bluuebunny/crossref_metadata_2025_split huggingface dataset:
More QR‐SCMEH‐MO calculations on group VIB transition metal molecules, M2 (M = Cr, Mo, W, Sg): Valence and valence‐core effects
Authors: Boudreaux E. A. , Baxter E. 
Published: September 2004

AbstractAt the 2001 Sanibel Symposium a presentation of MO calculations derived from the QR‐SCMEH‐MO method applied to Cr2 and Mo2 was made and subsequently published in the proceedings 22. This was followed by similar unpublished calculations on W2 and Sg2 presented at the 43rd Sanibel Symposium in 2003. Unfortunately, in neither of these instances were specific evaluations regarding magnitudes of spin‐pairing energies versus MO eigenvalues taken into account. However, when these factors were subsequently examined in detail, we found that the pattern of MO occupancies and overall bonding features were significantly altered from that reported previously. Among these M2 molecules (Cr2 and Mo2) are found to have open‐shell, triplet delta HOMOs, in which the spins are antiferromagnetically coupled to produce spin singlet ground states. It has been observed that the electronic structures of these molecules must be ascribed apparently to correlation effects confined not only to the valence electrons, but to valence/valence‐core electrons as well. Within a transition metal series the atomic configurations are: ns2np6nda(n + 1)sb; 1 ≤ a ≤ 10; 1 ≤ b ≤ 2. The nda(n + 1)sb portion is naturally the valence component, and the ns2np6 portion is the valence‐core component. All levels below the latter are the inner core, which are frozen in these calculations. Consequently, in molecular bonding there is not only valence correlation, but the likelihood of valence/valence‐core correlation as well; particularly since these are no longer necessarily correlated as they were in the separated atoms. There apparently are no influences from the inner core. Of course, these features apply specifically to the SCMEH‐MO method. Because the SCMEH‐MO method, in general, is not an ab initio type of routine, wherein all electron correlation is explicitly accounted for, it is essential to limit correlation only to those AOs specifically affected by bonding. Furthermore, these effects seem to be uniquely associated with the abnormally short bond distances in these particular molecules. All of the features of this study will be presented and contrasted. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
A portable automated system for trace gas sampling in the field and stable isotope analysis in the laboratory
Authors: Theis Daniel E. , Saurer Matthias , Blum Herbert , Frossard Emmanuel , Siegwolf Rolf T. W. 
Published: September 2004

AbstractA computer‐controllable mobile system is presented which enables the automatic collection of 33 air samples in the field and the subsequent analysis for δ13C and δ18O stable isotope ratios of a carbon‐containing trace gas in the laboratory, e.g. CO2, CO or CH4. The system includes a manifold gas source input for profile sampling and an infrared gas analyzer for in situ CO2 concentration measurements. Measurements of δ13C and δ18O of all 33 samples can run unattended and take less than six hours for CO2. Laboratory tests with three gases (compressed air with different pCO2 and stable isotope compositions) showed a measurement precision of 0.03‰ for δ13C and 0.02‰ for δ18O of CO2 (standard error (SE), n = 11). A field test of our system, in which 66 air samples were collected within a 24‐hour period above grassland, showed a correlation of 0.99 (r2) between the inverse of pCO2 and δ13C of CO2. Storage of samples until analysis is possible for about 1 week; this can be an important factor for sampling in remote areas. A wider range of applications in the field is open with our system, since sampling and analysis of CO and CH4 for stable isotope composition is also possible. Samples of compressed air had a measurement precision (SE, n = 33) of 0.03‰ for δ13C and of 0.04‰ for δ18O on CO and of 0.07‰ for δ13C on CH4. Our system should therefore further facilitate research of trace gases in the context of the carbon cycle in the field, and opens many other possible applications with carbon‐ and possibly non‐carbon‐containing trace gases. Copyright © 2004 John Wiley & Sons, Ltd.
Vicinal hydroxylation of unsaturated fatty acids for structural characterization of intact neutral phospholipids by negative electrospray ionization tandem quadrupole mass spectrometry
Authors: Moe Morten K. , Anderssen Trude , Strøm Morten B. , Jensen Einar 
Published: September 2004

