bluuebunny/crossref_metadata_2025 huggingface dataset:
Mesenchymal stem cell‐based angiopoietin‐1 gene therapy for acute lung injury induced by lipopolysaccharide in mice
Authors: Xu J , Qu J , Cao L , Sai Y , Chen C , He L , Yu L
Published: January 2008

Bone marrow‐derived mesenchymal stem cells (MSCs) can serve as a vehicle for gene therapy. Angiopoietin‐1 (Ang1) is a critical factor for endothelial survival and vascular stabilization via the inhibition of endothelial permeability and leukocyte–endothelium interactions. We hypothesized that MSC‐based Ang1 gene therapy might be a potential therapeutic approach for lipopolysaccharide (LPS)‐induced lung injury. MSCs were isolated from 6 week‐old inbred male mice and transduced with the Ang1 gene, using a lentivirus vector. The MSCs showed no significant phenotypic changes after transduction. In the in vivo mouse model, the LPS‐induced lung injury was markedly alleviated in the group treated with MSCs carrying Ang1 (MSCs–Ang1), compared with groups treated with MSCs or Ang1 alone. The expression of Ang1 protein in the recipient lungs was increased after MSCs–Ang1 administration. The histopathological and biochemical indices of LPS‐induced lung injury were improved after MSCs‐based Ang1 gene treatment. MSCs–Ang1 administration also reduced pulmonary vascular endothelial permeability and the recruitment of inflammatory cells into the lung. Cells of MSC origin could be detected in the recipient lungs for 2 weeks after injection with MSCs. These results suggest that MSCs and Ang1 have a synergistic role in the treatment of LPS‐induced lung injury. MSC‐based Ang1 gene therapy may be developed as a potential novel strategy for the treatment of acute lung injury. Copyright © 2008 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Preparation and characterization of polypropylene/solid‐state organomodified montmorillonite nanocomposites
Authors: Yu‐hai Sun , Yuan‐Fang Luo , De‐Min Jia
Published: January 2008

A novel organomodified montmorillonite prepared by solid‐state method and its nanocomposites with polypropylene were studied. The interaction between modifying agent and montmorillonite was investigated by X‐ray diffraction (XRD) analysis, contact angle determination, and Fourier‐transform infrared spectroscopy. The results showed that the modifying agent behaves as an effective intercalating agent, enlarging the interlayer spacing of montmorillonite and making montmorillonite more hydrophobic. Polypropylene/solid‐state organomodified montmorillonite composites were prepared by melt‐mixing method. The dispersion of the silicates was investigated by XRD analysis and transmission electron microscopy. It was found that the nanocomposites are formed with solid‐state organomodified montmorillonite and polypropylene. The thermogravimetric analysis and differential scanning calorimetry results showed that the organoclay could enhance the thermal stability and decrease the relative crystallinity of polypropylene. Mechanical and rheological tests indicated that the organoclay improves the mechanical properties but has no obvious effect on rheological properties of polypropylene. POLYM. COMPOS., 2008. © 2008 Society of Plastics Engineers
Real‐time measurement of flow front kinematics using quantitative visualization in injection molding process
Authors: Fathi S. , Behravesh A.H.
Published: January 2008

This article presents an experimental method for measuring the kinematics of the melt flow front, during the filling stage of the plastic injection molding process. The three main steps were: (i) visualization of the flow front advancement, (ii) image processing of the recorded results, and (iii) calculation of the flow front kinematics. The designed visual mold was capable of monitoring the flow advancement in two different cases: (i) a simple (nonconstrained) plate and (ii) a constrained plate (with an obstacle pin). Variations in instant flow rate, melt front area (MFA), and average melt front velocity (MFV) during filling stage were measured as a function of time. The applied technique could clearly show the flow behavior from which the flow front parameters could be extracted. A particle tracking velocimetry (PTV) method was also applied to study the orientation behavior of the advancing melt front. The time history of the particle's velocity components at the flow front could be easily extracted using the method. POLYM. ENG SCI., 2008. © 2008 Society of Plastics Engineers
Why 3‐D? Gel‐based microarrays in proteomics
Authors: Rubina Alla Yu. , Kolchinsky Alexander , Makarov Alexander A. , Zasedatelev Alexander S.
Published: January 2008

Gel‐based microarrays (biochips) consisting of nanoliter and sub‐nanoliter gel drops on hydrophobic substrate are a versatile technology platform for immobilization of proteins and other biopolymers. Biochips provide a highly hydrophilic environment, which stabilizes immobilized molecules and facilitates their interactions with analytes. The probes are immobilized simultaneously with gel polymerization, evenly distributed throughout individual elements, and are easily accessible because of large pores. Each element is an isolated nanotube. Applications of biochips in the studies of protein interactions with other proteins, nucleic acids, and glycans are described. In particular, biochips are compatible with MALDI‐MS. Biochip‐based assay of prostate‐specific antigen became the first protein microarray approved for clinical use by a national regulatory agency. In this review, 3‐D immobilization is compared with mainstream technologies based on surface immobilization.
Informatics for peptide retention properties in proteomic LC‐MS
Authors: Shinoda Kosaku , Sugimoto Masahiro , Tomita Masaru , Ishihama Yasushi
Published: January 2008

