bluuebunny/crossref_metadata_2025 huggingface dataset:
Prostate cell lines secrete IL‐8 in response to mycoplasma hominis through Toll‐like receptor 2‐mediated mechanism
Authors: Takeyama Koh , Mitsuzawa Hiroaki , Shimizu Takeyuki , Konishi Masanori , Nishitani Chiaki , Sano Hitomi , Kunishima Yasuharu , Matsukawa Masanori , Takahashi Satoshi , Shibata Ken‐ichiro , Tsukamoto Taiji , Kuroki Yoshio
Published: November 2005

Background

The roles of Toll‐like receptor 2 (TLR2) and Mycoplasma in prostate inflammation remain unclear. We investigated whether Mycoplasma induced inflammatory cytokine secretion through TLR2‐mediated mechanism in prostate cancer cell line.

Methods

Cell surface expression of TLR2 on PC‐3 cells were examined by flowcytometry. PC‐3 cells were stimulated with Mycoplasma hominis (M. hominis), and IL‐8 secretion and NF‐κB activation were examined.

Results

PC‐3 cells expressed TLR2 mRNA and cell surface TLR2 protein. The membrane fraction of M. hominis induced IL‐8 secretion from PC‐3 cells and NF‐κB activation in a concentration‐dependent manner. Transient transfection of the dominant negative mutant TLR2P681H into PC‐3 cells attenuated M. hominis‐induced IL‐8 secretion and NF‐κB activation. Antibody against the extracellular TLR2 domain significantly suppressed M. homnis‐induced IL‐8 secretion from the prostate cell lines including PC‐3, PrEC, and transformed myofibroblasts.

Conclusions

These results clearly demonstrate that the prostate cell line can secrete inflammatory cytokine in response to M. hominis through a TLR2‐mediated mechanism. © 2005 Wiley‐Liss, Inc.
Comparative structure–function analysis of cytolethal distending toxins
Authors: Hu Xin , Nesic Dragana , Stebbins C. Erec
Published: November 2005

Cytolethal distending toxins (CDTs) constitute a family of bacterial proteins that enter eukaryotic cells with genotoxic activity leading to cell cycle arrest and apoptosis. CDTs are widespread, having been found in a variety of Gram‐negative pathogens with a broad tissue tropism. The recently determined crystal structure of the Haemophilus ducreyi CDT provides a powerful starting point for analysis of the structure and function in this toxin family. In this study, we apply comparative modeling and structural analysis to extend the experimental structural information to multiple CDT toxins from a diverse species. Analysis of structurally and functionally important residues in the active subunit, CdtB, and putative cell delivery elements, CdtA and CdtC, begins to establish the fundamental, mechanistic elements of this unique holotoxin. The results reveal that key structural features with important functional consequences are highly conserved across different CDTs, providing a blueprint for directed examination of functional hypotheses in a variety of pathogenic contexts. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Electrical barriers in the ZnO varistor grain boundaries
Authors: Alim Mohammad A. , Li Shengtao , Liu Fuyi , Cheng Pengfei
Published: November 2005

In this paper a detailed nature of the electrical potential barriers in ZnO based varistors are presented. The excellent nonlinear current–voltage (I–V) characteristic of these varistors is attributed to the potential barriers formed between the successive ZnO grains during the processing cycle. These grain boundaries in the microstructure results in a few device‐related parameters such as built‐in‐potential, barrier height, barrier width, grain carrier density, Fermi level position in the grains, etc. Thermal activation energy is determined from the status of the leakage current of this device. Substantial studies conducted to comprehend possible conduction processes in the grain boundary regions under applied bias (electric field). It is understood that electron transport dominate the grain boundary regions based on electrical potential barrier consideration across the grain boundaries. The free electrons overcome potential barrier at elevated temperatures as well as under bias. These carriers fill trap sites (charged defect states) both in the bulk ZnO and in the grain surfaces (surface states). The formation of space charge region within the successive ZnO grains across the grain boundaries is a result of the equilibrium state of the device. Based on the findings an expression of the Schottky potential barrier width is proposed satisfying relevant expression of the current caused by the application of the electric field. It is observed that the potential barrier width is sharply reduced in the temperature range 320 K ≤ T ≤ 350 K. This reduction in the potential barrier width is likely to be associated with the relaxation process of the trap filled (trapped) carriers, usually monitored by the dielectric response (in the form of differential capacitance) of the device. Thus, the results provide an improved understanding of the nonlinear conduction behavior in ZnO varistors. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Haptic interaction in robot‐assisted endoscopic surgery: a sensorized end‐effector
Authors: Tavakoli M , Patel R V , Moallem M
Published: November 2005

Conventional endoscopic surgery has some drawbacks that can be addressed by using robots. The robotic systems used for surgery are still in their infancy. A major deficiency is the lack of haptic feedback to the surgeon. In this paper, the benefits of haptic feedback in robot‐assisted surgery are discussed. A novel robotic end‐effector is then described that meets the requirements of endoscopic surgery and is sensorized for force/ torque feedback. The endoscopic end‐effector is capable of non‐invasively measuring its interaction with tissue in all the degrees of freedom available during endoscopic manipulation. It is also capable of remotely actuating a tip and measuring its interaction with the environment without using any sensors on the jaws. The sensorized end‐effector can be used as the last arm of a surgical robot to incorporate haptic feedback and/or to evaluate skills and learning curves of residents and surgeons in endoscopic surgery. Copyright © 2005 Robotic Publications Ltd.
Multi‐imager compatible actuation principles in surgical robotics
Authors: Stoianovici D
Published: November 2005

