bluuebunny/crossref_metadata_2025 huggingface dataset:
Neglect of four‐ and approximation of one‐, two‐, and three‐center two‐electron integrals in a symmetrically orthogonalized basis
Authors: Laikov Dimitri N.
Published: December 2006

A new integral approximation for use in molecular electronic structure calculations is proposed as an alternative to the traditional neglect of diatomic differential overlap models. The similarity between the symmetrically orthogonalized and the original basis functions (assumed orthonormal within each atomic set but nonorthogonal between different centers) is used to construct a robust approximation for the two‐electron integrals, with the error being quadratic in the deviation between the products of the functions. Invariance properties of this procedure are rigorously proved. Numerical studies on a representative set of molecules at valence‐only minimal basis Hartree–Fock level show that the approximation introduces relatively small errors, encouraging its future application in the semiempirical field. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 698–702, 2007
Modifying the OPLS‐AA force field to improve hydration free energies for several amino acid side chains using new atomic charges and an off‐plane charge model for aromatic residues
Authors: Xu Zhitao , Luo Harry H. , Tieleman D. Peter
Published: December 2006

The hydration free energies of amino acid side chains are an important determinant of processes that involve partitioning between different environments, including protein folding, protein complex formation, and protein–membrane interactions. Several recent papers have shown that calculated hydration free energies for polar and aromatic residues (Trp, His, Tyr, Asn, Gln, Asp, Glu) in several common molecular dynamics force fields differ significantly from experimentally measured values. We have attempted to improve the hydration energies for these residues by modifying the partial charges of the OPLS‐AA force field based on natural population analysis of density functional theory calculations. The resulting differences between calculated hydration free energies and experimental results for the seven side chain analogs are less than 0.1 kcal/mol. Simulations of the synthetic Trp‐rich peptide Trpzip2 show that the new charges lead to significantly improved geometries for interacting Trp‐side chains. We also investigated an off‐plane charge model for aromatic rings that more closely mimics their electronic configuration. This model results in an improved free energy of hydration for Trp and a somewhat altered benzene–sodium potential of mean force with a more favorable energy for direct benzene–sodium contact. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 689–697, 2007
Computational alanine scanning mutagenesis—An improved methodological approach
Authors: Moreira Irina S. , Fernandes Pedro A. , Ramos Maria J.
Published: December 2006

Alanine scanning mutagenesis of protein–protein interfacial residues can be applied to a wide variety of protein complexes to understand the structural and energetic characteristics of the hot‐spots. Binding free energies have been estimated with reasonable accuracy with empirical methods, such as Molecular Mechanics/Poisson‐Boltzmann surface area (MM‐PBSA), and with more rigorous computational approaches like Free Energy Perturbation (FEP) and Thermodynamic Integration (TI). The main objective of this work is the development of an improved methodological approach, with less computational cost, that predicts accurately differences in binding free energies between the wild‐type and alanine mutated complexes (ΔΔGbinding). The method was applied to three complexes, and a mean unsigned error of 0.80 kcal/mol was obtained in a set of 46 mutations. The computational method presented here achieved an overall success rate of 80% and an 82% success rate in residues for which alanine mutation causes an increase in the binding free energy > 2.0 kcal/mol (warm‐ and hot‐spots). This fully atomistic computational methodological approach consists in a computational Molecular Dynamics simulation protocol performed in a continuum medium using the Generalized Born model. A set of three different internal dielectric constants, to mimic the different degree of relaxation of the interface when different types of amino acids are mutated for alanine, have to be used for the proteins, depending on the type of amino acid that is mutated. This method permits a systematic scanning mutagenesis of protein–protein interfaces and it is capable of anticipating the experimental results of mutagenesis, thus guiding new experimental investigations. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 644–654, 2007
Nearest‐neighbor nonparametric method for estimating the configurational entropy of complex molecules
Authors: Hnizdo Vladimir , Darian Eva , Fedorowicz Adam , Demchuk Eugene , Li Shengqiao , Singh Harshinder
Published: December 2006

A method for estimating the configurational (i.e., non‐kinetic) part of the entropy of internal motion in complex molecules is introduced that does not assume any particular parametric form for the underlying probability density function. It is based on the nearest‐neighbor (NN) distances of the points of a sample of internal molecular coordinates obtained by a computer simulation of a given molecule. As the method does not make any assumptions about the underlying potential energy function, it accounts fully for any anharmonicity of internal molecular motion. It provides an asymptotically unbiased and consistent estimate of the configurational part of the entropy of the internal degrees of freedom of the molecule. The NN method is illustrated by estimating the configurational entropy of internal rotation of capsaicin and two stereoisomers of tartaric acid, and by providing a much closer upper bound on the configurational entropy of internal rotation of a pentapeptide molecule than that obtained by the standard quasi‐harmonic method. As a measure of dependence between any two internal molecular coordinates, a general coefficient of association based on the information‐theoretic quantity of mutual information is proposed. Using NN estimates of this measure, statistical clustering procedures can be employed to group the coordinates into clusters of manageable dimensions and characterized by minimal dependence between coordinates belonging to different clusters. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 655–668, 2007
Efficient combination of Wang–Landau and transition matrix Monte Carlo methods for protein simulations
Authors: Ghulghazaryan Ruben G. , Hayryan Shura , Hu Chin‐Kun
Published: December 2006

