bluuebunny/crossref_metadata_2025 huggingface dataset:
Cold winter soils enhance dissolved organic carbon concentrations in soil and stream water
Authors: Haei Mahsa , Öquist Mats G. , Buffam Ishi , Ågren Anneli , Blomkvist Peder , Bishop Kevin , Ottosson Löfvenius Mikaell , Laudon Hjalmar
Published: April 2010

Concentrations of dissolved organic carbon ([DOC]) have increased in lakes, streams and rivers across a large part of the northern hemisphere and raised an animated scientific debate about the underlying mechanisms. The lack of consensus about the role of climate in controlling the DOC trends highlights the need for understanding the regulation of surface water DOC. We found that longer and colder winters result in higher [DOC] in a boreal headwater stream during the subsequent snowmelt. In addition, prolonged soil frost increases the spring and summer [DOC] in the riparian soil water, which is a major contributor of stream water DOC in the studied area. We conclude that winter climatic conditions can play a substantial role in controlling stream [DOC] in ways not previously understood. These findings are especially important for northern latitude regions expected to be most affected by climate change.
Laser wakefield acceleration at reduced density in the self-guided regime
Authors: Ralph J. E. , Clayton C. E. , Albert F. , Pollock B. B. , Martins S. F. , Pak A. E. , Marsh K. A. , Shaw J. L. , Till A. , Palastro J. P. , Lu W. , Glenzer S. H. , Silva L. O. , Mori W. B. , Joshi C. , Froula D. H.
Published: April 2010

Experiments conducted using a 200 TW 60 fs laser have demonstrated up to 720 MeV electrons in the self-guided laser wakefield regime using pure helium gas jet targets. The self-trapped charge in a helium plasma was shown to fall off with decreasing electron density with a threshold at 2.5×1018 cm−3, below which no charge is measured above 100 MeV. Self-guiding, however, is shown to continue below this density limitation over distances of 14 mm with an exit spot size of 25 μm. Simulations show that injection of electrons at these densities can be assisted through ionization induced trapping in a mix of helium with 3% oxygen.
Demagnetizing factors for disk samples of nonideal soft magnetic materials
Authors: Graham C. D. , Lorenz B. E.
Published: April 2010

To find out whether experimental magnetometric demagnetizing factors for disk samples of permalloy are valid for other magnetic materials with significant values of coercive field, we measured demagnetizing factors for disk samples of 1095 (high carbon) steel shim stock (Hc≅45 Oe), and for cold-rolled pure nickel (Hc≅23 Oe). The observed demagnetizing factors for steel agree well with those for permalloy but the values for cold-rolled nickel do not, at least for disk samples with diameter-to-thickness ratios d/t greater than 100. The criterion for agreement appears to be a hysteresis loop (M versus H) with straight, parallel sides up to at least half the saturation magnetization, implying a magnetization process controlled by the magnitude of the demagnetizing field.
Silicon nanowire polarizers for far ultraviolet (sub-200 nm) applications: Modeling and fabrication
Authors: Papalia John M. , Adamson Douglas H. , Chaikin Paul M. , Register Richard A.
Published: April 2010

We have previously demonstrated a fabrication technique for the creation of silicon wire grid polarizers (WGPs) for far (deep) ultraviolet applications utilizing a shear-aligned cylinder-forming polystyrene-b-poly(n-hexyl methacrylate) diblock copolymer as a mask for reactive ion etching of an amorphous silicon substrate. In our current work, a numerical model is refined and applied to our experimental systems to describe the impact of wire height and periodicity, and tradeoffs between the two, on polarization efficiency. We focus our attention at a wavelength of 193 nm, the emission wavelength of the ArF excimer laser currently in use in advanced photolithographic processes. Through application of the model’s predictions we have achieved marked improvement in the polarization efficiency of our WGPs by increasing the block copolymer molecular weight, thereby increasing the thickness of the Si wires, which compensates for a simultaneous increase in wire periodicity; the resulting arrays of parallel Si nanowires exhibit polarization efficiencies approaching 64% at 193 nm, a 68% relative increase over our previous Si WGPs.
Wheatstone bridge sensor composed of linear MgO magnetic tunnel junctions
Authors: Cao J. , Freitas P. P.
Published: April 2010

A full Wheatstone bridge sensor composed of linear MgO based magnetic tunnel junctions (MTJ) was designed and achieved. The magnetization direction of reference layers in the required bridge arms was successfully switched by using local current heating method, also demonstrating a viable method of manipulation of pinning direction for exchange bias system on a chip level. The final bridge output shows approximately full signal of individual MTJ but almost null output in the absence of any applied sensing field and small offset of voltage and field.
Shock-tuned cryogenic-deuterium-tritium implosion performance on Omega
Authors: Sangster T. C. , Goncharov V. N. , Betti R. , Boehly T. R. , Casey D. T. , Collins T. J. B. , Craxton R. S. , Delettrez J. A. , Edgell D. H. , Epstein R. , Fletcher K. A. , Frenje J. A. , Glebov Y. Yu. , Harding D. R. , Hu S. X. , Igumenschev I. V. , Knauer J. P. , Loucks S. J. , Li C. K. , Marozas J. A. , Marshall F. J. , McCrory R. L. , McKenty P. W. , Meyerhofer D. D. , Nilson P. M. , Padalino S. P. , Petrasso R. D. , Radha P. B. , Regan S. P. , Seguin F. H. , Seka W. , Short R. W. , Shvarts D. , Skupsky S. , Smalyuk V. A. , Soures J. M. , Stoeckl C. , Theobald W. , Yaakobi B.
Published: April 2010

