bluuebunny/crossref_metadata_2025_split huggingface dataset:
Osmolyte‐induced protein folding free energy changes
Authors: Wu Peng , Bolen D.W. 
Published: February 2006

AbstractUpon addition of protecting osmolyte to an aqueous solution of an intrinsically unstructured protein, spectral observables are often seen to change in a sigmoid fashion as a function of increasing osmolyte concentration. Commonly, such data are analyzed using the linear extrapolation model (LEM), a method that defines a scale from 0%–100% folded species at each osmolyte concentration by means of extending pre‐ and post‐folding baselines into the transition region. Defining the 0%–100% folding scale correctly for each osmolyte is an important part of the analysis, leading to evaluation of the fraction of folded protein existing in the absence of osmolytes. In this study, we used reduced and carboxyamidated RNase T1 (RCAM‐T1) as an intrinsically unstructured protein, and determined the thermodynamic stability of RCAM‐T1 induced by naturally occurring osmolytes. Because the folded fraction of the protein population determined by experiments of thermal and urea‐induced denaturation is nonzero in the absence of osmolytes at 15°C, the commonly used LEM can lead to false values of ΔG for protein folding due to the arbitrary assumption that the protein is 100% unfolded in the presence of buffer alone. To correct this problem, titration of the protein solution with urea and extrapolating back to zero urea concentration gives the spectral value for 100% denatured protein. With fluorescence as the observable we redefine F/F0 to F/F = 1.0 and require that the denatured‐state baseline have this value as its intercept. By so doing, the 0%–100% scale‐corrected ΔG values of RCAM‐T1 folding in the presence of various osmolytes are then found to be identical, with small error, demonstrating that ΔG is independent of the osmolytes used. Such a finding is an important step in validating this quantity derived from the LEM as having the properties expected of an authentic thermodynamic parameter. The rank order of osmolyte efficacies in stabilizing RCAM‐T1 is sarcosine > sucrose > sorbitol > proline > betaine > glycerol. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Two‐stage support vector regression approach for predicting accessible surface areas of amino acids
Authors: Nguyen Minh N. , Rajapakse Jagath C. 
Published: February 2006

AbstractWe address the problem of predicting solvent accessible surface area (ASA) of amino acid residues in protein sequences, without classifying them into buried and exposed types. A two‐stage support vector regression (SVR) approach is proposed to predict real values of ASA from the position‐specific scoring matrices generated from PSI‐BLAST profiles. By adding SVR as the second stage to capture the influences on the ASA value of a residue by those of its neighbors, the two‐stage SVR approach achieves improvements of mean absolute errors up to 3.3%, and correlation coefficients of 0.66, 0.68, and 0.67 on the Manesh dataset of 215 proteins, the Barton dataset of 502 nonhomologous proteins, and the Carugo dataset of 338 proteins, respectively, which are better than the scores published earlier on these datasets. A Web server for protein ASA prediction by using a two‐stage SVR method has been developed and is available (http://birc.ntu.edu.sg/∼pas0186457/asa.html). Proteins 2006. © 2006 Wiley‐Liss, Inc.
Predicting protease types by hybridizing gene ontology and pseudo amino acid composition
Authors: Zhou Guo‐Ping , Cai Yu‐Dong 
Published: February 2006

AbstractProteases play a vitally important role in regulating most physiological processes. Different types of proteases perform different functions with different biological processes. Therefore, it is highly desired to develop a fast and reliable means to identify the types of proteases according to their sequences, or even just identify whether they are proteases or nonproteases. The avalanche of protein sequences generated in the postgenomic era has made such a challenge become even more critical and urgent. By hybridizing the gene ontology approach and pseudo amino acid composition approach, a powerful predictor called GO‐PseAA predictor was introduced to address the problems. To avoid redundancy and bias, demonstrations were performed on a dataset where none of proteins has ≥ 25% sequence identity to any other. The overall success rates thus obtained by the jackknife cross‐validation test in identifying protease and nonprotease was 91.82%, and that in identifying the protease type was 85.49% among the following five types: (1) aspartic, (2) cysteine, (3) metallo, (4) serine, and (5) threonine. The high jackknife success rates yielded for such a stringent dataset indicate the GO‐PseAA predictor is very powerful and might become a useful tool in bioinformatics and proteomics. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Comment on: “Energy landscape of a small peptide revealed by dihedral angle principal component analysis”
Authors: Hinsen Konrad 
Published: February 2006

