References of "Lins, Laurence"
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See detailSurface and lipid interaction properties of novel rhamnolipids to explain their eliciting activity
Nasir, Mehmet Nail ULg; Monhonval, Pierre; Nott, Katherine ULg et al

in European Biophysics Journal [=EBJ] (2013), 42(S1), 168

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See detailAnalysis of calcium-induced effects on the conformation of fengycin
Nasir, Mehmet Nail ULg; Laurent, Pascal ULg; Flore, Christelle ULg et al

in Spectrochimica Acta Part A : Molecular and Biomolecular Spectroscopy (2013), 110

A combination of CD, FT-IR, NMR and fluorescence spectroscopic techniques was applied to elucidate the conformation of fengycin, a natural lipopeptide with antifungal and eliciting activities, in a ... [more ▼]

A combination of CD, FT-IR, NMR and fluorescence spectroscopic techniques was applied to elucidate the conformation of fengycin, a natural lipopeptide with antifungal and eliciting activities, in a membrane-mimicking environment and to investigate the effect of calcium ions on the conformation. We mainly observed that fengycin adopts a turn conformation and that the side chain of glutamate residues plays a key role on the stabilization of the peptide ring backbone conformation. More particularly, the binding of calcium ions by the carboxylic moieties has a consequence on the environment of the tyrosine residues. Our data suggest also an arrangement of fengycin molecules into “-sheet like micelles” in a membrane-mimicking environment and the enhancement of this aggregating effect in presence of calcium ions. The modulation of the fengycin conformation by the environmental conditions may influence its biological properties. [less ▲]

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See detailEffects of surfactin on membrane models displaying lipid phase separation.
Deleu, Magali ULg; Lorent, Joseph; Lins, Laurence ULg et al

in Biochimica et Biophysica Acta (2013), 1828(2), 801-815

Surfactin, a bacterial amphiphilic lipopeptide is attracting more and more attention in view of its bioactive properties which are in relation with its ability to interact with lipids of biological ... [more ▼]

Surfactin, a bacterial amphiphilic lipopeptide is attracting more and more attention in view of its bioactive properties which are in relation with its ability to interact with lipids of biological membranes. In this work, we investigated the effect of surfactin on membrane structure using model of membranes, vesicles as well as supported bilayers, presenting coexistence of fluid-disordered (DOPC) and gel (DPPC) phases. A range of complementary methods was used including AFM, ellipsometry, dynamic light scattering, fluorescence measurements of Laurdan, DPH, calcein release, and octadecylrhodamine B dequenching. Our findings demonstrated that surfactin concentration is critical for its effect on the membrane. The results suggest that the presence of rigid domains can play an essential role in the first step of surfactin insertion and that surfactin interacts both with the membrane polar heads and the acyl chain region. A mechanism for the surfactin lipid membrane interaction, consisting of three sequential structural and morphological changes, is proposed. At concentrations below the CMC, surfactin inserted at the boundary between gel and fluid lipid domains, inhibited phase separation and stiffened the bilayer without global morphological change of liposomes. At concentrations close to CMC, surfactin solubilized the fluid phospholipid phase and increased order in the remainder of the lipid bilayer. At higher surfactin concentrations, both the fluid and the rigid bilayer structures were dissolved into mixed micelles and other structures presenting a wide size distribution. [less ▲]

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See detailSynthesis and physico-chemical characterization of fatty esters
Sainvitu, Pauline ULg; Nott, Katherine ULg; Nicks, Francois ULg et al

Poster (2012, November 16)

Specific antioxidant molecules (e.g. phenolics) help to prevent oxidation reaction of the cell membrane. A fatty chain grafted on these compounds should enhance their capacity to interact with the ... [more ▼]

