bluuebunny/crossref_metadata_2025 huggingface dataset:
Adsorption of intact methanol on Ru(0001)
Authors: Gazdzicki Pawel , Uvdal Per , Jakob Peter
Published: June 2009

Fourier transform infrared absorption spectroscopy has been used to study the adsorption of methanol on the clean Ru(0001) surface at T≤80 K. Thereby, clear evidence for intact adsorption has been found. This observation contradicts previous studies which suggested an OH (OD) bond scission upon adsorption of methanol on Ru(0001), even at low temperatures, as well as partial recombinative desorption at higher T. Our conclusion is based on isotopic shifts of vibrational modes associated with the OH (OD) group of adsorbed CH3OH and CH3OD. Density functional theory (B3LYP) confirms these findings, as it reproduces the observed frequencies and isotopic shifts well. Additional support for our conclusion of nondissociative adsorption of methanol on Ru(0001) is provided by thermal desorption experiments of CH3OH coadsorbed with deuterium on Ru(0001). We find that CH3OD formation is clearly below detection threshold, while desorption of CH3OH is quite prominent; a recombinative desorption of dissociated methanol and hydrogen/deuterium as suggested in the literature is therefore discarded. At very low coverages and temperatures the presence of isolated methanol molecules or dimers is suggested. With increasing density or by annealing a low coverage methanol layer, hydrogen bonding leads to cluster formation, as evidenced by an intensity loss of those vibrational modes affected by hydrogen bonds, in conjunction with a substantial line broadening.
The nature of interactions between clusters of Mg and Zn with HCN from symmetry-adapted perturbation theory based of DFT
Authors: Snyder Desirée N. , Szczęśniak Małgorzata M. , Chałasiński Grzegorz
Published: June 2009

The donor-acceptor complexes HCN–Mgn and HCN–Znn (n=1,…,4), which were recently detected in helium nanodroplet infrared spectroscopy experiments by Miller and co-workers [Science 292, 481 (2001); J. Phys. Chem. A 110, 5620 (2006)] are investigated by the symmetry-adapted perturbation theory based on the density functional monomer description [SAPT(DFT)]. The interaction energy components, such as the electrostatic, exchange, induction, and dispersion, are calculated as a function of the metal cluster size. We find that the donor-acceptor interactions manifest themselves by the large induction and dispersion interactions, which counteract the unusually large exchange repulsion. The dependence of the components on the clusters size n follows different patterns in the complexes of magnesium and zinc. In HCN–Mgn the induction effect increases in magnitude much faster than the dispersion effect. In HCN–Znn there is a slight decrease in both dispersion and induction terms between n=2 and n=3. Then dispersion rises faster than induction between n=3 and n=4. The exchange effects are also much different in both types of complexes. The first-order exchange energy rises much faster with n in the magnesium complexes than in the zinc complexes. Furthermore, in the latter there is a significant drop in the exchange energy between n=2 and n=3. The second-order exchange effects tend to quench a larger percentage of the induction and dispersion contributions in the Mgn complexes than in Znn. These different patterns of the interaction energy variations with n are related to the different nature of nonadditive effects in the neat metal clusters.
Theory of void formation in dusty plasmas
Authors: Hu Zuquan , Chen Yinhua , Zheng Xiang , Huang Feng , Shi Gei-fen , Yu M. Y.
Published: June 2009

A fluid theory of void formation in dusty plasmas taking into account ionization is proposed. It is shown that if the ionization rate is larger than a threshold, an initial steady-state dust-density distribution can evolve into a stable distribution containing a void. As the ionization rate is further increased, the time required for void formation decreases. The void size first increases, but then decreases. However, for still larger ionization rates, the dusty region of the plasma becomes ringlike, including the convection term in dust momentum equation. The results are in agreement with existing experiments and theories.
Computational investigation on bubble detachment from submerged orifice in quiescent liquid under normal and reduced gravity
Authors: Chakraborty I. , Ray B. , Biswas G. , Durst F. , Sharma A. , Ghoshdastidar P. S.
Published: June 2009

In this work numerical simulations have been carried out to study the problem of dynamic air bubble formation from a submerged orifice in quiescent liquid, under constant inflow condition, at normal and reduced gravity levels. A coupled level-set and volume-of-fluid method is used to simulate the bubble formation, bubble detachment, and the bubble rise above the orifice. For the described study, the authors have mainly focused on low and medium air flow rate for simulation of bubble formation at the orifice. The employed gravity levels g/ge are in the range of 100, 10−1, and 10−2. The influence of buoyancy on the bubble shape has been studied. The study includes the bubble volume, formation frequency, pinch-off rate, detached bubble diameter, and the bubble growth history for different air flow rates. Even for the static contact angle θs=00, it is observed that at low gravity levels the bubble base spreads along the surface of the orifice plate away from the orifice rim during the expansion stage, and during the detachment stage the bubble base again comes back to the orifice rim. As the air flow rate is increased under normal and low gravity conditions, coalescence between the rising bubbles or between the detached bubble and the forming bubble at the orifice is observed. It is shown that the increasing trend of bubble size at detachment, with increasing air flow rate under normal gravity is reversed in the case of reduced gravity (g/ge=10−2).
Formation and photodestruction of dual dipole-bound anion (H2O)6{e−}CH3NO2
Authors: Nakanishi Ryuzo , Nagata Takashi
Published: June 2009

