bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparative effects of herbicide dicamba and related compound on plant mitochondrial bioenergetics
Authors: Peixoto Francisco , Vicente Joaquim A. F. , Madeira Vítor M. C.
Published: June 2003

The herbicide dicamba (3,6‐dichloro‐2‐methoxybenzoic acid) was evaluated for its effects on bioenergetic activities of potato tuber mitochondria to elucidate putative mechanisms of action and to compare its toxicity with 2‐chlorobenzoic acid. Dicamba (4 μmol/mg mitochondrial protein) induces a limited stimulation of state 4 respiration of ca. 10%, and the above concentrations significantly inhibit respiration, whereas 2‐chlorobenzoic acid maximally stimulates state 4 respiration (ca. 50%) at about 25 μmol/mg mitochondrial protein. As opposed to these limited effects on state 4 respiration, transmembrane electrical potential is strongly decreased by dicamba and 2‐chlorobenzoic acid. Dicamba (25 μmol/mg mitochondrial protein) collapses, almost completely, Δψ; similar concentrations of 2‐chlorobenzoic acid promote Δψ drops of about 50%. Proton permeabilization partially contributes to Δψ collapse since swelling in K‐acetate medium is stimulated, with dicamba promoting a stronger stimulation. The Δψ decrease induced by dicamba is not exclusively the result of a stimulation on the proton leak through the mitochondrial inner membrane, since there was no correspondence between the Δψ decrease and the change on the O2 consumption on state 4 respiration; on the contrary, for concentrations above 8 μmol/mg mitochondrial protein a strong inhibition was observed. Both compounds inhibit the activity of respiratory complexes II and III but complex IV is not significantly affected. Complex I seems to be sensitive to these xenobiotics. In conclusion, dicamba is a stronger mitochondrial respiratory chain inhibitor and uncoupler as compared to 2‐chlorobenzoic acid. Apparently, the differences in the lipophilicity are related to the different activities on mitochondrial bioenergetics. © 2003 Wiley Periodicals, Inc. J Biochem Mol Toxicol 17:185–192, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/jbt.10077
Effects of pycnogenol treatment on oxidative stress in streptozotocin‐induced diabetic rats
Authors: Maritim A. , Dene B. A. , Sanders R. A. , Watkins J. B.
Published: June 2003

Free radicals and oxidative stress have been implicated in the etiology of diabetes and its complications. This in vivo study has examined whether subacute administration of pycnogenol, a French pine bark extract containing procyanidins that have strong antioxidant potential, alters biomarkers of oxidative stress in normal and diabetic rats. Diabetes was induced in female Sprague‐Dawley rats by a single injection of streptozotocin (90 mg/kg body weight, ip), resulting (after 30 days) in subnormal body weight, increased serum glucose concentrations, and an increase in liver weight, liver/body weight ratios, total and glycated hemoglobin, and serum aspartate aminotransferase activity. Normal and diabetic rats were treated with pycnogenol (10 mg/kg body weight/day, ip) for 14 days. Pycnogenol treatment significantly reduced blood glucose concentrations in diabetic rats. Biochemical markers for oxidative stress were assessed in the liver, kidney, and heart. Elevated hepatic catalase activity in diabetic rats was restored to normal levels after pycnogenol treatment. Additionally, diabetic rats treated with pycnogenol had significantly elevated levels of reduced glutathione and glutathione redox enzyme activities. The results demonstrate that pycnogenol alters intracellular antioxidant defense mechanisms in streptozotocin‐induced diabetic rats. © 2003 Wiley Periodicals, Inc. J Biochem Mol Toxicol 17:193–199, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/jbt.10078
Gene expression in rat skin induced by irritating chemicals
Authors: Rogers James V. , Garrett Carol M. , McDougal James N.
Published: June 2003

Occupational skin disease is the second most significant cause of occupational disease, after accidents. Irritation from occupational chemicals such as solvents, hydrocarbons, and surfactants are one cause of this disease. Gene expression studies provide useful information about normal processes in the skin and responses of the skin to exogenous chemicals. We exposed rats, cutaneously, to sodium lauryl sulfate (SLS, 1% and 10% aqueous solution), m‐xylene (pure liquid), and d‐limonene (pure liquid) for 1 h and measured transcriptional responses at the end of the exposure and 3 h later for comparison with untreated skin samples. Total skin RNA was isolated and analyzed using the Affymetrix RatTox U34 array. Using the Affymetrix software, we found that 234 of approximately 850 genes were detected as present in at least 80% of the normal skin samples. The largest number of these genes was related to metabolism, oxidative/cellular stress, and signal transduction. Limonene caused the largest change in mRNA levels with a total of 34 increased transcripts and 4 decreased transcripts. Xylene treatment resulted in 6 increased transcripts and 14 decreased transcripts, while 10% SLS caused 5 transcripts to increase and 17 to decrease. Only two transcripts were observed to change in skin following a 1% SLS exposure. Sodium lauryl sulfate transcript changes increased with dose and were maximum at 4 h. Limonene transcript changes were more numerous at 1 h than at 4 h. The observed differences may reflect different mechanisms of irritation. © 2003 Wiley Periodicals, Inc. J Biochem Mol Toxicol 17:123–137, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/jbt.10079
Stochastic proximity embedding
Authors: Agrafiotis Dimitris K.
Published: June 2003

