bluuebunny/crossref_metadata_2025 huggingface dataset:
Unified analysis of thermodynamic and rheological properties of high polymer solutions. I. Binary systems
Authors: Grigera Tomás S. , Irurzun Isabel M. , Cortizo M. Susana , Figini Rubén V. , Marx‐Figini Marianne
Published: August 2002

We present a comprehensive experimental study of thermodynamic and rheological properties of semidilute polymer solutions in good solvent. Osmotic pressure and viscosity measurements have been done in several polymer‐solvent systems at different temperatures. A renormalization group technique was applied to analyze the data using de Gennes's blobs model to connect dynamic and conformational quantities. The behavior of polymer systems in the whole range from dilute to semidilute solutions can be satisfactorily described using only a few nonuniversal quantities experimentally determined. An adequate agreement between experiments and theory was found, showing universal behavior with a system‐dependent constant β that does not depend on molecular weight or concentration. © 2001 John Wiley & Sons, Inc. J Polym Sci Part B: Polym Phys 40: 290–301, 2002
Block copolymer compatibilizers for polystyrene/poly(dimethylsiloxane) blends
Authors: Marić M. , Macosko C. W.
Published: August 2002

Symmetric polystyrene (PS)–poly(dimethylsiloxane) (PDMS) diblock copolymers were mixed into a 20% dispersion of PDMS in PS. The effect of adding the block copolymer on the blend morphology was examined as a function of the block copolymer molecular weight (Mn,bcp), concentration, and viscosity ratio (ηr). When blended together with the PS and PDMS homopolymers, most of the block copolymer appeared as micelles in the PS matrix. Even when the copolymer was preblended into the PDMS dispersed phase, block copolymer micelles in the PS matrix phase were observed with transmission electron microscopy after mixing. Adding 16 kg/mol PS–PDMS block copolymer dramatically reduced the PDMS particle size, but the morphology, as examined by scanning electron microscopy, was unstable upon thermal annealing. Adding 156 kg/mol block copolymer yielded particle sizes similar to those of blends with 40 or 83 kg/mol block copolymers, but only blends with 83 kg/mol block copolymer were stable after annealing. For a given value of Mn,bcp, a minimum PDMS particle size was observed when ηr ∼ 1. When ηr = 2.6, thermally stable, submicrometer particles as small as 0.6 μm were observed after the addition of only 3% PS–PDMS diblock (number‐average molecular weight = 83 kg/mol) to the blend. As little as 1% 83 kg/mol block copolymer was sufficient to stabilize a 20% dispersion of 1.1‐μm PDMS particles in PS. Droplet size reduction was attributed to the prevention of coalescence caused by small amounts of block copolymer at the interface. The conditions under which block copolymer interfacial adsorption and interpenetration were facilitated were explained with Leibler's brush theory. © 2002 John Wiley & Sons, Inc. J Polym Sci Part B: Polym Phys 40: 346–357, 2002; DOI 10.1002/polb.10098
Round‐robin experiment in high‐temperature gel permeation chromatography
Authors: D'Agnillo Luigi , Soares J. B. P. , Penlidis A.
Published: August 2002

The results of an interlaboratory or round‐robin experiment in high‐temperature gel permeation chromatography (HT‐GPC) analysis are presented. The intention was to determine and raise awareness of interlaboratory reproducibility of HT‐GPC techniques. Fifteen laboratories performed analyses of five polyethylene samples and standards SRM 1475 and 1476. Reproducibility, as measured by the interlaboratory standard deviation (sLAB), was greatly influenced by the breadth of the molecular weight distribution (MWD) and branching. The sLAB values for the weight‐average molecular weight (Mw) of linear polyethylenes of narrow and broad MWDs were 4 and 14%, respectively. For branched polymers, GPC viscometry methods are shown to measure significantly higher molecular weights than the noncoupled GPC method, with higher variance. For branched polyethylenes measured with GPC viscometry, the reproducibility of Mw was characterized by sLAB = 18%. Reproducibility of the SRM 1475 standard was better than for unknowns. The results for branched standard SRM 1476 emphasize the important role of the detection method in GPC but call into question the use of this material as a molecular weight standard. For single‐site polyethylene, only a handful of labs measured an MWD that closely matched the Flory distribution. Qualitatively, the responses indicate that many variations in instrument and analytical methods exist among laboratories; this is partly a reflection of the development and refinements that this technique must yet undergo before a truly standard method is widely accepted and practiced. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 905–921, 2002
Conformational characteristics of poly(ethylene phthalate)s
Authors: Tonelli Alan E.
Published: August 2002

The conformational characteristics, as embodied in the unperturbed mean‐square end‐to‐end distances (〈r2〉o) and the characteristic ratios of the dimensions [Cn = 〈r2〉o/(n〈l2〉] are calculated for the para, meta, and ortho isomers of poly(ethylene phthalate)s: poly(ethylene terephthalate) (PET), poly(ethylene isophthalate) (PEI), and poly(ethylene phthalate) (PEP), respectively. Although each of these isomeric and partially aromatic polyesters has identical permissible conformations available to their ethylene glycol fragments, their connections through the ester bonds to the phenyl rings are quite distinct. In addition, for the ortho isomer (PEP), the close spatial proximity of the ester groups bonded to the same phenyl ring results in an interdependence of their orientations with respect to each other and the phenyl ring to which they are attached, unlike the independent orientations of ester groups in the para and meta isomers (PET and PEI). Conformational energy calculations, dependent on the orientation of the ester groups in PEP, are used to characterize their rotational interdependence to modify the rotational isomeric state (RIS) conformational models for PET and PEI and thereby obtain an RIS model appropriate for PEP. This leads to calculated relative dimensions (〈r2〉o) of 1.0:0.70:0.37 PET:PEI:PEP and characteristic ratios [Cn = 〈r2〉o/(n〈l2〉)] of 4.13:4.67:2.49 PET:PEI:PEP. These results are discussed in an effort to obtain some understanding of the inherent static (or equilibrium) and dynamic flexibilities of the isomeric poly(ethylene phthalate)s. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 1254–1260, 2002
Effect of pressure and temperature on chromophore reorientation in a new syndioregic main‐chain hydrazone nonlinear optical polymer
Authors: Hayden L. Michael , Kim Won‐Kook , Chafin Andrew P. , Lindsay Geoffrey A.
Published: August 2002

