bluuebunny/crossref_metadata_2025_split huggingface dataset:
Passive perception of odors and semantic circuits
Authors: Savic Ivanka , Berglund Hans 
Published: March 2004

AbstractThe sense of smell has been traditionally assumed to be different from other sensory modalities in that odors are encoded perceptually, without a semantic component. Recent findings of improved odor memory upon encoding with verbal cues question this view. Furthermore, familiar odors are easier to remember and discriminate than are unfamiliar ones, and odor familiarity is reported to predict odor naming. To investigate whether familiar odors are processed by different cerebral structures than those that process unfamiliar odors, 15O H2O‐positron emission tomography (PET) measurements of cerebral blood flow were carried out in 14 healthy men. The task was passive, birhinal, smelling of familiar odors (FAM), unfamiliar odors (uFAM), and odorless air (AIR). Significant activations (P < 0.05) were calculated using the contrasts FAM–AIR, uFAM–AIR, and FAM–uFAM, and deactivations running these contrasts in the opposite direction. In relation to AIR, both FAM and uFAM activated amygdala, piriform cortex, and parts of anterior cingulate cortex. FAM activated, in addition, left frontal cortex (Brodmann's areas 44,45,47), left parietal cortex incorporating precuneus, and right parahippocampus. Clusters covering parahippocampus and precuneus were observed also in FAM–uFAM. The activation of left frontal cortex and right parahippocampus was positively correlated with familiarity ratings. Smelling of familiar but not unfamiliar odorants seems to engage cerebral circuits mediating memory and language functions, in addition to the engagement of olfactory cortex. Already the most elemental form of odor processing, passive perception thus seems to engage semantic circuits. This is achieved by the ability of odorants to immediately elicit associations and judgments of odor characteristics. Hum. Brain Mapping 21:271–278, 2004. © 2004 Wiley‐Liss, Inc.
The effect of training systemic information on the retention of fault‐finding skills in manufacturing industries
Authors: Linou Nadia , Kontogiannis* Tom 
Published: March 2004

AbstractThis study examines how the process of skill retention (including both recall and reconstruction) can benefit from systemic training information that covers several structural, functional, physical (e.g., causal links), and supervisory features (e.g., system control and instrumentation). An experiment was carried out in which a group of participants who received systemic information was compared to a group trained in plant theory and to another three groups trained in heuristics that ranged in terms of high‐ and low‐level diagnostic information. Learning curves revealed that all groups achieved high accuracy scores in diagnosing faults in a distillation plant. Six weeks later, a retention test showed that the systemic group (S) had a better recall score than the groups trained in theory (T) and high‐level heuristics (HH). In addition, the S group had a better reconstruction score than the groups receiving the high‐ and low‐level heuristics (H+) and the low‐level diagnostic information (HL). An interesting finding was that high‐level diagnostic information seemed to support the reconstruction phase of the retention process, whereas low‐level information better supported the recall phase. Overall, it appeared that systemic information enabled trainees to acquire task cues to help recall and reconstruct diagnostic heuristics. © 2004 Wiley Periodicals, Inc. Hum Factors Man 14: 197–217, 2004.
How do employees perceive their organization and job when companies adopt principles of lean production?
Authors: Seppälä Pentti , Klemola Soili 
Published: March 2004

AbstractThe concept of lean production originally emerged in the beginning of the 1990s in the automobile industry, but its principles were adopted in other industries as well. According to the literature, the principles of lean production are controversial from the point of view of human well being. This study examined: 1) the extent to which lean production and related technologies were adopted in four Finnish manufacturing companies; 2) the way different occupational groups experienced their organization and work when principles of lean production had been implemented; and 3) which factors in the organization and change processes were associated with the employees' positive or negative perceptions of production, job satisfaction, and stress. © 2004 Wiley Periodicals, Inc. Hum Factors Man 14: 157–180, 2004.
Pattern recognition strategies for molecular surfaces: III. Binding site prediction with a neural network
Authors: Keil Matthias , Exner Thomas E. , Brickmann Jürgen 
Published: March 2004