An efficient combination of the Wang‐Landau and transition matrix Monte Carlo methods for protein and peptide simulations is described. At the initial stage of simulation the algorithm behaves like the Wang‐Landau algorithm, allowing to sample the entire interval of energies, and at the later stages, it behaves like transition matrix Monte Carlo method and has significantly lower statistical errors. This combination allows to achieve fast convergence to the correct values of density of states. We propose that the violation of TTT identities may serve as a qualitative criterion to check the convergence of density of states. The simulation process can be parallelized by cutting the entire interval of simulation into subintervals. The violation of ergodicity in this case is discussed. We test the algorithm on a set of peptides of different lengths and observe good statistical convergent properties for the density of states. We believe that the method is of general nature and can be used for simulations of other systems with either discrete or continuous energy spectrum. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 715–726, 2007
Effects of entropy on the gas‐phase pyrolysis of ethyl N,N‐dimethylcarbamate
Authors: Kim Chang K. , Kim Dong J. , Hsieh Y. , Lee Hai W. , Lee Bon‐Su , Kim Chan K.
Published: December 2006

In this study, we examined the gas‐phase pyrolysis of ethyl N,N‐dimethylcarbamate theoretically at various theoretical levels. The reaction consists of a two‐step mechanism, with N,N‐dimethylcarbamic acid and ethylene as reaction intermediates. In the first step, the reaction proceeds via a six‐membered cyclic transition state (TS), which is more favorable than that via a four‐membered cyclic TS. Here, the contribution of entropy to the overall potential energy surface was found to play an important role in determining the rate‐limiting step, which was found to be the second step when viewed in terms of the enthalpy of activation (ΔH≠), but the first step when entropy changes (−TΔS≠) were considered. These results are consistent with experimental findings. Moreover, the experimental activation entropy can be reproduced by using the hindered rotor approximation, which converts some low vibration frequencies that correspond to internal rotational modes into hindered rotors. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 625–631, 2007
Electronic structures and chemical bonding in diatomic ScX to ZnX (X = S, Se, Te)
Authors: Wu Z. J. , Wang M. Y. , Su Z. M.
Published: December 2006

Bond distances, vibrational frequencies, electron affinities, ionization potentials, dissociation energies, and dipole moments of the title molecules in neutral, positively, and negatively charged ions were studied using density functional method. Ground electronic state was assigned for each molecule. The bonding patterns were analyzed and compared with both the available data and across the series. It was found that, besides ionic component, covalent bonds are formed between the metal s, d orbitals, and the p orbital of S, Se, and Te. For neutral and cationic molecules, the covalent character increases from ScX to CrX and from FeX to CuX with an exception of decrease at MnX and ZnX, while for anionic molecules, the trend is not obvious. For both neutral and charged molecules, the sulfides have the shortest bond distance and largest vibrational frequency, while tellurides have the largest bond distance and smallest vibrational frequency. For neutral and anionic molecules, the dissociation energy of sulfides is the largest, that of tellurides is the smallest, while this only remains true for cationic molecules from ScX+ to FeX+. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 703–714, 2007
Implementation and application of helix–helix distance and crossing angle restraint potentials
Authors: Lee Jinhyuk , Im Wonpil
Published: December 2006

Based on the definition of helix–helix distance and crossing angle introduced by Chothia et al. (J Mol Biol 1981, 145, 215), we have developed the restraint potentials by which the distance and crossing angle of two selected helices can be maintained around target values during molecular dynamics simulations. A series of assessments show that calculated restraint forces are numerically accurate. Since the restraint forces are only exerted on atoms which define the helical principal axes, each helix can rotate along its helical axis, depending on the helix–helix intermolecular interactions. Such a restraint potential enables us to characterize the helix–helix interactions at atomic details by sampling their conformational space around specific distance and crossing angle with (restraint) force‐dependent fluctuations. Its efficacy is illustrated by calculating the potential of mean force as a function of helix–helix distance between two transmembrane helical peptides in an implicit membrane model. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 669–680, 2007
Transcription and epigenetic profile of the promoter, first exon and first intron of the human tyrosine hydroxylase gene
Authors: Romano Gaetano , Macaluso Marcella , Lucchetti Chiara , Iacovitti Lorraine
Published: December 2006

