bluuebunny/crossref_metadata_2025 huggingface dataset:
Organocatalytic enantioselective aza-Henry reaction of ketimines derived from isatins: access to optically active 3-amino-2-oxindoles
Authors: Kumar Akshay , Kaur Jasneet , Chimni Swapandeep Singh , Jassal Amanpreet Kaur
Published: May 2014

An organocatalytic asymmetric aza-Henry reaction of ketimines derived from isatins with nitroalkanes has been achieved using Cinchona alkaloid organocatalysts.
Synthesis and electrochemical properties of conducting polyaniline/graphene hybrids by click chemistry
Authors: Ramasamy Madeshwaran Sekkarapatti , Mahapatra Sibdas Singha , Yi Dong Hun , Yoo Hye Jin , Cho Jae Whan
Published: May 2014

Conducting polyaniline nanofiber-grafted graphene oxide (PANINF-GO) hybrids were prepared by click chemistry reaction and in situ rapid mixing polymerization. The resulting composites exhibited excellent electrochemical properties.
Design and synthesis of a new phosphinite-functionalized clay composite for the stabilization of palladium nanoparticles. Application as a recoverable catalyst for C–C bond formation reactions
Authors: Firouzabadi Habib , Iranpoor Nasser , Ghaderi Arash , Gholinejad Mohammad , Rahimi Sajjad , Jokar Safura
Published: May 2014

Pd-catalyzed C–C bond formation in green media, combining the advantages of homogeneous IL phase, phosphorylated ligands and a new heterogeneous clay support.
Supramolecular chemistry with ureido-benzoic acids
Authors: Appel Wilco P. J. , Nieuwenhuizen Marko M. L. , Lutz Martin , de Waal Bas F. M. , Palmans Anja R. A. , Meijer E. W.
Published: May 2014

A novel, complementary quadruple hydrogen-bonding motif is presented that shows very strong dimerization and is switchable with pH.
A versatile stable platform for multifunctional applications: synthesis of a nitroDOPA–PEO–alkyne scaffold for iron oxide nanoparticles
Authors: Stone R. C. , Qi B. , Trebatoski D. , Jetti R. , Bandera Y. P. , Foulger S. H. , Mefford O. T.
Published: May 2014

A simple but powerful design of contemporary magnetic nanoparticle composites for biomedical applications.
Robust biopolymer based ionic–covalent entanglement hydrogels with reversible mechanical behaviour
Authors: Kirchmajer Damian M. , Panhuis Marc in het
Published: May 2014

A robust ionic–covalent entanglement hydrogel from gum and gelatin with reversible mechanical characteristics is reported.
Study of the influences of molecular planarity and aluminum evaporation rate on the performances of electrical memory devices
Authors: Liu Hongzhang , Bo Rongcheng , Liu Haifeng , Li Najun , Xu Qingfeng , Li Hua , Lu Jianmei , Wang Lihua
Published: May 2014

We achieve different storage types by increasing the rate of evaporation of aluminum for the device based on TPA-BT, which has poor planarity.
Ubiquitin-like modifiers
Authors: Taherbhoy Asad M. , Schulman Brenda A. , Kaiser Stephen E.
Published: May 2014

UBLs (ubiquitin-like proteins) are a major class of eukaryotic post-translational modifiers. UBLs are attached to numerous cellular proteins and to other macromolecules, thereby regulating a wide array of cellular processes. In this chapter we highlight a subset of UBLs and describe their regulatory roles in the cell.
Polo-like kinase 1 (PLK1) and protein phosphatase 6 (PP6) regulate DNA-dependent protein kinase catalytic subunit (DNA-PKcs) phosphorylation in mitosis
Authors: Douglas Pauline , Ye Ruiqiong , Trinkle-Mulcahy Laura , Neal Jessica A. , De Wever Veerle , Morrice Nick A. , Meek Katheryn , Lees-Miller Susan P.
Published: May 2014

The protein kinase activity of the DNA-PKcs (DNA-dependent protein kinase catalytic subunit) and its autophosphorylation are critical for DBS (DNA double-strand break) repair via NHEJ (non-homologous end-joining). Recent studies have shown that depletion or inactivation of DNA-PKcs kinase activity also results in mitotic defects. DNA-PKcs is autophosphorylated on Ser2056, Thr2647 and Thr2609 in mitosis and phosphorylated DNA-PKcs localize to centrosomes, mitotic spindles and the midbody. DNA-PKcs also interacts with PP6 (protein phosphatase 6), and PP6 has been shown to dephosphorylate Aurora A kinase in mitosis. Here we report that DNA-PKcs is phosphorylated on Ser3205 and Thr3950 in mitosis. Phosphorylation of Thr3950 is DNA-PK-dependent, whereas phosphorylation of Ser3205 requires PLK1 (polo-like kinase 1). Moreover, PLK1 phosphorylates DNA-PKcs on Ser3205in vitro and interacts with DNA-PKcs in mitosis. In addition, PP6 dephosphorylates DNA-PKcs at Ser3205 in mitosis and after IR (ionizing radiation). DNA-PKcs also phosphorylates Chk2 on Thr68 in mitosis and both phosphorylation of Chk2 and autophosphorylation of DNA-PKcs in mitosis occur in the apparent absence of Ku and DNA damage. Our findings provide mechanistic insight into the roles of DNA-PKcs and PP6 in mitosis and suggest that DNA-PKcs’ role in mitosis may be mechanistically distinct from its well-established role in NHEJ.
Design of a fully-fiber multi-chord interferometer and a new phase-shift demodulation method for field-reversed configuration
Authors: Fang Dongfan , Sun Qizhi , Zhao Xiaoming , Jia Yuesong
Published: May 2014

