bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolution of a confined turbulent jet in a long cylindrical cavity: Homogeneous fluids
Authors: Voropayev S. I. , Sanchez X. , Nath C. , Webb S. , Fernando H. J. S.
Published: December 2011

The flow induced in a long cylinder by an axially discharging round turbulent jet was investigated experimentally with applications to crude oil storage in the U.S. strategic petroleum reserves (SPR). It was found that the flow does not reach a true steady state, but vacillates periodically. Digital video recordings and particle image velocimetry were used to map the flow structures and velocity/vorticity fields, from which the frequency of jet switching, jet stopping distance, mean flow, turbulence characteristics, and the influence of end-wall boundary conditions were inferred. The results were parameterized using the characteristic length D and velocity J1/2/D scales based on the jet kinematic momentum flux J and cylinder width D. The scaling laws so developed could be used to extrapolate laboratory observations to SPR flows.
Improvement of the quantum confined Stark effect characteristics by means of energy band profile modulation: The case of Gaussian quantum wells
Authors: Ramírez-Morales A. , Martínez-Orozco J. C. , Rodríguez-Vargas I.
Published: December 2011

We study the quantum confined stark effect (QCSE) characteristics in Gaussian quantum wells (GQW). This special energy band profile is built varying the aluminum concentration of the AlGaAs ternary alloy in Gaussian fashion. The semi-empirical sp3s* tight-binding model including spin is used to obtain the energy Stark shifts (ESS) and the wave-function Gaussian spatial overlap (GSO) between electrons and holes for different electric field strengths, quantum well widths and aluminum concentrations. We find that both the ESS and the GSO depend parabolically with respect to the electric field strength and the quantum well width. These QCSE characteristics show an asymmetry for the electric field in the forward and reverse directions, related directly to the different band-offset of electrons and holes, being the negative electric fields (reverse direction) more suitable to reach greater ESS. Two important features are presented by this special energy band profile: (1) reductions of the ESS and (2) enhancements of the GSO of tents to hundreds with respect to parabolic and rectangular quantum wells. Even more, tailoring the quantum well width it is possible to reach GSO of thousands with respect to rectangular quantum wells. Finally, it is important to mention that similar results could be obtained in other quantum well heterostructures of materials such as nitrides, oxides (ZnO), and SiGe whenever the confinement band profiles are modulated in Gaussian form.
Giant magnetoelectric torque effect and multicoupling in two phases ferromagnetic/piezoelectric system
Authors: Xing Zengping , Xu Kai , Dai Guangyu , Li Jiefang , Viehland Dwight
Published: December 2011

The physical mechanism of a non-magnetostrictive magnetoelectric (ME) effect was revealed and designated as the ME torque (MET) effect. Experimental results showed that the MET effect could be huge; a simple MET device could achieve giant ME voltage coefficients of 100 V/cm.Oe at 1 Hz and 2100 V/cm.Oe at the first order resonant frequency. These are the highest reported ME coefficients in a bulk device ever. We then proposed the multicoupling ME effect, which comes from the interaction of magnetostriction, magnetic torque, and piezoelectricity, and rewrite the ME constitutive tensor equation. The abnormal phenomenon in the (1-3) structure ME thin film that T-L mode might bring larger ME coupling than L-L mode was successfully explained from the multicoupling concept. These researches have extended the giant ME effect from the traditional magnetostrictive/piezoelectric system to a common ferromagnetic/piezoelectric system, and gave more choices to scientists/engineers for constructing the giant ME device.
Eliminating the broadening by finite aperture in Brillouin spectroscopy
Authors: Vialla R. , Rufflé B. , Guimbretière G. , Vacher R.
Published: December 2011

We present a new optical arrangement which allows to avoid the broadening by finite aperture in Brillouin spectroscopy. In this system, all the rays scattered at the same angle by the whole scattering volume are collected on a single pixel of the area detector. This allows to use large collection angles, increasing the luminosity without lowering the accuracy of the frequency-shift and linewidth measurements. Several results of experimental checks are provided, showing the efficiency of the device.
Simulation of heterogeneous end-coupling reactions in polydisperse polymer blends
Authors: Guseva Daria V. , Kudryavtsev Yaroslav V. , Berezkin Anatoly V.
Published: December 2011

The influence of polydispersity on the interfacial kinetics of end-coupling and microstructure formation in the melt of immiscible polymers was studied using dissipative particle dynamics simulations. The irreversible reaction started at a flat interface between two layers, each of which contained polymer chains of two different lengths with functionalized or unreactive end groups. As in the case of fully functionalized monodisperse reactants [A. V. Berezkin and Y. V. Kudryavtsev, Macromolecules 44, 112 (2011)10.1021/ma101285m], four kinetic regimes were observed: linear (mean field coupling at the initial interface), saturation (decreasing the reaction rate due to the copolymer brush formation or reactant depletion near the interface), autocatalytic (loss of the initial interface stability and formation of a lamellar microstructure), and terminal (microstructure ripening under diffusion control). The interfacial instability is caused by overcrowding the interface with the reaction product, and it can be kinetically suppressed by increasing chain length of the reactants. Main effects of polydispersity are as follows: (i) the overall end-coupling rate is dominated by the shortest reactive chains; (ii) the copolymer concentration at the interface causing its instability can be not the same as in the lamellas formed afterwards; (iii) mean length of the copolymer product considerably changes with conversion passing through a minimum when a microstructure is just formed.
Photoelectron spectroscopy of HC4N−
Authors: Vogelhuber Kristen M. , Wren Scott W. , Shaffer Christopher J. , McMahon Robert J. , McCoy Anne B. , Lineberger W. Carl
Published: December 2011

