bluuebunny/crossref_metadata_2025_split huggingface dataset:
C‐terminal tail derived from the neighboring subunit is critical for the activity of Thermoplasma acidophilumD‐aldohexose dehydrogenase
Authors: Nishioka Taiki , Yasutake Yoshiaki , Nishiya Yoshiaki , Tamura Noriko , Tamura Tomohiro 
Published: October 2008

AbstractThe D‐aldohexose dehydrogenase from the thermoacidophilic archaeon Thermoplasma acidophilum (AldT) is a homotetrameric enzyme that catalyzes the oxidation of several D‐aldohexoses, especially D‐mannose. AldT comprises a unique C‐terminal tail motif (residues 247–255) that shuts the active‐site pocket of the neighboring subunit. The functional role of the C‐terminal tail of AldT has been investigated using mutational and crystallographic analyses. A total of four C‐terminal deletion mutants (Δ254, Δ253, Δ252, and Δ249) and two site‐specific mutants (Y86G and P254G) were expressed by Escherichia coli and purified. Enzymatic characterization of these mutants revealed that the C‐terminal tail is a requisite and that the interaction between Tyr86 and Pro254 is critical for enzyme activity. The crystal structure of the Δ249 mutant was also determined. The structure showed that the active‐site loops undergo a significant conformational change, which leads to the structural deformation of the substrate‐binding pocket. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Defining and characterizing protein surface using alpha shapes
Authors: Albou Laurent‐Philippe , Schwarz Benjamin , Poch Olivier , Wurtz Jean Marie , Moras Dino 
Published: October 2008

AbstractThe alpha shape of a molecule is a geometrical representation that provides a unique surface decomposition and a means to filter atomic contacts. We used it to revisit and unify the definition and computation of surface residues, contiguous patches, and curvature. These descriptors are evaluated and compared with former approaches on 85 proteins for which both bound and unbound forms are available. Based on the local density of interactions, the detection of surface residues shows a sensibility of 98%, whereas preserving a well‐formed protein core. A novel conception of surface patch is defined by traveling along the surface from a central residue or atom. By construction, all surface patches are contiguous and, therefore, allows to cope with common problems of wrong and nonselection of neighbors. In the case of protein‐binding site prediction, this new definition has improved the signal‐to‐noise ratio by 2.6 times compared with a widely used approach. With most common approaches, the computation of surface curvature can be locally biased by the presence of subsurface cavities and local variations of atomic densities. A novel notion of surface curvature is specifically developed to avoid such bias and is parametrizable to emphasize either local or global features. It defines a molecular landscape composed on average of 38% knobs and 62% clefts where interacting residues (IR) are 30% more frequent in knobs. A statistical analysis shows that residues in knobs are more charged, less hydrophobic and less aromatic than residues in clefts. IR in knobs are, however, much more hydrophobic and aromatic and less charged than noninteracting residues (non‐IR) in knobs. Furthermore, IR are shown to be more accessible than non‐IR both in clefts and knobs. The use of the alpha shape as a unifying framework allows for formal definitions, and fast and robust computations desirable in large‐scale projects. This swiftness is not achieved to the detriment of quality, as proven by valid improvements compared with former approaches. In addition, our approach is general enough to be applied on nucleic acids and any other biomolecules. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Effect of pressure on helix‐coil transition of an alanine‐based peptide: An FTIR study
Authors: Imamura Hiroshi , Kato Minoru 
Published: October 2008

