bluuebunny/crossref_metadata_2025 huggingface dataset:
Enzymatic hydrolysis of dissolved corn stalk hemicelluloses: reaction kinetics and modeling
Authors: Belkacemi Khaled , Hamoudi Safia
Published: June 2003

The enzymatic hydrolysis of hemicelluloses as a filtrate originating from aqueous/steam pretreated corn stalks was carried out using commercial enzyme systems of several activities composed of cellulases and β‐D‐xylosidases from Aspergillus niger. The hydrolysis was conducted using free enzymes in aqueous substrate solution at a temperature of 30 °C and a pH of 5. Saccharification corresponding to 90% of potential simple sugar release was obtained after 10 h using 0.12 activity units (U) of Cellulases_1 complex per mg of dissolved solids present in the filtrate. Synergetic action of Cellulases_1 enzyme complex and β‐D‐xylosidases proved to be effective for the hydrolysis of plant hemicelluloses. A lumped model based on the Michaelis–Menten approach successfully described the fate of the lumped variables describing the hydrolysis of the overall kinetics of corn stalk hemicelluloses. The maximum saccharification rate evolved with the cellulases concentration as $V_{{\max_{i}}}^{{\rm app}} = K \cdot [{Cellulases}]^{n}$. This overall and pseudokinetic tendency was comparable to those reported in the literature for more simple systems employing a defined substrate and a pure hydrolytic enzyme. The n‐value was found to be in the range of 0.1–0.9 depending on the substrate lump involved in the reaction system. Copyright © 2003 Society of Chemical Industry
Synthesis, characterization and immunochemical evaluation of cephalosporin antigenic determinants
Authors: Sánchez‐Sancho Francisco , Perez‐Inestrosa Ezequiel , Suau Rafael , Montañez María I. , Mayorga Cristobalina , Torres Maria J. , Romano Antonino , Blanca Miguel
Published: June 2003

Lack of knowledge of the exact chemical structure of cephalosporin antigenic determinants has hindered clinical interpretation of adverse reactions to these drugs and delayed understanding of the mechanisms involved in the specific recognition and binding of IgE molecules to these antigenic determinants. We further resolve the relationship between structure and activity of proposed antigenic chemicals, including the rational design and synthesis of these haptenic structures. Comparative RAST inhibition studies of the synthesized molecules revealed that they were recognized by IgE antibodies induced by cephalosporin antibiotics. Thus, these data indicate that recognition is mainly directed to the acyl side chain and to the β‐lactam fragment that remains linked to the carrier protein in the cephalosporin conjugation course. Copyright © 2003 John Wiley & Sons, Ltd.
Effect of tillage and rotation on organic carbon forms of chernozemic soils in Saskatchewan
Authors: Wu Tianyun , Schoenau Jeff J. , Li Fengmin , Qian Peiyuan , Malhi Sukhdev S. , Shi Yuanchun
Published: June 2003

The effects of selected tillage and rotation systems on soil organic carbon and its fractions were studied on Chernozemic soils in south‐western and east‐central Saskatchewan. After practicing a no‐till fallow unfertilized‐wheat rotation for 7 years on an Orthic Brown Chernozem in south‐western Saskatchewan, total soil organic carbon (TOC) in the 0 – 5 cm and 5 – 10 cm layers was slightly lower than the tillage fallow‐unfertilized wheat comparable treatment. However, light fraction of organic carbon (LFOC) was similar in the two treatments. Comparison of the tillage fallow‐unfertilized wheat to a treatment involving conversion to a fertilized continuous cropping system for 10 years showed TOC increased slightly in the two depths and LFOC increased by 24 % and 29 % in the 0 – 5 cm and 5 – 10 cm layer, respectively, of the continuous cropping treatment. Microbial biomass carbon (MB‐C) was increased significantly at the 5 – 10 cm depth. After conversion of fallow‐wheat to alfalfa as perennial forage for 10 years, TOC increased by 80 % and 27 %, LFOC by 245 % and 286 %, and HFOC by 63 % and 20 % at 0 – 5 cm and 5 – 10 cm depths, respectively, compared to the tilled cereal‐fallow system. Meanwhile, water soluble organic carbon (WSOC) was not affected but MB‐C increased significantly.