Second harmonic generation (SHG) was used to measure the temperature dependence of the reorientation activation volume (ΔV*) of a syndioregic main‐chain hydrazone (SMCH) nonlinear optical polymer. The decay of the SHG signal from poled films of SMCH was recorded at hydrostatic pressures up to 2924 atm and at temperatures between 25 °C below the glass‐transition temperature (Tg) to 20 °C above it. ΔV* for pressures less than 500–1000 atm and T > Tg decreased as the temperature was increased. For pressures greater than 1000 atm, ΔV* was essentially constant for all temperatures. In addition, the size of ΔV* indicated that the chromophore in this main chain was internally flexible. © 2001 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 39: 895–900, 2001
Physical sequelae and self‐perceived attachment in adult survivors of childhood cancer
Authors: Joubert David , Sadéghi M. Réza , Elliott Mary , Devins Gerald M. , Laperrière Normand , Rodin Gary
Published: August 2002

The association between the physical sequelae of childhood cancer and self‐reported attachment behavior was investigated in 97 adult survivors. Attachment was assessed using standardized self‐report questionnaires. Functional disability and cosmetic sequelae of the cancer and its treatment were evaluated by the attending oncologist using a standardized rating scale. Results suggest that attachment is not significantly associated with physician‐rated physical sequelae, but may be related to the time of onset of the functional deficits, independent of the current age or age at diagnosis. Further, survivors with functional sequelae in adulthood describe themselves as more insecure in their relationships in general and more ambivalent in their relationship with their parents. These findings, if replicated, suggest that the duration of the functional deficits as well as the developmental stage of the individual when they began may be important variables which affect the survivor's capacity to develop and maintain intimate relationships that are secure and satisfying. Copyright © 2001 John Wiley & Sons, Ltd.
Quality of life in patients attending a low‐risk gynaecological oncology follow‐up clinic
Authors: Leake Robyn L. , Gurrin Lyle C. , Hammond Ian G.
Published: August 2002

Objectives: (1) To assess the quality of life (QOL) of patients who had been treated for gynaecological malignancies and who were attending a low risk follow‐up clinic. (2) To determine the accuracy of the clinic physicians' assessment of patients' QOL compared with the Functional Living Index—Cancer (FLI‐C) [Schipper et al., 1984. Measuring the quality of life of cancer patients: the Functional Living Index—Cancer: development and validation. J Clin Oncol 2(5): 472–483]. (3) To examine a single subjective question about change in QOL. (4) To assess patient fear of cancer recurrence.

Design: Self‐administered patient questionnaire. The questionnaire contained the FLI‐C, with four additional questions.

Setting: Low risk (good prognosis) follow‐up clinics in the Department of Gynaecological Oncology at King Edward Memorial Hospital (the tertiary centre for obstetrics and gynaecology for the state of Western Australia).

Patients: 202 consecutive attendees of the clinic. Non‐English speaking patients attending without an interpreter were excluded.

Results: Most patients reported a good QOL. The range of FLI‐C scores was 59–154 (possible range 22–154), with a median score of 140 and a mean of 134. Younger patients were more fearful of cancer recurrence. Radiotherapy was associated with a worsening of QOL. Patients living with partners experienced deterioration in sexual functioning.

Conclusions: Patients attending the low risk follow‐up clinic after gynaecological malignancy have a good overall QOL. Copyright © 2001 John Wiley & Sons, Ltd.
A structural model of the relationships among self‐efficacy, psychological adjustment, and physical condition in Japanese advanced cancer patients
Authors: Hirai Kei , Suzuki Yoko , Tsuneto Satoru , Ikenaga Masayuki , Hosaka Takashi , Kashiwagi Tetsuo
Published: August 2002

We made detailed research for relationships among physical condition, self‐efficacy and psychological adjustment of patients with advanced cancer in Japan. The sample consisted of 85 (42 males and 43 females) advanced cancer patients. Interviews were conducted with some measurement scales including the Self‐efficacy scale for Advanced Cancer (SEAC), and the Hospital Anxiety and Depression Scale (HADS). Karnofsky Performance Status (KPS) and medication status were also recorded from the evaluation by physicians. We used structural equation modeling (SEM) for statistical analysis. The analysis revealed that the model, including three self‐efficacy subscales, depression, anxiety, KPS, meal‐, liquid‐intake, prognosis and three latent variables: ‘Self‐efficacy’, ‘Emotional Distress’, and ‘Physical Condition,’ fit the data (chi‐square(24)=28.67, p=0.23; GFI=0.93; CFI=0.98; RMSEA=0.05). In this model, self‐efficacy accounted for 71% of the variance in emotional distress and physical condition accounted for 8% of the variance in self‐efficacy. Overall, our findings suggest clearly that close relationships existed among physical condition, self‐efficacy and emotional distress. That is, patients in good physical condition had a high self‐efficacy, and patients with high self‐efficacy were less emotionally distressed. These results imply that psychological intervention which emphasizes self‐efficacy would be effective for advanced cancer patients. Copyright © 2002 John Wiley & Sons, Ltd.
Communication in the cancer ‘bad news’ consultation: patient perceptions and psychological adjustment
Authors: Mager Wendy M. , Andrykowski Michael A.
Published: August 2002

