bluuebunny/crossref_metadata_2025_split huggingface dataset:
DFT study of the carbon‐ and nitrogen‐pivot lariat crown ethers and their complexes with alkali metal cations: Na+, K+
Authors: Zheng Xiaoyan , Wang Xueye , Yi Shanfeng , Wang Nuanqing , Peng Yueming 
Published: April 2009

AbstractIn this work, a quantum mechanical research of five lariat crown ethers(LCEs), 2‐methoxy‐15‐crown‐5(A), N‐methoxy‐4‐aza‐15‐crown‐5(B), N‐methoxy‐4‐aza‐18‐crown‐6(C), N‐methoxyethyl‐4‐aza‐18‐crown‐6(D), N,N′‐bis(2‐metho xyethyl)‐4,13‐diaza‐18‐crown‐6(E), which are based on either 15‐crown‐5 or 18‐crown‐6 frameworks and contain various pendant arms extending from either carbon or nitrogen atoms on the crown frameworks, had been done using density functional theory with B3LYP/6‐31G* method to obtain the electronic and geometrical structures of the LCEs and their complexes with alkali metal ions: Na+ and K+. The nucleophilicity of LCEs had been investigated by the Fukui functions. For complexes, the match between the cation and cavity size, the status of interaction between alkali metal ions and donor atoms in the LCEs, and the sidearm effect of the LCEs had been analyzed through the other calculated parameters, such as, highest occupied molecular orbital energy, lowest unoccupied molecular orbital energy, and energy gaps. In addition, the enthalpies of complexation reaction had been studied by the calculated thermodynamic data (298 K). The calculated results are all in a good agreement with the experimental data for the complexes. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009
QSAR of antilipid peroxidative activity of substituted benzodioxoles using chemometric tools
Authors: Mitra Indrani , Roy Kunal , Saha Achintya 
Published: April 2009

AbstractSearch and development of new effective antioxidant molecules with improved activity is of both biological and commercial importance. In this background, we have modeled antioxidant activities of a series of benzodioxoles for their ability to inhibit lipid peroxidation (pC) using quantitative structure activity relationship (QSAR) technique. The QSAR models were developed using different chemometric tools such as GFA and G/PLS techniques. Two different sets of descriptors were used for developing these QSAR models. Molecular shape analysis (MSA) and spatial (charged partial surface area and shadow) descriptors were included in the one set, whereas quantum chemical (Mulliken charges on common atoms of the molecules calculated at the AM1 level) and physicochemical (hydrophobic parameter and molar refractivity) descriptors were included in the other set. All the models developed were validated internally by leave‐one‐out cross‐validation and randomization techniques. The model predictivity was judged by their cross‐validated squared correlation coefficient (Q2) and the modified r2 (r) values, whereas the robustness of the models was judged from the value of R (Roy and Paul, QSAR Comb Sci DOI:10.1002/qsar.200810130). The developed models suggest that the antilipid peroxidative activity of the molecules largely depends on the charges of the carbon atoms connected to the oxygen atoms of the dioxole ring. Besides this, the activity also depends on the charged surface area of the molecules and the dipole moment of the molecules. Presence of the methoxy substituents (ortho or meta) on the phenyl ring at the R1 position of the benzodioxoles significantly lowers the antioxidant activity of these molecules. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009
Geometric similarity between protein–RNA interfaces
Authors: Zhou Peng , Zou Jianwei , Tian Feifei , Shang Zhicai 
Published: April 2009

AbstractA new method is described to measure the geometric similarity between protein–RNA interfaces quantitatively. The method is based on a procedure that dissects the interface geometry in terms of the spatial relationships between individual amino acid nucleotide pairs. Using this technique, we performed an all‐on‐all comparison of 586 protein–RNA interfaces deposited in the current Protein Data Bank, as the result, an interface–interface similarity score matrix was obtained. Based upon this matrix, hierarchical clustering was carried out which yielded a complete clustering tree for the 586 protein–RNA interfaces. By investigating the organizing behavior of the clustering tree and the SCOP classification of protein partners in complexes, a geometrically nonredundant, diverse data set (representative data set) consisting of 45 distinct protein–RNA interfaces was extracted for the purpose of studying protein–RNA interactions, RNA regulations, and drug design. We classified protein–RNA interfaces into three types. In type I, the families and interface structural classes of the protein partners, as well as the interface geometries are all similar. In type II, the interface geometries and the interface structural classes are similar, whereas the protein families are different. In type III, only the interface geometries are similar but the protein families and the interface structural classes are distinct. Furthermore, we also show two new RNA recognition themes derived from the representative data set. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009
On list coloring Steiner triple systems
Authors: Haxell P. E. , Pei M. 
Published: April 2009

