bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative Studies of Dispersant Optimization Techniques for Evaluating Stability of Alumina Slurries
Authors: Gaydardzhiev Stoyan , Ay Peter , Janeczko Marta 
Published: August 2006

AbstractThe choice of a reliable method for the testing of dispersant efficiency is an important issue in ceramics processing by emerging near net shape methods. The present paper presents the comparison of four methods for evaluation of the dispersibility properties of a commercial deflocculant Dolapix CE64, towards stabilization of submicron alumina powder suspended in water. The following techniques have been investigated for this purpose: zeta potential obtained from CVI measurement, specific surface charge based on streaming current, sedimentation and capillary suction time. A good correlation between the zeta potential and the streaming current as a means for determining the optimal dispersant dose and improved understanding of the dispersion mechanisms were obtained.
Structure determination of symmetric homo‐oligomers by a complete search of symmetry configuration space, using NMR restraints and van der Waals packing
Authors: Potluri Shobha , Yan Anthony K. , Chou James J. , Donald Bruce R. , Bailey‐Kellogg Chris 
Published: August 2006

AbstractStructural studies of symmetric homo‐oligomers provide mechanistic insights into their roles in essential biological processes, including cell signaling and cellular regulation. This paper presents a novel algorithm for homo‐oligomeric structure determination, given the subunit structure, that is both complete, in that it evaluates all possible conformations, and data‐driven, in that it evaluates conformations separately for consistency with experimental data and for quality of packing. Completeness ensures that the algorithm does not miss the native conformation, and being data‐driven enables it to assess the structural precision possible from data alone. Our algorithm performs a branch‐and‐bound search in the symmetry configuration space, the space of symmetry axis parameters (positions and orientations) defining all possible Cn homo‐oligomeric complexes for a given subunit structure. It eliminates those symmetry axes inconsistent with intersubunit nuclear Overhauser effect (NOE) distance restraints and then identifies conformations representing any consistent, well‐packed structure to within a user‐defined similarity level.For the human phospholamban pentamer in dodecylphosphocholine micelles, using the structure of one subunit determined from a subset of the experimental NMR data, our algorithm identifies a diverse set of complex structures consistent with the nine intersubunit NOE restraints. The distribution of determined structures provides an objective characterization of structural uncertainty: backbone RMSD to the previously determined structure ranges from 1.07 to 8.85 Å, and variance in backbone atomic coordinates is an average of 12.32 Å2. Incorporating vdW packing reduces structural diversity to a maximum backbone RMSD of 6.24 Å and an average backbone variance of 6.80 Å2. By comparing data consistency and packing quality under different assumptions of oligomeric number, our algorithm identifies the pentamer as the most likely oligomeric state of phospholamban, demonstrating that it is possible to determine the oligomeric number directly from NMR data. Additional tests on a number of homo‐oligomers, from dimer to heptamer, similarly demonstrate the power of our method to provide unbiased determination and evaluation of homo‐oligomeric complex structures. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Symmetry‐adapted tight‐binding calculations of the phonon dispersion and the resonant Raman intensity of the totally symmetric phonons of single‐walled carbon nanotubes
Authors: Popov Valentin N. , Lambin Philippe 
Published: August 2006

AbstractThe atomistic calculations of the physical properties of perfect single‐walled carbon nanotubes based on the use of the translational symmetry of the nanotubes face increasing computational difficulties for most of the presently synthesized nanotubes, which have up to a few thousand atoms in the unit cell. This difficulty can be circumvented by use of the helical symmetry of the nanotubes. We present the results of such symmetry‐adapted tight‐binding calculations of the phonon dispersion and resonant Raman intensity of the totally symmetric A 1 phonons of several hundred nanotubes. In particular, we show that 1) the frequencies and the resonant Raman intensity of the RBM and the G‐band modes show radius and chirality dependence and family patterns, 2) the strong electron – A 1(LO) phonon interactions in metallic nanotubes lead to Kohn anomalies of the phonon branches and to their softening at the zone‐center, 3) the G‐band consists of a subband due to A 1(LO) phonons of semiconducting tubes centered at ≈1593 cm–1, a subband of A 1(TO) phonons at ≈1570 cm–1, and a subband of A 1(LO) phonons of metallic tubes at ≈1540 cm–1. The latter prediction confirms previous theoretical results but disagrees with the assignment of the G‐band features adopted by other authors. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Theoretical study of the dissociation process by multiphoton absorption in the diatomic molecule
Authors: Sugimori Kimikazu , Ito Tomoya , Takata Yusuke , Ichitani Kazuhiro , Nagao Hidemi , Nishikawa Kiyoshi 
Published: August 2006

