bluuebunny/crossref_metadata_2025 huggingface dataset:
The epidemiology of fatalities reported to the Vaccine Adverse Event Reporting System 1990–1997
Authors: Silvers Linda E. , Ellenberg Susan S. , Wise Robert P. , Varricchio Frederick E. , Mootrey Gina T. , Salive Marcel E.
Published: August 2002

Purpose

To examine the fatalities reported to the federally administered Vaccine Adverse Event Reporting System (VAERS), a passive surveillance system, in its first 7 years.

Methods

The working data set included variables such as demographic information, dates of vaccination, adverse event onset and death, vaccines administered, and vaccination facility data. Frequencies for these data and state reporting rates were calculated.

Results

A total of 1266 fatalities were reported to VAERS during July 1990 through June 1997. The number of death reports peaked in 1992–1993 and then declined. The overall median age of cases was 0.4 years, with a range of 1 day to 104 years. Nearly half of the deaths were attributed to sudden infant death syndrome (SIDS).

Conclusions

The trend of decreasing numbers of deaths reported to VAERS since 1992–1993 follows that observed for SIDS overall for the US general population following implementation of the ‘Back to Sleep’ program. These data may support findings of past controlled studies showing that the association between infant vaccination and SIDS is coincidental and not causal. VAERS reports of death after vaccination may be stimulated by the temporal association, rather than by any causal relationship. Published in 2001 by John Wiley & Sons, Ltd.
Ultraviolet‐induced crosslinking of poly(vinyl alcohol) evaluated by principal component analysis of FTIR spectra
Authors: Miranda Teresa M R , Gonçalves Adilson R , Amorim M T Pessoa
Published: August 2002

The crosslinking of poly(vinyl alcohol) (PVA) films under ultraviolet irradiation for between 1 and 4 h was studied in air at 25 °C in the presence of sodium benzoate by Fourier‐transform infrared spectroscopy (FTIR) using the attenuated total reflectance technique (ATR). Principal component analysis (PCA) is a mathematical procedure that allows treatment of the entire infrared spectrum and is very appropriate for analysing the chemical modifications initiated by sodium benzoate which occur in PVA upon UV irradiation. By PCA it was possible to clarify the mechanism of crosslinking of PVA. From this FTIR–PCA study, it is suggested that a free radical arising from the photolysis of sensitizer would abstract a tertiary hydrogen atom from the polymer chain to yield a polymeric radical. This radical reacts with OH groups, leading to the formation of ether bonds between the polymeric chains and hence to crosslinking and insolubilization of the PVA.

© 2001 Society of Chemical Industry
Strong effects of counterions on the electrochemistry of poly(N‐methylaniline) thin films
Authors: Planes Gabriel A , Miras María C , Barbero Cesar
Published: August 2002

Poly(N‐methylaniline) thin films show different cyclic voltammetric behaviour when cycled in HClO4, HBF4, HCl or HNO3. While in the first two acids the film shows profiles peak potentials similar to those of polyaniline, profiles in HCl and HNO3 show higher peak potentials for oxidation and a different shape. The free energy for the process, calculated from the oxidation peak potential, shows a linear correlation with the free energy of hydration of the anions present in the test solution. An energy cycle for the oxidation process is proposed to explain the results. The reaction mechanism assumes that anions have to lose their hydration shell to form the polymer salt during electrochemical oxidation of the films. Electropolymerization also depends on the anion present in the solution. While this is possible with low hydration energy anions (ClO4−, BF4−), it is difficult or impossible when the electrolyte solution contains other anions (Cl−, NO3−) where a higher oxidation potential of the preformed polymer is observed.

© 2002 Society of Chemical Industry
Introduction to the special issue on the appraisal and prediction of school violence
Authors: Furlong Michael J. , Kingery Paul M. , Bates Michael P.
Published: August 2002

This article provides an overview of a special issue of Psychology in the Schools that critically examines issues related to the appraisal of the risk for violence among students. It is argued that school psychologists can assume the important role of informing communities about the limitations of school violence screening and assessment procedures and can implement student‐appraisal techniques that focus on long‐term student development. They can also work toward more accurate measurement of general school violence trends and intervention needs. © 2001 John Wiley & Sons, Inc.
Studies on copolymerization of n‐isopropylacrylamide and glycidyl methacrylate
Authors: Virtanen Janne , Tenhu Heikki
Published: August 2002

Free‐radical homopolymerization of N‐isopropyl acrylamide (NIPA, monomer 1) and copolymerizations of NIPA with glycidyl methacrylate (GMA, monomer 2) were conducted in deuterated dioxane at 70 °C. The conversion of the monomers was followed by 1H NMR spectroscopy. After the polymerization reactions the polymers were precipitated and analyzed. Reactivity ratios were determined using both Fineman–Ross and extended Kelen–Tüdős methods. Values obtained by these two methods were r1 = 0.39, r2 = 2.69 and r1 = 0.30, r2 = 2.66, respectively. In both cases, r ∼ 1, which is indicative of an ideal copolymerization resulting in a first‐order Markov distribution of the monomers in the final copolymer. The compositional heterogeneities of the polymers were estimated by following the instantaneous copolymer compositions as functions of conversion. Given the different reactivities of the two monomers it is concluded that a copolymer with a homogeneous distribution of monomers may be obtained not by a batch reaction, but by slowly and continuously adding GMA into the polymerizing reaction mixture. © 2001 John Wiley & Sons, Inc. J Polym Sci Part A: Polym Chem 39: 3716–3725, 2001
Compatibility and thermal properties of poly(3‐hydroxybutyrate)/poly(glycidyl methacrylate) blends
Authors: Lee Moo Sung , Park Won Ho
Published: August 2002