The transcriptional and chromatin profile of the promoter, first exon and first intron of the human TH gene were analyzed in human neuroblastoma BE(2)‐C‐16 and human renal carcinoma 293FT cell lines. The latter is a cell culture system that is not permissive for TH gene expression, whereas the former has a 50% cell fraction that tests positive for TH. The engineering of a 6.3 kb recombinant human TH promoter revealed the presence of repressors of transcription between positions (−6,244/−194). The addition of a 1.2 kb fragment of the first intron of the human TH gene (+730/+1,653) enhanced transcriptional activity of the recombinant promoter. However, both constructs were not specific for TH‐positive BE(2)‐C‐16 cells. Chromatin immunoprecipitation (Chip) analysis was carried out on BE(2)‐C‐16 and 293FT cells to probe sequences of promoter, first exon and first intron of the human TH gene from position (−448/+1,204). The presence of nucleosomes was observed approximately from position (−20/+473) in both cell lines. Chip analysis was then conducted to determine the acetylation of various lysine residues of H3 and H4 in both cell lines. All analyzed lysine residues of H3 and H4 were acetylated in BE(2)‐C‐16 cells, whereas 293FT cells tested positive for acetylation only in the external lysine residues of the histone tail. Our data are compatible with an active TH gene expression in a 50% cell fraction of BE(2)‐C‐16 cells. Further analysis of epigenetic programming might lead to the identification of the factors that determine TH gene expression specifically in dopaminergic neurons. J. Cell. Physiol. 211: 431–438, 2007. © 2006 Wiley‐Liss, Inc.
Molecular mechanisms involved in self‐renewal and pluripotency of embryonic stem cells
Authors: Liu Na , Lu Min , Tian Xuemei , Han Zhongchao
Published: December 2006

Embryonic stem cells (ES cells) are derived from inner cell mass (ICM). The self‐renewal and pluripotency are the main specificities of ES cells, which are likely to reveal a deeper understanding of human cellular biology and which are considered to be promising sources for cell therapy to treat patients with degenerative diseases in clinical. Growth of ES cells as a pluripotent population requires a balance between survival, proliferation, and self‐renewal signals. In fact, the precise mechanism that regulates stem cell self‐renewal and pluripotency remains largely unknown. Recently, in vitro and in vivo studies have identified several genetic regulators that may play important roles in the self‐renewal and pluripotency process of human and mouse ES cells, including extracellular signaling factors, transcription factors, cell‐cycle regulators, microRNA, genes implicated in chromosomal stability, and DNA methylation. In this review, we will summarize the currently known molecular regulators for ES cells self‐renewal, and we will propose some possibilities to explain the ways in which these distinct pathways might interact. J. Cell. Physiol. 211: 279–286, 2007. © 2006 Wiley‐Liss, Inc.
CO2‐enhanced sonographically guided radiofrequency ablation and transcatheter arterial chemoembolization for small hepatocellular carcinoma poorly defined on conventional sonography
Authors: Ohmoto Kenji , Yoshioka Naoko , Tomiyama Yasuyuki , Shibata Norikuni , Kawase Tomoya , Yoshida Koji , Kuboki Makoto , Yamamoto, Shinichiro
Published: December 2006

We report a case of hepatocellular carcinoma located just below the right hemidiaphragm that was diagnosed as having hepatitis C virus–related cirrhosis 12 years ago. Although the lesion was not clear on conventional sonography, it was clearly defined on CO2‐enhanced sonography, allowing safe and accurate radiofrequency ablation. By combining radiofrequency ablation with transcatheter arterial chemoembolization, extensive cauterization and complete tumor necrosis were obtained with only 1 session of treatment. The patient had no serious adverse effects and has shown no recurrence during 35 months of follow‐up. © 2006 Wiley Periodicals, Inc. J Clin Ultrasound, 2007.
Production of steviosides in ex vitro and in vitro grown Stevia rebaudiana Bertoni
Authors: Rajasekaran T , Giridhar P , Ravishankar GA
Published: December 2006

Stevia rebaudiana Bertoni plants grown in vitro and ex vitro were investigated for variations in the profile of steviosides in their leaves, shoots, roots and flowers. Steviosides were extracted by hydrolysis and esterification, evaporated to dryness and dissolved in methanol for quantitative analysis by high‐performance liquid chromatography (HPLC). The HPLC analysis and separation profiles indicated the presence of several different steviosides, predominantly eight known sweet diterpene glycosides. The most abundant compounds identified were steviolbioside, stevioside, rebaudiosides C and A and dulcoside A. The highest stevioside contents were recorded in 1‐month‐old greenhouse leaves (64.80 g steviolbioside kg−1 dried plant material) and in vitro leaves (0.99 g rebaudioside A kg−1 dried plant material). The recovery of steviosides from the leaves by methanol extraction was 90%. This is the first time that the eight predominant sweet diterpene glycosides in the various plant parts of S. rebaudiana have been investigated. Copyright © 2006 Society of Chemical Industry
Optimisation of flours for chapatti preparation using a mixture design
Authors: Rehman Salim Ur , Paterson Alistair , Piggott John R
Published: December 2006

A mixture design was evaluated for the preparation of composite chapatti flours from two wheat cultivars, Mercia and Galahad, as single cultivars did not yield flours suitable for chapatti production. Physicochemical and rheological tests were applied to determine flour quality. Dough development time (Peak time) and dough stability increased and tolerance index decreased with increasing level of Mercia in the composite flour. Instron and sensory tests were applied to evaluate changes in softness of chapattis at different intervals of storage. Maximum response in texture softness was found with 500 g kg−1 Mercia in the composite flour. Dough prepared from this composite flour showed low stickiness, moderate sheeting resistance and moderate subsequent shrinkage, making it of suitable sheeting quality for chapatti production. It yielded chapatti of soft texture whose scoop formation capability did not change significantly during storage. Copyright © 2006 Society of Chemical Industry
Quality of grated carrot (var. Nantes) packed under vacuum
Authors: Rocha Ada MCN , Ferreira João FFC , Silva Ângelo MM , Almeida Gonçalo N , Morais Alcina MMB
Published: December 2006

