bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optical coherence tomography and Raman spectroscopy of the ex‐vivo retina
Authors: Evans Julia W. , Zawadzki Robert J. , Liu Rui , Chan James W. , Lane Stephen M. , Werner John S. 
Published: June 2009

AbstractImaging the structure and correlating it with the biochemical content of the retina holds promise for fundamental research and for clinical applications. Optical coherence tomography (OCT) is commonly used to image the 3D structure of the retina and while the added functionality of biochemical analysis afforded by Raman scattering could provide critical molecular signatures for clinicians and researchers, there are many technical challenges to combine these imaging modalities. We describe an OCT microscope for ex‐vivo imaging combined with Raman spectroscopy capable of collecting morphological and molecular information about a sample simultaneously. We present our first results and discuss the challenges to further development of this dual‐mode instrument and limitations for future in‐vivo retinal imaging. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Reconstruction of peri‐implant bone defects using impacted bone allograft and BMP‐2 gene‐modified bone marrow stromal cells
Authors: Yan Meng‐Ning , Dai Ke‐Rong , Tang Ting‐Ting , Zhu Zhen‐An , Lou Jue‐Ren 
Published: June 2009

AbstractImpaction bone allografting represents an attractive procedure for bone defects reconstruction in joint replacement. And it was found that bone morphogenetic protein‐2(BMP‐2) gene therapy can enhance bone healing. The purpose of this study was to determine if combined adenovirus mediated human BMP‐2(Adv‐hBMP‐2) gene‐modified bone marrow stromal cells(BMSCs) with allograft enhanced the defects healing and improved the strength of implant fixation in 3‐mm bone defect around a titanium alloy implant. Using the impaction grafting technique, the defects were reconstructed using freeze‐dried allograft, freeze‐dried allografts loaded with autogenous BMSCs, or freeze‐dried allografts loaded with autogenous BMSCs modified with the human bone morphogenetic protein‐2 (hBMP‐2) gene. At 6 and 12 weeks, the Bone‐implant Contact rate and strength of the interface in the group with BMP‐2 gene medication were significantly higher than those of the non‐cell or cell groups. BMP‐2 gene medication also showed significant effects on allograft healing and replacement compared with those of two other groups, as evidenced by increased new bone formation and reduced graft remnants. The results suggest that BMP‐2 gene medication can enhance allograft healing and osseointegration of the bone‐implant interface. © 2009 Wiley Periodicals, Inc. J Biomed Mater Res 2010
In vitro macrophage response to polyethylene and polycarbonate‐urethane particles
Authors: Smith Richard A. , Hallab Nadim James 
Published: June 2009

AbstractThis study was undertaken to compare macrophage response to polycarbonate‐urethane (PCU), a proposed alternative material to polyethylene in acetabular components of total hip arthroplasty to cross‐linked ultra‐high molecular weight polyethylene (xUHMWPE) in the presence or absence of endotoxin. Polyethylene wear debris that is generated by total hip and knee replacements has been linked to osteolysis and limiting the lifespan of the implant. We added both lipopolysaccharide (LPS)‐free and endotoxin‐associated xUHMWPE and PCU particles to a human monocyte cell line (TH1) in culture and measured cell viability and tumor necrosis factor (TNF)α, interleukin (IL)‐1β, and prostaglandin E2 (PGE2) in the medium after 24 h. Results indicate that particles (both xUHMWPE and PCU) free of endotoxin did not significantly induce secretion of TNFα, IL‐1β, or PGE2 above basal levels. However, endotoxin‐exposed PCU particles induced significantly less TNFα and IL‐1β than endotoxin‐exposed xUHMWPE particles. This indicates that if endotoxin is available for binding to particles in vivo, then xUHMWPE may be more inflammatory to periprosthetic tissue and bone in part because of its affinity/reactivity with endotoxin when compared with PCU. © 2009 Wiley Periodicals, Inc. J Biomed Mater Res 2010
In vitro cytotoxicity evaluation of biomedical nanoparticles and their extracts
Authors: Das Gautom Kumar , Chan Peggy P. Y. , Teo Ailing , Loo Joachim Say Chye , Anderson James M. , Tan Timothy Thatt Yang 
Published: June 2009

