bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Thickness of Shock Layers in Liquid Chromatography
Authors: Zhu Jie , Ma Zidu , Guiochon Georges 
Published: March 2005

AbstractAt high concentrations, one boundary (the front if the isotherm is convex upward) of the elution band of a single component becomes very steep. Similarly, in frontal analysis, the same boundary is self‐sharpening. These steep boundaries are called shock layers. They result from the steady‐state equilibrium between a nonlinear thermodynamics of phase equilibrium on the one hand, which tends to create a concentration discontinuity, and axial dispersion and a finite rate of mass transfer on the other hand, which tend to relax the concentration gradient. We show that the width of experimental breakthrough curves recorded in frontal analysis agrees well with the prediction of the shock layer theory of Rhee and Amundson in the high concentration range. It is a function of the coefficients of the column HETP equation and the height of the concentration step and is independent of the column length, after the steady state is achieved. In the low concentration range, a discrepancy is observed when the column length is short and the migration distance is insufficient to achieve constant pattern behavior.
Mathematical Modeling of Inhibition Kinetics in Acetone–Butanol Fermentation by Clostridium acetobutylicum
Authors: Yang Xiaoping , Tsao George T. 
Published: March 2005

AbstractAcetone–butanol fermentation by Clostridium acetobutylicum suffers from severe product inhibition effects. This paper presents the results of studies on the cell growth kinetics of the culture under the inhibition of multiple products/byproducts. The inhibition effects caused by multiple components simultaneously as well as a single product alone were examined. Fractional factorial experiments were conducted, and statistical analysis of the study results was performed. Acetate, butyrate, butanol, and pH were found to exhibit synergistic inhibitory effects on the cell growth of C. acetobutylicum. Ethanol and acetone alone or in the presence of other products did not show inhibitory effects under the experimental conditions. Among the various mathematical forms of equations that were evaluated, a parabolic form was found to be most suitable for describing the overall synergistic inhibitory effects caused by acetate, butyrate, butanol, and pH. The simulation results achieved by using the model were promising.
Indicators of AEI Applied to the Delaware Estuary
Authors: Barnthouse Lawrence W. , Heimbuch Douglas G. , Anthony Vaughn C. , Hilborn Ray W. , Myers Ransom A. 
Published: March 2005

We evaluated the impacts of entrainment and impingement at the Salem Generating Station on fish populations and communities in the Delaware Estuary. In the absence of an agreed-upon regulatory definition of “adverse environmental impact” (AEI), we developed three independent benchmarks of AEI based on observed or predicted changes that could threaten the sustainability of a population or the integrity of a community.Our benchmarks of AEI included: (1) disruption of the balanced indigenous community of fish in the vicinity of Salem (the “BIC” analysis); (2) a continued downward trend in the abundance of one or more susceptible fish species (the “Trends” analysis); and (3) occurrence of entrainment/impingement mortality sufficient, in combination with fishing mortality, to jeopardize the future sustainability of one or more populations (the “Stock Jeopardy” analysis).The BIC analysis utilized nearly 30 years of species presence/absence data collected in the immediate vicinity of Salem. The Trends analysis examined three independent data sets that document trends in the abundance of juvenile fish throughout the estuary over the past 20 years. The Stock Jeopardy analysis used two different assessment models to quantify potential long-term impacts of entrainment and impingement on susceptible fish populations. For one of these models, the compensatory capacities of the modeled species were quantified through meta-analysis of spawner-recruit data available for several hundred fish stocks.All three analyses indicated that the fish populations and communities of the Delaware Estuary are healthy and show no evidence of an adverse impact due to Salem. Although the specific models and analyses used at Salem are not applicable to every facility, we believe that a weight of evidence approach that evaluates multiple benchmarks of AEI using both retrospective and predictive methods is the best approach for assessing entrainment and impingement impacts at existing facilities.
Side‐chain flexibility in protein–ligand binding: The minimal rotation hypothesis
Authors: Zavodszky Maria I. , Kuhn Leslie A. 
Published: March 2005

