bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ti5Se4: The First Step of Cluster Condensation with Titanium Selenides
Authors: He Meng , Simon Arndt , Duppel Viola 
Published: March 2004

AbstractA new Ti5Te4‐type compound, Ti5Se4, has been identified and its structure is refined against x‐ray powder diffraction data with the Rietveld method. It has a body‐centered tetragonal unit cell with lattice parameters a = 9.6728(1) Å, c = 3.5083(1) Å, space group I4/m. This compound is the first titanium selenide which consists of separated M5X4 (M = metal, X = metalloid) chains. The effect of atomic radii on the formation of the Ti5Te4‐type structure is discussed.
Synthese, Kristallstruktur und thermischer Abbau von Mg(H2O)6[B12H12] · 6 H2O
Authors: Tiritiris Ioannis , Schleid Thomas 
Published: March 2004

AbstractBei der Umsetzung einer wäßrigen Lösung der Säure (H3O)2[B12H12] mit MgCO3 und anschließendem isothermen Eindampfen der erhaltenen Lösung entstehen farblose, polyederförmige Einkristalle von Magnesium‐Dodekahydro‐closo‐Dodekaborat‐Dodekahydrat Mg(H2O)6[B12H12] · 6 H2O (kubisch, F4132; a = 1643, 21(9) pm, Z = 8). Die Kristallstruktur läßt sich auf den NaTl‐Strukturtyp zurückführen, wobei die Schwerpunkte der quasi‐ikosaedrischen [B12H12]2—‐Anionen (d(B—B) = 178—180 pm, d(B—H) = 109 pm) die Tl—‐ und die Mg2+‐Kationen die Na+‐Positionen besetzen. Ein direkter koordinativer Einfluß der [B12H12]2—‐Einheiten auf die Mg2+‐Kationen ist nicht festzustellen. Letztere werden lediglich von sechs Sauerstoffatomen der umgebenden Wassermoleküle oktaedrisch koordiniert und bilden isolierte Hexaaqua‐Komplexkationen [Mg(H2O)6]2+ (d(Mg—O) = 206 pm, 6×). Zusätzlich dazu sind in der Kristallstruktur sechs „zeolithische”︁ Wassermoleküle lokalisiert, die für die Bildung eines starken O—Hδ+···δ—O‐Wasserstoffbrückenbindungssystems sorgen. Die Ausbildung schwacher B—Hδ—···δ+H—O‐Wasserstoffbrücken wird ebenfalls diskutiert. Differenzthermoanalytische und thermogravimetrische Studien zum thermischen Verhalten des Dodekahydrats Mg[B12H12] · 12 H2O (≡ Mg(H2O)6[B12H12] · 6 H2O) belegen erwartungsgemäß einen zweistufigen Abbau im Temperaturbereich zwischen 71 und 76 °C sowie bei 202 °C, der schließlich zum wasserfreien Magnesium‐Dodekahydro‐closo‐Dodekaborat Mg[B12H12] führt.
A Novel 3‐D Heterobimetallic Cyano‐bridged Coordination Polymer Incorporating Ag···Ag Interaction: [Cu(dien)Ag(CN)2]2[Ag2(CN)3][Ag(CN)2]
Authors: Zhou Hui‐Bo , Dong Wen , Liang Mao , Liao Dai‐Zheng , Jiang Zong‐Hui , Yan Shi‐Ping , Cheng Peng 
Published: March 2004

AbstractA three‐dimensional cyano‐bridged copper(II) complex, [Cu(dien)Ag(CN)2]2[Ag2(CN)3][Ag(CN)2] (1) (dien = diethylenetriamine), has been prepared and characterized by X‐ray crystallography. Complex 1 crystallized in the monoclinic space group P21/n with a = 6.988(2), b = 17.615(6), c = 12.564(4) Å, β = 90.790(5)°. The crystal consists of cis‐[Cu(dien)]2+ units bridged by [Ag(CN)2]— to form a zig‐zag chain. The Ag atoms of the free and bridging [Ag(CN)2]— link together to form additional infinite zig‐zag chains with short Ag···Ag distances. The presence of Ag···Ag interactions effectively increases the dimensionality from a 1‐D chain to a 3‐D coordination polymer.
Syntheses and Crystal Structures of Two Sodium Ruthenates: Na2RuO4 and Na2RuO3
Authors: Mogare Kailash M. , Friese Karen , Klein Wilhelm , Jansen Martin 
Published: March 2004