AbstractWe report a novel method allowing the complete structural characterization of intact species of the phospholipid classes phosphatidylcholine and phosphatidylethanolamine by utilizing negative electrospray ionization quadrupole tandem mass spectrometry (MS/MS). Information on the molecular weight of the intact phospholipid species, the class to which it belongs, the molecular mass of the fatty acid substituents and their regioisomerism, is easily revealed by MS/MS. Throughout our investigations the R2COO− ions were more abundant than the R1COO− ions, and this observation is used for regioisomeric assignment of the two fatty acids. However, for phospholipid species containing an unsaturated fatty acid, information on the position of the double bond is not achieved in this way. By converting the olefinic sites to their 1,2‐dihydroxylated derivatives, information on the position of the hydroxyl groups (and hence of the double bond) is obtained by performing a second MS/MS experiment. Thus, a complete structural characterization of intact phosphatidylcholine and phosphatidylethanolamine species is obtained by performing these two MS/MS experiments. In order to ensure structural distinction of isobaric species, a number of phosphatidylethanolamine and phosphatidylcholine species were synthesized from lyso‐phosphatidylcholine and analyzed by the present method. The applicability of the method to real samples is also demonstrated by the complete structural elucidation of the two phosphatidylcholine species 16:0/18:1Δ9 and 16:0/18:1Δ11 from egg yolk. Copyright © 2004 John Wiley & Sons, Ltd.
Toward a systematic approach for selection of NASA technology portfolios
Authors: Weisbin Charles R. , Rodriguez Guillermo , Elfes Alberto , Smith Jeffrey H. 
Published: September 2004

AbstractThere is an important need for a consistent analytical foundation supporting the selection and monitoring of R&D tasks that support new system concepts that enable future NASA missions. This capability should be applicable at various degrees of abstraction, depending upon whether one is interested in formulation, development, or operations. It should also be applicable to a single project, a program comprised of a group of projects, an enterprise typically including multiple programs, and the overall agency itself. Emphasis here is on technology selection and new initiatives, but the same approach can be generalized to other applications, dealing, for example, with new system architectures, risk reduction, and task allocation among humans and machines. The purpose of this paper is to describe one such approach, which is in its early stages of implementation within NASA programs, and to discuss several illustrative examples. © 2004 Wiley Periodicals, Inc. Syst Eng 7: 285–302, 2004
CO Sniffing through Heme‐based Sensor Proteins
Authors: Ascenzi Paolo , Bocedi Alessio , Leoni Livia , Visca Paolo , Zennaro Elisabetta , Milani Mario , Bolognesi Martino 
Published: September 2004

AbstractO2, NO, and CO are substrates, products, and/or modulators in many enzymatic reactions including O2 respiration, denitrification, N2 fixation, and methanogenesis. Over the last decade, O2, NO, and CO have been reported to act as signaling molecules in the control of several distinct biological functions. Here, the heme‐based mechanisms of CO sensing by the bacterial homodimeric CooA and the mammalian heterodimeric NPAS2‐BMAL1 transcriptional factors are reviewed, and the signal transduction pathways are discussed.
IUBMB Life, 56: 309‐315, 2004
Induction of Drug‐metabolizing Enzymes and Transporters in Human Bronchial Epithelial Cells by Beclomethasone Dipropionate
Authors: Kuzuya Y. , Adachi T. , Hara H. , Anan A. , Izuhara K. , Nagai H. 
Published: September 2004

AbstractInhaled steroids are the most potent anti‐inflammatory therapy commonly used in bronchial asthma. There are, however, a small number of asthmatic patients who do not respond to inhaled steroid‐treatment. The stimulation of metabolism and excretion of inhaled drugs at bronchial tissues might lead to a decrease in the effect of the drugs, although the molecular mechanism of this resistance is unclear. In this study, we found that beclomethasone dipropionate (BDP) stimulated the expression of mRNAs for uridine 5'‐diphosphate glucuronosyl transferase 2B4 and 2B11, and transporters such as multidrug resistance P‐glycoprotein, multidrug resistance‐associated protein 1 and 2 in cultured bronchial epithelial cells. It is possible that the individual differences of expression of drug metabolizing enzymes and transporters and their enhancement with BDP are implicated in the individual differences of reactivity over steroid medical treatment.
IUBMB Life, 56: 355‐359, 2004
Development of Anti‐Retroviral Resistance of HIV‐1 Infected Individuals on Therapy: Is it inevitable?
Authors: Kolber Michael A. , Campo Rafael E. , Dickinson Gordon M. 
Published: September 2004