The quality of grated carrot (variety Nantes) was evaluated throughout 10 days of storage in two different atmospheres: air and vacuum at 2 °C. The parameters of quality were microbiological and physico‐chemical. Sensory evaluation of vacuum‐packed grated carrots was performed after the microbiology study. The objective was to study the use of a vacuum for preservation of this type of product. The use of a vacuum was sufficiently promising with respect to the capacity to extend the shelf life of grated carrot by reducing microbial load and by minimising physico‐chemical changes. The shelf life of grated carrot under vacuum was extended to 8 days at 2 °C. Copyright © 2006 Society of Chemical Industry
Influence of fried and fried‐treated oils with different filter aids on rat health
Authors: Farag Radwan S , El‐Anany Ayman M
Published: December 2006

Soybean, sunflower, palm and cottonseed oils were fried continuously at 180 ± 5 °C for 12 h. Fried oil quality was regenerated by adding individually Magnesol XL, diatomaceous earth and kaolin at 2% level, then stirring mechanically at 105 °C for 15 min and filtering. A set of nutritional experiments was conducted in which rats were administered standard diets containing non‐fried, fried and fried‐treated oils with various filter aids. The safety limits of the fried‐treated oils were recognized by measuring the activities of alanine aminotransferase (ALT), aspartate aminotransferase (AST) and alkaline phosphatase (AP), and levels of total lipids, total cholesterol, HDL cholesterol and LDL cholesterol of rat sera. Also, histopathological evaluation of rat liver tissues was microscopically done to detect any damage that might occur due to feeding rats on non‐fried, fried and fried‐treated oils. Administration of fried oils to rats induced significant rises in activities of ALT, AST and AP, and increases in the levels of total lipids and total cholesterol. The results demonstrate that there were non‐significant changes in sera levels of LDL and HDL cholesterol in rats fed diets containing various types of soybean, sunflower and cottonseed oils. Administration of fried‐treated oils to rat diets indicates that the activities of ALT, AST and AP and levels of sera constituents were similar to those of rats given non‐fried oils. Palm oil exceptionally behaved differently from the other oils. Palm oil raised sera total cholesterol and LDL cholesterol and lowered HDL cholesterol level. Histopathological examination of rat liver tissues indicated that changes paralleled the biochemical data. Copyright © 2006 Society of Chemical Industry
Secretagogue and bacteriostatic active fractions derived from a peptic hydro‐ lysate of alfalfa RuBisCO small purified subunit
Authors: Trovaslet Marie , Kapel Romain , Ravallec‐Plé Rozenn , Mouni Fadoua , Clarisse Martine , Faille Christine , Dhulster Pascal , Guillochon Didier , Vercaigne‐Marko Dominique
Published: December 2006

For the first time a purification process for small RuBisCO (ribulose‐1,5‐bisphosphate carboxylase/oxygenase) subunit (SRS) was developed from an industrial by‐product of alfalfa, taking advantage of its solubility at low pH. Only one protein strip (14 kDa) was clearly detected in the sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS‐PAGE) profile of the supernatant at pH 2. The recovery of SRS was 48% by this method, with a purity estimated as 98% by densitometry and reverse phase high‐performance liquid chromatography (RP‐HPLC). Moreover, most polyphenolic compounds were discarded, as confirmed by spectrophotometry and RP‐HPLC. SRS hydrolysis was performed for 20 h at 37 °C using pepsin in ammonia/formic acid buffer at pH 3. The hydrolysate was fractionated on a Sephadex G25 column equilibrated with ethanolamine/HCl buffer. Biological activities were found in two fractions. The first fraction showed slight bacteriostatic properties against two pathogenic bacteria, Salmonella arizonae and Shigella sonnei. The second fraction, tested by radioimmunoassay (RIA), presented a secretagogue activity comparable to that of gastrin. Copyright © 2006 Society of Chemical Industry
Antibiotics: Has the magic gone?
Authors: Chander Yogesh , Gupta Satish C , Goyal Sagar M , Kumar Kuldip
Published: December 2006

The emergence of antibiotic resistant bacteria has diminished the efficacy of several antibiotics that were used to treat infectious diseases in humans and animals. In recent years, the problem of antibiotic resistance has become more apparent as increasing numbers of bacteria have acquired resistance to multiple antibiotics. Antibiotics inhibit bacterial growth through a variety of mechanisms including inhibition of cell wall or protein synthesis, interference with DNA (or RNA) replication, and disruption of metabolic pathways or cell membrane. Bacteria develop resistance through genetic mutations or by acquiring resistant genes involved in the production of antibiotic degrading enzymes, overproduction of target molecules, efflux pumps to drain out antibiotics, and/or altered cell wall permeability to survive adverse physiological conditions. Published literature suggests that sub‐therapeutic feeding of food animals for growth promotion along with casual use of antibiotics in household products such as soaps and creams is contributing to increased antimicrobial resistance in the environment. If steps are not taken to minimize selective pressure on bacteria, the effectiveness of antibiotics (hailed as ‘magic bullets’) may be marginalized. Important steps in the judicious use of antibiotics on the farm are: (1) education of farmers on the pitfalls of using antibiotics sub‐therapeutically in the production of food animals; (2) development of animal production practices that reduce dependence on antibiotics; and (3) development of manure disposal practices that minimize the spread of residual antibiotics and antibiotic resistant bacteria into the environment. In addition, educating the general public on the use and misuse of antibiotics in daily life is also important if there is to be any significant impact on reducing the environmental spread of antibiotic resistance. Copyright © 2006 Society of Chemical Industry
The production of provitamin A‐rich vegetables in home‐gardens as a means of addressing vitamin A deficiency in rural African communities
Authors: Faber Mieke , van Jaarsveld Paul J
Published: December 2006

