bluuebunny/crossref_metadata_2025_split huggingface dataset:
Statistical models of shape for the analysis of protein spots in two‐dimensional electrophoresis gel images
Authors: Rogers Mike , Graham Jim , Tonge Robert P. 
Published: June 2003

AbstractIn image analysis of two‐dimensional electrophoresis gels, individual spots need to be identified and quantified. Two classes of algorithms are commonly applied to this task. Parametric methods rely on a model, making strong assumptions about spot appearance, but are often insufficiently flexible to adequately represent all spots that may be present in a gel. Nonparametric methods make no assumptions about spot appearance and consequently impose few constraints on spot detection, allowing more flexibility but reducing robustness when image data is complex. We describe a parametric representation of spot shape that is both general enough to represent unusual spots, and specific enough to introduce constraints on the interpretation of complex images. Our method uses a model of shape based on the statistics of an annotated training set. The model allows new spot shapes, belonging to the same statistical distribution as the training set, to be generated. To represent spot appearance we use the statistically derived shape convolved with a Gaussian kernel, simulating the diffusion process in spot formation. We show that the statistical model of spot appearance and shape is able to fit to image data more closely than the commonly used spot parameterizations based solely on Gaussian and diffusion models. We show that improvements in model fitting are gained without degrading the specificity of the representation.
Influence of the crosslink network structure on stress‐relaxation behavior: Viscoelastic modeling of the compression set experiment
Authors: Joubert C. , Michel A. , Choplin L. , Cassagnau P. 
Published: June 2003

AbstractA viscoelastic approach of the compression set test is addressed in this work. This test measures the ability of rubber compounds to retain elastic properties after prolonged action of compressive stresses. Elastic properties were tested by recording the normal stress under a constant deformation of 25% with a laboratory rheometer. Considering the Boltzmann superposition principle, compression set data were modeled from the relaxation of Young's modulus, described by a Maxwell spectrum plus a constant E∞ defining the elastic properties at the long times. This approach was developed with the copolymer of ethylene and vinyl acetate (EVA) networks crosslinked by radical chemistry and by an exchange reaction between acetate groups and silane compounds as crosslinking agents. Regarding the recovery of the elastic properties, radical chemistry provided better results than the exchange reaction for the identical crosslinking density of the network. Then, the Curro–Pincus molecular approach was developed to understand the influence of the microstructure of the EVA network on the elastic properties. The difference of the elastic properties between the two networks crosslinked by two different chemistry means was accounted for by considering the probability of having a dangling end of n units for a random crosslinking process. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 1779–1790, 2003
Finding help for sexual problems after prostate cancer treatment: A phone survey of men's and women's perspectives
Authors: Neese Leah E. , Schover Leslie R. , Klein Eric A. , Zippe Craig , Kupelian Patrick A. 
Published: June 2003

AbstractAs part of a larger postal survey, 320 survivors of prostate cancer who reported they were likely to seek help in the next year for a sexual problem were interviewed by phone about their strategies for finding help and the types of treatment that would help resolve post‐cancer sexual problems. In addition, 164 sexual partners (including 160 wives, three female partners in committed relationships, and one gay male partner) were interviewed. Educational materials were used by patients and partners to answer questions about sexual dysfunction but were less useful in helping to find professional referrals or in actually resolving sexual problems, particularly for African–American couples. Men's preferred method of finding help was to consult a urologist or prostate cancer specialist to find a medical treatment for erectile dysfunction. Ninety‐one percent of men had already tried to find medical help for erectile dysfunction, but previous attempts remained unsuccessful. Men wanted an oral medication that would resolve their sexual problem naturally, without major side effects. Only 43% of men said their partners had encouraged them to find help, and indeed a large minority of women had resigned themselves to having unsatisfying sex lives. These data suggest that including the partner in counseling about medical treatments for sexual function, and giving both men and partners realistic expectations about the limitations of existing treatments could boost the success of sexual rehabilitation after prostate cancer. Copyright © 2003 John Wiley & Sons, Ltd.
Respiratory damage in children exposed to urban pollution
Authors: Calderón‐Garcidueñas Lilian , Mora‐Tiscareño Antonieta , Fordham Lynn A. , Valencia‐Salazar Gildardo , Chung Charles J. , Rodriguez‐Alcaraz Antonio , Paredes Rogelio , Variakojis Daina , Villarreal‐Calderón Anna , Flores‐Camacho Lourdes , Antunez‐Solis Angelina , Henríquez‐Roldán Carlos , Hazucha Milan J. 
Published: June 2003

