bluuebunny/crossref_metadata_2025 huggingface dataset:
HB tag modules for PCR‐based gene tagging and tandem affinity purification in Saccharomyces cerevisiae
Authors: Tagwerker Christian , Zhang Hongwei , Wang Xiaorong , Larsen Liza S. Z. , Lathrop Richard H. , Hatfield G. Wesley , Auer Bernhard , Huang Lan , Kaiser Peter
Published: July 2006

We have recently developed the HB tag as a useful tool for tandem‐affinity purification under native as well as fully denaturing conditions. The HB tag and its derivatives consist of a hexahistidine tag and a bacterially‐derived in vivo biotinylation signal peptide, which support sequential purification by Ni2+‐chelate chromatography and binding to immobilized streptavidin. To facilitate tagging of budding yeast proteins with HB tags, we have created a series of plasmids with various selectable markers. These plasmids allow single‐step PCR‐based tagging and expression under control of the endogenous promoters or the inducible GAL1 promoter. HB tagging of several budding yeast ORFs demonstrated efficient biotinylation of the HB tag in vivo by endogenous yeast biotin ligases. No adverse effects of the HB tag on protein function were observed. The HB tagging plasmids presented here are related to previously reported epitope‐tagging plasmids, allowing PCR‐based tagging with the same locus‐specific primer sets that are used for other widely used epitope‐tagging strategies. The Sequences for the described plasmids were submitted to GenBank under Accession Numbers

DQ407918–pFA6a‐HBH‐kanMX6
DQ407927–pFA6a‐RGS18H‐kanMX6

DQ407919–pFA6a‐HBH‐hphMX4
DQ407928–pFA6a‐RGS18H‐hphMX4

DQ407920–pFA6a‐HBH‐TRP1
DQ407929–pFA6a‐RGS18H‐TRP1

DQ407921–pFA6a‐HTB‐kanMX6
DQ407930–pFA6a‐kanMX6‐PGAL1‐HBH

DQ407922–pFA6a‐HTB‐hphMX4
DQ407931–pFA6a‐TRP1‐PGAL1‐HBH

DQ407923–pFA6a‐HTB‐TRP1

DQ407924–pFA6a‐BIO‐kanMX6

DQ407925–pFA6a‐BIO‐hphMX4

DQ407926–pFA6a‐BIO‐TRP1

Copyright © 2006 John Wiley & Sons, Ltd.
The relationships between supplier development, commitment, social capital accumulation and performance improvement
Authors: Krause Daniel R. , Handfield Robert B. , Tyler Beverly B.
Published: July 2006

This study investigates the relationships between U.S. buying firms’ supplier development efforts, commitment, social capital accumulation with key suppliers, and buying firm performance. We identify linkages between supply chain management research on supplier development and organization theory research on social capital to consider how buying firm commitment to a long‐term relationship, cognitive capital (goals and values), structural capital (information sharing, supplier evaluation, supplier development), and relational capital (length of relationship, buyer dependency, supplier dependency) are related to buying firm performance improvements (cost improvements, and quality, delivery, flexibility improvements). Analysis of buying firms from the U.S. automotive and electronics industries provides support for the theory that buyer commitment and social capital accumulation with key suppliers can improve buying company performance. Moreover, the findings suggest that the relationships of structural and relational capital vary depending on the type of performance improvement considered.
Predictive display and interaction of telerobots based on augmented reality
Authors: Xiong Youjun , Li Shiqi , Xie Ming
Published: July 2006

A predictive display method and man-virtual robot interaction based on augmented reality are applied to control a telerobot. We first discuss the process of the augmented reality environment development. Then, we present the advantages of predictive display. Simulation of virtual robot's tasks in the augmented environment improves the safety of the telerobot when it executes the planned tasks. In addition, the immediate feedback from the virtual robot avoids the exacerbation of maneuverability caused by time-delay. For a more natural operation process, we apply multi man-virtual robot interactive methods. Lastly, the experiment of pick & place is conducted to validate the system.
Mao Zedong and the Famine of 1959–1960: A Study in Wilfulness
Authors: Bernstein Thomas P.
Published: July 2006

In late autumn 1958, Mao Zedong strongly condemned widespread practices of the Great Leap Forward (GLF) such as subjecting peasants to exhausting labour without adequate food and rest, which had resulted in epidemics, starvation and deaths. At that time Mao explicitly recognized that anti-rightist pressures on officialdom were a major cause of “production at the expense of livelihood.” While he was not willing to acknowledge that only abandonment of the GLF could solve these problems, he did strongly demand that they be addressed. After the July 1959 clash at Lushan with Peng Dehuai, Mao revived the GLF in the context of a new, extremely harsh anti-rightist campaign, which he relentlessly promoted into the spring of 1960 together with the radical policies that he previously condemned. Not until spring 1960 did Mao again express concern about abnormal deaths and other abuses, but he failed to apply the pressure needed to stop them. Given what he had already learned about the costs to the peasants of GLF extremism, the Chairman should have known that the revival of GLF radicalism would exact a similar or even bigger price. Instead, he wilfully ignored the lessons of the first radical phase for the sake of achieving extreme ideological and developmental goals.
In vitrocapacitation of bull spermatozoa by oviductal fluid and its components
Authors: Bergqvist Ann-Sofi , Ballester Joan , Johannisson Anders , Hernandez Marta , Lundeheim Nils , Rodríguez-Martínez Heriberto
Published: July 2006

