bluuebunny/crossref_metadata_2025 huggingface dataset:
Sucrose and ABA regulate starch biosynthesis in maize through a novel transcription factor, ZmEREB156
Authors: Huang Huanhuan , Xie Sidi , Xiao Qianlin , Wei Bin , Zheng Lanjie , Wang Yongbin , Cao Yao , Zhang Xiangge , Long Tiandan , Li Yangping , Hu Yufeng , Yu Guowu , Liu Hanmei , Liu Yinghong , Huang Zhi , Zhang Junjie , Huang Yubi
Published: June 2016

Sucrose is not only the carbon source for starch synthesis, but also a signal molecule. Alone or in coordination with ABA, it can regulate the expression of genes involved in starch synthesis. To investigate the molecular mechanisms underlying this effect, maize endosperms were collected from Zea mays L. B73 inbred line 10 d after pollination and treated with sucrose, ABA, or sucrose plus ABA at 28 °C in the dark for 24 h. RNA-sequence analysis of the maize endosperm transcriptome revealed 47 candidate transcription factors among the differentially expressed genes. We therefore speculate that starch synthetic gene expression is regulated by transcription factors induced by the combination of sucrose and ABA. ZmEREB156, a candidate transcription factor, is induced by sucrose plus ABA and is involved in starch biosynthesis. The ZmEREB156-GFP-fused protein was localized in the nuclei of onion epidermal cells and ZmEREB156 protein possessed strong transcriptional activation activity. Promoter activity of the starch-related genes Zmsh2 and ZmSSIIIa increased after overexpression of ZmEREB156 in maize endosperm. ZmEREB156 could bind to the ZmSSIIIa promoter but not the Zmsh2 promoter in a yeast one-hybrid system. Thus, ZmEREB156 positively modulates starch biosynthetic gene ZmSSIIIa via the synergistic effect of sucrose and ABA.
Resolving new ultrastructural features of cytokinetic abscission with soft-X-ray cryo-tomography
Authors: Sherman Shachar , Kirchenbuechler David , Nachmias Dikla , Tamir Adi , Werner Stephan , Elbaum Michael , Elia Natalie
Published: June 2016

Mammalian cytokinetic abscission is mediated by the ESCRT membrane fission machinery. While much has been clarified on the topology and kinetics of abscission through high-resolution microscopy, key questions regarding the mechanism of abscission remain open. Here we apply cryogenic soft-X-ray tomography to elucidate new ultrastructural details in the intercellular membrane bridge connecting cells undergoing abscission. In particular, we resolve defined ring-like structures inside the midbody dark zone that have been inaccessible to EM and identify membrane extrusions at the abscission sites. In cells at late stages of abscission we resolve a complex array of helical spirals, extending the structural information obtained by EM. Our results highlight the advantages of soft-X-ray tomography and emphasize the importance of using complementary approaches for characterizing cellular structures. Notably, by providing new structural data from intact cells we present a realistic view on the topology of abscission and suggest new mechanistic models for ESCRT mediated abscission.
A simple strategy guides the complex metabolic regulation in Escherichia coli
Authors: Facchetti Giuseppe
Published: June 2016

A way to decipher the complexity of the cellular metabolism is to study the effect of different external perturbations. Through an analysis over a sufficiently large set of gene knockouts and growing conditions, one aims to find a unifying principle that governs the metabolic regulation. For instance, it is known that the cessation of the microorganism proliferation after a gene deletion is only transient. However, we do not know the guiding principle that determines the partial or complete recovery of the growth rate, the corresponding redistribution of the metabolic fluxes and the possible different phenotypes. In spite of this large variety in the observed metabolic adjustments, we show that responses of E. coli to several different perturbations can always be derived from a sequence of greedy and myopic resilencings. This simple mechanism provides a detailed explanation for the experimental dynamics both at cellular (proliferation rate) and molecular level (13C-determined fluxes), also in case of appearance of multiple phenotypes. As additional support, we identified an example of a simple network motif that is capable of implementing this myopic greediness in the regulation of the metabolism.
Attention enhances stimulus representations in macaque visual cortex without affecting their signal-to-noise level
Authors: Daliri Mohammad Reza , Kozyrev Vladislav , Treue Stefan
Published: June 2016

