bluuebunny/crossref_metadata_2025 huggingface dataset:
Ion source development for various applications in Korea (invited) (abstract)
Authors: Hwang Y. S.
Published: February 2008

Ion source development in Korea has been related with various applications from accelerator to nanotechnology. Conventional ion sources such as Duoplasmatron and PIG ion sources were developed for high power proton accelerator and small cyclotron accelerators. To improve lifetime of the high current proton ion source, helicon plasma ion sources were developed with external rf antenna and applied for neutron generation in drive-in-target configuration. Negative hydrogen ion sources were also developed for tandem and cyclotron accelerators by using both rf and filament discharges. Large-area high-current ion sources for the KSTAR NBI system were developed and successfully tested for long-pulse operation of up to 300s. Several broad beam ion sources for industrial applications such as ion implantation and surface treatment were also developed by using arc, rf, and microwave discharges. Recently, ion source applications become diversified to the area of nano- and biotechnologies. For example, C60 ion source was developed for the use of bioapplications in nanometer scale. For focused ion beam as a nanofabrication tool, liquid metal ion sources were improved and a novel plasma ion source was developed by utilizing localized sheath discharges. Research and development activities of these ion sources will be discussed with short description of appropriate applications.
Magnetostructural transition in Nd5Si2.335Ge1.665
Authors: Wang H. B. , Altounian Z. , Ryan D. H. , Cadogan J. M. , Swainson I. P. , Cranswick L. M. D.
Published: February 2008

Neutron diffraction and χac data show that the first order magnetostructural transition in the Nd5SixGe4−x system takes place over a very narrow composition range (2.25<x<2.5) and does not appear to be controlled by the presence of light element impurities in the Nd metal. The structural change in Nd5Si2.335Ge1.665 is from the Gd5Si2Ge2-type monoclinic P1121∕a structure (M) (room temperature) to the Gd5Si4-type orthorhombic Pnma [O(I)] structure (low temperature).
Enhancement of normally directed light outcoupling from organic light-emitting diodes using nanoimprinted low-refractive-index layer
Authors: Jeong Soon Moon , Araoka Fumito , Machida Yoshimi , Ishikawa Ken , Takezoe Hideo , Nishimura Suzushi , Suzaki Goro
Published: February 2008

The authors have demonstrated increased light outcoupling from organic light-emitting diodes (OLEDs) based on nanoimprinted amorphous fluoropolymer, poly[perfluoro(4-vinyloxy-l-butene)] (PPFVB). Because PPFVB has a low refractive index and a high transmittance over wide wavelength range, the first-order Bragg diffracted light shows high directionality and decreased waveguide absorption. These characteristics provide an advantage for small- or medium-sized OLEDs, which are mainly viewed from the normal direction.
Discrete sums for the rapid determination of exponential decay constants
Authors: Everest Michael A. , Atkinson Dean B.
Published: February 2008

Several computational methods are presented for the rapid extraction of decay time constants from discrete exponential data. Two methods are found to be comparably fast and highly accurate. They are corrected successive integration and a method involving the Fourier transform (FT) of the data and the application of an expression that does not assume continuous data. FT methods in the literature are found to introduce significant systematic error owing to the assumption that data are continuous. Corrected successive integration methods in the literature are correct, but we offer a more direct way of applying them which we call linear regression of the sum. We recommend the use of the latter over FT-based methods, as the FT methods are more affected by noise in the original data.
Modeling of the Barkhausen jump in low carbon steel
Authors: Pérez-Benitez J. A. , Capó-Sánchez J. , Padovese L. R.
Published: February 2008

This work presents a model for the magnetic Barkhausen jump in low carbon content steels. The outcomes of the model evidence that the Barkhausen jump height depends on the coercive field of the pinning site and on the mean free path of the domain wall between pinning sites. These results are used to deduce the influence of the microstructural features and of the magnetizing parameters on the amplitude and duration of the Barkhausen jumps. In particular, a theoretical expression, establishing the dependence of the Barkhausen jump height on the carbon content and grain size, is obtained. The model also reveals the dependence of the Barkhausen jump on the applied frequency and amplitude. Theoretical and experimental results are presented and compared, being in good agreement.
Studies of the photonic and optical-frequency phonon properties of arrays of selectively grown GaN micropyramids
Authors: Coquillat D. , Le Vassor d’Yerville M. , Kazan M. , Liu C. , Watson I. M. , Edwards P. R. , Martin R. W. , Chong H. M. H. , De La Rue R. M.
Published: February 2008

An array of GaN micropyramids containing a near-surface InxGa1−xN∕GaN single quantum well has been fabricated using selective area epitaxial overgrowth above a patterned silica mask. The pyramid array has been studied by means of angle-resolved reflection measurements using s- and p-polarized incident light in the near- and mid-infrared optical ranges. We have found that the periodic array of flat-topped pyramids shows marked resonances in the near-infrared optical range due to resonant Bloch modes within the extraction cone and that the angular dispersion of these modes exhibits strong photonic crystal characteristics. The experimental results are in good agreement with the photonic band structure calculated using a scattering matrix formalism. The mid-infrared optical anisotropy properties of the micropyramids were investigated to probe the infrared active phonons of the pyramid array. The A1(LO) phonon of the InxGa1−xN∕GaN single quantum well was identified and the InN mole fraction was estimated from the mode behavior.
Half-metallic ferromagnetism in zinc-blende CaM (M=C,N)
Authors: Zhang Chang-wen
Published: February 2008

