bluuebunny/crossref_metadata_2025 huggingface dataset:
Plasma expansion and impedance collapse in a foil-less diode for a klystronlike relativistic backward wave oscillator
Authors: Xiao Renzhen , Sun Jun , Huo Shaofei , Li Xiaoze , Zhang Ligang , Zhang Xiaowei , Zhang Lijun
Published: December 2010

Klystronlike relativistic backward wave oscillator (RBWO) can produce microwave power exceeding 5 GW with a high efficiency larger than 40%. In the experiment of klystronlike RBWO, for about 1 MV peak diode voltages, increasing magnetic field from 1.43 to 1.89 T slowed the impedance collapse until it was suppressed completely. The introduction of a stainless steel obstructing ring aggravated the impedance collapse, whereas replacing the stainless steel obstructing ring with a flat stainless steel provided a more stable impedance variation during the pulse duration. These impedance collapses did not affect microwave generation seriously and may be attributed to the radial expansion of cathode plasma initialing from the cathode shank so that part of reverse currents were collected at the anode wall, contributing to the measured diode current. On the other hand, it was found that microwave generation shot-to-shot reproducibility was closely related to the diode impedance variation. When there was no or very low microwave measured, diode impedance collapse appeared at the latter of the pulse. The microwave generation shot-to-shot reproducibility was improved greatly after the electron collector was enlarged on radius with 1 mm. A possible explanation is that the anode plasma produced from electron collector expands axially and enters the diode region at a very high velocity of several mm/ns. The movement of the anode plasma in the beam-wave interaction region affects the microwave generation, which reduces the microwave power during the whole pulse duration significantly.
A novel large-orbit electron beam generated by a Cuccia coupler for a Ka-band third-harmonic slotted peniotron
Authors: Zhao Xiaoyun , Li Jiayin , Zou Huan , Wang Haiyang , Wu Xinhui , Hu Biao , Li Hao , Li Tianming
Published: December 2010

In this work, a novel large-orbit electron beam generated by a Cuccia coupler for a Ka-band third-harmonic slotted is proposed. The Cuccia coupler was originally used in the electron coupler for amplitude modulation and power control at ultrahigh frequencies. It is demonstrated by the 3D-PIC simulation that a 6 kV, 0.5 A beam will be gyroresonantly accelerated when a microwave power of 16 kW at 10 GHz is injected into the coupler, from which a 37 kV, 0.5 A large-orbit electron beam will be obtained; it is characterized by a relative velocity spread lower than 1% and a velocity ratio α (υ⊥/υz) up to 2.3. Moreover, other electron beam parameters including transverse velocity (υ⊥), longitudinal velocity (υz) and deviation of guiding center could be adjusted independently, whereas these are rather difficult for the cusp gun. Finally, the Ka-band third-harmonic slotted peniotron in 2π mode driven by such a beam is verified by 3D-PIC simulation, which is predicted to yield an output power of 8 kW at 30 GHz, with a microwave power conversion efficiency up to 50% and a device efficiency up to 43%, respectively.
Indium oxide octahedra optical microcavities
Authors: Dong Hongxing , Sun Liaoxin , Sun Shulin , Xie Wei , Zhou Lei , Shen Xuechu , Chen Zhanghai
Published: December 2010

Nearly perfect In2O3 octahedra were fabricated and studied as optical resonators. Electron microscopy images revealed that the octahedra have single-crystal structures, very smooth surfaces, and regular geometric morphologies. Bow-tielike modes in the visible spectral range were clearly observed at room temperature by using the spatially resolved spectroscopic technique. The experimental observations are described and fitted well with the plane wave interference model and Cauchy dispersion formula for refractive indices.
Strongly enhanced tunable photoluminescence in polymorphous silicon carbon thin films via excitation-transfer mechanism
Authors: Wang Junzhuan , Suendo V. , Abramov A. , Yu Linwei , Roca i Cabarrocas Pere
Published: December 2010

Here, we investigate the enhanced tunable photoluminescence (PL) of hydrogenated polymorphous silicon carbon (pm-Si1−xCx:H) thin films fabricated in a plasma enhanced chemical vapor deposition system. The silicon nanocrystal (nc-Si) inclusions are formed during gas-phase nucleation and incorporated in the hydrogenated amorphous silicon carbon (a-SiC:H) matrix. The nc-Si provides high-quality recombination centers for the photogenerated carriers in the pm-Si1−xCx:H material, while the a-SiC:H matrix plays a role of sensitizer. We elucidate and provide experimental evidence for this excitation-transfer mechanism. Strongly enhanced PL performance can be achieved by effective matrix passivation that favors a diffusion-driven carrier recombination in the nc-Si centers.
Magnetization dynamics triggered by surface acoustic waves
Authors: Davis S. , Baruth A. , Adenwalla S.
Published: December 2010

Investigations into fast magnetization switching are of both fundamental and technological interest. Here we present a low-power, remote method for strain driven magnetization switching. A surface acoustic wave propagates across an array of ferromagnetic elements, and the resultant strain switches the magnetization from the easy axis into the hard axis direction. Investigations as a function of applied magnetic field as well as unidirectional anisotropy (the exchange bias) reveal excellent agreement with prediction, confirming the viability of this method.
Ga induced superstructures as templates for lattice matched hetroepitaxial growth of GaN on Si(111) substrate
Authors: Kumar Praveen , Kuyyalil Jithesh , Shivaprasad S. M.
Published: December 2010

