bluuebunny/crossref_metadata_2025 huggingface dataset:
Functional potential of P2P‐R: A role in the cell cycle and cell differentiation related to its interactions with proteins that bind to matrix associated regions of DNA?
Authors: Scott Robert E. , Giannakouros Thomas , Gao Sizhi , Peidis Philippos
Published: August 2003

P2P‐R is the alternately spliced product of the P2P‐R/PACT gene in that P2P‐R lacks one exon encoding 34 amino acids. The 250 kDa P2P‐R protein is the predominate product expressed in multiple murine cell lines. It is a highly basic protein that contains multiple domains including an N‐terminal RING type zinc finger, a proline rich domain, an RS region, and a C‐terminal lysine‐rich domain. P2P‐R binds the p53 and the Rb1 tumor suppressors and is phosphorylated by the cdc2 and SRPK1a protein kinases. P2P‐R also interacts with scaffold attachment factor‐B (SAF‐B), a well characterized MARs (for matrix attachment regions) binding factor, and may interact with nucleolin, another MARs binding factor. In addition, P2P‐R binds single strand DNA (ssDNA). The expression of P2P‐R is regulated by differentiation and cell cycle events. P2P‐R mRNA is markedly repressed during differentiation, whereas immunoreactive P2P‐R protein levels are >10‐fold higher in mitotic than in G0 cells. The localization of P2P‐R also is modulated during the cell cycle. During interphase, P2P‐R is present primarily in nucleoli and nuclear speckles whereas during mitosis, P2P‐R associates with the periphery of chromosomes. Overexpression of near full length P2P‐R induces mitotic arrest in prometaphase and mitotic apoptosis, and overexpression of selected P2P‐R segments also can promote apoptosis. This compendium of data supports the possibility that P2P‐R may form complexes with the Rb1 and/or p53 tumor suppressors and MARs‐related factors, in a cell cycle and cell differentiation‐dependent manner, to influence gene transcription/expression and nuclear organization. J. Cell. Biochem. 90: 6–12, 2003. © 2003 Wiley‐Liss, Inc.
Network visualization system for computational chemistry
Authors: Kozhin Mikhail , Yanov Ilya , Leszczynski Jerzy
Published: August 2003

Network Visualization System for Computational Chemistry (NVSCC) is a molecular graphics program designed for the visualization of molecular assemblies. NVSCC accepts the output files from the most popular ab initio quantum chemical programs, GAUSSIAN and GAMESS, and provides visualization of molecular structures based on atomic coordinates. The main differences between NVSCC and other programs are:

Network support due to built‐in FTP and telnet clients, which allows for the processing of output from and the sending of input to different computer systems and operating systems.

The possibility of working with output files in real time mode.

The possibility of animation from an output file during all steps of optimization.

The quick processing of huge volumes of data.

The development of custom interfaces.

© 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1678–1688, 2003
Regional self‐interaction correction of density functional theory
Authors: Tsuneda Takao , Kamiya Muneaki , Hirao Kimihiko
Published: August 2003

We propose a new simple scheme for self‐interaction correction (SIC) of exchange functionals in the density functional theory. In the new scheme, exchange energies are corrected by substituting exchange self‐interactions for exchange functionals in regions of self‐interaction. To classify the regions of self‐interaction, we take advantage of the property of the total kinetic energy density approaching the Weizsäcker density in the case of electrons in isolated orbitals. The scheme differs from conventional SIC methods in that it produces optimized molecular structures. Applying the scheme to the calculation of reaction energy barriers showed that it provides a clear improvement in cases where the barriers are underestimated by conventional “pure” functionals. In particular, we found that this scheme even reproduces a transition state that is not given by pure functionals. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1592–1598, 2003
A comparison of the mechanism for the reductive half‐reaction between pea seedling and other copper amine oxidases (CAOs)
Authors: Prabhakar Rajeev , Siegbahn Per E. M.
Published: August 2003

In a previous DFT study a mechanism for the reductive half‐reaction of pea seedling amine oxidase (PSAO) was suggested. In many of the suggested steps a lysine at the active site plays an important role. However, this lysine is not found in other amine oxidases. The primary aim of the present DFT study is therefore to investigate alternative mechanisms for those amine oxidases (CAO) where the lysine residue is not present. One of the most important roles suggested for the lysine in PSAO was to protonate the O2‐site of TPQ before the critical CH bond cleavage of the substrate. In the absence of lysine the O2‐site of TPQ is now suggested to be protonated by a water ligand on the copper metal complex, in line with experimental suggestions. In other steps the role of lysine is taken over by an asparagine. All results are compared with experimental observations and good agreement is generally found. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1599–1609, 2003
FDS: Flexible ligand and receptor docking with a continuum solvent model and soft‐core energy function
Authors: Taylor Richard D. , Jewsbury Philip J. , Essex Jonathan W.
Published: August 2003