Electronic structures and magnetic properties of CaN and CaC in the zinc-blende (ZB) phase are systematically explored by using an accurate density-functional method. From the analysis of the spin-dependent density of states, band structure and magnetic moments, we predict that ZB-structure CaN and CaC at their respective equilibrium lattice constant are half-metallic (HM) ferromagnets with a magnetic moment of 1.00μB∕f.u. and 2.00μB∕f.u., respectively. Magnetism comes from spin-polarization of electrons in Ca d-orbitals and N (C) p-orbitals. We also find that their half-metallicity can be maintained within a wide range of lattice constants, which is helpful for applications in the field of spintronics.
Pitch angle scattering and effective collision frequency caused by stochastic magnetic fields
Authors: Neuer Marcus , Spatschek Karl H.
Published: February 2008

The motion of charged particles in a plasma with stochastic magnetic field lines is investigated on the basis of the so-called A-Langevin equation. In contrast to the well-known perpendicular (to an external magnetic field) transport, here the parallel transport is considered. The two cases of a strong guiding field and a weak mean magnetic field, respectively, are investigated. The A-Langevin equation is solved under the assumption that the Lagrangian correlation function for the magnetic field fluctuations is related to the Eulerian correlation function (in Gaussian form) via the Corrsin approximation. The latter is justified for small Kubo numbers. Generalizations to large Kubo numbers are discussed. It is shown that the magnetic field fluctuations are the source of diffusive motion along a strong guiding field even if binary collisions are absent. The case of small (or vanishing) mean fields is also investigated in the quasilinear limit. An effective collision frequency is derived which is consistent with the result for perpendicular quasilinear diffusion in strong guiding fields. The analytical results are checked by numerical simulations of the A-Langevin equation.
Drift-Alfvén vortices at the ion Larmor radius scale
Authors: Onishchenko O. G. , Krasnoselskikh V. V. , Pokhotelov O. A.
Published: February 2008

The theory of nonlinear drift-Alfvén waves with the spatial scales comparable to the ion Larmor radius is developed. It is shown that the set of equations describing the nonlinear dynamics of drift-Alfvén waves in a quasistationary regime admits a solution in the form of a solitary dipole vortex. The vortex structures propagating perpendicular to the ambient magnetic field faster than the diamagnetic ion drift velocity possess spatial scales larger than the ion Larmor radius, and vice versa. The variation of the vortex impedance and spatial scale as the function of the vortex velocity is analyzed. It is shown that incorporation of the finite electron temperature effects results in the appearance of a minimum in the dependence of the vortex impedance on the vortex velocity. This leads to the existence of the vortex structures with the smallest impedance. These structures are probably the most favorable energetically and can easily be excited in space plasmas. The relevance of theoretical results obtained to the Cluster observations in the magnetospheric cusp and magnetosheath is stressed.
Two-phase flow pattern transition across micropillars: Size scale effect at the microscale
Authors: Krishnamurthy Santosh , Peles Yoav
Published: February 2008

Size scale effect of adiabatic two-phase cross-flow over micropillars was experimentally investigated, and the mechanisms controlling the formation and transition of the recently discovered bridge flow was examined. A transition criterion, based on the Weber and Euler numbers, for the breakage of the bridges, is provided. The bridges break from the surface when the product of the Weber and Euler numbers is larger than ∼1; otherwise, the bridges cease to exist by coalescing with liquid slugs.
Space partitioning via Hilbert transform for symbolic time series analysis
Authors: Subbu Aparna , Ray Asok
Published: February 2008

Symbol sequence generation is a crucial step in symbolic time series analysis of dynamical systems, which requires phase-space partitioning. This letter presents analytic signal space partitioning (ASSP) that relies on Hilbert transform of the observed real-valued data sequence into the corresponding complex-valued analytic signal. ASSP yields comparable performance as other partitioning methods, such as symbolic false nearest neighbor partitioning (SFNNP) and wavelet-space partitioning (WSP). The execution time of ASSP is several orders of magnitude smaller than that of SFNNP. Compared to WSP, the ASSP algorithm is analytically more rigorous and is approximately five times faster.
Structural evolution of a high Tc ferroelectric (x)Bi(Zn1∕2Ti1∕2)O3–(1−x)PbTiO3 solid solution
Authors: Zhang X. D. , Kwon Daeyoung , Kim Bog G.
Published: February 2008

We have studied the structural phase transition of solid solutions (x)Bi(Zn1∕2Ti1∕2)O3–(1−x)PbTiO3. The temperature evolution of the x-ray diffraction patterns of the θ-2θ scans around {110} has been performed to check the structural phase transitions: The (101)∕(011) peak shifts to a larger value, while the (110) peak shifts to a smaller value with increasing temperature. Finally, the peaks merge to the same value at the Curie temperature, indicating a tetragonal to the cubic phase transition. The structural phase transition temperature Tc coincides with the Curie temperature and increases as the increasing Bi(Zn1∕2Ti1∕2)O3 composition (x). The evolution of the lattice constant, unit cell volume, and tetragonality as functions of temperature and composition is discussed.
Terahertz wave generation from a dc-biased multimode laser
Authors: Latkowski Sylwester , Surre Frederic , Landais Pascal
Published: February 2008