High quality GaN is grown by plasma assisted molecular beam epitaxy on Ga induced superstructural phases of Si(111)7×7. Three stable surface phases induced by Ga adsorption, viz., (1×1), (6.3×6.3), and (√3×√3)R30°, are employed as templates to grow epitaxial (0001) GaN thin films. GaN grown on Si(√3×√3)R30°-Ga is found to be highly crystalline with intense (0002) x-ray diffraction and photoluminescence peaks with low full width at half maximum, low surface roughness, and stoichiometric surface composition. The high quality of these GaN films formed at a low temperature of 400 °C is explained by the integral (×2) lattice matching between the unit cell of GaN and the (√3×√3) phase. The experiments demonstrate a plausible approach of adsorbate induced surface modifications as templates for III-V hetroepitaxy on Si surfaces.
Behavior of a train of droplets in a fluidic network with hydrodynamic traps
Authors: Bithi Swastika S. , Vanapalli Siva A.
Published: December 2010

The behavior of a droplet train in a microfluidic network with hydrodynamic traps in which the hydrodynamic resistive properties of the network are varied is investigated. The flow resistance of the network and the individual droplets guide the movement of droplets in the network. In general, the flow behavior transitions from the droplets being immobilized in the hydrodynamic traps at low flow rates to breaking up and squeezing of the droplets at higher flow rates. A state diagram characterizing these dynamics is presented. A simple hydrodynamic circuit model that treats droplets as fluidic resistors is discussed, which predicts the experimentally observed flow rates for droplet trapping in the network. This study should enable the rational design of microfuidic devices for passive storage of nanoliter-scale drops.
Passive optical separation and enrichment of cells by size difference
Authors: Hoi Siew-Kit , Kim Vuong Hoang , Huy Nguyen Manh , Sow Chorng-Haur , Ow Yueh-Sheng , Bettiol Andrew A.
Published: December 2010

A size-selective cell sorting microfluidic device that utilizes optical force is developed. The device consists of a three-dimensional polydimethylsiloxane microstructure comprised of two crossed microchannels in a three-dimensional configuration. A line shaped focused laser beam is used for automatic size-selective cell sorting in a continuous flow environment. As yeast cells in an aqueous medium are fed continuously into a lower channel, the line shaped focused laser beam is applied (perpendicular to the direction of flow) at the junction of the two crossed channels. The scattering force of the laser beam was employed to push cells matching specific criteria upward from one channel to another. The force depends on the size of the cells, the laser power, and the fluid flow speed. The variation in size of yeast cells causes them to follow different routes at the intersection. For flow speeds below 30 μm/s, all yeast cells larger than 3 μm were removed from the main stream. As a result, a high purity sample of small cells can be collected at the outlet of bottom channel.
Magnetic imaging of the pinning mechanism of asymmetric transverse domain walls in ferromagnetic nanowires
Authors: Petit Dorothée , Zeng Huang T. , Sampaio Joao , Lewis Emma , O’Brien Liam , Jausovec Ana-Vanessa , Read Dan , Cowburn Russell P. , O’Shea Kerry J. , McVitie Stephen , Chapman John N.
Published: December 2010

The pinning of asymmetric transverse magnetic domain walls by constrictions and protrusions in thin permalloy nanowires is directly observed using the Fresnel mode of magnetic imaging. Different domain wall (DW)/trap configurations are initialized using in situ applied magnetic fields, and the resulting configurations are imaged both at remanence and under applied fields. The nature of the chirality dependent pinning potentials created by the traps is clearly observed. The effect of the asymmetry of the DW is discussed. Micromagnetic simulations are also presented, which are in excellent agreement with the experiments.
High temperature ultrasonic transducer up to 1000 °C using lithium niobate single crystal
Authors: Baba Atsushi , Searfass Clifford T. , Tittmann Bernhard R.
Published: December 2010

Structural health monitoring (SHM) techniques are needed to maintain the reliability of aging power plants. The high temperature transducers are necessary to realize SHM under the working condition of power plants. In this paper, a high temperature transducer was developed using lithium niobate (LiNbO3) single crystal, which is well known as a high Curie temperature piezoelectric material. The LiNbO3 was bonded onto a stainless steel substrate. The transducer was heated in an electric furnace while measuring the bottom echoes from the substrate. We confirmed that the high temperature transducer could work up to 1000 °C.
A unidirectional quantum cascade ring laser
Authors: Nshii C. C. , Ironside C. N. , Sorel M. , Slight T. J. , Zhang S. Y. , Revin D. G. , Cockburn J. W.
Published: December 2010

We report on the design, fabrication, and characterization of a unidirectional quantum cascade ring laser operating at a wavelength of around 3.4 μm at 200 K. A unidirectional operation is achieved by incorporating an “S-shaped” crossover waveguide in a manner that it couples light from the counterclockwise direction to the preferred clockwise direction. The ring laser unidirectionality is confirmed by measuring the counterpropagating wave suppression ratio (CWSR) as a function of injection current. At 1.5 times the threshold current, the CWSR is 9 that is 90% of the light is emitted in the favored (clockwise) direction.
Dielectric, magnetic, and magnetoelectric properties of La and Ti codoped BiFeO3
Authors: Cui Y. F. , Zhao Y. G. , Luo L. B. , Yang J. J. , Chang H. , Zhu M. H. , Xie D. , Ren T. L.
Published: December 2010

