bluuebunny/crossref_metadata_2025 huggingface dataset:
Isotopic labelling in the study of organic and organometallic mechanism and structure: an account
Authors: Lloyd‐Jones Guy C. , Muñoz M. Paz
Published: October 2007

An account of the use of stable isotopes (2H, 13C, 15N, 18O, 34S) for the study of organic and organometallic reaction mechanism and structure, by way of kinetic determinations and modelling, NMR spectroscopy and mass spectrometry is presented. The techniques discussed include use of kinetic isotope effects, label‐facilitated nOe experiments, cross‐over experiments, stereoisotopochemical analysis, label‐facilitated NMR analysis of enantiomers using chiral‐shift reagents and NMR in chiral liquid crystal matrices. The reactions in which these tools have been applied are β‐H elimination in Pd‐σ‐alkyl complexes, the Bayliss–Hilman reaction, C–H insertion of stable carbenes, ring‐closing metathesis reactions, palladium‐catalysed hydrosilyation, palladium‐catalysed cycloisomerization, anionic thia‐Fries rearrangements, synthesis of proton sponges and their nitrogen stereodynamics, and transition metal (Pd, Mo) catalysed allylic alkylation. Copyright © 2007 John Wiley & Sons, Ltd.
Factors affecting the labeling yield of F‐18‐labeled AS1411
Authors: Li Junling , Trent John O. , Bates Paula J. , Ng Chin K.
Published: October 2007

The labeling of AS1411, a guanine (G)‐rich oligonucleotide (ON), conjugated with [18F]SFB was evaluated at different experimental conditions: ON concentration, base composition (G‐rich [AS1411] vs cytosine‐rich [CRO]), ON purity (desalted vs high‐pressure liquid chromatography (HPLC)‐purified) and buffers (tris‐HCl, sodium borate, and potassium phosphate (PBK)). The labeling yield, defined as % F‐18 incorporated into the ON, of HPLC‐purified AS1411 was significantly improved with increasing concentration – 7±3, 12±2, and 25±5% (n=5) at 56, 93, and 160 nmol/100 µL, respectively. The labeling yields, however, were much higher if guanines of AS1411 were completely replaced by cytosines – 22±1, 41±2, and 59±3% (n=3), respectively, at the same corresponding concentration (p<0.05). The specific activity of 18F‐AS1411 and 18F‐CRO was 4.2–12.6 and 4.2–25 mCi/µmol, respectively, after alcohol precipitation. If desalted grade of AS1411 and CRO was used instead for the conjugation, the yields were dropped to only 0–5 and 0–1 (n=5), respectively, regardless of the concentration used. The labeling yields were 5±2, 12±3, and 31±4 (n=3) at 200 nmol/100 µL of AS1411; and 30±2, 45±3, and 68±4 (n=3) at 200 nmol/100 µL of CRO for tris‐buffer, sodium borate, and PBK, respectively, at pH of 8.5 (p<0.05). Copyright © 2007 John Wiley & Sons, Ltd.
Synthesis of radiolabelled photolabile fusidic acid analogues
Authors: Schou Søren Christian , Riber Ditte , Grue‐Sørensen Gunnar
Published: October 2007

Two analogues of the antibiotic fusidic acid with photolabile groups, 4‐azidophenyl and 4‐benzoylphenyl, were successfully labelled with tritium via Pd/C catalysed tritiation of unsaturated precursors. Specific activities of 36 and 44 Ci/mmol were obtained. Copyright © 2007 John Wiley & Sons, Ltd.
Atomic force microscopy characterization of supported planar bilayers that mimic the mitochondrial inner membrane
Authors: Domènech Òscar , Redondo Lorena , Picas Laura , Morros Antoni , Montero M. Teresa , Hernández‐Borrell Jordi
Published: October 2007

In this study we examined the properties of supported planar bilayers (SPBs) formed from phospholipid components that comprise the mitochondrial inner membrane. We used 1‐palmitoyl‐2‐oleoyl‐sn‐glycero‐ 3‐phosphocholine (POPC), 1‐palmitoyl‐2‐oleoyl‐sn‐glycero‐3‐phosphoethanolamine (POPE) and cardiolipin (CL). Liposomes of binary POPE:POPC (1:1, mol:mol) and ternary (POPE:POPC:CL (0.5:0.3:0.2, mol:mol:mol) composition were used in the formation of SPBs on mica. The characterization of the SPBs was carried out below (4°C) and above (24 and 37°C) the phase transition temperature (Tm) of the mixtures in solution. We observed: (i) that the thickness of the bilayers, calculated from a cross‐sectional analysis, decreased as the visualization temperature increased; (ii) the existence of laterally segregated domains that respond to temperature in SPBs of POPE:POPC:CL; (iii) a decrease in height and an increase in roughness (Ra) of SPBs after cytochrome c (cyt c) injection at room temperature. To obtain further insight into the nature of the interaction between cyt c and the bilayers, the competition between 8‐anilino‐1‐naphthalene sulfonate (ANS) and the protein for the same binding sites in liposomes was monitored by fluorescence. The results confirm the existence of preferential interaction of cyt c with CL containing liposomes. Taking these results and those of previous papers published by the group, we discuss the preferential adsorption of cyt c in CL domains. This provides support for the relevance of these phospholipids as a proton trap in the oxidative phosphorylation process that occurs in the energy transducing membranes. Copyright © 2007 John Wiley & Sons, Ltd.
A knowledge‐based neuromodeling using space mapping technique: Compound space mapping‐based neuromodeling
Authors: Simsek Murat , Serap Sengor N.
Published: October 2007