We introduce stochastic proximity embedding (SPE), a novel self‐organizing algorithm for producing meaningful underlying dimensions from proximity data. SPE attempts to generate low‐dimensional Euclidean embeddings that best preserve the similarities between a set of related observations. The method starts with an initial configuration, and iteratively refines it by repeatedly selecting pairs of objects at random, and adjusting their coordinates so that their distances on the map match more closely their respective proximities. The magnitude of these adjustments is controlled by a learning rate parameter, which decreases during the course of the simulation to avoid oscillatory behavior. Unlike classical multidimensional scaling (MDS) and nonlinear mapping (NLM), SPE scales linearly with respect to sample size, and can be applied to very large data sets that are intractable by conventional embedding procedures. The method is programmatically simple, robust, and convergent, and can be applied to a wide range of scientific problems involving exploratory data analysis and visualization. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1215–1221, 2003
An algorithm to delineate and integrate topological basins in a three‐dimensional quantum mechanical density function
Authors: Malcolm Nathaniel O. J. , Popelier Paul L. A.
Published: June 2003

The growing activity in the area of Quantum Chemical Topology warrants a new algorithm to delineate topological basins in 3D scalar fields other than the electron density. A method based on the “octal tree search algorithm” of computer graphics is proposed to reach this goal. We illustrate the algorithm on the L(r) function, which is the negative of the Laplacian of the electron density. Because of its complicated topology, even in a simple test molecule such as water, it benefits from the octal tree algorithm as a robust, compact, and general technique to find the boundaries of topological basins. For the first time, we are able to compute the population and volume of the core and valence (bonding and nonbonding, i.e., lone pair) basins given by L(r)'s topology. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1276–1282, 2003
The SAAP force field. A simple approach to a new all‐atom protein force field by using single amino acid potential (SAAP) functions in various solvents*
Authors: Iwaoka Michio , Tomoda Shuji
Published: June 2003

A simple strategy to compose a new all‐atom protein force field (named as the SAAP force field), which utilizes the single amino acid potential (SAAP) functions obtained in various solvents by ab initio molecular orbital calculation applying the isodensity polarizable continuum model (IPCM), is presented. We considered that the total energy function of a protein force field (ETOTAL) is divided into three components; a single amino acid potential term (ESAAP), an interamino acid nonbonded interaction term (EINTER), and a miscellaneous term (EOTHERS), which is ignored (or considered to be constant) at the current version of the force field. The EINTER term consists of electrostatic interactions (EES') and van der Waals interactions (ELJ'). Despite simplicity, the SAAP force field implicitly involves the correlation among individual terms of the Lifson's potential function within a single amino acid unit and can treat solvent effects unambiguously by choosing the SAAP function in an appropriate solvent and the dielectric constant (D) of medium. Application of the SAAP force field to the Monte Carlo simulation of ForAla2NH2 in vacuo reasonably reproduced the results of the extensive conformational search by ab initio molecular orbital calculation. In addition, the preliminary Monte Carlo simulations for ForGly10NH2 and ForAla10NH2 showed reversible transitions from the extended to the pseudosecondary structures in water (D = 78.39) as well as in ether (D = 4.335). The result suggested that the new approach is efficient for fast modeling of protein structures in various environments. Decomposition analysis of the total energy function (ETOTAL) by using the SAAP force field suggested that conformational propensities of single amino acids (i.e., the ESAAP term) may play definitive roles on the topologies of protein secondary structures. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1192–1200, 2003
Energy decomposition in molecular complexes: Implications for the treatment of polarization in molecular simulations
Authors: Curutchet Carles , Bofill Josep María , Hernández Begoña , Orozco Modesto , Luque F. Javier
Published: June 2003

This study examines the contribution of electrostatic and polarization to the interaction energy in a variety of molecular complexes. The results obtained from the Kitaura–Morokuma (KM) energy decomposition analysis at the HF/6‐31G(d) level indicate that, for intermolecular distances around the equilibrium geometries, the polarization energy can be determined as the addition of the polarization energies of interacting blocks, as the mixed polarization term is typically negligible. Comparison of KM and QM/MM results shows that the electrostatic energy determined in the KM method is underestimated (in absolute value) by QM/MM methods. The reason of such underestimation can be attributed to the simplified representation of treating the interaction between overlapping charge distribution by the interaction of a QM molecule with a set of point charges. Nevertheless, the polarization energies calculated by KM and QM/MM methods are in close agreement. Finally, a consistent, automated strategy to derive charge distributions that include implicitly polarization effects in pairwise, additive force fields is presented. The strategy relies in the simultaneous fitting of electrostatic and polarization energies computed by placing a suitable perturbing particle at selected points around the molecule. The suitability of these charges to describe molecular interactions is discussed. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1263–1275, 2003
Performance of hybrid methods for large‐scale unconstrained optimization as applied to models of proteins
Authors: Das B. , Meirovitch H. , Navon I. M.
Published: June 2003

