bluuebunny/crossref_metadata_2025_split huggingface dataset:
ATP‐dependent active transport simulations based on a phosphatase–channel–kinase membrane structure
Authors: Fiaty K. , Charcosset C. , Perrin B. , Couturier R. , Maïsterrena B. 
Published: April 2004

AbstractSimulations of coupled interactions involving enzymatic reaction diffusion and electrostatic interactions were conducted under a fixed phosphatase–channel–kinase (PCK) topology oriented from the outside to the inside of a charged membrane structure. Depending on the phosphatase and kinase locations, we recently demonstrated that active transport of a phosphorylated substrate may occur via this PCK topology. The present analysis demonstrates that, if in addition to this topology, a phosphatase activity (P1) is also present on the inner side of the membrane, but outside the unstirred layer surrounding the inner membrane surface, then active transport of the corresponding unphosphorylated substrate may also occur. Therefore, this PCK membrane topology, which behaves as a specific ATP‐dependent transporter, appears as a general topology permitting; first, on its own the active transport of a phosphorylated substrate; second, when associated with a phosphatase acting in the bulk of the receiver compartment, the active transport of the corresponding unphosphorylated substrate, that is, in most cases, the transport of an uncharged substrate. The general mathematical model given permits the active transport of a phosphorylated substrate to be analyzed (in the absence of P1), the active transport of an unphosphorylated substrate (in the presence of P1), whatever the charge distributions on both sides of the membrane surface and whatever the positions of the membrane‐bound phosphatase and the membrane‐bound kinase. This general model also takes into account the consumption of ATP occurring into the receiver compartment during the time course of these transport phenomena. A broad analysis of the role played by the main parameters taken into account in the model was conducted to precisely define the physicochemical conditions and the membrane topology needed for the highest active transports within the shortest time. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1264–1276, 2004
Disruption of the actin cytoskeleton results in nuclear factor‐κB activation and inflammatory mediator production in cultured human intestinal epithelial cells
Authors: Németh Zoltán H. , Deitch Edwin A. , Davidson Marson T. , Szabó Csaba , Vizi E. Sylvester , Haskó György 
Published: April 2004

AbstractThe cytoskeleton in eukaryotic cells is composed of two major filament systems, the microtubule system and the actin cytoskeleton. The microtubule system has recently emerged as an important regulator of NF‐κB function. However, the role that the actin microfilament system plays in controlling NF‐κB activation is incompletely understood. In this study, we examined the effect of actin cytoskeleton disruption on NF‐κB activation in human intestinal epithelial cells. Treatment of HT‐29 or Caco‐2 cells with the prototypic actin disrupting agents cytochalasin D or latrunculin B resulted in increased NF‐κB DNA binding and NF‐κB‐dependent transcriptional activity. This NF‐κB activation by cytochalasin D was secondary to an effect on IκB, because cytochalasin D‐induced IκB degradation and the cytochalasin D‐induced increase in NF‐κB‐dependent transcriptional activity was prevented by a dominant negative IκB mutant. Exposure of the cells to cytochalasins or latrunculin B increased gene expression and release of the NF‐κB‐dependent chemokines IL‐8 and GRO‐α. Cytochalasin D also activated p38 MAP kinase, which pathway contributed to the cytochalasin D‐induced increase in IL‐8 production. These results demonstrate that the actin cytoskeleton plays an important role in the regulation of NF‐κB activation and inflammatory events in intestinal epithelial cells. © 2004 Wiley‐Liss, Inc.
Extracellular myocilin affects activity of human trabecular meshwork cells
Authors: Wentz‐Hunter Kelly , Kubota Ryo , Shen Xiang , Yue Beatrice Y.J.T. 
Published: April 2004

