bluuebunny/crossref_metadata_2025 huggingface dataset:
Mapping cyclic change of regional myocardial blood volume using steady‐state susceptibility effect of iron oxide nanoparticles
Authors: Wu Ed X. , Tang Haiying , Wong Kelvin K. , Wang Jie
Published: December 2003

Purpose

To demonstrate an in vivo magnetic resonance imaging (MRI) technique that maps the cyclic change of regional myocardial blood volume (MBV) during the cardiac cycle.

Materials and Methods

The method is based on the dominant T2* shortening effect of iron oxide nanoparticle‐induced magnetic susceptibility perturbation in myocardium in the steady state. The technique was demonstrated in vivo with normal mouse hearts at 9.4 T. The regional MBV maps in left ventricular myocardium were computed from the steady‐state pre‐ and post‐monocrystalline iron oxide nanoparticle (MION) gradient echo (GE) cine images. Cyclic changes of MBV in normal mice were analyzed quantitatively in different transmural and angular locations.

Results

High‐resolution MBV maps at various cardiac points were obtained. The study showed a general regional MBV decrease from end‐diastole (ED) to end‐systole (ES). Percentage reductions were 18.2 ± 6.6%, P < 0.03 in the lateral wall and 24.7 ± 3.1%, P < 0.0002 in the interventricular septum. The heterogeneous characteristics of MBV transmural distribution were also reported.

Conclusion

The steady‐state susceptibility effect of intravascular superparamagnetic contrast agent (CA) can be used to map the cyclic change of regional MBV. This imaging approach is relatively simple and may provide a new perspective for functional assessment of the microvasculature in myocardium. J. Magn. Reson. Imaging 2004;19:50–58. © 2003 Wiley‐Liss, Inc.
Comparison of spiral and FLASH phase velocity mapping, with and without breath‐holding, for the assessment of left and right coronary artery blood flow velocity
Authors: Keegan Jennifer , Gatehouse Peter D. , Mohiaddin Raad H. , Yang Guang‐Zhong , Firmin David N.
Published: December 2003

Purpose

To develop high temporal resolution coronary artery spiral phase velocity mapping sequences and to compare the results obtained with those from FLASH sequences.

Materials and Methods

Velocity curves were obtained in eight left and eight right coronary arteries using breath‐hold interleaved spiral (BH_SP), free‐breathing interleaved spiral (FB_SP), breath‐hold segmented FLASH (BH_FL), and free‐breathing FLASH (FB_FL) sequences. Spatial resolution, temporal resolution, and acquisition durations (cardiac cycles) were as follows—BH_SP: 0.9 mm × 0.9 mm, 30 msec, 20 cycles; FB_SP: 0.9 mm × 0.9 mm, 42 msec, 100 cycles; BH_FL: 0.9 mm × 1.8 mm, 70 msec (effective), 20 cycles; FB_FL: 0.9 mm × 1.8 mm, 30 msec, 480 cycles. Peak systolic, peak diastolic, and mean velocities were compared between sequences.

Results

For left and right arteries, the FB_SP velocity profiles closely followed those from the FB_FL sequence. By comparison, the BH_FL sequence failed to resolve the sharp peaks in the temporal velocity profiles of the right coronary artery, significantly underestimating the peak systolic (88 mm/second vs. 252 mm/second, P < 0.001), peak diastolic (114 mm/second vs. 153 mm/second, P < 0.01), and mean (56 mm/second vs. 93 mm/second, P < 0.001) velocities. For the less mobile left artery, the peak systolic, peak diastolic, and mean velocities were also underestimated by the BH_FL sequence, although this only reached statistical significance for the systolic peak (80 mm/second vs. 135 mm/second, P < 0.01), 142 mm/second vs. 168 mm/second, (P = ns), and 87 mm/second vs. 101 mm/second, (P = ns) respectively.

Conclusion

We have shown that the FB_SP sequence developed agrees well with the FB_FL sequence, while the study duration is reduced by a factor of 10 for the same spatial resolution. By comparison, the BH_FL sequence underestimates flow velocities, particularly in the more mobile right coronary artery. J. Magn. Reson. Imaging 2004;19:40–49. © 2003 Wiley‐Liss, Inc.
Safety assessment of gadoversetamide (OptiMARK®) administered by power injector
Authors: Abdou Nancy , Napoli Alicia M. , Hynes Michael R. , Allen John C. , Wible James H.
Published: December 2003

Purpose

To evaluate the safety of OptiMARK® (gadoversetamide injection) administered via power injector.

Materials and Methods

The study population included 144 healthy volunteers aged 18 years or older randomly assigned to one of seven treatment groups (N = 20/group). The safety assessment was based on changes in physical examination, vital signs, electrocardiograms (ECGs), standard clinical laboratory tests, and adverse events (AEs) through a 24‐hour postinjection period.

Results

OptiMARK caused no serious AEs or unexpected changes in physical examinations or laboratory parameters. The changes observed in vital signs and ECG intervals did not vary with changes in injection rate and were not significantly (P < 0.05) different from those elicited by saline administration at the same rates.