Energy minimization plays an important role in structure determination and analysis of proteins, peptides, and other organic molecules; therefore, development of efficient minimization algorithms is important. Recently, Morales and Nocedal developed hybrid methods for large‐scale unconstrained optimization that interlace iterations of the limited‐memory BFGS method (L‐BFGS) and the Hessian‐free Newton method (Computat Opt Appl 2002, 21, 143–154). We test the performance of this approach as compared to those of the L‐BFGS algorithm of Liu and Nocedal and the truncated Newton (TN) with automatic preconditioner of Nash, as applied to the protein bovine pancreatic trypsin inhibitor (BPTI) and a loop of the protein ribonuclease A. These systems are described by the all‐atom AMBER force field with a dielectric constant ϵ = 1 and a distance‐dependent dielectric function ϵ = 2r, where r is the distance between two atoms. It is shown that for the optimal parameters the hybrid approach is typically two times more efficient in terms of CPU time and function/gradient calculations than the two other methods. The advantage of the hybrid approach increases as the electrostatic interactions become stronger, that is, in going from ϵ = 2r to ϵ = 1, which leads to a more rugged and probably more nonlinear potential energy surface. However, no general rule that defines the optimal parameters has been found and their determination requires a relatively large number of trial‐and‐error calculations for each problem. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1222–1231, 2003
Many‐body effects on structure and dynamics of aqueous ionic solutions
Authors: Loeffler Hannes H.
Published: June 2003

We performed several molecular dynamic studies of metal cations in aqueous solution. The alkali metal ion Li+ and the first‐row transition metal ion Mn2+ have been chosen as model systems. Two different three‐body corrections are proposed to mimic the crucial many‐body effects of electrolyte solutions. The correction function, which includes attractive features of the three‐body potential, performs considerably better than the purely repulsive interaction function. Structural and dynamic results show that this simple enhancement is able to satisfactorily reproduce experimental and higher‐level results for the first hydration shell. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1232–1239, 2003
Assessment of the OLYP and O3LYP density functionals for first‐row transition metals
Authors: Baker Jon , Pulay Peter
Published: June 2003

We have investigated the performance of the OLYP and O3LYP density functionals for predicting atomic excitation energies and ionization potentials, and bond dissociation energies, geometries, and vibrational frequencies for selected first‐row transition metal compounds, including hydrides (MH) and singly charged methylene and methyl cations. The OLYP and O3LYP functionals are similar to the well‐known BLYP and B3LYP functionals, respectively, but use a new optimized exchange functional (OPTX) developed by Handy and Cohen (Mol Phys 2001, 99, 403) in place of the standard B88 exchange. A previous study by us on organic reactions (J Chem Phys 2002, 117, 1331) indicated that both OLYP and O3LYP gave results for heats of reaction and barrier heights that were overall superior to those using the popular B3LYP functional. For transition metals, however, although OLYP is overall superior to BLYP for molecular calculations, it is inferior to B3LYP. O3LYP provides results for molecules of about the same quality as B3LYP. For atomic excitation and 4s ionization energies, unless relativistic effects are included, OLYP and O3LYP are clearly worse than both BLYP and B3LYP. There is thus no real incentive to use either OLYP or O3LYP in place of B3LYP for calculations involving first‐row transition metals. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1184–1191, 2003
A computational study of the LiH dimer
Authors: McDowell Sean A. C.
Published: June 2003

A theoretical study of the properties of the linear LiH dimer was undertaken. In this dimer, an unusual type of hydrogen bonding (termed “inverse” hydrogen bonding by some authors), which involves the hydrogen bonded molecule acting as an electron donor (rather than as a proton donor), is exhibited. The optimized geometry, dipole moment, interaction energy, atomic charges, harmonic vibrational frequencies, and frequency shifts for the dimer are computed at the SCF, MP2, and QCISD levels of theory using mainly a 6‐31++G(d,p) basis set. We also examined the relative stability of the mono‐deuterated isotopomers of linear (LiH)2, i.e., LiH … LiD and LiD … LiH. Analysis of the normal vibrational modes, changes in the partial atomic charges, and changes in the vibrational frequencies of LiH on complexation were used to gain insight into the bonding and properties of the linear LiH dimer and its isotopomers. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1201–1207, 2003
A QM–MM interface between CHARMM and TURBOMOLE: Implementation and application to systems in bulk phase and biologically active systems
Authors: Loferer Markus J. , Loeffler Hannes H. , Liedl Klaus R.
Published: June 2003

The implementation of a hybrid QM–MM approach combining ab initio and density functional methods of TURBOMOLE with the molecular mechanics program package CHARMM is described. An interface has been created to allow data exchange between the two applications. With this method the efficient multiprocessor capabilities of TURBOMOLE can be utilized with CHARMM running as a single processor application. Therefore, features of nonparallel running code in CHARMM like the TRAVEL module for locating saddle points or VIBRAN for the calculation of second derivatives can be exploited by running the CPU intensive QM calculations in parallel. To test the methodology, several small systems are studied with both Hartree–Fock and density functional methods and varying QM–MM boundaries. Also, the computationally efficient RI‐J method has been examined for use in QM–MM applications. A B12 cofactor containing cobalt has been studied, to examine systems with a large QM region and transition metals. All tested methods perform satisfactory in comparison with pure quantum calculations. Additionally, algorithms for the characterization of saddle points have been tested for their potential use in QM–MM problems. The TRAVEL module of CHARMM has been applied to the Menshutkin reaction in the condensed phase, and a saddle point was located. This saddle point was verified by calculation of a steepest descent path connecting educt, transition state, and product, and by calculation of vibrational modes. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1240–1249, 2003
Toward direct determination of conformations of protein building units from multidimensional NMR experiments. V. NMR chemical shielding analysis of N‐formyl‐serinamide, a model for polar side‐chain containing peptides
Authors: Perczel András , Füzéry Anna K. , Császár Attila G.
Published: June 2003