AbstractThe trabecular meshwork (TM), a specialized eye tissue, is a major site for regulation of the aqueous humor outflow. Malfunctioning of this tissue is believed to be responsible for development of glaucoma, a blinding disease. Myocilin is a gene linked to the most common form of glaucoma. The protein product has been localized to both intra and extracellular sites, but its function still remains unclear. This study was to determine whether extracellular myocilin presented in the matrix affects adhesion, morphology, and migratory and phagocytic activities of human TM cells in culture. Cell adhesion assays indicated that TM cells, while adhering readily on fibronectin, failed to attach on recombinant myocilin purified from bacterial cultures. Adhesion on fibronectin was also compromised by myocilin in a dose dependent manner. Myocilin in addition triggered TM cells to assume a stellate appearance with broad cell bodies and microspikes. Loss of actin stress fibers and focal adhesions was observed. TM cell migration on fibronectin/myocilin to scratched wounds was reduced compared to fibronectin controls. Myocilin, however, had little impact on phagocytic activities of TM cells. Cell attachment on fibronectin and migration of corneal fibroblasts, a control cell type, were not altered by myocilin. These results demonstrate that extracellular myocilin elicits anti‐adhesive and counter‐migratory effects on TM cells. Myocilin in the matrix of tissues could be exerting a similar influence on TM cells in vivo, impacting the flexibility and resilience required for maintenance of the normal aqueous outflow. © 2004 Wiley‐Liss, Inc.
Expression of Concern: HER2 signaling enhances 5′UTR‐mediated translation of c‐Myc mRNA
Authors: Galmozzi Enrico , Casalini Patrizia , Iorio Marilena Valeria , Casati Barbara , Olgiati Clelia , Ménard Sylvie 
Published: April 2004

AbstractThe increased levels of c‐Myc protein observed previously in an ovarian carcinoma cell line stably transfected to express HER2 has suggested a role for the HER2 pathway in c‐Myc expression. Analysis of HER2‐transfected cells stimulated with heregulin β1 (HRG) revealed increased c‐Myc protein levels but not a corresponding increase in c‐Myc mRNA expression or any change in c‐Myc protein half‐life. Transfection of HER2‐overexpressing cells with a construct containing the 5′ untranslated region (5′UTR) of c‐Myc mRNA originated from the P2 promoter and placed upstream of the Renilla luciferase gene, enhanced reporter expression upon stimulation with HRG. The HRG‐mediated increase in reporter activity correlated with the HRG‐mediated induction observed for c‐Myc protein, identifying the P2‐derived leader (P2L) of c‐Myc mRNA as the cis‐element involved in c‐Myc translational induction. Both the increase in c‐Myc protein levels and P2L‐enhanced translational activity were inhibited by the PI3K inhibitor wortmannin. Together, these results demonstrate that HRG stimulation of HER2 overexpressing cells leads to enhanced c‐Myc protein synthesis through activation of the PI3K/Akt/mTOR pathway and that the P2L of c‐Myc mRNA is the element responsible for induction of c‐Myc translation. © 2004 Wiley‐Liss, Inc.
Roles of stromal cell RANKL, OPG, and M‐CSF expression in biphasic TGF‐β regulation of osteoclast differentiation
Authors: Karst Mary , Gorny Genevieve , Galvin Rachelle J. Sells , Oursler Merry Jo 
Published: April 2004

AbstractTo better understand the complex roles of transforming growth factor‐beta (TGF‐β) in bone metabolism, we examined the impact of a range of TGF‐β concentrations on osteoclast differentiation. In co‐cultures of support cells and spleen or marrow osteoclast precursors, low TGF‐β concentrations stimulated while high concentrations inhibited differentiation. We investigated the influences of TGF‐β on macrophage colony stimulating factor (M‐CSF), receptor activator of NF‐κB ligand (RANKL), and osteoprotegerin (OPG) expression and found a dose dependent inhibition of M‐CSF expression. RANKL expression was elevated at low TGF‐β concentrations with a less dramatic increase in OPG. Addition of OPG blocked differentiation at the stimulatory TGF‐β dose. Thus, low TGF‐β concentrations elevated the RANKL/OPG ratio while high concentrations did not, supporting that, at low TGF‐β concentrations, there is sufficient M‐CSF and a high RANKL/OPG ratio to stimulate differentiation. At high TGF‐β concentrations, the RANKL/OPG ratio and M‐CSF expression were both repressed and there was no differentiation. We examined whether TGF‐β‐mediated repression of osteoclasts differentiation is due to these changes by adding M‐CSF and/or RANKL and did not observe any impact on differentiation repression. We studied direct TGF‐β impacts on osteoclast precursors by culturing spleen or marrow cells with M‐CSF and RANKL. TGF‐β treatment dose‐dependently stimulated osteoclast differentiation. These data indicate that low TGF‐β levels stimulate osteoclast differentiation by impacting the RANKL/OPG ratio while high TGF‐β levels repress osteoclast differentiation by multiple avenues including mechanisms independent of the RANKL/OPG ratio or M‐CSF expression regulation. © 2004 Wiley‐Liss, Inc.
SPR for molecular interaction analysis: a review of emerging application areas
Authors: Karlsson Robert 
Published: April 2004