Today's most successful surgical robots are perhaps surgeon‐driven systems, such as the daVinci (Intuitive Surgical Inc., USA, www.intuitivesurgical.com). These have already enabled surgery that was unattainable with classic instrumentation; however, at their present level of development, they have limited utility. The drawback of these systems is that they are independent self‐contained units, and as such, they do not directly take advantage of patient data. The potential of these new surgical tools lies much further ahead. Integration with medical imaging and information are needed for these devices to achieve their true potential. Surgical robots and especially their subclass of image‐guided systems require special design, construction and control compared to industrial types, due to the special requirements of the medical and imaging environments. Imager compatibility raises significant engineering challenges for the development of robotic manipulators with respect to imager access, safety, ergonomics, and above all the non‐interference with the functionality of the imager. These apply to all known medical imaging types, but are especially challenging for achieving compatibility with the class of MRI systems. Even though a large majority of robotic components may be redesigned to be constructed of MRI compatible materials, for other components such as the motors used in actuation, prescribing MRI compatible materials alone is not sufficient. The electromagnetic motors most commonly used in robotic actuation, for example, are incompatible by principle. As such, alternate actuation principles using “intervention friendly” energy should be adopted and/or devised for these special surgical and radiological interventions.

This paper defines the new concept of Multi‐Imager Compatibility of surgical manipulators and describes its requirements. Subsequently, the paper gives several recommendations and proposes new actuation principles for this concept. Several implementations have been constructed and tested, and the results are presented here. This is the first paper addressing these issues. Copyright © 2005 Robotic Publications Ltd.
Human papillomaviruses: basic mechanisms of pathogenesis and oncogenicity
Authors: Hebner Christy M. , Laimins Laimonis A.
Published: November 2005

Human papillomaviruses (HPVs) are small double‐stranded DNA viruses that infect the cutaneous and mucosal epithelium. Infection by specific HPV types has been linked to the development of cervical carcinoma. HPV infects epithelial cells that undergo terminal differentiation and so encode multiple mechanisms to override the normal regulation of differentiation to produce progeny virions. Two viral proteins, E6 and E7, alter cell cycle control and are the main arbitrators of HPV‐induced oncogenesis. Recent data suggest that E6 and E7 also play a major role in the inhibition of the host cell innate immune response to HPV. The E1 and E2 proteins, in combination with various cellular factors, mediate viral replication. In addition, E2 has been implicated in both viral and cellular transcriptional control. Despite decades of research, the function of other viral proteins still remains unclear. While prophylactic vaccines to block genital HPV infection will soon be available, the widespread nature of HPV infection requires greater understanding of both the HPV life cycle as well as the mechanisms underlying HPV‐induced carcinogenesis. Copyright © 2005 John Wiley & Sons, Ltd.
Estimating vaccine effects from studies of outbreaks in household pairs
Authors: Becker Niels G. , Britton Tom , O'Neill Philip D.
Published: November 2005

The traditional way to measure efficacy of a vaccine, with respect to reduced susceptibility and reduced infectivity once infected, is to look at relative attack rates. Although straightforward to apply, such measures do not take disease transmission into account, with the consequence that they can depend strongly on the community setting, the duration of the study period, the way participants are recruited into the study and the virulence of the infection. Sometimes they give a very misleading assessment of the vaccine, as we illustrate by examples. Here measures of vaccine efficacy are considered that avoid these defects, and estimation procedures are presented for studies based on outbreaks in household pairs. Such studies enable estimation of vaccine effects on susceptibility, infectivity and transmission. We propose that the vaccine efficacy measures be estimated, without making any assumptions about the nature of the vaccine response, by consistent estimates of bounds for the measures. Copyright © 2005 John Wiley & Sons, Ltd.
Matching statistics: efficient computation and a new practical algorithm for the multiple common substring problem
Authors: Maaß Moritz G.
Published: November 2005

We present new algorithms for computing matching statistics with suffix arrays. We show how the Multiple Common Substring Problem can be solved efficiently in practice with a new approach using matching statistics. This problem consists of finding the common substrings of a set of strings. For the computation of matching statistics we compare seven different methods based on suffix trees and suffix arrays. Most of the suffix array algorithms have an inferior asymptotic worst case running time but a very low memory overhead and small constants in the running time complexity. Our experiments show a good performance in practice. Copyright © 2005 John Wiley & Sons, Ltd.
Histological and Molecular Structure Characterization of Annular Collagen after Intradiskal Electrothermal Annuloplasty
Authors: Southern Daniel , Lutz Gregory , Bracilovic Ana , West Paul , Spevak Mila , Camacho Nancy Pleshko , Doty Stephen
Published: November 2005

The mechanism of pain relief of intradiskal electrothermal annuloplasty (IDET) in the treatment of lumbar diskogenic pain is uncertain. Theories include sealing of annular fissures via collagen denaturation and contraction. Prior studies offer conflicting qualitative data on the ability of IDET to denature collagen. The objective of the present study is to evaluate IDET treatment effect onannular collagen using quantitative data supplied by Fourier-transform infrared imaging spectroscopy.