AbstractThe present study presents a new approach for evaluating in vitro cytotoxicity of nanoparticles. The approach is based on American National Standard ISO 10993‐5. Hepatoma HepG2 and fibroblast NIH3T3 cell lines were incubated with nanoparticles, and their associated extracts were derived at 70 and 121°C. Nanoparticles proposed as potential biomedical imaging probes were evaluated on the basis of the detection of metabolic activities and cell‐morphology changes. In general, nanoparticles incubated directly with cells showed higher cytotoxicity than their associated extracts. CdSe and core‐shell CdSe@ZnS quantum dots resulted in low cell viability for both cell lines. The cytotoxicity of the quantum dots was attributed to the Cd ion and the presence of the nanoparticle itself. A statistically significant (p < 0.05) decrease in cell viability was found in higher dosage concentrations. Rare earth nanoparticles and their extracts appear to affect NIH3T3 cells only, with cell viability as low as 71.4% ± 4.8%. Magnetic nanoparticles have no observable effects on the cell viabilities for both cell lines. In summary, we found the following: (1) both direct incubation and extracts of nanoparticles are required for complete assessment of nanoparticle cytotoxicity, (2) the rare earth oxide nanoparticles are less cytotoxic than the Cd‐based quantum dots, and (3) the extent of cytotoxicity is dependent upon the cell line. © 2009 Wiley Periodicals, Inc. J Biomed Mater Res, 2010
Proliferation, behavior, and cytokine gene expression of human umbilical vascular endothelial cells in response to different titanium surfaces
Authors: An Na , Schedle Andreas , Wieland Marco , Andrukhov Oleh , Matejka Michael , Rausch‐Fan Xiaohui 
Published: June 2009

AbstractSuccess of dental implantation is initially affected by wound healing of both, hard and soft tissues. Endothelial cells (ECs) are involved as crucial cells in the angiogenesis and inflammation process of wound healing. In the present study, proliferation, mobility, cluster formation, and gene expression of angiogenesis‐related molecules of human umbilical vascular endothelial cells (HUVECs) were investigated on titanium surfaces with different roughnesses: acid‐etched (A), coarse‐grit‐blasted and acid‐etched (SLA) surfaces, as well as on hydrophilic modified modA and modSLA surfaces. Cell behaviors were analyzed by proliferation assay and time‐lapse microscopy, gene expression was analyzed by real time PCR. Results showed that cell proliferation, mobility, and cluster formation were highest on modA surfaces compared with all other surfaces. HUVECs moved slowly and exhibited seldom cell aggregation on SLA and modSLA surfaces during the whole observing period of 120 h. The gene expressions of the angiogenesis‐related factors von Willebrand factor, thrombomodulin, endothelial cell protein C receptor, and adhesion molecules intercellular adhesion molecule‐1 and E‐selectin were most enhanced on modSLA surfaces. These results suggest that modA surface is optimal for proliferation and angiogenic behavior of ECs. However, modSLA surface seems to promote ECs to express angiogenesis‐related factor genes, which play essential roles in controlling inflammation and revascularization of wound healing. © 2009 Wiley Periodicals, Inc. J Biomed Mater Res 2010
A role for decorin in controlling proliferation, adhesion, and migration of murine embryonic fibroblasts
Authors: Ferdous Z. , Peterson S. B. , Tseng H. , Anderson D. K. , Iozzo R. V. , Grande‐Allen K. J. 
Published: June 2009

AbstractThe proteoglycan decorin putatively inhibits cell adhesion and cell migration on various extracellular matrix substrates through interactions with β1 integrins. This study, therefore, examined the adhesive, migration, and proliferative characteristics of decorin knockout (Dcn−/−) murine embryonic fibroblasts compared to wild‐type controls on collagen‐coated, fibronectin‐coated, and uncoated tissue culture plates. The Dcn−/− cells showed significantly greater proliferation than wild‐type controls on all substrates. The Dcn−/− cells also showed significantly greater adhesion to both collagen and fibronectin; both cell types showed greater adhesion to collagen. The addition of exogenous decorin had a differential effect on adhesion to collagen between cell types, but not on fibronectin. For collagen, blocking either α2 or β1 integrin subunits significantly reduced adhesion for Dcn−/− cells; whereas for fibronectin, blocking either the α5 or β1 integrin subunits reduced adhesion for both cell types. Decorin and the α5β1 integrin may have lesser roles in adhesion to fibronectin than previously presumed. Finally, compared to wild‐type cells, Dcn−/− cells showed greater migration on both uncoated and collagen substrates. This study demonstrates that decorin affects the biology of various integrins that participate in cell proliferation, adhesion, and migration on various substrates. © 2009 Wiley Periodicals, Inc. J Biomed Mater Res, 2010
Effect of implant surface microtopography on proliferation, neurotrophin secretion, and gene expression of Schwann cells
Authors: Yuan Quan , Liao Dapeng , Yang Xingmei , Li Xiaoyu , Wei Na , Tan Zhen , Gong Ping 
Published: June 2009

