bluuebunny/crossref_metadata_2025 huggingface dataset:
Response-dependent dynamics of cell-specific inhibition in cortical networks in vivo
Authors: El-Boustani Sami , Sur Mriganka
Published: December 2014

In the visual cortex, inhibitory neurons alter the computations performed by target cells via combination of two fundamental operations, division and subtraction. The origins of these operations have been variously ascribed to differences in neuron classes, synapse location or receptor conductances. Here, by utilizing specific visual stimuli and single optogenetic probe pulses, we show that the function of parvalbumin-expressing and somatostatin-expressing neurons in mice in vivo is governed by the overlap of response timing between these neurons and their targets. In particular, somatostatin-expressing neurons respond at longer latencies to small visual stimuli compared with their target neurons and provide subtractive inhibition. With large visual stimuli, however, they respond at short latencies coincident with their target cells and switch to provide divisive inhibition. These results indicate that inhibition mediated by these neurons is a dynamic property of cortical circuits rather than an immutable property of neuronal classes.
Controlling coherence via tuning of the population imbalance in a bipartite optical lattice
Authors: Di Liberto M. , Comparin T. , Kock T. , Ölschläger M. , Hemmerich A. , Smith C. Morais
Published: December 2014

The control of transport properties is a key tool at the basis of many technologically relevant effects in condensed matter. The clean and precisely controlled environment of ultracold atoms in optical lattices allows one to prepare simplified but instructive models, which can help to better understand the underlying physical mechanisms. Here we show that by tuning a structural deformation of the unit cell in a bipartite optical lattice, one can induce a phase transition from a superfluid into various Mott insulating phases forming a shell structure in the superimposed harmonic trap. The Mott shells are identified via characteristic features in the visibility of Bragg maxima in momentum spectra. The experimental findings are explained by Gutzwiller mean-field and quantum Monte Carlo calculations. Our system bears similarities with the loss of coherence in cuprate superconductors, known to be associated with the doping-induced buckling of the oxygen octahedra surrounding the copper sites.
Spartan deficiency causes genomic instability and progeroid phenotypes
Authors: Maskey Reeja S. , Kim Myoung Shin , Baker Darren J. , Childs Bennett , Malureanu Liviu A. , Jeganathan Karthik B. , Machida Yuka , van Deursen Jan M. , Machida Yuichi J.
Published: December 2014

Spartan (also known as DVC1 and C1orf124) is a PCNA-interacting protein implicated in translesion synthesis, a DNA damage tolerance process that allows the DNA replication machinery to replicate past nucleotide lesions. However, the physiological relevance of Spartan has not been established. Here we report that Spartan insufficiency in mice causes chromosomal instability, cellular senescence and early onset of age-related phenotypes. Whereas complete loss of Spartan causes early embryonic lethality, hypomorphic mice with low amounts of Spartan are viable. These mice are growth retarded and develop cataracts, lordokyphosis and cachexia at a young age. Cre-mediated depletion of Spartan from conditional knockout mouse embryonic fibroblasts results in impaired lesion bypass, incomplete DNA replication, formation of micronuclei and chromatin bridges and eventually cell death. These data demonstrate that Spartan plays a key role in maintaining structural and numerical chromosome integrity and suggest a link between Spartan insufficiency and progeria.
MORC1 represses transposable elements in the mouse male germline
Authors: Pastor William A. , Stroud Hume , Nee Kevin , Liu Wanlu , Pezic Dubravka , Manakov Sergei , Lee Serena A. , Moissiard Guillaume , Zamudio Natasha , Bourc’his Déborah , Aravin Alexei A. , Clark Amander T. , Jacobsen Steven E.
Published: December 2014

The Microrchidia (Morc) family of GHKL ATPases are present in a wide variety of prokaryotic and eukaryotic organisms but are of largely unknown function. Genetic screens in Arabidopsis thaliana have identified Morc genes as important repressors of transposons and other DNA-methylated and silent genes. MORC1-deficient mice were previously found to display male-specific germ cell loss and infertility. Here we show that MORC1 is responsible for transposon repression in the male germline in a pattern that is similar to that observed for germ cells deficient for the DNA methyltransferase homologue DNMT3L. Morc1 mutants show highly localized defects in the establishment of DNA methylation at specific classes of transposons, and this is associated with failed transposon silencing at these sites. Our results identify MORC1 as an important new regulator of the epigenetic landscape of male germ cells during the period of global de novo methylation.
Detection of interaction between protein trytophan residues and small or macromolecular ligands by synchrotron radiation magnetic circular dichroism
Authors: Hughes Ashley J. , Rudd Timothy R. , Wright Gareth S. A. , Fernig David G. , Siligardi Giuliano , Yates Edwin A.
Published: December 2014

Magnetic circular dichroism selectively detects interactions between macromolecules in solution that involve tryptophan–ligand interactions, through changes at 286 nm, and also between proteins and small molecules, such as 5-fluorouridine and superoxide dismutase.
Stable dispersions of azide functionalized ferromagnetic metal nanoparticles
Authors: Hofer C. J. , Zlateski V. , Stoessel P. R. , Paunescu D. , Schneider E. M. , Grass R. N. , Zeltner M. , Stark W. J.
Published: December 2014

Stable dispersions of azide functionalized ferromagnetic metal nanoparticles were synthesized by covalent attachment of a block-copolymer to the nanoparticles surface via SI-ATRP and subsequent post-modification.
A new strategy for synthesis of porous magnetic supraparticles with excellent biodegradability
Authors: Li Dian , Zhang Yuting , Yu Meng , An Qiao , Guo Jia , Lu Jennifer Q. , Wang Changchun
Published: December 2014