Sperm capacitation is crucial for fertilization. However, debate continues on exactly how, where and when capacitation is elicited in the bovine female genital tract. In this study we used merocyanine-540 and the chlortetracycline (CTC) assay to test how capacitation of bull spermatozoa is affectedin vitroby exposure to oviductal fluid (ODF) collectedin vivo, various glycosaminoglycans (GAGs) or bicarbonate. Following different durations of exposure, spermatozoa were stained with CTC or merocyanine-540, and evaluated with epifluorescent light microscopy or flow cytometry, respectively. Incubation time did not significantly affect capacitation. Exposure (30–120 min) to ODF capacitated (p< 0.05) bull spermatozoa as measured by either merocyanine-540 or CTC. Hyaluronan was the only GAG that induced a significant increase in B-pattern spermatozoa (capacitated;p= 0.012) compared with controls. Dermatan sulphate also induced capacitation (merocyanine-540 high fluorescence;p= 0.035). Exposure to bicarbonate-enriched media also yielded an increase in merocyanine-540 high fluorescence (p< 0.0001). When bicarbonate was added to the other treatments (ODF or GAGs) an equal increase in merocyanine-540 high fluorescence was noted (p< 0.0001), compared with before addition of bicarbonate and independent of the treatment before exposure. There was no significant difference in the number of B-pattern spermatozoa when bicarbonate was added, but an significant increase in spermatozoa with an acrosome-reacted (AR)-pattern (p< 0.0001) was observed. Exposure of spermatozoa to solubilized zonae pellucidae significantly increased the AR-pattern spermatozoa (p= 0.016). In conclusion, ODF was more potent in inducing capacitation of bull spermatozoa than the individual GAGs. Our results also indicate that bicarbonate is an effector of bull sperm capacitation.
Abbreviated text input using language modeling
Authors: SHIEBER STUART M. , NELKEN RANI
Published: July 2006

We address the problem of improving the efficiency of natural language text input under degraded conditions (for instance, on mobile computing devices or by disabled users), by taking advantage of the informational redundancy in natural language. Previous approaches to this problem have been based on the idea of prediction of the text, but these require the user to take overt action to verify or select the system's predictions. We propose taking advantage of the duality between prediction and compression. We allow the user to enter text in compressed form, in particular, using a simple stipulated abbreviation method that reduces characters by 26.4%, yet is simple enough that it can be learned easily and generated relatively fluently. We decode the abbreviated text using a statistical generative model of abbreviation, with a residual word error rate of 3.3%. The chief component of this model is an n-gram language model. Because the system's operation is completely independent from the user's, the overhead from cognitive task switching and attending to the system's actions online is eliminated, opening up the possibility that the compression-based method can achieve text input efficiency improvements where the prediction-based methods have not. We report the results of a user study evaluating this method.
Further evidence for intercity co-operation among Neo-Babylonian temples
Authors: MacGinnis J.
Published: July 2006

Recent work among the Sippar Collections of the British Musuem has brought to light a number of interesting texts, among which is the fragment BM 63570. This text lists the qīpu's of numerous temples along with other officials, associating them all with bundles of reeds measured in hundreds. This is of unusual interest, however it is not the first time such a text has come to light as a similar fragment, BM 68777, was identified and published by the present author in 1993. Indeed, without a doubt the two pieces belong to the same tablet. BM 68777 is the beginning of the text, while BM 63570 carries on the obverse from this after a very small break and then gives some lines from the top of the reverse. The reverse of BM 68777 was uninscribed.
The Role of the Karguzar in the Foreign Relations of State and Society of Iran from the mid-nineteenth century to 1921 Part III: The Karguzar and Disputes over Foreign Trade
Authors: Nouraei Morteza , Martin Vanessa
Published: July 2006

Continuing our theme of looking at foreign relations between Iran and Britain from the point of view of the popular level through the role of the karguzar (the Ministry of Foreign Affairs Agent), this article will consider cases concerning foreign trade and disputes over property. It will examine the popular response to the growth of the foreign presence through expansion of foreign trade and the way Iranians handled their situation in a system that was dominated by Europeans. As trade grew in the late nineteenth century, so did the number and workload of karguzars.
Welche Störungen behandeln Kinder- und Jugendlichenverhaltenstherapeuten in der Gesetzlichen Krankenversicherung?
Authors: Sinzig Judith , Plück Julia , Schmidt Martin H.
Published: July 2006

Zusammenfassung. Seit 1998 besteht bei Neufassung der Psychotherapie-Richtlinien das Gutachterverfahren, das vor Beginn einer Verhaltenstherapie und vor Kostenübernahme durch die gesetzlichen Krankenkassen durchlaufen werden muss. Derzeit liegen Auswertungen für den Erwachsenenbereich, nicht jedoch für den Kinder- und Jugendbereich, vor. 1021 Anträgen auf Verhaltenstherapie aus dem Jahrgang 2001, konnten als anfallende Stichprobe retrospektiv Variablen u. a. zu Diagnosen, soziodemografischem Status und schulischer Situation entnommen werden. Es ergab sich, dass einfache Aktivitäts- und Aufmerksamkeitsstörungen (16,8 %) bzw. Emotionale Störungen des Kindesalters (15,2 %) in den Anträgen am häufigsten als Diagnosen angegeben wurden. Faktorenanalytisch war für sieben von 16 Faktoren ein inhaltlicher Zusammenhang mit Diagnosenvariablen erkennbar. In dieser Faktorenanalyse auf gleichen Faktoren hoch ladende Variablen und Diagnosen wurden mithilfe von Chi-Quadrat-Tests auf Verteilungsabweichungen untersucht. Detaillierte Ergebnisse werden beschrieben. Es wird deutlich, dass die Stichprobe hinsichtlich Diagnosen und Zusammenhängen mit Geschlecht und Alter bereits bekannten empirischen Befunden entspricht. Spezifische Gruppen von Diagnosen sind mit familiären und schulbezogenen Aspekten verknüpft, die Fragen zu Prävention, verbesserter Therapie und schulischer Förderung aufwerfen. Generell wird kassenfinanzierte Verhaltenstherapie dem Spektrum psychischer Störungen bei Kindern und Jugendlichen gerecht.
Übereinstimmung von Diagnosen und Symptomen in der Verhaltenstherapie bei Kindern und Jugendlichen
Authors: Schmidt Martin H. , Sinzig Judith
Published: July 2006

