bluuebunny/crossref_metadata_2025_split huggingface dataset:
Synthesis of ω‐pyrenyl‐functionalized poly(1,3‐cyclohexadiene)
Authors: Natori Itaru , Natori Shizue 
Published: November 2008

Abstractω‐Pyrenyl‐functionalized poly(1,3‐cyclohexadiene) (PCHD) was successfully synthesized by the postpolymerization reaction of poly(1,3‐cyclohexadienyl)lithium (PCHDLi) with 1‐chloromethylpyrene (ClMe‐PY). This postpolymerization reaction consisted of two competitive reactions: the addition reaction of the pyrenyl group, and a hydrogen abstraction reaction (lithiation) as a side reaction. The degree of nucleophilicity of PCHDLi was a very important factor for suppression of the side reaction, and the PCHDLi/amine system, which has high nucleophilicity, produced high ω‐pyrenyl‐functionalization for PCHD. The UV/vis and fluorescence spectra for ω‐pyrenyl‐functionalized PCHD were bathochromically shifted, relative to that of pyrene. © 2008 Wiley Periodicals, Inc. J Appl Polym Sci, 2009
Substituent effects on trithiocarbonates‐mediated polymerization of styrene
Authors: Ran Rong , Chen Zhi , Wang Xiao Long 
Published: November 2008

AbstractIn the present work, the effectiveness of five trithiocarbonates (TTCs) as mediating agents in the reversible addition fragmentation chain transfer (RAFT) polymerization and photopolymerization of styrene (St) were investigated. The five TTCs including S,S′‐bis(α, α′‐dimethyl‐α″‐acetic acid) trithiocarbonate (TTC1), bis(2‐oxo‐2‐phenyl‐ethyl) trithiocarbonate (TTC2), 3‐(2‐carboxyethylsulfanylthiocarbonylsulfanyl)‐propionic acid (TTC3), 2‐(2‐carboxyethylsulfanylthiocarbonylsulfanyl)propionic acid (TTC4), and 2‐(2‐carboxyethylsulfanylthiocarbonylsulfanyl)‐2‐methylpropionic acid (TTC5) were synthesized, in which the substitution patterns (groups Z and R) of the TTCs were varied. The dynamic behavior of TTC1, TTC2, TTC4, and TTC5‐mediated polymerization of St was well described by pseudo first‐order kinetics. In the presence of TTC1, TTC2, TTC4, and TTC5, the polydispersity indices changed with increasing conversion in the range of 1.10–1.25 typical for RAFT‐prepared (co)polymers, and were well below the theoretical lower limit of 1.50 for a normal free radical polymerization. Transfer coefficients of TTCs in St polymerization at 70°C were estimated by using the Mayo method. Density functional theory calculations successfully predicted the effect of the structure of TTCs on the activity of RAFT agents in a qualitative manner. The calculated results for RAFT agents agreed well with the experimental results. © 2008 Wiley Periodicals, Inc. J Appl Polym Sci, 2009
How to interpret PubMed queries and why it matters
Authors: Yeganova Lana , Comeau Donald C. , Kim Won , Wilbur W. John 
Published: November 2008

AbstractA significant fraction of queries in PubMed™ are multiterm queries without parsing instructions. Generally, search engines interpret such queries as collections of terms, and handle them as a Boolean conjunction of these terms. However, analysis of queries in PubMed™ indicates that many such queries are meaningful phrases, rather than simple collections of terms. In this study, we examine whether or not it makes a difference, in terms of retrieval quality, if such queries are interpreted as a phrase or as a conjunction of query terms. And, if it does, what is the optimal way of searching with such queries. To address the question, we developed an automated retrieval evaluation method, based on machine learning techniques, that enables us to evaluate and compare various retrieval outcomes. We show that the class of records that contain all the search terms, but not the phrase, qualitatively differs from the class of records containing the phrase. We also show that the difference is systematic, depending on the proximity of query terms to each other within the record. Based on these results, one can establish the best retrieval order for the records. Our findings are consistent with studies in proximity searching.
“Backstage solidarity” in Spanish‐ and English‐written medical research papers: Publication context and the acknowledgment paratext
Authors: Salager‐Meyer Françoise , Ariza María Ángeles Alcaraz , Berbesí Maryelis Pabón 
Published: November 2008