Cryogenic-deuterium-tritium (DT) target compression experiments with low-adiabat (α), multiple-shock drive pulses have been performed on the Omega Laser Facility [T. R. Boehly, D. L. Brown, R. S. Craxton et al., Opt. Commun. 133, 495 (1997)] to demonstrate hydrodynamic-equivalent ignition performance. The multiple-shock drive pulse facilitates experimental shock tuning using an established cone-in-shell target platform [T. R. Boehly, R. Betti, T. R. Boehly et al., Phys. Plasmas 16, 056301 (2009)]. These shock-tuned drive pulses have been used to implode cryogenic-DT targets with peak implosion velocities of 3×107 cm/s at peak drive intensities of 8×1014 W/cm2. During a recent series of α∼2 implosions, one of the two necessary conditions for initiating a thermonuclear burn wave in a DT plasma was achieved: an areal density of approximately 300 mg/cm2 was inferred using the magnetic recoil spectrometer [J. A. Frenje, C. K. Li, F. H. Séguin et al., Phys. Plasmas 16, 042704 (2009)]. The other condition—a burn-averaged ion temperature ⟨Ti⟩n of 8–10 keV—cannot be achieved on Omega because of the limited laser energy; the kinetic energy of the imploding shell is insufficient to heat the plasma to these temperatures. A ⟨Ti⟩n of approximately 3.4 keV would be required to demonstrate ignition hydrodynamic equivalence [Betti et al., Phys. Plasmas17, 058102 (2010)]. The ⟨Ti⟩n reached during the recent series of α∼2 implosions was approximately 2 keV, limited primarily by laser-drive and target nonuniformities. Work is underway to improve drive and target symmetry for future experiments.
Visualization of electronic structures in the two-dimensional Hubbard model—Spinons, polarons, and stripes
Authors: Tomita Norikazu , Watanabe Shuji
Published: April 2010

Quantum fluctuations (QFs) in the two-dimensional Hubbard model are visualized by using a resonating Hartree-Fock method. Wave functions of optimized multi-Slater determinants show that QFs in the half-filled system are described by vibration, translation, and rotation of spinon-antispinon pairs, while those motions of polarons constitute dominant QFs in the lightly doped systems. We show that an attractive interaction works between two polarons in the framework of a projected Hartree-Fock approximation. The ground states at about 10% doping have a stripe structure and Q’s due to deviations from a uniform stripe.
Charge variation induced nonlinear wave damping in a nonthermal plasma
Authors: Younsi Smain , Tribeche Mouloud
Published: April 2010

A theoretical attempt is made to investigate the charge variation induced nonlinear wave damping in a dusty plasma with nonthermal electrons. Contrary to what has been already reported in the dusty plasma literature, our results show that faster waves suffer stronger anomalous damping than slower ones. As the nonthermal character of the plasma increases, the strength of the anomalous dissipation becomes more important and causes the fast solitary wave amplitude to decay more rapidly. The results complement and provide new insight into the previous work on this problem.
Dust in tokamaks: An overview of the physical model of the dust in tokamaks code
Authors: Bacharis Minas , Coppins Michael , Allen John E.
Published: April 2010

The dynamical behavior of dust produced in tokamaks is an important issue for fusion. In this work, the current status of the dust in tokamaks (DTOKS) [J. D. Martin et al., Europhys Lett. 83, 65001 (2008)] dust transport code will be presented. A detailed description of the various elements of its underlying physical model will be given together with representative simulation results for the mega amp spherical tokamak (MAST) [A. Sykes et al., Nucl. Fusion 41, 1423 (2001)]. Furthermore, a brief description of the various components of the dust transport (DUSTT) [R. D. Smirnov et al., Plasma Phys. Controlled Fusion 49, 347 (2007)] code will also be presented in comparison with DTOKS.
Effect of surface passivation on generation and recombination lifetimes in silicon wafer studied by impedance spectroscopy
Authors: Kumar Sanjai , Singh P. K. , Dhariwal S. R.
Published: April 2010

Impedance spectroscopy is used to study the effect of surface passivation on minority carrier lifetimes. The technique allows measurement of generation and recombination lifetimes separately. Induced p+-p-n structures are prepared by depositing semitransparent layers of high and low work function metals (Pd and Al, respectively) on the two sides of silicon wafers. Hydrogen adsorption property of Pd surface has been utilized for passivation. The generation lifetimes remain almost unaffected but recombination lifetimes enhance many folds after passivations which are in agreement with values obtained by microwave photoconductive decay technique after chemical passivation. Variations are analyzed for estimation of bulk recombination lifetime.
Outer synchronization of coupled networks using arbitrary coupling strength
Authors: Li Zhuchun , Xue Xiaoping
Published: April 2010

This paper mainly studies synchronization between two coupled networks, which is called “outer synchronization.” On the basis of Lyapunov function approach, we prove that for networks with balanced structure topology, outer synchronization can be asymptotically reached by using arbitrary coupling strength. We employ a concept which arises in studying the average-consensus problem. Some numerical examples are presented to illustrate the result in the end. The examples indicate that the coupling strength has real influence on the performance of outer synchronization for a short time. The numerical examples also show that the transverse Lyapunov exponent is independent of the value of coupling strength.
Electrical current suppression in Pd-doped vanadium pentoxide nanowires caused by reduction in PdO due to hydrogen exposure
Authors: Kim Byung Hoon , Oh Soon-Young , Jeong Hu Young , Yu Han Young , Yun Yong Ju , Kim Yark Yeon , Hong Won G. , Lee Jeong Yong , Kim Hae Jin
Published: April 2010

