bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of an enzyme immunoassay to detect and quantify psoralen and bergapten in plants
Authors: Bourgaud F. , Bouque V. , Marchal S. , Innocenti G. , Dall'Acqua F. , Guckert A.
Published: March 2007

A competitive enzyme immunoassay has been developed in order to quantify furanocoumarins. 5‐Hydroxypsoralen was modified and linked to bovine serum albumin to obtain an antigenic response. The rabbit serum that was collected was highly specific to 5‐methoxypsoralen and psoralen but did not recognize angelicin (a psoralen angular isomer), 8‐methoxypsoralen or 5,8‐dimethoxypsoralen, coumarin and related molecules. The detection limit was about 5 ng/mL for 5‐methoxypsoralen and 30 ng/mL for psoralen. The test was applied to plants that contain furanocoumarins i.e. species of Psoralea. The correlation with a classical high‐pressure liquid chromatographic method was satisfactory with both dry and fresh matter. With reference to the extraction method used with the plant material, the detection limit in the plant samples was about 15 μg/g for the dry matter and 20 μg/g for the fresh matter. This technique is a useful tool to detect and quantify psoralen and 5‐methoxypsoralen in plant samples.
Methods for the purification of ubiquitinated Proteins
Authors: Tomlinson Emma , Palaniyappan Naaventhan , Tooth David , Layfield Robert
Published: March 2007

Post‐translational protein modification by the covalent conjugation of ubiquitin, originally implicated as a signal for proteolytic degradation by 26S proteasome, has now been realised to play important roles in the regulation of almost all biological processes in eukaryotes. In order to understand these processes in greater detail there is a requirement for techniques that can purify mixtures of ubiquitin‐conjugated proteins, as a prerequisite to their identification and characterisation. Here we review the methods that have been applied to the bulk purification of ubiquitinated proteins and discuss their applications in proteomic analyses of the ‘ubiquitome’.
Synthesis, characterization, and biodegradation of copolymers of unsaturated and saturated poly(ester amide)s
Authors: Guo Kai , Chu C. C.
Published: March 2007

A new family of biodegradable copolymers of unsaturated poly(ester amide)s (UPEAs) and saturated poly(ester amide)s (SPEAs) based on L‐phenylalanine, aliphatic dicarboxylic acids, and aliphatic dialcohols was synthesized by solution polycondensation and characterized. These unsaturated/saturated poly(ester amide) copolymers (USPEAs) were obtained in fairly good yields with N,N‐dimethylacetamide as the solvent. The molecular weights (Mn and Mw) of the USPEAs measured by GPC ranged from 15 to 60 kg/mol with a molecular weight distribution of 1.07–1.63. The chemical structures of the USPEAs were confirmed by both IR and NMR spectra. The USPEA copolymers had glass transition temperatures lower than that of pure UPEA but higher than that of pure SPEA. An increase in the unsaturated component in the USPEA copolymers led to an increase in their glass transition temperatures. The solubility of the copolymers was good in N,N‐dimethylacetamide and dimethyl sulfoxide but poor in water, acetone, methanol, and ethyl acetate. The preliminary in vitro biodegradation properties of the USPEA copolymers were investigated in both pure phosphate buffered saline (PBS) buffer and α‐chymotrypsin solutions. The copolymers showed significantly faster weight loss in an enzyme solution than in a pure PBS buffer. Upon the adjustment of the unsaturated‐to‐saturated diester monomer feed ratio, the obtained USPEA copolymers could have controlled chemical and physical properties, such as glass transition temperatures, solubility, and biodegradability, which could easily extend their applications to biomedical and pharmaceutical areas. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 1595–1606, 2007
Combined effects of conjugation pattern and alkoxy side chains on the photovoltaic properties of thiophene‐containing PPE‐PPVs
Authors: Ayuk Mbi Egbe Daniel , Nguyen Le Huong , Schmidtke Kathy , Wild Andreas , Sieber Christoph , Guenes Serap , Serdar Sariciftci Niyazi
Published: March 2007

This contribution presents the synthesis and properties of four thiophene‐containing poly(‐p‐arylene‐ethynylene)/poly(‐p‐arylene‐vinylene)s, PIa‐b and PIIa‐b, whose repeating units (RU) consist either of 1:2 or 2:2 triple bond/double bond ratio, and which bear linear alkoxy side chains not longer than octyloxy and branched 2‐ethylhexyloxy. PIa‐b and PIIa‐b exhibit similar absorption and emission behaviour in dilute solution (λa = 483–486 nm, λe = 540 nm) as well as in solid state (λa = 500, 530 nm, λe = 560 nm), whereby slightly higher fluorescence quantum yields (Φf) were obtained for PI than for PII systems, as a result of higher number of thiophene units within the RU of PII. An enhancement of the Φf‐value from 0% to 3% is obtained after replacing linear octadecyloxy in PIIc‐e by bulky branched 2‐ethylhexyloxy in PIIa‐b. Nonoptimized solar cells of configuration ITO/PEDOT:PSS/polymer: PCBM (1:3 weight ratio)/LiF/Al show open circuit voltages as high as 900 mV for PIa‐b and 800 mV for PIIa‐b. Reducing the size of the side chain from R = 2‐ethylhexyl in PIa to R = methyl in PIb leads to a significant increase of the short circuit current, ISC, from ca. 2.5 mA to ca. 3.7 mA and consequently to an enhancement of the energy conversion efficiency, ηAM1.5, from ca. 1.2% to ca. 1.7%. This is due to an extended donor‐acceptor interfacial area, as evidenced by AFM topology pictures showing smaller nanoscale clusters size in PIb than in PIa active layer. The same change led to minimal effect in PII systems. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 1619–1631, 2007
Block copolymers of dodecafluoroheptyl methacrylate and butyl methacrylate by RAFT miniemulsion polymerization
Authors: Qinghua Zhang , Xiaoli Zhan , Fengqiu Chen , Ying Shi , Qiongyan Wang
Published: March 2007