The docking of flexible small molecule ligands to large flexible protein targets is addressed in this article using a two‐stage simulation‐based method. The methodology presented is a hybrid approach where the first component is a dock of the ligand to the protein binding site, based on deriving sets of simultaneously satisfied intermolecular hydrogen bonds using graph theory and a recursive distance geometry algorithm. The output structures are reduced in number by cluster analysis based on distance similarities. These structures are submitted to a modified Monte Carlo algorithm using the AMBER‐AA molecular mechanics force field with the Generalized Born/Surface Area (GB/SA) continuum model. This solvent model is not only less expensive than an explicit representation, but also yields increased sampling. Sampling is also increased using a rotamer library to direct some of the protein side‐chain movements along with large dihedral moves. Finally, a softening function for the nonbonded force field terms is used, enabling the potential energy function to be slowly turned on throughout the course of the simulation. The docking procedure is optimized, and the results are presented for a single complex of the arabinose binding protein. It was found that for a rigid receptor model, the X‐ray binding geometry was reproduced and uniquely identified based on the associated potential energy. However, when side‐chain flexibility was included, although the X‐ray structure was identified, it was one of three possible binding geometries that were energetically indistinguishable. These results suggest that on relaxing the constraint on receptor flexibility, the docking energy hypersurface changes from being funnel‐like to rugged. A further 14 complexes were then examined using the optimized protocol. For each complex the docking methodology was tested for a fully flexible ligand, both with and without protein side‐chain flexibility. For the rigid protein docking, 13 out of the 15 test cases were able to find the experimental binding mode; this number was reduced to 11 for the flexible protein docking. However, of these 11, in the majority of cases the experimental binding mode was not uniquely identified, but was present in a cluster of low energy structures that were energetically indistinguishable. These results not only support the presence of a rugged docking energy hypersurface, but also suggest that it may be necessary to consider the possibility of more than one binding conformation during ligand optimization. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1637–1656, 2003
A partition function algorithm for nucleic acid secondary structure including pseudoknots
Authors: Dirks Robert M. , Pierce Niles A.
Published: August 2003

Nucleic acid secondary structure models usually exclude pseudoknots due to the difficulty of treating these nonnested structures efficiently in structure prediction and partition function algorithms. Here, the standard secondary structure energy model is extended to include the most physically relevant pseudoknots. We describe an O(N5) dynamic programming algorithm, where N is the length of the strand, for computing the partition function and minimum energy structure over this class of secondary structures. Hence, it is possible to determine the probability of sampling the lowest energy structure, or any other structure of particular interest. This capability motivates the use of the partition function for the design of DNA or RNA molecules for bioengineering applications. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1664–1677, 2003
Ab initio study of the mechanism of the atmospheric reaction: NO2 + O3 → NO3 + O2
Authors: Peiró‐García Julio , Nebot‐Gil Ignacio
Published: August 2003

The atmospheric reaction NO2 + O3 → NO3 + O2 (1) has been investigated theoretically by using the MP2, G2, G2Q, QCISD, QCISD(T), CCSD(T), CASSCF, and CASPT2 methods with various basis sets. The results show that the reaction pathway can be divided in two different parts at the MP2 level of theory. At this level, the mechanism proceeds along two transition states (TS1 and TS2) separated by an intermediate, designated as A. However, when the single‐reference higher correlated QCISD methodology has been employed, the minimum A and the transition state TS2 are not found on the hypersurface of potential energy, which confirms a direct reaction mechanism. Single‐reference high correlated and multiconfigurational methods consistently predict the barrier height of reaction (1) to be within the range 2.5–6.1 kcal mol−1, in reasonable agreement with experimental data. The calculated reaction enthalpy is −24.6 kcal mol−1 and the reaction rate calculated at the highest CASPT2 level, of k = 6.9 × 10−18 cm3 molecule−1 s−1. Both results can be regarded also as accurate predictions of the methodology employed in this article. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1657–1663, 2003
Structural and dynamical properties of methane clathrate hydrates
Authors: English Niall J. , Macelroy J. M. D.
Published: August 2003

Equilibrium molecular dynamics (MD) simulations have been performed in both the NVT and NPT ensembles to study the structural and dynamical properties of fully occupied methane clathrate hydrates at 50, 125, and 200 K. Five atomistic potential models were used for water, ranging from fully flexible to rigid polarizable and nonpolarizable. A flexible and a rigid model were utilized for methane. The phonon densities of states were evaluated and the localized rattling modes for the methane molecules were found to couple to the acoustic phonons of the host lattice. The calculated methane density of states was found to be in reasonable agreement with available experimental data. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1569–1581, 2003
Detailed analysis of grid‐based molecular docking: A case study of CDOCKER—A CHARMm‐based MD docking algorithm
Authors: Wu Guosheng , Robertson Daniel H. , Brooks Charles L. , Vieth Michal
Published: August 2003

The influence of various factors on the accuracy of protein‐ligand docking is examined. The factors investigated include the role of a grid representation of protein‐ligand interactions, the initial ligand conformation and orientation, the sampling rate of the energy hyper‐surface, and the final minimization. A representative docking method is used to study these factors, namely, CDOCKER, a molecular dynamics (MD) simulated‐annealing‐based algorithm. A major emphasis in these studies is to compare the relative performance and accuracy of various grid‐based approximations to explicit all‐atom force field calculations. In these docking studies, the protein is kept rigid while the ligands are treated as fully flexible and a final minimization step is used to refine the docked poses. A docking success rate of 74% is observed when an explicit all‐atom representation of the protein (full force field) is used, while a lower accuracy of 66–76% is observed for grid‐based methods. All docking experiments considered a 41‐member protein‐ligand validation set. A significant improvement in accuracy (76 vs. 66%) for the grid‐based docking is achieved if the explicit all‐atom force field is used in a final minimization step to refine the docking poses. Statistical analysis shows that even lower‐accuracy grid‐based energy representations can be effectively used when followed with full force field minimization. The results of these grid‐based protocols are statistically indistinguishable from the detailed atomic dockings and provide up to a sixfold reduction in computation time. For the test case examined here, improving the docking accuracy did not necessarily enhance the ability to estimate binding affinities using the docked structures. © 2003 Wiley Periodicals, Inc. J Comput Chem 13: 1549–1562, 2003
Deriving effective mesoscale potentials from atomistic simulations
Authors: Reith Dirk , Pütz Mathias , Müller‐Plathe Florian
Published: August 2003

