bluuebunny/crossref_metadata_2025_split huggingface dataset:
Side chain‐to‐side chain cyclization by click reaction
Authors: Le Chevalier Isaad Alexandra , Papini Anna Maria , Chorev Michael , Rovero Paolo 
Published: May 2009

AbstractCuI‐catalyzed azide‐alkyne 1,3‐dipolar Huisgen's cycloaddition (CuAAC) is a click reaction that has drawn a lot of attention, in general, and in the field of peptide and protein sciences, in particular. Among several reported applications, the preparation of novel heterodetic cyclopeptides by an intramolecular side chain‐to‐side chain CuAAC, forming a 1,4‐disubstituted[1,2,3]triazolyl‐containing bridge, is of great interest. Herein, we provide a detailed protocol for the syntheses of model heterodetic cyclopeptides as a prototypical intramolecular CuAAC, using as a model a sequence derived from parathyroid hormone‐related protein. Copyright © 2009 European Peptide Society and John Wiley & Sons, Ltd.
Different mechanisms of action of antimicrobial peptides: insights from fluorescence spectroscopy experiments and molecular dynamics simulations
Authors: Bocchinfuso Gianfranco , Palleschi Antonio , Orioni Barbara , Grande Giacinto , Formaggio Fernando , Toniolo Claudio , Park Yoonkyung , Hahm Kyung‐Soo , Stella Lorenzo 
Published: May 2009

AbstractMost antimicrobial peptides exert their activity by interacting with bacterial membranes, thus perturbing their permeability. They are investigated as a possible solution to the insurgence of bacteria resistant to the presently available antibiotic drugs. However, several different models have been proposed for their mechanism of membrane perturbation, and the molecular details of this process are still debated. Here, we compare fluorescence spectroscopy experiments and molecular dynamics (MD) simulations regarding the association with lipid bilayers and lipid perturbation for two different amphiphilic helical antimicrobial peptides, PMAP‐23 and trichogin GA IV. PMAP‐23, a cationic peptide member of the cathelicidin family, is considered to induce membrane permeability according to the Shai‐Matsuzaki‐Huang “carpet” model, while trichogin GA IV is a neutral peptide, member of the peptaibol family. Although several lines of evidence suggest a “barrel‐stave” mechanism of pore formation for the latter peptide, its length is only half the normal thickness of a lipid bilayer. Both fluorescence spectroscopy experiments and MD simulations indicated that PMAP‐23 associates with membranes close to their surface and parallel to it, and in this arrangement it causes a severe perturbation to the bilayer, both regarding its surface tension and lipid order. By contrast, trichogin GA IV can undergo a transition from a surface‐bound state to a transmembrane orientation. In the first arrangement, it does not cause any strong membrane perturbation, while in the second orientation it might be able to span the bilayer from one side to the other, despite its relatively short length, by causing a significant thinning of the membrane. Copyright © 2009 European Peptide Society and John Wiley & Sons, Ltd.
Identification of Novel Scaffolds from an Original Chemical Library as Potential Antipsychotics
Authors: Gutiérrez‐de‐Terán Hugo , Correia Carla , Rodríguez David , Carvalho Maria Alice , Brea Jose , Cadavid María Isabel , Loza María Isabel , Proença Maria Fernanda , Areias Filipe 
Published: May 2009

AbstractThe ligand‐based virtual screening of an original chemical library, using atypical antipsychotics as query compounds led to the identification of a novel scaffold with inhibitory activity at the 5‐HT2Aserotonin receptor. The hit compounds were confirmed by pharmacological evaluation at the 5‐HT2Areceptor and complemented by the selection of other representatives of the same chemical family within our chemical library. A promising scaffold of 6‐(pyperazin‐1‐yl) purine was identified, and the binding mode is illustrated with an automated docking exploration on a homology built model of the 5‐HT2Areceptor. The present results constitute an excellent starting point for the discovery of new chemical entities with antipsychotic activity.
Peculiarities of conductance of carbon nanotube‐based quantum dots
Authors: Ogloblya O. V. , Prylutskyy Yu. I. , Strzhemechny Yu. M. 
Published: May 2009