A 633 nm laser interferometer has been designed based on a novel concept, which, without the acousto-optic modulator or the demodulator circuit, adopts the fibers to connect all elements except photodetectors and oscilloscope in this system to make it more compact, portable, and efficient. The noteworthy feature is to mathematically compare the two divided interference signals, which have the same phase-shift caused by the electron density but possess the different initial phase and low angular frequencies. It is possible to read the plasma density directly on the oscilloscope by our original mathematic demodulation method without a camera. Based on the Abel inversion algorithm, the radial electron density profiles versus time can be obtained by using the multi-chord system. The designed measurable phase shift ranges from 0 to 2π rad corresponding to the maximum line integral of electron density less than 3.5 × 1017 cm−2, and the phase accuracy is about 0.017 rad corresponding to the line integral of electron density accuracy of 1 × 1015 cm−2. After the construction of eight-chord interferometer, it will provide the detailed time resolved information of the spatial distribution of the electron density in the field-reversed configuration (FRC) plasma target produced by the “Yingguang-1” programmed-discharge device, which is being constructed in the Key Laboratory of Pulsed Power, China Academy of Engineering Physics.
Ab initio and relativistic DFT study of spin–rotation and NMR shielding constants in XF6 molecules, X = S, Se, Te, Mo, and W
Authors: Ruud Kenneth , Demissie Taye B. , Jaszuński Michał
Published: May 2014

We present an analysis of the spin–rotation and absolute shielding constants of XF6 molecules (X = S, Se, Te, Mo, W) based on ab initio coupled cluster and four-component relativistic density-functional theory (DFT) calculations. The results show that the relativistic contributions to the spin–rotation and shielding constants are large both for the heavy elements as well as for the fluorine nuclei. In most cases, incorporating the computed relativistic corrections significantly improves the agreement between our results and the well-established experimental values for the isotropic spin–rotation constants and their anisotropic components. This suggests that also for the other molecules, for which accurate and reliable experimental data are not available, reliable values of spin–rotation and absolute shielding constants were determined combining ab initio and relativistic DFT calculations. For the heavy nuclei, the breakdown of the relationship between the spin–rotation constant and the paramagnetic contribution to the shielding constant, due to relativistic effects, causes a significant error in the total absolute shielding constants.
Free energy of cluster formation and a new scaling relation for the nucleation rate
Authors: Tanaka Kyoko K. , Diemand Jürg , Angélil Raymond , Tanaka Hidekazu
Published: May 2014

Recent very large molecular dynamics simulations of homogeneous nucleation with (1 − 8) × 109 Lennard-Jones atoms [J. Diemand, R. Angélil, K. K. Tanaka, and H. Tanaka, J. Chem. Phys. 139, 074309 (2013)] allow us to accurately determine the formation free energy of clusters over a wide range of cluster sizes. This is now possible because such large simulations allow for very precise measurements of the cluster size distribution in the steady state nucleation regime. The peaks of the free energy curves give critical cluster sizes, which agree well with independent estimates based on the nucleation theorem. Using these results, we derive an analytical formula and a new scaling relation for nucleation rates: ln J′/η is scaled by ln S/η, where the supersaturation ratio is S, η is the dimensionless surface energy, and J′ is a dimensionless nucleation rate. This relation can be derived using the free energy of cluster formation at equilibrium which corresponds to the surface energy required to form the vapor-liquid interface. At low temperatures (below the triple point), we find that the surface energy divided by that of the classical nucleation theory does not depend on temperature, which leads to the scaling relation and implies a constant, positive Tolman length equal to half of the mean inter-particle separation in the liquid phase.
Ferromagnetic resonance study of the misalignment between anisotropy axes in exchange-biased NiFe/FeMn/Co trilayers
Authors: Barreto P. G. , Sousa M. A. , Pelegrini F. , Alayo W. , Litterst F. J. , Baggio-Saitovitch E.
Published: May 2014

Exchange-biased NiFe/FeMn/Co trilayers were grown by dc magnetron sputtering and analyzed by in-plane ferromagnetic resonance using Q-band microwaves. The experiments revealed that distinct Co and NiFe resonance modes were excited by the microwave field. A misalignment between the anisotropy axes of the magnetic layers was deduced from the angular variations of the resonance fields, which also showed the effects of uniaxial and unidirectional anisotropies. A phenomenological model was used to fit the experimental results taking also into account a rotatable anisotropy field associated to the domain structure of the FeMn layer and the magnetic history of the films.
Superconducting magnetic Wollaston prism for neutron spin encoding
Authors: Li F. , Parnell S. R. , Hamilton W. A. , Maranville B. B. , Wang T. , Semerad R. , Baxter D. V. , Cremer J. T. , Pynn R.
Published: May 2014