The posterior annulus of disks ( n = 3) from an intact human cadaveric spine at room temperature were treated with two different radiothermal catheters using standard intradiskal electrothermal annuloplasty (IDET) heating protocols. Disks were dissected free with catheters in place and fixed in formalin. Channels created by the catheters were marked and catheters were removed. Tissue samples of treated areas adjacent to the channels and internal control areas from the same disk were stained for light microscopy and placed on barium sulfate windows for Fourier transform infrared imaging spectroscopy (FT-IRIS) analysis.

Treated areas showed evidence of disruption in the fibrillar organization of annular collagen by light microscopy compared to intact stroma from control areas. Quantitative FT-IRIS analysis compared ratios of wavenumber regions known to be sensitive to collagen denaturation. Mean values for the ratios amide II/1,338 cm−1 (137.21 ± 25.84 treated, 76.94 ± 16.77 control) and 1,640/1,660 cm−1 (0.98 ± 0.03 treated, 0.89 ± 0.03 control) were significantly different between treated and control samples ( p < 0.001), indicating a breakdown in collagen integrity. Separate analysis by catheter type suggests that catheter design may impact treatment effect.
Localization of the nuclear receptor CAR at the cell membrane of mouse liver
Authors: Koike Chika , Moore Rick , Negishi Masahiko
Published: November 2005

The nuclear receptor constitutive active/androstane receptor CAR is a drug‐sensing transcription factor. Upon activation by various drugs such as phenobarbital (PB), CAR translocates from the cytoplasm into the nucleus to regulate the genes that encode enzymes and proteins involved in hepatic metabolism. Here, we have shown the presence of CAR at the cell membrane of mouse livers, using Car
+/+ and Car
−/− mice. Levels of the cell membrane CAR increased after PB treatment. The CAR exists as a large approximately 160 kDa complex. Thus, CAR undergoes PB‐induced translocation to the cell membrane, indicating that CAR may exert a non‐genomic action.
The putative protein 6 of the severe acute respiratory syndrome‐associated coronavirus: Expression and functional characterization
Authors: Geng Hua , Liu Yuet-Man , Chan Wai-Sing , Lo Anthony Wing-Ip , Au Deborah Mun-Yee , Waye Mary Miu-Yee , Ho Yuan-Yuan
Published: November 2005

The SARS‐CoV open reading frame 6 (ORF6) is transcribed into mRNA6 and encodes a putative 7.5 kDa accessory protein, SARS 6, with unknown function. In this study, we have confirmed the SARS 6 protein expression in lung and intestine tissues of the SARS patients and in SARS‐CoV infected Vero E6 cells by immunohistochemistry. Further studies by immunoblot and confocal microscopy analyses revealed the expression and the endoplasmic reticulum (ER) localization of the recombinant SARS 6 protein in mammalian cells. Expression of SARS 6 protein in mammalian cells elicits biological activity of stimulating cellular DNA synthesis.
Functional sulfurtransferase is associated with mitochondrial complex I from Yarrowia lipolytica, but is not required for assembly of its iron–sulfur clusters
Authors: Abdrakhmanova Albina , Dobrynin Krzysztof , Zwicker Klaus , Kerscher Stefan , Brandt Ulrich
Published: November 2005

Here, we report that in the obligate aerobic yeast Yarrowia lipolytica, a protein exhibiting rhodanese (thiosulfate:cyanide sulfurtransferase) activity is associated with proton pumping NADH:ubiquinone oxidoreductase (complex I). Complex I is a key enzyme of the mitochondrial respiratory chain that contains eight iron–sulfur clusters. From a rhodanese deletion strain, we purified functional complex I that lacked the additional protein but was fully assembled and displayed no functional defects or changes in EPR signature. In contrast to previous suggestions, this indicated that the sulfurtransferase associated with Y. lipolytica complex I is not required for assembly of its iron–sulfur clusters.
Micromapping of Mg/Ca values in cultured specimens of the high‐magnesium benthic foraminifera
Authors: Toyofuku Takashi , Kitazato Hiroshi
Published: November 2005

This study measured Mg/Ca values in cross sections of the benthic foraminifer Planoglabratella opercularis (d'Orbigny) using an electron probe microanalyzer (EPMA) (spot size, 2 μm; >1000 analyses). We cultured clonal juveniles of this species under controlled temperatures. This species precipitates high‐magnesium calcite as its test material. Mean Mg/Ca values increased linearly with the culture temperature; therefore Mg/Ca values in walls of subsequently formed chambers reflected changes in temperature during the experiment. Foraminiferal specimens yielded variable Mg/Ca values within their test walls, which resulted from the pattern of chamber formation and from minor variations of Mg/Ca within one chamber wall.
Coseismic slip distribution of the 1923 Kanto earthquake, Japan
Authors: Pollitz Fred F. , Nyst Marleen , Nishimura Takuya , Thatcher Wayne
Published: November 2005