This paper presents two new methods, space mapping (SM) with prior knowledge input (PKI‐D) with difference and compound space mapping‐based neuromodeling. Both methods combine two powerful techniques, space mapping‐based neuromodeling and PKI‐D with difference. The knowledge‐based modeling methods in the RF/microwave literature merge the prior knowledge about the device to be modeled with neural network structures while a knowledge‐based method, SP, focuses on reducing the computational burden. The main advantage of the proposed methods over these already existing knowledge‐based methods are their better extrapolation capability and reduced number of training set data. The simulation results obtained reveal that both methods decrease the cost of training and improve the extrapolation capability and output performance of the SP‐based neuromodeling. Copyright © 2007 John Wiley & Sons, Ltd.
Comparison of in vitro degradation of temperate forages using the gas production and filter bag techniques
Authors: Hetta Mårten , Nordheim Hege , Gustavsson Anne‐Maj , Martinsson Kjell
Published: October 2007

BACKGROUND: Two of the most promising in vitro techniques for dynamic forage evaluation are the gas production (GP) and filter bag (FB) techniques. To improve our understanding of how these techniques describe the dynamic degradation of forages, 20 temperate forage samples were analysed by each method at different time points during a 96 h incubation period. The results of the recordings were fitted to a biphasic Michaelis–Menten model describing the degradation of rapidly and slowly degrading forage fractions.

RESULTS: GP and disappearance from the FB measurements were correlated at all time points from 6 to 96 h (R2 = 0.27–0.74), except at the 24 h incubation point. When GP was transformed into organic matter degradation (OMD), there was an even stronger correlation (R2 = 0.54–0.75) between the techniques at all intervals. Comparison of the parameters from the Michaelis–Menten model resulted in correlations (R2 = 0.83) between the sizes of the estimated forage fractions, but not between parameter determining the rates of their degradation.

CONCLUSIONS: Both the GP and FB techniques have the potential to estimate the degradation of individual feed fractions in forages. Further studies in which the in vitro parameters are evaluated against livestock data, are needed to confirm the findings of this study, however. Copyright © 2007 Society of Chemical Industry
Alzheimer's disease in Down syndrome: Neurobiology and risk
Authors: Zigman Warren B. , Lott Ira T.
Published: October 2007

Down syndrome (DS) is characterized by increased mortality rates, both during early and later stages of life, and age‐specific mortality risk remains higher in adults with DS compared with the overall population of people with mental retardation and with typically developing populations. Causes of increased mortality rates early in life are primarily due to the increased incidence of congenital heart disease and leukemia, while causes of higher mortality rates later in life may be due to a number of factors, two of which are an increased risk for Alzheimer's disease (AD) and an apparent tendency toward premature aging. In this article, we describe the increase in lifespan for people with DS that has occurred over the past 100 years, as well as advances in the understanding of the occurrence of AD in adults with DS. Aspects of the neurobiology of AD, including the role of amyloid, oxidative stress, Cu/ZN dismutase (SOD‐1), as well as advances in neuroimaging are presented. The function of risk factors in the observed heterogeneity in the expression of AD dementia in adults with DS, as well as the need for sensitive and specific biomarkers of the clinical and pathological progressing of AD in adults with DS is considered. © 2007 Wiley‐Liss, Inc. MRDD Research Reviews 2007;13:237–246.
A cap model for partially saturated soils
Authors: Kohler R. , Hofstetter G.
Published: October 2007

The present paper deals with the extension of a cap model in order to describe the material behavior of partially saturated soils, in particular, of partially saturated sands and silts. The soil model is formulated in terms of two stress state variables, using net stress and matric suction and, alternatively, the average soil skeleton stress and suction, the latter playing the role of a stress‐like plastic internal variable. The yield surface, consisting of a shear failure surface and a hardening cap surface, the plastic potentials for the non‐associated flow rule and the hardening law for the cap are extended by taking into account the effects of matric suction on the material behavior. Furthermore, the third invariant of the deviatoric stress tensor is taken into account in the formulation of the yield surfaces. The developed model is validated by the numerical simulation of an extensive series of suction controlled tests for a silty sand, which were conducted at different constant values of suction. Although both versions of the soil model yield identical results for stress paths at constant values of matric suction, differences are encountered for stress paths involving wetting. Copyright © 2007 John Wiley & Sons, Ltd.
Reduced brain glutamate in patients with Parkinson's disease
Authors: Griffith H. Randall , Okonkwo Ozioma C. , O'Brien Timothy , Hollander Jan A. den
Published: October 2007

An understanding of the role played by glutamate (Glu) in idiopathic Parkinson's disease (PD) has remained somewhat elusive. Animal models of PD suggest that over‐activity of Glu receptors complicates the motor symptoms of PD and that Glu blockade may be a pharmacologic target in PD, whereas patient autopsy studies have proved less convincing for changes in Glu. No previous 1H MRS patient studies have documented changes in glutamate. All but one of these previous studies were performed at 1.5 T. We performed 3 T 1H MRS of the posterior cingulate gyrus in 12 non‐demented patients with PD and 12 age‐matched, neurologically normal control participants. Glu, N‐acetylaspartate (NAA) and choline‐containing compounds (Cho) measured in reference to creatine + phosphocreatine (Cr) were determined from single‐voxel proton MR spectra measured by PRESS at TE of 80 ms. The results show that the Glu/Cr ratio was reduced in patients with PD compared with controls (t = 2.54; P = 0.019), whereas no differences were observed in NAA/Cr or Cho/Cr ratios. These findings suggest that a reduction in Glu occurs in the cerebral cortex of patients with PD. 1H MRS at 3 T should be investigated in future studies as a means of tracking the course of metabolic brain changes in association with progression of disease in patients with PD. Copyright © 2007 John Wiley & Sons, Ltd.
Silica nanospheres as back surface reflectors for crystalline silicon thin‐film solar cells
Authors: Inns Daniel , Shi Lei , Aberle Armin G.
Published: October 2007

