bluuebunny/crossref_metadata_2025 huggingface dataset:
Continuously perfused microbubble array for 3D tumor spheroid model
Authors: Agastin Sivaprakash , Giang Ut-Binh T. , Geng Yue , DeLouise Lisa A. , King Michael R.
Published: June 2011

Multi-cellular tumor spheroids (MCTSs) have been established as a 3D physiologically relevant tumor model for drug testing in cancer research. However, it is difficult to control the MCTS testing parameters and the entire process is time-consuming and expensive. To overcome these limitations, we developed a simple microfluidic system using polydimethylsiloxane (PDMS) microbubbles to culture tumor spheroids under physiological flow. The flow characteristics such as streamline directions, shear stress profile, and velocity profile inside the microfluidic system were first examined computationally using a COMSOL simulation. Colo205 tumor spheroids were created by a modified hanging drop method and maintained inside PDMS microbubble cavities in perfusion culture. Cell viability inside the microbubbles was examined by live cell staining and confocal imaging. E-selectin mediated cell sorting of Colo205 and MDA-MB-231 cell lines on functionalized microbubble and PDMS surfaces was achieved. Finally, to validate this microfluidic system for drug screening purposes, the toxicity of the anti-cancer drug, doxorubicin, on Colo205 cells in spheroids was tested and compared to cells in 2D culture. Colo205 spheroids cultured in flow showed a threefold increase in resistance to doxorubicin compared to Colo205 monolayer cells cultured under static conditions, consistent with the resistance observed previously in other MCTS models. The advantages presented by our microfluidic system, such as the ability to control the size uniformity of the spheroids and to perform real-time imaging on cells in the growth platform, show potential for high throughput drug screening development.
Fast fiber-optic multi-wavelength pyrometer
Authors: Fu Tairan , Tan Peng , Pang Chuanhe , Zhao Huan , Shen Yi
Published: June 2011

A fast fiber-optic multi-wavelength pyrometer was developed for the ultraviolet-visible-near infrared spectra from 200 nm to 1700 nm using a CCD detector and an InGaAs detector. The pyrometer system conveniently and quickly provides the sufficient choices of multiple measurement wavelengths using optical diffraction, which avoids the use of narrow-band filters. Flexible optical fibers are used to transmit the radiation so the pyrometer can be used for temperature measurements in harsh environments. The setup and calibrations (wavelength calibration, nonlinearity calibration, and radiation response calibration) of this pyrometer system were described. Development of the multi-wavelength pyrometer involved optimization of the bandwidth and temperature discrimination of the multiple spectra data. The analysis results showed that the wavelength intervals, ΔλCCD = 30 nm and ΔλInGaAs = 50 nm, are the suitable choices as a tradeoff between the simple emissivity model assumption and the multiple signal discrimination. The temperature discrimination was also quantificationally evaluated for various wavelengths and temperatures. The measurement performance of the fiber-optic multi-wavelength pyrometer was partially verified through measurements with a high-temperature blackbody and actual hot metals. This multi-wavelength pyrometer can be used for remote high-temperature measurements.
Ab initio characterization of the Ne–I2 van der Waals complex: Intermolecular potentials and vibrational bound states
Authors: Delgado-Tellez Laura , Valdés Álvaro , Prosmiti Rita , Villarreal Pablo , Delgado-Barrio Gerardo
Published: June 2011

A theoretical study of the potential energy surface and bound states is performed for the ground state of the NeI2 van der Waals (vdW) complex. The three-dimensional interaction energies are obtained from ab initio coupled-cluster, coupled-cluster single double (triple)/complete basis set, calculations using large basis sets, of quadruple- through quintuple-zeta quality, in conjunction with relativistic effective core potentials for the heavy iodine atoms. For the analytical representation of the surface two different schemes, based on fitting and interpolation surface generation techniques, are employed. The surface shows a double-minimum topology for linear and T-shaped configurations. Full variational quantum mechanical calculations are carried out using the model surfaces, and the vibrationally averaged structures and energetics for the NeI2 isomers are determined. The accuracy of the potential energy surfaces is validated by a comparison between the present results and the corresponding experimental data available. In lieu of more experimental measurements, we also report our results/predictions on higher bound vibrational vdW levels, and the influence of the employed surface on them is discussed.
Electron hopping interactions in amorphous ZnO films probed by x-ray absorption near edge structure analysis
Authors: Cho Deok-Yong , Kim Jeong Hwan , Hwang Cheol Seong
Published: June 2011

The x-ray absorption near edge structures of amorphous ZnO (a-ZnO) films were examined. The near-edge structure, which reflects the virtual electron hopping interactions in the photoabsorption final states, increased in intensity compared to crystalline ZnO. Theoretical path-by-path analyses revealed that this reflects the extinction of the multiple hopping processes found in paths such as Zn→O→O′→Zn or Zn→O→Zn′→Zn while the Zn–(O or Zn) hopping interactions remain. This suggests that the structural disorders in a-ZnO can induce the localization of the conduction band through the limited hopping interactions.
Adhesive transitions in Newton black films: A computer simulation study
Authors: Bresme Fernando , Chacón Enrique , Martínez Héctor , Tarazona Pedro
Published: June 2011