In an Orthic Black Chernozem in east‐central Saskatchewan, the depletion and restoration of organic carbon was observed when native sod was changed into cropland and then back to grassland. For example, the TOC of cropland under cereal‐fallow rotation for 62 years decreased by 42 % and 33 % at 0 – 5 cm and 5 – 10 cm depths, respectively, compared to native sod. The LFOC decreased by 79 % and 74 % in the layers, and reductions in WSOC and MB‐C were even greater. After cropland was re‐seeded to grassland for 12 years, the concentration of total organic carbon was increased by 16 % and 22 % while the mass of organic carbon was the same as the cropland in the two layers. The LFOC and MB‐C amounts in the grass seed‐down were double that of the cropped land, but the amounts of TOC, LFOC, and MB‐C in grass seed‐down were still significantly lower than the native sod.
Epoetin alpha, epoetin beta and darbepoetin alfa: Two‐dimensional gel electrophoresis isoforms characterization and mass spectrometry analysis
Authors: Caldini Anna , Moneti Gloriano , Fanelli Alessandra , Bruschettini Alessia , Mercurio Stefano , Pieraccini Giuseppe , Cini Elisabetta , Ognibene Agostino , Luceri Francesca , Messeri Gianni
Published: June 2003

Since 1989 recombinant human erythropoietin (rhEPO) has been used as a drug for the correction of anemia, but the misuse of rhEPO as an ergogenic agent among athletes is a widespread doping practice. As a consequence there is a need for developing reference methods for the detection of rhEPO in biological fluids, and to be able to differentiate the recombinant from the natural protein. Recombinant human erythropoietin differs from its natural counterpart in the glycidic part of the molecule. Three different commercial recombinant products Epoetin alpha (Eprex, Janssen Cilag), Epoetin beta (Neorecormon, Roche) and Darbepoetin alfa (Nespo, Dompè) have been used to evaluate the performance of two‐dimensional gel electrophoresis (2‐DE) and mass spectrometry (MS) for the separation of isoforms and the identification of the proteins respectively. All the compounds studied were well separated by means of 2‐DE: Epoetin alpha and beta focused in the same isoelectric point region giving rise to six and eight spots respectively, whereas Darbepoetin alfa was found in a more acidic zone with two spots. Results obtained with micro high‐performance liquid chromatography‐electrospray ionization‐time of flight (TOF) MS and matrix‐assisted laser desorption/ionization‐time of flight MS for the three rhEPOs are reported. These preliminary results suggest that by means of 2‐DE and MS it should be possible to reveal the presence of rhEPOs for antidoping purposes.
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

In 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

A 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

As 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

Southwest 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

Non 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

Toric 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

We 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.
Verification of non-functional programs using interpretations in type theory
Authors: FILLIÂTRE JEAN-CHRISTOPHE
Published: June 2003

We study the problem of certifying programs combining imperative and functional features within the general framework of type theory. Type theory is a powerful specification language which is naturally suited for the proof of purely functional programs. To deal with imperative programs, we propose a logical interpretation of an annotated program as a partial proof of its specification. The construction of the corresponding partial proof term is based on a static analysis of the effects of the program which excludes aliases. The missing subterms in the partial proof term are seen as proof obligations, whose actual proofs are left to the user. We show that the validity of those proof obligations implies the total correctness of the program. This work has been implemented in the Coq proof assistant. It appears as a tactic taking an annotated program as argument and generating a set of proof obligations. Several nontrivial algorithms have been certified using this tactic.
Heparan sulphate glycosaminoglycans derived from endothelial cells and smooth muscle cells differentially modulate fibroblast growth factor-2 biological activity through fibroblast growth factor receptor-1
Authors: BERRY David , SHRIVER Zachary , NATKE Barbara , KWAN Chi-Pong , VENKATARAMAN Ganesh , SASISEKHARAN Ram
Published: June 2003

