bluuebunny/crossref_metadata_2025_split huggingface dataset:
Polypeptide folding on a conformational‐space network: Dependence of network topology on the structural discretization procedure
Authors: Affentranger Roman , Daura Xavier 
Published: January 2010

AbstractMapping the conformational space of a polypeptide onto a network of conformational states involves a number of subjective choices, mostly in relation to the definition of conformation and its discrete nature in a network framework. Here, we evaluate the robustness of the topology of conformational‐space networks derived from Molecular Dynamics (MD) simulations with respect to the use of different discretization (clustering) methods, variation of their parameters, simulation length and analysis time‐step, and removing high‐frequency motions from the coordinate trajectories. In addition, we investigate the extent to which polypeptide dynamics can be reproduced on the resulting networks when assuming Markovian behavior. The analysis is based on eight 500 ns and eight 400 ns MD simulations in explicit water of two 10‐residue peptides. Three clustering algorithms were used, two of them based on the pair‐wise root‐mean‐square difference between structures and one on dihedral‐angle patterns. A short characteristic path length and a power‐law behavior of the probability distribution of the node degree are obtained irrespective of the clustering method or the value of any of the tested parameters. The average cliquishness is consistently one or two orders of magnitude larger than that of a random realization of a network of corresponding size and connectivity. The cliquishness as function of node degree and the kinetic properties of the networks are found to be most dependent on clustering method and/or parameters. Although Markovian simulations on the networks reproduce cluster populations accurately, their kinetic properties most often differ from those observed in the MD simulations. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010
A new Lamarckian genetic algorithm for flexible ligand‐receptor docking
Authors: Fuhrmann Jan , Rurainski Alexander , Lenhof Hans‐Peter , Neumann Dirk 
Published: January 2010

AbstractWe present a Lamarckian genetic algorithm (LGA) variant for flexible ligand‐receptor docking which allows to handle a large number of degrees of freedom. Our hybrid method combines a multi‐deme LGA with a recently published gradient‐based method for local optimization of molecular complexes. We compared the performance of our new hybrid method to two non gradient‐based search heuristics on the Astex diverse set for flexible ligand‐receptor docking. Our results show that the novel approach is clearly superior to other LGAs employing a stochastic optimization method. The new algorithm features a shorter run time and gives substantially better results, especially with increasing complexity of the ligands. Thus, it may be used to dock ligands with many rotatable bonds with high efficiency. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010
Carbondioxide rare‐gas systems: Sensitivity of basis sets and double‐hybrid density functionals
Authors: Seal Prasenjit 
Published: January 2010

AbstractThis study emphasizes on the performance of six newly developed double‐hybrid density functionals (DHDF) in explaining the potential energy curves of different carbondioxide rare‐gas systems. The basis set sensitivity has also been explored with the use of three basis sets. Our results suggest that for lighter He/Ne‐CO2 complexes, proper choice of DHDF and basis set lead to results those matches exactly with earlier calculations and also with the experiment. On the other hand, for heavier Ar/Kr‐CO2 complexes although the equilibrium separation distance matches exactly with earlier observations, the interaction energy values lie far apart. The overall investigation emphasizes on the fact that one has to tune the methods and basis sets properly to achieve good and satisfactory results. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010
Cytokine‐dependent balance of mitogenic effects in primary human lung fibroblasts related to cyclic AMP signaling and phosphodiesterase 4 inhibition
Authors: Selige Jens , Tenor Hermann , Hatzelmann Armin , Dunkern Torsten 
Published: January 2010