The authors report on the dielectric, magnetic, and magnetoelectric (ME) properties of La and Ti codoped BiFeO3 (LBFTO). Codoping changes the structure of BiFeO3 from rhombohedral to tetragonal and the ferromagnetic properties of LBFTO are remarkably improved. More interestingly, the dielectric constant of LBFTO shows a linear increase with magnetic field and the slope decreases linearly with increasing temperature. The electric polarization of LBFTO also increases upon applying a magnetic field. The ME coupling coefficients of different orders were obtained by analyzing these data. The results were discussed by considering the doping induced destruction of the cycloidal structure in LBFTO.
Catastrophic optical damage at front and rear facets of diode lasers
Authors: Hempel Martin , Tomm Jens W. , Ziegler Mathias , Elsaesser Thomas , Michel Nicolas , Krakowski Michel
Published: December 2010

Single-pulse tests of the catastrophic optical damage (COD) are performed for three batches of diode lasers with different gain-regions. The tests involve in situ inspection of front, rear, and side of the devices by a thermocamera. Devices with an Al-containing gain-region show COD at the front facet, as expected for strong facet heating via surface recombination and reabsorption of laser light. In contrast, Al-free devices with low surface recombination rates tend to fail at the rear facet, pointing to a different heating scenario. The high carrier density at the rear facet favors heating and COD via Auger recombination processes.
Observation of large electric polarization in orthorhombic TmMnO3 thin films
Authors: Han T. C. , Chao H. H.
Published: December 2010

High-quality orthorhombic (OT) TmMnO3 (TMO) thin films with a-axis perpendicular to the film surface are grown epitaxially on Nb-doped SrTiO3(110) substrates using pulsed laser deposition. The structural, magnetic, and electric properties of OT-TMO films are measured. We found that a strong coupling between the magnetic structure and the electric polarization. Our experimental results also show that ferroelectricity in OT-TMO thin films below 32 K. Furthermore, the large electric polarization up to 0.45 μC/cm2 is observed at 10 K, supporting a theoretical prediction of large polarization in the E-type spin structure in this system.
Electrodeless electrohydrodynamic printing of personalized medicines
Authors: Elele Ezinwa , Shen Yueyang , Khusid Boris
Published: December 2010

We report on a method for drop-on-demand printing of personalized medicines. A fluid is infused into an electrically insulating nozzle to form a pendant drop that will serve as a floating electrode that is capacitively coupled to external electrodes during a voltage pulse. An electric force is directly applied to the pendant drop to produce a sessile drop on an insulating polymer film. Versatility is proved on fluids spanning over three orders of magnitude in viscosity and conductivity. Scaling analysis captures the essential physics of drop dynamics and provides critical design guideline.
Influence of streaming potential on the elastic response of a compliant microfluidic substrate subjected to dynamic loading
Authors: Chakraborty Jeevanjyoti , Chakraborty Suman
Published: December 2010

In the present study, we investigate the effect of streaming potential on the elastic response of a compliant surface subjected to dynamic loading conditions. For illustrating the pertinent physical phenomena, we analyze in particular the dynamical characteristics of the system on squeezing out of a liquid layer through a narrow gap formed between an elastic fluidic surface and an incipient rigid oscillating sphere. We reveal that the streaming potential effects may amplify the elastic force response of the substrate to a considerable extent. Interestingly and nontrivially, this increment turns out not only to be a function of the pertinent electrokinetic parameters dictating the establishment of the streaming potential, but also a combined consequence of the oscillation frequency and the stiffness of the substrate, consistent with a dynamical interaction between interfacial electrochemical-hydrodynamics and structural responsive characteristics that has hitherto not been emphatically explored.
Ponderomotive acceleration of electrons by a self focused laser pulse
Authors: Singh Rohtash , Sharma A. K.
Published: December 2010

Ponderomotive acceleration of electrons by a short laser pulse undergoing relativistic self-focusing in a plasma is investigated. The saturation in nonlinear plasma permittivity causes periodic self-focusing of the laser. The periodicity lengths are different for different axial segments of the pulse. As a result, pulse shape is distorted. An electron initially on the laser axis and at the front of the self-focusing pulse gains energy from the pulse until it is run over by the pulse peak. By the time electron reaches the tail, if pulse begins diverging, the deceleration of the electron is slower and the electron is left with net energy gain. The electrons slightly off the laser axis see a radial ponderomotive force too. Initially, when they are accelerated by the pulse front the acceleration is strong as they are closer to the axis. When they see the tail of the pulse (after being run by the pulse), they are farther from the axis and the retardation ponderomotive force is weaker. Thus, there is net energy gain.
Air-stable Curved π-Radical Based on Corannulene: Dynamic Electronic-spin Structure Induced by Temperature-dependent Conformational Changes
Authors: Ueda Akira , Ogasawara Kanako , Nishida Shinsuke , Fukui Kozo , Sato Kazunobu , Takui Takeji , Nakasuji Kazuhiro , Morita Yasushi
Published: December 2010