AbstractThe dihedral angle principal component analysis method published recently by Mu, Nguyen, and Stock, is shown to produce distortions of the free energy landscape due to the neglect of constraints in the coordinates. It is further shown that these distortions can create artificial minima and energy barriers. The rugged energy landscape that the authors find for a small peptide chain might thus be an artifact of their method. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Compton profile study of tin
Authors: Ahuja B. L. , Khera S. , Mathur S. , Heda N. L. 
Published: February 2006

AbstractIn this paper we report the Compton profile of β‐tin, measured at an intermediate resolution, using 661.65‐keV γ‐radiation from a 137Cs source. We have also computed the Compton profiles for α‐ and β‐tin using the CRYSTAL03 code. The Compton profiles within the framework of linear combination of atomic orbitals (LCAO) using Hartree–Fock (HF), density functional (DF) and pseudopotential‐HF schemes embodied in the CRYSTAL03 code have been reported for both phases. Good accordance of the experiment for β‐tin with the corresponding theoretical profiles has been observed for the LCAO‐HF and DF schemes. A real‐space analysis of the experimental Compton profile shows the metal‐like behavior of β‐tin. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Hydrostatic‐pressure effects on the correlated electron–hole transition energies in GaAs–Ga1–xAlxAs semiconductor quantum wells
Authors: Raigoza N. , Duque C. A. , Reyes‐Gómez E. , Oliveira L. E. 
Published: February 2006

AbstractThe effects of hydrostatic pressure on the correlated e–h transition energies in single GaAs–Ga1–xAlxAs quantum wells are calculated via a variational procedure, in the framework of the effective‐mass and non‐degenerate parabolic‐band approximations. The valence‐band anisotropy is included in our theoretical model by using different hole masses in different spatial directions. Both heavy‐ and light‐hole exciton energies are obtained, and correlated e–h transition energies are found in good agreement with available experimental measurements. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Raman spectroscopy of open‐ended Single Wall Carbon Nanotubes under pressure: effect of the pressure transmitting medium
Authors: Merlen A. , Toulemonde P. , Bendiab N. , Aouizerat A. , Sauvajol J. L. , Montagnac G. , Cardon H. , Petit P. , San Miguel A. 
Published: February 2006

AbstractWe performed high pressure Raman experiments on purified open‐ended single wall carbon nanotubes using different pressure transmitting media (paraffin oil, argon and 4:1 methanol ethanol mixture) and two excitating wavelength (514.5 nm and 632.8 nm). We state that the behavior of the Raman spectrum under pressure is significantly dependent on the pressure transmitting medium. This result points out the relevance of the interactions between the medium and the nanotubes, at the origin of the disagreement between the phase transition sequences reported in literature. The comparaison of tangential modes profiles clearly shows that 4:1 methanol ethanol induces few strain on nanotubes in the opposite of what is observed for argon and paraffin oil pressure transmitting media. These observations are discussed in terms of intercalation and stress due to non hydrostatic conditions. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Effect of electric current on the Jahn–Teller distortion modes in La0.67–yPryCa0.33MnO3
Authors: Ma Y. Q. , Yang J. , Zhao B. C. , Du J. J. , Sun Y. P. 
Published: February 2006

AbstractThe sensitivity of transport and the lattice to a direct current has been investigated by means of in situ measurements of resistivity ϱ and Young's modulus E along with magnetic measurements in La0.67–yPryCa0.33MnO3 (y = 0, 0.15, 0.25, and 0.30) compounds. Increasing the Pr doping level enhances the softening of the magnitude of E with the appearance of a minimum in the curve of the temperature dependence of the modulus, E(T). The direct current depresses the resistivity and shifts the E(T) minimum to lower temperatures dramatically for the compounds with y ≥ 0.25, which exhibit a distinct magnetic hysteresis loop. The resistivity drop caused by the larger current may result from the depression of the Q3‐type distortion mode of Mn3+O6 octahedra by the current, which may favor the lower resistivity. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
(II,Mn)VI nanostructures in mesoporous silica hosts – from powder samples to thin films
Authors: Chen L. , Klar P. J. , Heimbrodt W. , Kurz T. , Krug von Nidda H.‐A. , Loidl A. , Kouzema A. V. , Fröba M. 
Published: February 2006