Conclusion

This study demonstrated the safety of OptiMARK when administered via a power injector at rates of 2, 4, and 6 mL/second. J. Magn. Reson. Imaging 2004;19:133–140. © 2003 Wiley‐Liss, Inc.
EPI‐BOLD fMRI of human motor cortex at 1.5 T and 3.0 T: Sensitivity dependence on echo time and acquisition bandwidth
Authors: Fera Francesco , Yongbi Martin N. , van Gelderen Peter , Frank Joseph A. , Mattay Venkata S. , Duyn Jeff H.
Published: December 2003

Purpose

To investigate the sensitivity dependence of BOLD functional imaging on MRI acquisition parameters in motor stimulation experiments using a finger tapping paradigm.

Materials and Methods

Gradient‐echo echo‐planar fMRI experiments were performed at 1.5 T and 3.0 T with varying acquisition echo time and bandwidth, and with a 4 mm isotropic voxel size. To analyze the BOLD sensitivity, the relative contributions of BOLD signal amplitude and thermal and physiologic noise sources were evaluated, and statisticalt‐scores were compared in the motor area.

Results

At 1.5 T, the number of activated pixels and the averaget‐score showed a relatively broad optimum over a TE range of 60–160 msec. At 3.0 T, an optimum range was observed between TEs of 30–130 msec. Averaged over nine subjects, maxima in the number of pixels andt‐score values were 59% and 18% higher at 3.0 T than at 1.5 T, respectively, an improvement that was lower than the observed 100% to 110% increase in signal‐to‐noise ratio at 3.0 T.

Conclusion

The somewhat disappointing increase int‐scores at 3.0 T was attributed to the increased contribution of physiologic noise at the higher field strength under the given experimental conditions. At both field strengths, reducing the effective image acquisition bandwidth from 35 to 17 Hz per pixel did not affect or only marginally affect the BOLD sensitivity. J. Magn. Reson. Imaging 2004;19:19–26. Published 2003 Wiley‐Liss, Inc.
A variational approach to boundary elements—two dimensional Helmholtz problems
Authors: Kagawa Y. , Sun Y. , Chai L.
Published: December 2003

The boundary element method is a discretized version of the boundary integral equation method. The variational formulation is presented for the boundary element approach to Helmholtz problems. The numerical calculation of the eigenvalues in association with hollow waveguides demonstrates that the variational approach provides the upper and lower bounds of the eigenvalues.

The drawback of the discretized system equation must be solved by a trial and error approach, which is shown to be removed by the introduction of the dual reciprocity method. Copyright © 2003 John Wiley & Sons, Ltd.
Distribution in TLM models for diffusion (Part II: multi‐dimensional treatment)
Authors: Chardaire P. , de Cogan D.
Published: December 2003

The signals obtained at each time step of a transmission line matrix (TLM) simulation of Gaussian diffusion are analysed for two‐ and three‐dimensional cases. A combinatorial formula is derived to provide the signal magnitude at any spatial position and any time step after a single‐shot excitation in the two‐dimensional link‐line model. Formulae for the expectation and variance of the axial positions of a particle are determined for two‐ and three‐dimensional link‐line and link‐resistor models. A generalization of these formulae is proposed for higher dimensions, and an entirely numerical proving scheme is devised. Finally, we briefly compare the resulting variances and that of the underlying diffusion process. Copyright © 2003 John Wiley & Sons, Ltd.
Expectations of organizational mobility, workplace social inclusion, and employee job performance
Authors: Pearce Jone L. , Randel Amy E.
Published: December 2003

Two new concepts, employees' Expectations of Organizational Mobility (EOM) and Workplace Social Inclusion (WSI), were developed in part from the burgeoning literature on social capital. Two independent tests of the hypotheses in two different organizations found that the greater employees' EOM, the lower their WSI, which in turn was associated with lower employee job performance ratings. Further, the mediating role of WSI was confirmed. Our findings support the arguments of those who have warned that employees' EOM, and implicitly the human resources philosophy of ‘employability’ that encourages such expectations, is associated with comparatively worse individual job performance via lower levels of employee WSI. The value of these concepts for current employability debates, for the use of subjective supervisory judgments in performance appraisal ratings and for researchers interested in organization‐based communal social capital, is discussed. Copyright © 2004 John Wiley & Sons, Ltd.
Workplace deviance, organizational citizenship behavior, and business unit performance: the bad apples do spoil the whole barrel
Authors: Dunlop Patrick D. , Lee Kibeom
Published: December 2003

The influences of organizational citizenship behavior (OCB) and workplace deviant behavior (WDB) on business unit performance were investigated using data from branches of a fast food organization. Data included measures of WDB and OCB obtained from staff, ratings of performance provided by supervisors, and objective measures of performance. It was found that WDB was negatively and significantly associated with business unit performance measured both subjectively and objectively. OCB, however, failed to contribute to the prediction of business unit performance beyond the level that was achieved by WDB. It appeared, therefore, that the presence of deviant employees among business units impinges upon the performance of the business unit as a whole, whereas OCBs had comparatively little effect. Copyright © 2004 John Wiley & Sons, Ltd.
Transition to self‐directed work teams: implications of transition time and self‐monitoring for managers' use of influence tactics
Authors: Douglas Ceasar , Gardner William L.
Published: December 2003

In the face of heightened competitive pressures, elevated quality expectations, and calls for worker empowerment, more and more organizations have turned to self‐directed work teams (SDWTs). A review of the literature devoted to SDWTs suggests that managers often struggle with the transition to SDWTs because of the required shift in control to SDWT members. To promote the development of work teams, managers must modify their use of influence tactics in direct response to the control shift.

