bluuebunny/crossref_metadata_2025 huggingface dataset:
Spatial distributions of particle number concentrations in the global troposphere: Simulations, observations, and implications for nucleation mechanisms
Authors: Yu Fangqun , Luo Gan , Bates Timothy S. , Anderson Bruce , Clarke Antony , Kapustin Vladimir , Yantosca Robert M. , Wang Yuxuan , Wu Shiliang
Published: September 2010

Particle number concentration in the troposphere is an important parameter controlling the climate and health impacts of atmospheric aerosols. We show that nucleation rates and total particle number concentrations in the troposphere, predicted by different nucleation schemes, differ significantly. Our extensive comparisons of simulated results with land‐, ship‐, and aircraft‐based measurements indicate that, among six widely used nucleation schemes involving sulfuric acid, only the ion‐mediated nucleation (IMN) scheme can reasonably account for both absolute values (within a factor of ∼2) and spatial distributions of particle number concentrations in the whole troposphere. Binary homogeneous nucleation (BHN) schemes significantly underpredict particle number concentration in the lower troposphere (below ∼500 mbar), especially in the boundary layer over major continents (by a factor of up to ∼10). BHN is also insignificant in the upper troposphere based on a recent kinetically self‐consistent nucleation model constrained by multiple independent laboratory data. Previous conclusions about the importance of BHN in the upper troposphere should be revisited. Empirical activation and kinetic nucleation formulas significantly overpredict the particle number concentrations over tropical and subtropical oceans (by a factor of up to ∼10 in the boundary layer), and the overpredictions extend from ocean surface to around ∼400 mbar. This study represents the first comprehensive comparison of global particle number simulations with relevant measurements that have a 3‐D global spatial coverage. Our results suggest that ion‐mediated H2SO4‐H2O nucleation appears to dominate over neutral H2SO4‐H2O nucleation, not only in the lower troposphere but also in the middle and upper troposphere.
Managing the Water Footprint of Irrigated Food Production in England and Wales
Authors: Hess Tim , Knox Jerry , Kay Melvyn , Weatherhead Keith
Published: September 2010

This chapter discusses the concept of a water footprint in relation to irrigated food production in England and Wales and the opportunities to reduce its environmental impact. It is split into three parts. The first considers the definition of a water footprint and how it differs from a carbon footprint. The distinction between different types of water (“blue” and “green”) commonly referred to in water footprint studies and the problems associated with interpreting the data are described. The second part reviews the current state and underlying trends in irrigated agriculture, including the volumes abstracted and water sources used. An important component of a water footprint is the environmental impact of the water abstracted. Using a geographical information system (GIS), data on the spatial distribution of irrigation abstractions is combined with information on water resource availability to identify catchments where irrigated production (footprint) is likely to be having an environmental impact. The final part assesses the options for managing water better in irrigated agriculture, both on-farm and from a catchment (water regulation) perspective. Measures to reduce the water footprint on-farm include better management (scheduling) and the adoption of new technologies to improve irrigation application uniformity and water efficiency. Water regulation measures include limiting abstractions in catchments where environmental damage is known to be occurring, using water trading to reallocate water to higher value agricultural uses and changing the timing of abstraction to encourage winter reservoir storage. Finally, there is a discussion of the implications of increasing our dependence on overseas markets for food supply and the consequences for the agricultural sector's broader role in environmental sustainability and rural employment.
Nanotechnology for Sustainable Water Treatment
Authors: Hotze Matt , Lowry Greg
Published: September 2010

As world water demand continues to grow there is a critical need to develop sustainable water treatment solutions. This chapter describes the potential for nanomaterials to improve the sustainability of water treatment. Nanomaterial-driven advances in disinfection, oxidation, membrane separation and groundwater remediation are discussed with a view towards their potential to improve existing technologies. Disinfection technologies include oligodynamic processes with silver nanoparticles to effectively inactivate microorganisms without disinfection byproducts being formed. Oxidation technologies include metal oxide semiconductors and fullerene-based sensitisers acting as light-driven catalysts. Membrane separation processes include the embedding of materials such as zeolites, carbon nanotubes and metal oxides to improve selectivity and reduce fouling. Remediation technologies include iron particles designed to target and transform waste compounds in situ. These and other emerging water treatment technologies must be assessed with life-cycle analysis to determine the full materials and embodied energy costs of acquiring raw materials, manufacturing, use and end of life for the materials contained within each process. These costs must be weighed against the potential benefits for water treatment to determine their sustainability.
Akt inhibitors reduce glucose uptake independently of their effects on Akt
Authors: Tan Shi-Xiong , Ng Yvonne , James David E.
Published: September 2010