A new corannulene-based curved neutral π-radical bearing a tert-butylnitroxide moiety has been synthesized and isolated as an air-stable solid. Direct attachment of the spin centre to the corannulene skeleton gives rise to an extensive spin-delocalization onto the curved π-conjugated system from the nitroxide moiety. This salient electronic feature in the curved neutral radical system and its high stability have allowed us to find a dynamic electronic-spin behaviour induced by the temperature-dependent conformational change of the nitroxide moiety, as studied by liquid-phase variable-temperature electron spin resonance and 1H electron-nuclear double resonance and electron-nuclear-nuclear triple resonance spectroscopies with the help of density functional theory calculations.
Demethylation of an Allene Bearing Two Dimethoxythioxanthene Groups by Oxidation via a Vinyl Cation Intermediate
Authors: Yamaguchi Torahiko , Fuku-en Shin-ichi , Sugawara Shun , Kojima Satoshi , Yamamoto Yohsuke
Published: December 2010

With the objective of preparing an isolable triplet carbene, we have carried out the oxidation of an allenic compound bearing two thioxanthene moieties (5). Relatively weak oxidants such as Ph3C+BF4 – gave 8, which is the conjugate acid of 5, as a result of a one-electron oxidation followed by hydrogen abstraction, whereas relatively strong oxidants such as SbCl5 furnished a dicationic ketal (9) as a consequence of oxidation and demethylation. Computations on the supposed dicationic intermediate suggest that the singlet state is more stable than the triplet state by 6.7 kcal mol–1 and that the reason for this peculiarity is because the singlet state is essentially a vinyl cation stabilized by a coordinating methoxy group.
New Syntheses and Ring Expansion Reactions of Cyclobutenimines
Authors: Schaumann Ernst , Oppermann Gerrit , Stranberg Michael , Moore Harold W.
Published: December 2010

Two routes are reported for the synthesis of iminocyclobutenones having N-(het)aryl substitution: an addition/substitution sequence starting with cyclobutenediones and an aza-Wittig method. A new synthetic route to N-alkyl derivatives is also presented. This involves O-alkylation of 3-alkylamino-1,2-cyclobutenediones using Meerwein’s reagent and subsequent deprotonation under non-hydrolytic conditions. Lithium organyls were found to add to the remaining carbonyl group. The resulting tertiary alcohols undergo ring enlargement on heating in xylene to give 4-aminophenols, 4-amino-1-naphthols, or cyclopenta-annulated quinolines from 4-vinyl, 4-aryl, and 4-alkynyl derivatives, respectively.
The Pd-Catalyzed Alder - Ene Reactions of N-Protected and Propargylated 1-Amino-2-aryl-2-cyclohexenes as a New Route to C3a-Arylhexahydroindoles: Towards the Total Synthesis of Tazettine
Authors: Lehmann Anna L. , Willis Anthony C. , Banwell Martin G.
Published: December 2010

A series of N-protected and propargylated 1-amino-2-aryl-2-cyclohexenes (4) has been prepared. Several of these have been shown to undergo an intramolecular Alder–ene reaction in the presence of palladium acetate and the ligand BBEDA to afford C3a-arylhexahydroindoles of the general form 1. Certain of these products may serve as precursors to the alkaloid tazettine (2).
Supermarket revolution in Asia and emerging development strategies to include small farmers
Authors: Reardon Thomas , Timmer C. Peter , Minten Bart
Published: December 2010

A “supermarket revolution” has occurred in developing countries in the past 2 decades. We focus on three specific issues that reflect the impact of this revolution, particularly in Asia: continuity in transformation, innovation in transformation, and unique development strategies. First, the record shows that the rapid growth observed in the early 2000s in China, Indonesia, Malaysia, and Thailand has continued, and the “newcomers”—India and Vietnam—have grown even faster. Although foreign direct investment has been important, the roles of domestic conglomerates and even state investment have been significant and unique. Second, Asia's supermarket revolution has exhibited unique pathways of retail diffusion and procurement system change. There has been “precocious” penetration of rural towns by rural supermarkets and rural business hubs, emergence of penetration of fresh produce retail that took much longer to initiate in other regions, and emergence of Asian retail developing-country multinational chains. In procurement, a symbiosis between modern retail and the emerging and consolidating modern food processing and logistics sectors has arisen. Third, several approaches are being tried to link small farmers to supermarkets. Some are unique to Asia, for example assembling into a “hub” or “platform” or “park” the various companies and services that link farmers to modern markets. Other approaches relatively new to Asia are found elsewhere, especially in Latin America, including “bringing modern markets to farmers” by establishing collection centers and multipronged collection cum service provision arrangements, and forming market cooperatives and farmer companies to help small farmers access supermarkets.
Synchronous environmental and cultural change in the prehistory of the northeastern United States
Authors: Munoz Samuel E. , Gajewski Konrad , Peros Matthew C.
Published: December 2010

Climatic changes during the late Quaternary have resulted in substantial, often abrupt, rearrangements of terrestrial ecosystems, but the relationship between these environmental changes and prehistoric human culture and population size remains unclear. Using a database of archaeological radiocarbon dates alongside a network of paleoecological records (sedimentary pollen and charcoal) and paleoclimatic reconstructions, we show that periods of cultural and demographic change in the northeastern United States occurred at the same times as the major environmental-climatic transitions of that region. At 11.6, 8.2, 5.4, and 3.0 kyr BP (10
3
calendar years before present), changes in forest composition altered the distribution, availability, and predictability of food resources which triggered technological adjustments manifested in the archaeological record. Human population level has varied in response to these external changes in ecosystems, but the adoption of maize agriculture during the late Holocene also resulted in a substantial population increase. This study demonstrates the long-term interconnectedness of prehistoric human cultures and the ecosystems they inhabited, and provides a consolidated environmental-cultural framework from which more interdisciplinary research and discussion can develop. Moreover, it emphasizes the complex nature of human responses to environmental change in a temperate region.
Massive alterations of sarcoplasmic reticulum free calcium in skeletal muscle fibers lacking calsequestrin revealed by a genetically encoded probe
Authors: Canato M. , Scorzeto M. , Giacomello M. , Protasi F. , Reggiani C. , Stienen G. J. M.
Published: December 2010