AbstractWe investigate multiphoton absorption, including the dissociation process in the OH molecule by means of wavepacket dynamics. The time‐development scheme is the so‐called split‐operator method, which conserves the norm of the state vector. The resultant wavepacket involves the information of all discrete vibrational states and the dissociative continuum state substantially, so we are able to treat all the bound–bound, the bound–continuum and the continuum–continuum transitions. The energy spectra of the system under the strong laser pulse can also be obtained by the spectrum method, where the autocorrelation function of the wavepacket under consideration is Fourier transformed. First, we discuss the field intensity dependence of the population and the competition between dissociation and absorption processes in multiphoton processes of above‐threshold dissociation (ATD). Then, we analyze the above‐threshold dissociation due to the continuum–continuum transition in detail. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Branch and bound computation of exact p-values
Authors: Bejerano Gill 
Published: August 2006

Abstract
Summary: P-value computation is often used in bioinformatics to quantify the surprise, or significance, associated with a given observation. An implementation is provided that computes the exact p-value associated with any observed sample, against a null multinomial distribution, using the likelihood-ratio statistic. The efficient branch and bound code, far exceeding the full enumeration implemented by commercial packages, is especially useful with small sample, sparse data and rare events, common scenarios in bioinformatics, where approximations are often inaccurate and inappropriate. This code base can also be adapted to compute exact p-values of other statistics in diverse sampling scenarios.
Availability: Freely available at
Contact: jill@soe.ucsc.edujill
UniGene Tabulator: a full parser for the UniGene format
Authors: Lenzi Luca , Frabetti Flavia , Facchin Federica , Casadei Raffaella , Vitale Lorenza , Canaider Silvia , Carinci Paolo , Zannotti Maria , Strippoli Pierluigi 
Published: August 2006

Abstract
Summary: UniGene Tabulator 1.0 provides a solution for full parsing of UniGene flat file format; it implements a structured graphical representation of each data field present in UniGene following import into a common database managing system usable in a personal computer. This database includes related tables for sequence, protein similarity, sequence-tagged site (STS) and transcript map interval (TXMAP) data, plus a summary table where each record represents a UniGene cluster.
UniGene Tabulator enables full local management of UniGene data, allowing parsing, querying, indexing, retrieving, exporting and analysis of UniGene data in a relational database form, usable on Macintosh (OS X 10.3.9 or later) and Windows (2000, with service pack 4, XP, with service pack 2 or later) operating systems-based computers.
Availability: The current release, including both the FileMaker runtime applications, is freely available at
Contact: pierluigi.strippoli@unibo.it
Supplementary information: We also distribute a precalculated implementation for current Homo sapiens (build #190, March 2006) and Danio rerio (zebrafish, build #90, March 2006) UniGene data.
Characterization of a Susceptibility Locus for SLE, SLEB5, on Chromosome 4p14‐13
Authors: Johansson C. M. , Kristjánsdottir H. , Gröndal G. , Steinsson K. , Alarcón‐Riquelme M. E. 
Published: August 2006