We report molecular dynamics simulations of Newton black films (NBFs), ultra thin films of aqueous solutions stabilized with two monolayers of ionic surfactants, sodium dodecyl sulfate. We show that at low water content conditions and areas per surfactant corresponding to experimental estimates in NBFs, homogeneous films undergo an adhesion “transition,” which results in a very thin adhesive film coexisting with a thicker film. We identify the adhesive film with the equilibrium structure of the Newton black film. We provide here a direct microscopic view of the formation of these important structures, which have been observed in experimental studies of emulsions and foams. We also report a detailed investigation of the structural properties and interfacial fluctuation spectrum of the adhesive film. Our analysis relies on the definition of an “intrinsic surface,” which is used to remove the averaging effect that the capillary waves have on the film properties.
Nanocomposite exchange-spring magnet synthesized by gas phase method: From isotropic to anisotropic
Authors: Liu Xiaoqi , He Shihai , Qiu Jiao-Ming , Wang Jian-Ping
Published: June 2011

The fabrication of anisotropic nanocomposite exchange-spring magnets is demonstrated experimentally by using a gas-phase nanoparticle deposition technique. High resolution transmission electron microscopy images prove the experimental easy-axis definition of embedded hard magnetic nanoparticles in soft magnetic matrix. Exchange coupling between the hard and soft phases is confirmed by measuring recoil loops and δ M-H curve of the anisotropic FePt/Fe0.8Ni0.2 nanocomposite. The magnetic energy product for the anisotropic exchange-spring magnet is 224% higher than the isotropic case.
Formation of Zn defects in willemite-type Zn2GeO4 during supercooled liquid-crystal phase transition
Authors: Takahashi Yoshihiro , Ando Masataka , Ihara Rie , Fujiwara Takumi
Published: June 2011

This letter elucidates the formation mechanism of interstitial Zn defects in wide band-gap semiconductive willemite-type Zn2GeO4 via nanocrystallization in a zincogermanate glass. The results of time-development structural observations suggest that Zn2GeO4 nanocrystals precipitate in the nanometric Zn-condensed region, which occurs prior to nanocrystallization. The Zn-condensed environment probably promotes the capture of Zn ions in the interstitial sites of the Zn2GeO4 structure during the structural ordering of the supercooled liquid phase. The Zn-condensation mechanism is also discussed.
Anisotropy induced large exchange bias behavior in ball milled Ni–Co–Mn–Sb alloys
Authors: Nayak Ajaya K. , Sahoo Roshnee , Suresh K. G. , Nigam A. K. , Chen X. , Ramanujan R. V.
Published: June 2011

We report the effect of decrease in the grain size on the structural, magnetic and exchange bias (EB) behavior in ball milled Ni50−xCoxMn38Sb12 (x=0 and 5) Heusler alloys. The existence of a wide range of grain sizes in the ball milled samples results in dramatic changes in the structural and magnetic properties. For x=0, a large EB field of 3.2 kOe is observed in the ball milled sample, compared to a value of 245 Oe of the bulk sample. This increase is attributed to the enhanced exchange coupling between the soft and hard magnetic particles.
Effects of substrate orientation on the structural and electronic properties of epitaxial graphene on SiC(0001)
Authors: Robinson Joshua A. , Trumbull Kathleen A. , LaBella Michael , Cavalero Randall , Hollander Matthew J. , Zhu Michael , Wetherington Maxwell T. , Fanton Mark , Snyder David W.
Published: June 2011

We investigate graphene transport and structural properties as a function of silicon carbide (SiC) wafer orientation. Terrace step edge density is found to increase with wafer misorientation from SiC(0001). This results in a monotonic increase in average graphene thickness, as well as a 30% increase in carrier density and 40% decrease in mobility up to 0.45° miscut toward (11¯00). Beyond 0.45°, average thickness and carrier density continues to increase; however, carrier mobility is similar to low-miscut angles, suggesting that the interaction between graphene and SiC(0001) may be fundamentally different that of graphene/SiC(11¯0n).
High-efficiency silicon-compatible photodetectors based on Ge quantum dots
Authors: Cosentino S. , Liu Pei , Le Son T. , Lee S. , Paine D. , Zaslavsky A. , Pacifici D. , Mirabella S. , Miritello M. , Crupi I. , Terrasi A.
Published: June 2011

We report on high responsivity, broadband metal/insulator/semiconductor photodetectors with amorphous Ge quantum dots (a-Ge QDs) as the active absorbers embedded in a silicon dioxide matrix. Spectral responsivities between 1–4 A/W are achieved in the 500–900 nm wavelength range with internal quantum efficiencies (IQEs) as high as ∼700%. We investigate the role of a-Ge QDs in the photocurrent generation and explain the high IQE as a result of transport mechanisms via photoexcited QDs. These results suggest that a-Ge QDs are promising for high-performance integrated optoelectronic devices that are fully compatible with silicon technology in terms of fabrication and thermal budget.
De-embedding parasitic elements of GaN nanowire metal semiconductor field effect transistors by use of microwave measurements
Authors: Gu Dazhen , Wallis T. M. , Blanchard P. , Lim Sang-Hyun , Imtiaz A. , Bertness K. A. , Sanford N. A. , Kabos P.
Published: June 2011

We present a de-embedding roadmap for extracting parasitic elements of a nanowire (NW) metal semiconductor field effect transistor (MESFET) from full two-port scattering-parameter measurements in 0.1–25 GHz range. The NW MESFET is integrated in a microwave coplanar waveguide structure. A conventional MESFET circuit model is modified to include capacitors of small value that is non-negligible in NW devices. We follow a step-by-step removal of external elements and an iteration search for optimized model data. The fitted model indicates good agreement with experimental data. This letter reflects a significant step toward full circuit modeling of NW MESFETs under normal operating conditions.
Rare earth chalcogenide Ce3Te4 as high efficiency high temperature thermoelectric material
Authors: Wang Xiaochun , Yang Ronggui , Zhang Yong , Zhang Peihong , Xue Yu
Published: June 2011