Reversible addition‐fragmentation chain transfer (RAFT) miniemulsion polymerization of butyl methacrylate (BMA) and dodecafluoroheptyl methacrylate (DFMA) was carried out with 2‐cyanoprop‐2‐yl dithiobenzoate (CPDB) as chain transfer agent (CTA). Concentration effects of RAFT agent and initiator on kinetics and molecular weight were investigated. No obvious red oil layer (phase's separation) and coagulation was observed in the first stage of homopolymerization of BMA. The polymer molecular weights increased linearly with the monomer conversion with polydispersities lower than 1.2. At 75 °C, the monomer conversion could achieve above 96% in 3 h with [momomer]:[RAFT]:[KPS] = 620:4:1 (mole ratio). The results showed excellent controlled/living polymerization characteristics and a very fast polymerization rate. Furthermore, the synthesis of poly(BMA‐b‐DFMA) diblock copolymers with a regular structure (PDI < 1.30, PMMA calibration) was performed by adding the monomer of DFMA at the end of the RAFT miniemulsion polymerization of BMA. The success of diblock copolymerization was showed by the molecular weight curves shifting toward higher molar mass, recorded by gel permeation chromatography before and after block copolymerization. Compositions of block copolymers were further confirmed by 1H NMR, FTIR, and DSC analysis. The copolymers exhibited a phase‐separated morphology and possessed distinct glass transition temperatures associated with fluoropolymer PDFMA and PBMA domains. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 1585–1594, 2007
Biomarkers in drug development: friend or foe? A personal reflection gained working within oncology
Authors: Carroll Kevin J.
Published: March 2007

Hopes and expectations for the use and utility of new, emerging biomarkers in drug development have probably never been higher, especially in oncology. Biomarkers are exalted as vital patient selection tools in an effort to target those most likely to benefit from a new drug, and so to reduce development costs, lessen risk and expedite developments times. It is further hoped that biomarkers can be used as surrogate endpoints for clinical outcomes, to demonstrate effectiveness and, ultimately, to support drug approval. However, I perceive that all is not straightforward, and, particularly in terms of the promise of accelerated drug development, biomarker strategies may not in all cases deliver the advances and advantages hoped for. Copyright © 2007 John Wiley & Sons, Ltd.
Direct mass spectrometric analysis of flavors and fragrances in real applications using DART
Authors: Haefliger Olivier P. , Jeckelmann Nicolas
Published: March 2007

DART (Direct Analysis in Real Time) is an innovative technology to analyze complex solid samples at atmospheric pressure and ground potential by simply placing them between a DART ion source and a mass spectrometer. The analytes are ionized by a gun of neutral metastable species. The first examples of the application of DART to the analysis of flavor and fragrance raw materials in real, complex applications are reported here. A remarkably high potential of the technique is demonstrated. DART was applied to semi‐quantitative analyses of perfumery raw materials deposited on smelling strips. In optimal cases, limits of detection around 100 pg were achieved. DART also allowed the assessment of the deposition and release of fragrance on surfaces such as fabric and hair. Finally, DART permitted the screening of twelve chewing gum samples for the possible presence of taste‐refreshing compounds in less than 30 min. Copyright © 2007 John Wiley & Sons, Ltd.
The influence of river regulation and land use on floodplain forest regeneration in the semi‐arid upper Colorado River Basin, USA
Authors: Northcott Krista , Andersen Douglas C. , Cooper David J.
Published: March 2007

Flow regulation effects on floodplain forests in the semi‐arid western United States are moderately well understood, whereas effects associated with changes in floodplain land use are poorly documented. We mapped land cover patterns from recent aerial photos and applied a classification scheme to mainstem alluvial floodplains in 10 subjectively selected 4th order hydrologic units (subbasins) in the Upper Colorado River Basin (UCRB) in order to document land use patterns (floodplain development) and assess their effects on Fremont cottonwood forest (CF) regeneration. Three of the mainstem rivers were unregulated, five were moderately regulated and two were highly regulated. We classified polygons as Undeveloped (with two categories, including CF) and Developed (with five categories). We ground‐truthed 501 randomly selected polygons (4–28% of the floodplain area in each subbasin) to verify classification accuracy and to search for cottonwood regeneration, defined as stands established since regulation began or 1950, whichever is most recent. From 40% to 95% of the floodplain area remained undeveloped, but only 19–70% of the floodplain area was classified as forest. Regeneration occupied a mean of 5% (range 1–17%) of the floodplain. The likelihood of the presence of regeneration in a polygon was reduced 65% by development and independently in a complex manner by flow regulation. Our analyses indicate that floodplain forests may be in jeopardy on both regulated and unregulated rivers and that information on historical forest extent is needed to better understand their current status in the UCRB. Conservation efforts need to be coordinated at a regional level and address the potentially adverse affects of both flow regulation and floodplain development. Published in 2007 by John Wiley & Sons, Ltd.
Osmoresistant yeast Zygosaccharomyces rouxii: the two most studied wild‐type strains (ATCC 2623 and ATCC 42981) differ in osmotolerance and glycerol metabolism
Authors: Pribylova Lenka , de Montigny Jacky , Sychrova Hana
Published: March 2007