The magnitude of the attentional modulation of neuronal responses in visual cortex varies with stimulus contrast. Whether the strength of these attentional influences is similarly dependent on other stimulus properties is unknown. Here we report the effect of spatial attention on responses in the medial-temporal area (MT) of macaque visual cortex to moving random dots pattern of various motion coherences, i.e. signal-to-noise ratios. Our data show that allocating spatial attention causes a gain change in MT neurons. The magnitude of this attentional modulation is independent of the attended stimulus’ motion coherence, creating a multiplicative scaling of the neuron’s coherence-response function. This is consistent with the characteristics of gain models of attentional modulation and suggests that attention strengthens the neuronal representation of behaviorally relevant visual stimuli relative to unattended stimuli, but without affecting their signal-to-noise ratios.
A faulty interaction between SOD1 and hCCS in neurodegenerative disease
Authors: Wright Gareth S. A. , Antonyuk Svetlana V. , Hasnain S. Samar
Published: June 2016

A proportion of Amyotrophic lateral sclerosis (ALS) cases result from impaired mutant superoxide dismutase-1 (SOD1) maturation. The copper chaperone for SOD1 (hCCS) forms a transient complex with SOD1 and catalyses the final stages of its maturation. We find that a neurodegenerative disease-associated hCCS mutation abrogates the interaction with SOD1 by inhibiting hCCS zinc binding. Analogously, SOD1 zinc loss has a detrimental effect on the formation, structure and disassociation of the hCCS-SOD1 heterodimer. This suggests that hCCS functionality is impaired by ALS mutations that reduce SOD1 zinc affinity. Furthermore, stabilization of wild-type SOD1 by chemical modification including cisplatination, inhibits complex formation. We hypothesize that drug molecules designed to stabilize ALS SOD1 mutants that also target the wild-type form will lead to characteristics common in SOD1 knock-outs. Our work demonstrates the applicability of chromatographic SAXS when studying biomolecules predisposed to aggregation or dissociation; attributes frequently reported for complexes involved in neurodegenerative disease.
Mechanobiological induction of long-range contractility by diffusing biomolecules and size scaling in cell assemblies
Authors: Dasbiswas K. , Alster E. , Safran S. A.
Published: June 2016

Mechanobiological studies of cell assemblies have generally focused on cells that are, in principle, identical. Here we predict theoretically the effect on cells in culture of locally introduced biochemical signals that diffuse and locally induce cytoskeletal contractility which is initially small. In steady-state, both the concentration profile of the signaling molecule as well as the contractility profile of the cell assembly are inhomogeneous, with a characteristic length that can be of the order of the system size. The long-range nature of this state originates in the elastic interactions of contractile cells (similar to long-range “macroscopic modes” in non-living elastic inclusions) and the non-linear diffusion of the signaling molecules, here termed mechanogens. We suggest model experiments on cell assemblies on substrates that can test the theory as a prelude to its applicability in embryo development where spatial gradients of morphogens initiate cellular development.
E2F1-miR-20a-5p/20b-5p auto-regulatory feedback loop involved in myoblast proliferation and differentiation
Authors: Luo Wen , Li Guihuan , Yi Zhenhua , Nie Qinghua , Zhang Xiquan
Published: June 2016