A new type of dipole-bound anion composed of water and nitromethane (CH3NO2) is formed via the incorporation of CH3NO2 into argon-solvated water hexamer anions, (H2O)6−Arm. The reaction proceeds as an Ar-mediated process such that an effective energy dissipation through sequential Ar evaporation gives rise to the formation of [CH3NO2⋅(H2O)6]−. Photoelectron spectroscopy is employed to probe the electronic properties of the [CH3NO2⋅(H2O)6]− anion, which reveals that the dipole-bound nature of (H2O)6− remains almost intact in the product anion; the vertical detachment energy of [CH3NO2⋅(H2O)6]− is determined to be 0.65±0.02 eV. This spectroscopic finding, together with other suggestive evidences, allows us to refer to [CH3NO2⋅(H2O)6]− as a dual dipole-bound anion described as (H2O)6{e−}CH3NO2, where the diffuse excess electron interacts with both the (H2O)6 and CH3NO2 moieties via the electron-dipole interactions. The photodestruction of (H2O)6{e−}CH3NO2 at 2134 nm (0.58 eV) occurs with a competition between electron detachment and fragmentation. The latter leads exclusively to the formation of CH3NO2−⋅(H2O)3, indicating that the dual dipole-bound anion serves as a precursor to the hydrated valence anion of CH3NO2.
Effect of mechanical load on the shuttling operation of molecular muscles
Authors: Lee Seungjun , Lu Wei
Published: June 2009

We use molecular dynamics simulations to investigate the effect of mechanical force on stimulus-induced deformation of rotaxane-based artificial molecular muscles. The study shows that a small external force slows down the shuttling motion and leads to longer actuation time for a muscle to reach its full extension. Further increase in the force can significantly reduce the traveling distance of the ring, leading to reduced strain output. A force larger than 28 pN can completely suppress the shuttling motion, suggesting a limit of force output of molecular muscles.
Oscillating two stream instability of electromagnetic pump in the ion cyclotron range of frequency in a plasma
Authors: Ahmad Nafis , Tripathi V. K. , Rafat M. , Husain Mudassir M.
Published: June 2009

An analytical formalism of oscillating two stream instability of a large amplitude electromagnetic wave in the ion cyclotron range of frequency in a plasma is developed. The instability produces electrostatic ion cyclotron sidebands and a driven low frequency mode. The nonlinear coupling arises primarily due to the motion of ions and is strong when the pump frequency is close to ion cyclotron frequency and the oscillatory ion velocity is a significant fraction of acoustic speed. For propagation perpendicular to the ambient magnetic field, the X-mode pump wave produces flute type perturbation with maximum growth rate at some specific wavelengths, which are three to four times larger than the ion Larmor radius. For propagation at oblique angles to ambient magnetic field, the ion cyclotron O-mode, the growth rate increases with the wave number of the low frequency mode.
Alteration of the mechanical properties of azopolymer film in the process of surface relief grating formation
Authors: Veer Padmanabh U. , Pietsch Ullrich , Mueller Anne D.
Published: June 2009

Alterations of local hardness in azopolymer films have been investigated using atomic force microscope after light-induced surface relief gratings inscribed at temperatures between 25 °C and the glass transition. Compared to nonpatterned regions of same material, local hardness is increased at positions of crests but reduced in troughs. Surface relief gratings on films at room temperature show relative hardness variation up to 50% and decreases linearly with grating height and temperature. The findings can be explained by increased/decreased density of parallel-aligned polymer chains in crests/troughs as result of cooperative motion due to trans-cis-trans isomerisation during grating formation in competition with thermal disorder.
Comparison of wind power estimates from the ECMWF reanalyses with direct turbine measurements
Authors: Kiss Péter , Varga László , Jánosi Imre M.
Published: June 2009

Reanalysis data are rarely used for wind power estimates because of the limited spatial and temporal resolution. Here we report on a detailed comparison of wind speed and electric power time series recorded at a continental location in Hungary and estimates provided by the European Centre for Medium-Range Weather Forecasts (ECMWF) ERA-40 and Interim databases at nearby grid points. The results show that the temporal behavior is adequately represented in reanalysis records with damped magnitudes, as expected. However, characteristic shape differences in the wind speed histograms for turbine measurements and reanalysis hinder a perfect match of statistics. A satisfying agreement of histograms for measured and modeled output powers is achieved by scaling up surface wind speeds to have the same long time average value as for the turbine records. The presented calibration permits us to provide wind power estimates for large geographic areas, where the wind field is similarly coherent as around the test site.
Transport properties in heterogeneous compacted granular media made of carbon nanotubes and potassium bromide
Authors: Depriester Michael , Hadj Sahraoui Abdelhak , Hus Philippe , Roussel Frédérick
Published: June 2009

Thermal properties of pellets composed of carbon nanotubes (CNTs), single-walled or multiple-walled, and potassium bromide have been investigated via photothermal radiometry. Pellets containing 2 wt % CNT show a significant enhancement in thermal conductivity (k) by at least four times. However, when the concentration of a CNT is raised to 3 wt % or higher, a sudden drop in k is observed whereas the electrical conductivity keeps increasing and follows the percolation law. The thermal conductivity data have been modeled and interpreted in terms of a morphological transition between a compacted and an unconsolidated granular media.
Optically transparent nanofiber sheets by deposition of transparent materials: A concept for a roll-to-roll processing
Authors: Nogi Masaya , Yano Hiroyuki
Published: June 2009

