bluuebunny/crossref_metadata_2025_split huggingface dataset:
Density Mapping in Poly(Ethylene Terephthalate) Using a Fiber-Coupled Raman Microprobe and Partial Least-Squares Calibration
Authors: Everall Neil , Davis Kevin , Owen Harry , Pelletier M. J. , Slater Joe 
Published: May 2005

Partial least-squares (PLS) analysis has been used to calibrate Raman microprobe spectra of poly(ethylene terephthalate) films in terms of density, in order to give insight into changes in crystallinity through the film thickness. The microprobe utilizes a static multiplexed holographic grating to obtain the entire Raman spectrum (-1600-4000 cm-1) in a “single-shot” at ∼ 5-cm−1 resolution. Because there are no moving parts, frequency registration and repeatability are excellent and ideally suited for multivariate calibration. In addition, the high spectral throughput allows the whole spectrum to be collected in a few seconds with high signal-to-noise ratio. With this equipment, cross-validated calibration precisions as low as - 0.0021 g cm−3 were achieved. In this work we considered two ways of removing fluorescence backgrounds prior to carrying out multivariate calibration. The first involved manually fitting a baseline using a polynomial curve and subtracting it. The second approach simply takes the second derivative of the spectrum to attenuate the low-frequency components (i.e., the curved baseline). It was found that either pretreatment gave good calibration precision provided that the resultant spectra were intensity-normalized to correct for variations in laser power, sample alignment, and so on. Surprisingly, it was found that the best precision was obtained by grouping the spectral resolution elements into blocks of eight data points, thereby improving the signal-to-noise but effectively degrading the spectral resolution by a factor of three. This was especially important for the derivative spectra. Alternatively, Savitsky-Golay smoothing of the second derivative data was applied to the same effect but also at the expense of degrading spectral resolution. The implication of this work is that instruments intended for multivariate calibration applications could perhaps be designed to work at rather lower spectral resolutions (but higher signal-to-noise) than might otherwise be considered.
Endogenous κ-Opioid Receptor Systems Regulate Mesoaccumbal Dopamine Dynamics and Vulnerability to Cocaine
Authors: Chefer Vladimir I. , Czyzyk Traci , Bolan Elizabeth A. , Moron Jose , Pintar John E. , Shippenberg Toni S. 
Published: May 2005

Genetic and pharmacological approaches were used to examine κ-opioid receptor (KOR-1) regulation of dopamine (DA) dynamics in the nucleus accumbens and vulnerability to cocaine. Microdialysis revealed that basal DA release and DA extraction fraction (Ed), an indirect measure of DA uptake, are enhanced in KOR-1 knock-out mice. Analysis of DA uptake revealed a decreasedKmbut unchangedVmaxin knock-outs. Knock-out mice exhibited an augmented locomotor response to cocaine, which did not differ from that of wild-types administered a behavioral sensitizing cocaine treatment. The ability of cocaine to increase DA was enhanced in knock-outs, whereas c-fos induction was decreased. Although repeated cocaine administration to wild types produced behavioral sensitization, knock-outs exhibited no additional enhancement of behavior. Administration of the long-acting KOR antagonist nor-binaltorphimine to wild-type mice increased DA dynamics. However, the effects varied with the duration of KOR-1 blockade. Basal DA release was increased whereasEdwas unaltered after 1 h blockade. After 24 h, release andEdwere increased. The behavioral and neurochemical effects of cocaine were enhanced at both time points.These data demonstrate the existence of an endogenous KOR-1 system that tonically inhibits mesoaccumbal DA neurotransmission. Its loss induces neuroadaptations characteristic of “cocaine-sensitized” animals, indicating a critical role of KOR-1 in attenuating responsiveness to cocaine. The increased DA uptake after pharmacological inactivation or gene deletion highlights the plasticity of mesoaccumbal DA neurons and suggests that loss of KOR-1 and the resultant disinhibition of DA neurons trigger short- and long-term DA transporter adaptations that maintain normal DA levels, despite enhanced release.
Selectivity of Canary HVC Neurons for the Bird's Own Song: Modulation by Photoperiodic Conditions
Authors: Del Negro Catherine , Lehongre Katia , Edeline Jean-Marc 
Published: May 2005