A magnetic Wollaston prism can spatially split a polarized neutron beam into two beams with different neutron spin states, in a manner analogous to an optical Wollaston prism. Such a Wollaston prism can be used to encode the trajectory of neutrons into the Larmor phase associated with their spin degree of freedom. This encoding can be used for neutron phase-contrast radiography and in spin echo scattering angle measurement (SESAME). In this paper, we show that magnetic Wollaston prisms with highly uniform magnetic fields and low Larmor phase aberration can be constructed to preserve neutron polarization using high temperature superconducting (HTS) materials. The Meissner effect of HTS films is used to confine magnetic fields produced electromagnetically by current-carrying HTS tape wound on suitably shaped soft iron pole pieces. The device is cooled to ∼30 K by a closed cycle refrigerator, eliminating the need to replenish liquid cryogens and greatly simplifying operation and maintenance. A HTS film ensures that the magnetic field transition within the prism is sharp, well-defined, and planar due to the Meissner effect. The spin transport efficiency across the device was measured to be ∼98.5% independent of neutron wavelength and energizing current. The position-dependent Larmor phase of neutron spins was measured at the NIST Center for Neutron Research facility and found to agree well with detailed simulations. The phase varies linearly with horizontal position, as required, and the neutron beam shows little depolarization. Consequently, the device has advantages over existing devices with similar functionality and provides the capability for a large neutron beam (20 mm × 30 mm) and an increase in length scales accessible to SESAME to beyond 10 μm. With further improvements of the external coupling guide field in the prototype device, a larger neutron beam could be employed.
Direct numerical simulation of steady state, three dimensional, laminar flow around a wall mounted cube
Authors: Liakos Anastasios , Malamataris Nikolaos A.
Published: May 2014

The topology and evolution of flow around a surface mounted cubical object in three dimensional channel flow is examined for low to moderate Reynolds numbers. Direct numerical simulations were performed via a home made parallel finite element code. The computational domain has been designed according to actual laboratory experiment conditions. Analysis of the results is performed using the three dimensional theory of separation. Our findings indicate that a tornado-like vortex by the side of the cube is present for all Reynolds numbers for which flow was simulated. A horseshoe vortex upstream from the cube was formed at Reynolds number approximately 1266. Pressure distributions are shown along with three dimensional images of the tornado-like vortex and the horseshoe vortex at selected Reynolds numbers. Finally, and in accordance to previous work, our results indicate that the upper limit for the Reynolds number for which steady state results are physically realizable is roughly 2000.
Influence of bias voltage and temperature on charge transfer states in organic photovoltaic and electroluminescent integrated device
Authors: Huang Jiang , Wang Hanyu , Qi Yige , Yu Junsheng
Published: May 2014

Based on the organic photovoltaic (PV) and electroluminescent (EL) integrated device with a structure of SubPc/C60 heterojunction, both PV and EL properties of charge transfer states (CTSs) were simultaneously investigated. By means of infrared and visible isolating method, the EL characteristics of CTSs and singlet-triplet excitons were separated, and their properties dependence on bias voltage and temperature was analyzed by introducing modified diode models. From the simulation on the emissive photons from CTSs, the temperature independent parameters of CTSs were extracted, which have close relationship with thermal activation energy and effective emissive state number of CTSs at the SubPc/C60 interface.
Iterative derivation of effective potentials to sample the conformational space of proteins at atomistic scale
Authors: Capelli Riccardo , Paissoni Cristina , Sormanni Pietro , Tiana Guido
Published: May 2014

The current capacity of computers makes it possible to perform simulations of small systems with portable, explicit-solvent potentials achieving high degree of accuracy. However, simplified models must be employed to exploit the behavior of large systems or to perform systematic scans of smaller systems. While powerful algorithms are available to facilitate the sampling of the conformational space, successful applications of such models are hindered by the availability of simple enough potentials able to satisfactorily reproduce known properties of the system. We develop an interatomic potential to account for a number of properties of proteins in a computationally economic way. The potential is defined within an all-atom, implicit solvent model by contact functions between the different atom types. The associated numerical values can be optimized by an iterative Monte Carlo scheme on any available experimental data, provided that they are expressible as thermal averages of some conformational properties. We test this model on three different proteins, for which we also perform a scan of all possible point mutations with explicit conformational sampling. The resulting models, optimized solely on a subset of native distances, not only reproduce the native conformations within a few Angstroms from the experimental ones, but show the cooperative transition between native and denatured state and correctly predict the measured free-energy changes associated with point mutations. Moreover, differently from other structure-based models, our method leaves a residual degree of frustration, which is known to be present in protein molecules.
Curvature suppresses the Rayleigh-Taylor instability
Authors: Trinh Philippe H. , Kim Hyoungsoo , Hammoud Naima , Howell Peter D. , Chapman S. Jonathan , Stone Howard A.
Published: May 2014

The dynamics of a thin liquid film on the underside of a curved cylindrical substrate is studied. The evolution of the liquid layer is investigated as the film thickness and the radius of curvature of the substrate are varied. A dimensionless parameter (a modified Bond number) that incorporates both geometric parameters, gravity, and surface tension is identified, and allows the observations to be classified according to three different flow regimes: stable films, films with transient growth of perturbations followed by decay, and unstable films. Experiments and linear stability theory confirm that below a critical value of the Bond number curvature of the substrate suppresses the Rayleigh-Taylor instability.
Synthesis of rock-salt type lithium borohydride and its peculiar Li+ ion conduction properties
Authors: Miyazaki R. , Maekawa H. , Takamura H.
Published: May 2014