Retention times in HPLC yield valuable information for the identification of various analytes and the prediction of peptide retention is useful for the identification of peptides/proteins in LC‐MS‐based proteomics. Informatics methods such as artificial neural networks and support vector machines capable of solving nonlinear problems made possible the accurate modeling of quantitative structure‐retention relationships of peptides (including large polymers) up to 5 kDa to which classical linear models cannot be applied, as well as the proteome‐wide prediction of peptide retention. Proteome‐wide retention prediction and accurate mass‐information facilitate the identification of peptides in complex proteomic samples. In this review, we address recent developments in solid informatics methods and their application to peptide‐retention properties in ‘bottom‐up’ shotgun proteomics. We also describe future prospects for the standardization and application of retention times.
Feasibility of the spontaneous gas‐phase proton transfer equilibria between neutral Brønsted acids and Brønsted bases
Authors: Burk Peeter , Koppel Ivar , Trummal Aleksander , Koppel Ilmar A.
Published: January 2008

The computational investigation of interactions of different acid–base pairs regarding the nature and extent of spontaneous proton transfer was carried out at B3LYP/6‐311 + G** level. The selected acid–base pairs include the interactions of strong base (K2O) with acids of different strength (HClO4, HCl, and HF), and strong acid (HClO4) with bases ranging from K2O (GB = 322.8 kcal/mol) to H2O (GB = 157.6 kcal/mol). It was shown that spontaneus, unassisted proton transfer can take place in the gas‐phase reactions of strong neutral Brønsted acids and bases. The reaction might be barrierless as in case of interactions between strong acids and bases, for example perchloric acid and alkali metal oxides or potassium oxide and halogen hydrides, or involve the encounter complex (hydrogen bonded acid–base cluster), which is separated from ion‐pair by the transition state. Copyright © 2008 John Wiley & Sons, Ltd.
The synthesis and characterization of new thermoplastic poly(thiourethane‐urethane)s
Authors: Kultys Anna , Rogulska Magdalena , Pikus Stanisław
Published: January 2008

New thermoplastic segmented poly(thiourethane‐urethane)s (SPTUUs) were prepared by a one‐step melt polymerization from 20 to 80 mol % poly(tetramethylene oxide) of $\overline M _{\rm n}$ = 1000 or poly(hexamethylene carbonate) diol (PHCD) of $\overline M _{\rm n}$ = 860 as soft segments, hexamethylene diisocyanate (HDI) and bis[4‐(mercaptomethyl)phenyl]methanone (BMMPM) as a new dithiol chain extender at the NCO/(OH + SH) molar ratio of 1 in the presence of dibutyltin dilaurate as a catalyst. The structures of the SPTUUs were examined by FTIR, X‐ray diffraction analysis, and scanning electron microscopy. The SPTUUs were also characterized by physicochemical, thermal, and tensile properties as well as Shore A/D hardness. The SPTUUs with the PHCD soft segments showed better tensile properties than those with the PTMO soft segments. A nonsegmented polythiourethane based on BMMPM and HDI is also described. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 1770–1782, 2008
Inhaled furosemide in hospitalized infants with viral bronchiolitis: A randomized, double‐blind, placebo‐controlled pilot study
Authors: Bar Amir , Srugo Isaac , Amirav Israel , Tzverling Chana , Naftali Gabi , Kugelman Amir
Published: January 2008

Objective

To evaluate the short and long‐term clinical effects and the treatment‐feasibility of inhaled‐furosemide (IF) as compared with placebo via hood in hospitalized infants with viral‐bronchiolitis (VB).

Study‐Design

A randomized, double‐blind, placebo‐controlled pilot‐study was performed in previously healthy infants (0–12 months). Enrolled infants were randomized to receive either IF (2 mg/kg), or placebo nebulized by hood three times daily throughout the hospitalization. Clinical assessment (respiratory distress assessment instrument [RDAI]) was performed before, 30 and 60 min after the 1st daily inhalation. The short‐term effects were evaluated by the RDAI, respiratory assessment change score (RACS) and oxygen requirement and the long‐term effects by time to be weaned off oxygen, time to full enteral feeding, length of stay, and “ready to discharge” time.

Results

Both groups (16 infants each) had comparable characteristics at study entry. Mean (±SD) age was 72 ± 43 days, and 29/32 infants were RSV positive. Oxygen requirement (FiO2) decreased significantly at 30 min post‐inhalation (30 ± 9.2% to 26 ± 7.1%, P < 0.05) only in the IF group. RACSs and long‐term effects of both groups were comparable. Analysis of IF particles generated by the hood‐nebulizer demonstrated that 36% and 49% of the particles were <3 and 5 µm, respectively. No side effects were observed during IF treatment.