We report the 364-nm photoelectron spectrum of HC4N−. We observe electron photodetachment from the bent $\tilde X$X̃2A″ state of HC4N− to both the near-linear $\tilde X$X̃3A″ and the bent ã 1A′ states of neutral HC4N. We observe an extended, unresolved vibrational progression corresponding to $\tilde X$X̃3A″ ← $\tilde X$X̃2A″ photodetachment, and we measure the electron affinity (EA) of the $\tilde X$X̃3A″ state of HC4N to be 2.05(8) eV. Photodetachment to the bent ã 1A′ state results in a single intense origin peak at a binding energy of 2.809(4) eV, from which we determine the singlet-triplet splitting (ΔEST) of HC4N: 0.76(8) eV. For comparison and to aid in the interpretation of the HC4N− spectrum, we also report the 364-nm photoelectron spectra of HCCN− and DCCN−. Improved signal-to-noise over the previous HCCN− and DCCN− photoelectron spectra allows for a more precise determination of the EAs and ΔESTs of HCCN and DCCN. The EAs of HCCN and DCCN are measured to be 2.001(15) eV and 1.998(15) eV, respectively; ΔEST(HCCN) is 0.510(15) eV and ΔEST(DCCN) is 0.508(15) eV. These results are discussed in the context of other organic carbene chains.
Effects of non-ideal energy selective contacts and experimental carrier cooling rate on the performance of an indium nitride based hot carrier solar cell
Authors: Aliberti P. , Feng Y. , Shrestha S. K. , Green M. A. , Conibeer G. , Tu L. W. , Tseng P. H. , Clady R.
Published: December 2011

The performance of an InN based hot carrier solar cell with a bulk InN absorber has been evaluated using an innovative approach that takes into account absorber energy-momentum dispersion relations, energy conservation, Auger recombination and impact ionization mechanisms simultaneously. The non ideality of the energy selective filters has also been included in the model. In order to obtain practical achievable values of conversion efficiency, the actual thermalisation velocity of hot carriers in InN has been measured using time resolved photoluminescence. Results of the computations shown limiting efficiencies of 24% for 1000 suns and 36.2% for maximal concentration.
Energy-level and optical properties of nitrogen doped TiO2: An experimental and theoretical study
Authors: González-Borrero P. P. , Bernabé H. S. , Astrath N. G. C. , Bento A. C. , Baesso M. L. , Castro Meira M. V. , de Almeida J. S. , Ferreira da Silva A.
Published: December 2011

Photoacoustic spectroscopy was used to study nitrogen-doped titanium dioxide film. The energy positions of defect and impurity centre levels are reported. The energy levels were obtained using the excitation method and the mechanisms of the photoacoustic signal generation are discussed. The visible light absorption of the yellow film was explained considering electronic transitions between localized states within the band gap and the transitions from these states into the conduction band. Moreover, first principles calculations revealed that nitrogen doping and oxygen vacancies in titanium dioxide induce defect levels within the gap which account for the absorption in the visible light.
Even-odd symmetry and the conversion efficiency of ideal and practical graphene transistor frequency multipliers
Authors: Parrish Kristen N. , Akinwande Deji
Published: December 2011

The conversion efficiency of field-effect transistors with even-odd symmetry is elucidated in this work. From symmetry considerations, this work reveals that even symmetry, due to electron-hole symmetry in graphene, affords efficient even-harmonic multiplication. Odd symmetry, associated with linear charge transport, affords suppression of odd-harmonic signals. For the ideal symmetric transistor multiplier, conversion efficiency with relatively large power gain is achievable, while for practical graphene transistors, the efficiency can be substantially less than unity due to non-idealities such as contact resistance, high impurity densities, and low gate capacitance. In the quantum capacitance limit of graphene transistor, near-lossless conversion efficiency is available.
Large photoinduced conductivity reduction in thin films of metallic ferromagnetic manganites
Authors: Smolyaninova V. N. , Yong G. , Kolagani Rajeswari M. , Biswas Amlan , Ermer H. K. , Wang K. , Piazza A.
Published: December 2011

This paper reports on a study of photoinduced resistivity changes in thin films of ferromagnetic metallic (FMM) manganites. We have observed a significant increase of resistance in La0.7Ba0.3MnO3 thin film under continuous wave argon ion laser illumination presumably associated with photoinduced demagnetization. Strong dependence of resistance on thermal/illumination history is consistent with the coexistence of two phases: ferromagnetic metallic phase and photoinduced less conductive phase.
A sequential two-step near-infrared quantum splitting in Ho3+ singly doped NaYF4
Authors: Yu D. C. , Huang X. Y. , Ye S. , Zhang Q. Y. , Wang J.
Published: December 2011

We demonstrated an efficient sequential two-step near-infrared (NIR) quantum splitting (QS) in a Ho3+ singly doped β-NaYF4. An incident high-energy ultraviolet (UV)-to-visible photon in the wavelength range of 300−560 nm, which enables the Ho3+:5F4,5S2 states excited, could be efficiently split into two NIR photons at 1015 and 1180 nm. Underlying mechanisms for the sequential two-step NIR-QS process are analyzed in terms of the diffuse reflection spectrum, static and dynamic photoemission spectra and monitored excitation spectra. Internal quantum yield is obtained up to 110% on the basis of experimental and theoretical calculation results.
Insights from the great 2011 Japan earthquake
Authors: Lay Thorne , Kanamori Hiroo
Published: December 2011

