bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel silicate‐doped calcium‐based composite dental pulp capping agent
Authors: Chen Fangping , Mao Yuhao , Liu Changsheng , Yu Miaogen 
Published: March 2009

AbstractThe development of a dental pulp capping agent (DPCA) requires suitable setting time, acceptable compressive strength, favorable bioactivity, and to facilitate cementum tissue regeneration. Calcium phosphate cement (CPC) is widely used for its self‐setting, biodegradability, biocompatibility, and formability. However, a relative low strength and lack of bioactivity have limited its application. Herein, dicalcium silicate (Ca2SiO4, C2S) was introduced into CPC to prepare a novel silicate‐doped CPC/C2S composite DPCA by self‐setting in situ and its setting time, compressive strength, bioactivity, and biomineralization behaviors were investigated. The results indicated that the mechanical strength and setting time of DPCA were higher than those of pure CPC. C2S transformed into a CSH gel without disturbing the hydration of DPCA after soaking in SBF for 5 days. Moreover, much more bone‐like hydroxyapatite layers were formed, and DPCA exhibited higher bioactivity mainly in virtue of the rapid formation of CSH. DPCA with 15 wt% C2S, suggested to be the optimized composite, exhibited significantly improved bioactivity and high compressive strength, indicating that DPCA with 15 wt % C2S might have a significant pulp capping therapy advantage over the pure CPC. Copyright © 2009 Curtin University of Technology and John Wiley & Sons, Ltd.
Patterns of query reformulation during Web searching
Authors: Jansen Bernard J. , Booth Danielle L. , Spink Amanda 
Published: March 2009

AbstractQuery reformulation is a key user behavior during Web search. Our research goal is to develop predictive models of query reformulation during Web searching. This article reports results from a study in which we automatically classified the query‐reformulation patterns for 964,780 Web searching sessions, composed of 1,523,072 queries, to predict the next query reformulation. We employed an n‐gram modeling approach to describe the probability of users transitioning from one query‐reformulation state to another to predict their next state. We developed first‐, second‐, third‐, and fourth‐order models and evaluated each model for accuracy of prediction, coverage of the dataset, and complexity of the possible pattern set. The results show that Reformulation and Assistance account for approximately 45% of all query reformulations; furthermore, the results demonstrate that the first‐ and second‐order models provide the best predictability, between 28 and 40% overall and higher than 70% for some patterns. Implications are that the n‐gram approach can be used for improving searching systems and searching assistance.
Restraint safety in a residential setting for persons with intellectual disabilities
Authors: Tilli David M. , Spreat Scott 
Published: March 2009

AbstractThe primary purpose of this study was to estimate the risks associated with the use of emergency personal restraints at a residential facility for persons with intellectual and developmental disabilities. A secondary purpose was to determine if correlates of restraint‐related injury could be determined. One in three restraints resulted in an injury, but all of the injuries were minor. In terms of prediction, frequency of aggressive behavior use was the best single predictor of restraint‐related injury. Copyright © 2009 John Wiley & Sons, Ltd.
High biological activity of a recombinant protein immobilized onto polystyrene
Authors: Kumada Yoichi , Shiritani Yuki , Hamasaki Kyoko , Ohse Takuhito , Kishimoto Michimasa 
Published: March 2009

AbstractThe adsorption characteristics of glutathione S‐transferases (GST) genetically fused with polystyrene (PS)‐binding peptides (PS‐tags) on PS plates with increase in hydrophilicity were studied to clarify the mechanisms of the specific interaction between the PS‐tag‐fused protein and PS plates. GST fused with the PS‐tag PS19 (RAFIASRRIKRP) preferentially interacted with hydrophilic PS plates, even in the presence of high concentrations of competitors such as Tween 20 and BSA. Both basic and aliphatic amino acids in the PS‐tags were involved in the specific interaction of PS‐tags with the surface of the hydrophilic PS plate. Genetic fusion of the PS19 variants, PS19‐4 (RAIARRIRR) and PS19‐6 (RIIIRRIRR), further improved the immobilization yield of GST in the presence of a high concentration of the competitor BSA (50 mg/mL). The PS19‐6 peptide specifically interacted with the surfaces of various hydrophilic PS plates, especially in the presence of Tween 20. Higher remaining activity was detected on all of the hydrophilic PS plates immobilized with GST‐PS19‐6 in comparison with those with wild‐type GST and GST‐PS19, and the remaining activity was further increased by the addition of Tween 20 in the adsorption state. The PS19‐6 peptide developed in this study is therefore very useful as an affinity tag that can immobilize a target protein directly onto various hydrophilic PS supports with high remaining activity.
Free heme in micromolar amounts enhances the attraction between sickle cell hemoglobin molecules
Authors: Pan Weichun , Uzunova Veselina V. , Vekilov Peter G. 
Published: March 2009