AbstractWe study the list chromatic number of Steiner triple systems. We show that for every integer s there exists n0=n0(s) such that every Steiner triple system on n points STS(n) with n≥n0 has list chromatic number greater than s. We also show that the list chromatic number of a STS(n) is always within a log n factor of its chromatic number. © 2009 Wiley Periodicals, Inc. J Combin Designs 17: 314–322, 2009
Role of connective tissue growth factor and its interaction with basic fibroblast growth factor and macrophage chemoattractant protein‐1 in skin fibrosis
Authors: Chujo Sonoko , Shirasaki Fumiaki , Kondo‐Miyazaki Miki , Ikawa Yuka , Takehara Kazuhiko 
Published: April 2009

AbstractActivation of the immune system and abnormal growth of skin fibroblasts cause systemic sclerosis. Growth factors have various biological activities, including mediation of immune reactions. The growth factor family includes basic fibroblast growth factor (bFGF), transforming growth factor‐beta (TGF‐β), and connective tissue growth factor (CTGF). CTGF, an important downstream mediator of TGF‐β in fibrosis, has been suggested to play a specific role in fibrotic disorders. We have directed our attention to the role of CTGF in sustaining skin fibrosis. To better understand its effects in vivo, we established an animal model of skin fibrosis induced by exogenous application of growth factors. In this model, bFGF transiently induced subcutaneous fibrosis. Simultaneous injection of bFGF and CTGF increased skin fibrosis compared with a single injection of bFGF. Serial injections of bFGF for 3 days followed by CTGF for 4 days, or of CTGF followed by bFGF, did not cause skin fibrosis but simultaneous injections increased macrophage chemoattractant protein‐1 (MCP‐1) mRNA expression levels. To further define the mechanisms of skin fibrosis in vivo, bFGF and CTGF were injected simultaneously into MCP‐1 knockout mice, resulting in decreased collagen levels in granulation tissues on day 8. The number of inflammatory cells, such as mast cells, macrophages and lymphocytes, was significantly decreased in MCP‐1 knockout mice compared with wild‐type mice. These results suggest that bFGF induces collagen production by stimulating skin fibroblasts and CTGF cooperates with bFGF. Our results indicate that the induction of MCP‐1 is necessary for infiltration of inflammatory cells. J. Cell. Physiol. 220: 189–195, 2009. © 2009 Wiley‐Liss, Inc.
Glial cell‐derived neurotrophic factor increases migration of human chondrosarcoma cells via ERK and NF‐κB pathways
Authors: Su Chen‐Ming , Lu Dah‐Yuu , Hsu Chin‐Jung , Chen Hsien‐Te , Huang Chun‐Yin , Yang Wei‐Hung , Su Yi‐Chang , Yang Shu‐Ning , Fong Yi‐Chin , Tseng Wen‐Pei , Tang Chih‐Hsin 
Published: April 2009

AbstractInvasion of tumor cells is the primary cause of therapeutic failure in the treatment of malignant chondrosarcomas. Glial cell‐derived neurotrophic factor (GDNF) plays a crucial role in migration and metastasis of human cancer cells. Integrins are the major adhesive molecules in mammalian cells. Here we found that GDNF directed the migration and increased cell surface expression of αv and β3 integrin in human chondrosarcoma cells. Pretreated of JJ012 cells with MAPK kinase (MEK) inhibitors PD98059 or U0126 inhibited the GDNF‐mediated migration and integrin expression. Stimulation of cells with GDNF increased the phosphorylation of MEK and extracellular signal‐regulating kinase (ERK). In addition, NF‐κB inhibitor (PDTC) or IκB protease inhibitor (TPCK) also inhibited GDNF‐mediated cells migration and integrin up‐regulation. Stimulation of cells with GDNF induced IκB kinase (IKKα/β) phosphorylation, IκB phosphorylation, p65 Ser536 phosphorylation, and κB‐luciferase activity. Furthermore, the GDNF‐mediated increasing of κB‐luciferase activity was inhibited by PD98059, U0126, PDTC and TPCK or MEK, ERK, IKKα, and IKKβ mutants. Taken together, these results suggest that the GDNF acts through MEK/ERK, which in turn activates IKKα/β and NF‐κB, resulting in the activations of αvβ3 integrin and contributing the migration of human chondrosarcoma cells. J. Cell. Physiol. 220: 499–507, 2009. © 2009 Wiley‐Liss, Inc.
Intranuclear fluorescence resonance energy transfer analysis of plasmid DNA decondensation from nonviral gene carriers
Authors: Matsumoto Yu , Itaka Keiji , Yamasoba Tatsuya , Kataoka Kazunori 
Published: April 2009