We present results achieved in the generation of terahertz wave by a semiconductor laser. It is a Fabry–Pérot based device with shallow grooves implemented on its p-side to engineer the longitudinal mode spectrum. The laser is dc-biased and temperature controlled at 298K. The main two modes are separated by 3nm at 1550nm with a side-mode-suppression ratio of 25dB. Using a frequency resolved optical gating, evidence of mode beating at 373GHz is observed. With a bolometer interfaced to a Fourier transform interferometer, the second harmonic signal is measured at 690GHz.
Near-infrared luminescent polymer waveguide with a 20dB small-signal gain
Authors: Djiango Martin , Kobayashi Takeyuki , Blau Werner J. , Cai Bin , Komatsu Kyoji , Kaino Toshikuni
Published: February 2008

Near-infrared optical gain in luminescent polymeric slab asymmetric waveguides has been investigated by use of amplified spontaneous emission. Upon nanosecond photopumping, the waveguides have shown a small-signal gain coefficient of 37.2±2.1cm−1 at 820nm for a pump fluence of 1.57mJ∕cm2 (314kW∕cm2). The loss coefficient and transparency fluence have been found to be 7.3±1.0cm−1 at 820nm and 0.14mJ∕cm2 (28kW∕cm2), respectively. Furthermore, we show that a small-signal gain of 19.7±2.3dB is achievable in a 1.2-mm-long waveguide.
New analysis of electron energy exchange and cooling in semiconductors
Authors: Chung M. S. , Hong S. C. , Mayer A. , Cutler P. H. , Weiss B. L. , Miskovsky N. M.
Published: February 2008

Energy exchange Δε is investigated in field emission from semiconductors. For the first time, a formal theory is developed for the replacement process of the injected charge carriers. It leads to analytic expressions for Δε, which exhibit the dependence on field, temperature, and doping concentration in a parametric form. The analytic and numeric results reveal the important feature that Δε is positive for all temperatures. This implies that field emission from semiconductors always produces cooling of an emitter. When Joule heating is included, there is still a net cooling for a wide range of emitted current densities.
Simulating and interpreting Kelvin probe force microscopy images on dielectrics with boundary integral equations
Authors: Shen Yongxing , Barnett David M. , Pinsky Peter M.
Published: February 2008

Kelvin probe force microscopy (KPFM) is designed for measuring the tip-sample contact potential differences by probing the sample surface, measuring the electrostatic interaction, and adjusting a feedback circuit. However, for the case of a dielectric (insulating) sample, the contact potential difference may be ill defined, and the KPFM probe may be sensing electrostatic interactions with a certain distribution of sample trapped charges or dipoles, leading to difficulty in interpreting the images. We have proposed a general framework based on boundary integral equations for simulating the KPFM image based on the knowledge about the sample charge distributions (forward problem) and a deconvolution algorithm solving for the trapped charges on the surface from an image (inverse problem). The forward problem is a classical potential problem, which can be efficiently solved using the boundary element method. Nevertheless, the inverse problem is ill posed due to data incompleteness. For some special cases, we have developed deconvolution algorithms based on the forward problem solution. As an example, this algorithm is applied to process the KPFM image of a gadolinia-doped ceria thin film to solve for its surface charge density, which is a more relevant quantity for samples of this kind than the contact potential difference (normally only defined for conductive samples) values contained in the raw image.
Capacitance transient study of the influence of iron contamination on the electrical characteristics of silicon grain boundaries
Authors: Lu Jinggang , Rozgonyi George
Published: February 2008

The influence of iron contamination on the electrical characteristics of an interfacial grain boundary created by bonding two (110)∕(100) silicon wafers was examined by a capacitance transient technique. Compared with the clean sample, iron contamination increases both the density of boundary states (by at least three times) and the zero-bias barrier height (by 70meV), while dramatically reducing by two orders of magnitude the electron/hole capture cross-section ratio. These results suggest that a larger barrier will be sustained at the iron contaminated boundary under low injection condition, thereby enabling more effective minority carrier collection and associated enhanced recombination activity.
Nanometer-scale mapping and single-molecule detection with color-coded nanoparticle probes
Authors: Agrawal Amit , Deo Rajesh , Wang Geoffrey D. , Wang May D. , Nie Shuming
Published: February 2008

We report a method for single-molecule detection and biomolecular structural mapping based on dual-color imaging and automated colocalization of bioconjugated nanoparticle probes at nanometer precision. In comparison with organic dyes and fluorescent proteins, nanoparticle probes such as fluorescence energy-transfer nanobeads and quantum dots provide significant advantages in signal brightness, photostability, and multicolor-light emission. As a result, we have achieved routine two-color superresolution imaging and single-molecule detection with standard fluorescence microscopes and inexpensive digital color cameras. By using green and red nanoparticles to simultaneously recognize two binding sites on a single target, individual biomolecules such as nucleic acids are detected and identified without target amplification or probe/target separation. We also demonstrate that a powerful astrophysical method (originally developed to analyze crowded stellar fields) can be used for automated and rapid statistical analysis of nanoparticle colocalization signals. The ability to rapidly localize bright nanoparticle probes at nanometer precision has implications not only for ultrasensitive medical detection but also for structural mapping of molecular complexes in which individual components are tagged with color-coded nanoparticles.
TDP-43 regulates retinoblastoma protein phosphorylation through the repression of cyclin-dependent kinase 6 expression
Authors: Ayala Youhna M. , Misteli Tom , Baralle Francisco E.
Published: February 2008