AbstractAn algorithm for the identification of possible binding sites of biomolecules, which are represented as regions of the molecular surface, is introduced. The algorithm is based on the segmentation of the molecular surface into overlapping patches as described in the first article of this series.1The properties of these patches (calculated on the basis of physical and chemical properties) are used for the analysis of the molecular surfaces of 7821 proteins and protein complexes. Special attention is drawn to known protein binding sites. A binding site identification algorithm is realized on the basis of the calculated data using a neural network strategy. The neural network is able to classify surface patches as protein–protein, protein–DNA, protein–ligand, or nonbinding sites. To show the capability of the algorithm, results of the surface analysis and the predictions are presented and discussed with representative examples. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 779–789, 2004
Performance of SuSi: A method for generating atomistic models of amorphous polymers based on a random search of energy minima
Authors: Curcó David , Alemán Carlos 
Published: March 2004

AbstractThe performance of a recently developed method to generate representative atomistic models of amorphous polymers has been investigated. This method, which is denoted SuSi, can be defined as a random generator of energy minima. The effects produced by different parameters used to define the size of the system and the characteristics of the generation algorithm have been examined. Calculations have been performed on poly(L,D‐lactic) acid (ρ = 1.25 g/cm3) and nylon 6 (ρ = 1.084 g/cm3), which are important commercial polymers. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 790–798, 2004
Intramolecular interaction energies in model alanine and glycine tetrapeptides. Evaluation of anisotropy, polarization, and correlation effects. A parallel ab initio HF/MP2, DFT, and polarizable molecular mechanics study
Authors: Gresh Nohad , Kafafi Sherif A. , Truchon Jean‐François , Salahub Dennis R. 
Published: March 2004

AbstractAn extension of the SIBFA polarizable molecular mechanics procedure to flexible oligopeptides is reported. The procedure is evaluated by computing the relative conformational energies, δEconf, of the alanine tetrapeptide in 10 representative conformations, which were originally derived by Beachy et al. (J Am Chem Soc 1997, 119, 5908) to benchmark molecular mechanics procedures with respect to ab initio computations. In the present study, a particular emphasis is on the separable nature of the components of the energy and the particular impact of the polarization energy component on δEconf. We perform comparisons with respect to single‐point HF, DFT, LMP2, and MP2 computations done at the SIBFA‐derived energy minima. Such comparisons are made first for the 10 conformers derived from ϕ/ψ torsional angle energy‐minimization (the rigid rotor approach), and, in a second step, after allowing additional relaxation of the Cα centered valence angles. In both series of energy‐minimization, the SIBFA δEconf compared best with the LMP2 results using the 6‐311G** basis set, the rms being 1.3 kcal/mol. In the absence of the polarization component, the rms is 3.5 kcal/mol. In both series of minimizations, the magnitudes of δEconf, computed as differences with respect to the most stable conformer taken as energy zero, decrease along the series: HF > DFT > LMP2 > SIBFA > MP2, indicative of increasing stabilization of the most highly folded conformers. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 823–834, 2004
Development and evaluation of a generic evolutionary method for protein–ligand docking
Authors: Yang Jinn‐Moon 
Published: March 2004

AbstractWe have developed a generic evolutionary method with an empirical scoring function for the protein–ligand docking, which is a problem of paramount importance in structure‐based drug design. This approach, referred to as the GEMDOCK (Generic Evolutionary Method for molecular DOCKing), combines both continuous and discrete search mechanisms. We tested our approach on seven protein–ligand complexes, and the docked lowest energy structures have root‐mean‐square derivations ranging from 0.32 to 0.99 Å with respect to the corresponding crystal ligand structures. In addition, we evaluated GEMDOCK on crossdocking experiments, in which some complexes with an identical protein used for docking all crystallized ligands of these complexes. GEMDOCK yielded 98% docked structures with RMSD below 2.0 Å when the ligands were docked into foreign protein structures. We have reported the validation and analysis of our approach on various search spaces and scoring functions. Experimental results show that our approach is robust, and the empirical scoring function is simple and fast to recognize compounds. We found that if GEMDOCK used the RMSD scoring function, then the prediction accuracy was 100% and the docked structures had RMSD below 0.1 Å for each test system. These results suggest that GEMDOCK is a useful tool, and may systematically improve the forms and parameters of a scoring function, which is one of major bottlenecks for molecular recognition. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 843–857, 2004
Hydrogen bonding and solvent effects on the lowest 1(n, π*) excitations of triazines in water
Authors: Zeng Jun , Xie Daiqian 
Published: March 2004