Deposition of transparent materials on cellulose nanofiber sheets enhanced the transparency of nanofiber sheets. The coated nanofiber sheets exhibited high transparency regardless of the wide distribution of refractive indexes of the coated resins, and the loss of transparency compared with the theoretical values was less than 2.5%. The low coefficient of thermal expansion of the nanofiber sheets (8.5 ppm/K) was maintained after the coating. The continuous coating of functional transparent materials on the nanofiber sheets is a promising approach toward accomplishing a simple roll-to-roll manufacturing process.
Efficient generation and sorting of orbital angular momentum eigenmodes of light by thermally tuned q-plates
Authors: Karimi Ebrahim , Piccirillo Bruno , Nagali Eleonora , Marrucci Lorenzo , Santamato Enrico
Published: June 2009

We present methods for generating and for sorting specific orbital angular momentum (OAM) eigenmodes of a light beam with high efficiency, using a liquid crystal birefringent plate with unit topological charge known as “q-plate.” The generation efficiency has been optimized by tuning the optical retardation of the q-plate with temperature. The measured OAM m=±2 eigenmodes generation efficiency from an input TEM00 beam was of 97%. Mode sorting of the two input OAM m=±2 eigenmodes was achieved with an efficiency of 81%.
Infrared emission from tunneling electrons: The end of the rainbow in scanning tunneling microscopy
Authors: Boyle Michael G. , Mitra J. , Dawson P.
Published: June 2009

Electromagnetic radiation originating with localized surface plasmons in the metal-tip/metal-sample nanocavity of a scanning tunneling microscope is demonstrated to extend to a wavelength λ of at least 1.7 μm. Progressive spectral extension beyond λ∼1.0 μm occurs for increasing tip radius above ∼15 nm, reaching λ∼1.7 μm for tip radius ∼100 nm; these observations are corroborated by use of a simple physical model that relates the discrete plasmon mode frequencies to the tip radius. This spectral extension opens up a new regime for scanning tunneling microscope-based optical spectroscopy.
Tilted-charge high speed (7 GHz) light emitting diode
Authors: Walter G. , Wu C. H. , Then H. W. , Feng M. , Holonyak N.
Published: June 2009

We demonstrate a higher speed form of light emitting diode (LED), an asymmetrical two-junction tilted-charge LED, utilizing an n-type buried “drain” layer beneath the p-type “base” quantum-well (carrier and photon) active region. The drain layer tilts and pins the charge in the manner of a heterojunction bipolar light emitting transistor (HBLET), selecting and allowing only “fast” recombination (recombination lifetime τB of the order of base transit time τt). The tilted-charge LED, simple in design and construction, is capable of operation at low current in spontaneous recombination at a 7 GHz bandwidth or even higher with more refinement.
Temperature-dependent bending rigidity of graphene
Authors: Liu P. , Zhang Y. W.
Published: June 2009

Both previous theoretical and experimental work showed that the bending rigidity of a liquid membrane decreases with increasing temperature. We demonstrate that the elastic energy forms for a solid membrane and a liquid membrane are identical under equal-biaxial stretching, implying the bending rigidity of a solid membrane should decrease with increasing temperature. We perform molecular dynamics simulations to study how thermal fluctuation affects the bending rigidity of graphene, and find that the bending rigidity decreases exponentially with increasing temperature. This is in contrast with recent atomistic Monte Carlo simulation result that the bending rigidity of graphene increases with increasing temperature.
Transport properties of a quantum dot in quantum Hall regimes probed by a single-electron transistor
Authors: Chen J. C. , Li Ming-Yang , Ueda T. , Komiyama S.
Published: June 2009

Coulomb blockade oscillations in a semiconductor quantum dot (QD) with two confined Landau levels are investigated by probing a current through a single-electron transistor (SET) fabricated directly on top of the QD. The intradot tunneling events between the compressible regions in the dot are mapped out by measuring SET currents. Our results demonstrate that a SET can be an excellent electrometer that is extremely responsive to the local individual electron tunneling events in a closed electronic system.
Row spacing and planting density effects on the growth and yield of sugarcane. 2. Strategies for the adoption of controlled traffic
Authors: Garside A. L. , Bell M. J. , Robotham B. G.
Published: June 2009

Controlled traffic (matching wheel and row spacing) is being promoted as a means to manage soil compaction in the Australian sugar industry. However, machinery limitations dictate that wider row spacings than the standard 1.5-m single row will need to be adopted to incorporate controlled traffic and many growers are reluctant to widen row spacing for fear of yield penalties. To address these concerns, contrasting row configuration and planting density combinations were investigated for their effect on cane and sugar yield in large-scale experiments in the Gordonvale, Tully, Ingham, Mackay, and Bingera (near Bundaberg) sugarcane-growing regions of Queensland, Australia. The results showed that sugarcane possesses a capacity to compensate for different row configurations and planting densities through variation in stalk number and individual stalk weight. Row configurations ranging from 1.5-m single rows (the current industry standard) to 1.8-m dual rows (50 cm between duals), 2.1-m dual (80 cm between duals) and triple (65 cm between triples) rows, and 2.3-m triple rows (65 cm between triples) produced similar yields. Four rows (50 cm apart) on a 2.1-m configuration (quad rows) produced lower yields largely due to crop lodging, while a 1.8-m single row configuration produced lower yields in the plant crop, probably due to inadequate resource availability (water stress/limited radiation interception).
The results suggest that controlled traffic can be adopted in the Australian sugar industry by changing from a 1.5-m single row to 1.8-m dual row configuration without yield penalty. Further, the similar yields obtained with wider row configurations (2 m or greater with multiple rows) in these experiments emphasise the physiological and environmental plasticity that exists in sugarcane. Controlled traffic can be implemented with these wider row configurations (>2 m), although it will be necessary to carry out expensive modifications to the current harvester and haul-out equipment.
There were indications from this research that not all cultivars were suited to configurations involving multiple rows. The results suggest that consideration be given to assessing clones with different growth habits under a range of row configurations to find the most suitable plant types for controlled traffic cropping systems.
Replacement series studies of competition between tropical perennial and annual grasses and perennial grass mixtures in northern New South Wales
Authors: Lodge G. M. , Boschma S. P. , Harden S.
Published: June 2009