AbstractBackgroundThere has been considerable interest in researching the regulatory mechanisms that control transgene expression. In particular, there is impetus to investigate the intranuclear mechanisms for gene expression in order to improve the transfection efficiency of nonviral gene carriers.MethodsTo clarify the direct relationship between DNA decondensation and gene expression, plasmid DNA encoding Keima‐Red fluorescent protein was doubly‐labeled by a pair of donor–acceptor fluorescent dyes (fluorescein and Cy3), and transfected to HuH‐7 cells using nonviral gene carriers: polyethylenimine (polyplex) and LipofectAMINE 2000 (lipoplex). Fluorescence resonance energy transfer analysis between the two dyes represents the condensation state of the pDNA. The intranuclear trafficking and condensation state of the pDNA were explored in transgene expressing and non‐expressing cells under confocal laser scanning spectromicroscopy.ResultsThe majority of transgene positively expressing cells transfected with polyplex and lipoplex had decondensed pixels in the nucleus. The majority of non‐expressing cells transfected with polyplex had only condensed pixels in the nucleus. The majority of non‐expressing cells transfected with lipoplex had no pixels in the nucleus.ConclusionsBoth polyplex and lipoplex marked a strong correlation between pDNA decondensation and transgene expression, yet the major limiting factor for transgene expression was different. In polyplex, the pDNA decondensation after nuclear entry was the major determining factor for transgene expression, whereas the nuclear entry itself was the chief determining step for transgene expression by lipoplex. This imaging technique allowed in situ observation of pDNA in the nucleus, providing important information about DNA behavior for gene expression. Copyright © 2009 John Wiley & Sons, Ltd.
Totally symmetric colored graphs
Authors: Grech Mariusz , Kisielewicz Andrzej 
Published: April 2009

AbstractIn this paper we describe almost all edge‐colored complete graphs that are fully symmetric with respect to colors and transitive on every set of edges of the same color. This generalizes the recent description of self‐complementary symmetric graphs by Peisert and gives examples of permutation groups that require more than 5 colors to be represented as the automorphism group of a k ‐colored graph. This also contributes to the recent study of homogeneous factorizations of complete graphs. The result relies on the classification of finite simple groups. © 2009 Wiley Periodicals, Inc. J Graph Theory 62: 329–345, 2009
d‐Regular graphs of acyclic chromatic index at least d+2
Authors: Basavaraju Manu , Chandran L. Sunil , Kummini Manoj 
Published: April 2009

AbstractAn acyclic edge coloring of a graph is a proper edge coloring such that there are no bichromatic cycles. The acyclic chromatic index of a graph is the minimum number k such that there is an acyclic edge coloring using k colors and is denoted by a′(G). It was conjectured by Alon, Sudakov and Zaks (and earlier by Fiamcik) that a′(G)⩽Δ+2, where Δ=Δ(G) denotes the maximum degree of the graph. Alon et al. also raised the question whether the complete graphs of even order are the only regular graphs which require Δ+2 colors to be acyclically edge colored. In this article, using a simple counting argument we observe not only that this is not true, but in fact all d‐regular graphs with 2n vertices and d>n, requires at least d+ 2 colors. We also show that a′(Kn, n)⩾n+ 2, when n is odd using a more non‐trivial argument. (Here Kn, n denotes the complete bipartite graph with n vertices on each side.) This lower bound for Kn, n can be shown to be tight for some families of complete bipartite graphs and for small values of n. We also infer that for every d, n such that d⩾5, n⩾2d+ 3 and dn even, there exist d‐regular graphs which require at least d+2‐colors to be acyclically edge colored. © 2009 Wiley Periodicals, Inc. J Graph Theory 63: 226–230, 2010
Selective reduction in microglia density and function in the white matter of colony‐stimulating factor‐1–deficient mice
Authors: Kondo Yoichi , Duncan Ian D. 
Published: April 2009

