bluuebunny/crossref_metadata_2025 huggingface dataset:
Hydrogen-doped In2O3 transparent conducting oxide films prepared by solid-phase crystallization method
Authors: Koida Takashi , Kondo Michio , Tsutsumi Koichi , Sakaguchi Akio , Suzuki Michio , Fujiwara Hiroyuki
Published: February 2010

We have characterized amorphous to crystalline transformation of hydrogen (H)-doped In2O3 (In2O3:H) films by transmission electron microscopy, thermal desorption spectroscopy, spectroscopic ellipsometry, and Hall measurements. The In2O3:H films that show a mixed-phase structure embedded with small density of crystalline grains in a large volume fraction of amorphous phase have been fabricated at room temperature by the sputtering of an In2O3 ceramic target with introduction of H2O vapor, and the films have been postannealed in vacuum to crystallize the amorphous phase. With increasing annealing temperature up to 200 °C, the film shows a large increase in Hall mobility (μHall) from 42 to 110 cm2/V s and a decrease in carrier density (NHall) from 4.6×1020 to 2.1×1020 cm−3 with slight decrease in resistivity. The change in μHall and NHall with annealing temperature is strongly correlated with the volume fractions of the amorphous and crystalline phases in the films. Analyses of dielectric functions of the films using the Drude model revealed that the high electron mobility in the crystallized films is attributed mainly to longer relaxation time rather than smaller effective mass, as compared with as-deposited films. Temperature-dependent Hall analysis, relationship between NHall and μHall, and comparison between μHall and optical mobility showed that (i) scattering processes inside amorphous and/or crystalline matrices limit the mobility, (ii) doubly charged ionized impurity scattering is reduced by crystallization, and (iii) phonon scattering becomes dominant after crystallization in the In2O3:H films. The above results suggest that H-doping reduces carrier scattering in the crystallized In2O3:H and structural rearrangements during crystallization eliminate oxygen deficiency and generate H+ that acts as a singly charged donor. In this article, we discuss the transport properties with the variation in microscopic and chemical structures in the In2O3:H films.
First-principles study of alkali-atom doping in a series of zigzag and armchair carbon nanotubes
Authors: Wen Y. W. , Liu H. J. , Tan X. J. , Pan L. , Shi J.
Published: February 2010

First-principles calculations are performed to study the Li doping in a series of carbon nanotubes with different diameters and chiralities. It is found that the Li–Li interaction inside or outside zigzag tubes is repulsive but strongly screened. Moreover, small diameter zigzag tubes are energetically more favorable than larger ones for Li doping. In contrast, almost all the armchair tubes have the same Li binding energy, especially for the outside doping. Our theoretical results suggest that small diameter zigzag tubes could be plausible candidates for Li-ion battery application. In addition, the doping of other alkali atoms in zigzag tubes is also investigated and the optimal binding distance between them are determined.
Photoconductivity in single AlN nanowires by subband gap excitation
Authors: Huang H. M. , Chen R. S. , Chen H. Y. , Liu T. W. , Kuo C. C. , Chen C. P. , Hsu H. C. , Chen L. C. , Chen K. H. , Yang Y. J.
Published: February 2010

Photoconductivity of individual aluminum nitride (AlN) nanowires has been characterized using different subband gap excitation sources. It is interesting that both positive (under 1.53 and 2.33 eV excitations) and negative (under 3.06 and 3.81 eV excitations) photocurrent responses are observed from the wide band gap nitride nanowires. The negative photoconductivity, which is attributed to the presence of electron trap and recombination center in the bulk of AlN, is capable to be inversed by a strong positive photoconductive mechanism of surface while changes the ambience from the atmosphere to the vacuum. An oxygen molecular sensitization effect is proposed to be the reason resulting in the enhancement of positive photocurrent and the inversion of negative photoresponse in the vacuum. Understanding of the diverse photoconductivity and its molecular effect is of great importance in the development of energy-selective and highly sensitive nanowire photodetector of AlN in the visible and ultraviolet ranges.
Statistical model for small clusters transforming from one isomer to another
Authors: Han Xiao-Jing , Wang Yin , Lin Zheng-Zhe , Zhang Wenxian , Zhuang Jun , Ning Xi-Jing
Published: February 2010

Based on the fact that the kinetic energy of one atom in small cluster still obeys the Boltzmann distribution, a statistical model is developed to predict the time consumed by a small cluster transforming from one isomer to another and is tested by vast molecular dynamics simulations of C12 isomers transformation in helium gas at high temperatures (2000–3500 K). Extrapolating the model to lower temperatures, we found that the time for the most probable isomer of C12 formed at 2500 K turning into the most stable one is more than 1012 years at room temperature.
Suppression of complex domain wall behavior in Ni80Fe20 nanowires by oscillating magnetic fields
Authors: Weerts K. , Van Roy W. , Borghs G. , Lagae L.
Published: February 2010

We have studied the field-induced propagation of domain walls (DW) in 750 nm wide magnetic nanowires by time-resolved magneto-optical Kerr microscopy. Two different DW propagation modes are observed, separated by the so-called Walker breakdown (WB), with velocities ranging from 250 till 500 m/s. At WB, a velocity decrease occurs because of a complex evolution of the DW shape. Through simulations and experiments, we demonstrate a method to suppress this complex DW behavior at WB by superimposing an oscillating magnetic field Hosc, parallel to the switching field Heff, at frequencies ranging from 200 to 600 MHz.
Minimum-error state discrimination constrained by the no-signaling principle
Authors: Hwang Won-Young , Bae Joonwoo
Published: February 2010