Vitamin A deficiency remains a public health problem in the developing world. The highest prevalence of vitamin A deficiency is in Africa and Asia (>30%). Dietary modification, a long‐term strategy to address vitamin A deficiency, complements food fortification and vitamin A supplementation programmes. Provitamin A carotenoids from foods of plant origin are more affordable than preformed vitamin A from animal foods, and many resource‐poor households rely on yellow/orange‐fleshed vegetables and fruits and dark‐green leafy vegetables as their main source of vitamin A. The provitamin A carotenoid content in plant foods varies widely and differences among cultivars of the same food exist. Several factors influence the bioavailability of provitamin A carotenoids. The potential contribution of plant foods to vitamin A status depends on the retention of provitamin A carotenoids after storage, preparation and processing. Home‐gardens can provide households with direct access to provitamin A‐rich vegetables that are not readily available or within their financial reach. The components and critical issues of home‐garden projects are described. Copyright © 2006 Society of Chemical Industry
Predictors for long‐term survival after interdisciplinary salvage surgery for advanced or recurrent gynecologic cancers
Authors: Fleisch M.C. , Pantke P. , Beckmann M.W. , Schnuerch H.G. , Ackermann R. , Grimm M.O. , Bender H.G. , Dall P.
Published: December 2006

Background and Objectives

We wanted to identify factors which allow predicting long‐term survival after pelvic exenteration (PE) for locally advanced or recurrent gynecologic malignancies.

Methods

All patients undergoing PE at our institution from 1983 to 2002 were screened. In 203 cases data were obtainable and analyzed with respect to factors predicting outcome considering morbidity, mortality, and survival. Follow‐up data and data concerning late complications not documented in our records were obtained by telephone interviews.

Results

Mean age was 55 (22–77) years. PE was performed for locally advanced (36%) or recurrent (64%) cervical (n = 133), endometrial (n = 26), vaginal (n = 23), vulvar (n = 10), and ovarian cancer (n = 11, cases with rectum and/or bladder resections). In 13.4% (n = 26) the intent of the procedure was palliation in the remaining cure. Procedures performed were anterior (n = 91), posterior (45), or total (n = 67) PE. 53% of patients underwent preoperative radio‐chemotherapy, 11.8% as a neoadjuvant treatment. Mean OR time was 8.1 hr, an average of 5.6 units of packed red blood cells were perioperatively transfused. Microscopically complete resection was achievable in n = 69 patients. Perioperative mortality was 1% (n = 2). Seventy‐one percent (n = 144) of patients were available for follow‐up. Five‐year overall survival in patients treated with a curative intent was 21%, 5‐year survival in those patients with complete resection was 32%. Forty‐two percent of patients with a complete resection without lymph node involvement, age 30–50, curative intention, and the absence of a pelvic sidewall infiltration survived 5 years or longer.

Conclusion

In our series a 5‐year survival rate of over 40% could be achieved for nodal‐negative patients without pelvic sidewall infiltration when treated with curative intent and after complete resection. J. Surg. Oncol. 2007; 95: 476–484. © 2006 Wiley‐Liss, Inc.
Decisions for extent of gastric surgery in gastric cancer patients: Younger patients require more attention than the elderly
Authors: Lee Jun Ho , Ryu Keun Won , Lee Jong Seok , Lee Jong Ryeol , Kim Chan Gyoo , Choi Il Ju , Park Sook Ryun , Kook Myeong‐Cherl , Kim Young‐Woo , Bae Jae‐Moon
Published: December 2006

Background and Objectives

There is a prevailing belief that young patients with gastric adenocarcinomas have a more aggressive disease.

Methods

We reviewed the prospectively collected database of 753 gastric adenocarcinomas patients who had undergone curative gastrectomy. Clinicopathological factors and the survival rates for each pathological TNM stage were compared between patients younger than 40 years of age and the others.

Results

Fifty‐four (9.8%) patients were younger than 40 years of age. The overall accuracy of the intra‐operative stage was 62.5%; 54.0% in the young patients and 63.5% in older patients (P = 0.006). Intraoperative under‐staging was more commonly seen in the younger patients when compared to the older patients. These trends were more prominent in patients with surgical stage I disease. Age proved to be an independent risk factor influencing the accuracy of intraoperative staging using a logistic regression analysis. There was no difference in overall 3‐year survival rate between the two age groups for each pathological TNM stage.