TDP-43 (for
T
AR
D
NA binding
p
rotein) is a highly conserved heterogeneous nuclear ribonucleoprotein (hnRNP) involved in specific pre-mRNA splicing and transcription events. TDP-43 recently has been identified as the main component of cytoplasmic inclusions in frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS), two neurodegenerative disorders. The cellular role of this protein remains to be identified. Here, we show that loss of TDP-43 results in dysmorphic nuclear shape, misregulation of the cell cycle, and apoptosis. Removal of TDP-43 in human cells significantly increases cyclin-dependent kinase 6 (Cdk6) protein and transcript levels. The control of Cdk6 expression mediated by TDP-43 involves GT repeats in the target gene sequence. Cdk6 up-regulation in TDP-43-depleted cells is accompanied by an increase in phosphorylation of two of its major targets, the retinoblastoma protein pRb and pRb-related protein pRb2/p130. TDP-43 silencing also is followed by changes in the expression levels of several factors that control cell proliferation. Morphological nuclear defects and increased apoptosis upon TDP-43 loss are mediated via the pRb pathway because pRb-negative cells (Saos-2) do not undergo programmed cell death or nuclear shape deformation upon TDP-43 removal. Our results identify a regulatory target of TDP-43 and show that TDP-43 depletion has important consequences in essential metabolic processes in human cells.
No association between maternal recurrent genital herpes in pregnancy and higher risk for congenital abnormalities
Authors: ÁCS NÁNDOR , BÁNHIDY FERENC , PUHÓ ERZSÉBET , CZEIZEL ANDREW E.
Published: February 2008

Objective. To study the possible links between recurrent symptomatic genital herpes during pregnancy and risk for congenital abnormalities (CAs). Method. The occurrence of prospectively and medically‐recorded recurrent genital herpes during pregnancy in the mothers of cases with different congenital abnormalities and in the mothers of matched controls without CAs was compared in the population‐based large data set of the Hungarian Case‐Control Surveillance System of Congenital Abnormalities. Results. Of 22,843 cases with CAs, 59 (0.26%) were born to mothers with recurrent symptomatic genital herpes, while of 38,151 control newborns without CAs, 86 (0.23%) were born to mothers with recurrent genital herpes during the study pregnancy (adjusted OR: 1.1, 95% CI: 0.8–1.6). Pregnant women with clinically recognised recurrent genital herpes in the first trimester of pregnancy are not linked with a higher risk for any CAs. Conclusion. Recurrent genital herpes during pregnancy does not associate with a higher risk of CAs.
Tocolytic effectiveness of nifedipine versus ritodrine and follow‐up of newborns: a randomised controlled trial
Authors: VAN DE WATER M. , TIMMERMAN‐VAN KESSEL E. , DE KLEINE M.J. , OEI S.G.
Published: February 2008

Background. Several studies have demonstrated the superior tocolytic effectiveness of nifedipine over ritodrine. Only 1 trial conducted a long‐term follow‐up of newborns and found no difference in psychosocial and motor functioning. In a randomised, multicentre trial, we compared the tocolytic effectiveness of nifedipine and ritodrine and included a long‐term follow‐up of the newborns after 2 years of age. Methods. Patients with imminent preterm labour were randomised and received either nifedipine or ritodrine. Side‐effects, tocolytic effectiveness and neonatal outcome were studied. Development of the children was studied after the age of 2 years by a parental questionnaire. Results. Ninety‐three patients were included. Birth was postponed for an average of 4.3 weeks in the ritodrine group and 5.0 weeks in the nifedipine group (p = 0.4). Patients who received ritodrine experienced significantly more side‐effects compared to patients who received nifedipine (29 versus 4%, p<0.05). No significant differences were found in either group for average birth weight, Apgar scores after 1 min, neonatal intensive care unit (NICU) admission and neonatal complications. Parental questionnaires after 2 years had a response rate of 70%. Two‐thirds of the children had developed normally in both groups. In both groups, only a few children were severely retarded (n = 4). No significant differences in development were found between the 2 groups. Conclusions. Both nifedipine and ritodrine proved effective tocolytic drugs, however ritodrine caused significantly more maternal side‐effects. Neonatal outcome and long‐term development after 2 years of age were not significantly different. We favour nifedipine over ritodrine as a tocolytic drug.
Adenocarcinoma of the uterine cervix: prognostic significance of clinicopathologic parameters, flow cytometry analysis and HPV infection
Authors: DABIĆ MIRELA M. , NOLA MARIN , TOMIČIĆ IVANA , DOTLIĆ SNJEŽANA , PETROVEČKI MARKO , JUKIĆ STANKO
Published: February 2008

Background. This study was designed to determine the possible impact of status of human papillomavirus (HPV) infection (no infection, single, multiple infections) on the survival of patients with cervical adenocarcinoma, to correlate the HPV status with other clinicopathologic parameters, and to examine clinical, histological and flow cytometric parameters as predictors of survival in cervical adenocarcinoma. Methods. The clinical data of 51 patients with adenocarcinoma of the cervix who were treated at the Department of Gynecology and Obstetrics, Zagreb University School of Medicine, from 1978 to 2004 were analysed: age at presentation, menstrual status, clinical stage, relapse, survival. Exact histologic subtype, architectural grade and nuclear grade were determined. DNA flow cytometry was performed to determine DNA ploidy and proliferative index. Polymerase chain reaction (SPF primers), followed by reverse hybridisation for genotyping, was used to determine the HPV status. Results. The status of HPV infection had no impact on patient survival, and could not be correlated with any of the analysed clinicopathologic parameters. Univariate analysis showed significant association between patient survival and clinical stage (p = 0.002) and architectural grade (p = 0.033). Multivariate analysis confirmed both parameters as significantly associated with survival. Menstrual status, nuclear grade, DNA ploidy and proliferative activity had no impact on patient survival. Conclusion. Clinical stage and architectural grade are significant predictors for survival of patients with cervical adenocarcinoma. Status of HPV infection, flow cytometric parameters, nuclear grade and menstrual status do not predict patient survival.
Responding to Simulated Pandemic Influenza in San Antonio, Texas
Authors: Miller George , Randolph Stephen , Patterson Jan E.
Published: February 2008

Objective.