We provide a bound on the minimum error when discriminating among quantum states, using the no-signaling principle. The bound is general in that it depends on neither dimensions nor specific structures of given quantum states to be discriminated among. We show that the bound is tight for the minimum-error state discrimination between symmetric (both pure and mixed) qubit states. Moreover, the bound can be applied to a set of quantum states for which the minimum-error state discrimination is not known yet. Finally, our results strengthen the quantitative connection between two no-go theorems, the no-signaling principle, and the no perfect state estimation.
Thermoreflectance characterization of band-edge excitonic transitions in CuAlS2 ultraviolet solar-cell material
Authors: Ho Ching-Hwa
Published: February 2010

Near band edge transitions of CuAlS2 chalcopyrite crystals have been characterized using temperature-dependent thermoreflectance (TR) spectroscopy in the temperature range between 30 and 340 K. A lot of interband transition features of EAn=2, EAn=3, EBn=2, EC, ED, EE, and EF were detected in the low-temperature TR spectrum of 3–6 eV at 30 K. Transition energies of the TR features of CuAlS2 are analyzed. Transition origins of the features are evaluated. Optical-electric conversion behavior of CuAlS2 was evaluated by photoconductivity (PC) measurement at 300 K. The PC spectrum reveals that the maximum photoresponse occurs near the energy positions of EAn=2, EAn=3, and EBn=2 features. The features are the fundamental band edge excitons which dominate photoelectric conversion behavior of CuAlS2 ultraviolet solar-energy material.
Single-walled carbon-nanotube-deposited tapered fiber for four-wave mixing based wavelength conversion
Authors: Chow K. K. , Tsuji M. , Yamashita S.
Published: February 2010

We report the observation of four-wave mixing (FWM) in single-walled carbon nanotubes (CNTs) deposited around a tapered fiber. The third-order nonlinearity of CNTs is originated from the interband transitions of the π-electrons causing nonlinear polarization similar to other highly-nonlinear organic optical materials. CNTs with suitable distributed tube diameter are optically deposited around a tapered fiber and FWM effect is generated by launching a probe and a pump light into the fiber device. FWM-based wavelength conversion is further demonstrated using the generated nonlinear effects and tunable conversion of 10 Gb/s nonreturn-to-zero signal is obtained.
Scanning tunneling microscopic analysis of Cu(In,Ga)Se2 epitaxial layers
Authors: Mayer Marie A. , Ruppalt Laura B. , Hebert Damon , Lyding Joseph , Rockett Angus A.
Published: February 2010

Scanning tunneling microscopy (STM) measurements have been made on single-crystal epitaxial layers of CuInSe2 grown on GaAs substrates. Results were obtained for as-grown, air-exposed, and cleaned surfaces; in situ cleaved surfaces; surfaces sputtered and annealed in the STM system; and samples prepared by a light chemical etch. Conventional constant-current topographs, current-voltage curves, and current imaging tunneling spectroscopy (CITS) scans were obtained. Topographic images show that the surfaces appear rough on the atomic scale and often exhibit regular features consistent with a previously proposed surface ad-dimer reconstruction. CITS scans show a spatially varying energy gap consistent with band-edge fluctuations on a scale of a few atomic spacings. Energy variations were observed in both band edges. Although quantitative description of the magnitude of these fluctuations is difficult, the fluctuations on the atomic scale appear much larger than observed by methods such as photoluminescence, which average over larger volumes.
Ta
2
O
5
polymorphs: Structural motifs and dielectric constant from first principles
Authors: Andreoni Wanda , Pignedoli Carlo A.
Published: February 2010

Using large-scale simulations based on density-functional theory we determine the structural properties of several polymorphs of tantalia, their vibrational spectra and dielectric properties. Our calculations indicate that structurally distinct configurations can coexist, having coordination polyhedra that are dissimilar or have different relative arrangements. Interpolyhedra vibrations are discovered to be responsible for sizable changes of the static dielectric constant from one polymorph to the other. Our results for the dielectric constant (both at high and low frequency) are in excellent agreement with experiment and provide an explanation for the different measured values and their claimed dependence on growth conditions.
Hierarchical nanostructured spherical carbon with hollow core/mesoporous shell as a highly efficient counter electrode in CdSe quantum-dot-sensitized solar cells
Authors: Fan Sheng-Qiang , Fang Baizeng , Kim Jung Ho , Kim Jeum-Jong , Yu Jong-Sung , Ko Jaejung
Published: February 2010

Hierarchical nanostructured spherical carbon with hollow core/mesoporous shell (HCMS) was explored as a counter electrode in CdSe quantum-dot-sensitized solar cells. Compared with conventional Pt electrodes and commercially available activated carbon, the HCMS carbon counter electrode exhibits a much larger fill factor due to the considerably decreased charge transfer resistance at the interface of the counter electrode/polysulfide electrolyte. Furthermore, a solar cell with the HCMS carbon counter electrode presents a high power conversion efficiency of up to 3.90% as well as an incident photon-to-current conversion efficiency peak of 80%.
Consistency in seed-deposition patterns and the distribution of mistletoes among its host trees in an Amazonian savanna
Authors: Fadini Rodrigo Ferreira , Gonçalves Danielly Caroline Miléo , Reis Rúbia Patrícia Fernandes
Published: February 2010