Conclusion

Based on our pilot study, IF has no significant clinical effects in hospitalized infants with VB. IF via hood seems to be feasible and safe. Pediatr Pulmonol. 2008; 43:261–267. © 2008 Wiley‐Liss, Inc.
Effect of zinc supplementation on respiratory tract infections in children with cystic fibrosis
Authors: Abdulhamid I. , Beck F.W.J. , Millard S. , Chen X. , Prasad A.
Published: January 2008

Zinc (Zn) has significant anti‐oxidant and anti‐inflammatory activity. Zn deficiency can occur in subsets of patients with cystic fibrosis (CF) especially those with malabsorption and impaired growth. Although supplemental Zn has significantly reduced infections in various disorders, its efficacy has not been thoroughly investigated in CF. We performed a double blind placebo controlled pilot study to investigate the effect of daily 30 mg elemental Zn for 1 year on the rate of respiratory tract infections (RTIs), use of antibiotics and plasma cytokines in 26 children with CF (ages 7–18 years). Plasma Zn, Cu, inflammatory cytokines and ex vivo generation of IL‐2 were measured at baseline and at the end of the study. The number of days of oral antibiotics was lower in Zn treated patients compared to placebo (P = 0.05). However, compared to placebo, the effect of Zn was greater in patients who exhibited low plasma Zn at baseline (P = 0.02) than those who had plasma Zn levels identical to normal subjects (P = 0.55). Zn supplementation was marginally effective in reducing percentage increase in plasma IL‐6 and IL‐8 while increasing the percentage change in ex vivo generation of IL‐2 in isolated mononuclear cell. In conclusion, oral intake of 30 mg/day of Zn reduced the number of days of oral antibiotics used to treat RTIs in children with CF. A higher daily Zn dose may be needed to decrease RTIs and modify immune responses. Pediatr Pulmonol. 2008; 43:281–287. © 2008 Wiley‐Liss, Inc.
Quantum field theories coupled to supergravity
Authors: Große J.
Published: January 2008

This article is devoted to the investigation of the interplay of supersymmetric Yang–Mills theories (SYM) and supergravity (SUGRA). The topic is studied from two points of view: Firstly from the point of view of AdS/CFT correspondence, which realises the coupling of four dimensional superconformal 𝒩 = 4 SYM theory and ten dimensional type IIB SUGRA in a holographic way. In order to arrive at theories that resemble quantum chromodynamics (QCD) more closely, fundamental fields are introduced using probe D7‐branes and non‐trivial background configuration are considered. In particular supergravity solutions that are only asymptotically anti‐de Sitter and break supersymmetry are used. This allows the description of spontaneous chiral symmetry breaking. The meson spectrum is calculated and the existence of an associated Goldstone mode is demonstrated. Moreover it is shown that highly radially excited mesons are not degenerate. Additionally instanton configurations on the D7‐branes are investigated, which lead to a holographic description of the dual field theory's Higgs branch. Finally a holographic description of heavy‐light mesons is developed, which are mesons consisting of quarks with a large mass difference, such that a treatment of B mesons can be achieved The second approach is the technique of so‐called space‐time dependent couplings (also known as “local couplings”), where coupling constants are promoted to external sources. This allows to explore the conformal anomaly of quantum field theories coupled to a classical gravity background. The technique is extended to the superfield description of 𝒩 = 1 supergravity, a complete basis for the anomaly is given and the consistency conditions that arise from a cohomological treatment are calculated. Possible implications for an extension of Zamolodchikov's c‐theorem to four dimensional supersymmetric quantum field theories are discussed.
Comprehensive analysis of the helix‐X‐helix motif in soluble proteins
Authors: Deville Julie , Rey Julien , Chabbert Marie
Published: January 2008

α‐Helices are the most common secondary structures found in globular proteins. In this report, we analyze the stereochemical and sequence properties of helix‐X‐helix (HXH) motifs in which two α‐helices are linked by a single residue, in search of characteristic structures and sequence signals. The analysis is carried out on a database of 837 nonredundant HXH motifs. The kinks are characterized by the bend angle between the axes of the N‐terminal and C‐terminal helices and the wobble angle corresponding to the rotation of C‐terminal helix axis on the plane perpendicular to the N‐terminal one. The phi‐psi dihedral angles of the linker residue are clustered in six distinct areas of the Ramachandran plot: two areas are located in the additional allowed α region (α1 and α2), two areas are in the additional allowed β region (β1 and β2) and two areas have positive phi values (αL and βM). Each phi/psi region corresponds to characteristic bend and wobble angles and amino acid distributions. Bend angles can vary from 0° to 160°. Most wobble angles correspond to a counter‐clockwise rotation of the C‐terminal helix. Proline residues are rigorously excluded from the linker position X but have a high propensity at position X+1 of the β1 and β2 motifs (12 and 7, respectively) and at position X+3 of the α1 motifs (9). Glycine linkers are located either in the αL region (20%) or in the βM region (80%). This latter conformation is characterized by a marked bend angle (124° ± 18°) and a clockwise wobble. Among other amino acids, Asn is remarkable for its high propensity (>3) at the linker position of the α2, β1, and β2 motifs. Stabilization of HXH motifs by H‐bonds between polar side chains of the linker and polar groups of the backbone is determined. A method based on position‐specific scoring matrices is developed for conformational prediction. The accuracy of the predictions reaches 80% when the method is applied to proline‐induced kinks or to kinks with bend angles in the 50°–100° range. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Rational design of peptides active against the gram positive bacteria Staphylococcus aureus
Authors: Landon Céline , Barbault Florent , Legrain Michèle , Guenneugues Marc , Vovelle Françoise
Published: January 2008