To describe the results of a simulation study of the spread of pandemic influenza, the effects of public health measures on the simulated pandemic, and the resultant adequacy of the surge capacity of the hospital infrastructure and to investigate the adequacy of key elements of the national pandemic influenza plan to reduce the overall attack rate so that surge capacity would not be overwhelmed.

Design.

We used 2 discrete-event simulation models: the first model simulates the contact and disease transmission process, as affected by public health interventions, to produce a stream of arriving patients, and the second model simulates the diagnosis and treatment process and determines patient outcomes.

Setting.

Hypothetical scenarios were based on the response plans, infrastructure, and demographic data of the population of San Antonio, Texas.

Results.

Use of a mix of strategies, including social distancing, antiviral medications, and targeted vaccination, may limit the overall attack rate so that demand for care would not exceed the capacity of the infrastructure. Additional simulations to assess social distancing as a sole mitigation strategy suggest that a reduction of infectious community contacts to half of normal levels would have to occur within approximately 7 days.

Conclusions.

Under ideal conditions, the mix of strategies may limit demand, which can then be met by community surge capacity. Given inadequate supplies of vaccines and antiviral medications, aggressive social distancing alone might allow for the control of a local epidemic without reliance on outside support.
From pull-down data to protein interaction networks and complexes with biological relevance
Authors: Zhang Bing , Park Byung-Hoon , Karpinets Tatiana , Samatova Nagiza F.
Published: February 2008

Motivation:  Recent improvements in high-throughput Mass Spectrometry (MS) technology have expedited genome-wide discovery of protein–protein interactions by providing a capability of detecting protein complexes in a physiological setting. Computational inference of protein interaction networks and protein complexes from MS data are challenging. Advances are required in developing robust and seamlessly integrated procedures for assessment of protein–protein interaction affinities, mathematical representation of protein interaction networks, discovery of protein complexes and evaluation of their biological relevance.

Results: A multi-step but easy-to-follow framework for identifying protein complexes from MS pull-down data is introduced. It assesses interaction affinity between two proteins based on similarity of their co-purification patterns derived from MS data. It constructs a protein interaction network by adopting a knowledge-guided threshold selection method. Based on the network, it identifies protein complexes and infers their core components using a graph-theoretical approach. It deploys a statistical evaluation procedure to assess biological relevance of each found complex. On Saccharomyces cerevisiae pull-down data, the framework outperformed other more complicated schemes by at least 10% in F1-measure and identified 610 protein complexes with high-functional homogeneity based on the enrichment in Gene Ontology (GO) annotation. Manual examination of the complexes brought forward the hypotheses on cause of false identifications. Namely, co-purification of different protein complexes as mediated by a common non-protein molecule, such as DNA, might be a source of false positives. Protein identification bias in pull-down technology, such as the hydrophilic bias could result in false negatives.

Contact:  samatovan@ornl.gov

Supplementary information: Supplementary data are available at Bioinformatics online.
AIMIE: a web-based environment for detection and interpretation of significant sequence motifs in prokaryotic genomes
Authors: Mrázek Jan , Xie Shaohua , Guo Xiangxue , Srivastava Anuj
Published: February 2008

Motivation: Genomes contain biologically significant information that extends beyond that encoded in genes. Some of this information relates to various short dispersed repeats distributed throughout the genome. The goal of this work was to combine tools for detection of statistically significant dispersed repeats in DNA sequences with tools to aid development of hypotheses regarding their possible physiological functions in an easy-to-use web-based environment.

Results:  Ab Initio Motif Identification Environment (AIMIE) was designed to facilitate investigations of dispersed sequence motifs in prokaryotic genomes. We used AIMIE to analyze the Escherichia coli and Haemophilus influenzae genomes in order to demonstrate the utility of the new environment. AIMIE detected repeated extragenic palindrome (REP) elements, CRISPR repeats, uptake signal sequences, intergenic dyad sequences and several other over-represented sequence motifs. Distributional patterns of these motifs were analyzed using the tools included in AIMIE.

Availability: AIMIE and the related software can be accessed at our web site http://www.cmbl.uga.edu/software.html.