AbstractThe goal of this work is to learn from nature about the magnitudes of side‐chain motions that occur when proteins bind small organic molecules, and model these motions to improve the prediction of protein–ligand complexes. Following analysis of protein side‐chain motions upon ligand binding in 63 complexes, we tested the ability of the docking tool SLIDE to model these motions without being restricted to rotameric transitions or deciding which side chains should be considered as flexible. The model tested is that side‐chain conformational changes involving more atoms or larger rotations are likely to be more costly and less prevalent than small motions due to energy barriers between rotamers and the potential of large motions to cause new steric clashes. Accordingly, SLIDE adjusts the protein and ligand side groups as little as necessary to achieve steric complementarity. We tested the hypothesis that small motions are sufficient to achieve good dockings using 63 ligands and the apo structures of 20 different proteins and compared SLIDE side‐chain rotations to those experimentally observed. None of these proteins undergoes major main‐chain conformational change upon ligand binding, ensuring that side‐chain flexibility modeling is not required to compensate for main‐chain motions. Although more frugal in the number of side‐chain rotations performed, this model substantially mimics the experimentally observed motions. Most side chains do not shift to a new rotamer, and small motions are both necessary and sufficient to predict the correct binding orientation and most protein–ligand interactions for the 20 proteins analyzed.
The flexibility in the proline ring couples to the protein backbone
Authors: Ho Bosco K. , Coutsias Evangelos A. , Seok Chaok , Dill Ken A. 
Published: March 2005

AbstractIn proteins, the proline ring exists predominantly in two discrete states. However, there is also a small but significant amount of flexibility in the proline ring of high‐resolution protein structures. We have found that this side‐chain flexibility is coupled to the backbone conformation. To study this coupling, we have developed a model that is simply based on geometric and steric factors and not on energetics. We show that the coupling between ϕ and χ1 torsions in the proline ring can be described by an analytic equation that was developed by Bricard in 1897, and we describe a computer algorithm that implements the equation. The model predicts the observed coupling very well. The strain in the Cγ‐Cδ‐N angle appears to be the principal barrier between the UP and DOWN pucker. This strain is relaxed to allow the proline ring to flatten in the rare PLANAR conformation.
Regulation of YKL‐40 expression during genotoxic or microenvironmental stress in human glioblastoma cells
Authors: Junker Nanna , Johansen Julia S. , Hansen Lasse T. , Lund Eva L. , Kristjansen Paul E.G. 
Published: March 2005

YKL‐40 is a 40 kDa secreted glycoprotein belonging to the family of ‘mammalian chitinase‐like proteins’, but without chitinase activity. YKL‐40 has a proliferative effect on fibroblasts, chondrocytes and synoviocytes, and chemotactic effect on endothelium and vascular smooth muscle cells. Elevated YKL‐40 levels are found in serum of patients with diseases characterized by inflammation, fibrosis and tissue remodeling. Several studies have reported that high serum YKL‐40 levels in patients with cancer are associated with poor prognosis. YKL‐40 expression is strongly elevated in serum and biopsy material from glioblastomas patients. We investigated the expression of YKL‐40 in three human malignant glioma cell lines exposed to different types of stress. Whereas a polymerase chain reaction transcript was detectable in all three cell lines, only U87 produced measurable amounts of YKL‐40 protein. In U87, hypoxia and ionizing radiation induced a significant increase in YKL‐40 after 24–48 h. The hypoxic induction of YKL‐40 was independent of HIF1. Etoposide, ceramide, serum depletion and confluence all led to elevated YKL‐40. Inhibition of p53 augmented the YKL‐40 expression indicating that YKL‐40 is attenuated by p53. In contrast, both basic fibroblast growth factor and tumor necrosing factor‐α repressed YKL‐40. These are the first data on regulation of YKL‐40 in cancer cells. Diverse types of stress resulted in YKL‐40 elevation, which strongly supports an involvement of YKL‐40 in the malignant phenotype as a cellular survival factor in an adverse microenvironment. (Cancer Sci 2005; 96: 183–190)
Correlation between subjective and objective measures of outcome in staffed community housing
Authors: Perry J. , Felce D. 
Published: March 2005