Pd nanoparticle-doped vanadium pentoxide nanowires (Pd-VONs) were synthesized. Electrical current suppression was observed when the Pd-VON was exposed to hydrogen gas, which cannot be explained by the work function changes mentioned in previous report such as Pd-doped carbon nanotubes and SnO2 nanowires. Using the x-ray photoelectron spectroscopy, we found that the reduction in PdO due to hydrogen exposure plays an important role in the current suppression of the Pd-VON.
Spectroscopy of 1.55μm PbS quantum dots on Si photonic crystal cavities with a fiber taper waveguide
Authors: Rakher M. T. , Bose R. , Wong C. W. , Srinivasan K.
Published: April 2010

We use an optical fiber taper waveguide to probe PbS quantum dots (QDs) dried on Si photonic crystal cavities near 1.55μm. We demonstrate that a low density (≲100 μm−2) of QDs does not significantly degrade cavity quality factors as high as ≈3×104. We also show that the tapered fiber can be used to excite the QDs and collect the subsequent cavity-filtered photoluminescence, and present measurements of reversible photodarkening and QD saturation. This method represents an important step toward spectroscopy of single colloidal QDs in the telecommunications band.
Band alignment at the BaCuSeF/ZnTe interface
Authors: Zakutayev Andriy , Tate Janet , Platt Heather A. S. , Keszler Douglas A. , Barati Alireza , Klein Andreas , Jaegermann Wolfram
Published: April 2010

In situ photoemission spectroscopy experiments are used to characterize the interface between ZnTe and the wide band gap p-type semiconductor BaCuSeF. The contact is characterized by a null valence-band offset, a large conduction-band offset, and a chemically graded interface. By applying the transitivity rule for band offset and on the basis of similarities in chemical composition, BaCuSeF contact to chalcogenide photovoltaic absorber materials would be expected to have similar properties. By extension, BaCuChF (Ch=S,Se,Te) materials are suitable as p-layers in p-i-n double-heterojunction solar cells fabricated with CdTe, Cu(InGa)Se2, and Cu2ZnSnS4 absorbers.
Lamellar nanostructures of silicon heterogeneously solidified on graphite sheets
Authors: Li Y. F. , Yu H. Q. , Li H. , Liew K. M. , Liu X. F.
Published: April 2010

Molecular dynamics simulations are performed to examine the heterogeneous solidification of silicon on foreign graphite sheets (GSs). It clearly indicates that silicon atoms are concentrated to form hierarchical nanostructures composed of equidistant nanolayers. Graphite plate induces strong ordered liquid silicon layers near the surfaces of GSs. This study suggests ordered liquid layers should be the early form of the solid crystal, which determine the subsequent nucleation. The confined nanospace between two GSs favors the solidification and results in the decrease in the distance between layers. GSs make silicon atoms solidify into an hcp crystal rather than fcc structure.
Optimal time-dependent current pattern for domain wall dynamics in nanowires
Authors: Yan P. , Wang X. R.
Published: April 2010

Optimal current pattern for domain wall (DW) dynamics in nanowires is investigated. Based on the modified Landau–Lifshitz–Gilbert equation with both the Slonczewski spin-transfer torque and the fieldlike torque, the optimal current pattern for either the maximal DW propagation velocity or the maximal DW-motion-induced spin electromotive voltage is found. Possible experimental realizations are discussed.
The Jaggy Diamonds Illusion
Authors: Kawabe Takahiro , Qian Kun , Yamada Yuki , Miura Kayo
Published: April 2010

We report a new illusion in which the edges of diamonds placed at the intersections of grids are perceived to be jaggy (the jaggy diamonds illusion). Interestingly, the illusion disappears when the stimulus is rotated by 45°, when the stimuli are observed at a close distance, and on the diamond at which the observers stare. Luminance contrast between diamonds, grids, and background is a strong determinant for this illusion.
Assessing the effect of marine isoprene and ship emissions on ozone, using modelling and measurements from the South Atlantic Ocean
Authors: Williams J. , Custer T. , Riede H. , Sander R. , Jöckel P. , Hoor P. , Pozzer A. , Wong-Zehnpfennig S. , Hosaynali Beygi Z. , Fischer H. , Gros V. , Colomb A. , Bonsang B. , Yassaa N. , Peeken I. , Atlas E. L. , Waluda C. M. , van Aardenne J. A. , Lelieveld J.
Published: April 2010

Environmental context. Air over the remote Southern Atlantic Ocean is amongst the cleanest anywhere on the planet. Yet in summer a large-scale natural phytoplankton bloom emits numerous natural reactive compounds into the overlying air. The productive waters also support a large squid fishing fleet, which emits significant amounts of NO and NO2. The combination of these natural and man-made emissions can efficiently produce ozone, an important atmospheric oxidant.
Abstract. Ship-borne measurements have been made in air over the remote South Atlantic and Southern Oceans in January–March 2007. This cruise encountered a large-scale natural phytoplankton bloom emitting reactive hydrocarbons (e.g. isoprene); and a high seas squid fishing fleet emitting NOx (NO and NO2). Using an atmospheric chemistry box model constrained by in-situ measurements, it is shown that enhanced ozone production ensues from such juxtaposed marine biogenic and anthropogenic emissions. The relative impact of shipping and phytoplankton emissions on ozone was examined on a global scale using the EMAC model. Ozone in the marine boundary layer was found to be over ten times more sensitive to NOx emissions from ships, than to marine isoprene in the region south of 45°. Although marine isoprene emissions make little impact on the global ozone budget, co-located ship and phytoplankton emissions may explain the increasing ozone reported for the 40–60°S southern Atlantic region.
Bombesin functionalized gold nanoparticles show in vitro and in vivo cancer receptor specificity
Authors: Chanda Nripen , Kattumuri Vijaya , Shukla Ravi , Zambre Ajit , Katti Kavita , Upendran Anandhi , Kulkarni Rajesh R. , Kan Para , Fent Genevieve M. , Casteel Stan W. , Smith C. Jeffrey , Boote Evan , Robertson J. David , Cutler Cathy , Lever John R. , Katti Kattesh V. , Kannan Raghuraman
Published: April 2010