AbstractWe probe the role of free heme in the interactions between sickle cell hemoglobin (HbS) molecules in simulated physiological solutions: polymerization of deoxy‐HbS is the primary pathogenic event of sickle cell anemia, and HbS releases heme after autoxidation more readily than normal adult hemoglobin. We characterize these interactions in terms of osmotic virial coefficients, which we determine by static light scattering. We analyze the results in the heme‐hemoglobin system using the Kirkwood‐Goldberg model. We show that in the absence of heme, the HbS molecules weakly attract and the attraction is not due to the lowered—as a result of the sickle cell mutation—molecular charge. We show that the part of the interface between the two αβ dimers, exposed in the deoxy‐state, plays a crucial role in this attraction. We show that heme at micromolar concentrations induces strong attraction between the hemoglobin molecules. We show that the high efficacy of the heme results from the statistics of electrostatic and hydrophobic interactions between the heme and hemoglobin molecules. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 1108–1116, 2009.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Gene‐expression‐based quality scores indicate optimal harvest point in Bordetella pertussis cultivation for vaccine production
Authors: van de Waterbeemd Bas , Streefland Mathieu , Pennings Jeroen , van der Pol Leo , Beuvery Coen , Tramper Johannes , Martens Dirk 
Published: March 2009

AbstractThe evolution of vaccine product quality during batch cultivation of Bordetella pertussis, the causative agent of whooping cough, was investigated with the goal to determine the optimal harvest point. The process was explored by measuring mRNA expression at frequent intervals during cultivation. The genes that are involved in virulence are already known for this product and changes in their expression levels are proposed to be indicative for product quality. A quantitative product quality score is calculated based on the expression levels of these virulence genes, which allows comparison of expected product quality between culture samples. Product quality scores were maximal throughout the logarithmic growth phase, but dropped significantly at the start of the stationary phase. This showed that the decreasing lactate and glutamate concentrations towards the end of the batch are critical for product quality. On‐line measurement of these nutrients allows the cultivation process to be harvested at the optimal harvest point, increasing process robustness and consistency. Biotechnol. Bioeng. 2009;103: 900–908. © 2009 Wiley Periodicals, Inc.
Tissue printing to visualize polyphenol oxidase and peroxidase in vegetables, fruits, and mushrooms
Authors: Melberg Amanda R. , Flurkey William H. , Inlow Jennifer K. 
Published: March 2009

AbstractA simple tissue‐printing procedure to determine the tissue location of the endogenous enzymes polyphenol oxidase and peroxidase in a variety of vegetables, fruits, and mushrooms is described. In tissue printing, cell contents from the surface of a cut section of the tissue are transferred to an adsorptive surface, commonly a nitrocellulose membrane. Because of the considerable expense of nitrocellulose, our procedure utilizes artists' hot‐press watercolor paper as a novel and more economical alternative. Tissue prints are then exposed to an enzyme substrate from which an insoluble, colored product is produced. The appearance of color in specific areas of the print is an indication of the presence of the enzyme in those tissue locations. The experiment is designed to enable students to learn some fundamental concepts about enzymes. It has been used in an introductory‐level organic and biochemistry course for nonscience majors, but would also be appropriate for advanced high school students or could be adapted for an upper‐level undergraduate biochemistry course.
Red seaweed enzyme‐catalyzed bromination of bromophenol red: An inquiry‐based kinetics laboratory experiment for undergraduates
Authors: Jittam Piyachat , Boonsiri Patcharee , Promptmas Chamras , Sriwattanarothai Namkang , Archavarungson Nattinee , Ruenwongsa Pintip , Panijpan Bhinyo 
Published: March 2009