AbstractNa2RuO4, prepared from Na2O2 and RuO2 via high oxygen pressure synthesis, crystallises monoclinic in space group P21/c (a = 10.721(6), b = 7.033(4), c = 10.871(6) Å, β = 119.10(4)°, Z = 8, 2503 unique reflections, R1 = 0.049). Structure determination from single crystal data shows that the compound consists of infinite chains of RuO5 trigonal bipyramids connected through their axial vertices. The Na cations connect the pseudohexagonally packed [RuO3O2/2] chains and are coordinated by six or seven oxygen atoms, respectively. The compound exhibits an one‐dimensional spin system with μ = 2.80 μB and Θ = —222 K and a three‐dimensional antiferromagnetic ordering below 50 K. Na2RuO3 was obtained from Na2RuO4 at 850 °C under a flow of argon. The structure was determined from X‐ray powder diffraction. It is closely related to the α‐NaFeO2 and the Li2SnO3 structure types, layered variants of the NaCl type. In Na2RuO3 the Na and Ru atoms are partially disordered. This partially disordered state was approximated by a Rietveld refinement of two superimposed structural models (model I: R 3¯ m, a = 3.12360(5), c = 16.0370(4) Å, Z = 2; model II: C2/c, a = 5.4141(4), b = 9.3663(6), c = 10.8481(4) Å, β = 99.636(9)°, Z = 8).
Normal Reference Value of Hemoglobin of Older Boys and Geographical Factors
Authors: Miao Ge 
Published: March 2004

In order to supply a scientific basis for uniting the normal reference value standard of hemoglobin of Chinese older boys. Methods: A research is made about the relationship between the normal reference value of 14751 examples of hemoglobin of older boys and five geographical factors in 92 areas in China, which are determined by the hemoglobincyanide method. Results: It is found that the correlation of geographical factors and the normal reference value of hemoglobin of older boys are quite significant (F = 9.68). By using the method of multiple linear regression analysis, one regression equation is inferred:
Ŷ = 108.0 + 0.003633X1 + 0.003945X2 + 0.1680X3 − 0.6310X4 + 0.005518X5 ± 8.3
Conclusion: If geographical values are obtained in some areas, the normal reference value of hemoglobin of older boys of this area can be reckoned by using the regression equation. Furthermore, the depending on the geographical factors, China can be divided into six districts: Qingzang, Southwest, Northwest, Southeast, North and Northeast district.
Real‐time data received from Mount Erebus Volcano, Antarctica
Authors: Aster R. , MacIntosh W. , Kyle P. , Esser R. , Bartel B. , Dunbar N. , Johnson J. , Karstens R. , Kurnik C. , McGowan M. , McNamara S. , Meertens C. , Pauly B. , Richmond M. , Ruiz M. 
Published: March 2004

Internal and eruptive volcano processes involve complex interactions of multi‐phase fluids with the solid Earth and the atmosphere, and produce diverse geochemical, visible, thermal, elastic, and anelastic effects. Multidisciplinary experimental agendas are increasingly being employed to meet the challenge of understanding active volcanoes and their hazards [e.g.,Ripepe et al., 2002; Wallace et al., 2003].Mount Erebus is a large (3794 m) stratovolcano that forms the centerpiece of Ross Island, Antarctica, the site of the principal US. (McMurdo) and New Zealand (Scott) Antarctic bases. With an elevation of 3794 m and a volume of ∼1670 km3, Erebus offers exceptional opportunities for extended study of volcano processes because of its persistent, low‐level, strombolian activity (Volcano Explosivity Index 0–1) and exposed summit magma reservoir (manifested as a long‐lived phonolitic lava lake). Key scientific questions include linking conduit processes to near‐field deformations [e.g., Aster et al., 2003] ,explosion physics [ e.g., Johnson et al., 2003], magmatic differentiation and residence [e.g., Kyle et al., 1992], and effects on Antarctic atmospheric and ice geochemistry [e.g., Zreda‐Gostynska et al., 1997]. The close proximity of Erebus (35 km) to McMurdo, and its characteristic dry, windy, cold, and high‐elevation Antarctic environment, make the volcano a convenient test bed for the general development of volcano surveillance and other instrumentation under extreme conditions.
Assessing the Probability That a Positive Report is False: An Approach for Molecular Epidemiology Studies
Authors: Wacholder Sholom , Chanock Stephen , Garcia-Closas Montserrat , El ghormli Laure , Rothman Nathaniel 
Published: March 2004