The diverse set of waves generated in Earth’s interior, oceans, and atmosphere during the devastating Tohoku-oki earthquake reveal some extraordinary geophysics.
Patterns of plant abundances in natural systems: is there value in modelling both species abundance and distribution?
Authors: Duff Thomas J. , Bell Tina L. , York Alan
Published: November 2011

In plant ecology it is common to use biophysical models to predict species distribution; however, spatial quantitative models of plant species remain rare. In practice, occupancy models are often assumed to indicate habitant quality and are used as surrogate abundance models. This study assessed the potential value of quantitative models of plants for ecosystem management applications by assessing patterns of occupancy and abundance within two closely related understorey plant species, Xanthorrhoea australis and X. caespitosa. Vegetation quadrats were surveyed in Eucalyptus woodland and cover-abundances were assessed using a metric pin intersection technique. A zero inflated generalised additive modelling process was used to assess the relationship of species occupancies and cover-abundances to environmental properties. The models were applied to mapped environmental data to create spatial predictions of occupancy and cover-abundance. Both species shared several predictor variables, but differing responses to these variables resulted in mutually exclusive distributions. No significant correlation was observed between occupancy and cover-abundance for X. australis, but strong correlation was evident for X. caespitosa. The strength of the occupancy and abundance relationship was found to differ greatly between the two species and is therefore likely to be species specific. Occupancy models have been used successfully as proxies for habitat quality models of plant species; however where occupancy and abundance of plants are driven by different influences occupancy will be a poor surrogate for abundance. Outcomes may be improved if occupancy models are validated for abundance or quantitative models are developed and tested for individual species.
Growth rates of juvenile southern rock lobster (Jasus edwardsii) estimated through a diver-based tag - recapture program
Authors: Linnane Adrian , Hobday David , Frusher Stewart , Gardner Caleb
Published: November 2011

Despite being one of the most economically important fisheries in south-eastern Australia, growth rates of juvenile southern rock lobster (Jasus edwardsii) have not previously been quantified in the wild. This study utilised a diver-based tag–recapture program to estimate growth rates of individuals between 40–80 mm carapace length (CL) in temperate reef sites across south-eastern Australia. Of the 7064 lobsters tagged and released, 978 (14%) were recaptured with recapture rates of 23, 5 and 7% in the States of Tasmania, South Australia and Victoria respectively. Although individual growth increments were similar between the sexes, differences in annual growth rates were evident at 50 mm CL, with males growing ~1.4 times faster than females. Increased levels of growth in males resulted from a higher moult frequency, which was found to significantly reduce in females as they reached sexual maturity at ~70–80 mm CL. No significant difference was found in growth rates of males or females between the States when all sites within each State were combined. The growth estimates from this work contribute to the understanding of juvenile lobster population dynamics and will improve current fishery models by confirming relationships between early juvenile, pre-recruit abundance and entry to the fishable biomass.
Natural C-14 provides new data for stream food-web studies: a comparison with C-13 in multiple stream habitats
Authors: Ishikawa Naoto F. , Uchida Masao , Shibata Yasuyuki , Tayasu Ichiro
Published: November 2011

In stream food-web analysis, the contributions of carbon from periphyton (an autochthonous source) and terrestrial litter (an allochthonous source) are estimated by isotopic difference. We hypothesised that periphyton δ13C varies among stream habitats, whereas Δ14C does not because Δ14C is corrected with δ13C, by definition. To test this hypothesis, we compared the variability of δ13C and Δ14C of periphyton and dissolved inorganic carbon (DIC) in four habitats (open v. shaded, riffle v. pool) within a limestone-based upland stream in Japan. Periphyton δ13C values (from –31.9‰ to –16.3‰) were significantly different among the habitats whereas the Δ14C values (from –379‰ to –141‰) were not. Periphyton δ13C values depended on both algal photosynthetic activity and δ13C of the DIC, whereas periphyton Δ14C depended only on DIC Δ14C. The δ13C and Δ14C values of litter were constant. Thus, the difference between the periphyton and litter δ13C values (Δδ13C) varied among habitats, but their Δ14C differences (ΔΔ14C) did not. Our results indicate that Δ14C is spatially stable among stream habitats and that Δ14C measurements can be used to precisely determine carbon sources for stream food-web analysis within individual reaches.
Effects of anthocyanin extracted from black soybean seed coat on spermatogenesis in a rat varicocele-induced model
Authors: Jang Hoon , Kim Su Jin , Yuk Seung Mo , Han Dong Seok , Ha U.-Syn , Hong Sung Hoo , Lee Ji Yeol , Hwang Tae Kon , Hwang Seong Yeon , Kim Sae Woong
Published: November 2011