Development of cancer receptor-specific gold nanoparticles will allow efficient targeting/optimum retention of engineered gold nanoparticles within tumors and thus provide synergistic advantages in oncology as it relates to molecular imaging and therapy. Bombesin (BBN) peptides have demonstrated high affinity toward gastrin-releasing peptide (GRP) receptors in vivo that are overexpressed in prostate, breast, and small-cell lung carcinoma. We have synthesized a library of GRP receptor-avid nanoplatforms by conjugating gold nanoparticles (AuNPs) with BBN peptides. Cellular interactions and binding affinities (IC
50
) of AuNP–BBN conjugates toward GRP receptors on human prostate cancer cells have been investigated in detail. In vivo studies using AuNP–BBN and its radiolabeled surrogate
198
AuNP–BBN, exhibiting high binding affinity (IC
50
in microgram ranges), provide unequivocal evidence that AuNP–BBN constructs are GRP-receptor-specific showing accumulation with high selectivity in GRP-receptor-rich pancreatic acne in normal mice and also in tumors in prostate-tumor-bearing, severe combined immunodeficient mice. The i.p. mode of delivery has been found to be efficient as AuNP–BBN conjugates showed reduced RES organ uptake with concomitant increase in uptake at tumor targets. The selective uptake of this new generation of GRP-receptor-specific AuNP–BBN peptide analogs has demonstrated realistic clinical potential in molecular imaging via x-ray computed tomography techniques as the contrast numbers in prostate tumor sites are severalfold higher as compared to the pretreatment group (Hounsfield unit = 150).
Nonlinear interplay of TEM and ITG turbulence and its effect on transport
Authors: Merz F. , Jenko F.
Published: April 2010

The dominant source of anomalous transport in fusion plasmas on ion scales is turbulence driven by trapped electron modes (TEMs) and ion temperature gradient (ITG) modes. While the individual properties of each of these two instabilities and the corresponding microturbulence have been examined in detail in the past, the effects of a coexistence of the two modes and the phenomena of transitions between the TEM and ITG dominated regimes are not well studied. In many experimental situations, the temperature and density gradients support both microinstabilities simultaneously, so that transitional regimes are important for a detailed understanding of fusion plasmas. In this paper, this issue is addressed, using the gyrokinetic code GENE for a detailed investigation of the dominant and subdominant linear instabilities and the corresponding nonlinear system. A simple quasilinear model based on eigenvalue computations is presented which is shown to reproduce important features of the nonlinear TEM–ITG transition.
BiP Availability Distinguishes States of Homeostasis and Stress in the Endoplasmic Reticulum of Living Cells
Authors: Lai Chun Wei , Aronson Deborah E. , Snapp Erik Lee
Published: April 2010

Accumulation of misfolded secretory proteins causes cellular stress and induces the endoplasmic reticulum (ER) stress pathway, the unfolded protein response (UPR). Although the UPR has been extensively studied, little is known about the molecular changes that distinguish the homeostatic and stressed ER. The increase in levels of misfolded proteins and formation of complexes with chaperones during ER stress are predicted to further crowd the already crowded ER lumen. Surprisingly, using live cell fluorescence microscopy and an inert ER reporter, we find the crowdedness of stressed ER, treated acutely with tunicamycin or DTT, either is comparable to homeostasis or significantly decreases in multiple cell types. In contrast, photobleaching experiments revealed a GFP-tagged variant of the ER chaperone BiP rapidly undergoes a reversible quantitative decrease in diffusion as misfolded proteins accumulate. BiP mobility is sensitive to exceptionally low levels of misfolded protein stressors and can detect intermediate states of BiP availability. Decreased BiP availability temporally correlates with UPR markers, but restoration of BiP availability correlates less well. Thus, BiP availability represents a novel and powerful tool for reporting global secretory protein misfolding levels and investigating the molecular events of ER stress in single cells, independent of traditional UPR markers.
AS160 Modulates Aldosterone-stimulated Epithelial Sodium Channel Forward Trafficking
Authors: Liang Xiubin , Butterworth Michael B. , Peters Kathryn W. , Frizzell Raymond A.
Published: April 2010