In this paper, fabrication of a non‐continuous silicon dioxide layer from a silica nanosphere solution followed by the deposition of an aluminium film is shown to be a low‐cost, low‐thermal‐budget method of forming a high‐quality back surface reflector (BSR) on crystalline silicon (c‐Si) thin‐film solar cells. The silica nanosphere layer has randomly spaced openings which can be used for metal‐silicon contact areas. Using glass/SiN/p+nn+c‐Si thin‐film solar cells on glass as test vehicle, the internal quantum efficiency (IQE) at long wavelengths (>900 nm) is experimentally demonstrated to more than double by the implementation of this BSR, compared to the baseline case of a full‐area Al film as BSR. The improved optical performance of the silica nanosphere/aluminium BSR is due to reduced parasitic absorption in the Al film. Copyright © 2007 John Wiley & Sons, Ltd.
Crisis response in the public schools: A survey of school psychologists' experiences and perceptions
Authors: Adamson Austin D. , Peacock Gretchen Gimpel
Published: October 2007

In this study, 228 school psychologists completed a survey regarding crisis intervention teams and plans. The majority of respondents indicated their schools had crisis plans (95.1%) and teams (83.6%). The most common team activities endorsed by participants involved providing direct assistance and services to students, staff, and the media. The majority of participants (93%) reported that their schools had experienced and responded to serious crises. Respondents indicated that psychological debriefing was frequently used (generic 49.1% and standardized 17.9%). Less than half of the participants (44.3%) reported that meetings were conducted with parents and community members following a crisis. Nearly all of the participants (98.2%) reported that they had some type of crisis intervention training. However, many participants suggested that additional training and practice with crisis intervention would improve schools' crisis responses. Results are discussed with implications for school psychologists to improve their schools' crisis intervention plans and teams' responses. © 2007 Wiley Periodicals, Inc. Psychol Schs 44: 749–764, 2007.
Modifying socially withdrawn behavior: A playground intervention for students with internalizing behaviors
Authors: Marchant Michelle R. , Solano Brock R. , Fisher Adam K. , Caldarella Paul , Young K. Richard , Renshaw Tyler L.
Published: October 2007

There is little research regarding interventions for children with internalizing behaviors in schools, both within classrooms and in nonclassroom environments. In response to this need, a nonclassroom treatment package, consisting of (a) social skills instruction, (b) mediated self‐management, and (c) a reinforcement system, was implemented to modify the socially withdrawn behavior of 3 elementary students. The effects of this treatment package were evaluated on the school playground—during recess—by recording both the number of communicative acts and the total time spent engaged in appropriate peer play for each target student. All target students showed marked improvement in their playground, social interaction. Future research should be conducted with similar populations, using variations of the described methods in other school settings. © 2007 Wiley Periodicals, Inc. Psychol Schs 44: 779–794, 2007.
School‐based support for GLBT students: A review of three levels of research
Authors: Hansen Anastasia L.
Published: October 2007

Gay, lesbian, bisexual, and transgender (GLBT) students experience harassment, alienation, and violence in schools. Several school‐based interventions have been suggested to provide a safe and effective learning environment for these students, but few have been evaluated or investigated experimentally. This review utilizes A.K. Ellis' (2001) model to review the research on school‐based interventions for GLBT youth at the levels of theory, applied investigation, and widespread implementation. Results suggest that, although the research base for psychological needs of GLBT youth is well established, applied investigation of small‐ and large‐scale implementation is in the early stages. © 2007 Wiley Periodicals, Inc. Psychol Schs 44: 839–848, 2007.
International Symposium on High Performance Proteomics 2007: A contribution to Proteomics May 14–16, 2007 Dortmund, Germany
Authors: Hamacher Michael , Grünewald Petra , Rammert Klaus , Bustamante Nadine Palacios , Hardt Tanja , van Hall André , Meyer Helmut E.
Published: October 2007

The symposium High Performance Proteomics was held in Dortmund on May 14‐16, 2007, to celebrate the opening of the Zentrum für Angewandte Proteomik as well as the 6th anniversary of the German Human Brain Proteome Project. It offered an outstanding opportunity to obtain a broad overview about all fields of proteomics and related fields, combining the expertise of biochemists, physicians, bioinformatics, mathematicians and other researchers in Life Sciences. The main topics were the presentation of state‐of‐the‐art proteomics technologies as well as possible transfer models for industrial applications. An accompanying industrial exhibition, as well as a discussion panel, offered the possibility to get in contact with colleagues and potential industrial partners. A visit to the former colliery Zeche Zollern and the social event at the Harenberg City‐Center with an excellent view around Dortmund also left time for further communication between the more than 200 attendees.
Preparation of poly(styrene‐b‐N‐isopropylacrylamide) micelles surface‐linked with gold nanoparticles and thermo‐responsive ultraviolet–visible absorbance
Authors: Li Jian , He Wei‐Dong , Sun Xiao‐Li
Published: October 2007