The yeast Zygosaccharomyces rouxii is known for its high tolerance to osmotic stress, which is thought to be caused by sets of specific genes. Relatively few Z. rouxii genes have been identified so far, all of them having homologues in Saccharomyces cerevisiae; none of them was Z. rouxii‐specific. Most of the known Z. rouxii genes were isolated from two wild‐type strains, ATCC 2623 and ATCC 42981. In this study, we compared these two strains with regard to some of their morphological, physiological and genomic properties. Important differences were found in their salt tolerance and assimilation of glycerol and karyotype; slight differences were also present in their cell morphology. The ATCC 42981 strain showed a higher resistance to salts, higher glycerol production and, unlike ATCC 2623, was able to assimilate glycerol. Under conditions of osmotic stress, the glycerol production in both Z. rouxii strains was much lower than in a S. cerevisiae S288c culture, which suggested the presence of a system that efficiently retains glycerol inside Z. rouxii cells. The karyotype analysis revealed that ATCC 42981 cells contain more chromosomes and have a bigger genome size than those of ATCC 2623. Copyright © 2007 John Wiley & Sons, Ltd.
Attenuation of stress-induced anorexia in brown trout (Salmo trutta) by pre-treatment with dietaryl-tryptophan
Authors: Höglund Erik , Sørensen Christina , Bakke Marit Jørgensen , Nilsson Göran E. , Øverli Øyvind
Published: March 2007

The general consensus is that brain serotonin (5-HT) inhibits feed intake in teleost fishes and other vertebrates. Dietary manipulations with the 5-HT precursor tryptophan (TRP) have, however, yielded contradictory effects on feed intake, while studies of the endocrine response to stress indicate that the effects of TRP-enriched feed are context dependent. A characteristic behavioural response to stress is a reduction in feed intake, and in the present study we investigated whether pre-treatment with TRP-enriched feed affected stress-induced changes in feeding behaviour in brown trout (Salmo trutta). After acclimatisation in observation aquaria, isolated fish were fed control or TRP-supplemented feed for 7 d, whereupon they were transferred to a novel environment, in which all fish were fed control feed. Transfer to a new environment resulted in decreased feeding in both the TRP pre-treated and the control-treated group. However, this decrease was more pronounced in the control-treated group. Previous experiments have concluded that stimulation of brain 5-HT systems by TRP enhancement does not affect feed intake in salmonid fishes, but in these studies food intake was observed in unstressed animals only. The present study suggests that pre-treatment with dietary TRP attenuates stress-induced anorexia. Hence, it appears that the effect of dietary manipulations of TRP on feeding behaviour is dependent on the stress levels experienced by experimental animals. These behavioural data are discussed in the context of the involvement of 5-HT in appetite regulation.
THE RESTORATION OF THE PORTICUS OCTAVIAE AND SEVERAN IMPERIAL POLICY
Authors: GORRIE CHARMAINE
Published: March 2007

The Porticus Octaviae was built in the Campus Martius sometime between 33 and 23 BC (Figure 1). There is controversy as to whether it was built by Augustus and dedicated to his sister, or commissioned by Octavia herself. The complex, however, which included a library and senate house was closely associated with Octavia and her son. The Porticus Octaviae fell victim to the fire of ad 80 and was probably restored by Domitian. An inscription on the propylon of the complex records its restoration, also after a fire, by Septimius Severus and Caracalla in AD 203. Little consideration, however, has been given to the importance of the Severan restoration in the context of this emperor's building programme. This article will examine the messages conveyed by the restoration of the Porticus Octaviae in terms of Severus' imperial policy, and in particular his desire to connect himself to the legacy of Augustus.
CICERO AND THE TREVERI: NEW LIGHT ON AN OLD PUN
Authors: SHOTTER DAVID
Published: March 2007

Sed, ut ego quoque te aliquid admoneam de vestris cautionibus, Treveros vites censeo: audio capitales esse: mallem auro, argento, aere essent.

However, if I may give you a caveat from your own legal arsenal, I advise you to keep clear of the Treveri: I hear that they are deadly customers, like their Roman namesakes. If you want a Board of Three, better try the Masters of the Mint.

The letter, from which this passage is taken, is one of a number that passed between Cicero and a young lawyer, Gaius Trebatius Testa, who was serving with Julius Caesar's army in Gaul in the late 50s BC.