Contact:  mrazek@uga.edu
Hochuekkito, a Kampo (Traditional Japanese Herbal) Medicine, and its Polysaccharide Portion Stimulate G‐CSF Secretion from Intestinal Epithelial Cells
Authors: Matsumoto Tsukasa , Moriya Michiyo , Kiyohara Hiroaki , Tabuchi Yoshiaki , Yamada Haruki
Published: February 2008

Kampo (traditional Japanese herbal) medicines are taken orally due to which the gastric mucosal immune system may act as one of the major targets for the expression of pharmacological activity. The inner surface of the intestinal tract possesses a large area of mucosal membranes, and the intestinal epithelial cells sit at the interface between a lumen and a lymphocyte‐rich lamina propria. The cross talk that occurs between these compartments serves to maintain intestinal homeostasis, and the cytokine network plays an important role in the cross talk. In this study, the effect of Hochuekkito (HET), one of Kampo medicines, on cytokine secretion of intestinal epithelial cells was investigated. When murine normal colonic epithelial cell‐line MCE301 cells were stimulated with HET, the contents of granulocyte colony‐stimulating factor (G‐CSF) in the conditioned medium were significantly increased in dose‐ and time‐dependent manners. The enhanced G‐CSF gene transcription in MCE301 cells by the stimulation of HET was observed by RT‐PCR. The enhanced G‐CSF secretion by HET was also observed in C3H/HeJ mice‐derived primary cultured colonic epithelial cells. When the HET was fractionated, only the polysaccharide fraction (F‐5) enhanced the G‐CSF secretion of MCE301 cells, and the activity of F‐5 lost after the treatment of periodate that can degrade the carbohydrate moiety. These results suggest that HET enhances secretion of G‐CSF from colonic epithelial cells and the polysaccharide is one of the active ingredients of HET. The enhanced G‐CSF secretion by HET may partly contribute to the clinically observed various pharmacological activities of HET including immunomodulating activity.
Aspects of Sino‐Japan Complementary and Alternative Medicine and Development on the Traditional Uighur Medicine
Authors: Yusup Abdiryim , Yamaguchi Nobuo
Published: February 2008

Two consecutive conferences on ‘Sino‐Japan Complementary and Alternative Medicine and Development on the Traditional Uighur Medicine’ were held in Xinjiang Medical University on July 3 and Kanazawa Medical University on October 6, 2007. The Vice president Halmurat Upur presided over the meeting and gave congratulatory address on holding of the conference. In order to understand mutually and discuss the possibility of the Uighur Medicine as CAM and the situation of medicine in the global sense, specialist scholars of Traditional Uighur Medicine and postgraduates attended this conference. In the meeting of the CAM, the achievements on the research of Traditional Uighur Medicine were exchanged and warmly discussed. Presentations were made in the consecutive conference.
Effects of Satureja khuzestanica on Serum Glucose, Lipids and Markers of Oxidative Stress in Patients with Type 2 Diabetes Mellitus: A Double‐Blind Randomized Controlled Trial
Authors: Vosough-Ghanbari Sanaz , Rahimi Roja , Kharabaf Shabnam , Zeinali Shima , Mohammadirad Azadeh , Amini Somayeh , Yasa Nargues , Salehnia Alinazar , Toliat Tayebeh , Nikfar Shekoufeh , Larijani Bagher , Abdollahi Mohammad
Published: February 2008

Satureja khuzestanica is an endemic plant of Iran that is widely distributed in the Southern part of the country. It has antioxidant properties and thus it seems to be useful in diseases related to oxidative stress such as diabetes and hyperlipidemia. The present study investigates the effect of S. khuzestanica supplement in metabolic parameters of hyperlipidemic patients with type 2 diabetes mellitus. Twenty‐one hyperlipidemic patients with type 2 diabetes mellitus were randomized in a double blind, placebo controlled clinical trial to receive either S. khuzestanica (tablets contain 250 mg dried leaves) or placebo once a day for 60 days. Blood samples were obtained at baseline and at the end of the study. Samples were analyzed for levels of glucose, total cholesterol, LDL‐cholesterol, HDL‐cholesterol, triglyceride, creatinine, thiobarbituric acid reactive substances (TBARS) as marker of lipid peroxidation and ferric reducing ability (total antioxidant power, TAP). Treatment of patients by S. khuzestanica for 60 days induced significant decrease in total cholesterol (P = 0.008) and LDL‐cholesterol (P = 0.03) while increased HDL‐cholesterol (P = 0.02) and TAP (P = 0.007) in comparison with the baseline values. S. khuzestanica did not alter blood glucose, triglyceride, creatinin and TBARS levels. In comparison with baseline values, no significant change was observed in blood glucose, total cholesterol, LDL‐cholesterol, HDL‐cholesterol, triglyceride, creatinine, TBARS and TAP in placebo‐treated group. Usage of S. khuzestanica as a supplement to drug regimen of diabetic type 2 patients with hyperlipidemia is recommended.
Growth and biochemical responses of the offspring of mussels directly affected by the “Prestige” oil spill
Authors: Peteiro Laura G. , Filgueira Ramón , Labarta Uxío , Fernández-Reiriz María José
Published: February 2008

Peteiro, L. G., Filgueira, R., Labarta, U., and Fernández-Reiriz, M. J. 2008. Growth and biochemical responses of the offspring of mussels directly affected by the “Prestige” oil spill. – ICES Journal of Marine Science, 65: 509–513. We investigated whether perturbations to growth and biochemistry, detected in Mytilus galloprovincialis mussel seed cultured after the “Prestige” oil spill (2003), were evident in its offspring (2004). Sublethal effects in the 2003 mussels or, alternatively, direct exposure to remobilization of fuel on the seabed, might have detrimental effects on mussel juveniles in 2004. However, the absence of differences in lipid composition and growth performance between mussel seed gathered from the area most affected by the spill (Pindo) and the reference population (Miranda) seems to indicate the absence of sublethal effects related to hydrocarbon exposure in the offspring of mussels directly exposed to the “Prestige” oil spill.
Arabidopsis PPR40 Connects Abiotic Stress Responses to Mitochondrial Electron Transport
Authors: Zsigmond Laura , Rigó Gábor , Szarka András , Székely Gyöngyi , Ötvös Krisztina , Darula Zsuzsanna , Medzihradszky Katalin F. , Koncz Csaba , Koncz Zsuzsa , Szabados László
Published: February 2008