AbstractInterleukin‐1β (IL‐1β) and basic fibroblast growth factor (bFGF) are important regulators of proliferation, and their expression is increased in lungs of patients with asthma, idiopathic pulmonary fibrosis (IPF), or chronic obstructive pulmonary disease (COPD). We investigated the effect of IL‐1β and bFGF on proliferation of human lung fibroblasts and the role of COX‐2, PGE2, and cAMP in this process. Furthermore, the effect of phosphodiesterase (PDE) 3 and 4 inhibition was analyzed. In primary human lung fibroblasts low concentrations of IL‐1β (<10 pg/ml) potentiated the bFGF‐induced DNA synthesis, whereas higher concentrations revealed antiproliferative effects. Higher concentrations of IL‐1β‐induced COX‐2 mRNA and protein associated with an increase in PGE2and cAMP, and all of these parameters were potentiated by bFGF. The PDE4 inhibitor piclamilast concentration‐dependently reduced proliferation by a partial G1 arrest. The PDE3 inhibitor motapizone was inactive by itself but enhanced the effect of the PDE4 inhibitor. This study demonstrates that bFGF and IL‐1β act in concert to fine‐tune lung fibroblast proliferation resulting in amplification or reduction. The antiproliferative effect of IL‐1β is likely attributed to the induction of COX‐2, which is further potentiated by bFGF, and the subsequent generation of PGE2and cAMP. Inhibition of PDE4 inhibition (rather than PDE3) may diminish proliferation of human lung fibroblasts and therefore could be useful in the therapy of pathological remodeling in lung diseases. J. Cell. Physiol. 223: 317–326, 2010. © 2010 Wiley‐Liss, Inc.
Evidence of lysosomal membrane permeabilization in mucopolysaccharidosis type I: Rupture of calcium and proton homeostasis
Authors: Pereira Vanessa Gonçalves , Gazarini Marcos L. , Rodrigues Lara Cheliz , da Silva Flávia Helena , Han Sang Won , Martins Ana Maria , Tersariol Ivarne L.S. , D'Almeida Vânia 
Published: January 2010

AbstractMucopolysaccharidosis type I (MPS I) is caused by a deficiency of α‐iduronidase (IDUA), which leads to intralysosomal accumulation of glysosaminoglycans. Patients with MPS I present a wide range of clinical manifestations, but the mechanisms by which these alterations occur are still not fully understood. Genotype–phenotype correlations have not been well established for MPS I; hence, it is likely that secondary and tertiary alterations in cellular metabolism and signaling may contribute to the physiopathology of the disease. The aim of this study was to analyze Ca2+ and H+ homeostasis, lysosomal leakage of cysteine proteases, and apoptosis in a murine model of MPS I. After exposition to specific drugs, cells from Idua−/− mice were shown to release more Ca2+ from the lysosomes and endoplasmic reticulum than Idua+/+ control mice, suggesting a higher intraorganelle store of this ion. A lower content of H+ in the lysosomes and in the cytosol was found in cells from Idua−/− mice, suggesting an alteration of pH homeostasis. In addition, Idua−/− cells presented a higher activity of cysteine proteases in the cytosol and an increased rate of apoptotic cells when compared to the control group, indicating that lysosomal membrane permeabilization might occur in this model. Altogether, our results suggest that secondary alterations—as changes in Ca2+ and H+ homeostasis and lysosomal membrane permeabilization—may contribute for cellular damage and death in the physiopathology of MPS I. J. Cell. Physiol. 223: 335–342, 2010. © 2010 Wiley‐Liss, Inc.
Prognostic role of human equilibrative transporter 1 (hENT1) in patients with resected gastric cancer
Authors: Santini Daniele , Vincenzi Bruno , Fratto Maria Elisabetta , Perrone Giuseppe , Lai Raymond , Catalano Vincenzo , Cass Carol , Ruffini Pier Adelchi , Spoto Chiara , Muretto Pietro , Rizzo Sergio , Muda Andrea Onetti , Mackey John R. , Russo Antonio , Tonini Giuseppe , Graziano Francesco 
Published: January 2010

AbstractNucleoside transporter proteins are specialized proteins that mediate the transport of nucleosides and nucleoside analog drugs across the plasma membrane. The human equilibrative nucleoside transporter 1 (hENT1) is a member of these proteins and mediates cellular entry of gemcitabine, cytarabine, and fludarabine. The hENT1 expression has been demonstrated to be related with prognosis and activity of gemcitabine‐based therapy in breast, ampullary, lung, and pancreatic cancer. We investigated the immunohistochemical expression of hENT in tumor samples from 111 patients with resected gastric adenocarcinoma, correlating these data with clinical parameters and disease outcomes. None of the patients received chemotherapy or radiation therapy before or after surgery as a part of an adjuvant or neoadjuvant program. On univariate survival analysis, the hENT1 expression was associated with overall survival (OS) and disease free survival (DFS). Specifically, those patients with overexpression of hENT1 showed a shorter OS (P = 0.021) and a shorter DFS (P = 0.033). Considering only the node positive patients, higher hENT levels were associated with significantly shorter median DFS (21.7 months; 95% CI 11.1–32.4) compared with patients with low expression of hENT1. The hENT1 expression was defined, in the lymph‐node positive patients, as an independent prognostic factor (P = 0.019). Furthermore, considering only patients with diffuse or mixed tumors and lymph‐node positive, the expression of hENT1 was strongly related with DFS and OS. Immunohistochemistry for the hENT1 protein carries prognostic information in patients with resected gastric cancer and holds promise as a predictive factor in chemotherapy decisions. J. Cell. Physiol. 223: 384–388, 2010. © 2010 Wiley‐Liss, Inc.
Effect of cryopreservation on biological and immunological properties of stem cells from apical papilla
Authors: Ding Gang , Wang Wei , Liu Yi , An Yunqing , Zhang Chunmei , Shi Songtao , Wang Songlin 
Published: January 2010