Poly(3‐hydroxybutyrate) (PHB)/poly(glycidyl methacrylate) (PGMA) blends were prepared by a solution‐precipitation procedure. The compatibility and thermal decomposition behavior of the PHB/PGMA blends was studied with differential scanning calorimetry, thermogravimetric analysis, and differential thermal analysis (DTA). The blends were immiscible in the as‐blended state, but for the blends with PGMA contents of 50 wt % or more, the compatibility was dramatically changed after 1 min of annealing at 200 °C. In addition, PHB/PGMA blends showed higher thermal stability, as measured by maximum decomposition temperatures and residual weight during thermal degradation. This was probably due to crosslinking reactions of the epoxide groups in the PGMA component with the carboxyl chain ends of PHB fragments during the degradation process, and the occurrence of such reactions can be assigned to the exothermic peaks in the DTA thermograms. © 2001 John Wiley & Sons, Inc. J Polym Sci Part A: Polym Chem 40: 351–358, 2002
Methyl methacrylate emulsion polymerization at low monomer concentration: Kinetic modeling of nucleation, particle size distribution, and rate of polymerization
Authors: Herrera‐Ordóñez Jorge , Olayo Roberto
Published: August 2002

The results of a mathematical model developed in the authors' previous work are discussed and compared against final number (N) and size distribution of particles (PSD) and the rate of polymerization (RP) experimental data of methyl methacrylate (MMA) emulsion polymerization above the critical micelle concentration (cmc) of the surfactant. On the basis of the model results, the hypothesis that the observed bimodal PSD can be ascribed to secondary nucleation as proposed in the literature is questionable. It is discussed that this PSD can also be caused by differences in the growing rate of different‐size particles as predicted for styrene emulsion polymerization. Because of the small particle size obtained at low initial monomer concentration, the high rate of free‐radical desorption reduces the accumulation of these species; therefore, the autoacceleration effect is less pronounced for the conditions under study compared with the usual behavior of the RP during MMA emulsion polymerization above cmc. Similarities and differences between model predictions and experimental data are discussed. © 2001 John Wiley & Sons, Inc. J Polym Sci Part A: Polym Chem 39: 2547–2556, 2001
On the wall slip of polymer blends
Authors: Maciel A. , Salas V. , Soltero J. F. A. , Guzmán J. , Manero O.
Published: August 2002

The slip flow of the polypropylene (PP)/poly[ethylene‐co‐(vinyl acetate)] (EVA) system was studied in a capillary rheometer for shear rates of 40–1000 s−1 at four temperatures. Three dies made of aluminum with a length/diameter (L/D) ratio of 15 and diameters of 1.59, 1.19, and 0.79 mm provided the flow data. Calculations of the slip velocity by the Mooney method showed power‐law behavior with the stress. Blends were prepared at various proportions of PP and EVA for observation of the variation of the slip velocity for different compositions and temperatures. Direct microscopic observations of the slip layer on extruded samples showed domains of the dispersed phase unevenly distributed between the slip layer and the core and provided estimates of the thickness of the layer adjacent to the capillary wall. Results showed that the viscosity in the slip layer was 10–100 times lower than that in the bulk for the same value of the shear stress. In terms of the extrapolation length, the development of the slip layer was the result of different disentanglement dynamics of the molecules in the slip layer in comparison with those in the bulk. © 2002 John Wiley & Sons, Inc. J Polym Sci Part B: Polym Phys 40: 303–316, 2002
Relationship between trait anxiety, brain activity and natural killer cell activity in cancer patients: a preliminary PET study
Authors: Tashiro Manabu , Itoh Masatoshi , Kubota Kazuo , Kumano Hiroaki , Masud Mehedi M. , Moser Ernst , Arai Hiroyuki , Sasaki Hidetada
Published: August 2002

The purpose of this study is to examine the relationship between psychological factors, regional brain activity and natural killer cell activity (NKA). Eight patients with malignant diseases were studied by FDG‐PET under a resting condition. NKA and degree of anxiety and depression were measured using Taylor's manifest anxiety scale (MAS) and Zung's self‐rating depression scale (SDS). Linear correlation of NKA and psychological measures to the regional brain metabolism in cancer patients was examined using statistical parametric mapping (SPM).

Positive linear correlation between NKA and regional metabolic rate ratios was identified in the visual association cortex, anterior cingulate gyrus (CG) and sensorimotor area, and negative correlation was identified in the inferolateral prefrontal cortex (ILPFC), prefrontal cortex (PFC), orbitofrontal cortex (OFC) and anterior temporal cortex. Positive linear correlation to the MAS score was identified in the visual association cortex, anterior CG, primary sensorimotor area and the posterior parietal cortex, and negative correlation was detected in the ILPFC, PFC, OFC and anterior temporal cortex. The NKA and MAS scores positively correlated with each other (p<0.001).