AbstractOur method for estimating solvent effects on electronic spectra in media with strong solute–solvent interactions is applied here to calculate the absorption and fluorescence solvatochromatic shifts of dilute triazines in water. First, the ab initio CASSCF method is used to estimate the gas‐phase electronic excitation properties and state charge distributions; second, Monte Carlo simulations are performed to elucidate liquid structures around the ground and excited state solute; finally, the solvent shift is evaluated based on the gas‐phase charge distributions and the explicit solvent structures. For the dilute triazine solutions, simulations predict one linear (different) hydrogen bond attached to each nitrogen atom. Upon the first 1(n, π*)electronic excitation one hydrogen bond is completely broken. For the absorption and fluorescence spectra, our calculations demonstrated that the specific solvent–solute interaction, in any electronic state, plays a critical role in the determination of solvent shifts. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 813–822, 2004
Simultaneous quantification of cyclophosphamide, 4‐hydroxycyclophosphamide, N,N′,N″‐triethylenethiophosphoramide (thiotepa) and N,N′,N″‐triethylenephosphoramide (tepa) in human plasma by high‐performance liquid chromatography coupled with electrospray ionization tandem mass spectrometry
Authors: de Jonge Milly E. , van Dam Selma M. , Hillebrand Michel J. X. , Rosing Hilde , Huitema Alwin D. R. , Rodenhuis Sjoerd , Beijnen Jos H. 
Published: March 2004

AbstractThe alkylating agents cyclophosphamide (CP) and N, N′, N″‐triethylenethiophosphoramide (thiotepa) are often co‐administered in high‐dose chemotherapy regimens. Since these regimens can be complicated by the occurrence of severe and sometimes life‐threatening toxicities, pharmacokinetically guided administration of these compounds, to reduce variability in exposure, may lead to improved tolerability. For rapid dose adaptations during a chemotherapy course, we have developed and validated an assay, using liquid chromatography coupled with electrospray tandem mass spectrometry (LC/MS/MS), for the routine quantification of CP, thiotepa and their respective active metabolites 4‐hydroxycyclophosphamide (4OHCP) and N, N′, N″‐triethylenephosphoramide (tepa) in plasma. Because of the instability of 4OHCP in plasma, the compound is derivatized with semicarbazide (SCZ) immediately after sample collection and quantified as 4OHCP‐SCZ. Sample pretreatment consisted of protein precipitation with a mixture of methanol and acetronitrile using 100 µl of plasma. Chromatographic separation was performed on an Zorbax Extend C18 column (150 × 2.1 mm i.d., particle size 5 µm), with a quick gradient using 1 mM ammonia solution and acetonitrile, at a flow‐rate of 0.4 ml min−1. The analytical run time was 10 min. The triple quadrupole mass spectrometer was operating in the positive ion mode and multiple reaction monitoring was used for drug quantification. The method was validated over the concentration ranges 200–40 000 ng ml−1 for CP, 50–5000 ng ml−1 for 4OHCP‐SCZ and 5–2500 ng ml−1 for thiotepa and tepa, using 100 µl of human plasma. These dynamic concentration ranges proved to be relevant in daily practice. Hexamethylphosphoramide was used as an internal standard. The coefficients of variation were <12% for both intra‐day and inter‐day precisions for each compound. Mean accuracies were also between the designated limits (±15%). This robust and rapid LC/MS/MS assay is now successfully applied for routine therapeutic drug monitoring of CP, thiotepa and their metabolites in our hospital. Copyright © 2004 John Wiley & Sons, Ltd.
Electrospray ionization mass spectrometric study of 1,3,4‐oxadiazole–copper complexes
Authors: Frański Rafał 
Published: March 2004