AbstractThe purpose of this study was to evaluate the effect of different implant surface properties on the morphology, proliferation, neurotrophin secretion, and gene expression of Schwann cells. Four types of implant surfaces, including ground (smooth surface), sandblasted and acid‐etched (SLA), hydroxyapatite‐coated (HA), and titanium plasma spray (TPS) surfaces were fabricated and photographed by a scanning electron microscopy (SEM). Schwann cells derived from neonatal rats were cultured on the implant surfaces and assessed via SEM observation and methylthiazol tetrazolium (MTT) colorimetric assay. The secretions and mRNA levels of brain‐derived neurotrophic factor (BDNF) and nerve growth factor (NGF) were measured by enzyme‐linked immunosorbent assay (ELISA) and quantitative real time RT‐PCR, respectively, on days 3 and 7. Tissue culture plastic was used as a control. The results demonstrated that Schwann cells exhibited typical bipolar spindle morphology on various surfaces, and proliferated faster than the control. Neurotrophin secretion and gene expression of both BDNF and NGF were also increased by implant surfaces. This study suggests that the function of Schwann cells can be enhanced by implant implants. © 2009 Wiley Periodicals, Inc. J Biomed Mater Res 2010
Characterization of dextrin‐based hydrogels: Rheology, biocompatibility, and degradation
Authors: Carvalho Joana , Moreira Susana , Maia João , Gama Francisco M. 
Published: June 2009

AbstractA new class of degradable dextrin‐based hydrogels (dextrin‐HEMA) was developed. The hydroxyethyl methacrylate ester (HEMA) hydroxyl groups were activated with N,N′‐carbonyldiimidazole (CDI), followed by their coupling to dextrin, yielding a derivatized material that can be polymerized in aqueous solution to form hydrogels. A comparative study of the stability of the dextrin‐HEMA hydrogels and dextrin‐vinyl acrylate (dextrin‐VA, produced in previous work) revealed that only the firsts are effectively hydrolyzed under physiological conditions. A severe mass loss of dextrin‐HEMA gels occurs over time, culminating in the complete dissolution of the gels. Rheologic analysis confirmed that physical structuring is less pronounced when dextrin is modified with methacrylate side groups. The biocompatibility results revealed that the dextrin hydrogels have negligible cell toxicity, irrespective of the hydrogel type (HEMA and VA), allowing cell adhesion and proliferation. Gathering the biocompatibility and the ability to tailor the release profiles, we consider dextrin a promising biomaterial for biomedical applications, namely for controlled release. © 2009 Wiley Periodicals, Inc. J Biomed Mater Res 2010
A systematic SPR study of human plasma protein adsorption behavior on the controlled surface packing of self‐assembled poly(ethylene oxide) triblock copolymer surfaces
Authors: Chang Yung , Chu Wan‐Ling , Chen Wen‐Yih , Zheng Jie , Liu Lingyun , Ruaan Ruoh‐Chyu , Higuchi Akon 
Published: June 2009