AbstractWithin the framework of the surface Green's function matching method, we carried out calculations of the differential conductance of symmetrically and asymmetrically connected armchair (n, n)—zigzag (2n, 0)—armchair (n, n) carbon nanotubes with different lengths of the middle section and infinitely long ends. It is shown that the (n, n)/(2n, 0)/(n, n) segment, when n is not a multiple of 3, behaves as a quantum dot and has a conduction gap even for short middle segments. The position of the conductance peeks closest to the Fermi energy is determined by the interface states of the (n, n)/(2n, 0) junction. In addition to conductance peaks originating from the interface states of the (n, n)/(2n, 0) heterojunction, for sufficiently long middle zigzag nanotube, there are more conductance peaks in the vicinity of the Fermi energy, and those stem from the electronic structure of an individual finite (2n, 0) zigzag nanotube. However, positions of the peaks farther away from the Fermi energy cannot be found in such a simple way. Thus, such (n, n)/(2n, 0)/(n, n) quantum dot has singularities in its electronic properties, which may yield the Coulomb blockade effect should those strongly localized discrete levels become occupied. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Lipid–nucleic acids interactions as base for organization and expression of cellular genome
Authors: Kuvichkin V. V. 
Published: May 2009

AbstractAlthough lipid–nucleic acid interactions have been studied, with certain or little progress, for more than 30 years, it is only in recent years that the problem has received particular attention. It should, however, be noted that most studies deal with DNA‐cationic surfactants interactions, whereas DNA‐zwitterionic interactions, which are more complex and close to nature, are poorly investigated. The long‐standing studies of the triple complexes: DNA–phosphatidylcholine liposomes–divalent metal cations allow us to confirm that these complexes are responsible for the formation of not only the structures existing in DNA–cationic liposome complexes but also some other cellular structures. The author proposed hypothesis about the involvement of direct DNA–lipid interactions in the nuclear pore assembly. Only taking into account interactions between DNA and lipids of cellular membrane, one can explain the origin of such structures as nucleoid, nuclear pore, and nuclear matrix. The formation of triple complexes was accompanied by the aggregation and partial fusion of liposomes as was shown by cryo‐TEM technique. The author has presented new data on the structure of triple complexes, which were obtained by phase contrast cryo‐TEM. Biophysical data on the liposomes fusion during triple complex formation and perspective of their computer simulation are also presented. DNA acts as a fusogen in this process and it unwinds in the region of liposomes fusion. The nuclear envelope and pore complexes assembly is provided by membrane vesicles fusion. Author has proposed that the DNA‐induced fusion of zwitterionic liposomes in vitro may suggest the involvement of direct lipids–DNA interaction in nuclear envelope assembly. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Three‐dimensional H‐bonding and ferroelectric transition in KDP. Quantum‐chemical study
Authors: Dolin S. P. , Mikhailova T. Yu. , Solin M. V. , Breslavskaya N. N. , Levin A. A. 
Published: May 2009

AbstractOn basis of the nonempirical methods (SCF, B3LYP, MP2‐MP4) and several cluster models, the ferroelectric KH2PO4 (KDP) and its deuteroanalogue are studied. The tunneling integrals Ω and the parameters of the effective coupling of protons/deuterons U,V (the Ising parameters) are calculated for these materials with the 3d network of H/D‐bonds. Using the obtained U,V and Ω values in the frames of molecular field approximation, it is found that the structural phase (ferroelectric) transition occurs for both crystals within the lowering of temperature. Such low‐temperature behavior differs the 3d KDP‐family materials from 0d systems, where the low‐temperature phase transition takes place only upon deuteration. It is demonstrated that this difference is associated with an abrupt Ising parameters growth for KDP if compared with the nondeuterated 0d materials. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Interplaying roles of native topology and chain length in marginally cooperative and noncooperative folding of small protein fragments
Authors: Badasyan Artem , Liu Zhirong , Chan Hue Sun 
Published: May 2009