Aldosterone-induced increases in apical membrane epithelial sodium channel (ENaC) density and Na transport involve the induction of 14-3-3 protein expression and their association with Nedd4-2, a substrate of serum- and glucocorticoid-induced kinase (SGK1)-mediated phosphorylation. A search for other 14-3-3 binding proteins in aldosterone-treated cortical collecting duct (CCD) cells identified the Rab-GAP, AS160, an Akt/PKB substrate whose phosphorylation contributes to the recruitment of GLUT4 transporters to adipocyte plasma membranes in response to insulin. In CCD epithelia, aldosterone (10 nM, 24 h) increased AS160 protein expression threefold, with a time-course similar to increases in SGK1 expression. In the absence of aldosterone, AS160 overexpression increased total ENaC expression 2.5-fold but did not increase apical membrane ENaC or amiloride-sensitive Na current (Isc). In AS160 overexpressing epithelia, however, aldosterone increased apical ENaC and Isc 2.5-fold relative to aldosterone alone, thus recruiting the accumulated ENaC to the apical membrane. Conversely, AS160 knockdown increased apical membrane ENaC and Isc under basal conditions to ∼80% of aldosterone-stimulated values, attenuating further steroid effects. Aldosterone induced AS160 phosphorylation at five sites, predominantly at the SGK1 sites T568 and S751, and evoked AS160 binding to the steroid-induced 14-3-3 isoforms, β and ε. AS160 mutations at SGK1 phospho-sites blocked its selective interaction with 14-3-3β and ε and suppressed the ability of expressed AS160 to augment aldosterone action. These findings indicate that the Rab protein regulator, AS160, stabilizes ENaC in a regulated intracellular compartment under basal conditions, and that aldosterone/SGK1-dependent AS160 phosphorylation permits ENaC forward trafficking to the apical membrane to augment Na absorption.
Supersplat—spliced RNA-seq alignment
Authors: Bryant Douglas W. , Shen Rongkun , Priest Henry D. , Wong Weng-Keen , Mockler Todd C.
Published: April 2010

Motivation: High-throughput sequencing technologies have recently made deep interrogation of expressed transcript sequences practical, both economically and temporally. Identification of intron/exon boundaries is an essential part of genome annotation, yet remains a challenge. Here, we present supersplat, a method for unbiased splice-junction discovery through empirical RNA-seq data.

Results: Using a genomic reference and RNA-seq high-throughput sequencing datasets, supersplat empirically identifies potential splice junctions at a rate of ∼11.4 million reads per hour. We further benchmark the performance of the algorithm by mapping Illumina RNA-seq reads to identify introns in the genome of the reference dicot plant Arabidopsis thaliana and we demonstrate the utility of supersplat for de novo empirical annotation of splice junctions using the reference monocot plant Brachypodium distachyon.

Availability: Implemented in C++, supersplat source code and binaries are freely available on the web at http://mocklerlab-tools.cgrb.oregonstate.edu/

Contact:  tmockler@cgrb.oregonstate.edu
The lantern shark's light switch: turning shallow water crypsis into midwater camouflage
Authors: Claes Julien M. , Mallefet Jérôme
Published: April 2010

Bioluminescence is a common feature in the permanent darkness of the deep-sea. In fishes, light is emitted by organs containing either photogenic cells (intrinsic photophores), which are under direct nervous control, or symbiotic luminous bacteria (symbiotic photophores), whose light is controlled by secondary means such as mechanical occlusion or physiological suppression. The intrinsic photophores of the lantern shark
Etmopterus spinax
were recently shown as an exception to this rule since they appear to be under hormonal control. Here, we show that hormones operate what amounts to a unique light switch, by acting on a chromatophore iris, which regulates light emission by pigment translocation. This result strongly suggests that this shark's luminescence control originates from the mechanism for physiological colour change found in shallow water sharks that also involves hormonally controlled chromatophores: the lantern shark would have turned the initial shallow water crypsis mechanism into a midwater luminous camouflage, more efficient in the deep-sea environment.
A moving topic: control and dynamics of animal locomotion
Authors: Biewener Andrew , Daniel Thomas
Published: April 2010

Animal locomotion arises from complex interactions among sensory systems, processing of sensory information into patterns of motor output, the musculo-skeletal dynamics that follow motor stimulation, and the interaction of appendages and body parts with the environment. These processes conspire to produce motions and forces that permit stunning manoeuvres with important ecological and evolutionary consequences. Thus, the habitats that animals may exploit, their ability to escape predators or attack prey, their capacity to manoeuvre and turn, or the use of their available energy all depend upon the processes that determine locomotion. Here, we summarize a series of 10 papers focused on this integrative research topic.
Sir John Royden Maddox. 27 November 1925 — 12 April 2009
Authors: Gratzer Walter
Published: April 2010

John Maddox was a man of prodigious energy, blessed by an astonishing memory, and with a deep understanding of broad swathes of science. As a lecturer at the University of Manchester he seemed set on an academic career and was widely regarded as the most promising member of an outstanding group of young theoreticians. Yet during five years he published no papers, other than an unsigned account in
Nature
in 1951 of the newly opened Joule Museum in Salford. He suffered, it was thought, from want of confidence in writing up his work, but then came his precipitate move to the
Manchester Guardian
, where he at once began to publish profusely. From then on, printer's ink coursed through his veins: his devotion to journalism endured to the end of his life, and brought him high distinction.
Edwin Ernest Salpeter. 3 December 1924 — 26 November 2008
Authors: Terzian Yervant
Published: April 2010

Edwin E. Salpeter was a towering figure in twentieth-century astrophysics. Among his major scientific accomplishments is his 1955 paper ‘The luminosity function and stellar evolution’, where he first derived the empirical stellar initial mass function and estimated the probability for the creation of stars of given mass at a particular time, known as the Salpeter initial mass function. Just before this major achievement he had explained how giant stars burn helium to form carbon in the triple-alpha process, in which three helium nuclei combine to form carbon. This crucial step opened the path for the formation of elements as heavy as iron in the core of the stars. Salpeter showed the way to put physics into astronomy, and astrophysics has made enormous strides to understand the Universe. He once observed that most successful scientists are golf players; that is, they map out their own strategy and then write a unified theory. Salpeter said that he belonged to the minority of scientists who are Ping-pong players that react to influences from outside players. This approach made Salpeter a generalist.
Fish in a ring: spatio-temporal pattern formation in one-dimensional animal groups
Authors: Abaid Nicole , Porfiri Maurizio
Published: April 2010