In this study, we explore changes in managers' usage of influence tactics during the transition to SDWTs within a large aluminum manufacturing plant. Analyses of longitudinal data show that despite the new team environment, managers' use of influence tactics was focused at the individual level. We also found that transition time accounts for variance in managers' choices of influence tactics. Finally, an exploratory analysis suggests that high as opposed to low self‐monitoring managers may be more prone to increase their usage of soft influence tactics and decrease their usage of hard influence tactics over the course of the transition; the influence behavior of low self‐monitoring managers remained unchanged. Implications for future research are discussed. Copyright © 2004 John Wiley & Sons, Ltd.
An empirical investigation of interviewer‐related factors that discourage the use of high structure interviews
Authors: Lievens Filip , de Paepe Anneleen
Published: December 2003

High structure interviews appear to be less frequently used in personnel management practice than might be expected given their good reliability and validity. Although several authors have speculated on the factors of resistance to high structure interviews, empirical research is very scarce. Two studies are conducted among experienced human resources representatives who frequently conduct employment interviews. The first study provides a fine‐grained description of the degree of structure used in interviews, showing that in most interviews constraints are placed only on the topical areas to be covered and that scoring is done only on multiple criteria. The second study tests various hypotheses regarding interviewer‐related factors, which may lead to lower levels of structure in interviews. Results show that when interviewers are concerned about establishing an informal contact with interviewees, want to have discretion over interview questions, and want to develop interviews efficiently, they are less inclined to use higher levels of structure in interviews. Conversely, people who participated in interviewing workshops and Conventional types report using significantly higher levels of structure. Implications for improving interviewer motivation to use higher levels of structure in interviews are discussed. Copyright © 2004 John Wiley & Sons, Ltd.
Go and Chess as prognosis instruments for understanding competitive positions
Authors: Hoffjan Andreas
Published: December 2003

Asians play Go and Europeans play Chess. These two games reflect the strategic thinking which is often typical of the Asian and the European manager. Whoever understands and masters the games will be better able to understand the competitive behaviour of their international competitors and secure competitive advantage.

This paper deals primarily with the explanatory power of both board games for international business strategies of Japanese and European companies.

While a strategy of sequential market entry is typical for many Japanese companies, European firms often prefer quick market entry by company takeovers.

Many elements of strategy in the game of Go can be found again in Japanese firms: the strong position on the domestic market, the strategy of exercising restraint, the readiness to make strategic sacrifices, the development of a sense for the direction as well as strategic flexibility.

In contrast, European firms often court market entry by acquisition. This strategy is also reflected in the game of Chess: the objective of destruction of the opponent requires an offensive strategy in the opposing sphere of influence, tactical skills and distinctive analytical skills.

Copyright © 2003 John Wiley & Sons, Ltd.
The apparent dependence of the diffusion coefficient of N‐acetylaspartate upon magnetic field strength: evidence of an interaction with NMR methodology
Authors: Guilfoyle David N. , Suckow Raymond F. , Baslow Morris H.
Published: December 2003

An inverse relationship between applied magnetic field strength and the apparent diffusion coefficient (ADC) of several important brain metabolites including N‐acetyl‐l‐aspartate (NAA), choline and creatine, measured in vivo using proton magnetic resonance spectroscopy (MRS), has been reported. In this investigation, using phantom studies of NAA at magnetic field strengths of 3 and 7 T, these observations have been verified under controlled MRS conditions in vitro, and the ADC of NAA has been found to vary inversely with magnetic field strength, decreasing at a rate of 2.5%/T at 20°C. We have also assessed whether the effect is a function of a systemic bias in methodology, or if the effect is actually on the rate of molecular diffusion. This was done using an MRS‐independent method for measurement of molecular diffusion in NAA phantoms at 0, 0.025 and 7 T applied magnetic field strengths. As a result, it has been demonstrated that the observed apparent magnetic field dependence of the ADC of NAA is a consequence of the NMR measurement and is apparently not a real effect on molecular diffusion. Copyright © 2003 John Wiley & Sons, Ltd.
MRCP in the diagnosis of iatrogenic bile duct injury
Authors: Bujanda Luis , Calvo Mari M. , Cabriada José L. , Orive Victor , Capelastegui Angel
Published: December 2003

Postoperative biliary tract lesions are becoming increasingly common. The diagnosis is made by direct cholangiography via endoscopic retrograde cholangiopancreatography (ERCP) or percutaneous transhepatic cholangiography (PTC). The present comparative study evaluates the diagnostic efficacy of magnetic resonance cholangiopancreatography (MRCP) in application to iatrogenic bile duct injury. A prospective blind study was performed, contrasting MRCP and ERCP in 10 patients with suspected postoperative biliary tract lesions. MRCP was performed less than 72 h before ERCP. Final diagnosis was made on the basis of findings at surgery and ERCP. The presence of biliary dilatation, excision injury, stricture, fluid collection and free fluid was analyzed. The mean patient age was 66.5 years. There were three males and seven females. The type of postoperative lesion (Bergman classification) are five patients type C, three type D, one type B and one type A. Diagnostic failure was recorded in two cases with ERCP, while in five patients it was unable to define a therapeutic approach. In contrast, MRCP correctly diagnosed all patients. MRCP is effective in diagnosing postoperative biliary tract lesions, and can help decide the best therapeutic approach. Copyright © 2003 John Wiley & Sons, Ltd.
In‐vivo high resolution three‐dimensional MRI studies of rat joints at 7 T
Authors: Faure P. , Doan B.‐T. , Beloeil J.‐C.
Published: December 2003