AbstractThe diluted magnetic semiconductor Cd1–x Mnx S with x up to 0.2 was synthesized within the pores of mesoporous thin film (MTF) silica host structures by a wet impregnation technique from an aqueous solution of the respective metal acetates, followed by drying steps and a conversion to sulfides by thermal H2S treatment. The presence of Cd1–x Mnx S nanoparticles inside the pores was confirmed by Raman spectroscopy. Photoluminescence excitation (PLE) measurements clearly reveal quantum confinement of the electronic states of the nanostructured Cd1–x Mnx S. Electron‐paramagnetic resonance (EPR) measurements on low x samples are used to prove that Mn is incorporated on cation site of the II–VI host and to demonstrate that the magnetic properties of Cd1–x Mnx S nanostructures are strongly affected by the reduction of the lateral dimensions. The quality of the Cd1–x Mnx S nanostructures synthesized in MTF silica hosts is comparable to that of Cd1–x Mnx S nanostructures inside MCM‐41 mesoporous silica powder. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Observation of Zn vacancies in ZnO grown by chemical vapor transport
Authors: Tuomisto F. , Saarinen† K. , Grasza K. , Mycielski A. 
Published: February 2006

AbstractWe have used positron annihilation spectroscopy to study the vacancy defects in ZnO crystals grown by both the conventional and contactless chemical vapor transport (CVT and CCVT). Our results show that Zn vacancies or Zn vacancy related defects are present in as‐grown ZnO, irrespective of the growth method. Zn vacancies are observed in CVT‐grown undoped ZnO and (Zn,Mn)O. The Zn vacancies present in undoped CCVT‐ZnO are the dominant negatively charged point defect in the material. Doping the material with As introduces also Zn vacancy‐related defect complexes with larger open volume. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Optical probing of spin‐dependent interactions in II–VI semiconductor structures
Authors: Gaj J. A. , Cibert J. , Ferrand D. , Golnik A. , Goryca M. , Karczewski G. , Kossacki P. , Kossut J. , Kowalik K. , Krebs O. , Kudelski A. , Kutrowski M. , Lemaitre A. , Maślana W. , Nawrocki M. , Pacuski W. , Płochocka P. , Senellart P. , Tatarenko S. , Voisin P. , Wojtowicz T. 
Published: February 2006

AbstractWe present a selection of optical experiments, providing information on several spin‐dependent interactions in II–VI semiconductor structures. Exciton–exciton and exciton–carrier interactions were studied by time‐resolved picosecond pump–probe measurements. Several examples of recent studies involving ion‐carrier exchange interaction in quantum wells and layers are discussed, concerning the quest for room temperature ferromagnetic semiconductors, spin temperature of Mn ions in (Cd,Mn)Te quantum wells, and spin relaxation in such wells under pulsed magnetic field. Finally, anisotropic electron–hole exchange in semiconductor quantum dots is discussed in the context of efforts to obtain generation of entangled photon pairs in a biexciton–exciton cascade in a semiconductor quantum dot. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Nanosecond spin memory of electrons in CdTe/CdMgTe quantum wells
Authors: Astakhov G. V. , Kiessling T. , Yakovlev D. R. , Zhukov E. A. , Bayer M. , Ossau W. , Zakharchenya B. P. , Karczewski G. , Wojtowicz T. , Kossut J. 
Published: February 2006

AbstractWe report on spin memory relaxation time τ s of free electrons in CdTe‐based quantum wells which is found to be in the nanosecond range. In these studies two different techniques have been exploited: (i) the Hanle effect under cw excitation and (ii) the time‐resolved pump‐&‐probe Kerr rotation measured under excitation by 1.8‐ps optical pulses. These independent techniques give very close results τ s ns and τ s = 14 ns, respectively. To our knowledge this is by two orders of magnitude longer than the electron spin relaxation times reported for CdTe‐based quantum wells so far. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
III–V/II–VI heterovalent double quantum wells
Authors: Toropov A. A. , Sedova I. V. , Sorokin S. V. , Terent'ev Ya. V. , Ivchenko E. L. , Lykov D. N. , Ivanov S. V. , Bergman J. P. , Monemar B. 
Published: February 2006