AbstractA well‐controlled biocompatible nonfouling surface is significant for biomedical requirements, especially for the improvement of biocompatibility. We demonstrate the low or nonbiofouling surfaces by coating hydrophobic–hydrophilic triblock copolymers of poly(ethylene oxide)‐poly(propylene oxide)‐poly(ethylene oxide) (PEO‐PPO‐PEO) on the CH3‐terminated self‐assembled monolayer (SAM). Two types of copolymers are used to modify the surface, one with different PEO/PPO ratios (∼20/80, 40/60, and 80/20, w/w) but the same PPO molecular weight (∼2 k), the other with different copolymer MWs (∼9, 11, and 15 k) but the same PEO/PPO ratio (80/20, w/w). In situ surface plasmon resonance (SPR) sensor is used to evaluate polymer adsorption on the SAMs and subsequent protein adsorption on the copolymer‐treated surface. The effects of PEO‐PPO‐PEO molecular weight, PPO‐to‐PEO ratio, and ionic strength on protein adsorption from single protein solutions of fibrinogen, BSA, and complex mixed proteins are systematically investigated. A Pluronic™ F108 treated surface is highly resistant to nonspecific protein adsorption under the optimized conditions (MW of 15 k and PEO/PPO ratio of 80/20). This work demonstrates that the PEO‐PPO‐PEO polymer is able to achieve ultra low fouling surface via surface modification by controlling surface packing density of polymers (molecular weight, hydrophobic/hydrophilic ratio, and hydrophilic group coverage). © 2009 Wiley Periodicals, Inc. J Biomed Mater Res 2010
Ligand and structure‐based models for the prediction of ligand‐receptor affinities and virtual screenings: Development and application to the β2‐adrenergic receptor
Authors: Vilar Santiago , Karpiak Joel , Costanzi Stefano 
Published: June 2009

AbstractIn this study, we evaluated the applicability of ligand‐based and structure‐based models to quantitative affinity predictions and virtual screenings for ligands of the β2‐adrenergic receptor, a G protein‐coupled receptor (GPCR). We also devised and evaluated a number of consensus models obtained through partial least square regressions, to combine the strengths of the individual components. In all cases, the bioactive conformation of each ligand was derived from molecular docking at the crystal structure of the receptor. We identified the most effective models applicable to the different scenarios, in the presence or in the absence of a training set. For ranking the affinity of closely related analogs when a training set is available, a ligand‐based consensus model (LI‐CM) seems to be the best choice, while the structure‐based MM‐GBSA score seems the best alternative in the absence of a training set. For virtual screening purposes, the structure‐based MM‐GBSA score was found to be the method of choice. Consensus models consistently had performances superior or close to those of the best individual components, and were endowed with a significantly increased robustness. Given multiple models with no a priori knowledge of their predictive capabilities, constructing a consensus model ensures results very close to those that the best model alone would have yielded. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010
An N log N approximation based on the natural organization of biomolecules for speeding up the computation of long range interactions
Authors: Anandakrishnan Ramu , Onufriev Alexey V. 
Published: June 2009

AbstractPresented here is a method, the hierarchical charge partitioning (HCP) approximation, for speeding up computation of pairwise electrostatic interactions in biomolecular systems. The approximation is based on multiple levels of natural partitioning of biomolecular structures into a hierarchical set of its constituent structural components. The charge distribution in each component is systematically approximated by a small number of point charges, which, for the highest level component, are much fewer than the number of atoms in the component. For short distances from the point of interest, the HCP uses the full set of atomic charges available. For long‐distance interactions, the approximate charge distributions with smaller sets of charges are used instead. For a structure consisting of N charges, the computational cost of computing the pairwise interactions via the HCP scales as O(N log N), under assumptions about the structural organization of biomolecular structures generally consistent with reality. A proof‐of‐concept implementation of the HCP shows that for large structures it can lead to speed‐up factors of up to several orders of magnitude relative to the exact pairwise O(N2) all‐atom computation used as a reference. For structures with more than 2000–3000 atoms the relative accuracy of the HCP (relative root‐mean‐square force error per atom), approaches the accuracy of the particle mesh Ewald (PME) method with parameter settings typical for biomolecular simulations. When averaged over a set of 600 representative biomolecular structures, the relative accuracies of the two methods are roughly equal. The HCP is also significantly more accurate than the spherical cutoff method. The HCP has been implemented in the freely available nucleic acids builder (NAB) molecular dynamics (MD) package in Amber tools. A 10 ns simulation of a small protein indicates that the HCP based MD simulation is stable, and that it can be faster than the spherical cutoff method. A critical benefit of the HCP approximation is that it is algorithmically very simple, and unlike the PME, the HCP is straightforward to use with implicit solvent models. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010
Stability of the hydration layer of tropocollagen: A QM study
Authors: Pálfi Villő K. , Perczel András 
Published: June 2009