The high energy density and excellent cycle performance of lithium ion batteries makes them superior to all other secondary batteries and explains why they are widely used in portable devices. However, because organic liquid electrolytes have a higher operating voltage than aqueous solution, they are used in lithium ion batteries. This comes with the risk of fire due to their flammability. Solid electrolytes are being investigated to find an alternative to organic liquid. However, the nature of the solid-solid point contact at the interface between the electrolyte and electrode or between the electrolyte grains is such that high power density has proven difficult to attain. We develop a new method for the fabrication of a solid electrolyte using LiBH4, known for its super Li+ ion conduction without any grain boundary contribution. The modifications to the conduction pathway achieved by stabilizing the high pressure form of this material provided a new structure with some LiBH4, more suitable to the high rate condition. We synthesized the H.P. form of LiBH4 under ambient pressure by doping LiBH4 with the KI lattice by sintering. The formation of a KI - LiBH4 solid solution was confirmed both macroscopically and microscopically. The obtained sample was shown to be a pure Li+ conductor despite its small Li+ content. This conduction mechanism, where the light doping cation played a major role in ion conduction, was termed the “Parasitic Conduction Mechanism.” This mechanism made it possible to synthesize a new ion conductor and is expected to have enormous potential in the search for new battery materials.
Computational insights of water droplet transport on graphene sheet with chemical density
Authors: Zhang Liuyang , Wang Xianqiao
Published: May 2014

Surface gradient has been emerging as an intriguing technique for nanoscale particle manipulation and transportation. Owing to its outstanding and stable chemical properties, graphene with covalently bonded chemical groups represents extraordinary potential for the investigation of nanoscale transport in the area of physics and biology. Here, we employ molecular dynamics simulations to investigate the fundamental mechanism of utilizing a chemical density on a graphene sheet to control water droplet motions on it. Simulation results have demonstrated that the binding energy difference among distinct segment of graphene in terms of interaction between the covalently bonded oxygen atoms on graphene and the water molecules provides a fundamental driving force to transport the water droplet across the graphene sheet. Also, the velocity of the water droplet has showed a strong dependence on the relative concentration of oxygen atoms between successive segments. Furthermore, a multi-direction channel provides insights to guide the transportation of objects towards a targeted position, separating the mixtures with a system of specific chemical functionalization. Our findings shed illuminating lights on the surface gradient method and therefore provide a feasible way to control nanoscale motion on the surface and mimic the channelless microfluidics.
Structural transformations in NiTi shape memory alloy nanowires
Authors: Mirzaeifar Reza , Gall Ken , Zhu Ting , Yavari Arash , DesRoches Reginald
Published: May 2014

Martensitic phase transformation in bulk Nickle-Titanium (NiTi)—the most widely used shape memory alloy—has been extensively studied in the past. However, the structures and properties of nanostructured NiTi remain poorly understood. Here, we perform molecular dynamics simulations to study structural transformations in NiTi nanowires. We find that the tendency to reduce the surface energy in NiTi nanowires can lead to a new phase transformation mechanism from the austenitic B2 to the martensitic B19 phase. We further show that the NiTi nanowires exhibit the pseudoelastic effects during thermo-mechanical cycling of loading and unloading via the B2 and B19 transformations. Our simulations also reveal the unique formation of compound twins, which are expected to dominate the patterning of the nanostructured NiTi alloys at high loads. This work provides the novel mechanistic insights into the martensitic phase transformations in nanostructured shape memory alloy systems.
Emergent behaviors of a holonomic particle system on a sphere
Authors: Chi Dongpyo , Choi Sun-Ho , Ha Seung-Yeal
Published: May 2014

We study sufficient conditions for the asymptotic emergence of synchronous behaviors in a holonomic particle system on a sphere, which was recently introduced by Lohe [“Non-Abelian Kuramoto model and synchronization,” J. Phys. A: Math. Theor. 42, 395101–395126 (2009)]. These conditions depend only on the coupling strength and initial position diameter. For identical particles, we show that the position diameter approaches zero asymptotically under these sufficient conditions, i.e., all particles approach to the same position. For non-identical particles, the particle positions do not shrink to one point, but can be squeezed into some small region whose diameter is inversely proportional to the coupling strength, when the coupling strength is large. We also provide several numerical results to confirm our analytical findings.
Multiple double-metal bias-free terahertz emitters
Authors: McBryde D. , Gow P. , Berry S. A. , Barnes M. E. , Aghajani A. , Apostolopoulos V.
Published: May 2014

We demonstrate multiplexed terahertz emitters that exhibits 2 THz bandwidth that do not require an external bias. The emitters operate under uniform illumination eliminating the need for a micro-lens array and are fabricated with periodic Au and Pb structures on GaAs. Terahertz emission originates from the lateral photo-Dember effect and from the different Schottky barrier heights of the chosen metal pair. We characterize the emitters and determine that most terahertz emission at 300 K is due to band-bending due to the Schottky barrier of the metal.
Ferromagnetism in undoped One-dimensional GaN Nanowires
Authors: Jeganathan K. , Purushothaman V. , Debnath R. , Arumugam S.
Published: May 2014

We report an intrinsic ferromagnetism in vertical aligned GaN nanowires (NW) fabricated by molecular beam epitaxy without any external catalyst. The magnetization saturates at ∼0.75 × emu/gm with the applied field of 3000 Oe for the NWs grown under the low-Gallium flux of 2.4 × 10−8 mbar. Despite a drop in saturation magnetization, narrow hysteresis loop remains intact regardless of Gallium flux. Magnetization in vertical standing GaN NWs is consistent with the spectral analysis of low-temperature photoluminescence pertaining to Ga-vacancies associated structural defects at the nanoscale.
Enhanced broadband wide-angle light-graphene interactions in visible wavelengths assisted by nanoporous gold structure
Authors: Hao Y. , Zhao X. , Song C. , Chen L. , Shi W. , Liu F.
Published: May 2014