AbstractBackground  A distinction is made between objective and subjective assessment when quality of life evaluation is considered. The aim was to explore the association between objective and subjective appraisals within similar quality of life domains.Methods  Correlations between scores on objective and subjective quality of life measures concerning choice, activity and integration were investigated by administering measures to the residents of a random sample of 47 small community housing services. Correlations between the measures and resident adaptive behaviour were also investigated.Results  All objective measures were significantly correlated with adaptive behaviour but only one subjective measure was. With level of adaptive behaviour controlled, 6/7 correlations between pairs of objective measures were significant. Fifteen of the 16 correlations between objective and subjective measures were insignificant.Conclusions  Assessments of objective life conditions and personal satisfaction appear to be distinct. Their suitability for different purposes and the notion that subjective appraisal of life may be under homeostatic regulation are discussed.
Dispersal, habitat differences, and comparative phylogeography of Southeast Asian seahorses (Syngnathidae:Hippocampus)
Authors: LOURIE S. A. , GREEN D. M. , VINCENT A. C. J. 
Published: March 2005

AbstractFour distinct phylogeographical patterns across Southeast Asia were observed for four species of seahorse (genusHippocampus) with differing ecologies. For all species, genetic differentiation (based on cytochromebsequence comparisons) was significantly associated with sample site (ΦST = 0.190–0.810,P < 0.0001) and with geographical distance (Mantel'sr = 0.37–0.59,P < 0.019). Geographic locations of genetic breaks were inconsistent across species in 7/10 comparisons, although some similarities across species were also observed. The two shallow‐water species (Hippocampus barbouriandHippocampus kuda) have colonized the Sunda Shelf to a lesser degree than the two deeper‐water species (Hippocampus spinosissimusandHippocampus trimaculatus). In all species the presence of geographically restricted haplotypes in the Philippines could indicate past population fragmentation and/or long‐distance colonization. A nested clade analysis (NCA) revealed that long‐distance colonization and/or fragmentation were likely the dominant forces that structure populations of the two shallow‐water species, whereas range expansion and restricted dispersal with isolation by distance were proportionally more important in the history of the two deeper‐water species.H. trimaculatushas the most widespread haplotypes [average clade distance (Dc) of nonsingleton haplotypes = 1169 km], indicating potentially high dispersal capabilities, whereasH. barbourihas the least widespread haplotypes (averageDc = 67 km) indicating potentially lower dispersal capabilities. Pleistocene separation of marine basins and postglacial flooding of the Sunda Shelf are extrinsic factors likely to have contributed to the phylogeographical structure observed, whereas differences among the species appear to reflect their individual ecologies.
Phylogeography of the Russian flying squirrel (Pteromys volans): implication of refugia theory in arboreal small mammal of Eurasia
Authors: OSHIDA TATSUO , ABRAMOV ALEXEI , YANAGAWA HISASHI , MASUDA RYUICHI 
Published: March 2005

AbstractA phylogeographical study of the Russian (Siberian) flying squirrel (Pteromys volans) was carried out using the complete mitochondrial (mt) cytochrome b gene sequences with special reference to the refugia theory for the arboreal traits of this species. We examined 31 specimens from 24 localities, resulting in 28 haplotypes. One breeding specimen with a unique haplotype from Hokkaido, Japan was included in the phylogenetic analysis. There were three mtDNA lineages: Hokkaido, Far Eastern, and northern Eurasia. Divergence data among lineages demonstrated that the Hokkaido group separated from the other groups during the Holsteinian interglacial. The phylogeographical pattern of P. volans is different from that previously reported for terrestrial rodents associated with treeless habitats. Unlike grasslands, forests decreased during glaciation and moved southward because of the cold and arid environmental conditions. The glacial refugia of P. volans would have been associated with forest dynamics in the Pleistocene.
Microsatellite variation and structure of 28 populations of the common wetland plant, Lychnis flos‐cuculi L., in a fragmented landscape
Authors: GALEUCHET D. J. , PERRET C. , FISCHER M. 
Published: March 2005