The result might serve as supporting data for a hypothesis that psycho‐immune interaction is also mediated by the cerebral cortex and limbic system. Copyright © 2001 John Wiley & Sons, Ltd.
Cancer patients' perceptions of do not resuscitate orders
Authors: Olver Ian N. , A. Eliott Jaklin , Blake‐Mortimer Jane
Published: August 2002

Patients' perceptions of do not resuscitate (DNR) orders and how and when to present the information were sought to aid in framing DNR policy. Semi‐structured interviews of 23 patients being treated for cancer, were conducted by a clinical psychologist. The interviews were transcribed and analysed with the aid of a qualitative software package. Discourse analysis enabled hypotheses to be formed based on consistencies and variations of the language used. Most patients understood what DNR meant and preferred DNR orders to ‘good palliative care’ orders. They saw it as their autonomous right and responsibility to make such decisions. They would seek information on the likely medical outcomes of resuscitation but also would use non‐rational criteria based on emotional and social factors to make their decisions. Family considerations suggest that personal autonomy is not the overriding basis of the decision. Patients were unsure of the best timing of a DNR discussion and were prepared to defer to doctors' intuition. Most advocated written DNR orders but few had them. Families were construed as advocates but also seen as constraining individual autonomy. When considering DNR orders, patients recognise the diversity of preferences likely to exist that belie a one policy fits all approach Copyright © 2002 John Wiley & Sons, Ltd.
Genetic differences of rock glaciers and the discontinuous mountain permafrost zone in Kanchanjunga Himal, Eastern Nepal
Authors: Ishikawa Mamoru , Watanabe Teiji , Nakamura Naohiro
Published: August 2002

A number of rock glaciers, including glacier‐derived and talus‐derived rock glaciers, were identified in Kanchanjunga Himal, easternmost Nepal. DC resistivity imagings were applied to representative rock glaciers of both types. The distribution of resistivity values in the subsurface within these rock glaciers was significantly different. A massive glacial ice body was found within the glacier‐derived rock glacier, suggesting this rock glacier originated from glacial dead ice (ice‐cored rock glacier). The lower limits of discontinuous mountain permafrost zone in Kanchanjunga Himal were inferred from the distribution of talus‐derived rock glaciers (ice‐cemented rock glaciers) and the estimated mean annual air temperature. The lower limit of the discontinuous mountain permafrost zone is 4800 m ASL on the north‐facing slopes, while 5300 m ASL on the south‐ to east‐facing slopes. These altitudes were considerably higher than those of the western Himalaya, which are under dry continental climatic conditions. Copyright © 2001 John Wiley & Sons, Ltd.
Use of nasal potential difference and sweat chloride as outcome measures in multicenter clinical trials in subjects with cystic fibrosis**
Authors: Ahrens Richard C. , Standaert Thomas A. , Launspach Janice , Han Seung‐Ho , Teresi Mary E. , Aitken Moira L. , Kelley Thomas J. , Hilliard Kathleen A. , Milgram Laura J.H. , Konstan Michael W. , Weatherly Mark R. , McCarty Nael A.
Published: August 2002

One of the goals of current research in cystic fibrosis (CF) is to develop treatments that correct or compensate for defects in function of the cystic fibrosis transmembrane regulator (CFTR) gene. The use of outcome measures that assess CFTR function such as nasal potential difference (NPD) measurements and sweat chloride determinations will be required to evaluate the efficacy of such treatments in multicenter clinical trials. The purpose of this work was to identify the sources and magnitude of variability in NPD and sweat chloride measurements when performed at multiple centers. For the variance component analysis presented here, we used NPD and sweat chloride measurements from 37 subjects with CF participating in a phase I, four‐center clinical trial of CPX (8‐cyclopentyl‐1,3‐dipropylxanthine), a drug intended to enhance trafficking of ΔF508 CFTR to the cell membrane. The specific techniques used to measure these outcomes were not standardized, and varied between the four sites.

Variability of both NPD measurements (baseline potential difference during infusion with Ringer's solution; change in response to addition of 0.1 mM amiloride; and subsequent change in response to perfusion with low chloride solution containing 0.1 mM amiloride and 0.01 mM isoproterenol) and sweat chloride measurements differed significantly between study sites. For change in NPD, one study site had significantly greater variability (lower reproducibility) of measurement than the other three sites. For sweat chloride measurements, reproducibility was lower at two of the sites relative to the other two sites.

Sample size calculations showed that lower reproducibility at one or more sites can substantially reduce the power of studies using NPD or sweat chloride determinations as outcome measures. Standardization of measurement protocols, careful operator training and certification, and ongoing monitoring of individual operator performance may help to improve reliability in multicenter trials. Pediatr Pulmonol. 2002; 33:142–150. © 2002 Wiley‐Liss, Inc.
Effect of choice of reference equation on analysis of pulmonary function in cystic fibrosis patients*
Authors: Rosenfeld Margaret , Pepe Margaret S. , Longton Gary , Emerson Julia , FitzSimmons Stacey , Morgan Wayne
Published: August 2002

Pulmonary function is an important measure of disease severity and prognosis in cystic fibrosis (CF). It is generally expressed as a percentage of a predicted value, calculated using regression equations derived from a reference population. A number of reference equations are in widespread use. The purposes of this study were to determine: 1) the extent to which, for a given absolute FEV1 value, percent of predicted (PPFEV1) values vary when derived by different reference equations; and 2) whether these differences affect conclusions of longitudinal and cross‐sectional analyses. Subjects were all Caucasians 6–18 years old in the 1990 Cystic Fibrosis Foundation Registry.

We found clinically important discrepancies in PPFEV1 when calculated by the methods of Dockery et al. [Am Rev Respir Dis 1983;128:405–412] and Wang et al. [Pediatr Pulmonol 1993;15:75–78] as compared to Knudson et al. [Am Rev Respir Dis 1983;127:725–734] or Polgar and Promadhat [Pulmonary Function Testing in Children 1971; Philadelphia: W.B. Saunders]. In longitudinal analyses, the choice of reference equation resulted in varying apparent rates of decline in FEV1. For example, among subjects ages 12–14 years in 1990, the decline in PPFEV1 from 1990–1995 varied between 2–11%, depending on the choice of reference equation. In cross‐sectional analyses, the choice of reference equation affected the distribution of subjects classified as having mild, moderate, or severe lung disease.