Varicocele is the most common cause of primary male infertility and is associated with oxidative stress. The aim of the present study was to investigate the effects of anthocyanin on a rat model of varicocele. Twenty-four male rats were divided into four experimental groups: a normal control group, a varicocele-induced control group and two varicocele-induced groups treated with either 40 or 80 mg kg–1, p.o., anthocyanin for 4 weeks. Varicocele was induced by the partial obstruction of the left renal vein. After 8 weeks, the testes and epididymides from rats in all groups were removed, weighed and subjected to histological examination and semen analysis. Apoptosis in the testes was determined by terminal deoxyribonucleotidyl transferase-mediated dUTP–digoxigenin nick end-labelling (TUNEL) and oxidative stress was assessed by measuring 8-hydroxy-2′-deoxyguanosine (8-OHdG) levels. Although no significant differences in sperm counts were observed among the groups, anthocyanin treatment of the varicocele-induced groups resulted in significantly increased testes weight, sperm motility and spermatogenic cell density (P < 0.05). Anthocyanin treatment also significantly decreased apoptotic body count and 8-OHdG concentrations (P < 0.05). We suggest that the antioxidant effect of anthocyanin prevented the damage caused by varicocele-induced reactive oxygen species.
Rats in rice: linking crop and pest models to explore management strategies
Authors: Brown Peter R. , My Phung Nguyen Thi , Gaydon Donald S.
Published: December 2011

Context
Rodents cause yield losses of 10–15% in irrigated lowland rice crops in Vietnam, with farmers spending a lot of time and money trying to control them. Despite this, there is little understanding about the optimal timing of rodent control and the level of reduction required to maximise rice crop yields. This is compounded by the ability of rice crops to compensate for damage, and farmers applying control at the wrong time.

Aims
We explored the optimal timing and intensity of rodent control required to increase yields of irrigated lowland rice crops in the Mekong Delta, Vietnam.

Methods
We developed a system analysis framework using the rice model APSIM-Oryza validated against a hand-clipped field experiment, linked with a rodent population model and field data on rodent damage rates in rice crops. A range of intensities of reduced feeding rates and timing were explored in simulated scenarios. The responses were examined over three rice crop seasons in An Giang province, Mekong Delta, Vietnam.

Key results
The rice crop model was benchmarked, validated and shown to adequately compensate for rodent damage. Highest yield losses occurred in the third rice crop (16% yield loss). A one-off rodent control action at the booting stage of the rice crop with 50% control effectiveness achieved a 5% yield increase. The community trap barrier system (CTBS) with 30% control effectiveness achieved a 5% yield increase.

Conclusions
The modelling demonstrated the importance of rodent management timing and that control should be applied before the onset of the rodent breeding season, which normally starts at maximum tillering or booting stages.

Implications
We conclude that modelling can improve pest management decisions by optimising timing and level of effectiveness to achieve yield increases.
Dynamic control of protein diffusion within the granal thylakoid lumen
Authors: Kirchhoff Helmut , Hall Chris , Wood Magnus , Herbstová Miroslava , Tsabari Onie , Nevo Reinat , Charuvi Dana , Shimoni Eyal , Reich Ziv
Published: December 2011

The machinery that conducts the light-driven reactions of oxygenic photosynthesis is hosted within specialized paired membranes called thylakoids. In higher plants, the thylakoids are segregated into two morphological and functional domains called grana and stroma lamellae. A large fraction of the luminal volume of the granal thylakoids is occupied by the oxygen-evolving complex of photosystem II. Electron microscopy data we obtained on dark- and light-adapted
Arabidopsis
thylakoids indicate that the granal thylakoid lumen significantly expands in the light. Models generated for the organization of the oxygen-evolving complex within the granal lumen predict that the light-induced expansion greatly alleviates restrictions imposed on protein diffusion in this compartment in the dark. Experiments monitoring the redox kinetics of the luminal electron carrier plastocyanin support this prediction. The impact of the increase in protein mobility within the granal luminal compartment in the light on photosynthetic electron transport rates and processes associated with the repair of photodamaged photosystem II complexes is discussed.
High-efficiency homologous recombination in the oil-producing alga
Nannochloropsis
sp.
Authors: Kilian Oliver , Benemann Christina S. E. , Niyogi Krishna K. , Vick Bertrand
Published: November 2011

Algae have reemerged as potential next-generation feedstocks for biofuels, but strain improvement and progress in algal biology research have been limited by the lack of advanced molecular tools for most eukaryotic microalgae. Here we describe the development of an efficient transformation method for
Nannochloropsis
sp., a fast-growing, unicellular alga capable of accumulating large amounts of oil. Moreover, we provide additional evidence that
Nannochloropsis
is haploid, and we demonstrate that insertion of transformation constructs into the nuclear genome can occur by high-efficiency homologous recombination. As examples, we generated knockouts of the genes encoding nitrate reductase and nitrite reductase, resulting in strains that were unable to grow on nitrate and nitrate/nitrite, respectively. The application of homologous recombination in this industrially relevant alga has the potential to rapidly advance algal functional genomics and biotechnology.
Palmitoylation influences the function and pharmacology of sodium channels
Authors: Bosmans Frank , Milescu Mirela , Swartz Kenton J.
Published: November 2011