AbstractSouthwest Metropolitan Mexico City (SWMMC) children are chronically exposed to complex mixtures of air pollutants. In a cross‐sectional arm of our study, we investigated the association between exposure to SWMMC atmosphere and nasal abnormalities, hyperinflation, and interstitial markings assessed by chest X‐rays, lung function changes, several serum cytokines, and endothelin‐1 in 174 children aged 5–17 years vs. 27 control children residents in low‐polluted areas. Control children had no nasal lesions, and only one child showed an abnormal chest X‐ray. SWMMC children exhibited nasal abnormalities (22%), hyperinflation (67%), interstitial markings (49%), and a mild restrictive pattern by spirometry (10%). Interstitial markings were associated with a decrease in predicted values of FEF25–75, FEF75, and the FEV1/FVC ratio. Boys had a higher probability of developing interstitial markings with age (P = 0.004). Blood smear findings included toxic granulations in neutrophils and schistocytes. SWMMC children had more serum IL10 and IL6 and less IL8 than controls. In a longitudinal arm of our study, we found a significant seasonal drop in FVC and FEV1 associated with a 6‐month period of high ozone and PM10 levels. Our data strongly suggest that a lifelong exposure to urban air pollution causes respiratory damage in children. Moreover, a cytokine network becomes imbalanced, with a shift towards upregulation of anti‐inflammatory cytokines. Consequently, these children are potentially at risk for developing chronic lung disease and other systemic effects later in life. Pediatr Pulmonol. 2003; 36:148–161. © 2003 Wiley‐Liss, Inc.
Retrospective review of children presenting with non cystic fibrosis bronchiectasis: HRCT features and clinical relationships
Authors: Edwards E.A. , Metcalfe R. , Milne D.G. , Thompson J. , Byrnes C.A. 
Published: June 2003

AbstractNon cystic fibrosis (CF) bronchiectasis in children presents with a spectrum of disease severity. Our aims were to document the extent and severity of disease in children with non‐CF bronchiectasis, to review the inter‐ and intraobserver agreement for the high‐resolution computed tomography (HRCT) features examined, and to assess correlations between HRCT features and clinical measures of severity. We performed a retrospective review of 56 children from the Starship Children's Hospital. HRCT scans were scored by a modified Bhalla system, and the chest X‐rays using the Brasfield score. Scores were correlated with demographics, number of hospitalizations, disease duration, pulmonary function, clinical examination, and chronic sputum infection. The bronchiectasis seen was widespread and severe, particularly in Maori and Pacific Island children. The kappa coefficient for intraobserver agreement was better than that for interobserver agreement. Comparisons between HRCT scan and lung function parameters showed that the strongest relationships were between forced expiratory volume in 1 sec (FEV1) and forced expiratory flow between 25–75% of forced vital capacity (FEF25–75) with the extent of bronchiectasis, bronchial wall thickening, and air trapping. Children with digital clubbing and chest deformity showed significantly higher scores for extent of bronchiectasis, bronchial wall dilatation and thickness, and overall computed tomography (CT) score. No relationship was demonstrated between chronic sputum infection and CT score. The HRCT score demonstrated a stronger correlation between the extent and severity of bronchiectasis, and spirometry values, than the chest X‐ray score. In conclusion, pediatric non‐CF bronchiectasis in Auckland is extensive and severe. The good intraobserver ratings mean that consistency of scoring is possible on repeated scans. This study cannot comment on the relationships of CT and less severe disease. Pediatr Pulmonol. 2003; 36:87–93. © 2003 Wiley‐Liss, Inc.
Toric duality, Seiberg duality and Picard‐Lefschetz transformations
Authors: Franco S. , Hanany A. 
Published: June 2003