Zusammenfassung. Die Ergebnisse einer Verhaltenstherapie hängen von einer sorgfältigen Behandlungsplanung ab. Ausschlaggebend für die Qualität der Behandlungsplanung ist die Diagnostik. Sie führt zu kategorialen Diagnosen, die für die Verlaufsprognosen bestimmend sind, und zu Symptomausprägungen im Sinne einer dimensionalen Diagnostik als Basis für die engere Zielplanung. Kategoriale Diagnosen beruhen auf der richtigen und vollständigen Erfassung des Symptomspektrums. Die Übereinstimmung zwischen Symptomen und Diagnosen wurde anhand von 1018 sukzessiv angefallenen Berichten zu Anträgen für eine Kinderverhaltenstherapie an die gesetzlichen Krankenkassen überprüft. Klinische Kinderpsychologen erreichen dabei bei knapp der Hälfte der von ihnen bei Kindern und Jugendlichen behandelten Störungsbilder für ICD-10-Diagnosen Übereinstimmung größer .50, ähnlich wie Kinder- und Jugendpsychiater. Die Beziehungen zwischen Symptomen und einzelnen Diagnosen entsprachen den von ICD-10 erwarteten. Besonders leicht war die Diagnose monosymptomatischer Störungen, Schwierigkeiten bereitete die Diagnose depressiver Syndrome, von Anpassungsstörungen und kombinierten Störungen des Sozialverhaltens und der Emotionen. Die Gründe für mangelnde Übereinstimmung zwischen Symptomspektrum und Diagnose werden erörtert und Empfehlungen für die Ausbildung von Kinder- und Jugendlichenpsychotherapeuten gegeben.
North Pacific carbon cycle response to climate variability on seasonal to decadal timescales
Authors: McKinley G. A. , Takahashi T. , Buitenhuis E. , Chai F. , Christian J. R. , Doney S. C. , Jiang M.‐S. , Lindsay K. , Moore J. K. , Le Quéré C. , Lima I. , Murtugudde R. , Shi L. , Wetzel P.
Published: July 2006

Climate variability drives significant changes in the physical state of the North Pacific, and there may be important impacts of this variability on the upper ocean carbon balance across the basin. We address this issue by considering the response of seven biogeochemical ocean models to climate variability in the North Pacific. The models' upper ocean pCO2 and air‐sea CO2 flux respond similarly to climate variability on seasonal to decadal timescales. Modeled seasonal cycles of pCO2 and its temperature‐ and non‐temperature‐driven components at three contrasting oceanographic sites capture the basic features found in observations (Takahashi et al., 2002, 2006; Keeling et al., 2004; Brix et al., 2004). However, particularly in the Western Subarctic Gyre, the models have difficulty representing the temporal structure of the total pCO2 seasonal cycle because it results from the difference of these two large and opposing components. In all but one model, the air‐sea CO2 flux interannual variability (1σ) in the North Pacific is smaller (ranges across models from 0.03 to 0.11 PgC/yr) than in the Tropical Pacific (ranges across models from 0.08 to 0.19 PgC/yr), and the time series of the first or second EOF of the air‐sea CO2 flux has a significant correlation with the Pacific Decadal Oscillation (PDO). Though air‐sea CO2 flux anomalies are correlated with the PDO, their magnitudes are small (up to ±0.025 PgC/yr (1σ)). Flux anomalies are damped because anomalies in the key drivers of pCO2 (temperature, dissolved inorganic carbon (DIC), and alkalinity) are all of similar magnitude and have strongly opposing effects that damp total pCO2 anomalies.
A synchronized dating of three Greenland ice cores throughout the Holocene
Authors: Vinther B. M. , Clausen H. B. , Johnsen S. J. , Rasmussen S. O. , Andersen K. K. , Buchardt S. L. , Dahl‐Jensen D. , Seierstad I. K. , Siggaard‐Andersen M.‐L. , Steffensen J. P. , Svensson A. , Olsen J. , Heinemeier J.
Published: July 2006

As part of the effort to create the new Greenland Ice Core Chronology 2005 (GICC05) a synchronized stratigraphical timescale for the Holocene parts of the DYE‐3, Greenland Ice Core Project (GRIP), and North Greenland Ice Core Project (NGRIP) ice cores is made by using volcanic reference horizons in electrical conductivity measurements to match the cores. The main annual layer counting is carried out on the most suited records only, exploiting that the three ice cores have been drilled at locations with different climatic conditions and differences in ice flow. However, supplemental counting on data from all cores has been performed between each set of reference horizons in order to verify the validity of the match. After the verification, the main dating is transferred to all records using the volcanic reference horizons as tie points. An assessment of the mean annual layer thickness in each core section confirms that the new synchronized dating is consistent for all three cores. The data used for the main annual layer counting of the past 7900 years are the DYE‐3, GRIP, and NGRIP stable isotope records. As the high accumulation rate at the DYE‐3 drill site makes the seasonal cycle in the DYE‐3 stable isotopes very resistant to firn diffusion, an effort has been made to extend the DYE‐3 Holocene record. The new synchronized dating relies heavily on this record of ∼75,000 stable isotope samples. The dating of the early Holocene consists of an already established part of GICC05 for GRIP and NGRIP which has now been transferred to the DYE‐3 core. GICC05 dates the Younger Dryas termination, as defined from deuterium excess, to 11,703 years before A. D. 2000 (b2k), 130 years earlier than the previous GRIP dating.
The gut flora as a forgotten organ
Authors: O'Hara Ann M , Shanahan Fergus
Published: July 2006