The present paper describes the spatial distribution of the mistletoe Psittacanthus plagiophyllus Eichl. (Loranthaceae) on its host, the cashew tree Anacardium occidentale L., in a Brazilian Amazonian savanna. Our aim was to understand the roles of bird-seed dispersers and host quality in determining the mistletoe distribution among its host trees. In 2006, we marked 118 cashews in a 4.5-ha plot and counted the number of mistletoes and the presence of seeds attached to host branches in 2006, 2007 and 2008. On average, 36% of the hosts were infected each year. The infection load and the probability of being infected increased significantly with host crown diameter. On average, 25% of the hosts received at least one mistletoe seed in each year, being taller and previously infected hosts more prone to receive seeds in all 3 years. Elaenia cristata was the main seed disperser, visiting P. plagiophyllus 48 times in 35 h of focal records. Additionally, in a field experiment, we used the presence of an infection and the host size as surrogates for host quality and tested their effect on mistletoe survivorship. After 9 months, 16.5% of seeds survived and 14% had established, but neither host conditions nor host size influenced seed survivorship. Therefore, we suggest that mistletoe distribution is a consequence of a consistent dispersal of seeds onto larger and previously parasitised hosts across years.
Reproductive biology and intergeneric breeding compatibility of ornamental Portulaca and Calandrinia (Portulacaceae)
Authors: Wickramasinghe Priyanka , Harrison Dion K. , Johnston Margaret E.
Published: February 2010

Portulaca grandiflora Hook and P. umbraticola Kunth (Portulacaceae) are popular garden annuals, and have been bred for improved ornamental value. However, limited research has been published on hybridisation of Portulaca, with no reports on intergeneric hybridisation. Calandrinia balonensis Lindley and Calandrinia sp. nov. (not yet fully classified) are floriferous Australian Portulacaceae species, with potential as novel flowering pot plants, and are potential candidates for breeding with ornamental Portulaca. We studied the reproductive biology of these four species and breeding compatibility for reciprocal crosses of P. grandiflora × C. balonensis (2n = 18) and P. umbraticola × C. sp. nov. (2n = 24). All four species produced seeds for intraspecific outcrosses. P. grandiflora and C. sp. nov. are partially self-compatible whereas P. umbraticola and C. balonensis are highly self-incompatible. Autogamy was detected only for P. grandiflora. Reciprocal crosses of P. grandiflora × C. balonensis and P. umbraticola × C. sp. nov. with similar chromosome numbers did not produce seeds, primarily because of pollen–pistil incompatibility that prevents pollen-tube growth within the stigmata. Methods to overcome hybridisation barriers of these species combinations need to be established to create novel products for ornamental horticulture.
Seed persistence of the invasive aquatic plant, Gymnocoronis spilanthoides (Asteraceae)
Authors: Panetta F. Dane
Published: February 2010

Seed persistence of Gymnocoronis spilanthoides (D.Don) DC.; Asteraceae (Senegal tea), a serious weed of freshwater habitats, was examined in relation to burial status and different soil moisture regimes over a 3-year period. Seeds were found to be highly persistent, especially when buried. At the end of the experiment, 42.0%, 27.3% and 61.4% of buried seeds were viable following maintenance at field capacity, water logged and fluctuating (cycles of 1week at field capacity followed by 3weeks’ drying down) soil moisture conditions, respectively. Comparable viability values for surface-situated seeds were ~3% over all soil moisture regimes. Predicted times to 1% viability are 16.2 years for buried seed and 3.8 years for surface-situated seed. Persistence was attributed primarily to the absence of light, a near-obligate requirement for germination in this species, although secondary dormancy was induced in some seeds. Previous work has demonstrated low fecundity in field populations of G. spilanthoides, which suggests that soil seed banks may not be particularly large. However, high levels of seed persistence, combined with ostensibly effective dispersal mechanisms, indicate that this weed may prove a difficult target for regional or state-wide eradication.
Endogenous hormones in seed, leaf, and pod wall and their relationship to seed filling in soybeans
Authors: Liu Bing , Liu Xiao-bing , Wang Cheng , Jin Jian , Herbert S. J.
Published: February 2010