AbstractToric Duality arises as an ambiguity in computing the quiver gauge theory living on a D3‐brane which probes a toric singularity. It is reviewed how, in simple cases Toric Duality is Seiberg Duality. The set of all Seiberg Dualities on a single node in the quiver forms a group which is contained in a larger group given by a set of Picard‐Lefschetz transformations. This leads to elements in the group (sometimes called fractional Seiberg Duals) which are not Seiberg Duality on a single node, thus providing a new set of gauge theories which flow to the same universality class in the Infra Red.
Nontrivial RR two‐form field strength and SU(3)‐structure
Authors: Kaste P. , Minasian R. , Petrini M. , Tomasiello A. 
Published: June 2003

AbstractWe discuss how in the presence of a nontrivial RR two‐form field strength and nontrivial dilaton the conditions of preserving supersymmetry on six‐dimensional manifolds lead to generalized monopole and Killing spinor equations. We construct an SU(3)‐structure on these manifolds and give the explicit expression of its intrinsic torsion in terms of the RR two‐form field strength and dilaton. We show that the manifold is Kähler if F(1,1) = 0.
Memory conformity: can eyewitnesses influence each other's memories for an event?
Authors: Gabbert Fiona , Memon Amina , Allan Kevin 
Published: June 2003

AbstractThe current study investigated memory conformity effects between individuals who witness and then discuss a criminal event, employing a novel procedure whereby each member of a dyad watches a different video of the same event. Each video contained unique items that were thus seen only by one witness. Dyads in one condition were encouraged to discuss the event before each witness (individually) performed a recall test, while in a control condition dyads were not allowed to discuss the event prior to recall. A significant proportion (71%) of witnesses who had discussed the event went on to mistakenly recall items acquired during the discussion. There were no age‐related differences in susceptibility to these memory conformity effects in younger (18–30 years) as compared to older (60–80 years) participants. Possible social and cognitive mechanisms underlying the distortions of memory due to conformity are discussed. Copyright © 2003 John Wiley & Sons, Ltd.
The role of competition and knowledge in the Ellsberg task
Authors: Kühberger Anton , Perner Josef 
Published: June 2003

AbstractAmbiguity avoidance denotes people's preference for gambling situations with known over unknown, or ambiguous, probability distributions. In four experiments we provide evidence for the interaction between competitiveness and knowledge in Ellsberg's task, in which people have a choice between a risky box (distribution of balls known) and an ambiguous box (distribution of balls not known). If the situation is perceived as competitive (the experimenter or an opponent is responsible for composing the boxes) people avoid ambiguity by betting on the box with the known probability distribution. If the task is perceived as cooperative (a partner or friend is composing the boxes) people are indifferent toward ambiguity or even ambiguity seeking. In addition, we find that people expect their winning odds to be less than even in the ambiguous box. Copyright © 2003 John Wiley & Sons, Ltd.
Predicting the conformational states of cyclic tetrapeptides
Authors: Loiseau Nicolas , Gomis Jean‐Marie , Santolini Jérôme , Delaforge Marcel , André François 
Published: June 2003

AbstractBiologically active cyclic tetrapeptides, usually found among fungi metabolites, exhibit phytotoxic or cytostatic activities that are likely to be governed by specific conformations adopted in solution. For conformational studies and drug design, there is a strong interest in using fast and reliable methods to determine correctly the conformational population of cyclotetrapeptides. We show here that standard molecular mechanics computational approach gives satisfactory results. The method was validated step by step by experimental data either obtained after synthesis and NMR analysis, or found in the literature. The cyclo(Gly)4, cyclo(Ala)4, cyclo(Sar)4, and cyclo(SarGly)2 peptides were used to evaluate the prediction of the peptide backbone conformation, and the detailed conformational analysis of tentoxin, a natural phytotoxic cyclotetrapeptide in which N‐alkylated peptide bonds alternate with regular secondary ones, was used to validate the computation of conformers proportions. From the knowledge of an initial cyclic primary structure and of the D or L configuration of the amino acids, we show that it is possible to determine the exact orientation of carbonyl groups and to predict the nature of conformers present in solution. The proportion of each conformer can be inferred from a statistical thermodynamics approach by using the potential energy values of each conformer, computed by molecular mechanics methods with the TRIPOS force field, which allowed us to account for the solvent. The solvent contribution was processed by two different methods according to the nature of the interactions: whether through the dielectric constant introduced in the electrostatic potential, when interaction with solute molecules are weak or negligible, or through the computation of free energy of solvation using the algorithm SILVERWARE© for solvents explicitly interacting with the solute. When applied to tentoxin, this conformational analysis yielded results in very good agreement with the experimental data reported by Pinet et al. (Biopolymers, 1995, Vol. 36, pp. 135–152), on both the nature of existing conformers and their relative proportions, whatever the nature of the considered solvent. © 2003 Wiley Periodicals, Inc. Biopolymers 69:363–385, 2003
Structure and function of integral membrane protein domains resolved by peptide‐amphiphiles: Application to phospholamban
Authors: Lockwood Nathan A. , Tu Raymond S. , Zhang Zhiwen , Tirrell Matthew V. , Thomas David D. , Karim Christine B. 
Published: June 2003