The protein kinase Akt is involved in various cellular processes, including cell proliferation, growth and metabolism. Hyperactivation of Akt is commonly observed in human tumours and so this pathway has been the focus of targeted drug discovery. However, Akt also plays an essential role in other physiological processes, such as the insulin-regulated transport of glucose into muscle and fat cells. This process, which is essential for whole-body glucose homoeostasis in mammals, is thought to be mediated via Akt-dependent movement of GLUT4 glucose transporters to the plasma membrane. In the present study, we have investigated the metabolic side effects of non-ATP-competitive allosteric Akt inhibitors. In 3T3-L1 adipocytes, these inhibitors caused a decrease in the Akt signalling pathway concomitant with reduced glucose uptake. Surprisingly, a similar reduction in GLUT4 translocation to the plasma membrane was not observed. Further investigation revealed that the inhibitory effects of these compounds on glucose uptake in 3T3-L1 adipocytes were independent of the Akt signalling pathway. The inhibitors also inhibited glucose transport into other cell types, including human erythrocytes and T-47D breast cancer cells, suggesting that these effects are not specific to GLUT4. We conclude that these drugs may, at least in part, inhibit tumorigenesis through inhibition of tumour cell glucose transport.
RNA-directed epigenetic regulation of DNA rearrangements
Authors: Mochizuki Kazufumi
Published: September 2010

Ciliated protozoa undergo extensive DNA rearrangements, including DNA elimination, chromosome breakage and DNA unscrambling, when the germline micronucleus produces the new macronucleus during sexual reproduction. It has long been known that many of these events are epigenetically controlled by DNA sequences of the parental macronuclear genome. Recent studies in some model ciliates have revealed that these epigenetic regulations are mediated by non-coding RNAs. DNA elimination in Paramecium and Tetrahymena is regulated by small RNAs that are produced and operated by an RNAi (RNA interference)-related mechanism. It has been proposed that the small RNAs from the micronuclear genome can be used to identify eliminated DNAs by whole-genome comparison of the parental macronucleus and the micronucleus. In contrast, DNA unscrambling in Oxytricha is guided by long non-coding RNAs that are produced from the somatic parental macronuclear genome. These RNAs are proposed to act as templates for the direct unscrambling events that occur in the developing macronucleus. The possible evolutionary benefits of these RNA-directed epigenetic regulations of DNA rearrangement in ciliates are discussed in the present chapter.
Microstructural characteristics and phonon structures in luminescence from surface oxidized Ge nanocrystals embedded in HfO2 matrix
Authors: Das S. , Singha R. K. , Gangopadhyay S. , Dhar A. , Ray S. K.
Published: September 2010

Ge nanocrystals embedded in HfO2 matrices were prepared by rf magnetron sputtering technique. Transmission electron micrographs reveal the formation of spherical shape Ge nanocrystals of 4–6 nm diameters for 800 °C and 6–9 nm for 900 °C annealed samples. X-ray photoelectron spectroscopy confirms the formation of surface oxidized Ge nanocrystals. Embedded Ge nanocrystals show strong photoluminescence peaks in visible and ultraviolet region even at room temperature. Spectral analysis suggests that emission in 1.58 and 3.18 eV bands originate from TΣ(TΠ)→S0, and TΠ′→S0 optical transitions in GeO color centers, respectively, and those in the range 2.0–3.0 eV are related to Ge/O defects at the interface of the oxidized nanocrystals. Temperature dependent photoluminescence study has revealed additional fine structures with lowering of temperature, the origin of which is attributed to the strong coupling of electronic excitations with local vibration of germanium oxides at the surface.
Device reliability study of high gate electric field effects in AlGaN/GaN high electron mobility transistors using low frequency noise spectroscopy
Authors: Rao Hemant , Bosman Gijs
Published: September 2010

Low frequency noise characteristics of gate and drain currents are investigated for prestressed and poststressed AlGaN/GaN high electron mobility transistors. High reverse bias voltage stresses on the gate stack changes both drain and gate current noise. A temporary increase in drain current noise was observed during stress which recovered to prestress level a few weeks later. This is explained via a positive and negative threshold voltage shift due to electron trapping under the gate during and after stress, respectively. On the other hand, gate current noise shows a permanent increase after the stress which is not seen to recover once the stress is removed. It is proposed that new defect states are created below the metal AlGaN layer of the gate edges which leads to a permanent degradation of gate current noise.
Magnetically responsive bacterial cellulose: Synthesis and magnetic studies
Authors: Vitta Satish , Drillon Marc , Derory A.
Published: September 2010

Bacterial cellulose with its porous network structure was used as a support to precipitate Ni nanoparticles by room temperature chemical reduction of Ni-chloride hexahydrate. The room temperature reduction in an aqueous environment results in the formation of crystalline Ni nanoparticles of size 10 to 60 nm inside the bacterial cellulose along with Ni(OH)2. The nanocrystals have an equiaxed shape and are found both as individual particles as well as small aggregates depending on the porous network structure of cellulose matrix. The bacterial cellulose does not undergo any change and retains its crystal structure even after chemical reduction reaction. The Ni loaded bacterial cellulose is found to be ferromagnetic at room temperature with a saturation magnetization of 2.81 emu g−1 which increases by an order of magnitude to 21.8 emu g−1 at 1.8 K. The coercive field also increases by two orders of magnitude from 28 G at 300 K to 2900 G at 1.8 K. The zero field cooled magnetization however exhibits a superparamagnetic behavior with a peak at 20 K, the blocking temperature and this behavior is observed even in ac magnetization. The magnetization decrease with increasing temperature up to 400 K, when extrapolated to high temperatures using a power law indicates a Curie transition at 500 K, much lower than the Curie temperature of bulk Ni. The fraction of isolated superparamagnetic nanoparticles present in the composite was estimated from the saturation magnetization and is found to be ∼88%. These results clearly highlight the presence of two separate magnetic phases, superparamagnetic, and ferromagnetic, and the role of various magnetic interactions in the collective magnetic behavior of Ni nanoparticles in the composite structure.
Steady interaction of a vortex street with a shear flow
Authors: Crowdy Darren , Nelson Rhodri
Published: September 2010