Knowledge of chemical shift–structure relationships could greatly facilitate the NMR chemical shift assignment and structure refinement processes that occur during peptide/protein structure determination via NMR spectroscopy. To determine whether such correlations exist for polar side chain containing amino acid residues the serine dipeptide model, For‐L‐Ser‐NH2, was studied. Using the GIAO‐RHF/6‐31+G(d) and GIAO‐RHF/TZ2P levels of theory the NMR chemical shifts of all hydrogen (1HN,1Hα,1Hβ1,1Hβ2), carbon (13Cα,13Cβ,13C′) and nitrogen (15N) atoms have been computed for all 44 stable conformers of For‐L‐Ser‐NH2. An attempt was made to establish correlation between chemical shift of each nucleus and the major conformational variables (ω0, ϕ, ψ, ω1, χ,1and χ2). At both levels of theory a linear correlation can be observed between1Hα/ϕ,13Cα/ϕ, and13Cα/ψ. These results indicate that the backbone and side‐chain structures of For‐L‐Ser‐NH2have a strong influence on its chemical shifts. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1157–1171, 2003
A MCSCF method for ground and excited states based on full optimizations of successive Jacobi rotations
Authors: Ivanic Joseph , Ruedenberg Klaus
Published: June 2003

A new multiconfigurational self‐consistent field (MCSCF) method based on successive optimizations of Jacobi rotation angles is presented. For given one‐ and two‐particle density matrices and an initial set of corresponding integrals, a technique is developed for the determination of a Jacobi angle for the mixing of two orbitals, such that the exact energy, written as a function of the angle, is fully minimized. Determination of the energy‐minimizing orbitals for given density matrices is accomplished by successive optimization and updating of Jacobi angles and integrals. The total MCSCF energy is minimized by alternating between CI and orbital optimization steps. Efficiency is realized by optimizing CI and orbital vectors quasi‐simultaneously by not fully optimizing each in each improvement step. On the basis of the Jacobi‐rotation based approach, a novel MCSCF procedure is formulated for excited states, which avoids certain shortcomings of traditional excited‐state MCSCF methods. Applications to specific systems show the practicability of the developed methods. Published 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1250–1262, 2003
Synthesis of tritium‐labelled 3′‐azido‐3′‐deoxythymidine
Authors: Sidorov G.V. , Zverkov Yu.B. , Myasoedov N.F. , Jasko M.V. , Skoblov Yu.S.
Published: June 2003

New approaches to the synthesis of 3′‐azido‐3′‐deoxythymidine labelled with tritium in the heterocyclic base have been developed. With this aim, enzymatic transribosylation with [3H]thymine using the enzyme preparation from rat liver and a three‐step chemical synthesis with use of the tritium labelled precursor were studies. The enzyme preparation did not catalyse the transfer of the 3′‐azido‐3′‐deoxyribosyl fragment to the [3H]thymine residue. 5′‐O‐Benzoyl‐2,3′‐anhydrothymidine was taken as a precursor for the tritium labelling by the chemical methods. The resulting [3H]3′‐azido‐3′‐deoxythymidine was obtained with a specific radioactivity of 18.3 Ci/mmol, the tritium is located in the C‐6 position of the thymine residue. Copyright © 2003 John Wiley & Sons, Ltd.
High‐resolution three‐dimensional MR angiography of rodent tumors: Morphologic characterization of intratumoral vasculature
Authors: Fink Christian , Kiessling Fabian , Bock Michael , Lichy Matthias Philipp , Misselwitz Bernd , Peschke Peter , Fusenig Norbert E. , Grobholz Rainer , Delorme Stefan
Published: June 2003

Purpose

To evaluate high‐resolution three‐dimensional MR angiography (MRA) for the visualization and morphologic characterization of intratumoral vasculature.

Materials and Methods

Two subcutaneous rodent tumor models (human skin carcinoma HaCaT‐ras‐A‐5RT3 grown in nude mice and rat prostate carcinoma R3327‐AT1 grown in Copenhagen rats) were examined with a clinical 1.5 T MR‐system. For MRA a dedicated high‐resolution three‐dimensional gradient echo pulse sequence with a voxel size of 166 × 206 × 320 μm3 was performed after injection of Gadomer‐17. The image analysis included a correlation of intratumoral vessels with histology. Signal intensity measurements were performed in the vena cava, the tumor underlying muscle, and in various regions of the tumor. Signal‐to‐noise‐ratios (SNR) and contrast‐to‐noise‐ratios (CNR) were calculated from this measurement.

Results

High‐resolution MRA allowed a clear distinction of intratumoral blood vessels. The mouse tumor model tended to be strongly vascularized with several intratumoral blood vessels clearly displayed by MRA. When correlated with histology, these intratumoral blood vessels had a size in the range of 300 to 400 μm. In contrast, rat tumors had only sparse capillary intratumoral blood vessels that could only be demonstrated by histology. In both tumor models, dilated blood vessels were observed in the subcutaneous tissue near the tumor. In general, areas with a strong contrast enhancement correlated with viable, well vascularized tumor regions, whereas non‐enhancing tumor areas correlated with tumor necrosis or hypoxic areas.

Conclusion

High‐resolution three‐dimensional MRA allows the visualization of intratumoral vasculature in rodent models. With minimal hardware and software modifications, high‐resolution MRA could be performed on a clinical 1.5 T MRI scanner. Morphologic characterization of intratumoral blood vessels could add important insights into the process of tumor angiogenesis. J. Magn. Reson. Imaging 2003;18:59–65. © 2003 Wiley‐Liss, Inc.
Accelerated dynamic MR imaging with a parallel imaging technique for hypervascular hepatocellular carcinomas: Usefulness of a test bolus in examination and subtraction imaging
Authors: Takahashi Nobuyuki , Yoshioka Hiroshi , Yamaguchi Masayuki , Saida Yukihisa , Itai Yuji
Published: June 2003

Purpose

To assess the impact of the accelerated dynamic MR imaging (ADMRI) approach using parallel imaging for detecting hypervascular hepatocellular carcinomas (HCCs) and to evaluate the usefulness of a test bolus in examination and subtraction imaging in this setting.