Palmitoylation is a common lipid modification known to regulate the functional properties of various proteins and is a vital step in the biosynthesis of voltage-activated sodium (Nav) channels. We discovered a mutation in an intracellular loop of rNav1.2a (G1079C), which results in a higher apparent affinity for externally applied PaurTx3 and ProTx-II, two voltage sensor toxins isolated from tarantula venom. To explore whether palmitoylation of the introduced cysteine underlies this observation, we compared channel susceptibility to a range of animal toxins in the absence and presence of 2-Br-palmitate, a palmitate analog that prevents palmitate incorporation into proteins, and found that palmitoylation contributes to the increased affinity of PaurTx3 and ProTx-II for G1079C. Further investigations with 2-Br-palmitate revealed that palmitoylation can regulate the gating and pharmacology of wild-type (wt) rNav1.2a. To identify rNav1.2a palmitoylation sites contributing to these phenomena, we substituted three endogenous cysteines predicted to be palmitoylated and found that the gating behavior of this triple cysteine mutant is similar to wt rNav1.2a treated with 2-Br-palmitate. As with chemically depalmitoylated rNav1.2a channels, this mutant also exhibits an increased susceptibility for PaurTx3. Additional mutagenesis experiments showed that palmitoylation of one cysteine in particular (C1182) primarily influences PaurTx3 sensitivity and may enhance the inactivation process of wt rNav1.2a. Overall, our results demonstrate that lipid modifications are capable of altering the gating and pharmacological properties of rNav1.2a.
Tripartite motif containing protein 27 negatively regulates CD4 T cells by ubiquitinating and inhibiting the class II PI3K-C2β
Authors: Cai Xinjiang , Srivastava Shekhar , Sun Yi , Li Zhai , Wu Haiyan , Zuvela-Jelaska Ljiljana , Li Jun , Salamon Rachel S. , Backer Jonathan M. , Skolnik Edward Y.
Published: December 2011

The K
+
channel KCa3.1 is required for Ca
2+
influx and the subsequent activation of CD4 T cells. The class II phosphatidylinositol 3 kinase C2β (PI3KC2β) is activated by the T-cell receptor (TCR) and is critical for KCa3.1 channel activation. Tripartite motif containing protein 27 (TRIM27) is a member of a large family of proteins that function as Really Interesting New Gene (RING) E3 ubiquitin ligases. We now show that TRIM27 functions as an E3 ligase and mediates lysine 48 polyubiquitination of PI3KC2β, leading to a decrease in PI3K enzyme activity. By inhibiting PI3KC2β, TRIM27 also functions to negatively regulate CD4 T cells by inhibiting KCa3.1 channel activity and TCR-stimulated Ca
2+
influx and cytokine production in Jurkat, primary human CD4 T cells, and Th0, Th1, and Th2 CD4 T cells generated from

TRIM27
−/−

mice. These findings provide a unique mechanism for regulating class II PI3Ks, and identify TRIM27 as a previously undescribed negative regulator of CD4 T cells.
“I saw the yellowish going south”
Authors: de Villiers Jessica
Published: December 2011

This paper uses discourse analysis techniques to analyze communication breakdown in the conversation of a youth with autism spectrum disorder (ASD). In demonstrating how discourse analysis can reveal unexpected and ordinarily unperceived meanings in unorthodox forms of expression in ways that are clinically relevant, this text analysis uncovers and examines not only ambiguities and conversational breakdown, but also unexpected coherence, in a discourse that appears to be incomprehensible. Beginning with a brief account of ASD, the paper goes on to present the linguistic framework for analysis, phasal analysis (Asp and de Villiers 2010; Gregory 1985a; Malcolm 2010), a contextually based model for the description of English discourse. Specifically, the approach is used for an analysis of prosodic, grammatical and discourse features. Analysis reveals meaningful linguistic patterning that indicates conversational participation, engagement and coherence not previously supposed, with important social and clinical implications.
Piecemeal acquisition of boundedness
Authors: Tribushinina Elena
Published: December 2011

Recent semantic studies show that adjectives differ in terms of the scalar structures associated with them, which has implications for patterns of degree modification. For example, relative adjectives in Dutch are associated with unbounded (open) scales and are, therefore, incompatible with maximizing adverbs (e.g. #helemaal groot ‘completely big’, #helemaal klein ‘completely small’). This paper tests the hypothesis that children acquire the relevant distinctions in the domain of boundedness in a piecemeal fashion by storing ready-made modifier-adjective pairings from the input and later generalizing over them. The results of the longitudinal corpus study of four degree adverbs in the spontaneous speech of nine children acquiring Netherlandic Dutch are consistent with the idea that language learners start by reproducing target-like modifier-adjective combinations stored as prefabs from the input. Once a critical mass of such adverb-adjective pairings has been stored, children make generalizations over the stored instances and proceed to productive use. This phase is marked by over-generalization errors that are attested, on average, six months after the emergence of a degree adverb. Most of the over-generalization errors involved combining a degree adverb with an adjective of an incompatible scalar structure. It is concluded that the acquisition of boundedness has a more protracted time course than has been hitherto assumed on the basis of comprehension experiments.
Automatic registration between 3D intra-operative ultrasound and pre-operative CT images of the liver based on robust edge matching
Authors: Nam Woo Hyun , Kang Dong-Goo , Lee Duhgoon , Lee Jae Young , Ra Jong Beom
Published: November 2011

The registration of a three-dimensional (3D) ultrasound (US) image with a computed tomography (CT) or magnetic resonance image is beneficial in various clinical applications such as diagnosis and image-guided intervention of the liver. However, conventional methods usually require a time-consuming and inconvenient manual process for pre-alignment, and the success of this process strongly depends on the proper selection of initial transformation parameters. In this paper, we present an automatic feature-based affine registration procedure of 3D intra-operative US and pre-operative CT images of the liver. In the registration procedure, we first segment vessel lumens and the liver surface from a 3D B-mode US image. We then automatically estimate an initial registration transformation by using the proposed edge matching algorithm. The algorithm finds the most likely correspondences between the vessel centerlines of both images in a non-iterative manner based on a modified Viterbi algorithm. Finally, the registration is iteratively refined on the basis of the global affine transformation by jointly using the vessel and liver surface information. The proposed registration algorithm is validated on synthesized datasets and 20 clinical datasets, through both qualitative and quantitative evaluations. Experimental results show that automatic registration can be successfully achieved between 3D B-mode US and CT images even with a large initial misalignment.
Accounting for Heterogeneity in Multicrop Micro‐Econometric Models: Implications for Variable Input Demand Modeling
Authors: Carpentier Alain , Letort Elodie
Published: November 2011