AbstractEffects of pressure and temperature on the helix‐coil transition of an alanine‐based peptide (Ac‐ AA(AAKAA)3AAY‐NH2) have been investigated using CD and FTIR spectroscopy. From the correlation between CD and FTIR data, we showed that the change in infrared intensity of the amide I′ band at 1633 cm−1 is almost identical to the change in the helical content calculated from the CD result. Thus, we monitored the amide I′ band intensity at 1633 cm−1 to determine the helical content at high pressures. We determined free energy, enthalpy, and volume changes upon unfolding of the α‐helix. The obtained volume change (0.98 ± 0.04 cm3 mol−1 res−1 at 25.4°C) is not consistent with a recent molecular dynamics simulation study by Pascheck et al. who used temperature‐pressure replica exchange methods (Paschek, Gnanakaran, and Garcia, Proc Natl Acad Sci USA 2005;102:6765–6770). They reported a small negative volume change upon unfolding of the α‐helix, indicating that pressure induced the peptide to unfold. Pressure dependence of the band‐width of the amide I′ band also supported the present experimental results in which pressure induces the peptide to fold, which is also apparently inconsistent with the pressure‐induced protein unfolding that is generally observed. We propose a hypothesis to unravel the paradox of pressure‐induced peptide folding and protein unfolding. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Degradation kinetics and safety evaluation of buprofezin residues in grape (Vitis vinifera L.) and three different soils of India
Authors: Oulkar Dasharath P , Banerjee Kaushik , Patil Sangram H , Upadhyay Ajay K , Taware Praveen B , Deshmukh Madhukar B , Adsule Pandurang G 
Published: October 2008

AbstractBACKGROUND: This work was undertaken to determine the preharvest interval (PHI) of buprofezin to minimize its residues in grapes and thereby ensure consumer safety and avoid possible non‐compliance in terms of residue violations in export markets. Furthermore, the residue dynamics in three grapevine soils of India was explored to assess its environmental safety.RESULTS: Residues dissipated following non‐linear two‐compartment first + first‐order kinetics. In grapes, the PHI was 31 days at both treatments (312.5 and 625 g a.i. ha−1), with the residues below the maximum permissible intake even 1 h after foliar spraying. Random sampling of 5 kg comprising small bunchlets (8–10 berries) collected from a 1 ha area gave satisfactory homogeneity and representation of the population. A survey on the samples harvested after the PHI from supervised vineyards that received treatment at the recommended dose showed residues below the maximum residue limit (MRL) of 0.02 mg kg−1 applicable for the European Union. In soil, the degradation rate was fastest in clay soil, followed by sandy loam and silty clay, with a half‐life within 16 days in all the soils.CONCLUSION: The recommendation of the PHI proved to be effective in minimizing buprofezin residues in grapes. Thus, this work is of high practical significance to the domestic and export grape industry of India to ensure safety compliance in respect of buprofezin residues, keeping in view the requirements of international trade. Copyright © 2008 Society of Chemical Industry
A Dual‐Response Partial Least Squares Regression QSAR Model and its Application in Design of Dual Activators of PPARα and PPARγ
Authors: Ajmani Subhash , Kulkarni Sudhir A. 
Published: October 2008

AbstractIn this paper, an attempt was made to develop a dual‐response Quantitative Structure–Activity Relationship (QSAR) model on a series of 5‐aryl thiazolidinedione and oxazolidinedione derivatives acting as dual activators of PPARα and PPARγ (Peroxisome Proliferator‐Activated Receptors) using partial least squares regression method. Various 2D descriptors were calculated and used in the present analysis. For model validation, the dataset was divided into various training and test sets using both rational and random selection procedures. The developed QSAR models were found to be statistically significant with respect to training (r2>0.8), cross‐validation (q2>0.7), and external validation (pred_r2>0.8). The developed dual‐response model suggests that descriptors such as HBA, HBD, Xlog P, polar surface area play an important role in determining both biological activities. In addition, it allows comparison of the behavior of common subset descriptors toward each activity which may aid in the rational design of novel selective/non‐selective potent molecules.
Stable isotope natural abundance of nitrous oxide emitted from Antarctic tundra soils: effects of sea animal excrement depositions
Authors: Zhu Renbin , Liu Yashu , Li Xianglan , Sun Jianjun , Xu Hua , Sun Liguang 
Published: October 2008

