bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation on in vitro biocompatibility of silk fibroin‐based biomaterials with primarily cultured hippocampal neurons
Authors: Tang Xin , Ding Fei , Yang Yumin , Hu Nan , Wu Hong , Gu Xiaosong 
Published: September 2008

AbstractSilk fibroin‐based biomaterials have recently found increasing applications in the tissue‐engineering field including the generation of artificial nerve guides for peripheral nerve repair. The aim of this study was to investigate the suitability of silk fibroin as a candidate biomaterial for central nervous system (CNS) therapy. We found that substrates made up of silk fibroin fibers supported the survival and growth of the attached hippocampal neurons by using morphological observation. We also cultured the hippocampal neurons in silk fibroin extract for different times, and observed no significant difference occurring in their morphology, cell viability for these cultured hippocampal neurons as compared to those cultured in plain neuronal culture medium. Moreover, immunocytochemistry, RT‐PCR, and Western blot analysis revealed that no significant difference was found in mRNA or protein levels of the growth‐associated molecules, such as brain‐derived neurotrophic factor, growth‐associated protein‐43, neurofilament, nerve growth factor, and nerve growth factor‐receptor P75, between the hippocampal neurons cultured in the silk fibroin extract and in plain neuronal culture medium. Taken together, all the results demonstrate that silk fibroin has good biocompatibility with primarily cultured hippocampal neurons without any significant cytotoxic effects on their cell phenotype and functions, suggesting a potential possible use of silk fibroin for preparing the tissue‐engineered nerve guides or drug delivery vehicles to treat CNS injuries or diseases. © 2008 Wiley Periodicals, Inc. J Biomed Mater Res, 2009
Macroporous hydroxyapatite scaffolds for bone tissue engineering applications: Physicochemical characterization and assessment of rat bone marrow stromal cell viability
Authors: Oliveira Joaquim M. , Silva Simone S. , Malafaya Patricia B. , Rodrigues Marcia T. , Kotobuki Noriko , Hirose Motohiro , Gomes Manuela E. , Mano Joao F. , Ohgushi Hajime , Reis Rui L. 
Published: September 2008

AbstractIn this work, a new methodology is reported for developing hydroxyapatite (HA) scaffolds using an organic sacrifice template. The novelty of work consists of possibility of obtaining porous and highly interconnected scaffolds mimicking the sacrificial component. Our purpose consisted of evaluating the physicochemical properties of the HA scaffolds by means of Fourier transform infra‐red spectroscopy, X‐ray diffraction analysis, and scanning electron microscopy (SEM) attached with an X‐ray detector. The HA scaffolds obtained possess a porosity of ∼70%, and macropores diameter in the range of 50–600 μm. In contrast, results regarding the microcomputed tomography analysis have demonstrated both high pore uniformity and interconnectivity across the scaffolds. The compressive strength of the HA scaffolds was found to be 30.2 ± 6.0 MPa. Bioactivity of the HA scaffolds was assessed by immersion into a simulated body fluid solution, in vitro. SEM observations have showed a deposition of apatite on the surface of the HA scaffolds, with a “cauliflower‐like” morphology after 1 day, and tend to be more pronounced with the immersion time. The changes in calcium and phosphorus concentration were monitored by inductively‐coupled plasma optical emission spectrometry. Cytotoxicity of the HA scaffolds was preliminarily investigated by carrying direct observation of mouse fibroblasts cells (L929 cell‐line) death in the inverted microscope, and then cell viability was determined by means of carrying out a MTS assay. Complementarily, a luminescent cell viability assay based on the quantification of adenosine triphosphate was performed using rat bone marrow stromal cells (RBMSCs). A LIVE/DEAD assay and SEM analysis allowed the visualization of the RBMSCs adhesion and proliferation on the surface of the HA scaffolds. According to the results obtained from 3D architecture, mechanical properties, biocompatibility, and adhesion tests, it is suggested that HA scaffolds has potential to find applications in bone tissue engineering scaffolding. © 2008 Wiley Periodicals, Inc. J Biomed Mater Res, 2009
Synthesis and characterization of semi‐interpenetrating polymer networks based on polyurethane and N‐isopropylacrylamide for wound dressing
Authors: Thimma Reddy Thatiparti , Kano Arihiro , Maruyama Atsushi , Hadano Michiko , Takahara Atsushi 
Published: September 2008