Fibroblast growth factor (FGF) signalling is involved in a wide range of important biological activities with differential effects in various cell types. The activity of FGF is modulated by heparin/heparan sulphate-like glycosaminoglycans (HSGAGs), found both in the extracellular matrix and on the cell surface. HSGAGs affect FGF signalling by interacting with both the growth factor and the FGF receptor (FGFR). In this study we sought to investigate whether HSGAGs at the cell surface of bovine aortic endothelial cells (BAEC) and smooth muscle cells (SMC) can differentially modulate FGF signalling in these cell types and modulate their differential response to FGF. We find that SMC and BAEC express the same FGFR isoforms and bind FGF2 with equal affinity at the cell surface, yet FGF has a markedly higher proliferative effect on SMC than on BAEC. Isolated HSGAGs from these two cell types were found to elicit distinct patterns of proliferation in chlorate-treated cells. Furthermore, examination of focal sequences reveals that HSGAGs from SMC, but not those from BAEC, retain the sulphation pattern necessary to induce FGF2 activity. As such, the differences in FGF2-mediated proliferation can be explained by the distinct cell surface HSGAGs of the two cell types. We conclude that the focal sequences of cell surface HSGAGs from SMC and BAEC govern, at least in part, the differential activity of FGF2 on these two cell types.
Substrate (aglycone) specificity of human cytosolic beta-glucosidase
Authors: BERRIN Jean-Guy , CZJZEK Mirjam , KROON Paul A. , MCLAUCHLAN W. Russell , PUIGSERVER Antoine , WILLIAMSON Gary , JUGE Nathalie
Published: June 2003

Human cytosolic β-glucosidase (hCBG) is a xenobiotic-metabolizing enzyme that hydrolyses certain flavonoid glucosides, with specificity depending on the aglycone moiety, the type of sugar and the linkage between them. Based upon the X-ray structure of Zea mays β-glucosidase, we generated a three-dimensional model of hCBG by homology modelling. The enzyme exhibited the (β/α)8-barrel fold characteristic of family 1 β-glucosidases, with structural differences being confined mainly to loop regions. Based on the substrate specificity of the human enzymes, sequence alignment of family 1 enzymes and analysis of the hCBG structural model, we selected and mutated putative substrate (aglycone) binding site residues. Four single mutants (Val168→Tyr, Phe225→Ser, Tyr308→Ala and Tyr308→Phe) were expressed in Pichia pastoris, purified and characterized. All mutant proteins showed a decrease in activity towards a broad range of substrates. The Val168→Tyr mutation did not affect Km on p-nitrophenyl (pNP)-glycosides, but increased Km 5-fold on flavonoid glucosides, providing the first biochemical evidence supporting a role for this residue in aglycone-binding of the substrate, a finding consistent with our three-dimensional model. The Phe225→Ser and Tyr308→Ala mutations, and, to a lesser degree, the Tyr308→Phe mutation, resulted in a drastic decrease in specific activities towards all substrates tested, indicating an important role of those residues in catalysis. Taken together with the three-dimensional model, these mutation studies identified the amino-acid residues in the aglycone-binding subsite of hCBG that are essential for flavonoid glucoside binding and catalysis.
Activation of phosphoinositide 3-kinase by D2 receptor prevents apoptosis in dopaminergic cell lines
Authors: NAIR Venugopalan D. , OLANOW C. Warren , SEALFON Stuart C.
Published: June 2003