AbstractThe purpose of this article is to analyze the acknowledgment (ACK) paratext of medical research articles written in English and Spanish in three geographical contexts: Venezuela, Spain, and the United States of America. We thus randomly selected 150 research articles from leading medical journals in each country. The frequency and length of ACKs, the number of named and unnamed acknowledgees, the reasons why they were acknowledged, the number of grants received, and the sources of funding were recorded. The motivations that underpinned each ACK were classified according to B. Cronin's (1995) and C.L. Giles & I.G. Councill's (2004) typology. Results were analyzed by means of chi‐square tests. Our results show that ACKs from the English‐language corpus are significantly more frequent and longer than those from both the Spanish and Venezuelan samples. The number of persons acknowledged and the number of grants received also were significantly greater in the U.S. sample than they were in the two Spanish‐language corpora. Differences were found in the number and types of funding sources. Moreover, in the three corpora, technical/instrumental assistance was more frequently acknowledged than was peers' ideational input. A small‐scale ethnographic research study was conducted with Spanish and Venezuelan researchers to get firsthand feedback on the motivations that could lie behind their ACK behavior. We conclude that “backstage solidarity” (E. Goffman, 1959, p. 177; also see B. Cronin & S. Franks, 2006, p. 1915) significantly differs from one context to another, and that the communicative and sociocultural conventions of academic contributorship are not only discipline‐dependent but also language‐ and context‐dependent.
The impact of frame semantic annotation levels, frame‐alignment techniques, and fusion methods on factoid answer processing
Authors: Ofoghi Bahadorreza , Yearwood John , Ma Liping 
Published: November 2008

AbstractThe impact of frame semantic enrichment of texts on the task of factoid question answering (QA) is studied in this paper. In particular, we consider different techniques for answer processing with frame semantics: the level of semantic class identification and role assignment to texts, and the fusion of frame semantic‐based answer‐processing approaches with other methods used in the Text REtrieval Conference (TREC). The impact of each of these aspects on the overall performance of a QA system is analyzed in this paper. The TREC 2004 and TREC 2006 factoid question sets were used for the experiments. These demonstrate that the exploitation of encapsulated frame semantics in FrameNet in a shallow semantic parsing process can enhance answer‐processing performance in factoid QA systems. This improvement is dependent on the level of semantic annotation, the frame semantic alignment method, and the method of fusing frame semantic‐based answer‐processing models with other existing models. A more comprehensively annotated environment with all different part‐of‐speech target predicates provides a higher chance of correct factoid answer retrieval where semantic alignment is based on both semantic classes and a relaxed set of semantic roles for answer span identification. Our experiments on fusion techniques of frame semantic‐based and entity‐based answer‐processing models show that merging answer lists with respect to their scores and redundancy by exploiting a fusion function leads to a more effective overall factoid QA system compared to the use of individual models.
Prediction of human oral pharmacokinetics using nonclinical data: examples involving four proprietary compounds
Authors: Fura Aberra , Vyas Viral , Humphreys William , Chimalokonda Anjaneya , Rodrigues David 
Published: November 2008

AbstractThe oral pharmacokinetics (concentration‐time profile) of four proprietary compounds in humans were predicted using theCvss‐MRTmethod. The first step was to demonstrate superposition of intravenous (i.v.) pharmacokinetic profiles of preclinical species following mathematical transformation of their respective concentration‐time curves using the correspondingCvss(whereCvss=dose/Vss;Vss is the volume of distribution at steady state) and mean residence time (MRT) values. The resultant profiles were then back‐transformed to estimate human i.v. plasma concentration‐time profiles using humanCvssandMRTvalues. HumanCvssandMRTvalues were estimated from projected humanVss andCLvalues. Projection ofCLwas based on scaled (in vitro) metabolic clearance, simple allometry with and without various correction factors and the unbound fraction corrected intercept method.Vss values were estimated by allometric scaling with and without correction for interspecies differences in plasma protein binding. The predicted human i.v. profiles, in combination with the estimated mean absorption rate constants and bioavailability, were then used to simulate the oral pharmacokinetics in human using one‐ or multi‐compartment kinetic models. Overall, with this approach, key oral pharmacokinetic parameters such asAUC,Cmax,Cminand oral plasmaT½were projected to be within two‐fold of the actual values in humans. Copyright © 2008 John Wiley & Sons, Ltd.
Kinetic modeling for enzymatic hydrolysis of pretreated creeping wild ryegrass
Authors: Zheng Yi , Pan Zhongli , Zhang Ruihong , Jenkins Bryan M. 
Published: November 2008

