bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tumor interstitial fluid pressure may regulate angiogenic factors in osteosarcoma
Authors: Nathan Saminathan S. , Huvos Andrew G. , Casas‐Ganem Jorge E. , Yang Rui , Linkov Irina , Sowers Rebecca , DiResta Gene R. , Gorlick Richard , Healey John H. 
Published: May 2008

AbstractWe have previously shown that osteosarcomas (OS) have states of increased interstitial fluid pressure (IFP), which correlate with increased proliferation and chemosensitivity. In this study, we hypothesized that constitutively raised IFP in OS regulates angiogenesis. Sixteen patients with the clinical diagnosis of OS underwent blood flow and IFP readings by the wick‐in‐needle method at the time and location of open biopsy. Vascularity was determined by capillary density in the biopsy specimens. We performed digital image analysis of immunohistochemical staining for CD31, VEGF‐A, VEGF‐C, and TPA on paraffin‐embedded tissue blocks of the biopsy samples. Clinical results were validated in a pressurized cell culture system. Interstitial fluid pressures in the tumors (mean 33.5 ± SD 17.2 mmHg) were significantly higher (p = 0.00001) than that in normal tissue (2.9 ± 5.7 mmHg). Pressure readings were significantly higher in low vascularity tumors compared to high vascularity tumors (p < 0.001). In the OS cell lines, growth in a pressurized environment was associated with VEGF‐A downregulation, VEGF‐C upregulation, and TPA upregulation. The reverse was seen in the OB cell line. Growth in the HUVEC cell line was not significantly inhibited in a pressurized environment. Immunohistochemical assessment for VEGF‐A (p = 0.01), VEGF‐C (p = 0.008), and TPA (p = 0.0001) translation were consistent with the findings on PCR. Our data suggests that some molecules in angiogenesis are regulated by changes in IFP. © 2008 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 26:1520–1525, 2008
Muscle strength quantification in small animals: A new transcutaneous technique in rabbits
Authors: Meffert Rainer H. , Frey Sönke P. , Jansen Hendrik , Ochman Sabine , Raschke Michael J. , Langer Martin 
Published: May 2008

AbstractThe objective of this study was to develop a new, simple, and noninvasive technique to measure the force produced by dorsi‐flexion of the foot in small animals. In addition, this study aimed to quantitatively describe changes in muscle and soft tissue structures using histomorphometry. The recovery of the dorsi‐flexing muscles in the tibialis anterior compartment in New Zealand White rabbits was evaluated after musculoskeletal trauma by measuring isometric contractions after submaximal transcutaneous electrical stimulation of the peroneal nerve. The trauma included muscle and bone trauma that was treated with limb shortening followed by distraction osteogenesis. Muscle contractions were initiated at an amplitude of 5.1 mA for a duration of 2.56 ms at intervals of 50 ms. Based on consecutive measurements of the force on days 5, 10, 15, 20, 25, and 30 postsurgery, a positive trend in recovery of the stimulated force produced by dorsi‐flexion of the foot was observed. The muscle strength at 30 days postsurgery was compared to that measured presurgery (baseline): 55% of the animals had dorsi‐flexion strength that was 60% below that of the presurgery baseline muscle strength; 36% of the animals had dorsi‐flexion strength that was greater than 60% of the baseline measure, indicating that there was a significant decrease in force produced by dorsi‐flexion of the foot after trauma on all testing days (p < 0.01) and that a severe muscular injury was set with limited recovery. This technique provides a new option for examining muscle regeneration and rehabilitation in small animals. © 2008 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 26:1526–1532, 2008
Non‐enzymatic glycation of chondrocyte‐seeded collagen gels for cartilage tissue engineering
Authors: Roy Rani , Boskey Adele L. , Bonassar Lawrence J. 
Published: May 2008

AbstractCollagen glycated with ribose (250 mM) in solution (pre‐glycation) and as a gel (post‐glycation) was seeded with chondrocytes and the effects of glycation on chondrocyte matrix assembly in culture were determined. Pre‐glycation enhanced GAG accumulation significantly over controls at both 2 and 4 weeks (p < 0.05), although at both time points there were no statistical differences in cell number between pre‐glycated and control gels. The increased proteoglycan accumulation was shown to be in part due to significantly increased GAG retention by the pre‐glycated constructs (p < 0.05). Total collagen content in these pre‐glycated gels was also significantly higher than unglycated gels at 4 weeks (p < 0.05). With post‐glycation of collagen gels, chondrocyte number and GAG accumulation were all significantly lower than controls (p < 0.05). Post‐glycation also inhibited GAG retention by the constructs (p < 0.05). Given these results, pre‐glycation may be an improved processing method for collagen gels for tissue engineering techniques. © 2008 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 26:1434–1439, 2008
The canine bilateral groove model of osteoarthritis
Authors: Intema Femke , DeGroot Jeroen , Elshof Bram , Vianen Marieke E. , Yocum Sue , Zuurmond Annemarie , Mastbergen Simon C. , Lafeber Floris P. 
Published: May 2008