Conclusions

The present study showed that intra‐operative under‐staging was more common in young patients with gastric cancer, especially with stage I disease. This finding raises the concern for inaccurate diagnosis and surgical under treatment in younger patients with stage I gastric cancer. J. Surg. Oncol. 2007; 95: 485–490. © 2006 Wiley‐Liss, Inc.
Analysis of germline and tumor mutations of p53 gene in familial occurrence of soft tissue sarcomas
Authors: Kudawara Ikuo , Matsumine Akihiko , Ohzono Kenji
Published: December 2006

Background

Familial soft tissue sarcomas are extremely rare. There is little information available on the clinical features and molecular findings of the hereditary occurrence of mesenchymal tumor.

Patients and Methods

A woman and her younger brother had malignant fibrous histiocytoma (pleomorphic type) and liposarcoma (pleomorphic type) in the lower limbs, respectively. Analysis of p53 mutations in exons 5–9 of the tumor and in germ‐line was done.

Results

A guanine to adenine substitution occurred in CGC, codon 175 of exon 5 in p53 gene, to CAC in the tumor sample of Case 1. Likewise, a thymine to cytosine substitution occurred in TTT, codon 270 of exon 8 in p53 gene, to TCT in tumor sample of Case 2. Germline mutations were not seen in the either patients.

Conclusions

Different missense mutations of p53 were detected in each tumor, however no germline mutations of p53 were found. The alteration of codon 175 in Case 1 is relatively common mutation. On the contrary, the mutation in codon 270 in Case 2 was extremely rare in cancers. Further molecular investigation is needed to understand the mechanism in familial occurrence of sarcomas. J. Surg. Oncol. © 2006 Wiley‐Liss, Inc.
Immediate dynamic lymphoscintigraphy delivers no additional value to lymphoscintigraphy 3 hr after tracer injection in sentinel lymph node biopsy in breast cancer patients
Authors: Edwina Doting M.H. , Annemiek Stiekema H.M. , de Vries Jakob , Lemstra Clara , Hoekstra Harald J. , Vrieling Mirjam , Rietman Lianne , Jager Pieter L.
Published: December 2006

Objective

Immediate dynamic imaging enables accurate definition of sentinel lymph nodes, whereas imaging 3 hr after tracer injection may lead to overestimation of the number of sentinel lymph nodes. A study was performed to define the value of lymphoscintigraphy immediately versus 3 hr after tracer injection in sentinel lymph node biopsy for breast cancer management.

Methods

In 165 sentinel lymph node biopsy procedures preoperative immediate and 3 hr post‐injection lymphoscintigraphy was performed after intraparenchymal tracer administration.

Results

Lymph node visualization occurred in 63 immediate procedures (38%) versus in 163 procedures 3 hr post‐injection (99%). In 17 procedures (10%) in which immediate lymphoscintigraphy had visualized sentinel lymph nodes, additional nodes had been seen on 3 hr post‐injection lymphoscintigraphy. In eight of these procedures (5%) all nodes were detected in the same draining lymph node basin. Non‐axillary sentinel lymph nodes were identified by preoperative lymphoscintigraphy in 28 procedures (17%) and improved staging in three patients (5%).

Conclusion

The only impact of immediate lymphoscintigraphy was the possible omission of removal of 1–2 sec‐echelon nodes per patient in 5% of patients. We consider this yield too low to continue immediate lymphoscintigraphy in breast cancer patients. J. Surg. Oncol. 2007;95:469–475. © 2006 Wiley‐Liss, Inc.
Posttraumatic stress disorder in female veterans with military and civilian sexual trauma
Authors: Himmelfarb Naomi , Yaeger Deborah , Mintz Jim
Published: December 2006

This study examines relationships among military sexual trauma (MST), nonmilitary sexual trauma, and posttraumatic stress disorder (PTSD). A sample of 196 female veterans was assessed for trauma occurring before, during, and after military service, and for current PTSD. The prevalence of MST was higher than that of premilitary and postmilitary sexual trauma. Premilitary trauma did not significantly increase the odds of experiencing MST, but did increase the odds of experiencing postmilitary sexual trauma. Logistic regression analyses revealed MST was more strongly associated with PTSD than was premilitary or postmilitary trauma. Women with MST had the greatest increased odds of developing PTSD. Understanding risk factors for and taking steps to prevent MST may reduce cases of PTSD in female veterans.
Latent difference score approach to longitudinal trauma research
Authors: King Lynda A. , King Daniel W. , McArdle John J. , Saxe Glenn N. , Doron‐LaMarca Susan , Orazem Robert J.
Published: December 2006

In this article, the authors introduce a latent difference score (LDS) approach to analyzing longitudinal data in trauma research. The LDS approach accounts for internal sources of change in an outcome variable, including the influence of prior status on subsequent levels of that variable and the tendency for individuals to experience natural change (e.g., a natural decrease in posttraumatic stress disorder [PTSD] symptoms over time). Under traditional model assumptions, the LDSs are maximally reliable and therefore less likely to introduce biases into model testing. The authors illustrate the method using a sample of children who experienced significant burns or other injuries to examine potential influences (i.e., age of child–adolescent at time of trauma and ongoing family strains) on PTSD symptom severity over time.
A guide to economic evaluation: Methods for cost‐effectiveness analysis of person‐level data
Authors: Hoch Jeffrey S. , Smith Mark W.
Published: December 2006