The intestinal microflora is a positive health asset that crucially influences the normal structural and functional development of the mucosal immune system. Mucosal immune responses to resident intestinal microflora require precise control and an immunosensory capacity for distinguishing commensal from pathogenic bacteria. In genetically susceptible individuals, some components of the flora can become a liability and contribute to the pathogenesis of various intestinal disorders, including inflammatory bowel diseases. It follows that manipulation of the flora to enhance the beneficial components represents a promising therapeutic strategy. The flora has a collective metabolic activity equal to a virtual organ within an organ, and the mechanisms underlying the conditioning influence of the bacteria on mucosal homeostasis and immune responses are beginning to be unravelled. An improved understanding of this hidden organ will reveal secrets that are relevant to human health and to several infectious, inflammatory and neoplastic disease processes.
Termolecular kinetics for the Mu+CO+M recombination reaction: A unique test of quantum rate theory
Authors: Pan James J. , Arseneau Donald J. , Senba Masayoshi , Garner David M. , Fleming Donald G. , Xie Tiao , Bowman Joel M.
Published: July 2006

The room-temperature termolecular rate constants, k0, for the Mu+CO+M⇌MuCO+M (M=He, N2, Ar) recombination reaction have been measured by the μSR technique, and are reported for moderator gas pressures of up to ∼200bar (densities ≲0.4×1022moleccm−3). The experimental relaxation rates reveal an unusual signature, in being dominated by the electron spin-rotation interaction in the MuCO∙ radical that is formed in the addition step. In N2 moderator, k0=1.2±0.1×10−34cm6s−1, only about 30% higher than found in Ar or He. The experimental results are compared with theoretical calculations carried out on the Werner-Keller-Schinke (WKS) surface [Keller et al., J. Chem. Phys. 105, 4983 (1996)], within the framework of the isolated resonance model (IRM). The positions and lifetimes of resonance states are obtained by solving the complex Hamiltonian for the nonrotating MuCO system, using an L2 method, with an absorbing potential in the asymptotic region. Accurate values of the vibrational bound and resonance states of MuCO reveal unprecedented isotope effects in comparisons with HCO, due to the remarkable effect of replacing H by the very light Mu atom (mMu≈19mH). Due to its pronounced zero-point energy shift, there are only two (J=0) bound states in MuCO. Contributions from nonzero J states to the termolecular rate constants are evaluated through the J-shifting approximation, with rotational constants evaluated at the potential minimum. The value of the important A constant (181cm−1) used in this approximation was supported by accurate J=K=1 calculations, from which A=180cm−1 was obtained by numerical evaluation. The calculations presented here, with a “weak collision factor” βc=0.001, indicative of the very sparse density of MuCO states, give a very good account of both the magnitude and pressure dependence of the experimental rates, but only when the fact that the two initially bound (J=0) states become resonances for J>0 is taken into account. This is the first time in IRM calculations of atom-molecule recombination reactions where J≠0 states have proven to be so important, thus providing a truly unique test of quantum rate theory.
Semiquantal analysis of hydrogen bond
Authors: Ando Koji
Published: July 2006

The semiquantal time-dependent Hartree (SQTDH) theory is applied to the coupled Morse and modified Lippincott-Schroeder (LS) model potentials of hydrogen bond. The structural correlation between the heavy atoms distance and the proton position, the geometric isotope effect, the energy of hydrogen bond formation, and the proton vibrational frequency shift are examined in a broad range of structural parameters. In particular, the geometric isotope effect is found to depend notably on the choice of the potential model, for which the LS potential gives the isotope shift of the heavy atoms distance in the range of 0.02–0.04Å, in quantitative agreement with the experimental findings from assortment of hydrogen bonding crystals. The fourth-order expansion approximation to the semiquantal extended potential was confirmed to be highly accurate in reproducing the full SQTDH results. The approximation is computationally efficient and flexible enough to be applied to general models of hydrogen bond.
Quantum graphs as holonomic constraints
Authors: Dell’Antonio Gianfausto , Tenuta Lucattilio
Published: July 2006

We consider the dynamics on a quantum graph as the limit of the dynamics generated by a one-particle Hamiltonian in R2 with a potential having a deep strict minimum on the graph, when the width of the well shrinks to zero. For a generic graph we prove convergence outside the vertices to the free dynamics on the edges. For a simple model of a graph with two edges and one vertex, we prove convergence of the dynamics to the one generated by the Laplacian with Dirichlet boundary conditions in the vertex.
Excess electron localization sites in neutral water clusters
Authors: Turi László , Madarász Ádám , Rossky Peter J.
Published: July 2006