AbstractA semimechanistic multi‐reaction kinetic model was developed to describe the enzymatic hydrolysis of a lignocellulosic biomass, creeping wild ryegrass (CWR; Leymus triticoides). This model incorporated one homogeneous reaction of cellobiose‐to‐glucose and two heterogeneous reactions of cellulose‐to‐cellobiose and cellulose‐to‐glucose. Adsorption of cellulase onto pretreated CWR during enzymatic hydrolysis was modeled via a Langmuir adsorption isotherm. This is the first kinetic model which incorporated the negative role of lignin (nonproductive adsorption) using a Langmuir‐type isotherm adsorption of cellulase onto lignin. The model also reflected the competitive inhibitions of cellulase by glucose and cellobiose. The Matlab optimization function of “lsqnonlin” was used to fit the model and estimate kinetic parameters based on experimental data generated under typical conditions (8% solid loading and 15 FPU/g‐cellulose enzyme concentration without the addition of background sugars). The model showed high fidelity for predicting cellulose hydrolysis behavior over a broad range of solid loading (4–12%, w/w, dry basis), enzyme concentration (15–150 FPU/ g‐cellulose), sugar inhibition (glucose of 30 and 60 mg/mL and cellobiose of 10 mg/mL). In addition, sensitivity analysis showed that the incorporation of the nonproductive adsorption of cellulase onto lignin significantly improved the predictability of the kinetic model. Our model can serve as a robust tool for developing kinetic models for system optimization of enzymatic hydrolysis, hydrolysis reactor design, and/or other hydrolysis systems with different type of enzymes and substrates. Biotechnol. Bioeng. 2009;102: 1558–1569. © 2008 Wiley Periodicals, Inc.
Utilization of cross‐linked laccase aggregates in a perfusion basket reactor for the continuous elimination of endocrine‐disrupting chemicals
Authors: Cabana Hubert , Jones J. Peter , Agathos Spiros N. 
Published: November 2008

AbstractA perfusion basket reactor (BR) was developed for the continuous utilization of insolubilized laccase as cross‐linked enzyme aggregates (CLEAs). The BR consisted of an unbaffled basket made of a metallic filtration module filled with CLEAs and continuously agitated by a 3‐blade marine propeller. The agitation conditions influenced both the apparent laccase activity in the reactor and the stability of the biocatalyst. Optimal laccase activity was obtained at a rotational speed of 12.5 rps and the highest stability was reached at speeds of 1.7 rps or lower. The activity and stability of the biocatalyst were affected drastically upon the appearance of vortices in the reaction medium. This reactor was used for the continuous elimination of the endocrine disrupting chemicals (EDCs) nonylphenol (NP), bisphenol A (BPA), and triclosan (TCS). Optimization of EDC elimination by laccase CLEAs as a function of temperature and pH was achieved by response surface methodology using a central composite factorial design. The optimal conditions of pH and temperature were, respectively, 4.8 and 40.3°C for the elimination of p353NP (a branched isomer of NP), 4.7 and 48.0°C for BPA, and 4.9 and 41.2°C for TCS. Finally, the BR was used for the continuous elimination of these EDCs from a 5 mg L−1 aqueous solution using 1 mg of CLEAs at pH 5 and room temperature. Our results showed that at least 85% of these EDCs could be eliminated with a hydraulic retention time of 325 min. The performances of the BR were quite stable over a 7‐day period of continuous treatment. Furthermore, this system could eliminate the same EDCs from a 100 mg L−1 solution. Finally, a mathematical model combining the Michaelis–Menten kinetics of the laccase CLEAs and the continuous stirred tank reactor behavior of the BR was developed to predict the elimination of these xenobiotics. Biotechnol. Bioeng. 2009;102: 1582–1592. © 2008 Wiley Periodicals, Inc.
Hemoglobin‐based oxygen carrier and convection enhanced oxygen transport in a hollow fiber bioreactor
Authors: Chen Guo , Palmer Andre F. 
Published: November 2008