AbstractIt is still debated whether microglia play a beneficial or harmful role in myelin disorders such as multiple sclerosis and leukodystrophies as well as in other pathological conditions of the central nervous system. The osteopetrotic (op/op) mouse has reduced numbers of cells of monocyte lineage as a result of an inactivating mutation in the colony stimulating factor‐1 gene. To determine whether this mutant mouse might be used to study the role of microglia in myelin disorders, we quantified the number of microglia in the central nervous system of op/op mice and explored their ability to respond to brain injury created by a stab wound. Microglial density in the 2‐month‐old op/op mice was significantly decreased in the white matter tracts compared with the ‐ge matched wild‐type controls (by 63.6% in the corpus callosum and 86.4% in the spinal dorsal column), whereas the decrease was less in the gray matter, cerebral cortex (24.0%). A similar decrease was seen at 7 months of age. Morphometric studies of spinal cord myelination showed that development of myelin was not affected in op/op mice. In response to a stab wound, the increase in the number of microglia/macrophages in op/op mice was significantly less pronounced than that in wild‐type control. These findings demonstrate that this mutant is a valuable model in which to study roles of microglia/macrophages in the pathophysiology of myelin disorders. © 2009 Wiley‐Liss, Inc.
Adaptations in 5‐HT receptor expression and function: Implications for treatment of cognitive impairment in aging
Authors: Mitchell Ellen S. , McDevitt Ross A. , Neumaier John F. 
Published: April 2009

AbstractMalfunction of the serotonin system may contribute to memory deficits during aging. We evaluated the 5‐HT6antagonist RO4368554 in two models of learning and memory in aged rats. Male rats (18 months) were assigned to two groups of equal cognitive performance. After 2 weeks of 5‐HT6antagonist RO4368554 (5 mg/kg, i.p.) treatment, rats showed significant improvement in object recognition and social discrimination compared with rats given chronic vehicle. Brains from these animals were examined for changes in plasticity‐associated proteins Ki‐67 and PCNA. No differences were seen between groups in any of these markers. We also measured mRNA expression of 5‐HT6, along with 5‐HT1A, 5‐HT1B, and tryptophan hydroxylase‐2 mRNAs in 4‐month‐old and 24‐month‐old F344 rats. Decreases in 5‐HT1Bexpression were observed in several forebrain regions in the old rats. These results demonstrate that 5‐HT6and 5‐HT1Breceptors are potential targets for treatment of age‐related memory disorders. © 2009 Wiley‐Liss, Inc.
Expression of SLURP‐1, an endogenous α7 nicotinic acetylcholine receptor allosteric ligand, in murine bronchial epithelial cells
Authors: Horiguchi Kazuhide , Horiguchi Satomi , Yamashita Naomi , Irie Kaoru , Masuda Junya , Takano‐Ohmuro Hiromi , Himi Toshiyuki , Miyazawa Mai , Moriwaki Yasuhiro , Okuda Takashi , Misawa Hidemi , Ozaki Hiroshi , Kawashima Koichiro 
Published: April 2009