As in most of his letters to Trebatius, Cicero revels in jokes and word-play with a legal flavour which, of course, would have suited this particular recipient. This passage is far from easy to translate adequately into English because it contains a ‘developing’ pun, the full force of which is inevitably lost in translation. The actual structure of the pun, however, is obvious enough: Trebatius' proximity to the tribe of the Treveri leads to a word-play with the Latin word, Tresviri (‘Board of Three’). The fact that the Treveri had a reputation for ferocity in battle causes Cicero to call them ‘deadly’ (capitales) which, in its turn, leads to an implied reference to the Tresviri Capitales, three junior officials in Rome who were in charge of executions and prisons.
Adaptive motion selection for online hand–eye calibration
Authors: Zhang Jing , Shi Fanhuai , Liu Yuncai
Published: March 2007

While a robot moves, online hand–eye calibration to determine the relative pose between the robot gripper/end-effector and the sensors mounted on it is very important in a vision-guided robot system. During online hand–eye calibration, it is impossible to perform motion planning to avoid degenerate motions and small rotations, which may lead to unreliable calibration results. This paper proposes an adaptive motion selection algorithm for online hand–eye calibration, featured by dynamic threshold determination for motion selection and getting reliable hand–eye calibration results. Simulation and real experiments demonstrate the effectiveness of our method.
A prototype for convective margin shifts
Authors: Lintner B. R. , Neelin J. D.
Published: March 2007

Regional precipitation anomalies under El Niño or global warming scenarios manifest considerable spatial variability, especially in the vicinity of tropical deep convective zones. Using a simplified set of equations, we develop an analytic prototype of convective margins for tropical land regions subject to inflow from adjacent ocean regions. The approach yields an expression for the location of the convective margin from which it is straightforward to deduce how climate perturbations impact the margin. We compare the results of the prototype to full model simulations of the equatorial South American precipitation response to El Niño forcing and find general agreement. Analysis of the observations supports the convective inflow margin prototype's applicability to appropriately simple basic state configurations.
Simultaneous retrieval of volcanic ash and SO2 using MSG‐SEVIRI measurements
Authors: Prata A. J. , Kerkmann J.
Published: March 2007

Volcanic ash and sulphur dioxide masses from the November 2005 eruption of Karthala volcano, Comoros Islands, are simultaneously retrieved using rapid‐scan, multispectral infrared measurements from the Spin Enhanced Visible and Infrared Imager on board the Meteosat Second Generation geosynchronous satellite. Retrievals are made every 15 min, which show that the ash and SO2 separate in the vertically sheared atmosphere producing a fast moving upper level (∼12 km) SO2 cloud, a slower moving middle level (∼8 km) ash cloud and a boundary layer (<3 km) SO2 plume. The total mass of fine ash is 0.1 ± 0.05 Tg (SiO2), the upper level SO2 mass is 0.19 ± 0.01 Tg (S) while the boundary layer SO2 mass is 0.009 ± 0.01 Tg (S). These are the first simultaneous satellite measurements of ash and SO2 from an erupting volcano and confirm previous ideas about vertical separation. We suggest care must be exercised when using SO2 as a tracer for volcanic ash in aviation hazard warning systems.
Impacts of land use/cover classification accuracy on regional climate simulations
Authors: Ge Jianjun , Qi Jiaguo , Lofgren Brent M. , Moore Nathan , Torbick Nathan , Olson Jennifer M.
Published: March 2007

Land use/cover change has been recognized as a key component in global change. Various land cover data sets, including historically reconstructed, recently observed, and future projected, have been used in numerous climate modeling studies at regional to global scales. However, little attention has been paid to the effect of land cover classification accuracy on climate simulations, though accuracy assessment has become a routine procedure in land cover production community. In this study, we analyzed the behavior of simulated precipitation in the Regional Atmospheric Modeling System (RAMS) over a range of simulated classification accuracies over a 3 month period. This study found that land cover accuracy under 80% had a strong effect on precipitation especially when the land surface had a greater control of the atmosphere. This effect became stronger as the accuracy decreased. As shown in three follow‐on experiments, the effect was further influenced by model parameterizations such as convection schemes and interior nudging, which can mitigate the strength of surface boundary forcings. In reality, land cover accuracy rarely obtains the commonly recommended 85% target. Its effect on climate simulations should therefore be considered, especially when historically reconstructed and future projected land covers are employed.
Ergodicity of pumping tests
Authors: Sanchez‐Vila Xavier , Tartakovsky Daniel M.
Published: March 2007

Standard interpretations of pumping tests in heterogeneous formations rely on effective representations of porous media, which replace spatially varying hydraulic properties with their constant counterparts averaged over the support volume of a test. Rigorous approaches for deriving representative (effective, apparent, upscaled, etc.) parameters employ either ensemble or spatial averaging. We derive a set of conditions under which these two paradigms yield identical results. We refer to them as conditions for the ergodicity of pumping tests. This allows one to use stochastic approaches to estimate the statistics of the spatial variability of hydraulic parameters on scales smaller than the support volume of a pumping test.
Effect of ultrasound on the heterogeneous nucleation of BaSO4 during reactive crystallization
Authors: Guo Z. , Jones A. G. , Hao H. , Patel B. , Li N.
Published: March 2007

The effect of ultrasound on reactive crystallization is studied by measuring the induction time when nucleation is predominantly heterogeneous. Barium sulphate is used as the working substance precipitated by mixing aqueous BaCl2 and Na2SO4 solutions with relatively low concentrations compared to experiments for homogeneous nucleation. It is observed that at a given supersaturation level, the induction time significantly decreases with increasing ultrasonic energy input. The mechanism of the ultrasonic effect on heterogeneous nucleation is analyzed. The effect of ultrasound is to increase the diffusion coefficient (DAB) while reducing the contact angle (θ) and geometric factor (f). This gives rise to an increase in the heterogeneous nucleation rate and shorter induction time. The ultrasonic effect on critical supersaturation ratio (Scrit) is also investigated to determine the mechanism of ultrasonic effect on f and θ. Both the force from the cavitational bubble implosion and the nucleation process occurring at bubble/solution/foreign solid interface are proposed as the predominant reasons why contact angle (θ) decreases with the increase of energy input.
Resonance of relaxation time in the temperature modulated Schlögl model
Authors: Antoine C. , Lemarchand A.
Published: March 2007