AbstractCoarse‐grained chain simulations were used to study fragments of two homologous proteins of the peripheral subunit‐binding domain (PSBD) family, Bacillus stearothermophilus PSBD (E3BD) and Escherichia coli 2‐oxo‐glutarate dehydrogenase PSBD (BBL). To ascertain a robust rank order of folding cooperativity, native‐centric intraprotein interactions were modeled by (i) a common Gō‐like potential, and (ii) native‐centric potentials with desolvation barriers or (iii) many‐body terms. Homologous proteins can possess substantially different folding cooperativity. Consistent with experiment, our calculations indicated that E3BD fragments fold more cooperatively than BBL fragments of approximately the same chain length. For a given fragment, native contacts deduced from Protein Data Bank structures can vary significantly depending on the number of residues that the structure encompasses in addition to those of the fragment itself, resulting in variation in model folding cooperativity predicted using different native contact sets for the same fragment. This observation underscores that folding cooperativity of these fragments can be extremely sensitive to change in chain length. Thus, a ∼40‐residue protein fragment's folding cooperativity, or lack thereof, does not necessarily imply essentially identical behaviors for super‐ or sub‐fragments with only several residues more, or less, than the given fragment. Ramifications for experimental investigations of downhill folding are discussed. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Image‐guided navigation: the surgeon's perspective on performance consequences and human factors issues
Authors: Manzey Dietrich , Röttger Stefan , Bahner‐Heyne J. Elin , Schulze‐Kissing Dirk , Dietz Andreas , Meixensberger Jürgen , Strauss Gero 
Published: May 2009

AbstractBackgroundImage‐guided navigation (IGN) represents a first step in the automation of surgical functions. The use of IGN can involve several human factors issues that must be taken into account when evaluating their impact on surgical performance and patient safety.MethodsA nationwide survey was conducted among 213 surgeons from 112 German hospitals in order to assess the perceived performance consequences and human factors issues of IGN, including changes of situation awareness, performance and workload, as well as issues of overreliance, skill degradation and usability.ResultsGenerally, surgeons report improved performance and patient safety related to the use of IGN. However, issues of increased time pressure and mental demands were reported by inexperienced users. Furthermore, overreliance on IGN represents a risk, albeit only in a minority of respondents.ConclusionsIGN is evaluated as a helpful tool for surgeons. However, special care should be taken to provide surgeons with sufficient time and training during familiarization with an IGN system. Copyright © 2009 John Wiley & Sons, Ltd.
Syntheses and Crystal Structures of PbSbO2Br, PbSbO2I, and PbBiO2Br
Authors: Pfitzner Arno , Pohla Patrick 
Published: May 2009

AbstractTransparent single crystals of PbSbO2Br (green), PbSbO2I, and PbBiO2Br (yellow) were obtained by solid state reactions of stoichiometric amounts of PbO, Pn2O3 (Pn = Sb, Bi) and PnX3 (X = Br, I). The crystal structures were determined from single‐crystal X‐ray data. The title compounds crystallize tetragonally in the space group I4/mmm (No. 139): Lattice constants and refinement values are: PbSbO2Br: a = 3.9463(3), c = 12.849(1) Å, V = 200.10(3) Å3, and Z = 2, R1 = 0.0236, and wR2 = 0.0513. PbSbO2I: a = 4.0074(3), c = 13.627(2) Å, V = 218.84(3) Å3, and Z = 2, R1 = 0.0244, and wR2 = 0.0538. PbBiO2Br: a = 3.9818(2), c = 12.766(2) Å, V = 202.39(4) Å3, and Z = 2, R1 = 0.0276, and wR2 = 0.0715. The compounds are isotypic and crystallize in the anti‐ThCr2Si2 structure type with lead and Pn statistically disordered on one common position. In case of Pn = Sb a slight separation of the positions of the cations becomes obvious. Optical bandgaps were determined by UV/Vis spectroscopy. They are 2.67 eV (PbSbO2Br), 2.48 eV (PbSbO2I), and 2.47 eV (PbBiO2Br).
The two major capitals in the crypt of Saint-Bénigne at Dijon
Authors: Wood Rita 
Published: May 2009

AbstractThe three-storey rotunda at Dijon, built by William of Volpiano and consecrated in 1018, has been reduced to its crypt, but an impressive pair of capitals survive adjacent to the burial place of St Bénigne. In modern times these capitals have repeatedly been described as full of monsters, and their significance for Romanesque sculpture has consequently been neglected. Enough remains of their dense, three-dimensional sculpture for them to be identified as representing, in fact, a lesson commonly read in masses for the dead. Numerous saints and martyrs were marked by burials in the crypt or by altars in the rotunda. All Saints’ Day was celebrated on 1 November, so that the main feast day of St Bénigne was transferred to 2 November. About 998, the commemoration of All Souls, also on 2 November, had been introduced by Odilo, Abbot of Cluny, and is likely to have been adopted by Abbot William. The text from 1 Thessalonians suggests the imaginative use of the rotunda’s vertical dimension, at this particular season and others.
Resonant Weibel instability in counterstreaming plasmas with temperature anisotropies
Authors: LAZAR M. , DIECKMANN M. E. , POEDTS S. 
Published: May 2009