AbstractHaloperoxidase enzymes are of interest for basic and applied bioscientists because of their increasing importance in pharmaceutical industry and environmental cleanups. In a guided inquiry‐based laboratory experiment for life‐science, agricultural science, and health science undergraduates, the bromoperoxidase from a red seaweed was used to brominate bromophenol red, a novel starting substrate. Substrate and enzyme concentration dependence of this enzyme‐catalyzed reaction as followed colorimetrically yielded initial rates of reaction that the students compared with those of their peers. The students worked as collaborative groups partially designing their own experiments and carrying them out. In performing the laboratory experiment, they were minimally guided by the instructor and teaching assistants. To engage the students before the laboratory, a short activity involving the enzyme‐induced color change was carried out. At the end of the laboratory session, student groups discussed their results in front of the class and reached their own conclusions. Most students had better understanding of important concepts in enzyme kinetics and showed good attitude toward the overall student‐centered laboratory exercise.
Problem‐solving test: The mechanism of action of a human papilloma virus oncoprotein
Authors: Szeberényi József 
Published: March 2009

AbstractTerms to be familiar with before you start to solve the test: human papilloma virus; cervical cancer; oncoproteins; malignant transformation; retinoblastoma protein; cell cycle; quiescent and cycling cells; cyclin/cyclin‐dependent kinase (Cdk) complexes; E2F; S‐phase genes; enhancer element; proto‐oncogenes; tumor suppressor genes; radioactive labeling; immunoprecipitation; SDS‐polyacrylamide gel electrophoresis; autoradiography; protein phosphorylation and dephosphorylation; gene induction; agarose beads; centrifugation; Western blot analysis; phases of cell cycle; generation time.
Using clickers to improve student engagement and performance in an introductory biochemistry class
Authors: Addison Stephen , Wright Adrienne , Milner Rachel 
Published: March 2009

AbstractAs part of ongoing efforts to enhance teaching practices in a large‐class introductory biochemistry course, we have recently tested the effects of using a student response system (clickers) on student exam performances and engagement with the course material. We found no measurable difference in class mean composite examination score for students taught with clickers than for those taught in traditional lectures. However, there were significantly more students in the highest achievement category (91–100%) in the section that incorporated clickers than in any other section over five academic terms. Overall, students gave high approval ratings for the use of the clickers, particularly in increasing their participation and engagement in lectures. However, students who reported their performance to be in the lowest performance categories gave a lower level of approval for the use of the clickers than those who reported their performance to be in the higher performance categories. The implications for using clickers to improve teaching in biochemistry are discussed.
Enzymatic digestibility and pretreatment degradation products of AFEX‐treated hardwoods (Populus nigra)
Authors: Balan Venkatesh , Sousa Leonardo da Costa , Chundawat Shishir P. S. , Marshall Derek , Sharma Lekh N. , Chambliss C. Kevin , Dale Bruce E. 
Published: March 2009

AbstractThere is a growing need to find alternatives to crude oil as the primary feed stock for the chemicals and fuel industry and ethanol has been demonstrated to be a viable alternative. Among the various feed stocks for producing ethanol, poplar (Populus nigra × Populus maximowiczii) is considered to have great potential as a biorefinery feedstock in the United States, due to their widespread availability and good productivity in several parts of the country. We have optimized AFEX pretreatment conditions (180°C, 2:1 ammonia to biomass loading, 233% moisture, 30 minutes residence time) and by using various combinations of enzymes (commercical celluloses and xylanases) to achieve high glucan and xylan conversion (93 and 65%, respectively). We have also identified and quantified several important degradation products formed during AFEX using liquid chromatography followed by mass spectrometry (LC‐MS/MS). As a part of degradation product analysis, we have also quantified oligosaccharides in the AFEX water wash extracts by acid hydrolysis. It is interesting to note that corn stover (C4 grass) can be pretreated effectively using mild AFEX pretreatment conditions, while on the other hand hardwood poplar requires much harsher AFEX conditions to obtain equivalent sugar yields upon enzymatic hydrolysis. Comparing corn stover and poplar, we conclude that pretreatment severity and enzymatic hydrolysis efficiency are dictated to a large extent by lignin carbohydrate complexes and arabinoxylan cross‐linkages for AFEX. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009
Plant Cytochrome CYP74 Family: Biochemical Features, Endocellular Localisation, Activation Mechanism in Plant Defence and Improvements for Industrial Applications
Authors: Hughes Richard K. , De Domenico Stefania , Santino Angelo 
Published: March 2009