AbstractStem cells from apical papilla (SCAP) are a novel population of multipotent stem cells that, although similar to dental pulp stem cells, are a discrete source of dental stem cells. SCAP have potential roles in root development, apexogenesis, pulp/dentin regeneration, and bioroot engineering. However, procedures to store and preserve SCAP for future clinical applications have not been explored. In this study, we compared human freshly isolated SCAP (fSCAP) with cryopreserved SCAP (cSCAP) in terms of cell viability, colony‐forming efficiency, cell proliferation rate, multilineage differentiation potential, profiles of mesenchymal stem cell (MSC) markers, karyotype analysis, and immunological assays. cSCAP showed a similar viable cell ratio, colony‐forming efficiency, cell proliferation rate, multilineage differentiation potential, MSC surface markers, apoptotic rate, and G‐banded karyotype when compared to fSCAP. There was no significant difference between fSCAP and cSCAP with regard to immune properties. In addition, cSCAP of miniature pig possessed the similar proliferation rate, differentiation potential, and immunomodulatory function as seen in fSCAP. This study demonstrates that cryopreservation does not affect the biological and immunological properties of SCAP, supporting the feasibility of SCAP cryopreservation in nitrogen. J. Cell. Physiol. 223: 415–422, 2010. © 2010 Wiley‐Liss, Inc.
Claw‐free circular‐perfect graphs
Authors: Pêcher Arnaud , Zhu Xuding 
Published: January 2010

AbstractThe circular chromatic number of a graph is a well‐studied refinement of the chromatic number. Circular‐perfect graphs form a superclass of perfect graphs defined by means of this more general coloring concept. This article studies claw‐free circular‐perfect graphs. First, we prove that if G is a connected claw‐free circular‐perfect graph with χ(G)>ω(G), then min{α(G), ω(G)}=2. We use this result to design a polynomial time algorithm that computes the circular chromatic number of claw‐free circular‐perfect graphs. A consequence of the strong perfect graph theorem is that minimal imperfect graphs G have min{α(G), ω(G)}=2. In contrast to this result, it is shown in Z. Pan and X. Zhu [European J Combin 29(4) (2008), 1055–1063] that minimal circular‐imperfect graphs G can have arbitrarily large independence number and arbitrarily large clique number. In this article, we prove that claw‐free minimal circular‐imperfect graphs G have min{α(G), ω(G)}≤3. © 2010 Wiley Periodicals, Inc. J Graph Theory 65: 163–172, 2010
Cycle and cocycle coverings of graphs
Authors: McGuinness Sean 
Published: January 2010

AbstractIn this article, we show that for any simple, bridgeless graph G on n vertices, there is a family 𝒞 of at most n−1 cycles which cover the edges of G at least twice. A similar, dual result is also proven for cocycles namely: for any loopless graph G on n vertices and ε edges having cogirth g*⩾3 and k(G) components, there is a family of at most ε−n+k(G) cocycles which cover the edges of G at least twice. © 2010 Wiley Periodicals, Inc. J Graph Theory 65: 270–284, 2010
Recent advances in space‐mapping‐based modeling of microwave devices
Authors: Koziel Slawomir , Bandler John W. 
Published: January 2010

AbstractWe review the latest developments in space‐mapping‐based modeling techniques with applications in microwave engineering. We discuss the two techniques that utilize a combination of standard space mapping and function approximation methodologies, in particular fuzzy systems and support vector regression (SVR). In both cases, the initial space‐mapping model is enhanced by an additional term that approximates the differences between the fine model and the initial space‐mapping surrogate. We compare the standard and enhanced space‐mapping models, as well as the fuzzy systems and SVR directly used for modeling fine model data. A discussion of the advantages and disadvantages of the presented methods is also given. Copyright © 2010 John Wiley & Sons, Ltd.
Adenylyl cyclase regulates heavy metal sensitivity, bikaverin production and plant tissue colonization in Fusarium proliferatum
Authors: Kohut Gábor , Oláh Brigitta , Ádám Attila L. , García‐Martínez Jorge , Hornok László 
Published: January 2010