In order to investigate the possible relationship between endogenous hormones and seed filling in soybeans, concentrations of abscisic acid (ABA), gibberellins (GA3), indole-3-acetic acid (IAA), and cytokinins (ZR) in seed, leaf, and pod wall were determined during seed filling of 3 soybean cultivars differing in seed size and quality. All cultivars were grown at 3 densities. The large-seeded cultivar had a strong and greater ability to accumulate photosynthate during seed filling. The genetic trait of seed size was fully expressed at low density. The large-seeded cultivar had a much higher ABA concentration in seed than the moderate and small-seeded cultivars before physiological maturity. ABA concentration in the large-seeded cultivar seed was 40% greater than that of the small-seeded cultivar at 30 days after flowering. Higher densities increased ABA concentrations in seeds. Two peaks of seed GA3 concentration were observed during seed filling. GA3 concentrations at all densities were similar. The peaks of IAA concentration in the 3 cultivars uniformly occurred at 50 days after flowering. The large-seeded cultivar had greater peak concentrations of GA3 and IAA in seed than the other cultivars, while the peak concentration of ZR was highest in the small-seeded cultivar. The concentrations of ABA in leaf increased with time while that of GA3 decreased. The large-seeded cultivar had higher ABA and IAA concentration in leaf while the small-seeded cultivar consistently had higher GA3 concentration in leaf. ZR was present in a smaller amount in the leaf, and was not detected in the pod wall. The large-seeded cultivar maintained higher IAA concentration in pod wall. ABA concentration in seed was positively correlated with seed-filling rate (P < 0.01, r = 0.85**, 0.92**, and 0.83** for large-, moderate- and small-seeded cultivars respectively).The concentration of GA3 in seed was significantly correlated with the seed-filling rate in large- and moderate-seeded cultivars (P < 0.01, r = 0.87**; P < 0.05, r = 0.63*), and no correlation was found for the small-seeded cultivar. There was no correlation between the concentrations of seed IAA, ZR, and seed-filling rate. There was a parallel relationship between seed growth and leaf/pod wall ABA concentration. Thus, ABA might offer a driving force for photosynthate phloem unloading in the seed coat. Lower concentration of ABA and GA3 in the leaf than in seed suggests that most of the two hormones is transported to seed. The mechanism of IAA in seed growth and GA3 concentration and its dynamic in seed quality need further investigation.
Impacts of grazing management options on pasture and animal productivity in a Heteropogon contortus (black speargrass) pasture in central Queensland. 1. Pasture yield and composition
Authors: Orr D. M. , Burrows W. H. , Hendricksen R. E. , Clem R. L. , Back P. V. , Rutherford M. T. , Myles D. J. , Conway M. J.
Published: February 2010

An extensive grazing study was conducted between 1988 and 2001 in a Heteropogon contortus (black speargrass) pasture in central Queensland. The study was designed to measure the effects of stocking rate on native pasture, native pasture with legume oversown, and native pasture with animal diet supplement/spring burning on pasture and animal production. Summer rainfall throughout the study was below the long-term mean. Mean annual pasture utilisation ranged from 13% at 8 ha/steer up to 61% at 2 ha/steer. Increasing stocking rate treatments reduced total pasture yields while total yields in legume oversown treatments were similar to those in native pasture at the same stocking rate. When spring burning was possible, total yields were reduced in the subsequent autumn. Increasing stocking rate in native pasture tended to reduce H. contortus and Bothriochloa bladhii, increased the composition of intermediate species, such as B. decipiens and Chloris divaricata, and also changed the frequencies of a range of minor species. Oversowing legumes resulted in Stylosanthes scabra cv. Seca increasing from <1% of pasture composition in 1988 to 50% in 2000 and was associated with a reduction in H. contortus and changes in the frequencies of some minor species. Stocking rates heavier than 4 ha/steer resulted in annual pasture utilisation greater than 30% and were unsustainable because they reduced total yield and resulted in undesirable changes in species composition. It was concluded that pasture production was sustainable when stocking rates were maintained at 4 ha/steer, which equates to 30% annual pasture utilisation, and through the judicious use of spring burning.
Root hair morphology and mycorrhizal colonisation of pasture species in response to phosphorus and nitrogen nutrition
Authors: Hill J. O. , Simpson R. J. , Ryan M. H. , Chapman D. F.
Published: February 2010

Root hairs and arbuscular mycorrhizal fungi (AMF) increase the absorptive surface area of a root and the volume of soil explored and as such are important for nutrient acquisition in infertile soil. Root hair morphology and colonisation by AMF were compared for 10 temperate pasture species, and responses to N and P deficiency characterised. Vulpia spp., Holcus lanatus, and Lolium rigidum had the longest root hairs (range 1.02–2.36 mm) while Trifolium subterraneum had the shortest (~0.27 mm). In contrast, T. subterraneum had a much higher density of root hairs than any of the other species. In response to P deficiency, the length and density of root hairs generally increased; in response to N deficiency, both increases and decreases in the length and density of root hairs were observed. The annual dicotyledons T. subterraneum and Arctotheca calendula had much higher mycorrhizal colonisation on roots grown at low P availability than the grasses. Root colonisation decreased with increasing P availability in all species. A yield advantage from mycorrhizal colonisation was demonstrated only for T. subterraneum when P was deficient. The potential root cylinder volume of each species was calculated as an index of the ability of the species to explore soil. Although all plant species were colonised by AMF, a positive linear relationship was observed between relative P uptake rate from the soil and the rate at which potential root cylinder volumes were developed by most species. Development of potential root cylinder volume also largely explained the critical external P requirements of most species. No such relationships were observed for N. It was concluded that knowledge of root length and the length of root hairs grown in nutrient-poor conditions may be used to predict the potential of many plant species to acquire P, and also their critical external P requirement for maximum growth. However, the study also highlighted some exceptional species.
Bat heart mass: correlation with foraging niche and roost preference
Authors: Bullen R. D. , McKenzie N. L. , Bullen K. E. , Williams M. R.
Published: February 2010

