bluuebunny/crossref_metadata_2025_split huggingface dataset:
MALDI‐TOF mass spectrometry of bacteria*
Authors: Lay Jackson O. 
Published: October 2004

Abstract

I.
Introduction
172

II.
Bacterial RNA and DNA
174

III.
Recombinant Proteins
175

IV.
Protein Identification
176

V.
Proteomics
178

VI.
Other Applications that Involve Cellular Isolates
180

VII.
Whole Cells
180

VIII.
Interpretation of Data from Whole Cells
187

IX.
Identification of Proteins and Metabolites in Cells
188

X.
Isolate‐Related Strain Differences in Human Pathogenic Bacteria
190

XI.
Conclusion and Future Prospects
190

References
191

The development of MALDI‐TOF mass spectrometry methods for the characterization of bacteria is reviewed and discussed. The general use of MALDI for the characterization of large biomolecules led directly to obvious applications involving the analysis of isolated bacterial proteins. More surprising was the observation that MALDI‐TOF mass spectrometry could be applied directly to crude cellular fractions or cellular suspensions and that the resulting data from such complex mixtures could provide evidence for chemotaxonomic classification. Versatility and the rapidity of analysis led to the rapid development of a number of MALDI‐TOF methods involving bacteria. Examples of some of the applications covered in this review are the analysis of bacterial RNA and DNA, the detection of recombinant proteins, the characterization of targeted or unknown proteins, bacterial proteomics, the detection of virulence markers, and the very rapid characterization of bacteria at the genus, species, and strain level. The demonstrated capability of taxonomic classification at the strain level, using unprocessed cells, opens the possibility that MALDI‐TOF and similar mass spectrometry approaches may contribute significantly to fulfilling emerging needs for the development of near real‐time methods for the characterization of bacteria. © 2002 John Wiley & Sons, Inc., Mass Spec Rev 20:172–194, 2001
Computational chemistry: A useful (sometimes mandatory) tool in mass spectrometry studies
Authors: Alcamí Manuel , Mó Otilia , Yáñez Manuel 
Published: October 2004

AbstractI.Introduction196II.Theoretical Models197A.   Hartree‐Fock (HF) Theory197B.   Configuration Interaction (CI)197C.   Perturbation Theory198D.   Coupled Cluster Theory198E.   Quadratic Configuration Interaction199F.   Composite Procedures199G.   Multiconfiguration Interaction Theories199H.   Density Functional Theory200I.   CASSCF‐DFT Approaches201J.   Wave Function Analysis202III.Performance of the Model203A.   Geometries203B.   Harmonic Vibrational Frequencies and Infrared Intensities206C.   Energies206D.   Entropies208E.   Convergency Problems of the Moller Plesset Series209F.   Radicals and Other Open‐Shell Systems210G.   Dications213IV.Bond Weakening vs. Bond Reinforcement in Ion‐Molecule Interactions214A.   Dissociative Proton Attachment219B.   Ionization Effects in Three‐Membered Rings221V.Theoretical Characterization of Elusive or Non‐Conventional Structures of Relevance in Gas‐Phase Ion Chemistry Confirmed by Experiment223A.   Oxywater224B.   Ammonia Oxide224C.   Silicon‐Containing Molecules225D.   Fluoroformic Acid225E.   Sulfur‐ and Phosphorus‐Containing Molecules225F.   Ylides226G.   Ethylenedione227H.   Cumulenes and Heterocumulenes227I.   Carbenes230J.   Hydrogen‐Bridged Radical Cations230VI.The Role of Non‐Classical Structures in Ion‐Molecule Interactions231A.   Hydrocarbon Protonated Forms231B.   Protonated Forms of X4(X=P, As, Sb, Bi) and Other Small Clusters233C.   Molecular Planetary Systems234Acknowledgments235References235In this review, we present a brief summary of the theoretical methods most frequently used in gas‐phase ion chemistry. In subsequent sections, the performance of these methods is analyzed, paying attention to the reliability of geometries, vibrational frequencies, energies, and entropies. The possible pathologies of the different methods, in the form of instabilities of the wave function or spin contamination problems, are discussed. Several examples are presented to illustrate the usefulness ofab initioor density functional theory (DFT) methods to predict the existence of elusive molecules and/or to characterize non‐conventional structures, and to rationalize the charge redistributions normally associated with ion–molecule interactions and which result in bond‐weakening or bond‐reinforcement effects. Finally, the role of non‐classical structures in ion–molecule interactions is also illustrated with different examples. © 2002 John Wiley & Sons, Inc., Mass Spec Rev 20:195–245, 2001
Genetic testing in Parkinson's disease
Authors: McInerney‐Leo Aideen , Hadley Donald W. , Gwinn‐Hardy Katrina , Hardy John 
Published: October 2004

