bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thermally reversible novel photochromic dihydroindoles
Authors: Eguchi Nobutaka , Ubukata Takashi , Yokoyama Yasushi 
Published: September 2007

AbstractThermally reversible novel photochromic 4,5‐ and 6,7‐dihydroindoles possessing a hexafluoropropano‐bridge, a spiro‐adamantane moiety and a phenyl group were synthesized and their photochemical forward as well as thermal back reactions were investigated. While the open coloured form of 4,5‐dihydroindole had an absorption maximum at 417 nm in toluene, that of 6,7‐dihydroindole at 553 nm. Although the thermal back reaction of the former took about 2 h at r.t., that of the latter completed within a few minutes. Copyright © 2007 John Wiley & Sons, Ltd.
Effect of introducing a cationic system into a thiol‐ene photopolymerizable formulation
Authors: Ortiz Ricardo Acosta , Urbina Bertha A. Puente , Valdez Liliana V. Cabello , Duarte Lydia Berlanga , Santos Ramiro Guerrero , Valdez Aída E. García , Soucek Mark D. 
Published: September 2007

AbstractHybrid materials derived from a thiol‐ene and cationic polymerization were obtained from concomitant polymerization. The hybrid materials were cured by both photopolymerization and thermally induced polymerization. The kinetics of the photopolymerization were measured using time resolved‐IR and optical pyrometry. The nucleophilic character of the polysulfide obtained initially in the thiol‐ene polymerization inhibited the development of the cationic photoinitiated polymerization of epoxy monomers. Besides, the epoxide groups underwent a proton catalyzed addition reaction with the thiols to form new sulfides groups in the reaction mixture. It is proposed that the formed sulfides can terminate the growing polyether chains forming dormant species like trialkylsulfonium salts. These salts promote the thermal polymerization of the epoxy monomer in a post treatment, producing hard and transparent materials. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 4829–4843, 2007
Copper binding sites in the C‐terminal domain of mouse prion protein: A hybrid (QM/MM) molecular dynamics study
Authors: Colombo Maria Carola , VandeVondele Joost , Van Doorslaer Sabine , Laio Alessandro , Guidoni Leonardo , Rothlisberger Ursula 
Published: September 2007

AbstractWe present a hybrid QM/MM Car–Parrinello molecular dynamics study of the copper‐loaded C‐terminal domain of the mouse prion protein. By means of a statistical analysis of copper coordination in known protein structures, we localized the protein regions with the highest propensity for copper ion binding. The identified candidate structures were subsequently refined via QM/MM simulations. Their EPR characteristics were computed to make contact with the experimental data and to probe the sensitivity to structural and chemical changes. Overall best agreement with the experimental EPR data (Van Doorslaer et al., J Phys Chem B 2001; 105: 1631–1639) and the information currently available in the literature is observed for a binding site involving H187. Moreover, a reinterpretation of the experimental proton hyperfine couplings was possible in the light of the present computational findings. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Predicting experimental properties of integral membrane proteins by a naive Bayes approach
Authors: Martin‐Galiano Antonio J. , Smialowski Pawel , Frishman Dmitrij 
Published: September 2007

AbstractIntegral membrane proteins (iMPs) are challenging targets for structure determination because of the substantial experimental difficulties involved in their sample preparation. Accordingly, success rates of large‐scale structural genomics consortia are much lower for this class of molecules compared to globular targets, underscoring the pressing need for predictive strategies to identify iMPs that are more likely to overcome laboratory bottlenecks. On the basis of the target status information available in the TargetDB repository, we describe the first large‐scale analysis of experimental behavior of iMPs. Using information on recalcitrant and propagating iMP targets as negative and positive sets, respectively, we present naive Bayes classifiers capable of predicting, from sequence alone, those proteins that are more amenable to cloning, expression, and solubilization studies. Protein sequences are represented in the space of 72 features, including amino acid composition, occurrence of amino acid groups, ratios between residue groups, and hydrophobicity measures. Taking into account unequal representation of main taxonomic groups in the TargetDB, sequence database had a beneficial effect on the prediction results. The classifiers achieve accuracies of 70%, 63–70%, and 61% in predicting the amenability of iMPs for cloning, expression, and solubilization, respectively, thus making them useful tools in target selection for structure determination. Our assessment of prediction results clearly demonstrates that classifiers based on single features do not possess acceptable discriminative power and that the experimental behavior of iMPs is imprinted in their primary sequence through relationships between a restricted set of key properties. In most cases, sets of 10–20 protein features were found actually relevant, most notably, the content of isoleucine, valine, and positively‐charged residues. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Thermostable variants of the recombinant xylanase a from Bacillus subtilis produced by directed evolution show reduced heat capacity changes
Authors: Ruller Roberto , Deliberto Laila , Ferreira Tatiana Lopes , Ward Richard J. 
Published: September 2007