In this work, we study the collective behaviour of fish shoals in annular domains. Shoal mates are modelled as self-propelled particles moving on a discrete lattice. Collective decision-making is determined by information exchange among neighbours. Neighbourhoods are specified using the perceptual limit and numerosity of fish. Fish self-propulsion and obedience to group decisions are described through random variables. Spatio-temporal schooling patterns are measured using coarse observables adapted from the literature on coupled oscillator networks and features of the time-varying network describing the fish-to-fish information exchange. Experiments on zebrafish schooling in an annular tank are used to validate the model. Effects of group size and obedience parameter on coarse observables and network features are explored to understand the implications of perceptual numerosity and spatial density on fish schooling. The proposed model is also compared with a more traditional metric model, in which the numerosity constraint is released and fish interactions depend only on physical configurations. Comparison shows that the topological regime on which the proposed model is constructed allows for interpreting characteristic behaviours observed in the experimental study that are not captured by the metric model.
Natural catalytic activity in a marine shale for generating natural gas
Authors: Mango Frank D. , Jarvie Daniel M. , Herriman Eleanor
Published: April 2010

Many organic-rich rocks are major sources of oil and gas in sedimentary basins presumably through high-temperature thermal cracking. This view was brought into question with recent reports of marine shales generating catalytic gas in the laboratory at 50
°
C, 300
°
C below thermal-cracking temperatures. Gas forms under natural conditions without artificial stimulation. Compositions of methane, ethane and propane are near thermodynamic equilibrium (2C
2
H
6
=CH
4
+C
3
H
8
) mirroring those in natural deposits. It is significant because thermal cracking can neither generate hydrocarbons at equilibrium nor can it bring them to equilibrium over geological time. Thus, catalysis must be the source of equilibrium in natural gas habitats and in marine shales. There is experimental evidence for metathesis (

) as the catalytic path to equilibrium. However, it is without example in contemporary catalysis, and therefore, calls for extraordinary empirical support. Here, we report independent and unequivocal evidence of natural catalytic activity in a marine shale linking metathesis and thermodynamic equilibrium. A Cretaceous Mowry shale catalysed the dimerization of propylene (C
3
H
6
) to methyl cyclopentane (MCP, C
6
H
12
) and
n
-hexane (
n
-C
6
, C
6
H
14
) at 50
°
C in greater than 99 per cent selectivity. Propylene increased the rate of
n
-C
6
generation by a factor of 100 with 100 per cent selectivity to the straight-chain hexane (
n
-C
6
). Propylene also suppressed the generation of all hydrocarbons except cyclopentane, MCP and
n
-C
6
. The ratio MCP/
n
-C
6
, which swung chaotically between 1 and 25 before propylene addition, was rendered invariant with propylene addition (
R
2
=0.99; MCP/
n
-C
6
=1.20±0.034 s.d.). These uniquely catalytic reactions confirm natural catalytic activity in this shale. It appears to be ‘palaeoactivity’ possibly conceived in early diagenesis and sustained over geological time.
Excavated substrate modulates growth instability during nest building in ants
Authors: Toffin Etienne , Kindekens Jonathan , Deneubourg Jean-Louis
Published: April 2010

In social insects, the nests of the same species can show a large difference in size and shape. Despite these large variations, the nests share the same substructures, some appearing during nest growth. In ants, the interplay between nest size and digging activity leads to two successive morphological transitions from circular to branched shapes (budding along the perimeter of the circular cavity and tunnelling of the galleries). Like several other self-organized collective behaviours, this phenomenon, as well as the entire nest-digging process, is thought to be modulated by environmental properties. The present study investigates the effect of excavated substrate on the nest morphogenesis and the morphological transitions by using two materials with different cohesions. Here, we show that the two morphological transitions occur more frequently with a cohesive substrate than with a granular one: 96 per cent of cohesive experiments showed both transitions, whereas only 50 per cent did in granular experiments. We found that transitions and excavation cessation follow area–response thresholds: the shape transitions take place and the digging activity stops when the dug area reaches the corresponding threshold values. The shape transition thresholds are lower with the cohesive substrate and that of stopping digging is independent of nest shape and material. According to simulations, the experimental frequencies of transitions found their origin in the competition between transitions and activity cessation and in the difference between the transition threshold values of each substrate. Our results demonstrate how the substrate properties modulate the collective response and lead to various patterns. Considering the non-specific mechanisms at work, such effects of substrate coarseness have their counterparts in various collective behaviours, generating alternative patterns to colonize and exploit the environment.
Divergence in behaviour between the European corn borer,Ostrinia nubilalis, and its sibling speciesOstrinia scapulalis: adaptation to human harvesting?
Authors: Calcagno Vincent , Bonhomme Vincent , Thomas Yan , Singer Michael C. , Bourguet Denis
Published: April 2010

Divergent adaptation to host plant species may be the major mechanism driving speciation and adaptive radiations in phytophagous insects. Host plants can differ intrinsically in a number of attributes, but the role of natural enemies in host plant specialization is often underappreciated. Here, we report behavioural divergence between the European corn borer (ECB,Ostrinia nubilalis) and its sibling speciesOstrinia scapulalis, in relation to a major enemy: humans. Harvesting maize imposes selective mortality onOstrinialarvae: those located above the cut-off line of the stalk face almost certain death. We show that ECB larvae diapause closer to the ground than those ofO. scapulalis, which is sympatric but feeds mainly on weeds. The difference in diapause height results from genetically determined differences in geotactic behaviour. ECB larvae descend towards the ground specifically at harvest time, increasing their chances of surviving harvesting by about 50 per cent overO. scapulalislarvae. Natural enemies appear as a major driver of host-plant specialization in this example, stressing the need to consider ‘tri-trophic’ ecological niches to understand insect diversification. Our results also strongly suggest that geotaxis evolved as a singular instance of behavioural resistance in a major agricultural pest.
Balitora eddsi, a new species of hillstream loach (Ostariophysi: Balitoridae) from Nepal
Authors: Conway K. W. , Mayden R. L.
Published: April 2010