We experimentally demonstrate enhanced light-graphene interactions aided by the surface plasmons sustained in bicontinuous structure of nanoporous gold (NPG) film in visible wavelengths. Coupling with such amorphous metallic structure enables broadband and wide-angle absorption enhancement of graphene. The average absorption enhancement at normal incidence is at one-order of magnitude larger than that of pristine graphene, to be 25.6%. In addition, the strong near electric fields at the surface proximity of NPG film greatly promote the Raman scattering of graphene up to one order of magnitude for either 514.5- or 632.8-nm laser excitation. Our study shows that NPG film is a promising platform in graphene-integrated applications in visible regime such as photodetectors and light-harvesting devices.
Coherent and tunable terahertz radiation from graphene surface plasmon polaritons excited by an electron beam
Authors: Liu Shenggang , Zhang Chao , Hu Min , Chen Xiaoxing , Zhang Ping , Gong Sen , Zhao Tao , Zhong Renbin
Published: May 2014

Although surface plasmon polaritons (SPPs) resonance in graphene can be tuned in the terahertz regime, transforming such SPPs into coherent terahertz radiation has not been achieved. Here, we propose a graphene-based coherent terahertz radiation source with greatly enhanced intensity. The radiation works at room temperature, it is tunable and can cover the whole terahertz regime. The radiation intensity generated with this method is 400 times stronger than that from SPPs at a conventional dielectric or semiconducting surface and is comparable to that from the most advanced photonics source such as a quantum cascade laser. The physical mechanism for this strong radiation is presented. The phase diagrams defining the parameters range for the occurrence of radiation is also shown.
Bioisosteric Fluorine in the Clandestine Design of Synthetic Cannabinoids
Authors: Wilkinson Shane M. , Banister Samuel D. , Kassiou Michael
Published: May 2014

Over the past decade, a plethora of indole-based synthetic cannabinoids (SCs) have emerged with their structures clearly inspired by scientific literature. Their structures continually evolve to elude detection by law enforcement and circumvent finite scheduling laws. The latest generation of SCs follow patent literature that encompasses a bioisosteric fluorine-for-hydrogen replacement commonly applied in medicinal chemistry. Unlike traditional pharmaceutical development, where rigorous preclinical evaluation is completed before human administration, these SCs are distributed for intended recreational consumption with little-to-no pharmacological data known. This highlight explores the evolution of SCs to this latest generation of fluorinated SCs where accumulating evidence indicates increased health concerns.
The unique regulation of iron-sulfur cluster biogenesis in a Gram-positive bacterium
Authors: Santos Joana A. , Alonso-García Noelia , Macedo-Ribeiro Sandra , Pereira Pedro José Barbosa
Published: May 2014

Significance

Iron-sulfur clusters are ubiquitous cofactors of proteins intervening in disparate biological processes. Iron-sulfur cluster biosynthesis pathways are tightly regulated in Gram-negative bacteria. One of the participating transcription factors, iron-sulfur cluster pathway (ISC) regulator (IscR), can itself bind an iron-sulfur cluster. Depending on its ligation status, IscR recognizes and binds to distinct promoters, therefore modulating cluster biosynthesis. This unique protein at the crossroad between the ISC and sulfur assimilation (SUF) iron-sulfur cluster biosynthetic pathways was thought to be restricted to Gram-negative bacteria. We demonstrated the existence of a functional IscR in the unique Gram-positive bacterium
Thermincola potens
. Structural and functional analysis of
T. potens
and
Escherichia coli
IscR unveiled a conserved mechanism of promoter discrimination, along with subtle structural differences that explain their distinct DNA sequence recognition specificity.
Ecological Risk of Live Bait Fisheries: A New Angle on Selective Fishing
Authors: Drake D Andrew R , Mandrak Nicholas E
Published: May 2014

The use of live baitfish is a cultural norm in many jurisdictions across North America. Because baitfish are often harvested from mixed stocks in the wild, the potential for bycatch exists, leading to the inadvertent relocation of nontarget species via distribution networks and anglers; therefore, like many fisheries, core issues revolve around selective fishing. We assess selectivity of bait fisheries in Ontario, focusing on the prevalence of bycatch within the commercial supply chain and the propensity for nontarget species introductions by anglers. Selection for target stocks was strong; however, species assemblages in retail tanks and angler purchases included game, imperiled, invasive, and other nontarget species. The combination of bycatch, a large volume of angling trips, and risky angler behavior results in high probabilities of introducing the suite of nontarget species contained incidentally. Pathway approaches to management provide opportunities to increase selectivity, manage the risk of species introductions, and sustain the integrity of bait operations throughout North America.