AbstractThe complexes of 2,5‐disubstituted‐1,3,4‐oxadiazoles, namely 2,5‐diphenyl‐1,3,4‐oxadiazole (1), 2,5‐bis(2‐pyridyl)‐1,3,4‐oxadiazole (2) and 2,5‐bis(4‐pyridyl)‐1,3,4‐oxadiazole (3), with copper cation were studied by electrospray ionization mass spectrometry (ESI‐MS). The ability of the compounds studied to form complexes with copper (under the ESI conditions) can be ordered as 2 > 1 > 3. The compounds studied tend to form both 1 : 1 and 2 : 1 chelate complexes with both copper(II) and copper(I). The complexes with copper(I) are formed in the ESI process. The influence of solvent polarity, solution flow‐rate, counter ions (Cl−, NO3−, CH3COO−, SO42−, acetylacetonates) on the type of the ions observed was studied. Copyright © 2004 John Wiley & Sons, Ltd.
Quantitative analysis of the novel anticancer drug ABT‐518, a matrix metalloproteinase inhibitor, plus the screening of six metabolites in human plasma using high‐performance liquid chromatography coupled with electrospray tandem mass spectrometry
Authors: Stokvis E. , Rosing H. , Crul M. , Rieser M. J. , Heck A. J. R. , Schellens J. H. M. , Beijnen J. H. 
Published: March 2004

AbstractA liquid chromatographic/tandem mass spectrometric (LC/MS/MS) assay for the quantitative analysis of the novel anticancer drug ABT‐518 and the screening of six potential metabolites in human plasma has been developed and validated to support a phase I study with the drug. ABT‐518 is an inhibitor of matrix metalloproteinases, which are associated with tumor growth and development of metastasis. Plasma samples were prepared for analysis using a simple solid‐phase extraction method on phenyl cartridges. LC separation was performed on a Zorbax extend C18 column (150 × 2.1 mm i.d., 5 µm particle size) using a mobile phase of methanol–aqueous 10 mM ammonium hydroxide (80:20, v/v) pumped at a flow‐rate of 0.2 ml min−1. An API2000 triple‐quadrupole mass spectrometer was used for specific and sensitive detection. The best chromatographic speed (total run time 8 min) and peak shapes were obtained by employing an alkaline mobile phase (pH in aqueous phase ∼10). Furthermore, an alkaline eluent was favored in order to obtain a better overall sensitivity for the protonated analytes. The dynamic range was from 10 to 1000 ng ml−1 from 500 µl of plasma for ABT‐518 and the metabolites were detected at levels of the same order of magnitude. Inter‐assay accuracies for ABT‐518 at five concentration levels were between −9.24 and 6.93% and inter‐assay precisions were always <10.7%. Analyte stability was not critical during either storage or processing. This method was successfully applied in a phase I clinical study of ABT‐518. The active drug, ABT‐518, and all of the metabolites included in the assay could be identified in plasma from dosed patients. We believe that the method described in this paper using an alkaline mobile phase in combination with a basic stable analytical column may also be generally useful for the bioanalysis of other basic drugs. Copyright © 2004 John Wiley & Sons, Ltd.
Accurate mass measurement and tandem mass spectrometry of intact globin chains identify the low proportion variant hemoglobin Lepore–Boston–Washington from the blood of a heterozygote
Authors: Rai Dilip K. , Green Brian N. , Landin Britta , Alvelius Gunvor , Griffiths William J. 
Published: March 2004

AbstractWithin a mixture of proteins, minor polymorphic components are difficult to identify using a conventional proteomic approach. Their identification generally requires multi‐dimensional separation steps, before or after proteolytic cleavage, followed by sequence analysis of the proteolytic products. In this study, we investigated the potential of tandem mass spectrometry for protein characterization by identifying the δ–β hybrid human hemoglobin variant Lepore–Boston–Washington using electrospray ionization tandem mass spectrometry. Hemoglobin Lepore–Boston–Washington occurs mainly in heterozygotes, where it comprises ∼10% of the total non‐α‐chains, the dominant non‐α‐chain being the normal β(∼90%). Furthermore, Hemoglobin Lepore–Boston–Washington has an average molecular mass (15 865.23 Da) that is only 2 Da lower than that of the normal β‐chain (15 867.24 Da). Consequently, it cannot be resolved from the normal β‐chain by mass spectrometry. Here we show how Hemoglobin Lepore–Boston–Washington was identified directly from the diluted blood of a heterozygote by analyzing the product ions from the Lepore–Boston–Washington and normal β‐chain ions without prior separation of the individual chains. This study shows the potential of the tandem mass spectrometry for identifying a minor component in an unseparated mixture of proteins. Copyright © 2004 John Wiley & Sons, Ltd.
Collision‐induced dissociation of valdecoxib metabolites: a novel rearrangement involving an isoxazole ring
Authors: Zhang Ji Y. , Xu Fran , Breau Alan P. 
Published: March 2004

