bluuebunny/crossref_metadata_2025_split huggingface dataset:
Synergistic effect of high‐affinity binding and flow preconditioning on endothelial cell adhesion
Authors: Mathur Anshu B. , Truskey George A. , Reichert William M. 
Published: December 2002

AbstractThe current study examined whether the combined introduction of high‐affinity avidin–biotin bonds and fibronectin–integrin bonds (i.e., dual ligand treatment) would further augment the adhesion of flow‐preconditioned endothelial cells to model substrates via contributions to the actin cytoskeleton and the formation of focal contacts. Human umbilical vein endothelial cells (HUVEC) were grown under static conditions or exposed to a flow‐preconditioning regimen for 24 h. Cell retention was determined by exposure to 75 dynes/cm2. The combination of flow preconditioning and the dual ligand treatment yielded higher cell retention under flow compared to the cells adherent via fibronectin–integrin bonds only. This increase in adhesion strength correlated with a greater focal contact area. Elongation of the HUVEC occurred after exposure to flow preconditioning; however, orientation of dual ligand adherent cells was restricted due to the presence of the high‐affinity ligand. Flow‐preconditioned cells showed increased stress fiber formation compared to nonconditioned cells although the stress fibers per cell for flow‐preconditioned cells were the same on both the ligand systems employed. The results indicate that enhanced adhesion strength is due to a combination of increased focal contact area, stress fiber formation, and cell alignment. © 2002 Wiley Periodicals, Inc. J Biomed Mater Res 64A: 155–163, 2003
Structural dependence of apatite formation on titania gels in a simulated body fluid
Authors: Uchida Masaki , Kim Hyun‐Min , Kokubo Tadashi , Fujibayashi Shunsuke , Nakamura Takashi 
Published: December 2002

AbstractThe apatite‐forming ability of titania gels with different structures has been investigated in a simulated body fluid with ion concentrations nearly equal to those of human blood plasma. Titania gels with an amorphous structure or with an anatase or rutile structure were prepared by the sol‐gel process with a subsequent heat treatment at various temperatures. The titania gels with an amorphous structure did not induce apatite formation on their surfaces in the simulated body fluid , whereas gels with an anatase or rutile structure induced apatite formation on their surfaces. The deposition of apatite was more pronounced on the anatase gels than on the rutile gels. This indicates that a specific structure of titania is effective in inducing apatite formation in a body environment. Such a specific structure was assumed in this study to be the crystalline planar arrangement in the anatase structure, which facilitates epitaxy of the apatite crystal. © 2002 Wiley Periodicals, Inc. J Biomed Mater Res 64A: 164–170, 2003
Type I collagen production by osteoblast‐like cells cultured in contact with different bioactive glasses
Authors: Bosetti Michela , Zanardi Laura , Hench Larry , Cannas Mario 
Published: December 2002

AbstractBioactive glasses are silica‐based, surface‐active bone substitutes that have shown good biocompatibility both in bone and in soft tissue and are used in oral and maxillofacial bone augmentation. Previous in vitro studies showing that bioactive glasses support the growth and maturation of rat osteoblast‐like cells and promote the expression and maintenance of the osteoblastic phenotype have suggested that there is both a solution‐mediated and a surface‐controlled effect on cell activity. In this study, we investigated the behavior of human primary osteoblast‐like cells cultured in contact with three different bioactive glasses and compared them with amorphous silica (SiO2) used in the form of granules. The specific activity of alkaline phosphatase determined biochemically was significantly higher at 2 and 4 days on the bioactive glass with 46.1 mol % silica content (45S5 Bioglass®) cultures than in the control cultures and in the bioactive gel‐glass cultures, which had 60 mol % (58S) and 80 mol % (77S) silica content. Osteoblasts synthesize collagen type I, which is subsequently mineralized. Immunoblot and biochemical studies showed increased collagen release from osteoblast‐like cells cultured in contact with bioactive glasses over that of controls. Among the three bioactive glasses, 45S5 is the highest inducer of osteoblast‐like cell collagen release; moreover, mRNA for type I collagen was stimulated approximately three‐ to fivefold after 45S5 treatment. 77S bioactive glass similarly increased type I collagen synthesis even though alkaline phosphatase was not higher. These results suggest that 45S5 Bioglass® not only induces osteogenic differentiation of human primary osteoblast‐like cells, but can also increase collagen synthesis and release. The newly formulated bioactive gel‐glass 77S seems to have potential applications for tissue engineering, inducing increased collagen synthesis. © 2002 Wiley Periodicals, Inc. J Biomed Mater Res 64A: 189–195, 2003
Effect of the chemical composition of Ricinus communis polyurethane on rat bone marrow cell attachment, proliferation, and differentiation
Authors: Beloti Márcio M. , Hiraki Karen R. N. , Barros Valdemar M. R. , Rosa Adalberto L. 
Published: December 2002

