bluuebunny/crossref_metadata_2025_split huggingface dataset:
User preference: A measure of query‐term quality
Authors: Wacholder Nina , Liu Lu 
Published: August 2006

AbstractThe goal of this research is to understand what characteristics, if any, lead users engaged in interactive information seeking to prefer certain sets of query terms. Underlying this work is the assumption that query terms that information seekers prefer induce a kind of cognitive efficiency: They require less mental effort to process and therefore reduce the energy required in the interactive information‐seeking process. Conceptually, this work applies insights from linguistics and cognitive science to the study of query‐term quality. We report on an experiment in which we compare user preference for three sets of terms; one had been preconstructed by a human indexer, and two were identified automatically. Twenty‐four participants used a merged list of all terms to answer a carefully created set of questions. By design, the interface constrained users to access the text exclusively via the displayed list of query terms. We found that participants displayed a preference for the human‐constructed set of terms eight times greater than the preference for either set of automatically identified terms. We speculate about reasons for this strong preference and discuss the implications for information access. The primary contributions of this research are (a) explication of the concept of user preference as a measure of query‐term quality and (b) identification of a replicable procedure for measuring preference for sets of query terms created by different methods, whether human or automatic. All other factors being equal, query terms that users prefer clearly are the best choice for real‐world information‐access systems.
Fluorescence and bioluminescence analysis of sequential UV‐biological degradation of p‐cresol in water
Authors: Tchaikovskaya O. , Sokolova I. , Svetlichnyi V. , Karetnikova E. , Fedorova E. , Kudryasheva N. 
Published: August 2006

AbstractThe photolysis and Penicillium tardum H‐2 degradation of p‐cresol in water containing humic acids was investigated by fluorescence and bioluminescence methods. Humic acids extracted from peat (the Vasuygan bog, Tomsk region of Russia) induce the phototransformation of p‐cresol. The influence of humic acids on the phototransformation of p‐cresol under different irradiation conditions was investigated. Comparison of the data on the KrCl* (λ = 222 nm) and XeCl* (λ = 308 nm) excilamps light showed that the most effective p‐cresol degradation was observed with mercury lamp irradiation in the presence of humic acids. Copyright © 2006 John Wiley & Sons, Ltd.
Peptide design of a competitive inhibitor for HMG‐CoA reductase based on statin structure
Authors: Pak Valeriy V. , Kim Sung Hee , Koo Minseon , Lee Nari , Shakhidoyatov K. M. , Kwon Dae Young 
Published: August 2006

AbstractThis study investigates a proposed design of a peptide sequence that is based on a bioactive conformation of statins that act as the competitive inhibitors of HMG–CoA for HMGR. To bridge these heterogeneous organic compounds, a conformational aspect relating to an analysis of the flexibility of the peptide molecules and their occupied volumes was applied to the peptide design. The design criterion was formulated in terms of a proximity parameter (Pr), reflecting the probability of an active peptide conformation to approximate the statin. Through a structure–functional analysis of previously synthesized peptides and statin molecules, nine peptides were selected for the peptide library. Comparing the calculated proximity parameters, four peptides (IAVE, YAVE, IVAE, and YVAE) from the library were selected and synthesized. In vitro assays elucidated the inhibition properties for HMGR that are exhibited by these peptides. Among all peptides, YVAE showed the highest ability to inhibit HMGR. A kinetic analysis revealed that this peptide is a competitive inhibitor of HMG–CoA with an equilibrium constant of inhibitor binding (Ki) of 15.2 ± 1.4 μM. The calculated coefficient correlation (R) between log (IC50) and the inverse value of proximity parameter (1/Pr) was found to be 0.99, indicating a high degree of correlation and efficacy of the given approach in the peptide sequence design. © 2006 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 84: 586–594, 2006This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Vibrational spectroscopic characteristics of secondary structure polypeptides in liquid water: Constrained MD simulation studies
Authors: Choi Jun‐Ho , Hahn Seungsoo , Cho Minhaeng 
Published: August 2006