We found that the spirit-preserved hearts of 34 species of Australian bat, representing 6 families, weighed from 0.3 to 0.65% of bat mass (mbat), a variation factor of two. The average mass of the heart specimens of the 34 species was 0.501% of bat mass and this did not vary with bat mass. This value was much lower than the average of the available published data, 0.991%. Insectivorous bats that forage or fly in and near three-dimensional clutter have heart mass fractions ~0.04% larger than average, whereas insectivorous bats that forage around and above the canopy in clear air have fractions ~0.16% smaller than average. Insectivorous bats that are obligate deep-cave roosters have significantly smaller fractions, 0.18% smaller than average, whereas those that hover have fractions ~0.08% larger than average. Available published data, although based on freshly sacrificed animals, show the same trends in relation to heart mass fraction and the same scatter and body-mass relationships. However, the magnitude of the fractions differs by a factor of two and may relate to our removal of all tissue except the musculature and walls of the four cardiac chambers.
Vigilance in a solitary marsupial, the common wombat (Vombatus ursinus)
Authors: Favreau François-René , Jarman Peter J. , Goldizen Anne W. , Dubot Anne-Laure , Sourice Stéphane , Pays Olivier
Published: February 2010

We studied vigilance activity in a wild population of the common wombat (Vombatus ursinus), a large, solitary, burrow-using, marsupial prey species in which individuals tolerate the presence of conspecifics within their home range. For the first time, we report postures and rates of vigilance in common wombats; our results show a limited repertoire of vigilant postures and low overall rates of vigilance. Because few studies of birds and mammals that have reported the effect of distance to conspecifics on the vigilance of focal animals have considered solitary prey species, we tested this effect in wombats. Our results show that a model including distance to cover and distance to the nearest conspecific, but not time of day, best explained the variation in the proportion of time that focal individuals spent in vigilance. Individual vigilance decreased when distance to cover increased. Vigilance of wombats increased when there was a conspecific within a radius of 70 m of the focal individual. In addition, we tested whether pairs of nearby wombats scanned independently of one another, coordinated their activity in non-overlapping bouts of vigilance or synchronised their bouts of vigilance. Wombats in close proximity exhibited independent bouts of individual vigilant and foraging activity. Thus, in this solitary species, our results support the assumption that individuals scan independently of each other.
Basking behaviour and torpor use in free-ranging Planigale gilesi
Authors: Warnecke Lisa , Geiser Fritz
Published: February 2010

We investigated the importance of energy-conserving strategies for free-ranging Planigale gilesi in arid Australia. We monitored torpor use and basking behaviour using internal temperature-sensitive transmitters. Torpor was used every day; the maximum torpor bout duration was 18.2 h and the minimum body temperature was 10.5°C. Basking behaviour was observed during rewarming from torpor as well as during normothermia. The use of torpor and basking is likely to reduce the energy requirements of P. gilesi, thus helping it to survive in a harsh and unpredictable environment.
Ultrahigh-throughput screening in drop-based microfluidics for directed evolution
Authors: Agresti Jeremy J. , Antipov Eugene , Abate Adam R. , Ahn Keunho , Rowat Amy C. , Baret Jean-Christophe , Marquez Manuel , Klibanov Alexander M. , Griffiths Andrew D. , Weitz David A.
Published: February 2010

The explosive growth in our knowledge of genomes, proteomes, and metabolomes is driving ever-increasing fundamental understanding of the biochemistry of life, enabling qualitatively new studies of complex biological systems and their evolution. This knowledge also drives modern biotechnologies, such as molecular engineering and synthetic biology, which have enormous potential to address urgent problems, including developing potent new drugs and providing environmentally friendly energy. Many of these studies, however, are ultimately limited by their need for even-higher-throughput measurements of biochemical reactions. We present a general ultrahigh-throughput screening platform using drop-based microfluidics that overcomes these limitations and revolutionizes both the scale and speed of screening. We use aqueous drops dispersed in oil as picoliter-volume reaction vessels and screen them at rates of thousands per second. To demonstrate its power, we apply the system to directed evolution, identifying new mutants of the enzyme horseradish peroxidase exhibiting catalytic rates more than 10 times faster than their parent, which is already a very efficient enzyme. We exploit the ultrahigh throughput to use an initial purifying selection that removes inactive mutants; we identify ∼100 variants comparable in activity to the parent from an initial population of ∼10
7
. After a second generation of mutagenesis and high-stringency screening, we identify several significantly improved mutants, some approaching diffusion-limited efficiency. In total, we screen ∼10
8
individual enzyme reactions in only 10 h, using < 150 μL of total reagent volume; compared to state-of-the-art robotic screening systems, we perform the entire assay with a 1,000-fold increase in speed and a 1-million-fold reduction in cost.
Formation of carcinogens indoors by surface-mediated reactions of nicotine with nitrous acid, leading to potential
thirdhand smoke
hazards
Authors: Sleiman Mohamad , Gundel Lara A. , Pankow James F. , Jacob Peyton , Singer Brett C. , Destaillats Hugo
Published: February 2010