Poly(styrene‐b‐N‐isopropylacrylamide) (PSt‐b‐PNIPAM) with dithiobenzoate terminal group was synthesized by reversible addition‐fragmentation‐transfer polymerization. The dithiobenzoate terminal group was converted into thiol terminal group with NaBH4, resulting thiol‐terminated PSt‐b‐PNIPAM‐SH. After PSt‐b‐PNIPAM‐SH assembled into core‐shell micelles in aqueous solution, gold nanoparticles were in situ surface‐linked onto the micelles through the reduction of gold precursor anions with NaBH4. Thus, temperature responsive core/shell micelles of PSt‐b‐PNIPAM surface‐linked with gold nanoparticles (PSt‐b‐PNIPAM‐Au micelles) were obtained. Transmission Electron Microscopy revealed the successful linkage of gold nanoparticles and the dependence of the number of gold nanoparticles per micelle on the molar ratio of HAuCl4 to thiol group of PSt‐b‐PNIPAM. Dynamic Light Scattering analysis demonstrated thermo‐responsive behavior of PSt‐b‐PNIPAM‐Au micelles. Changing the temperature of PSt‐b‐PNIPAM‐Au micelles led to the shrinkage of PNIPAM shell and allowed to tune the distance between gold nanoparticles. Ultraviolet–visible (UV–vis) spectroscopy clearly showed the reversible modulation of UV–vis absorbance of PSt‐b‐PNIPAM‐Au micelles upon heating and cooling. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 5156–5163, 2007
Synthesis and characterization of a biodegradable amphiphilic copolymer based on branched poly(ϵ‐caprolactone) and poly(ethylene glycol)
Authors: Zou Tao , Li Song‐Lin , Zhang Xian‐Zheng , Wu Xiao‐Jun , Cheng Si‐Xue , Zhuo Ren‐Xi
Published: October 2007

A novel biodegradable amphiphilic copolymer with hydrophobic poly(ε‐caprolactone) branches containing cholic acid moiety and a hydrophilic poly(ethylene glycol) chain was synthesized. The copolymer was characterized by FTIR, 1H NMR, gel permeation chromatography (GPC), differential scanning calorimetry (DSC), polarizing light microscopy (PLM), and wide‐angle X‐ray diffraction (WAXD) analysis. The amphiphilic copolymer could self‐assemble into micelles in an aqueous solution. The critical micelle concentration of the amphiphilic copolymer was determined by fluorescence spectroscopy. A nanoparticle drug delivery system with a regularly spherical shape was prepared with high encapsulation efficiency. The in vitro drug release from the drug‐loaded polymeric nanoparticles was investigated. Because of the branched structure of the hydrophobic part of the copolymer and the relatively fast degradation rate of the copolymer, an improved release behavior was observed. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 5256–5265, 2007
Synthesis and characterization of hyperbranched polyfluorenes containing triarylpyrazoline cores towards efficient blue light‐emitting diodes
Authors: Peng Qiang , Yan Liushui , Chen Dezhi , Wang Fuzhi , Wang Ping , Zou Dechun
Published: October 2007

New series of hyperbranched polyfluorenes containing triarylpyrazoline cores, PFZ10, PFZ20, PFNZ10, and PFNZ20, have been synthesized according to the “A2 + A′2 + B3” Suzuki coupling method. The structures and property of the monomers and conjugated polymers were characterized by elemental analysis, gel permeation chromatography, cyclic voltammetry, thermogravimetric analysis, differential scanning calorimetry, and UV–visible absorption, 1H NMR, 13C NMR, and photoluminescence spectroscopies. All these polymers exhibited good solubility in common organic solvents and good thermal stability. The long‐wavelength emission of polyfluorenes had been effectively reduced in these hyperbranched polymers. Standard polymer light emitting devices (PLEDs) from PFZ10, PFZ20, PFNZ10, and PFNZ20, with the configuration of ITO/PEDOT/polymer/TPBI/Alq3/Mg:Ag, exhibited good electroluminescence (EL) properties The PLED based on PFNZ10 emitted pure blue light with a low turn‐on voltage of 5.3 V and a high EL efficiency of about 1.93%. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 5296–5307, 2007
Synthesis and structural characterization of syndiotactic trans‐1,2 and cis‐1,2 polyhexadienes
Authors: Ricci Giovanni , Boglia Aldo , Motta Tiziano , Bertini Fabio , Boccia Antonella Caterina , Zetta Lucia , Alberti Enrica , Famulari Antonino , Arosio Paolo , Meille Stefano Valdo
Published: October 2007

The (E) isomer in mixtures of (E) and (Z) 1,3‐hexadiene was polymerized with the system CoCl2(PiPrPh2)2‐MAO, a highly active and stereospecific catalyst for the preparation of 1,2 syndiotactic polybutadiene. A new crystalline polymer with a melting point of 109 °C was obtained. The polymer was characterized by IR, NMR (13C, 1H in solution and 13C in the solid‐state), X‐ray diffraction, DSC, GPC and it was found to have a trans‐1,2 syndiotactic structure with a 5.18 ± 0.04 Å fiber periodicity. Since only the (E) isomer was polymerized, at the end of the reaction we were able to separate the (Z) isomer, which was ultimately polymerized with CpTiCl3‐MAO at low temperature, obtaining a low molecular weight, stereoregular polymer that, characterized by IR and NMR methods, was found to exhibit a cis‐1,2 syndiotactic structure, never reported before. Molecular mechanics calculations were carried out on the trans‐1,2 syndiotactic polymer and structural models consistent with the X‐ray diffraction data are proposed. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 5339–5353, 2007
Classifying protein kinase structures guides use of ligand‐selectivity profiles to predict inactive conformations: Structure of lck/imatinib complex
Authors: Jacobs Marc D. , Caron Paul R. , Hare Brian J.
Published: October 2007