AbstractNitrous oxide (N2O), a greenhouse gas, is mainly emitted from soils during the nitrification and denitrification processes. N2O stable isotope investigations can help to characterize the N2O sources and N2O production mechanisms. N2O isotope measurements have been conducted for different types of global terrestrial ecosystems. However, no isotopic data of N2O emitted from Antarctic tundra ecosystems have been reported although the coastal ice‐free tundra around Antarctic continent is the largest sea animal colony on the global scale. Here, we report for the first time stable isotope composition of N2O emitted from Antarctic sea animal colonies (including penguin, seal and skua colonies) and normal tundra soils using in situ field observations and laboratory incubations, and we have analyzed the effects of sea animal excrement depositions on stable isotope natural abundance of N2O. For all the field sites, the soil‐emitted N2O was 15N‐ and 18O‐depleted compared with N2O in local ambient air. The mean δ values of the soil‐emitted N2O were δ15N = −13.5 ± 3.2‰ and δ18O = 26.2 ± 1.4‰ for the penguin colony, δ15N = −11.5 ± 5.1‰ and δ18O = 26.4 ± 3.5‰ for the skua colony and δ15N = −18.9 ± 0.7‰ and δ18O = 28.8 ± 1.3‰ for the seal colony. In the soil incubations, the isotopic composition of N2O was measured under N2 and under ambient air conditions. The soils incubated under the ambient air emitted very little N2O (2.93 µg N2ON kg−1). Under N2 conditions, much more N2O was formed (9.74 µg N2ON kg−1), and the mean δ15N and δ18O values of N2O were −19.1 ± 8.0‰ and 21.3 ± 4.3‰, respectively, from penguin colony soils, and −17.0 ± 4.2‰ and 20.6 ± 3.5‰, respectively, from seal colony soils. The data from in situ field observations and laboratory experiments point to denitrification as the predominant N2O source from Antarctic sea animal colonies. Copyright © 2008 John Wiley & Sons, Ltd.
Accuracy assessment of aerial photographs acquired using lighter‐than‐air blimps: low‐cost tools for mapping river corridors
Authors: Vericat Damià , Brasington James , Wheaton Joe , Cowie Michaela 
Published: October 2008

AbstractMonitoring river systems with repeat aerial photography is a powerful tool although the temporal resolution of surveys is rarely performed at anything better than annual time‐scales. In recent years, a variety of low‐cost aerial platforms for acquiring aerial photography have emerged. While these economical options may facilitate more frequent repeat surveys, the accuracy of imagery needs further consideration.The accuracy of imagery obtained from a Lighter‐Than‐Air Blimp is investigated through two simple experiments. The first looks at the geospatial error of aerial photographs derived using five geometric transformation models, and the sensitivity of the photo registration quality to various ground control point (GCP) configurations and densities. At high GCP densities, higher order polynomial transformation models provide the highest quality registrations. However, at more modest GCP densities (i.e. 19–28 GCPs Ha−1), simple aerotriangulation and 2nd order polynomial transformation models perform modestly, resulting in registration errors at standards equal to or better than obtained with conventional aerial photography (e.g. 0.5–1 m). The quality of image registration is highly dependent on the configuration of GCPs. In a second experiment, the practical utility of producing a mosaic of blimp acquired imagery is explored over a kilometre long braided reach. Even at relatively low GCPs densities (e.g. 9 GCPs Ha−1), a mosaiced aerial of the entire reach can be produced of adequate quality to support bar‐scale mapping of patch‐scale features. The survey required less than a single day of field work and laboratory processing, and presents a cost‐effective alternative to traditionally commissioned flights. Copyright © 2008 John Wiley & Sons, Ltd.
Estimation of the error performance objectives for satellite communication systems
Authors: Kim Sooyoung , Yeo Sungmoon , Shin Dongseok , Song Sang Seob 
Published: October 2008