Seedlings of three perennial tropical grasses, Chloris gayana cv. Katambora (Rhodes grass), Panicum coloratum var. makarikariense cv. Bambatsi (panic grass), and Digitaria eriantha ssp. eriantha cv. Premier (digit grass), were each grown in replacement series mixtures with seedlings of the annual summer-growing grass weeds Urochloa panicoides (liverseed grass) and Echinochloa colona (awnless barnyard grass). A separate experiment examined the competitiveness of seedlings of the three perennial tropical grasses when two species were sown together. Plants were sown 50 mm apart in boxes at a density of 307 plants/m2. Maximum likelihood estimates were used to derive parameters of a non-linear competition model using the dry weights of perennial and annual grasses.
Seedlings of the summer-growing annual liverseed grass competed aggressively with those of the tropical perennial Katambora Rhodes grass. However, Bambatsi panic seedlings were equally competitive with those of awnless barnyard grass, while those in a Premier digit-barnyard grass mixture were inhibited by the presence of each other. In the perennial grass mixtures study, the performance of both Premier digit and Bambatsi panic was adversely affected by the presence of Katambora Rhodes grass.
QTL mapping for milling, gluten quality, and flour pasting properties in a recombinant inbred line population derived from a Chinese soft×hard wheat cross
Authors: Zhang Yelun , Wu Yunpeng , Xiao Yonggui , Yan Jun , Zhang Yong , Zhang Yan , Ma Chuanxi , Xia Xianchun , He Zhonghu
Published: June 2009

Improvement of processing quality is important for various wheat-based end products. A recombinant inbred line (RIL) population derived from a cross between the Chinese wheat cvv. PH82-2 (hard) and Neixiang 188 (soft) was sown at 3 locations across two seasons to map quantitative trait loci (QTLs) for milling, gluten quality, flour pasting properties, and Chinese white salted noodle (CWSN) qualities. One hundred and eighty-eight microsatellite loci, one rye secalin marker Sec1, one STS marker YP7A, one CAPs marker for the Pinb-D1b allele, and four glutenin subunit markers were used to genotype the population and construct a linkage map for subsequent QTL analysis. In total, 53 QTLs for 16 quality parameters were mainly mapped to glutenin loci Glu-A3 (Glu-A3a:Glu-A3d), Glu-B1 (Bx7+By9:Bx14+By15), and Glu-D1 (Bx2+By12:Bx5+By10), and the grain hardness (Pinb-D1a:Pinb-D1b) locus. The-high-molecular weight glutenin subunits (HMW-GS) 5+10 at the Glu-D1 locus showed large effects on mixograph peak time (MPT), mixograph 8 min width (MTxW), and weakening slope (WS), accounting for 43.1%, 24.2%, and 39.7% of the phenotypic variance, respectively. In contrast, the 1RS (1B.1R translocation) showed large negative effects on MTxW, explaining 42.2% of the phenotypic variance. Two important QTLs were detected for Rapid Viscosity Analyzer (RVA) parameters: one for RVA final viscosity (RFV) near the 1RS and the other for RVA setback (RSb) associated with the Glu-B1 locus, explaining 21.6% and 12.3% of the phenotypic variance, respectively. Two QTLs for noodle adhesiveness were identified: one occurred on chromosome 1A and the other was associated with Glu-B1. Two QTLs for noodle springiness, one associated with the 1RS showing a negative effect on noodle quality and the other mapped to the Ha locus on chromosome 5DS, accounted for 9.4% and 8.1% of the phenotypic variance, respectively. In addition, the Ha locus also showed large effects on flower protein content (FPC), mixograph peak width (MPW), and RVA parameters, especially RVA pasting temperature (RPT), explaining 71.5% of the phenotypic variance.
Do spring cover crops rob water and so reduce wheat yields in the northern grain zone of eastern Australia?
Authors: Whish J. P. M. , Price L. , Castor P. A.
Published: June 2009