Porous biodegradable magnetic supraparticles with surface area up to 285.4 m2g−1have been fabricated by a one-step etching method.
Diboron as a reductant for nickel-catalyzed reductive coupling: rational design and mechanistic studies
Authors: Zhang Guoying , Xie Yinjun , Wang Zhengkun , Liu Yang , Huang Hanmin
Published: December 2014

Diboron (B2pin2) has been identified as an efficient and environmentally benign reducing reagent for reductive coupling reactions for the first time, which enables the nickel-catalyzed reductive tetramerization of alkynes to be performed with high efficiency in the presence of formal substoichiometric amounts of (0.3 equiv.) the reductant.
Energy frameworks: insights into interaction anisotropy and the mechanical properties of molecular crystals
Authors: Turner Michael J. , Thomas Sajesh P. , Shi Ming W. , Jayatilaka Dylan , Spackman Mark A.
Published: December 2014

Energy frameworks provide an approach to understanding crystal packing by combining quantitative intermolecular interaction energies with qualitative and appealing graphics.
Prediction of enhanced solvent-induced enantioselectivity for a ring opening with a bifurcating reaction path
Authors: Carpenter Barry K. , Harvey Jeremy N. , Glowacki David R.
Published: December 2014

A fully atomistic molecular dynamics simulation predicts enhance induction of enantiomeric excess in the products of a reaction with a bifurcating reaction coordinate, when run in a chiral solvent.
How determinant is N-terminal to C-terminal coupling for protein folding?
Authors: Krobath Heinrich , Rey Antonio , Faísca Patrícia F. N.
Published: December 2014

The existence of native interactions between the protein termini is a major determinant of the free energy barrier in a two-state folding transition being therefore a critical modulator of protein folding cooperativity.
Comparative study of new chromium-based catalysts for the selective tri- and tetramerization of ethylene
Authors: Härzschel Stefan , Kühn Fritz E. , Wöhl Anina , Müller Wolfgang , Al-Hazmi Mohammed H. , Alqahtani Abdullah M. , Müller Bernd H. , Peulecke Normen , Rosenthal Uwe
Published: December 2014

Small changes in ligand structure and conditions make a chromium ethylene oligomerization catalyst to switch from 1-hexene to 1-octene selectivity.
Ionothermal synthesis and crystal structures of novel aluminum phosphates with in situ generated templates
Authors: Man Shanshan , Wang Zenglong , Zhao Boya , Liu Lei , Dong Jinxiang
Published: December 2014

Two new crystalline aluminophosphates were successfully synthesized for the first time from a protic ionic liquid, 3-dimethylaminopropylamine acetate.
Linear trinuclear cobalt(ii) single molecule magnet
Authors: Zhang Yuan-Zhu , Brown Andrew J. , Meng Yin-Shan , Sun Hao-Ling , Gao Song
Published: December 2014

The first linear trinuclear [CoII3] SMM was achieved due to significant intracluster ferromagnetic coupling. This study shows that miniscule changes in the coordination environment of the cobalt centers in this structural archetype can have a drastic effect on the observation of SMM behavior.
Application of disposable starch-based platforms for sample introduction and determination of refractory elements using graphite furnace atomic absorption spectrometry and direct solid sample analysis
Authors: Colares Lígia , Pereira Éderson R. , Merib Josias , Silva Julyetty C. , Silva Jaqueline M. , Welz Bernhard , Carasek Eduardo , Borges Daniel L. G.
Published: December 2014

We propose starch-based platforms for direct solid sample introduction in GF AAS. Signal tailing for refractory elements is significantly reduced.
Influence of the solvent on the complexation of Cm(iii) and Eu(iii) with nPr–BTP studied by time-resolved laser fluorescence spectroscopy
Authors: Bremer Antje , Müllich Udo , Geist Andreas , Panak Petra J.
Published: December 2014

The systematic investigation of the influence of the water content in methanol–water mixtures on the complexation of Cm(iii) and Eu(iii) with nPr–BTP revealed an immense influence of the solvent.
Sulfur-containing species in the extraction residue from Xianfeng lignite characterized by X-ray photoelectron spectrometry and electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry
Authors: Liu Fang-Jing , Wei Xian-Yong , Wang Yu-Gao , Li Peng , Li Zhan-Ku , Zong Zhi-Min
Published: December 2014

Detailed composition of sulfur-containing species in the extraction residue from Xianfeng lignite was characterized by XPS and ESI FT-ICR MS.
Instability of carbon nanoparticles interacting with lipid bilayers
Authors: Baowan Duangkamon , Cox Barry J. , Hill James M.
Published: December 2014

For nanoparticles penetrating biological tissue, modelling indicates that without external forces, carbon nanoparticles will remain trapped in lipid bilayers.
Preparation and characterization of activated montmorillonite clay supported 11-molybdo-vanado-phosphoric acid for cyclohexene oxidation
Authors: Boudjema S. , Vispe E. , Choukchou-Braham A. , Mayoral J. A. , Bachir R. , Fraile J. M.
Published: December 2014

Heterogenization of homogenous catalysts consisting of vanadium substituted polyphosphomolybdate with Keggin structure supported on activated bentonite for epoxidation of cyclohexene.
The first 4,4′-imidazolium-tagged C2-symmetric bis(oxazolines): application in the asymmetric Henry reaction
Authors: Tang Li-Wei , Dong Xiao , Zhou Zhi-Ming , Liu Ying-Qiang , Dai Li , Zhang Man
Published: December 2014