AbstractParkinson's disease (PD) is a common neurodegenerative disorder of adulthood characterized clinically by rigidity, bradykinesia, resting tremor, and postural instability. The annual incidence of PD ranges between 16 and 19 individuals per 100,000 (Twelves et al., Mov Disord 2003;18:19–31). Historically, PD has been commonly viewed as an idiopathic or environmentally triggered condition. However, as is true with most common conditions, there have been several families reported with PD who demonstrate a classic Mendelian pattern of inheritance. To date, nine genetic loci have been reported and four pathogenic genes have been identified: α‐synuclein, parkin, DJ1, and PINK1. Families with alterations in these genes or linked sites demonstrate either recessive or dominant inheritance patterns and may have typical and/or atypical symptoms, with an age of onset extending from the second to the sixth decade. Commercial tests for parkin and α‐synuclein mutations are now available. We predict that physicians, particularly neurologists, increasingly will be approached for information and referrals regarding genetic testing. To assist patients and their families, physicians will not only need to know when such testing is likely to yield a meaningful result but also be aware of the possible social and emotional consequences of testing. The following is a review of what is currently known about the genetics of PD within this context. We discuss what is known about genetic testing for Huntington's disease, a well‐described model for genetic testing in a neurodegenerative disorder. We explore the utility, appropriateness, and possible implications of genetic testing for diagnostic and presymptomatic purposes. Published 2004 John Wiley & Sons
The ubiquitin‐proteasome pathway and proteasome inhibitors
Authors: Myung Jayhyuk , Kim Kyung Bo , Crews Craig M. 
Published: October 2004

AbstractThe ubiquitin‐proteasome pathway has emerged as a central player in the regulation of several diverse cellular processes. Here, we describe the important components of this complex biochemical machinery as well as several important cellular substrates targeted by this pathway and examples of human diseases resulting from defects in various components of the ubiquitin‐proteasome pathway. In addition, this review covers the chemistry of synthetic and natural proteasome inhibitors, emphasizing their mode of actions toward the 20S proteasome. Given the importance of proteasome‐mediated protein degradation in various intracellular processes, inhibitors of this pathway will continue to serve as both molecular probes of major cellular networks as well as potential therapeutic agents for various human diseases. © 2001 John Wiley & Sons, Inc. Med Res Rev, 21, No. 4, 245–273, 2001
Arterial calcification: A review of mechanisms, animal models, and the prospects for therapy
Authors: Wallin Reidar , Wajih Nadeem , Greenwood G. Todd , Sane David C. 
Published: October 2004

AbstractThe causes of arterial calcification are beginning to be elucidated. Macrophages, mast cells, and smooth muscle cells are the primary cells implicated in this process. The roles of a variety of bone‐related proteins including bone morphogenetic protein‐2 (BMP‐2), matrix Gla protein (MGP), osteoprotegerin (OPG), osteopontin, and osteonectin in regulating arterial calcification are reviewed. Animals lacking MGP, OPG, smad6, carbonic anhydrase isoenzyme II, fibrillin‐1, and klotho gene product develop varying extents of arterial calcification. Hyperlipidemia, vitamin D, nicotine, and warfarin, alone or in various combinations, produce arterial calcification in animal models. MGP has recently been discovered to be an inhibitor of bone morphogenetic protein‐2, the principal osteogenic growth factor. Many of the forces that induce arterial calcification may act by disrupting the essential post‐translational modification of MGP, allowing BMP‐2 to induce mineralization. MGP requires gamma‐carboxylation before it is functional, and this process uses vitamin K as an essential cofactor. Vitamin K deficiency, drugs that act as vitamin K antagonists, and oxidant stress are forces that could prevent the formation of GLA residues on MGP. The potential role of arterial apoptosis in calcification is discussed. Potential therapeutic options to limit the rate of arterial calcification are summarized. © 2001 John Wiley & Sons, Inc. Med Res Rev, 21, No. 4, 274–301, 2001
The active site of HIV‐1 protease
Authors: Mager Peter P. 
Published: October 2004