AbstractThermosensitive semi‐interpenetrating polymer networks (semi‐IPNs) composed of crosslinked poly(N‐isopropylacrylamide) (PNiPAAm) and linear segmented polyurethane urea (SPUU) were synthesized via thermal initiated free radical polymerization. Synthesized semi‐IPNs of various compositions were characterized by Fourier transform infrared spectroscopy, water equilibrium swelling at different temperatures, drug lading, drug release, cell adhesion, and detachment. The semi‐IPN films of all the compositions were transparent in dry state and negative thermosensitivity in their swelling ratio, that is, lower swelling levels with increasing temperature. The drug release study revealed that the rate of drug release is fast in case of pure SPUU compared to PNiPAAm and semi‐IPN film. Drug release depended mainly on solubility of the drugs and physical networks between SPUU and PNiPAAm. Finally NIH3T3 cells were seeded on the semi‐IPN films and found that cells were securely attached and proliferated to confluence. Upon cooling, cells were detached from the semi‐IPN films. Therefore, the semi‐IPN films may be good candidate materials for wound dressing applications. © 2008 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2009
Demineralized bone matrix as an osteoinductive biomaterial andin vitropredictors of its biological potential
Authors: Katz Jordan M. , Nataraj Chandra , Jaw Rebecca , Deigl Elizabeth , Bursac Predrag 
Published: September 2008

AbstractThe osteoinductivity of demineralized bone matrix (DBM) varies from donor to donor as a result of varying levels of multiple growth factors, matrix integrity, and artifacts from material processing. Manyin vitroassays are currently used for screening the osteoinductivity of DBM. The objectives of this study were to determine the correlation of specific growth factors andin vitromitotic stimulation toin vivoectopic bone formation capacity with a large number of DBM samples. Samples were assayed using ELISA methods for BMP‐2/4 and TGF‐β1 (n= 304) and cell proliferation using SAOS‐2 osteoblasts (n= 239). All samples were then implanted intramuscularly in the abdomen of nude rats. Allin vitroassays showed significant variability for any particular level of ostoinductivity determined byin vivomodel. A significant, but only very weak, positive correlation toin vivoresults was found for TGF‐β1 (r2= 0.016), BMP 2/4 (r2= 0.065), and SAOS‐2 cell proliferation (r2= 0.053). The results of this study amplify the notion that a multitude of factors and their relative interplay, rather than a single factor are likely to determine the potency of any particular lot of DBM. © 2008 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2009
In vivo evaluation of anodic TiO2 nanotubes: An experimental study in the pig
Authors: von Wilmowsky Cornelius , Bauer Sebastian , Lutz Rainer , Meisel Mark , Neukam Friedrich Wilhelm , Toyoshima Takeshi , Schmuki Patrik , Nkenke Emeka , Schlegel Karl Andreas 
Published: September 2008

AbstractBecause of their ability to mimic the dimensions of constituent components of natural bone and the possibility to serve as a gene and drug‐delivery carrier, nanotubes seem to be a promising coating for medical implants. Aim of this study was to investigate the effects of a TiO2 nanotube structured surface on periimplant bone formation in vivo when compared with an untreated standard titanium surface. Twenty‐five titanium implants covered with an ordered TiO2 nanotube layer with an individual tube diameter of 30 nm and 25 commercially pure titanium (cp‐Ti) implants were placed in the frontal skull of 25 domestic pigs. To evaluate the effects of the nanotube structured implants on the periimplant bone formation, bone‐implant contact (BIC), and immunohistochemistry analysis were performed at day 3, 7, 14, 30, and 90. Evaluating immunohistochemistry, a significantly higher collagen type‐ I expression occurred at day 7 (p = 0.003), day 14 (p = 0.016), and day 30 (p = 0.044), for the nanostructured implants in comparison with the control group. It could be found that a nanotube structured implant surface with a diameter of 30 nm does influence bone formation and bone development by enhancing osteoblast function. SEM evaluation of the specimen surfaces revealed that the nanotube coatings do resist shearing forces that evoked by implant insertion. Because of their simple, low cost, flexible manufacturing and the possibility for the usage as drug or growth factor delivery system, nanotubes seem to be a promising method for future medical implant coatings. © 2008 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2009
Theoretical studies of the reactions of CF3CHCLOCHF2/CF3CHFOCHF2 with OH radical and Cl atom and their product radicals with OH
Authors: Yang Lei , Liu Jing‐Yao , Wan Su‐Qin , Li Ze‐Sheng 
Published: September 2008