The electronic band structures of Ce3Te4 have been studied using the first-principles density-functional theory calculations. It is found that the density of states of Ce3Te4 has a very high delta-shaped peak appearing 0.21 eV above the Fermi level, which mainly comes from the f orbital electrons of the rare-earth element Ce. Using the simple theory proposed by Mahan and Sofo, [Proc. Natl. Acad. Sci. U.S.A. 93, 7436 (1996)], we obtain an ideal value of zT=13.5 for Ce3Te4 at T=1200 K, suggesting that the rare-earth chalcogenide Ce3Te4 could be a promising high efficiency high temperature thermoelectric material.
Rise and fall of defect induced ferromagnetism in SiC single crystals
Authors: Li Lin , Prucnal S. , Yao S. D. , Potzger K. , Anwand W. , Wagner A. , Zhou Shengqiang
Published: June 2011

6H–SiC (silicon carbide) single crystals containing VSi–VC divacancies are investigated with respect to magnetic and structural properties. We found that an initial increase in structural disorder leads to pronounced ferromagnetic properties at room temperature. Further introduction of disorder lowers the saturation magnetization and is accompanied with the onset of lattice amorphization. Close to the threshold of full amorphization, also divacancy clusters are formed and the saturation magnetization nearly drops to zero.
On the mechanical efficiency of dielectric barrier discharge plasma actuators
Authors: Giepman R. H. M. , Kotsonis M.
Published: June 2011

The mechanical power production and electrical power consumption of the dielectric barrier discharge plasma actuator is investigated for different operating conditions. The ratio of these two values delivers the mechanical efficiency of the actuator as a flow acceleration device. The general trend is that higher carrier frequencies and voltages lead to higher values of the efficiency. The values that were found for the mechanical efficiency are very small, the highest recorded value is only 0.18%.
Phase behavior of binary symmetric mixtures in pillared slit-like pores: A density functional approach
Authors: Pizio O. , Sokołowski S. , Sokołowska Z.
Published: June 2011

Density functional approach is applied to study the phase behavior of symmetric binary Lennard-Jones(12,6) mixtures in pillared slit-like pores. Our focus is in the evaluation of the first-order phase transitions in adsorbed phases and lines delimiting mixed and demixed adsorbed phases. The scenario of phase changes is sensitive to the pore width, to the energy of fluid-solid interaction, the amount, and the length of the pillars. Quantitative trends and qualitative changes of the phase diagrams topology are examined depending on the values of these parameters. The presence of pillars provides additional excluded volume effects, besides the confinement due to the pore walls. The effects of attraction between fluid species and pillars counteract this additional confinement. We have observed that both the increasing surface pillar density and the augmenting strength of fluid-solid interactions can qualitatively change the phase diagrams topology for the model with sufficiently strong trends for demixing. If the length of pillars is sufficiently large comparing to the pore width at low temperatures, we observe additional phase transitions of the first and second order due to the symmetry breaking of the distribution of chain segments and fluid species with respect to the slit-like pore center. Re-entrant symmetry changes and additional critical points then are observed.
Electric field modulation of magnetoresistance in multiferroic heterostructures for ultralow power electronics
Authors: Liu Ming , Li Shandong , Obi Ogheneyunume , Lou Jing , Rand Scott , Sun Nian X.
Published: June 2011

An energy-efficiency technique for electrically modulating magnetoresistance was demonstrated in multiferroic anisotropic magnetoresistance (AMR) and giant magnetoresistance (GMR) heterostructures. A giant electric field (E-field) induced magnetic anisotropy caused by a strong magnetoelectric coupling was utilized to control the orientation of magnetization and thus dynamically manipulate magnetoresistance in AMR and GMR devices. A multiband tunable AMR field sensor was designed and developed to dramatically enhance the measurement range by 15 times. In addition, two types of E-field determination of GMR in spin-valve structures are studied. The results indicate an energy efficiency approach to controlling magnetoresistance by E-field rather than magnetic field, which shows great potential for novel low power electronic and spintronic devices.
Vibrational relaxation of azide ions in liquid-to-supercritical water
Authors: Olschewski Martin , Knop Stephan , Lindner Jörg , Vöhringer Peter
Published: June 2011

The dynamics of vibrational energy relaxation (VER) of the aqueous azide anion was studied over a wide temperature (300 K ≤ T ≤ 663 K) and density (0.6 g cm−3 ≤ ρ ≤ 1.0 g cm−3) range thereby covering the liquid and the supercritical phase of the water solvent. Femtosecond mid-infrared spectroscopy on the ν3 band associated with the asymmetric stretching vibration of the azide anion was used to monitor the relaxation dynamics in a time-resolved fashion. The variation of the vibrational relaxation rate constant with temperature and density was found to be rather small. Surprisingly, the simple isolated binary collision model is able to fully reproduce the experimentally observed temperature and density dependence of the relaxation rate provided a local density correction around the vibrationally excited solute based on classical molecular dynamics simulations is used. The simulations further suggest that head-on collisions of the solvent with the terminal nitrogen atoms rather than side-on collisions with the central nitrogen atom of the azide govern the vibrational energy relaxation of this system. Finally, the importance of hydrogen bonding for the VER dynamics in this system is briefly discussed.
Clouds of atoms with opposite spins bounce off one another
Authors: Levi Barbara Goss
Published: June 2011

A gas of strongly interacting ultracold atoms offers extremely high resistance to the flow of spin; its spin diffusion reaches a minimum, universal value.
A mirror gives light an extra twist
Authors: Smart Ashley G.
Published: June 2011

The contorted optical field aids the differentiation of chiral molecules, a result that confirms ideas first proposed last year.
Singapore applies itself to science
Authors: Day Charles
Published: June 2011