To what extent seasonal factors modify the neuronal functional properties within the nuclei of the avian song system remains an open question. In adult songbirds, neurons of the song premotor nucleus HVC (used as a proper name) exhibit selective responses for the bird's own song (BOS). Here we examine whether, outside the breeding season, when songs are less stereotyped, HVC neurons of male canaries still respond selectively to the BOS produced during this period. In an initial experiment, single-unit recordings (n= 114) revealed that the neuronal selectivity for the current BOS was attenuated in males exposed to a short-day photoperiod (typical of the nonbreeding season) compared with that found in males exposed to a long-day photoperiod. In long-day conditions, 35% of the cells responded to the BOS, whereas only 12% did in short-day conditions; there were four times more selective cells (d′ > 1) in long-day than in short-day conditions.To determine whether these effects were the consequence of differences in acoustic features between breeding and nonbreeding songs, neurons (n= 72) recorded in short-day conditions were tested with both a short-day BOS and a long-day BOS. A low percentage of neurons exhibited responses to short-day or to long-day BOS (11% for each song). Responses of putative interneurons (spike duration <0.4 ms) and of putative relay cells were similarly attenuated by the short-day conditions. These results strongly suggest that, in canary, rather than being a fixed property, the selectivity for the BOS moves along a continuum and peaks when the day length mimics the breeding conditions.
First-principle studies of the lattice dynamics of crystals, and related properties
Authors: Gonze Xavier , Rignanese Gian-Marco , Caracas Razvan 
Published: May 2005

Abstract
The crystal lattice is never rigid. Due to temperature, external fields or pressure, the nuclei vibrate, the lattice distorts, and instabilities can induce phase transitions. We review the basic concepts of density-functional perturbation theory, a computational method especially suited to determine from first-principles the microscopic parameters governing such behaviour. Then, we present the additional formalism leading to the following properties of minerals: the infra-red and Raman spectra; the prediction of (meta)stability or instability of a crystalline phase, based on the phonon spectrum; the computation of thermodynamics quantities like the free energy, entropy, specific heat; the atomic temperature factors. For each property, examples are given. When appropriate, we mention the computation of related properties, like dielectric tensor and Born effective charges that are needed to get infra-red spectra. Finally, we discuss briefly, on one hand, other applications of the density-functional perturbation theory, and, on the other hand, an alternative technique, the finite-difference computation of dynamical matrices.
First-principle study of materials involved in incommensurate transitions
Authors: Caracas Razvan , Gonze Xavier 
Published: May 2005

Abstract
We discuss the applicability of the density functional theory to the study of incommensurate crystals. After a brief introduction to these aperiodic but ordered materials we present several types of ab initio methodologies that are adequate in the context of incommensurate transitions and phases. We also give a survey of the corresponding applications, while providing two case studies: Pb2MgTeO6 and K2SeO4.
Ab initio theory of planetary materials
Authors: Oganov Artem R. , Price G. David , Scandolo Sandro 
Published: May 2005

Abstract

Ab initio simulations play an increasingly important role in the studies of deep planetary interiors. Here we review the current state of this field, concentrating on studies of the materials of the Earth’s deep interior (MgO—SiO2—FeO—Al2O3, Fe—Si—S—O) and of the interiors of giant planets (H—He system, H2O—CH4—NH3 system). In particular, novel phases and phase diagrams, insights into structural and electronic phase transitions, melting curves, thermoelasticity and the effects of impurities on physical properties of planet-forming materials are discussed.
The DL_POLY molecular dynamics package
Authors: Smith William , Todorov Ilian T. , Leslie Maurice 
Published: May 2005