miR-17 family microRNAs (miRNAs) are crucial for embryo development, however, their role in muscle development is still unclear. miR-20a-5p and miR-20b-5p belong to the miR-17 family and are transcribed from the miR-17~92 and miR-106a~363 clusters respectively. In this study, we found that miR-20a-5p and miR-20b-5p promoted myoblast differentiation and repressed myoblast proliferation by directly binding the 3′ UTR of E2F transcription factor 1 (E2F1) mRNA. E2F1 is an important transcriptional factor for organism’s normal development. Overexpression of E2F1 in myoblasts promoted myoblast proliferation and inhibited myoblast differentiation. Conversely, E2F1 inhibition induced myoblast differentiation and repressed myoblast proliferation. Moreover, E2F1 can bind directly to promoters of the miR-17~92 and miR-106a~363 clusters and activate their transcription and E2F1 protein expression is correlated with the expression of pri-miR-17~92 and pri-miR-106a~363 during myoblast differentiation. These results suggested an auto-regulatory feedback loop between E2F1 and miR-20a-5p/20b-5p and indicated that miR-20a-5p, miR-20b-5p and E2F1 are involved in myoblast proliferation and differentiation through the auto-regulation between E2F1 and miR-20a-5p/20b-5p. These findings provide new insight into the mechanism of muscle differentiation and further shed light on the understanding of muscle development and muscle diseases.
Refraction-Assisted Solar Thermoelectric Generator based on Phase-Change Lens
Authors: Kim Myoung-Soo , Kim Min-Ki , Jo Sung-Eun , Joo Chulmin , Kim Yong-Jun
Published: June 2016

Solar thermoelectric generators (STEGs), which are used for various applications, (particularly small size electronic devices), have optical concentration systems for high energy conversion efficiency. In this study, a refraction-assisted STEG (R-STEG) is designed based on phase-change materials. As the phase-change material (PCM) changes phase from solid to liquid, its refractive index and transmittance also change, resulting in changes in the refraction of the sunlight transmitted through it, and concentration of solar energy in the phase-change lens. This innovative design facilitates double focusing the solar energy through the optical lens and a phase-change lens. This mechanism resulted in the peak energy conversion efficiencies of the R-STEG being 60% and 86% higher than those of the typical STEG at solar intensities of 1 kW m−2 and 1.5 kW m−2, respectively. In addition, the energy stored in PCM can help to generate steady electrical energy when the solar energy was removed. This work presents significant progress regarding the optical characteristic of PCM and optical concentration systems of STEGs.
Formation of simple nitrogen hydrides NH and NH2 at cryogenic temperatures through N + NH3 → NH + NH2 reaction: dark cloud chemistry of nitrogen
Authors: Nourry Sendres , Krim Lahouari
Published: June 2016

Formation of NH and NH2 at 10 K through N + NH3 → NH + NH2 reaction.
Manganese doped-iron oxide nanoparticle clusters and their potential as agents for magnetic resonance imaging and hyperthermia
Authors: Casula Maria F. , Conca Erika , Bakaimi Ioanna , Sathya Ayyappan , Materia Maria Elena , Casu Alberto , Falqui Andrea , Sogne Elisa , Pellegrino Teresa , Kanaras Antonios G.
Published: June 2016

A method for water-soluble Mn doped iron oxide clusters and their magnetic properties.
Structural and mechanistic basis for the high activity of Fe–N–C catalysts toward oxygen reduction
Authors: Li Jingkun , Ghoshal Shraboni , Liang Wentao , Sougrati Moulay-Tahar , Jaouen Frédéric , Halevi Barr , McKinney Samuel , McCool Geoff , Ma Chunrong , Yuan Xianxia , Ma Zi-Feng , Mukerjee Sanjeev , Jia Qingying
Published: June 2016

The biomimetic dynamic nature of the Fe–N–C active site with a near-optimal Fe2+/3+redox potential facilitates ORR by balancing the site-blocking effect and O2dissociation.
No measurable “cleaning” of polychlorinated biphenyls from Rainbow Trout in a 9 week depuration study with dietary exposure to 40% polyethylene microspheres
Authors: Rummel Christoph Daniel , Adolfsson-Erici Margaretha , Jahnke Annika , MacLeod Matthew
Published: June 2016