It is important to obtain high resolution images of joints for the study of disease, especially in rodent experimental models. We optimized 1H magnetic resonance imaging three‐dimensional sequences at 7 T, with lipid signal suppression, and T1 and T2 measurements for in‐vivo experiments on rat joints, in order to assess the effectiveness of high‐field MRI. The method was validated by applying it to the early diagnosis of arthritis. We studied the progress of rheumatoid arthritis in an arthritic rat model. We observed the rats' knees for 21 days after inducing arthritis. The images acquired over one hour had a high resolution of 1.75 × 10−3 mm3, (105 × 105 × 145 μm3) which allowed us to spot the early stages of joint degeneration, such as bone erosion, and to observe an apparent ‘MRI’ loss of cartilage thickness, attributed to dehydration of the cartilage tissue. The MR images obtained during the early stages of rheumatoid arthritis enabled us to study joint changes accurately before any histological signs of attack were visible. Copyright © 2003 John Wiley & Sons, Ltd.
Diabetes self‐management: how are we doing?
Authors: Reed JA , Ashton H , Lawrence JM , Hollinghurst S , Higgs ER
Published: December 2003

Modern management of diabetes places a high burden on patients. New insulin delivery devices and blood glucose monitoring equipment may aid self‐care, but only if they are used appropriately and do not malfunction. This study of 130 insulin treated patients aimed to assess their skills in using, their knowledge of and the functioning integrity of their diabetes equipment.

Each patient had a one‐hour appointment with a diabetes nurse specialist. Patients were interviewed using a structured questionnaire assessing knowledge of self‐care and were asked to demonstrate use of their meter and their insulin injection technique.

In total, 80% of patients felt confident with the condition of their equipment and ability to use it appropriately. This contrasted with the assessment of the diabetes nurse specialist. Only 8/130 patients did not demonstrate any problems with blood glucose testing, meter use or insulin administration. In all, 19% carried no form of identification to say they have diabetes and up to 40% were inadequately prepared to manage episodes of hypoglycaemia. Disposal of sharps is another area for concern, with 50% of patients disposing of sharps directly into the household waste.

Empowering patients to manage their diabetes relies on providing effective education. Our study demonstrates that despite patient perceptions there is a significant shortfall in self‐management skills and understanding. Addressing this shortfall remains a challenge for the future. Copyright © 2003 John Wiley & Sons, Ltd.
Transepidermal elimination in diabetes mellitus
Authors: Rajeswaran C
Published: December 2003

The incidence of diabetes mellitus and its complications is on the increase. The skin lesions associated with diabetes mellitus are varied. In this article, acquired perforating dermatosis characterised by transepidermal elimination is reported in a 61‐year‐old male with diabetes mellitus and chronic renal failure. The incidence of skin lesions is increasing, especially among diabetic patients with renal failure. A high index of suspicion is required for early detection and management. The pathogenesis and natural history of this group of skin disorders are not clear. Correction of glycaemic control and stabilisation of renal failure are known to cause remission of these lesions. Copyright © 2003 John Wiley & Sons, Ltd.
Atypical antipsychotic drugs and diabetes
Authors: Livingstone C , Rampes H
Published: December 2003

The atypical antipsychotic drugs have enhanced the quality of life in many patients with schizophrenia. Their main advantage over conventional antipsychotic drugs is their propensity to cause fewer extrapyramidal adverse effects. However, there is increasing evidence that atypical antipsychotic drugs are associated with metabolic adverse effects including weight gain, new onset diabetes (both type 2 diabetes and diabetic ketoacidosis) and hypertriglyceridaemia. These problems are most common with clozapine. We discuss the mechanism of the association and recommendations for screening and monitoring in order that metabolic problems can be detected and treated early. Copyright © 2003 John Wiley & Sons, Ltd.
Diabetes and coronary heart disease NSFs: what comparisons can we make and what lessons can we learn?
Authors: Begg A
Published: December 2003

In England both diabetes and coronary heart disease are now covered for a 10‐year period by national service frameworks. National directors have been appointed to provide high profile leadership with responsibility for achieving overall success. Significant progress to date is claimed for the improvement in the prevention, diagnosis and treatment of patients with coronary heart disease. Systematic care increases workload, requires more staff and additional financial resources. Implementation of the frameworks is dependent on funding from the general National Health Service allocation with specific money only being available for certain components.

A significant opportunity is provided to prevent the development of diabetes in those most at risk and to enhance the role of the user in ongoing diabetic care. Fewer national targets have been set for diabetes and locally agreed targets need to be achievable and realistic.

Meeting the proposed quality indicators for both conditions, with a financial incentive, is likely to become the main priority within general practice. A variation in approach within the devolved countries of the United Kingdom may in time lead to a recordable difference in clinical outcomes. For both frameworks to remain relevant for the full 10 years a mechanism is required for regular updating.