The slip distribution associated with the 1923 M = 7.9 Kanto, Japan, earthquake is reexamined in light of new data and modeling. We utilize a combination of first‐order triangulation, second‐order triangulation, and leveling data in order to constrain the coseismic deformation. The second‐order triangulation data, which have not been utilized in previous studies of 1923 coseismic deformation, are associated with only slightly smaller errors than the first‐order triangulation data and expand the available triangulation data set by about a factor of 10. Interpretation of these data in terms of uniform‐slip models in a companion study by Nyst et al. shows that a model involving uniform coseismic slip on two distinct rupture planes explains the data very well and matches or exceeds the fit obtained by previous studies, even one which involved distributed slip. Using the geometry of the Nyst et al. two‐plane slip model, we perform inversions of the same geodetic data set for distributed slip. Our preferred model of distributed slip on the Philippine Sea plate interface has a moment magnitude of 7.86. We find slip maxima of ∼8–9 m beneath Odawara and ∼7–8 m beneath the Miura peninsula, with a roughly 2:1 ratio of strike‐slip to dip‐slip motion, in agreement with a previous study. However, the Miura slip maximum is imaged as a more broadly extended feature in our study, with the high‐slip region continuing from the Miura peninsula to the southern Boso peninsula region. The second‐order triangulation data provide good evidence for ∼3 m right‐lateral strike slip on a 35‐km‐long splay structure occupying the volume between the upper surface of the descending Philippine Sea plate and the southern Boso peninsula.
A diagnostic model of the diurnal cycle of sea surface temperature for use in coupled ocean‐atmosphere models
Authors: Schiller A. , Godfrey J. S.
Published: November 2005

On the basis of a method of estimating the diurnal amplitude of sea surface temperature (SST) as a function of the diurnal integrals of surface heat and momentum fluxes, a parameterization scheme of the diurnal cycle of SST is implemented in a one‐dimensional ocean mixed‐layer model. Many coupled ocean‐atmosphere models using bulk mixed‐layer schemes underestimate the diurnal cycle in sea surface temperature by up to 2°C. This discrepancy is caused by coarse vertical resolution in the upper grid boxes of the ocean components. A simple solution is suggested by adding one extra transient level: a variable‐depth diurnal sublayer within the top model level which accommodates the diurnal buoyancy cycle. A one‐dimensional mixed‐layer model with 10‐m resolution and with sublayer simulates diurnal SSTs close to those observed from the Tropical Ocean Global Atmosphere/Coupled Ocean Atmosphere Response Experiment (TOGA/COARE) with typical errors of about 0.1°C. The impact of improved SSTs on surface heat fluxes is also shown by coupling the one‐dimensional mixed‐layer model with sublayer to an atmospheric boundary layer model.
Automated daily processing of more than 1000 ground‐based GPS receivers for studying intense ionospheric storms
Authors: Komjathy Attila , Sparks Lawrence , Wilson Brian D. , Mannucci Anthony J.
Published: November 2005

As the number of ground‐based and space‐based receivers tracking the Global Positioning System (GPS) satellites steadily increases, it is becoming possible to monitor changes in the ionosphere continuously and on a global scale with unprecedented accuracy and reliability. As of August 2005, there are more than 1000 globally distributed dual‐frequency GPS receivers available using publicly accessible networks including, for example, the International GPS Service and the continuously operating reference stations. To take advantage of the vast amount of GPS data, researchers use a number of techniques to estimate satellite and receiver interfrequency biases and the total electron content (TEC) of the ionosphere. Most techniques estimate vertical ionospheric structure and, simultaneously, hardware‐related biases treated as nuisance parameters. These methods often are limited to 200 GPS receivers and use a sequential least squares or Kalman filter approach. The biases are later removed from the measurements to obtain unbiased TEC. In our approach to calibrating GPS receiver and transmitter interfrequency biases we take advantage of all available GPS receivers using a new processing algorithm based on the Global Ionospheric Mapping (GIM) software developed at the Jet Propulsion Laboratory. This new capability is designed to estimate receiver biases for all stations. We solve for the instrumental biases by modeling the ionospheric delay and removing it from the observation equation using precomputed GIM maps. The precomputed GIM maps rely on 200 globally distributed GPS receivers to establish the “background” used to model the ionosphere at the remaining 800 GPS sites.
AMMONIUM AND UV RADIATION STIMULATE THE ACCUMULATION OF MYCOSPORINE‐LIKE AMINO ACIDS IN PORPHYRA COLUMBINA (RHODOPHYTA) FROM PATAGONIA, ARGENTINA1
Authors: Peinado Nathalie Korbee , Abdala Díaz Roberto T. , Figueroa Félix L. , Helbling E. Walter
Published: November 2005

The combined effects of ammonium concentration and UV radiation on the red alga Porphyra columbina (Montagne) from the Patagonian coast (Chubut, Argentina) was determined using short‐term (less than a week) experimentation. Discs of P. columbina were incubated with three ammonium concentrations (0, 50, and 300 μM NH4Cl) in anilluminated chamber (PAR=300 μmol photons·m−2·s−1, UVA=15 W·m−2, UVB=0.7 W·m−2) at 15°C. Algae incubated at 300 μM ammonium showed a significant increase (P<0.05) in the concentration of mycosporine‐like amino acids (MAAs) compared with the initial value or with the other ammonium treatments. The increase of MAAs was, however, a function of the quality of irradiance received, with a higher increase in samples exposed to UVA compared with UVB (29% and 5% increase, respectively). However, UVB radiation was more effective in inducing MAA synthesis per unit energy received by the algae. Samples exposed to PAR only had an intermediate increase in MAA concentration of 16%. Chl a concentration decreased through the incubation with the greatest decrease at high ammonium concentration. Phycobiliprotein (BP) decreased through time with the smallest decrease occurring at high ammonium concentration. Photoinhibition (as a decrease of optimal quantum yield) was significantly greater under nitrogen‐deprived conditions than that under replete ammonium levels. Maximal gross photosynthesis (GPmax), as oxygen evolution, and maximal electron transport rate (ETRmax), as chl fluorescence, increased with the ammonium concentration. Positive relationships between maximal GP or ETR and pigment ratios (BP/chl a and MAAs/chl a) and negative relationships with chl a concentration were found.
AMPHIDINIUM REVISITED. II. RESOLVING SPECIES BOUNDARIES IN THE AMPHIDINIUM OPERCULATUM SPECIES COMPLEX (DINOPHYCEAE), INCLUDING THE DESCRIPTIONS OF AMPHIDINIUM TRULLA SP. NOV. AND AMPHIDINIUM GIBBOSUM. COMB. NOV.1
Authors: Murray Shauna , Flø Jørgensen Mårten , Daugbjerg Niels , Rhodes Leslie
Published: November 2005