The cytosolic free Ca
2+
transients elicited by muscle fiber excitation are well characterized, but little is known about the free [Ca
2+
] dynamics within the sarcoplasmic reticulum (SR). A targetable ratiometric FRET-based calcium indicator (D1ER Cameleon) allowed us to investigate SR Ca
2+
dynamics and analyze the impact of calsequestrin (CSQ) on SR [Ca
2+
] in enzymatically dissociated flexor digitorum brevis muscle fibers from WT and CSQ-KO mice lacking isoform 1 (CSQ-KO) or both isoforms [CSQ-double KO (DKO)]. At rest, free SR [Ca
2+
] did not differ between WT, CSQ-KO, and CSQ-DKO fibers. During sustained contractions, changes were rather small in WT, reflecting powerful buffering of CSQ, whereas in CSQ-KO fibers, significant drops in SR [Ca
2+
] occurred. Their amplitude increased with stimulation frequency between 1 and 60 Hz. At 60 Hz, the SR became virtually depleted of Ca
2+
, both in CSQ-KO and CSQ-DKO fibers. In CSQ-KO fibers, cytosolic free calcium detected with Fura-2 declined during repetitive stimulation, indicating that SR calcium content was insufficient for sustained contractile activity. SR Ca
2+
reuptake during and after stimulation trains appeared to be governed by three temporally distinct processes with rate constants of 50, 1–5, and 0.3 s
−1
(at 26 °C), reflecting activity of the SR Ca
2+
pump and interplay of luminal and cytosolic Ca
2+
buffers and pointing to store-operated calcium entry (SOCE). SOCE might play an essential role during muscle contractures responsible for the malignant hyperthermia-like syndrome in mice lacking CSQ.
Dynamic macrophage “probing” is required for the efficient capture of phagocytic targets
Authors: Flannagan Ronald S. , Harrison Rene E. , Yip Christopher M. , Jaqaman Khuloud , Grinstein Sergio
Published: December 2010

Binding of ligands by immunoreceptors is thought to be a passive, stochastic process. Contrary to this notion, we found that binding of IgG-opsonized particles by Fcγ receptors was inhibited in macrophages, dendritic and microglial cells by agents that interfere with actin assembly or disassembly. Changes in the lateral mobility of the receptors—assessed by single-particle tracking—or in the microelasticity of the membrane—determined by atomic-force microscopy—could not account for the effects of actin disruption on particle binding. Instead, we found that the macrophages contact their targets by actively extending actin-rich structures. Formation of these protrusions is driven by Rac and requires phosphatidylinositol 4,5-bisphosphate and phosphatidylinositol 3,4,5-trisphosphate. Capture of C3bi-opsonized as well as unopsonized targets by macrophages was also dependent on actin. Thus, phagocytes continuously probe their environment for foreign particles in a manner akin to the constitutive sampling of the fluid milieu by dendritic cells. Active probing by phagocytes is most important when confronted by scarcely opsonized and/or highly mobile targets.
Therapy-induced selective loss of leukemia-initiating activity in murine adult T cell leukemia
Authors: El Hajj Hiba , El-Sabban Marwan , Hasegawa Hideki , Zaatari Ghazi , Ablain Julien , Saab Shahrazad T. , Janin Anne , Mahfouz Rami , Nasr Rihab , Kfoury Youmna , Nicot Christophe , Hermine Olivier , Hall William , de Thé Hugues , Bazarbachi Ali
Published: December 2010

Chronic HTLV-I (human T cell lymphotropic virus type I) infection may cause adult T cell leukemia/lymphoma (ATL), a disease with dismal long-term prognosis. The HTLV-I transactivator, Tax, initiates ATL in transgenic mice. In this study, we demonstrate that an As2O3 and IFN-α combination, known to trigger Tax proteolysis, cures Tax-driven ATL in mice. Unexpectedly, this combination therapy abrogated initial leukemia engraftment into secondary recipients, whereas the primary tumor bulk still grew in the primary hosts, only to ultimately abate later on. This loss of initial transplantability required proteasome function. A similar regimen recently yielded unprecedented disease control in human ATL. Our demonstration that this drug combination targeting Tax stability abrogates tumor cell immortality but not short-term growth may foretell a favorable long-term efficiency of this regimen in patients.
Chemorepulsion by blood S1P regulates osteoclast precursor mobilization and bone remodeling in vivo
Authors: Ishii Masaru , Kikuta Junichi , Shimazu Yutaka , Meier-Schellersheim Martin , Germain Ronald N.
Published: December 2010