AbstractWe consider the physical layer error performance parameters and design criteria for digital satellite systems established by ITU‐R Recommendation S.1062, where the performance objectives are given in terms of the bit error rate (BER) divided by the average number of errors within a cluster. It is well known that errors on satellite links employing forward error correction (FEC) schemes tend to occur in clusters. The resulting block error rate is the same as if it was caused by randomly occurring bit errors with an error‐event ratio of BER/α, whereαis the average number of errors within a cluster. The factor,α, accounts for the burstiness of the errors and also represents the ratio between the BER and the error‐event ratio. This paper proposes theoretical methods to estimate the factor,α. Using the weight distributions of the FEC codes, we derive a set of expressions for the factor,α, as well as their compact lower bounds. We present lower bounds for various FEC schemes including binary BCH codes, block turbo codes, convolutional codes, and turbo codes. The simulation results show that the proposed lower bounds are good estimates in the high signal‐to‐noise ratio region. Copyright © 2008 John Wiley & Sons, Ltd.
Low‐complexity unambiguous acquisition methods for BOC‐modulated CDMA signals
Authors: Lohan Elena Simona , Burian Adina , Renfors Markku 
Published: October 2008

AbstractThe new M‐code signals of GPS and the signals proposed for the future Galileo systems are of split‐spectrum type, where the pseudorandom (PRN) code is multiplied with rectangular sub‐carriers in one or several stages. Sine and cosine binary‐offset‐carrier (BOC) modulations are examples of modulations, which split the signal spectrum and create ambiguities in the envelope of the autocorrelation function (ACF) of the modulated signals. Thus, the acquisition of split‐spectrum signals, based on the ambiguous ACF, poses some challenges, which might be overcome at the expense of higher complexity (e.g. by decreasing the step in searching the timing hypotheses). Recently, two techniques that deal with the ambiguities of the ACF have been proposed, and they were referred to as ‘sideband (SB) techniques’ (by Betz, Fishmanet al.) or ‘BPSK‐like’ techniques (by Martin, Heirieset al.), since they use SB correlation channels and the obtained ACF looks similar to the ACF of a BPSK‐modulated PRN code. These techniques allow the use of a higher search step compared with the ambiguous ACF situation. However, both these techniques use SB‐selection filters and modified reference PRN codes at the receivers, which affect the implementational complexity. Moreover, the ‘BPSK‐like’ techniques have been so far studied for even BOC‐modulation orders (i.e. integer ratio between the sub‐carrier frequency and the chip rate) and they fail to work for odd BOC‐modulation orders (or equivalently for split‐spectrum signals with significant zero‐frequency content). We propose here three reduced‐complexity methods that remove the ambiguities of the ACF of the split‐spectrum signals and work for both even and odd BOC‐modulation orders. Two of the proposed methods are extensions of the previously mentioned techniques, and the third one is introduced by the authors and called the unsuppressed adjacent lobes (UAL) technique. We argue via theoretical analysis the choice of the parameters of the proposed methods and we compare the alternative methods in terms of complexity and performance. Copyright © 2008 John Wiley & Sons, Ltd.
Microwave depolarization versus rain attenuation on earth space in Malaysia
Authors: Mandeep J. S. 
Published: October 2008

AbstractThe wave propagation experiments using Japanese geostationary satellite Superbird‐C have been performed at the Universiti Sains Malaysia earth station. A relationship between rain depolarization and attenuation, valid for earth‐space path at microwave wavelengths, is presented. Cumulative rain attenuation and cross‐polarization discrimination (XPD) statistics are given for the period of 4 years (2002–2005) at 12.255 GHz. XPD varied from 44 dB at 1% to 16 dB at 0.001% of time the abscissa is exceeded. Comparisons were made with available data sets and with five simple XPD models and the results indicate a good performance by the simple isolation model and the CHU model compared with the others. These results serve as checks on the theoretical models needed for predicting communication system performance in geographical regions especially for equatorial climate where measurements are not available. Copyright © 2008 John Wiley & Sons, Ltd.
Multiphoton microscopic imaging of adipose tissue based on second‐harmonic generation and two‐photon excited fluorescence
Authors: Huang Zufang , Zhuo Shuangmu , Chen Jianxin , Chen Rong , Jiang Xingshan 
Published: October 2008

