bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alendronate regulates cell invasion and MMP‐2 secretion in human osteosarcoma cell lines
Authors: Cheng Y.Y. , Huang L. , Lee K.M. , Li K. , Kumta S.M. 
Published: March 2004

AbstractBackgroundOsteosarcoma is the most common malignant bone tumor of childhood. Significant proportions of these patients eventually develop pulmonary metastases and succumb to their disease even after conventional multi‐agent chemotherapy and surgical excision. Matrix metalloproteinase (MMP)‐2 induced degradation of blood vessel basement membranes is an important pre‐requisite for tumor invasion and metastasis. Bisphosphonates (BPs) have been known to inhibit tumor growth and metastasis in some tumors such as breast cancer, renal cell carcinoma, and prostate cancer, and may do so through inhibition of MMP secretion. We, therefore, tested the effect of BPs on tumor cell invasion, MMP‐2 secretion, and apoptosis of osteosarcoma cell lines.ProcedureTwo osteosarcoma cell lines (SaOS‐2, U2OS) were treated with alendronate (50, 100, and 150 μM) for 24 and 48 hr. Matrigel invasion assay was used to investigate the invasive potential of osteosarcoma cell lines before and after alendronate treatment. Real‐time quantitative RT‐PCR was used to determine the mRNA level of MMP‐2 with and without alendronate treatment. Enzyme‐linked immunosorbent assay (ELISA) was used to quantify the cytokine level of MMP‐2 secreted in the condition medium. BP‐induced cell apoptosis was evaluated by fluorescent flow cytometric analysis.Results and ConclusionsThe results showed that alendronate inhibited cell invasion of both osteosarcoma cell lines in a dose‐dependent manner. Alendronate reduced the mRNA level and cellular level of MMP‐2 in both cell lines in a time and dose‐dependent manner. Alendronate also induced significant apoptosis in both cell lines. Our finding suggests that alendronate downregulates MMP‐2 secretion and induces apoptosis in osteosarcoma cells, which may both contribute to the reduction of invasive potential of the tumor cells. © 2004 Wiley‐Liss, Inc.
Fetal open spina bifida: a natural history of disease progression in utero
Authors: Biggio Joseph R. , Wenstrom Katharine D. , Owen John 
Published: March 2004

AbstractObjectiveTo determine the natural history of the prenatal development of ventriculomegaly and talipes in fetuses with open spina bifida.Study designAll fetuses with isolated open spina bifida and managed at our center between January 1996 and March 2000 were retrospectively evaluated. Ultrasonographic images and reports were reviewed from examinations performed every 3 to 4 weeks from the time of diagnosis to delivery for lesion level and type, ventriculomegaly (defined as an atrial width of ≥10 mm), and lower extremity appearance.ResultsOf the 53 pregnancies identified, 20 (38%) were electively terminated. In the 33 ongoing gestations, the lesions ranged from lower thoracic to sacral; 79% were characterized as meningomyeloceles and 21% as myeloschises. Fifty‐five percent (n = 18) had ventriculomegaly at diagnosis (early onset, mean gestational age at diagnosis 22 ± 5 weeks), 33% (n = 11) subsequently developed ventriculomegaly (late onset, mean 29 ± 6 weeks), and 12% (n = 4) had normal ventricle size at the last sonogram before birth (mean 38 ± 1 weeks). The ventricular size prior to delivery was significantly smaller with late‐onset ventriculomegaly than with early‐onset: 15 ± 4 mm versus 28 ± 10 mm, (p = 0.001). Only 6% (n = 2) had talipes at the initial sonogram, and 18% (n = 6) were subsequently determined to have talipes (mean 30 ± 6 weeks).ConclusionMost fetuses with open spina bifida develop ventriculomegaly, and the majority do so by 21 weeks' gestation. Fetuses that develop ventriculomegaly later in gestation have less severe ventricular dilation at birth. In contrast, a minority of fetuses have congenital talipes, and because most cases develop after 20 weeks, they are not predicted by early midtrimester sonographic evaluation. Copyright © 2004 John Wiley & Sons, Ltd.
Structural organization and drawability in polyamide blends
Authors: Persyn O. , Miri V. , Lefebvre J. M. , Depecker C. , Gors C. , Stroeks A. 
Published: March 2004