AbstractThe active site of the homodimeric HIV‐1 protease includes six amino acids (triads AspThrGly found in each monomer) in amino acid positions 25 to 27 and 25′ to 27′. Up to now, the role of Thr26 and Thr26′, and Gly27 and Gly27′, is unknown. It is hypothesized that strong hydrogen‐bonding forces between the Thr26 and Thr26′ residues stabilize the conformational state of the active site, and that the function of Gly27 and Gly27′ is to accommodate and bind a substrate in a position in which the catalytic Asp25 and Asp25′ carboxylate groups can attack the amide moiety of a substrate. © 2001 John Wiley & Sons, Inc. Med Res Rev, 21, No. 4, 348–353, 2001
Normal‐appearing white matter in multiple sclerosis has heterogeneous, diffusely prolonged T2
Authors: Whittall Kenneth P. , MacKay Alex L. , Li David K.B. , Vavasour Irene M. , Jones Craig K. , Paty Donald W. 
Published: October 2004

AbstractT2 relaxation in normal‐appearing white matter (NAWM) of multiple sclerosis (MS) patients was reexamined using more complete sampling and analysis of decay curves, and to assess focal vs. diffuse abnormalities. Nine MS patients and 10 controls were scanned using a single‐slice 32‐echo pulse sequence with a 10‐ms echo spacing. Decay curves from outlined white and gray matter structures were analyzed using non‐negative least‐squares (NNLS). Resulting T2 distributions were each summarized by the geometric mean T2, T2. Different white matter structures had different mean (over the subjects in a group) T2. Mean T2 in NAWM was always greater than that of controls. Differences were not caused by a few voxels with extreme T2 (i.e., focal lesions), but rather by shifts of the entire T2 distribution (diffuse prolongation). This T2 increase suggests diffuse myelin or axonal pathology. Magn Reson Med 47:403–408, 2002. © 2002 Wiley‐Liss, Inc.
Nuclear magnetic relaxation dispersion of ferritin and ferritin‐like magnetic particle solutions: A pH‐effect study
Authors: Gossuin Yves , Roch Alain , Lo Bue Francesco , Muller Robert N. , Gillis Pierre 
Published: October 2004

AbstractThe relaxation mechanism of water protons in the presence of ferritin is still being debated. In this work, the pH dependence of the relaxation induced by ferritin and Fercayl®, a ferritin‐like akaganeite particle, is studied through T1 and T2 nuclear magnetic relaxation dispersion (NMRD) profiles. To differing extents, the relaxation brought about by both systems is significantly affected by pH. A proton exchange time of 33 ns (at pH 6 and 37°C) is deduced from the fittings of Fercayl® T1 NMRD profiles. The linearity of the relationship between 1/T2 and the magnetic field B0 for ferritin and Fercayl® solutions is not altered by changes in pH. The parameters of this linearity strongly depend on pH for the latter, while remaining unchanged for the former. These results are interpreted in terms of an exchange between protons belonging to hydroxyl groups at the surface of the particle and bulk water protons. Magn Reson Med 46:476–481, 2001. © 2001 Wiley‐Liss, Inc.
Positive effects of polyethylene glycol conjugation to generation‐4 polyamidoamine dendrimers as macromolecular MR contrast agents
Authors: Kobayashi Hisataka , Kawamoto Satomi , Saga Tsuneo , Sato Noriko , Hiraga Akira , Ishimori Takayoshi , Konishi Junji , Togashi Kaori , Brechbiel Martin W. 
Published: October 2004

AbstractMacromolecules conjugated with polyethylene glycol (PEG) acquire more hydrophilicity, resulting in a longer half‐life in circulation and lower immunogenicity. Two novel conjugates for MRI contrast agents were synthesized from a generation‐4 polyamidoamine dendrimer (G4D), 2‐(p‐isothiocyanatobenzyl)‐6‐methyl‐diethylenetriaminepentaacetic acid (1B4M), and one or two PEG molecules with a molecular weight of 20000 Da (PEG2‐G4D‐(1B4M‐Gd)62 (MW: 96 kD), PEG1‐G4D‐(1B4M‐Gd)63 (MW: 77 kD)). Their pharmacokinetics, excretion, and properties as vascular MRI contrast agents were evaluated and compared with those of G4D‐(1B4M‐Gd)64 (MW: 57 kD). PEG2‐G4D‐(1B4M‐Gd)62 remained in the blood significantly longer and accumulated significantly less in the liver and kidney than the other two preparations (P < 0.01). Although the blood clearance was slower, PEG2‐G4D‐(1B4M‐Gd)62 was excreted more readily without renal retention than the other two preparations. In conclusion, the positive effects of PEG conjugation on a macromolecular MRI contrast agent were found to be prolonged retention in the circulation, increased excretion, and decreased accumulation in the organs. Magn Reson Med 46:781–788, 2001. © 2001 Wiley‐Liss, Inc.
Active acoustic control in gradient coils for MRI
Authors: Mansfield P. , Haywood B. , Coxon R. 
Published: October 2004