AbstractThe fresh adipose tissue was investigated by the use of multiphoton microscopy (MPM) based on two‐photon excited fluorescence and second‐harmonic generation (SHG). Microstructure of collagen and adipose cells in the adipose tissue is clearly imaged at a subcellular level with the excitation light wavelengths of 850 and 730 nm, respectively. The emission spectrum of collagen SHG signal and NADH and FAD fluorescence signal can also be obtained, which can be used to quantify the content of collagen and adipose cells and reflect the degree of pathological changes when comparing normal tissue with abnormal adipose tissue in the same condition. The results indicate that MPM has the potential to be applied to investigate the adipose tissue and can be used in the research field of lipid and connective tissues. SCANNING 30, 452–456, 2008. © 2008 Wiley Periodicals, Inc.
The virtuous cycle of discovery and creation of entrepreneurial opportunities
Authors: Zahra Shaker A. 
Published: October 2008

AbstractResearchers have debated whether entrepreneurial opportunities are discovered or created. However, they have often overlooked the importance of the contextual variables that stimulate, shape, and define the entrepreneurial act. This article focuses on entrepreneurial activities within technology‐based established companies and shows how and why certain contexts are more conducive for discovery, while others promote the discovery and creation of opportunities. The article suggests a virtuous and dynamic cycle where discovery enriches creation which, in turn, fosters the discovery of new opportunities. The focus on the context and key features of entrepreneurial search contributes to the behavioral theory of and the debate on the origins of opportunities. Copyright © 2008 Strategic Management Society.
Selected variation: the population‐level implications of multistage selection in entrepreneurship
Authors: Eckhardt Jonathan T. , Ciuchta Michael P. 
Published: October 2008

AbstractThis article examines the population level implications of microlevel theories of entrepreneurship. The actions of those who seek to organize opportunities, as well as the hurdles that they must overcome to successfully exploit them, give rise to an evolutionary multistage selection process. The article indicates that the consideration of selection events leads to a more complete understanding of the entrepreneurial process and how microlevel theories influence important outcomes in entrepreneurship. Other theoretical and empirical implications of staged selection for research in entrepreneurship are discussed. Copyright © 2008 Strategic Management Society.
Understanding opportunity discovery and sustainable advantage: the role of transaction costs and property rights
Authors: Foss Kirsten , Foss Nicolai J. 
Published: October 2008

AbstractTo add insight in new value creation, opportunity discovery should be integrated with strategic management theory. Based on the resource‐based view and the economics of property rights, we build a framework that accomplishes this. Our key argument is that property rights and transaction costs are important antecedents of opportunity discovery. We identify two mechanisms that establish this influence and examine alternative ways in which knowledge, transaction costs, and property rights influence opportunity discovery and sustainable advantage. Copyright © 2008 Strategic Management Society.
Inside opportunity formation: enterprise failure, cognition, and the creation of opportunities
Authors: Mitchell Ronald K. , Mitchell J. Robert , Smith J. Brock 
Published: October 2008

AbstractTo better understand opportunity creation, we investigate the extent to which recognition of failure impacts the new transaction commitment mindset of entrepreneurs. In a PLS model, we utilize data gathered from a sample of 220 entrepreneurs, and augment these results with an ANOVA analysis that provides a deeper exploration of the theory. In this article, we: (1) elaborate on the critical dimensions that represent a multi‐construct view of the new transaction commitment mindset and describe ways that these dimensions can be measured; (2) examine the extent to which the recognition of new venture failure impacts the new transaction commitment mindset; and (3) explore the implications of the interaction between failure recognition and the new transaction commitment mindset for an entrepreneur's decision to continue or abandon opportunity creation efforts. Our results suggest that recognition of failure does indeed impact the new transaction commitment mindset and, by extension, can enable opportunity creation. Copyright © 2008 Strategic Management Society.