Materials and Methods

Thirty patients with 135 HCCs underwent ADMRI using a two‐dimensional gradient‐recalled echo sequence with parallel imaging. Seventeen patients were evaluated without a test bolus and 13 patients with a test bolus. The detectability of HCCs was calculated between the groups with and without a test bolus. ADMRI was evaluated regarding the signal‐to‐noise ratio (SNR) of the lesion and the liver, the contrast‐to‐noise ratio (CNR) of the lesion vs. the liver, and the feasibility of subtraction images.

Results

ADMRI with and without a test bolus had almost equal sensitivity (92.5% and 92.6%). No significant difference was seen in the SNR of lesions and the CNR of lesions vs. livers between both groups. With a test bolus, ADMRI could depict the peak enhancement of nodules on the 2nd or 3rd dynamic phases and optimized the timing of peak lesion enhancement. Subtraction images could be obtained regarding minimal slice misregistration.

Conclusion

ADMRI had high detectability of HCCs with and without a test bolus. J. Magn. Reson. Imaging 2003;18:80–89. © 2003 Wiley‐Liss, Inc.
Imaging of the articular cartilage in osteoarthritis of the knee joint: 3D spatial‐spectral spoiled gradient‐echo vs. fat‐suppressed 3D spoiled gradient–echo MR imaging
Authors: Yoshioka Hiroshi , Alley Marcus , Steines Daniel , Stevens Kathryn , Rubesova Erika , Genovese Mark , Dillingham Michael F. , Lang Philipp
Published: June 2003

Purpose

To compare three‐dimensional (3D) spatial‐spectral (SS) spoiled gradient‐recalled acquisition in the steady state (SPGR) imaging with fat‐suppressed 3D SPGR sequences in MR imaging of articular cartilage of the knee joint in patients with osteoarthritis.

Materials and Methods

MR images of six patients with osteoarthritis of the knee were prospectively examined with a 1.5T MR scanner. For quantitative analyses, the signal‐to‐noise ratios, contrast‐to‐noise ratios, and contrast of cartilage and adjacent structures including meniscus, synovial fluid, muscle, fat tissue, and bone marrow were measured.

Results

In patients with osteoarthritis, 3DSS‐SPGR images demonstrated higher spatial resolution and higher mean signal‐to‐noise (S/N) ratios (cartilage, 24.9; synovial fluid, 12.3; muscle, 20.7; meniscus, 21.6), with shorter acquisition times (7 minutes 20 seconds), when compared to fat‐suppressed 3D SPGR images (cartilage, 22.3; synovial fluid, 10.8; muscle, 16.7; meniscus, 13.4).

Conclusion

3DSS‐SPGR imaging is a promising method for evaluating cartilage pathology in patients with osteoarthritis of the knee and has the potential to replace fat‐suppressed 3D SPGR imaging. J. Magn. Reson. Imaging 2003;18:66–71. © 2003 Wiley‐Liss, Inc.
An inductively‐coupled, detachable receiver coil system for use with magnetic resonance compatible endoscopes
Authors: Gilderdale David J. , Williams Andreanna D. , Dave Umakant , deSouza Nandita M.
Published: June 2003

Purpose

To construct an inductively‐coupled receiver coil system for use with a magnetic resonance (MR) compatible endoscope, and to evaluate its use in a pilot group of patients with esophageal cancer.

Materials and Methods

An inductively‐coupled coil system, comprising a saddle geometry cylindrical receiver coil fitted as a sleeve around the endoscope tip and a pick‐up coil housed within a channel of an MR‐compatible endoscope, was designed and developed for use at 0.5 T. Twenty‐three patients with esophageal cancer were recruited for MR endoscopy. In 17 cases, the endoscopic coil system was used in conjunction with an external surface coil in order to obtain information from the surrounding mediastinum. The examination took 40–50 minutes.

Results

MR imaging using the inductively‐coupled endoscopic coil was successful in 21 cases (one failed intubation and one artifact from unrelated external source). Image artifact was largely due to respiration and global patient motion in sedated individuals undergoing endoscopy.

Conclusion

Inductively‐coupled coil systems may be used with endoscopes to allow improved safety through increased patient‐system isolation and detachability of coils and electronics for repair or replacement with coils tuned for different frequencies. J. Magn. Reson. Imaging 2003;18:131–135. © 2003 Wiley‐Liss, Inc.
The need for phase‐encoding flow compensation in high‐resolution intracranial magnetic resonance angiography
Authors: Parker Dennis L. , Goodrich K. Craig , Roberts John A. , Chapman Brian E. , Jeong Eun‐Kee , Kim Seong‐Eun , Tsuruda Jay S. , Katzman Gregory L.
Published: June 2003

Purpose

To demonstrate that the time delay between phase and frequency encoding and the presence of pulsatile blood flow in high‐resolution time‐of‐flight (TOF) imaging of the intracranial arteries (especially near the circle of Willis) can distort the appearance of blood vessels and result in a cross‐hatch—appearing artifact in surrounding tissue.