A one parameter family of explicit solutions of the Euler equations is presented comprising a steadily propagating point vortex street situated in a region of uniform vorticity below a periodically deformed vortex jump separating a region of irrotational flow from a uniform shear flow. Various features of the new solutions are described. The limiting solutions are such that the vortex jump develops a periodic sequence of cusps. The stability of the equilibria is investigated numerically using a cylindrical contour dynamics algorithm. The equilibria not too close to the limiting case are found to be structurally robust for a large range of parameter values.
Fluid to solid transition in magnetofluidized beds of fine powders
Authors: Valverde J. M. , Espin M. J. , Quintanilla M. A. S. , Castellanos A.
Published: September 2010

Experimental observations on the fluid to solid transition in beds of magnetized fine particles fluidized by gas are reported for different particle sizes (dp). Contrarily to stability analysis prediction, the fluidized bed is stabilized by a sufficiently strong magnetic field in the cross-flow configuration. As the strength H of the horizontally applied magnetic field is increased, particle chaining in the bubbling bed becomes apparent due to the induced attractive magnetostatic forces between the particles. In close analogy with magnetorheological fluids chain stability is determined by the balance between gas flow shear and the interparticle magnetostatic force. The jamming transition occurs at a gas velocity scaling proportionally to dp2H2 when the length of the stable chains reaches a critical size which is independent of particle size.
Stabilization of a passively mode-locked laser by continuous wave optical injection
Authors: Rebrova Natalia , Habruseva Tatiana , Huyet Guillaume , Hegarty Stephen P.
Published: September 2010

We investigate numerically and experimentally the properties of a passively mode locked quantum dot semiconductor laser under the influence of cw optical injection. We demonstrate that the waveform instability at high pumping for these devices can be overcome when one mode of the device is locked to the injected master laser and additionally show spectral narrowing and tunability. Experimental and numerical analyses demonstrate that the stable locking boundaries are similar to these obtained for optical injection in CW lasers.
Solvothermal synthesis of designed nonstoichiometric strontium titanate for efficient visible-light photocatalysis
Authors: Sulaeman Uyi , Yin Shu , Sato Tsugio
Published: September 2010

SrTiO 3 powders with various Sr/Ti atomic ratios were synthesized by microwave-assisted solvothermal reactions of SrCl2 and Ti(OC3H7)4 in KOH aqueous solutions. The nanoparticles of perovskite type SrTiO3 structure with the particle size of 30–40 nm were synthesized. The photocatalytic activity was determined by deNOx ability using light emitting diode lamps of various wavelengths such as 627 nm (red), 530 nm (green), 445 nm (blue), and 390 nm (UV). The photocatalytic activity significantly changed depending on the Sr/Ti atomic ratio, i.e., the strontium rich sample (Sr/Ti atomic ratio>1) showed excellent visible light responsive photocatalytic activity for the oxidative destruction of NO.
Environmental influence on the physico-chemical and physiological properties of Jatropha curcas seeds
Authors: Pompelli Marcelo Francisco , Ferreira Débora Teresa da Rocha Gomes , Cavalcante Polyana Geysa da Silva , Salvador Taciana de Lima , Shiue de Hsie Bety , Endres Laurício
Published: September 2010

The present study investigated the influence of two Brazilian environments on the physico-chemical and physiological properties of Jatropha curcas L. (physic nut) – an oilseed plant of great potential in biodiesel production. Fruits and seeds of plants grown in the Brazilian Atlantic rainforest (AF) and in the semiarid climate of Caatinga (SA) were compared. Fruits from the SA were longer, wider and heavier than those from the AF. In contrast, the AF seeds were larger and heavier than the SA seeds. Soluble sugars, protein, relative water content and electrical conductivity of the SA seeds significantly exceeded that of the AF seeds by 28%, 23%, 32% and 94%, respectively. Seeds of the AF had a significantly greater percentage germination (17.5%) and needed less time to germinate (10%) than did the SA seeds. Shoot dry biomass of seedlings grown from the AF seeds significantly exceeded that of the SA by 18.5%. Results suggest this pattern may be due to the higher carbon storage (i.e. sugars, proteins and oil) in the AF than SA seeds. Further studies are warranted to verify whether the differences observed between the seed sources investigated in the present study could be due to varietal or biotype factors.
A sensitive period for environmental regulation of eating behavior and leptin sensitivity
Authors: Mainardi Marco , Scabia Gaia , Vottari Teresa , Santini Ferruccio , Pinchera Aldo , Maffei Lamberto , Pizzorusso Tommaso , Maffei Margherita
Published: September 2010