The purpose of this study was to explore relationships between breast cancer survivors' experiences during the diagnostic consultation and their subsequent long‐term psychological adjustment. Sixty women (M age=53 years) who had been diagnosed with local or regional breast cancer (Stage 0–IIIA) an average of 28 months prior were interviewed by telephone. Measures included: Cancer Diagnostic Interview Scale, Anxiety subscale of the Hospital Anxiety and Depression Scale, Posttraumatic Stress Disorder Checklist – Civilian Version, Center for Epidemiologic Studies Depression Scale, and ad hoc items regarding memory for, and satisfaction with, the diagnostic consultation. After controlling for demographic and clinical variables, the three CDIS subscales accounted for 12% of the variance in women's PCL‐C scores (F change=3.46, p<0.05). The CDIS‐Caring subscale was a significant predictor in the ‘best‐fit’ regression model for each of the three indices of long‐term distress (all B's>−0.23, p<0.05). In contrast, the CDIS‐Competence subscale was not a significant predictor in any of the ‘best‐fit’ models. Additionally, women's satisfaction with physician behavior during the diagnostic consultation was unrelated to all adjustment measures (r's<0.10, p's>0.50). Findings suggest that women's perceptions of physicians' interpersonal skills during the diagnostic consultation are associated with later psychological adjustment. Copyright © 2002 John Wiley & Sons, Ltd.
Ground thermal conditions in a frost‐crack polygon, a palsa and a mineral palsa (lithalsa) in the discontinuous permafrost zone, northern Sweden
Authors: Westin Bo , Zuidhoff Frieda S.
Published: August 2002

Ground temperature measurements were collected during 1997 to 1998 at three locations in the discontinuous permafrost zone in northern Sweden. Measurements were made in two frost‐crack polygons, two palsas and a mineral palsa (lithalsa). Important for the formation of permafrost at all locations are (i) the absence of snow and, (ii) local soil properties. The seasonal variation in apparent thermal diffusivity—with higher diffusivities in summer than in winter in the mineral soil of the frost‐crack polygon and relatively little seasonal variation in the peat of the palsas—is the main cause for the cooler conditions in the palsas in summer. Morphology adds to the temperature fluctuations as indicated by highly fluctuating ground temperatures in the dome‐shaped mineral palsa as compared to the frost‐crack polygon. Occasional ground temperature gradients of more than −10 °C/m are probably sufficient for seasonal frost cracking. Copyright © 2001 John Wiley & Sons, Ltd.
Normal volume of distribution of tobramycin in a mother and daughter with a CFTR splice mutation (1717 − 1G → A)
Authors: Simon Dawn , Cimino Michael , Borowitz Drucy
Published: August 2002

A mother and daughter pair with CF who shared a splice mutation (1717 − 1G → A) had a normal volume of distribution of tobramycin. The literature on tobramycin pharmacokinetics, which was published before the genetic defect was identified, is discussed. The authors speculate on the role of CFTR in the distribution of aminoglycosides and recommend that CFTR mutations should be clarified in all future studies of tobramycin pharmacokinetics in patients with CF. Pediatr Pulmonol. 2002; 33:315‐317. © 2002 Wiley‐Liss, Inc.
Exhaled nitric oxide and asthma in young children
Authors: Avital Avraham , Uwyyed Kamal , Berkman Neville , Godfrey Simon , Bar‐Yishay Ephraim , Springer Chaim
Published: August 2002

Exhaled nitric oxide (eNO) has been used to diagnose asthma in adults and children using either the slow vital capacity method (SVCm) or, in younger children, the tidal breathing method (TBm). Adenosine 5′‐monophosphate (AMP) challenge also has been found to be a sensitive and specific test for the diagnosis of asthma. In the present study, we used the AMP provocation concentration that caused wheezing (PCW) to confirm the diagnosis of asthma (PCW ≤ 200 mg/mL). We studied 36 children (2–7 years) with mild intermittent asthma, 13 children (3–7 years) with moderate persistent asthma treated with inhaled steroids, 20 nonasthmatic children (2–7 years) with chronic cough and recurrent pneumonia, and 15 healthy children (4–6 years). Expired gas was collected in collection bags by the TBm, and eNO was measured. We evaluated the efficacy of eNO values in diagnosing asthma.

The mean eNO level of the mild intermittent asthmatic children (5.6 ± 0.4 ppb) not receiving inhaled corticosteroids was significantly higher (ANOVA P < 0.0001) than that of the moderate persistent asthmatics who were treated with inhaled steroids, the nonasthmatic children with chronic cough, and the group of healthy children (3.7 ± 0.6 ppb, P < 0.05; 3.2 ± 0.3 ppb, P < 0.001; 2.2 ± 0.2 ppb, P < 0.001, respectively). The points of intersection for sensitivity and specificity curves of eNO to differentiate mild intermittent asthmatics from nonasthmatic children with chronic cough and from healthy children were 77% and 88% for eNO values of 3.8 ppb and 2.9 ppb, respectively.