RESUMEN

el uso de carnada viva es una norma cultural en varias jurisdicciones de Norte América. Debido a que los peces que se utilizan como carnada a veces son capturados junto con una mezcla de stocks silvestres, existe el potencial de que se vuelvan fauna de acompañamiento, lo que tiene como consecuencia que especies no objetivo sean reubicadas de forma inadvertida a través pescadores y de redes de distribución; por esta razón, como sucede en muchas pesquerías, el problema medular gira en torno a la pesca selectiva. En este trabajo se evalúa la selectividad de las pesquerías de carnada en Ontario, Canadá, haciendo enfasis en la prevalencia de la fauna de acompañamiento en la cadena productiva y en la propensión que existe por parte de los pescadores a reubicar especies no objetivo. La selectividad que existe para los stocks objetivo es intensa, sin embargo las asociaciones de peces que comercializan los pescadores incluyen especies de pesca deportiva, especies en peligro, especies invasivas y otras especies no objetivo. La combinación de fauna de acompañamiento, una enorme cantidad de viajes de pesca y un comportamiento riesgoso por parte de los pescadores, da como resultado una alta probabilidad de introducir una amplia gama de especies no objetivo que son contenidas incidentalmente. El manejo utilizando corredores, podria incrementar la selectividad, controlar la introducción de especies y mantener la integridad de las operaciones pesqueras con carnada a lo largo de Norte América.
Identification and functional analysis of peroxiredoxin isoforms in Euglena gracilis
Authors: Tamaki Shun , Maruta Takanori , Sawa Yoshihiro , Shigeoka Shigeru , Ishikawa Takahiro
Published: May 2014

Euglena gracilis lacks catalase and contains ascorbate peroxidase (APX) which is localized exclusively in the cytosol. Other enzymes that scavenge reactive oxygen species (ROS) in Euglena have not yet been identified; therefore, ROS metabolism, especially in organelles, remains unclear in Euglena. The full-length cDNAs of four Euglena peroxiredoxins (EgPrxs) were isolated in this study. EgPrx1 and -4 were predicted to be localized in the cytosol, and EgPrx2 and -3 in plastids and mitochondria, respectively. The catalytic efficiencies of recombinant EgPrxs were similar to those of plant thiol-peroxidases, but were markedly lower than those of APX from Euglena. However, transcript levels of EgPrx1, -2, and -3 were markedly higher than those of APX. The growth rate of Euglena cells, in which the expression of EgPrx1 and -4 was suppressed by gene silencing, was markedly reduced under normal conditions, indicating physiological significance of Prx proteins.
Efficient screening of environmental isolates for Saccharomyces cerevisiae strains that are suitable for brewing
Authors: Fujihara Hidehiko , Hino Mika , Takashita Hideharu , Kajiwara Yasuhiro , Okamoto Keiko , Furukawa Kensuke
Published: May 2014

We developed an efficient screening method for Saccharomyces cerevisiae strains from environmental isolates. MultiPlex PCR was performed targeting four brewing S. cerevisiae genes (SSU1, AWA1, BIO6, and FLO1). At least three genes among the four were amplified from all S. cerevisiae strains. The use of this method allowed us to successfully obtain S. cerevisiae strains.
The multivariate arithmetic Tutte polynomial
Authors: Brändén Petter , Moci Luca
Published: May 2014

We introduce an arithmetic version of the multivariate Tutte polynomial and a quasi-polynomial that interpolates between the two. A generalized Fortuin-Kasteleyn representation with applications to arithmetic colorings and flows is obtained. We give a new and more general proof of the positivity of the coefficients of the arithmetic Tutte polynomial and (in the representable case) a geometrical interpretation of them.
Parity sheaves
Authors: Juteau Daniel , Mautner Carl , Williamson Geordie
Published: May 2014

Given a stratified variety

X
X

with strata satisfying a cohomological parity-vanishing condition, we define and show the uniqueness of “parity sheaves,” which are objects in the constructible derived category of sheaves with coefficients in an arbitrary field or complete discrete valuation ring. This construction depends on the choice of a parity function on the strata.

If

X
X

admits a resolution also satisfying a parity condition, then the direct image of the constant sheaf decomposes as a direct sum of parity sheaves, and the multiplicities of the indecomposable summands are encoded in certain refined intersection forms appearing in the work of de Cataldo and Migliorini. We give a criterion for the Decomposition Theorem to hold in the semi-small case.

Our framework applies to many stratified varieties arising in representation theory such as generalised flag varieties, toric varieties, and nilpotent cones. Moreover, parity sheaves often correspond to interesting objects in representation theory. For example, on flag varieties we recover in a unified way several well-known complexes of sheaves. For one choice of parity function we obtain the indecomposable tilting perverse sheaves. For another, when using coefficients of characteristic zero, we recover the intersection cohomology sheaves and in arbitrary characteristic the special sheaves of Soergel, which are used by Fiebig in his proof of Lusztig’s conjecture.
Marmoset monkeys evaluate third-party reciprocity
Authors: Kawai Nobuyuki , Yasue Miyuki , Banno Taku , Ichinohe Noritaka
Published: May 2014

Many non-human primates have been observed to reciprocate and to understand reciprocity in one-to-one social exchanges. A recent study demonstrated that capuchin monkeys are sensitive to both third-party reciprocity and violation of reciprocity; however, whether this sensitivity is a function of general intelligence, evidenced by their larger brain size relative to other primates, remains unclear. We hypothesized that highly pro-social primates, even with a relatively smaller brain, would be sensitive to others' reciprocity. Here, we show that common marmosets discriminated between human actors who reciprocated in social exchanges with others and those who did not. Monkeys accepted rewards less frequently from non-reciprocators than they did from reciprocators when the non-reciprocators had retained all food items, but they accepted rewards from both actors equally when they had observed reciprocal exchange between the actors. These results suggest that mechanisms to detect unfair reciprocity in third-party social exchanges do not require domain-general higher cognitive ability based on proportionally larger brains, but rather emerge from the cooperative and pro-social tendencies of species, and thereby suggest this ability evolved in multiple primate lineages.
Reinitiation enhances reliable transcriptional responses in eukaryotes
Authors: Liu Bo , Yuan Zhanjiang , Aihara Kazuyuki , Chen Luonan
Published: May 2014