AbstractWe have used synthetic lipidated peptides (“peptide‐amphiphiles”) to study the structure and function of isolated domains of integral transmembrane proteins. We used 9‐fluorenylmethyloxycarbonyl (Fmoc) solid‐phase peptide synthesis to prepare full‐length phospholamban (PLB1–52) and its cytoplasmic (PLB1–25K: phospholamban residues 1–25 plus a C‐terminal lysine), and transmembrane (PLB26–52) domains, and a 38‐residue model α‐helical sequence as a control. We created peptide‐amphiphiles by linking the C‐terminus of either the isolated cytoplasmic domain or the model peptide to a membrane‐anchoring, lipid‐like hydrocarbon tail. Circular dichroism measurements showed that the model peptide‐amphiphile, either in aqueous suspension or in lipid bilayers, had a higher degree of α‐helical secondary structure than the unlipidated model peptide. We hypothesized that the peptide‐amphiphile system would allow us to study the function and structure of the PLB1–25K cytoplasmic domain in a native‐like configuration. We compared the function (inhibition of the Ca‐ATPase in reconstituted membranes) and structure (via CD) of the PLB1–25 amphiphile to that of PLB and its isolated transmembrane and cytoplasmic domains. Our results indicate that the cytoplasmic domain PLB1–25K has no effect on Ca‐ATPase (calcium pump) activity, even when tethered to the membrane in a manner mimicking its native configuration, and that the transmembrane domain of PLB is sufficient for inhibition of the Ca‐ATPase. © 2003 Wiley Periodicals, Inc. Biopolymers 69: 283–292, 2003
Thermodynamical properties of simple models of protein‐like heteropolymers
Authors: Sikorski Andrzej , Romiszowski Piotr 
Published: June 2003

AbstractThe lattice approximation of a heteropolymer chain as a model of a single polypeptide was used in the computer simulation. The residues of a model polypeptide were represented by the chain of α‐carbons located on a very flexible [310] lattice. The force field that mimic the intramolecular interactions contained the long‐range contact potential between the residues and the local preferences in forming helical structures. The chain consisted of two types of residues that had different hydrophobicity. The simulations were performed by means of the Replica Exchange Monte Carlo method combined with the Histogram method. The series of simulations were carried out to investigate the influence of both components of the force field on the transition temperature and the characteristics of the coil‐to‐globule transition. The properties of low‐temperature ordered structures were determined. The thermodynamical description of the model chain was also given. The phase transition was found to be sharp and cooperative for longer chains and strong helical potential. The collapsed globule contained the strongly hydrophobic residues inside the globule while the remaining residues were mainly located close to the globule surface. © 2003 Wiley Periodicals, Inc. Biopolymers 69: 391–398, 2003
Size and shape of the repetitive domain of high molecular weight wheat gluten proteins. I. Small‐angle neutron scattering
Authors: Egelhaaf Stefan U. , Swieten Eric van , Bosma Tjibbe , Boef Esther de , Dijk Alard A. van , Robillard George T. 
Published: June 2003