A new species of hillstream loach Balitora eddsi is described from the Karnali River drainage in south‐western Nepal. The new species is distinguished from all its congeners by possessing the following combination of characters: six to seven unbranched pectoral‐fin rays, pelvic‐fin length 12–14% standard length (LS), dorsal surface without circular or irregular shaped dark blotches, snout pointed, median lobe between anterior rostral barbels pointed posteriorly, dorsal‐fin origin posterior to pelvic‐fin origin, lateral line scales 66–67, caudal peduncle length 22–23·2% LS, caudal peduncle depth 4·1–4·2 times its length.
The stem canker (blackleg) fungus, Leptosphaeria maculans, enters the genomic era
Authors: ROUXEL T. , BALESDENT M. H.
Published: April 2010

Leptosphaeria maculans is the most ubiquitous pathogen of Brassica crops, and mainly oilseed brassicas (oilseed rape, canola), causing the devastating ‘stem canker’ or ‘blackleg’. This review summarizes our current knowledge on the pathogen, from taxonomic issues to specific life traits. It mainly illustrates the importance of formal genetics approaches on the pathogen side to dissect the interaction with the host plants. In addition, this review presents the main current research topics on L. maculans and focuses on the L. maculans genome initiative recently begun, including its main research issues.

Taxonomy:  Leptosphaeria maculans (Desm.) Ces. & de Not. (anamorph Phoma lingam Tode ex Fr.). Kingdom Fungi, Phylum Ascomycota, Class Dothideomycetes (Loculoascomycetes), Order Pleosporales, Genus Leptosphaeria, Species maculans.

Host range:  cultivated Brassicas such as Brassica napus (oilseed rape, canola), B. rapa, B. juncea, B. oleracea, etc., along with numerous wild crucifers species. Arabidopsis thaliana was recently reported to be a potential host for L. maculans. Primary disease symptoms are greyish‐green collapse of cotyledon or leaf tissue, without a visible margin, bearing tiny black spots (pycnidia). The fungus then develops an endophytic symptomless growth for many months. Secondary symptoms, at the end of the growing season, are dry necroses of the crown tissues with occasional blackening (stem canker or blackleg) causing lodging of the plants. Pseudothecia differentiate on leftover residues. Seedling damping‐off and premature ripening are also reported under certain environmental conditions.

Useful websites:  Leptosphaeria maculans sequencing project at Genoscope: http://www.genoscope.cns.fr/externe/English/Projets/Projet_DM/organisme_DM.html; the SECURE site: http://www.secure.rothamsted.ac.uk/ the ‘Blackleg’ group at the University of Melbourne: http://www.botany.unimelb.edu.au/blackleg/overview.htm
Salicylic acid (SA)‐dependent gene activation can be uncoupled from cell death‐mediated gene activation: the SA‐inducible NIMIN‐1 and NIMIN‐2 promoters, unlike the PR‐1a promoter, do not respond to cell death signals in tobacco
Authors: GLOCOVA IVANA , THOR KATHRIN , ROTH BERNHARD , BABBICK MAREN , PFITZNER ARTUR J. P. , PFITZNER URSULA M.
Published: April 2010

Tobacco pathogenesis‐related (PR) genes of group 1 are induced during pathogen defence (hypersensitive response, HR, and systemic acquired resistance, SAR), after exogenous application of salicylic acid (SA), and by developmental cues. Likewise, SA enhances transcripts for Arabidopsis NIMIN‐1 and NIMIN‐2, which interact with NPR1/NIM1, a key regulator of SAR. To further illuminate gene activation during pathogen defence, reporter gene expression from the NIMIN‐1 and NIMIN‐2 promoters was analysed in transgenic tobacco plants in direct comparison to PR‐1 gene expression. NIMIN[GUS] chimeric genes were highly sensitive to SA, whereas NIMIN[GUS], unlike PR1a[GUS], expression was only weak in necrotic tissue exhibiting HR. Furthermore, PR‐1a, but not NIMIN, promoter constructs were activated systemically in response to local cell death elicited by expression of the proapoptotic Bax gene. Conversely, NIMIN‐1[GUS] expression was completely suppressed during pathogen defence in plants depleted from SA, whereas PR‐1 proteins still accumulated in necrotic tissue. These findings demonstrate that SA‐dependent gene activation can be uncoupled from cell death‐induced gene activation. Whereas PR‐1a induction during the HR and SAR responses is mediated by HR‐associated signals and SA, activation of the NIMIN‐1 and NIMIN‐2 promoters in infected tobacco relies on SA, but not on cell death signals.
Clinical trial: gastric acid suppression in Hispanic adults with symptomatic gastro‐oesophageal reflux disease – comparator study of esomeprazole, lansoprazole and pantoprazole
Authors: Morgan D. , Pandolfino J. , Katz P. O. , Goldstein J. L. , Barker P. N. , Illueca M.
Published: April 2010

Aliment Pharmacol Ther 2010; 32: 200–208

Background  Hispanic‐Americans are a rapidly growing population in the United States, yet gastro‐oesophageal reflux disease (GERD) is not well studied in this population.

Aim  To compare the efficacy of esomeprazole, lansoprazole and pantoprazole in suppressing gastric acid, including the area of the ‘acid pocket,’ in Hispanics with GERD.