Western lifestyle contributes to body weight dysregulation. Leptin down-regulates food intake by modulating the activity of neural circuits in the hypothalamic arcuate nucleus (ARC), and resistance to this hormone constitutes a permissive condition for obesity. Physical exercise modulates leptin sensitivity in diet-induced obese rats. The role of other lifestyle components in modulating leptin sensitivity remains elusive. Environmentally enriched mice were used to explore the effects of lifestyle change on leptin production/action and other metabolic parameters. We analyzed adult mice exposed to environmental enrichment (EE), which showed decreased leptin, reduced adipose mass, and increased food intake. We also analyzed 50-d-old mice exposed to either EE (YEE) or physical exercise (YW) since birth, both of which showed decreased leptin. YEE mice showed no change in food intake, increased response to leptin administration, increased activation of STAT3 in the ARC. The YW leptin-induced food intake response was intermediate between young mice kept in standard conditions and YEE. YEE exhibited increased and decreased ratios of excitatory/inhibitory synapses onto α-melanocyte-stimulating hormone and agouti-related peptide neurons of the ARC, respectively. We also analyzed animals as described for YEE and then placed in standard cages for 1 mo. They showed no altered leptin production/action but demonstrated changes in excitatory/inhibitory synaptic contacts in the ARC similar to YEE. EE and physical activity resulted in improved insulin sensitivity. In conclusion, EE and physical activity had an impact on feeding behavior, leptin production/action, and insulin sensitivity, and EE affected ARC circuitry. The leptin-hypothalamic axis is maximally enhanced if environmental stimulation is applied during development.
Breakdown of the first hyperpolarizability/bond-length alternation parameter relationship
Authors: Murugan N. Arul , Kongsted Jacob , Rinkevicius Zilvinas , Ågren Hans
Published: September 2010

We have investigated the dependence of the static first hyperpolarizability on the bond-length alternation (BLA) parameter. Our analysis indicates that the validity of the first hyperpolarizability/BLA parameter relationship is restricted to the no-field, vacuum, limit, while it successively breaks down along with increasing polarity of a surrounding medium, becoming invalid, for instance, in an aqueous solution. This contention is based on a series of TD-DFT, TD-DFT/PCM and hybrid TD-DFT/MM calculations of the first hyperpolarizability for a set of molecular configurations generated from Car–Parrinello hybrid QM/MM simulations of the stilbazolium merocyanine chromophore in chloroform and water solvents, and on a rationalization by means of the two-state model for the first hyperpolarizability. The BLA dependence of the three parameters entering the two-state model is shown to be qualitatively different in vacuum and in solvents. Particularly, in the vacuum case, the difference between ground and excited state dipole moments goes to zero for a vanishing BLA, which is not true in the presence of an aqueous medium. In the aqueous medium, an opposing behavior of the parameters involved in the two-state model results in an almost constant first hyperpolarizability with varying BLA parameter.
Interface Based on Electrooculography for Velocity Control of a Robot Arm
Authors: Iáñez Eduardo , Azorín José M. , Fernández Eduardo , Úbeda Andrés
Published: September 2010

This paper describes a technique based on electrooculography to control a robot arm. This technique detects the movement of the eyes, measuring the difference of potential between the cornea and the retina by placing electrodes around the ocular area. The processing algorithm developed to obtain the position of the eye at the blink of the user is explained. The output of the processing algorithm offers, apart from the direction, four different values (zero to three) to control the velocity of the robot arm according to how much the user is looking in one direction. This allows controlling two degrees of freedom of a robot arm with the eyes movement. The blink has been used to mark some targets in tests. In this paper, the experimental results obtained with a real robot arm are shown.
Robotics as a Support Tool for Experimental Optimisation of Surgical Strategies in Orthopaedic Surgery
Authors: Frigola Manel , Vinagre Manuel , Casals Alicia , Amat Josep , Santana Fernando , Torrens Carlos
Published: September 2010

Robotics has shown its potential not only in assisting the surgeon during an intervention but also as a tool for training and for surgical procedure′s evaluation. Thus, robotics can constitute an extension of simulators that are based on the high capabilities of computer graphics. In addition, haptics has taken a first step in increasing the performance of current virtual reality systems based uniquely on computer simulation and their corresponding interface devices. As a further step in the field of training and learning in surgery, this work describes a robotic experimental workstation composed of robots and specific measuring devices, together with their corresponding control and monitoring strategies for orthopaedic surgery. Through a case study, humerus arthroplasty, experimental evaluation shows the possibilities of having a test bed available for repetitive and quantifiable trials, which make a reliable scientific comparison between different surgical strategies possible.
Upregulation of Tim-3 and PD-1 expression is associated with tumor antigen–specific CD8+ T cell dysfunction in melanoma patients
Authors: Fourcade Julien , Sun Zhaojun , Benallaoua Mourad , Guillaume Philippe , Luescher Immanuel F. , Sander Cindy , Kirkwood John M. , Kuchroo Vijay , Zarour Hassane M.
Published: September 2010