We report a clustering of public human protein kinase structures based on the conformations of two structural elements, the activation segment and the C‐helix, revealing three discrete clusters. One cluster includes kinases in catalytically active conformations. Each of the other clusters contains a distinct inactive conformation. Typically, kinases adopt at most one of the inactive conformations in available X‐ray structures, implying that one of the conformations is preferred for many kinases. The classification is consistent with selectivity profiles of several well‐characterized kinase inhibitors. We show further that inhibitor selectivity profiles guide kinase classification. For example, selective inhibition of lck among src‐family kinases by imatinib (Gleevec) suggests that the relative stabilities of inactive conformations of lck are different from other src‐family kinases. We report the X‐ray structure of the lck/imatinib complex, confirming that the conformation adopted by lck is distinct from other structurally‐characterized src‐family kinases and instead resembles kinases abl1 and kit in complex with imatinib. Our classification creates new paths for designing small‐molecule inhibitors. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Assembly of the oncogenic DNA‐binding complex LMO2‐Ldb1‐TAL1‐E12
Authors: Ryan Daniel P. , Duncan Jaimee L. , Lee Christopher , Kuchel Philip W. , Matthews Jacqueline M.
Published: October 2007

The nuclear proteins TAL1 (T‐cell acute leukaemia protein 1) and LMO2 (LIM‐only protein 2) have critical roles in haematopoietic development, but are also often aberrantly activated in T‐cell acute lymphoblastic leukaemia. TAL1 and LMO2 operate within multifactorial protein–DNA complexes that regulate gene expression in the developing blood cell. TAL1 is a tissue‐specific basic helix–loop–helix (bHLH) protein that binds bHLH domains of ubiquitous E‐proteins, (E12 and E47), to bind E‐box (CANNTG) DNA motifs. TAL1bHLH also interacts specifically with the LIM domains of LMO2, which in turn bind Ldb1 (LIM‐domain binding protein 1). Here we used biophysical methods to characterize the assembly of a five‐component complex containing TAL1, LMO2, Ldb1, E12, and DNA. The bHLH domains of TAL1 and E12 alone primarily formed helical homodimers, but together preferentially formed heterodimers, to which LMO2 bound with high affinity (KA ∼ 108M−1). The resulting TAL1/E12/LMO2 complex formed in the presence or absence of DNA, but the different complexes preferentially bound different Ebox‐sequences. Our data provide biophysical evidence for a mechanism, by which LMO2 and TAL1 both regulate transcription in normal blood cell development, and synergistically disrupt E2A function in T‐cells to promote the onset of leukaemia. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Interaction cutoff effect on ruggedness of protein–protein energy landscape
Authors: Ruvinsky Anatoly M. , Vakser Ilya A.
Published: October 2007

The concept of the energy landscape is important for better understanding of protein–protein interactions and for designing adequate docking procedures. The intermolecular landscape has a rugged terrain that impedes search procedures. Its inherent ruggedness is related to the conformational characteristics of the molecules and to the form of the potential function—more rugged for short‐range potentials and less rugged for “soft,” typically long‐range potentials. Our study determined that the landscape ruggedness is further substantially exacerbated by truncation of the potentials. This additional ruggedness appears below certain critical interaction ranges that depend on the form of the potential. The theoretical model describing the cutoff effect on the landscape ruggedness is confirmed by the energy calculation on a dataset of protein–protein complexes. The negative effect of the potentials cutoff is well known. However, revealing its physical basis in terms of the energy landscape is important for better understanding of intermolecular interactions. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Automated prediction of ligand‐binding sites in proteins
Authors: Harris Rodney , Olson Arthur J. , Goodsell David S.
Published: October 2007

We present a method, termed AutoLigand, for the prediction of ligand‐binding sites in proteins of known structure. The method searches the space surrounding the protein and finds the contiguous envelope with the specified volume of atoms, which has the largest possible interaction energy with the protein. It uses a full atomic representation, with atom types for carbon, hydrogen, oxygen, nitrogen and sulfur (and others, if desired), and is designed to minimize the need for artificial geometry. Testing on a set of 187 diverse protein‐ligand complexes has shown that the method is successful in predicting the location and approximate volume of the binding site in 73% of cases. Additional testing was performed on a set of 96 protein‐ligand complexes with crystallographic structures of apo and holo forms, and AutoLigand was able to predict the binding site in 80% of the apo structures. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Tuning the shape of macroporous silicon
Authors: Trifonov T. , Garín M. , Rodríguez A. , Marsal L. F. , Alcubilla R.
Published: October 2007

The cover picture shows SEM images of the porous silicon membranes with controlled pore geometry which are subject to this issue's Editor's Choice article [1]. The authors demonstrate how the rounded‐square shape of pores in a silicon membrane prepared by photo‐electrochemical etching can be turned into a circular cross section using multiple oxidation/oxide‐stripping cycles.

The image on the left is a side view onto a cleaved sample after eleven oxidation steps. The enlarged inset shows pore walls as thin as about 250 nm, including one set of the slightly thicker marks produced by reducing the current in order to obtain feedback on the etching rate. One oxidation step further, the membrane releases individual silicon pillars with a very large aspect ratio, as is illustrated by the top view on the right.

The first author holds a post‐doctoral position at the Electronics Department of the Technical University of Catalonia, where his research focuses on the fabrication of 2D and 3D photonic crystals based on macroporous silicon.