We demonstrate how an iterative method for potential inversion from distribution functions developed for simple liquid systems can be generalized to polymer systems. It uses the differences in the potentials of mean force between the distribution functions generated from a guessed potential and the true distribution functions to improve the effective potential successively. The optimization algorithm is very powerful: convergence is reached for every trial function in few iterations. As an extensive test case we coarse‐grained an atomistic all‐atom model of polyisoprene (PI) using a 13:1 reduction of the degrees of freedom. This procedure was performed for PI solutions as well as for a PI melt. Comparisons of the obtained force fields are drawn. They prove that it is not possible to use a single force field for different concentration regimes. © 2003 Wiley Periodicals, Inc. J Comput Chem 13: 1624–1636, 2003
STO and GTO field‐induced polarization functions for H to Kr
Authors: Chong Delano P. , Grüning Myrta , Baerends Evert Jan
Published: August 2003

Field‐induced polarization (FIP) functions were proposed over two decades ago to improve the accuracy of calculated response properties, and the FIP functions in GTO form for H and C to F were tested on small molecules, with encouraging results. The concept of FIP is now extended to all atoms up to Kr. New simplifying approximations for the description of asymptotic highest occupied atomic orbitals (HOAOs) are introduced in this study. They provide the basis for STO and GTO exponents of a complete set of FIP functions from H to Kr, which are both listed for the convenience of the users. Tests on the polarizabilities of a series of atoms and molecules demonstrate that addition of the FIP basis functions to a series of standard basis sets drastically improves the performance of all these basis sets compared to converged results. Moreover, the byproduct of this study (approximate asymptotic HOAOs) provides information for the construction of accurate basis sets for long‐range ground state properties. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1582–1591, 2003
A multicentered approach to integrated QM/QM calculations. Applications to multiply hydrogen bonded systems
Authors: Hopkins Brian W. , Tschumper Gregory S.
Published: August 2003

A multicentered integrated QM/QM technique has been developed. By separating high‐level calculations in distinct regions of molecules, the multicentered approach supplants a single large high‐level calculation with several smaller calculations. Due to the steep polynomial scaling of traditional ab initio quantum chemical methods, this separation significantly enhances the computational efficiency of QM/QM methods. The straightforward implementation of this multicentered approach is illustrated with several large poly‐alcohols that form hydrogen bonds with water. The largest alcohol–water complex contains 81 atoms. For properly selected model systems, this multicentered approach introduces essentially no error in the dissociation energies of these complexes relative to conventional QM/QM schemes. This multicentered technique should be easily extended to other, more general integrated methods (QM/MM, ONIOM, etc). © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1563–1568, 2003
Improved third‐order Møller–Plesset perturbation theory
Authors: Grimme Stefan
Published: August 2003

Based on a partitioning of the total correlation energy into contributions from parallel‐ and antiparallel‐spin pairs of electrons, a modified third‐order Møller–Plesset (MP) perturbation theory is developed. The method, termed SCS–MP3 (SCS for spin‐component‐scaled) continues previous work on an improved version of MP2 (S. Grimme, J Chem Phys 2003, 118, 9095). A benchmark set of 32 isogyric reaction energies, 11 atomization energies, and 11 stretched geometries is used to assess to performance of the model in comparison to the standard quantum chemical approaches MP2, MP3, and QCISD(T). It is found, that the new method performs significantly better than usual MP2/MP3 and even outperforms the more costly QCISD method. Opposite to the usual MP series, the SCS third‐order correction uniformly improves the results. Dramatic enhancements are especially observed for the more difficult atomization energies, some of the stretched geometries, and reaction and ionization energies involving transition metal compounds where the method seems to be competitive or even superior to the widely used density functional approaches. Further tests performed for other complex systems (biradicals, C20 isomers, transition states) demonstrate that the SCS–MP3 model yields often results of QCISD(T) accuracy. The uniformity with which the new approach improves for very different correlation problems indicates significant robustness, and suggests it as a valuable quantum chemical method of general use. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1529–1537, 2003
Continuum and discrete calculation of fractional contributions to solvation free energy
Authors: Morreale Antonio , Gelpí Josep Lluis , Luque F. Javier , Orozco Modesto
Published: August 2003

Approaches to compute fractional contributions to the solvation free energy are developed in the context of continuum self consistent reaction field calculations (both classical and quantum mechanical), as well as in the framework of discrete molecular dynamics simulations. It is found that for a series of typical pharmacological drugs there is a good agreement between the different fractional descriptions. Algorithms reported here can be easily applied as molecular descriptors in the context of quantitative structure‐activity relationships. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1610–1623, 2003
Ab initioinvestigation on the reaction path and rate for the gas‐phase reaction of HO + H2O ↔ H2O + OH
Authors: Uchimaru Tadafumi , Chandra Asit K. , Tsuzuki Seiji , Sugie Masaaki , Sekiya Akira
Published: August 2003