Specific antioxidant molecules (e.g. phenolics) help to prevent oxidation reaction of the cell membrane. A fatty chain grafted on these compounds should enhance their capacity to interact with the membrane lipids. In our study, three fatty esters comprising an aromatic part were synthesized. They differentiate the aromatic substituent and the number of carbons between the aromatic ring and the ester function. A structure-function relationships study was performed to identify the structural pattern affecting the interfacial properties and the membrane interaction properties. The behavior of their monolayer film at an air-water interface was studied. The interactions with membrane were assessed on living cells and were predicted by a computational approach. In the future, we will investigate the effect of the presence of a sugar unit on these molecules. [less ▲]

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See detailMolecular analysis of the interfacial and membrane-interacting properties of D-xylose-based bolaforms
Nasir, Mehmet Nail ULg; Legrand, Vincent; Gatard, Sylvain et al

Poster (2012, October)

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See detailReplacing explicit water and lipids by implicit representation in molecular dynamics simulations
Steinhauer, Sven ULg; Crowet, Jean-Marc ULg; Lins, Laurence ULg et al

Poster (2012, September 11)

Molecular dynamics (MD) is an appropriate method for investigation of biomolecular systems and helps in explaining results from wet lab experiments or in getting further insight into details, which are ... [more ▼]

Molecular dynamics (MD) is an appropriate method for investigation of biomolecular systems and helps in explaining results from wet lab experiments or in getting further insight into details, which are not accessible by experimental methods(Lindahl, 2008). By now, many biologically relevant processes for drug design, toxicological studies and other fields of application, can not be performed by atomistic MD simulations (Lindahl, 2008). <br />In MD, the necessary time effort for carrying out a simulation is considerable and depends mainly on (1) the complexity of the simulated system (2) the simulated time scale (3) the simulation method (4) the efficiency of used hardware and software algorithms. Carried out MD simulations nowadays may still take weeks of calculation on high end computers. <br /> <br />In practice, biologically relevant processes, as e.g. protein folding, take usually place above the time scale of milli seconds. They can take up to the order of some thousands of seconds (in case of the folding of membrane proteins). Molecular dynamics computer simulations have reached the scale of micro seconds for simulations of systems where each atom was described and simulated over time.(Lindahl, 2008) <br /> <br />Nevertheless, MD has risen to an important promoter methodology for many different fields of application. By replacing bunches of atoms by artificial particles, complexity of the systems can be reduced. This method is called the coarse grain method (CG). Biggin and Bond (2008) found an acceleration of their simulation processes for self assembling membrane / protein systems in water by factor 100. They estimated one to two days of calculation for a simulated time scale of 0.1 to 0.2 micro seconds for their systems. <br /> <br />Implicit force fields like "IMPALA", aim to describe water and/or membrane molecules in simulations by a couple of simple and partially precalculable equations. “IMPALA” is a force field initially developed by our laboratory. Using this method, thousands of water and lipid molecules can be replaced, leading to a reduced complexity of the system to be simulated. <br />"IMPALA"(Ducarme et al., 1998) based on the assumption of rigid peptides and aimed to find the insertion characteristics of such in membranes. Elimination of the necessity for simulating the aqueous and lipid phase atom by atom in the software package "Gromacs"(Berendsen et al., 1995) will permit both: a gain of speed, as it was already the case for the introduction of the coarse grain method, and a gain of precision by turning rigid molecules flexible through "Gromacs". Our current work is the integration of the "IMPALA" implicit force field into "Gromacs". <br /> <br />Biggin, P.C. & Bond, P.J. Molecular dynamics simulations of membrane proteins. Methods Mol. Biol. 443, 147-60(2008). <br />Berendsen, et al. (1995) Comp. Phys. Comm. 91: 43-56. <br />Ducarme, P., Rahman, M. & Brasseur, R. IMPALA: a simple restraint field to simulate the biological membrane in molecular structure studies. Proteins 30, 357-71(1998). <br />Lindahl, E.R. (2008). Molecular dynamics simulations. Methods Mol. Biol. 443, 3-23. [less ▲]

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See detailCharacterizing of protein dataset with GO ontology
Dmitrieva, Joelia Borisnova; Florea, B; Li, N et al

Poster (2012, September 09)