AbstractCollagen is a triple helical protein, highly hydrated in nature. Bella and Berman (J Mol Biol 1996, 264, 734) have reported the structure of the first hydration layer. Water molecules form bridges of different length around the POG repeats and self assemble into left‐handed helical water threads. To explore the stability of these specifically hydrated places, we have designed suitable QM models: each comprises a triple helix formed by 18 residues surrounded by 8 to 12 explicit waters. Two sets of amino acids were used, one standing for the core structural subunit of tropocollagen (POG‐model) and one for its natural enzyme recognition sites (AAG‐model). We have determined the stability order of the water binding places, the strongest being −8.1 kcal mol−1, while the weakest −6.1 kcal mol−1 per hydrogen bond. In X‐ray structures, each triplet of tropocollagen is shielded by six to nine water molecules. Beside the mandatory six, the “surplus” three water molecules further strengthen the binding of all the others. However, the displacement of selected water molecules turns out to be energy neutral. These water binding places on the surface of the triple helix can provide explanation on how an almost liquid‐like hydration environment exists between the closely packed tropocollagens (Henkelman et al., Magn Reson Med 1994, 32, 592). It seems that these water reservoirs or buffers can provide space for “hole conduction” of water molecules and thus contribute to the elasticity of collagen. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010
Ligand shape emerges in solvent dipole ordering region at ligand binding site of protein
Authors: Murata Katsumi , Nagata Naoya , Nakanishi Isao , Kitaura Kazuo 
Published: June 2009

AbstractSolvent dipole ordering (SDO), introduced by Higo et al. (Proteins Struct Funct Genet 2000, 40, 193), is an entity that captures an aspect of hydration structure. We have studied SDO in the ligand binding site of two proteins (FK506 binding protein and dihydrofolate reductase) and found that the high SDO regions overlap significantly with the 3D structures of known inhibitors bound to the proteins. Thus, the SDO region might be used to predict the preferred molecular shape of ligands that bind to a protein. Based on this finding, we propose a novel docking procedure using model molecules that mimic the shape of the SDO region. To prove the validity of thisapproach, we performed a redocking experiment for p38 mitogen‐activated protein kinase ligands using model molecules for search queries; we succeeded in identifying the binding conformations and binding modes of known inhibitors. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010
Energy gradients in combined fragment molecular orbital and polarizable continuum model (FMO/PCM) calculation
Authors: Li Hui , Fedorov Dmitri G. , Nagata Takeshi , Kitaura Kazuo , Jensen Jan H. , Gordon Mark S. 
Published: June 2009

AbstractThe analytic energy gradients for the combined fragment molecular orbital and polarizable continuum model (FMO/PCM) method are derived and implemented. Applications of FMO/PCM geometry optimization to polyalanine show that the structures obtained with the FMO/PCM method are very close to those obtained with the corresponding full ab initio PCM methods. FMO/PCM (RHF/6‐31G* level) is used to optimize the solution structure of the 304‐atom Trp‐cage miniprotein and the result is in agreement with NMR experiments. The key factors determining the relative stability of the α‐helix, β‐turn and the extended form in solution are elucidated for polyalanine. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010
A fast method for large‐scale De Novo peptide and miniprotein structure prediction
Authors: Maupetit Julien , Derreumaux Philippe , Tufféry Pierre 
Published: June 2009

AbstractAlthough peptides have many biological and biomedical implications, an accurate method predicting their equilibrium structural ensembles from amino acid sequences and suitable for large‐scale experiments is still missing. We introduce a new approach—PEP‐FOLD—to the de novo prediction of peptides and miniproteins. It first predicts, in the terms of a Hidden Markov Model‐derived structural alphabet, a limited number of local conformations at each position of the structure. It then performs their assembly using a greedy procedure driven by a coarse‐grained energy score. On a benchmark of 52 peptides with 9–23 amino acids, PEP‐FOLD generates lowest‐energy conformations within 2.8 and 2.3 Å Cα root‐mean‐square deviation from the full nuclear magnetic resonance structures (NMR) and the NMR rigid cores, respectively, outperforming previous approaches. For 13 miniproteins with 27–49 amino acids, PEP‐FOLD reaches an accuracy of 3.6 and 4.6 Å Cα root‐mean‐square deviation for the most‐native and lowest‐energy conformations, using the nonflexible regions identified by NMR. PEP‐FOLD simulations are fast—a few minutes only—opening therefore, the door to in silico large‐scale rational design of new bioactive peptides and miniproteins. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010