In an attempt to increase the antimicrobial activity of the insect defensin from Anopheles gambiae, which is active against Staphylococcus aureus at low concentration, hybrid defensins were designed by combining conserved sequence regions and variable regions of insect defensins. Their activity against S. aureus strains sensitive and resistant to conventional antibiotics was evaluated, and the toxicity of the most active molecules was tested. The three‐dimensional structure of Anopheles gambiae defensin and five hybrids were determined by NMR and molecular modelling. This strategy led to the design of two chimeric defensins with increased activity compared with the native molecule, but one of them appears to be toxic to mice at a rather low concentration. The structure of the CSαβ motif, which is a characteristic of insect defensin, is sensitive to sequence modifications, in particular in the N‐terminal loop. The existence of the CSαβ is most probably a prerequisite for the stability and the activity of the molecule, but is not sufficient by itself since the hybrid displaying the best defined structure is not active against the tested strains. The analysis of the structure, in relation with the activity and the toxicity data, underlines the importance of turns and of the N‐terminal loop. Residues located in the turns contributing to the preservation of positive electrostatic areas at the surface of the molecules seem particularly important for the activity of the molecule, while residues involved in the N‐terminal loop are both involved in the modulation of the activity and the toxicity of the molecule. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Mechanism of inhibition of wt‐dihydrofolate reductase from E. coli by tea epigallocatechin‐gallate
Authors: Spina Michele , Cuccioloni Massimiliano , Mozzicafreddo Matteo , Montecchia Francesca , Pucciarelli Stefania , Eleuteri Anna Maria , Fioretti Evandro , Angeletti Mauro
Published: January 2008

Dihydrofolate reductase (DHFR) is a ubiquitous enzyme involved in major biological process, including DNA synthesis and cancer inhibition, and its modulation is the object of extensive structural, kinetic, and pharmacological studies. In particular, earlier studies showed that green tea catechins are powerful inhibitors of bovine liver and chicken liver DHFR. In this article, we report the results of inhibition kinetics for the enzyme from another source (DHFR from E. coli) exerted by (−)‐epigallocatechingallate (EGCG). Using different analytical techniques, we reported that EGCG acts as a bisubstrate inhibitor on the bacterial DHFR. Moreover, the combined approach of biosensor, kinetic, and molecular modelling analysis disclosed the ability of EGCG to bind to the enzyme both on substrate (DHF) and cofactor (NADPH) site. Collectively, our data have confirmed the selectivity of antifolate compounds with respect to the different source of enzyme (bacterial or mammalian DHFR) and the possible role of tea catechins as chemopreventive agents. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Cloning and characterization of a caesalpinoid (Chamaecrista fasciculata) hemoglobin: The structural transition from a nonsymbiotic hemoglobin to a leghemoglobin
Authors: Gopalasubramaniam Sabarinathan K. , Kovacs Frank , Violante‐Mota Fernando , Twigg Paul , Arredondo‐Peter Raúl , Sarath Gautam
Published: January 2008

Nonsymbiotic hemoglobins (nsHbs) and leghemoglobins (Lbs) are plant proteins that can reversibly bind O2 and other ligands. The nsHbs are hexacoordinate and appear to modulate cellular concentrations of NO and maintain energy levels under hypoxic conditions. The Lbs are pentacoordinate and facilitate the diffusion of O2 to symbiotic bacteroids within legume root nodules. Multiple lines of evidence suggest that all plant Hbs evolved from a common ancestor and that Lbs originated from nsHbs. However, little is known about the structural intermediates that occurred during the evolution of pentacoordinate Lbs from hexacoordinate nsHbs. We have cloned and characterized a Hb (ppHb) from the root nodules of the ancient caesalpinoid legume Chamaecrista fasciculata. Protein sequence, modeling data, and spectral analysis indicated that the properties of ppHb are intermediate between that of nsHb and Lb, suggesting that ppHb resembles a putative ancestral Lb. Predicted structural changes that appear to have occurred during the nsHb to Lb transition were a compaction of the CD‐loop and decreased mobility of the distal His inhibiting its ability to coordinate directly with the heme‐Fe, leading to a pentacoordinate protein. Other predicted changes include shortening of the N‐ and C‐termini, compaction of the protein into a globular structure, disappearance of positive charges outside the heme pocket and appearance of negative charges in an area located between the N‐ and C‐termini. A major consequence for some of these changes appears to be the decrease in O2‐affinity of ancestral nsHb, which resulted in the origin of the symbiotic function of Lbs. Proteins 2008. © 2008 Wiley‐Liss, Inc.
A combination of rescoring and refinement significantly improves protein docking performance
Authors: Pierce Brian , Weng Zhiping
Published: January 2008