AbstractUsing the constrained MD simulation method in combination with quantum chemistry calculation, Hessian matrix reconstruction, and fragmentation approximation methods, we established a computational scheme for numerical simulations of amide I IR absorption, vibrational circular dichroism (VCD), and 2D IR photon echo spectra of peptides in solution. Six different secondary structure peptides, i.e., α‐helix, 310‐helix, π‐helix, antiparallel and parallel β‐sheets, and polyproline II (PII), are considered, and the vibrational characteristic features in their linear and nonlinear spectra in the amide I band region are discussed. Isotope‐labeling effects on IR and VCD spectra are notable only for α‐ and π‐helical peptides due to the strong vibrational couplings between two nearest neighboring amide I local oscillators. The amplitudes of difference 2D IR spectra are shown to be strongly dependent on both the extent of mode delocalization and the relative orientation of local mode transition dipoles determined by secondary structure. © 2006 Wiley Periodicals, Inc. Biopolymers 83: 519–536, 2006This article was originally published online as an accepted preprint. The “Published Online“ date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Randomized clinical trial assessing the effect of Doppler-optimized fluid management on outcome after elective colorectal resection
Authors: Noblett S E , Snowden C P , Shenton B K , Horgan A F 
Published: August 2006

Abstract

Background
Protocolized fluid administration using oesophageal Doppler monitoring may improve the postoperative outcome in patients undergoing surgery.

Methods
A total of 108 patients undergoing elective colorectal resection were recruited into a double-blind prospective randomized controlled trial. An oesophageal Doppler probe was placed in all patients. The control group received perioperative fluid at the discretion of the anaesthetist, whereas the intervention group received additional colloid boluses based on Doppler assessment. Primary outcome was length of postoperative hospital stay. Secondary outcomes were morbidity, return of gastrointestinal function and cytokine markers of the systemic inflammatory response. Standard preoperative and postoperative management was used in all patients.

Results
Demographic and surgical details were similar in the two groups. Aortic flow time, stroke volume, cardiac output and cardiac index during the intraoperative period were higher in the intervention group (P &lt; 0·050). The intervention group had a reduced postoperative hospital stay (7 versus 9 days in the control group; P = 0·005), fewer intermediate or major postoperative complications (2 versus 15 per cent; P = 0·043) and tolerated diet earlier (2 versus 4 days; P = 0·029). There was a reduced rise in perioperative level of the cytokine interleukin 6 in the intervention group (P = 0·039).

Conclusion
A protocol-based fluid optimization programme using intraoperative oesophageal Doppler monitoring leads to a shorter hospital stay and decreased morbidity in patients undergoing elective colorectal resection.
A Simple and Powerful Flow Cytometric Method for the Simultaneous Determination of Multiple Parameters at G Protein‐Coupled Receptor Subtypes
Authors: Schneider Erich , Mayer Matthias , Ziemek Ralf , Li Liantao , Hutzler Christoph , Bernhardt Günther , Buschauer Armin 
Published: August 2006

AbstractThe quantification of pharmacological parameters at G protein‐coupled receptors (GPCRs) is indispensable in drug research but costly and time‐consuming when conventional methods are sequentially applied. With neuropeptide Y (NPY) Y1, Y2, and Y5 receptors as model systems, a homogenous flow cytometric method for the simultaneous determination of the affinity, selectivity, and activity of GPCR ligands was developed. Mixtures of cells expressing the receptors of interest and cyanine‐labeled NPY as a universal fluorescent Y1, Y2, and Y5 receptor agonist were used. Calcium mobilization was measured in different channels with the aid of fluo‐4 and fura red. A combination of dye‐loaded HEL‐Y1 and CHO‐Y2‐Gαqi5 cells with unloaded HEC‐1B‐Y5 cells allowed the simultaneous determination of Y1, Y2, and Y5 receptor selectivity preceded by the Y1 and Y2 receptor‐mediated response with one and the same sample. The data are in good agreement with those determined by radioligand binding and spectrofluorimetry. The convenient, robust, and inexpensive multiparametric procedure offers a broad range of applications in the pharmacological characterization of GPCR ligands.
Molecular Basis of Substrate Recognition in D‐3‐Hydroxybutyrate Dehydrogenase from Pseudomonas putida
Authors: Feller Claudia , Günther Robert , Hofmann Hans‐Jörg , Grunow Marlis 
Published: August 2006