AbstractMammalian secreted lymphocyte antigen‐6/urokinase‐type plasminogen activator receptor‐related peptide‐1 (SLURP‐1) is a positive allosteric ligand for α7 nicotinic acetylcholine (ACh) receptors (α7 nAChRs) that potentiates responses to ACh and elicits proapoptotic activity in human keratinocytes. Mutations in the gene encoding SLURP‐1 have been detected in patients with Mal de Meleda, a rare autosomal recessive skin disorder characterized by transgressive palmoplantar keratoderma. On the basis of these findings, SLURP‐1 is postulated to be involved in regulating tumor necrosis factor‐α (TNF‐α) release from keratinocytes and macrophages via α7 nAChR‐mediated pathways. In the present study, we assessed SLURP‐1 expression in lung tissue from C57BL/6J mice to investigate the functions of SLURP‐1 in pulmonary physiology and pathology. Immunohistochemical and in situ hybridization analyses revealed expression of SLURP‐1 protein and mRNA, respectively, exclusively in ciliated bronchial epithelial cells. This was supported by Western blotting showing the presence of the 9.5‐kDa SLURP‐1 protein in whole‐lung tissue and trachea. In addition, high‐affinity choline transporter (CHT1) was detected in apical regions of bronchial epithelial cells and in neurons located in the lamina propria of the bronchus, suggesting that bronchial epithelial cells are able to synthesize both SLURP‐1 and ACh. We also observed direct contact between F4/80‐positive macrophages and bronchial epithelial cells and the presence of invading macrophages in close proximity to CHT1‐positive nerve elements. Collectively, these results suggest that SLURP‐1 contributes to the maintenance of bronchial epithelial cell homeostasis and to the regulation of TNF‐α release from macrophages in bronchial tissue. © 2009 Wiley‐Liss, Inc.
Isatin binding proteins in rat brain: In situ imaging, quantitative characterization of specific [3H]isatin binding, and proteomic profiling
Authors: Crumeyrolle‐Arias Michele , Buneeva Olga , Zgoda Victor , Kopylov Arthur , Cardona Ana , Tournaire Marie‐Claude , Pozdnev Vladimir , Glover Vivette , Medvedev Alexei 
Published: April 2009

AbstractIsatin (indole‐2,3‐dione) is an endogenous indole that has a distinct and discontinuous distribution in the brain and in other mammalian tissues and body fluids. Its output is increased under conditions of stress and anxiety. Its biological targets remain poorly characterized, although [3H]isatin binding sites have been demonstrated in various brain structures. In this study, by using a real‐time beta‐imager, [3H]isatin radioligand binding analysis, and proteomic identification of proteins specifically bound to the affinity sorbent 5‐aminocaproyl‐isatin‐Sepharose, we have investigated the distribution of [3H]isatin specific binding sites in the rat brain, characterized their Kd and Bmax, and identified some individual brain isatin binding proteins. The binding of [3H]isatin to rat brain sections was saturable and characterized by Kd values (of 0.2–0.3 μM) consistent with physiological concentrations. The highest Bmax was found in the hypothalamus, consistent with a role in stress. In most brain regions, the homologous inhibition of [3H]isatin binding by increasing concentrations of cold isatin demonstrated complex behavior suggesting involvement of various binding proteins characterized by different affinity to isatin. Affinity chromatography of Triton X‐100 lysates of whole‐brain homogenates on 5‐aminocaproyl‐isatin‐Sepharose followed by subsequent proteomic analysis resulted in identification of 25 individual proteins, including glyceraldehyde‐3‐phosphate dehydrogenase, one of few previously reported isatin binding proteins, and a group of cytoskeleton‐related proteins. These binding sites may be related to the known antiproliferative and proapoptotic activities of isatin. © 2009 Wiley‐Liss, Inc.
Localization of the full‐thickness cartilage lesions in medial and lateral unicompartmental knee osteoarthritis
Authors: Gulati Aashish , Chau Ryan , Beard David J. , Price Andrew J. , Gill Harinderjit S. , Murray David W. 
Published: April 2009

AbstractThis study's aim was to determine the patterns of osteoarthritis (OA) in both unicompartmental medial and lateral OA of the knee. Forty patients with medial and 20 with lateral unicompartmental knee osteoarthritis were studied to determine the location of full‐thickness cartilage lesions. Intraoperatively, the distance between margins of the lesion and reference lines were measured. The femoral measurements were transposed onto lateral radiographs to determine the relationship between the lesion site and knee flexion angles. Both tibial and femoral lesions were significantly (p < 0.01) more posterior in lateral OA than medial OA. In medial OA, the lesion center was, on average, at 11° (SD 3°) of flexion, whereas in lateral OA, it was at 40° (SD 3°). The smallest medial femoral lesions were near full extension and, as they enlarged, they extended posteriorly. The smallest lateral femoral lesions extended from 20° to 60° flexion. As these lesions enlarged, they extended both anteriorly and posteriorly. There was a well‐defined relationship between the site of the lesions and their size, suggesting that they develop and progress in a predictable manner. The relationship was different for medial and lateral OA, suggesting that different mechanical factors are important in initiating the different types of OA. The lesions in medial OA occur in extension, perhaps initiated by events occurring at heel strike. The lesions in lateral OA begin at flexion angles above those occurring during the single leg stance phase of the gait cycle, so activities other than gait are likely to induce lateral OA. © 2009 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 27:1339–1346, 2009