We conclude that eNO collected by the TBm can differentiate steroid‐naive young children with intermittent asthma from healthy children, from nonasthmatic children with chronic cough, and from asthmatic children treated with inhaled steroids. Pediatr Pulmonol. 2001; 32:308–313. © 2001 Wiley‐Liss, Inc.
Immunohistochemical studies on the distribution of nerve fibers in the human prostate with special reference to the anterior fibromuscular stroma
Authors: Iwata Tsuyoshi , Ukimura Osamu , Inaba Mitsuhiko , Kojima Munekado , Kumamoto Kenzo , Ozawa Hitoshi , Kawata Mitsuhiro , Miki Tsuneharu
Published: August 2002

BACKGROUND

Although the anterior fibromuscular stroma (AFMS) comprises up to one third of the total bulk of the prostate, its physiological function remains unknown. We recently reported the possible contribution of the AFMS to micturition. The aim of this study is to reveal the differences in the distribution of innervation between the AFMS and the other regions of the prostate.

METHODS

We performed immunohistochemical stainings using antibodies such as protein gene product (PGP) 9.5, tyrosine hydroxylase(TH), neuropeptide Y (NPY), and vasoactive intestinal peptide (VIP). Morphometric analysis was made to examine the density of peripheral nerve fibers containing PGP 9.5, TH, NPY, and VIP by using a computer‐assisted imaging system.

RESULTS

The number of PGP 9.5‐immunoreactive (IR) nerve fibers and the smooth muscle in the AFMS decreased from the base to the apex of the prostate. TH‐IR nerve fibers were more abundant in the AFMS than in the transition zone. NPY‐ and VIP‐IR nerve fibers were less numerous in the AFMS than in the peripheral zone.

CONCLUSIONS

This study is the first to demonstrate that the AFMS has peculiar neuronal innervation. We observed significantly different innervation in the AFMS compared with the other regions of the prostate. Prostate 48:242–247, 2001. © 2001 Wiley‐Liss, Inc.
Weak temperature dependence of the free energy surface and folding pathways of structured peptides
Authors: Cavalli Andrea , Ferrara Philippe , Caflisch Amedeo
Published: August 2002

The thermodynamics and energetics of a 20‐residue synthetic peptide with a stable three‐stranded antiparallel β‐sheet fold are investigated by implicit solvent molecular dynamics (MD) at 330 K (slightly above the melting temperature in the model) and compared with previous simulation results at 360 K. At both temperature values, the peptide folds reversibly to the NMR solution conformation, irrespective of the starting conformation. The sampling of the conformational space (2.3 μs and 25 folding events at 330 K, and 3 μs and 50 folding events at 360 K) is sufficient to obtain a thermodynamic description of minima and transition states on the free energy surface, which is determined near equilibrium by counting populations. The free energy surface, plotted as a function of two‐order parameters that monitor formation of either of the β‐hairpins, is similar at both temperature values. The statistically predominant folding pathway and its frequency (about two‐thirds of the folding events) are the same at 330 K and 360 K. Furthermore, the main unfolding route is the reverse of the predominant folding pathway. The effective energy and its electrostatic and van der Waals contributions show a downhill profile at both temperatures, implying that the free energy barrier is of entropic origin and corresponds to the freezing of about two‐thirds of the chain into a β‐hairpin conformation. The average folding rate is nearly the same at 330 K and 360 K, while the unfolding rate is about four times slower at 330 K than at 360 K. Taken together with previous MD analysis of α‐helices and β‐hairpins, the present simulation results indicate that the free energy surface and folding mechanism of structured peptides have a weak temperature dependence. Proteins 2002;47:305–314. © 2002 Wiley‐Liss, Inc.
A study on protein sequence alignment quality
Authors: Elofsson Arne
Published: August 2002

One of the most central methods in bioinformatics is the alignment of two protein or DNA sequences. However, so far large‐scale benchmarks examining the quality of these alignments are scarce. On the other hand, recently several large‐scale studies of the capacity of different methods to identify related sequences has led to new insights about the performance of fold recognition methods. To increase our understanding about fold recognition methods, we present a large‐scale benchmark of alignment quality. We compare alignments from several different alignment methods, including sequence alignments, hidden Markov models, PSI‐BLAST, CLUSTALW, and threading methods. For most methods, the alignment quality increases significantly at about 20% sequence identity. The difference in alignment quality between different methods is quite small, and the main difference can be seen at the exact positioning of the sharp rise in alignment quality, that is, around 15–20% sequence identity. The alignments are improved by using structural information. In general, the best alignments are obtained by methods that use predicted secondary structure information and sequence profiles obtained from PSI‐BLAST. One interesting observation is that for different pairs many different methods create the best alignments. This finding implies that if a method that could select the best alignment method for each pair existed, a significant improvement of the alignment quality could be gained. Proteins 2002;46:330–339. © 2002 Wiley‐Liss, Inc.
Optimizing the hydrogen‐bond network in Poisson–Boltzmann equation‐based pKa calculations
Authors: Nielsen Jens E. , Vriend Gerrit
Published: August 2002

pKa calculation methods that are based on finite difference solutions to the Poisson–Boltzmann equation (FDPB) require that energy calculations be performed for a large number of different protonation states of the protein. Normally, the differences between these protonation states are modeled by changing the charges on a few atoms, sometimes the differences are modeled by adding or removing hydrogens, and in a few cases the positions of these hydrogens are optimized locally. We present an FDPB‐based pKa calculation method in which the hydrogen‐bond network is globally optimized for every single protonation state used. This global optimization gives a significant improvement in the accuracy of calculated pKa values, especially for buried residues. It is also shown that large errors in calculated pKa values are often due to structural artifacts induced by crystal packing. Optimization of the force fields and parameters used in pKa calculations should therefore be performed with X‐ray structures that are corrected for crystal artifacts. Proteins 2001;43:403–412. © 2001 Wiley‐Liss, Inc.
PRED‐CLASS: Cascading neural networks for generalized protein classification and genome‐wide applications
Authors: Pasquier Claude , Promponas Vassilis J. , Hamodrakas Stavros J.
Published: August 2002