This review compares the two national service frameworks and looks at the lessons that can be learned in order to ensure successful implementation. Copyright © 2003 John Wiley & Sons, Ltd.
Optimizing physical energy functions for protein folding
Authors: Fujitsuka Yoshimi , Takada Shoji , Luthey‐Schulten Zaida A. , Wolynes Peter G.
Published: December 2003

We optimize a physical energy function for proteins with the use of the available structural database and perform three benchmark tests of the performance: (1) recognition of native structures in the background of predefined decoy sets of Levitt, (2) de novo structure prediction using fragment assembly sampling, and (3) molecular dynamics simulations. The energy parameter optimization is based on the energy landscape theory and uses a Monte Carlo search to find a set of parameters that seeks the largest ratio δEs/ΔE for all proteins in a training set simultaneously. Here, δEs is the stability gap between the native and the average in the denatured states and ΔE is the energy fluctuation among these states. Some of the energy parameters optimized are found to show significant correlation with experimentally observed quantities: (1) In the recognition test, the optimized function assigns the lowest energy to either the native or a near‐native structure among many decoy structures for all the proteins studied. (2) Structure prediction with the fragment assembly sampling gives structure models with root mean square deviation less than 6 Å in one of the top five cluster centers for five of six proteins studied. (3) Structure prediction using molecular dynamics simulation gives poorer performance, implying the importance of having a more precise description of local structures. The physical energy function solely inferred from a structural database neither utilizes sequence information from the family of the target nor the outcome of the secondary structure prediction but can produce the correct native fold for many small proteins. Proteins 2004;54:000–000. © 2003 Wiley‐Liss, Inc.
Loss of translational entropy in molecular associations
Authors: Siebert Xavier , Amzel L. Mario
Published: December 2003

Molecular associations in solution are opposed by the loss of entropy (ΔS) that results from the restriction of motion of each component in the complex. Theoretical estimates of ΔS are essential for rationalizing binding affinities, as well as for calculating entropic contribution to enzyme catalysis. Recently a statistical–mechanical framework has been proposed for estimating efficiently the translational entropy loss (ΔStrsl), while taking explicitly into account the complex intermolecular interactions between the solute and the solvent. This framework relates the translational entropy of a solute in solution to its “free volume,” defined as the volume accessible to the center of mass of the solute in the presence of the solvent and calculated by using an extension of the cell model (CM) for condensed phases. The translational entropy of pure water, estimated with the CM algorithm, shows good agreement with the experimental information. The free volume of various solutes in water, calculated within the CM by using molecular dynamics simulations with explicit solvent, displays a strong correlation with the solutes' polar and total surface areas. This correlation is used to propose a parameterization that can be used to calculate routinely the translational entropy of a solute in water. We also applied the CM formalism to calculate the free volume and translational entropy loss (ΔStrsl) on binding of benzene to a cavity in a mutant T4‐lysozyme. Our results agree with previously published estimates of the binding of benzene to this mutant T4‐lysozyme. These and other considerations suggest that the cell model is a simple yet efficient theoretical framework to evaluate the translational entropy loss on molecular association in solution. Proteins 2004. © 2003 Wiley‐Liss, Inc.
Molecular dynamics simulations of peptides containing an unnatural amino acid: Dimerization, folding, and protein binding
Authors: Yu Haibo , Daura Xavier , van Gunsteren Wilfred F.
Published: December 2003

We have performed molecular dynamics (MD) simulations to study the dimerization, folding, and binding to a protein of peptides containing an unnatural amino acid. NMR studies have shown that the substitution of one residue in a tripeptide β‐strand by the unnatural amino acid Hao (5‐HO2CCONH‐2‐MeO‐C6H3‐CO‐NHNH2) modifies the conformational flexibility of the β‐strand and the hydrogen‐bonding properties of its two edges: The number of hydrogen‐bond donors and acceptors increases at one edge, whereas at the other, they are sterically hindered. In simulations in chloroform, the Hao‐containing peptide 9 (i‐PrCO‐Phe‐Hao‐Val‐NHBu) forms a β‐sheet–like hydrogen‐bonded dimer, in good agreement with the available experimental data. Addition of methanol to the solution induces instability of this β‐sheet, as confirmed by the experiments. MD simulations also reproduce the folding of the synthetic peptide 1a (i‐PrCO‐Hao‐Ut‐Phe‐Ile‐Leu‐NHMe) into a β‐hairpin–like structure in chloroform. Finally, the Hao‐containing peptide, Ac‐Ala‐Hao‐Ala‐NHMe, is shown to form a stable complex with the Ras analogue, Rap1 A, in water at room temperature. Together with the available experimental data, these simulation studies indicate that Hao‐containing peptides may serve as inhibitors of β‐sheet interactions between proteins. Proteins 2003. © 2003 Wiley‐Liss, Inc.
Detection of functional modules from protein interaction networks
Authors: Pereira‐Leal Jose B. , Enright Anton J. , Ouzounis Christos A.
Published: December 2003