To determine the structures of protein–protein interactions, protein docking is a valuable tool that complements experimental methods to characterize protein complexes. Although protein docking can often produce a near‐native solution within a set of global docking predictions, there are sometimes predictions that require refinement to elucidate correct contacts and conformation. Previously, we developed the ZRANK algorithm to rerank initial docking predictions from ZDOCK, a docking program developed by our lab. In this study, we have applied the ZRANK algorithm toward refinement of protein docking models in conjunction with the protein docking program RosettaDock. This was performed by reranking global docking predictions from ZDOCK, performing local side chain and rigid‐body refinement using RosettaDock, and selecting the refined model based on ZRANK score. For comparison, we examined using RosettaDock score instead of ZRANK score, and a larger perturbation size for the RosettaDock search, and determined that the larger RosettaDock perturbation size with ZRANK scoring was optimal. This method was validated on a protein–protein docking benchmark. For refining docking benchmark predictions from the newest ZDOCK version, this led to improved structures of top‐ranked hits in 20 of 27 cases, and an increase from 23 to 27 cases with hits in the top 20 predictions. Finally, we optimized the ZRANK energy function using refined models, which provides a significant improvement over the original ZRANK energy function. Using this optimized function and the refinement protocol, the numbers of cases with hits ranked at number one increased from 12 to 19 and from 7 to 15 for two different ZDOCK versions. This shows the effective combination of independently developed docking protocols (ZDOCK/ZRANK, and RosettaDock), indicating that using diverse search and scoring functions can improve protein docking results. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Crystal structure of glycerophosphodiester phosphodiesterase (GDPD) from Thermoanaerobacter tengcongensis, a metal ion‐dependent enzyme: Insight into the catalytic mechanism
Authors: Shi Liang , Liu Jun‐Feng , An Xiao‐Min , Liang Dong‐Cai
Published: January 2008

Glycerophosphodiester phosphodiesterase (GDPD; EC 3.1.4.46) catalyzes the hydrolysis of a glycerophosphodiester to an alcohol and glycerol 3‐phosphate in glycerol metabolism. It has an important role in the synthesis of a variety of products that participate in many biochemical pathways. We report the crystal structure of the Thermoanaerobacter tengcongensis GDPD (ttGDPD) at 1.91 Å resolution, with a calcium ion and glycerol as a substrate mimic coordinated at this calcium ion (PDB entry 2pz0). The ttGDPD dimer with an intermolecular disulfide bridge and two hydrogen bonds is considered as the potential functional unit. We used site‐directed mutagenesis to characterize ttGDPD as a metal ion‐dependent enzyme, identified a cluster of residues involved in substrate binding and the catalytic reaction, and we propose a possible general acid‐base catalytic mechanism for ttGDPD. Superposing the active site with the homologous structure GDPD from Agrobacterium tumefaciens (PDB entry 1zcc), which binds a sulfate ion in the active site, the sulfate ion can represent the phosphate moiety of the substrate, simulating the binding mode of the true substrate of GDPD. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Detailed conformational dynamics of juxtamembrane region and activation loop in c‐Kit kinase activation process
Authors: Zou Jun , Wang Yi‐Dong , Ma Fan‐Xin , Xiang Ming‐Li , Shi Bing , Wei Yu‐Quan , Yang Sheng‐Yong
Published: January 2008

The stem cell factor receptor (c‐Kit) plays critical roles in initiating cell growth and proliferation. Its kinase functional abnormity has been thought to associate with several human cancers. The regulation of c‐Kit kinase activity is achieved by phosphorylation on the residues Tyr568 and Tyr570 within juxtamembrane region (JMR) and subsequent structural transition of JMR and activation loop (A‐loop). However, the detailed conformational dynamics of JMR and A‐loop are far from clear, especially whether their conformational changes are coupled or not during the kinase activation transition. In this investigation, the complete conformational transition pathway was determined using a series of nanosecond conventional molecular dynamics (MD) and targeted molecular dynamics (TMD) simulations in explicit water systems. The results of the MD simulations show that the phosphorylation of residues Tyr568 and Tyr570 within JMR induces the detachment of JMR from the kinase C‐lobe and increases the fluctuation in the structure of JMR, thus appearing to initiate the kinase activation process. During the course of the TMD simulation, which characterizes the conformational transition of c‐Kit from autoinhibitory to activated state, the JMR undergoes a rapid departure from the allosteric binding site and drifts into solvent, followed by the conformational flip of A‐loop from inactive (fold) state to active (extended) state. A change in the orientation of helix αC in response to the motion of JMR and A‐loop has also been observed. The computational results presented here indicate that the dissociation of JMR from the kinase domain is prerequisite to c‐Kit activation, which is consistent with previous experiments. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Comprehensive description of protein structures using protein folding shape code
Authors: Yang Jiaan
Published: January 2008

Understanding and describing three‐dimensional (3D) protein structures have dominated biological and biochemistry research for many years. A comprehensive description of protein folding structure is essential for the advancement of protein research. In this study, a novel description method is developed to generate a set of folding patterns with specific shape features, as well as vector characteristics in space. To accomplish the goal, this method embeds features from geometry, morphology and topology together into an algorithmic approach to achieve a full description for proteins. A set of 27 vectors is derived mathematically from an enclosed space, and each vector represents a 3D folding shape of five successive Cα atoms in the protein backbone. The 27 vectors are represented by 27 symbols, which are called as the protein folding shape code (PFSC). The PFSC method offers a digital description of folding shapes along a protein backbone, which facilitates protein structure analysis. The PFSC method provides a tool to study the similarity and dissimilarity for protein or protein conformers. The PFSC results show overall agreement with structural assignments from the protein data bank, as well as results from other methods. All results show that the PFSC method is a reliable tool with explicit meaning for protein folding shape description. Protiens 2008. © 2008 Wiley‐Liss, Inc.
Molecular dynamics study of Pseudomonas aeruginosa lectin‐II complexed with monosaccharides
Authors: Mishra Navnit Kumar , Kulhánek Petr , Šnajdrová Lenka , Petřek Martin , Imberty Anne , Koča Jaroslav
Published: January 2008