AbstractThe new principles of active acoustic control in gradient coil design recently introduced by Mansfield and Haywood (MAGMA 1999;8(Suppl 1):55) are further developed theoretically for the far‐field acoustic output for a single sector of a coil system comprising four or more flat rectangular coil sectors. Each sector consists of a split plate arrangement in which are embedded two windings, an outer primary winding and a narrow inner re‐entrant loop control winding immediately adjacent to and surrounding the split or air gap. The wire spacing of the control winding is made small so as not to affect substantially the magnetic field created by the primary winding. Experimental results are presented for two sectors each made of a different readily available plastic material and tested over a range of frequencies. They both show substantial average reductions in acoustic output over the full output when the control winding is appropriately driven. New theoretical expressions are derived for particular frequencies based on normal mode expansions for the plate. This new approach is better able to explain the acoustic output difference between the full and reduced output modes. Empirical expressions are also developed which include longitudinal as well as transverse plate characteristics and used to fit the experimental acoustic output data as a function of frequency and indicate good agreement with regard to both the form and amplitude of the acoustic output response. Magn Reson Med 46:807–818, 2001. © 2001 Wiley‐Liss, Inc.
3D coronary vessel wall imaging utilizing a local inversion technique with spiral image acquisition
Authors: Botnar René M. , Kim Won Y. , Börnert Peter , Stuber Matthias , Spuentrup Elmar , Manning Warren J. 
Published: October 2004

AbstractCurrent 2D black blood coronary vessel wall imaging suffers from a relatively limited coverage of the coronary artery tree. Hence, a 3D approach facilitating more extensive coverage would be desirable. The straightforward combination of a 3D‐acquisition technique together with a dual inversion prepulse can decrease the effectiveness of the black blood preparation. To minimize artifacts from insufficiently suppressed blood signal of the nearby blood pools, and to reduce residual respiratory motion artifacts from the chest wall, a novel local inversion technique was implemented. The combination of a nonselective inversion prepulse with a 2D selective local inversion prepulse allowed for suppression of unwanted signal outside a user‐defined region of interest. Among 10 subjects evaluated using a 3D‐spiral readout, the local inversion pulse effectively suppressed signal from ventricular blood, myocardium, and chest wall tissue in all cases. The coronary vessel wall could be visualized within the entire imaging volume. Magn Reson Med 46:848–854, 2001. © 2001 Wiley‐Liss, Inc.
Characterization of the macromolecule baseline in localized 1H‐MR spectra of human brain
Authors: Hofmann L. , Slotboom J. , Boesch C. , Kreis R. 
Published: October 2004

AbstractShort‐echo‐time magnetic resonance spectra of human brain contain broad contributions from macromolecules. As they are a priori of unknown shape and intensity, they pose a problem if one wants to quantitate the overlying spectral features from low‐molecular‐weight metabolites. On the other hand, the macromolecular contributions may provide relevant clinical information themselves, if properly evaluated. Several methods, based on T1, T2, or spectral shape, have previously been suggested to suppress or edit the macromolecule contributions. Here, a method is presented based on a series of saturation recovery scans and that allows for simultaneous recording of the macromolecular baseline and the fully relaxed metabolite spectrum. In comparison to an inversion recovery technique aimed at nulling signals from long‐T1 components, the saturation recovery method is less susceptible to T1 differences inherent in signals from different metabolites or introduced by pathology. The saturation recovery method was used to quantitate the macromolecular baseline in white and/or gray matter locations of the human brain in 40 subjects. It was found that the content and composition of MR visible macromolecules depends on cerebral location, as well as the age of the investigated subject, while no gender dependence could be found. Magn Reson Med 46:855–863, 2001. © 2001 Wiley‐Liss, Inc.
Quantitative imaging of magnetization transfer exchange and relaxation properties in vivo using MRI
Authors: Sled John G. , Pike G. Bruce 
Published: October 2004

AbstractWe describe a novel imaging technique that yields all of the observable properties of the binary spin‐bath model for magnetization transfer (MT) and demonstrate this method for in vivo studies of the human head. Based on a new model of the steady‐state behavior of the magnetization during a pulsed MT‐weighted imaging sequence, this approach yields parametric images of the fractional size of the restricted pool, the magnetization exchange rate, the T2 of the restricted pool, as well as the relaxation times in the free pool. Validated experimentally on agar gels and samples of uncooked beef, we demonstrate the method's application on two normal subjects and a patient with multiple sclerosis. Magn Reson Med 46:923–931, 2001. © 2001 Wiley‐Liss, Inc.
Coronary magnetic resonance angiography: Experimental evaluation of the new rapid clearance blood pool contrast medium P792
Authors: Taupitz Matthias , Schnorr Jörg , Wagner Susanne , Kivelitz Dietmar , Rogalla Patrik , Claaßen Gerlind , Dewey Marc , Robert Philippe , Corot Claire , Hamm Bernd 
Published: October 2004