During the 14-month-long fallow that arises when moving from summer to winter crops, stubble breakdown can denude the soil surface and leave it vulnerable to erosion. Cover crops of millet have been proposed as a solution, but this then raises the question, how often is there sufficient water in the system to grow a cover crop without reducing the soil water reserves to the point of prejudicing the following wheat crop? An on-farm research approach was used to compare the traditional long fallow (TF) with a millet fallow (MF) in a total of 31 commercial paddocks over 3 years. Each treatment was simulated using the simulation-modelling framework (APSIM) to investigate the outcomes over a longer timeframe and to determine how often a millet fallow could be successfully included within the farming system.
The on-farm trials showed that early-sown millet cover crops removed before December had no effect on wheat yield, but this was not true of millet cover crops that were allowed to grow through to maturity. Long-term simulations estimated that a spring cover crop of millet would adversely affect wheat yields in only 2% of years if planted early and removed after 50% cover had been achieved.
Comparing the nitrogen and phosphorus requirements of canola and wheat for grain yield and quality
Authors: Brennan R. F. , Bolland M. D. A.
Published: June 2009

Canola (oilseed rape, Brassica napus L.) is now grown in rotation with spring wheat (Triticum aestivum L.) on the predominantly sandy soils of south-western Australia. For both crop species, fertiliser nitrogen (N) and phosphorus (P) need to be applied for profitable grain production. The fertiliser N requirements have been determined separately for canola or wheat when adequate P was applied. By contrast, the fertiliser P requirements of the 2 species have been compared in the same experiment when adequate N was applied and showed that canola consistently required ~25–60% less P than wheat to produce 90% of the maximum grain yield. We report results of a field experiment conducted at 7 sites from 2000 to 2003 in the region to compare grain yield responses of canola and wheat to application of N and P in the same experiment. Four levels of N (0–138 kg N/ha as urea [46% N]) and 6 levels of P (0–40 kg P/ha as superphosphate [9.1%P]) were applied. Significant grain yield responses to applied N and P occurred for both crop species at all sites of the experiment, and the N × P interaction for grain production was always significant. To produce 90% of the maximum grain yield, canola required ~40% more N (range 16–75%) than wheat, and ~25% less P (range 12–43%) than wheat. For both crop species at 7 sites, applying increasing levels of N had no significant effect on the level of P required for 90% of maximum grain yield, although at 1 site the level of P required to achieve the target yield for both crop species when no N was applied (nil-N treatment) was significantly lower than for the other 3 treatments treated with N. For both crop species at all 7 sites, applying increasing levels of P increased the level of N required for 90% of the maximum grain yield. Fertiliser P had no significant effect on protein concentration in canola and wheat grain, and oil concentration in canola grain. As found in previous studies, application of increasing levels of N decreased oil concentration while increasing protein concentration in canola grain, and increased protein concentration in wheat grain. The N × P interaction was not significant for protein or oil concentration in grain. Protein concentrations in canola grain were about double those found in wheat grain.
Waterlogging affects the growth, development of tillers, and yield of wheat through a severe, but transient, N deficiency
Authors: Robertson Drew , Zhang Heping , Palta Jairo A. , Colmer Timothy , Turner Neil C.
Published: June 2009

Tiller production and survival are suppressed on soils prone to waterlogging. The tiller production and growth of wheat (Triticum aestivum cv. Wyalkatchem) was investigated in a glasshouse experiment during and after a transient waterlogging to examine its effect on grain yield. Wheat plants received either a high or low nitrogen (N) application at sowing and were waterlogged at 22 days after sowing for 14 days. Plants received a second either high or low N application after waterlogging was released. Waterlogging induced a transient N deficiency. The N concentration of the youngest expanded leaf on the mainstem and tillers declined markedly during waterlogging, but its recovery 14 days after the waterlogging was ended was independent of treatment, reaching a greater than the critical minimum concentration of 3.5%. The growth of primary tillers 1 and 2 was severely inhibited by waterlogging while the exsertion of new tillers was delayed by 9 days. Shoot dry weight of the waterlogged plants at final harvest was reduced by 37% compared with the non-waterlogged plants. During the recovery period, the waterlogged plants produced higher order tillers that produced late ears. As a result, the number of ears per plant was similar in plants in continuously drained or previously waterlogged soil. Waterlogging reduced the number of grains per ear on the mainstem and tillers, and consequently grain yield by 32%. High N application after waterlogging increased grain yield by ~20%, but high N applied at sowing had no effect on yield. This suggests that N application after waterlogging can reduce the detrimental effect of waterlogging on grain yields in areas prone to waterlogging.
Growth retardation and altered autonomic control in mice lacking brain serotonin
Authors: Alenina Natalia , Kikic Dana , Todiras Mihail , Mosienko Valentina , Qadri Fatimunnisa , Plehm Ralph , Boyé Philipp , Vilianovitch Larissa , Sohr Reinhard , Tenner Katja , Hörtnagl Heide , Bader Michael
Published: June 2009

Serotonin synthesis in mammals is initiated by 2 distinct tryptophan hydroxylases (TPH), TPH1 and TPH2. By genetically ablating TPH2, we created mice (
Tph2
−/−
) that lack serotonin in the central nervous system. Surprisingly, these mice can be born and survive until adulthood. However, depletion of serotonin signaling in the brain leads to growth retardation and 50% lethality in the first 4 weeks of postnatal life. Telemetric monitoring revealed more extended daytime sleep, suppressed respiration, altered body temperature control, and decreased blood pressure (BP) and heart rate (HR) during nighttime in
Tph2
−/−
mice. Moreover,
Tph2
−/−
females, despite being fertile and producing milk, exhibit impaired maternal care leading to poor survival of their pups. These data confirm that the majority of central serotonin is generated by TPH2. TPH2-derived serotonin is involved in the regulation of behavior and autonomic pathways but is not essential for adult life.
Newborn infants perceive abstract numbers
Authors: Izard Véronique , Sann Coralie , Spelke Elizabeth S. , Streri Arlette
Published: June 2009