We present approximate pseudopotential quantum-mechanical calculations of the excess electron states of equilibrated neutral water clusters sampled by classical molecular dynamics simulations. The internal energy of the clusters are representative of those present at temperatures of 200 and 300K. Correlated electronic structure calculations are used to validate the pseudopotential for this purpose. We find that the neutral clusters support localized, bound excess electron ground states in about 50% of the configurations for the smallest cluster size studied (n=20), and in almost all configurations for larger clusters (n>66). The state is always exterior to the molecular frame, forming typically a diffuse surface state. Both cluster size and temperature dependence of energetic and structural properties of the clusters and the electron distribution are explored. We show that the stabilization of the electron is strongly correlated with the preexisting instantaneous dipole moment of the neutral clusters, and its ground state energy is reflected in the electronic radius. The findings are consistent with electron attachment via an initial surface state. The hypothetical spectral dynamics following such attachment is also discussed.
Gas bubble phenomenon in nanoscale liquid film under external electric field
Authors: Luo Jianbin , He Yu , Zhong Min , Jin Zhongmin
Published: July 2006

The effects of an external electric field on liquid films confined within a nanogap between a smooth plate and a highly polished steel ball have been investigated. It was found that some gas microbubbles emerged around the edge of the Hertz central region and then moved off the central region. Experimental results indicated that the emergence of the bubbles was largely dependent on the liquid polarity and the external voltage. It is thought that the emergence of the bubbles is due to the liquid surface vibration.
Structure and photoluminescence properties of evaporated GeOx thin films
Authors: Ardyanian M. , Rinnert H. , Devaux X. , Vergnat M.
Published: July 2006

Amorphous GeOx alloys were prepared by evaporation of GeO2 powder on substrates maintained at 100°C. The evolution of the structure was investigated by infrared-absorption spectrometry, Raman spectrometry and transmission electron microscopy experiments for annealing temperatures less than 600°C. These experiments allowed us to follow the phase separation of the alloy and to observe the appearance of amorphous and crystallized Ge aggregates. The evolution of the photoluminescence in the range of 560–1550nm was correlated to the structure of the films.
Thermal resistance of the nanoscale constrictions between carbon nanotubes and solid substrates
Authors: Maune Hareem , Chiu Hsin-Ying , Bockrath Marc
Published: July 2006

We have determined the thermal resistance for transferring heat between individual single-walled carbon nanotube devices and solid substrates. Using sapphire and comparing our results to previous results obtained from SiO2, we find that the resistance is dominated by interfacial resistance rather than the spreading resistance of heat for diffusing into the substrate. Our results are in agreement to a recent model for the thermal resistance of nanoscale constrictions. Our results suggest that relatively short contact lengths (∼10–30nm) to a typical solid should be sufficient to transfer heat efficiently into carbon nanotubes, underscoring the potential of carbon nanotubes for nanoscale thermal management.
Optical gain in dye-impregnated oxidized porous silicon waveguides
Authors: Oton C. J. , Navarro-Urrios D. , Capuj N. E. , Ghulinyan M. , Pavesi L. , González-Pérez S. , Lahoz F. , Martín I. R.
Published: July 2006

Positive optical gain under pulsed excitation in oxidized porous silicon planar waveguides impregnated with Nile blue (LC 6900) is reported. Amplified spontaneous emission measurements show a dramatic line narrowing when the pump energy is increased, together with a strong superlinear behavior. Variable stripe length measurements were performed to characterize quantitatively the amplification, and an unambiguous transition from losses to gain is observed with a threshold of ∼3mJ∕cm2 at 700nm. A maximum gain coefficient of 8.7cm−1 (∼40dB∕cm) is reported. Shifting excitation spot measurements confirm the reliability of our results. This system is interesting in view of an optically pumped silicon-based pulsed laser.
Carrier trap passivation in multicrystalline Si solar cells by hydrogen from SiNx:H layers
Authors: Dekkers H. F. W. , Carnel L. , Beaucarne G.
Published: July 2006

Hydrogenation by high temperature rapid annealing of SiNx:H is found to be very effective on the defects responsible for the carrier trapping effect in multicrystalline silicon. The passivation effect is reversible and is annihilated by a long thermal annealing. As for the passivation of deep, lifetime killing defects, the efficiency of “trap” removal by the short thermal treatment depends on the density of the SiNx:H layer. This effect is, in fact, well correlated with performance improvement observed in solar cells. The parallelism between the trap and recombination center passivation effects suggests that they originate from the same defect.
Multilevel conductance switching in polymer films
Authors: Lauters M. , McCarthy B. , Sarid D. , Jabbour G. E.
Published: July 2006

Multilevel conductance switching in poly[2-methoxy-5-(2′-ethyl-hexyloxy)-1,4-phenylene vinylene] (MEH-PPV) films is demonstrated. A thin-film structure, ITO-coated glass/MEH-PPV/Al, has shown the ability to store a continuum of conductance states. These states are nonvolatile and can be switched reproducibly by applying appropriate programing biases above a certain threshold voltage. The electrical conductivity of the highest and lowest states can differ by five orders of magnitude. Furthermore, these devices exhibit good cyclic switching characteristics and retention times of several weeks.
High-temperature random lasing in ZnO nanoneedles
Authors: Yang H. Y. , Lau S. P. , Yu S. F. , Abiyasa A. P. , Tanemura M. , Okita T. , Hatano H.
Published: July 2006

We report the high-temperature ultraviolet random laser action in ZnO nanoneedles. The characteristic temperature of the ZnO nanoneedle lasers was derived to be 138K in the temperature range from 300to615K. The cavity length of the random lasers as a function of temperature was determined by Fourier transform spectroscopy. The cavity length decreased with an increase in temperature from ∼14μm at 300Kto∼2μm at 550K. The optical gain of the ZnO nanoneedle lasers at high temperature is attributed to a self-compensation mechanism in the cavity length.
Design of a ZnMnSe∕ZnMgSe spin-polarized terahertz quantum cascade laser tunable by magnetic field
Authors: Savić Ivana , Ikonić Zoran , Vukmirović Nenad , Indjin Dragan , Harrison Paul , Milanović Vitomir
Published: July 2006