AbstractThe thermal behavior of polyamide 6/amorphous polyamide blends has been investigated as a function of blend composition and temperature. Crystal phase nature and stability are probed by a combination of thermal analysis, X‐ray diffraction and Fourier transform infrared spectroscopy. Ductility appears to be strongly affected by the addition of the amorphous polyamide, but the corresponding decrease of the yield stress, either taken at the same draw temperature or under a comparable state of mobility of the amorphous phase, may not be simply accounted for by the reduction of overall ordered phase content.
Bubble removal in rotational molding
Authors: Gogos George 
Published: March 2004

AbstractClosed form solutions have been obtained for bubble dissolution in typical polymer melts encountered in rotational molding. The solutions are in excellent agreement with experimental data available in the literature. Using these solutions, it is shown that under typical rotational molding conditions the polymer melts may be almost saturated. As a result, bubble shrinkage occurs over long periods. Depending on the degree of saturation, surface tension may contribute substantially to the concentration gradient that drives bubble shrinkage. It is also shown that a pressure increase imposed on a nearly saturated polymer melt leads to a steep concentration gradient at the bubble/melt interface that can cause extremely fast bubble shrinkage. Applied to the rotational molding process, such a pressure increase can result in substantial cycle‐time shortening through elimination (or reduction) of the currently used excessive heating. A further benefit may be that additional resins, which at present cannot be used because of oxidation at sustained high‐temperatures, can become available to the rotational molding industry. Under the under‐saturated conditions created by a pressure increase, the effect of surface tension on the rate of bubble shrinkage is negligible.
Effect of high concentration of Co (II) on Enterobacter liquefaciens strain C‐1: A bacterium highly resistant to heavy metals with an unknown genome.
Authors: Marrero Jeannette , González Luis Javier , Sánchez Aniel , Ayala Marta , Paz‐Lago Dalila , González Wendy , Fallarero Adyary , Castellanos‐Serra Lila , Coto Orquídea 
Published: March 2004

AbstractHeavy metals are required as nutrients for essential functions in microorganisms. However, higher concentrations of these cations are generally toxic and may produce contrasting effects on living organisms. Enterobacter liquefaciens strain C‐1, a bacterium isolated from the Moa mine in Cuba, is able to survive in the presence of high concentrations of heavy metals. The proteomes of Enterobacter liquefaciens strain C‐1, grown under aerobic conditions in the presence and absence of Co (II) were compared using two‐dimensional gel electrophoresis analysis in the isoelectric point range of 4–7 and the mass range of 15–120 kDa. Significant changes in the expression level (> two‐fold) were detected for 13 spots: seven and six were up‐ and down‐regulated, respectively. Because the genome of this bacterium is unknown, identification by peptide mass fingerprinting only succeeded in four cases and most of the cross‐species identifications were supported by de novo sequencing of tryptic peptides followed by sequence alignment using the MS BLAST program. Twelve different proteins were identified, ten are involved in cellular antioxidant defence probably induced by the presence of Co (II). This is the first step towards understanding the role of proteins participating in the mechanism of resistance to heavy metals in this bacterium.
Proteomics analysis of human endothelial cell line EA.hy926 after exposure to GSM 900 radiation
Authors: Nylund Reetta , Leszczynski Dariusz 
Published: March 2004

AbstractThe human endothelial cell line EA.hy926 was exposed to mobile phone radiation and the effect on protein expression was examined using two‐dimensional electrophoresis (2‐DE). Up to 38 various proteins have statistically significantly altered their expression levels following the irradiation. Four proteins were identified with matrix‐assisted laser desorption/ionization‐mass spectrometry (MALDI‐MS). Two of the affected proteins were determined to be isoforms of cytoskeletal vimentin. This finding supports our earlier presented working hypothesis which indicated that the mobile phone radiation might affect the cytoskeleton and might have an effect on the physiological functions that are regulated by the cytoskeleton.
Selective growth of epithelial basal cells from human prostate in a three‐dimensional organ culture
Authors: Papini Sandra , Rosellini Alfredo , Campani Daniela , DeMatteis Anna , Selli Cesare , Revoltella Roberto Paolo 
Published: March 2004