We show the possibility to accelerate—in a resonant way—a nonlinear chemical reaction by imposing a small temperature modulation. This classical resonance, which happens for particular modulation frequencies, is illustrated on the athermic cubic Schlögl model, which allows us to get analytical expressions for both the reaction relaxation time and the frequency-resonant delay.
Frequency oscillations of the Shapiro steps
Authors: Hu Bambi , Tekić Jasmina
Published: March 2007

The frequency dependence of the dynamical-mode locking phenomena in the ac driven dissipative Frenkel-Kontorova model is studied by the molecular-dynamics simulations. It was found that the Shapiro steps exhibit very strong frequency dependence influenced by the amplitude of ac force. At the low frequencies, in the large amplitude regime, the oscillations of the step width and the critical depinning force have been observed. These oscillations are directly related to the stability and the existence of the interference effects in the real systems.
Self-assembly morphology effects on the crystallization of semicrystalline block copolymer thin film
Authors: Wei Yuhan , Pan Caiyuan , Li Binyao , Han Yanchun
Published: March 2007

Self-assembly morphology effects on the crystalline behavior of asymmetric semicrystalline block copolymer polystyrene-block-poly(L-lactic acid) thin film were investigated. Firstly, a series of distinctive self-assembly aggregates, from spherical to ellipsoid and rhombic lamellar micelles (two different kinds of rhombic micelles, defined as rhomb 1 and rhomb 2) was prepared by means of promoting the solvent selectivity. Then, the effects of these self-assembly aggregates on crystallization at the early stage of film evolution were investigated by in situ hot stage atomic force microscopy. Heterogeneous nucleation initiated from the spherical micelles and dendrites with flat on crystals appeared with increasing temperature. At high temperature, protruding structures were observed due to the thickening of the flat-on crystals and finally more thermodynamically stable crystallization formed. Annealing the rhombic lamellar micelles resulted in different phenomena. Turtle-shell-like crystalline structure initiated from the periphery of the rhombic micelle 1 and spread over the whole film surface in the presence of mostly noncrystalline domain interior. Erosion and small hole appeared at the surface of the rhombic lamellar micelle 2; no crystallization like that in rhomb 1 occurred. It indicated that the chain-folding degree was different in these two micelles, which resulted in different annealing behaviors.
Effect of percolation on thermal transport in nanotube composites
Authors: Kumar S. , Alam M. A. , Murthy J. Y.
Published: March 2007

The effective thermal conductivity of two-dimensional (2D) nanocomposites composed of carbon nanotubes (CNTs) dispersed in a host substrate is simulated to quantify the role of tube percolation on the thermal transport. The model is in excellent agreement with a 2D effective medium theory for low tube densities, but departs significantly from it when tube-tube interaction becomes significant. It is found that percolation effects may play a role for tube-tube and tube-substrate thermal resistance parameters typical of CNT composites. They are quantified in terms of a conductivity exponent for a range of governing parameters.
Orientation dependence of magnetic moment on double-walled nanotubes with topological line defects
Authors: Okada Susumu , Nakada Kyoko , Kawai Takazumi
Published: March 2007

The authors propose a double-walled structure of carbon nanotubes with topological line defects as a structure that exhibits magnetic moment depending on the mutual orientation of constituent nanotubes. In a short distance between the defects on each nanotube, the hybridization between the localized states on each nanotube results in a low-spin state as the ground state. In other orientations, the polarized electron spins localized around the defect on each tube are in parallel direction to each other resulting in a high-spin state. Local density of states around the Fermi level indicates that the double-walled nanotube exhibits spin-dependent transport properties.
Detection of terahertz waves using low-temperature-grown InGaAs with 1.56μm pulse excitation
Authors: Takazato A. , Kamakura M. , Matsui T. , Kitagawa J. , Kadoya Y.
Published: March 2007

The authors have investigated the dc and terahertz-detection characteristics of the photoconductive antennas made on low-temperature-grown (LTG) InxGa1−xAs (0.4<x<0.53). It was found that the resistivity of the LTG In0.4Ga0.6As can be as high as 700Ωcm, with which the resistance of the antenna becomes higher than 3MΩ. Terahertz waves were detected by the antennas with the pulse excitation at 1.56μm, with a spectral range exceeding 3THz, and a dynamic range of about 55dB. The results also indicate that the photocarrier dynamics depend on the In content.
Evidence for “superfilling” of submicrometer trenches with electroless copper deposit
Authors: Hasegawa Madoka , Yamachika Noriyuki , Shacham-Diamand Yosi , Okinaka Yutaka , Osaka Tetsuya
Published: March 2007

Void-free copper filling of trenches for ultralarge scale integrated interconnect structure was demonstrated by electroless deposition technique using polyethylene glycol as an inhibiting bath additive. With this electroless plating bath, the authors succeeded in demonstrating superfilling. Of particular interest is that the deposition at trench opening was nil during the filling process, while that at the bottom was very fast. This letter presents a demonstration and a proof of superfilling of trenches by electroless copper deposition.
Real-time plasmon resonance tuning of liquid Ga nanoparticles by in situ spectroscopic ellipsometry
Authors: Wu Pae C , Kim Tong-Ho , Brown April S. , Losurdo Maria , Bruno Giovanni , Everitt Henry O.
Published: March 2007