AbstractD‐3‐Hydroxybutyrate dehydrogenase from Pseudomonas putida (EC 1.1.1.30) belongs to the family of short‐chain dehydrogenases/reductases (SDRs). It catalyzes the reversible and stereospecific oxidation of D‐3‐hydroxybutyrate (D‐3‐HB) to acetoacetate with the aid of NAD+ as coenzyme. This study contributes to understanding the mechanism and the high specificity of this enzyme towards its negatively charged and hydrophilic substrate. Sequence comparison of 44 bacterial HBDHs shows the residues Gln91, His141, Lys149, Lys192, and Gln193 to be strictly conserved. Site‐directed mutagenesis of these amino acids to alanine and subsequent kinetic characterization of the mutated enzymes provides insight into the importance of these residues for substrate recognition and catalysis. Docking studies and molecular‐dynamics simulations based on a three‐dimensional structure model of a complex between P. putida HBDH and its coenzyme obtained by comparative molecular modeling were performed and provided deeper insight into the binding of the ligands at the molecular level. They show the residues Gln91, His141, Gln193, and, in particular, Lys149 to be involved in a hydrogen‐bonding network with the carboxylate group of the substrate.
Silica Pattern Formation in Diatoms: Species‐Specific Polyamine Biosynthesis
Authors: Sumper Manfred , Lehmann Gerhard 
Published: August 2006

AbstractDiatoms are eukaryotic, unicellular algae that are well known for the intricate architecture of their silica‐based cell walls. Species identification is mainly based on variations of their hierarchically organized silica structures. Particularly striking silica frameworks are found among diatoms that belong to the genus Coscinodiscus. Recent work indicates an important role for long‐chain polyamines in guiding silica precipitation as well as in silica‐pattern formation. Here we demonstrate that polyamines, even if isolated from closely related diatom species, exhibit substantial structural differences. Structural variations include the overall chain length, the degree of methylation, positions of secondary amino functionalities, and, unexpectedly, site‐specific incorporation of a quaternary ammonium functionality. These findings support a specific role for polyamines in creating silica nanostructures.
Kinetic, Thermodynamic, and Mechanistic Patterns for Free (Unbound) Cytochrome c at Au/SAM Junctions: Impact of Electronic Coupling, Hydrostatic Pressure, and Stabilizing/Denaturing Additives
Authors: Khoshtariya Dimitri E. , Dolidze Tina D. , Seifert Stefan , Sarauli David , Lee Geoffrey , van Eldik Rudi 
Published: August 2006

AbstractCombined kinetic (electrochemical) and thermodynamic (calorimetric) investigations were performed for an unbound (intact native‐like) cytochrome c (CytC) freely diffusing to and from gold electrodes modified by hydroxyl‐terminated self‐assembled monolayer films (SAMs), under a unique broad range of experimental conditions. Our approach included: 1) fine‐tuning of the charge‐transfer (CT) distance by using the extended set of Au‐deposited hydroxyl‐terminated alkanethiol SAMs [‐S‐(CH2)n‐OH] of variable thickness (n=2, 3, 4, 6, 11); 2) application of a high‐pressure (up to 150 MPa) kinetic strategy toward the representative Au/SAM/CytC assemblies (n=3, 4, 6); 3) complementary electrochemical and microcalorimetric studies on the impact of some stabilizing and denaturing additives. We report for the first time a mechanistic changeover detected for “free” CytC by three independent kinetic methods, manifested through 1) the abrupt change in the dependence of the shape of the electron exchange standard rate constant (ko) versus the SAM thickness (resulting in a variation of estimated actual CT range within ca. 15 to 25 Å including ca. 11 Å of an “effective” heme‐to‐ω‐hydroxyl distance). The corresponding values of the electronic coupling matrix element vary within the range from ca. 3 to 0.02 cm−1; 2) the change in activation volume from +6.7 (n=3), to ≈0 (n=4), and −5.5 (n=6) cm3 mol−1 (disclosing at n=3 a direct pressure effect on the protein's internal viscosity); 3) a “full” Kramers‐type viscosity dependence for ko at n=2 and 3 (demonstrating control of an intraglobular friction through the external dynamic properties), and its gradual transformation to the viscosity independent (nonadiabatic) regime at n=6 and 11. Multilateral cross‐testing of “free” CytC in a native‐like, glucose‐stabilized and urea‐destabilized (molten‐globule‐like) states revealed novel intrinsic links between local/global structural and functional characteristics. Importantly, our results on the high‐pressure and solution‐viscosity effects, together with matching literature data, strongly support the concept of “dynamic slaving”, which implies that fluctuations involving “small” solution components control the proteins' intrinsic dynamics and function in a highly cooperative manner as far as CT processes under adiabatic conditions are concerned.
Acid–Base and Metal‐Ion‐Binding Properties of Xanthosine 5′‐Monophosphate (XMP) in Aqueous Solution: Complex Stabilities, Isomeric Equilibria, and Extent of Macrochelation
Authors: Sigel Helmut , Massoud Salah S. , Song Bin , Griesser Rolf , Knobloch Bernd , Operschall Bert P. 
Published: August 2006