AbstractThe Weibel instability, driven by a plasma temperature anisotropy, is non-resonant with plasma particles: it is purely growing in time, and does not oscillate. The effect of a counterstreaming plasma is examined. In a counterstreaming plasma with an excess of transverse temperature, the Weibel instability arises along the streaming direction. Here it is proved that for large wave-numbers the instability becomes resonant with a finite real (oscillation) frequency, ωr ≠ 0. When the plasma flows faster, with a bulk velocity larger than the parallel thermal velocity, the instability becomes dominantly resonant. This new feature of the Weibel instability can be relevant for astrophysical sources of non-thermal emissions and the stability of counterflowing plasma experiments.
Stability of ion–acoustic solitary waves in a multi-species magnetized plasma consisting of non-thermal and isothermal electrons
Authors: ISLAM SK. ANARUL , BANDYOPADHYAY A. , DAS K. P. 
Published: May 2009

AbstractA theoretical study of the first-order stability analysis of an ion–acoustic solitary wave, propagating obliquely to an external uniform static magnetic field, has been made in a plasma consisting of warm adiabatic ions and a superposition of two distinct populations of electrons, one due to Cairns et al. and the other being the well-known Maxwell–Boltzmann distributed electrons. The weakly nonlinear and the weakly dispersive ion–acoustic wave in this plasma system can be described by the Korteweg–de Vries–Zakharov–Kuznetsov (KdV-ZK) equation and different modified KdV-ZK equations depending on the values of different parameters of the system. The nonlinear term of the KdV-ZK equation and the different modified KdV-ZK equations is of the form [φ(1)]ν(∂φ(1)/∂ζ), where ν = 1, 2, 3, 4; φ(1) is the first-order perturbed quantity of the electrostatic potential φ. For ν = 1, we have the usual KdV-ZK equation. Three-dimensional stability analysis of the solitary wave solutions of the KdV-ZK and different modified KdV-ZK equations has been investigated by the small-k perturbation expansion method of Rowlands and Infeld. For ν = 1, 2, 3, the instability conditions and the growth rate of instabilities have been obtained correct to order k, where k is the wave number of a long-wavelength plane-wave perturbation. It is found that ion–acoustic solitary waves are stable at least at the lowest order of the wave number for ν = 4.
THE EVOLVING CONTEXT OF THE FUNDAMENTAL DIFFERENCE HYPOTHESIS
Authors: Bley-Vroman Robert 
Published: May 2009

Foreign language learning contrasts with native language development in two key respects: It is unreliable and it is nonconvergent. At the same time, it is clear that foreign languages are languages. The fundamental difference hypothesis (FDH) was introduced as a way to account for the general characteristics of foreign language learning. The FDH was originally formulated in the context of the theory of rich Universal Grammar, and this theory has guided much foreign language acquisition research over the past two decades. However, advances in the understanding of language have undermined much of the supporting framework.The FDH—indeed all of SLA research—must be rethought in light of these advances. It is proposed here that (a) foreign language grammars make central use of patches, which are also seen as peripheral phenomena in native languages; (b) non-domain-specific processes are used in foreign language acquisition, but that these are also employed—although more effectively because they are integrated into the language system—by native language development; and (c) foreign language online processing relies heavily on the use of shallow parses, but these are also available in native language processing, although less crucially.
Automatic ontology creation using adaptation
Authors: Cross Valerie , Bathija Vishal 
Published: May 2009