AbstractDirected evolution techniques have been used to improve the thermal stability of the xylanase A from Bacillus subtilis (XylA). Two generations of random mutant libraries generated by error prone PCR coupled with a single generation of DNA shuffling produced a series of mutant proteins with increasing thermostability. The most Thermostable XylA variant from the third generation contained four mutations Q7H, G13R, S22P, and S179C that showed an increase in melting temperature of 20°C. The thermodynamic properties of a representative subset of nine XylA variants showing a range of thermostabilities were measured by thermal denaturation as monitored by the change in the far ultraviolet circular dichroism signal. Analysis of the data from these thermostable variants demonstrated a correlation between the decrease in the heat capacity change (ΔCp) with an increase in the midpoint of the transition temperature (Tm) on transition from the native to the unfolded state. This result could not be interpreted within the context of the changes in accessible surface area of the protein on transition from the native to unfolded states. Since all the mutations are located at the surface of the protein, these results suggest that an explanation of the decrease in ΔCp should include effects arising from the protein/solvent interface. Proteins 2008. © 2007 Wiley‐Liss, Inc.
More compact protein globules exhibit slower folding rates
Authors: Galzitskaya Oxana V. , Reifsnyder Danielle C. , Bogatyreva Natalya S. , Ivankov Dmitry N. , Garbuzynskiy Sergiy O. 
Published: September 2007

AbstractWe have demonstrated that, among proteins of the same size, α/β proteins have on the average a greater number of contacts per residue due to their more compact (more “spherical”) structure, rather than due to tighter packing. We have examined the relationship between the average number of contacts per residue and folding rates in globular proteins according to general protein structural class (all‐α, all‐β, α/β, α+β). Our analysis demonstrates that α/β proteins have both the greatest number of contacts and the slowest folding rates in comparison to proteins from the other structural classes. Because α/β proteins are also known to be the oldest proteins, it can be suggested that proteins have evolved to pack more quickly and into looser structures. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Computational analysis of folding and mutation properties of C5 domain of myosin binding protein C
Authors: Guardiani Carlo , Cecconi Fabio , Livi Roberto 
Published: September 2007

AbstractThermal folding molecular dynamics simulations of the domain C5 of Myosin binding protein C were performed using a native‐centric model to study the role of three mutations related to Familial Hypertrophic Cardiomyopathy. Mutation of Asn755 causes the largest shift of the folding temperature, and the residue is located in the CFGA′ β‐sheet featuring the highest Φ‐values. The mutation thus appears to reduce the thermodynamic stability in agreement with experimental data. The mutations on Arg654 and Arg668, conversely, cause little change in the folding temperature and they reside in the low Φ‐value BDE β‐sheet, so that their pathological role cannot be related to impairment of the folding process but possibly to the binding with target molecules. As the typical signature of Domain C5 is the presence of a longer and destibilizing CD‐loop with respect to the other Ig‐like domains, we completed the work with a bioinformatic analysis of this loop showing a high density of negative charge and low hydrophobicity. This indicates the CD‐loop as a natively unfolded sequence with a likely coupling between folding and ligand binding. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Sampling of near‐native protein conformations during protein structure refinement using a coarse‐grained model, normal modes, and molecular dynamics simulations
Authors: Stumpff‐Kane Andrew W. , Maksimiak Katarzyna , Lee Michael S. , Feig Michael 
Published: September 2007