AbstractA homologue of the adenylyl cyclase (AC) gene of Neurospora crassa, named Fpacy1 was cloned from the genomic library of Fusarium proliferatum ITEM 2287 by screening the library with a DNA fragment amplified by using PCR primers designed from conserved sequences of the catalytic domain of AC genes from other fungi. The deduced FPACY1 protein had 53–77% identity with the AC proteins of other fungi. ΔFpacy1 mutants obtained by targeted gene disruption showed retarded vegetative growth, increased conidiation and delayed conidial germination. Colonization capability of the mutants, assessed on maize seedlings and tomato fruits also was adversely affected. In sexual crosses the AC mutants retained full male fertility, but their female fertility decreased significantly. Disruption of Fpacy1 abolished vegetative self‐incompatibility, suggesting that the AC gene is involved in multiple developmental processes related to vegetative growth, as well as sexual and parasexual events. The elevated thermo‐ and H2O2‐tolerance of the ΔFpacy1 mutants was coupled to an increased sensitivity towards Cd and Cu, indicating that the cAMP signaling pathway may have both negative and positive regulatory roles on the stress response mechanisms of fungal cells. When grown under nitrogen limitation conditions, the ΔFpacy1 mutants produced an average of ∼274 μg g–1 bikaverin, whereas only traces of this metabolite was detected in the wild type. This finding provides further evidence of the role of the cAMP‐PKA pathway in regulating bikaverin production. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Effect of environmental conditions on extracellular lipases production and fungal morphology from Aspergillus niger MYA 135
Authors: Colin Veronica Leticia , Baigori Mario Domingo , Pera Licia Maria 
Published: January 2010

AbstractUnder the current assay conditions, lipase production in mineral medium was only detected in the presence of vegetable oils, reaching the highest specific activity with olive oil. In this way, effect of different environmental conditions on fungal morphology and olive oil‐induced extracellular lipases production from Aspergillus niger MYA 135 was studied. It was observed that addition of 1.0 g l–1 FeCl3to the medium encouraged filamentous growth and increased the specific activity 6.6 fold after 4 days of incubation compared to the control. However, major novelty of this study was the satisfactory production of an acidic lipase at initial pH 3 of the culture medium (1.74 ± 0.06 mU μg–1), since its potencial applications in food and pharmaceutical industry are highly promising. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Isolation, structure elucidation and biological activity of angucycline antibiotics from an epiphytic yew streptomycete
Authors: Maruna Michal , Sturdikova Maria , Liptaj Tibor , Godany Andrej , Muckova Marta , Certik Milan , Pronayova Nadezda , Proksa Bohumil 
Published: January 2010

AbstractIn the course of study of epiphytic microorganisms occurring on the surface of roots of Taxus baccata L. a new strain Streptomyces sp. AC113 was isolated. According to 16S ribosomal DNA‐based identification the new strain is 99% identical with Streptomyces flavidofuscus. This strain cultivated in an arginine glycerol medium produced three major metabolites identified as (–)‐8‐O ‐methyltetrangomycin (1), 8‐O ‐methyltetrangulol (2) and 8‐O ‐methyl‐7‐deoxo‐7‐hydroxytetrangomycin (3). The chemical structures of these angucyclines were elucidated by 1D and 2D NMR as well as by mass spectrometry. Isolated angucycline metabolites showed significant antimicrobial activity against Bacillus cereus and Listeria mocytogenes. Cytotoxic activities of compounds 1, 2 and 3 against four cell lines (B16, HT‐29 and non – tumor V79, L929) were evaluated. Compound 3 was the most potent anticancer agents with IC50 0.054 μg/ml against cell line B16. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Axillary staging prior to or after neoadjuvant systemic therapy? A single institutional experience
Authors: Mushawah Fatema Al , Tan Marcus C. , Margenthaler Julie A. 
Published: January 2010