AbstractSystemic lupus erythematosus is a systemic autoimmune disorder of unknown aetiology but is most likely caused by an interaction between several genetic factors and the environment. In a previously published genome scan we presented linkage to a marker on chromosome 4p13 in Icelandic families. Fine mapping of the region has been performed using 10 multicase families from Iceland and the maximum two‐point LOD score was given by marker D4S2974 (Z = 3.57, α = 1). Multipoint analyses of the markers in the region suggest a putative disease gene to be located between markers D4S405 and D4S2381. The maximum multipoint LOD score (Z = 3.76) was given for marker D4S2974 in combination with the novel repeat GT4C2. A family‐specific haplotype was segregating with the disease in each of eight families although a founder haplotype could not be identified. Analysis of recombination events in the patients delimited the susceptibility locus to approximately 3 cM. The susceptibility locus identified probably contains a mutation that has been enriched in the Icelandic population but is less common in other populations. We also show that this region is not identical to a susceptibility locus for SLE located on 4p16 where we detect no linkage.
Th1/Th2 Imbalance, Measured by Circulating and Intracytoplasmic Inflammatory Cytokines – Immunological Alterations in Acute Coronary Syndrome and Stable Coronary Artery Disease
Authors: Szodoray P. , Timar O. , Veres K. , Der H. , Szomjak E. , Lakos G. , Aleksza M. , Nakken B. , Szegedi G. , Soltesz P. 
Published: August 2006

AbstractTo describe how peripheral immune‐parameters reflect the inflammatory alterations of the atherosclerotic plaques in coronary atherosclerosis. We measured general inflammatory markers C‐reactive protein (CRP) and granulocyte activity, lymphocyte subpopulations and their state of activation, evaluated circulating Th1/Th2‐type cytokines, and specific intracytoplasmic cytokines. We investigated the association of immune‐parameters with disease outcome and mortality. Thirty‐three patients with acute coronary syndrome (ACS), 62 with stable coronary artery disease (CAD) and 58 healthy controls were studied. Peripheral blood lymphocyte subgroups were quantified by flow cytometry, soluble cytokines and autoantibodies were assessed using enzyme‐linked immunosorbent assay (ELISA), while intracellular cytokine levels were measured by flow cytometry after intracellular staining. We found elevated levels of CRP and granulocyte activity in ACS versus CAD (P < 0.001, P = 0.017, respectively). Natural killer (NK) cell percentages were elevated, while percentage of T cells to the total lymphocyte count was slightly decreased in ACS compared to controls (P < 0.0001, P = 0.012, respectively). Both forms of coronary atherosclerosis showed significantly higher percentages of activated T cells than controls when stained for the activation markers HLA‐DR3 and CD69+ (ACS: P < 0.0001, P = 0.002, CAD: P < 0.0001, P = 0.018, respectively). IL‐1, IL‐4 and IL‐10 proved significantly higher in ACS versus controls (P = 0.036, P = 0.01, P < 0.0001 respectively). Th1 to Th2 ratio shifted towards a Th1 dominance in both diseases. Both general proinflammatory markers and activated T cells signify CAD. The orchestrated proinflammatory cascade eventually leads to the development of the disease.
The Generation of Extracellular DNA in SLE: the Role of Death and Sex
Authors: Pisetsky D. S. , Jiang N. 
Published: August 2006

AbstractDNA is a large macromolecule that plays a central role in the pathogenesis of systemic lupus erythematosus (SLE), serving as a target antigen of autoantibodies as well as a major component of immune complexes. These complexes can both promote immune disturbances as well as deposit in the kidney to incite inflammation. While the origin of anti‐DNA autoantibodies in SLE has received intense investigation, the mechanisms by which DNA exits cells to form immune complexes in the circulation is not well understood. To determine the origin of DNA circulating in the blood in SLE, our laboratory has been using a murine model system to track the in vivo fate of DNA from Jurkat T cells that have been made apoptotic or necrotic in vitro and then administered to mice. Results of these studies indicate that DNA from apoptotic and necrotic cells appears in the blood in a time‐ and dose‐dependent manner. Irrespective of origin, this DNA has properties of nucleosomes as shown by its molecular weight. The process of release requires the presence of macrophages and can be modified by glucocorticoids as well as inflammation. In addition, sex may play a role in the generation of extracellular DNA from dead cells as male and female mice differ in their responses in this model. Together, these studies clarify the origin of extracellular DNA circulating in the blood in SLE and suggest steps in this process that can be interdicted by novel therapy.
Cicatricial ectropion: repair with myocutaneous flaps and canthopexy
Authors: Manku Kiran , Leong James K , Ghabrial Raf 
Published: August 2006