Abstract
The DL_POLY package provides a set of classical molecular dynamics programs that have application over a wide range of atomic and molecular systems. Written for parallel computers they offer capabilities stretching from small systems consisting of a few hundred atoms running on a single processor, up to systems of several million atoms running on massively parallel computers with thousands of processors. In this article we describe the structure of the programs and some applications.
STM3: a chemistry visualization platform
Authors: Valle Mario 
Published: May 2005

Abstract
To support CSCS research users we built STM3, a software platform on which advanced chemistry visualization techniques can be integrated. Its main goal is not to replace existing tools, but to provide functionalities not covered by them. STM3’s unusual characteristic among chemistry visualization tools is its ability to combine chemistry and general visualization techniques in the same view. STM3 is built on top of a proven visualization environment (AVS/Express) that lets CSCS’s visualization staff concentrate its efforts on developing new technologies rather than investing time on graphical and user interface implementation issues.
Interaction of 2‐Hydroxy‐substituted Nile Red Fluorescent Probe with Organic Nitrogen Compounds
Authors: Sebök‐Nagy Krisztina , Miskolczy Zsombor , Biczók László 
Published: May 2005

ABSTRACTThe fluorescent properties of 2‐hydroxy Nile red dye (HONR) proved to be highly sensitive to the basicity of hydrogen bond acceptors. Fluorescence quantum yields and fluorescence decay profiles were measured as the function of the concentration of organic nitrogen compounds in solvents of various polarities. The detailed mechanism and the kinetics of the fluorescence quenching were revealed with the combined analysis of the steady‐state and time‐resolved spectroscopic data. The relative contribution of the competing reaction steps was found to be very sensitive to the basicity of the additive and to solvent polarity. The most profound change appeared in the unimolecular deactivation pathways of the excited hydrogen‐bonded HONR, whereas the formation rate of this species varied to a lesser extent. The dissociation into excited HONR and ground‐state base was able to compete with the energy dissipation only when 2,4,6‐trimethylpyridine was used as hydrogen bond acceptor in toluene. The bimolecular quenching of the excited hydrogen‐bonded complex played significant role in apolar solvents. Proton displacement along the hydrogen bond in the excited complex led to excited ion pairs in polar media.
Circular Dichroism of the Photoreceptor Pigment Oxyblepharismin
Authors: Pieroni Osvaldo , Plaza Pascal , Mahet Mathilde , Angelini Nicola , Checcucci Giovanni , Malatesta Manuela , Martin Monique M. , Lenci Francesco 
Published: May 2005

ABSTRACTCircular dichroism (CD) was used to study the structure of oxyblepharismin (OxyBP), the photoreceptor chromophore for the photophobic response of the blue form of Blepharisma japonicum. Both the chromophore associated to its native protein and the free chromophore in ethanol solution were investigated. CD spectra in the far‐UV range indicate that OxyBP induces a slight increase in the α‐helix content of the protein matrix. CD spectra in the near‐UV and visible region of the spectrum show that OxyBP adopts a chiral conformation with a preferential geometry not only when associated to its protein matrix, but also when isolated and dissolved in ethanol. This experimental result is related to the existence of a high‐energy interconversion barrier between two enantiomeric structures of the molecule and discussed on the basis of an asymmetric biosynthesis of its precursor, blepharismin.
Syndecan‐1 Expression During the Formation of Junctional Epithelium
Authors: Dias Rubia A. , Shibata Shunichi , Hashimoto‐Uoshima Mariko , Podyma‐Inoue Katarzyna A. , Ishikawa Isao , Yanagishita Masaki 
Published: May 2005