AbstractThe mechanisms and dynamics studies of the OH radical and Cl atom with CF3CHClOCHF2 and CF3CHFOCHF2 have been carried out theoretically. The geometries and frequencies of all the stationary points are optimized at the B3LYP/6‐311G(d,p) level, and the energy profiles are further refined by interpolated single‐point energies (ISPE) method at the G3(MP2) level of theory. For each reaction, two H‐abstraction channels are found and four products (CF3CHFOCF2, CF3CFOCHF2, and CF3CHClOCF2, CF3CClOCHF2) are produced during the above processes. The rate constants for the CF3CHClOCHF2/CF3CHFOCHF2 + OH/Cl reactions are calculated by canonical variational transition‐state theory (CVT) within 200–2000 K, and the small‐curvature tunneling is included. The total rate constants calculated from the sum of the individual rate constants and the branching ratios are in good agreement with the experimental data. The Arrhenius expressions for the reactions are obtained. Our calculation shows that the substitution of Cl by F decreases the reactivity of CF3CHClOCHF2 toward OH and Cl. In addition, the mechanisms of subsequent reactions of product radicals and OH radical are further investigated at the G3(MP2)//B3LYP/6‐311G(d,p) level, and the main products are predicted in the this article. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009
Role of the variable active site residues in the function of thioredoxin family oxidoreductases
Authors: Carvalho Alexandra T. P. , Fernandes Pedro A. , Swart Marcel , Van Stralen Joost N. P. , Bickelhaupt F. Matthias , Ramos Maria J. 
Published: September 2008

AbstractThe enzymes of the thioredoxin family fulfill a wide range of physiological functions. Although they possess a similar CXYC active site motif, with identical environment and stereochemical properties, the redox potential and pKa of the cysteine pair varies widely across the family. As a consequence, each family member promotes oxidation or reduction reactions, or even isomerization reactions. The analysis of the three‐dimensional structures gives no clues to identify the molecular source for the different active site properties. Therefore, we carried out a set of quantum mechanical calculations in active site models to gain more understanding on the elusive molecular‐level origin of the differentiation of the properties across the family. The obtained results, together with earlier quantum mechanical calculations performed in our laboratories, gave rise to a consistent line of evidence, which points to the fact that both active site cysteines play an important role in the differentiation. In contrary to what was assumed, differentiation is not achieved through a different stabilization of the solvent exposed cysteine but, instead, through a fine tuning of the nucleophilicity of both active site cysteines. Reductant enzymes have both cysteine thiolates poorly stabilized, oxidant proteins have both cysteine thiolates highly stabilized, and isomerases have one thiolate (solvent exposed) poorly stabilized and the other (buried) thiolate highly stabilized. The feasibility of shifting the chemical equilibrium toward oxidation, reduction, or isomerization only through subtle electrostatic effects is quite unusual, and it relies on the inherent thermoneutrality of the catalytic steps carried out by a set of chemically equivalent entities all of which are cysteine thiolates. Such pattern of stabilization/destabilization, detected in our calculations is fully consistent with the observed physiological roles of this family of enzymes. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009
Refining the description of peptide backbone conformations improves protein simulations using the GROMOS 53A6 force field
Authors: Cao Zanxia , Lin Zhixiong , Wang Jun , Liu Haiyan 
Published: September 2008