AbstractAlterations in the chemical composition of a polymer may be undertaken to improve its biological properties. The aim of this study was to investigate the in vitro biocompatibility of Ricinus communis polyurethane (RCP) with three different chemical compositions: RCPp (pure RCP), RCP+CaCO3, and RCP+Ca3(PO4)2. Rat bone marrow cells were cultivated under conditions that allowed osteoblastic differentiation and were evaluated for cell attachment, cell proliferation, cell morphology, total protein content, alkaline phosphatase (ALP) activity, and bonelike nodule formation. For the evaluation of attachment, cells were cultured for 4 h. After 3 days, cell morphology was evaluated. Cell proliferation was evaluated after 7 and 14 days. Total protein content and ALP activity were evaluated after 14 days. For bonelike nodule formation, cells were cultured for 21 days. Data were compared with an analysis of variance and Duncan's multiple range test when appropriate. Cell attachment and ALP activity were not affected by RCP chemical composition. Proliferation, total protein content, and bonelike nodule formation were all affected by RCP chemical composition. These results suggest that initial cell events are not affected by RCP chemical composition, whereas RCPs blended with calcium carbonate or, better yet, calcium phosphate, by favoring events that promote matrix mineralization, are more biocompatible materials. © 2002 Wiley Periodicals, Inc. J Biomed Mater Res 64A: 171–176, 2003
Maximal flow rates and sieving coefficients in different plasmafilters: Effects of increased membrane surfaces and effective length under standardized in vitro conditions
Authors: Unger J.K. , Haltern C. , Dohmen B. , Rossaint R. 
Published: December 2002

AbstractIn Europe, capillary membrane filters are the favored method for plasmapheresis and detoxification systems including a plasma separation unit. Using capillary membrane filters clearance depends on the filtration rate and the sieving coefficient (Qs) for the plasma substrates. We investigated whether the increase of the effective membrane surface of plasmafilters enables higher clearance rates than a small plasmafilter. Heparinized porcine blood (5 I.U./l) of healthy pigs was used for an in vitro circuit. Filter types used were from GAMBRO: n = 5 PF1000N (effective membrane surface: 0.15 m2), n = 4 PF2000N (0.35) and from ASAHI: n = 4 PLASMAFLO OP‐05W (L) (0.5). Spontaneous hemolysis was chosen to indicate the individual threshold limit for maximal flow rates. Sieving coefficient was determined for ten parameters at lowest and highest blood flow (Qb) and filtration rates (Qf). PF1000N enabled maximal flow rates as high as PF2000N and PLASMAFLO (Qb/Qf in ml/min: 200/40). Qs for most substrates were similar between the filter types and the flow rates. Compared to PLASMAFLO, the filter type with the largest membrane surface, the PF1000N provided significantly better Qs for triglycerides and albumin and a trend for a better elimination of cholesterol, GGT, and LDH. The sieving properties of the PF2000N ranged between PF1000N and PLASMAFLO. Under standardized in vitro conditions, the larger plasmafilters tested did not improve the overall performance of the plasmapheresis procedure. Thus, enlargement of the membrane surface such as provided by two commercially available and clinically well‐established plasmafilters could not be proven to enable higher clearance rates. J. Clin. Apheresis 17:190–198, 2002. © 2002 Wiley‐Liss, Inc.
A randomized comparison of plateletpheresis with the same donors using four blood separators at a single blood center
Authors: Tenorio Grace C. , Strauss Ronald G. , Wieland Martha J. , Behlke Timothy A. , Ludwig Gerald A. 
Published: December 2002