Despite its small size, the Lion City has become an influential exemplar of investing in science to promote industry.
Listening in on the listening brain
Authors: Kraus Nina
Published: June 2011

The measured response of the auditory brainstem to complex aural stimuli does more than reveal hearing acumen. It also gives insight into how experience molds the perception of sound.
The City as Assemblage: Dwelling and Urban Space
Authors: McFarlane Colin
Published: June 2011

In this paper I consider what ‘assemblage’ might offer a conception of the city. Although assemblage is gaining currency in geography and beyond, there has been little effort to consider how it might be conceptualised and what its specificity might be. In offering a conceptualisation of assemblage, I bring assemblage into conversation with particular debates around dwelling and argue, first, that assemblage provides a useful basis for thinking of the city as a dwelling process and, second, that it is particularly useful for conceiving the spatiality of the city as processual, relational, mobile, and unequal. Despite their distinct intellectual histories, I suggest there is a productive debate to be had by bringing assemblage and dwelling into dialogue. I examine some of the ways in which assemblage and dwelling might interact and reflect on particular moments of fieldwork conducted in São Paulo and Mumbai and on diverse examples ranging from ‘slum’ housing to urban policy and mobility.
Bidirectional plasticity in the primate inferior olive induced by chronic ethanol intoxication and sustained abstinence
Authors: Welsh John P. , Han Victor Z. , Rossi David J. , Mohr Claudia , Odagiri Misa , Daunais James B. , Grant Kathleen A.
Published: June 2011

The brain adapts to chronic ethanol intoxication by altering synaptic and ion-channel function to increase excitability, a homeostatic counterbalance to inhibition by alcohol. Delirium tremens occurs when those adaptations are unmasked during withdrawal, but little is known about whether the primate brain returns to normal with repeated bouts of ethanol abuse and abstinence. Here, we show a form of bidirectional plasticity of pacemaking currents induced by chronic heavy drinking within the inferior olive of cynomolgus monkeys. Intracellular recordings of inferior olive neurons demonstrated that ethanol inhibited the tail current triggered by release from hyperpolarization (

I
tail

). Both the slow deactivation of hyperpolarization-activated cyclic nucleotide-gated channels conducting the hyperpolarization-activated inward current and the activation of Ca
v
3.1 channels conducting the T-type calcium current (

I
T

) contributed to

I
tail

, but ethanol inhibited only the

I
T

component of

I
tail

. Recordings of inferior olive neurons obtained from chronically intoxicated monkeys revealed a significant up-regulation in

I
tail

that was induced by 1 y of daily ethanol self-administration. The up-regulation was caused by a specific increase in

I
T

which (
i
) greatly increased neurons’ susceptibility for rebound excitation following hyperpolarization and (
ii
) may have accounted for intention tremors observed during ethanol withdrawal. In another set of monkeys, sustained abstinence produced the opposite effects: (
i
) a reduction in rebound excitability and (
ii
) a down-regulation of I

tail

caused by the down-regulation of both the hyperpolarization-activated inward current and

I
T

. Bidirectional plasticity of two hyperpolarization-sensitive currents following chronic ethanol abuse and abstinence may underlie persistent brain dysfunction in primates and be a target for therapy.
Structural model of the TRPP2/PKD1 C-terminal coiled-coil complex produced by a combined computational and experimental approach
Authors: Zhu Jiang , Yu Yong , Ulbrich Maximilian H. , Li Ming-hui , Isacoff Ehud Y. , Honig Barry , Yang Jian
Published: June 2011

Autosomal dominant polycystic kidney disease (ADPKD) is caused by mutations in TRPP2 and PKD1, which form an ion channel/receptor complex containing three TRPP2 and one PKD1. A TRPP2 C-terminal coiled-coil trimer, critical for the assembly of this complex, associates with a single PKD1 C-terminal coiled-coil. Many ADPKD pathogenic mutations result in the abolishment of the TRPP2/PKD1 coiled-coil complex. To gain molecular and functional insights into this heterotetrameric complex, we computationally constructed a structural model by using a two-step docking strategy, based on a known crystal structure of the TRPP2 coiled-coil trimer. The model shows that this tetrameric complex has a novel di-trimer configuration: An upstream trimer made of three TRPP2 helices and a downstream trimer made of two TRPP2 helices and one PKD1 helix. Mutagenesis and biochemical analysis identified critical TRPP2/PKD1 interface contacts essential for the heteromeric coiled-coil complex. Mutation of these interface positions in the full-length proteins showed that these interactions were critical for the assembly of the full-length complex in cells. Our results provide a means to specifically weaken the TRPP2 and PKD1 association, thus facilitating future in vitro and in vivo studies on the functional importance of this association.
Evolutionarily conserved surface residues constitute actin binding sites of tropomyosin
Authors: Barua Bipasha , Pamula Melissa C. , Hitchcock-DeGregori Sarah E.
Published: June 2011