Complex cellular processes are modular and are accomplished by the concerted action of functional modules (Ravasz et al., Science 2002;297:1551–1555; Hartwell et al., Nature 1999;402:C47–52). These modules encompass groups of genes or proteins involved in common elementary biological functions. One important and largely unsolved goal of functional genomics is the identification of functional modules from genomewide information, such as transcription profiles or protein interactions. To cope with the ever‐increasing volume and complexity of protein interaction data (Bader et al., Nucleic Acids Res 2001;29:242–245; Xenarios et al., Nucleic Acids Res 2002;30:303–305), new automated approaches for pattern discovery in these densely connected interaction networks are required (Ravasz et al., Science 2002;297:1551–1555; Bader and Hogue, Nat Biotechnol 2002;20:991–997; Snel et al., Proc Natl Acad Sci USA 2002;99:5890–5895). In this study, we successfully isolate 1046 functional modules from the known protein interaction network of Saccharomyces cerevisiae involving 8046 individual pair‐wise interactions by using an entirely automated and unsupervised graph clustering algorithm. This systems biology approach is able to detect many well‐known protein complexes or biological processes, without reference to any additional information. We use an extensive statistical validation procedure to establish the biological significance of the detected modules and explore this complex, hierarchical network of modular interactions from which pathways can be inferred. Proteins 2003. © 2003 Wiley‐Liss, Inc.
Gaps in structurally similar proteins: Towards improvement of multiple sequence alignment
Authors: Wrabl James O. , Grishin Nick V.
Published: December 2003

An algorithm was developed to locally optimize gaps from the FSSP database. Over 2 million gaps were identified from all versus all FSSP structure comparisons, and datasets of non‐identical gaps and flanking regions comprising between 90,000 and 135,000 sequence fragments were extracted for statistical analysis. Relative to background frequencies, gaps were enriched in residue types with small side chains and high turn propensity (D, G, N, P, S), and were depleted in residue types with hydrophobic side chains (C, F, I, L, V, W, Y). In contrast, regions flanking a gap exhibited opposite trends in amino acid frequencies, i.e., enrichment in hydrophobic residues and a high degree of secondary structure. Log‐odds scores of residue type as a function of position in or around a gap were derived from the statistics. Three simple experiments demonstrated that these scores contained significant predictive information. First, regions where gaps were observed in single sequences taken from HOMSTRAD structure‐based multiple sequence alignments generally scored higher than regions where gaps were not observed. Second, given the correct pairwise‐aligned cores, the actual positions of gaps could be reproduced from sequence more accurately using the structurally‐derived statistics than by using random pairwise alignments. Finally, revision of the Clustal‐W residue‐specific gap opening parameters with this new information improved the agreement of Clustal‐W alignments with the structure‐based alignments. At least three applications for these results are envisioned: improvement of gap penalties in pairwise (or multiple) sequence alignment, prediction of regions of single sequences likely (or unlikely) to contain indels, and more accurate placement of gaps in automated pairwise structure alignment. Proteins 2003;53:000–000. © 2003 Wiley‐Liss, Inc.
Proteomic signatures: Amino acid and oligopeptide compositions differentiate among phyla
Authors: Pe'er Itsik , Felder Clifford E. , Man Orna , Silman Israel , Sussman Joel L. , Beckmann Jacques S.
Published: December 2003

Availability of complete genome sequences allows in‐depth comparison of single‐residue and oligopeptide compositions of the corresponding proteomes. We have used principal component analysis (PCA) to study the landscape of compositional motifs across more than 70 genera from all three superkingdoms. Unexpectedly, the first two principal components clearly differentiate archaea, eubacteria, and eukaryota from each other. In particular, we contrast compositional patterns typical of the three superkingdoms and characterize differences between species and phyla, as well as among patterns shared by all compositional proteomic signatures. These species‐specific patterns may even extend to subsets of the entire proteome, such as proteins pertaining to individual yeast chromosomes. We identify factors that affect compositional signatures, such as living habitat, and detect strong eukaryotic preference for homopeptides and palindromic tripeptides. We further detect oligopeptides that are either universally over‐ or underabundant across the whole proteomic landscape, as well as oligopeptides whose over‐ or underabundance is phylum‐ or species‐specific. Finally, we report that species composition signatures preserve evolutionary memory, providing a new method to compare phylogenetic relationships among species that avoids problems of sequence alignment and ortholog detection. Proteins 2004. © 2003 Wiley‐Liss, Inc.
First principles computational study of the active site of arginase
Authors: Ivanov Ivaylo , Klein Michael L.
Published: December 2003

Ab initio density functional theory (DFT) methods were used to investigate the structural features of the active site of the binuclear enzyme rat liver arginase. Special emphasis was placed on the crucial role of the second shell ligand interactions. These interactions were systematically studied by performing calculations on models of varying size. It was determined that a water molecule, and not hydroxide, is the bridging exogenous ligand. The carboxylate ligands facilitate the close approach of the Mn (II) ions by attenuating the metal–metal electrostatic repulsion. Of the two metals, MnA was shown to carry a larger positive charge. Analysis of the electronic properties of the active site revealed that orbitals involving the terminal Asp234 residue, as well as the flexible μ‐1,1 bridging Asp232, lie at high energies, suggesting weaker coordination. This is reflected in certain structural variability present in our models and is also consistent with recent experimental findings. Finally, implications of our findings for the biological function of the enzyme are delineated. Proteins 2004. © 2003 Wiley‐Liss, Inc.
Sequence‐based study of two related proteins with different folding behaviors
Authors: Favrin Giorgio , Irbäck Anders , Wallin Stefan
Published: December 2003