AbstractThe four acidity constants of threefold protonated xanthosine 5′‐monophosphate, H3(XMP)+, reveal that at the physiological pH of 7.5 (XMP−H)3− strongly dominates (and not XMP2− as given in textbooks); this is in contrast to the related inosine (IMP2−) and guanosine 5′‐monophosphate (GMP2−) and it means that XMP should better be named as xanthosinate 5′‐monophosphate. In addition, evidence is provided for a tautomeric (XMP−H⋅N1)3−/(XMP−H⋅N3)3− equilibrium. The stability constants of the M(H;XMP)+ species were estimated and those of the M(XMP) and M(XMP−H)− complexes (M2+=Mg2+, Ca2+, Sr2+, Ba2+, Mn2+, Co2+, Ni2+, Cu2+, Zn2+, Cd2+) measured potentiometrically in aqueous solution. The primary M2+ binding site in M(XMP) is (mostly) N7 of the monodeprotonated xanthine residue, the proton being at the phosphate group. The corresponding macrochelates involving P(O)2(OH)− (most likely outer‐sphere) are formed to ≈65 % for nearly all M2+. In M(XMP−H)− the primary M2+ binding site is (mostly) the phosphate group; here the formation degree of the N7 macrochelates varies widely from close to zero for the alkaline earth ions, to ≈50 % for Mn2+, and ≈90 % or more for Co2+, Ni2+, Cu2+, Zn2+, and Cd2+. Because for (XMP−H)3− the micro stability constants quantifying the M2+ affinity of the xanthosinate and ${{\rm PO}{{2- \hfill \atop 3\hfill}}}$ residues are known, one may apply a recently developed quantification method for the chelate effect to the corresponding macrochelates; this chelate effect is close to zero for the alkaline earth ions and it amounts to about one log unit for Co2+, Ni2+, Cu2+. This method also allows calculation of the formation degrees of the monodentatally coordinated isomers; this information is of relevance for biological systems because it demonstrates how metal ions can switch from one site to another through macrochelate formation. These insights are meaningful for metal‐ion‐dependent reactions of XMP in metabolic pathways; previous mechanistic proposals based on XMP2− need revision.
A New Basic Motif in Cyanometallate Coordination Polymers: Structure and Magnetic Behavior of M(μ‐OH2)2[Au(CN)2]2(M=Cu, Ni)
Authors: Lefebvre Julie , Callaghan Fergal , Katz Michael J. , Sonier Jeff E. , Leznoff Daniel B. 
Published: August 2006

AbstractThe structures of two cyanoaurate‐based coordination polymers, M(μ‐OH2)2[Au(CN)2]2(M=Cu, Ni), were determined by using a combination of powder and single‐crystal X‐ray diffraction techniques. The basic structural motif for both polymers contains rarely observed M(μ‐OH2)2M double aqua‐bridges, which generate an infinite chain; twotrans[Au(CN)2]−units also dangle from each metal center. The chains form ribbons that interact three dimensionally through CN⋅⋅⋅H hydrogen bonding. The magnetic properties of both compounds and of the dehydrated analogue Cu[Au(CN)2]2were investigated by direct current (dc) and alternating current (ac) magnetometry; muon spin‐relaxation data was also obtained to probe their magnetic properties in zero‐field. In M(μ‐OH2)2[Au(CN)2]2, ferromagnetic chains of M(μ‐OH2)2M are present below 20 K. Interchain magnetic interactions mediated through hydrogen bonding, involving water and cyanoaurate units, yield a long‐range magnetically ordered system in Cu(μ‐OH2)2[Au(CN)2]2below 0.20 K, as indicated by precession in the muon spin polarization decay. Ni(μ‐OH2)2[Au(CN)2]2undergoes a transition to a spin‐glass state in zero‐field at 3.6 K, as indicated by a combination of muon spin‐relaxation and ac‐susceptibility data. This transition is probably due to competing interactions that lead to spin frustration. A phase transition to a paramagnetic state is possible for Ni(μ‐OH2)2[Au(CN)2]2upon application of an external field; the critical field was determined to be 700 Oe at 1.8 K. The dehydrated compound Cu[Au(CN)2]2shows weak antiferromagnetic interactions at low temperatures.
Investigation of a Molecular Morphology Effect on Polyphenylazomethine Dendrimers; Physical Properties and Metal‐Assembling Processes
Authors: Imaoka Takane , Tanaka Reiko , Yamamoto Kimihisa 
Published: August 2006