AbstractBackground:  To evaluate the effectiveness of myocutaneous upper eyelid flaps combined with canthopexy to treat cicatricial lower eyelid ectropion.Methods:  A prospective non‐comparative case series undertaken in a private practice setting. Consecutive patients with moderate lower eyelid cicatricial ectropion and upper eyelid dermatochalasis underwent transfer of a bipedicle or monopedicle flap from the upper eyelid combined with canthopexy. The main outcome measures included the occurrence of complications, eyelid position and cosmesis.Results:  Sixty‐two consecutive cases of cicatricial ectropion repair using myocutaneous flaps and canthopexy. After a mean follow up of 20 months, 58 (93.5%) of the cases had the lower lid punctum facing posterosuperior into the tear lake, showed lid globe apposition and satisfactory eyelid position. There was mild recurrence of cicatricial ectropion in four patients (6.5%). There were no cases of graft failure or granuloma formation.Conclusion:  The use of a myocutaneous flap from the upper eyelid combined with a canthopexy suspension suture for repair of cicatricial ectropion may offer good eyelid position and function. This technique has the advantage of avoiding full thickness blepharotomy and was associated with a low incidence of early recurrence.
Assisted hatching using a 1.48‐µm diode laser: Evaluation of zona opening and zona thinning techniques in human embryos
Authors: YANO KOHJI , KUBO TOSHIKO , ÔHASHI IKUKO , YANO CHIEKO 
Published: August 2006

Aim:  We assessed the effectiveness of assisted hatching using a 1.48‐µm diode laser in human embryos, comparing zona opening and zona thinning techniques.Methods:  A total of 56 day 3 embryos were assigned randomly to a zona opening group, a zona thinning group, or a control group. We then carried out assisted hatching using the OCTAX Laser Shot system (MTG Medical Technology, Altdorf, Germany) in the first two groups. In the zona opening group, the inner membrane of the zona pellucida was broken to create a full‐thickness opening. In the zona thinning group, the inner membrane of the zona pellucida was not breached. After the laser procedure, embryos were cultured to the hatched blastocyst stage.Results:  Blastocyst development rates did not differ significantly between the three groups. In the zona opening group, blastocysts were significantly more likely to hatch than those in the control group (P ≤ 0.05) and no arrested hatching of blastocysts was observed.Conclusions:  Assisted hatching using a 1.48‐µm diode laser in the zona opening technique increases the likelihood of blastocyst hatching in human embryos and does not adversely effect subsequent embryo development. (Reprod Med Biol 2006; 5: 221–226)
A meso‐level approach to the 3D numerical analysis of cracking and fracture of concrete materials
Authors: CABALLERO A. , CAROL I. , LÓPEZ C. M. 
Published: August 2006

ABSTRACTA meso‐mechanical model for the numerical analysis of concrete specimens in 3D has been recently proposed. In this approach, concrete is represented as a composite material with the larger aggregates embedded in a mortar‐plus‐aggregates matrix. Both continuum‐type components are considered linear elastic, while the possibilities of failure are provided with the systematic use of zero‐thickness interface elements equipped with a cohesive fracture constitutive law. These elements are inserted along all potential crack planes in the mesh a priori of the analysis. In this paper, the basic features of the model are summarized, and then results of calculations are presented, which include uniaxial tension and compression loading of 14‐aggregate cubical specimen along X, Y and Z axes. The results confirm the consistency of the approach with physical phenomena and well‐known features of concrete behaviour, and show low scatter when different loading directions are considered. Those cases can also be considered as different specimens subjected to the same type of loading.
MODELING THE ANNUAL PRODUCTION OF INTERTIDAL BENTHIC MICROALGAE IN ESTUARINE ECOSYSTEMS1
Authors: Pinckney James L. , Zingmark Richard G. 
Published: August 2006