AbstractBACKGROUNDA three‐dimensional organotypic culture method has been developed for selectively growing epithelial basal cells from human benign prostate.METHODSTissue fragments were cultured on sponges for several weeks and the viability of luminal and basal epithelium and cellular responses to 4,5α‐dihydrotesterone (DHT) stimulation were studied.RESULTSThe gland tissue could be successfully maintained showing preservation of ducts and lobules as in vivo. Without DHT, a progressive hyperplasia of basal cells was observed: these cells proliferated with retention of the lumen or forming nests with squamous differentiation, lining the surface of the fragment and migrating to the underlying sponge. In contrast, secretory cells disappeared. Epithelial cells isolated from long‐term cultures showed a typical basal cell‐immunophenotype. DHT‐treated tissues maintained a much higher percentage of luminal cells than untreated tissues.CONCLUSIONSThese systems allow the study of proliferation and differentiation of basal cells within their natural microenvironment as well as prostate pathobiology. © 2004 Wiley‐Liss, Inc.
The extended left‐handed helix: A simple nucleic acid‐binding motif
Authors: Hicks Joshua M. , Hsu Victor L. 
Published: March 2004

AbstractThe poly‐proline type II extended left‐handed helical structure is well represented in proteins. In an effort to determine the helix's role in nucleic acid recognition and binding, a survey of 258 nucleic acid‐binding protein structures from the Protein Data Bank was conducted. Results indicate that left‐handed helices are commonly found at the nucleic acid interfacial regions. Three examples are used to illustrate the utility of this structural element as a recognition motif. The third K homology domain of NOVA‐2, the Epstein‐Barr nuclear antigen‐1, and the Drosophila paired protein homeodomain all contain left‐handed helices involved in nucleic acid interactions. In each structure, these helices were previously unidentified as left‐handed helices by secondary structure algorithms but, rather, were identified as either having small amounts of hydrogen bond patterns to the rest of the protein or as being “unstructured.” Proposed mechanisms for nucleic acid interactions by the extended left‐handed helix include both nonspecific and specific recognition. The observed interactions indicate that this secondary structure utilizes an increase in protein backbone exposure for nucleic acid recognition. Both main‐chain and side‐chain atoms are involved in specific and nonspecific hydrogen bonding to nucleobases or sugar‐phosphates, respectively. Our results emphasize the need to classify the left‐handed helix as a viable nucleic acid recognition and binding motif, similar to previously identified motifs such as the helix‐turn‐helix, zinc fingers, leucine zippers, and others. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Identification of structural proteins from shrimp white spot syndrome virus (WSSV) by 2DE‐MS
Authors: Zhang Xiaobo , Huang Canhua , Tang Xuhua , Zhuang Ying , Hew Choy Leong 
Published: March 2004

AbstractWhite spot syndrome virus (WSSV) is a major shrimp pathogen that also infects many other species of crustaceans. Its 305‐kb double‐stranded DNA genome has the capacity to encode 181 presumptive proteins. In an attempt to identify the viral proteins from the 181 theoretical proteins, proteins of the purified WSSV were separated by two‐dimensional electrophoresis (2‐DE). More than 60 protein spots were revealed, as detected by silver staining, from which 12 viral proteins were identified by mass spectrometry. In total, 25 WSSV proteins, including those reported in one of our earlier studies (Huang et al., Mol Cell Proteomics 2002;1:223–231), were revealed by this proteomic approach, and their corresponding genes were further confirmed by reverse transcription‐polymerase chain reaction (RT‐PCR). Two of them were characterized to be WSSV envelope proteins using immuno‐electron microscopy. Our study showed that the proteomic approach is a powerful method for discovering the viral structural proteins and their corresponding genes. Proteins 2004;9999:000–000. © 2004 Wiley‐Liss, Inc.
High‐resolution prediction of protein helix positions and orientations
Authors: Li Xin , Jacobson Matthew P. , Friesner Richard A. 
Published: March 2004