Also featured on the cover is a Review Article by Chivukula et al., surveying the various types of acoustic‐wave devices utilizing surface‐acoustic, acousto‐optic and photo‐acoustic effects for applications in biology and medicine [2]. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The effect of SWCNT and nano‐diamond films on human osteoblast cells
Authors: Kalbacova M. , Kalbac M. , Dunsch L. , Kromka A. , Vaněček M. , Rezek B. , Hempel U. , Kmoch S.
Published: October 2007

Human osteoblasts (SAOS‐2) are cultured on single‐walled carbon nanotube (SWCNT) and nanocrystalline diamond (NCD) films in order to evaluate their potential for biological application. We present dependence of metabolic activity and morphology of osteoblasts on (i) material substrate (NCD or SWCNT films), (ii) surface termination – O‐termination causing hydrophilic surface and H‐termination (as deposited NCDs) causing hydrophobic surface, (iii) surface roughness in the range of 11–39 nm RMS and (iv) SWCNT production technique – laser ablation, arc‐discharge and HiPco. The metabolic activity decreases to the same non‐toxic level on SWCNT films produced by different techniques as well as on H‐terminated NCD compared to tissue culture polystyrene. The metabolic activity is increasing on O‐terminated NCD films as a function of their roughness. Morphological observations support superior properties of O‐terminated NCD films. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Experimental observation and numerical simulation of guided modes in Nd:YLiF4 channel waveguides produced by carbon ion implantation
Authors: Tan Yang , Chen Feng
Published: October 2007

We report on, to our knowledge the first time, the channel waveguide formation in Nd:YLiF4 laser crystal produced by 6 MeV carbon ion implantation. The guided modes are observed by using an end‐face arrangement. We construct the two‐dimensional (2D) refractive index profile of the channel waveguide cross section, which is based on the related planar waveguide index distribution as well as the rectangular shape of the waveguide cross sections. The modal intensity distribution is numerically calculated by using the beam propagation method according to the reconstructed index profile, which shows a reasonable agreement with the experimental result. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Theoretical study of hydrogen‐bonded complexes of benzene with hydrides of astrochemical interest
Authors: Nait Achour M. , Belmecheri M. R. , Berthier G. , Savinelli R.
Published: October 2007

Post Hartree–Fock and DFT calculations have been performed for studying the possibility for a benzene support to be linked to various hydrides through a quasi Bz···HA bond. Interaction energy of compounds, including CH bonds (CH4, CH3F, CH2O, CHN, CHNO), NH bonds (NH3, NH2F, NHC, NHCO, NH3O), and OH bonds (OH2, OHF, NCOH), were evaluated, taking basis set superposition error (BSSE) and zero point vibrational energy (ZPVE) corrections into account. Numerical convergence of results with respect to the ingredients included at different steps of theory (basis set, DFT functionals, correlation treatments, geometry optimization) was tested mainly on the example of the water adduct and, for comparison, the Bz···H3O+ system containing a cation instead of a neutral molecule. A rather large range of adsorption energies is obtained, from about 1 kcal/mol for methane to more than 6 kcal/mol for cyanic acid, according to the acidic character of the adsorbed species in each family of Bz···HA bonds. Some consequences for astrophysical problems involving PAHs in the interstellar medium are pointed out. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
The use of Gaussian quadrature for estimation in frailty proportional hazards models
Authors: Liu Lei , Huang Xuelin
Published: October 2007

In this paper, we propose a novel Gaussian quadrature estimation method in various frailty proportional hazards models. We approximate the unspecified baseline hazard by a piecewise constant one, resulting in a parametric model that can be fitted conveniently by Gaussian quadrature tools in standard software such as SAS Proc NLMIXED. We first apply our method to simple frailty models for correlated survival data (e.g. recurrent or clustered failure times), then to joint frailty models for correlated failure times with informative dropout or a dependent terminal event such as death. Simulation studies show that our method compares favorably with the well‐received penalized partial likelihood method and the Monte Carlo EM (MCEM) method, for both normal and Gamma frailty models. We apply our method to three real data examples: (1) the time to blindness of both eyes in a diabetic retinopathy study, (2) the joint analysis of recurrent opportunistic diseases in the presence of death for HIV‐infected patients, and (3) the joint modeling of local, distant tumor recurrences and patients survival in a soft tissue sarcoma study. The proposed method greatly simplifies the implementation of the (joint) frailty models and makes them much more accessible to general statistical practitioners. Copyright © 2007 John Wiley & Sons, Ltd.
Understanding complexity, challenging traditional ways of thinking
Authors: Wulun Jin
Published: October 2007

This paper discusses the historic evolutionary process of thinking patterns since modern science, which can be divided into three stages: modernism, systems thinking and postmodernism. The paper proposes that the main form of thinking pattern of modernism is mechanism which accompanies modern science. Systems thinking set its aim on holism, but its approach is still inseparable from division and reduction. Both the thinking patterns of modernism and systems thinking are of the category of constitutive theory. However, the rise of complexity sciences has brought great changes to thinking patterns and moved toward postmodernism that has the characteristic of generative theory. In this paper, the function of both convergent and divergent patterns of thinking in the evolution of holistic thinking is interspersed. Copyright © 2007 John Wiley & Sons, Ltd.
A new approach to studying complex systems
Authors: Zexian Yan
Published: October 2007

This paper introduces a new approach to the studies of complex systems, which is based on conceptual entanglement of science and philosophy. On the basis of ‘two umbrellas’ by Checkland, we raise a ‘third umbrella’, namely, self‐organization and evolution, which extends systems thinking to complex system thinking. This paper also talks about the mechanisms of the operation and evolution of complex systems, puts forth an interactive model of three mechanisms and two feedback loops and finally presents its implication to the management of social organizations. Copyright © 2007 John Wiley & Sons, Ltd.
Wölbkrafttorsion bei veränderlichem, offenem Querschnitt – hat die Biegezugstabanalogie noch Gültigkeit?
Authors: Rubin Helmut , Aminbaghai Mehdi
Published: October 2007