A design of a magnetic field tunable ZnMnSe∕ZnMgSe terahertz quantum cascade laser is proposed. It relies on the spin-dependent potential induced by a magnetic field. The electron dynamics are calculated using the Boltzmann equation approach, with electron-longitudinal optical phonon, electron-longitudinal acoustic phonon, and electron-electron scattering included. Tunability of the emission energy between 10 and 26meV, and 38 and 42meV, for transitions of spin-down and spin-up electrons, respectively, may be achieved by varying a magnetic field up to 5T, at a temperature of 1.5K. Population inversion of up to 42% for spin-down and 27% for spin-up electrons is predicted, which in conjunction with the estimated waveguide losses, yields sufficient gain for laser operation.
The STE20/Germinal Center Kinase POD6 Interacts with the NDR Kinase COT1 and Is Involved in Polar Tip Extension inNeurospora crassa
Authors: Seiler Stephan , Vogt Nico , Ziv Carmit , Gorovits Rena , Yarden Oded
Published: July 2006

Members of the Ste20 and NDR protein kinase families are important for normal cell differentiation and morphogenesis in various organisms. We characterized POD6 (NCU02537.2), a novel member of the GCK family of Ste20 kinases that is essential for hyphal tip extension and coordinated branch formation in the filamentous fungus Neurospora crassa. pod-6 and the NDR kinase mutant cot-1 exhibit indistinguishable growth defects, characterized by cessation of cell elongation, hyperbranching, and altered cell-wall composition. We suggest that POD6 and COT1 act in the same genetic pathway, based on the fact that both pod-6 and cot-1 can be suppressed by 1) environmental stresses, 2) altering protein kinase A activity, and 3) common extragenic suppressors (ropy, as well as gul-1, which is characterized here as the ortholog of the budding and fission yeasts SSD1 and Sts5, respectively). Unlinked noncomplementation of cot-1/pod-6 alleles indicates a potential physical interaction between the two kinases, which is further supported by coimmunoprecipitation analyses, partial colocalization of both proteins in wild-type cells, and their common mislocalization in dynein/kinesin mutants. We conclude that POD6 acts together with COT1 and is essential for polar cell extension in a kinesin/dynein-dependent manner in N. crassa.
Akt Down-Regulates ERK1/2 Nuclear Localization and Angiotensin II-induced Cell Proliferation through PEA-15
Authors: Gervais Marianne , Dugourd Céline , Muller Laurent , Ardidie Corinne , Canton Brigitte , Loviconi Laetitia , Corvol Pierre , Chneiweiss Hervé , Monnot Catherine
Published: July 2006

Angiotensin II (AngII) type 1 receptors (AT1) regulate cell growth through the extracellular signal-regulated kinase (ERK)1/2 and phosphatidylinositol 3-kinase (PI3K) pathways. ERK1/2 and Akt/protein kinase B, downstream of PI3K, are independently activated but both required for mediating AngII-induced proliferation when expressed at endogenous levels. We investigate the effect of an increase in the expression of wild-type Akt1 by using Chinese hamster ovary (CHO)-AT1 cells. Unexpectedly, Akt overexpression inhibits the AT1-mediated proliferation. This effect could be generated by a cross-talk between the PI3K and ERK1/2 pathways. A functional partner is the phosphoprotein enriched in astrocytes of 15 kDa (PEA-15), an Akt substrate known to bind ERK1/2 and to regulate their nuclear translocation. We report that Akt binds to PEA-15 and that Akt activation leads to PEA-15 stabilization, independently of PEA-15 interaction with ERK1/2. Akt cross-talk with PEA-15 does not affect ERK1/2 activation but decreases their nuclear activity as a result of the blockade of ERK1/2 nuclear accumulation. In response to AngII, PEA-15 overexpression displays the same functional consequences on ERK1/2 signaling as Akt overactivation. Thus, Akt overactivation prevents the nuclear translocation of ERK1/2 and the AngII-induced proliferation through interaction with and stabilization of endogenous PEA-15.
Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching
Authors: Du Pan , Kibbe Warren A. , Lin Simon M.
Published: July 2006

Motivation: A major problem for current peak detection algorithms is that noise in mass spectrometry (MS) spectra gives rise to a high rate of false positives. The false positive rate is especially problematic in detecting peaks with low amplitudes. Usually, various baseline correction algorithms and smoothing methods are applied before attempting peak detection. This approach is very sensitive to the amount of smoothing and aggressiveness of the baseline correction, which contribute to making peak detection results inconsistent between runs, instrumentation and analysis methods.

Results: Most peak detection algorithms simply identify peaks based on amplitude, ignoring the additional information present in the shape of the peaks in a spectrum. In our experience, ‘true’ peaks have characteristic shapes, and providing a shape-matching function that provides a ‘goodness of fit’ coefficient should provide a more robust peak identification method. Based on these observations, a continuous wavelet transform (CWT)-based peak detection algorithm has been devised that identifies peaks with different scales and amplitudes. By transforming the spectrum into wavelet space, the pattern-matching problem is simplified and in addition provides a powerful technique for identifying and separating the signal from the spike noise and colored noise. This transformation, with the additional information provided by the 2D CWT coefficients can greatly enhance the effective signal-to-noise ratio. Furthermore, with this technique no baseline removal or peak smoothing preprocessing steps are required before peak detection, and this improves the robustness of peak detection under a variety of conditions. The algorithm was evaluated with SELDI-TOF spectra with known polypeptide positions. Comparisons with two other popular algorithms were performed. The results show the CWT-based algorithm can identify both strong and weak peaks while keeping false positive rate low.

