bluuebunny/crossref_metadata_2025_split huggingface dataset:
The interactive online SKY/M‐FISH & CGH Database and the Entrez Cancer Chromosomes search database: Linkage of chromosomal aberrations with the genome sequence
Authors: Knutsen Turid , Gobu Vasuki , Knaus Rodger , Padilla‐Nash Hesed , Augustus Meena , Strausberg Robert L. , Kirsch Ilan R. , Sirotkin Karl , Ried Thomas 
Published: June 2005

AbstractTo catalog data on chromosomal aberrations in cancer derived from emerging molecular cytogenetic techniques and to integrate these data with genome maps, we have established two resources, the NCI and NCBI SKY/M‐FISH & CGH Database and the Cancer Chromosomes database. The goal of the former is to allow investigators to submit and analyze clinical and research cytogenetic data. It contains a karyotype parser tool, which automatically converts the ISCN short‐form karyotype into an internal representation displayed in detailed form and as a colored ideogram with band overlay, and also has a tool to compare CGH profiles from multiple cases. The Cancer Chromosomes database integrates the SKY/M‐FISH & CGH Database with the Mitelman Database of Chromosome Aberrations in Cancer and the Recurrent Chromosome Aberrations in Cancer database. These three datasets can now be searched seamlessly by use of the Entrez search and retrieval system for chromosome aberrations, clinical data, and reference citations. Common diagnoses, anatomic sites, chromosome breakpoints, junctions, numerical and structural abnormalities, and bands gained and lost among selected cases can be compared by use of the “similarity” report. Because the model used for CGH data is a subset of the karyotype data, it is now possible to examine the similarities between CGH results and karyotypes directly. All chromosomal bands are directly linked to the Entrez Map Viewer database, providing integration of cytogenetic data with the sequence assembly. These resources, developed as a part of the Cancer Chromosome Aberration Project (CCAP) initiative, aid the search for new cancer‐associated genes and foster insights into the causes and consequences of genetic alterations in cancer. Published 2005 Wiley‐Liss, Inc.
In vivo imaging of neuromodulatory synaptic transmission using PET: A review of relevant neurophysiology
Authors: Fisher Ronald E. , Morris Evan D. , Alpert Nathaniel M. , Fischman Alan J. 
Published: May 2005

AbstractRecent data from positron emission tomography (PET) imaging studies suggest the possibility of studying synaptic transmission in vivo in humans. The approach will require a synthesis of two established techniques: brain activation studies (conventionally performed by measuring regional cerebral blood flow or metabolism) and neurotransmitter receptor imaging (using radiolabelled ligands that bind to specific neuroreceptors). By comparing neuroreceptor binding in subjects at rest and while performing an activation task, it may be possible to determine whether a particular neurotransmitter is involved in performance of the task. The underlying principle is that endogenous neurotransmitter competes with the injected radioligand for the same receptors, thereby inhibiting ligand binding. This effect will be even more pronounced during activation, as the synaptic concentration of transmitter rises. Thus, activation of a specific neurotransmitter will be detected as a decrease in specific binding of the radioligand. In this paper we review neurophysiological and biochemical literature to estimate the endogenous neurotransmitter concentration changes that will be expected to occur during an activation task, using the dopamine system as an example. We calculate that the average synaptic dopamine concentration is ≈ 100 nM and that it approximately doubles during activation. This, along with consideration of the concentration of radioligand and affinities of the ligand and dopamine for dopamine receptors, suggests that physiological activation of a specific neurotransmitter system is likely to be detectable with PET. © 1995 Wiley‐Liss, Inc.
Regulation of rCBF by diffusible signals: An analysis of constraints on diffusion and elimination
Authors: Friston K. J. 
Published: May 2005