AbstractToo many reports of associations between genetic variants and common cancer sites and other complex diseases are false positives. A major reason for this unfortunate situation is the strategy of declaring statistical significance based on a P value alone, particularly, any P value below .05. The false positive report probability (FPRP), the probability of no true association between a genetic variant and disease given a statistically significant finding, depends not only on the observed P value but also on both the prior probability that the association between the genetic variant and the disease is real and the statistical power of the test. In this commentary, we show how to assess the FPRP and how to use it to decide whether a finding is deserving of attention or “noteworthy.” We show how this approach can lead to improvements in the design, analysis, and interpretation of molecular epidemiology studies. Our proposal can help investigators, editors, and readers of research articles to protect themselves from overinterpreting statistically significant findings that are not likely to signify a true association. An FPRP-based criterion for deciding whether to call a finding noteworthy formalizes the process already used informally by investigators—that is, tempering enthusiasm for remarkable study findings with considerations of plausibility.
Heme as an optical probe of a conformational transition of ovine recPrP
Authors: Pato Christine , Célier Chantal , Rezaei Human , Grosclaude Jeanne , Marden Michael C. 
Published: March 2004

AbstractThe prion protein occurs as a globular domain and a leading fragment whose structure is not well‐defined. For the ovine species, all of the tryptophan residues are in the initial fragment, while the globular domain is rich in tyrosine residues. Using heme as a spectroscopic probe, we have studied the recombinant prion protein before and after a temperature‐induced conformational change. As for most heme proteins, the absorption spectrum of heme‐CO displays a red shift upon binding to the protein, and both the Y and W fluorescence are highly quenched. Flash photolysis kinetics of the PrP–heme‐CO complex shows a low yield for the bimolecular phase, indicating a pocket around the hemes. By comparing the holoprotein and the truncated sequence corresponding to the globular domain, the stoichiometry was determined to be five hemes for the globular domain and two hemes for the leading fragment. At high temperature, the hemes are released; upon cooling, only two hemes bind, and only the tryptophan fluorescence is quenched; this would indicate that the globular domain has formed a more compact structure, which is inert with respect to the hydrophobic probe. The final state of polymerization is perturbed if the synthetic peptide “N3” (PrP residues 142–166, which include the first helix) is added to the prion protein solution; the temperature cycle no longer reduces the number of heme binding sites. This would indicate that the peptide may alter or inhibit the polymer formation.
Sites of interaction between SecA and the chaperone SecB, two proteins involved in export
Authors: Randall Linda L. , Crane Jennine M. , Liu Gseping , Hardy Simon J.S. 
Published: March 2004

AbstractSecB, a small tetrameric cytosolic chaperone in Escherichia coli, facilitates the export of precursor poly‐peptides by maintaining them in a nonnative conformation and passing them to SecA, which is a peripheral member of the membrane‐bound translocation apparatus. It has been proposed by several laboratories that as SecA interacts with various components along the export pathway, it undergoes conformational changes that are crucial to its function. Here we report details of molecular interactions between SecA and SecB, which may serve as conformational switches. One site of interaction involves the final C‐terminal 21 amino acids of SecA, which are positively charged and contain zinc. The C terminus of each subunit of the SecA dimer makes contact with the flat β‐sheet that is formed by each dimer of the SecB tetramer. Here we demonstrate that a second interaction exists between the extreme C‐terminal α‐helix of SecB and a site on SecA, as yet undefined but different from the C terminus of SecA. We investigated the energetics of the interactions by titration calorimetry and characterized the hydrodynamic properties of complexes stabilized by both interactions or each interaction singly using sedimentation velocity centrifugation.
Tissue transglutaminase acylation: Proposed role of conserved active site Tyr and Trp residues revealed by molecular modeling of peptide substrate binding
Authors: Chica Roberto A. , Gagnon Paul , Keillor Jeffrey W. , Pelletier Joelle N. 
Published: March 2004