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See detailPlasma membrane localization of StREM1.3 Remorin is mediated by conformational changes in a novel C-terminal anchor and required for the restriction of PVX movement.
Perraki, Artemis; Cacas, Jean-Luc; Crowet, Jean-Marc ULg et al

in Plant Physiology (2012), 160(1),

The formation of plasma membrane (PM) micro-domains plays a crucial role in the regulation of membrane signalling and trafficking. Remorins are a plant-specific family of proteins organized in six ... [more ▼]

The formation of plasma membrane (PM) micro-domains plays a crucial role in the regulation of membrane signalling and trafficking. Remorins are a plant-specific family of proteins organized in six phylogenetic groups, and Remorins of the group 1 are among the few plant proteins known to specifically associate with membrane rafts. As such, they are valuable to understand the molecular bases for PM lateral organization in plants. However, little is known about the structural determinants underlying group 1 Remorins specific association with membrane rafts. We used a structure-function approach to identify a short C-terminal anchor (RemCA) indispensable and sufficient for tight direct binding of Solanum tuberosum REMORIN 1.3 (StREM1.3) to the PM. RemCA switches from unordered to an alpha-helical structure in a non-polar environment. Protein structure modelling indicates that RemCA folds into a tight hairpin of amphipathic helices. Consistently, mutations reducing RemCA amphipathy abolished StREM1.3 PM localization. Furthermore, RemCA directly binds to biological membranes in vitro, shows higher affinity for Detergent-Insoluble Membranes (DIM) lipids, and targets YFP to DIMs in vivo. Mutations in RemCA resulting in cytoplasmic StREM1.3 localization abolish StREM1.3 function in restricting potato virus X movement. The mechanisms described here provide new insights on the control and function of lateral segregation of plant PM. [less ▲]

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See detailCharacterization of the interaction of xylose-based bolaamphiphiles with biomimetic membrane systems
Nasir, Mehmet Nail ULg; Legrand, Vincent; Gatard, Sylvain et al

Conference (2012, July)

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See detailCalcium-induced conformational changes of the elicitor and membrane-active fengycin
Nasir, Mehmet Nail ULg; Lins, Laurence ULg; Ongena, Marc ULg et al

Poster (2012, April)

Fengycin is a natural lipopeptide synthetized by Bacillus subtilis strains. It is characterized by strong antifungal and low hemolytic activities. It seems also play a role in the promoting of elicitor ... [more ▼]

Fengycin is a natural lipopeptide synthetized by Bacillus subtilis strains. It is characterized by strong antifungal and low hemolytic activities. It seems also play a role in the promoting of elicitor activities of other compounds. The target of the biological activities of fengycin is supposed to be plasma membrane of sensitive cells. Even though the natural fengycin from has been discovered 25 years ago, nowadays, there is an increase of interest for this compound because of its potent applications. Until 15 years ago, the primary structure of fengycin was a matter of open debate before the publication of the corrected structure obtained by nuclear magnetic resonance and mass spectroscopy techniques. Although the infrared and ultraviolet absorption spectra of the lipopeptide were measured, no detailed analysis of these data was performed probably because of the unconventional sequence of the lipopeptide making these kinds of analyses complicated. In this work, our attempt was to analyze the conformational properties of fengycin as well as the calcium-induced changes using two complementary spectroscopic methods, Fourrier transformed infrared spectroscopy (FTIR) and circular dichroism (CD). In a first step, we have characterized the conformational properties of pure fengycin. The lipopeptide adopts turn conformation in trifluoroethanol, a membrane-mimicking solvent. D-aminoacids seem to be involved in intra molecular hydrogen bonds. In a second step, we have investigated the role played by Ca2+ ions on the possible conformational changes of fengycin. The addition of calcium gives rise to important modifications of the conformation. As fengycin has two glutamate residues, calcium is supposed to bind to their side chains. In conclusion, we have demonstrated that the conformation of fengycin is closely depending of the environment and the presence of calcium ions play an important role on the conformational changes of the lipopeptide. Moreover, spectra obtained both FTIR and CD methods ascertain the presence of turn conformation. [less ▲]