The paradoxical coexistence of spontaneous tumor antigen–specific immune responses with progressive disease in cancer patients furthers the need to dissect the molecular pathways involved in tumor-induced T cell dysfunction. In patients with advanced melanoma, we have previously shown that the cancer-germline antigen NY-ESO-1 stimulates spontaneous NY-ESO-1–specific CD8+ T cells that up-regulate PD-1 expression. We also observed that PD-1 regulates NY-ESO-1–specific CD8+ T cell expansion upon chronic antigen stimulation. In the present study, we show that a fraction of PD-1+ NY-ESO-1–specific CD8+ T cells in patients with advanced melanoma up-regulates Tim-3 expression and that Tim-3+PD-1+ NY-ESO-1–specific CD8+ T cells are more dysfunctional than Tim-3−PD-1+ and Tim-3−PD-1− NY-ESO-1–specific CD8+ T cells, producing less IFN-γ, TNF, and IL-2. Tim-3–Tim-3L blockade enhanced cytokine production by NY-ESO-1–specific CD8+ T cells upon short ex vivo stimulation with cognate peptide, thus enhancing their functional capacity. In addition, Tim-3–Tim-3L blockade enhanced cytokine production and proliferation of NY-ESO-1–specific CD8+ T cells upon prolonged antigen stimulation and acted in synergy with PD-1–PD-L1 blockade. Collectively, our findings support the use of Tim-3–Tim-3L blockade together with PD-1–PD-L1 blockade to reverse tumor-induced T cell exhaustion/dysfunction in patients with advanced melanoma.
Targeting Tim-3 and PD-1 pathways to reverse T cell exhaustion and restore anti-tumor immunity
Authors: Sakuishi Kaori , Apetoh Lionel , Sullivan Jenna M. , Blazar Bruce R. , Kuchroo Vijay K. , Anderson Ana C.
Published: September 2010

The immune response plays an important role in staving off cancer; however, mechanisms of immunosuppression hinder productive anti-tumor immunity. T cell dysfunction or exhaustion in tumor-bearing hosts is one such mechanism. PD-1 has been identified as a marker of exhausted T cells in chronic disease states, and blockade of PD-1–PD-1L interactions has been shown to partially restore T cell function. We have found that T cell immunoglobulin mucin (Tim) 3 is expressed on CD8+ tumor-infiltrating lymphocytes (TILs) in mice bearing solid tumors. All Tim-3+ TILs coexpress PD-1, and Tim-3+PD-1+ TILs represent the predominant fraction of T cells infiltrating tumors. Tim-3+PD-1+ TILs exhibit the most severe exhausted phenotype as defined by failure to proliferate and produce IL-2, TNF, and IFN-γ. We further find that combined targeting of the Tim-3 and PD-1 pathways is more effective in controlling tumor growth than targeting either pathway alone.
CD11c depletion severely disrupts Th2 induction and development in vivo
Authors: Phythian-Adams Alexander T. , Cook Peter C. , Lundie Rachel J. , Jones Lucy H. , Smith Katherine A. , Barr Tom A. , Hochweller Kristin , Anderton Stephen M. , Hämmerling Günter J. , Maizels Rick M. , MacDonald Andrew S.
Published: September 2010

Although dendritic cells (DCs) are adept initiators of CD4+ T cell responses, their fundamental importance in this regard in Th2 settings remains to be demonstrated. We have used CD11c–diphtheria toxin (DTx) receptor mice to deplete CD11c+ cells during the priming stage of the CD4+ Th2 response against the parasitic helminth Schistosoma mansoni. DTx treatment significantly depleted CD11c+ DCs from all tissues tested, with 70–80% efficacy. Even this incomplete depletion resulted in dramatically impaired CD4+ T cell production of Th2 cytokines, altering the balance of the immune response and causing a shift toward IFN-γ production. In contrast, basophil depletion using Mar-1 antibody had no measurable effect on Th2 induction in this system. These data underline the vital role that CD11c+ antigen-presenting cells can play in orchestrating Th2 development against helminth infection in vivo, a response that is ordinarily balanced so as to prevent the potentially damaging production of inflammatory cytokines.
MHC class I–deficient natural killer cells acquire a licensed phenotype after transfer into an MHC class I–sufficient environment
Authors: Elliott Julie M. , Wahle Joseph A. , Yokoyama Wayne M.
Published: September 2010

In MHC class I–deficient hosts, natural killer (NK) cells are hyporesponsive to cross-linking of activation receptors. Functional competence requires engagement of a self–major histocompatability complex (MHC) class I–specific inhibitory receptor, a process referred to as “licensing.” We previously suggested that licensing is developmentally determined in the bone marrow. In this study, we find that unlicensed mature MHC class I–deficient splenic NK cells show gain-of-function and acquire a licensed phenotype after adoptive transfer into wild-type (WT) hosts. Transferred NK cells produce WT levels of interferon-γ after engagement of multiple activation receptors, and degranulate at levels equivalent to WT NK cells upon coincubation with target cells. Only NK cells expressing an inhibitory Ly49 receptor specific for a cognate host MHC class I molecule show this gain-of-function. Therefore, these findings, which may be relevant to clinical bone marrow transplantation, suggest that neither exposure to MHC class I ligands during NK development in the BM nor endogenous MHC class I expression by NK cells themselves is absolutely required for licensing.
First-principles study of the structural and magnetic properties of graphene on a Fe/Ni(1 1 1) surface
Authors: Sun X , Pratt A , Yamauchi Y
Published: September 2010