Although infants and animals respond to the approximate number of elements in visual, auditory, and tactile arrays, only human children and adults have been shown to possess abstract numerical representations that apply to entities of all kinds (e.g., 7 samurai, seas, or sins). Do abstract numerical concepts depend on language or culture, or do they form a part of humans' innate, core knowledge? Here we show that newborn infants spontaneously associate stationary, visual-spatial arrays of 4–18 objects with auditory sequences of events on the basis of number. Their performance provides evidence for abstract numerical representations at the start of postnatal experience.
Acid–base-driven matrix-assisted mass spectrometry for targeted metabolomics
Authors: Shroff Rohit , Rulíšek Lubomír , Doubský Jan , Svatoš Aleš
Published: June 2009

The ability to charge huge biomolecules without breaking them apart has made matrix-assisted laser desorption/ionization (MALDI) mass spectrometry an indispensable tool for biomolecular analysis. Conventional, empirically selected matrices produce abundant matrix ion clusters in the low-mass region (<500 Da), hampering the application of MALDI-MS to metabolomics. An ionization mode of MAILD, a rational protocol for matrix selection based on Brønsted–Lowry acid–base theory and its application to metabolomics, biological screening/profiling/imaging, and clinical diagnostics is illustrated. Numerous metabolites, covering important metabolic pathways (Krebs' cycle, fatty acid and glucosinolate biosynthesis), were detected in extracts, biofluids, and/or in biological tissues (Arabidopsis thaliana,Drosophila melanogaster,Acyrthosiphon pisum, and human blood). This approach moves matrix selection from “black art” to rational design and sets a paradigm for small-molecule analysis via MALDI-MS.
Universal oscillations in counting statistics
Authors: Flindt C. , Fricke C. , Hohls F. , Novotný T. , Netočný K. , Brandes T. , Haug R. J.
Published: June 2009

Noise is a result of stochastic processes that originate from quantum or classical sources. Higher-order cumulants of the probability distribution underlying the stochastic events are believed to contain details that characterize the correlations within a given noise source and its interaction with the environment, but they are often difficult to measure. Here we report measurements of the transient cumulants 〈〈

n
m

〉〉 of the number
n
of passed charges to very high orders (up to
m
= 15) for electron transport through a quantum dot. For large
m
, the cumulants display striking oscillations as functions of measurement time with magnitudes that grow factorially with
m
. Using mathematical properties of high-order derivatives in the complex plane we show that the oscillations of the cumulants in fact constitute a universal phenomenon, appearing as functions of almost any parameter, including time in the transient regime. These ubiquitous oscillations and the factorial growth are system-independent and our theory provides a unified interpretation of previous theoretical studies of high-order cumulants as well as our new experimental data.
Universal behavior of the osmotically compressed cell and its analogy to the colloidal glass transition
Authors: Zhou E. H. , Trepat X. , Park C. Y. , Lenormand G. , Oliver M. N. , Mijailovich S. M. , Hardin C. , Weitz D. A. , Butler J. P. , Fredberg J. J.
Published: June 2009

Mechanical robustness of the cell under different modes of stress and deformation is essential to its survival and function. Under tension, mechanical rigidity is provided by the cytoskeletal network; with increasing stress, this network stiffens, providing increased resistance to deformation. However, a cell must also resist compression, which will inevitably occur whenever cell volume is decreased during such biologically important processes as anhydrobiosis and apoptosis. Under compression, individual filaments can buckle, thereby reducing the stiffness and weakening the cytoskeletal network. However, the intracellular space is crowded with macromolecules and organelles that can resist compression. A simple picture describing their behavior is that of colloidal particles; colloids exhibit a sharp increase in viscosity with increasing volume fraction, ultimately undergoing a glass transition and becoming a solid. We investigate the consequences of these 2 competing effects and show that as a cell is compressed by hyperosmotic stress it becomes progressively more rigid. Although this stiffening behavior depends somewhat on cell type, starting conditions, molecular motors, and cytoskeletal contributions, its dependence on solid volume fraction is exponential in every instance. This universal behavior suggests that compression-induced weakening of the network is overwhelmed by crowding-induced stiffening of the cytoplasm. We also show that compression dramatically slows intracellular relaxation processes. The increase in stiffness, combined with the slowing of relaxation processes, is reminiscent of a glass transition of colloidal suspensions, but only when comprised of deformable particles. Our work provides a means to probe the physical nature of the cytoplasm under compression, and leads to results that are universal across cell type.
A common toxin fold mediates microbial attack and plant defense
Authors: Ottmann Christian , Luberacki Borries , Küfner Isabell , Koch Wolfgang , Brunner Frédéric , Weyand Michael , Mattinen Laura , Pirhonen Minna , Anderluh Gregor , Seitz Hanns Ulrich , Nürnberger Thorsten , Oecking Claudia
Published: June 2009