This study shows that residual nicotine from tobacco smoke sorbed to indoor surfaces reacts with ambient nitrous acid (HONO) to form carcinogenic tobacco-specific nitrosamines (TSNAs). Substantial levels of TSNAs were measured on surfaces inside a smoker’s vehicle. Laboratory experiments using cellulose as a model indoor material yielded a > 10-fold increase of surface-bound TSNAs when sorbed secondhand smoke was exposed to 60 ppbv HONO for 3 hours. In both cases we identified 1-(
N
-methyl-
N
-nitrosamino)-1-(3-pyridinyl)-4-butanal, a TSNA absent in freshly emitted tobacco smoke, as the major product. The potent carcinogens 4-(methylnitrosamino)-1-(3-pyridinyl)-1-butanone and
N
-nitroso nornicotine were also detected. Time-course measurements revealed fast TSNA formation, with up to 0.4% conversion of nicotine. Given the rapid sorption and persistence of high levels of nicotine on indoor surfaces—including clothing and human skin—this recently identified process represents an unappreciated health hazard through dermal exposure, dust inhalation, and ingestion. These findings raise concerns about exposures to the tobacco smoke residue that has been recently dubbed “thirdhand smoke.” Our work highlights the importance of reactions at indoor interfaces, particularly those involving amines and NO

x

/HONO cycling, with potential health impacts.
Wolf Reik: Inheritance beyond DNA
Authors: LeBrasseur Nicole
Published: February 2010

Reik takes on the dual nature of epigenetic regulation and finds that it can satisfy his dual tastes for basic research and medicine.
Synaptobrevin N-terminally bound to syntaxin–SNAP-25 defines the primed vesicle state in regulated exocytosis
Authors: Walter Alexander M. , Wiederhold Katrin , Bruns Dieter , Fasshauer Dirk , Sørensen Jakob B.
Published: February 2010

Rapid neurotransmitter release depends on the ability to arrest the SNAP receptor (SNARE)–dependent exocytosis pathway at an intermediate “cocked” state, from which fusion can be triggered by Ca2+. It is not clear whether this state includes assembly of synaptobrevin (the vesicle membrane SNARE) to the syntaxin–SNAP-25 (target membrane SNAREs) acceptor complex or whether the reaction is arrested upstream of that step. In this study, by a combination of in vitro biophysical measurements and time-resolved exocytosis measurements in adrenal chromaffin cells, we find that mutations of the N-terminal interaction layers of the SNARE bundle inhibit assembly in vitro and vesicle priming in vivo without detectable changes in triggering speed or fusion pore properties. In contrast, mutations in the last C-terminal layer decrease triggering speed and fusion pore duration. Between the two domains, we identify a region exquisitely sensitive to mutation, possibly constituting a switch. Our data are consistent with a model in which the N terminus of the SNARE complex assembles during vesicle priming, followed by Ca2+-triggered C-terminal assembly and membrane fusion.
Localized topological changes of the plasma membrane upon exocytosis visualized by polarized TIRFM
Authors: Anantharam Arun , Onoa Bibiana , Edwards Robert H. , Holz Ronald W. , Axelrod Daniel
Published: February 2010

Total internal reflection fluorescence microscopy (TIRFM) images the plasma membrane–cytosol interface and has allowed insights into the behavior of individual secretory granules before and during exocytosis. Much less is known about the dynamics of the other partner in exocytosis, the plasma membrane. In this study, we report the implementation of a TIRFM-based polarization technique to detect rapid submicrometer changes in plasma membrane topology as a result of exocytosis. A theoretical analysis of the technique is presented together with image simulations of predicted topologies of the postfusion granule membrane–plasma membrane complex. Experiments on diI-stained bovine adrenal chromaffin cells using polarized TIRFM demonstrate rapid and varied submicrometer changes in plasma membrane topology at sites of exocytosis that occur immediately upon fusion. We provide direct evidence for a persistent curvature in the exocytotic region that is altered by inhibition of dynamin guanosine triphosphatase activity and is temporally distinct from endocytosis measured by VMAT2-pHluorin.
Dual action of epidermal growth factor: extracellular signal-stimulated nuclear–cytoplasmic export and coordinated translation of selected messenger RNA
Authors: Tsai Nien-Pei , Lin Ya-Lun , Tsui Yao-Chen , Wei Li-Na
Published: February 2010

We report the first example of a coordinated dual action of epidermal growth factor (EGF) in stimulating the nuclear–cytoplasmic export and translation of a select messenger RNA (mRNA). The effect of EGF is mediated by the RNA-binding protein Grb7 (growth factor receptor–bound protein 7), which serves as an adaptor for a specific mRNA–protein export complex and a translational regulator. Using the κ–opioid receptor (OR [KOR]) as a model, we demonstrate that EGF activates nuclear SHP-2 (Src homology region 2–containing tyrosine phosphatase), which dephosphorylates Grb7 in the nucleus. Hypophosphorylated Grb7 binds to the KOR mRNA and recruits the Hu antigen R–exportin-1 (CRM1) complex to form a nuclear–cytoplasmic export complex that exports KOR mRNA. EGF also activates focal adhesion kinase in the cytoplasm to rephosphorylate Grb7, releasing KOR mRNA for active translation. In summary, this study uncovers a coordinated, dual activity of EGF in facilitating nuclear export of a specific mRNA–protein complex as well as translational activation of the exported mRNA.
Molecular endpoints of Ca2+/calmodulin- and voltage-dependent inactivation of Cav1.3 channels
Authors: Tadross Michael R. , Johny Manu Ben , Yue David T.
Published: February 2010