AbstractValdecoxib is a potent COX‐2 inhibitor. During metabolism studies of valdecoxib by liquid chromatography/tandem mass spectrometry, we observed a novel mass spectral rearrangement involving an isoxazole ring for some of the metabolites in the negative ion mode. Accurate mass measurements were performed with quadrupole time‐of‐flight mass spectrometry to determine the elemental compositions of the fragments. Additionally, two types of stable‐isotope labeled analogues were prepared to assist with the assignments of these fragments and possible mechanistic rearrangements resulting from collision‐induced dissociation (CID). Detailed analyses of the CID mass spectra suggest that the fragmentation process involves a novel two‐step rearrangement. The first step consists of an intramolecular SN2 reaction with a five‐membered ring rearrangement to form an intermediate. The second step involves a four‐membered ring intramolecular rearrangement followed by a cleavage of the N—O bond on the isoxazole ring to form a unique fragment ion at m/z 196. The same phenomenon was observed for a group of structurally related metabolites that also contain a 5‐hydroxymethyl or 5‐carboxylic acid moieties. A mechanism for the novel rearrangement involving an isoxazole ring is proposed. Copyright © 2004 John Wiley & Sons, Ltd.
Characterization of the interglycosidic linkage in di‐, tri‐, tetra‐ and pentaglycosylated flavonoids and differentiation of positional isomers by liquid chromatography/electrospray ionization tandem mass spectrometry
Authors: Ferreres F. , Llorach R. , Gil‐Izquierdo A. 
Published: March 2004

AbstractThe LC/UV‐DAD/ESI‐MSn negative fragmentation mode of 23 O‐glycosylated flavonoids with two, three, four and five hexoses was studied. The results show that it is possible to differentiate the (1 → 2) and (1 → 6) interglucosidic linkages and also to discern between the flavonoid isomers with two glucoses (sophorosides, gentiobiosides and X,Y‐diglucosides), three glucoses (sophorotriosides and X‐sophoroside‐Y‐glucoside) and four glucoses (X‐sophorotriosides‐Y‐glucoside and X‐sophoroside‐Y‐sophoroside). In the characterization of the (1 → 2) and (1 → 6) interglycosidic linkages, the Y1− (−162 u) and Z1− (−180 u) ions play a relevant role. In the first case ions with high relative abundance (13–79%) are found, whereas in the other cases they are in very low abundance or absent. X,Y‐di‐O‐glucoside flavonoids can be differentiated from the O‐diglucoside flavonoids by the presence of Y1− (base peak) and Y0− (∼30%) ions and the absence of Z1− ions. Regarding flavonoids glycosylated with three glucoses, X‐sophoroside‐Y‐glucoside flavonoids show the Y70− (−162 u) ion as the only peak in MS2 events whereas in sophorotrioside flavonoids various ions due to intermediate fragmentations are observed. These ions are characteristic of a (1 → 2) interglucosidic linkage. In MS2 experiments on flavonoids with four glucoses (X‐sophorotrioside‐Y‐glucoside and X‐sophoroside‐Y‐sophoroside), the base peak indicated the total loss of the sugar moieties in position 7. In addition, the characterization of the type of interglycosidic linkage in flavonoids glycosylated with five sugars can be achieved. On the other hand, in tetra‐ and pentaglycosylated flavonoids, the ions that characterize the (1 → 2) interglucosidic linkage formed by intermediate fragmentation of the oligosacharide residues (sophorosides and sophorotriosides) are found in much higher relative abundance in MS3 than in MS2 experiments, where they are almost not detected. Copyright © 2004 John Wiley & Sons, Ltd.