AbstractA mathematical model was developed to study O2 transport in a convection enhanced hepatic hollow fiber (HF) bioreactor, with hemoglobin‐based O2 carriers (HBOCs) present in the flowing cell culture media stream of the HF lumen. In this study, four HBOCs were evaluated: PEG‐conjugated human hemoglobin (MP4), human hemoglobin (hHb), bovine hemoglobin (BvHb) and polymerized bovine hemoglobin (PolyBvHb). In addition, two types of convective flow in the HF extra capillary space (ECS) were considered in this study. Starling flow naturally occurs when both of the ECS ports are closed. If one of the ECS ports is open, forced convective flow through the ECS will occur due to the imposed pressure difference between the lumen and ECS. This type of flow is referred to as cross‐flow in this work, since some of the fluid entering the HF lumen will pass across the HF membrane and exit via the open ECS port. In this work, we can predict the dissolved O2 concentration profile as well as the O2 transport flux in an individual HF of the bioreactor by solving the coupled momentum and mass transport equations. Our results show that supplementation of the cell culture media with HBOCs can dramatically enhance O2 transport to the ECS (containing hepatocytes) and lead to the formation of an in vivo‐like O2 spectrum for the optimal culture of hepatocytes. However, both Starling flow and cross‐flow have a very limited effect on O2 transport in the ECS. Taken together, this work represents a novel predictive tool that can be used to design or analyze HF bioreactors that expose cultured cells to defined overall concentrations and gradients of O2. Biotechnol. Bioeng. 2009;102: 1603–1612. © 2008 Wiley Periodicals, Inc.
Synthesis and Investigation of a Chiral Enterobactin Analogue Based on a Macrocyclic Peptide Scaffold
Authors: Pintér Áron , Haberhauer Gebhard 
Published: November 2008

AbstractA chiral C3‐symmetric enterobactin analogue (1) has been synthesized by attachment of three 2,3‐dihydroxybenzoyl units to a chiral oxazole‐containing macrocyclic peptide scaffold. Complex formation kinetics and stoichiometry with various metal ions were investigated by spectrophotometric methods. In the cases of AlIII, InIII and FeIII complexes, UV absorption and CD kinetics showed nonlinearity, which results from slow conformational changes of the octahedral complexes. Virtual binding constants were determined from UV absorption data and showed selective binding of GaIII in preference to FeIII, by two orders of magnitude. CD spectroscopy revealed highly diastereoselective binding of AlIII, GaIII, InIII, FeIII and GeIV ions at room temperature, corresponding to the helical chirality opposite to that of the analogous enterobactin complexes. Ab initio calculations confirmed the energetic stabilization of the Λ isomers relative to the Δ isomers.
pH‐Dependent Catalytic Activity and Chemoselectivity in Transfer Hydrogenation Catalyzed by Iridium Complex with 4,4′‐Dihydroxy‐2,2′‐bipyridine
Authors: Himeda Yuichiro , Onozawa‐Komatsuzaki Nobuko , Miyazawa Satoru , Sugihara Hideki , Hirose Takuji , Kasuga Kazuyuki 
Published: November 2008

AbstractTransfer hydrogenation catalyzed by an iridium catalyst with 4,4′‐dihydroxy‐2,2′‐bipyridine (DHBP) in an aqueous formate solution exhibits highly pH‐dependent catalytic activity and chemoselectivity. The substantial change in the activity is due to the electronic effect based on the acid–base equilibrium of the phenolic hydroxyl group of DHBP. Under basic conditions, high turnover frequency values of the DHBP complex, which can be more than 1000 times the value of the unsubstituted analogue, are obtained (up to 81 000 h−1 at 80 °C). In addition, the DHBP catalyst exhibits pH‐dependent chemoselectivity for α,β‐unsaturated carbonyl compounds. Selective reduction of the CC bond of enone with high activity are observed under basic conditions. The ketone moieties can be reduced with satisfactory activity under acidic conditions. In particular, pH‐selective chemoselectivity of the CO versus CC bond reduction was observed in the transfer hydrogenation of cinnamaldehyde.
Discovery of DPP IV Inhibitors by Pharmacophore Modeling and QSAR Analysis followed by in silico Screening
Authors: Al‐masri Ihab M. , Mohammad Mohammad K. , Taha Mutasem O. 
Published: November 2008

AbstractDipeptidyl peptidase IV (DPP IV) deactivates the natural hypoglycemic incretin hormones. Inhibition of this enzyme should restore glucose homeostasis in diabetic patients making it an attractive target for the development of new antidiabetic drugs. With this in mind, the pharmacophoric space of DPP IV was explored using a set of 358 known inhibitors. Thereafter, genetic algorithm and multiple linear regression analysis were employed to select an optimal combination of pharmacophoric models and physicochemical descriptors that yield selfconsistent and predictive quantitative structure–activity relationships (QSAR) (r2287=0.74, F‐statistic=44.5,r2BS=0.74,r2 LOO=0.69,r2PRESSagainst 71 external testing inhibitors=0.51). Two orthogonal pharmacophores (of cross‐correlationr2=0.23) emerged in the QSAR equation suggesting the existence of at least two distinct binding modes accessible to ligands within the DPP IV binding pocket. Docking experiments supported the binding modes suggested by QSAR/pharmacophore analyses. The validity of the QSAR equation and the associated pharmacophore models were established by the identification of new low‐micromolar anti‐DPP IV leads retrieved by in silico screening. One of our interesting potent anti‐DPP IV hits is the fluoroquinolone gemifloxacin (IC50=1.12 μM). The fact that gemifloxacin was recently reported to potently inhibit the prodiabetic target glycogen synthase kinase 3β(GSK‐3β) suggests that gemifloxacin is an excellent lead for the development of novel dual antidiabetic inhibitors against DPP IV and GSK‐3β.
Multicenter phase 2 study of neoadjuvant paclitaxel, estramustine phosphate, and carboplatin plus androgen deprivation before radiation therapy in patients with unfavorable‐risk localized prostate cancer
Authors: Kelly William Kevin , Halabi Susan , Elfiky Aymen , Ou San‐San , Bogart Jeff , Zelefsky Michael , Small Eric 
Published: November 2008