Many plant pathogens secrete toxins that enhance microbial virulence by killing host cells. Usually, these toxins are produced by particular microbial taxa, such as bacteria or fungi. In contrast, many bacterial, fungal and oomycete species produce necrosis and ethylene-inducing peptide 1 (Nep1)-like proteins (NLPs) that trigger leaf necrosis and immunity-associated responses in various plants. We have determined the crystal structure of an NLP from the phytopathogenic oomycete
Pythium aphanidermatum
to 1.35Å resolution. The protein fold exhibits structural similarities to cytolytic toxins produced by marine organisms (actinoporins). Computational modeling of the 3-dimensional structure of NLPs from another oomycete,
Phytophthora parasitica,
and from the phytopathogenic bacterium,
Pectobacterium carotovorum,
revealed a high extent of fold conservation. Expression of the 2 oomycete NLPs in an
nlp
-deficient
P. carotovorum
strain restored bacterial virulence, suggesting that NLPs of prokaryotic and eukaryotic origins are orthologous proteins. NLP mutant protein analyses revealed that identical structural properties were required to cause plasma membrane permeabilization and cytolysis in plant cells, as well as to restore bacterial virulence. In sum, NLPs are conserved virulence factors whose taxonomic distribution is exceptional for microbial phytotoxins, and that contribute to host infection by plasma membrane destruction and cytolysis. We further show that NLP-mediated phytotoxicity and plant defense gene expression share identical fold requirements, suggesting that toxin-mediated interference with host integrity triggers plant immunity-associated responses. Phytotoxin-induced cellular damage-associated activation of plant defenses is reminiscent of microbial toxin-induced inflammasome activation in vertebrates and may thus constitute another conserved element in animal and plant innate immunity.
Controls on development and diversity of Early Archean stromatolites
Authors: Allwood Abigail C. , Grotzinger John P. , Knoll Andrew H. , Burch Ian W. , Anderson Mark S. , Coleman Max L. , Kanik Isik
Published: June 2009

The ≈3,450-million-year-old Strelley Pool Formation in Western Australia contains a reef-like assembly of laminated sedimentary accretion structures (stromatolites) that have macroscale characteristics suggestive of biological influence. However, direct microscale evidence of biology—namely, organic microbial remains or biosedimentary fabrics—has to date eluded discovery in the extensively-recrystallized rocks. Recently-identified outcrops with relatively good textural preservation record microscale evidence of primary sedimentary processes, including some that indicate probable microbial mat formation. Furthermore, we find relict fabrics and organic layers that covary with stromatolite morphology, linking morphologic diversity to changes in sedimentation, seafloor mineral precipitation, and inferred microbial mat development. Thus, the most direct and compelling signatures of life in the Strelley Pool Formation are those observed at the microscopic scale. By examining spatiotemporal changes in microscale characteristics it is possible not only to recognize the presence of probable microbial mats during stromatolite development, but also to infer aspects of the biological inputs to stromatolite morphogenesis. The persistence of an inferred biological signal through changing environmental circumstances and stromatolite types indicates that benthic microbial populations adapted to shifting environmental conditions in early oceans.
Mrc1 phosphorylation in response to DNA replication stress is required for Mec1 accumulation at the stalled fork
Authors: Naylor Maria L. , Li Ju-mei , Osborn Alex J. , Elledge Stephen J.
Published: June 2009

DNA replication stress activates a response pathway that stabilizes stalled forks and promotes the completion of replication. The budding yeast Mec1 sensor kinase, Mrc1 mediator, and Rad53 effector kinase are central to this signal transduction cascade in S phase. We report that Mec1-dependent, Rad53-independent phosphorylation of Mrc1 is required to establish a positive feedback loop that stabilizes Mec1 and the replisome at stalled forks. A structure–function analysis of Mrc1 also uncovered a central region required for proper mediator function and association with replisome components. Together these results reveal new insight into how Mrc1 facilitates checkpoint signal amplification at stalled replication forks.
Uncertainty evaluation for linking a bilateral key comparison with the corresponding CIPM key comparison
Authors: Ojanen M , Shpak M , Kärhä P , Leecharoen R , Ikonen E
Published: June 2009

A method for evaluating the uncertainty in linking a bilateral key comparison to another key comparison with several participants is presented theoretically and demonstrated with an actual comparison. Equations are derived for the uncertainties of the unilateral and mutual degrees of equivalence for the linked participant in the bilateral comparison. It is shown that the uncertainty components related to uncorrelated effects in the measurements of the linking participant play a critical role in determining the additional uncertainties due to the linking process. As a practical example, the results are applied to a bilateral comparison of the spectral irradiance scales of MIKES (Finland) and NIMT (Thailand) in the spectral range from 290 nm to 900 nm.
Suppression of error-field-induced magnetic islands by Alfvén resonance effect in rotating plasmas
Authors: Furukawa M. , Zheng L.-J.
Published: June 2009

Error-field penetration is numerically studied in cylindrical tokamak geometry with plasma rotation. For a static error field, non-rotating magnetic islands are generated in the steady state. The penetrated perturbed magnetic flux is effectively reduced by the plasma rotation at small resistivity. Twin current sheets are formed at the Alfvén resonance positions when the plasma rotation is fast enough, and thereby the error-field penetration is significantly changed. The electromagnetic torque increases linearly in the plasma rotation velocity especially at high rotation velocity and low resistivity regime, which agrees with previous theoretical prediction, although the linear scaling can be easily affected if the Alfvén resonance is located close to the plasma edge. The electromagnetic torque in this regime does not depend on the resistivity. For high beta or small resistivity plasmas, the resultant volume-integrated electromagnetic torque, which brakes the plasma rotation, becomes maximum at very small, almost zero experimentally, rotation velocity.
Feasibility of electron Bernstein wave coupling via O-X-B mode conversion in the RFX-mod reversed field pinch device
Authors: Bilato R. , Volpe F. , Köhn A. , Paccagnella R. , Farina D. , Poli E. , Brambilla M.
Published: June 2009