Liquid Ga nanoparticles have been deposited on sapphire substrates at room temperature. The optical evolution of Ga nanoparticle surface plasmon resonance during deposition has been characterized by in situ real-time spectroscopic ellipsometry to control and tune the plasmon resonance photon energy. The existence of both longitudinal and transverse modes for spheroidal Ga nanoparticles supported on a sapphire substrate is demonstrated and the dependence of the longitudinal and transverse plasmon energies on particle size is discussed. Stability of the Ga surface plasmon resonance to air exposure and high temperature is also demonstrated.
Are predatory arthropods useful indicators in Australian agroecosystems?
Authors: New T. R.
Published: March 2007

Information on the diversity and roles of two groups of arthropod predators (Neuroptera and Araneae) in Australian cropping systems is reviewed, as a foundation for discussing the properties of such predators that may render them useful bioindicators, and for discussing their ecological roles in agroecosystems. Predators are a prime target for conservation and augmentation, reflecting their perceived or actual positive roles in pest management, but most appear to have little value as true bioindicators in agricultural environments. In Australia, Neuroptera are represented by very few species in most agroecosystems, and all of these species are polyphagous generalists. Biological knowledge of Araneae, and of the factors that influence their species richness, is too scanty to enable sound understanding of changes in assemblage composition that might otherwise be regarded as ‘indication’. The current value of these groups as bioindicators is minimal.
Distinctive features of large complex virus genomes and proteomes
Authors: Mrázek Jan , Karlin Samuel
Published: March 2007

More than a dozen large DNA viruses exceeding 240-kb genome size were recently discovered, including the “giant”
mimivirus
with a 1.2-Mb genome size. The detection of
mimivirus
and other large viruses has stimulated new analysis and discussion concerning the early evolution of life and the complexity and mechanisms of evolutionary transitions. This paper presents analysis in three contexts. (
i
) Genome signatures of large viruses tend to deviate from the genome signatures of their hosts, perhaps indicating that the large viruses are lytic in the hosts. (
ii
) Proteome composition within these viral genomes contrast with cellular organisms; for example, most eukaryotic genomes, with respect to acidic residue usages, select Glu over Asp, but the opposite generally prevails for the large viral genomes preferring Asp more than Glu. In comparing Phe vs. Tyr usage, the viral genomes select mostly Tyr over Phe, whereas in almost all bacterial and eukaryotic genomes, Phe is used more than Tyr. Interpretations of these contrasts are proffered with respect to protein structure and function. (
iii
) Frequent oligonucleotides and peptides are characterized in the large viral genomes. The frequent words may provide structural flexibility to interact with host proteins.
Discovery of microRNA–mRNA modules via population-based probabilistic learning
Authors: Joung Je-Gun , Hwang Kyu-Baek , Nam Jin-Wu , Kim Soo-Jin , Zhang Byoung-Tak
Published: March 2007

Motivation: MicroRNAs (miRNAs) and mRNAs constitute an important part of gene regulatory networks, influencing diverse biological phenomena. Elucidating closely related miRNAs and mRNAs can be an essential first step towards the discovery of their combinatorial effects on different cellular states. Here, we propose a probabilistic learning method to identify synergistic miRNAs involving regulation of their condition-specific target genes (mRNAs) from multiple information sources, i.e. computationally predicted target genes of miRNAs and their respective expression profiles.

Results: We used data sets consisting of miRNA–target gene binding information and expression profiles of miRNAs and mRNAs on human cancer samples. Our method allowed us to detect functionally correlated miRNA–mRNA modules involved in specific biological processes from multiple data sources by using a balanced fitness function and efficient searching over multiple populations. The proposed algorithm found two miRNA–mRNA modules, highly correlated with respect to their expression and biological function. Moreover, the mRNAs included in the same module showed much higher correlations when the related miRNAs were highly expressed, demonstrating our method's ability for finding coherent miRNA–mRNA modules. Most members of these modules have been reported to be closely related with cancer. Consequently, our method can provide a primary source of miRNA and target sets presumed to constitute closely related parts of gene regulatory pathways.

Contact:  btzhang@bi.snu.ac.kr

Supplementary information: Supplementary data are available at Bioinformatics online.
Low copy repeats mediate distal chromosome 22q11.2 deletions: Sequence analysis predicts breakpoint mechanisms
Authors: Shaikh Tamim H. , O’Connor Ronald J. , Pierpont Mary Ella , McGrath James , Hacker April M. , Nimmakayalu Manjunath , Geiger Elizabeth , Emanuel Beverly S. , Saitta Sulagna C.
Published: March 2007

Genomic disorders contribute significantly to genetic disease and, as detection methods improve, greater numbers are being defined. Paralogous low copy repeats (LCRs) mediate many of the chromosomal rearrangements that underlie these disorders, predisposing chromosomes to recombination errors. Deletions of proximal 22q11.2 comprise the most frequently occurring microdeletion syndrome, DiGeorge/Velocardiofacial syndrome (DGS/VCFS), in which most breakpoints have been localized to a 3 Mb region containing four large LCRs. Immediately distal to this region, there are another four related but smaller LCRs that have not been characterized extensively. We used paralog-specific primers and long-range PCR to clone, sequence, and examine the distal deletion breakpoints from two patients with de novo deletions mapping to these distal LCRs. Our results present definitive evidence of the direct involvement of LCRs in 22q11 deletions and map both breakpoints to the BCRL module, common to most 22q11 LCRs, suggesting a potential region for LCR-mediated rearrangement both in the distal LCRs and in the DGS interval. These are the first reported cases of distal 22q11 deletions in which breakpoints have been characterized at the nucleotide level within LCRs, confirming that distal 22q11 LCRs can and do mediate rearrangements leading to genomic disorders.
A Novel Bioinformatics Approach Identifies Candidate Genes for the Synthesis and Feruloylation of Arabinoxylan
Authors: Mitchell Rowan A.C. , Dupree Paul , Shewry Peter R.
Published: March 2007