AbstractWe have developed a new method for predicting helix positions in globular proteins that is intended primarily for comparative modeling and other applications where high precision is required. Unlike helix packing algorithms designed for ab initio folding, we assume that knowledge is available about the qualitative placement of all helices. However, even among homologous proteins, the corresponding helices can demonstrate substantial differences in positions and orientations, and for this reason, improperly positioned helices can contribute significantly to the overall backbone root‐mean‐square deviation (RMSD) of comparative models. A helix packing algorithm for use in comparative modeling must obtain high precision to be useful, and for this reason we utilize an all‐atom protein force field (OPLS) and a Generalized Born continuum solvent model. To reduce the computational expense associated with using a detailed, physics‐based energy function, we have developed new hierarchical and multiscale algorithms for sampling the helices and flanking loops. We validate the method using a test suite of 33 cases, which are drawn from a diverse set of high‐resolution crystal structures. The helix positions are reproduced with an average backbone RMSD of 0.6 Å, while the average backbone RMSD of the complete loop–helix–loop region (i.e., the helix with the surrounding loops, which are also repredicted) is 1.3 Å. Proteins 2004;55:000–000. © 2004 Wiley‐Liss, Inc.
A novel method of resistance for influenza against a channel‐blocking antiviral drug
Authors: Astrahan Peleg , Kass Itamar , Cooper Matthew A. , Arkin Isaiah T. 
Published: March 2004

AbstractEffective antivirals are few and far between, and as such, the appearance of resistance toward such treatments is an obvious medical concern. In this article, we analyze the mechanism by which influenza attains resistance toward amantadine, a blocker of the viral M2 H+ channel. Binding analyses of amantadine to M2 peptides from different viral strains showed that the virus has developed two alternate routes to avoid blockage of its channel: (1) a conventional route, in which the channel no longer binds the blocker and, hence, the blocker cannot exert its inhibitory function; and (2) a novel mechanism, in which binding of the blocker is retained, yet the function of the protein is unaffected. Pore diameter profiles revealed the molecular mechanism by which the virus may attain this novel type of resistance: an increase in the size of the channel. Thus, despite the drug binding the channel, it may not be able to block the pore, since the channel diameter has increased. Our findings may have broad ramifications in the design of new antivirals, and of novel blockers against malfunctioning human channels implicated in disease. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Analysis of CDK2 active‐site hydration: A method to design new inhibitors
Authors: Kříž Zdeněk , Otyepka Michal , Bártová Iveta , Koča Jaroslav 
Published: March 2004

AbstractThe interactions between the protein and the solvent were analyzed, and protein regions with a high density of water molecules, as well as structural water molecules, were determined by using molecular dynamics (MD) simulations. A number of water molecules that were in contact with the protein for the whole trajectory were determined. Their interaction energies and hydrogen bonds with protein residues were analyzed. Altogether, 39, 27, 49, and 32 water molecules bound to the protein were found for trajectories of the free CDK2, CDK2/ATP, CDK2/roscovitine, and CDK2/isopentenyladenine complexes, respectively. Positions of observed water molecules were compared with X‐ray crystallography data. Special attention was paid to water molecules in the active site of the enzyme, and especially to the deep pocket, where the N9 roscovitine side‐chain is buried. Exchange of active‐site water molecules with bulk water through the tunnel from the pocket was observed. In the CDK2/isopentenyladenine complex simulation, two water molecules that arrange interaction between the inhibitor and the enzyme via an H‐bond were observed. Two stable water molecules in the trajectory of the free CDK2 were found that occupy the same position as the nitrogens N3 and N9 of the isopentenyladenine or N1 and N6 nitrogens of the adenosine triphosphate (ATP). The positions of structural water molecules were compared with the positions of substrate polar groups and crystallographic water molecules found in the Brookhaven Protein Data Bank for various CDK2 complexes. It was concluded that tracing tightly bound water molecules may substantially help in designing new inhibitors. Proteins 2004. © 2004 Wiley‐Liss, Inc.
The mechanism of proton exclusion in aquaporin channels
Authors: Ilan Boaz , Tajkhorshid Emad , Schulten Klaus , Voth Gregory A. 
Published: March 2004

AbstractThe mechanism of proton exclusion in aquaporin channels is elucidated through free energy calculations of the pathway of proton transport. The second generation multistate empirical valence bond (MS‐EVB2) model was applied to simulate the interaction of an excess proton with the channel environment. Jarzynski's equality was employed for rapid convergence of the free energy profile. A barrier sufficiently high to block proton transport is located near the channel center at the NPA motif—a site involved in bi‐orientational ordering of the embedded water‐wire in absence of the excess proton. A second and lower barrier is observed at the selectivity filter near the periplasmic outlet where the channel is narrowest. This secondary barrier may be essential in filtering other large solutes and cations. Proteins 2004;9999:000–000. © 2004 Wiley‐Liss, Inc.
Different propensity to form amyloid fibrils by two homologous proteins—Human stefins A and B: Searching for an explanation
Authors: Jenko Saša , Škarabot Miha , Kenig Manca , Gunčar Gregor , Muševič Igor , Turk Dušan , Žerovnik Eva 
Published: March 2004