ZSPA–1 is an engineered protein that binds to its parent, the three‐helix‐bundle Z domain of staphylococcal protein A. Uncomplexed ZSPA–1 shows a reduced helix content and a melting behavior that is less cooperative, compared with the wild‐type Z domain. Here we show that the difference in folding behavior between these two sequences can be partly understood in terms of an off‐lattice model with 5–6 atoms per amino acid and a minimalistic potential, in which folding is driven by backbone hydrogen bonding and effective hydrophobic attraction. Proteins 2004;54:000–000. © 2003 Wiley‐Liss, Inc.
The influence of uniaxial stress on the electrical properties of TMA‐CuBr4 crystals
Authors: Kallaev S. N. , Kamilov I. K. , Djabrailov A. M. , Sadykov S. A. , Amirova A. A.
Published: December 2003

Anomalously large variations in the electrical properties of [N(CH3)4]2CuBr4 crystals are manifested by the disappearance of the spontaneous polarization (ferroelectricity) under the action of small uniaxial mechanical stresses. The observed effect is reversible and non‐linear. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
EPR of [Li]0, [Na]0, and [K]0 centres in SrS and CaS polycrystals
Authors: Seeman V. , Danilkin M. , Ots A. , Pedak E. , Pung L. , Pärnoja E.
Published: December 2003

Connected with alkaline metal impurities axial V centres were studied by EPR in SrS and CaS polycrystals. A paramagnetic S− ion arises near an alkaline metal ion substituting for a cation of the host lattice after a hole produced by X‐raying at 77 K is captured. The centres are observable at low temperatures of 10–25 K. The superhyperfine structure from a 23Na nucleus and a 7Li nucleus was observed. Parameters of V centres (g‐tensor and A‐tensor values, thermal decay) are determined. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Effect of gallium doping on the electronic structure of lead‐telluride‐based alloys
Authors: Skipetrov E. , Zvereva E. , Kovalev B. , Slyn'ko E.
Published: December 2003

Galvanomagnetic and photoelectric properties of the Pb1−ySnyTe (0 ≤ y ≤ 0.06) and Pb1−xGexTe (0.04 ≤ x ≤ 0.08) single crystals doped with gallium (CGa = 0.3–3 mol%) have been investigated. Low‐temperature activation ranges of the impurity conductivity on the dark curves of the resistivity ρ(1/T) and Hall coefficient RH(1/T) were revealed and attributed to the appearance of gallium‐induced deep levels in the gap of the alloys. It was shown that the alloys possess high infrared photosensitivity at temperatures below Tc = 50–60 K. The results are discussed in the frame of the model assuming that doping with gallium leads to the formation of two different gallium‐related defect levels in the energy spectrum of the PbTe‐based alloys. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Expanded Bethe–Peierls approximation for the Ising model with S = 1/2 and 1
Authors: Du A. , Liu H. J. , Yü Y. Q.
Published: December 2003

A expanded Bethe–Peierls approximation has been used to study the Ising model on honeycomb lattice, square lattice, kagomé lattice, triangular lattice and simple cubic lattice with spin S = 1/2 and 1. The spatial dimensionality of system is distinguished for different lattices. It is found that the transition temperatures on different lattices are much closer to the real values than those obtained by the effective field theory and the Bethe lattice approximation, and the transition temperatures of systems on kagomé lattice (z = 4) and trianguilar lattice (z = 6) are lower than those on square lattice (z = 4) and simple cubic lattice (z = 6), respectively. The static magnetic susceptibilities are also calculated. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Interlayer coupling in magnetic superlattices with electron density inhomogeneities
Authors: Gruhn W. , Bąk Z.
Published: December 2003

We discuss the influence of spatial inhomogeneities of the free electron density on the magnetic interaction between magnetic layers of the superlattice, mediated across nonmagnetic, metallic spacer. Using the modified total energy approach, we prove that the TM or RE superlattices the additional scattering of free electrons on magnetic ion multipole moment increases the ferroquadrupolar biquadratic coupling between magnetic layers. It is shown also that the nonuniform free electron density generates contribution to the interlayer coupling being of the Dzialoshinsky‐Moriya type. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Spin surfaces and trajectories in valence bands of tetrahedral semiconductors
Authors: Dargys A.
Published: December 2003

Surfaces and trajectories traced out by spin vectors in spin space are calculated and systematized for holes in tetrahedral semiconductors. It is shown how various trajectories are related to the wave‐function phases and amplitudes of the doubly degenerated heavy‐mass, light‐mass, or split‐off bands. Relations between hole wave vectors and spin surface shapes are examined for high symmetry directions. The presented results may be useful in ultrafast spintronics, where both the spin state and the wave vector of a hole should be taken into account simultaneously in the description of the hole spin dynamics. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Ionic conductivity and chemical diffusion in superionic LixCu2−xS (0 ≤ x ≤ 0.25)
Authors: Balapanov M. Kh. , Gafurov I. G. , Mukhamed'yanov U. Kh. , Yakshibaev R. A. , Ishembetov R. Kh.
Published: December 2003