AbstractNot just another P450: Shown here is a model of the overall structure of CYP74C3 with the putative membrane‐binding region that is required for enzyme activation. Members of the CYP74 family of cytochrome P450 enzymes are specialised in the metabolism of hydroperoxides and play an important role in oxylipin metabolism, which is one of the main defence mechanisms employed by plants.magnified imageIn order to respond to their rapidly changing environments, plants have evolved complex signalling pathways, which enable tight control over stress responses. Recent work has shed new light on one of these pathways that involves the different classes of plant oxylipins that are produced through the CYP74 pathway. These phytochemicals play an important role in plant defence, and can act as direct antimicrobials or as signalling molecules that inducing the expression of defence genes. The fine‐tuning regulation of defence responses, which depends on the precise cross‐talk among different signalling pathways, has important consequences for plant fitness and is a new, challenging area of research. In this review we focus on new data relating to the physiological significance of different phyto‐oxylipins and related enzymes. Moreover, recent advances in the biotechnological production of oxylipins are also discussed.
A co‐training algorithm for multi‐view data with applications in data fusion
Authors: Culp Mark , Michailidis George 
Published: March 2009

AbstractIn several scientific applications, data are generated from two or more diverse sources (views) with the goal of predicting an outcome of interest. Often it is the case that the outcome is not associated with any single view. However, the synergy of all measurements from each view may yield a more predictive classifier. For example, consider a drug discovery application in which individual molecules are described partially by several assay screens based on diverse profiles and partially by their chemical structural fingerprints. A common classification problem is to determine whether the molecule is associated with a particular disease. In this paper, a co‐training algorithm is developed to utilize data from diverse sources to predict the common class variable. Novel enhancements for variable importance, robustness to a mislabeled class variable, and a technique to handle unbalanced classes are applied to the motivating data set, highlighting that the approach attains strong performance and provides useful diagnostics for data analytic purposes. In addition, comparisons to a framework with data fusion using partial least squares (PLS) are also assessed on real data. An R package for performing the proposed approach is provided as Supporting information. Copyright © 2003 John Wiley & Sons, Ltd.
Oxidation of Tertiary Amines by Cytochrome P450—Kinetic Isotope Effect as a Spin‐State Reactivity Probe
Authors: Li Chunsen , Wu Wei , Cho Kyung‐Bin , Shaik Sason 
Published: March 2009

AbstractTwo types of tertiary amine oxidation processes, namely, N‐dealkylation and N‐oxygenation, by compound I (Cpd I) of cytochrome P450 are studied theoretically using hybrid DFT calculations. All the calculations show that both N‐dealkylation and N‐oxygenation of trimethylamine (TMA) proceed preferentially from the low‐spin (LS) state of Cpd I. Indeed, the computed kinetic isotope effects (KIEs) for the rate‐controlling hydrogen abstraction step of dealkylation show that only the KIELS fits the experimental datum, whereas the corresponding value for the high‐spin (HS) process is much higher. These results second those published before for N,N‐dimethylaniline (DMA), and as such, they further confirm the conclusion drawn then that KIEs can be a sensitive probe of spin state reactivity. The ferric‐carbinolamine of TMA decomposes most likely in a non‐enzymatic reaction since the FeO bond dissociation energy (BDE) is negative. The computational results reveal that in the reverse reaction of N‐oxygenation, the N‐oxide of aromatic amine can serve as a better oxygen donor than that of aliphatic amine to generate Cpd I. This capability of the N‐oxo derivatives of aromatic amines to transfer oxygen to the heme, and thereby generate Cpd I, is in good accord with experimental data previously reported.
Base‐Catalyzed Highly Stereoselective Conversion of γ‐Hydroxy‐α,β‐acetylenic Esters to γ‐Acetoxy Dienoates
Authors: Yue Yang , Yu Xiao‐Qi , Pu Lin 
Published: March 2009