A cascading system of hierarchical, artificial neural networks (named PRED‐CLASS) is presented for the generalized classification of proteins into four distinct classes—transmembrane, fibrous, globular, and mixed—from information solely encoded in their amino acid sequences. The architecture of the individual component networks is kept very simple, reducing the number of free parameters (network synaptic weights) for faster training, improved generalization, and the avoidance of data overfitting. Capturing information from as few as 50 protein sequences spread among the four target classes (6 transmembrane, 10 fibrous, 13 globular, and 17 mixed), PRED‐CLASS was able to obtain 371 correct predictions out of a set of 387 proteins (success rate ∼ 96%) unambiguously assigned into one of the target classes. The application of PRED‐CLASS to several test sets and complete proteomes of several organisms demonstrates that such a method could serve as a valuable tool in the annotation of genomic open reading frames with no functional assignment or as a preliminary step in fold recognition and ab initio structure prediction methods. Detailed results obtained for various data sets and completed genomes, along with a web sever running the PRED‐CLASS algorithm, can be accessed over the World Wide Web at http://o2.biol.uoa.gr/PRED‐CLASS. Proteins 2001;44:361–369. © 2001 Wiley‐Liss, Inc.
Aromatic di‐alanine repeats (AdAR) are structural motifs characteristic of the soluble N‐ethylmaleimide‐sensitive factor attachment protein (SNAP) family
Authors: Bruckert Franz , Casavant Thomas , Satre Michel
Published: August 2002

The aromatic di‐alanine repeat is a novel 12‐amino acid‐long motif constituting alternate small and large hydrophobic residues that mediate the close packing of α‐helices. A hidden Markov model profile was constructed from the motifs initially described in Soluble N‐ethyl maleimide‐sensitive factor attachment proteins (SNAP), a family of soluble proteins involved in intracellular membrane fusion. Scanning different sets of protein sequences showed unambiguously that this profile defines a structural motif independent of the tetratrico peptide repeat, another widespread α‐helical motif. In addition to SNAP, aromatic di‐alanine repeats are found in selective LIM homeodomain binding proteins (SLB) and in proteins from the Pyrococcus and Archaeoglobus prokaryotes. Proteins 2001;45:40–46. © 2001 Wiley‐Liss, Inc.
Structure‐based inhibitor screening: A family of sulfonated dye inhibitors for malaria parasite triosephosphate isomerase
Authors: Joubert F. , Neitz A.W.H. , Louw A.I.
Published: August 2002

The crystal structure of malaria triosephosphate isomerase (TIM) was screened against the National Cancer Institute database of three‐dimensional molecular structures. Ten top‐scoring commercially available compounds were analyzed for inhibition of recombinant TIM. Two anionic dyes showed inhibition of TIM at concentrations of <100 mM. Four related sulfonated dyes were identified from the literature, docked, and screened in vitro. All showed inhibition of malaria TIM. Models indicate that these compounds bind in two suggested conformations to the active site region of the TIM enzyme. These compounds may be used in rational modification procedures for the synthesis of lead anti‐TIM drugs. Proteins 2001;45:136–143. © 2001 Wiley‐Liss, Inc.
Computer simulations aimed at structure prediction of supersecondary motifs in proteins
Authors: Forcellino François , Derreumaux Philippe
Published: August 2002

It is well established that protein structures are more conserved than protein sequences. One‐third of all known protein structures can be classified into ten protein folds, which themselves are composed mainly of α‐helical hairpin, β hairpin, and βαβ supersecondary structural elements. In this study, we explore the ability of a recent Monte Carlo–based procedure to generate the 3D structures of eight polypeptides that correspond to units of supersecondary structure and three‐stranded antiparallel beta sheet. Starting from extended or misfolded compact conformations, all Monte Carlo simulations show significant success in predicting the native topology using a simplified chain representation and an energy model optimized on other structures. Preliminary results on model peptides from nucleotide binding proteins suggest that this simple protein folding model can help clarify the relation between sequence and topology. Proteins 2001;45:159–166. © 2001 Wiley‐Liss, Inc.
RunMACRO: a program to facilitate sensitivity analyses using the water flow and solute movement model MACRO
Authors: Hansen Martin
Published: August 2002

Sensitivity analyses of pesticide leaching often involve a large range of simulations based on nearly identical set‐ups. Using RunMACRO it is possible to make large numbers of simulations with a minimum of exertion. Running many nearly identical model set‐ups is tedious and might introduce errors in selecting the correct values from a long range of parameter files that are appropriate to the model set‐up. RunMACRO makes the task easier and minimises the risk of errors in the generation of parameter files and model executions. Using RunMACRO, it is possible to create a suite of MACRO simulations based on a single parameter file where the range or a list of values for one to three parameters is specified. RunMACRO then creates a parameter file for each of the simulations and runs the simulations one by one. RunMACRO can easily be modified to be used with other simulation programs that use ASCII‐based parameter files and can be started from a command prompt. RunMACRO is available free to use and modify from the Geological Survey of Denmark and Greenland's home page.