Amphidinium operculatum Claparède et Lachmann, the type species of the dinoflagellate genus Amphidinium, has long had an uncertain identity. It has been considered to be either difficult to distinguish from other similar species or a morphologically variable species itself. This has led to the hypothesis that A. operculatum represents a “species complex.” Recently, the problem of distinguishing A. operculatum from similar species has become particularly acute, because several morphologically similar species have been found to produce bioactive compounds of potential interest to the pharmaceutical industry. In this study, we cultured and examined existing cultures of several species of Amphidinium, most of which have been previously identified as A. operculatum or as species considered by some to be synonyms or varieties of A. operculatum. Thirty strains were examined using comparative LM, SEM, and partial large subunit (LSU) rDNA sequence data. Through morphological and molecular phylogenetic analyses, six distinct species were identified, including Amphidinium trulla sp. nov. and Amphidinium gibbosum comb. nov. Amphidinium operculatum was redescribed based on four cultures. Genetic variability within the examined Amphidinium species varied greatly. There was little difference among strains in partial LSU rDNA for most species, but strains of A. carterae and A. massartii Biencheler differed by as much as 4%. In both A. carterae and A. massartii, three distinct genotypes based on partial LSU rDNA were found, but no morphological differences among strains could be observed using LM or SEM. In the case of A. carterae, no biogeographically related molecular differences were found.
PHYLOGENETIC PLACEMENT OFBOTRYOCOCCUS BRAUNII(TREBOUXIOPHYCEAE) ANDBOTRYOCOCCUS SUDETICUSISOLATE UTEX 2629 (CHLOROPHYCEAE)1
Authors: Senousy Hoda H. , Beakes Gordon W. , Hack Ethan
Published: November 2005

The phylogenetic placement of four isolates ofBotryococcus brauniiKützing and ofBotryococcus sudeticusLemmermann isolate UTEX 2629 was investigated using sequences of the nuclear small subunit (18S) rRNA gene. TheB. brauniiisolates represent the A (two isolates), B, and L chemical races. One isolate ofB. braunii(CCAP 807/1; A race) has a group I intron atEscherichia coliposition 1046 and isolate UTEX 2629 has group I introns atE. colipositions 516 and 1512. The rRNA sequences were aligned with 53 previously reported rRNA sequences from members of the Chlorophyta, including one reported forB. braunii(Berkeley strain). Phylogenetic trees were constructed using distance, weighted maximum parsimony, and maximum likelihood, and their reliability was estimated using bootstrap analysis for distance and parsimony and Bayesian inference for likelihood. All methods showed, with high bootstrap or credibility support, that the four isolates ofB. brauniiform a monophyletic group whose closest relatives are in the genusChoricystisin the Trebouxiophyceae, whereas the previously reportedB. brauniisequence is from a member of the Chlamydomonadales in the Chlorophyceae and isolate UTEX 2629 is a member of the Sphaeropleales in the Chlorophyceae. Polyphyly of these sequences was confirmed by Kishino‐Hasegawa tests on artificial trees in which sequences were moved to a single lineage.
Dynamic arrest in a liquid of symmetric dumbbells: Reorientational hopping for small molecular elongations
Authors: Moreno Angel J. , Chong Song-Ho , Kob Walter , Sciortino Francesco
Published: November 2005

We present extensive equilibrium and out-of-equilibrium molecular-dynamics simulations of a liquid of symmetric dumbbell molecules, for constant packing fraction, as a function of temperature and molecular elongation. We compute diffusion constants as well as odd and even orientational correlators. The notations odd and even refer to the parity of the order l of the corresponding Legendre l polynomial, evaluated for the orientation of the molecular axis relative to its initial position. Rotational degrees of freedom of order l are arrested if, in the long-time limit, the corresponding orientational l correlator does not decay to zero. It is found that for large elongations translational and rotational degrees of freedom freeze at the same temperature. For small elongations only the even rotational degrees of freedom remain coupled to translational motions and arrest at a finite common temperature. On the contrary, the odd rotational degrees of freedom remain ergodic at all investigated temperatures. Hence, in the translationally arrested state, each molecule remains trapped in the cage formed by its neighboring molecules, but is able to perform 180° rotations, which lead to relaxation only for the odd orientational correlators. The temperature dependence of the characteristic time of these residual rotations is well described by an Arrhenius law. Finally, we discuss the evidence in favor of the presence of the type-A transition for the odd rotational degrees of freedom, as predicted by mode-coupling theory for small molecular elongations. This transition is distinct from the type-B transition, associated with the arrest of the translational and even rotational degrees of freedom for small elongations, and with all degrees of freedom for large elongations. Odd orientational correlators are computed for small elongations at very low temperatures in the translationally arrested state. The obtained results suggest that hopping events restore the ergodicity of the odd rotational degrees of freedom at temperatures far below the A transition.
Random multi-overlap structures for optimization problems
Authors: De Sanctis Luca
Published: November 2005