AbstractTransglutaminases (TGases) catalyze the cross‐linking of peptides and proteins by the formation of γ‐glutamyl‐ε‐lysyl bonds. Given the implication of tissue TGase in various physiological disorders, development of specific tissue TGase inhibitors is of current interest. To aid in the design of peptide‐based inhibitors, a better understanding of the mode of binding of model peptide substrates to the enzyme is required. Using a combined kinetic/molecular modeling approach, we have generated a model for the binding of small acyl‐donor peptide substrates to tissue TGase from red sea bream. Kinetic analysis of various N‐terminally derivatized Gln‐Xaa peptides has demonstrated that many CBz‐Gln‐Xaa peptides are typical in vitro substrates with KM values between 1.9 mM and 9.4 mM, whereas Boc‐Gln‐Gly is not a substrate, demonstrating the importance of the CBz group for recognition. Our binding model of CBz‐Gln‐Gly on tissue TGase has allowed us to propose the following steps in the acylation of tissue TGase. First, the active site is opened by displacement of conserved W329. Second, the substrate Gln side chain enters the active site and is stabilized by hydrophobic interaction with conserved residue W236. Third, a hydrogen bond network is formed between the substrate Gln side chain and conserved residues Y515 and the acid‐base catalyst H332 that helps to orient and activate the γ‐carboxamide group for nucleophilic attack by the catalytic sulphur atom. Finally, an H‐bond with Y515 stabilizes the oxyanion formed during the reaction.
Mimicking the action of folding chaperones in molecular dynamics simulations: Application to the refinement of homology‐based protein structures
Authors: Fan Hao , Mark Alan E. 
Published: March 2004

AbstractA novel method for the refinement of misfolded protein structures is proposed in which the properties of the solvent environment are oscillated in order to mimic some aspects of the role of molecular chaperones play in protein folding in vivo. Specifically, the hydrophobicity of the solvent is cycled by repetitively altering the partial charges on solvent molecules (water) during a molecular dynamics simulation. During periods when the hydrophobicity of the solvent is increased, intramolecular hydrogen bonding and secondary structure formation are promoted. During periods of increased solvent polarity, poorly packed regions of secondary structures are destabilized, promoting structural rearrangement. By cycling between these two extremes, the aim is to minimize the formation of long‐lived intermediates. The approach has been applied to the refinement of structural models of three proteins generated by using the ROSETTA procedure for ab initio structure prediction. A significant improvement in the deviation of the model structures from the corresponding experimental structures was observed. Although preliminary, the results indicate computationally mimicking some functions of molecular chaperones in molecular dynamics simulations can promote the correct formation of secondary structure and thus be of general use in protein folding simulations and in the refinement of structural models of small‐ to medium‐size proteins.
An improved crystal form of Plasmodium falciparum peptide deformylase
Authors: Robien Mark A. , Nguyen Kiet T. , Kumar Abhinav , Hirsh Irwin , Turley Stewart , Pei Dehua , Hol Wim G.J. 
Published: March 2004

AbstractAn altered version of peptide deformylase from Plasmodium falciparum (PfPDF), the organism that causes the most devastating form of malaria, has been cocrystallized with a synthesized inhibitor that has submicromolar affinity for its target protein. The structure is solved at 2.2 Å resolution, an improvement over the 2.8 Å resolution achieved during the structural determination of unliganded PfPDF. This represents the successful outcome of modifying the protein construct in order to overcome adverse crystal contacts and other problems encountered in the study of unliganded PfPDF. Two molecules of PfPDF are found in the asymmetric unit of the current structure. The active site of each monomer of PfPDF is occupied by a proteolyzed fragment of the tripeptide‐like inhibitor. Unexpectedly, each PfPDF subunit is associated with two nearly complete molecules of the inhibitor, found at a protein–protein interface. This is the first structure of a eukaryotic PDF protein, a potential drug target, in complex with a ligand.
Prediction of functional sites by analysis of sequence and structure conservation
Authors: Panchenko Anna R. , Kondrashov Fyodor , Bryant Stephen 
Published: March 2004

AbstractWe present a method for prediction of functional sites in a set of aligned protein sequences. The method selects sites which are both well conserved and clustered together in space, as inferred from the 3D structures of proteins included in the alignment. We tested the method using 86 alignments from the NCBI CDD database, where the sites of experimentally determined ligand and/or macromolecular interactions are annotated. In agreement with earlier investigations, we found that functional site predictions are most successful when overall background sequence conservation is low, such that sites under evolutionary constraint become apparent. In addition, we found that averaging of conservation values across spatially clustered sites improves predictions under certain conditions: that is, when overall conservation is relatively high and when the site in question involves a large macromolecular binding interface. Under these conditions it is better to look for clusters of conserved sites than to look for particular conserved sites.
Energy functions for protein design I: Efficient and accurate continuum electrostatics and solvation
Authors: Pokala Navin , Handel Tracy M. 
Published: March 2004