Sphingosine-1-phosphate (S1P), a lipid mediator enriched in blood, controls the dynamic migration of osteoclast (OC) precursors (OPs) between the blood and bone, in part via the S1P receptor 1 (S1PR1) which directs positive chemotaxis toward S1P. We show that OPs also express S1PR2, an S1P receptor which mediates negative chemotaxis (or chemorepulsion). OP-positive chemotaxis is prominent in gradients with low maximal concentrations of S1P, whereas such behavior is minimal in fields with high maximal S1P concentrations. This reverse-directional behavior is caused by S1PR2-mediated chemorepulsion acting to override S1PR1 upgradient motion. S1PR2-deficient mice exhibit moderate osteopetrosis as a result of a decrease in osteoclastic bone resorption, suggesting that S1PR2 contributes to OP localization on the bones mediated by chemorepulsion away from the blood where S1P levels are high. Inhibition of S1PR2 function by the antagonist JTE013 changed the migratory behavior of monocytoid cells, including OPs, and relieved osteoporosis in a mouse model by limiting OP localization and reducing the number of mature OCs attached to the bone surface. Thus, reciprocal regulation of S1P-dependent chemotaxis controls bone remodeling by finely regulating OP localization. This regulatory axis may be promising as a therapeutic target in diseases affecting OC-dependent bone remodeling.
RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries
Authors: Habegger Lukas , Sboner Andrea , Gianoulis Tara A. , Rozowsky Joel , Agarwal Ashish , Snyder Michael , Gerstein Mark
Published: December 2010

Summary: The advent of next-generation sequencing for functional genomics has given rise to quantities of sequence information that are often so large that they are difficult to handle. Moreover, sequence reads from a specific individual can contain sufficient information to potentially identify and genetically characterize that person, raising privacy concerns. In order to address these issues, we have developed the Mapped Read Format (MRF), a compact data summary format for both short and long read alignments that enables the anonymization of confidential sequence information, while allowing one to still carry out many functional genomics studies. We have developed a suite of tools (RSEQtools) that use this format for the analysis of RNA-Seq experiments. These tools consist of a set of modules that perform common tasks such as calculating gene expression values, generating signal tracks of mapped reads and segmenting that signal into actively transcribed regions. Moreover, the tools can readily be used to build customizable RNA-Seq workflows. In addition to the anonymization afforded by MRF, this format also facilitates the decoupling of the alignment of reads from downstream analyses.

Availability and implementation: RSEQtools is implemented in C and the source code is available at http://rseqtools.gersteinlab.org/.

Contact:  lukas.habegger@yale.edu; mark.gerstein@yale.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
MSPocket: an orientation-independent algorithm for the detection of ligand binding pockets
Authors: Zhu Hongbo , Pisabarro M. Teresa
Published: December 2010

Motivation: Identification of ligand binding pockets on proteins is crucial for the characterization of protein functions. It provides valuable information for protein–ligand docking and rational engineering of small molecules that regulate protein functions. A major number of current prediction algorithms of ligand binding pockets are based on cubic grid representation of proteins and, thus, the results are often protein orientation dependent.

Results: We present the MSPocket program for detecting pockets on the solvent excluded surface of proteins. The core algorithm of the MSPocket approach does not use any cubic grid system to represent proteins and is therefore independent of protein orientations. We demonstrate that MSPocket is able to achieve an accuracy of 75% in predicting ligand binding pockets on a test dataset used for evaluating several existing methods. The accuracy is 92% if the top three predictions are considered. Comparison to one of the recently published best performing methods shows that MSPocket reaches similar performance with the additional feature of being protein orientation independent. Interestingly, some of the predictions are different, meaning that the two methods can be considered complementary and combined to achieve better prediction accuracy. MSPocket also provides a graphical user interface for interactive investigation of the predicted ligand binding pockets. In addition, we show that overlap criterion is a better strategy for the evaluation of predicted ligand binding pockets than the single point distance criterion.

Availability: The MSPocket source code can be downloaded from http://appserver.biotec.tu-dresden.de/MSPocket/. MSPocket is also available as a PyMOL plugin with a graphical user interface.

Contact:  hongboz@biotec.tu-dresden.de; mayte@biotec.tu-dresden.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Oxford Handbook of Critical Care
Authors: Singer Mervyn , Webb Andrew
Published: December 2010

Patient-centred and practical, the Oxford Handbook of Critical Care serves the consultant, trainee, nurse, and other allied health professionals as both a reference and aide memoir, as an indispensable guide to all aspects of critical care.
Oxford Handbook of Ophthalmology
Authors: Denniston Alastair K. O. , Murray Philip I.
Published: December 2010

The Oxford Handbook of Ophthalmology offers a systematic summary of ophthalmic disease directed towards diagnosis, interim assessment and ongoing management. The content covers key areas for the trainee include clinical skills, aids to diagnosis, and investigations and their interpretation. Newly-added content includes material on refractive ophthalmology and evidence-based ophthalmology.
Protective Effect of Pioglitazone Against Endotoxin‐Induced Liver Injury through Prevention of Kupffer Cell Sensitization
Authors: Enomoto Nobuyuki , Takei Yoshiyuki , Yamashima Shunhei , Ikejima Kenichi , Kitamura Tsuneo , Sato Nobuhiro
Published: December 2010

Abstract: Background: Activation of Kupffer cells by lipopolysaccharide (LPS) plays a pivotal role in the onset of pathophysiological events that occur during endotoxemia and intracellular calcium ([Ca2+]i) is involved in LPS‐stimulated cytokine production. TNF‐α is produced exclusively by the monocyte‐macrophage lineage, including Kupffer cells, and pioglitazone has been shown to reduce TNF‐α production from macrophages. On the other hand, there is increasing evidence that TNF‐α plays a major role in the initiation and/or progression of multiple organ failure syndrome. Therefore, the purpose of this work was to determine whether pioglitazone could prevent LPS‐induced liver injury