AbstractProtein structure refinement from comparative models with the goal of predicting structures at near‐experimental accuracy remains an unsolved problem. Structure refinement might be achieved with an iterative protocol where the most native‐like structure from a set of decoys generated from an initial model in one cycle is used as the starting structure for the next cycle. Conformational sampling based on the coarse‐grained SICHO model, atomic level of detail molecular dynamics simulations, and normal‐mode analysis is compared in the context of such a protocol. All of the sampling methods can achieve significant refinement close to experimental structures, although the distribution of structures and the ability to reach native‐like structures differs greatly. Implications for the practical application of such sampling methods and the requirements for scoring functions in an iterative refinement protocol are analyzed in the context of theoretical predictions for the distribution of protein‐like conformations with a random sampling protocol. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Recognizing in situ oxygen analyzers as ignition sources in fired equipment
Authors: Van Geffen Sheila , Corripio Bernardo , Weber Andy 
Published: September 2007

AbstractMost modern ethylene cracking furnaces use close‐coupled extractive or in situ oxygen analyzers based on a zirconium oxide sensor in the stack area to provide fast and reliable measurement of the oxygen content of the flue gas exiting the firebox. This allows for precise control of the excess combustion air in the firebox, resulting in higher energy efficiency for the furnace than is typical using conventional extractive sample‐based analyzer systems where the analyzer might be several hundred feet away from the sample point. These analyzers use a zirconium oxide sensing element that operates at 700°C, which is well above the auto‐ignition temperature of many flammable hydrocarbon mixtures. Although flame arrestors can be installed on these analyzers to prevent flame propagation from the probe element into the firebox there are still situations that can exist that the analyzer can pose as an ignition source. This paper will discuss the two typical zirconium oxide oxygen analyzer designs and how the analyzer can be a source of ignition, and review an incident in a Dow cracking furnace, which resulted from an in situ oxygen analyzer igniting a flammable mixture in a furnace. Corrective actions are included in this paper. © 2007 American Institute of Chemical Engineers Process Saf Prog, 2007
Quantitative Structure‐Properties Relationship in Stilbene‐Triazine Optical Brightener Design
Authors: Wilkowska Ewa , Konopski Leszek 
Published: September 2007

AbstractThe Quantitative Structure‐Property Relationship (QSPR) has been studied in a group of bis(s‐triazin‐2‐yl)‐4,4′‐diamino‐2,2′‐disulphostilbene Fluorescent Brightening Agents (FBAs). The degree of whiteness, tint and Yellowness Index (YI) were studied as parameters determining the brightening properties using surface‐size press method on neutral printing papers, and the degree of whiteness W was chosen as the most appropriate for QSPR studies. The effectiveness of brightening depended on the substituent R in positions 4‐(sulphophenylamino, disulphophenylamino or methoxy groups), and especially at position 6 of the triazine ring (disubstituted amino group NYZ). The best results were obtained when an amino acid moiety was built in the 6‐substituent. Hammett electron constants and Taft induction constants were used as substituent descriptors. A quantitative correlation was found using simple and multiple regression analysis. The constructed model allowed to design two new brighteners containing R=2,5‐disulphoaniline group, Y=H and Z=appropriately taurine and N‐cyanoethyltaurine. To validate the model, the high values of whiteness predicted by the regression equation were confirmed by synthesis. The Taft σ*‐constant values for CH(CH3)COOH and CH(CH2COOH)COOH substituents were calculated using the developed equation.
Theoretical Modeling of PrkCc, Serine–Threonine Protein Kinase Intracellular Domain, Complexed with ATP Derivatives
Authors: Gruszczyński Paweł , Kaźmierkiewicz Rajmund , Obuchowski Michał , Lammek Bernard 
Published: September 2007