Materials and Methods

Two techniques to reduce the artifact, tri‐directional flow compensation (3DFC) and elliptical‐centric (EC) phase‐encoding order, are investigated in five volunteer studies.

Results

3DFC eliminates the pulsation‐related artifacts and the vessel distortion. A residual amplitude variation artifact is observed. EC phase encoding nearly eliminates the pulsatile motion‐related artifact, but it does not eliminate vessel distortion.

Conclusion

The combination of 3DFC and EC phase encoding appears to provide the greatest artifact reduction in the five volunteer studies performed. J. Magn. Reson. Imaging 2003;18:121–127. © 2003 Wiley‐Liss, Inc.
Keyhole Dixon method for faster, perceptually equivalent fat suppression
Authors: Flask Chris A. , Salem Kyle A. , Moriguchi Hisamoto , Lewin Jonathan S. , Wilson David L. , Duerk Jeffrey L.
Published: June 2003

Purpose

To reduce the acquisition time associated with the two‐point Dixon fat suppression technique by combining a keyhole in‐phase (Water + Fat) k‐space data set with a full out‐of‐phase (Water – Fat) k‐space data set and optimizing the keyhole size with a perceptual difference model.

Materials and Methods

A set of keyhole Dixon images was created by varying the number of lines in the keyhole data set. Off‐resonance correction was incorporated into the image reconstruction process to improve the homogeneity of the fat suppression. A perceptual difference model (PDM) was validated with human observer experiments and used to compare the keyhole images to images from a full two‐point Dixon acquisition. The PDM was used to determine the smallest keyhole width required to obtain perceptual equivalence to images obtained from the full two‐point Dixon method.

Results

In experimental phantom studies, the keyhole Dixon image reconstructed from 96 of 192 Water + Fat k‐space lines and 192 Water – Fat k‐space lines was perceptually equivalent to the full (192 + 192) two‐point Dixon images, resulting in a 25% reduction in scan time. Clinical images of a volunteer's knee, orbits, and abdomen created from the smallest, perceptually equivalent keyhole width resulted in a 27%–38% reduction in total scan time.

Conclusion

This method improves the temporal efficiency of the conventional two‐point Dixon technique and may prove especially useful for high‐field systems where specific absorption rate (SAR) limits will constrain radiofrequency (RF)‐based fat suppression techniques. J. Magn. Reson. Imaging 2003;18:103–112. © 2003 Wiley‐Liss, Inc.
Three‐dimensional method for comparing in vivo interventional MR images of thermally ablated tissue with tissue response
Authors: Breen Michael S. , Lancaster Tanya L. , Lazebnik Roee S. , Nour Sherif G. , Lewin Jonathan S. , Wilson David L.
Published: June 2003

Purpose

To investigate the ability of magnetic resonance (MR) to monitor radio‐frequency (RF) ablation treatments by comparing MR images of thermal lesions to histologically assayed cellular damage. We developed a new methodology using three‐dimensional registration for making spatial correlations.

Materials and Methods

A low‐field, open MRI system was used to guide an ablation probe into rabbit thigh muscle and acquire MR volumes after ablation. After fixation, we sliced and photographed the tissue at 3‐mm intervals, using a specially designed apparatus, to obtain a volume of tissue images. Histologic samples were digitized using a video microscopy system. For our three‐dimensional registration method, we used the tissue images as the reference, and registered histology and MR images to them using two different computer alignment steps. First, the MR volume was aligned to the volume of tissue images by registering needle fiducials placed near the tissue of interest. Second, we registered the histology images with the tissue images using a two‐dimensional warping technique that aligned internal features and the outside boundary of histology and tissue images.

Results

The MR and histology images were very well aligned, and registration accuracy, determined from displacement of needle fiducials, was 1.32 ± 0.39 mm (mean ± SD), which compared favorably to the MR voxel dimensions (0.70 mm in‐plane and 3.0 mm thick). A preliminary comparison of MR and tissue response showed that the region inside the elliptical hyperintense rim in MR closely corresponds to the region of necrosis as established by histology, with a mean absolute distance between MR and histology boundaries of 1.17 mm, slightly smaller than the mean registration error. The MR region slightly overestimated the region of necrosis, with a mean signed distance between boundaries of 0.85 mm.

Conclusion

Our results suggest that our methodology can be used to achieve three‐dimensional registration of histology and in vivo MR images. In MR lesion images, the inner border of the hyperintense region corresponds to the border of irreversible cell damage. This is good evidence that during RF ablation treatments, iMRI lesion images can be used for real‐time feedback. J. Magn. Reson. Imaging 2003;18:90–102. © 2003 Wiley‐Liss, Inc.
Methodological considerations for measuring rates of brain atrophy
Authors: Gunter Jeffrey L. , Shiung Maria M. , Manduca Armando , Jack Clifford R.
Published: June 2003

Purpose

To systematically compare two techniques for measuring brain atrophy rates from serial magnetic resonance imaging (MRI) studies.

Materials and Methods

Using the separation in atrophy rate between cohorts of cognitively normal elderly subjects and patients with Alzheimer's disease (AD) as the gold standard, we evaluated 1) different methods of computing volume change; 2) different methods for steps in image preprocessing—intensity normalization, alignment mask used, and bias field correction; 3) the effect of MRI acquisition hardware changes; and 4) the sensitivity of the method to variations in initial manual volume editing. For each of the preceding evaluations, measurements of whole‐brain and ventricular atrophy rates were calculated.