This article describes anab initioinvestigation on the potential surfaces for one of the simplest hydrogen atom abstraction reactions, that is, HO + H2O ↔ H2O + OH. In accord with the findings in the previously reported theoretical investigations, two types of the hydrogen‐bonding complexes [HOHOH] and [H2OHO] were located on the potential energy surface. The water molecule acts as a hydrogen donor in the [HOHOH] complex, while the OH radical acts as a hydrogen donor in the [H2OHO] complex. The energy evaluations at the MP2(FC) basis set limit, as well as those through the CBS‐APNO procedure, have provided estimates for enthalpies of association for these complexes at 298 K as −2.1 ≈ −2.3 and −4.1 ≈ −4.3 kcal/mol, respectively. The IRC calculations have suggested that the [H2OHO] complex should be located along the reaction coordinate for the hydrogen abstraction. Our best estimate for the classical barrier height for the hydrogen abstraction is 7.8 kcal/mol, which was obtained from the CBS‐APNO energy evaluations. After fitting the CBS‐APNO potential energy curve to a symmetrical Eckart function, the rate constants were calculated by using the transition state theory including the tunneling correction. Our estimates for the Arrhenius parameters in the temperature region from 300 to 420 K show quite reasonable agreement with the experimentally derived values. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1538–1548, 2003
Coronary heart disease, hypertension, and angiotensinogen gene variants in indian opulation
Authors: Nair K.G. , Shalia K.K. , Ashavaid T.F. , Dalal J.J.
Published: August 2003

Gene encoding components of the renin angiotensin system (RAS) have been implicated with the increased risk of cardiovascular disease (CVD). Two variants of the angiotensinogen (AGT) gene, M235T and T174M, have been shown to be associated with increased risk of hypertension. In the present study, we examined the association of these two polymorphisms and their synergistic interaction with the angiotensin I‐converting enzyme (ACE) deletion homozygote genotype (D/D) on subjects with coronary heart disease (CHD) and hypertension. We studied 131 healthy individuals, 141 angiographically verified CHD patients, and 159 hypertensive subjects. The identification of the ACE and AGT gene polymorphisms was carried out using a PCR‐based restriction endonuclease digestion method. There was no significant difference in the distribution of the M235T and T174M variants between the two test groups and the control group. Association was also not seen when analysis was carried out in patients when subgrouped according to the extent of the severity of the disease. In addition, the risk was not restricted to subjects carrying the D allele of the ACE gene and T235T of AGT. M235T and T174M variants do not contribute to the increased risk of CHD or hypertension in the Indian population. J. Clin. Lab. Anal. 17:141–146, 2003. © 2003 Wiley‐Liss, Inc.
Development of a new method for measuring total urinary protein using acid violet 6B pigment
Authors: Iijima Shiro , Cho Hiroko , Sakai Nobue , Shiba Kiyoko , Toyoshima Yayoi , Nishida Kenji , Kobayashi Shizuko
Published: August 2003

We have developed a new method for measuring total urinary protein using acid violet 6B (AV6B) pigment. Nine purified components of human urinary proteins and urine samples collected randomly from 123 diabetic outpatients were used. There were 62, 36, and 25 cases of prenephropathy, early nephropathy, and overt nephropathy, respectively. All samples were measured by Coomassie brilliant blue G 250 (CBB), pyrogallol red‐molybdate (PRM), and AV6B methods using an optical photometer. In healthy subjects, the major components of urinary proteins, such as γ‐globulins, IgG, IgA Tamm‐Horsfall protein, and transferrin, the reactivity values of the AV6B and PRM methods were similar. The CBB method was the least sensitive of the three methods. In the urine samples from diabetic patients, the urinary protein values measured by the AV6B method were higher than those measured by the CBB method in the prenephropathy stage. The values obtained by the AV6B method (y) correlated well with those from the CBB method (x) (y = 1.243x+ 3.61, r = 0.904). When the values from the AV6B method (y) were compared to those from the PRM method (x), correlation was low (y = 1.406x−29.15, r = 0.786). In conclusion, the AV6B method was more useful than the CBB and PRM methods for low levels of urinary protein. J. Clin. Lab. Anal. 17: 147–154, 2003. © 2003 Wiley‐Liss, Inc.
Diagnosis of tuberculosis: Available technologies, limitations, and possibilities
Authors: Garg Sanjay K. , Tiwari R. P. , Tiwari Dileep , Singh Rupinder , Malhotra Dolly , Ramnani V. K. , Prasad G.B.K.S. , Chandra Ramesh , Fraziano M. , Colizzi V. , Bisen Prakash S.
Published: August 2003

Rapid diagnosis and treatment are important for preventing transmission of Mycobacterium tuberculosis. However, the diagnosis of tuberculosis continues to pose serious problems, mainly because of difficulties in differentiating between patients with active tuberculosis and those with healed lesions, normal mycobacterium boris BCG (Bacillus Calmette Guerin) vaccinated individuals, and unvaccinated Manteux positives. Physicians still rely on conventional methods such as Ziehl‐Neelsen (ZN) staining, fluorochrome staining, sputum culture, gastric lavage, and other non‐traditional methods. Although the tuberculin test has aided in the diagnosis of tuberculosis for more than 85 years, its interpretation is difficult because sensitization with nontuberculous mycobacteria leads to false‐positive tests. There have been numerous unsuccessful attempts to develop clinically useful serodiagnostic kits for tuberculosis. A number of proteinaceous and nonprotein antigens (such as acyltrehaloses and phenolglycolipids) have been explored from time to time for the development of such assays but they have not proved to be clinically useful. It has been difficult to develop an ELISA utilizing a suitable antigen because M. tuberculosis shares a large number of antigenic proteins with other microorganisms that may or may not be pathogenic. With the advent of molecular biology techniques, there have been significant advances in nucleic acid‐based amplification and hybridization, which are helping to rectify existing flaws in the diagnosis of tuberculosis. The detection of mycobacterial DNA in clinical samples by polymerase chain reaction (PCR) is a promising approach for the rapid diagnosis of tuberculous infection. However, the PCR results must be corrected for the presence of inhibitors as well as for DNA contamination. In the modern era of genetics, marked by proteomics and genomics, the day is not far off when DNA chip‐based hybridization assays will instantly reveal mycobacterial infections. J. Clin. Lab. Anal. 17: 155–163, 2003. © 2003 Wiley‐Liss, Inc.
Serum cystatin C may predict the early prognostic stages of patients with type 2 diabetic nephropathy
Authors: Shimizu Ayumi , Horikoshi Satoshi , Rinnno Hisaki , Kobata Mami , Saito Kensuke , Tomino Yasuhiko
Published: August 2003