AbstractThe GROMOS 53A6 parameter sets have been shown to reproduce an extensive range of thermodynamics data in condensed phase (Oostenbrink et al., J Comput Chem 2004, 25, 1656), mainly due to the reoptimized nonbonded interactions. Here, we derive refinements for the descriptions of peptide backbone conformations for thisparameter set. A two‐dimensional adaptive umbrella sampling procedure was employed to determine the free energy surfaces of model alanine and glycine dipeptides in solution to high accuracy, with sampling errors below 0.8 kJ mol−1 for relative free energies between major minima. Comparisons of these surfaces with quantum mechanical ones and conformation distributions in protein crystal structures indicated that refined treatments of backbone torsional angle terms are necessary. The high accuracy of the computed free energy surfaces allowed us to consider two types of corrections, one numerically and exactly reproducing the quantum mechanical results, and the other using small analytical terms to correct major deficiencies for the dipeptide systems. In addition, aiming at improving the directionality of backbone–backbone hydrogen bonds, we optimized and tested an off‐center charge model for the peptide backbone carbonyl oxygen. Extensive molecular dynamics simulations of five proteins and two peptides in solution indicate that refined treatments of backbone dihedral angles lead to substantial improvements of the simulations. Being much simpler, the analytical terms perform as good as or even slightly better than the exact numerical corrections. Although using off‐center charges brought some improvements, the directionality of hydrogen bonds have not been significantly improved. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009
Performance of density functional models to reproduce observed 13Cα chemical shifts of proteins in solution
Authors: Vila Jorge A. , Baldoni Héctor A. , Scheraga Harold A. 
Published: September 2008

AbstractThe purpose of this work is to test several density functional models (namely, OPBE, O3LYP, OPW91, BPW91, OB98, BPBE, B971, OLYP, PBE1PBE, and B3LYP) to determine their accuracy and speed for computing 13Cα chemical shifts in proteins. The test is applied to 10 NMR‐derived conformations of the 76‐residue α/β protein ubiquitin (protein data bank id 1D3Z). With each functional, the 13Cα shielding was computed for 760 amino acid residues by using a combination of approaches that includes, but is not limited to, treating each amino acid X in the sequence as a terminally blocked tripeptide with the sequence Ac‐GXG‐NMe in the conformation of the regularized experimental protein structure. As computation of the 13Cα chemical shifts, not their shielding, is the main goal of this work, a computation of the 13Cα shielding of the reference, namely, tetramethylsilane, is investigated here and an effective and a computed tetramethylsilane shielding value for each of the functionals is provided. Despite observed small differences among all functionals tested, the results indicate that four of them, namely, OPBE, OPW91, OB98, and OLYP, provide the most accurate functionals with which to reproduce observed 13Cα chemical shifts of proteins in solution, and are among the faster ones. This study also provides evidence for the applicability of these functionals to proteins of any size or class, and for the validation of our previous results and conclusions, obtained from calculations with the slower B3LYP functional. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009
One‐electron spin‐orbit contribution by effective nuclear charges
Authors: Chiodo Sandro G. , Russo Nino 
Published: September 2008

AbstractEffective nuclear charges of the main group elements from the second up to the fifth row have been developed for the one‐electron part of the spin‐orbit (SO) coupling Hamiltonian. These parameters, suitable to be used for SO calculations of large molecular systems, provide a useful and remarkably good approximation to the full SO Hamiltonian. We have derived atomic effective nuclear charges by fitting procedure. Computed fine‐structure splitting (FSS) of the doublet and triplet II states of AH species (A is one of the abovementioned elements) have been chosen for this purpose. We have adopted the noniterative scheme, previously reported, according to which SO contributions can be calculated through direct coupling between the II states. The latter have been optimized at B3LYP level using DZVP basis sets. As surrogates for a large number of possible applications, we have widely employed the empirical parameters to compute II‐FSSs of diatomic species for which experimental data are available. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009
Gadd45 modulation of intrinsic and extrinsic stress responses in myeloid cells
Authors: Hoffman Barbara , Liebermann Dan A. 
Published: September 2008