Whereas dopamine agonists are known to provide symptomatic benefits for Parkinson's disease, recent clinical trials suggest that they might also be neuroprotective. Laboratory studies demonstrate that dopamine agonists can provide neuroprotective effects in a number of model systems, but the role of receptor-mediated signalling in these effects is controversial. We find that dopamine agonists have robust, concentration-dependent anti-apoptotic activity in PC12 cells that stably express human D2L receptors from cell death due to H2O2 or trophic withdrawal and that the protective effects are abolished in the presence of D2-receptor antagonists. D2 agonists are also neuroprotective in the nigral dopamine cell line SN4741, which express endogenous D2 receptors, whereas no anti-apoptotic activity is observed in native PC12 cells, which do not express detectable D2 receptors. Notably, the agonists studied differ in their relative efficacy to mediate anti-apoptotic effects and in their capacity to stimulate [35S]guanosine 5′-[γ-thio]triphosphate ([35S]GTP[S]) binding, an indicator of G-protein activation. Studies with inhibitors of phosphoinositide 3-kinase (PI 3-kinase), extracellular-signal-regulated kinase or p38 mitogen-activated protein kinase indicate that the PI 3-kinase pathway is required for D2 receptor-mediated cell survival. These studies indicate that certain dopamine agonists can complex with D2 receptors to preferentially transactivate neuroprotective signalling pathways and to mediate increased cell survival.
UK Food Standards Agency Optimal Nutrition Status Workshop: environmental factors that affect bone health throughout life
Authors: Burns Lynn , Ashwell Margaret , Berry Jacqueline , Bolton-Smith Caroline , Cassidy Aedin , Dunnigan Matthew , Khaw Kay Tee , Macdonald Helen , New Susan , Prentice Ann , Powell Jonathan , Reeve Jonathan , Robins Simon , Teucher Birgit
Published: June 2003

The UK Food Standards Agency (FSA) convened a group of expert scientists to discuss and review UK FSA- and Department of Health-funded research on diet and bone health. This research focused on the lifestyle factors that are amenable to change and may significantly affect bone health and the risk of osteoporotic fracture. The potential benefits of fruits and vegetables, meat, Ca, vitamins D and K and phyto-oestrogens were presented and discussed. Other lifestyle factors were also discussed, particularly the effect of physical activity and possible gene–nutrient interactions affecting bone health.
APPROXIMATE-OPTIMAL DETECTOR FOR CHAOS COMMUNICATION SYSTEMS
Authors: LAU FRANCIS C. M. , TSE CHI K.
Published: June 2003

Recently, an optimal noncoherent detection technique for chaos-shift-keying digital communication system has been proposed. The computational intensity required, however, increases exponentially with the spreading factor. In this Letter, we propose an approximate-optimal detection technique, whose computational effort increases only linearly with the spreading factor. In particular, we use the chaotic sequences generated by a skew tent map as an example to illustrate the approximate-optimal detection method. The bit error performance of the proposed detector is evaluated by computer simulations and the results are compared with those obtained using the optimal detector.
THE HOMFLY POLYNOMIAL OF THE DECORATED HOPF LINK
Authors: MORTON HUGH R. , LUKAC SASCHA G.
Published: June 2003

The main goal is to find the Homfly polynomial of a link formed by decorating each component of the Hopf link with the closure of a directly oriented tangle. Such decorations are spanned in the Homfly skein of the annulus by elements Qλ, depending on partitions λ. We show how the 2-variable Homfly invariant <λ, μ> of the Hopf link arising from decorations Qλand Qμcan be found from the Schur symmetric function sμof an explicit power series depending on λ. We show also that the quantum invariant of the Hopf link coloured by irreducible sl(N)qmodules Vλand Vμ, which is a 1-variable specialisation of <λ, μ>, can be expressed in terms of an N × N minor of the Vandermonde matrix (qij).
NAKED SINGULARITIES IN THE CHARGED VAIDYA–De SITTER SPACETIME
Authors: BEESHAM A. , GHOSH S. G.
Published: June 2003

We study the occurrence of naked singularities in the spherically symmetric collapse of a charged null fluid in an expanding de Sitter background — a piece of charged Vaidya–de Sitter spacetime. The naked singularities are found to be gravitationally strong in Tipler's sense and thus violate the cosmic censorship hypothesis.
FRACTAL DUST MODEL OF THE UNIVERSE BASED ON MANDELBROT'S CONDITIONAL COSMOLOGICAL PRINCIPLE AND GENERAL THEORY OF RELATIVITY
Authors: MITTAL A. K. , LOHIYA DAKSH
Published: June 2003