We determined the relationship between levels of serum cystatin C or serum creatinine (s‐Cr) and prognostic stages of type 2 diabetic nephropathy. Serum samples from 174 patients with type 2 diabetes were obtained from Juntendo University Hospital, Tokyo and Juntendo Urayasu Hospital, Chiba, Japan. They were classified into four groups according to the Report of the Ministry of Health and Welfare of Japan as follows: Stage I (normoalbuminuric stage), Stage II (microalbuminuric stage), Stage IIIA (macroalbuminuric stage without renal dysfunction), Stage IIIB (macroalbuminuric stage with renal dysfunction), and Stage IV (renal failure stage). Among these patients, 68 were Stage I, 29 Stage II, 32 Stage IIIA, 17 Stage IIIB, and 28 Stage IV. The levels of serum cystatin C were measured using the Dade Behring Cystatin C assay with automated Dade Behring Nephelometer II (BNII) (Dade Behring Marburg GmbH, Germany). The mean levels of serum cystatin C in Stage IIIA were significantly higher than those in Stage I or II (P<0.00001, P<0.0005, respectively). The mean levels of serum cystatin C in Stage IIIB and Stage IV were also significantly higher than those in Stage I (P<0.00001). However, the mean levels of serum creatinine (s‐Cr) in Stage IIIA were not significantly higher than those in Stage I or II. The levels of s‐Cr in Stage IIIB and Stage IV were significantly higher than those in Stage I (P<0.00001). Receiver operating characteristic (ROC) plots demonstrated that the area under the curve (AUC) of cystatin C (0.76) was greater than that of s‐Cr (0.66). As an early prognostic marker of type 2 diabetic nephropathy, serum cystatin C was better than s‐Cr in terms of sensitivity and specificity. It appears that the levels of serum cystatin C may predict early prognostic stages of patients with type 2 diabetic nephropathy. J. Clin. Lab. Anal. 17:164–167, 2003. © 2003 Wiley‐Liss, Inc.
Interleukin‐10 gene –627 allele variants, not interleukin‐I beta gene and receptor antagonist gene polymorphisms, are associated with atopic bronchial asthma
Authors: Hang Liang‐Wen , Hsia Te‐Chun , Chen Wen‐Chi , Chen Huey‐Yi , Tsai Jeffrey J.P. , Tsai Fuu‐Jen
Published: August 2003

Asthma is an airway hyperresponsive disease characterized by the expression of multiple inflammatory genes, including cytokines. Interleukin‐I and interleukin‐10 (IL‐1 and IL‐10) are cytokines that might play a role in the process of inflammation and are therefore considered to be involved in the pathogenesis of bronchial asthma. The aim of this study was to test whether the polymorphisms of the promoter region and exon 5 of the IL‐1 gene, intron 2 of the IL‐1Ra gene, and –627 nucleotide (C/A) of the IL‐10 gene could be genetic markers for the susceptibility of bronchial asthma. A normal control group made up of 47 healthy volunteers and 117 patients with bronchial asthma were examined in this study. We analyzed the variable number of tandem repeats at intron 2 of the IL‐1Ra gene for the polymorphisms by polymerase chain reaction (PCR). PCR‐based restriction analysis of the IL‐1 gene polymorphisms of the promoter region and exon 5 was carried out by the endonucleases Ava I and Taq I, respectively. The IL‐10 gene –627 C/A polymorphisms were investigated by PCR‐based restriction analysis. The distribution of CC homozygotes in the IL‐10 gene was significantly lower in asthma patients than in controls (P=0.013, OR=3.599, 95% CI=1.240∼10.441). The polymorphisms studied in the IL‐1 genes did not reveal any significant association with bronchial asthma when compared with the control group (promoter region by chi‐square test, P=0.627; exon 5 region by Fisher's exact test, P=0.403). Only two alleles of the IL‐1Ra gene corresponding to one and two copies of an 86‐base pair sequence repeat were identified by PCR in the control group. There were three alleles found in the asthmatic patient group. The results revealed no significant differences between normal individuals and asthma patients (P=0.454, Fisher's exact test). The IL‐10 gene –627 “A” allele is an associated risk factor of developing atopic asthma. J. Clin. Lab. Anal. 17:168–173, 2003. © 2003 Wiley‐Liss, Inc.
Evaluation of an automated chemiluminescent immunoassay for complexed PSA on the Bayer ACS:180™ system
Authors: Datta Pradip , Dasgupta Amitava
Published: August 2003