Arabinoxylans (AXs) are major components of graminaceous plant cell walls, including those in the grain and straw of economically important cereals. Despite some recent advances in identifying the genes encoding biosynthetic enzymes for a number of other plant cell wall polysaccharides, the genes encoding enzymes of the final stages of AX synthesis have not been identified. We have therefore adopted a novel bioinformatics approach based on estimation of differential expression of orthologous genes between taxonomic divisions of species. Over 3 million public domain cereal and dicot expressed sequence tags were mapped onto the complete sets of rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana) genes, respectively. It was assumed that genes in cereals involved in AX biosynthesis would be expressed at high levels and that their orthologs in dicotyledonous plants would be expressed at much lower levels. Considering all rice genes encoding putative glycosyl transferases (GTs) predicted to be integral membrane proteins, genes in the GT43, GT47, and GT61 families emerged as much the strongest candidates. When the search was widened to all other rice or Arabidopsis genes predicted to encode integral membrane proteins, cereal genes in Pfam family PF02458 emerged as candidates for the feruloylation of AX. Our analysis, known activities, and recent findings elsewhere are most consistent with genes in the GT43 families encoding β-1,4-xylan synthases, genes in the GT47 family encoding xylan α-1,2- or α-1,3-arabinosyl transferases, and genes in the GT61 family encoding feruloyl-AX β-1,2-xylosyl transferases.
Nitric Oxide and cGMP Signaling in Calcium-Dependent Development of Cell Polarity inCeratopteris richardii
Authors: Salmi Mari L. , Morris Kacey E. , Roux Stanley J. , Porterfield D. Marshall
Published: March 2007

Single-celled spores of the fern Ceratopteris richardii undergo gravity-directed cell polarity development that is driven by polar calcium currents. Here we present results that establish a role for nitric oxide (NO)/cGMP signaling in transducing the stimulus of gravity to directed polarization of the spores. Application of specific NO donors and scavengers inhibited the calcium-dependent gravity response in a dose-dependent manner. The effects of NO donor exposure were antagonized by application of NO scavenger compounds. Similarly, the guanylate cyclase inhibitors 6-anilino-5,8-quinolinedione and 1H-[1,2,4]oxadiazolo[4,3-a]quinoxalin, and the phosphodiesterase inhibitor Viagra, which modulate NO-dependent cGMP levels in the cells, disrupted gravity-directed cell polarity in a dose-dependent manner. Viagra effects were antagonized by application of NO scavengers, consistent with the postulate that NO and cGMP are linked in the signaling pathway. To identify other components of the signaling system we analyzed gene expression changes induced by Viagra treatment using microarrays and quantitative real-time reverse transcription-polymerase chain reaction. Preliminary microarray analysis revealed several genes whose expression was significantly altered by Viagra treatment. Three of these genes had strong sequence similarity to key signal transduction or stress response genes and quantitative real-time reverse transcription-polymerase chain reaction was used to more rigorously quantify the effects of Viagra on their expression in spores and to test how closely these effects could be mimicked by treatment with dibutyryl cGMP. Taken together our results implicate NO and cGMP as downstream effectors that help link the gravity stimulus to polarized growth in C. richardii spores.
Nitric Oxide Synthase-Dependent Nitric Oxide Production Is Associated with Salt Tolerance in Arabidopsis
Authors: Zhao Min-Gui , Tian Qiu-Ying , Zhang Wen-Hao
Published: March 2007

Nitric oxide (NO) has emerged as a key molecule involved in many physiological processes in plants. To characterize roles of NO in tolerance of Arabidopsis (Arabidopsis thaliana) to salt stress, effect of NaCl on Arabidopsis wild-type and mutant (Atnoa1) plants with an impaired in vivo NO synthase (NOS) activity and a reduced endogenous NO level was investigated. Atnoa1 mutant plants displayed a greater Na+ to K+ ratio in shoots than wild-type plants due to enhanced accumulation of Na+ and reduced accumulation of K+ when exposed to NaCl. Germination of Atnoa1 seeds was more sensitive to NaCl than that of wild-type seeds, and wild-type plants exhibited higher survival rates than Atnoa1 plants when grown under salt stress. Atnoa1 plants had higher levels of hydrogen peroxide than wild-type plants under both control and salt stress, suggesting that Atnoa1 is more vulnerable to salt and oxidative stress than wild-type plants. Treatments of wild-type plants with NOS inhibitor and NO scavenger reduced endogenous NO levels and enhanced NaCl-induced increase in Na+ to K+ ratio. Exposure of wild-type plants to NaCl inhibited NOS activity and reduced quantity of NOA1 protein, leading to a decrease in endogenous NO levels measured by NO-specific fluorescent probe. Treatment of Atnoa1 plants with NO donor sodium nitroprusside attenuated the NaCl-induced increase in Na+ to K+ ratio. Therefore, these findings provide direct evidence to support that disruption of NOS-dependent NO production is associated with salt tolerance in Arabidopsis.
Impairment of Cellulose Synthases Required forArabidopsisSecondary Cell Wall Formation Enhances Disease Resistance
Authors: Hernández-Blanco Camilo , Feng Dong Xin , Hu Jian , Sánchez-Vallet Andrea , Deslandes Laurent , Llorente Francisco , Berrocal-Lobo Marta , Keller Harald , Barlet Xavier , Sánchez-Rodríguez Clara , Anderson Lisa K. , Somerville Shauna , Marco Yves , Molina Antonio
Published: March 2007