AbstractLocal changes in cerebral hemodynamics are observed within a few hundred milliseconds of changes in neural activity. If hemodynamic responses are mediated by passive diffusion of a spatial signal (from the site of neural activity to the microvessels) then the dynamics of the response suggest a lower limit on the signal's apparent diffusion and elimination. The aim of this work was to estimate these limits and narrow the field of possible candidate substances.A simple biophysical simulation was used to examine how the time course of concentration changes in a spatial signal, at the site of action (microvessels), depends on key diffusion parameters (source geometry, apparent diffusion and elimination half‐life). The simulations suggested (1) that the rise in signal concentration is mostly a function of source geometry and diffusion. Conversely falls in concentration depend on elimination and (2) even when sources are very sparsely distributed Nitric Oxide would have a sufficiently fast diffusion and elimination to signal the early components of activity‐dependent hemodynamic response by passive diffusion. © 1995 Wiley‐Liss, Inc.
Surface modification of interconnected porous scaffolds
Authors: Liu Xiaohua , Won Youngjun , Ma Peter X. 
Published: June 2005

AbstractSurface properties of scaffolds play an important role in cell adhesion and growth. Biodegradable poly(α‐hydroxy acids) have been widely used as scaffolding materials for tissue engineering; however, the lack of functional groups is a limitation. In this work, gelatin was successfully immobilized onto the surface of poly(α‐hydroxy acids) films and porous scaffolds by a new entrapment process. The surface composition and properties were examined using attenuated total reflection–Fourier transform infrared spectroscopy (ATR‐FTIR), X‐ray photoelectron spectra (XPS), and contact angle measurements. Control over the amount of entrapped gelatin was achieved by varying the solvent composition, the duration of soaking, the concentration of gelatin in solution, and chemical crosslinking. The amount of entrapped gelatin increased with the ratio of dioxane/water in the solvent mixture used. Chemical crosslinking after physical entrapment considerably increased the amount of retained gelatin on the surface of poly(α‐hydroxy acids). Osteoblasts were cultured on these films and scaffolds. The surface modification significantly improved cell attachment and proliferation. Cell numbers on the surface‐modified films and scaffolds were significantly higher than those on controls 4 h and 1 day after cell seeding. The osteoblasts showed higher proliferation on surface‐modified scaffolds than on the control during 4 weeks of in vitro cultivation. More collagen fibers and other cell secretions were deposited on the surface‐modified scaffolds than on the control scaffolds. This novel surface treatment strategy provides a convenient and universal way to modify the surface properties of three‐dimensional scaffolds and thus promote cell adhesion and proliferation for tissue engineering. © 2005 Wiley Periodicals, Inc. J Biomed Mater Res, 2005
Comparison of one‐dimensional and two‐dimensional functionally graded materials for the backing shell of the cemented acetabular cup
Authors: Hedia H. S. 
Published: June 2005

AbstractAmong the factors that have been suggested as contributing to the failure of a total joint replacement are stress shielding and the subsequent bone resorption. Recent studies have shown that when a backing shell made from a Ti alloy is used, high stresses are generated in the cement at the edges of the cup, and low stresses are generated at the dome of the bone in the acetabulum; thus, the bone at the dome suffers stress shielding and the cement edge suffers high stresses. The aim of this study was to investigate the effect of using a functionally graded material (FGM), instead of Ti alloy, for the backing shell (BS) on the stress distribution in the BS–cement–bone system. Finite‐element and optimization techniques were used to obtain the optimal distribution of materials in the tangential direction only of the backing (1D FGM) as well as in the tangential and radial directions of the backing (2D FGM). It was found that the stress distribution in the BS–cement–bone system was about the same, regardless of whether the BS was fabricated from a 1D or 2D FGM. The stress‐shielding factor in the bone at the dome of the acetabulum and the maximum von Mises stress in cement at the cement interfaces for 1D and 2D FGM were reduced by about 51%, 69%, and 50%, respectively, compared to the case when the shell was fabricated from a Ti alloy. The optimal elastic modulus of the 1D FGM was obtained with the materials graded from HA at the dome of the acetabulum to a Ti alloy at the rim of the shell. The optimal elastic modulus of the 2D FGM was obtained with the materials graded from Ti alloy at the right edge of the rim, to Bioglass 45S5 at the left edge of the rim, and to HA at the dome of the shell. © 2005 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2005
Protective effect of NAC on formaldehyde‐containing–ZOE‐based root‐canal‐sealers–induced cyclooxygenase‐2 expression and cytotoxicity in human osteoblastic cells
Authors: Huang Fu‐Mei , Chou Lin Shin‐Shen , Chou Ming‐Yung , Chang Yu‐Chao 
Published: June 2005