Methods: Rats were given a single oral dose of pioglitazone (500 μg/kg). To assess the sensitization of Kupffer cells, LPS (5 mg/kg) was administered IV and transaminases were evaluated 24 hr later. Kupffer cells were isolated 2 hr after pioglitazone treatment. After addition of LPS, [Ca2+]i was measured using a microspectrofluorometer with the fluorescent indicator, fura‐2, and TNF‐α was measured by ELISA

Results: LPS increased transaminases dramatically and elevation of serum transaminases were diminished markedly by pioglitazone. In isolated Kupffer cells, the LPS‐induced increase in [Ca2+]i and TNF‐α production were suppressed by treated with pioglitazone

Conclusions: Therefore, it is concluded that pioglitazone prevents LPS induced liver injury via a mechanism dependent on suppression of TNF‐α production from Kupffer cells.
Comparing the performance of multiple mitochondrial genes in the analysis of Australian freshwater fishes
Authors: Page T. J. , Hughes J. M.
Published: December 2010

In this study, four mitochondrial genes (cytochrome oxidase I, ATPase, cytochrome b and control region) were amplified from most of the fish species found in the fresh waters of south‐eastern Queensland, Australia. The performance of these different gene regions was compared in terms of their ability to cluster fish families together in a neighbour‐joining tree, both individually by gene and in all combinations. The relative divergence rates of each of these genes were also calculated. The three coding genes (cytochrome oxidase I, ATPase and cytochrome b) recovered similar number of families and had broadly similar divergence rates. ATPase diverged a little more quickly than cytochrome oxidase I and cytochrome b slightly more slowly than cytochrome oxidase I. All two‐gene combinations recovered the same number of families. Results from the control region were much more variable, and, although generally possessing more diversity than the other regions, were sometimes less variable.
Neural correlates of verbal learning in adolescent alcohol and marijuana users
Authors: Schweinsburg Alecia Dager , Schweinsburg Brian C. , Nagel Bonnie J. , Eyler Lisa T. , Tapert Susan F.
Published: December 2010

Aims  Alcohol and marijuana are the most widely used intoxicants among adolescents, yet their potential unique and interactive influences on the developing brain are not well established. Brain regions subserving learning and memory undergo continued maturation during adolescence, and may be particularly susceptible to substance‐related neurotoxic damage. In this study, we characterize brain response during verbal learning among adolescent users of alcohol and marijuana.

Design  Participants performed a verbal paired associates encoding task during functional magnetic resonance imaging (fMRI) scanning.

Setting  Adolescent subjects were recruited from local public schools and imaged at a university‐based fMRI center.

Participants  Participants were 74 16–18‐year‐olds, divided into four groups: (i) 22 controls with limited alcohol and marijuana experience, (ii) 16 binge drinkers, (iii) eight marijuana users and (iv) 28 binge drinking marijuana users.

Measurements  Diagnostic interview ensured that all teens were free from neurological or psychiatric disorders; urine toxicology and breathalyzer verified abstinence for 22–28 days before scanning; a verbal paired associates task was administered during fMRI.

Findings  Groups demonstrated no differences in performance on the verbal encoding task, yet exhibited different brain response patterns. A main effect of drinking pointed to decreased inferior frontal but increased dorsal frontal and parietal fMRI response among binge drinkers (corrected P < 0.05). There was no main effect of marijuana use. Binge drinking × marijuana interactions were found in bilateral frontal regions (corrected P < 0.05), where users of either alcohol or marijuana showed greater response than non‐users, but users of both substances resembled non‐users.

Conclusions  Adolescent substance users demonstrated altered fMRI response relative to non‐using controls, yet binge drinking appeared to be associated with more differences in activation than marijuana use. Alcohol and marijuana may have interactive effects that alter these differences, particularly in prefrontal brain regions.
Organ identity and environmental conditions determine the effectiveness of nonhost resistance in the interaction between Arabidopsis thaliana and Magnaporthe oryzae
Authors: SCHREIBER CHRISTINE , SLUSARENKO ALAN J. , SCHAFFRATH ULRICH
Published: December 2010

Mechanisms leading to nonhost resistance of plants against nonadapted pathogens are thought to have great potential for the future management of agriculturally important diseases. In this article, we report an investigation of nonhost resistance motivated by the advantages of studying an interaction between two model organisms, namely Arabidopsis thaliana and Magnaporthe oryzae. During the course of our studies, however, we discovered an unexpected plasticity in the responses of Arabidopsis against this ostensibly nonhost pathogen. Thus, we elucidated that certain experimental conditions, such as the growth of plants under long days at constantly high humidity and the use of high inoculum concentrations of M. oryzae conidia, forced the interaction in leaves of some Arabidopsis ecotypes towards increased compatibility. However, sporulation was never observed. Furthermore, we observed that roots were generally susceptible to M. oryzae, whereas leaves, stems and hypocotyls were not infected. It must be concluded, therefore, that Arabidopsis roots lack an effective defence repertoire against M. oryzae, whereas its leaves possess such nonhost defence mechanisms. In summary, our findings point to organ‐specific determinants and environmental conditions influencing the effectiveness of nonhost resistance in plants.
Underwater‐seal nasogastric tube drainage to relieve gastric distension caused by air swallowing
Authors: Solomon A. W. , Bramall J. C. , Ball J.
Published: December 2010