Tropomyosin (Tm) is a two-chained, α-helical coiled-coil protein that associates end-to-end to form a continuous strand along actin filaments and regulates the functions and stability of actin in eukaryotic muscle and nonmuscle cells. Mutations in Tm cause skeletal and cardiac myopathies. We applied a neoteric molecular evolution approach to gain insight into the fundamental unresolved question of what makes the Tm coiled coil an actin binding protein. We carried out a phylogenetic analysis of 70 coding sequences of Tm genes from 26 animal species, from cnidarians to chordates, and evaluated the substitution rates (ω) at individual codons to identify conserved sites. The most conserved residues at surface
b
,
c
,
f
heptad repeat positions were mutated in rat striated muscle αTm and expressed in
Escherichia coli
. Each mutant had 3–4 sites mutated to Ala within the first half or the second half of periods 2–6. Actin affinity and thermodynamic stability were determined in vitro. Mutations in the first half of periods 2, 4, and 5 resulted in the largest reduction in actin affinity (> 4-fold), indicating these mutations include residues in actin-binding sites. Mutations in the second half of the periods had a ≤ 2-fold effect on affinity indicating these residues may be involved in other conserved regulatory functions. The structural relevance of these results was assessed by constructing molecular models for the actin-Tm filament. Molecular evolution analysis is a general approach that may be used to identify potential binding sites of a protein for a conserved protein.
Structural basis for the neutralization and genotype specificity of hepatitis E virus
Authors: Tang Xuhua , Yang Chunyan , Gu Ying , Song Cuiling , Zhang Xiao , Wang Yingbin , Zhang Jun , Hew Choy Leong , Li Shaowei , Xia Ningshao , Sivaraman J.
Published: June 2011

Hepatitis E virus (HEV) causes acute hepatitis in humans, predominantly by contamination of food and water, and is characterized by jaundice and flu-like aches and pains. To date, no vaccines are commercially available to prevent the disease caused by HEV. Previously, we showed that a monoclonal antibody, 8C11, specifically recognizes a neutralizing conformational epitope on HEV genotype I. The antibody 8C11 blocks the virus-like particle from binding to and penetrating the host cell. Here, we report the complex crystal structure of 8C11 Fab with HEV E2s(I) domain at 1.9 Å resolution. The 8C11 epitopes on E2s(I) were identified at Asp
496
-Thr
499
, Val
510
-Leu
514
, and Asn
573
-Arg
578
. Mutations and cell-model assays identified Arg
512
as the most crucial residue for 8C11 interaction with and neutralization of HEV. Interestingly, 8C11 specifically neutralizes HEV genotype I, but not the other genotypes. Because HEV type I and IV are the most abundant genotypes, to understand this specificity further we determined the structure of E2s(IV) at 1.79 Å resolution and an E2s(IV) complex with 8C11 model was generated. The comparison between the 8C11 complexes with type I and IV revealed the key residues that distinguish these two genotypes. Of particular interest, the residue at amino acid position 497 at the 8C11 epitope region of E2s is distinct among these two genotypes. Swapping this residue from one genotype to another inversed the 8C11 reactivity, demonstrating the essential role played by amino acid 497 in the genotype recognition. These studies may lead to the development of antibody-based drugs for the specific treatment against HEV.
Convexity of quantum
χ
2
-divergence
Authors: Hansen Frank
Published: June 2011

The general quantum
χ
2
-divergence has recently been introduced by Temme et al. [Temme K, Kastoryano M, Ruskai M, Wolf M, Verstrate F (2010)
J Math Phys
51:122201] and applied to quantum channels (quantum Markov processes). The quantum
χ
2
-divergence is not unique, as opposed to the classical
χ
2
-divergence, but depends on the choice of quantum statistics. It was noticed that the elements in a particular one-parameter family

of quantum
χ
2
-divergences are convex functions in the density matrices (
ρ
,
σ
), thus mirroring the convexity of the classical
χ
2
(
p
,
q
)-divergence in probability distributions (
p
,
q
). We prove that any quantum
χ
2
-divergence is a convex function in its two arguments.
Multiplexed RNA structure characterization with selective 2′-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)
Authors: Lucks Julius B. , Mortimer Stefanie A. , Trapnell Cole , Luo Shujun , Aviran Sharon , Schroth Gary P. , Pachter Lior , Doudna Jennifer A. , Arkin Adam P.
Published: June 2011

New regulatory roles continue to emerge for both natural and engineered noncoding RNAs, many of which have specific secondary and tertiary structures essential to their function. Thus there is a growing need to develop technologies that enable rapid characterization of structural features within complex RNA populations. We have developed a high-throughput technique, SHAPE-Seq, that can simultaneously measure quantitative, single nucleotide-resolution secondary and tertiary structural information for hundreds of RNA molecules of arbitrary sequence. SHAPE-Seq combines
s
elective 2′-
h
ydroxyl
a
cylation analyzed by
p
rimer
e
xtension (SHAPE) chemistry with multiplexed paired-end deep sequencing of primer extension products. This generates millions of sequencing reads, which are then analyzed using a fully automated data analysis pipeline, based on a rigorous maximum likelihood model of the SHAPE-Seq experiment. We demonstrate the ability of SHAPE-Seq to accurately infer secondary and tertiary structural information, detect subtle conformational changes due to single nucleotide point mutations, and simultaneously measure the structures of a complex pool of different RNA molecules. SHAPE-Seq thus represents a powerful step toward making the study of RNA secondary and tertiary structures high throughput and accessible to a wide array of scientific pursuits, from fundamental biological investigations to engineering RNA for synthetic biological systems.
Modeling and automation of sequencing-based characterization of RNA structure
Authors: Aviran Sharon , Trapnell Cole , Lucks Julius B. , Mortimer Stefanie A. , Luo Shujun , Schroth Gary P. , Doudna Jennifer A. , Arkin Adam P. , Pachter Lior
Published: June 2011

Sequence census methods reduce molecular measurements such as transcript abundance and protein-nucleic acid interactions to counting problems via DNA sequencing. We focus on a novel assay utilizing this approach, called
s
elective 2′-
h
ydroxyl
a
cylation analyzed by
p
rimer
e
xtension sequencing (SHAPE-Seq), that can be used to characterize RNA secondary and tertiary structure. We describe a fully automated data analysis pipeline for SHAPE-Seq analysis that includes read processing, mapping, and structural inference based on a model of the experiment. Our methods rely on the solution of a series of convex optimization problems for which we develop efficient and effective numerical algorithms. Our results can be easily extended to other chemical probes of RNA structure, and also generalized to modeling polymerase drop-off in other sequence census-based experiments.
Optical structures, algebraically special spacetimes, and the Goldberg–Sachs theorem in five dimensions
Authors: Taghavi-Chabert Arman
Published: June 2011