We extend to the K-SAT and p-XOR-SAT optimization problems the results recently achieved, by introducing the concept of random multi-overlap structure, for the Viana-Bray model of diluted mean field spin glass. More precisely we can prove a generalized bound and an extended variational principle for the free energy per site in the thermodynamic limit. Moreover a trial function implementing ultrametric breaking of replica symmetry is exhibited. The ultrametric structure exhibits the same factorization property as the optimal structures for the Viana-Bray model and the Sherrington-Kirkpatrick nondiluted model.
Thermometric characteristics approximation of germanium film temperature microsensors by orthonormal polynomials
Authors: Bogdanova Nina B. , Terziyska B. M. , Madge H.
Published: November 2005

Approximations of thermometric characteristics of germanium film temperature microsensors are presented using a mathematical approach based on their expansion with orthonormal polynomials. A weighted orthonormal polynomial expansion method (OPEM) is applied, involving the experimental errors of calibration test data at every point. The thermometric functions R(T) and T(R) of resistance and temperature are described in the whole temperature range (1.7–300K) and in three subintervals (1.7–20, 20–150, and 150–300K). The absolute, relative, and specific sensitivities of the sensor, as well as the main approximation characteristics, are discussed. The OPEM is extended to obtain a mathematical description of R(T) and T(R) functions by usual polynomial coefficients calculated by orthonormal ones. A comparison between maximal relative deviations of R(T) and T(R) three-interval approximations, correspondingly, by usual and orthonormal polynomials, is presented. Numerical results of the approximation parameters of these type of temperature sensors are shown in the figures and tables.
Distorted wave Born and three-body distorted wave Born approximation calculations of the fully differential cross section for electron-impact ionization of nitrogen molecules
Authors: Gao Junfang , Madison D. H. , Peacher J. L.
Published: November 2005

Currently there are no reliable theoretical approaches for calculating fully differential cross sections (FDCSs) for low-energy electron-impact ionization of large molecules. We have recently proposed the orientation-averaged molecular orbital (OAMO) for calculating cross sections averaged over molecular orientations. In this paper, we use the OAMO to calculate distorted wave Born approximation (DWBA) and molecular three-body distorted wave (M3DW) Born approximation FDCS for electron-impact ionization of the nitrogen molecule. Both coplanar symmetric and asymmetric FDCSs are investigated in the energy range of 35.6–400eV. By comparing with the experimental data, we found that the M3DW is reasonably accurate in this energy range. We also found that the postcollision interaction plays a sufficiently important role and that the DWBA is not reliable.
Correlated complex independent particle potential for calculating electronic resonances
Authors: Sajeev Y. , Santra Robin , Pal Sourav
Published: November 2005

We have formulated and applied an analytic continuation method for the recently formulated correlated independent particle potential [A. Beste and R. J. Bartlett J. Chem. Phys. 120, 8395 (2004)] derived from Fock space multireference coupled cluster theory. The technique developed is an advanced ab initio tool for calculating the properties of resonances in the low-energy electron-molecule collision problem. The proposed method quantitatively describes elastic electron-molecule scattering below the first electronically inelastic threshold. A complex absorbing potential is utilized to define the analytic continuation for the potential. A separate treatment of electron correlation and relaxation effects for the projectile-target system and the analytic continuation using the complex absorbing potential is possible, when an approximated form of the correlated complex independent particle potential is used. The method, which is referred to as complex absorbing potential-based correlated independent particle (CAP-CIP), is tested by application to the well-known Πg2 shape resonance of e-N2 and the B2g2 shape resonance of e-C2H4 (ethylene) with highly satisfactory results.
Digital ultrasonic pulse-echo overlap system and algorithm for unambiguous determination of pulse transit time
Authors: Pantea Cristian , Rickel Dwight G. , Migliori Albert , Leisure Robert G. , Zhang Jianzhong , Zhao Yusheng , El-Khatib Sami , Li Baosheng
Published: November 2005

We report an evolution of an all-digital ultrasonic pulse technique for measurements of elastic constants of solids. An unambiguous analytical procedure is described for determining the correct time delay of echoes without any need for actual echo overlap. We also provide a simple procedure for making corrections for transducer-bond-induced phase shifts. The precision of a measurement made with this system at ambient temperature exceeds one part in 107 without the use of mixers, gates, time delays, and other complications normally associated with such measurements.
50
-
Ω
-matched system for low-temperature measurements of the time-resolved conductance of low-dimensional semiconductors
Authors: Naser B. , Heeren J. , Ferry D. K. , Bird J. P.
Published: November 2005