This article aims to show that if the farm sample under consideration is characterized by significant heterogeneity, recovering output‐specific input uses or modeling farm‐level input uses may be more complicated than previously recognized. The article theoretically investigates the problems implied by farm heterogeneity in input allocation equations and multicrop econometric models, proposes an empirically tractable solution for overcoming these problems, and assesses the empirical relevance of the theoretically identified problems. The results demonstrate that heterogeneity matters, but that the revealed heterogeneity bias has a limited impact on the empirical results.
Hand attractiveness—its determinants and associations with facial attractiveness
Authors: Kościński Krzysztof
Published: November 2011

Although attractiveness of the human hand seems to be of some importance in the social and mating context, it has attracted little scientific interest thus far. Here, we investigated physical determinants of hand attractiveness and its associations with facial appeal. Photographs of faces and the dorsal and ventral side of hands of young women and men were measured and assessed for attractiveness and several other features. Typicality and femininity of shape, perceived fattiness and skin healthiness, the appearance of nail vicinity, and grooming influenced hand attractiveness in men and women. Hand and facial attractiveness were correlated with each other for each sex. This relationship was mediated by shape typicality and fattiness in men and by grooming and, possibly, fattiness in women. Results are discussed from an evolutionary psychology perspective with special reference to biological signaling and mate selection.
Inferring sequence regions under functional divergence in duplicate genes
Authors: Huang Yi-Fei , Golding G. Brian
Published: November 2011

Motivation: A number of statistical phylogenetic methods have been proposed to identify type-I functional divergence in duplicate genes by detecting heterogeneous substitution rates in phylogenetic trees. A common disadvantage of the existing methods is that autocorrelation of substitution rates along sequences is not modeled. This reduces the power of existing methods to identify regions under functional divergence.

Results: We design a phylogenetic hidden Markov model to identify protein regions relevant to type-I functional divergence. A C++ program, HMMDiverge, has been developed to estimate model parameters and to identify regions under type-I functional divergence. Simulations demonstrate that HMMDiverge can successfully identify protein regions under type-I functional divergence unless the discrepancy of substitution rates between subfamilies is very limited or the regions under functional divergence are very short. Applying HMMDiverge to G protein α subunits in animals, we identify a candidate region longer than 20 amino acids, which overlaps with the α-4 helix and the α4-β6 loop in the GTPase domain with divergent rates of substitutions. These sites are different from those reported by an existing program, DIVERGE2. Interestingly, previous biochemical studies suggest the α-4 helix and the α4-β6 loop are important to the specificity of the receptor–G protein interaction. Therefore, the candidate region reported by HMMDiverge highlights that the type-I functional divergence in G protein α subunits may be relevant to the change of receptor–G protein specificity after gene duplication. From these results, we conclude that HMMDiverge is a useful tool to identify regions under type-I functional divergence after gene duplication.

Availability: C++ source codes of HMMDiverge and simulation programs used in this study, as well as example datasets, are available at http://info.mcmaster.ca/yifei/software/HMMDiverge.html

Contact:  golding@mcmaster.ca

Supplementary Information:  Supplementary data are available at Bioinformatics online.
A novel specific edge effect correction method for RNA interference screenings
Authors: Carralot Jean-Philippe , Ogier Arnaud , Boese Annette , Genovesio Auguste , Brodin Priscille , Sommer Peter , Dorval Thierry
Published: November 2011

Motivation: High-throughput screening (HTS) is an important method in drug discovery in which the activities of a large number of candidate chemicals or genetic materials are rapidly evaluated. Data are usually obtained by measurements on samples in microwell plates and are often subjected to artefacts that can bias the result selection. We report here a novel edge effect correction algorithm suitable for RNA interference (RNAi) screening, because its normalization does not rely on the entire dataset and takes into account the specificities of such a screening process. The proposed method is able to estimate the edge effects for each assay plate individually using the data from a single control column based on diffusion model, and thus targeting a specific but recurrent well-known HTS artefact. This method was first developed and validated using control plates and was then applied to the correction of experimental data generated during a genome-wide siRNA screen aimed at studying HIV–host interactions. The proposed algorithm was able to correct the edge effect biasing the control data and thus improve assay quality and, consequently, the hit-selection step.

Contact:  dorvalt@ip-korea.org; jean-philippe.carralot@roche.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Modelling time course gene expression data with finite mixtures of linear additive models
Authors: Grün Bettina , Scharl Theresa , Leisch Friedrich
Published: November 2011

Summary: A model class of finite mixtures of linear additive models is presented. The component-specific parameters in the regression models are estimated using regularized likelihood methods. The advantages of the regularization are that (i) the pre-specified maximum degrees of freedom for the splines is less crucial than for unregularized estimation and that (ii) for each component individually a suitable degree of freedom is selected in an automatic way. The performance is evaluated in a simulation study with artificial data as well as on a yeast cell cycle dataset of gene expression levels over time.

Availability: The latest release version of the R package flexmix is available from CRAN (http://cran.r-project.org/).