AbstractA series of novel dendritic polyphenylazomethines (DPA) with asymmetric morphologies was synthesized. Their physical properties, such as encapsulating effect, molecular dynamics, and metal assembly, are strongly dependent on the entire conformation of the molecules. The most important property is layer‐by‐layer metal assembly in the dendrimer structure from the core to the outside. Bis‐ and tris‐substituted DPAs of the fourth generation also act as frameworks for stepwise assembly of a metal component (SnCl2), like the fully substituted symmetric DPA. However, extensive investigation of metal assembly in specific DPAs revealed that they do not follow the stepwise process. The molecular density calculated from the experimental hydrodynamic volume indicated that bis‐ and tris‐substituted DPAs with asymmetric morphology still retain a free space similar to that of fully substituted symmetric DPA. The monosubstituted DPA, however, displayed a slightly higher density (smaller space) than the other DPAs. The experimental results suggest a bent conformation of the dendrimer in which the core moiety is folded into the dendron structure. In addition, the molecular dynamics were probed by means of the 1H NMR signals of the porphyrin core. It was demonstrated that the conformation is not fixed at room temperature in solvated DPAs, especially in monosubstituted DPA. A similar observation was for the smaller DPAs (third generations) with asymmetric morphologies. These dendrimers do not follow the stepwise complexation process. The structures of bis‐ and tris‐substituted dendrimers which accurately follow the stepwise process are fixed. These observations provide a new insight into the finely controlled metal‐assembly chemistry of dendritic macromolecules, and a rigid and fixed conformation is one of important factors for their unique properties.
Alternative Einsatzmöglichkeiten der „Bevorzugten Kristallisation”︁ zur Enantiomerentrennung
Authors: Polenske D. , Elsner M. P. , Lorenz H. , Seidel‐Morgenstern A. 
Published: August 2006

AbstractDie Enantiomerentrennung aus racemischen Mischungen mittels der „Bevorzugten Kristallisation”︁ wird bisher ausschließlich bei konglomeratbildenden Stoffsystemen im Batch‐ bzw. in einigen Fällen im zyklischen Modus durchgeführt. Für die wesentlich häufiger vorkommenden verbindungsbildenden Stoffsysteme wurde die „Bevorzugte Kristallisation”︁ bisher nicht eingesetzt. Der Beitrag gibt einen Überblick über die Möglichkeiten und Grenzen der Enantiomerentrennung in konglomerat‐ und verbindungsbildenden Stoffsystemen mittels der „Bevorzugten Kristallisation”︁. Dabei wird auf den Einfluss der Fest/Flüssig‐Phasengleichgewichte‐ sowie auf alternative Konzepte der Prozessführung eingegangen. Für das konglomeratbildende Stoffsystem Threonin/Wasser werden experimentelle Ergebnisse zur Maßstabsvergrößerung des Batch‐Prozesses sowie zur zyklischen Betriebsweise vorgestellt. Des Weiteren werden erste erfolgreiche Resultate zum Einsatz der „Bevorzugten Kristallisation”︁ zur Enantiomerengewinnung im verbindungsbildenden Stoffsystem Mandelsäure/Wasser präsentiert.
Temperatur‐ und Wasserverteilung bei der konvektiven Trocknung mittels Inline‐Magnetresonanztomographie
Authors: Regier M. , Idda P. , Knoerzer K. , Hardy E. H. , Schuchmann H. P. 
Published: August 2006

AbstractMit Hilfe eines Konvektionstrockners ist die Trocknung von Lebensmitteln direkt in einem Magnetresonanztomographen möglich. Dabei können Wasserverteilungen innerhalb eines Trocknungsgutes inline und nicht‐invasiv erfasst werden. So lässt sich die ortsaufgelöste Trocknung verfolgen, und es können bestehende und neue Trocknungsmodelle evaluiert werden.
Doing Homogeneous Catalysis between Basic Research and Application
Authors: Beller M. 
Published: August 2006

AbstractRecent achievements in applied homogeneous catalysis are described. Special focus is given on the development of novel palladium catalysts which are of industrial interest for the synthesis of bulk and fine chemicals. Most of the reported work has been done in an intensive collaboration between the Degussa AG (DHC) and the Leibniz‐Institut für Katalyse e.V. The clear vision of the goal and a close interaction of basic research and applied catalysis have led to a fast development from the initial discovery to the upscaling of the ligands. Such a combination of know how from academic and industrial partners will provide the basis for further innovations in catalysis in future.