Gene transcription is a noisy process carried out by the transcription machinery recruited to the promoter. Noise reduction is a fundamental requirement for reliable transcriptional responses which in turn are crucial for signal transduction. Compared with the relatively simple transcription initiation in prokaryotes, eukaryotic transcription is more complex partially owing to its additional reinitiation mechanism. By theoretical analysis, we showed that reinitiation reduces noise in eukaryotic transcription independent of the transcription level. Besides, a higher reinitiation rate enables a stable scaffold complex an advantage in noise reduction. Finally, we showed that the coupling between scaffold formation and transcription can further reduce transcription noise independent of the transcription level. Furthermore, compared with the reinitiation mechanism, the noise reduction effect of the coupling can be of more significance in the case that the transcription level is low and the intrinsic noise dominates. Our results uncover a mechanistic route which eukaryotes may use to facilitate a more reliable response in the noisy transcription process.
Synergy between shear-induced migration and secondary flows on red blood cells transport in arteries: considerations on oxygen transport
Authors: Biasetti Jacopo , Spazzini Pier Giorgio , Hedin Ulf , Gasser T. Christian
Published: May 2014

Shear-induced migration of red blood cells (RBCs) is a well-known phenomenon characterizing blood flow in the small vessels (micrometre to millimetre size) of the cardiovascular system. In large vessels, like the abdominal aorta and the carotid artery (millimetre to centimetre size), the extent of this migration and its interaction with secondary flows has not been fully elucidated. RBC migration exerts its influence primarily on platelet concentration, oxygen transport and oxygen availability at the luminal surface, which could influence vessel wall disease processes in and adjacent to the intima. Phillips' shear-induced particle migration model, coupled to the Quemada viscosity model, was employed to simulate the macroscopic behaviour of RBCs in four patient-specific geometries: a normal abdominal aorta, an abdominal aortic aneurysm (AAA), a normal carotid bifurcation and a stenotic carotid bifurcation. Simulations show a migration of RBCs from the near-wall region with a lowering of wall haematocrit (volume fraction of RBCs) on the posterior side of the normal aorta and on the lateral-external side of the iliac arteries. A marked migration is observed on the outer wall of the carotid sinus, along the common carotid artery and in the carotid stenosis. No significant migration is observed in the AAA. The spatial and temporal patterns of wall haematocrit are correlated with the near-wall shear layer and with the secondary flows induced by the vessel curvature. In particular, secondary flows accentuate the initial lowering in RBC near-wall concentration by convecting RBCs from the inner curvature side to the outer curvature side. The results reinforce data in literature showing a decrease in oxygen partial pressure on the inner curvature wall of the carotid sinus induced by the presence of secondary flows. The lowering of wall haematocrit is postulated to induce a decrease in oxygen availability at the luminal surface through a diminished concentration of oxyhaemoglobin, hence contributing, with the reported lowered oxygen partial pressure, to local hypoxia.
Evidence of VX nerve agent use from contaminated white mustard plants
Authors: Gravett Matthew R. , Hopkins Farrha B. , Self Adam J. , Webb Andrew J. , Timperley Christopher M. , Baker Matthew J.
Published: May 2014

The Chemical Weapons Convention prohibits the development, production, acquisition, stockpiling, retention, transfer or use of chemical weapons by Member States. Verification of compliance and investigations into allegations of use require accurate detection of chemical warfare agents (CWAs) and their degradation products. Detection of CWAs such as organophosphorus nerve agents in the environment relies mainly upon the analysis of soil. We now present a method for the detection of the nerve agent VX and its hydrolysis products by gas chromatography and liquid chromatography mass spectrometry of ethanol extracts of contaminated white mustard plants (
Sinapis alba
) which retained the compounds of interest for up to 45 days. VX is hydrolysed by the plants to ethyl methylphosphonic acid and then to methylphosphonic acid. The utility of white mustard as a nerve agent detector and remediator of nerve agent-polluted sites is discussed. The work described will help deter the employment of VX in conflict.
Protein-poor diet reduces host-specific immune gene expression in
Bombus terrestris
Authors: Brunner Franziska S. , Schmid-Hempel Paul , Barribeau Seth M.
Published: May 2014

Parasites infect hosts non-randomly as genotypes of hosts vary in susceptibility to the same genotypes of parasites, but this specificity may be modulated by environmental factors such as nutrition. Nutrition plays an important role for any physiological investment. As immune responses are costly, resource limitation should negatively affect immunity through trade-offs with other physiological requirements. Consequently, nutritional limitation should diminish immune capacity in general, but does it also dampen differences among hosts? We investigated the effect of short-term pollen deprivation on the immune responses of our model host
Bombus terrestris
when infected with the highly prevalent natural parasite
Crithidia bombi
. Bumblebees deprived of pollen, their protein source, show reduced immune responses to infection. They failed to upregulate a number of genes, including antimicrobial peptides, in response to infection. In particular, they also showed less specific immune expression patterns across individuals and colonies. These findings provide evidence for how immune responses on the individual-level vary with important elements of the environment and illustrate how nutrition can functionally alter not only general resistance, but also alter the pattern of specific host–parasite interactions.
Phylogenomic analysis of echinoderm class relationships supports Asterozoa
Authors: Telford Maximilian J. , Lowe Christopher J. , Cameron Christopher B. , Ortega-Martinez Olga , Aronowicz Jochanan , Oliveri Paola , Copley Richard R.
Published: May 2014