© 2001 Society of Chemical Industry
Long term effect of aflatoxin B1 on lipid peroxidation in rat liver and kidney: effect of picroliv and silymarin
Authors: Rastogi Ravi , Srivastava Arvind Kumar , Rastogi Anil Kumar
Published: August 2002

Aflatoxin B1 (AFB1) is a potent hepatotoxic and hepatocarcinogenic mycotoxin. The mechanism of cellular damage caused by AFB1 has not been fully elucidated. Lipid peroxidation is one of the main manifestations of oxidative damage and has been found to play an important role in the toxicity and carcinogenesis of many carcinogens. The present investigation aims at assessing the comparative antioxidant effet of picroliv, a standardized iridoid glycoside fraction of Picrorhiza kurroa and silymarin, a well known standard hepatoprotective, on aflatoxin B1 induced lipid‐peroxidation in rat liver and kidney. Marked increases in lipid peroxide levels and a concomitant decrease in enzymic antioxidant levels were observed in aflatoxin B1 (2 mg/kg, i.p) ‐toxicated rats, while drug (picroliv and silymarin both) treatment reversed the condition to near normal levels. The effects of picroliv and silymarin were comparable. Copyright © 2001 John Wiley & Sons, Ltd.
Experimental treatment of chronic Trypanosoma cruzi infection in mice with 2‐n‐propylquinoline
Authors: Nakayama Hector , Ferreira Maria Elena , Arias Antonieta Rojas de , Bilbao Ninfa Vera de , Torres Susana , Schinini Alicia , Fournet Alain
Published: August 2002

It was reported previously that 2‐n‐propylquinoline was active against the epimastigote form of Trypanosoma cruzi. The effects of oral treatments with benznidazole and 2‐n‐propylquinoline were evaluated in Balb/c mice infected with T. cruzi chronically. The reference drug and 2‐n‐propylquinoline were administered 60 days post‐infection for 30 days at 25 mg/mL. At 35 days post‐treatment, the serological tests (ELISA) of the 2‐n‐ propylquinoline‐treated mice were significantly different from the controls (p = 0.01) and the benznidazole‐treated mice (p = 0.03), while this was not the case at 85 days post‐treatment. These results are encouraging for continuing the investigation of other analogues of 2‐n‐propylquinoline in experimental chronic Chagas' disease. Copyright © 2001 John Wiley & Sons, Ltd.
The range of pro‐ecological activities concerning packaging in Poland against the background of the European Union (EU)
Authors: Lisińska‐Kuśnierz Małgorzata
Published: August 2002

The aim of this work was to present the legal status relating to fundamental issues of packaging ecology. Next, the fundamental requirements established for packaging from the point of view of environmental protection are analysed. For this reason requirements related to the manufacture of packaging and its raw material composition, to returnable packaging, suitability for various forms of processing, marking of packaging and the content of heavy metals in packaging are presented. These requirements may significantly influence the manufacturing technologies of packaging materials and packaging, as well as the packaging systems applied. It should be remembered that manufacturers and users of packaging are responsible for the quantity and types of packaging introduced to the market. The amount and the nature of waste depend on them. These links are of major influence on the final form of packaging as well as on creating and shaping consumer habits, which are not always justified in terms of ecological requirements established for packaging. Copyright © 2001 John Wiley & Sons, Ltd.
Coupling crystallography and computational biochemistry in understanding heme enzyme structure and function
Authors: Poulos Thomas L. , Barrows Tiffany , Bhaskar B. , Bonagura Christopher A. , Li Huiying
Published: August 2002

Computational methods and crystallography have been coupled to study structure–function relationships in cytochrome c peroxidase (CCP) and nitric oxide synthase (NOS). NOS is an important drug target and the structural details of NOS–inhibitor interactions are essential if structure‐based drug design is to be of any use in the development of therapeutic agents targeted to NOS. The structure of 7‐nitroindazole, a potent NOS inhibitor, complexed to one NOS isoform left some ambiguity in the precise orientation of the inhibitor. Various computational approaches were used to resolve this ambiguity as well as revealing the energetic basis for tight binding. With CCP site directed mutagenesis, crystallography and various computational tools have been used to understand why CCP is unique among the peroxidases in its ability to stabilize a tryptophan cation radical during catalysis. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
Unexpectedly large basis set effects on the binding of O2 to heme complexes
Authors: Barea Guada , Maseras Feliu , Lledós Agustí
Published: August 2002

IMOMM(Becke3LYP:MM3) geometry optimizations on the Fe(P)(H2O)(O2) (P=porphyrin) system with different basis sets are shown to provide large differences in the iron–oxygen bond distance. This difference is found to be not in the basis set superposition error or in the description of the interaction between iron and dioxygen. Instead, the origin of the difference is shown to be in the relative energies of the FeII(P)(O2) and FeIII(P)(O2−) descriptions emerging from the stabilities of the separate FeII/O2 and FeIII/O2− fragments. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001
New computational algorithm for the prediction of protein folding types
Authors: Štambuk Nikola , Konjevoda Paško
Published: August 2002