AbstractWith the advent of the Molecular Dynamics (MD) methods two complexes of PrkC catalytic domain with N6‐methoxy‐ATP and N6‐pyrrolidino‐ATP analogues were studied. Structures of the intracellular domain of the enzyme and the ATP derivatives were modeled theoretically. We report here the spatial arrangement of the PrkC kinase and its two complexes as well as their behavior during the MD simulations.
Development and Evaluation of a QSPR Model for the Prediction of Diamagnetic Susceptibility
Authors: Afantitis Antreas , Melagraki Georgia , Sarimveis Haralambos , Koutentis Panayiotis A. , Markopoulos John , Igglessi‐Markopoulou Olga 
Published: September 2007

AbstractA novel QSPR model is developed and evaluated for the prediction of diamagnetic susceptibility. The model was produced using the Multiple Linear Regression (MLR) technique on a database that consists of 406 organic compounds involving a diverse set of chemical structures. The accuracy of the QSPR model (R2=0.88) is illustrated using various evaluation techniques, such as leave‐one‐out procedure (Q2=0.87) and validation through an external test set (R$\rm{ {_{pred}^{2}}}$=0.89). The study leads to the conclusion that three physical–topological descriptors affect significantly the diamagnetic susceptibility: Polar Surface Area (PSAr), Principal Moment of Inertia X (PMIX), and Diameter (Diam).
Adaptive Dunnett tests for treatment selection
Authors: Koenig Franz , Brannath Werner , Bretz Frank , Posch Martin 
Published: September 2007

AbstractClinical trials incorporating treatment selection at pre‐specified interim analyses allow to integrate two clinical studies into a single, confirmatory study. In an adaptive interim analysis, treatment arms are selected based on interim data as well as external information. The specific selection rule does not need to be pre‐specified in advance in order to control the multiple type I error rate. We propose an adaptive Dunnett test procedure based on the conditional error rate of the single‐stage Dunnett test. The adaptive procedure uniformly improves the classical Dunnett test, which is shown to be strictly conservative if treatments are dropped at interim. The adaptive Dunnett test is compared in a simulation with the classical Dunnett test as well as with adaptive combination tests based on the closure principle. The method is illustrated with a real‐data example. Copyright © 2007 John Wiley & Sons, Ltd.
Markovian power curves for wind turbines
Authors: Anahua E. , Barth St. , Peinke J. 
Published: September 2007

AbstractThis paper shows a novel method to characterize wind turbine power performance directly from high‐frequency fluctuating measurements. In particular, we show how to evaluate the dynamic response of the wind turbine system on fluctuating wind speed in the range of seconds. The method is based on the stochastic differential equations known as the Langevin equations of diffusive Markov processes. Thus, the fluctuating wind turbine power output is decomposed into two functions: (i) the relaxation, which describes the deterministic dynamic response of the wind turbine to its desired operation state, and (ii) the stochastic force (noise), which is an intrinsic feature of the system of wind power conversion. As a main result, we show that independently of the turbulence intensity of the wind, the characteristic of the wind turbine power performance is properly reconstructed. This characteristic is given by their fixed points (steady states) from the deterministic dynamic relaxation conditioned for given wind speed values. The method to estimate these coefficients directly from the data is presented and applied to numerical model data, as well as to real‐world measured power output data. The method is universal and is not only more accurate than the current standard procedure of ensemble averaging (IEC‐61400‐12) but it also allows a faster and robust estimation of wind turbines' power curves. Copyright © 2007 John Wiley & Sons, Ltd.
Combination of enzyme analysis, allele‐specific PCR and sequencing to detect mutations in the GALT gene
Authors: Calderon F. R. O. , Nelson L. , Dobrowolski P. , Sinitsyna I. , Phansalkar A. , Longo N. , Pasquali M. , Mao R. 
Published: September 2007