A diet containing microplastic at the highest feasible concentration did not measurably enhance fecal elimination of PCBs by Rainbow Trout.
Modern advances in heterocyclic chemistry in drug discovery
Authors: Taylor Alexandria P. , Robinson Ralph P. , Fobian Yvette M. , Blakemore David C. , Jones Lyn H. , Fadeyi Olugbeminiyi
Published: June 2016

New advances in functionalized heterocyclic chemistry are of critical importance to the medicinal chemist as it provides the ability to expand the available drug-like chemical space and drive more efficient delivery of drug discovery programs.
Research progress in electroanalytical techniques for determination of antimalarial drugs in pharmaceutical and biological samples
Authors: Thapliyal Neeta , Chiwunze Tirivashe E. , Karpoormath Rajshekhar , Goyal Rajendra N. , Patel Harun , Cherukupalli Srinivasulu
Published: June 2016

The review focusses on the role of electroanalytical methods for determination of antimalarial drugs in biological matrices and pharmaceutical formulations with a critical analysis of published voltammetric and potentiometric methods.
Phosphorus removal and recovery from dairy manure by electrocoagulation
Authors: Zhang Xin , Lin Hongjian , Hu Bo
Published: June 2016

Removal of 96.7% of phosphorus from dairy manure via electrocoagulation with low carbon steel electrodes.
Interfacial effect on Mn-doped TiO2 nanoparticles: from paramagnetism to ferromagnetism
Authors: Zhang Le , Zhu Liping , Hu Liang , Li Yaguang , Song Hui , Ye Zhizhen
Published: June 2016

Interfacial defects created during phase-transformation leads to room temperature ferromagnetism of manganese-doped TiO2 nanoparticles.
Influences of melting method on fused iron catalysts for Fischer–Tropsch synthesis
Authors: Zhang Juan , Sun Taomei , Ding Jian , Xiao Haicheng , Kong Fanhua , Chen Jiangang
Published: June 2016

The melting method for fused iron catalysts was found to be vital and those prepared by AAW performed best for the Fischer–Tropsch synthesis.
Hybrid polymer matrix composite containing polyaniline and Nafion as novel precursor of the enhanced catalyst for oxygen reduction reaction
Authors: Fu Xudong , Wang Suli , Li Huanqiao , Xia Zhangxun , Jiang Luhua , Sun Gongquan
Published: June 2016

A kind of hybrid polymer matrix composite serves as a novel nitrogen precursor for enhanced metal–nitrogen-doped carbon catalyst.
Large-scale conversion of helical-ribbon carbon nanofibers to a variety of graphene-related materials
Authors: Lobato B. , Merino C. , Barranco V. , Centeno T. A.
Published: June 2016

The control of the oxidation time of helical-ribbon carbon nanofibers enables the production of a wide variety of graphene materials.
One-step synthesis of nickel cobalt sulphides particles: tuning the composition for high performance supercapacitors
Authors: Zhang Huaihao , Guan Bing , Gu Jiangna , Li Yu , Ma Chi , Zhao Jing , Wang Tianyi , Cheng Changjing
Published: June 2016

NiS2–CoS2 composites with different Ni and Co molar ratios for supercapacitors (SCs) were synthesized by one-step hydrothermal co-deposition method. Among them, Ni/Co/S-1 (Ni : Co ratio of 1 : 1) possesses the highest Cm value at the same current densities.
A highly sensitive non-enzymatic hydrogen peroxide and hydrazine electrochemical sensor based on 3D micro-snowflake architectures of α-Fe2O3
Authors: Majumder S. , Saha B. , Dey S. , Mondal R. , Kumar S. , Banerjee S.
Published: June 2016