The authors introduce economic evaluation with particular attention to cost‐effectiveness analysis. They begin by establishing why health care decisions should be guided by economics. They then explore different types of economic evaluations. To illustrate how to conduct and evaluate a cost‐effectiveness analysis, a hypothetical study about the treatment of posttraumatic stress disorder with psychotherapy versus pharmacotherapy is considered. The authors conclude with recommendations for increasing the strength and relevance of economic evaluations.
Customized PEG‐Derived Copolymers for Tissue‐Engineering Applications
Authors: Tessmar Joerg K. , Göpferich Achim M.
Published: December 2006

PEG‐containing copolymers play a prominent role as biomaterials for different applications ranging from drug delivery to tissue engineering. These custom‐designed materials offer enormous possibilities to change the overall characteristics of biomaterials by improving their biocompatibility and solubility, as well as their ability to crystallize in polymer blends and to resist protein adsorption. This article demonstrates various principles of PEG‐based material design that are applied to fine tune the properties of biomaterials for different tissue engineering applications. More specifically, strategies are described to develop PEG copolymers with various block compositions and specific bulk properties, including low melting points and improved surface hydrophilicity. Highly hydrated polymer gel networks for promoting cellular growth or suppressing protein adsorption and cell adhesion are introduced. By incorporating selectively cleavable cross‐links, these hydrophilic polymers can also serve as smart hydrogel scaffolds, mimicking the natural extracellular matrix for cell cultivation and tissue growth. Ultimately, these developments lead to the creation of biomimetic materials to immobilize bioactive compounds, allowing precise control of cellular adhesion and tissue growth.

magnified image
Homotopy classification of module bundles via Grassmannians
Authors: Papatriantafillou Maria H.
Published: December 2006

Given a Waelbroeck ring R, we prove that the Grassmannian of a projective finitely generated R ‐module is a topological manifold modeled on a topological abelian group of R ‐linear maps. Fibre bundles of fibre type a module as above, over a compact base space B, admitting R ‐valued partitions of unity, are classified by the homotopy classes of continuous maps on B with values in the respective Grassmannian. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
IgE‐Mediated food allergy diagnosis: Current status and new perspectives
Authors: Asero Riccardo , Ballmer‐Weber Barbara K. , Beyer Kirsten , Conti Amedeo , Dubakiene Ruta , Fernandez‐Rivas Montserrat , Hoffmann‐Sommergruber Karin , Lidholm Jonas , Mustakov Tihomir , Oude Elberink Joanne N. G. , Pumphrey Richard S. H. , Stahl Skov Per , van Ree Ronald , Vlieg‐Boerstra Berber J. , Hiller Reinhard , Hourihane Jonathan O. , Kowalski Marek , Papadopoulos Nikos G. , Wal Jean‐Michel , Mills E. N. Clare , Vieths Stefan
Published: December 2006

In June 2005, the work of the EU Integrated Project EuroPrevall was started. EuroPrevall is the largest research project on food allergy ever performed in Europe. Major aims of the project are to generate for the first time reliable data on the prevalence of food allergies across Europe and on the natural course of food allergy development in infants. Improvement of in vitro diagnosis of food allergies is another important aim of the project. The present review summarizes current knowledge about the clinical presentation of food allergy and critically reviews available diagnostic tools at the beginning of the project period. A major problem in diagnosis is a relatively poor ‘clinical specificity’, i. e. both positive skin tests and in vitro tests for specific IgE are frequent in sensitized subjects without food allergy symptoms. So far, no in vitro test reliably predicts clinical food allergy. EuroPrevall aims at improving the predictive value of such tests by proceeding from diagnosis based on allergen extracts to purified allergen molecules, taking into account the affinity of the IgE–allergen interaction, and evaluating the potential of biological in vitro tests such as histamine release tests or basophil activation tests including assays performed with permanently growing cell lines.
Ochratoxin A: An overview on toxicity and carcinogenicity in animals and humans
Authors: Pfohl‐Leszkowicz Annie , Manderville Richard A.
Published: December 2006

Ochratoxin A (OTA) is a ubiquitous mycotoxin produced by fungi of improperly stored food products. OTA is nephrotoxic and is suspected of being the main etiological agent responsible for human Balkan endemic nephropathy (BEN) and associated urinary tract tumours. Striking similarities between OTA‐induced porcine nephropathy in pigs and BEN in humans are observed. International Agency for Research on Cancer (IARC) has classified OTA as a possible human carcinogen (group 2B). Currently, the mode of carcinogenic action by OTA is unknown. OTA is genotoxic following oxidative metabolism. This activity is thought to play a central role in OTA‐mediated carcinogenesis and may be divided into direct (covalent DNA adduction) and indirect (oxidative DNA damage) mechanisms of action. Evidence for a direct mode of genotoxicity has been derived from the sensitive32P‐postlabelling assay. OTA facilitates guanine‐specific DNA adductsin vitroand in rat and pig kidney orally dosed, one adduct comigrates with a synthetic carbon (C)‐bonded C8‐dG OTA adduct standard. In this paper, our current understanding of OTA toxicity and carcinogenicity are reviewed. The available evidence suggests that OTA is a genotoxic carcinogen by induction of oxidative DNA lesions coupled with direct DNA adductsviaquinone formation. This mechanism of action should be used to establish acceptable intake levels of OTA from human food sources.
Intestinal absorption of dietary carotenoids
Authors: Yonekura Lina , Nagao Akihiko
Published: December 2006