We present the results of a series of 10‐ns molecular dynamics simulations on Pseudomonas aeruginosa lectin‐II (PA‐IIL) and its complexes with four different monosaccharides. We compare the saccharide‐free, saccharide‐occupied, and saccharide‐ and ion‐free forms of the lectin. The results are coupled with analysis of the water density map and calcium coordination. The water density pattern around the binding site in the free lectin molecular dynamics was fitted with that in the X‐ray and with the hydroxyl groups of the monosaccharide within the lectin/monosaccharide complexes and the best ligand was predicted based on the best fit. Interestingly, the water density pattern around the binding site in the uncomplexed lectin exactly fitted the O2, O3, and O4 hydroxyl groups of the fucose complex with the lectin. This observation could lead to a hypothesis that the replacement of these three water molecules from the binding site by the monosaccharide decreases the entropy of the complex and increases the entropy of the water molecules, which favors the binding. It suggests that the high density peaks of the solvent around the binding site in the free protein could be the tool to predict hydroxyl group orientation of the sugar in the protein/sugar complexes. The high affinity of PA‐IIL binding site is also attributed to the presence of two calcium ions, each of them making five to six coordinations with the protein part and two coordinations with either water or the monosaccharide. When the calcium ions are removed from the simulated system, they are replaced by sodium ions from the solvent. These observations rationalize the high binding affinity of PA‐IIL towards fucose. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Identifying stabilizing key residues in proteins using interresidue interaction energy matrix
Authors: Bendová‐Biedermannová Lada , Hobza Pavel , Vondrášek Jiří
Published: January 2008

We are proposing an interresidue interaction energy map (IEM) – a new tool for protein structure analysis and protein bioinformatics. This approach employs the sum of pair‐wise interaction energies of a particular residue as a measure of its structural importance. We will show that the IEM can serve as a means for identifying key residues responsible for the stability of a protein. Our method can be compared with the interresidue contact map but has the advantage of weighting the contacts by the stabilization energy content which they bring to the protein structure. For the theoretical adjustment of the proposed method, we chose the Trp‐cage mini protein as a model system to compare a spectrum of computational methods ranging from the ab initio MP2 level through the DFT method to empirical force‐field methods. The IEM method correctly identifies Tryptophane 6 as the key residue in the Trp‐cage. The other residues with the highest stabilizing contributions correspond to the structurally important positions in the protein. We have further tested our method on the Trp2Cage miniprotein – a P12W mutant of the Trp‐cage and on two proteins from the rubredoxin family that differ in their thermostability. Our method correctly identified the thermodynamically more stable variants in both cases and therefore can also be used as a tool for the relative measurement of protein stability. Finally, we will point out the important role played by dispersion energy, which contributes significantly to the total stabilization energy and whose role in aromatic pairs is clearly dominant. Surprisingly, the dispersion energy plays an even more important role in the interaction of prolines with aromatic systems. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Structural properties of the DNA‐bound form of a novel tandem repeat DNA‐binding domain, STPR
Authors: Saito Shin , Yokoyama Takuya , Aizawa Tomoyasu , Kawaguchi Kyosuke , Yamaki Takeshi , Matsumoto Daisuke , Kamijima Tatsuro , Kamiya Masakatsu , Kumaki Yasuhiro , Mizuguchi Mineyuki , Takiya Sigeharu , Demura Makoto , Kawano Keiichi
Published: January 2008

Fibroin‐modulator‐binding protein 1 (FMBP‐1) is a predicted transcription factor of the silkworm fibroin gene. The DNA‐binding domain of FMBP‐1 consists of four almost perfect tandem repeats of 23 amino acids each (R1–R4), and is referred to as the score and three amino acid peptide repeat (STPR) domain. This characteristic domain is conserved in eukaryotes, but the DNA‐binding mode is not known. In this study, the structural properties of the DNA‐bound form of the STPR domain were characterized. The combined experiments indicated that the STPR domain bound to the DNA duplex with a 1:1 binding ratio. The specific DNA caused considerable changes in the thermal unfolding profile and the digestion pattern of the STPR domain. These data suggested that the domain adapts a quite rigid helix‐rich structure in the DNA‐bound state, even though it moves flexibly in the absence of DNA. Furthermore, mutual induced‐fit conformational change was also observed in DNA. Finally, we determined the DNA‐binding surface of the STPR third repeat (R3) by alanine scanning mutagenesis; a particular site, composed of hydrophobic and hydrophilic residues, was identified. Notably, the substitution of Arg‐9 in R3 with alanine residue, which is located in the middle of the surface, drastically abolished the α‐helix‐inducing and DNA‐binding abilities. From these results, we predicted the DNA‐binding mode of the STPR domain. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Real‐value prediction of backbone torsion angles
Authors: Xue Bin , Dor Ofer , Faraggi Eshel , Zhou Yaoqi
Published: January 2008