AbstractHighly active antiretroviral therapy directed against HIV‐1 has dramatically modified morbidity and mortality in infected individuals. Enthusiasm for the success of these medications have been tempered by an inability to clear virus from the infected host leaving a virus poised to leverage any advantage into one of productive survival. One mechanism used to accomplish escape from suppression secondary to antiretroviral therapy is by developing mutations. The goal of therapy has been to diminish viral replication, thereby effectively abrogating the development of these resistance‐bearing mutations. This strategy has met with significant success but numerous host‐viral factors impact on the ability of the clinician to persistently suppress viral load, thereby providing a window of opportunity for the virus to mutate. In particular we review evidence for ongoing viral replication in the face of suppressive antiretroviral therapy and viral replication in tissue compartments. We discuss whether viral resistance can develop during transient elevations in viral load (viral blips) or as a function of the rate of viral load decay while on therapy. Finally, we touch on the therapeutic strategy that diminished viral replication capacity of mutational species can maintain host immunity.
IUBMB Life, 56: 301‐307, 2004
Anti‐Oxidative Response of Carbonic Anhydrase III in Skeletal Muscle
Authors: Zimmerman Un‐Jin P. , Wang Ping , Zhang Xiangming , Bogdanovich Sasha , Forster Robert E. 
Published: September 2004

AbstractWe propose that carbonic anhydrase III (CAIII) functions as an anti‐oxidant agent in skeletal muscle. To explore this hypothesis, we analyzed the gene expression profile of skeletal muscle in mice deficient in CAIII gene utilizing the murine genome U74Av2 set microarray. Pairwise comparison between CAIII knockout mice and their wild‐type littermates revealed that more than 500 of 12,000 genes in the array showed an altered level of transcription. Of particular note were transcriptional alterations among genes associated with the glutathione redox cycle, suggesting a possible involvement of CAIII in the glutathione‐mediated anti‐oxidant activity. We therefore investigated S‐glutathiolation and irreversible oxidation of the 2 reactive sulfhyryls of CAIII in skeletal muscle under oxidative stresses of ischemia, or exhaustive exercise. Analysis by isoelectric focusing followed by Western blot revealed that the two sulfhydryls were differentially and progressively oxidized. Brief ischemia of 10 ‐ 20 min provoked partial (one of the suflhydryls) modification of CAIII via reversible S‐glutathiolation. Protracted 60 min ischemia yielded equal amounts of both partially and completely (both sulfhydryls) modified CAIII due to irreversible oxidization. Twenty minutes of repetitive electrical stimulation, simulating exhaustive exercise, produced a mixed yield: partial modification by reversible S‐glutathiolation and complete modification by irreversible oxidation. Thus CAIII responds to oxidative stress with a distinctive sulfhydryl oxidation patterns reflecting duration and severity that may prove sensitive indices of extent and type of damage in muscle injury.
IUBMB Life, 56: 343‐347, 2004
Branched Mitochondrial Electron Transport in the Animalia: Presence of Alternative Oxidase in Several Animal Phyla
Authors: McDonald Allison E. , Vanlerberghe Greg C. 
Published: September 2004