In the present work, well crystalline 3D micro-snowflake structured α-Fe2O3has been successfully synthesized on a large scaleviaa simple hydrothermal reaction by hydrolysis of a K3Fe(CN)6precursor.
Stabilization of alkali metal ions interaction with OH-functionalized graphene via clustering of OH groups – implications in charge storage applications
Authors: Dobrota Ana S. , Gutić Sanjin , Kalijadis Ana , Baljozović Miloš , Mentus Slavko V. , Skorodumova Natalia V. , Pašti Igor A.
Published: June 2016

Clustering of OH groups over graphene basal plane stabilizes the interaction with alkali metal ions, preventing irreversible reduction, while the charge is stored in OH groups interacting with ions and the π electronic system.
Two- and four-probe field-effect and Hall mobilities in transition metal dichalcogenide field-effect transistors
Authors: Nazir Ghazanfar , Khan Muhammad Farooq , Iermolenko Volodymyr M. , Eom Jonghwa
Published: June 2016

We have fabricated WS2 and MoS2 multilayer field-effect transistors to compare two-probe and four-probe field-effect and Hall mobility measurements.
Nucleophile promoted gold redox catalysis with diazonium salts: C–Br, C–S and C–P bond formation through catalytic Sandmeyer coupling
Authors: Peng Haihui , Cai Rong , Xu Chang , Chen Hao , Shi Xiaodong
Published: June 2016

Gold-catalyzed C-heteroatom (C–X) coupling reactions are evaluated without using sacrificial oxidants.
Alginate/graphene double-network nanocomposite hydrogel beads with low-swelling, enhanced mechanical properties, and enhanced adsorption capacity
Authors: Zhuang Yuan , Yu Fei , Chen Hong , Zheng Jie , Ma Jie , Chen Junhong
Published: June 2016

We designed and prepared a novel alginate/reduced graphene oxide double-network hydrogel and investigated its mechanical properties, stability and adsorption capacity in comparison with a single network.
Conversion of inert cryptomelane-type manganese oxide into a highly efficient oxygen evolution catalyst via limited Ir doping
Authors: Sun Wei , Cao Li-mei , Yang Ji
Published: June 2016

Inert cryptomelane oxide doping with Ir results in both higher OER performance and substantially reduced Ir consumption compared to IrO2.
Ultrasmall SnS2nanoparticles anchored on well-distributed nitrogen-doped graphene sheets for Li-ion and Na-ion batteries
Authors: Jiang Yong , Feng Yazhi , Xi Baojuan , Kai Shuangshuang , Mi Kan , Feng Jinkui , Zhang Junhao , Xiong Shenglin
Published: June 2016

SnS2–NGS hybrid materials: ultrasmall SnS2–NGS hybrids have been first synthesized by a convenient annealing–hydrothermal-combined route. The excellent Li and Na storage ability is attributed to the unique structure of SnS2–NGS and the synergistic function between NGSs and SnS2.
Al0.3Ga0.7N PN diode with breakdown voltage >1600 V
Authors: Allerman A.A. , Armstrong A.M. , Fischer A.J. , Dickerson J.R. , Crawford M.H. , King M.P. , Moseley M.W. , Wierer J.J. , Kaplar R.J.
Published: June 2016

Demonstration of Al0.3Ga0.7N PN diodes grown with breakdown voltages in excess of 1600 V is reported. The total epilayer thickness is 9.1 μm and was grown by metal‐organic vapour‐phase epitaxy on 1.3‐mm‐thick sapphire in order to achieve crack‐free structures. A junction termination edge structure was employed to control the lateral electric fields. A current density of 3.5 kA/cm2 was achieved under DC forward bias and a reverse leakage current <3 nA was measured for voltages <1200 V. The differential on‐resistance of 16 mΩ cm2 is limited by the lateral conductivity of the n‐type contact layer required by the front‐surface contact geometry of the device. An effective critical electric field of 5.9 MV/cm was determined from the epilayer properties and the reverse current–voltage characteristics. To our knowledge, this is the first aluminium gallium nitride (AlGaN)‐based PN diode exhibiting a breakdown voltage in excess of 1 kV. It is noted that a Baliga figure of merit (Vbr2/Rspec,on) of 150 MW/cm2 found is the highest reported for an AlGaN PN diode and illustrates the potential of larger‐bandgap AlGaN alloys for high‐voltage devices.
Continuous finite‐time output consensus tracking of high‐order agents with matched and unmatched disturbances
Authors: Yu Shuanghe , Long Xiaojun , Guo Ge
Published: June 2016