Availability: The algorithm is implemented in R and will be included as an open source module in the Bioconductor project.

Contact:  s-lin2@northwestern.edu

Supplementary material:  . Colour versions of the figures in this article can be found at Bioinformatics Online.
VAMP: Visualization and analysis of array-CGH, transcriptome and other molecular profiles
Authors: Rosa Philippe La , Viara Eric , Hupé Philippe , Pierron Gaëlle , Liva Stéphane , Neuvial Pierre , Brito Isabel , Lair Séverine , Servant Nicolas , Robine Nicolas , Manié Elodie , Brennetot Caroline , Janoueix-Lerosey Isabelle , Raynal Virginie , Gruel Nadège , Rouveirol Céline , Stransky Nicolas , Stern Marc-Henri , Delattre Olivier , Aurias Alain , Radvanyi François , Barillot Emmanuel
Published: July 2006

Motivation: Microarray-based CGH (Comparative Genomic Hybridization), transcriptome arrays and other large-scale genomic technologies are now routinely used to generate a vast amount of genomic profiles. Exploratory analysis of this data is crucial in helping to understand the data and to help form biological hypotheses. This step requires visualization of the data in a meaningful way to visualize the results and to perform first level analyses.

Results: We have developed a graphical user interface for visualization and first level analysis of molecular profiles. It is currently in use at the Institut Curie for cancer research projects involving CGH arrays, transcriptome arrays, SNP (single nucleotide polymorphism) arrays, loss of heterozygosity results (LOH), and Chromatin ImmunoPrecipitation arrays (ChIP chips). The interface offers the possibility of studying these different types of information in a consistent way. Several views are proposed, such as the classical CGH karyotype view or genome-wide multi-tumor comparison. Many functionalities for analyzing CGH data are provided by the interface, including looking for recurrent regions of alterations, confrontation to transcriptome data or clinical information, and clustering. Our tool consists of PHP scripts and of an applet written in Java. It can be run on public datasets at

Availability: The VAMP software (Visualization and Analysis of array-CGH,transcriptome and other Molecular Profiles) is available upon request. It can be tested on public datasets at . The documentation is available at

Contact:  vamp@curie.fr
Clinical significance of β1 integrin expression as a prediction marker for radiotherapy in early glottic carcinoma
Authors: Choi Seung‐Ho , Cho Kyung‐Ja , Nam Soon‐Yuhl , Lee Sang‐wook , Kang Joon , Kim Sang Yoon
Published: July 2006

Objective: To determine the significance of β1 integrin expression as a prediction marker for the response to radiotherapy in patients with early glottic carcinoma.

Study Design: Retrospective study in a tertiary referral center.

Methods: Among the T1/T2 glottic carcinoma patients treated with radiotherapy from 1992 to 2002, 52 had more than 2 years of follow‐up and available pretreatment biopsy specimens. The immunohistochemical staining was performed for the assay of β1 integrin expression, and the staining pattern of each was classified as diffuse, localized, or negative. The associations between the patterns of β1 integrin expression and clinicopathologic parameters, including response to radiotherapy, involvement of the anterior commissure, and grade of histologic differentiation, were evaluated.

Results: After radiotherapy, 42 patients remained tumor free, and 10 patients had recurrent or persistent disease. Six (12%) specimens were negative for β1 integrin expression, 39 (75%) had a localized staining pattern, and 7 (13%) had a diffuse staining pattern. Recurrence rate was significantly higher in the diffuse group (53%) than in the localized (13%) or negative (17%) groups (P = .023). The pattern of β1 integrin expression was also closely related to histologic differentiation (P = .008), although the association between response to radiotherapy and histologic differentiation was not significant

Conclusion: The pattern of expression of β1 integrin, which has been known as a stem cell marker of the epidermis, may be helpful in predicting the response to radiation in patients with early glottic carcinoma.
Patients Undergoing Sinus Surgery: Constructing a Demographic Profile
Authors: Martin Timothy J. , Yauck Jennifer S. , Smith Timothy L.
Published: July 2006

Objectives: The objective of this study is to construct an accurate and representative demographic profile of patients undergoing sinus surgery for chronic rhinosinusitis (CRS). This will enable future studies to enroll representative samples so that results can be more easily compared across studies and generalized to the U.S. population.

Methods: The investigators interrogated the databases of the National Survey of Ambulatory Surgery to gather demographic data. Whenever the NSAS provided incomplete characterization, deficiencies were corrected using state‐level data provided by the Health care Cost and Utilization Project. The constructed profile was compared with available profiles of patients with CRS and demographic data provided by the U.S. Census Bureau.

Results: The demographic profile of patients undergoing sinus surgery is 52.7% female with a mean age of 38.5 years. A total of 93.5% of surgery is performed on an outpatient basis with 78.8% of patients having private insurance sources. No significant difference in occurrence of surgery was found between months of the year or between regions of the country. The constructed race profile is 85.7% white, 5% black, 1.2% Asian/Pacific Islander, 0.2% Native American, and 7.8% other.