Background: Syndecans are cell surface heparan sulfate proteoglycans (PG) which can bind to and modulate the action of growth factors and extracellular matrix components (ECM). Syndecan‐ 1 has been shown to play important roles during early tooth development and wound healing and repair. Among diverse cells and tissues that comprise the periodontium, the junctional epithelium (JE) constitutes a region of significant anatomic and clinical importance, but the nature of inductive signals and molecules involved in its formation is still unclear. Therefore, this work examines if syndecan‐1 is associated with formation of JE, and the distribution of other syndecan family members in the epithelium.Methods:In situ hybridization and immunohistochemical techniques were performed using oral tissues from 4‐day‐old to 10‐week‐old mice to investigate the expression of syndecan‐ 1, ‐2, ‐3 and ‐4 mRNAs and their corresponding proteins.Results: Based on in situ hybridization experiments, all syndecan mRNAs were detected in sulcular epithelium (SE), gingival epithelium (GE), and JE with varying intensity and distribution. Syndecan‐1 immunostaining was localized on the cell surface while that of syndecan‐2 did not show clear membrane localization. Our experiments in the developing tooth demonstrated that syndecan‐1 protein followed characteristic patterns of expression during JE formation and that immunoreactivity for syndecan‐1 protein decreased with age when JE cells underwent terminal differentiation.Conclusion: Results of syndecan‐1 mRNA and protein expression patterns suggested that this proteoglycan might be an important molecule during the formation of JE. J Periodontol 2005;76:696‐704.
Characteristics of Periodontal Microflora in Acute Myocardial Infarction
Authors: Doĝan Başak , Buduneli Eralp , Emingil Gülnur , Atilla Gül , Akilli Azem , Antinheimo Johanna , Lakio Laura , Asikainen Sirkka 
Published: May 2005

Background: Periodontitis has been linked to increased risk of cardiovascular diseases. Systemic reactions associated with cardiovascular events may depend on characteristics of the subgingival microflora in periodontitis. Our objectives were to compare the numbers of cultivable bacteria, composition of subgingival microflora and clonal distribution of Actinobacillus actinomycetemcomitans (A. actinomycetemcomitans) in two groups of patients with generalized chronic periodontitis (GCP), one with an acute myocardial infarction (AMI‐GCP) and the other one without AMI (non–AMI‐GCP).Methods: In all, 150 dentate individuals were screened for suitability to this study. Subgingival bacterial samples were collected from 11 AMI‐GCP and 11 non–AMI‐GCP patients who had been selected using strict inclusion criteria in an attempt to exclude confounding factors and to increase comparability of periodontal conditions by matching for periodontal probing depths and attachment levels. Culture methods were used to determine the total viable counts and occurrence and proportions of six periodontal bacterial species and yeasts. Polymerase chain reaction (PCR) technique was used to detect A. actinomycetemcomitans and Porphyromonas gingivalis (P. gingivalis). Intraspecies characterization of A. actinomycetemcomitans included serotyping and genotyping.Results: The mean proportions of P. gingivalis (P = 0.05) and Tannerella forsythensis (T. forsythensis) (P = 0.01) were significantly lower, but the numbers of Micromonas micros (M. micros) and A. actinomycetemcomitans were up to nine times higher and the mean total number of cultivable bacteria per sample higher (P <0.01) in AMI‐GCP than in non–AMI‐GCP.Conclusion: The findings that no target subgingival species were overrepresented but the total bacterial number was higher in AMI‐GCP than non–AMI‐GCP patients may provide support to the hypothesis that elevated numbers of bacteria in close vicinity to sterile parenteral area present a risk for systemic health.J Periodontol 2005;76:740‐748.
In Vitro Evidence That the Biological Effects of Platelet‐Rich Plasma on Periodontal Ligament Cells Is Not Mediated Solely by Constituent Transforming‐Growth Factor‐β or Platelet‐Derived Growth Factor
Authors: Kawase Tomoyuki , Okuda Kazuhiro , Saito Yoshinori , Yoshie Hiromasa 
Published: May 2005