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See detailHow does elicitor and antimicrobial fengycin interact with plasma membranes of sensitive cells ?
Nasir, Mehmet Nail ULg; Eeman, Marc; Lins, Laurence ULg et al

Conference (2012, April)

Fengycin is characterized by its strong antifungal and low hemolytic activities. It has also been recently demonstrated that it has plant elicitor properties and is also able to enhance the elicitors’ ... [more ▼]

Fengycin is characterized by its strong antifungal and low hemolytic activities. It has also been recently demonstrated that it has plant elicitor properties and is also able to enhance the elicitors’ activity of surfactin. The cell target of its biological activities is supposed to be plasma membrane. In spite of these interesting biological activities, fengycin has not been extensively investigated probably because of the difficulties related to its production. In a first time; we have characterized the interfacial properties of fengycin by tensiometry measurements and demonstrated that this surface activity was pH-dependent. In a second time; we have investigated the interactions of the lipopeptide with membrane lipids using model membranes such as Langmuir monolayers and multilammelar vesicles (MLVs). Our results indicate that the lipopeptide was able to penetrate into different lipid monolayers showing a preference for sterol-containing monolayers. In order to better understand the mechanism of the interactions of fengycin with membranes at the molecular level, MLVs with or without fengycin have been analyzed by spectroscopic techniques. We have shown that conformational changes of the lipopeptide occurred in the presence of lipids and they were more significant in the presence of sterol. Moreover, tyrosine residues of the lipopeptide seem to play an important role in these interactions. In conclusion, we have determined that the surface-active behavior as well as the conformation of fengycin depends on its environment. We have also showed that the lipopeptide does not interact with all class of lipids in the same way and presents a preference for sterols. The presence of key groups within peptide cycle has also been supposed for the biological activities of the lipopeptide. [less ▲]

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See detailReplacing explicit water and membrane molecules in molecular dynamics simulation to boost simulation speed
Steinhauer, Sven ULg; Crowet, Jean-Marc ULg; Lins, Laurence ULg et al

Poster (2012, February 10)

Molecular dynamics (MD) is an appropriate method for investigation of biomolecular systems and helps in explaining results from wet lab experiments or in getting further insight into details, which are ... [more ▼]

Molecular dynamics (MD) is an appropriate method for investigation of biomolecular systems and helps in explaining results from wet lab experiments or in getting further insight into details, which are not accessible by experimental methods(Lindahl, 2008). By now, many biologically relevant processes for drug design, toxicological studies and other fields of application, can not be performed by atomistic MD simulations (Lindahl, 2008). In MD, the necessary time effort for carrying out a simulation is considerable and depends mainly on (1) the complexity of the simulated system (2) the simulated time scale (3) the simulation method (4) the efficiency of used hardware and software algorithms. Carried out MD simulations nowadays may still take weeks of calculation on high end computers. In practice, biologically relevant processes, as e.g. protein folding, take usually place above the time scale of milli seconds. They can take up to the order of some thousands of seconds (in case of the folding of membrane proteins). Molecular dynamics computer simulations have reached the scale of micro seconds for simulations of systems where each atom was described and simulated over time.(Lindahl, 2008) Nevertheless, MD has risen to an important promoter methodology for many different fields of application. By replacing bunches of atoms by artificial particles, complexity of the systems can be reduced. This method is called the coarse grain method (CG). Biggin and Bond (2008) found an acceleration of their simulation processes for self assembling membrane / protein systems in water by factor 100. They estimated one to two days of calculation for a simulated time scale of 0.1 to 0.2 micro seconds for their systems. Implicit force fields like "IMPALA", aim to describe water and/or membrane molecules in simulations by a couple of simple and partially precalculable equations. “IMPALA” is a force field initially developed by our laboratory. Using this method, thousands of water and lipid molecules can be replaced, leading to a reduced complexity of the system to be simulated. "IMPALA"(Ducarme et al., 1998) based on the assumption of rigid peptides and aimed to find the insertion characteristics of such in membranes. Elimination of the necessity for simulating the aqueous and lipid phase atom by atom in the software package "Gromacs"(Berendsen et al., 1995) will permit both: a gain of speed, as it was already the case for the introduction of the coarse grain method, and a gain of precision by turning rigid molecules flexible through "Gromacs". Our current work is the integration of the "IMPALA" implicit force field into "Gromacs". Biggin, P.C. & Bond, P.J. Molecular dynamics simulations of membrane proteins. Methods Mol. Biol. 443, 147-60(2008). Berendsen, et al. (1995) Comp. Phys. Comm. 91: 43-56. Ducarme, P., Rahman, M. & Brasseur, R. IMPALA: a simple restraint field to simulate the biological membrane in molecular structure studies. Proteins 30, 357-71(1998). Lindahl, E.R. (2008). Molecular dynamics simulations. Methods Mol. Biol. 443, 3-23. [less ▲]