The structure and spin-resolved electronic states of a graphene-adsorbed Fe/Ni(1 1 1) surface are investigated and compared with a graphene/Ni(1 1 1) surface using first-principles calculations. Nine possible geometries are studied with Fe and C atoms at different sites with respect to the topmost Ni atoms. Geometries with one C atom located on top of an Fe atom (C1) and one at a hollow (fcc or hcp) site (C2) are the most energetically favourable. The electronic states of graphene are significantly modified by the interaction with the Fe/Ni(1 1 1) surface. The dominant π states of the C2 atom are drastically shifted towards the Fermi level and become highly positive-spin-polarized due to the corresponding spin-down states located above the Fermi level. The level shift is very small for the spin-up π states of the C1 atom but obvious for the spin-down states due to spin splitting induced by Fe atoms, resulting in a negative spin polarization at shallow levels and a positive one at deeper levels. The adsorption of graphene on Fe/Ni(1 1 1) is stronger than that on the clean Ni(1 1 1) surface.
PCBM : P3HT polymer composites for photonic crystal all-optical switching applications
Authors: Li Zhiqiang , Hu Xiaoyong , Zhang Jiaxiang , Yang Hong , Gong Qihuang
Published: September 2010

An all-optical switching with an operating pump intensity of 1 MW cm−2 is realized in a one-dimensional nonlinear organic photonic crystal made of poly(3-hexylthiophene) doped with 1-(3-methoxycarbonyl)propyl-1-phenyl-(6,6)C61, fabricated by focused ion-beam etching. The femtosecond pump and probe method is adopted to measure the transmittance changes of the probe laser based on the photonic bandgap shift induced by the pump laser. Under resonant excitation, a large nonlinear refractive index of the order of 10−9 cm2 W−1 is obtained for the polymer composite. A switching time of 58.9 ps is maintained due to intermolecular charge transfer and exciton–exciton annihilation.
RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming
Authors: Kato Yuki , Sato Kengo , Hamada Michiaki , Watanabe Yoshihide , Asai Kiyoshi , Akutsu Tatsuya
Published: September 2010

Motivation: Considerable attention has been focused on predicting RNA–RNA interaction since it is a key to identifying possible targets of non-coding small RNAs that regulate gene expression post-transcriptionally. A number of computational studies have so far been devoted to predicting joint secondary structures or binding sites under a specific class of interactions. In general, there is a trade-off between range of interaction type and efficiency of a prediction algorithm, and thus efficient computational methods for predicting comprehensive type of interaction are still awaited.

Results: We present RactIP, a fast and accurate prediction method for RNA–RNA interaction of general type using integer programming. RactIP can integrate approximate information on an ensemble of equilibrium joint structures into the objective function of integer programming using posterior internal and external base-paring probabilities. Experimental results on real interaction data show that prediction accuracy of RactIP is at least comparable to that of several state-of-the-art methods for RNA–RNA interaction prediction. Moreover, we demonstrate that RactIP can run incomparably faster than competitive methods for predicting joint secondary structures.

Availability:  RactIP is implemented in C++, and the source code is available at http://www.ncrna.org/software/ractip/

Contact:  ykato@kuicr.kyoto-u.ac.jp; satoken@k.u-tokyo.ac.jp

Supplementary information:  Supplementary data are available at Bioinformatics online.
Discovering graphical Granger causality using the truncating lasso penalty
Authors: Shojaie Ali , Michailidis George
Published: September 2010

Motivation: Components of biological systems interact with each other in order to carry out vital cell functions. Such information can be used to improve estimation and inference, and to obtain better insights into the underlying cellular mechanisms. Discovering regulatory interactions among genes is therefore an important problem in systems biology. Whole-genome expression data over time provides an opportunity to determine how the expression levels of genes are affected by changes in transcription levels of other genes, and can therefore be used to discover regulatory interactions among genes.

Results: In this article, we propose a novel penalization method, called truncating lasso, for estimation of causal relationships from time-course gene expression data. The proposed penalty can correctly determine the order of the underlying time series, and improves the performance of the lasso-type estimators. Moreover, the resulting estimate provides information on the time lag between activation of transcription factors and their effects on regulated genes. We provide an efficient algorithm for estimation of model parameters, and show that the proposed method can consistently discover causal relationships in the large p, small n setting. The performance of the proposed model is evaluated favorably in simulated, as well as real, data examples.

Availability: The proposed truncating lasso method is implemented in the R-package ‘grangerTlasso’ and is freely available at http://www.stat.lsa.umich.edu/∼shojaie/

Contact:  shojaie@umich.edu
How threshold behaviour affects the use of subgraphs for network comparison
Authors: Rito Tiago , Wang Zi , Deane Charlotte M. , Reinert Gesine
Published: September 2010

Motivation: A wealth of protein–protein interaction (PPI) data has recently become available. These data are organized as PPI networks and an efficient and biologically meaningful method to compare such PPI networks is needed. As a first step, we would like to compare observed networks to established network models, under the aspect of small subgraph counts, as these are conjectured to relate to functional modules in the PPI network. We employ the software tool GraphCrunch with the Graphlet Degree Distribution Agreement (GDDA) score to examine the use of such counts for network comparison.

Results: Our results show that the GDDA score has a pronounced dependency on the number of edges and vertices of the networks being considered. This should be taken into account when testing the fit of models. We provide a method for assessing the statistical significance of the fit between random graph models and biological networks based on non-parametric tests. Using this method we examine the fit of Erdös–Rényi (ER), ER with fixed degree distribution and geometric (3D) models to PPI networks. Under these rigorous tests none of these models fit to the PPI networks. The GDDA score is not stable in the region of graph density relevant to current PPI networks. We hypothesize that this score instability is due to the networks under consideration having a graph density in the threshold region for the appearance of small subgraphs. This is true for both geometric (3D) and ER random graph models. Such threshold behaviour may be linked to the robustness and efficiency properties of the PPI networks.