The assessment of carotenoid bioavailability has long been hampered by the limited knowledge of their absorption mechanisms. However, recent reports have elucidated important aspects of carotenoid digestion and absorption. Disruption of food matrix and increasing amounts of fat seem to enhance the absorption of carotenes to a larger extent than that of xanthophylls. Comparing different carotenoid species, xanthophylls seem to be more easily released from the food matrix and more efficiently micellized than the carotenes. On the other hand, carotenes are more efficiently taken up by the enterocytes. However, carotenoid emulsification and micellization steps are largely affected by the food matrix and dietary components, being the main determinant of carotenoid bioavailability from foodstuffs. Although the intestinal uptake of carotenoids has been thought to occur by simple diffusion, recent studies reported the existence of receptor‐mediated transport of carotenoids in enterocytes. Comparisons between the intestinal absorption of a wide array of carotenoids would be useful to elucidate the absorption mechanism of each carotenoid species, in view of the recent indications that intestinal carotenoid uptake may involve the scavenger receptor class B type I and possibly other epithelial transporters. The unraveling of the whole mechanism underlying the absorption of carotenoids will be the challenge for future studies.
Overview of antibacterial, antitoxin, antiviral, and antifungal activities of tea flavonoids and teas
Authors: Friedman Mendel
Published: December 2006

Tea leaves produce organic compounds that may be involved in the defense of the plants against invading pathogens including insects, bacteria, fungi, and viruses. These metabolites include polyphenolic compounds, the six so‐called catechins, and the methyl‐xanthine alkaloids caffeine, theobromine, and theophylline. Postharvest inactivation of phenol oxidases in green tea leaves prevents oxidation of the catechins, whereas postharvest enzyme‐catalyzed oxidation (fermentation) of catechins in tea leaves results in the formation of four theaflavins as well as polymeric thearubigins. These substances impart the black color to black teas. Black and partly fermented oolong teas contain both classes of phenolic compounds. A need exists to develop a better understanding of the roles of polyphenolic tea compounds in food and medical microbiology. This overview surveys and interprets our present knowledge of activities of tea flavonoids and teas against foodborne and other pathogenic bacteria, virulent protein toxins produced by some of the bacteria, virulent bacteriophages, pathogenic viruses and fungi. Also covered are synergistic, mechanistic, and bioavailability aspects of the antimicrobial effects. Further research is suggested for each of these categories. The herein described findings are not only of fundamental interest, but also have practical implications for nutrition, food safety, and animal and human health.
Poly(N,N‐dimethylacrylamide)‐Based Microspheres Prepared by Heterogeneous Polymerizations
Authors: Babič Michal , Horák Daniel
Published: December 2006

PDMAAm microspheres have been obtained by inverse suspension, inverse emulsion, and dispersion polymerization. Conventional inverse suspension polymerization in toluene/trichloroethene is modified by the use of ultrasound. The resulting hydrogel microspheres are examined by dynamic light scattering and scanning electron microscopy to afford the morphology, dispersity, and size of the microspheres. Inverse suspension polymerization yields 100‐µm particles, while those obtained by inverse emulsion polymerization are 0.13–1 µm in diameter. While the inverse techniques produce particles of broad size distribution, monodisperse microspheres are obtained by the Kraton G 1650‐stabilized dispersion polymerization of DMAAm in a toluene/heptane medium. The particle size and polydispersity could be controlled by the addition of water into the dispersed phase, and by varying the cellulose acetate butyrate or Kraton G 1650 concentration and the toluene/trichloroethene or toluene/heptane ratio.

magnified image
Bayesian parallel imaging with edge‐preserving priors
Authors: Raj Ashish , Singh Gurmeet , Zabih Ramin , Kressler Bryan , Wang Yi , Schuff Norbert , Weiner Michael
Published: December 2006

Existing parallel MRI methods are limited by a fundamental trade‐off in that suppressing noise introduces aliasing artifacts. Bayesian methods with an appropriately chosen image prior offer a promising alternative; however, previous methods with spatial priors assume that intensities vary smoothly over the entire image, resulting in blurred edges. Here we introduce an edge‐preserving prior (EPP) that instead assumes that intensities are piecewise smooth, and propose a new approach to efficiently compute its Bayesian estimate. The estimation task is formulated as an optimization problem that requires a nonconvex objective function to be minimized in a space with thousands of dimensions. As a result, traditional continuous minimization methods cannot be applied. This optimization task is closely related to some problems in the field of computer vision for which discrete optimization methods have been developed in the last few years. We adapt these algorithms, which are based on graph cuts, to address our optimization problem. The results of several parallel imaging experiments on brain and torso regions performed under challenging conditions with high acceleration factors are shown and compared with the results of conventional sensitivity encoding (SENSE) methods. An empirical analysis indicates that the proposed method visually improves overall quality compared to conventional methods. Magn Reson Med 57:8–21, 2007. © 2006 Wiley‐Liss, Inc.