AbstractIn studies aimed at local treatment of experimental osteoarthritis (OA) it is optimal to have an internal (untreated) OA control. Such an approach excludes interanimal variation, and allows paired statistical evaluation of treatment efficacy. For this purpose, we developed and characterized a bilateral version of the canine Groove model. We hypothesized that the bilateral version of the canine Groove model would show consistent and clear development of features of OA similar to those found in the unilateral version. In six Beagle dogs, grooves were surgically made in the articular cartilage of the femoral condyles of both knee joints. Six additional dogs underwent bilateral sham surgery. The degree of OA was quantified 20 weeks after surgery and was compared in retrospect to 23 animals that undergone the same procedure in a single knee joint with the contralateral knee serving as a non‐OA control. Bilateral groove surgery resulted in OA. This was based on the observed ineffective repair response in which an increase in proteoglycan synthesis, a diminished retention of these newly formed proteoglycans, and an enhanced loss of resident proteoglycans resulted in a decreased cartilage proteoglycan content. These biochemical effects were corroborated by clear histological features of OA. All these effects were found in femor as well as in the (surgically untouched) tibia. Interestingly, features of OA were slightly more severe in the bilateral model than in the unilateral variant. The bilateral canine Groove model showed consistent and clear development of features of OA, comparable to the unilateral model. © 2008 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 26:1471–1477, 2008
Densitometric determination of zinc bacitracin and nystatin in animal feed
Authors: Injac Rade , Strukelj Borut , Djordjevic‐Milic Vukosava , Karljikovic‐Rajic Katarina , Lingeman Henk 
Published: May 2008

AbstractBACKGROUND: The European Union has forbidden the use of antibiotics as additives in animal feed. Zn‐bacitracin (Zn‐BC) and nystatin (NYS) were frequently used for their growth‐promoting effects and for feed conversion in poultry, pigs and cattle. An HPTLC method has been developed for separating Zn‐BC and NYS in the mixture, for routine quality control.RESULTS: The separation was obtained using RP‐18 F254S coated HPTLC plates with acetonitrile/methanol (equal volumes):toluene:KH2PO4/KOH (buffer, pH 6.8) = 57:3:40 (v/v/v), adjusted with HCl to pH 8.2, as a mobile phase. The densitograms were monitored at 192, 215 and 305 nm and both antibiotics were assayed at 215 nm. The method was shown to be specific, accurate (recoveries were 98.7 ± 0.5% and 104.8 ± 0.7% for Zn‐BC and NYS, respectively), linear over the tested range (correlation coefficients, 0.9982 and 0.9884), and precise (intermediate precision RSD below 2.2% for both analytes) with efficient separation (Rs = 3.5).CONCLUSION: The method was applied for determining Zn‐BC and NYS as additives in spiked matrices of commercial animal feedstuffs. According to LOD values for each antibiotic, the minimum detectable amount in feed is 4.5 and 5.5 ppm of Zn‐BC and NYS, respectively. Copyright © 2008 Society of Chemical Industry
Architectures and performance evaluation of bandwidth brokers
Authors: Bouras Christos , Primpas Dimitris 
Published: May 2008

AbstractDiffServ is the basis of contemporary QoS‐enabled networks. Setting up DiffServ QoS requires extensive engineering effort in dimensioning and provisioning, especially for adjacent networks under different administrations linked in a ‘federated’ hierarchy. The bandwidth broker is an entity that is responsible for the management of the resources and the QoS service operation in an automated way. In this paper, we present, test and compare two different architectures of bandwidth brokers: a centralized one and a distributed one. We also deal with the inter‐domain operation of the bandwidth broker in order to perform end‐to‐end provisioning. The paper presents the relevant aspects for inter‐domain operation of a bandwidth broker and focuses on pathfinding issues. We discuss two models for inter‐domain routing through bandwidth brokers, analyzing their advantages and comparing them. Copyright © 2008 John Wiley & Sons, Ltd.
Preparation of a variety of fluoroalkyl end‐capped N‐(1,1‐dimethyl‐3‐oxobutyl)acrylamide oligomer/silica nanocomposites possessing no weight loss characteristic at 800°C
Authors: Sawada Hideo , Tashima Tsukasa , Kodama Shun 
Published: May 2008