AbstractBy using ThT fluorescence, X‐ray diffraction, and atomic force microscopy (AFM), it has been shown that human stefins A and B (subfamily A of cystatins) form amyloid fibrils. Both protein fibrils show the 4.7 Å and 10 Å reflections characteristic for cross β‐structure. Similar height of ∼3 nm and longitudinal repeat of 25–27 nm were observed by AFM for both protein fibrils. Fibrils with a double height of 5.6 nm were only observed with stefin A. The fibril's width for stefin A fibrils, as observed by transmission electron microsopy (TEM), was in the same range as previously reported for stefin B (Žerovnik et al., Biochem Biophys Acta 2002;1594:1–5). The conditions needed to undergo fibrillation differ, though. The amyloid fibrils start to form at pH 5 for stefin B, whereas in stefin A, preheated sample has to be acidified to pH < 2.5. In both cases, adding TFE, seeding, and alignment in a strong magnetic field accelerate the fibril growth. Visual analysis of the three‐dimensional structures of monomers and domain‐swapped dimers suggests that major differences in stability of both homologues stem from arrangement of specific salt bridges, which fix α‐helix (and the α‐loop) to β‐sheet in stefin A monomeric and dimeric forms. Proteins 2004;55:000–000. © 2004 Wiley‐Liss, Inc.
New vision of emergency response planning
Authors: Al‐qurashi Fahad 
Published: March 2004

AbstractIn an emergency situation, seconds can mean the difference between relief and tragedy. Important information must be presented clearly and cohesively to enable decision making under crisis conditions.This paper describes a project in which an Emergency Response System (ERS) has been developed for the Uthmaniyah gas plant (UGP). The ERS is essentially made up of two applications: the SAFER Real‐Time application made by SAFER Systems of the United States and a customized Geographical Information System (GIS) application developed by the Saudi Aramco Information Technology group. The SAFER system provides the user with immediate plume graphics based on local topography, maps, real‐time weather, chemical release specifics, and gas sensors data. This information is fed to a scientific gas dispersion model to predict the movement and concentration of gas or liquid release. The GIS allows the effect of the plume on people and structures to be analyzed in detail. Combined together, the ERS provides a tool for modeling and monitoring an accidental release. It will improve emergency planning, decision making, and response within the UGPD.The above information is shared with emergency responders such as the fire department, security, and medical personnel via the network. As a result, they would dispatch their resources via the safest route. As weather conditions change, the plume dispersion will change and, hence, emergency response efforts will shift accordingly. © 2004 American Institute of Chemical Engineers Process Saf Prog 23: 56–61, 2004
Ferromagnetism of amorphous LaCo2 hydride
Authors: Nakamura H. , Nakahara A. , Shiga M. , Ito K. , Yamaguchi M. , Tsvyashchenko A. V. , Fomicheva L. N. 
Published: March 2004

AbstractMagnetic properties of hydrogen‐amorphized LaCo2 with a relatively high hydrogen concentration, LaCo2H3.8, were investigated by magnetization and NMR measurements. The hydride behaves as a ferromagnet with TC = 400–500 K and averaged moment ∼0.5 μB/Co (at 1.5 K). The Co moment amplitude was found to distribute considerably from 0 to ∼1 μB. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Specific heat anomalies in ferroelectrics LiNaGe4O9 and Li1.1Na0.9Ge4O9
Authors: Cach R. , Cebula I. , Volnyanskii M. D. 
Published: March 2004

AbstractThe heat capacity of LiNaGe4O9 and Li1.1Na0.9Ge4O9 crystals has been measured using AC calorimetry method. It is shown, that the temperature evolution of the excess heat capacity and the excess entropy of both crystals, in the ferroelectric phase, can be described by the formulas resulting from the classical Landau theory of phase transition. The values of the Landau expansion coefficients are determined. The obtained results lead to the conclusion that the spontaneous polarization can be reckoned as an order parameter in the phase transition of the weak ferroelectric LiNaGe4O9. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)