Prostate‐specific antigen (PSA), the most important tumor marker for the detection of prostate cancer, exists in serum in a free, uncomplexed form (free PSA [fPSA]), and as bound to protease inhibitors (mainly α1‐antichymotrypsin [ACT]). The measurement of complexed PSA (cPSA) concentration in serum has been shown to have better sensitivity and specificity than serum total PSA concentration. A new chemiluminescent immunoassay for cPSA for use on the Bayer ACS:180™ fully automated system (Bayer Corp., Tarrytown, NY) has been developed and evaluated. The precision of the new assay was <3.9% (within‐run coefficient of variation [CV]) and <5.0% (total CV). The analytical sensitivity (95% upper limit of noise at zero calibrator) was <0.03 ng/mL. A comparison of the ACS:180™ cPSA results with the cPSA concentrations calculated from the ACCESS (Beckman‐Coulter) PSA and fPSA assays yielded the following regression equation: ACS:180™ cPSA=0.93* (calculated ACCESS cPSA) +0.43, R=0.993, n=95. The mean dilution and spike recovery for five samples were both 98%. No interference was observed from hemoglobin, triglyceride, or bilirubin (NCCLS protocol). These results indicate that the ACS:180™ cPSA assay is precise, and compares well with the calculated cPSA from ACCESS total and free‐PSA results. J. Clin. Lab. Anal. 17:174–178, 2003. © 2003 Wiley‐Liss, Inc.
Impaired protein binding of Chinese medicine DanShen in uremic sera and sera with hyperbilirubinemia: Rapid assessment of total and free Danshen concentrations using the fluorescence polarization immunoassay for digoxin
Authors: Wahed Amer , Pollard John , Wells Alice , Dasgupta Amitava
Published: August 2003

DanShen is a Chinese medicine that is used to treat cardiovascular disorders. DanShen is moderately to strongly protein bound, mainly to albumin. Because impaired protein binding of albumin‐bound drugs in uremia has been reported, we studied protein binding of DanShen by measuring the digoxin‐like immunoreactive component of this Chinese medicine. We observed a significantly higher percentage of free fraction of DanShen in uremic sera in vitro. Impaired protein binding of DanShen was also observed in sera from patients with liver disease, who had elevated concentrations of bilirubin. Treating uremic sera with activated charcoal significantly improved the protein binding of DanShen, indicating that uremic compounds are responsible for the impaired protein binding of DanShen. On the other hand, when various amounts of bilirubin were added to aliquots of the normal pool supplemented with DanShen, we observed only a modest displacement of DanShen from the protein‐binding sites by bilirubin, indicating that hypoalbuminemia may play a major role in impaired protein binding of DanShen in sera with elevated bilirubin concentrations. We conclude that protein binding of DanShen is lower in uremic sera and in sera with elevated bilirubin concentrations. J. Clin. Lab. Anal. 17:179–183, 2003. © 2003 Wiley‐Liss, Inc.
Quantification of chemotherapeutic target gene mRNA expression in human breast cancer biopsies: Comparison of real‐time reverse transcription‐PCR vs. Relative quantification reverse transcription‐PCR utilizing DNA sequencer analysis of PCR products
Authors: Juhasz Agnes , Frankel Paul , Cheng Catherine , Rivera Hector , Vishwanath Reena , Chiu Alice , Margolin Kim , Yen Yun , Newman Edward M. , Synold Tim , Wilczynski Sharon , Lenz Heinz‐Josef , Gandara David , Albain Kathy S. , Longmate Jeffrey , Doroshow James H.
Published: August 2003

The solid tumor mRNA expression of genes related to the mechanism of action of certain antineoplastic agents is often predictive of clinical efficacy. We report here on the development of a rapid and practical real‐time RT‐PCR method to quantify genetic expression in solid tumors. The genes examined are related to the intracellular pharmacology of gemcitabine and cisplatin, two drugs that are used in the treatment of several types of advanced cancer. We evaluated target gene mRNA levels from breast tumor samples using two quantitative RT‐PCR methods: 1) an improved relative RT‐PCR method using fluorescence‐labeled primers, automated PCR set up, and GeneScan® analysis software; and 2) real‐time RT‐PCR with redesigned primers using an ABI 7900HT instrument, with additional postprocessing of the data to adjust for efficiency differences across the target genes. Using these methods, we quantified mRNA expression levels of deoxycytidine kinase (dCK), deoxycytidylate deaminase (dCDA), the M1 and M2 subunits of ribonucleotide reductase (RRM1, RRM2), and excision cross complementation group 1 (ERCC1) in 35 human “fresh” frozen breast cancer biopsies. While both assay methods were substantially more rapid than traditional RT‐PCR, real‐time RT‐PCR appeared to be superior to the amplification end‐point measurement in terms of precision and high throughput, even when a DNA sequencer was used to assess fluorescence‐labeled PCR products. This reproducible, highly sensitive real‐time RT‐PCR method for the detection and quantification of the mRNAs for dCK, dCDA, RRM1, RRM2, and ERCC1 in human breast cancer biopsies appears to be more informative and less time‐consuming than either classical radioisotope‐dependent RT‐PCR or the technique utilizing GeneScan® analysis described herein. By allowing the measurement of intratumoral target gene expression, these new methods may prove useful in predicting the clinical utility of gemcitabine‐ and platinum‐containing chemotherapy programs in patients with solid tumors. J. Clin. Lab. Anal. 17:184–194, 2003. © 2003 Wiley‐Liss, Inc.
Prenatal diagnosis of Machado‐Joseph disease/spinocerebellar ataxia type 3 in Taiwan: Early detection of expanded ataxin‐3
Authors: Tsai Hui‐Fang , Liu Chin‐San , Chen Gin‐Den , Lin Mei‐Ling , Li Chuan , Chen Yi‐Yun , Wang Bao‐Tyan , Hsieh Mingli
Published: August 2003