AbstractAt one blood center, each of 20 donors underwent plateletpheresis on four blood cell separators in random order. We compared the CS3000+, Amicus V 2.41, MCS Plus, and Spectra LRS V 7 Turbo regarding platelet (PLT) yield, pre‐ and post‐procedure PLT counts, percent fall in donor PLT count, process time, efficiency, PLT product and donor PLT volume (MPV). Using ≥ 150 × 109 PLTs/L pre‐donation counts, a goal was set of 4.5 × 1011 PLTs unit in up to 100 minutes processing time. Results were (mean values) PLT yields of Amicus, Spectra, CS3000+, and MCS Plus: 4.3, 4.6, 4.3, 4.0 × 1011 PLTS, respectively; percent donor PLT fall: 24, 32, 30, 29%, respectively; processing times: 50, 74, 87, 101 minutes, respectively; relative efficiency (RE): 2.2, 1.6, 1.2,1.0, respectively (based on the MCS Plus performance with RE of 1 = 4 × 109 PLTS/min); PLT product MPV: 6.7, 7.4, 6.8,7.1 fL, respectively; pre‐procedure donor MPV: 7.7, 7.3, 7.6 and 7.6 fL, respectively; and percent donor MPV change: −5.2, 0, −6.6, and −10%, respectively. Significant changes in the donor MPV were noted (P < 0.05) but could not be related to product MPV. Spectra seemed to collect larger PLTs (higher MPV); the significance remains unknown for both donors and recipients. Importantly, all four separators gave acceptable and comparable PLT yields (P < 0.05) with Spectra trending higher. The short process time and high RE together indicate highly efficient collections particularly by Amicus and Spectra. J. Clin. Apheresis 17:170–176, 2002. © 2002 Wiley‐Liss, Inc.
First two patients with ulcerative colitis who developed classical thrombotic thrombocytopenic purpura successfully treated with medical therapy and plasma exchange
Authors: Baron Beverly W. , Jeon Hye‐Ran , Glunz Catherine , Peterson Amy , Cohen Russell , Hanauer Stephen , Rubin David , Hart John , Baron Joseph M. 
Published: December 2002

AbstractThe association of ulcerative colitis (UC) and thrombotic thrombocytopenic purpura (TTP) is rare. Only one prior patient with these two syndromes has been reported in the literature. In that case, splenectomy and proctectomy were performed to control the symptoms of TTP. We present two patients with UC who developed TTP and were successfully treated with multiple plasma exchanges (PEXs) in conjunction with medical therapy without the necessity for surgical intervention. Acquired TTP may be another extraintestinal autoimmune feature of UC. TTP in association with UC may be refractory to high‐dose steroids and PEX, possibly requiring vincristine and splenectomy, as in the one previously reported case, to achieve remission. J. Clin. Apheresis 17:204–206, 2002. © 2002 Wiley‐Liss, Inc.
Extracorporeal photopheresis reduces the number of mononuclear cells that produce pro‐inflammatory cytokines, when tested ex‐vivo
Authors: Bladon John , Taylor Peter 
Published: December 2002

AbstractExtracorporeal photopheresis (ECP) has been shown to be clinically effective in the treatment of many T cell–mediated conditions. ECP's mechanism of action includes the induction of apoptosis and the release of pro‐inflammatory cytokines. Recently, we have observed early lymphoid apoptosis, detectable immediately post ECP. We were interested to determine what influence ECP has on pro‐inflammatory cytokine secretion at this early pre‐infusion stage. Samples from 6 cutaneous T cell lymphoma (CTCL) and 5 graft versus host disease (GvHD) patients were taken pre ECP and immediately post ECP, prior to re‐infusion. Following separation, the PBMCs were added to a cell culture medium and stimulated with PMA, Ionomycin, and Brefeldin A for 6 hours. Using flow cytometry, intracellular cytokine expression of IFNγ and TNFα was determined in the T cell population. The monocytes were evaluated for IL6, IFNγ, IL12, and TNFα. For both patient groups, the number of IFNγ‐expressing T cells fell significantly at re‐infusion, whilst both T cell‐ and monocyte‐expressing TNFα levels were reduced at re‐infusion. All other cytokines tested showed no significant change post ECP. For GvHD, pro‐inflammatory cytokines have a pathological role. Their down‐regulation may have a direct clinical benefit. However, the reduction in the number of IFNγ‐ and TNFα‐expressing mononuclear cells means, at this early stage, it is unlikely that these cytokines assist in the removal of the malignant Th2 cells present in CTCL. J. Clin. Apheresis 17:177–182, 2002. © 2002 Wiley‐Liss, Inc.
MOPED: Method for optimizing physical energy parameters using decoys
Authors: Seok Chaok , Rosen J. B. , Chodera John D. , Dill Ken A. 
Published: December 2002