Contact:  Bettina.Gruen@jku.at
An infrastructure for ontology-based information systems in biomedicine: RICORDO case study
Authors: Wimalaratne Sarala M. , Grenon Pierre , Hoehndorf Robert , Gkoutos Georgios V. , de Bono Bernard
Published: December 2011

Summary: The article presents an infrastructure for supporting the semantic interoperability of biomedical resources based on the management (storing and inference-based querying) of their ontology-based annotations. This infrastructure consists of: (i) a repository to store and query ontology-based annotations; (ii) a knowledge base server with an inference engine to support the storage of and reasoning over ontologies used in the annotation of resources; (iii) a set of applications and services allowing interaction with the integrated repository and knowledge base. The infrastructure is being prototyped and developed and evaluated by the RICORDO project in support of the knowledge management of biomedical resources, including physiology and pharmacology models and associated clinical data.

Availability and implementation: The RICORDO toolkit and its source code are freely available from http://ricordo.eu/relevant-resources.

Contact:  sarala@ebi.ac.uk
GbPDF1 Is Involved in Cotton Fiber Initiation via the Core cis-Element HDZIP2ATATHB2
Authors: Deng Fenglin , Tu Lili , Tan Jiafu , Li Yang , Nie Yichun , Zhang Xianlong
Published: November 2011

Cotton (Gossypium spp.) fiber cells are seed trichomes derived from the epidermal layer of the cotton seed coat. The molecular components responsible for regulating fiber cell differentiation have not been fully elucidated. A cotton PROTODERMAL FACTOR1 gene (GbPDF1) was found to be expressed preferentially during fiber initiation and early elongation, with highest accumulation in fiber cells 5 d post anthesis. PDF1 silencing caused retardation of fiber initiation and produced shorter fibers and lower lint percentage compared with the wild type, indicating that the gene is required for cotton fiber development. Further analysis showed that a higher accumulation of hydrogen peroxide occurred in the RNA interference transgenic cotton lines. Meanwhile, the expression of several genes related to ethylene and pectin synthesis or sugar transport during cotton fiber growth was found to be significantly reduced in the PDF1-suppressed cotton. Three proteins interacting with GbPDF1 in yeast and in planta might involve cellular signaling or metabolism. GbPDF1 promoter::GUS constructs in transgenic cotton were predominantly expressed in the epidermis of ovules and developing fibers. Progressive deletions of the GbPDF1 promoter showed that a 236-bp promoter fragment was sufficient for basal GbPDF1 transcription in cotton. Mutation of putative regulatory sequences showed that HDZIP2ATATHB2, an element within the fragment, was essential for PGbPDF1-1 expression. The binding activity between this cis-element and nuclear extracts from fiber-bearing cotton ovules at 5 d post anthesis was specific. We conclude that GbPDF1 plays a critical role together with interaction partners in hydrogen peroxide homeostasis and steady biosynthesis of ethylene and pectin during fiber development via the core cis-element HDZIP2ATATHB2.
Evidence for a SAL1-PAP Chloroplast Retrograde Pathway That Functions in Drought and High Light Signaling in Arabidopsis
Authors: Estavillo Gonzalo M. , Crisp Peter A. , Pornsiriwong Wannarat , Wirtz Markus , Collinge Derek , Carrie Chris , Giraud Estelle , Whelan James , David Pascale , Javot Hélène , Brearley Charles , Hell Rüdiger , Marin Elena , Pogson Barry J.
Published: December 2011

Compartmentation of the eukaryotic cell requires a complex set of subcellular messages, including multiple retrograde signals from the chloroplast and mitochondria to the nucleus, to regulate gene expression. Here, we propose that one such signal is a phosphonucleotide (3′-phosphoadenosine 5′-phosphate [PAP]), which accumulates in Arabidopsis thaliana in response to drought and high light (HL) stress and that the enzyme SAL1 regulates its levels by dephosphorylating PAP to AMP. SAL1 accumulates in chloroplasts and mitochondria but not in the cytosol. sal1 mutants accumulate 20-fold more PAP without a marked change in inositol phosphate levels, demonstrating that PAP is a primary in vivo substrate. Significantly, transgenic targeting of SAL1 to either the nucleus or chloroplast of sal1 mutants lowers the total PAP levels and expression of the HL-inducible ASCORBATE PEROXIDASE2 gene. This indicates that PAP must be able to move between cellular compartments. The mode of action for PAP could be inhibition of 5′ to 3′ exoribonucleases (XRNs), as SAL1 and the nuclear XRNs modulate the expression of a similar subset of HL and drought-inducible genes, sal1 mutants accumulate XRN substrates, and PAP can inhibit yeast (Saccharomyces cerevisiae) XRNs. We propose a SAL1-PAP retrograde pathway that can alter nuclear gene expression during HL and drought stress.
Cloning, purification and crystallographic analysis of a hypothetical protein, BPSL1549, from Burkholderia pseudomallei
Authors: Cruz-Migoni Abimael , Ruzheinikov Sergey N. , Sedelnikova Svetlana E. , Obeng Barbara , Chieng Sylvia , Mohamed Rahmah , Nathan Sheila , Baker Patrick J. , Rice David W.
Published: December 2011