AbstractThe solution structure of the central repetitive domain of high molecular weight (HMW) wheat gluten proteins has been investigated for a range of concentrations and temperatures using mainly small‐angle neutron scattering. A representative part of the repetitive domain (dB1) was studied as well as an “oligomer” basically consisting of four dB1 units, which has a length similar to the complete central domain. The scattering data over the entire angular range of both proteins are in quantitative agreement with a structural model based on a worm‐like chain, a model frequently used in polymer theory. This model describes the “supersecondary structure” of dB1 and dB4 as a semiflexible cylinder with a length of about 235 and 900 Å, respectively, and a cross‐sectional diameter of about 15 Å. The flexibility of both proteins is characterized by a persistence length of about 13 Å. Their structures are thus quantitatively identical, which implies that the central HMW domain can be elongated while retaining its structural characteristics. It seems conceivable that the flexible cylinder results from a helical structure, which resembles the β‐spiral observed in earlier studies on gluten proteins and elastin. However, compared to the previously proposed structure of a (stiff) rod, our experiments clearly indicate flexibility of the cylinder. © 2003 Wiley Periodicals, Inc. Biopolymers 69: 311–324, 2003
Spectroscopic study of human lung epithelial cells (A549) in culture: Living cells versus dead cells
Authors: Notingher I. , Verrier S. , Haque S. , Polak J. M. , Hench L. L. 
Published: June 2003

AbstractThe noninvasive analysis of living cells grown on 3‐dimensional scaffold materials is a key point in tissue engineering. In this work we show the capability of Raman spectroscopy for use as a noninvasive method to distinguish cells at different stages of the cell cycle and living cells from dead cells. The spectral differences between cells in different stages of the cell cycle are characterized mainly by variations in DNA vibrations at 782, 788, and 1095 cm−1. The Raman spectrum of dead human lung derived (A549 line) cells indicates the breakdown of both phosphodiester bonds and DNA bases. The most sensitive peak for identifying dead cells is the 788 cm−1 peak corresponding to DNA OPO backbone stretching. The magnitude of this peak is reduced by 80% in the spectrum of dead cells. Changes in protein peaks suggest significant conformational changes; for example, the magnitude of the 1231 cm−1 peak assigned to random coils is reduced by 63% for dead cells. The sharp peak of phenylalanine at 1005 cm−1 drops to half, indicating a decrease of stable proteins associated with cell death. The differences in the 1190–1385 cm−1 spectral region also suggest a decrease in the amount of nucleic acids and proteins. Using curve fitting, we quantify these spectral differences that can be used as markers of cell death. © 2003 Wiley Periodicals, Inc. Biopolymers (Biospectroscopy), 2003
Novel fluorescence based receptor binding assay method for receptors lacking ligand conjugates with preserved affinity: Study on estrogen receptor α
Authors: Christoph Silke , Meyer‐Almes Franz‐Josef 
Published: June 2003

AbstractIn this study a novel general approach is presented that allows for a straightforward design of receptor binding assays. This principle of a receptor binding assay is applied to the estrogen receptor, which is important in the management of breast cancer and for the estimation of the estrogenic potency of chemicals in the environment. The inhibitory concentrations to reduce cell proliferation in 50% of controls for 17‐β‐estradiol, 4‐hydroxy tamoxifen, and tamoxifen are determined to be 61 nM, 33 nM, and 17 μM, respectively. The measurement time of the nanoparticle based immunoassay format is 3 s. The Z′ factor, which is calculated to be 0.89, reflects the excellent assay performance. © 2003 Wiley Periodicals, Inc. Biopolymers (Biospectroscopy), 2003
Direct enantiomeric resolution of (±)‐atenolol, (±)‐metoprolol, and (±)‐propranolol by impregnated TLC using L‐aspartic acid as chiral selector
Authors: Bhushan R. , Arora Meenakshi 
Published: June 2003

AbstractResolution of three commonly used β‐blockers, (±)‐atenolol, (±)‐metoprolol and (±)‐propranolol, into their enantiomers has been achieved using normal‐phase TLC on silica gel plates impregnated with L‐aspartic acid as the chiral selector. Different combinations of acetonitrile–methanol–water as mobile phase were found to be successful in resolving the enantiomers. The spots were detected with iodine and the detection limits were found to be 0.26 µg for atenolol and 0.23 µg for each of metoprolol and propranolol as racemate. Copyright © 2003 John Wiley & Sons, Ltd.