We describe the construction of a low-temperature cryostat that may be used to study the time-dependent conductivity of low-dimensional semiconductors with time resolution of a few-hundred picoseconds. The system makes use of semirigid coaxial cables to provide the necessary connections from room-temperature instrumentation to the low-temperature stage, and features a specially designed launch that provides efficient 50Ω impedance matching to the semiconductor system of interest. In order to explore the capabilities of the system, we perform time-resolved measurements of the magnetotransport properties of a high mobility GaAs∕AlGaAs two-dimensional electron gas.
Local electronic structures of ZnSe∕Si nanotapes and their luminescence properties
Authors: Li Quan , Hark S. K. , Wang Juan , Xu Y. M. , Wang C. R. , Lau W. M.
Published: November 2005

Zn Se ∕ Si nanotapes have been fabricated via a co-assisted vapor-phase transfer mechanism. Local electronic structure investigation along the nanotape radial direction suggests that the Si surface can be terminated by the ZnSe, leading to the one-dimensional (1D) anisotropic growth of Si, and further results in direct interface between ZnSe and Si in the nanotapes. The co-growth mechanism not only results in nanowire heterostructures, but also effectively incorporates Si into ZnSe and thus modifies its luminescence properties, leading to luminescence peak both above and below the original band gap of pure phase ZnSe.
Room-temperature excitonic absorption in quantum wires
Authors: Takahashi Yasushi , Hayamizu Yuhei , Itoh Hirotake , Yoshita Masahiro , Akiyama Hidefumi , Pfeiffer Loren N. , West Ken W.
Published: November 2005

We measured the absorption spectra of T-shaped quantum wires at room temperature using waveguide-transmission spectroscopy. A strong and narrow room-temperature one-dimensional-exciton absorption peak was observed, which indicates a peak modal absorption coefficient of 160cm−1 per 20 wires with a Γ-factor of 4.3×10−3, a width of 7.2meV, and strong polarization anisotropy.
Growth and properties of GaN and AlN layers on silver substrates
Authors: Mikulics Martin , Kočan Martin , Rizzi Angela , Javorka Peter , Sofer Zdeněk , Stejskal Josef , Marso Michel , Kordoš Peter , Lüth Hans
Published: November 2005

We report on the preparation and properties of GaN and AlN layers grown by molecular-beam epitaxy on silver metal substrates. X-ray diffraction rocking curves show polycrystalline character of GaN with high preferential GaN(11-22) orientation. An intermetallic phase of Ga3Ag is found at the GaN∕Ag interface. On the other hand, AlN layers exhibit a monocrystalline structure with a growth direction of (0002). Schottky diodes prepared on GaN layers show good rectifying behavior and relatively low leakage current (∼10−3A∕cm2). These results indicate that the III-nitride growth on metallic substrates might be used for low-cost and large-area electronic and photonic devices.
Ferroelectric switch for spin injection
Authors: Zhuravlev M. Ye. , Jaswal S. S. , Tsymbal E. Y. , Sabirianov R. F.
Published: November 2005

A method for the switching of the spin polarization of the electric current injected into a semiconductor is proposed, based on injecting spins from a diluted magnetic semiconductor through a ferroelectric tunnel barrier. We show that the reversal of the electric polarization of the ferroelectric results in a sizable change in the spin polarization of the injected current, thereby providing a two-state electrical control of this spintronic device. We also predict a possibility of switching of tunneling magnetoresistance in magnetic tunnel junctions with a ferroelectric barrier and coexistence of tunneling magnetoresistance and giant electroresistance effects in these multiferroic tunnel junctions.
Control the relative length of carbon nanotubes from site to site on one silicon substrate
Authors: Zhang Zhengjun , Zhou Ya , Yue Yang
Published: November 2005

Carbon nanotubes were grown on silicon substrates by chemical vapor deposition with a mixture of ferrocene and xylene by suppressing the reaction of Fe with silicon. We also found a way to control the relative length of carbon nanotubes grown on one substrate by using Au thin films with different thickness (at the nanometer scale) as the block material, whose vaporization postponed the growth of carbon nanotubes. We can thus use Au films as a “shutter” to adjust the growth time of the nanotubes, leading to the control in the relative length of carbon nanotubes from site to site on one substrate.
Enhanced electroluminescence and color purity in conjugated polymer with nano-porous morphology
Authors: Kim Tae-Ho , Im Sang Hyuk , Park O Ok
Published: November 2005

The luminescent properties of conjugated polymers are seriously affected by concentration of the conjugated chains and the degree of polymer chain packing. We examined the effect of nanoporous morphology in the emitting layer of poly[2-methoxy-5-(2′-ethylhexyloxy)-1,4-phenylene vinylene] to hope that it would prevent polymer chain packing so that effectively decrease interchain interaction caused by interchain species and aggregates. High luminance is obtained at relatively low current density since the annihilation of singlet excitons is decreased. Redshifted emission due to the interchain aggregates and excimers are also suppressed, so that the color purity of the devices is greatly improved.
Growth characteristics associated with biomass production in three varieties of Trichloris crinita (Poaceae), a forage grass native to the arid regions of Argentina
Authors: Greco S. A. , Cavagnaro J. B.
Published: November 2005