Highly efficient and recyclable imidazolium-tagged bis(oxazolines), with an imidazolium tagged onto the 4,4′-position of the box, have been designed and prepared for the first time.
Synthesis of NaCl single crystals with defined morphologies as templates for fabricating hollow nano/micro-structures
Authors: Wang Bingbing , Jin Ping , Yue Yuanzheng , Ji Shidong , Li Yamei , Luo Hongjie
Published: December 2014

Hollow structured SiO2, TiO2 and related XRD patterns before and after removal of the NaCl template.
Atom-economical chemoselective synthesis of furocoumarins via cascade palladium catalyzed oxidative alkoxylation of 4-oxohydrocoumarins and alkenes
Authors: Tan Xian-chun , Zhao Hai-yuan , Pan Ying-ming , Wu Na , Wang Heng-shan , Chen Zhen-feng
Published: December 2014

A novel and efficient procedure for the synthesis of furo[3,2-c]coumarins from readily available 4-oxohydrocoumarins and alkenes in the presence of a catalytic amount of Pd(CF3COO)2 has been developed.
Synthesis, characterization, and tuning of the liquid crystal properties of ionic materials based on the cyclic polyoxothiometalate [{Mo4O4S4(H2O)3(OH)2}2(P8W48O184)]36−
Authors: Watfa Nancy , Floquet Sébastien , Terazzi Emmanuel , Haouas Mohamed , Salomon William , Korenev Vladimir S. , Taulelle Francis , Guénée Laure , Hijazi Akram , Naoufal Daoud , Piguet Claude , Cadot Emmanuel
Published: December 2014

Ionic associations between a polyoxometalate cluster and organic cations leads to the formation of ionic liquid crystals.
Photolinker-free photoimmobilization of antibodies onto cellulose for the preparation of immunoassay membranes
Authors: Credou Julie , Volland Hervé , Berthelot Thomas
Published: December 2014

Immunoassay membranes were produced by photoimmobilization of antibodies onto cellulose without any photocoupling intermediate nor any biomolecule or substrate pretreatment.
Tracking mesenchymal stem cell tumor-homing using fluorescent silica nanoparticles
Authors: Gao Yu , Wang Yaqi , Fu Afu , Shi Wei , Yeo David , Luo Kathy Qian , Ow Hooisweng , Xu Chenjie
Published: December 2014

Core–shell fluorescent silica nanoparticles for in vitro and in vivo tracking of tumor tropism of human mesenchymal stem cells.
Silencing of ANGPTL 3 (angiopoietin-like protein 3) in human hepatocytes results in decreased expression of gluconeogenic genes and reduced triacylglycerol-rich VLDL secretion upon insulin stimulation
Authors: Tikka Anna , Soronen Jarkko , Laurila Pirkka-Pekka , Metso Jari , Ehnholm Christian , Jauhiainen Matti
Published: December 2014

Homozygosity of loss-of-function mutations in ANGPTL3 (angiopoietin-like protein 3)-gene results in FHBL2 (familial combined hypolipidaemia, OMIM #605019) characterized by the reduction of all major plasma lipoprotein classes, which includes VLDL (very-low-density lipoprotein), LDL (low-density lipoprotein), HDL (high-density lipoprotein) and low circulating NEFAs (non-esterified fatty acids), glucose and insulin levels. Thus complete lack of ANGPTL3 in humans not only affects lipid metabolism, but also affects whole-body insulin and glucose balance. We used wild-type and ANGPTL3-silenced IHHs (human immortalized hepatocytes) to investigate the effect of ANGPTL3 silencing on hepatocyte-specific VLDL secretion and glucose uptake. We demonstrate that both insulin and PPARγ (peroxisome-proliferator-activated receptor γ) agonist rosiglitazone down-regulate the secretion of ANGPTL3 and TAG (triacylglycerol)-enriched VLDL1-type particles in a dose-dependent manner. Silencing of ANGPTL3 improved glucose uptake in hepatocytes by 20–50% and influenced down-regulation of gluconeogenic genes, suggesting that silencing of ANGPTL3 improves insulin sensitivity. We further show that ANGPTL3-silenced cells display a more pronounced shift from the secretion of TAG-enriched VLDL1-type particles to secretion of lipid poor VLDL2-type particles during insulin stimulation. These data suggest liver-specific mechanisms involved in the reported insulin-sensitive phenotype of ANGPTL3-deficient humans, featuring lower plasma insulin and glucose levels.
Impulse responses and the late time stability properties of time‐domain integral equations
Authors: Xiao Gaobiao , Tian Xuezhe , Luo Wei , Fang Jinpeng
Published: December 2014

Impulse responses to the time‐domain integral equations (TDIEs) using marching‐on‐in‐time (MOT) scheme are discussed in this study. It can be seen clearly that the interior resonance currents are included in the impulse responses of the time‐domain electric field integral equation (TDEFIE) and the time‐domain magnetic field integral equation (TDMFIE), but not in those of the time‐domain combined field integral equation (TDCFIE), while spurious DC solenoidal currents are only included in the TDEFIE. Analysis shows that the MOT‐TDMFIE is basically exponentially convergent, and the MOT‐TDCFIE usually converges to a small constant value, while the MOT‐TDEFIE is basically unstable. The stability properties are justified by the eigenvalues of the corresponding systems. This study also shows that it is possible to solve time‐domain integral equations (TDIEs) using their impulse responses truncated according to the maximum physical size of the scatterer.
Accelerated simulation‐driven design optimisation of compact couplers by means of two‐level space mapping
Authors: Bekasiewicz Adrian , Koziel Slawomir , Pankiewicz Bogdan
Published: December 2014