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See detailMulti-Scale Simulation of the Simian Immunodeficiency Virus Fusion Peptide.
Crowet, Jean-Marc ULg; Parton, Daniel L.; Hall, Benjamin A. et al

in Journal of Physical Chemistry B (2012)

Fusion peptides of type I fusion glycoproteins are structural elements of several enveloped viruses which enable the fusion between host and virus membranes. It is generally suggested that these peptides ... [more ▼]

Fusion peptides of type I fusion glycoproteins are structural elements of several enveloped viruses which enable the fusion between host and virus membranes. It is generally suggested that these peptides can promote the early fusion steps by inducing membrane curvature and that they adopt a tilted helical conformation in membranes. Although this property has been the subject of several experimental and in silico studies, an extensive sampling of the membrane peptide interaction has not yet been done. In this study, we performed coarse-grained molecular dynamic simulations in which the lipid bilayer self-assembles around the peptide. The simulations indicate that the SIV fusion peptide can adopt two different orientations in a DPPC bilayer, a major population which adopts a tilted interfacial orientation and a minor population which is perpendicular to the bilayer. The simulations also indicate that for the SIV mutant that does not induce fusion in vitro the tilt is abolished. [less ▲]

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See detailIn silico predictions of 3D structures of linear and cyclic peptides with natural and non-proteinogenic residues.
Beaufays, Jérôme ULg; Lins, Laurence ULg; Thomas, Annick ULg et al

in Journal of Peptide Science : An Official Publication of the European Peptide Society (2012), 18(1), 17-24

We extended the use of Peplook, an in silico procedure for the prediction of three-dimensional (3D) models of linear peptides to the prediction of 3D models of cyclic peptides and thanks to the ab initio ... [more ▼]

We extended the use of Peplook, an in silico procedure for the prediction of three-dimensional (3D) models of linear peptides to the prediction of 3D models of cyclic peptides and thanks to the ab initio calculation procedure, to the calculation of peptides with non-proteinogenic amino acids. Indeed, such peptides cannot be predicted by homology or threading. We compare the calculated models with NMR and X-ray models and for the cyclic peptides, with models predicted by other in silico procedures (Pep-Fold and I-Tasser). For cyclic peptides, on a set of 38 peptides, average root mean square deviation of backbone atoms (BB-RMSD) was 3.8 and 4.1 A for Peplook and Pep-Fold, respectively. The best results are obtained with I-Tasser (2.5 A) although evaluations were biased by the fact that the resolved Protein Data Bank models could be used as template by the server. Peplook and Pep-Fold give similar results, better for short (up to 20 residues) than for longer peptides. For peptides with non-proteinogenic residues, performances of Peplook are sound with an average BB-RMSD of 3.6 A for 'non-natural peptides' and 3.4 A for peptides combining non-proteinogenic residues and cyclic structure. These results open interesting possibilities for the design of peptidic drugs. Copyright (c) 2011 European Peptide Society and John Wiley & Sons, Ltd. [less ▲]

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See detailModeling of non-covalent complexes of the cell-penetrating peptide CADY and its siRNA cargo.
Crowet, Jean-Marc ULg; Lins, Laurence ULg; Deshayes, Sebastien et al

in Biochimica et Biophysica Acta (2012)