AbstractPubMed searches identified four emerging application areas for surface plasmon resonance systems. Food analysis, proteomics, immunogenicity and drug discovery. These application areas are reviewed. In connection with the review of drug discovery applications a case study is presented. This study demonstrates the value of combining results from drug–target and ADME predictive assays for compound selection. Copyright © 2004 John Wiley & Sons, Ltd.
Artificial metallo‐DNA towards discrete metal arrays
Authors: Shionoya Mitsuhiko 
Published: April 2004

AbstractDNA shows promise as a provider of a structural basis for the “bottom‐up” fabrication of functionalized molecular building blocks. In particular, the replacement of hydrogen‐bonded DNA base pairing for alternative one could possibly provide a novel tool for re‐engineering DNA as well as for biological applications. This review describes our recent approaches to metal‐based strategy directed towards self‐assembled metal arrays within DNAs. Recently, we reported the synthesis of a series of artificial oligonucleotides, d(5′‐GHnC‐3′) (n = 1‐5), using hydroxypyridone nucleobases (H) as flat bidentate ligands. Right‐handed double helices of the oligonucleotides, nCu2+·d(5′‐GHnC‐3′)2 (n = 1‐5), are quantitatively formed through Cu2+‐mediated alternative base pairing (H‐Cu2+‐H), where the Cu2+ ions are aligned along the helix axes inside the duplexes with the Cu2+‐Cu2+ distance of 3.7 ± 0.1 Å. The Cu2+ ions are coupled in a ferromagnetic manner with one another through unpaired d electrons to form magnetic chains. This strategy represents a new method for self‐assembled metal arrays in a predesigned fashion, leading to the possibility of metal‐based molecular devices such as molecular magnets and wires.
Synthesis of iron‐containing polymers with azo dyes in the backbones or side chains
Authors: Abd‐El‐Aziz Alaa S. , Okasha Rawda M. , Todd Erin K. , Afifi Tarek H. , Shipman Patrick O. , Copping K. Michelle D. 
Published: April 2004

AbstractThe synthesis of cationic cyclopentadienyliron‐containing polymers with pendent azobenzene chromophores was accomplished via metal‐mediated nucleophilic aromatic substitution reactions. All of the desired polymers were isolated as vibrantly coloured materials and displayed excellent solubility in polar aprotic solvents. Cationic and neutral cyclopentadienyliron polymers incorporating azo dyes in the backbone were also prepared. Reactions of azo dyes with dichlorobenzene complexes allowed for the isolation of cationic cyclopentdienyliron (CpFe+) complexes with azo dye chromophores. These complexes were then reacted with 1,1′‐ferrocenedicarbonyl chloride to produce the trimetallic monomers with terminal chloro groups. These monomers contained two pendent CpFe+ cations and a neutral iron moiety in the backbone. Nucleophilic substitution reactions of these monomers with oxygen and sulfur containing dinucleophiles gave rise to a new class of polymeric materials. The pendent CpFe+ moieties could also be cleaved from the polymer backbones using photolysis to afford novel ferrocene based polymers. The UV‐vis spectra of the organoiron monomers and polymers display similar wavelength maxima however incorporating azobenzene chromophores with electron‐withdrawing substituent into the polymer chains resulted in bathochromic shifts of the λmax values.
Parkinson's disease sleep scale: Validation study of a Spanish version
Authors: Martínez‐Martín Pablo , Salvador Carlos , Menéndez‐Guisasola Luis , González Sonia , Tobías Aurelio , Almazán Javier , Chaudhuri K. Ray 
Published: April 2004

AbstractThe Parkinson's Disease Sleep Scale (PDSS) is the first published bedside clinical tool to specifically measure sleep disturbances in Parkinson's disease (PD). The objective of the present study was to carry out a metric analysis of a Spanish version (PDSS‐SV) using a cross‐sectional study of 100 PD patients who participated in the study. Usual measures for PD and mental status were applied by neurologists. Patients completed the Epworth Sleepiness Scale, Parkinson's Disease Questionnaire‐39 Items (PDQ‐39), and PDSS‐SV. PDSS internal consistency (Cronbach's α, 0.77; significant item‐total correlation for 11 items) was satisfactory. PDSS showed high test–retest reliability (intraclass correlation coefficient for items, 0.79–0.99; for total score, 0.94). Standard error of measurement was 9.80 (crossover) and 5.01 (longitudinal). Scores were distributed uniformly, with low floor and ceiling effect (1%). PDSS scores were correlated significantly with depression (Hamilton Depression Rating Scale, rS = −0.55; P < 0.0001) and quality of life (PDQ‐39 Summary Index, rS = −0.26; P = 0.007), but not with clinical variables. Self‐perception of mood disorder, pain, or hallucinations correlated individually with PDSS scores, and a factor explaining 65% of the variance was found. The assessment of PD sleep disorders with the PDSS met some basic standards required for health status measures. © 2004 Movement Disorder Society
Complete binary trees in folded and enhanced cubes
Authors: Choudum S.A. , Nandini R. Usha 
Published: April 2004