Contact:  tiago@stats.ox.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Bayesian experts in exploring reaction kinetics of transcription circuits
Authors: Yoshida Ryo , Saito Masaya M. , Nagao Hiromichi , Higuchi Tomoyuki
Published: September 2010

Motivation Biochemical reactions in cells are made of several types of biological circuits. In current systems biology, making differential equation (DE) models simulatable in silico has been an appealing, general approach to uncover a complex world of biochemical reaction dynamics. Despite of a need for simulation-aided studies, our research field has yet provided no clear answers: how to specify kinetic values in models that are difficult to measure from experimental/theoretical analyses on biochemical kinetics.

Results: We present a novel non-parametric Bayesian approach to this problem. The key idea lies in the development of a Dirichlet process (DP) prior distribution, called Bayesian experts, which reflects substantive knowledge on reaction mechanisms inherent in given models and experimentally observable kinetic evidences to the subsequent parameter search. The DP prior identifies significant local regions of unknown parameter space before proceeding to the posterior analyses. This article reports that a Bayesian expert-inducing stochastic search can effectively explore unknown parameters of in silico transcription circuits such that solutions of DEs reproduce transcriptomic time course profiles.

Availability: A sample source code is available at the URL http://daweb.ism.ac.jp/∼yoshidar/lisdas/

Contact:  yoshidar@ism.ac.jp
Morphological and Molecular Analyses of Host and Nonhost Interactions Involving Barley and Wheat and the Covered Smut Pathogen Ustilago hordei
Authors: Gaudet Denis A. , Wang Yuanyuan , Penniket Carolyn , Lu Z. X. , Bakkeren Guus , Laroche André
Published: September 2010

Ustilago hordei interactions on coleoptiles of barley host cultivars Odessa (compatible), Hannchen (incompatible, carrying the Ruh1 resistance gene), and on nonhost Neepawa wheat were studied using light and fluorescent microscopy. Autofluorescence, mainly caused by callose accumulation, was more rapidly expressed in nonhost wheat at 30 to 72 h compared with the incompatible reaction between 72 and 144 h. Microarray results demonstrated that more than half of the 893 differentially regulated genes were observed in Neepawa; of these genes, 45% fell into the defense- and stress-related classes in Neepawa compared with 25 and 37% in Odessa and Hannchen, respectively. Their expression coincided with the early morphological defense responses observed and were associated with the jasmonic acid and ethylene (JA/ET) signaling pathway. Expression patterns in Odessa and Hannchen were similar, involving fewer genes and coinciding with later morphological defense responses of these varieties. Although no visible hypersensitive response was apparent in Hannchen or Neepawa, specific upregulation of hypersensitivity-related proteins was observed, such as beta-VPE at 48 h. Expression levels of the callose synthase gene were closely associated with callose accumulation. Differential responses in defense-gene expression among disease reaction types included upregulation of PR-1.1b and downregulation of a nonspecific lipid transfer protein in the incompatible and compatible interactions, respectively. Transcript levels of EDS1 and PAD4, involved in both basal resistance and R-mediated resistance to avirulent pathogens, were up-regulated during both nonhost and Ruh1-mediated resistance. Application of methyl-jasmonate, salicylic acid and ET to leaves revealed that only PR1.1b is strongly up-regulated by all three compounds, while the majority of the defense-related genes are only slightly up-regulated by these signaling compounds.
Nivalenol-Type Populations of Fusarium graminearum and F. asiaticum Are Prevalent on Wheat in Southern Louisiana
Authors: Gale Liane Rosewich , Harrison Stephen A. , Ward Todd J. , O'Donnell Kerry , Milus Eugene A. , Gale Samuel W. , Kistler H. Corby
Published: September 2010

U.S. populations of the Fusarium graminearum clade cause head blight on wheat and barley and usually contaminate grain with the trichothecene mycotoxin deoxynivalenol (DON). Recently, however, individual nivalenol (NIV)-type isolates from the United States were described that belonged to either the newly described species F. gerlachii or the genetically distinct Gulf Coast population of F. graminearum sensu stricto (s.s.). Here, we describe the discovery of NIV-type F. graminearum s.s. populations that were found in high proportion (79%) among isolates from small-grain-growing regions of Louisiana. We genotyped 237 isolates from Louisiana with newly developed polymerase chain reaction (PCR) restriction fragment length polymorphism markers and multiplex PCR primers that distinguish among the three trichothecene types: the two DON types (15ADON and 3ADON) and NIV. These isolates were compared with 297 isolates from 11 other U.S. states, predominantly from the Midwest. Using Bayesian-model-based clustering, we discovered a southern Louisiana population of F. graminearum s.s. that was genetically distinct from the previously recognized pathogen population in the Midwest (MW15ADON population). Population membership was correlated with trichothecene type. Most isolates from the southern Louisiana population were of the NIV type, while the majority of the isolates from the Midwest were of the 15ADON type. A smaller proportion of isolates from Louisiana belonged to the previously described Gulf Coast population that was mostly of the 3ADON type. The NIV type was also identified in collections from Arkansas (12%), North Carolina (40%), and Missouri (2%), with the collections from Arkansas and North Carolina being small and unrepresentative. F. asiaticum was detected from the two southern Louisiana parishes Acadia and Alexandria. All identified 41 F. asiaticum isolates were of the NIV type. Greenhouse tests indicated that U.S. NIV types accumulated four times less trichothecene toxin than DON types on inoculated wheat. This is the first report of NIV-type populations of F. graminearum s. s. and F. asiaticum in the United States.
Comparison of Soil Fungal Community Structure in Different Peanut Rotation Sequences Using Ribosomal Intergenic Spacer Analysis in Relation to Aflatoxin-Producing Fungi
Authors: Sudini H. , Arias C. R. , Liles M. R. , Bowen K. L. , Huettel R. N.
Published: September 2010