AbstractThe mitochondrion of most eukaryotes has multiple electron transport components that increase the points of entry and/or exit of electrons, thus giving a branched nature to the respiratory chain. In plants and many other organisms, a prominent example is alternative oxidase, a non‐energy conserving branch in the respiratory chain and an additional terminal oxidase for the exit of electrons. Our genome database searches have now revealed the presence of alternative oxidase in four animal species from three different phyla (Mollusca, Nematoda and Chordata), consistent with frequent reports of cyanide‐resistant respiration in the Animalia. In Ciona intestinalis and Crassostrea gigas, alternative oxidase is expressed in several different tissues. Phylogenetic analysis is consistent with the animal proteins having originated by vertical inheritance. We hypothesize that alternative oxidase is likely widespread in the Animalia and discuss some of the potential role(s) for such a branched respiratory chain.
IUBMB Life, 56: 333‐341, 2004
Structural and Functional Characterization of Gene Products Encoded in the Human Genome by Homology Detection
Authors: Pandit SB , Balaji S. , Srinivasan N. 
Published: September 2004

AbstractAvailability of the human genome data has enabled the exploration of a huge amount of biological information encoded in it. There are extensive ongoing experimental efforts to understand the biological functions of the gene products encoded in the human genome. However, computational analysis can aid immensely in the interpretation of biological function by associating known functional/structural domains to the human proteins. In this article we have discussed the implications of such associations. The association of structural domains to human proteins could help in prioritizing the targets for structure determination in the structural genomics initiatives. The protein kinase family is one of the most frequently occurring protein domain families in the human proteome while P‐loop hydrolase, which comprises many GTPases and ATPases, is a highly represented superfamily. Using the superfamily relationships between families of unknown and known structures we could increase structural information content of the human genome by about 5%. We could also make new associations of domain families to 33 human proteins that are potentially linked to genetically inherited diseases.
IUBMB Life, 56: 317‐331, 2004
A common aberration with water‐immersion objective lenses
Authors: ARIMOTO R. , MURRAY J. M. 
Published: September 2004

SummaryWe describe here an aberration that is frequently encountered with water‐immersion but not oil‐immersion objectives. The aberration is shown to be induced by tilt of the coverslip out of the plane normal to the optical axis. Model calculations taking into account the path‐length distortions introduced by a tilted coverslip satisfactorily reproduce the observed effect on the images of small subresolution fluorescent beads.
Quantification of micrometre‐sized porosity in quasicrystals using coherent synchrotron radiation imaging
Authors: AGLIOZZO S. , CLOETENS P. 
Published: September 2004

SummaryPhase contrast radiography has been applied to investigate porosity in the bulk of quasicrystals. The pores act on X‐rays as lenses, leading to drastic changes in the phase contrast images of pores. Depending on the recording conditions and pore features, different imaging regimes are accessed. The variation of the contrast makes the direct characterization of pores from image data, in terms of a precise determination of their size and volume, unreliable. The contrast in Fresnel diffraction images of pores was thus investigated with the support of numerical simulations. A phase retrieval procedure was carried out in order to obtain the correct information from the pore images.
Viability of endolithic micro‐organisms in rocks from the McMurdo Dry Valleys of Antarctica established by confocal and fluorescence microscopy
Authors: WIERZCHOS J. , DE LOS RÍOS A. , SANCHO L. G. , ASCASO C. 
Published: September 2004

SummaryThe rocks of the McMurdo Dry Valleys desert in Antarctica harbour endolithic communities of micro‐organisms such as lichens, fungi, cyanobacteria and bacteria. Establishing the physiological status and viability of these microbial colonies in their natural microhabitat has far‐reaching implications for understanding the microbial ecology of the harsh environment of this polar desert. Here we describe the use of confocal microscopy and a specific fluorescent probe (FUN‐1) to evaluate the metabolic activity of fungal cells. Application of confocal microscopy also served to identify living and dead bacteria or cyanobacteria using the fluorescent assay reagents Live/Dead SYTO 9 and propidium iodide or SYTOX Green, respectively. In addition, through the use of epifluorescence microscopy, live/dead bacteria and cyanobacteria could be detected by estimating fluorescence from their cell components provoked by simultaneously staining with nucleic acids stains such as DAPI and SYTOX Green.
Cytopathological changes induced by selected Brazilian flaviviruses in mouse macrophages
Authors: BARROS V. E. D. , THOMAZINI J. A. , FIGUEIREDO L. T. M. 
Published: September 2004