CADY is a cell-penetrating peptide spontaneously making non-covalent complexes with siRNAs in water. Neither the structure of CADY nor that of the complexes is resolved. We have calculated and analyzed 3D ... [more ▼]

CADY is a cell-penetrating peptide spontaneously making non-covalent complexes with siRNAs in water. Neither the structure of CADY nor that of the complexes is resolved. We have calculated and analyzed 3D models of CADY and of the non-covalent CADY-siRNA complexes in order to understand their formation and stabilization. Data from the ab initio calculations and molecular dynamics support that, in agreement with the experimental data, CADY is a polymorphic peptide partly helical. Taking into consideration the polymorphism of CADY, we calculated and compared several complexes with peptide/siRNA ratios of up to 40. Four complexes were run by using molecular dynamics. The initial binding of CADYs is essentially due to the electrostatic interactions of the arginines with siRNA phosphates. Due to a repetitive arginine motif (XLWR(K)) in CADY and to the numerous phosphate moieties in the siRNA, CADYs can adopt multiple positions at the siRNA surface leading to numerous possibilities of complexes. Nevertheless, several complex properties are common: an average of 14+/-1 CADYs is required to saturate a siRNA as compared to the 12+/-2 CADYs experimentally described. The 40 CADYs/siRNA that is the optimal ratio for vector stability always corresponds to two layers of CADYs per siRNA. When siRNA is covered by the first layer of CADYs, the peptides still bind despite the electrostatic repulsion. The peptide cage is stabilized by hydrophobic CADY-CADY contacts thanks to CADY polymorphism. The analysis demonstrates that the hydrophobicity, the presence of several positive charges and the disorder of CADY are mandatory to make stable the CADY-siRNA complexes. [less ▲]

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See detailInteraction network of antimicrobial peptides of Arabidopsis thaliana, based on hith-throughput yeast two-hybrid screening
Damon, Coralie ULg; Dmitrieva, Joelia Borisnova; Muhovski, Yordan et al

in Plant Physiology & Biochemistry (2012)

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See detailLiquid Crystalline Phases Induced by the Hydroxyl Group Stereochemistry of Amphiphilic Carbohydrate Bicatenary Derivatives
Razafindralambo, Hary ULg; Richel, Aurore ULg; Paquot, Michel ULg et al

in Journal of Physical Chemistry B (2012), 116(13), 3998-4005

Liquid-crystals (LC) may exist in different phases depending upon the orientational and positional orders of molecules in the material. Here, we demonstrate that the class of LC state induced by ... [more ▼]

Liquid-crystals (LC) may exist in different phases depending upon the orientational and positional orders of molecules in the material. Here, we demonstrate that the class of LC state induced by amphiphilic carbohydrate bicatenary derivatives is strictly a hydroxyl group stereochemistry-dependent. This statement results from the experimental and theoretical investigations of surface film (2D) and bulk solid (3D) thermal behavior of synthetic stereoisomers n-tetradecyl (-D-n-tetradecyl) galacto- and gluco-pyranosiduronate, with an axial (GalA-C14/14) or equatorial (GlcA-C14/14) hydroxyl group at the fourth carbon, respectively. Surface pressure-area isotherms (283 K to 310 K), differential scanning calorimetry thermograms (223 K to 573 K), and polarized optical textures (298-363 K) reveal that GlcA-C14/14 organizes as a smectic LC-like phase (positional or lateral order) whereas the analogous stereoisomeric GalA-C14/14 behaves as a nematic LC-like phase (orientational order). Thermodynamic investigations and molecular dynamics models computed under similar temperature conditions provide consistent data with physical properties resulting from experimental approaches. [less ▲]

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See detailInteraction of Hexadecylbetainate Chloride with Biological Relevant Lipids
Nsimba Zakanda, Francis; Lins, Laurence ULg; Nott, Katherine ULg et al

in Langmuir (2012), 28(7), 3524-3533

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