AbstractA convenient route with high stereo control to γ‐acetoxy dienoates is provided by the reaction of methyl propiolate with aldehydes in the presence of ZnEt2 and N‐methylimidazole at room temperature, followed by the catalytic conversion of the resulting γ‐hydroxy‐α,β‐acetylenic esters with p‐N,N‐dimethylaminopyridine (DMAP) in acetic anhydride (see scheme).magnified imageγ‐Hydroxy‐α,β‐acetylenic esters can be conveniently prepared from the reaction of methyl propiolate with aldehydes in the presence of ZnEt2 and N‐methylimidazole at room temperature. It is discovered that the γ‐hydroxy‐α,β‐acetylenic esters can be catalyzed by p‐N,N‐dimethylaminopyridine (DMAP) in acetic anhydride to generate the γ‐acetoxy dienoates with high stereo control. The mechanism of this conversion is investigated by NMR ananlyses and isotope labeling experiments. An intramolecular Diels–Alder reaction of a γ‐acetoxy dienoate is conducted to show the synthetic potential of these compounds.
A New Quantum Chemical Approach to the Magnetic Properties of Oligonuclear Transition‐Metal Complexes: Application to a Model for the Tetranuclear Manganese Cluster of Photosystem II
Authors: Pantazis Dimitrios A. , Orio Maylis , Petrenko Taras , Zein Samir , Bill Eckhard , Lubitz Wolfgang , Messinger Johannes , Neese Frank 
Published: March 2009

AbstractBroken‐symmetry DFT calculations on transition‐metal clusters with more than two centers allow the hyperfine coupling constants to be extracted. Application of the proposed theoretical scheme to a tetranuclear manganese complex that models the S2 state of the oxygen‐evolving complex of photosystem II yields hyperfine parameters that can be directly compared with experimental data. The picture shows the metal–oxo core of the model and the following parameters; exchange coupling constant Jij, the expectation value of the site‐spin operator ${{\left\langle {{\rm S}_{\rm z}^{({\rm{{\rm K}}})} } \right\rangle }}$, and the isotropic hyperfine coupling ${{{\rm A}_{{\rm{{\rm iso}}}}^{{\rm{({\rm K})}}} }}$ parameters.magnified imageThe reliable correlation of structural features and magnetic or spectroscopic properties of oligonuclear transition‐metal complexes is a critical requirement both for research into innovative magnetic materials and for elucidating the structure and function of many metalloenzymes. We have developed a novel method that for the first time enables the extraction of hyperfine coupling constants (HFCs) from broken‐symmetry density functional theory (BS‐DFT) calculations on clusters. Using the geometry‐optimized tetranuclear manganese complex [Mn4O6(bpy)6]4+/3+ as a model, we first examine in detail the calculation of exchange coupling constants J through the BS‐DFT approach. Complications arising from the indeterminacy of experimentally fitted J constants are identified and analyzed. It is found that only the energy levels derived from Hamiltonian diagonalization are a physically meaningful basis for comparing theory and experiment. Subsequently, the proposed theoretical scheme is applied to the calculation of 55Mn HFCs of the MnIII,IV,IV,IV state of the complex, which is similar to the S2 state of the oxygen‐evolving complex (OEC) in photosystem II of oxygenic photosynthesis. The new approach performs reliably and accurately, and yields calculated HFCs that can be directly compared with experimental data. Finally, we carefully examine the dependence of HFC on the J value and draw attention to the sensitivity of the calculated values to the exchange coupling parameters. The proposed strategy extends naturally to hetero‐oligonuclear clusters of arbitrary shape and nuclearity, and hence is of general validity and usefulness in the study of magnetic metal clusters. The successful application of the new approach presented here is a first step in the effort to establish correlations between the available spectroscopic information and the structural features of complex metalloenzymes like OEC.
A General Palladium‐Catalyzed Amination of Aryl Halides with Ammonia
Authors: Schulz Thomas , Torborg Christian , Enthaler Stephan , Schäffner Benjamin , Dumrath Andreas , Spannenberg Anke , Neumann Helfried , Börner Armin , Beller Matthias 
Published: March 2009

AbstractA new robust palladium/phosphine catalyst system for the selective monoarylation of ammonia with different aryl bromides and chlorides has been developed. The active catalyst is formed in situ from [Pd(OAc)2] and air‐ and moisture‐stable phosphines as easy‐to‐handle pre‐catalysts. The productivity of the catalyst system is comparable to that of competitive Pd/phosphine systems; full conversion is achieved with most substrates with 1–2 mol % of Pd source and a fourfold excess of ligand (L).magnified image