SummaryScanning and transmission electron microscopy were used to analyse the ultrastructure of peritoneal mouse macrophage cells infected with Brazilian flavivirus (yellow fever, Rocio, Bussuquara and Saint Louis encephalitis viruses). Macrophage cells collected 3 days after viral infection had a flattened shape, with an increased number of large spikes of cytoplasm prolongations, giving an appearance of hairy cells. Cytopathological changes to the macrophage cells were similar regardless of the infecting flavivirus. Rough and smooth endoplasmic reticulum of the macrophage cells infected with flavivirus were abundant, hypertrophic and enlarged. A large number of free ribosomes were seen in the cytoplasm of these infected cells. Spherical particles approximately 50–70 nm in diameter, some of which were empty, were observed in the cytoplasm, generally inside vesicles. These particles probably correspond to viral particles.
Image calibration in fluorescence microscopy
Authors: ZWIER J. M. , VAN ROOIJ G. J. , HOFSTRAAT J. W. , BRAKENHOFF G. J. 
Published: September 2004

SummaryA fluorescence image calibration method is presented based on the use of standardized uniformly fluorescing reference layers. It is demonstrated to be effective for the correction of non‐uniform imaging characteristics across the image (shading correction) as well as for relating fluorescence intensities between images taken with different microscopes or imaging conditions. The variation of the illumination intensity over the image can be determined on the basis of the uniform bleaching characteristics of the layers. This permits correction for the latter and makes bleach‐rate‐related imaging practical. The significant potential of these layers for calibration in quantitative fluorescence microscopy is illustrated with a series of applications. As the illumination and imaging properties of a microscope can be evaluated separately, the methods presented are also valuable for general microscope testing and characterization.
Watching molecular processes with the atomic force microscope: dynamics of polymer adsorption and desorption at the single molecule level
Authors: GUNNING A. P. , KIRBY A. R. , MACKIE A. R. , KROON P. , WILLIAMSON G. , MORRIS V. J. 
Published: September 2004

SummaryThe formation of networks is an important step in the synthesis of many biological assemblies. For example, during the synthesis of plant cell walls the factors which dictate the arrangement of the polymeric constituents that make up the cell wall are not yet understood. Factors such as site‐directed binding provide a possible theoretical background for beginning to understand the assembly of complex biological structures, but modelling of this process is difficult, time consuming and lacks experimental methods for verification. Through the use of atomic force microscopy (AFM) it has been demonstrated that changes in the binding of a single heterogeneous cell wall polysaccharide to a charged substrate can be followed in real time. Furthermore, subsequent image analysis allows the probability of binding of the molecule to be mapped to produce a real data set which is comparable with those obtained in simulation studies. In addition, these AFM studies have provided new mechanistic clues to the adsorption/desorption process of this polysaccharide.
Design‐based estimation of surface area in thick tissue sections of arbitrary orientation using virtual cycloids
Authors: GOKHALE A. M. , EVANS R. A. , MACKES J. L. , MOUTON P. R. 
Published: September 2004

SummarySurface area is a first‐order stereological parameter with important biological applications, particularly at the intersection of biological phases. To deal with the inherent anisotropy of biological surfaces, state‐of‐the‐art design‐based methods require tissue rotation around at least one axis prior to sectioning. This paper describes the use of virtual cycloids for surface area estimation of objects and regions in thick, transparent tissue sections cut at any arbitrary (convenient) orientation. Based on the vertical section approach of Baddeley et al., the present approach specifies the vertical axis as the direction of sectioning (i.e. the direction perpendicular to the tissue section), and applies computer‐generated cycloids (virtual cycloids) with their minor axis parallel to the vertical axis. The number of surface‐cycloid intersections counted on focal planes scanned through the z‐axis is proportional to the surface area of interest in the tissue, with no further assumptions about size, shape or orientation. Optimal efficiency at each x–y location can be achieved by three virtual cycloids orientated with their major axes (which are parallel to the observation planes) mutually at an angle of 120°. The major practical advantage of the present approach is that estimates of total surface area (S) and surface density (SV) can be obtained in tissue sections cut at any convenient orientation through the reference space.