CF physicians should be aware of the impact of choice of reference equation in both clinical care and research. Pediatr Pulmonol. 2001; 31:227–237. © 2001 Wiley‐Liss, Inc.
DNA methylation in the androgen receptor gene promoter region in rat prostate cancers
Authors: Takahashi Satoru , Inaguma Shingo , Sakakibara Michihisa , Cho Young‐Man , Suzuki Shugo , Ikeda Yoshihisa , Cui Lin , Shirai Tomoyuki
Published: August 2002

BACKGROUND

Invasive adenocarcinomas developing in the rat dorsolateral prostate on combined treatment with 3,2′‐dimethyl‐4‐aminobiphenyl (DMAB) and testosterone propionate (TP) are biologically androgen‐independent and lacking androgen receptor protein (AR) expression. The present study was conducted to assess the mechanisms underlying this loss of AR expression in rat prostate cancer.

METHODS

The methylation status of the AR gene promoter region in rat prostate cancer and cell lines (PLS10, 20, and 30) was examined by Southern blotting, methylation‐specific polymerase chain reaction, and methylation‐sensitive single‐strand conformation analysis (MS‐SSCA).

RESULTS

AR mRNA expression was not detected in any of the rat prostate cancers or cancer cell lines tested by Northern blot analysis. Higher levels of methylated CpGs were observed in PLS20 than PLS10 or 30. Demethylation treatment by 5‐aza‐2′‐deoxycytidine restored AR mRNA expression in PLS20. The CpGs suggested to be responsible for AR expression in rat prostate cancer were found to be located ‐9 and ‐1 nucleotides upstream of the transcriptional initiation site. All of the examined rat prostate and seminal vesicle cancers demonstrated hypermethylation at these CpG sites.

CONCLUSIONS

These data clearly demonstrate that aberrant hypermethylation in the AR promoter region may play a critical role in AR expression in rat prostate cancers. Prostate 52: 82–88, 2002. © 2002 Wiley‐Liss, Inc.
Primary culture of microvascular endothelial cells from human benign prostatic hyperplasia
Authors: Stachon Axel , Schlüter Tanja , Köller Manfred , Weisser Heike , Krieg Michael
Published: August 2002

Background

Prostate growth seems to be influenced by paracrine factors like IL‐6 originating from the microvascular endothelium. Therefore, our efforts were focused on the primary culture and behavior of microvascular endothelial cells (HPEC) derived from tissue of human benign prostatic hyperplasia (BPH). Until now, the isolation and culture of HPEC from BPH have not been reported.

Methods

BPH tissue was cut into small cubes and gently squeezed after incubation with dispase. HPEC were cultured from the resulting cell suspension after a stepwise selection by use of superparamagnetic beads coated with antibodies against endothelial specific antigens. HPEC were characterized by flow cytometry and immunohistochemistry. γ‐Glutamyl transpeptidase activity (specific for microvascular endothelium) was measured after dissolution of the HPEC with Triton X‐100. After the incubation of HPEC either with ATP, VEGF, or TNF‐α, the release of IL‐6 was measured by enzyme linked immunosorbent assay (ELISA).

Results

HPEC showed a typical endothelial morphology. They were positive for von Willebrand factor, CD31, CD62E (after stimulation with TNF‐α), α‐actin and were negative for fibroblastic antigens and PSA. Proliferation was stimulated by vascular endothelial growth factor (VEGF). γ‐Glutamyl transpeptidase activity in HPEC was 6.3 μIU/μg protein, whereas in human umbilical vein endothelial cells (HUVEC) no γ‐glutamyl transpeptidase activity was detectable. The IL‐6 secretion of HPEC was stimulated by VEGF and TNF‐α, but not by ATP and bradykinin.

Conclusions

For the first time, the primary culture of microvascular endothelial cells from BPH tissue was successfully performed. Our results suggest that HPEC may be actively involved in prostate growth, due to the secretion of regulatory factors such as IL‐6. Prostate 48:156–164, 2001. © 2001 Wiley‐Liss, Inc.
Hypermethylation of the CD44 gene is associated with progression and metastasis of human prostate cancer
Authors: Kito Hiroki , Suzuki Hiroyoshi , Ichikawa Tomohiko , Sekita Nobuyuki , Kamiya Naoto , Akakura Koichiro , Igarashi Tatsuo , Nakayama Tsuyoshi , Watanabe Masatoshi , Harigaya Kenichi , Ito Haruo
Published: August 2002

Background

CD44 is a metastasis suppressor gene for prostate cancer and the down‐regulation of CD44 and its variants is associated with the progression of prostate cancer. Also, hypermethylation of the CpG islands of the CD44 gene is closely associated with transcriptional inactivation, resulting in the decreased expression of CD44. To clarify the exact role of methylation status of CpG islands of CD44 gene in the progression and metastasis of prostate cancer, we investigated the methylation status of this gene in primary and metastatic human prostate tumors obtained from surgery or autopsy.

Methods

We examined 97 samples from 40 Japanese patients with adenocarcinoma of the prostate. Tumor tissues were obtained from radical prostatectomy specimens from eight patients with stage B, 12 patients with stage C and three patients with stage D1 and at autopsy from 17 hormone‐refractory metastatic cases, who had initially responded to the therapy and thereafter relapsed. Distant metastatic tissues were also obtained at autopsy (i.e., liver, lung, kidney, mammary gland, and pelvic lymph nodes) from 10 of 17 hormone‐refractory cases. We analyzed the hypermethylation status of CD44 promotor region by PCR using genomic DNAs digested with the m5C‐sensitive restriction enzyme HpaII.