AbstractIt is well known that the complete binary treeBn(n≥ 3) on 2n− 1 vertices is not embeddable into then‐dimensional hypercube. In this article, we describe a recursive technique to embedBninto then‐dimensional folded and enhanced cubes, ifnsatisfies certain necessary parity conditions. © 2004 Wiley Periodicals, Inc.
Cytotoxicity in cytokine stimulated astrocyte cultures: role of IL‐6 and nitric oxide
Authors: Yilmaz Ozlem , Taskiran Dilek , Aydar Sevgen 
Published: April 2004

AbstractThe cytokines interleukin 1 (IL‐1) and tumor necrosis factor alpha (TNF‐α), produced by glial cells within the brain, appear to contribute to the neuropathogenesis of several inflammatory neurodegenerative diseases. However, little is known about the mechanism underlying cytokine‐induced neurotoxicity. Using astroglial cultures obtained from fetal rat brain, we investigated the effects of lipopolysaccharides (LPS) and cytokines (IL‐1β and TNF‐α). Primary cell cultures treated with LPS, IL‐1β plus TNF‐α generated substantial amounts of nitric oxide (NO), elevated interleukin 6 (IL‐6) levels and caused astroglial injury measured by lactate dehydrogenase (LDH) activity. However, blockade of NO production with nitric oxide synthase (NOS) inhibitors did not affect cell death, suggesting that NO is not responsible for cytokine‐induced astroglial cell death under the experimental conditions employed.
BK virus‐associated nephropathy in kidney transplant recipients
Authors: de Bruyn Guy , Limaye Ajit P. 
Published: April 2004

AbstractPolyomavirus BK has emerged as an important cause of renal allograft infection leading to allograft dysfunction and loss in kidney transplant recipients. Significant progress has been made, particularly in the area of diagnostic methods for BK virus, thereby facilitating diagnosis, screening and monitoring of infection. This review outlines current concepts on the epidemiology, pathogenesis, diagnosis and therapy of BK virus nephropathy. The precise risk factors that are important for induction and progression of infection to invasive disease, the most effective diagnostic strategies, and the efficacy of current therapeutic approaches, all remain to be defined fully. It is to be hoped that these deficiencies will stimulate research to address these important questions. Copyright © 2004 John Wiley & Sons, Ltd.
Presentation of multivariate data for clinical use: The Framingham Study risk score functions
Authors: Sullivan Lisa M. , Massaro Joseph M. , D'Agostino Ralph B. 
Published: April 2004

AbstractThe Framingham Heart Study has been a leader in the development and dissemination of multivariable statistical models to estimate the risk of coronary heart disease. These models quantify the impact of measurable and modifiable risk factors on the development of coronary heart disease and can be used to generate estimates of risk of coronary heart disease over a predetermined period, for example the next 10 years. We developed a system, which we call a points system, for making these complex statistical models useful to practitioners. The system is easy to use, it does not require a calculator or computer and it simplifies the estimation of risk based on complex statistical models. This system represents an effort to make available a tool for clinicians to aid in their decision‐making process regarding treatment and to assist them in motivating patients toward healthy behaviours. The system is also readily available to patients who can easily estimate their own coronary heart disease risk and monitor this risk over time. Copyright © 2004 John Wiley & Sons, Ltd.
A risk‐adjusted Sets method for monitoring adverse medical outcomes
Authors: Grigg O. A. , Farewell V. T. 
Published: April 2004

AbstractThe Sets method has been advocated in previous work as a method for monitoring adverse medical outcomes where the adverse event rate is low. Here, a risk‐adjusted version of the refined Sets method is presented and an example is given to demonstrate its advantage over the unadjusted method. The method is suitable for any risk distribution and does not assume that changes in risk will be small. A graphical representation, referred to as the Grass plot, of the original and risk‐adjusted methods is also given. Copyright © 2004 John Wiley & Sons, Ltd.
Physicochemical Properties of Casein‐Starch Interaction Obtained by Extrusion Process
Authors: Fernández‐Gutiérrez Jaime Antonio , San Martín‐Martínez Eduardo , Martínez‐Bustos Fernando , Cruz‐Orea Alfredo 
Published: April 2004