AbstractGadd45 proteins modulate signaling in response to physiological and environmental stressors. Expression of gadd45 genes is rapidly induced by different stressors, including differentiation‐inducing cytokines and genotoxic stress. Induction of gadd45 genes at the onset of myeloid differentiation suggested that Gadd45 protein(s) play a role in hematopoiesis, yet no apparent abnormalities were observed in either the bone marrow (BM) or peripheral blood compartments of mice deficient for either gadd45a or gadd45b. However, under conditions of hematological stress, including acute stimulation with cytokines, myelo‐ablation and inflammation, both gadd45a‐deficient and gadd45b‐deficient mice exhibited deficiencies. This is discussed within the context of what is known about Gadd45 proteins in stress signaling, hematopoietic development and the innate immune response. Furthermore, myeloid enriched BM cells from gadd45a and gadd45b deficient mice were observed to be more sensitive to ultraviolet radiation (UVC), VP‐16 and daunorubicin (DNR) induced apoptosis compared to wild‐type (WT) cells, displaying defective G2/M arrest following exposure to UVC and VP‐16, but not to DNR. Novel mechanisms that mediate the pro‐survival functions of Gadd45 in hematopoietic cells following UV irradiation were demonstrated, involving activation of the Gadd45a‐p38‐NF‐κB survival pathway and Gadd45b mediated inhibition of the stress response MKK4‐JNK apoptotic pathway. The ramifications regarding the pathogenesis of different leukemias and the response of normal and malignant hematopoietic cells to chemo‐ and radiation‐therapy, as well as other challenges to the hematopoietic compartment, are discussed. J. Cell. Physiol. 218: 26–31, 2009. © 2008 Wiley‐Liss, Inc.
The ING gene family in the regulation of cell growth and tumorigenesis
Authors: Coles Andrew H. , Jones Stephen N. 
Published: September 2008

AbstractThe five members of the inhibitor of growth (ING) gene family have garnered significant interest due to their putative roles as tumor suppressors. However, the precise role(s) of these ING proteins in regulating cell growth and tumorigenesis remains uncertain. Biochemical and molecular biological analysis has revealed that all ING members encode a PHD finger motif proposed to bind methylated histones and phosphoinosital, and all ING proteins have been found as components of large chromatin remodeling complexes that also include histone acetyl transferase (HAT) and histone deacetylase (HDAC) enzymes, suggesting a role for ING proteins in regulating gene transcription. Additionally, the results of forced overexpression studies performed in tissue culture have indicated that several of the ING proteins can interact with the p53 tumor suppressor protein and/or the nuclear factor‐kappa B (NF‐κB) protein complex. As these ING‐associated proteins play well‐established roles in numerous cell processes, including DNA repair, cell growth and survival, inflammation, and tumor suppression, several models have been proposed that ING proteins act as key regulators of cell growth not only through their ability to modify gene transcription but also through their ability to alter p53 and NF‐κB activity. However, these models have yet to be substantiated by in vivo experimentation. This review summarizes what is currently known about the biological functions of the five ING genes based upon in vitro experiments and recent mouse modeling efforts, and will highlight the potential impact of INGs on the development of cancer. J. Cell. Physiol. 218: 45–57, 2009. © 2008 Wiley‐Liss, Inc.
Conjunctival sac fluid contains elevated levels of soluble TRAIL: Implications for the anti‐tumoral surveillance of the anterior surface of the eye
Authors: Secchiero Paola , Lamberti Giuseppe , Corallini Federica , Melloni Elisabetta , Guarnotta Carla , Sebastiani Adolfo , Zauli Giorgio 
Published: September 2008

AbstractLittle is known on the ability of different epithelia to release soluble TNF‐related apoptosis‐inducing ligand (TRAIL) and the relevance of TRAIL secretion by epithelial cells is still incompletely understood. On these bases, we have measured the concentration of soluble TRAIL by ELISA in the conjunctival sac fluid. It was the highest ever detected in a biological fluid (mean value of 26,800 pg/ml), being approximately 20‐fold greater than that found in human saliva and >200‐fold greater than that detected in human serum. On the other hand, osteoprotegerin, the soluble decoy receptor of TRAIL, was almost undetectable in the conjunctival sac fluid. Of note, the levels of soluble TRAIL measured in conjunctival sac fluid were in the range able to induce in vitro apoptosis of lymphoma cells. By in situ immunohistochemistry, TRAIL protein expression was predominantly detected in the corneal epithelium and, to a less extent, in the conjunctival epithelium. By flow cytometry analysis, membrane‐associated TRAIL was documented in isolated corneal epithelial cells obtained from patients undergoing photorefractive keratectomy (PRK). The key contribution provided by corneal epithelium to the production of soluble TRAIL was underscored in time‐course experiments, in which a marked decrease of the levels of soluble TRAIL in the conjunctival sac fluid was demonstrated 1 day after PRK followed by a progressive recovery at days 5–30 after PRK. Taken together, our findings strongly support a major role of soluble TRAIL in protecting cornea and conjunctiva from tumor formation and/or invasion. J. Cell. Physiol. 218: 199–204, 2009. © 2008 Wiley‐Liss, Inc.