AbstractWe report on design, fabrication by molecular beam epitaxy, and photoluminescence (PL) studies of III–V/II–VI heterovalent structures containing a GaAs/AlGaAs/ZnSe/ZnCdMnSe double quantum well (QW). The studies of temperature‐dependent and time‐resolved PL have provided an insight into the nature of the exciton localization potential induced by the heterovalent interface. It is found that under the resonant conditions the observed emission mostly originates from the recombination of excitons confined in type II quantum‐dot‐like structures, where the holes are localised within the GaAs QW due to the well width fluctuations and the electrons are localized in the plane of the ZnCdMnSe QW due to the fluctuations of the conduction band offset at the heterovalent interface, induced by random variation of the interface microscopic structure. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Identification of isoenzymes using matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry
Authors: Hardouin Julie , Hubert‐Roux Marie , Delmas Agnès F. , Lange Catherine 
Published: February 2006

AbstractThe identification of isoforms is one of the great challenges in proteomics due to the large number of identical amino acids preventing their separations by two‐dimensional electrophoresis. Matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOFMS) has become a rapid and sensitive tool in proteomics, notably with the new instrumental improvements. In this study, we used several acquisition modes of MALDI‐TOFMS to identify isoforms of porcine glutathiones S‐transferase. The use of multiple proteases coupled to the different acquisition modes of MALDI‐TOFMS (linear, reflectron, post‐source decay (PSD) and in‐source decay, positive and negative modes) allowed the identification of two sequences. Moreover, a third sequence is pointed out from a PSD study of a tryptic ion revealing the modification of the amino acid tyrosine 146 to phenylalanine. Copyright © 2006 John Wiley & Sons, Ltd.
Complementary structural information of positive‐ and negative‐ion MSn spectra of glycopeptides with neutral and sialylated N‐glycans
Authors: Deguchi Kisaburo , Ito Hiroki , Takegawa Yasuhiro , Shinji Nagai , Nakagawa Hiroaki , Nishimura Shin‐Ichiro 
Published: February 2006

AbstractPositive‐ and negative‐ion MSn spectra of chicken egg yolk glycopeptides binding a neutral and a sialylated N‐glycan were acquired by using electrospray ionization linear ion trap time‐of‐flight mass spectrometry (ESI‐LIT‐TOFMS) and collision‐induced dissociation (CID) with helium as collision gas. Several characteristic differences were observed between the positive‐ and negative‐ion CID MSn (n = 2, 3) spectra. In the positive‐ion MS2 spectra, the peptide moiety was presumably stable, but the neutral N‐glycan moiety caused several B‐type fragmentations and the sialylated N‐glycan almost lost sialic acid(s). In contrast, in the negative‐ion MS2 spectra, the peptide moiety caused several side‐chain and N‐glycan residue (e.g., N‐acetylglucosamine (GlcNAc) residue) fragmentations in addition to backbone cleavages, but the N‐glycan moieties were relatively stable. The positive‐ion MS3 spectra derived from the protonated peptide ion containing a GlcNAc residue (203.1 Da) provided enough information to determine the peptide amino‐acid sequence including the glycosylation site, while the negative‐ion MS3 spectra derived from the deprotonated peptide containing a 0,2X1‐type cross‐ring cleavage (83.1 Da) complicated the peptide sequence analysis due to side‐chain and 0,2X1 residue related fragmentations. However, for the structural information of the N‐glycan moiety of the glycopeptides, the negative‐ion CID MS3 spectra derived from the deprotonated 2,4A6‐type cross‐ring cleavage ion (neutral N‐glycan) or the doubly deprotonated B6‐type fragment ion (sialylated N‐glycan) are more informative than are those of the corresponding positive‐ion CID MS3 spectra. Thus, the positive‐ion mode of CID is useful for the analyses of peptide amino‐acid sequences including the glycosylation site. The negative‐ion mode of CID is especially useful for sialylated N‐glycan structural analysis. Therefore, in the structural analysis of N‐glycopeptides, their roles are complementary. Copyright © 2006 John Wiley & Sons, Ltd.
Electrospray ionization mass spectrometry: a key analytical tool for the characterization of regioselectively derivatized maltooligosaccharides obtained starting from natural β‐cyclodextrin
Authors: Lesur David , Gassama Abdoulaye , Moreau Vincent , Djedaïni‐Pilard Florence , Brique Arnaud , Pilard Serge 
Published: February 2006