The present study focuses on determining soil fungal community structure in different peanut-cropping sequences by using a high-resolution DNA fingerprinting technique: ribosomal intergenic spacer analysis (RISA). This study was initiated to determine fungal community profiles in four peanut-cropping sequences (continuous peanut, 4 years of continuous bahiagrass followed by peanut, peanut-corn-cotton, and peanut-cotton rotations), with a special focus to evaluate whether the profiles under investigation may have also indicated microbial differences that could affect Aspergillus flavus populations. Results indicated 75% similarities among fungal communities from the same cropping sequences as well as with similar times of sampling. Polymerase chain reaction (PCR)-based detection of A. flavus directly from these soils was carried out using A. flavus-specific primers (FLA1 and FLA2) and also through quantitative estimation on A. flavus and A. parasiticus agar medium. Population levels of A. flavus in soil samples ranged from zero to 1.2 × 103 CFU g–1 of soil (based on culturable methods); however, the fungus was not detected with A. flavus-specific primers. The minimum threshold limit at which these aflatoxin-producing fungi could be detected from the total soil genomic DNA was determined through artificial inoculation of samples with 10-fold increases in concentrations. The results indicated that a minimum population density of 2.6 × 106 CFU g–1 of soil is required for PCR detection in our conditions. These results are useful in further determining the relative population levels of these fungi in peanut soils with other soil fungi. This is a new approach to understanding soil fungal communities and how they might change over time and under different rotation systems.
Cytokinin Regulation of Auxin Synthesis in Arabidopsis Involves a Homeostatic Feedback Loop Regulated via Auxin and Cytokinin Signal Transduction
Authors: Jones Brian , Gunnerås Sara Andersson , Petersson Sara V. , Tarkowski Petr , Graham Neil , May Sean , Dolezal Karel , Sandberg Göran , Ljung Karin
Published: September 2010

Together, auxin and cytokinin regulate many of the processes that are critical to plant growth, development, and environmental responsiveness. We have previously shown that exogenous auxin regulates cytokinin biosynthesis in Arabidopsis thaliana. In this work, we show that, conversely, the application or induced ectopic biosynthesis of cytokinin leads to a rapid increase in auxin biosynthesis in young, developing root and shoot tissues. We also show that reducing endogenous cytokinin levels, either through the induction of CYTOKININ OXIDASE expression or the mutation of one or more of the cytokinin biosynthetic ISOPENTENYLTRANSFERASE genes leads to a reduction in auxin biosynthesis. Cytokinin modifies the abundance of transcripts for several putative auxin biosynthetic genes, suggesting a direct induction of auxin biosynthesis by cytokinin. Our data indicate that cytokinin is essential, not only to maintain basal levels of auxin biosynthesis in developing root and shoot tissues but also for the dynamic regulation of auxin biosynthesis in response to changing developmental or environmental conditions. In combination with our previous work, the data suggest that a homeostatic feedback regulatory loop involving both auxin and cytokinin signaling acts to maintain appropriate auxin and cytokinin concentrations in developing root and shoot tissues.
Elevated overdose mortality rates among First Nations individuals in a Canadian setting: a population‐based analysis
Authors: Milloy M‐J. , Wood Evan , Reading Charlotte , Kane Daniel , Montaner Julio , Kerr Thomas
Published: September 2010

Aims  To determine the total burden of illicit drug overdose mortality over the study period in the province of British Columbia and investigate possible population‐level determinants by estimating rates among subgroups including First Nations individuals.

Design  Review of coroner case files.

Setting  The province of British Columbia, Canada.

Participants  Individuals dying from an illicit drug overdose between 2001 and 2005.

Measurements  Age‐adjusted mortality rates, standardized mortality ratios (SMR) and years of potential life lost (YPLL), stratified by major population groups.

Findings  Over the study period, 909 individuals died from illicit drug overdoses, including 104 (11.4%) First Nations individuals. Compared to the general population, First Nations males and females suffered from substantially elevated SMR and YPLL. In a multivariate logistic regression analysis, First Nations deaths were significantly more likely to be among women, related to injection drug use and to have occurred in the Downtown Eastside area of Vancouver, the local epicentre of human immunodeficiency virus infection and open drug use (all P < 0.05).

Conclusions  This report found highly elevated overdose death rates and levels of premature mortality among First Nations Canadians in British Columbia compared to the general population. While previously unidentified, these findings are consistent with the poorer population health profile of First Nations Canadians. Although further research is needed to identify the causes of the elevated death rates, our findings support increased availability of evidence‐based overdose prevention measures.