Results

The correlation between the methylation status of CD44 gene and the stage progression of prostate cancer was statistically significant (P = 0.0438). In two of 10 hormone‐refractory cases, a comparison of the methylation status of the CD44 gene in metastases to that in primary tumors revealed interfocal heterogeneity of CD44 methylation status.

Conclusions

These results indicate an important role of CD44 methylation in the progression and metastasis of prostate cancer, although the amount of methylational heterogeneity is substantial among metastatic sites within the same patient. Prostate 49:110–115, 2001. © 2001 Wiley‐Liss, Inc.
Dynamic and structural analysis of isotropically distributed molecular ensembles
Authors: Prompers Jeanine J. , Brüschweiler Rafael
Published: August 2002

An efficient new method is presented for the characterization of motional correlations derived from a set of protein structures without requiring the separation of overall and internal motion. In this method, termed isotropically distributed ensemble (IDE) analysis, each structure is represented by an ensemble of isotropically distributed replicas corresponding to the situation found in an isotropic protein solution. This leads to a covariance matrix of the cartesian atomic positions with elements proportional to the ensemble average of scalar products of the position vectors with respect to the center of mass. Diagonalization of the covariance matrix yields eigenmodes and amplitudes that describe concerted motions of atoms, including overall rotational and intramolecular dynamics. It is demonstrated that this covariance matrix naturally distinguishes between “rigid” and “mobile” parts without necessitating a priori selection of a reference structure and an atom set for the orientational alignment process. The method was applied to the analysis of a 5‐ns molecular dynamics trajectory of native ubiquitin and a 40‐ns trajectory of a partially folded state of ubiquitin. The results were compared with essential dynamics analysis. By taking advantage of the spherical symmetry of the IDE covariance matrix, more than a 10‐fold speed up is achieved for the computation of eigenmodes and mode amplitudes. IDE analysis is particularly suitable for studying the correlated dynamics of flexible and large molecules. Proteins 2002;46:177–189. © 2001 Wiley‐Liss, Inc.
Role of hydrophilic and hydrophobic contacts in folding of the second β‐hairpin fragment of protein G: Molecular dynamics simulation studies of an all‐atom model
Authors: Zhou Yaoqi , Linhananta Apichart
Published: August 2002

Predicting the folding mechanism of the second β‐hairpin fragment of the Ig‐binding domain B of streptococcal protein G is unexpectedly challenging for simplified reduced models because the models developed so far indicated a different folding mechanism from what was suggested from high‐temperature unfolding and equilibrium free‐energy surface analysis based on established all‐atom empirical force fields in explicit or implicit solvent. This happened despite the use of empirical residue‐based interactions, multibody hydrophobic interactions, and inclusions of hydrogen bonding effects in the simplified models. This article employs a recently developed all‐atom (except nonpolar hydrogens) model interacting with simple square‐well potentials to fold the peptide fragment by molecular dynamics simulation methods. In this study, 193 out of 200 trajectories are folded at two reduced temperatures (3.5 and 3.7) close to the transition temperature T* ∼ 4.0. Each simulation takes <7 h of CPU time on a Pentium 800‐MHz PC. Folding of the new all‐atom model is found to be initiated by collapse before the formation of main‐chain hydrogen bonds. This verifies the mechanism proposed from previous all‐atom unfolding and equilibrium simulations. The new model further predicts that the collapse is initiated by two nucleation contacts (a hydrophilic contact between D46 and T49 and a hydrophobic contact between Y45 and F52), in agreement with recent NMR measurements. The results suggest that atomic packing and native contact interactions play a dominant role in folding mechanism. Proteins 2002;47:154–162. © 2002 Wiley‐Liss, Inc.
Analysis of a data set of paired uncomplexed protein structures: New metrics for side‐chain flexibility and model evaluation
Authors: Zhao Shanrong , Goodsell David S. , Olson Arthur J.
Published: August 2002

We compiled and analyzed a data set of paired protein structures containing proteins for which multiple high‐quality uncomplexed atomic structures were available in the Protein Data Bank. Side‐chain flexibility was quantified, yielding a set of residue‐ and environment‐specific confidence levels describing the range of motion around χ1 and χ2 angles. As expected, buried residues were inflexible, adopting similar conformations in different crystal structure analyses. Ile, Thr, Asn, Asp, and the large aromatics also showed limited flexibility when exposed on the protein surface, whereas exposed Ser, Lys, Arg, Met, Gln, and Glu residues were very flexible. This information is different from and complementary to the information available from rotamer surveys. The confidence levels are useful for assessing the significance of observed side‐chain motion and estimating the extent of side‐chain motion in protein structure prediction. We compare the performance of a simple 40° threshold with these quantitative confidence levels in a critical evaluation of side‐chain prediction with the program SCWRL. Proteins 2001;43:271–279. © 2001 Wiley‐Liss, Inc.
Optimization of solvation models for predicting the structure of surface loops in proteins
Authors: Das Bedamati , Meirovitch Hagai
Published: August 2002