AbstractBACKGROUND.A multicenter phase 2 trial was conducted to evaluate the safety and feasibility of radiotherapy after paclitaxel, estramustine phosphate, and carboplatin (TEC) plus androgen deprivation therapy in previously untreated unfavorable‐risk localized prostate cancer patients.METHODS.Patients with localized high‐risk prostate cancer were treated with 4 cycles (16 weeks) of continuous weekly paclitaxel at 80 mg/m2 intravenously with estramustine at 280 mg orally 3 times a day for 5 days a week and carboplatin (area under the curve of 6) on Day 1 of every cycle followed by 3‐dimensional conformal or intensity‐modulated radiotherapy (total dose of 77.4 gray [Gy] in 1.8‐Gy fractions). All patients received androgen deprivation therapy with either goserelin acetate at 3.6 mg subcutaneously or leuprolide acetate at 7.5 mg intramuscularly monthly for 6 months starting at Day 1 of therapy. Patients were evaluated for acute and late toxicities along with progression‐free survival and time to prostate‐specific antigen (PSA) failure associated with the multimodality therapy.RESULTS.Twenty‐seven of 34 patients completed therapy and were evaluable for safety and feasibility. There was 1 patient with grade 3 nausea during chemotherapy. No other grade 3 or 4 gastrointestinal, cardiovascular, or genitourinary acute or late toxicities were reported. The most common grade 1 to 2 late toxicities were proctitis (11%), dysuria (11%), and urinary frequency/urgency (33%). Two deaths due to prostate cancer were observed. Median follow‐up was 38 months among 24 surviving patients; median PSA progression‐free survival was 12.1 months (95% confidence interval, 13.3‐25.9).CONCLUSIONS.Neoadjuvant chemohormonal therapy with TEC followed by high‐dose radiation therapy is safe and feasible in a multicenter setting. Cancer 2008. © 2008 American Cancer Society.
On the modified Crank–Nicholson difference schemes for parabolic equation with non‐smooth data arising in biomechanics
Authors: Ashyralyev Allaberen , Erdogan Abdullah Said , Arslan Nurullah 
Published: November 2008

AbstractIn the present paper, we consider the mixed problem for one‐dimensional parabolic equation with non‐smooth data generated by the blood flow through glycocalyx on the endothelial cells. Stable numerical method is developed and solved by using the r‐modified Crank–Nicholson schemes. Numerical analysis is given for a constructed problem. Copyright © 2008 John Wiley & Sons, Ltd.
Unusual Complications Following Living Donor Nephrectomy
Authors: Akoh Jacob A. , Rana Tahawar A. , Stacey Sarah L. 
Published: November 2008

AbstractBACKGROUNDThe aim of this study was to highlight unusual complications following living‐donor nephrectomy within a single center.METHODSBetween January 2003 and February 2008, 58 donor nephrectomies (52 open and 6 laparoscopic hand‐assisted) were performed. All donors were followed up at 6 weeks and then discharged to regular yearly visits with their designated nephrologists. All complications were entered prospectively into a database used for this analysis.RESULTSForty‐four (76%) had a left donor nephrectomy, whereas 14 (24%) had a right nephrectomy. There were 22 men and 34 women with a median age of 48 years (range 27–70 years). Average length of hospital stay of the donors was 5 days (median 4 days). Fifty donors (86%) had no complications; the complications seen in the remaining 8 (14%) were hemorrhage in 4 donors, testicular pain treated by orchidectomy in 1 donor, neuropathic pain in 1 donor, and lymphoma in 1 transplanted kidney.CONCLUSIONSIn addition to rigorous and careful assessment of potential donors, every effort must be made to reduce the risk of postoperative complications by adopting a careful surgical technique, ensuring a high level of vigilance, and early detection of complications—bearing in mind some of the unusual complications detailed in this report.