Burkholderia pseudomallei BPSL1549, a putative protein of unknown function, has been overexpressed in Escherichia coli, purified and subsequently crystallized by the hanging-drop vapour-diffusion method using PEG as a precipitant to give crystals with overall dimensions of 0.15 × 0.15 × 0.1 mm. Native data were collected to 1.47 Å resolution at the European Synchrotron Radiation Facility (ESRF). The crystals belonged to space group P212121, with unit-cell parameters a = 37.1, b = 45.4, c = 111.9 Å and with a single polypeptide chain in the asymmetric unit.
Crystallization and preliminary X-ray diffraction analysis of mouse prostaglandin F2αsynthase, AKR1B3
Authors: Takashima Yasuhide , Hatanaka Seika , Mizohata Eiichi , Nagata Nanae , Fukunishi Yoshifumi , Matsumura Hiroyoshi , Urade Yoshihiro , Inoue Tsuyoshi
Published: December 2011

Aldo-keto reductase 1B3 (AKR1B3) catalyzes the NADPH-dependent reduction of prostaglandin H2(PGH2), which is a common intermediate of various prostanoids, to form PGF2α. AKR1B3 also reduces PGH2to PGD2in the absence of NADPH. AKR1B3 produced inEscherichia coliwas crystallized in complex with NADPH by the sitting-drop vapour-diffusion method. The crystal was tetragonal, belonging to space groupP41212 orP43212, with unit-cell parametersa = b = 107.62,c= 120.76 Å. X-ray diffraction data were collected to 2.4 Å resolution at 100 K using a synchrotron-radiation source.
Preliminary X-ray crystallographic studies on acetate kinase (AckA) fromSalmonella typhimuriumin two crystal forms
Authors: Chittori Sagar , Savithri H. S. , Murthy M. R. N.
Published: December 2011

Acetate kinase (AckA) catalyzes the reversible transfer of a phosphate group from acetyl phosphate to ADP, generating acetate and ATP, and plays a central role in carbon metabolism. In the present work, the gene corresponding to AckA fromSalmonella typhimurium(StAckA) was cloned in the IPTG-inducible pRSET C vector, resulting in the attachment of a hexahistidine tag to the N-terminus of the expressed enzyme. The recombinant protein was overexpressed, purified and crystallized in two different crystal forms using the microbatch-under-oil method. Form I crystals diffracted to 2.70 Å resolution when examined using X-rays from a rotating-anode X-ray generator and belonged to the monoclinic space groupC2, with unit-cell parametersa = 283.16,b= 62.17,c= 91.69 Å, β = 93.57°. Form II crystals, which diffracted to a higher resolution of 2.35 Å on the rotating-anode X-ray generator and to 1.90 Å on beamline BM14 of the ESRF, Grenoble, also belonged to space groupC2 but with smaller unit-cell parameters (a= 151.01,b= 78.50,c = 97.48 Å, β = 116.37°). Calculation of Matthews coefficients for the two crystal forms suggested the presence of four and two protomers ofStAckA in the asymmetric units of forms I and II, respectively. Initial phases for the form I diffraction data were obtained by molecular replacement using the coordinates ofThermotoga maritimaAckA (TmAckA) as the search model. The form II structure was phased using a monomer of form I as the phasing model. Inspection of the initial electron-density maps suggests dramatic conformational differences between residues 230 and 300 of the two crystal forms and warrants further investigation.
A randomized controlled trial of a brief intervention for illicit drugs linked to the Alcohol, Smoking and Substance Involvement Screening Test (ASSIST) in clients recruited from primary health‐care settings in four countries
Authors: Humeniuk Rachel , Ali Robert , Babor Thomas , Souza‐Formigoni Maria Lucia O. , de Lacerda Roseli Boerngen , Ling Walter , McRee Bonnie , Newcombe David , Pal Hemraj , Poznyak Vladimir , Simon Sara , Vendetti Janice
Published: December 2011

Aims  This study evaluated the effectiveness of a brief intervention (BI) for illicit drugs (cannabis, cocaine, amphetamine‐type stimulants and opioids) linked to the World Health Organization (WHO) Alcohol, Smoking and Substance Involvement Screening Test (ASSIST). The ASSIST screens for problem or risky use of 10 psychoactive substances, producing a score for each substance that falls into either a low‐, moderate‐ or high‐risk category.

Design  Prospective, randomized controlled trial in which participants were either assigned to a 3‐month waiting‐list control condition or received brief motivational counselling lasting an average of 13.8 minutes for the drug receiving the highest ASSIST score.

Setting  Primary health‐care settings in four countries: Australia, Brazil, India and the United States.

Participants  A total of 731 males and females scoring within the moderate‐risk range of the ASSIST for cannabis, cocaine, amphetamine‐type stimulants or opioids.

Measurements  ASSIST‐specific substance involvement scores for cannabis, stimulants or opioids and ASSIST total illicit substance involvement score at baseline and 3 months post‐randomization.

Findings  Omnibus analyses indicated that those receiving the BI had significantly reduced scores for all measures, compared with control participants. Country‐specific analyses showed that, with the exception of the site in the United States, BI participants had significantly lower ASSIST total illicit substance involvement scores at follow‐up compared with the control participants. The sites in India and Brazil demonstrated a very strong brief intervention effect for cannabis scores (P < 0.005 for both sites), as did the sites in Australia (P < 0.005) and Brazil (P < 0.01) for stimulant scores and the Indian site for opioid scores (P < 0.01).

Conclusions  The Alcohol, Smoking and Substance Involvement Screening Test‐linked brief intervention aimed at reducing illicit substance use and related risks is effective, at least in the short term, and the effect generalizes across countries.