Air swallowing can occur as a psychogenic phenomenon, because of abnormal anatomy, or during non‐invasive positive pressure ventilation. Gross distension of the stomach with air can have severe consequences for the respiratory and gastrointestinal systems. We report the case of a 62‐year‐old man with severe dynamic hyperinflation due to chronic obstructive pulmonary disease, who developed respiratory failure requiring intubation a few hours after radical prostatectomy. Following a percutaneous tracheostomy and weaning of sedation on day six, his abdomen began to enlarge progressively. X‐rays revealed massive gastric distension due to air swallowing, which continued despite all efforts to optimise therapy. The use of an underwater seal drainage system on a nasogastric tube improved ventilation and ultimately aided weaning from mechanical support.
Allogeneic haematopoietic stem cell transplantation for myelofibrosis: a report of the Société Française de Greffe de Moelle et de Thérapie Cellulaire (SFGM‐TC)
Authors: Robin Marie , Tabrizi Reza , Mohty Mohamad , Furst Sabine , Michallet Mauricette , Bay Jacques‐Olivier , Cahn Jean‐Yves , De Coninck Eric , Dhedin Nathalie , Bernard Marc , Rio Bernard , Buzyn Agnès , Huynh Anne , Bilger Karin , Bordigoni Pierre , Contentin Nathalie , Porcher Raphaël , Socié Gérard , Milpied Noel
Published: December 2010

Allogeneic haematopoietic stem‐cell transplantation (HSCT) is the only curative treatment for myelofibrosis. We report an analysis of the Société Française de Greffe de Moelle et de Thérapie Cellulaire (SFGM‐TC) registry including patients with myelofibrosis transplanted between 1997 and 2008. Potential risk factors affecting engraftment, non‐relapse mortality (NRM), overall survival (OS) and progression‐free survival (PFS) were analysed. One hundred and forty‐seven patients, aged 20–68 (median 53) years, diagnosed with primary (53%) or secondary myelofibrosis underwent HSCT; 59% of patients were transplanted from a matched sibling donor. The conditioning regimen was myeloablative in 31% of patients. Ninety percent of the patients engrafted. Factors affecting favourably engraftment were splenectomy before HSCT, human leucocyte antigen (HLA) matched sibling donor, peripheral stem cell use as source of stem cells and absence of pre‐transplant thrombocytopenia. Four‐year OS, PFS and NRM survival were 39% (95%confidence interval [CI]: 31–50), 32% (95%CI: 24–43) and 39% (95%CI 30–48), respectively. Multivariate analysis indicated that HLA‐identical sibling donor, chronic phase disease and splenectomy in men had favourable impact on OS.
Epistemic activities and collaborative learning: towards an analytical model for studying knowledge construction in networked learning settings
Authors: Zenios Maria
Published: December 2010

The aim of this paper is to provide an analytical model for studying knowledge creation among geographically dispersed students in an online postgraduate programme by using the concept of epistemic activity. Rooted in qualitative methodologies, it takes a case study approach which strengthens the grounding of theory on social learning by using triangulation of evidence from online discussions and seven semi‐structured interviews. The analytical model that emerges, distinguishes a set of moves that serve understanding negotiation of meaning and co‐construction of knowledge in online discussion. The findings of the study suggest that knowledge advancement processes can be understood as part of identifying key strategies in the form of online epistemic activities for postgraduate learners in a networked learning context. The paper offers a conceptual account for researching knowledge construction in higher education.
Multifaceted assessment of species validity in the Dasymutilla bioculata species group (Hymenoptera: Mutillidae)
Authors: WILLIAMS KEVIN A. , MANLEY DONALD G. , PILGRIM ERIK M. , VON DOHLEN CAROL D. , PITTS JAMES P.
Published: December 2010

This study examines the validity of the ten species and eight subspecies composing the Dasymutilla bioculata species group. Four lines of evidence are examined: morphological data derived from both sexes; behavioural data derived from the study of mating pairs; geographic distribution; and molecular data derived from the internal transcribed spacers 1 and 2 of the nuclear ribosomal RNA cistron (ITS1 and ITS2). Morphological studies reveal that none of the taxa in question can be consistently diagnosed by any synapomorphies or unique combinations of characters. Mating studies reveal that males of single nominal taxa are attracted to females of multiple nominal taxa, and that females of single nominal taxa attract multiple males. None of the nominal taxa are geographically isolated from the others. Genetic distances between these taxa are significantly lower than those seen in interspecific comparisons of other Dasymutilla species. Based on this evidence, we infer that the taxa in question share a recent common ancestor, and cannot be adequately differentiated using any of the available data sources. Therefore, employing the phylogenetic species concept, Dasymutilla bimaculata Manley & Pitts, Dasymutilla chiron chiron (Blake), Dasymutilla chiron ursula (Cresson), Dasymutilla creusa creusa (Cresson), Dasymutilla creusa bellona (Cresson), Dasymutilla lepeletierii (Fox), Dasymutilla medea (Cresson), Dasymutilla melanippe melanippe Mickel, Dasymutilla melanippe conformis Mickel, Dasymutilla praegrandis praegrandis Mickel, Dasymutilla praegrandis russata Mickel, Dasymutilla pyrrhus (Fox) and Dasymutilla sulcatulla Mickel must be considered junior synonyms of Dasymutilla bioculata (Cresson). We also discuss the identification of this species, as well as subspecific relationships and species‐group implications.