We present a fractal dust model of the Universe based on Mandelbrot's proposal to replace the standard Cosmological Principle by his Conditional Cosmological Principle within the framework of General Theory of Relativity. This model turns out to be free from the Hubble de-Vaucouleurs paradox and is consistent with the SNe1a observations. The expected galaxy count as a function of red-shift is obtained for this model. An interesting variation is a steady state version, which can account for an accelerating scale factor without any cosmological constant in the model.
A DYNAMICAL APPROACH TO FRACTIONAL BROWNIAN MOTION
Authors: MANNELLA RICCARDO , GRIGOLINI PAOLO , WEST BRUCE J.
Published: June 2003

Herein we develop a dynamical foundation for fractional Brownian motion. A clear relation is established between the asymptotic behavior of the correlation function and diffusion in a dynamical system. Then, assuming that scaling is applicable, we establish a connection between diffusion (either standard or anomalous) and the dynamical indicator known as the Hurst coefficient. We argue on the basis of numerical simulations that although we have been able to prove scaling only for "Gaussian" processes, our conclusions may well apply to a wider class of systems. On the other hand, systems exist for which scaling might not hold, so we speculate on the possible consequences of the various relations derived in the paper on such systems.
FRACTAL ANALYSIS OF NORMAL HUMAN RETINAL BLOOD VESSELS
Authors: MASTERS BARRY R.
Published: June 2003

The fractal dimension of the pattern of retinal blood vessels in the normal human eye was calculated. Photomontages were constructed from 10 red-free retinal photographs. Manual tracings of the vessels were made. Digital images of the tracings were analyzed on a computer using the box-counting method to determine the fractal dimension. The mean value and standard deviation of the fractal dimension (box-counting dimension), computed as described in the Methods section, is 1.70 ± 0.02 (N = 10). The use of standard methods for both data acquisition and computer assisted box-counting to determine the fractal dimension, resulted in reduced variance in the calculated data.
Lattice separation and measures
Authors: Ponnley James
Published: June 2003

The effects of lattice separation such as normality, almost normal, slightly normal on various lattice‐derived measure are investigated and generalizations of earlier work on 0‐1 valued measures are obtained.
Memory conformity: can eyewitnesses influence each other's memories for an event?
Authors: Gabbert Fiona , Memon Amina , Allan Kevin
Published: June 2003

The 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

Ambiguity 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

Biologically 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

We 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

The 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

The 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

The 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

In 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

Resolution 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.
Hybrid Bayesian networks: making the hybrid Bayesian classifier robust to missing training data
Authors: Woody Nathaniel A. , Brown Steven D.
Published: June 2003

Many standard classification methods are incapable of handling missing values in a sample. Instead, these methods must rely on external filling methods in order to estimate the missing values. The hybrid network proposed in this paper is an extension of the hybrid classifier that is robust to missing values. The hybrid network is produced by performing empirical Bayesian network structure learning to create a Bayesian network that retains its classification ability in the presence of missing data in both training and test cases. The performance of the hybrid network is measured by calculating a misclassification rate when data are removed from a dataset. These misclassification curves are then compared against similar curves produced from the hybrid classifier and from a classification tree. Copyright © 2003 John Wiley & Sons, Ltd.
SSRD: simple sequence repeats database of the human genome
Authors: Subramanian Subbaya , Madgula Vamsi M , George Ranjan , Kumar Satish , Pandit Madhusudhan W , Singh Lalji
Published: June 2003

Simple sequence repeats are predominantly found in most organisms. They play a major role in studies of genetic diversity, and are useful as diagnostic markers for many diseases. The simple sequence repeats database (SSRD) for the human genome was created for easy access to such repeats, for analysis, and to be used to understand their biological significance. The data includes the abundance and distribution of SSRs in the coding and non‐coding regions of the genome, as well as their association with the UTRs of genes. The exact locations of repeats with respect to genomic regions (such as UTRs, exons, introns or intergenic regions) and their association with STS markers are also highlighted. The resource will facilitate repeat sequence analysis in the human genome and the understanding of the functional and evolutionary significance of simple sequence repeats. SSRD is available through two websites, http://www.ccmb.res.in/ssr and http://www.ingenovis.com/ssr. Copyright © 2003 John Wiley & Sons, Ltd.
Perimeter Effects on Ring Currents in Polycyclic Aromatic Hydrocarbons: Circumcoronene and Two Hexabenzocoronenes
Authors: Soncini Alessandro , Steiner Erich , Fowler Patrick W. , Havenith Remco W. A. , Jenneskens Leonardus W.
Published: June 2003