AbstractCyclooxygenase‐2 (COX‐2) is an inducible enzyme believed to be responsible for prostaglandin synthesis at site of inflammation. Recently, the activation of COX‐2 expression may be one of the important pathogenesis of root‐canal‐sealers–induced periapical inflammation. However, little is known about whether chemical interaction can modulate the COX‐2 expression and cytotoxicity induced by formaldehyde‐containing–ZOE‐based root canal sealers. The aim of this study was to investigate the effects of antioxidants such as catalase, superoxide dismutase (SOD), and N‐acetyl‐L‐cysteine (NAC) on N2‐ and endomethasone‐induced COX‐2 mRNA gene and cytotoxicity in human osteoblastic cell line U2OS cells. Our data demonstrated that both formaldehyde‐containing–ZOE‐based root canal sealers were found to induce COX‐2 mRNA gene expression in U2OS cells. The addition of glutathione (GSH) precursor NAC led to decrease the induction of COX‐2 mRNA gene expression and cytotoxicity by both N2 and Endomethasone (p < 0.05). However, catalase and SOD lacked the ability to prevent cytotoxicity and COX‐2 mRNA gene expression induced by N2 and Endomethasone (p > 0.05). The data presented here demonstrated that the activation of COX‐2 mRNA gene expression may be one of the pathogenesis of formaldehyde‐containing–ZOE‐based root‐canal‐sealers–induced periapical inflammation. In addition, GSH depletion, but not the attack of oxygen free radicals, could be the mechanism for cytotoxicity and COX‐2 mRNA gene expression induced by formaldehyde‐containing–ZOE‐based root canal sealers. NAC appears as a useful agent in protecting cell damage mediated by formaldehyde‐containing–ZOE‐based root canal sealers. © 2005 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2005
Histone H4 post‐translational modifications in chordate mitotic and endoreduplicative cell cycles
Authors: Spada Fabio , Chioda Mariacristina , Thompson Eric M. 
Published: June 2005

AbstractHistone post‐translational modifications mark distinct structural and functional chromatin states but little is known of their involvement in the progression of different cell cycle types across phylogeny. We compared temporal and spatial dynamics of histone H4 post‐translational modifications during both mitotic and endoreduplicative cycles of the urochordate, Oikopleura dioica, and proliferating mammalian cells. Endocycling cells showed no signs of chromosome condensation or entry into mitosis. They exhibited an evolution of replication patterns indicative of reduced chromatin compartmentalization relative to proliferating mammalian cells. In the latter cells, published cell cycle profiles of histone H4 acetylated at lysine 16 (H4AcK16) or dimethylated at lysine 20 (H4Me2K20) are disputed. Our results, using different, widely used H4AcK16 antibodies, revealed significant antibody‐specific discrepancies in spatial and temporal cell cycle regulation of this modification, with repercussions for interpretation of previous immunofluorescence and immunoprecipitation data based on these reagents. On the other hand, three different antibodies to H4Me2K20 revealed similar cell cycle profiles of this modification that were conserved throughout the mitotic cell cycle in urochordate and mammalian cells, with accumulation at mitosis and a decrease during S‐phase. H4Me2K20 also cycled in endocycles, indicating that dynamics of this modification are not strictly constrained by the mitotic phase of the cell cycle and suggesting additional roles during G‐ and S‐phase progression. This article contains Supplementary Material available at http://www.mrw.interscience.wiley.com/suppmat/0730‐2312/suppmat/2005/95/spada.html. © 2005 Wiley‐Liss, Inc.
Andrograpanin, a compound isolated from anti‐inflammatory traditional Chinese medicine Andrographis paniculata, enhances chemokine SDF‐1α‐induced leukocytes chemotaxis
Authors: Ji Li‐Li , Wang Zhu , Dong Fang , Zhang Wen‐Bo , Wang Zheng‐Tao 
Published: June 2005