Oxidative respiration produces adenosine triphosphate through the mitochondrial electron transport system controlling the energy supply of plant cells. Here we describe a mitochondrial pentatricopeptide repeat (PPR) domain protein, PPR40, which provides a signaling link between mitochondrial electron transport and regulation of stress and hormonal responses in Arabidopsis (Arabidopsis thaliana). Insertion mutations inactivating PPR40 result in semidwarf growth habit and enhanced sensitivity to salt, abscisic acid, and oxidative stress. Genetic complementation by overexpression of PPR40 complementary DNA restores the ppr40 mutant phenotype to wild type. The PPR40 protein is localized in the mitochondria and found in association with Complex III of the electron transport system. In the ppr40-1 mutant the electron transport through Complex III is strongly reduced, whereas Complex IV is functional, indicating that PPR40 is important for the ubiqinol-cytochrome c oxidoreductase activity of Complex III. Enhanced stress sensitivity of the ppr40-1 mutant is accompanied by accumulation of reactive oxygen species, enhanced lipid peroxidation, higher superoxide dismutase activity, and altered activation of several stress-responsive genes including the alternative oxidase AOX1d. These results suggest a close link between regulation of oxidative respiration and environmental adaptation in Arabidopsis.
Iron-Induced Turnover of the Arabidopsis IRON-REGULATED TRANSPORTER1 Metal Transporter Requires Lysine Residues
Authors: Kerkeb Loubna , Mukherjee Indrani , Chatterjee Iera , Lahner Brett , Salt David E. , Connolly Erin L.
Published: February 2008

Iron is an essential micronutrient but is toxic if accumulated at high levels. Thus, iron uptake and distribution in plants are controlled by precise regulatory mechanisms. IRON-REGULATED TRANSPORTER1 (IRT1) is the major high affinity iron transporter responsible for iron uptake from the soil in Arabidopsis (Arabidopsis thaliana). Previously, we showed that IRT1 is subject to posttranscriptional regulation; when expressed from the constitutive cauliflower mosaic virus 35S promoter, IRT1 protein accumulates only in iron-deficient roots. IRT1 contains an intracellular loop that may be critical for posttranslational regulation by metals. Of particular interest are a histidine (His) motif (HGHGHGH) that might bind metals and two lysine residues that could serve as attachment sites for ubiquitin. We constructed a set of mutant IRT1 alleles: IRT1H154Q, IRT1H156Q, IRT1H158Q, IRT1H160Q, IRT14HQ (quadruple His mutant), IRT1K146R, IRT1K171R, and a double mutant (IRT1K146R,K171R). Mutation of the His or lysine residues did not eliminate the ability of IRT1 to transport iron or zinc. Expression of each of the IRT1 variants and an IRT1intact construct in plants from the 35S promoter revealed that either K146 or K171 is required for iron-induced protein turnover, and 35S-IRT1K146R,K171R plants contain higher levels of iron as compared to 35S-IRT1 and wild type. Furthermore, accumulation of metals in 35S-IRT1K146R,K171R plants was not associated with an increase in ferric chelate reductase activity; this result indicates that, at least under conditions when iron is abundant, reduction of ferric iron may not be the rate-limiting step in iron uptake by strategy I plants such as Arabidopsis.
Structural dependencies of protein backbone 2JNC′ couplings
Authors: Juranić Nenad , Dannenberg J.J. , Cornilescu Gabriel , Salvador Pedro , Atanasova Elena , Ahn Hee‐Chul , Macura Slobodan , Markley John L. , Prendergast Franklyn G.
Published: February 2008

Protein folding can introduce strain in peptide covalent geometry, including deviations from planarity that are difficult to detect, especially for a protein in solution. We have found dependencies in protein backbone 2JNC′ couplings on the planarity and the relative orientation of the sequential peptide planes. These dependences were observed in experimental 2JNC′ couplings from seven proteins, and also were supported by DFT calculations for a model tripeptide. Findings indicate that elevated 2JNC′ couplings may serve as reporters of structural strain in the protein backbone imposed by protein folds. Such information, supplemented with the H‐bond strengths derived from h3JNC′ couplings, provides useful insight into the overall energy profile of the protein backbone in solution.
Dopant Distribution in Grain‐Boundary Films in Calcia‐Doped Silicon Nitride Ceramics
Authors: Gu Hui , Pan Xiaoqing , Cannon Rowland M. , Rühle Manfred
Published: February 2008

Quantitative analyses of the local chemistry of amorphous films at the grain boundary (GB) were taken on hot isostatically pressed high‐purity Si3N4 doped with various amounts of calcium (up to 450 ppm). This work was mainly accomplished by using spatially resolved electron energy‐loss spectroscopy (EELS) in a dedicated scanning transmission electron microscope. The amount of calcium segregation, quantified in terms of GB excess, saturated in the films at a bulk‐doping level of ∼220 ppm. Extra additives did not stay at the triple‐point glass pockets, where the calcium was almost expelled completely; instead, the additives stayed at intersections between the films and pockets. Otherwise, the calcium distribution was uniform along and across GB films. The latter was determined from simulations of EELS profiling. At grain/pocket interfaces, a much‐lower segregation level occurred, ranging from one‐half to one‐tenth of the level at the GB. This observation indicates different segregation mechanisms in the two cases. Also, the calcium segregation in GB films changed the film composition dramatically, because more N3− ions were introduced and replaced O2− ions, to maintain the local stoichiometry. Reduction of the Van der Waals force has been proposed as being the origin of the film expansion with increasing calcium content.
Influence of Additives on Slag Resistance of Al2O3‐SiO2‐SiC‐C Refractory Bond Phases under Reducing Atmosphere
Authors: Chan Chen‐Feng , Argent Bernard B. , Lee William E.
Published: February 2008