A novel procedure for optimizing the atomic solvation parameters (ASPs) σi developed recently for cyclic peptides is extended to surface loops in proteins. The loop is free to move, whereas the protein template is held fixed in its X‐ray structure. The energy is Etot = EFF(ϵ = nr) + ∑ σiAi, where EFF(ϵ = nr) is the force‐field energy of the loop–loop and loop–template interactions, ϵ = nr is a distance‐dependent dielectric constant, and n is an additional parameter to be optimized. Ai is the solvent‐accessible surface area of atom i. The optimal σi and n are those for which the loop structure with the global minimum of Etot(n, σi) becomes the experimental X‐ray structure. Thus, the ASPs depend on the force field and are optimized in the protein environment, unlike commonly used ASPs such as those of Wesson and Eisenberg (Protein Sci 1992;1:227–235). The latter are based on the free energy of transfer of small molecules from the gas phase to water and have been traditionally combined with various force fields without further calibration. We found that for loops the all‐atom AMBER force field performed better than OPLS and CHARMM22. Two sets of ASPs [based on AMBER (n = 2)], optimized independently for loops 64–71 and 89–97 of ribonuclease A, were similar and thus enabled the definition of a best‐fit set. All these ASPs were negative (hydrophilic), including those for carbon. Very good (i.e., small) root‐mean‐square‐deviation values from the X‐ray loop structure were obtained with the three sets of ASPs, suggesting that the best‐fit set would be transferable to loops in other proteins as well. The structure of loop 13–24 is relatively stretched and was insensitive to the effect of the ASPs. Proteins 2001;43:303–314. © 2001 Wiley‐Liss, Inc.
How to guarantee optimal stability for most representative structures in the protein data bank
Authors: Bastolla Ugo , Farwer Jochen , Knapp Ernst Walter , Vendruscolo Michele
Published: August 2002

We proposed recently an optimization method to derive energy parameters for simplified models of protein folding. The method is based on the maximization of the thermodynamic average of the overlap between protein native structures and a Boltzmann ensemble of alternative structures. Such a condition enforces protein models whose ground states are most similar to the corresponding native states. We present here an extensive testing of the method for a simple residue‐residue contact energy function and for alternative structures generated by threading. The optimized energy function guarantees high stability and a well‐correlated energy landscape to most representative structures in the PDB database. Failures in the recognition of the native structure can be attributed to the neglect of interactions between different chains in oligomeric proteins or with cofactors. When these are taken into account, only very few X‐ray structures are not recognized. Most of them are short inhibitors or fragments and one is a structure that presents serious inconsistencies. Finally, we discuss the reasons that make NMR structures more difficult to recognize. Proteins 2001;44:79–96. © 2001 Wiley‐Liss, Inc.
Role of non‐glycine residues in left‐handed helical conformation for the conformational stability of human lysozyme
Authors: Takano Kazufumi , Yamagata Yuriko , Yutani Katsuhide
Published: August 2002

To understand the role of non‐Gly residues in the left‐handed helical conformation for the conformational stability of a protein, the non‐Gly to Gly and Ala mutations at six left‐handed residues (R21, Y38, R50, Q58, H78, and N118) of the human lysozyme were examined. The thermodynamic parameters for denaturation were determined using a differential scanning calorimeter, and the crystal structures were analyzed by X‐ray crystallography. If a left‐handed non‐Gly had an unfavorable steric interaction between the side‐chain Cβ and backbone, the Gly mutation would be expected to stabilize more than the Ala mutation at the same position. For the mutant human lysozymes, however, there were few differences in the denaturation Gibbs energy (ΔG) between the Gly and Ala mutants, except for the substitution at position 58. Analysis of the changes in stability (ΔΔG) based on the structures of the wild‐type and mutant proteins showed that the experimental ΔΔG value of Q58G was ∼7 kJ/mol higher than the estimated value without consideration of any local steric interaction. These results indicate that only Q58G increased the stability by elimination of local constraints. The residue 58 is located at the most rigid position in the left‐handed non‐Gly residues and is involved in its enzymatic function. It can be concluded that the left‐handed non‐Gly residues do not always have unfavorable strain energies as compared with Gly at the same position. Proteins 2001;44:233–243. © 2001 Wiley‐Liss, Inc.
Role of amino acid residues in left‐handed helical conformation for the conformational stability of a protein
Authors: Takano Kazufumi , Yamagata Yuriko , Yutani Katsuhide
Published: August 2002

Our previous study of six non‐Gly to Gly/Ala mutant human lysozymes in a left‐handed helical region showed that only one non‐Gly residue at a rigid site had unfavorable strain energy as compared with Gly at the same position (Takano et al., Proteins 2001; 44:233–243). To further examine the role of left‐handed residues in the conformational stability of a protein, we constructed ten Gly to Ala mutant human lysozymes. Most Gly residues in human lysozyme are located in the left‐handed helix region. The thermodynamic parameters for denaturation and crystal structures were determined by differential scanning calorimetry and X‐ray analysis, respectively. The difference in denaturation Gibbs energy (ΔΔG) for the ten Gly to Ala mutants ranged from + 1.9 to −7.5 kJ/mol, indicating that the effect of the mutation depends on the environment of the residue. We confirm that Gly in a left‐handed region is more favorable at rigid sites than non‐Gly, but there is little difference in energetic cost between Gly and non‐Gly at flexible sites. The present results indicate that dihedral angles in the backbone conformation and also the flexibility at the position should be considered for analyses of protein stability, and protein structural determination, prediction, and design. Proteins 2001;45:274–280. © 2001 Wiley‐Liss, Inc.
Crystal structure of non‐allosteric L‐lactate dehydrogenase from Lactobacillus pentosus at 2.3 Å resolution: Specific interactions at subunit interfaces
Authors: Uchikoba Hiroyuki , Fushinobu Shinya , Wakagi Takayoshi , Konno Michiko , Taguchi Hayao , Matsuzawa Hiroshi
Published: August 2002