Results

In general, greater separation between the clinical groups was seen with ventricular rather than whole‐brain measures. Surprisingly, neither the use of bias field correction nor a major hardware change between the scan pairs affected group separation.

Conclusion

Atrophy rate measurements from serial MRI are candidates for use as surrogate markers of disease progression in AD and other dementing neurodegenerative disorders. The final method has excellent precision and accurately captures the expected biology of AD—arguably the two most important features if this technique is to be used as a biomarker of disease progression. J. Magn. Reson. Imaging 2003;18:16–24. © 2003 Wiley‐Liss, Inc.
Echo planar imaging at 4 tesla with minimum acoustic noise
Authors: Tomasi Dardo G. , Ernst Thomas
Published: June 2003

Purpose

To minimize the acoustic sound pressure levels of single‐shot echo planar imaging (EPI) acquisitions on high magnetic field MRI scanners.

Materials and Methods

The resonance frequencies of gradient coil vibrations, which depend on the coil length and the elastic properties of the materials in the coil assembly, were measured using piezoelectric transducers. The frequency of the EPI‐readout train was adjusted to avoid the frequency ranges of mechanical resonances.

Results

Our MRI system exhibited two sharp mechanical resonances (at 720 and 1220 Hz) that can increase vibrational amplitudes up to six‐fold. A small adjustment of the EPI‐readout frequency made it possible to reduce the sound pressure level of EPI‐based perfusion and functional MRI scans by 12 dB.

Conclusion

Normal vibrational modes of MRI gradient coils can dramatically increase the sound pressure levels during echo planar imaging (EPI) scans. To minimize acoustic noise, the frequency of EPI‐readout trains and the resonance frequencies of gradient coil vibrations need to be different. J. Magn. Reson. Imaging 2003;18:128–130. © 2003 Wiley‐Liss, Inc.
Acromiohumeral distance in a seated position in persons with impingement syndrome
Authors: Hébert Luc J. , Moffet Hélène , Dufour Marie , Moisan Christian
Published: June 2003

Purpose

To compare the acromiohumeral distance (AHD) of both shoulders in subjects with a unilateral shoulder impingement syndrome (SIS) and healthy subjects in a seated position during free shoulder movements of large amplitude.

Materials and Methods

Using a 0.5‐Tesla SIGNA‐SP/i™ open‐configuration magnetic resonance imaging (MRI) system, the AHD was measured at several arm positions, in a standardized seated position.

Results

In flexion (rest to 130°), the mean AHD of SIS varied from 8.3 to 2.8 mm, as compared to from 8.7 to 4.1 mm for asymptomatic contralateral shoulders. In abduction (rest to 110°), the AHD varied from 8.1 to 3.4 mm and from 8.8 to 4.6 mm for SIS and asymptomatic shoulders, respectively. The smallest AHD (P < .01) was observed at 110°. From 80° of arm elevation, the AHD was significantly smaller in impingement than in asymptomatic shoulders (P < .05). The AHD of asymptomatic shoulders did not differ from that of healthy subjects. In SIS, the AHD at rest was correlated with its reduction at all shoulder positions (rp = 0.62–0.88), but was a poor predictor of the smallest AHD observed at 110° (flexion, R2 = 0.09; abduction, R2 = 0.08).

Conclusion

In the critical arm elevation positions for impingement, AHD is discriminative for SIS, compared to asymptomatic shoulders and healthy ones. AHD at rest is a good indicator of the magnitude of its reduction in elevation, but not of the smallest AHD in arm elevation. J. Magn. Reson. Imaging 2003;18:72–79. © 2003 Wiley‐Liss, Inc.
Perilesional hyperintense rim of malignant hepatic tumors on ferumoxide‐enhanced T1‐weighted gradient‐echo MR images: Correlation between MR imaging and histopathologic findings
Authors: Kanematsu Masayuki , Matsuo Masayuki , Yamada Yasuhiro , Semelka Richard C. , Kondo Hiroshi , Goshima Satoshi , Hoshi Hiroaki , Moriyama Noriyuki
Published: June 2003

Purpose

To correlate the perilesional hyperintense rim of malignant hepatic tumors seen on ferumoxide‐enhanced T1‐weighted gradient‐echo (GE) MR images with histopathologic findings.

Materials and Methods

In 13 tumors in 12 patients, T1‐weighted GE images (TE of 1.4 msec, flip angle of 90 degrees) obtained after IV administration of ferumoxide were evaluated. MR imaging was initiated within one hour of the completion of ferumoxide administration. Surgical resection for tumors was performed within an interval of two weeks of the MR imaging. Resected specimens were histopathologically examined for peritumoral sinusoidal congestion, desmoplastic reaction, compressed hepatic parenchyma, lymphocytic infiltration, and vascular proliferation.

Results

In twelve tumors (92%), prominently (N = 2), moderately (N = 5), and mildly to minimally (N = 5), a perilesional hyperintense rim was observed. Among histopathologic findings, the degree of peritumoral sinusoidal congestion correlated (R = .75, P < .04) with the degree of perilesional hyperintense rim. The thickness of the perilesional hyperintense rim showed a moderate positive correlation (R = .65, P < .02) with the thickness of peritumoral area with sinusoidal congestion.