AbstractAndrographis paniculata is a traditional Chinese medicine (TCM) that has been effectively used for treatment of infection, inflammation, cold, fever, and diarrhea in China. However, mechanism of its therapeutic function is not well known. In the current study, we showed one of its components, andrograpanin, could enhance chemokine stromal cell‐derived factor‐1α (SDF‐1α) induced chemotaxis in Jurkat and THP‐1 cells. Further study demonstrated that this kind of effect was CXC chemokine receptor‐4 (CXCR4) specific, since andrograpanin could not enhance other chemokines, such as RANTES, monocyte chemotactic protein‐1 (MCP‐1), etc. induced cell chemotaxis. Mechanisms of andrograpanin exerting its effect were not directly in the receptor and G protein coupling level because it had no effect on the binding of SDF‐1 to CXCR4, SDF‐1 induced G protein activation and adenyly cyclase inhibition. However, receptor internalization might be involved, since we found it significantly reduced SDF‐1α‐induced CXCR4 internalization. © 2005 Wiley‐Liss, Inc.
The ab initio limit quartic force field of BH3
Authors: Schuurman Michael S. , Allen Wesley D. , Schaefer Henry F. 
Published: June 2005

AbstractThe complete quartic force field of BH3 has been converged to the ab initio limit by extrapolation of core‐valence correlation‐consistent basis set series (cc‐pCVXZ, X = T, Q, 5) of all‐electron CCSD(T) (coupled‐cluster singles and doubles with perturbative triples) energy points. Additional computations including full coupled‐cluster treatments through quadruple excitations (CCSDTQ), scalar relativistic effects, and diagonal Born–Oppenheimer corrections (DBOC) were concurrently executed. Within second‐order vibrational perturbation theory (VPT2) our quartic force field yields the fundamental frequencies ν1 = 2502.3 cm−1, ν2 = 1147.2 cm−1, ν3 = 2602.1 cm−1, and ν4 = 1196.5 cm−1, in excellent agreement with observed gas‐phase fundamentals, displaying a mean absolute error of only 0.3 cm−1. Our converged prediction for the equilibrium bond length of BH3 is re = 1.1867 Å. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1106–1112, 2005
Representation of Zn(II) complexes in polarizable molecular mechanics. Further refinements of the electrostatic and short‐range contributions. Comparisons with parallel ab initio computations
Authors: Gresh Nohad , Piquemal Jean‐Philip , Krauss Morris 
Published: June 2005

AbstractWe present refinements of the SIBFA molecular mechanics procedure to represent the intermolecular interaction energies of Zn(II). The two first‐order contributions, electrostatic (EMTP), and short‐range repulsion (Erep), are refined following the recent developments due to Piquemal et al. (Piquemal et al. J Phys Chem A 2003, 107, 9800; and Piquemal et al., submitted). Thus, EMTP is augmented with a penetration component, Epen, which accounts for the effects of reduction in electronic density of a given molecular fragment sensed by another interacting fragment upon mutual overlap. Epen is fit in a limited number of selected Zn(II)–mono‐ligated complexes so that the sum of EMTP and Epen reproduces the Coulomb contribution Ec from an ab initio Hartree–Fock energy decomposition procedure. Denoting by S, the overlap matrix between localized orbitals on the interacting monomers, and by R, the distance between their centroids, Erep is expressed by a S2/R term now augmented with an S2/R2 one. It is calibrated in selected monoligated Zn(II) complexes to fit the corresponding exchange repulsion Eexch from ab initio energy decomposition, and no longer as previously the difference between (Ec + Eexch) and EMTP. Along with the reformulation of the first‐order contributions, a limited recalibration of the second‐order contributions was carried out. As in our original formulation (Gresh, J Comput Chem 1995, 16, 856), the Zn(II) parameters for each energy contribution were calibrated to reproduce the radial behavior of its ab initio HF counterpart in monoligated complexes with N, O, and S ligands. The SIBFA procedure was subsequently validated by comparisons with parallel ab initio computations on several Zn(II) polyligated complexes, including binuclear Zn(II) complexes as in models for the Gal4 and β‐lactamase metalloproteins. The largest relative error with respect to the RVS computations is 3%, and the ordering in relative energies of competing structures reproduced even though the absolute numerical values of the ab initio interaction energies can be as large as 1220 kcal/mol. A term‐to‐term identification of the SIBFA contributions to their ab initio counterparts remained possible even for the largest sized complexes. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1113–1130, 2005
Airway gene transfer using cationic emulsion as a mucosal gene carrier
Authors: Kim Tae Woo , Chung Hesson , Kwon Ick Chan , Sung Ha Chin , Shin Byung Chul , Jeong Seo Young 
Published: May 2005