Machado‐Joseph disease (MJD)/Spinocerebellar Ataxia Type 3 (SCA3) is a rare autosomal dominative disorder in which one of the neurodegenerative disorders is caused by a translated CAG repeat expansion. Here, we present the first prenatal diagnosis of MJD in Taiwan in a woman whose husband was known to carry an unstable CAG repeat expansion in the MJD gene. After evaluating the couples' motivation and psychological tolerance, amniocentesis was performed at gestation of 13 weeks. The diagnosis was made using a simple nonradioactive polymerase chain reaction (PCR) for rapid detection of the presence of an expanded MJD allele. Meanwhile, using radioactive PCR, we identified the presence of an unusual shortness of CAG expansion in the MJD gene with 74 repeats in the fetus compared with 78 repeats in the father. After termination of the pregnancy, Western blot analysis further confirmed the presence of normal and mutant ataxin‐3 in the fetal tissue. In summary, we have performed the first prenatal diagnosis of MJD in Taiwan, and described our experience with an at‐risk male requesting counseling, carrier testing, and prenatal diagnosis for Machado‐Joseph disease. Early detection of both normal and expanded ataxin‐3 in fetal tissues was first demonstrated in the present study. J. Clin. Lab. Anal. 17: 195–200, 2003. © 2003 Wiley‐Liss, Inc.
Evaluation of the Computerized Assessment System for Psychotherapy Evaluation and Research (CASPER) interview with a psychiatric inpatient population
Authors: Strong Joanna E. , Farrell Albert D.
Published: August 2003

The Computerized Assessment System for Psychotherapy Evaluation and Research (CASPER; Farrell & McCullough‐Vaillant, 1996) includes a computer‐based interview designed to assess functioning across a broad range of areas. The psychometric properties of scales derived from this interview were examined in a sample of 191 patients from the admissions wards of a state psychiatric hospital. Few participants had difficulty completing the computerized interview, and most rated their reactions to it positively. Item analyses and confirmatory factor analysis largely replicated the structure reported in a previous study of outpatients. Support was found for scales representing Physical Complaints, Worry, Hopelessness, Assertiveness, Hostility/Anger, Thought Problems, Psychotic Symptoms, Substance Use, and Suicidal Thoughts and Behavior. Comparison of scales from the CASPER and the Behavior and Symptom Identification Scale‐32 (BASIS‐32; Eisen & Culhane, 1999) supported the convergent and discriminant validity of several scales. Support also was found for the CASPER Global Functioning scale. Overall, results supported the use of the CASPER as a valuable tool for assessing inpatient functioning. © 2003 Wiley Periodicals, Inc. J Clin Psychol.
MMPI‐2: Confidence intervals for random responding to the F, F Back, and VRIN scales
Authors: Charter Richard A. , Lopez Michael N.
Published: August 2003

Several studies have investigated random responding to the F, F Back, and VRIN scales. Only one study attempted to provide practical cutoff scores for these scales, but was unable to reach definitive cutoffs. This study uses the normal approximation to the binomial distribution and provides confidence interval bounds for random responding at the 95, 90, and 85% levels for the F, F Back, and VRIN scales. The possibility that humans asked to respond randomly produce F, F Back, and VRIN scores different from computer‐generated random scores was investigated. The results show nonsignificant differences between human and computer responses for the F and F Back scales and mixed results for the VRIN scale. © 2003 Wiley Periodicals, Inc. J Clin Psychol.
Minimal model to document psychometric change after standard anterior temporal lobectomy for intractable seizure disorder
Authors: Costello Raymond M. , Mayes Bruce , Szabo C. Akos , Vollmer Dennis G.
Published: August 2003

Neuropsychological assessment of persons with epilepsy is recommended whenever neurosurgery is considered as an alternative therapy for seizure disorders refractory to ordinary medical management. Although psychological assessment is common in centers specialized in the care of epilepsy patients, standardized protocols are not common. This study addresses the question of the optimal minimal test battery necessary to differentiate groups of right‐handed patients with refractory, complex partial seizure disorder who receive either right or left anterior temporal lobectomy or no surgery. No variable differentiated the groups before surgery. Only Logical Memory–Immediate of the Wechsler Memory Scale differentiated the groups following surgery. This finding is consistent with the literature. © 2003 Wiley Periodicals, Inc. J Clin Psychol.
Measuring coping style and resistance among Spanish and Argentine samples: Development of the Systematic Treatment Selection Self‐Report in Spanish
Authors: Corbella Sergi , Beutler Larry E. , Fernández‐Álvarez Héctor , Botella Luis , Malik Mary L. , Lane Geoffrey , Wagstaff Nicole
Published: August 2003