Conclusions. A novel integration of national and state databases can be used to create a demographic profile of patients undergoing surgery for CRS. The creation of this profile enables further study of representative populations of patients with CRS and enables thoughtful analysis of the existing literature. The difficulty in creating the profile highlights the need for complete and accurate healthcare information collection by national and state agencies.
Persistent Inflammation and Hyperresponsiveness Following Viral Rhinosinusitis
Authors: Klemens James Joseph , Thompson Kenneth , Langerman Alexander , Naclerio Robert M.
Published: July 2006

Objectives: To develop a murine model of viral rhinosinusitis.

Study Design: Randomized, controlled, animal model.

Methods: Mice were intranasally inoculated with Sendai virus (SeV) or ultraviolet (UV)‐inactivated virus. On days 3 and 10 postinfection, nasal lavage fluid was obtained for viral culture. On days 4, 10, and 38 postinfection, sinus mucosa was harvested and analyzed by flow cytometry for CD3‐, CD4‐, CD8‐, CD25‐, CD11b‐, CCR3‐, and GR1‐positive cells. Nasal hyperresponsiveness to histamine challenge was measured on days 8 and 36 postinoculation.

Results: On day 3, viral cultures were positive from all SeV‐inoculated mice but from none of the UV‐inactivated mice (P ≤ .0039). There was no growth of virus from either group on day 10. On day 4, flow cytometry on SeV‐infected sinus cells showed a significant increase in macrophages (P ≤ .03) and neutrophils (P ≤ .02) compared with controls. This inflammation resolved by day 10. On day 38, mice inoculated with SeV had significantly more CD8+ (P ≤ .044) and CD4+CD25+ (P ≤ .017) cells than did controls. On day 8, there was a significant increase in both sneezing (P ≤ .002) and nasal rubbing (P ≤ .002) in the SeV‐infected group to histamine challenge compared with controls. This difference continued to day 36.

Conclusions: Inoculation with SeV results in an acute infection that resolves spontaneously within 10 days. Infected mice develop a significant increase in T‐suppressor and T‐regulatory cells after resolution of the acute infection, which persists for at least 38 days. The persistence of these T cells is associated with hyperresponsiveness to histamine. This mouse model has some parallels to chronic rhinosinusitis after a viral infection in humans and should allow us to clarify the pathophysiology of this disease.
Pterygopalatine Fossa Infiltration Through the Greater Palatine Foramen: Where to Bend the Needle
Authors: Douglas Richard , Wormald Peter‐John
Published: July 2006

Objective: In the literature, there has been controversy regarding the length of the greater palatine canal. If the pterygopalatine fossa is infiltrated in an attempt to reduce bleeding during sinus surgery, this information is important to be able to place local anesthetic with maximal effect and the least likelihood of complications.

Study Design: The authors conducted a prospective cadaver‐based study using high‐definition computed tomography (CT) scans.

Methods: Twenty‐two cadaver heads were CT scanned and the greater palatine canal length, pterygopalatine fossa height, and thickness of the soft tissue in the roof of the mouth were measured on parasagittal images using the CT scanner workstation.

Results: The mean length of the greater palatine canal was 18.5 mm (95% confidence interval [CI] = 17.9–19.1) and the mean height of the pterygopalatine fossa was 21.6 mm (95% CI = 20.7–22.5). The mean thickness of the soft tissue in the roof of the mouth overlying the foramen of the greater palatine canal was 6.9 mm (95% CI = 6.2–7.6).

Conclusion: To perform an effective infiltration of the pterygopalatine fossa, the needle should be bent at 25 mm from the tip at an angle of 45°.
Denitratisoma oestradiolicum gen. nov., sp. nov., a 17β-oestradiol-degrading, denitrifying betaproteobacterium
Authors: Fahrbach Michael , Kuever Jan , Meinke Ruth , Kämpfer Peter , Hollender Juliane
Published: July 2006

A Gram-negative, motile, denitrifying bacterium (strain AcBE2-1T) was isolated from activated sludge of a municipal wastewater treatment plant using 17β-oestradiol (E2) as sole source of carbon and energy. Cells were curved rods, 0.4–0.8×0.8–2.0 μm in size, non-fermentative, non-spore-forming, oxidase-positive and catalase-negative. E2 was oxidized completely to carbon dioxide and water by reduction of nitrate to a mixture of dinitrogen monoxide and dinitrogen, with the intermediate accumulation of nitrite. Electron recoveries were between 90 and 100 %, taking assimilated E2 into account. With nitrate as the electron acceptor, the bacterium also grew on fatty acids (C2to C6), isobutyrate, crotonate,dl-lactate, pyruvate, fumarate and succinate. Phylogenetic analysis of its 16S rRNA gene sequence revealed that strain AcBE2-1Trepresents a separate line of descent within the familyRhodocyclaceae(Betaproteobacteria). The closest relatives are the cholesterol-degrading, denitrifying bacteriaSterolibacterium denitrificansDSM 13999Tand strain 72Chol (=DSM 12783), with <93.9 % sequence similarity. The G+C content of the DNA was 61.4 mol%. Detection of a quinone system with ubiquinone Q-8 as the predominant compound and a fatty acid profile that included high concentrations of C16 : 1ω7c/iso-C15 : 02-OH and C16 : 0, in addition to C18 : 1ω7cand small amounts of C8 : 03-OH, supported the results of the phylogenetic analysis. On the basis of 16S rRNA gene sequence data in combination with chemotaxonomic and physiological data, strain AcBE2-1T(=DSM 16959T=JCM 12830T) is placed in a new genusDenitratisomagen. nov. as the type strain of the type speciesDenitratisoma oestradiolicumgen. nov., sp. nov.