Optical (or Robinson) structures are one generalization of four-dimensional shearfree congruences of null geodesics to higher dimensions. They are Lorentzian analogues of complex and CR structures. In this context, we extend the Goldberg–Sachs theorem to five dimensions. To be precise, we find a new algebraic condition on the Weyl tensor, which generalizes the Petrov type II condition, in the sense that it ensures the existence of such congruences on a five-dimensional spacetime, vacuum or under weaker assumptions on the Ricci tensor. This results in a significant simplification of the field equations. We discuss possible degenerate cases, including a five-dimensional generalization of the Petrov type D condition. We also show that the vacuum black ring solution is endowed with optical structures, yet fails to be algebraically special with respect to them. We finally explain the generalization of these ideas to higher dimensions, which has been checked in six and seven dimensions.
Clinical and prognostic effects of atrial fibrillation in heart failure patients with reduced and preserved left ventricular ejection fraction
Authors: Linssen Gerard C.M. , Rienstra Michiel , Jaarsma Tiny , Voors Adriaan A. , van Gelder Isabelle C. , Hillege Hans L. , van Veldhuisen Dirk J.
Published: June 2011

Aims

Atrial fibrillation (AF) is common in heart failure (HF), but few data regarding the prognostic relevance of AF are available in HF patients with preserved left ventricular ejection fraction (HF‐PEF). We aimed to study the clinical impact of AF vs. sinus rhythm (SR) in stabilized HF patients with reduced left ventricular ejection fraction (HF‐REF) and in those with preserved left ventricular ejection fraction (HF‐PEF).

Methods and results

We studied 927 patients with stable HF, of whom 336 (36%) had AF. N‐terminal pro‐B‐type natriuretic peptide (NT‐proBNP) concentrations were measured at baseline and patients were followed for 18 months. We compared time to first HF (re‐)hospitalization or death between patients with AF and SR.

Atrial fibrillation was present at baseline in 215 (35%) patients with HF‐REF (mean LVEF 0.25 + 0.08) and in 121 (40%) patients with HF‐PEF (mean LVEF 0.50 + 0.09). Plasma NT‐proBNP levels were similar in AF and SR patients (median 2398 vs. 2532 pg/mL, P = 0.74). Atrial fibrillation was independently associated with elevated NT‐proBNP levels in HF‐PEF, but not in HF‐REF patients (multivariable B = 0.33, P= 0.047 and B = 0.03; P = 0.89, respectively). After 18 months of follow‐up, the presence of AF was an independent predictor of death or HF hospitalization in HF‐PEF (multivariable hazard ratio 1.49 (95% CI 1.04–2.14), P = 0.03), but not in HF‐REF patients (1.05 (CI 95% 0.80–1.38), P = 0.72).

Conclusion

Atrial fibrillation is equally common in patients with HF‐PEF and HF‐REF. In HF‐PEF, but not in HF‐REF patients, AF was associated with higher NT‐proBNP levels and was independently related to death or HF hospitalization.
Three-dimensional reconstruction of the fast-start swimming kinematics of densely schooling fish
Authors: Butail Sachit , Paley Derek A.
Published: June 2011

Information transmission via non-verbal cues such as a fright response can be quantified in a fish school by reconstructing individual fish motion in three dimensions. In this paper, we describe an automated tracking framework to reconstruct the full-body trajectories of densely schooling fish using two-dimensional silhouettes in multiple cameras. We model the shape of each fish as a series of elliptical cross sections along a flexible midline. We estimate the size of each ellipse using an iterated extended Kalman filter. The shape model is used in a model-based tracking framework in which simulated annealing is applied at each step to estimate the midline. Results are presented for eight fish with occlusions. The tracking system is currently being used to investigate fast-start behaviour of schooling fish in response to looming stimuli.
Plant surfaces with cuticular folds are slippery for beetles
Authors: Prüm Bettina , Seidel Robin , Bohn Holger Florian , Speck Thomas
Published: June 2011

Plant surfaces covered with three-dimensional (3D) waxes are known to strongly reduce insect adhesion, leading to slippery surfaces. Besides 3D epicuticular waxes, cuticular folds are a common microstructure found on plant surfaces, which have not been quantitatively investigated with regard to their influence on insect adhesion. We performed traction experiments with Colorado potato beetles on five plant surfaces with cuticular folds of different magnitude. For comparison, we also tested (i) smooth plant surfaces and (ii) plant surfaces possessing 3D epicuticular waxes. Traction forces on surfaces with medium cuticular folds, of about 0.5 µm in both height and thickness and a spacing of 0.5–1.5 µm, were reduced by an average of 88 per cent in comparison to smooth plant surfaces. Traction forces were reduced by the same order of magnitude as on plant surfaces covered with 3D epicuticular waxes. For surface characterization, we performed static contact angle measurements, which proved a strong effect of cuticular folds also on surface wettability. Surfaces possessing cuticular folds of greater magnitude showed higher contact angles up to superhydrophobicity. We hypothesize that cuticular folds reduce insect adhesion mainly due to a critical roughness, reducing the real contact area between the surface and the insect's adhesive devices.
Lattice studies of quantum chromodynamics-like theories with many fermionic degrees of freedom
Authors: DeGrand Thomas
Published: June 2011