Trichloris crinita (Lag.) Parodi is an important perennial native grass widespread in the range areas of the arid and semi-arid phytogeographical region of Monte, Argentina. Previous studies have shown great variability in forage biomass production per plant among different varieties of this species. The aim of this work was to assess which morphological and physiological traits are associated with differential productivity of T. crinita varieties. Three varieties: Pichi, of high productivity, Arroyito, of medium productivity, and Encon, of low productivity were tested in a field experiment. Dry matter (DM) produced by different organs, assimilates partitioning, and leaf area per plant were measured on three different dates for each variety, during an annual growth cycle, under watered conditions. Relative growth rate (RGR), net assimilation rate (NAR), leaf area ratio (LAR), specific leaf area (SLA), leaf weight ratio (LWR) and leaf area development rate (LADR) were calculated at 72, 128 and 172 days after transplanting. Significant differences among varieties were found for DM production of blades, sheaths + culms, panicles, roots and shoot/root ratio. Pichi and Arroyito produced more total plant biomass than Encon and this was associated with higher dry matter accumulation in aboveground organs and larger leaf area. LADR, LAR and one of its components SLA were the parameters that best explained differences in biomass production. DM partitioning to roots (considered as the percentage of total DM) was very high in Encon, the least productive variety. Differences in productivity seem to be directly associated with the mean annual rainfall and inversely associated with the mean annual temperature of the environment where plants were collected. Thus, the growth characteristics of each variety reflect differential adaptation to their areas of origin.
Mutant mitochondrial helicase Twinkle causes multiple mtDNA deletions and a late-onset mitochondrial disease in mice
Authors: Tyynismaa Henna , Mjosund Katja Peltola , Wanrooij Sjoerd , Lappalainen Ilse , Ylikallio Emil , Jalanko Anu , Spelbrink Johannes N. , Paetau Anders , Suomalainen Anu
Published: November 2005

Defects of mitochondrial DNA (mtDNA) maintenance have recently been associated with inherited neurodegenerative and muscle diseases and the aging process. Twinkle is a nuclear-encoded mtDNA helicase, dominant mutations of which cause adult-onset progressive external ophthalmoplegia (PEO) with multiple mtDNA deletions. We have generated transgenic mice expressing mouse Twinkle with PEO patient mutations. Multiple mtDNA deletions accumulate in the tissues of these mice, resulting in progressive respiratory dysfunction and chronic late-onset mitochondrial disease starting at 1 year of age. The muscles of the mice faithfully replicate all of the key histological, genetic, and biochemical features of PEO patients. Furthermore, the mice have progressive deficiency of cytochrome
c
oxidase in distinct neuronal populations. These “deletor” mice do not, however, show premature aging, indicating that subtle accumulation of mtDNA deletions and progressive respiratory chain dysfunction are not sufficient to accelerate aging. This model is a valuable tool for therapy development and testing for adult-onset mitochondrial disorders.
β-Catenin regulates myogenesis by relieving I-mfa-mediated suppression of myogenic regulatory factors in P19 cells
Authors: Pan Weijun , Jia Yingying , Wang Jiyong , Tao Donglei , Gan Xiaoqing , Tsiokas Leonidas , Jing Naihe , Wu Dianqing , Li Lin
Published: November 2005

Wnt/β-catenin signaling plays a critical role in embryonic myogenesis. Here we show that, in P19 embryonic carcinoma stem cells, Wnt/β-catenin signaling initiates the myogenic process depends on β-catenin-mediated relief of I-mfa (inhibitor of MyoD Family a) suppression of myogenic regulatory factors (MRFs). We found that β-catenin interacted with I-mfa and that the interaction was enhanced by Wnt3a. In addition, we found that the interaction between β-catenin and I-mfa was able to attenuate the interaction of I-mfa with MRFs, relieve I-mfa-mediated suppression of the transcriptional activity and cytosolic sequestration of MRFs, and initiate myogenesis in a P19 myogenic model system that expresses exogenous myogenin. This work reveals a mechanism for the regulation of MRFs during myogenesis by elucidating a β-catenin-mediated, but lymphoid enhancing factor-1/T cell factor independent, mechanism in regulation of myogenic fate specification and differentiation of P19 mouse stem cells.
Transcriptome profiling of bacterial responses to root exudates identifies genes involved in microbe-plant interactions
Authors: Mark G. Louise , Dow J. Maxwell , Kiely Patrick D. , Higgins Hazel , Haynes Jill , Baysse Christine , Abbas Abdelhamid , Foley Tara , Franks Ashley , Morrissey John , O'Gara Fergal
Published: November 2005

Molecules exuded by plant roots are thought to act as signals to influence the ability of microbial strains to colonize the roots and to survive in the rhizosphere. Differential bacterial responses to signals from different plant species may mediate the selection of specific rhizosphere populations. Very little, however, is known about the effects of plant exudates on patterns of bacterial gene expression. Here, we have tested the concept that plant root exudates modulate expression of bacterial genes involved in establishing microbe-plant interactions. We have examined the influence on the
Pseudomonas aeruginosa
PA01 transcriptome of exudates from two varieties of sugarbeet that select for genetically distinct pseudomonad populations in the rhizosphere. The response to the two exudates showed only a partial overlap; the majority of those genes with altered expression was regulated in response to only one of the two exudates. Genes with altered expression included those with functions previously implicated in microbe-plant interactions, such as aspects of metabolism, chemotaxis and type III secretion, and a subset with putative or unknown function. Use of a panel of mutants with targeted disruptions allowed us to identify previously uncharacterized genes with roles in the competitive ability of
P. aeruginosa
in the rhizosphere within this subset. No genes with host-specific effects were identified. Homologues of the genes identified occur in the genomes of both beneficial and pathogenic root-associated bacteria, suggesting that this strategy may help to elucidate molecular interactions that are important for biocontrol, plant growth promotion, and plant pathogenesis.