Die weniger anschauliche Theorie der Wölbkrafttorsion kann durch die wesentlich anschaulichere Theorie II. Ordnung des Biegestabes mit Längszugkraft ersetzt werden, indem die Biegezugstabanalogie verwendet wird. Dass dieses Vorgehen nicht mehr zulässig ist, wenn es sich um einen Stab mit veränderlichem Querschnitt handelt, wird im vorliegenden Beitrag gezeigt. Für einen verallgemeinerten, einfachsymmetrischen I‐Querschnitt mit linear veränderlicher Steghöhe und Gurtbreite werden alle erforderlichen Formeln zur Berechnung der Schnitt‐ und Verschiebungsgrößen auf Basis der Übertragungsbeziehung entwickelt und die zur Ermittlung der Wölbnormal‐ und Wölbschubspannungen benötigten Beziehungen angegeben. Die Anwendung wird anhand von drei Beispielen gezeigt, beim ersten Beispiel sind auch die Ergebnisse nach der Biegezugstabanalogie angegeben, dabei zeigt sich, dass die Zustandsgrößen der sekundären Torsion i. d. R. nicht einmal das richtige Vorzeichen aufweisen.
An analytical model for high‐rise wall‐frame structures with outriggers
Authors: Lee Jaehong , Bang Minsik , Kim Jae‐Yeol
Published: October 2007

In this paper, the governing equations of wall‐frame structures with outriggers are formulated through the continuum approach and the whole structure is idealized as a shear–flexural cantilever with rotational springs. The effect of shear deformation and flexural deformation of the wall‐frame and outrigger trusses are considered and incorporated in the formulation of the governing equations. A displacement‐based one‐dimensional finite element model is developed to predict lateral drift of a wall‐frame with outriggers under horizontal loads. Numerical static results are obtained and compared with previously available results and the values obtained from the finite element package MIDAS. The proposed method is found to be simple and efficient, and provides reasonably accurate results in the early design stage of tall building structures. Copyright © 2007 John Wiley & Sons, Ltd.
Anbindung von Fluoreszenzfarbstoffen an plasmachemisch funktionalisierte und Cucurbituril‐modifizierte Oberflächen
Authors: Mix R. , Hoffmann K. , Buschmann H.‐J. , Friedrich J. F. , Resch‐Genger U.
Published: October 2007

Plasmapolymerisierte Allylaminschichten (50 nm) wurden auf Polypropylenfolien abgeschieden. Die auf diese Weise generierte NH2‐funktionalisierte Polymeroberfläche wurde mit Xanthen‐Fluorophoren chemisch umgesetzt. Da die Farbstoff‐gekoppelten Folien nur geringe Fluoreszenz aufwiesen, wurden zwei Wege zur möglichen Entkopplung der Farbstoffe von der Oberfläche und damit zur Erhöhung der Fluoreszenzintensität getestet. Als erstes wurde ein Spacer durch die Umsetzung der primären Aminogruppen mit Glutaraldehyd und der nachfolgenden Kettenverlängerung mit Diaminohexan eingeführt. Diese nachfolgende Reaktion ergab eine spacergebundene NH2‐Oberfläche, die analog der Allylaminschicht mit den Farbstoffen umgesetzt wurde. Als weiterer Weg wurde der Zusatz einer geeigneten Käfigverbindung, des Cucurbit[6]urils, getestet. Die spacergebundenen und zusätzlich mit Cucurbituril modifizierten aminofunktionellen Oberflächen zeigten nach der Farbstoffankopplung eine verbesserte Fluoreszenzintensität.
The characteristics of domestic tung oils
Authors: Holmes Raiford L. , Pack Frank C. , Minor Jacob C. , McKinney R. S.
Published: October 2007

Conclusion

Domestic tung oil is a very uniform product as shown by the determination of the chemical and physical properties of 74 samples taken over three successive milling seasons.

The refractive index, refractive dispersion, and heat test are correlated with the total eleostearic acid content, the correlation coefficients being 0.69, 0.73, and −0.62 respectively, which indicates that any one of these values can be taken as a rough measure of the elostearic acid content. The correlation of the eleostearic acid content with the Wijs and hydrogen iodine values was lower, 0.48 and 0.53, respectively. A correlation of −0.81 was found between refractive index and heat test.
The pigments of crude cottonseed oils. I. The inhibition of color reversion in crude cottonseed oils
Authors: Dechary J. M. , Kupperman R. P. , Thurber F. H. , O’Connor R. T.
Published: October 2007

Treatment of freshly prepared crude cottonseed oils withp‐aminobenzoic acid and subsequent removal of the di‐p‐carboxyanilinogossypol formed makes it possible to store the oils at a relatively high temperature (37–38°C.) and for an extended period of time (30 days) without incurring any adverse changes in the refining and bleaching properties of the oils. In addition, a considerable decrease in the refining loss of the crude oil is obtained, and the stability of the bleached oil is not affected by the treatment.

Spectrophotometric studies made during all phases of the chemical treatment and during the refining and bleaching procedures show that thep‐aminobenzoic acid removes almost completely the gossypol‐like pigments which are present in the crude oils and yields oils having the characteristic carotenoid spectrum.
Developing coping typologies of minority adolescents: A latent profile analysis
Authors: Aldridge Arianna A. , Roesch Scott C.
Published: October 2007

Latent profile analysis (LPA) was used to develop a coping typology of minority adolescents (M=15.5 years). A multiethnic sample (n=354) was recruited from a program aimed at serving low‐income students. LPA revealed three distinct coping profiles. The first comprised adolescents who used a number of specific coping strategies at a low level (low generic copers). The second comprised adolescents who emphasized active/approach strategies (e.g., planning; active copers). The third comprised adolescents who emphasized avoidant/passive strategies (e.g., substance abuse; avoidant copers). Active copers experienced significantly less depression and more stress‐related growth than low generic copers. Low generic copers not only experienced significantly less depression than avoidant copers but also significantly less stress‐related growth than active copers. Discussion focuses on integrating the current typology with traditional coping taxomonies.
The Ca2+‐dependent exocytosis of enlargeosomes is greatly reinforced by genistein via a non‐tyrosine kinase‐dependent mechanism
Authors: Prada Ilaria , Cocucci Emanuele , Racchetti Gabriella , Meldolesi Jacopo
Published: October 2007