Methods  In this open‐label, 3‐way crossover study, 83 Hispanics with symptomatic GERD were randomized to 1 of 6 possible treatment sequences of three 5–7‐day dosing periods with esomeprazole 40 mg, lansoprazole 30 mg and pantoprazole 40 mg daily separated by 10–17‐day washout periods. Intragastric pH was measured for 24 h using dual probes with a distal and proximal (area of the ‘acid pocket’) electrode.

Results  Esomeprazole suppressed intragastric acid (pH >4.0) significantly longer over 24 h (primary end point) compared with lansoprazole and pantoprazole (P < 0.0001), and proximal gastric acid (pH >4.0) significantly longer over 24 h compared with lansoprazole (P < 0.05) and pantoprazole (P < 0.0001).

Conclusions  Esomeprazole was more effective than lansoprazole and pantoprazole in suppressing gastric acidity at both intragastric distal and proximal (area of the acid pocket) sites in Hispanics with GERD. Future studies are warranted to understand better the role of the acid pocket in GERD (Clinical trial numbers: D9612L00106; ClinicalTrials.gov: NCT00410592).
ORIGINAL ARTICLE: Metabolic outcome of GH treatment in prepubertal short children with and without classical GH deficiency
Authors: Decker Ralph , Albertsson‐Wikland Kerstin , Kriström Berit , Nierop Andreas F. M. , Gustafsson Jan , Bosaeus Ingvar , Fors Hans , Hochberg Ze’ev , Dahlgren Jovanna
Published: April 2010

Context  Few studies have evaluated the metabolic outcomes of growth hormone (GH) treatment in idiopathic short stature (ISS). Moreover, children with ISS appear to need higher GH doses than children with GH deficiency (GHD) to achieve the same amount of growth and may therefore be at increased risk of adverse events during treatment. The individualized approach using prediction models for estimation of GH responsiveness, on the other hand, has the advantage of narrowing the range of growth response, avoiding too low or high GH doses.

Design  Short prepubertal children with either isolated GHD (39) or ISS (89) participated in a 2‐year randomized trial of either individualized GH treatment with six different GH doses (range, 17–100 μg/kg/day) or a standard dose (43 μg/kg/day).

Objective  To evaluate if individualized GH treatment reduced the variance of the metabolic measures as shown for growth response and to compare changes in metabolic variables in children with ISS and GHD.

Hypothesis  Individualized GH dose reduces the range of metabolic outcomes, and metabolic outcomes are similar in children with ISS and GHD.

Results  We observed a narrower variation for fasting insulin (−34·2%) and for homoeostasis model assessment (HOMA) (−38·9%) after 2 years of individualized GH treatment in comparison with standard GH dose treatment. Similar metabolic changes were seen in ISS and GHD. Delta (Δ) height SDS correlated with Δinsulin‐like growth factor I (IGF‐I), Δleptin and Δbody composition. Principal component analysis identified an anabolic and a lipolytic component. Anabolic variables [Δlean body mass (LBM) SDS and ΔIGF‐I SDS] clustered together and correlated strongly with Δheight SDS and GH dose, whereas lipolytic variables [Δfat mass (FM) SDS and Δleptin] were clustered separately from anabolic variables. Regression analysis showed GH dose dependency in ISS, and to a lesser degree in GHD, for ΔLBM SDS and Δheight SDS, but not for changes in FM.

Conclusions  Individualized GH dosing during catch‐up growth reduces the variance in insulin and HOMA and results in equal metabolic responses irrespective of the diagnosis of GHD or ISS.
HLA‐DR‐restricted T‐cell responses to factor VIII epitopes in a mild haemophilia A family with missense substitution A2201P
Authors: ETTINGER R. A. , JAMES E. A. , KWOK W. W. , THOMPSON A. R. , PRATT K. P.
Published: April 2010

Summary.  An HLA‐DRA‐DRB1*0101‐restricted T‐cell epitope in the factor VIII (FVIII) C2 domain occurred in a mild haemophilia A patient with missense substitution FVIII‐A2201P. His T cells responded to synthetic peptides FVIII2186–2205 and FVIII2194–2213 (J Thromb Haemost 2007; 5: 2399). T cells from family members with genotype FVIII‐A2201P were analysed to determine if FVIII‐specific T cells occur in individuals with a haemophilic mutation but no clinically significant inhibitor response. Fluorescent MHC class II tetramers corresponding to subjects’HLA‐DRB1 types were loaded with 20‐mer peptides and utilized to label antigen‐specific CD4+ T cells. T‐cell responses to peptides spanning the FVIII‐C2 sequence were evaluated. T cells recognizing specific peptides were cloned, and antigen specificity was verified by proliferation assays. Plasma and/or purified IgG samples were tested for FVIII inhibitory activity. CD4+ T cells and T‐cell clones from two brothers who shared the DRB1*0101 allele responded to FVIII2194–2213. A haemophilic cousin’s HLA‐DRA‐DRB1*1104‐restricted response to FVIII2202–2221 was detected only when CD4+CD25+ cells were depleted. A great uncle and two obligate carriers had no detectable FVIII‐C2‐specific T cells. Concentrated IgG from the brother without a clinical inhibitor response showed a low‐titre FVIII inhibitor. FVIII‐specific T cells and inhibitory IgG were found in a previously infused, haemophilic subject who had a sub‐clinical FVIII inhibitor. CD4+CD25+ depleted T cells from a non‐infused haemophilic cousin recognized an overlapping FVIII epitope, indicating a latent HLA‐DRA‐DRB1*1104‐restricted T‐cell response to FVIII. Specific T‐cell responses to FVIII can occur without clinically significant inhibitors.