Cellulose is synthesized by cellulose synthases (CESAs) contained in plasma membrane–localized complexes. In Arabidopsis thaliana, three types of CESA subunits (CESA4/IRREGULAR XYLEM5 [IRX5], CESA7/IRX3, and CESA8/IRX1) are required for secondary cell wall formation. We report that mutations in these proteins conferred enhanced resistance to the soil-borne bacterium Ralstonia solanacearum and the necrotrophic fungus Plectosphaerella cucumerina. By contrast, susceptibility to these pathogens was not altered in cell wall mutants of primary wall CESA subunits (CESA1, CESA3/ISOXABEN RESISTANT1 [IXR1], and CESA6/IXR2) or POWDERY MILDEW–RESISTANT5 (PMR5) and PMR6 genes. Double mutants indicated that irx-mediated resistance was independent of salicylic acid, ethylene, and jasmonate signaling. Comparative transcriptomic analyses identified a set of common irx upregulated genes, including a number of abscisic acid (ABA)–responsive, defense-related genes encoding antibiotic peptides and enzymes involved in the synthesis and activation of antimicrobial secondary metabolites. These data as well as the increased susceptibility of ABA mutants (abi1-1, abi2-1, and aba1-6) to R. solanacearum support a direct role of ABA in resistance to this pathogen. Our results also indicate that alteration of secondary cell wall integrity by inhibiting cellulose synthesis leads to specific activation of novel defense pathways that contribute to the generation of an antimicrobial-enriched environment hostile to pathogens.
The Arabidopsis aba4-1 Mutant Reveals a Specific Function for Neoxanthin in Protection against Photooxidative Stress
Authors: Dall'Osto Luca , Cazzaniga Stefano , North Helen , Marion-Poll Annie , Bassi Roberto
Published: March 2007

The aba4-1 mutant completely lacks neoxanthin but retains all other xanthophyll species. The missing neoxanthin in light-harvesting complex (Lhc) proteins is compensated for by higher levels of violaxanthin, albeit with lower capacity for photoprotection compared with proteins with wild-type levels of neoxanthin. Detached leaves of aba4-1 were more sensitive to oxidative stress than the wild type when exposed to high light and incubated in a solution of photosensitizer agents. Both treatments caused more rapid pigment bleaching and lipid oxidation in aba4-1 than wild-type plants, suggesting that neoxanthin acts as an antioxidant within the photosystem II (PSII) supercomplex in thylakoids. While neoxanthin-depleted Lhc proteins and leaves had similar sensitivity as the wild type to hydrogen peroxide and singlet oxygen, they were more sensitive to superoxide anions. aba4-1 intact plants were not more sensitive than the wild type to high-light stress, indicating the existence of compensatory mechanisms of photoprotection involving the accumulation of zeaxanthin. However, the aba4-1 npq1 double mutant, lacking zeaxanthin and neoxanthin, underwent stronger PSII photoinhibition and more extensive oxidation of pigments than the npq1 mutant, which still contains neoxanthin. We conclude that neoxanthin preserves PSII from photoinactivation and protects membrane lipids from photooxidation by reactive oxygen species. Neoxanthin appears particularly active against superoxide anions produced by the Mehler's reaction, whose rate is known to be enhanced in abiotic stress conditions.
Cathodic protection of concrete structures containing calcareous aggregates in tropical‐humid marine environments
Authors: Sosa M. , Camacho R. , Pérez T. , González‐Sánchez J.
Published: March 2007

Purpose

To evaluate the performance of two cathodic protection (CP) systems applied to steel reinforced concrete structures manufactured with calcareous aggregates and exposed to the tropical‐humid marine environment at the Yucatán peninsula in Mexico.

Design/methodology/approach

Rectangular concrete beams were manufactured using a water/cement ratio = 0.65, with and without the addition of NaCl in the mixing water. Specimens subjected to CP, eight to impressed current cathodic protection (ICCP) and eight to sacrificial anode cathodic protection (SACP) were partially immersed in natural seawater during 360 days. The half cell potential (HCP) and the current consumption were recorded during the total exposure time.

Findings

The measured HCP values of the steel rebar in the beams subjected to SACP did not attain protection potential levels. However, the galvanic couple Zn‐steel provided enough current for the protection of the steel. Visual inspection of concrete cores extracted from the beams indicated that corrosion products were not present at the steel‐concrete boundary. On the other hand, the ICCP applied to eight concrete beams provided excellent corrosion protection to the steel rebar.

Originality/value

This work revealed that the SACP system (thermally sprayed zinc) works well in high relative humidity environments and can be successfully used to protect steel reinforced concrete structures manufactured with calcareous aggregates which are endemic of the region and commonly used for infrastructure construction in the Yucatán peninsula.