The microstructures of Al2O3–SiO2–SiC–C refractory matrices with aluminum, silicon, Si3N4, BN, B2O3, and B4C additives are characterized before and after a crucible slag test, and the phases present are compared to those expected at thermodynamic equilibrium. The carbon content dominates the resistance to CaO–MgO–Al2O3–SiO2 slag penetration, while the viscosity of liquid phases present has a significant influence when the matrix carbon contents are similar. Silicon and Si3N4 additives reduce slag penetration resistance because of indirect oxidation of carbon to form SiC. B4C, in particular, and B2O3 also reduce slag penetration resistance because of formation of a more fluid boron‐containing liquid, while aluminum and BN addition have no significant effect. Carbon and BN hardly react with the slag, while SiC partially reacts with it, leading to deposition of carbon as a dense layer. Corundum present in the refractories also readily dissolves in the slag. Microstructurally, slag penetration resistance is associated with the dense carbon layer located at the slag‐refractory interface.
Simulation of Cold Compaction Densification Behavior of Silicon Nitride Ceramic Powder
Authors: Sun Xue‐Kun , Kim Ki‐Tae , Wang Guo‐Dong
Published: February 2008

The cold‐compaction densification behavior of silicon nitride (Si3N4) ceramic powder was analyzed using two models: the Shima model and the Cam‐Clay model. Triaxial‐compression experimental data were used to evaluate these two models. Shima models that used Si3N4 matrix material with different yield stresses were discussed. It is clear that the Cam‐Clay model can effectively simulate the cold‐compaction densification behavior of Si3N4 ceramic powder. The Shima model that used a very high yield stress for the Si3N4 matrix material slightly overestimated the experimental data, and the Shima model that used the actual yield stress for Si3N4 matrix material largely overestimated that data.
Effect of Lubricant on the Surface Structure of Aluminosilicate Fibers
Authors: Mitchell Brian S. , Fondeur Fernando , Xiao Zhijun , Li Wenyan , Bennett Stacey
Published: February 2008

Commercial aluminosilicate fibers of the nominal composition 45 wt% Al2O3, 54 wt% SiO2 have similar bulk properties but different surface chemistries, depending on whether they were formed with (WL) or without (NL) the aid of a mineral‐oil lubricant. Both fiber samples are X‐ray amorphous as formed; they have similar crystallization temperatures and have activation energies for crystallization of 751 and 854 kJ/mol for samples NL and WL, respectively. Fiber surface properties differ markedly, as indicated by diffuse reflectance infrared transmission spectroscopy and X‐ray photoelectron spectroscopy. These techniques show that carbon from the lubricant degradation and/or combustion is incorporated into the melt, whereupon it reacts with nonbonding oxygens in the Al‐O network to form network carbonates.
Interfacial Structure of Disordered‐Ordered Domain Boundaries in Lanthanum‐Doped Barium Magnesium Niobate
Authors: Lee Hwack Joo , Park Hyun Min , Ryu Hyun , Paik Jong Hoo , Nahm Sahn , Byun Jae‐Dong
Published: February 2008

Microstructural studies on the interfacial boundaries of disordered and 1:2 ordered domains in lanthanum‐doped (Ba0.975La0.025)(Mg0.34Nb0.66)O3 were performed using high‐resolution transmission electron microscopy and synchrotron powder X‐ray diffractometry. Disordered and 1:2 ordered domains both coexisted in a single grain. Each domain occupied its own region, and the interfaces were atomically sharp and coherent. The wavelength of the superlattice modulation in the 1:2 ordered domain was ∼0.71 nm. The transition from the 1:2 ordered region to the disordered one could be differentiated at the interface by using the superlattice modulations in the 1:2 ordered domain. From these observations, a deducible interfacial model also was presented.
Amorphous Silicoboron Carbonitride Ceramic with Very High Viscosity at Temperatures above 1500°C
Authors: Riedel Ralf , Ruswisch Lutz M. , An Linan , Raj Rishi
Published: February 2008

Recently, the viscosity of a predominantly amorphous silicon carbonitride (Si1.7C1.0±0.1N1.5) alloy with an apparent glass‐transition temperature (Tg) of 1400°–1500°C was studied. In this study, the creep behavior of silicoboron carbonitride (Si2B1.0C3.4N2.3), which seems to have a Tg value of >1700°C, was examined. Both materials exhibited a three‐stage creep behavior. In stage I, the creep rate declined, because of densification. In stage II, the strain rate approaches a steady state. In stage III, it resumes a declining strain rate, which ultimately decreased below the measurement limit of the system. At 1550°C in stage II, the viscosity of silicoboron carbonitride was six orders of magnitude higher than that of fused silica. Among the Si‐C‐N ceramics, only chemical‐vapor‐deposited and reaction‐bonded silicon carbides seem to have greater creep resistance than the silicoboron carbonitrides at temperatures >1550°C.