The backbone structure of a protein is largely determined by the ϕ and ψ torsion angles. Thus, knowing these angles, even if approximately, will be very useful for protein‐structure prediction. However, in a previous work, a sequence‐based, real‐value prediction of ψ angle could only achieve a mean absolute error of 54° (83°, 35°, 33° for coil, strand, and helix residues, respectively) between predicted and actual angles. Moreover, a real‐value prediction of ϕ angle is not yet available. This article employs a neural‐network based approach to improve ψ prediction by taking advantage of angle periodicity and apply the new method to the prediction to ϕ angles. The 10‐fold‐cross‐validated mean absolute error for the new method is 38° (58°, 33°, 22° for coil, strand, and helix, respectively) for ψ and 25° (35°, 22°, 16° for coil, strand, and helix, respectively) for ϕ. The accuracy of real‐value prediction is comparable to or more accurate than the predictions based on multistate classification of the ϕ−ψ map. More accurate prediction of real‐value angles will likely be useful for improving the accuracy of fold recognition and ab initio protein‐structure prediction. The Real‐SPINE 2.0 server is available on the website http://sparks.informatics.iupui.edu. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Terrain‐based vehicle orientation estimation combining vision and inertial measurements
Authors: Gupta Vishisht , Brennan Sean
Published: January 2008

A novel method for estimating vehicle roll, pitch, and yaw using machine vision and inertial sensors is presented that is based on matching images captured from an on‐vehicle camera to a rendered representation of the surrounding terrain obtained from a three‐dimensional (3D) terrain map. U.S. Geographical Survey Digital Elevation Maps were used to create a 3D topology map of the geography surrounding the vehicle, and it is assumed in this work that large segments of the surrounding terrain are visible, particularly the horizon lines. The horizon lines seen in the captured video from the vehicle are compared to the horizon lines obtained from a rendered geography, allowing absolute comparisons between rendered and actual scene in roll, pitch, and yaw. A kinematic Kalman filter modeling an inertial navigation system then uses the scene matching to generate filtered estimates of orientation. Numerical simulations verify the performance of the Kalman filter. Experiments using an instrumented vehicle operating at the test track of the Pennsylvania Transportation Institute were performed to check the validity of the method. When compared to estimates from a global positioning system/inertial measurement unit (IMU) system, the roll, pitch, and yaw estimates from vision/IMU Kalman filter show an agreement with a (2σ) bound of 0.5, 0.26, and 0.8 deg, respectively. © 2008 Wiley Periodicals, Inc.
Three Dimensional Computerized Microtomography in the Analysis of Sculpture
Authors: Badde Aurelia , Illerhaus Bernhard
Published: January 2008

The Alte Nationalgalerie, Staatliche Museen zu Berlin (SMB) and the Federal Institute for Materials Research and Testing (BAM) tested the accomplishment of the three dimensional computerized microtomography (3D‐µCT)—a new flat panel detector computerized tomography (CT) system at the BAM with extended energy range, with high voltage X‐ray tubes (330 and 225 kV), with micrometer focal spot size and micrometer resolution and enlarged object size (up to 70 cm diameter)—for examining plaster statues.

The high spatial and density resolution of the tomograph enable detailed insights into the individual work processes of the investigated cast plaster statues. While initiated in support of the conservation process, computed tomography (CT) analysis has assisted in revealing relative chronologies within the series of the cast works of art, thus serving as a valuable tool in the art‐historical appraisal of the oeuvres.

The image‐processing systems visualize the voids and cracks within and the cuts through the original cast works. Internal structures, armoring, sculptural reworking as well as restorative interventions are virtually reconstructed.

The authors are currently employing the 3D‐µCT systems at the BAM into the detection of defects in Carrara marble sculpture. Microcracks, fractures, and material flaws are visualized at spatial resolution down to 10µm. Computerized reconstruction of ultrasound tomography is verified by analyzing correlations in the results obtained from the complementary application of these two non‐destructive testing (NDT) methods of diagnosis. SCANNING 30: 000–000, 2008. © 2008 Wiley Periodicals, Inc.
Disciplinary authority and accountability in scientific practice and learning
Authors: Ford Michael
Published: January 2008

This article explores the relation between how scientific knowledge is created and the reasoning involved in learning content with understanding. Although an asserted parallel between these underpins reform, little is actually known about this relation. This article offers a model of this relation that draws coherent connections between the science studies literature, which suggests ways of conceiving how scientific knowledge is created; and sociocultural learning theory, which suggests ways of conceiving scientific reasoning. This model highlights a dialectic betweenconstructionandcritiqueof claims in both scientific reasoning and practice. A “grasp” of scientific practice as such is instrumental to learning because informational content of scientific knowledge lies not only on the level of facts, but also on the levels of methods and values, and coordinating information across these levels is crucial for understanding. In contrast to prevailing constructivist ideas that highlight studentauthorityto construct knowledge as scientists do, this model emphasizes the importance of knowing how to hold claimsaccountable. Thus, the ideal vision of students makingtheir own senseof content is superceded by a more defensible ideal vision of students learning how to makescientific senseof content. © 2008 Wiley Periodicals, Inc.Sci Ed92:404–423, 2008
Nondestructive quantitative XPS imaging of depth distribution of atoms on the nanoscale
Authors: Hajati Shaaker , Coultas Sarah , Blomfield Chris , Tougaard Sven
Published: January 2008