L‐Lactate dehydrogenase (LDH) from Lactobacillus pentosus is a non‐allosteric enzyme, which shows, however, high sequence similarity to allosteric LDHs from certain bacteria. To elucidate the structural basis of the absence of allostery of L. pentosus LDH (LPLDH), we determined the crystal structure of LPLDH at 2.3 Å resolution. Bacterial LDHs are tetrameric enzymes composed of identical subunits and exhibit 222 symmetry. The quaternary structure of LPLDH was similar to the active conformation of allosteric LDHs. Structural analysis revealed that the subunit interfaces of LPLDH are optimized mainly through hydrophilic interactions rather than hydrophobic interactions, compared with other LDHs. The subunit interfaces of LPLDH are more specifically stabilized by increased numbers of intersubunit salt bridges and hydrogen bonds, and higher geometrical complementarity. Such high specificity at the subunit interfaces should hinder the rearrangement of the quaternary structure needed for allosteric regulation and thus explain the “non‐allostery” of LPLDH. Proteins 2002;46:206–214. © 2001 Wiley‐Liss, Inc.
Metabolism of the phosphonate herbicide glyphosate by a non‐nitrate‐utilizing strain of Penicillium chrysogenum
Authors: Klimek Magdalena , Lejczak Barbara , Kafarski Paweł , Forlani Giuseppe
Published: August 2002

A Penicillium chrysogenum strain was isolated for its ability to grow in minimal medium containing the herbicide glyphosate as the only nitrogen source. The presence of concentrations up to 25 mM progressively stimulated the fungal growth rate, which was negligible in media lacking reduced nitrogen. However, glyphosate utilization never exceeded 1 mmol g−1 mycelial dry mass, and below a threshold concentration both herbicide uptake and fungal growth were subject to a lag phase, suggesting that the herbicide may enter the cell by either simple passive diffusion or inducible carriers. Amino acids, possible products of glyphosate breakdown, as well as ammonia, were found to replace the herbicide in restoring mycelial growth. Cells were devoid of detectable nitrate reductase activity, thus the isolate seems to be impaired in its ability to convert nitrate to ammonium. In vitro activity of 5‐enol‐pyruvyl‐shikimate‐3‐phosphate synthase, the target site of glyphosate action, was highly sensitive to the herbicide. Fungal growth rate was considerably lower when the herbicide was also the only phosphorus source, whereas glyphosate utilization was substantially unaffected, suggesting an unusual route for its degradation. Herbicide metabolism was strongly reduced when other sources of organic nitrogen were made available.

© 2001 Society of Chemical Industry
Wild salmonids and sea louse infestations on the west coast of Scotland: sources of infection and implications for the management of marine salmon farms
Authors: Butler James R A
Published: August 2002

The sea louse (Lepeophtheirus salmonis Krøyer) is a major health problem for both farmed and wild salmonids. This paper investigates louse epidemiology and management in the salmon‐farming zone of western Scotland. Based on a review of the marine ecology of wild salmon (Salmo salar L) and sea trout (Salmo trutta L), and catch and farm production statistics, best estimates were made for numbers of wild and farm hosts present in coastal waters in March–June 2000. Applying data for ovigerous female louse infections and fecundity, the sources and risks of larval transmission to wild salmon and sea trout were modelled. Farm salmon in the second spring of production were the primary host group (98% of fish), while numbers of wild salmonids (<1%) and escaped farm salmon (2%) were relatively insignificant. Farm salmon produced 97% of louse eggs at high levels (eight ovigerous lice per fish), and 78% at low levels (one per fish). Wild salmonids produced <1% of eggs under both scenarios, but escaped farm salmon produced 3% and 21%, respectively. All hosts potentially cross‐infect one another, but farm salmon are more likely to infect wild and farm smolts, and also other farm salmon. Monitoring of lice on sea trout in June 1998–2000 by the Association of West Coast Fisheries Trusts corroborated the model's conclusions. Localised epizootics occurred every year and coincided with the presence of ovigerous lice on local farms. In areas of mixed‐year class production on farms, epizootics were evident every spring, but occurred every second spring in areas of single‐year class production. In 1998–2000 at least 14–40% of sea trout were infected with potentially lethal infestations of lice. Ovigerous louse levels of <0.005 per fish were required on farm salmon in the spring of 2000 to produce less eggs than those emitted by wild salmonids. With the industry's continued expansion, and thus increased numbers of farm salmon, a target of zero ovigerous lice will be required on farms to minimise impacts on wild salmonids. Due to the limited long‐term efficacy and availability of louse medicines, management strategies are discussed which will improve control, including single‐year class production over large areas, alternate S1–S1/2 smolt inputs, and 11‐month production cycles.

© 2002 Society of Chemical Industry
Traffic load models for bridge design: recent developments and research
Authors: Prat Michel
Published: August 2002

The processes and methods used to achieve the load models of the Eurocode for traffic loads on road bridges pREN1991‐2 is now widely accepted. Various universities (Aaachen, Delft, Trinity College, Dublin, Liège, Pisa), consulting engineers (Flint & Neill Partnership) and organizations, notably the TRL (Transport Research Laboratory) and the BRE (British Research Establishement, Ltd), the main centres for civil engineering research in the United Kingdom, together with the SETRA and the LCPC who cover the major aspects of road transport for the Ministry of Transport in France, lead studies involving civil engineering companies, industrial manufacturers of heavy vehicles and manufacturers of tyres for the determination of loading levels for bridge design. This paper presents an overview of recent developments and some envisaged research.
Hypocholesterolaemic effect of the oleoresin of Capsicum annum L. in gerbils (Meriones hurrianae Jerdon)
Authors: Gupta R. S. , Dixit V. P. , Dobhal M. P.
Published: August 2002