AbstractA variety of fluoroalkyl end‐capped N‐(1,1‐dimethyl‐3‐oxobutyl)acrylamide oligomer [RF‐(DOBAA)n‐ RF]/silica nanocomposites, in which the oligomer contents are 18–96%, were prepared by reactions of the corresponding fluorinated oligomer with tetraethoxysilane and silica nanoparticles under alkaline conditions. Each fluorinated oligomer/silica composite thus obtained is nanometer size‐controlled very fine particles (22–68 nm) possessing a good dispersibility and stability in a variety of solvents including water. Interestingly, the weight loss of RF‐(DOBAA)n‐RF/silica nanocomposites, in which the oligomer contents are 18–72%, were not observed at all even at 800°C, as well as the original silica nanoparticles, although the corresponding sub‐micrometer size‐controlled RF‐ (DOBAA)n‐RF/silica composites (particle size: 359 nm) decomposed completely at 800°C to afford the weight loss in proportion to the content of RF‐(DOBAA)n‐RF oligomer in composites. On the other hand, a slight weight loss of RF‐(DOBAA)n‐RF/silica nanocomposites, in which the oligomer contents are 75–94%, was observed at 800°C compared to that of the original silica nanoparticles. Copyright © 2008 John Wiley & Sons, Ltd.
Quantification of seed oil from species with varying oil content using supercritical fluid extraction
Authors: Seal Charlotte E. , Kranner Ilse , Pritchard Hugh W. 
Published: May 2008

AbstractIntroduction: The quantity and composition of seed oil affects seed viability and storability and hence the value of a species as a resource for nutrition and plant conservation. Supercritical fluid extraction with carbon dioxide (SFE‐CO2) offers a rapid, environmentally friendly alternative to traditional solvent extraction.Objective: To develop a method using SFE‐CO2 to quantify the seed oil content in a broad range of species with high to low oil contents.Methodology: Seed oil was extracted using SFE‐CO2 from four crop species representing high, medium and low oil content: Helianthus annuus, Asteraceae, with ca. 55% oil; Brassica napus, Brassicaceae, with ca. 50% oil; Glycine max, Fabaceae, with ca. 20% oil; and Pisum sativum, Fabaceae, with ca. 2% oil. Extraction pressures of 5000, 6000 and 7500 psi and temperatures of 40, 60 and 80°C were examined and a second step using 15% ethanol as a modifier included. Oil yields were compared with that achieved from Smalley Butt extraction. The optimised SFE‐CO2 method was validated on six species from taxonomically distant families and with varying oil contents: Swietenia humilis (Meliaceae), Stenocereus thurberi (Cactaceae), Sinapis alba (Brassicaceae), Robinia pseudoacacia (Fabaceae), Poa pratensis (Poaceae) and Trachycarpus fortunei (Arecaceae).Results: The two‐step extraction at 6000 psi and 80°C produced oil yields equivalent to or higher than Smalley Butt extraction for all species, including challenging species from the Brassicaceae family.Conclusion: SFE‐CO2 enables the rapid analysis of seed oils across a broad range of seed oil contents. Copyright © 2008 John Wiley & Sons, Ltd.
Cyclic polypeptides by thermal polymerization of α‐amino acid N‐carboxyanhydrides
Authors: Kricheldorf Hans R. , Lossow Colin V. , Lomadze Nino , Schwarz Gert 
Published: May 2008

AbstractThe NCAs of the following five amino acids were polymerized in bulk at 120 °C without addition of a catalyst or initiator: sarcosine (Sar), L‐alanine (L‐Ala), D,L‐phenylalanine (D,L‐Phe), D,L‐leucine (D,L‐Leu) and D,L‐valine (D,L‐Val). The virgin reaction products were characterized by viscosity measurements 13C NMR spectroscopy and MALDI‐TOF mass spectrometry. In addition to numerous low molar mass byproducts cyclic polypeptides were formed as the main reaction products in the mass range above 800 Da. Two types of cyclic oligo‐ and polypeptides were detected in all cases with exception of sarcosine NCA, which only yielded one class of cyclic polypeptides. The efficient formation of cyclic oligo‐ and polypeptides explains why high molar mass polymers cannot be obtained by thermal polymerizations of α‐amino acid NCAs. Various polymerization mechanisms were discussed. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 4012–4020, 2008
Stimuli‐responsive cationic terpolymers by RAFT polymerization: Synthesis, characterization, and protein interaction studies
Authors: Rossi Nicholas A. A. , Jadhav Vaibhav , Lai Benjamin F. L. , Maiti Souvik , Kizhakkedathu Jayachandran N. 
Published: May 2008