AbstractBackgroundDelivery of genes to airway mucosa would be a very valuable method for gene therapy and vaccination. However, there have been few reports on suitable gene delivery systems for administration. In this study, we use a cationic emulsion system, which is physically stable and facilitates the transfer of genes in the presence of up to 90% serum, as a mucosal gene carrier.Methods and resultsCationic lipid emulsion was formulated with squalene and 1,2‐dioleoyl‐sn‐glycero‐3‐trimethylammoniumpropane (DOTAP) as major components. Emulsions formed stable complexes with DNA and protected and transferred DNA to target cells against DNase I digestion in the presence of mucosal destabilizers such as heparin sulfate (a polysaccharide of the glycosaminoglycan family in mucosa) and Newfectan (a natural lung extract of bovine) in an in vitro system. In contrast, commercial liposomes and counter liposomes, made with an identical lipid composition of emulsions, failed. After in vivo intranasal instillation, the cationic emulsion showed at least 200 times better transfection activity than the liposomal carriers in both nasal tissue and lung.ConclusionsThese findings show that cationic emulsions can mediate gene transfection into airway epithelium, making it a good choice for transferring therapeutic genes and for genetic vaccination against an pathogenic infection via an airway route. Copyright © 2005 John Wiley & Sons, Ltd.
Regular orientable embeddings of complete bipartite graphs
Authors: Kwak Jin Ho , Kwon Young Soo 
Published: June 2005

AbstractIn this paper, it will be shown that the isomorphism classes of regular orientable embeddings of the complete bipartite graph Kn,n are in one‐to‐one correspondence with the permutations on n elements satisfying a given criterion, and the isomorphism classes of them are completely classified when n is a product of any two (not necessarily distinct) prime numbers. For other n, a lower bound of the number of those isomorphism classes of Kn,n is obtained. As a result, many new regular orientable embeddings of the complete bipartite graph are constructed giving an answer of Nedela‐Škoviera's question raised in 12. © 2005 Wiley Periodicals, Inc. J Graph Theory
On graphs whose Laplacian matrices have distinct integer eigenvalues
Authors: Fallat Shaun M. , Kirkland Stephen J. , Molitierno Jason J. , Neumann M. 
Published: June 2005

AbstractIn this paper, we investigate graphs for which the corresponding Laplacian matrix has distinct integer eigenvalues. We define the set Si,n to be the set of all integers from 0 to n, excluding i. If there exists a graph whose Laplacian matrix has this set as its eigenvalues, we say that this set is Laplacian realizable. We investigate the sets Si,n that are Laplacian realizable, and the structures of the graphs whose Laplacian matrix has such a set as its eigenvalues. We characterize those i < n such that Si,n is Laplacian realizable, and show that for certain values of i, the set Si,n is realized by a unique graph. Finally, we conjecture that Sn,n is not Laplacian realizable for n ≥ 2 and show that the conjecture holds for certain values of n. © 2005 Wiley Periodicals, Inc. J Graph Theory
Analysis of normal human fetal eye lens crystallins by high‐performance liquid chromatography/mass spectrometry
Authors: He Shuming , Pan Suhua , Wu Kaili , Amster I. Jonathan , Orlando Ron 
Published: May 2005

AbstractHigh‐performance liquid chromatography/mass spectrometry (HPLC/MS) was used to characterize the water‐soluble and water‐insoluble fractions of human fetal eye lens crystallins. This age group was selected since their crystallins are not expected to have accumulated significant amounts of either age‐ or cataract‐related post‐translational modifications owing to their young age. This analysis permitted the identification and determination of the extent of post‐translational modifications for a range of crystallins in a single procedure. The excellent agreement between the calculated and experimental molecular weights from HPLC/MS implies that the published sequences for the crystallins αA2, αB2, βA3, βB2 and γC are correct. This agreement also demonstrates that these proteins do not contain any previously undetected post‐translational modifications. In addition, the molecular weights for many crystallins with unknown sequences and/or post‐translational modifications were determined to within several mass units. This appears to be the first reported analysis of the post‐translational modifications occurring in crystallins from this age group. By providing the molecular weights of the native human crystallins, this study provides a baseline for future comparisons of the age‐ and cataract‐related post‐translational modifications of human lens crystallins.