It is well known that XPS imaging based on the peak intensity gives limited quantitative information. Recently, we found Tougaard's algorithm [J. Vac. Sci. Technol. 2003; A21: 1081] very robust for automatic data processing and we made a qualitative test of its ability to give an image of the amount of substance (AOS) in the outermost few nanometers as well as images of surface and bulk localized atoms [Surf. Sci. 2006; 600: 3015]. In this work, we perform a quantitative test of the algorithm's ability to produce images of Ag taken from a series of samples with increasing thicknesses of plasma patterned octadiene (2, 4, 6 and 8 nm) on Ag substrates. The obtained images of the amount of silver atoms in the outermost few nanometers of the samples were in good agreement with the nominal thicknesses. For a given sample, different sectioning of depth distributions of atoms were made, which clearly prove the ability of the method for quantitative and nondestructive determination of in‐depth distribution of atoms. We have shown that the algorithm is suitable to make 3D image of the nanoscale. Copyright © 2008 John Wiley & Sons, Ltd.
Plasmon peak inhomogeneous broadening in reflection electron energy loss spectroscopy from carbon materials
Authors: Calliari L. , Fanchenko S. , Filippi M.
Published: January 2008

In addition to the damping effect on plasmon peak broadening in reflection electron energy loss spectroscopy (REELS), the effect of inhomogeneous broadening is considered. The analysis of experimental data from highly oriented pyrolytic graphite (HOPG) shows that the contribution of inhomogeneous broadening is of the same order as the contribution associated with damping. In other words, the width of plasmon peaks cannot be ascribed only to damping, which is just one among several other contributions in this respect. At variance with other broadening contributions, however, damping is responsible not only for the width of plasmon peaks but also for their energy. For this reason, by showing that accounting for inhomogeneous broadening leads to decrease of the damping parameter, we also show that the plasmon peak‐shift associated with damping is less than one could expect otherwise. Copyright © 2008 John Wiley & Sons, Ltd.
Electrolytical deposition of NiCo films on Fe micro‐particles
Authors: Oriňáková Renáta , Oriňák Andrej , Kupková Miriam , Kabátová Margita , Chovan Peter
Published: January 2008

Binary NiCo coating layer was deposited electrolytically onto Fe micro particles surface. Galvanostatic electrolysis was carried out in fluidised bed system using Ni anode as well stainless steel anode.

Surface morphology of coated micro particles and depth distribution of individual metals (Ni, Co) in coating layer on the cross‐section of coated particles was investigated by SEM/EDX analysis.

Composition of coatings formed on powder particles was determined by atomic absorption spectrometry (AAS) and the character of co‐deposition was studied. The electrochemical deposition of NiCo alloys can show anomalous behaviour, in which there is a preferential deposition of the less noble rather than the more noble metal. The anomaly of Ni‐Co electrodeposition was not observed even when the stainless steel anode was used. It was found that the ratio between Ni and Co in binary deposit is dependant on the anode material. Employment of Ni anode was reflected in higher content of Ni in binary layer and changed distribution of coating components on the surface of coated particles. Copyright © 2008 John Wiley & Sons, Ltd.
Surface properties of activated carbon prepared from wastes
Authors: Demiral Hakan , Demiral İlknur
Published: January 2008

In this study, activated carbons were produced from animal wastes (cow dung) by chemical activation. The effects of the activating agent and the impregnation ratio were investigated at constant temperature of 700 °C. Chemical activations were carried out by mixing the solution of ZnCl2 or KOH and animal wastes with a chemical agent/waste, ratio (wt/wt) varying from 0.5 to 2.5. The pore properties including the Brunauer‐Emmett‐Teller(BET) surface area, pore volume, pore size distribution and average pore diameter of the activated carbons were determined by physical adsorption of N2 at − 196 °C. The highest BET surface areas and total pore volumes were achieved as 1367 m2/g and 0.788 cm3/g for ZnCl2‐activated carbon and as 1916 m2/g and 1.13 cm3/g for KOH‐activated carbon, respectively. The microstructure of the activated carbons was examined by SEM. The surface functional groups were determined by Fourier transform infrared spectra (FTIR). This study has demonstrated that high surface area activated carbons can be prepared from the chemical activation of animal wastes with KOH and ZnCl2 as activating agents. Copyright © 2008 John Wiley & Sons, Ltd.
Reconciling perspectives of software logic testing
Authors: Kaminski Garrett , Williams Gregory , Ammann Paul
Published: January 2008

Many software logic test coverage criteria have emerged over the past several years; however, they are scattered throughout the literature. The goal of this paper is to describe the various logic tests and explain their rationale in a centralized location in order to aid software testers in their decisions about which to implement. Each logic test is examined in terms of its minimum and maximum test sizes, subsumption relationship to other logic tests, and its fault detection capability. It is shown that although semantic tests generally have a smaller test size, syntactic tests are better in terms of fault detection capability. Furthermore, it is shown that the syntactic tests subsume their semantic counterparts. Two new software faults are introduced to Kuhn's fault hierarchy, namely the term insertion fault and the term negation fault, and the fault detection capability of the logic tests with respect to these faults is examined. A new software testing criterion called multiple unique true point/near false point (MUTP/NFP) is also presented, with a description of its benefits and limitations. Specifically, a detailed comparison of the MUTP/NFP criterion and the CUTPNFP/MNFP/MUTP criterion is given. Copyright © 2008 John Wiley & Sons, Ltd.