In this study, the authors discuss a robust and efficient technique for rapid design of compact couplers. The approach exploits two‐level space mapping (SM) correction of an equivalent circuit model of the coupler structure under design. The first SM layer (local correction) is utilised to ensure good matching between the equivalent circuit and the electromagnetic model at the component level. Subsequent global correction allows for accounting the electromagnetic couplings between the components. The important advantage of two‐level model correction is that small number of parameter is utilised at each stage, which substantially simplifies and speeds up the parameters extraction procedure. Another advantage is that the local‐global SM results in considerably better generalisation capability of the surrogate model (as compared to conventional SM). This leads to improved reliability of the optimisation process and its reduced computational cost. The proposed technique is validated using an example of two compact microstrip rat‐race couplers and compared with other surrogate‐based optimisation techniques.
A gas-surface interaction kernel for diatomic rarefied gas flows based on the Cercignani-Lampis-Lord model
Authors: Hossein Gorji M. , Jenny Patrick
Published: December 2014

This work presents a kinetic wall boundary model for diatomic gas molecules. The model is derived by generalizing the Cercignani-Lampis-Lord gas-surface interaction kernel in order to account for the gas internal degrees of freedom. Here, opposed to the extensions by Lord [“Some extensions to the Cercignani-Lampis gas-surface scattering kernel,” Phys. Fluids 3, 706–710 (1991)], energy exchange between different molecular modes is honored and thus, different physical phenomena arising from inelastic gas–surface collisions can be described. For practical implementations of the model, a Monte–Carlo algorithm was devised, which significantly reduces the computational cost associated with sampling. Comparisons of model predictions with experimental and molecular dynamics data exhibit good agreement. Moreover, simulation studies are performed to demonstrate how energy transfers between different modes due to wall collisions can be exploited for gas separation.
Inducing chemotactic and haptotactic cues in microfluidic devices for three-dimensional in vitro assays
Authors: Moreno-Arotzena O. , Mendoza G. , Cóndor M. , Rüberg T. , García-Aznar J. M.
Published: December 2014

Microfluidic devices allow for the production of physiologically relevant cellular microenvironments by including biomimetic hydrogels and generating controlled chemical gradients. During transport, the biomolecules interact in distinct ways with the fibrillar networks: as purely diffusive factors in the soluble fluid or bound to the matrix proteins. These two main mechanisms may regulate distinct cell responses in order to guide their directional migration: caused by the substrate-bound chemoattractant gradient (haptotaxis) or by the gradient established within the soluble fluid (chemotaxis). In this work 3D diffusion experiments, in combination with ELISA assays, are performed using microfluidic platforms in order to quantify the distribution of PDGF-BB and TGF-β1 across collagen and fibrin gels. Furthermore, to gain a deeper understanding of the fundamental processes, the experiments are reproduced by computer simulations based on a reaction-diffusion transport model. This model yields an accurate prediction of the experimental results, confirming that diffusion and binding phenomena are established within the microdevice.
Time- and power-dependent operation of a parametric spin-wave amplifier
Authors: Brächer T. , Heussner F. , Pirro P. , Fischer T. , Geilen M. , Heinz B. , Lägel B. , Serga A. A. , Hillebrands B.
Published: December 2014

We present the experimental observation of the localized amplification of externally excited, propagating spin waves in a transversely in-plane magnetized Ni81Fe19 magnonic waveguide by means of parallel pumping. By employing microfocussed Brillouin light scattering spectroscopy, we analyze the dependency of the amplification on the applied pumping power and on the delay between the input spin-wave packet and the pumping pulse. We show that there are two different operation regimes: At large pumping powers, the spin-wave packet needs to enter the amplifier before the pumping is switched on in order to be amplified while at low powers the spin-wave packet can arrive at any time during the pumping pulse.
Benzoate pathway: members, biosynthesis and function.
Authors: Kulma A. , Żuk M. , Kostyn A. , Kostyn K. , Szopa J.
Published: December 2014

Efforts to treat diseases have long involved the use of natural materials placed in contact with human tissues. The main sources of these materials are plant products containing a broad spectrum of compounds capable of restoring, regenerating and even healing tissues. A unique, dual-purpose function is ascribed to benzoate derivatives. Plant protection against environmental stresses on the one hand and strong antimicrobial and antioxidant functions on the other are their potential functions. The benzoate pathway, although very rich in compounds of different and important functions for producers (plant) and consumers, is as yet not fully understood. Signal molecules (salicylate), antimicrobial and antifungal (benzoate, vanillin), local anaesthetic (cocaine) and anticancer (taxol) are all examples of simple benzoate derivatives. Thus, the challenge for biochemists and biotechnologists is to gain more knowledge about the identification and regulation of genes that control this pathway and its application for diversified compound production in plants. The main goal of this review is to summarize knowledge about the route/routes of biosynthesis of benzenoid derivatives (BP) from the phenylpropanoid pathway, as well as about the regulation of the biosynthesis of these compounds, their properties and biotechnological approaches for their production.
Resonance of automorphic forms for 𝐺𝐿(3)
Authors: Ren Xiumin , Ye Yangbo
Published: December 2014