We present a new computational algorithm for the prediction of a secondary protein structure. The method enables the evaluation of α‐ and β‐protein folding types from the nucleotide sequences. The procedure is based on the reflected Gray code algorithm of nucleotide–amino acid relationships, and represents the extension of Swanson's procedure in Ref. 4. It is shown that six‐digit binary notation of each codon enables the prediction of α‐ and β‐protein folds by means of the error‐correcting linear block triple‐check code. We tested the validity of the method on the test set of 140 proteins (70 α‐ and 70 β‐folds). The test set consisted of standard α‐ and β‐protein classes from Jpred and SCOP databases, with nucleotide sequence available in the GenBank database. 100% accurate classification of α‐ and β‐protein folds, based on 39 dipeptide addresses derived by the error‐correcting coding procedure was obtained by means of the logistic regression analysis (p<0.00000001). Classification tree and machine learning sequential minimal optimization (SMO) classifier confirmed the results by means 97.1% and 90% accurate classification, respectively. Protein fold prediction quality tested by means of leave‐one‐out cross‐validation was a satisfactory 82.1% for the logistic regression and 81.4% for the SMO classifier. The presented procedure of computational analysis can be helpful in detecting the type of protein folding from the newly sequenced exon regions. The method enables quick, simple, and accurate prediction of α‐ and β‐protein folds from the nucleotide sequence on a personal computer. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 84: 13–22, 2001
Quantum Monte Carlo calculations for ground and excited states
Authors: Needs R. J. , Kent P. R. C. , Porter A. R. , Towler M. D. , Rajagopal G.
Published: August 2002

A brief overview of the diffusion quantum Monte Carlo method is given. We illustrate the application to ground‐state calculations by a study of the relative stability of carbon clusters near the crossover to fullerene stability, thereby determining the smallest stable fullerene. The application to excited states is illustrated via a study of excitonic states in small hydrogenated silicon clusters. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001
Quantum manifestations of classical trajectories in molecular systems
Authors: Seidel L. , González‐Giralda C. , Benito R. M. , Borondo F.
Published: August 2002

Quantum chaos, understood as the effect of the underlying classical dynamics on the stationary quantum properties in classically chaotic systems, is examined in two molecular floppy systems. Realistic models of two degrees of freedom for HO2 and HCN/HNC are considered. The structure of the classical phase space is studied using Poincaré surfaces of section and the dynamical characteristics of the corresponding wave functions analyzed also in phase space with the aid of Husimi functions. Some wave functions show strong localization along periodic orbits. © 2002 John Wiley & Sons, Inc. Int J Quantum Chem, 2001
The effect of water on the ion trap analysis of trimethylsilyl derivatives of long‐chain fatty acids and alcohols
Authors: Wood Karl V. , Bonham Connie C. , Jenks Matthew A.
Published: August 2002

Gas chromatography/mass spectrometry (GC/MS), with an ion trap mass analyzer, was used to examine the very‐long‐chain cuticular acid and certain non‐acid wax constituents on the leaf sheath surface of Sorghum bicolor before and during 36 hours of light exposure. The mass spectra of the trimethylsilylated acids and alcohols did not match any of those published in searchable mass spectral libraries. The observed differences can be related to the interaction between water and the trimethylsilylated acids and alcohols. Understanding the observed mass spectra of the very‐long‐chain plant waxes is critical for studies that employ GC/MS with the ion trap mass analyzer to elucidate cuticular wax compositions on plants. Copyright © 2001 John Wiley & Sons, Ltd.
Supersonic gas chromatography/mass spectrometry
Authors: Amirav Aviv , Gordin Alexander , Tzanani Nitzan
Published: August 2002

A new gas chromatography/mass spectrometry (GC/MS) system was designed and evaluated which we have named ‘Supersonic GC/MS’. It is based on a modification of a commercially available GC/MS system to include a supersonic molecular beam (SMB) MS interface. In this system the standard electron ionization (EI) ion source was replaced with a fly‐through EI ion source mounted in the path of the SMB. A hyperthermal surface ionization (HSI) ion source combined with a 90 ° ion mirror (for the EI‐produced ions) was also added, and placed inside the quadrupole mass analyzer in place of its original EI ion source. The ‘Supersonic GC/MS’ system requires 18 cm added bench space plus the addition of an air‐cooled 60 L/s diffusion pump and a 537 L/min rotary pump. The system is user friendly since all the gas flow rates, heated zones, sampling and data analysis are performed the same way as the original system and are computer‐controlled via the original software. Similar EI sensitivity was obtained as with the original system for hexachlorobenzene and octafluoronaphthalene, while improved EI detection limits were demonstrated for methyl stearate and eicosane due to the significant enhancement of their molecular ion abundances. A GC/MS detection limit of 500 ag for pyrene was demonstrated using HSI. Good supersonic expansion cooling was achieved with large alkanes, despite the use of a rotary pump at the nozzle chamber instead of a diffusion pump. High temperature GC/MS analysis was demonstrated for large polycyclic aromatic hydrocarbons (PAHs) including ovalene and decacyclene (ten rings). Library searches with EI mass spectra are demonstrated, and it is explained why the enhancement of the molecular ion actually improves the library search in most cases. The analysis of large phthalate esters is also described, and the improvement obtained is shown to originate from their enhanced molecular and high mass fragment ions. Copyright © 2001 John Wiley & Sons, Ltd.
Estimation of proton affinity of proline and tryptophan under electrospray ionization conditions using the extended kinetic method
Authors: Mirza Shama P. , Prabhakar S. , Vairamani M.
Published: August 2002