ABSTRACTThe purpose of this study was to develop and validate a habitat‐specific production simulation model to quantify annual benthic microalgal production in North Inlet estuary, South Carolina. Using hourly measurements of incident irradiance during 1990–1991 as the forcing function, the simulation model was used to obtain hourly estimates of areal benthic microalgal gross primary production in five habitat types. The model, which was validated using actual measurements of production, showed good (r2= 0.63, P < 0.001) agreement between observed and predicted production in the short Spartina alterniflora Loisel zone habitats showed the highest mean hourly production (61.1 mg C m−2 h−1) while intertidal mudflats had the maximum hourly rate (166.9 mg C m−2 h−1). Daily production was highly variable, primarily due to daily fluctuations in irradiance. Annual estimates of habitat‐specific production were multiplied by the mates of habitat‐specific production were multiplied by the known area of each habitat type to determine total microalgal production for the estuary (3.423 × 109 g C yr−1). Short Spartina zone habitats provided 45% of total microalgal annual production, followed by intertidal mudflats (22%), tall Spartina zones (18%), shallow subtidal (13%) and microalgal production exceeds phytoplankton and microalgal production but is less than Spartina production.
INFECTION, GROWTH, AND COMMUNITY‐LEVEL CONSEQUENCES OF A DIATOM PATHOGEN IN A SONORAN DESERT STREAM1
Authors: Peterson Christopher G. , Dudley Tom L. , Hoagland Kyle D. , Johnson Lisa M. 
Published: August 2006

ABSTRACTWe describe effect of a pathogen that spread through a dense, rapidly growing, benthic diatom community during two infection periods (February and mid‐April 1991) in Sycamore Creek, Arizona. Infected areas appeared as gray rings within a matrix of healthy diatom growth and spread rapidly, eventually covering all benthic substrata and causing algal sloughing (within 2 wk in February and 1 wk in April). Examination of algal material with transmission electron microscopy revealed the presence of invasive bacteria within diatom cells from infected areas, suggesting a pathogenic bacterium as the most probable cause of this phenomenon. Infected area supported lower chlorophyll a concentrations and contained higher percentages of diatom cells with fragmented or reduced chloroplasts than uninfected areas. Spread of the pathogen appeared to be linked most strongly with diatom densities. The infection spread most rapidly in April, when cell densities were highest, and decimated all diatom species populations. The February infection was more species‐specific in its action, affecting large motile and rosetteforming taxa more strongly than small, adnate diatoms. This latter group likely resided at the base of communities and may have been buffered from pathogen transfer by mucilage and/or dentrital particles. Consequently, relative abundance of small, adnate diatom taxa increased in algal communities as a result of the February infection. Pathogen‐induced alteration of diatom species composition and abundance should influence primary production in this ecosystem and affect the dynamics of organisms that exploit algae as a resource.
THE FLAGELLAR APPARATUS OF CHRYSOLEPIDOMONAS DENDROLEPIDOTA (CHRYSOPHYCEAE), A SINGLE‐CELLED MONAD COVED WITH ORGANIC SCALES1
Authors: Peters Michael C. , Andersensp Robert A. 
Published: August 2006

ABSTRACTThe flagellar apparatus of Chrysolepidomonas dedrolepidota Peters et Andersen is similar to that of other members of the Ochromonadales, Chrysophyceae. there are four microtubular roots (R1‐4) and a system II fiber (= rhizoplast). the R1 root consists of three microtubules that nucleate many cytoplasmic microtubules. One compressed band of 10 or more cytoplasmic microtubules is directed black along the R1 root in an anti‐parallel direction. The R2 root consists of one to two microtubules, and it extends toward the distal end of the R1 root. The R3 root consists of six (?seven) microtubules near its proximal end. The “a” and “f” microtubules of the R3 root are under the short flagellum, and the “f” microtubule loops back and under the basal body, extending down to the nucleus. The R4 root consists of one to two microtubules extending along the left side of the shot flagellum and curving under the short flagellum where it terminates near the “a” microtubule of R3 Both flagella have a transitional plate and a transitional helix with five gyres. There is a thin, second plate in the basal body at the level of the distal end of the “c” tubules of the basal body triplets. The tripartite flagellar hairs have long lateral filaments but lack short lateral filaments. We compare the flagellar apparatus with that of other members of the Ochromonadales and members of the Hydrurales and Hibberdiales.