Letffbe a Maass form forSL3(Z)SL_3(\mathbb Z)with Fourier coefficientsAf(m,n)A_f(m,n). A smoothly weighted sum ofAf(m,n)A_f(m,n)against an exponential functione(αnβ)e(\alpha n^\beta )of fractional powernβn^\betaforX≤n≤2XX\leq n\leq 2Xis proved to have a main term of sizeX2/3X^{2/3}whenβ=1/3\beta =1/3andα\alphais close to3ℓ1/33\ell ^{1/3}for some integerℓ≠0\ell \neq 0. The sum becomes rapidly decreasing ifβ>1/3\beta >1/3. If such a sum is not smoothly weighted, the main term can only be detected under a conjectured bound toward the Ramanujan conjecture. The existence of such a main term manifests the vibration and resonance behavior of individual automorphic formsffforGL(3)GL(3). Applications of these results include a new modularity test on whether a two dimensional arraya(m,n)a(m,n)comes from Fourier coefficientsAf(m,n)A_f(m,n)of a Maass formffforSL3(Z)SL_3(\mathbb Z). Techniques used in the proof include a Voronoi summation formula, its asymptotic expansion, and the weighted stationary phase.
Genetic mosaic analysis of a deleterious mitochondrial DNA mutation inDrosophilareveals novel aspects of mitochondrial regulation and function
Authors: Chen Zhe , Qi Yun , French Stephanie , Zhang Guofeng , Garcia Raúl Covian , Balaban Robert , Xu Hong
Published: December 2014

Various human diseases are associated with mitochondrial DNA (mtDNA) mutations, but heteroplasmy—the coexistence of mutant and wild-type mtDNA—complicates their study. We previously isolated a temperature-lethal mtDNA mutation in Drosophila, mt:CoIT300I, which affects the cytochrome c oxidase subunit I (CoI) locus. In the present study, we found that the decrease in cytochrome c oxidase (COX) activity was ascribable to a temperature-dependent destabilization of cytochrome a heme. Consistently, the viability of homoplasmic flies at 29°C was fully restored by expressing an alternative oxidase, which specifically bypasses the cytochrome chains. Heteroplasmic flies are fully viable and were used to explore the age-related and tissue-specific phenotypes of mt:CoIT300I. The proportion of mt:CoIT300Igenome remained constant in somatic tissues along the aging process, suggesting a lack of quality control mechanism to remove defective mitochondria containing a deleterious mtDNA mutation. Using a genetic scheme that expresses a mitochondrially targeted restriction enzyme to induce tissue-specific homoplasmy in heteroplasmic flies, we found that mt:CoIT300Ihomoplasmy in the eye caused severe neurodegeneration at 29°C. Degeneration was suppressed by improving mitochondrial Ca2+uptake, suggesting that Ca2+mishandling contributed to mt:CoIT300Ipathogenesis. Our results demonstrate a novel approach for Drosophila mtDNA genetics and its application in modeling mtDNA diseases.
Comparison between Hinode/SOT and SDO/HMI, AIA data for the study of the solar flare trigger process
Authors: Bamba Yumi , Kusano Kanya , Imada Shinsuke , Iida Yusuke
Published: December 2014

Understanding the mechanism that produces solar flares is important not only from the scientific point of view but also for improving space weather predictability. There are numerous observational and computational studies that have attempted to reveal the onset mechanism of solar flares. However, the underlying mechanism of flare onset remains elusive. To elucidate the flare trigger mechanism, we analyzed several flare events which were observed by Hinode/Solar Optical Telescope (SOT) in our previous study. Because of the limitation of the SOT field of view, however, only four events in the Hinode data sets have been usable. Therefore, increasing the number of events is required for evaluating the flare trigger models. We investigated the applicability of data obtained by the Solar Dynamics Observatory (SDO) to increase the data sample for a statistical analysis of the flare trigger process. SDO regularly observes the full disk of the sun and all flares, although its spatial resolution is lower than that of Hinode. We investigated the M6.6 flare which occurred on 2011 February 13, and compared the analyzed data of SDO with the results of our previous study using Hinode/SOT data. Filter and vector magnetograms obtained by the Helioseismic and Magnetic Imager and filtergrams from the Atmospheric Imaging Assembly (AIA) 1600 Å were employed. From the comparison of small-scale magnetic configurations and chromospheric emission prior to the flare onset, we confirmed that the trigger region is detectable with the SDO data. We also measured the magnetic shear angles of the active region and the azimuth and strength of the flare trigger field. The results were consistent with our previous study. We concluded that statistical studies of the flare trigger process are feasible with SDO as well as Hinode data. We also investigated the temporal evolution of the magnetic field before the flare onset with SDO.
Deregulation of Plant Cell Death Through Disruption of Chloroplast Functionality Affects Asexual Sporulation of Zymoseptoria tritici on Wheat
Authors: Lee Wing-Sham , Devonshire B. Jean , Hammond-Kosack Kim E. , Rudd Jason J. , Kanyuka Kostya
Published: December 2014

Chloroplasts have a critical role in plant defense as sites for the biosynthesis of the signaling compounds salicylic acid (SA), jasmonic acid (JA), and nitric oxide (NO) and as major sites of reactive oxygen species production. Chloroplasts, therefore, regarded as important players in the induction and regulation of programmed cell death (PCD) in response to abiotic stresses and pathogen attack. The predominantly foliar pathogen of wheat Zymoseptoria tritici is proposed to exploit the plant PCD, which is associated with the transition in the fungus to the necrotrophic phase of infection. In this study virus-induced gene silencing was used to silence two key genes in carotenoid and chlorophyll biosynthesis, phytoene desaturase (PDS) and Mg-chelatase H subunit (ChlH). The chlorophyll-deficient, PDS- and ChlH-silenced leaves of susceptible plants underwent more rapid pathogen-induced PCD but were significantly less able to support the subsequent asexual sporulation of Z. tritici. Conversely, major gene (Stb6)-mediated resistance to Z. tritici was partially compromised in PDS- and ChlH-silenced leaves. Chlorophyll-deficient wheat ears also displayed increased Z. tritici disease lesion formation accompanied by increased asexual sporulation. These data highlight the importance of chloroplast functionality and its interaction with regulated plant cell death in mediating different genotype and tissue-specific interactions between Z. tritici and wheat.
Insights Into the Polerovirus–Plant Interactome Revealed by Coimmunoprecipitation and Mass Spectrometry
Authors: DeBlasio Stacy L. , Johnson Richard , Mahoney Jaclyn , Karasev Alexander , Gray Stewart M. , MacCoss Michael J. , Cilia Michelle
Published: December 2014