Studies carried out by immunofluorescence, patch‐clamping and FM dye fluorescence consistently showed that the Ca2+‐induced exocytosis of enlargeosomes, specific vesicles expressed by many cell types, is strongly reinforced by pre‐treatment of the cells with genistein, a wide spectrum blocker of tyrosine kinases, which also induces many additional effects. Various other blockers of tyrosine kinases, however, were ineffective, and the same occurred with drugs mimicking most of the rapid, non‐tyrosine kinase‐dependent effects of genistein. The reinforcement of enlargeosome‐regulated exocytosis, therefore, is a new effect of genistein and a peculiar property of the enlargeosome exocytosis, not shared by analogous processes.
Role of Ser216 in the mechanism of action of membrane‐bound lytic transglycosylase B: Further evidence for substrate‐assisted catalysis
Authors: Reid Christopher W. , Legaree Blaine A. , Clarke Anthony J.
Published: October 2007

Lytic transglycosylases cleave the β‐(1 → 4)‐glycosidic bond in the bacterial cell wall heteropolymer peptidoglycan between the N‐acetylmuramic acid (MurNAc) and N‐acetylglucosamine (GlcNAc) residues with the concomitant formation of a 1,6‐anhydromuramoyl residue. Based on sequence alignments, Ser216 in Pseudomonas aeruginosa membrane‐bound lytic transglycosylase B (MltB) was targeted for replacement with alanine to delineate its role in the enzyme's mechanism of action. The specific activity of the Ser216 → Ala MltB derivative was less than 12% of that for the wild‐type enzyme, while its substrate binding affinity remained virtually unaltered. These data are in agreement with a role of Ser216 in orienting the N‐acetyl group on MurNAc at the −1 subsite of MltB for its participation in a substrate‐assisted mechanism of action.
Adiponectin deficiency suppresses ABCA1 expression and ApoA‐I synthesis in the liver
Authors: Oku Hiroyuki , Matsuura Fumihiko , Koseki Masahiro , Sandoval Jose C. , Yuasa-Kawase Miyako , Tsubakio-Yamamoto Kazumi , Masuda Daisaku , Maeda Norikazu , Ohama Tohru , Ishigami Masato , Nishida Makoto , Hirano Ken-ichi , Kihara Shinji , Hori Masatsugu , Shimomura Iichiro , Yamashita Shizuya
Published: October 2007

Plasma high density lipoprotein (HDL)‐cholesterol levels are inversely correlated with the incidence of cardiovascular diseases. HDL is mainly assembled in the liver through the ATP‐binding cassette transporter (ABCA1) pathway. In humans, plasma HDL‐cholesterol levels are positively correlated with plasma adiponectin (APN) concentrations. Recently, we reported that APN enhanced apolipoprotein A‐I (apoA‐I) secretion and ABCA1 expression in HepG2 cells. In the present study, we investigated HDL assembly in APN‐knockout (KO) mice. The apoA‐I protein levels in plasma and liver were reduced in APN‐KO mice compared with wild‐type‐mice. The ABCA1 expression in liver was also decreased in APN‐KO mice. APN deficiency might cause the impaired HDL assembly by decreasing ABCA1 expression and apoA‐I synthesis in the liver.
Suppressive effect of reactive oxygen species on CD40‐induced B cell activation
Authors: Liu Jiqin , Yoshida Yasuhiro , Yamashita Uki
Published: October 2007

Reactive oxygen species (ROS) produced by the innate immune system work as effectors to destroy pathogens and to control cellular responses. However, their role in the adaptive immune response remains unclear. Here we studied the effect of exogenous ROS on CD40‐induced B cell activation. H2O2 treatment inhibited CD40‐induced immunoglobulin production of B cells, DNA binding of NF‐κB, IκBα degradation and IKK phosphorylation. On the other hand, H2O2 treatment did not induce obvious B cell death after 30 min of stimulation. Although the ligation of anti‐CD40 antibody was not disturbed by H2O2, TRAF2 recruitment to CD40 was inhibited. These results suggest that exogenous ROS play a negative role in CD40 signaling during B cell activation.
Protective effects of metallothionein against dopamine quinone‐induced dopaminergic neurotoxicity
Authors: Miyazaki Ikuko , Asanuma Masato , Hozumi Hiroaki , Miyoshi Ko , Sogawa Norio
Published: October 2007

Dopamine (DA) quinone as DA neuron‐specific oxidative stress conjugates with cysteine residues in functional proteins to form quinoproteins. Here, we examined the effects of cysteine‐rich metal‐binding proteins, metallothionein (MT)‐1 and ‐2, on DA quinone‐induced neurotoxicity. MT quenched DA semiquinones in vitro. In dopaminergic cells, DA exposure increased quinoproteins and decreased cell viability; these were ameliorated by pretreatment with MT‐inducer zinc. Repeated L‐DOPA administration markedly elevated striatal quinoprotein levels and reduced the DA nerve terminals specifically on the lesioned side in MT‐knockout parkinsonian mice, but not in wild‐type mice. Our results suggested that intrinsic MT protects against L‐DOPA‐induced DA quinone neurotoxicity in parkinsonian mice by its quinone‐quenching property.