AbstractThe controlled synthesis and characterization of a range of stimuli responsive cationic terpolymers containing varying amounts of N‐isopropylacrylamide (NIPAM), 3‐(methylacryloylamino)propyl trimethylammonium chloride (MAPTAC), and poly(ethylene glycol)monomethyl methacrylate (PEGMA) is presented. The terpolymers were synthesized using reversible addition‐fragmentation chain transfer (RAFT) polymerization. Compositions of the terpolymers determined using 1H NMR were in close agreement to the theoretical values determined from the monomer feed ratios. GPC‐MALLS was used to analyze the molecular weight characteristics of the polymers, which were found to have low polydispersities (Mw/Mn 1.1–1.4). The phase transitions were studied as a function of PEGMA and NIPAM content using temperature controlled 1H NMR and turbidity measurements (UV‐Vis). The relationship between thermal stability and the comonomer ratio of the polymers was measured using thermogravimetric analysis (TGA). Protein interaction studies were performed to determine the suitability of the polymers for biological applications. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 4021–4029, 2008
Ring‐opening copolymerization of ethylene carbonate and ε‐caprolactone catalyzed by neodymium tris(2,6‐di‐tert‐butyl‐4‐methylphenolate): Synthesis, characterization, and dynamic mechanic analysis
Authors: Chen Feng , Zhu Weipu , Xu Ning , Shen Zhiquan 
Published: May 2008

AbstractThe ring‐opening copolymerization of ethylene carbonate (EC) with ε‐caprolactone (CL) was carried out using neodymium tris(2,6‐di‐tert‐butyl‐4‐methylphenolate) as a single‐component catalyst. Copolymers containing up to 22.0% EC contents with high molecular weights (up to 23.97 × 104) and moderate molecular weight distributions (between 1.66 and 2.03) were synthesized at room temperature. Compared with homopoly(ε‐caprolactone), the copolymers with EC units exhibited increased glass transition temperatures (−35.6 °C), reduced melting temperatures (44.5 °C), and greatly enhanced elongation percentage at break (2383%) based on dynamic mechanic analysis. The crystallinities of the copolymers decreased with the increasing EC molar percentage in the products. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 4050–4055, 2008
Interactions of ionic liquids with polysaccharides. VI. Pure cellulose nanoparticles from trimethylsilyl cellulose synthesized in ionic liquids
Authors: Köhler Sarah , Liebert Tim , Heinze Thomas 
Published: May 2008

AbstractTrimethylsilyl cellulose (TMSC) can be efficiently synthesized with 1,1,1,3,3,3‐hexamethyldisilazane (HMDS) by applying the ionic liquids (ILs) 1‐ethyl‐3‐methylimidazolium acetate, 1‐ethyl‐3‐methylimidazolium chloride, and 1‐butyl‐3‐methylimidazolium chloride as reaction medium, yielding pure biopolymer derivatives with degrees of substitution (DS) up to 2.89. Cosolvents, for example, chloroform, could be used to adjust the viscosity of the system and to achieve the miscibility of the components. During the synthesis of highly functionalized derivatives precipitation of the TMSC occurred, which simplifies the recycling of the IL. The high tendency of TMSC toward the formation of supermolecular structures was exploited for the formation of nanoparticles studying a simple dialysis process. Amazingly, pure cellulose nanoparticles can be obtained by dissolving TMSC in tetrahydrofurane or N,N‐dimethyl acetamide and dialysis against water. FTIR spectroscopy confirmed the complete removal of the TMS functions during this process. Scanning electron microscopy, dynamic light scattering, atomic force microscopy, and particle size distribution analysis showed that cellulose particles down to a size of 170 nm are accessible in this simple manner. The nanoparticle suspensions exhibit viscosities in the range of water. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 4070–4080, 2008
In pursuit of virtual lead optimization: The role of the receptor structure and ensembles in accurate docking
Authors: Bolstad Erin S. D. , Anderson Amy C. 
Published: May 2008