The effect of capsicum oleoresin (CO) on dietary hypercholeterolaemia were observed in male gerbils at a dose of 75 mg/kg body wt/day. The oleoresin reduced serum cholesterol and triglycerides by 70% and 66%, whereas, liver cholesterol and triglycerides were lowered by 70.9% and 68.7% respectively, in comparison with atherogenic fed controls. CO feeding prevented the accumulation of cholesterol and triglycerides in the liver and aorta. The faecal excretion of cholesterol and triglycerides were significantly increased in oleoresin fed gerbils. Copyright © 2002 John Wiley & Sons, Ltd.
Antiulcerogenic effect of Hippophae rhamnoides L.
Authors: Süleyman H. , Demirezer L. Ö. , Büyükokuroglu M. E. , Akcay M. F. , Gepdiremen A. , Banoglu Z. N. , Göçer F.
Published: August 2002

The antiulcerogenic effect of a hexane extract (HRe‐1) from Hippophae rhamnoides (Eleagnaceae) was tested on indomethacin‐ and stress‐induced ulcer models. As a result HRe‐1 was found to be active in preventing gastric injury. Copyright © 2001 John Wiley & Sons, Ltd.
The in vitro effect of Viscum album (VA) extract on DNA repair of peripheral blood mononuclear cells (PBMC) in cancer patients
Authors: Kovacs Eva
Published: August 2002

Viscum album (VA) extract as an immunomodulator was tested in an in vitro model to investigate DNA repair in damaged peripheral blood mononuclear cells (PBMC) of ten breast cancer patients. The cells were exposed by gamma rays or 4‐hydroxycyclophosphamide (4‐HCy). Two hours after exposure the following were measured, without or with VA extract (1) DNA repair using the alkaline sucrose gradient for the sedimentation of DNA strand breaks, (2) DNA‐gamma‐production in the supernatant of the cultured cells. The VA extract led to an improvement of DNA repair in gamma‐ray or 4‐HCy damaged PBMC and to a significant increase of the IFN‐gamma‐production both in undamaged and in damaged cells.

The results indicate that the VA extract affects positively DNA repair in PBMC damaged by two different agents and suggest that an increased IFN‐gamma‐production may play an important role in the DNA repair process. Copyright © 2002 John Wiley & Sons, Ltd.
Antipruritic and antidermatitic effect of extract and compounds of Impatiens balsamina L. in atopic dermatitis model NC mice
Authors: Oku Hisae , Ishiguro Kyoko
Published: August 2002

We examined the effects of a 35% ethanol extract (IB) from the petals of Impatiens balsamina L. and the principal active compounds from IB on chronic and serious pruritus and the development of dermatitis using NC mice, a model of atopic dermatitis. IB at 100 mg/kg significantly inhibited serious scratching behaviour in the NC mouse with established dermatitis when administered i.v. 1 h before, or p.o. 24 h before the measurement. A 10 μg/kg dose of kaempferol 3‐rutinoside and 2‐hydroxy‐1, 4‐naphthoquinone (lawsone) isolated from IB also inhibited scratching behaviour in the NC mouse with established dermatitis. When 4‐week‐old NC mice with no symptoms were administered orally 100 mg/kg/day of IB until 13 weeks of age, protection was also noted against scratching behaviour during the development of dermatitis. IB was effective for the prevention and treatment of atopic dermatitis. Copyright © 2001 John Wiley & Sons, Ltd.
Evaluation of the potency activity of aphrodisiac in Eurycoma longifolia Jack
Authors: Ang H. H. , Ikeda S. , Gan E. K.
Published: August 2002

The butanol, methanol, water and chloroform extracts of the roots of Eurycoma longifolia Jack were studied using various tests of potency of treated male rats. The results showed that E. longifolia produced a dose‐dependent, recurrent and significant increase in the episodes of penile reflexes as evidenced by increases in quick flips, long flips and erections of the treated male rats during the 30 min observation period. These results provide further evidence that E. longifolia increases the aphrodisiac potency activity in treated animals. Copyright © 2001 John Wiley & Sons, Ltd.
Effects of Rosa canina fruit extract on neutrophil respiratory burst
Authors: Daels‐Rakotoarison D. A. , Gressier B. , Trotin F. , Brunet C. , Luyckx M. , Dine T. , Bailleul F. , Cazin M. , Cazin J‐C.
Published: August 2002

Respiratory burst leads polymorphonuclear neutrophils (PMN) to produce reactive oxygen species (ROS) such as superoxide anions (O2 °−), hypochlorous acid (HOCl) and hydrogen peroxide (H2O2) which may possess deleterious effects for the organism. Rosa canina fruits are well known to contain a large amount of vitamin C which is antioxidant. This study was focused on the polyphenolics contained in rose hips to evaluate their antioxidative properties.
 We prepared a rose hip extract deprived of vitamin C. The extract contained mainly phenolics such as proanthocyanidins and flavonoids. We investigated its effects directly against O2 °−, HOCl and H2O2 and investigated its effects on isolated PMN. For that, in vitro inflammatory conditions were reproduced by stimulating PMN with stimuli having different transductional pathways, in order to determine a possible mechanism of action.
 The results showed that the extract can inhibit ROS tested in acellular and cellular systems. The IC50 obtained were 5.73 mg/L, 1.33 mg/L and 2.34 mg/L respectively for O2 °−, HOCl and H2O2 in acellular experiments. For cellular experiments, the IC50 were quite similar. Thus, the extract did not present an effect on PMN metabolism. Therefore, the antioxidative effects of Rosa canina are due not only to vitamin C but also to polyphenolics. Copyright © 2002 John Wiley & Sons, Ltd.