AbstractWe present a method called MOPED for optimizing energetic and structural parameters in computational models, including all‐atom energy functions, when native structures and decoys are given. The present method goes beyond previous approaches in treating energy functions that are nonlinear in the parameters and continuous in the degrees of freedom. We illustrate the method by improving solvation parameters in the energy function EEF1, which consists of the CHARMM19 polar hydrogen force field augmented by a Gaussian solvation term. Although the published parameters for EEF1 correctly discriminate the native from decoys in the decoy sets of Levitt et al., they fail on several of the more difficult decoy sets of Baker et al. MOPED successfully finds improved parameters that allow EEF1 to discriminate native from decoy structures on all protein structures that do not have metals or prosthetic groups. © 2002 Wiley Periodicals, Inc. J Comput Chem 24: 89–97, 2003
Fast approximate methods for calculating nucleic acid base pair interaction energies
Authors: Sherer Edward C. , York Darrin M. , Cramer Christopher J. 
Published: December 2002

AbstractInteraction enthalpies for six base pairs have been computed at a variety of efficient levels of electronic structure theory and compared to experiment. In addition to previously defined levels of theory, modified Hamiltonians with adjusted parameters in hybrid Hartree–Fock/density functionals and semiempirical neglect‐of‐diatomic‐differential‐overlap models were examined. Of the pure and hybrid density functional levels, mPWPW91/MIDI! performed most satisfactorily, as judged by comparison not only to the available experimental data, but also to data from more robust electronic structure methods for 22 additional base pairs. The low computational cost of the mPWPW91/MIDI! model was further exploited in an investigation of various base trimers, tetramers, and one base pentamer. A carefully reparameterized semiempirical model, PM3BP, was able to achieve similar levels of accuracy at a still greater savings in terms of computational effort. © 2002 Wiley Periodicals, Inc. J Comput Chem 24: 57–67, 2003
Catalysis on the coastline: Theozyme, molecular dynamics, and free energy perturbation analysis of antibody 21D8 catalysis of the decarboxylation of 5‐nitro‐3‐carboxybenzisoxazole
Authors: Ujaque Gregori , Tantillo Dean J. , Hu Yunfeng , Houk K. N. , Hotta Kinya , Hilvert Donald 
Published: December 2002

AbstractAntibody 21D8 catalyzes the decarboxylation of 5‐nitro‐3‐carboxybenzisoxazole. The hapten used was designed to induce an antibody binding site with anion binders for the carboxylate, plus a nonpolar environment to accelerate decarboxylation. A recent X‐ray crystal structure of 21D8 has shown that the binding pocket contains an array of both polar and charged residues. Nevertheless, 21D8 is able to catalyze a reaction that involves a decrease in polarity from reactant to transition state. The origins of this phenomenon were explored using various computational strategies—quantum mechanics, theozyme models, docking, molecular dynamics, free energy perturbation, and linear interaction energy—the combination of which has produced a consistent picture of catalysis. By partially desolvating the charged carboxylate, 21D8 manages to effect “catalysis on the coastline,” without burying the carboxylate in a nonpolar region of the binding pocket. The results have implications for that broad class of enzyme and antibody catalyzed reactions that involve the conversion of a substrate with a relatively localized charge into a transition state with a highly dispersed charge. © 2002 Wiley Periodicals, Inc. J Comput Chem 24: 98–110, 2003
The intramolecular mechanism for the second proton transfer in triosephosphate isomerase (TIM): A QM/FE approach
Authors: Alagona Giuliano , Ghio Caterina , Kollman Peter A. 
Published: December 2002

AbstractThe intramolecular mechanism we earlier proposed [Alagona, G.; Desmeules, P.; Ghio, C.; Kollman, P. A. J Am Chem Soc 1984, 106, 3623] for the second proton transfer of the reaction catalyzed by triosephosphate isomerase (TIM) is examined ab initio at the HF and MP2/6‐31+G** levels in vacuo for two conformers of the enediolate phosphate (ENEP), with the ethereal oxygen of the phosphate group either syn (X), as in the crystal structure, or anti (Y) with respect to the enediolate carbonyl O. The barrier height for the intramolecular proton transfer occurring in enediolate is very sensitive to electron correlation corrections. The MP2 internal energy barrier is much lower than the HF one, while the free energy (FE) barrier is even more favorable, indicating that the enzyme presence is not requested to speed up that step. An investigation of the dynamical aspects of the mechanism, along the pathway from ENEP A (with H on O1) to TS and from TS to ENEP B (with H on O2), was, however, carried out in the presence of the enzyme field while using a neutral His‐95 with its proton on Nδ. To perform the FE simulations, it was necessary to parametrize in the AMBER force‐field the ENEP A, TS and B species, whose partial charges have been determined with the RESP procedure, with the X and Y arrangements of the phosphate head. Actually, the FE/QM approach produced a low barrier and a substantial balance between A and B, especially at the MP2 level. The trajectories, analyzed paying a particular attention to the positions assumed by His‐95 and by the other active site residues, put forward somewhat different H‐bond patterns around the X or Y enediolate phosphate. © 2002 Wiley Periodicals, Inc. J Comput Chem 1: 46–56, 2003
Transferability of fragmental contributions to the octanol/water partition coefficient: An NDDO‐based MST study
Authors: Curutchet C. , Salichs A. , Barril X. , Orozco Modesto , Javier Luque F. 
Published: December 2002