SummaryNewborn screening can identify patients with classical galactosaemia, and their diagnosis needs to be confirmed with assay of the activity of galactose‐1‐phosphate uridyltransferase (GALT). Unfortunately, in many cases the results can be ambiguous and further testing is required. Here we report a combination of biochemical analysis of GALT enzyme activity and mutation analysis of the most common mutations in the corresponding gene. Samples (n=43) submitted for confirmatory testing for classical galactosaemia were analysed simultaneously for GALT enzyme activity and allele‐specific PCR/fragment analysis for seven mutations and two polymorphisms in the GALT gene (mutations IVS2‐2A>G, p.S135L, p.T138M, p.L195P, p.K285N, p.Q188R, p.Y209C; polymorphisms p.N314D, p.L218L). Mutation detection accorded with biochemical analysis in 93% of samples. Subsequently, a total of 34 samples with either discordant results between the above methods or low enzyme activity were fully sequenced, identifying previously reported pathogenic mutations and seven novel variations (p.P185H, p.R201C, p.E220K, p.R223S, p.I278N, p.L289F and p.L218X) in the GALT gene. This approach further increased concordance between genetic and biochemical analysis to 99% of all alleles tested. Our results indicate that DNA testing can help to verify biochemical enzymatic data and improve distinction of borderline enzyme activities where a patient may still benefit from treatment.
Acid sphingomyelinase‐deficient Niemann–Pick disease: Novel findings in a Greek child
Authors: Fotoulaki M. , Schuchman E. H. , Simonaro C. M. , Augoustides‐Savvopoulou P. , Michelakakis H. , Panagopoulou P. , Varlamis G. , Nousia‐Arvanitakis S. 
Published: September 2007

SummaryNiemann–Pick Disease (NPD) is a heterogeneous group of autosomal recessive disorders characterized by progressive accumulation of sphingomyelin and cholesterol in lysosomes. Six types of NPD have been described based on clinical presentation and involved organs. The primary defect in NPD types A and B is a deficiency of lysosomal acid sphingomyelinase (ASM). We present a case of a 5‐year‐old boy with type B NPD who had severe clinical manifestations, including heart involvement. He was first admitted to the hospital at 2 months because of vomiting, refusal to feed, lethargy, hepatomegaly and mild transaminasaemia. Liver biopsy at 12 months showed lipid accumulation and fibrosis. Investigations for lysosomal storage disorders revealed increased plasma chitotriosidase (549 nmol/h per ml, normal value 0–150). At 18 months, no detectable ASM activity was observed in cultured fibroblasts (normal range 23–226 nmol/h per mg protein) confirming NPD B. Pulmonary involvement was detected with high‐resolution computerized tomography which revealed reticulonodular infiltrations and thickening of the interlobular septa. At 2 years growth retardation and kyphosis were noted. At 2.5 years he manifested neurodevelopment regression, indicating CNS involvement. Cardiac involvement (grade III mitral valve insufficiency) developed at 4 years and heart failure at 5 years. Genetic analysis revealed two mutations: a H421Y mutation that is common in Saudi Arabian and Turkish patients, and a W32X mutation, which has been found in other Mediterranean patients.
A severity scoring tool to assess the neurological features of neuronopathic Gaucher disease
Authors: Davies E. H. , Surtees R. , DeVile C. , Schoon I. , Vellodi A. 
Published: September 2007

SummaryType III Gaucher disease is one of the three recognized subtypes of Gaucher disease, an inherited deficiency of lysosomal glucocerebrosidase. Phenotypically there is a wide spectrum of visceral and neurological manifestations. Enzyme replacement is effective in managing the visceral disease; however, the neurological manifestations remain a more challenging obstacle. There is an unfulfilled need to reliably monitor neurological disease and its response to treatment. A severity scoring tool was developed through neurological domain identification, item generation and tool formation. Domain identification was established based on a retrospective single centre study (n=15) and a systematic review of publications. Forty‐seven patients with neuronopathic Gaucher disease were then assessed using the tool to establish the clinical and statistical reliability of each domain. Judgement quantification of the tool was established through a process of content validity involving five European experts. Content validity is considered to be most effective when undertaken systematically. Concurrent validity and feasibility of the tool was also highlighted. This process allowed a revised and validated version of the tool to be developed.