Identification of host proteins interacting with the aphidborne Potato leafroll virus (PLRV) from the genus Polerovirus, family Luteoviridae, is a critical step toward understanding how PLRV and related viruses infect plants. However, the tight spatial distribution of PLRV to phloem tissues poses challenges. A polyclonal antibody raised against purified PLRV virions was used to coimmunoprecipitate virus-host protein complexes from Nicotiana benthamiana tissue inoculated with an infectious PLRV cDNA clone using Agrobacterium tumefaciens. A. tumefaciens-mediated delivery of PLRV enabled infection and production of assembled, insect-transmissible virus in most leaf cells, overcoming the dynamic range constraint posed by a systemically infected host. Isolated protein complexes were characterized using high-resolution mass spectrometry and consisted of host proteins interacting directly or indirectly with virions, as well as the nonincorporated readthrough protein (RTP) and three phosphorylated positional isomers of the RTP. A bioinformatics analysis using ClueGO and STRING showed that plant proteins in the PLRV protein interaction network regulate key biochemical processes, including carbon fixation, amino acid biosynthesis, ion transport, protein folding, and trafficking.
Emerging Yr26-Virulent Races of Puccinia striiformis f. tritici Are Threatening Wheat Production in the Sichuan Basin, China
Authors: Han D. J. , Wang Q. L. , Chen X. M. , Zeng Q. D. , Wu J. H. , Xue W. B. , Zhan G. M. , Huang L. L. , Kang Z. S.
Published: December 2014

Stripe rust, caused by Puccinia striiformis f. tritici, is one of the most destructive diseases of wheat in the world. The Sichuan Basin is one of the most important regions of wheat production and stripe rust epidemics in China. Stripe rust resistance gene Yr26 (the same gene as Yr24) has been widely used in wheat breeding programs and in many cultivars grown in this region since the gene was discovered in the early 1990s. Virulence to Yr26 has increased in frequency since its first detection in 2008. The objective of this study was to assess the vulnerability of the wheat cultivars and breeding lines in the Sichuan Basin to Yr26-virulent races. In total, 85 wheat accessions were tested with Yr26-avirulent races CYR32, CYR33, and Su11-4 and two Yr26-virulent races, V26/CM42 and V26/Gui22. DNA markers for Yr26 were used to determine the presence and absence of Yr26 in the wheat accessions. Of the 85 wheat accessions, only 5 were resistant and 19 susceptible to all races tested, and the remaining 61 were resistant to at least one or more races tested in seedling stage. In all, 65 (76.5%) accessions were susceptible to the emerging Yr26-virulent race V26/Gui22. In field tests, susceptible accessions increased from 31.8% in a nursery inoculated with predominant and Yr26-avirulent races to 61.2% in the nursery inoculated with the predominant races mixed with V26/Gui22. Based on the results of the molecular marker and race tests, 33 (38.8%) accessions were determined to have Yr26, showing that the Yr26 virulence is a major threat to wheat production in the Sichuan Basin and potentially in other regions of China.
Generation of an Attenuated, Cross-Protective Pepino mosaic virus Variant Through Alignment-Guided Mutagenesis of the Viral Capsid Protein
Authors: Chewachong Godwill M. , Miller Sally A. , Blakeslee Joshua J. , Francis David M. , Morris T. Jack , Qu Feng
Published: December 2014

Mild variants of many viruses are able to protect infected plants from subsequent invasion by more severe variants of the same viruses through a process known as cross-protection. In the past, the cross-protective viral variants were commonly derived from mild field isolates that were sometimes genetically heterogeneous, providing variable levels of cross-protection. Here, we report a novel approach to rapidly generate cross-protective variants of the tomato-infecting Pepino mosaic virus (PepMV) independently of the availability of mild field isolates. Our approach sought to attenuate PepMV by mutating less conserved amino acid residues of the abundantly produced capsid protein (CP). These less-conserved amino acid residues were identified through multiple alignments of CPs of six potexviruses including PepMV, and were altered systematically to yield six PepMV mutants. These mutants were subsequently inoculated onto the model plant Nicotiana benthamiana, as well as tomato, to evaluate their accumulation levels, symptom severities, and cross-protection potentials. The mutant KD, in which the threonine (T) and alanine (A) residues at CP positions 66 and 67 were replaced with lysine (K) and aspartic acid (D), respectively, were found to accumulate to low levels in infected plants, cause very mild symptoms, and effectively protect both N. benthamiana and tomato against secondary infections by wild-type PepMV. These data suggest that our approach represents a simple, fast, and reliable way of generating attenuated viral variants capable of cross-protection.
Impact of Laurel Wilt, Caused byRaffaelea lauricola, on Leaf Gas Exchange and Xylem Sap Flow in Avocado,Persea americana
Authors: Ploetz Randy C. , Schaffer Bruce , Vargas Ana I. , Konkol Joshua L. , Salvatierra Juanpablo , Wideman Ronney
Published: December 2014