AbstractBackgroundThe study aim was to investigate our institutional strategies for axillary staging in breast cancer patients undergoing neoadjuvant therapy.MethodsWe identified 595 patients treated with neoadjuvant therapy between 2000 and 2007. Axillary staging occurred by four methods: (1) pre‐therapy fine needle aspiration biopsy (FNAB); (2) pre‐therapy sentinel lymph node biopsy (SLNB); (3) post‐therapy SLNB; or (4) post‐therapy axillary lymph node dissection (ALND).ResultsOf 595 patients, 115 underwent FNAB (Group 1; 36 N0, 79 N+), 88 underwent SLNB pre‐therapy (Group 2; 47 N0, 41 N+), 55 underwent SLNB post‐therapy (Group 3; 42 N0, 13 N+), and 337 underwent ALND post‐therapy (Group 4; 133 N0, 204 N+). There was no difference between groups according to patient age, race, stage of disease, estrogen/progesterone receptor and Her‐2neu status, or type of neoadjuvant therapy.ConclusionsThe lack of standardized recommendations for axillary staging in the setting of neoadjuvant therapy leads to variable approaches within an institution. The use of ALND without pre‐therapy axillary assessment may result in over‐treatment of patients. Randomized clinical trials are needed to determine the feasibility and accuracy of SLNB following neoadjuvant therapy. Until such data are available, pre‐therapy axillary staging may reduce the number of unnecessary lymph node dissections. J. Surg. Oncol. 2010;102:404–407. © 2010 Wiley‐Liss, Inc.
Should direct mesocolon invasion be included in T4 for the staging of gastric cancer?
Authors: Park Jung Hoon , Hyung Woo Jin , Choi Seung Ho , Noh Sung Hoon 
Published: January 2010

AbstractBackground and ObjectivesOne of the sites most frequently invaded by gastric cancer is the mesocolon; however, the UICC does not mention this anatomical site as an adjacent structure involved in gastric cancer. The purpose of this study was to characterize and classify mesocolon invasion from gastric cancer.MethodsWe examined 806 patients who underwent surgery for advanced gastric carcinoma from 1992 to 2007 at the Department of Surgery, Gangnam Severance Hospital, Korea. Among these, patients who showed macroscopically direct invasion into the mesocolon were compared to other patients with advanced gastric cancer.ResultsThe curability, number and extent of nodal metastasis, and the survival of the mesocolon invasion group were significantly worse than these factors in the T3 group. However, the survival of the mesocolon invasion group after curative resection was much better than that of patients who had incurable factors.ConclusionsMesocolon invasion should be included in T4 for the staging of gastric cancer. J. Surg. Oncol. 2010; 101:205–208. © 2010 Wiley‐Liss, Inc.
Pont hepatique (hepatic bridge), an important anatomic structure in cytoreductive surgery
Authors: Sugarbaker Paul H. 
Published: January 2010

AbstractBackground and ObjectivesCancer dissemination on peritoneal surfaces can be treated by cytoreductive surgery and perioperative intraperitoneal chemotherapy. To maximize benefits a complete cancer removal precedes the chemotherapy treatments.MethodsDuring cytoreductive surgical procedures a variable bridge of liver parenchyma that covers the round ligament of the liver was observed. This bridge of liver parenchyma is referred to as the pont hepatique (hepatic bridge). Failure to remove tumor nodules from beneath the pont hepatique will result in recurrent disease.ResultsIf the pont hepatique is opened as part of a cytoreductive procedure for peritoneal dissemination of cancer, cancer nodules will often be found beneath. These nodules can be removed using electrosurgical dissection taking care to avoid damage to the left hepatic artery.ConclusionsDivision of the pont hepatique and removal of cancer nodules around and on the round ligament will facilitate a complete cytoreduction. J. Surg. Oncol. 2010; 101:251–252. © 2010 Wiley‐Liss, Inc.
Tourism market segmentation in Iran
Authors: Najmi Manoochehr , Sharbatoghlie Ahmad , Jafarieh Ali 
Published: January 2010

AbstractThis study was a prototype segmentation of Iran's inbound tourism market with a concentration on culture. The focus of this paper was to introduce a step by step description of the methodology used to segment Iran's inbound tourism market. In the first phase, cluster analysis was employed to segment the entire market based on two dimensions of tourists' expenditure and cultural traits. In the second phase, the resulting clusters were divided into further subgroups using a common sense approach. Additional variables were utilised to profile the segments, and finally, the segmentation process was verified through outcome analysis. Copyright © 2010 John Wiley & Sons, Ltd.