I give an elementary introduction to the study of gauge theories coupled to fermions with many degrees of freedom. Besides their intrinsic interest, these theories are candidates for non-perturbative extensions of the Higgs sector of the standard model. While related to quantum chromodynamics, these systems can exhibit very different behaviour from it: they can possess a running gauge coupling with an infrared-attractive fixed point. I briefly survey recent lattice work in this area.
The renormalization group and nuclear forces
Authors: Birse Michael C.
Published: June 2011

I give an outline of recent applications of the renormalization group to effective theories of nuclear forces, focusing on the use of a Wilsonian approach to analyse systems of two or three non-relativistic particles.
Efimov physics from a renormalization group perspective
Authors: Hammer Hans-Werner , Platter Lucas
Published: June 2011

We discuss the physics of the Efimov effect from a renormalization group viewpoint using the concept of limit cycles. Furthermore, we discuss recent experiments providing evidence for the Efimov effect in ultracold gases and its relevance for nuclear systems.
Carboxydocella manganica sp. nov., a thermophilic, dissimilatory Mn(IV)- and Fe(III)-reducing bacterium from a Kamchatka hot spring
Authors: Slobodkina G. B. , Panteleeva A. N. , Sokolova T. G. , Bonch-Osmolovskaya E. A. , Slobodkin A. I.
Published: June 2011

A thermophilic, anaerobic, dissimilatory Mn(IV)- and Fe(III)-reducing bacterium (strain SLM 61T) was isolated from a terrestrial hot spring on the Kamchatka peninsula. The cells were straight rods, 0.5–0.6 µm in diameter and 1.0–6.0 µm long, and exhibited tumbling motility by means of peritrichous flagellation. The strain grew at 26–70 °C, with an optimum at 58–60 °C, and at pH 5.5–8.0, with an optimum at pH 6.5. Growth of SLM 61T was observed at 0–2.0 % (w/v) NaCl, with an optimum at 0.5 % (w/v). The generation time under optimal growth conditions was 40 min. Strain SLM 61T grew and reduced Mn(IV), Fe(III) or nitrate with a number of organic acids and complex proteinaceous compounds as electron donors. It was capable of chemolithoautotrophic growth using molecular hydrogen as an electron donor, Fe(III) but not Mn(IV) or nitrate as an electron acceptor and CO2 as a carbon source. It also was able to ferment pyruvate, yeast extract, glucose, fructose, sucrose and maltose. The G+C content of DNA of strain SLM 61T was 50.9 mol%. 16S rRNA gene sequence analysis revealed that the closest relative of the isolated organism was

Carboxydocella thermautotrophica

41T (96.9 % similarity). On the basis of its physiological properties and phylogenetic analyses, the isolate is considered to represent a novel species, for which the name Carboxydocella manganica sp. nov. is proposed. The type strain is SLM 61T ( = DSM 23132T  = VKM B-2609T). C. manganica is the first described representative of the genus

Carboxydocella

that possesses the ability to reduce metals and does not utilize CO.
Planococcus plakortidis sp. nov., isolated from the marine sponge Plakortis simplex (Schulze)
Authors: Kaur Ishwinder , Das A. P. , Acharya M. , Klenk H.-P. , Sree A. , Mayilraj S.
Published: June 2011

A novel coccoid-shaped strain, AS/ASP6 (II)T, was isolated from a sample taken from Plakortis simplex (Schulze), a marine sponge, collected at a depth of 30 m from the Bay of Bengal. This strain was identified by using a polyphasic taxonomic approach. The results of 16S rRNA gene sequence analysis showed that strain AS/ASP6 (II)T should be assigned to the genus

Planococcus

. Chemotaxonomic data (A4α-type peptidoglycan; MK-6, MK-7 and MK-8 menaquinones; mainly branched cellular fatty acids; and phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol as cellular phospholipids) supported taxonomic placement in the genus

Planococcus

. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain AS/ASP6 (II)T belonged to the genus

Planococcus

and was closely related to the type strains of

Planococcus maritimus

(99.1 %) followed by

Planococcus rifietoensis

(98.6 %),

Planococcus maitriensis

(98.5 %),

Planococcus citreus

(98.3 %),

Planococcus salinarum

(98.1 %),

Planococcus columbae

(97.9 %),

Planococcus donghaensis

(97.8 %) and

Planococcus antarcticus

(97.7 %); DNA–DNA hybridization values obtained were well below the threshold that is required for the proposal of a novel species. The G+C content of the genomic DNA was 51.0 mol%. The phenotypic and genotypic data showed that strain AS/ASP6 (II)T merits recognition as a representative of a novel species of the genus

Planococcus

, for which the name Planococcus plakortidis sp. nov. is proposed; the type strain is AS/ASP6 (II)T ( = MTCC 8491T = DSM 23997T).
Rhodococcus artemisiae sp. nov., an endophytic actinobacterium isolated from the pharmaceutical plant Artemisia annua L.
Authors: Zhao Guo-Zhen , Li Jie , Zhu Wen-Yong , Tian Shou-Zheng , Zhao Li-Xing , Yang Ling-Ling , Xu Li-Hua , Li Wen-Jun
Published: June 2011

A Gram-positive, non-motile actinobacterium, designated YIM 65754T, was isolated from the stem of Artemisia annua L., collected from Yunnan province, south-west China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YIM 65754T comprised an evolutionary lineage within the genus