The relative order of the proton affinity (PA) of 20 naturally occurring amino acids has been determined under electrospray ionization conditions and compared with earlier studies of different research workers. The order we obtained is similar to that reported by other groups except in three cases viz., valine–aspartic acid, asparagine–glutamic acid and tryptophan–proline. The PA values of proline and tryptophan are determined by the extended kinetic method using amino acids themselves as reference bases. The PA values we thus obtained for proline and tryptophan are 219.9 and 221.6 kcal/mol, respectively. Copyright © 2001 John Wiley & Sons, Ltd.
Investigation of synthetic peptide hormones by liquid chromatography coupled to pneumatically assisted electrospray ionization mass spectrometry: analysis of a synthesis crude of peptide triptorelin
Authors: Sanz‐Nebot V. , Toro I. , Castillo A. , Barbosa J.
Published: August 2002

Triptorelin, a synthetic peptide hormone used in the treatment of prostate cancer by means of reduction in the action of male hormone testosterone, is studied here. The synthetic procedure commonly results in unwanted side products that require extensive purification and characterization of the synthesis mixture. The chromatographic separation of triptorelin from the crude mixture was developed by applying the linear solvation energy relationship (LSER) methodology previously developed, to optimize the composition of the mobile phase in order to avoid lengthy empirical optimization procedures. Electrospray ionization mass spectrometry coupled to liquid chromatography (LC/ES‐MS) was used to obtain reliable information on the inevitable side products. The knowledge of the identity of these impurities allows fast optimization of the synthetic procedure and also the therapeutic use of triptorelin peptide hormone. Copyright © 2001 John Wiley & Sons, Ltd.
Practical aspects of liquid chromatography/electrospray tandem mass spectrometry for rapid identification of metabolites of a new antifungal agent SYN‐2836 in dog urine
Authors: Bu Hai‐Zhi , Poglod Marzena , Micetich Ronald G. , Khan Jehangir K.
Published: August 2002

This report presents the structural elucidation of 12 urinary metabolites of SYN‐2836, a new antifungal agent showing extensive metabolism in beagle dogs, using complementary liquid chromatography/tandem mass spectrometry (LC/MS/MS) methodologies. The 12 SYN‐2836 metabolites were readily divided into four groups by considering that all three members of each group, although differing in masses, exhibited highly similar product ion mass spectra. This suggests that the metabolites within each group share a common major substructure. Therefore, all the grouped SYN‐2836 metabolites were strategically identified by characterization of the major substructures followed by determination of the additional small substructures. This grouping strategy greatly facilitated the structural elucidation of these metabolites. Other strategies were also employed to achieve as rapid and unambiguous characterization of the SYN‐2836 metabolites as possible. Copyright © 2001 John Wiley & Sons, Ltd.
An investigation of cobalt oxide based nanocrystalline thin films by secondary ion mass spectrometry
Authors: Barison Simona , Barreca Davide , Daolio Sergio , Fabrizio Monica , Tondello Eugenio
Published: August 2002

An investigation of cobalt oxide based nanocrystalline thin films by secondary ion mass spectrometry (SIMS) is presented. The coatings, whose composition ranged between CoO and Co3O4, were synthesized by chemical vapor deposition (CVD) on indium tin oxide (ITO) substrates, using cobalt(II) β‐diketonate as precursor. The SIMS analysis revealed a satisfactory precursor conversion into the oxides and allowed distinction of regions in the films at different compositions. Film‐substrate intermixing phenomena were evidenced and studied as a function of deposition temperature, film thickness and composition. Copyright © 2001 John Wiley & Sons, Ltd.
Electrospray ionization mass spectrometric study of the hydrolysis‐polycondensation process of Sn(OBut)4
Authors: Armelao Lidia , Schiavon Giovanni , Seraglia Roberta , Tondello Eugenio , Russo Umberto , Traldi Pietro
Published: August 2002

The oligomerization of Sn(OBut)4 in the sol‐gel process has been studied by several different analytical approaches. Electrospray ionization (ESI) mass spectrometry was highly effective in describing the first species produced by the hydrolysis‐polycondensation reactions. Mössbauer spectroscopy has elucidated the fast behavior of the hydrolytic oligomerization process, while calorimetric data have demonstrated the high enthalpy of the reaction in the presence of different solvents. Copyright © 2001 John Wiley & Sons, Ltd.
Mass spectral study of O‐ and S‐aryl dimethylthiocarbamates under electron impact conditions: Newman‐Kwart rearrangement in the gas phase
Authors: Prabhakar S. , Kar Paramita , Mirza S. P. , Lakshmi V. V. S. , Nagaiah K. , Vairamani M.
Published: August 2002

The electron impact (EI) mass spectra of isomeric S‐ and O‐aryl (2‐naphthyl, R‐Ph‐ = aryl, where R = H, NO2, COOCH3, COCH3 and OCH3) dimethylthiocarbamates have been studied in detail. The EI spectra of O‐aryl dimethylthiocarbamates include some of the fragment ions that are characteristic of the corresponding S‐aryl isomer, which could be explained by a Newman‐Kwart rearrangement in the ion source of the mass spectrometer, after ionization. The EI mass spectra of S‐aryl dimethylthiocarbamates showed specific fragment ions resulting from cleavage of the molecular ion involving the bond between sulfur and the carbonyl group of the carbamate moiety (α‐cleavage). The EI mass spectra of O‐aryl dimethylthiocarbamates, however, showed the fragmentation of the molecular ion by α‐cleavage involving the bonds on both sides of oxygen atom. Further, the EI mass spectra of O‐aryl dimethylthiocarbamates containing an electron‐withdrawing substituent (‐R) on the aryl group showed a characteristic fragment ion corresponding to [M − R]+. Copyright © 2001 John Wiley & Sons, Ltd.