While some aspects of the phylogeny of the five living echinoderm classes are clear, the position of the ophiuroids (brittlestars) relative to asteroids (starfish), echinoids (sea urchins) and holothurians (sea cucumbers) is controversial. Ophiuroids have a pluteus-type larva in common with echinoids giving some support to an ophiuroid/echinoid/holothurian clade named Cryptosyringida. Most molecular phylogenetic studies, however, support an ophiuroid/asteroid clade (Asterozoa) implying either convergent evolution of the pluteus or reversals to an auricularia-type larva in asteroids and holothurians. A recent study of 10 genes from four of the five echinoderm classes used ‘phylogenetic signal dissection’ to separate alignment positions into subsets of (i) suboptimal, heterogeneously evolving sites (invariant plus rapidly changing) and (ii) the remaining optimal, homogeneously evolving sites. Along with most previous molecular phylogenetic studies, their set of heterogeneous sites, expected to be more prone to systematic error, support Asterozoa. The homogeneous sites, in contrast, support an ophiuroid/echinoid grouping, consistent with the cryptosyringid clade, leading them to posit homology of the ophiopluteus and echinopluteus. Our new dataset comprises 219 genes from all echinoderm classes; analyses using probabilistic Bayesian phylogenetic methods strongly support Asterozoa. The most reliable, slowly evolving quartile of genes also gives highest support for Asterozoa; this support diminishes in second and third quartiles and the fastest changing quartile places the ophiuroids close to the root. Using phylogenetic signal dissection, we find heterogenous sites support an unlikely grouping of Ophiuroidea + Holothuria while homogeneous sites again strongly support Asterozoa. Our large and taxonomically complete dataset finds no support for the cryptosyringid hypothesis; in showing strong support for the Asterozoa, our preferred topology leaves the question of homology of pluteus larvae open.
Role of the phosphopantetheinyltransferase enzyme, PswP, in the biosynthesis of antimicrobial secondary metabolites by Serratia marcescens Db10
Authors: Gerc Amy J. , Stanley-Wall Nicola R. , Coulthurst Sarah J.
Published: May 2014

Phosphopantetheinyltransferase (PPTase) enzymes fulfil essential roles in primary and secondary metabolism in prokaryotes, archaea and eukaryotes. PPTase enzymes catalyse the essential modification of the carrier protein domain of fatty acid synthases, polyketide synthases (PKSs) and non-ribosomal peptide synthetases (NRPSs). In bacteria and fungi, NRPS and PKS enzymes are often responsible for the biosynthesis of secondary metabolites with clinically relevant properties; these secondary metabolites include a variety of antimicrobial peptides. We have previously shown that in the Gram-negative bacteriumSerratia marcescensDb10, the PPTase enzyme PswP is essential for the biosynthesis of an NRPS-PKS dependent antibiotic called althiomycin. In this work we utilize bioinformatic analyses to classify PswP as belonging to the F/KES subfamily of Sfp type PPTases and to putatively identify additional NRPS substrates of PswP, in addition to the althiomycin NRPS-PKS, inSer. marcescensDb10. We show that PswP is required for the production of three diffusible metabolites by this organism, each possessing antimicrobial activity againstStaphylococcus aureus. Genetic analyses identify the three metabolites as althiomycin, serrawettin W2 and an as-yet-uncharacterized siderophore, which may be related to enterobactin. Our results highlight the use of an individual PPTase enzyme in multiple biosynthetic pathways, each contributing to the ability ofSer. marcescensto inhibit competitor bacteria by the production of antimicrobial secondary metabolites.
Low-temperature catalyst activator: mechanism of dense carbon nanotube forest growth studied using synchrotron radiation
Authors: Takashima Akito , Izumi Yudai , Ikenaga Eiji , Ohkochi Takuo , Kotsugi Masato , Matsushita Tomohiro , Muro Takayuki , Kawabata Akio , Murakami Tomo , Nihei Mizuhisa , Yokoyama Naoki
Published: May 2014

The mechanism of the one-order-of-magnitude increase in the density of vertically aligned carbon nanotubes (CNTs) achieved by a recently developed thermal chemical vapor deposition process was studied using synchrotron radiation spectroscopic techniques. In the developed process, a Ti film is used as the underlayer for an Fe catalyst film. A characteristic point of this process is that C2H2feeding for the catalyst starts at a low temperature of 450°C, whereas conventional feeding temperatures are ∼800°C. Photoemission spectroscopy using soft and hard X-rays revealed that the Ti underlayer reduced the initially oxidized Fe layer at 450°C. A photoemission intensity analysis also suggested that the oxidized Ti layer at 450°C behaved as a support for nanoparticle formation of the reduced Fe, which is required for dense CNT growth. In fact, a CNT growth experiment, where the catalyst chemical state was monitoredin situby X-ray absorption spectroscopy, showed that the reduced Fe yielded a CNT forest at 450°C. Contrarily, an Fe layer without the Ti underlayer did not yield such a CNT forest at 450°C. Photoemission electron microscopy showed that catalyst annealing at the conventional feeding temperature of 800°C caused excess catalyst agglomeration, which should lead to sparse CNTs. In conclusion, in the developed growth process, the low-temperature catalyst activation by the Ti underlayer before the excess Fe agglomeration realised the CNT densification.