The ionic conductivity and the conjugate chemical diffusion of cations and electron holes in LixCu2−xS (0 ≤ x ≤ 0.25) compositions are studied in the temperature range 623–467 K. In accordance with prediction of the known “mixed mobile ions effect” the partial substitution of copper by lithium in copper sulfide leads to decreasing of the ionic conductivity and it is linked to an increase of activation energy of the ionic conductivity. In comparison with pure copper sulfide the chemical diffusion coefficients in the lithium‐contained compounds are smaller too. The observed values of the activation energy of the chemical diffusion are close to those of the activation energy of the ionic conductivity. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The effective susceptibility exponent in transverse Ising thin films
Authors: Kaneyoshi T.
Published: December 2003

By the use of both the standard mean field theory and the effective field theory with correlations the phase transition of the transverse Ising thin films is investigated with special emphasis to the behavior of the susceptibility χ(T) outside the critical regime. The exchange interaction and transverse field at the surfaces of the thin film take values different from those in the bulk. Various non‐monotonic temperature dependences of the effective exponent γ(T) introduced by Kouvel and Fisher are found, depending on the ratios of these properties between the surfaces and the bulk as well as the value of film thickness L. They are clearly different from the behavior in the bulk. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Interwell exciton dispersion engineering, coherent phonons generation and optical detection of exciton condensate
Authors: Lozovik Yu. E. , Ovchinnikov I. V. , Ostroumov R. P. , Wang K. L.
Published: December 2003

We propose to use dispersion engineering of interwell excitons in coupled quantum wells with external electric and magnetic fields in order to generate coherent phonons and to detect exciton condensate. A parallel magnetic field moves the dispersion minimum of interwell excitons away from the radiative zone and thus reduces their recombination rate. Normal electric field moves an interwell excitons dispersion minimum on the energy scale. These two fields effect can be used to tune the resonance condition of the interwell excitons recombination process via an in‐well excitons level, which results in acoustic phonon emission. We show, that one can change recombination rate as well as intensity and angular distribution of the interwell excitons photoluminescence in the wide range by controlling the external fields. Based on this principle we propose and theoretically evaluate a procedure to detect the condensate of interwell excitons, as well as a scheme to obtain a coherent and monochromatic phonon beam (saser). The statistics of the phonon emission from the condensate of interwell excitons is studied. Numerical estimate for GaAs/AlGaAs coupled quantum wells is provided. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Hopping transport in 1D chains (DNA vs. DLC)
Authors: Kohary K. , Cordes H. , Baranovskii S. D. , Thomas P. , Wendorff J.‐H.
Published: December 2003

We discuss charge transport in one‐dimensional organic solids (DNA and discotic liquid‐crystalline glass (DLC)), focusing on the effects of static and dynamic disorder. In the presence of static disorder it can be shown that the temperature dependence of the low‐field mobility is μ ∝ exp [−(T0/T)2], with characteristic temperature T0 depending on the scale of the energy distribution of localized states responsible for transport. In the case of both static and dynamic disorder the situation is different. We obtain a temperature independent mobility in our molecular dynamics calculations in the case of large static and dynamic disorder compared to the energy overlap integral between the neighbouring sites. The theoretical results are in good agreement with experimental data. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Shot noise in mesoscopic transport through localised states
Authors: Savchenko A. K. , Safonov S. S. , Roshko S. H. , Bagrets D. A. , Jouravlev O. N. , Nazarov Y. V. , Linfield E. H. , Ritchie D. A.
Published: December 2003

We show that shot noise can be used for studies of hopping and resonant tunnelling between localised electron states. In hopping via several states, shot noise is seen to be suppressed compared with its classical Poisson value SI = 2eI (I is the average current) and the suppression depends on the distribution of the barriers between the localised states. In resonant tunnelling through a single impurity an enhancement of shot noise is observed. It has been established, both theoretically and experimentally, that a considerable increase of noise occurs due to Coulomb interaction between two resonant tunnelling channels. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Interwell exciton dispersion engineering, coherent phonons generation and optical detectionof exciton condensate
Authors: Lozovik Yu. E. , Ovchinnikov I. V. , Ostroumov R. P. , Wang K. L.
Published: December 2003

This issue's Editor's Choice [1] discusses interwell excitons in coupled quantum wells as a candidate for observation of different phases in an exciton system, including the very interesting phenomenon of Bose condensation.

The cover picture shows schematically how the generation of coherent phonons and the angular distribution of the exciton photoluminescence (PL) from the quantum well system can be controlled by the external electric and magnetic fields.

The first author, Yurii E. Lozovik, is head of the Laboratory of Spectroscopy of Nanostructures at the Institute of Spectroscopy and also Professor of Physics at the Moscow Physical and Technical Institute. His main interests are electron and electron–hole systems in nanostructures, cluster physics, quantum electrodynamics in a cavity, matter in strong magnetic fields, nanotechnology, ultrafast and near field optics, and computer simulations.
Error in an approximate wave function and an error minimization scheme
Authors: Mukhopadhyay S. , Bhattacharyya K.
Published: December 2003

An estimate of error in an approximate wave function for a stationary state is put forward that does not require any information about the exact state. The measure is sensitive and direct. Parameters embedded in a trial wave function can be varied to minimize this error as well, leading to a variational principle. Such a scheme works nicely for bound states and the more so for Siegert states, for which the standard energy minimization principle does not apply. Pilot calculations on the anharmonic oscillator system and the radial Stark effect in the hydrogen atom reveal the worth of the endeavor. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2004