AbstractThe development of natural cyclodextrins (CDs) for various industrial applications (agroalimentary, cosmetic or pharmaceutical) constitutes a continuous challenge. For the integration of these agricultural plant products in the creation of super‐absorbent biodegradable and hypoallergenic materials (water‐retaining agents, cosmetic hydrating and texturing, pharmaceutical and horticultural products) to replace synthetic polymers, we have developed chemical methods to access regioselectively C‐6‐derivatized maltooligosaccharides starting from CDs. These compounds are highly suitable for further chemical modifications and are expected to give access to a new class of polymeric materials with potential applications such as water‐retaining agents in the disposable nappies industry. For the structural analysis of carbohydrates, electrospray ionization mass spectrometry (ESI‐MS) offers precise results, analytical versatility and very high sensitivity. We report herein the rapid and convenient follow‐up of chemical reactions, the purity evaluation of intermediates and final products, and the structural characterization of derivatized maltooligosaccharides, obtained by acidic cleavage (acetolysis) of halogenated and esterified CDs, using ESI‐MS in combination with the high‐resolution (HRMS) and tandem mass spectrometry (MS/MS) capabilities of a quadrupole orthogonal time‐of‐flight (Q‐TOF) mass spectrometer. Copyright © 2006 John Wiley & Sons, Ltd.
Cluster detection diagnostics for small area health data: with reference to evaluation of local likelihood models
Authors: Monir Hossain Md. , Lawson Andrew B. 
Published: February 2006

AbstractThe focus of this paper is the development of a range of cluster detection diagnostics that can be used to assess the degree to which a clustering method recovers the true clustering behaviour of small area data. The diagnostics proposed range from individual region specific diagnostics to neighbourhood diagnostics, and assume either individual region risk as focus, or concern areas of maps defined to be clustered and the recovery ability of methods. A simulation‐based comparison is made between a small set of count data models: local likelihood, BYM and Lawson and Clark. It is found that local likelihood has good performance across a range of criteria when a CAR prior is assumed for the lasso parameter. Copyright © 2006 John Wiley & Sons, Ltd.
Evaluating spatial surveillance: detection of known outbreaks in real data
Authors: Kleinman Ken , Abrams Allyson , Katherine Yih W. , Platt Richard , Kulldorff Martin 
Published: February 2006

AbstractSince the anthrax attacks of October 2001 and the SARS outbreaks of recent years, there has been an increasing interest in developing surveillance systems to aid in the early detection of such illness. Systems have been established which do this is by monitoring primary health‐care visits, pharmacy sales, absenteeism records, and other non‐traditional sources of data. While many resources have been invested in establishing such systems, relatively little effort has as yet been expended in evaluating their performance.One way to evaluate a given surveillance system is to compare the signals it generates with known outbreaks identified in other systems. In public health practice, for example, public health departments investigate reports of illness and sometimes track hospital admissions. Comparison of new systems with extant systems cannot generate estimates of test characteristics such as sensitivity and specificity, since the actual number of positives and negatives cannot be known. However, the comparison can reveal whether a new or proposed system's signals match outbreaks detected by the existing system. This could help support or reject the new system as an alternative or complement to the extant system.We propose three methods to test the null hypothesis that the new system does not signal true outbreaks more often than would be expected by chance. The methods differ in the restrictiveness of the assumptions required. Each test may detect weaknesses in the new system, depending on the distribution of outbreaks and can be used to construct confidence limits on the agreement between the new system's signals and the outbreaks, given the distribution of the signals. They can be used to assess whether the new system works in that it detects the outbreaks better than chance would suggest and can also determine if the new systems' signals are generated earlier than an extant system. Copyright © 2006 John Wiley & Sons, Ltd.
A workflow spatial scan statistic
Authors: Duczmal Luiz , Buckeridge David L. 
Published: February 2006

AbstractWe propose a modification of the spatial scan statistic that takes account of workflow, which is the movement of individuals between home and work. The objective is to detect clusters of disease in situations where exposure occurs in the workplace, but only home address is available for analysis. In these situations, application of the usual spatial scan statistic does not account for possible differences between home and work address, thereby reducing the power of detection. We describe an extension to the usual spatial scan statistic that uses workflow data to search for disease clusters resulting from workplace exposure. We also present results from simulations that demonstrate the increased power of the workflow scan statistic over the usual scan statistic for detecting clusters arising from exposures in the workplace. Copyright © 2006 John Wiley & Sons, Ltd.