Conclusion

Perilesional hyperintense rim of malignant hepatic tumors on ferumoxide‐enhanced T1‐weighted GE images may correlate with sinusoidal congestion surrounding malignant hepatic tumors. J. Magn. Reson. Imaging 2003;18:40–48. © 2003 Wiley‐Liss, Inc.
Comparison of right ventricular volume measurements between axial and short axis orientation using steady‐state free precession magnetic resonance imaging
Authors: Alfakih Khaled , Plein Sven , Bloomer Tim , Jones Tim , Ridgway John , Sivananthan Mohan
Published: June 2003

Purpose

To compare right ventricular (RV) volume measurements and their reproducibility between axial and short axis orientation acquisition techniques.

Materials and Methods

Measurements of RV volumes from data sets acquired in axial and short axis orientations were compared in 20 normal subjects. The observer variabilities were assessed and the left ventricle (LV) and RV stroke volumes (SV) were compared.

Results

There was a significant and systematic difference in the EDV and ESV volumes between the axial and short axis methods. The latter method resulted in larger volumes (mean bias EDV 7.5 ± 13.2, 4.7% difference; ESV 7.2 ± 8.6, 10.7% difference). The axial method had lower intra‐ and interobserver variability than the short axis method. The standard deviation of the difference (SDD) and the limits of agreement were consistently lower for the axial method. The mean differences between LV and RV stroke volumes expressed as mean ± 1 SD (r2 =correlation coefficient) were: axial 7.6 ± 9.1 (r2 = 0.93); and short axis 7.4 ± 10.8 (r2 = 0.90).

Conclusion

There is a significant systematic difference between volumes measured using the two different orientations. The axial orientation resulted in better inter‐ and intraobserver reproducibility. J. Magn. Reson. Imaging 2003;18:25–32. © 2003 Wiley‐Liss, Inc.
Functional magnetic resonance imaging: A review of methodological aspects and clinical applications
Authors: Hennig Jürgen , Speck Oliver , Koch Martin A. , Weiller Cornelius
Published: June 2003

This paper gives an overview of the recent literature on methodological developments of functional magnetic resonance imaging (fMRI) and recent trends in clinical applications. With the recent introduction of high‐field systems and methodological developments leading to more robust signal behavior, fMRI is in a transition state from a research modality for use by experts to a standard procedure with useful applications in patient management. Compared to the use in neuroscientific research, which is often based on BOLD techniques alone, the application in patients is distinguished by a multiparametric characterization of the brain using a combination of several techniques. Neuronal fiber tracking based on diffusion anisotropy measurements, in particular, has already turned out to provide relevant supplementary information to the BOLD‐based cortical activation maps. J. Magn. Reson. Imaging 2003;18:1–15. © 2003 Wiley‐Liss, Inc.
Dynamic T1 estimation of brain tumors using double‐echo dynamic MR imaging
Authors: Ishimori Yoshiyuki , Kimura Hirohiko , Uematsu Hidemasa , Matsuda Tsuyoshi , Itoh Harumi
Published: June 2003

Purpose

To assess the clinical utility of a new method for real‐time estimation of T1 during the first pass of contrast agent by using this method to examine brain tumors.

Materials and Methods

The multi‐phase spoiled gradient‐echo pulse sequence using the double‐echo magnetic resonance (MR) technique was modified. In the first half of the pulse sequence, the flip angle was varied systematically. Then, static T1 values were calculated using differences in MR signal intensities between different flip angles. In the latter half of this sequence, changes in absolute T1 were calculated using differences in signal intensities before and after injection of contrast agent. The double‐echo MR data were used to minimize the T2* effect. Five cases of neurinoma and seven cases of meningioma were examined. Changes in T1 during the first pass of contrast agent were compared between neurinoma and meningioma.

Results

Changes in absolute T1 were clearly demonstrated on the parametric map. Although the changes in absolute T1 during the first pass of contrast agent did not allow differentiation between the two types of tumors, the mean gradient after the first pass was statistically higher for neurinoma than for meningioma (P < 0.05; meningioma, 0.011 ± 0.012 second−1/second; neurinoma, 0.034 ± 0.020 second−1/second).

Conclusion

The present method appears to be useful for estimation of dynamic T1 changes in brain tumors in clinical settings. J. Magn. Reson. Imaging 2003;18:113–120. © 2003 Wiley‐Liss, Inc.
A single breath‐hold multiecho T2* cardiovascular magnetic resonance technique for diagnosis of myocardial iron overload
Authors: Westwood Mark , Anderson Lisa J. , Firmin David N. , Gatehouse Peter D. , Charrier Clare C. , Wonke Beatrix , Pennell Dudley J.
Published: June 2003

Purpose

To assess tissue iron concentrations by the use of a gradient echo T2* multiecho technique.

Materials and Methods

We compared the results of measurements of heart T2* from 32 patients using the established multiple breath‐hold variable TR technique with a new multiecho sequence that acquires all images within a single breath‐hold with constant TR.

Results

There was good agreement of myocardial T2* values between both methods in the abnormal range of T2* < 20 msec (mean difference 0.2msec, 95% CI −1.3 to 0.9 msec, r = 0.97, P < 0.0001). The coefficient of variability between the methods was 3.5%. The interstudy reproducibility using the multiecho sequence had a variability coefficient of 2.3% in the abnormal T2* range and 5.8% over all T2* values. There was good agreement between the techniques for the liver T2* values.

Conclusions

The use of the single breath‐hold, multiecho acquisition allowed reliable quantification of myocardial T2*. The good reproducibility, speed, and T1 independence of this technique allows greater accuracy, faster patient throughput, and, therefore, reduced costs (which is important in developing countries where thalassemia is most prevalent). J. Magn. Reson. Imaging 2003;18:33–39. © 2003 Wiley‐Liss, Inc.