Ca2+/calmodulin- and voltage-dependent inactivation (CDI and VDI) comprise vital prototypes of Ca2+ channel modulation, rich with biological consequences. Although the events initiating CDI and VDI are known, their downstream mechanisms have eluded consensus. Competing proposals include hinged-lid occlusion of channels, selectivity filter collapse, and allosteric inhibition of the activation gate. Here, novel theory predicts that perturbations of channel activation should alter inactivation in distinctive ways, depending on which hypothesis holds true. Thus, we systematically mutate the activation gate, formed by all S6 segments within CaV1.3. These channels feature robust baseline CDI, and the resulting mutant library exhibits significant diversity of activation, CDI, and VDI. For CDI, a clear and previously unreported pattern emerges: activation-enhancing mutations proportionately weaken inactivation. This outcome substantiates an allosteric CDI mechanism. For VDI, the data implicate a “hinged lid–shield” mechanism, similar to a hinged-lid process, with a previously unrecognized feature. Namely, we detect a “shield” in CaV1.3 channels that is specialized to repel lid closure. These findings reveal long-sought downstream mechanisms of inactivation and may furnish a framework for the understanding of Ca2+ channelopathies involving S6 mutations.
Metscape: a Cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks
Authors: Gao Jing , Tarcea V. Glenn , Karnovsky Alla , Mirel Barbara R. , Weymouth Terry E. , Beecher Christopher W. , Cavalcoli James D. , Athey Brian D. , Omenn Gilbert S. , Burant Charles F. , Jagadish H. V.
Published: February 2010

Summary: Metscape is a plug-in for Cytoscape, used to visualize and interpret metabolomic data in the context of human metabolic networks. We have developed a metabolite database by extracting and integrating information from several public sources. By querying this database, Metscape allows users to trace the connections between metabolites and genes, visualize compound networks and display compound structures as well as information for reactions, enzymes, genes and pathways. Applying the pathway filter, users can create subnetworks that consist of compounds and reactions from a given pathway. Metscape allows users to upload experimental data, and visualize and explore compound networks over time, or experimental conditions. Color and size of the nodes are used to visualize these dynamic changes. Metscape can display the entire metabolic network or any of the pathway-specific networks that exist in the database.

Availability: Metscape can be installed from within Cytoscape 2.6.x under ‘Network and Attribute I/O’ category. For more information, please visit http://metscape.ncibi.org/tryplugin.html

Contact:  jinggao@umich.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Modeling macro–molecular interfaces with Intervor
Authors: Loriot Sébastien , Cazals Frédéric
Published: February 2010

Summary:  Intervor is a software computing a parameter-free representation of macro–molecular interfaces, based on the α-complex of the atoms. Given two interacting partners, possibly with water molecules squeezed in-between them, Intervor computes an interface model which has the following characteristics: (i) it identifies the atoms of the partners which are in direct contact and those whose interaction is water mediated, (ii) it defines a geometric complex separating the partners, the Voronoi interface, whose geometric and topological descriptions are straightforward (surface area, number of patches, curvature), (iii) it allows the definition of the depth of atoms at the interface, thus going beyond the traditional dissection of an interface into a core and a rim. These features can be used to investigate correlations between structural parameters and key properties such as the conservation of residues, their polarity, the water dynamics at the interface, mutagenesis data, etc.

Availability:  Intervor can be run from the web site http://cgal.inria.fr/abs/Intervor or upon downloading the binary file. Plugins are also made available for VMD and Pymol.

Contact:  frederic.cazals@sophia.inria.fr
Silent ships sometimes do encounter more fish. 2. Concurrent echosounder observations from a free-drifting buoy and vessels
Authors: De Robertis Alex , Wilson Christopher D.
Published: February 2010

De Robertis, A., and Wilson, C. D. 2010. Silent ships sometimes do encounter more fish. 2. Concurrent echosounder observations from a free-drifting buoy and vessels. – ICES Journal of Marine Science, 67: 996–1003. The reactions of walleye pollock (Theragra chalcogramma) to the NOAA ships “Miller Freeman” (MF), a conventionally designed research vessel, and the “Oscar Dyson” (OD), a noise-reduced research vessel, were compared near the Shumagin Islands, Alaska. Observations with a buoy-mounted echosounder indicated a stronger decrease in pollock backscatter strength and a greater increase in pollock backscatter depth associated with the passage of the MF than the OD. The pollock began to respond at a distance of ∼270 m from the vessel and were disturbed for several minutes after vessel passage. The reaction to the OD was weak, suggesting that measurements of pollock made by the OD in this environment are not strongly biased by vessel avoidance. Comparison of echosounder observations collected on board each vessel indicated that the MF measured less pollock backscatter, a deeper pollock depth distribution, and weaker single-target echoes than the OD. Together, the results indicate that acoustic measurements from the two vessels are not equivalent because of a reduced avoidance response to the noise-reduced vessel.
Picosecond and femtosecond X-ray absorption spectroscopy of molecular systems
Authors: Chergui Majed
Published: February 2010