AbstractElectrostatics and solvation energies are important for defining protein stability, structural specificity, and molecular recognition. Because these energies are difficult to compute quickly and accurately, they are often ignored or modeled very crudely in computational protein design. To address this problem, we have developed a simple, fast, and accurate approximation for calculating Born radii in the context of protein design calculations. When these approximate Born radii are used with the generalized Born continuum dielectric model, energies calculated by the 106‐fold slower finite difference Poisson‐Boltzmann model are faithfully reproduced. A similar approach can be used for estimating solvent‐accessible surface areas (SASAs). As an independent test, we show that these approximations can be used to accurately predict the experimentally determined pKas of >200 ionizable groups from 15 proteins.
Equilibrium thermal transitions of collagen model peptides
Authors: Persikov Anton V. , Xu Yujia , Brodsky Barbara 
Published: March 2004

AbstractThe folding of collagen in vitro is very slow and presents difficulties in reaching equilibrium, a feature that may have implications for in vivo collagen function. Peptides serve as good model systems for examining equilibrium thermal transitions in the collagen triple helix. Investigations were carried out to ascertain whether a range of synthetic triple‐helical peptides of varying sequences can reach equilibrium, and whether the triple helix to unfolded monomer transition approximates a two‐state model. The thermal transitions for all peptides studied are fully reversible given sufficient time. Isothermal experiments were carried out to obtain relaxation times at different temperatures. The slowest relaxation times, on the order of 10–15 h, were observed at the beginning of transitions, and were shown to result from self‐association limited by the low concentration of free monomers, rather than cis–trans isomerization. Although the fit of the CD equilibrium transition curves and the concentration dependence of Tm values support a two‐state model, the more rigorous comparison of the calorimetric enthalpy to the van't Hoff enthalpy indicates the two‐state approximation is not ideal. Previous reports of melting curves of triple‐helical host–guest peptides are shown to be a two‐state kinetic transition, rather than an equilibrium transition.
Does the Adoption of a Business Risk Audit Approach Change Internal Control Documentation and Testing Practices?
Authors: Bierstaker James Lloyd , Wright Arnold 
Published: March 2004

The purpose of this study is to investigate the impact of the adoption of a business risk audit approach on internal control documentation and testing. Data were collected from senior auditors before and after a change to a new business risk approach to determine if auditors’ preferred internal control documentation format, as well as the number of formats commonly used, had changed. In addition, corroborating data were collected from 23 experienced managers and partners regarding preferred documentation format and extent of control testing and reasons for changes in control evaluation and testing approaches.The results suggest that auditors use narratives significantly more often and rely on other formats significantly less than previously. In addition, results indicate that the primary reason auditors choose to rely on narratives is to enhance audit efficiency, and second, because the flexibility of this format works well with the new audit approach adopted. These findings have implications for audit effectiveness, since recent research suggests that significant internal control deficiencies may be overlooked if auditors rely on a single format. Finally, auditors indicated that the frequency of testing of controls has significantly increased as a result of the enhanced audit focus on business processes.
The tenth rib line as a new landmark of the lumbar vertebral level during spinal block
Authors: Jung C.‐W. , Bahk J.‐H. , Lee J.‐H. , Lim Y.‐J. 
Published: March 2004

SummaryThe purpose of this study was to assess whether the tenth rib line (an imaginary line that joins the lowest points of the rib cage on the flanks) could be used as a marker of the lumbar vertebral level. Simple X‐rays (n = 100) were taken with radiopaque markers attached on the lowest points of the rib cage and the uppermost points of the iliac crests on both flanks. The spinous process or interspinous space that the tenth rib or Tuffier's lines crossed was identified and recorded, respectively, in the neutral and fully flexed positions. With lumbar flexion, the tenth rib line (median (25th to 75th percentiles)) moved upward (L2 (L1−2 − L2) vs. L1–2 (L1–2 – L1–2); p < 0.01), but Tuffier's line moved downward (L4−5 (L4 − L4−5) vs. L4−5 (L4 − L5); p < 0.01). Because the ease of palpating the tenth rib line and its distribution patterns are comparable to those of the Tuffier's line, the tenth rib line may be useful as a new landmark of the lumbar vertebral level as well as a safeguard to prevent spinal puncture from being mistakenly performed at a dangerously high level.