Laurel wilt, caused by Raffaelea lauricola, is a destructive disease of avocado (Persea americana). The susceptibility of different cultivars and races was examined previously but more information is needed on how this host responds to the disease. In the present study, net CO2assimilation (A), stomatal conductance of H2O (gs), transpiration (E), water use efficiency (WUE), and xylem sap flow rates were assessed in cultivars that differed in susceptibility. After artificial inoculation with R. lauricola, there was a close relationship between symptom development and reductions in A, gs, E, WUE, and mean daily sap flow in the most susceptible cultivar, ‘Russell’, and significantly greater disease and lower A, gs, E, WUE, and sap flow rates were usually detected after 15 days compared with the more tolerant ‘Brogdon’ and ‘Marcus Pumpkin’. Significant differences in preinoculation A, gs, E, and WUE were generally not detected among the cultivars but preinoculation sap flow rates were greater in Russell than in Brogdon and Marcus Pumpkin. Preinoculation sap flow rates and symptom severity for individual trees were correlated at the end of an experiment (r = 0.46), indicating that a plant’s susceptibility to laurel wilt was related to its ability to conduct water. The potential management of this disease with clonal rootstocks that reduce sap flow rates is discussed.
Sodium Bicarbonate and Renal Function after Cardiac Surgery
Authors: Bailey Michael , McGuinness Shay , Haase Michael , Haase-Fielitz Anja , Parke Rachael , Hodgson Carol L. , Forbes Andrew , Bagshaw Sean M. , Bellomo Rinaldo
Published: December 2014

AbstractAbstract

The authors have performed a novel, prospectively planned individual patient data meta-analysis of the double-blind randomized trials in this important field. Urinary alkalinization with sodium bicarbonate infusion is not associated with a significant reduction in the overall risk of acute kidney injury in cardiac surgery patients. However, urinary alkalinization was associated with significant renal protection in the subgroup of patients undergoing elective coronary artery bypass graft surgery suggesting that further investigation in these patients is warranted.

Background:

The effect of urinary alkalinization in cardiac surgery patients at risk of acute kidney injury (AKI) is controversial and trial findings conflicting. Accordingly, the authors performed a prospectively planned individual patient data meta-analysis of the double-blind randomized trials in this field.

Methods:

The authors studied 877 patients from three double-blind, randomized controlled trials enrolled to receive either 24 h of intravenous infusion of sodium bicarbonate or sodium chloride. The primary outcome measure was a postoperative increase in serum creatinine concentration of greater than 25% or 0.5 mg/dl (> 44 μm/L) within the first five postoperative days. Secondary outcomes included the raw change in serum creatinine, greater than 50% and greater than 100% rises in serum creatinine, developing AKI (Acute Kidney Injury Network criteria), initiation of renal replacement therapy, morbidity, and mortality.

Results:

Patients were similar in demographics, comorbidities, and cardiac procedures. Sodium bicarbonate increased plasma bicarbonate (P < 0.001) and urine pH (P < 0.001). There were no differences in the development of the primary outcome (Bicarbonate 45% [39–51%] vs. Saline 42% [36–48%], P = 0.29). This result remained unchanged when controlling for study and covariates (odds ratio [OR], 99% confidence interval [CI]: Bicarbonate vs. Control, 1.11 [0.77–1.60], P = 0.45). There was, however, a significant study-adjusted benefit in elective coronary artery bypass surgery patients in terms of renal replacement therapy (Bicarbonate vs. Control, OR: 0.38 [99% CI: 0.25–0.58], P < 0.0001) and the development of an Acute Kidney Injury Network grade = 3 (Bicarbonate vs. Control, OR: 0.45 [99% CI: 0.43–0.48], P < 0.0001).

Conclusions:

Urinary alkalinization using sodium bicarbonate infusion is not associated with an overall lower incidence of AKI; however, it reduces severe AKI and need for renal replacement therapy in elective coronary artery bypass patients.
Two-week Course of Preoperative Radiotherapy for Locally Advanced Rectal Adenocarcinoma
Authors: Zhu Xiang-gao , Li Jin-luan , Li Xiao-fan , Li Yong-heng , Ni Qian-yu , Wang Lin , Zhang Shan-wen , Gu Jin , Cai Yong , Lin Chi
Published: December 2014

Objectives:

To evaluate local control and survival in locally advanced rectal adenocarcinoma patients who underwent a preoperative 2-week course of radiotherapy (RT) and to identify prognostic factors influencing the survival rate.

Methods:

We analyzed 377 consecutively treated patients with locally advanced (T3/T4 or node positive) rectal adenocarcinoma. All patients underwent a preoperative 2-week course of RT (30 Gy in 10 fractions) followed by curative surgery. Regression model was used to examine prognostic factors for the disease-free survival (DFS) and overall survival (OS) rates. The Statistical Analysis System software package, version 9.3, was used for analysis.

Results:

The median follow-up for all living patients was 63.8 months (range, 5.1 to 131.7). The 5-year DFS and OS rates were 64.5% (95% CI, 59.0-69.4) and 75.6% (95% CI, 70.5-80.0), respectively. The 5-year cumulative incidences of local recurrence and distant metastases were 5.4% (95% CI, 2.9-7.9) and 29.0% (95% CI, 23.9-30.1), respectively. The pathologic complete response rate was achieved in 17 patients (4.5%). The Multivariate Cox Regression model showed that factors affecting DFS were the surgical technique, pre-RT pathologic grade, ypT, ypN, and comorbidity; and factors improving OS were low anterior resection, low pre-RT grade, low ypT, and low ypN.

Conclusions:

Patients treated with preoperative RT with 30 Gy in 10 fractions had similar local control, 5-year DFS and OS to reported long course RT regimen. The surgical technique, pre-RT pathologic grade, ypT, and ypN seemed to affect the OS. Further study on combining a 2-week course of preoperative RT with concurrent chemotherapy would be warranted.
Thyroid V50 Highly Predictive of Hypothyroidism in Head-and-Neck Cancer Patients Treated With Intensity-modulated Radiotherapy (IMRT)
Authors: Sachdev Sean , Refaat Tamer , Bacchus Ian D. , Sathiaseelan Vythialinga , Mittal Bharat B.
Published: December 2014

Objectives:

Radiation-induced hypothyroidism affects a significant number of patients with head-and-neck squamous cell cancer (HNSCC). We examined detailed dosimetric and clinical parameters to better determine the risk of hypothyroidism in euthyroid HNSCC patients treated with intensity-modulated radiation therapy (IMRT).