AbstractHabitat fragmentation is known to cause genetic differentiation between small populations of rare species and decrease genetic variation within such populations. However, common species with recently fragmented populations have rarely been studied in this context. We investigated genetic variation and its relationship to population size and geographical isolation of populations of the common plant species, Lychnis flos‐cuculi L., in fragmented fen grasslands. We analysed 467 plants from 28 L. flos‐cuculi populations of different sizes (60 000–54 000 flowering individuals) in northeastern Switzerland using seven polymorphic microsatellite loci. Genetic differentiation between populations is small (FST = 0.022; amova; P < 0.001), suggesting that gene flow among populations is still high or that habitat fragmentation is too recent to result in pronounced differentiation. Observed heterozygosity (HO = 0.44) significantly deviates from Hardy–Weinberg equilibrium, and within‐population inbreeding coefficient FIS is high (0.30–0.59), indicating a mixed mating breeding system with substantial inbreeding in L. flos‐cuculi. Gene diversity is the only measure of genetic variation which decreased with decreasing population size (R = 0.42; P < 0.05). While our results do not indicate pronounced effects of habitat fragmentation on genetic variation in the still common L. flos‐cuculi, the lower gene diversity of smaller populations suggests that the species is not entirely unaffected.
Laser capture microdissection for the analysis of gene expression during embryogenesis of Arabidopsis
Authors: Casson Stuart , Spencer Matthew , Walker Katherine , Lindsey Keith 
Published: March 2005

SummaryIt is during embryogenesis that the body plan of the developing plant is established. Analysis of gene expression during embryogenesis has been limited due to the technical difficulty of accessing the developing embryo. Here we demonstrate that laser capture microdissection can be applied to the analysis of embryogenesis. We show how this technique can be used in concert with DNA microarray for the large‐scale analysis of gene expression in apical and basal domains of the globular‐stage and heart‐stage embryo, respectively, when critical events of polarity, symmetry and biochemical differentiation are established. This high resolution spatial analysis shows that up to approximately 65% of the genome is expressed in the developing embryo, and that differential expression of a number of gene classes can be detected. We discuss the validity of this approach for the functional analysis of both published and previously uncharacterized essential genes.
Substrate and cofactor requirements for RNA editing of chloroplast transcripts in Arabidopsis in vitro
Authors: Hegeman Carla E. , Hayes Michael L. , Hanson Maureen R. 
Published: March 2005

SummaryNone of the macromolecular components of the chloroplast RNA editing apparatus has yet been identified. In order to facilitate biochemical purification and characterization of the chloroplast RNA editing apparatus, we have identified conditions suitable for production of chloroplast extracts from the model plant Arabidopsis that are capable of editing exogenous substrates produced by in vitro transcription. A simple poisoned primer extension assay readily quantified editing extent of mutated and wild‐type substrates. Maximum editing efficiency typically varied from 10 to 40% with different chloroplast preparations. Substrates carrying as little as 47 nt surrounding the psbE editing site were as efficiently edited as longer substrates. Editing activity was stimulated when either ATP, CTP, or dCTP was provided to the extract, an unusual observation also recently seen with plant mitochondrial editing extracts. Editing was sensitive to a zinc chelator, also a characteristic of the mammalian APOBEC editing enzyme, which is a zinc‐dependent cytidine deaminase.
The Ligaments and Sesamoid Bones of Knee Joint in New Zealand Rabbits
Authors: Orhan I. O. , Haziroglu R. M. , Gultiken M. E. 
Published: March 2005

SummaryThis study has been conducted on the knee joints of the New Zealand rabbits. A total of 20 knee joints from 10 (five female, five male) adult New Zealand rabbits were studied in the study. Fourteen ligaments and four sesamoid bones including the patellar bone, the infrapatellar adipose body, and the suprapatellar cartilage specifically present in rabbits were grossly observed. The caudal meniscotibial ligaments of the lateral meniscus were noted to be lacking in these rabbits. Moreover, the medial collateral ligament did not have a capsular character in nature. Thus, adipose tissue was determined at a point where the suprapatellar cartilage and patella fused.
Stereological Study of the External Urethral Sphincter in the Female Urethra of the Lamb: A New Model for Studies on Urinary Continence
Authors: Rodríguez‐Veiga E. , Mestre‐Nieto L. , Martínez‐Sainz P. , García‐Pascual A. , Martín‐Palacios S. , Marín‐García P. , González‐Soriano J. 
Published: March 2005