AbstractAccurate ranking during in silico lead optimization is critical to drive the generation of new ligands with higher affinity, yet it is especially difficult because of the subtle changes between analogs. In order to assess the role of the structure of the receptor in delivering accurate lead ranking results, we docked a set of forty related inhibitors to structures of one species of dihydrofolate reductase (DHFR) derived from crystallographic, NMR solution data, and homology models. In this study, the crystal structures yielded the superior results: the compounds were placed in the active site in the conserved orientation and the docking scores for 80% percent of the compounds clustered into the same bins as the measured affinity. Single receptor structures derived from NMR data or homology models did not serve as accurate docking receptors. To our knowledge, these are the first experiments that assess ranking of homologous lead compounds using a variety of receptor structures. We then extended the study to investigate whether ensembles, either computationally or experimentally derived, of all of the single starting structures aid, hinder or have no effect on the performance of the starting template. Impressively, when ensembles of receptor structures derived from NMR data or homology models were employed, docking accuracy improved to a level equal to that of the high resolution crystal structures. The same experiments using a second species of DHFR and set of ligands confirm the results. A comparison of the structures of the individual ensemble members to the starting structures shows that the effect of the ensembles can be ascribed to protein flexibility in addition to absorption of computational error. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Threading without optimizing weighting factors for scoring function
Authors: Yang Yifeng David , Park Changsoon , Kihara Daisuke 
Published: May 2008

AbstractOptimizing weighting factors for a linear combination of terms in a scoring function is a crucial step for success in developing a threading algorithm. Usually weighting factors are optimized to yield the highest success rate on a training dataset, and the determined constant values for the weighting factors are used for any target sequence. Here we explore completely different approaches to handle weighting factors for a scoring function of threading. Throughout this study we use a model system of gapless threading using a scoring function with two terms combined by a weighting factor, a main chain angle potential and a residue contact potential. First, we demonstrate that the optimal weighting factor for recognizing the native structure differs from target sequence to target sequence. Then, we present three novel threading methods which circumvent training dataset‐based weighting factor optimization. The basic idea of the three methods is to employ different weighting factor values and finally select a template structure for a target sequence by examining characteristics of the distribution of scores computed by using the different weighting factor values. Interestingly, the success rate of our approaches is comparable to the conventional threading method where the weighting factor is optimized based on a training dataset. Moreover, when the size of the training set available for the conventional threading method is small, our approach often performs better. In addition, we predict a target‐specific weighting factor optimal for a target sequence by an artificial neural network from features of the target sequence. Finally, we show that our novel methods can be used to assess the confidence of prediction of a conventional threading with an optimized constant weighting factor by considering consensus prediction between them. Implication to the underlined energy landscape of protein folding is discussed. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Anchoring effects in a wide binding pocket: The molecular basis of regioselectivity in engineered cytochrome P450 monooxygenase from B. megaterium
Authors: Branco Ricardo J.F. , Seifert Alexander , Budde Michael , Urlacher Vlada B. , Ramos Maria J. , Pleiss Jürgen 
Published: May 2008

AbstractThe molecular basis of regioselectivity of cytochrome P450 monooxygenases from Bacillus megaterium (CYP102A1) with its flexible and widely opened active site is still not well understood. In the present work (−)‐α‐pinene bound complexes with two triple mutants were modeled to elucidate the contribution of the three major factors that mediate selectivity: active site shape, protein flexibility, and chemical reactivity of the substrate. For the triple mutant A74G F87V L188Q (GVQ), one stable, productive conformation of the substrate (conformation I) was identified by multiple molecular dynamics simulations. The model predicts pinene epoxide as a major product (42% pinene oxide, 23% verbenol) which is in agreement with the experimental product profile (70% pinene oxide, 20% verbenol). In contrast, for the triple mutant A74G F87G L188Q (GGQ) two stable productive substrate conformations were identified (conformations IIa and IIb), and verbenol was predicted as major product (81% verbenol, 16% myrtenol), which is in agreement with experimental results (77% verbenol, 10% myrtenol). The effect of chemical reactivity of the substrate was demonstrated by comparison of (−)‐α‐pinene to its regioisomer (−)‐β‐pinene, where the product profile is shifted from 68% pinocarveol and 32% myrtanal in mutant GVQ, to 40% pinocarveol and 60% myrtanal in mutant GGQ. Our results strongly suggest a major role of residue 87 in anchoring (−)‐α‐pinene during substrate binding which provides a simple and elegant rationalization of the dynamic structure of this enzyme‐substrate complex. Proteins 2008. © 2008 Wiley‐Liss, Inc.