Background: The biological actions of platelet‐rich plasma (PRP) are thought to be mediated primarily by constituent transforming‐growth factor‐β1 (TGF‐β1) and platelet‐derived growth factor‐AB (PDGF‐AB). However, we previously demonstrated that type I collagen expression in periodontal ligament (PDL) cells is acutely stimulated through fibrin clot formation produced by the fibrinogen within PRP, rather than by the known growth factors. To investigate the possible involvement of other unidentified components in PRP action, we have now compared the effects of PRP with those of known recombinant growth factors on cell proliferation, alkaline phosphatase (ALP) activity, and collagen synthesis in human PDL cell cultures.Methods: PRP was prepared by an established two‐step centrifugation protocol using blood obtained from adult human volunteers. Cells cultured in serum‐reduced medium on native or collagen‐coated plates were treated with PRP, TGF‐β1, or PDGF‐AB. Cellular DNA synthesis was evaluated by bromodeoxyuridine incorporation. ALP activity was assessed using p‐nitrophenylphosphate with formalin‐fixed cells, and cellular DNA content was subsequently quantified using bis‐benzimide. Collagen synthesis was evaluated using a specific dye‐based assay kit.Results: 1) As did both TGF‐β1 and PDGF‐AB, PRP stimulated cell proliferation. 2) However, only the initial mitogenic action of PRP was attenuated in collagen‐coated plates. 3) PRP, but neither growth factor, immediately induced fibrin clot formation and subsequently stimulated cellular adhesion and collagen synthesis. 4) These effects were significantly augmented on collagen‐coated plates. 5) PRP enhanced ALP activity, but neither TGF‐β1 nor PDGF‐AB replicated this effect.Conclusions: When evaluated versus the concentrations of growth factors known to be contained by our PRP preparations, these data support the concept that PRP‐constituent TGF‐β1 acts as a significant growth factor on PDL cells. However, our findings also strongly suggest that the PRP‐induced increase in ALP activity is mediated by an as‐yet‐unidentified component(s). In conjunction with previously demonstrated fi‐ brinogen‐mediated actions, our data provide evidence that PRP produces a number of potent effects on PDL cells that does not solely reflect simple combination of its major known growth factors.J Periodontol 2005; 76:760‐767.
Evaluation of Demineralized Bone Matrix Paste and Putty in Periodontal Intraosseous Defects
Authors: Bender Sara A. , Rogalski Joanna B. , Mills Michael P. , Arnold Ralph M. , Cochran David L. , Mellonig James T. 
Published: May 2005

Background: Demineralized bone matrix (DBX) paste and putty are particulate demineralized bone matrices in a 2% or 4% hyaluronate carrier, respectively. The purpose of this study was to determine the effectiveness of DBX paste and putty compared to demineralized freeze‐dried bone allograft (DFDBA) in the treatment of human intraosseous periodontal defects.Methods: Sixty systemically healthy individuals between the ages of 31 and 71 years with at least one intraosseous periodontal defect of≥3 mm in depth and radiographic evidence of at least 40% to 50% vertical bone loss were accrued. Following initial non‐surgical periodontal therapy, sites were randomly selected to receive either DBX paste, DBX putty, or DFDBA (control). Baseline and 6‐month reentry soft and hard tissue parameter measurements were made by calibrated examiners. Data were analyzed within and between groups utilizing analysis of variance (ANOVA) and paired and unpaired Student t tests.Results: Probing depth reductions were significantly improved in all treatment groups with DFDBA, DBX paste, and putty patients demonstrating 2.8 mm, 3.6 mm, and 2.3 mm, respectively. Attachment level gains were significantly improved from baseline for all treatment groups with DFDBA, DBX paste, and putty, respectively, demonstrating 2.4 mm, 2.9 mm, and 1.6 mm. Bone fill was similar between all groups with DBX paste, putty, and DFDBA control groups demonstrating 2.0 mm, 2.4 mm, and 2.2 mm, respectively. All groups yielded significant improvements in percent bone fill with DFDBA, DBX paste and putty, respectively, achieving 37%, 42.1%, and 50% with no significant differences between the groups.Conclusion: In summary, demineralized bone matrix paste, demineralized bone matrix putty, and demineralized freeze‐dried bone allograft all demonstrated similar favorable improvements in soft and hard tissue parameters in the treatment of human intraosseous defects. J Periodontol 2005;76:768‐777.