The need to visualize molecular structure in the course of a chemical reaction, a phase transformation or a biological function has been a dream of scientists for decades. The development of time-resolved X-ray and electron-based methods is making this true. X-ray absorption spectroscopy is ideal for the study of structural dynamics in liquids, because it can be implemented in amorphous media. Furthermore, it is chemically selective. Using X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) in laser pump/X-ray probe experiments allows the retrieval of the local geometric structure of the system under study, but also the underlying photoinduced electronic structure changes that drive the structural dynamics. Recent developments in picosecond and femtosecond X-ray absorption spectroscopy applied to molecular systems in solution are reviewed: examples on ultrafast photoinduced processes such as intramolecular electron transfer, low-to-high spin change, and bond formation are presented.
`Making the molecular movie': first frames
Authors: Miller R. J. Dwayne , Ernstorfer Ralph , Harb Maher , Gao Meng , Hebeisen Christoph T. , Jean-Ruel Hubert , Lu Cheng , Moriena Gustavo , Sciaini German
Published: February 2010

Recent advances in high-intensity electron and X-ray pulsed sources now make it possible to directly observe atomic motions as they occur in barrier-crossing processes. These rare events require the structural dynamics to be triggered by femtosecond excitation pulses that prepare the system above the barrier or access new potential energy surfaces that drive the structural changes. In general, the sampling process modifies the system such that the structural probes should ideally have sufficient intensity to fully resolve structures near the single-shot limit for a given time point. New developments in both source intensity and temporal characterization of the pulsed sampling mode have made it possible to make so-called `molecular movies',i.e.measure relative atomic motions faster than collisions can blur information on correlations. Strongly driven phase transitions from thermally propagated melting to optically modified potential energy surfaces leading to ballistic phase transitions and bond stiffening are given as examples of the new insights that can be gained from an atomic level perspective of structural dynamics. The most important impact will likely be made in the fields of chemistry and biology where the central unifying concept of the transition state will come under direct observation and enable a reduction of high-dimensional complex reaction surfaces to the key reactive modes, as long mastered by Mother Nature.
Photolysis of Br2in CCl4studied by time-resolved X-ray scattering
Authors: Kong Qingyu , Lee Jae Hyuk , Lo Russo Manuela , Kim Tae Kyu , Lorenc Maciej , Cammarata Marco , Bratos Savo , Buslaps Thomas , Honkimaki Veijo , Ihee Hyotcherl , Wulff Michael
Published: February 2010

A time-resolved X-ray solution scattering study of bromine molecules in CCl4is presented as an example of how to track atomic motions in a simple chemical reaction. The structures of the photoproducts are tracked during the recombination process, geminate and non-geminate, from 100 ps to 10 µs after dissociation. The relaxation of hot Br2*molecules heats the solvent. At early times, from 0.1 to 10 ns, an adiabatic temperature rise is observed, which leads to a pressure gradient that forces the sample to expand. The expansion starts after about 10 ns with the laser beam sizes used here. When thermal artefacts are removed by suitable scaling of the transient solvent response, the excited-state solute structures can be obtained with high fidelity. The analysis shows that 30% of Br2*molecules recombine directly along theXpotential, 60% are trapped in theA/A′ state with a lifetime of 5.5 ns, and 10% recombine non-geminatelyviadiffusive motion in about 25 ns. The Br—Br distance distribution in theA/A′ state peaks at 3.0 Å.
Serum lactoferrin level as a serologic biomarker for allergic rhinitis
Authors: Choi G. ‐S. , Shin S. ‐Y. , Kim J. ‐H. , Lee H. ‐Y. , Palikhe N. S. , Ye Y. ‐M. , Kim S. ‐H. , Park H. ‐S.
Published: February 2010

Background
Allergic rhinitis (AR) is a very common disease and a risk factor for allergic asthma. The discovery of new biomarkers for the early detection of AR would improve the clinical outcomes and reduce socio‐economic burden. We sought to identify a novel serologic marker for detection of AR using a proteomic approach.

Methods
To identify the proteins involved in AR, comparative proteomics was applied using nasal lavage fluids (NLFs) taken before and after a nasal provocation test (NPT) with Dermatophagoides pteronyssinus (Dpt) in a subject with AR sensitized to Dpt. The clinical relevance of the identified proteins was evaluated by ELISA using NLFs and sera from the three study groups: Dpt‐sensitive AR; asymptomatic Dpt‐sensitive controls; and non‐atopic healthy controls. The sensitivities and specificities of the candidate proteins for predicting AR were determined using receiver operating characteristic (ROC) curves.

Results
In proteomic analysis, lactoferrin expression was up‐regulated after NPT. The validation study using ELISA showed a significantly lower serum lactoferrin level in the AR group than those of the other two groups (P<0.05, respectively). To discriminate between subjects with or without AR, the optimal serum cut‐off level of lactoferrin was set at <307 ng/mL using the ROC curve. The sensitivity and specificity for predicting AR were 81.4% and 58%. When combined with serum Dpt‐specific IgE level, the sensitivity and specificity for predicting AR were 76.7% and 79.2%.

Conclusion
These results suggest that the serum lactoferrin level is associated with the phenotype of Dpt‐sensitive AR, and in combination with the serum Dpt‐specific IgE level, may be a potential serologic marker for early detection of AR.

Cite this as: G.‐S. Choi, S.‐Y. Shin, J.‐H. Kim, H.‐Y. Lee, N. S. Palikhe, Y.‐M. Ye, S.‐H. Kim and H.‐S. Park, Clinical & Experimental Allergy, 2010 (40) 403–410.