AbstractThe signal‐enhancing characteristics of a new monodisperse monogadolinated macromolecular MR contrast medium (P792) were evaluated for magnetic resonance angiography (MRA) of the coronary arteries. A total of 15 cardiac examinations were performed in pigs at 1.5 T using a 3D gradient‐echo sequence. Images were acquired during breath‐hold before and up to 35 min after IV injection of Gd‐DTPA (0.3 mmol Gd/kg), Gd‐BOPTA (0.2 mmol Gd/kg), and P792 (13 μmol Gd/kg). An increase in the signal‐to‐noise ratio (SNR) of 97% ± 17%, 108% ± 37%, and 109% ± 31% in coronary arteries and of 82% ± 19%, 82% ± 24%, and 28% ± 18% in myocardium, respectively, was measured during the first postcontrast acquisition. The blood‐to‐myocardium signal‐difference‐to‐noise ratio (SDNR) was significantly higher for P792 than for the other Gd compounds (P < .05) for up to 15 min after injection. Qualitative assessment showed that visualization of the coronary arteries and their branches was significantly better for P792 compared to the low‐molecular Gd compounds (P < .05). The blood pool contrast medium P792 is well suited for MRA of the coronary arteries. Magn Reson Med 46:932–938, 2001. © 2001 Wiley‐Liss, Inc.
Effects of flow and energy metabolism on injury and Rb+ uptake in pig hearts: An 87Rb and 31P NMR study
Authors: Kupriyanov Valery V. , Bo Xiang  , Sun Jiankang , Jilkina Olga , Dai Guangping , Deslauriers Roxanne 
Published: October 2004

AbstractIn this work the roles of coronary flow (CF) and metabolism in Rb+ (K+ congener) uptake were studied. In isolated pig hearts the left anterior descending artery (LAD) was cannulated to maintain adequate perfusion of the LAD bed. Rb+ loading was initiated and the LAD flow was either completely stopped (no flow (NF)) or reduced to 12% (low flow (LF)), or buffer was deoxygenated without change in flow (hypoxic flow (HYP)) for 2 h. CF through the LAD was then restored to normal, or perfusion was switched to oxygenated buffer. Serial 87Rb MR images or localized 31P spectra were acquired to compare the Rb+ uptake and energetics in the left ventricular (LV) anterior (ischemic/hypoxic) and posterior (normal) walls. End‐ischemic/hypoxic 87Rb signal intensities in the anterior wall were higher and the fluxes were greater in the HYP and LF groups than in the NF group. Phosphocreatine and ATP decreased less significantly and recovered better in the HYP and LF groups. Upon reperfusion/reoxygenation, the HYP and LF groups showed higher 87Rb signal intensities and smaller or no infarctions in the anterior wall compared to those in the NF group. Ischemia reduces Rb+ uptake due to both flow limitations and metabolic inhibition of cellular transport. 87Rb MRI has a potential for distinguishing necrotic and reversibly damaged tissue. Magn Reson Med 46:963–973, 2001. © 2001 Wiley‐Liss, Inc.
Improved harmonic phase myocardial strain maps
Authors: Kuijer Joost P.A. , Jansen E. , Marcus J. Tim , van Rossum Albert C. , Heethaar Robert M. 
Published: October 2004

AbstractMagnetic resonance tagging has proven a valuable tool in the quantification of myocardial deformation. However, time‐consuming postprocessing has discouraged the use of this technique in clinical routine. Recently, the harmonic phase (HARP) technique was introduced for automatic calculation of myocardial strain maps from tagged images. In this study, a comparison was made between HARP instantaneous strain maps calculated from single tagged images (SPAMM) and those calculated from subtracted tagged images (CSPAMM). The performance was quantified using simulated images of an incompressible cylinder in the ‘end‐systolic’ state with realistic image contrast and noise. The error in the second principal stretch ratio was 0.009 ± 0.032 (mean ± SD) for the SPAMM acquisition, and 0.007 ± 0.016 for CSPAMM at identical contrast‐to‐noise ratio. Furthermore, differences between the methods were illustrated with in vivo strain maps. Those calculated from CSPAMM images showed fewer artifacts and were less sensitive to the choice of cut‐off frequencies in the HARP band‐pass filter. A prerequisite for the method to become practical is that the CSPAMM images should be acquired in a single breathhold. Magn Reson Med 46:993–999, 2001. © 2001 Wiley‐Liss, Inc.