This article reports the reliability and validity of the Coping Style and Resistance subscales of the Systematic Treatment Selection Self‐Report (STS‐SR) scale after its translation to Spanish. The English versions of the STS system identify eight empirically derived patient variables that have been found to moderate the effects of various classes of mental health treatment procedures. Research on these dimensions as treatment indicators, as assessed both by clinicians and through patient self‐reports, indicates that they increase the efficiency and effectiveness of treatment among English‐speaking samples. This article reports a study of the convergent and discriminant validity of two of the subscales, Coping Style and Trait Resistance. The subscales were translated English into Spanish and administered to large Spanish and Argentinean subject pools, along with established measures of the same and related constructs. Results revealed that both scales possessed good internal consistency and adequate discriminant validity. The implications of these findings are discussed. © 2003 Wiley Periodicals, Inc. J Clin Psychol.
Evaluation of a meridian‐based intervention, Emotional Freedom Techniques (EFT), for reducing specific phobias of small animals
Authors: Wells Steve , Polglase Kathryn , Andrews Henry B. , Carrington Patricia , Baker A. Harvey
Published: August 2003

This study explored whether a meridian‐based procedure, Emotional Freedom Techniques (EFT), can reduce specific phobias of small animals underlaboratory‐controlled conditions. Randomly assigned participants were treated individually for 30 min with EFT (n = 18) or a comparison condition, diaphragmatic breathing (DB) (n = 17). ANOVAS revealed that EFT produced significantly greater improvement than did DB behaviorally and on three self‐report measures, but not on pulse rate. The greater improvement for EFT was maintained, and possibly enhanced, at six‐ to nine‐months follow‐up on the behavioral measure. These findings suggest that a single treatment session using EFT to reduce specific phobias can produce valid behavioral and subjective effects. Some limitations of the study also are noted and clarifying research suggested. © 2003 Wiley Periodicals, Inc. J Clin Psychol.
Neurokinin‐1 receptor (NK‐1R) expression is induced in human colonic epithelial cells by proinflammatory cytokines and mediates proliferation in response to substance P
Authors: Goode Triona , O'Connor Terry , Hopkins Ann , Moriarty Derek , O'Sullivan Gearld C. , Collins J. Kevin , O'Donoghue Diarmuid , Baird Alan W. , O'Connell Joe , Shanahan Fergus
Published: August 2003

We have previously shown that the receptor for substance P (SP), neurokinin‐1 receptor (NK‐1R), is a marker of human mucosal but not peripheral mononuclear cells. In the present study, we investigate NK‐1R expression in the human colonic mucosa in vivo, particularly in the epithelial cells. We investigate the influence of proinflammatory Th1 cytokines and SP on expression and function of NK‐1R in colonic epithelial cells in vitro. Using in situ hybridization to detect NK‐1R mRNA, and immunohistochemistry to detect NK‐1R protein, colonic epithelial cells were found to express NK‐1R in vivo. In contrast, colon epithelial cell lines (Caco‐2, HT29, SW620, T84) were negative for NK‐1R mRNA and protein. However, stimulation with a proinflammatory cytokine cocktail containing IFN‐γ, TNF‐α, and IL‐1β, caused induction of NK‐1R expression. Expression of NK‐1R in human colonic epithelial cells in vivo may therefore reflect cytokine conditioning by the mucosal microenvironment. SP did not alter ion transport in monolayers of cytokine‐treated T84 cells. While SP stimulated epithelial ion transport in colonic mucosae ex vivo, this was not a direct effect of SP on the epithelial cells, and appeared to be neurally mediated. However, SP (10−10–10−8 M) elicited a dose‐dependent proliferative effect on cytokine‐stimulated, but not unstimulated, SW620 cells. Proliferation of the epithelial cells in response to SP was mediated specifically via cytokine‐induced NK‐1R, since an NK‐1R‐specific antagonist (Spantide 1) completely blocked SP‐mediated proliferation in the cytokine‐treated cells. Our results therefore demonstrate that proinflammatory cytokines induce expression of NK‐1R in human colonic epithelial cell lines, and that SP induces proliferation of the epithelial cells via cytokine‐induced NK‐1R. J. Cell. Physiol. 197: 30–41, 2003© 2003 Wiley‐Liss, Inc.
Establishment of a human preadipose cell line, HPB‐AML‐I: Refractory to PPARγ‐mediated adipogenic stimulation
Authors: Torii Ikuko , Morikawa Shigeru , Nakano Akinobu , Morikawa Keiko
Published: August 2003

In this study, we established a unique cell line, HPB‐AML‐I (AML‐I), from peripheral blood mononuclear cells collected from a patient with acute myeloid leukemia (AML: M1). Morphological and phenotypical analyses of the established AML‐I cells demonstrated that they belong to a preadipocyte cell line as indicated by their storage of lipid droplets and expression of surface antigens similar to those found on bone marrow stromal cells (MSC). Through cell culture under adipogenic conditions, effective differentiation of AML‐I cells into adipocytes was induced by an adipogenesis inducing cocktail (INC) made up of a mixture of methylisobutylxanthine, hydrocortisone, and indomethacin. By contrast, activation of peroxisome proliferator‐activated receptor (PPARγ), which plays a key role in lipids metabolism and is highly expressed in AML‐I cells, decreased the number of lipid droplets in AML‐I cells. Here we report the establishment of a unique human derived‐preadipocyte cell line, AML‐I, and its bi‐directional adipogenic response to different type stimulation, i.e., one is a refractory response to troglitazone, a well‐known adipogenic stimulator, and a positive response to INC, an adipogenesis induction cocktail. These results suggest that, based on the adipogenic response, there might be some distinct lineages in human adipocytes and that the unique differentiation of AML‐I cells should be useful for analyzing both the differentiation and regulation of human preadipocytes. J. Cell. Physiol. 197: 42–52, 2003© 2003 Wiley‐Liss, Inc.