Rhodococcus

. The isolate clustered with

Rhodococcus pyridinivorans

PDB9T,

Rhodococcus gordoniae

W 4937T and

Rhodococcus rhodochrous

DSM 43241T, with which it shared 98.4, 97.9 and 97.8 % 16S rRNA gene sequence similarities, respectively. However, DNA–DNA relatedness demonstrated that strain YIM 65754T was distinct from its closest phylogenetic neighbours. The cell-wall peptidoglycan contained meso-diaminopimelic acid, arabinose, galactose, mannose and glucose (cell-wall chemotype IV). The major menaquinone was MK-8(H2) and the predominant fatty acids were C16 : 0 (27.83 %), iso-C15 : 0 2-OH and/or C16 : 1ω7c (20.21 %) and 10-methyl C18 : 0 (17.50 %). The DNA G+C content was 66.2 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic evidence, the isolate represents a novel species of the genus

Rhodococcus

, for which the name Rhodococcus artemisiae sp. nov. is proposed; the type strain is YIM 65754T ( = CCTCC AA 209042T = DSM 45380T).
Rhizobium skierniewicense sp. nov., isolated from tumours on chrysanthemum and cherry plum
Authors: Puławska Joanna , Willems Anne , Sobiczewski Piotr
Published: June 2011

Three isolates of Gram-negative, rod-shaped, non-spore-forming bacteria were recovered from galls on chrysanthemum (Chrysanthemum L.; Ch11T, Ch12) and cherry plum (Prunus cerasifera var. divaricata; AL9.3). All three isolates were able to cause crown galls on various plant species. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the three isolates were probably identical (100% sequence similarity) and closely related to

Rhizobium rubi

(99.6 %),

Rhizobium radiobacter

(98.7 %) and

Rhizobium larrymoorei

(98.1 %). Similar analysis based on the housekeeping genes glnA, gyrB and rpoB also indicated that the novel isolates were identical and closely related to

R. rubi

. The major cellular fatty acids of strain Ch11T were C18 : 1ω7c (62.1 %), summed feature 2 (comprising C12 : 0 aldehyde, iso-C16 : 1 I and/or C14 : 0 3-OH; 10.8 %), summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH; 7.7 %) and C10 : 0 3-OH (7.5 %). However, the DNA–DNA relatedness between Ch11T and

R. rubi

LMG 156T was only 48 % and, unlike phylogenetically related established

Rhizobium

species, the novel isolates were able to utilize β-hydroxybutyric acid but not l-fucose. Based on the phylogenetic and phenotypic evidence, the isolates are considered to represent a single novel species of the genus

Rhizobium

, for which the name Rhizobium skierniewicense sp. nov. is proposed; the type strain is Ch11T ( = LMG 26191T = CFBP 7420T).
Evolution of the PEBP Gene Family in Plants: Functional Diversification in Seed Plant Evolution
Authors: Karlgren Anna , Gyllenstrand Niclas , Källman Thomas , Sundström Jens F. , Moore David , Lascoux Martin , Lagercrantz Ulf
Published: June 2011

The phosphatidyl ethanolamine-binding protein (PEBP) gene family is present in all eukaryote kingdoms, with three subfamilies identified in angiosperms (FLOWERING LOCUS T [FT], MOTHER OF FT AND TFL1 [MFT], and TERMINAL FLOWER1 [TFL1] like). In angiosperms, PEBP genes have been shown to function both as promoters and suppressors of flowering and to control plant architecture. In this study, we focus on previously uncharacterized PEBP genes from gymnosperms. Extensive database searches suggest that gymnosperms possess only two types of PEBP genes, MFT-like and a group that occupies an intermediate phylogenetic position between the FT-like and TFL1-like (FT/TFL1-like). Overexpression of Picea abies PEBP genes in Arabidopsis (Arabidopsis thaliana) suggests that the FT/TFL1-like genes (PaFTL1 and PaFTL2) code for proteins with a TFL1-like function. However, PaFTL1 and PaFTL2 also show highly divergent expression patterns. While the expression of PaFTL2 is correlated with annual growth rhythm and mainly confined to needles and vegetative and reproductive buds, the expression of PaFTL1 is largely restricted to microsporophylls of male cones. The P. abies MFT-like genes (PaMFT1 and PaMFT2) show a predominant expression during embryo development, a pattern that is also found for many MFT-like genes from angiosperms. P. abies PEBP gene expression is primarily detected in tissues undergoing physiological changes related to growth arrest and dormancy. A first duplication event resulting in two families of plant PEBP genes (MFT-like and FT/TFL1-like) seems to coincide with the evolution of seed plants, in which independent control of bud and seed dormancy was required, and the second duplication resulting in the FT-like and TFL1-like clades probably coincided with the evolution of angiosperms.
Coping with Stresses: Roles of Calcium- and Calcium/Calmodulin-Regulated Gene Expression
Authors: Reddy Anireddy S.N. , Ali Gul S. , Celesnik Helena , Day Irene S.
Published: June 2011

Abiotic and biotic stresses are major limiting factors of crop yields and cause billions of dollars of losses annually around the world. It is hoped that understanding at the molecular level how plants respond to adverse conditions and adapt to a changing environment will help in developing plants that can better cope with stresses. Acquisition of stress tolerance requires orchestration of a multitude of biochemical and physiological changes, and most of these depend on changes in gene expression. Research during the last two decades has established that different stresses cause signal-specific changes in cellular Ca2+ level, which functions as a messenger in modulating diverse physiological processes that are important for stress adaptation. In recent years, many Ca2+ and Ca2+/calmodulin (CaM) binding transcription factors (TFs) have been identified in plants. Functional analyses of some of these TFs indicate that they play key roles in stress signaling pathways. Here, we review recent progress in this area with emphasis on the roles of Ca2+- and Ca2+/CaM-regulated transcription in stress responses. We will discuss emerging paradigms in the field, highlight the areas that need further investigation, and present some promising novel high-throughput tools to address Ca2+-regulated transcriptional networks.