Materials and Methods:

From 2006 to 2010, 75 clinically euthyroid patients with HNSCC were treated with sequential IMRT. The cohort included 59 men and 16 females with a median age of 55 years (range, 30 to 89 y) who were treated to a median dose of 70 Gy (range, 60 to 75 Gy) with concurrent chemotherapy in nearly all (95%) cases. Detailed thyroid dosimetric parameters including maximum dose, mean dose, and other parameters (eg, V50—percent volume receiving at least 50 Gy) were obtained. Freedom from hypothyroidism was evaluated using the Kaplan-Meier method. Univariate and multivariate analyses were conducted using Cox regression.

Results:

After a median follow-up period of 50 months, 25 patients (33%) became hypothyroid. On univariate analysis, thyroid V50 was highly correlated with developing hypothyroidism (P=0.035). Other dosimetric paramaters including mean thyroid dose (P=0.11) and maximum thyroid dose (P=0.39) did not reach statistical significance. On multivariate analysis incorporating patient, tumor, and treatment variables, V50 remained highly statistically significant (P=0.037). Regardless of other factors, for V50>60%, the odds ratio of developing hypothyroidism was 6.76 (P=0.002).

Conclusions:

In HNSCC patients treated with IMRT, thyroid V50 highly predicts the risk of developing hypothyroidism. V50>60% puts patients at a significantly higher risk of becoming hypothyroid. This can be a useful dose constraint to consider during treatment planning.
Graphlet signature-based scoring method to estimate protein–ligand binding affinity
Authors: Singh Omkar , Sawariya Kunal , Aparoy Polamarasetty
Published: December 2014

Over the years, various computational methodologies have been developed to understand and quantify receptor–ligand interactions. Protein–ligand interactions can also be explained in the form of a network and its properties. The ligand binding at the protein-active site is stabilized by formation of new interactions like hydrogen bond, hydrophobic and ionic. These non-covalent interactions when considered as links cause non-isomorphic sub-graphs in the residue interaction network. This study aims to investigate the relationship between these induced sub-graphs and ligand activity. Graphlet signature-based analysis of networks has been applied in various biological problems; the focus of this work is to analyse protein–ligand interactions in terms of neighbourhood connectivity and to develop a method in which the information from residue interaction networks, i.e. graphlet signatures, can be applied to quantify ligand affinity. A scoring method was developed, which depicts the variability in signatures adopted by different amino acids during inhibitor binding, and was termed as GSUS (graphlet signature uniqueness score). The score is specific for every individual inhibitor. Two well-known drug targets, COX-2 and CA-II and their inhibitors, were considered to assess the method. Residue interaction networks of COX-2 and CA-II with their respective inhibitors were used. Only hydrogen bond network was considered to calculate GSUS and quantify protein–ligand interaction in terms of graphlet signatures. The correlation of the GSUS with pIC
50
was consistent in both proteins and better in comparison to the Autodock results. The GSUS scoring method was better in activity prediction of molecules with similar structure and diverse activity and vice versa. This study can be a major platform in developing approaches that can be used alone or together with existing methods to predict ligand affinity from protein–ligand complexes.
Bacillus polymachus sp. nov., with a broad range of antibacterial activity, isolated from forest topsoil samples by using a modified culture method
Authors: Nguyen Tuan Manh , Kim Jaisoo
Published: December 2014

A new, modified culture method that utilizes a transwell plate with a 0.4 µm pore-size microporous membrane was developed. This system allows only trace nutrients from the soil into the liquid culture through the microporous membrane. The method is a more powerful tool for the discovery of novel species from soils than are traditional methods. Such newly identified species could potentially produce useful metabolites. A bacterial strain, T515T, was isolated using this modified culture method. Growth of strain T515Toccurred at pH 4–9 in a temperature range between 20 °C and 40 °C and in the presence of 0–2 % (w/v) NaCl on R2A agar. Colonies on the agar plates were tiny, white, and convex after 5 days incubation at 28 °C. Comparative analysis of the nearly full-length 16S rRNA gene sequence of strain T515Trevealed close pairwise similarity with species of the genusBacillus, and strain T515Twas most closely related toBacillus panaciterraeGsoil 1517T(96.7 %) andBacillus funiculusNAF001T(96.0 %). The major quinone of strain T515Twas menaquinone-7 (MK-7) and the major fatty acids were iso-C15 : 0(45.5 %), anteiso-C15 : 0(23.2 %) and C16 : 0(10.9 %). The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Strain T515Twas sensitive to streptomycin and tetracycline, but resistant to rifampicin (0.125 µg ml−1), ampicillin (0.5 µg ml−1) and chloramphenicol (1 µg ml−1). The strain showed antimicrobial activities against the six strains tested:Bacillus subtilisKEMB 51201-001,Staphylococcus aureusKEMB 4659,Pseudomonas aeruginosaKACC 10185,Staphylococcus epidermidisKACC 13234,Paenibacillus larvaeKACC 14031 andEscherichia coliKEMB 212-234. Based on these results, strain T515Trepresents a novel species of the genusBacilluswith the proposed name,Bacillus polymachussp. nov. The type strain is T515T( = KEMB 9005-168T = KACC 18242T = NBRC 110614T).