AbstractOntologies are an emerging means of knowledge representation to improve information organization and management, and they are becoming more prevalent in the domain of engineering design. The task of creating new ontologies manually is not only tedious and cumbersome but also time consuming and expensive. Research aimed at addressing these problems in creating ontologies has investigated methods of automating ontology reuse mainly by extracting smaller application ontologies from larger, more general purpose ontologies. Motivated by the wide variety of existing learning algorithms, this paper describes a new approach focused on the reuse of domain-specific ontologies. The approach integrates existing software tools for natural language processing with new algorithms for pruning concepts not relevant to the new domain and extending the pruned ontology by adding relevant concepts. The approach is assessed experimentally by automatically adapting a design rationale ontology for the software engineering domain to a new one for the related domain of engineering design. The experiment produced an ontology that exhibits comparable quality to previous attempts to automate ontology creation as measured by standard content performance metrics such as coverage, accuracy, precision, and recall. However, further analysis of the ontology suggests that the automated approach should be augmented with recommendations presented to a domain expert who monitors the pruning and extending processes in order to improve the structure of the ontology.
Enterobius vermicularis infection in schoolchildren: a large-scale survey 6 years after a population-based control
Authors: WANG L.-C. , HWANG K.-P. , CHEN E.-R. 
Published: May 2009

SUMMARYPinworm infection remains prevalent in children in many parts of the world. This study was designed to determine the prevalence of this infection in schoolchildren in Taiwan after the termination of the 15-year population-based control project in 2001. Our results showed that 2·4% of 118 190 children in 385 primary schools were found to have enterobiasis by two-consecutive-day adhesive cellophane perianal swabs. The prevalences were significantly different in the 25 counties/cities surveyed (0·6–6·6%). A significantly higher prevalence was found in boys (2·6%) than in girls (2·2%) and the prevalence decreased by grade from 3·8% in grade 1 to 1·0% in grade 6. In the primary schools, 9·1% had positive rates ⩾10%. In addition, pinworm infection was found to be significantly associated with the socioeconomic status, personal hygiene and sanitary conditions of the children. The results indicate that the overall prevalence of enterobiasis remains at a low level after the control programme was transferred to the local governments.
Pulmonary diffuse arterial calcifications: a very rare complication in the recipient of a twin-to-twin transfusion syndrome
Authors: Bassil Eter Rania , Dulac Yves , Acar Philippe 
Published: May 2009

AbstractThe syndrome of twin-to-twin transfusion is known potentially to be associated with the development of right ventricular obstruction, albeit rarely at supravalvar levels, in the recipient twin. We report the case of a recipient twin with diffuse hypoplasia and calcification of the pulmonary arterial tree, confirmed by postnatal thoracic angioscan. When aged 2 years, the child was moderately symptomatic with mild cyanosis, in spite of suprasystemic right ventricular systolic pressure as revealed by follow-up echocardiography.
Association of school performance indicators with implementation of the Healthy Kids, Smart Kids programme: case study
Authors: Nansel Tonja R , Huang Terry TK , Rovner Alisha J , Sanders-Butler Yvonne 
Published: May 2009

AbstractObjectiveThe purpose of the present analysis was to examine secular trends in school performance indicators in relationship to the implementation of a programme targeting the school food and physical activity environment.DesignData on available school performance indicators were obtained; retrospective analyses were conducted to assess trends in indicators in association with programme implementation; each outcome was regressed v. year, beginning with the year prior to programme implementation.SettingThe Healthy Kids, Smart Kids programme, a grass-roots effort to enhance the school food and physical activity environment in the Browns Mill Elementary School in Georgia.SubjectsData included publicly available school records from the years 1995 to 2006.ResultsThe number of nurse, counselling and disciplinary referrals per 100 students demonstrated a downward trend, while standardized test scores demonstrated an upward trend beginning in the year of programme implementation. School year was a significant predictor of all indicators.ConclusionsPromoting nutrition and physical activity within the school environment may be a promising approach for enhancing both student health and educational outcomes.
Chained to cannons or wearing targets on their T-shirts: human shields in international humanitarian law
Authors: de Belle Stéphanie Bouchié 
Published: May 2009

AbstractThis article examines the legal problems associated with human shields. The author begins by discussing the absolute nature of the prohibition on their use and goes on to consider the precautions to be observed by the party being attacked. A violation of the ban on use of human shields by the attacked party is not an act of perfidy and does not release the attacker from his obligations. Because human shields are civilians, they are not legitimate objects of attack, even where they are acting in a voluntary capacity, as they are not taking direct part in hostilities. Among the attacker's obligations to take precautions, the proportionality principle applies in the classic way, even in the case of voluntary human shields.