AbstractExtruded samples of starch‐casein blends were processed by using a single‐screw extruder. The independent variables in the process were temperature (126–194°C), moisture content (18–29%) and starch‐casein blend (5–95%). These independent variables affected significantly the physicochemical and textural properties of the biopolymers. The highest values for expansion (EXP) and water absorption index (WAI) were found when a higher starch proportion was present in the blends, at 126°C barrel temperature and moisture content higher than 25%. By increasing the barrel temperature, from 126°C to 194°C, the water solubility index (WSI) and color parameter were increased. Initial viscosity (IV) and viscosity at 90°C (V90) were mainly affected by the barrel temperature at 194°C. However, the viscosity at 50°C (V50) was affected neither by the different extrusion variables nor by the biopolymer proportion in the blends. Compression force (CF) was strongly dependent on moisture content and casein proportion in the blend. The higher CF values were found at starch concentrations around 50% and 25% moisture content, for higher or lower values than these the obtained extruded products were softer and consequently had lower CF values.
Starch Phosphates Produced by Extrusion: Physical Properties and Influence on Yogurt Stability
Authors: San Martín‐Martínez Eduardo , Aguilar‐Méndez Miguel A. , Espinosa‐Solares T. , Pless Reynaldo C. , Quintana Z. Delia 
Published: April 2004

AbstractStarch phosphorylation with sodium tripolyphosphate (STP) was performed using a single‐screw extrusion process. The extrusion variables studied were temperature (from 99.5°C to 200.4°C), water content (16.3% to 19.7%, w/w), and STP content (0.82% to 4.18%, w/w). The resulting phosphorylated starch was evaluated with respect to expansion, water solubility index (WSI), water absorption index (WAI), degree of substitution (DS), and viscosity. The phosphorylated starch was tested as a stabilizing additive in yogurt formulations, with respect to the syneresis index (SI) and the syneresis susceptibility coefficient (SSC). The results show that the expansion increases with increasing STP content, and decreases with increasing temperature and water content employed in the process. Increasing extrusion temperatures and decreasing water content resulted in increasing WSI and decreasing WAI. The DS was dependent on STP content, increasing as STP content increased, but appeared to be insensitive to changes in water content (between 16% and 20%, w/w). The highest level of yogurt stability, as measured by the syneresis index (SI) and the syneresis susceptibility coefficient (SSC), were obtained when the yogurt was formulated with the starch of the highest DS (0.018), which had been obtained at 150°C, 18% water content, and 4.12% (w/w) of STP.
Modern methods for the iterative computation of eigenpairs of matrices of high dimension
Authors: van der Vorst H.A. 
Published: April 2004

AbstractWe give an overview of computational methods for the eigenproblem Ax = λx and related eigenproblems, in particular those for large matrices. Subspace methods, including the Lanczos and Arnoldi methods, have become increasingly popular. We will highlight a quite recent subspace method for the iterative computation of a few eigenvalues and eigenvectors of high‐dimensional eigenproblems: The so‐called Jacobi‐Davidson method. The application of this method for standard, generalized, and quadratic eigenproblems will be discussed.
Effects of packaging type, gas atmosphere and storage temperature on survival and growth of Listeria spp. in shredded dry coleslaw and its components
Authors: Bourke Paula , O'Beirne David 
Published: April 2004

SummaryThe survival and growth of Listeria populations inoculated on to dry coleslaw mix and its components were investigated, focusing on effects of storage temperatures and gas atmospheres within packaging films or storage chambers. There were few significant effects of packaging film at 3 °C, but at 8 °C the elevated CO2/low O2 atmospheres generated within orientated polypropylene (OPP) packages and used in controlled atmosphere chambers were inhibitory. Although two strains of Listeria monocytogenes had survival characteristics comparable with Listeria innocua, L. monocytogenes ATCC 19114 survived better at 3 °C and also in the elevated CO2/low O2 atmospheres within OPP at 8 °C. The effects of product components on the survival of L. innocua were linked to storage temperature. Shredded carrot reduced initial counts and at 8 °C inhibited survival of L. innocua in comparison with shredded cabbage.