AbstractThis study examines the transferability of fragmental contributions to the octanol/water partition coefficient. As a previous step, we report the parameterization of the AM1 and PM3 versions of the MST model for n‐octanol. The final AM1 and PM3 MST models reproduce the experimental free energy of solvation and the octanol/water partition coefficient (log Pow) with a root‐mean‐square deviation of around 0.7 kcal/mol and 0.5 (in units of log P), respectively. Based on this parameterization, an NNDO‐based procedure is presented to dissect the free energy of transfer between octanol and water in contributions directly associated with specific atoms or functional groups. The application of this procedure to a set of representative molecular systems illustrates the dependence of the log Pow fragmental contribution due to electronic, hydrogen bonding, and steric effects, which cannot be easily accounted for in simple additive‐based empirical schemes. The results point out the potential use of theoretical methods to refine the fragmental contributions in empirical methods. © 2002 Wiley Periodicals, Inc. J Comput Chem 24: 32–45, 2003
Motifs in nucleic acids: Molecular mechanics restraints for base pairing and base stacking
Authors: Harvey Stephen C. , Wang Chunlin , Teletchea Stephane , Lavery Richard 
Published: December 2002

AbstractIn building and refining nucleic acid structures, it is often desirable to enforce particular base pairing and/or base stacking interactions. Energy‐based modeling programs with classical molecular mechanics force fields do not lend themselves to the easy imposition of penalty terms corresponding to such restraints, because the requirement that two bases lie in or near the same plane (pairing) or that they lie in parallel planes (stacking) cannot be easily expressed in terms of traditional interactions involving two atoms (bonds), three atoms (angles), or four atoms (torsions). Here we derive expressions that define a collection of pseudobonds and pseudoangles through which molecular mechanics restraints for base pairing and stacking can be imposed. We have implemented these restraints into the JUMNA package for modeling DNA and RNA structures. JUMNA scripts can specify base pairing with a variety of standard geometries (Watson–Crick, Hoogsteen, wobble, etc.), or with user‐defined geometries; they can also specify stacking arrangements. We have also implemented “soft‐core” functions to modify van der Waals and electrostatic interactions to avoid steric conflicts in particularly difficult refinements where two backbones need to pass through one another. Test cases are presented to show the utility of the method. The restraints could be adapted for implementation in other molecular mechanics packages. © 2002 Wiley Periodicals, Inc. J Comput Chem 24: 1–9, 2003
Molecular mechanics force‐field development for amino acid zwitterions
Authors: Kirschner K. N. , Lewin A. H. , Bowen J. P. 
Published: December 2002

AbstractUnderstanding the conformational flexibility of amino acid zwitterions (ZWs) and their associated conformational energies is crucial for predicting their interactions in biological systems. Gas‐phase ab initio calculations of ZWs are intractable. Molecular mechanics (MM), on the other hand, is able to handle large systems but lacks the necessary force field parameters to model ZWs. To develop force field parameters that are able to correctly model ZW geometries and energetics we used a novel combinatorial approach: amino acid ZWs were broken down structurally into key functional components, which were parameterized separately. Møller–Plesset second‐order perturbation calculations on small carboxylates, on the glycine cation, and on novel hydrogen bonded systems, coupled with available experimental data, were used to generate MM3(2000) ZW parameters (Allinger N. L.; Yuh, Y. H.; Lii, J.‐H. J Am Chem Soc 1989, 111, 8551). The MM3 results from this combinatorial approach gave geometries that are in good agreement with neutron diffraction experiments, plus their frequencies and energies appear to be reasonably modeled. Current limitations and future development of MM force fields are discussed briefly. © 2002 Wiley Periodicals, Inc. J Comput Chem 24: 111–128, 2003