Electron Bernstein wave coupling through the ordinary-extraordinary-Bernstein (O-X-B) scheme has been modelled for reversed field experiment-mod (RFX-mod) overdense plasmas. The compromise between constraints from plasma parameters and from a viable launcher design highlights the commercial frequency of 28 GHz as a promising candidate. At this frequency a steerable quasi-optical launch system has the flexibility necessary for tuning the optimal operational window for the O-X mode conversion. According to the results of a two-dimensional full-wave code (Köhn et al
2008 Plasma Phys. Control. Fusion
50 085018), the maximum O-X mode conversion efficiency amounts to 58% for a single pass.
Destabilization of the internal kink mode by energetic electrons on the HL-2A tokamak
Authors: Chen W. , Ding X.T. , Liu Yi. , Yuan G.L. , Zhang Y.P. , Dong Y.B. , Song X.Y. , Zhou J. , Song X.M. , Deng W. , Yang Q.W. , Ji X.Q. , Duan X.R. , Liu Y.
Published: June 2009

A strong burst of the internal kink mode has been observed during ECRH on the HL-2A. It has been experimentally identified that the energetic electrons, which deviate from Maxwell velocity distribution, excite the mode, which was a so-called electron fishbone (e-fishbone). The energy distribution of the electrons is indirectly measured by a hard x-ray detector (CdTe) with the pulse height analysis. When the counts of the energetic electrons with 35–70 keV increase to a higher level, the mode can be obviously observed. The e-fishbone can be excited during off-axis ECRH deposited on both the high field side and the low field side. The modes propagate toroidally parallel to the precession velocity of deeply trapped ions which is in the same direction as the plasma current (co-current) and poloidally parallel to the electron diamagnetic drift velocity. In order to further identify with the e-fishbone mode, the resonance condition of the wave–particle has been investigated. Comparing with experimental results, the calculation analyses show that the mode frequency is close to the precession frequency of the barely trapped electrons or barely circulating electrons when the magnetic shear is very weak or negative.
An Intramolecular Signaling Element that Modulates Dynamin Function In Vitro and In Vivo
Authors: Chappie Joshua S. , Acharya Sharmistha , Liu Ya-Wen , Leonard Marilyn , Pucadyil Thomas J. , Schmid Sandra L.
Published: June 2009

Dynamin exhibits a high basal rate of GTP hydrolysis that is enhanced by self-assembly on a lipid template. Dynamin's GTPase effector domain (GED) is required for this stimulation, though its mechanism of action is poorly understood. Recent structural work has suggested that GED may physically dock with the GTPase domain to exert its stimulatory effects. To examine how these interactions activate dynamin, we engineered a minimal GTPase-GED fusion protein (GG) that reconstitutes dynamin's basal GTPase activity and utilized it to define the structural framework that mediates GED's association with the GTPase domain. Chemical cross-linking of GG and mutagenesis of full-length dynamin establishes that the GTPase-GED interface is comprised of the N- and C-terminal helices of the GTPase domain and the C-terminus of GED. We further show that this interface is essential for structural stability in full-length dynamin. Finally, we identify mutations in this interface that disrupt assembly-stimulated GTP hydrolysis and dynamin-catalyzed membrane fission in vitro and impair the late stages of clathrin-mediated endocytosis in vivo. These data suggest that the components of the GTPase-GED interface act as an intramolecular signaling module, which we term the bundle signaling element, that can modulate dynamin function in vitro and in vivo.
Reordering contigs of draft genomes using the Mauve Aligner
Authors: Rissman Anna I. , Mau Bob , Biehl Bryan S. , Darling Aaron E. , Glasner Jeremy D. , Perna Nicole T.
Published: June 2009

Summary: Mauve Contig Mover provides a new method for proposing the relative order of contigs that make up a draft genome based on comparison to a complete or draft reference genome. A novel application of the Mauve aligner and viewer provides an automated reordering algorithm coupled with a powerful drill-down display allowing detailed exploration of results.

Availability: The software is available for download at http://gel.ahabs.wisc.edu/mauve.

Contact:  rissman@wisc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online and http://gel.ahabs.wisc.edu
Fungal Infections
Authors: Ali Nazia
Published: June 2009

Fungi are a common cause of skin infections. The pathogens involved are usually dermatophytes and yeasts. This article covers the common types of fungal infections and provides information on how they can be recognized and managed in a primary care setting. Providing patients with advice on the preventative measures that can be taken is essential to prevent recurrent infections.
Obsessive—Compulsive Disorder
Authors: Taylor Clare
Published: June 2009

Obsessive—compulsive disorder is a common psychiatric disorder characterized by intrusive thoughts or ‘obsessions’, which predispose to repetitive acts or rituals, known as ‘compulsions’. These compulsions are necessary to relieve the anxiety caused by the obsession. Patients have insight into the unnecessary nature of the symptoms but can find them hard to suppress. Inability to carry out everyday activities can lead to significant functional impairment. Many feel embarrassed and go to great lengths to conceal the disorder from others which can lead to a delay in diagnosis and management.