Current‐density maps are calculated at an ab initio level for the three symmetrical polycyclic aromatic hydrocarbons, circumcoronene [1 (D6h)], hexabenzo[bc,ef,hi,kl,no,qr]coronene [2 a (D6h) and 2 b (D3d)], and hexabenzo[a,d,g,j,m,p]coronene [3 a (D6h), 3 b (D6) and 3 c (D3d)], all of which can be formally derived by annelation of benzene rings to a coronene core. Whilst 1 is planar, 2 has a non‐planar minimum that is effectively isoenergetic with its planar form, and 3 has a well defined non‐planar structure. The shape of the molecular boundary rather than the planarity of the molecule plays the critical rôle in the character of the predicted currents. Formal deletion of outer hexagons from circumcoronene (1) in two different ways produces either hexabenzocoronene 2 with a prediction of disjoint local benzenoid diatropic currents linked by a global perimeter, or 3 with a giant diatropic perimeter current enclosing a weak paramagnetic circulation on the central hexagon. The current density map of 1 is effectively a superposition of those of 2 and 3. Its strong diatropic perimeter current subsumes the six weaker diatropic benzenoid circulations evident in 2, and bifurcates in the six outer benzenoid rings that form the corners of the giant hexagon; its benzene “hub” sustains a diatropic current, as would be expected from the partial cancellation of the strong diatropic hub current of 2 by the weaker paratropic hub current of 3. The relationship between the three molecules is rationalised by considering orbital contributions to their current density maps.
The Regioselectivity of the Asymmetric Intermolecular Heck Reaction with Planar Chiral Diphosphine–Oxazoline Ferrocenyl Ligands
Authors: Tu Tao , Deng Wei‐Ping , Hou Xue‐Long , Dai Li‐Xin , Dong Xi‐Cheng
Published: June 2003

A series of novel planar chiral diphosphine‐oxazoline ferrocenyl ligands were synthesized and used efficiently in the palladium‐catalyzed asymmetric intermolecular Heck reaction of 2,3‐dihydrofuran with aryl triflate and cyclohexenyl triflate. The tuning of the regioselectivity was realized by means of different palladium precursors and by changing the electronic factor of the ligands. A plausible rationale based on the existed mechanism is provided.
Cover Picture: Discrete Supramolecular Assemblies of Porphyrins Mediated by Coordination Compounds (Eur. J. Inorg. Chem. 13/2003)
Authors: Iengo Elisabetta , Zangrando Ennio , Alessio Enzo
Published: June 2003

The cover picture shows the X‐ray structure of an unprecedented supramolecular assembly comprising four porphyrins and six metal atoms (two Ru and four Zn); this very stable and symmetrical architecture was obtained by spontaneous self‐assembly through four 4′‐N(py)−Zn interactions of two equal bis(porphyrin)ruthenium self‐complementary building blocks. The design of this and other robust and shape‐persistent assemblies, obtained by coordination of meso‐pyridylporphyrins to ruthenium, palladium and zinc centers, is comprehensively discussed in the microreview by E. Alessio et al. on p. 2371 ff. NMR spectroscopy and X‐ray crystallography were used jointly for the unambiguous characterization of the new species in solution and solid state, respectively. Very often the adducts of nanoscopic dimensions, in which the number, position, relative distance and orientation of the chromophores is well defined, were obtained through hierarchical supramolecular self‐assembly: multi‐porphyrin components were used as building blocks for the metal‐mediated assembly of more elaborate architectures.