SummarySome of the morphometrical features and functional properties of the lamb external urethral sphincter (EUS) were determined by means of ATPase histochemistry. In this study, eight female urethras of 2‐ to 3‐month‐old lambs were used. The samples were studied by using an unbiased stereological design and were statistically evaluated with a Kolmogorov–Smirnov test. Additionally, the mechanical activity of the different fibre types was analysed by measuring the isometric changes in tension induced by electrical field stimulation (EFS) of intrinsic nerves. The lamb EUS has an average fibre density of 1142.37 fibres/mm2 (SD = 279.33). Our data showed the predominance of fast‐twitch fibres or type II fibres, with a proportion of 30% (type I) and 70% (type II) in all cases. These percentages remained the same along the length of the EUS. However, a clear tendency to increase the number of both fibre types in the mid‐EUS was observed. Interestingly, type I and II fibres are intermingled throughout the whole lamb EUS. Dynamic parameters of the contraction induced in lamb EUS preparations by EFS of intramural nerves, were intermediate between fast‐ and slow‐twitch muscles. Furthermore, contractile activity showed no decrease in amplitude upon repetitive stimulation, suggesting the presence of a mixture of fibre types, in which fast but fatigue‐resistant fibres (probably type IIA) seem to predominate. Our results indicate that lambs could be suggested as a new biological model to study those pathological processes, which involve the sphincteric regulation of the EUS.
Morphology and Histology of the Atlantic Bottlenose Dolphin (Tursiops truncatus) Adrenal Gland with Emphasis on the Medulla
Authors: Clark L. S. , Pfeiffer D. C. , Cowan D. F. 
Published: March 2005

SummaryThis study provides the first detailed description of the Atlantic bottlenose dolphin (Tursiops truncatus) adrenal gland with emphasis on the medulla. Thirty‐one dolphins of varying age and sex were used in this study. No statistical differences were found between the right and left gland mass, however, the left was typically greater. Mean mass for the right and left adrenal glands were 4.99 ± 0.513 and 5.36 ± 0.558 g, respectively. No statistical differences were found between average gland mass and sexual maturity or sex. The average cortex/medulla ratio was 1.22 ± 0.060 meaning approximately 48% is cortex, 41% is medulla, and 11% was categorized as other (i.e. blood vessels, connective tissue, etc.). The cortex contained pseudolobules and the typical zonation. A medullary band, consisting of highly basophilic staining cells was found at the periphery of the medulla. Projections of the medulla to the gland capsule were noted. Immunolabelling with polyclonal antibodies against the enzymes dopamineβhydroxylase and phenylethanolamine N‐methyl transferase indicated that noradrenaline producing cells are found throughout the medulla including the medullary band while adrenaline producing cells are only found within the medullary band. Transmission electron microscopy confirmed the presence of two distinct cell populations within the medullary band and a single cell population throughout the medulla.
Absence of hypercoagulability in acute Kawasaki disease
Authors: Lin Ming‐Tsan , Tsao Lon‐Yen , Cheng Ming‐Lin , Chang Yu‐Jun , Chiu Han‐Yao , Chen Hsiao‐Neng , Kuo Su‐Feng , Chiou Shwu‐Jin 
Published: March 2005

Abstract
Background
: Kawasaki disease (KD) is a systemic vasculitis syndrome with the striking feature of cardiovascular involvement. Endothelial cell (EC) damage has been suggested to predispose individuals to the development of coronary vascular disorders. When EC are perturbed, prethrombotic complications ensue. The purpose of this study was to examine the clinical relevance of EC activation and hypercoagulability in the pathogenesis of KD and to determine if plasma levels of these markers are correlated with the development of coronary aneurysms.
Methods
: EC function and coagulation status were assessed in 52 patients with acute KD, 20 febrile control subjects, and 20 healthy control subjects. Biological markers of EC and hypercoagulability were measured and included thrombomodulin, tissue factor, tissue factor pathway inhibitor, von Willebrand factor (vWF), coagulation factor VII (FVII), activated factor VII, prothrombin fragment 1 + 2 (F1 + 2), and D‐dimer.
Results
: Transient dilatation of coronary arteries was the most common complication (55.8%), and coronary aneurysm was noted in five patients (9.6%). Levels of vWF, FVII, F1 + 2 and D‐dimer were higher in acute KD patients compared with healthy controls but not febrile controls. Markers of EC and hypercoagulability were not different between patients with cardiac complications and those without cardiac complications. Biological and immunological assays did not demonstrate the prethrombotic state in acute KD.
Conclusions
: Our results suggest that hypercoagulability does not occur during the acute stage of KD. Markers of EC damage and hypercoagulability are not predictive of coronary aneurysms in KD.