Finite‐time output consensus tracking problem of n ‐order multi‐agent systems (MAS) with matched and unmatched disturbances is investigated in this study. First, a distributed protocol is given for the nominal MAS to achieve finite‐time consensus tracking. Second, the unmatched disturbances in every follower are converted to the matched ones through a state transformation, and a finite‐time disturbance observer is utilised to estimate its disturbances and their derivatives up to the (n  − l)‐order (1 ≤ l ≤ n) subject to the bounded (n  − l  + 1)‐order derivatives. Finally, the combined observer‐based protocol achieves the finite‐time output consensus tracking in spite of all the disturbances. Finally, simulation results validate the scheme.
Corrections for “Discretisation method and stability criteria for non‐linear systems under discrete‐time time delay control”
Authors: Lee Jinoh , Medrano‐Cerda Gustavo A. , Jung Je Hyung
Published: June 2016

Corrected proofs of Lemma 3, Theorem 1 and several typographical errors in [1] are provided.
Time‐varying threshold‐based fault detection for a class of uncertain non‐linear systems in strict‐feedback form
Authors: Zhang Zhi‐Hui , Yang Guang‐Hong
Published: June 2016

This study presents a time‐varying threshold‐based fault detection (FD) method for a class of single‐input single‐output non‐linear systems in strict‐feedback form with unmeasurable states, unmatched non‐linear fault functions and uncertainties. First, a residual generator with prescribed performance is designed in a framework of recursive technique. Then, the tight time‐varying thresholds are computed by using the prescribed performance bound (PPB) and the FD scheme is presented. Furthermore, the fault detectability is analysed to characterise the sensitivity to the faults. It is shown that the residual signal satisfies the PPB and all the estimation errors are uniformly bounded before fault occurrence. Compared with the method without considering the PPB, the proposed time‐varying thresholds improve the FD performance with fewer false alarms caused by overshoot during the transient process. Finally, a comparative simulation study illustrates the superiority of the proposed method.
Identification of critical generating units for maintenance: a game theory approach
Authors: Pourahmadi Farzaneh , Fotuhi‐Firuzabad Mahmud , Dehghanian Payman
Published: June 2016

With the rapid evolution of electricity markets and the need for higher economic efficiency of power industry, attempts for lowering down the maintenance costs as a large portion of system operation expenses seem imperative. Recognised as a crucial step in practical implementation of modern maintenance paradigms, e.g. reliability‐centred maintenance, this study proposes an efficient method to quantify the generating units’ criticality on the bulk power system reliability performance. The proposed approach utilises a solution concept of game theory and evaluates the contribution of each generating unit on the overall system reliability when a higher‐order contingency occurs. The suggested framework would lead to a fair identification of critical units in restructured power systems for more focused maintenance activities and also helps in recognising where investments should be made to improve the system reliability. The effectiveness of the proposed approach is confirmed through implementation on the IEEE 24‐bus reliability test system.
Non‐cooperative game theory based energy management systems for energy district in the retail market considering DER uncertainties
Authors: Marzband Mousa , Javadi Masoumeh , Domínguez‐García José Luis , Mirhosseini Moghaddam Maziar
Published: June 2016

In this study, a general framework for implementing a retail energy market based on the Nikaido–Isoda/relaxation algorithm is proposed as an electricity market structure with large distributed energy resources (DERs) penetration and demand side management of consumers. Moreover, the consumers are able to participate in the market as prosumers (i.e. producer and consumer at the same time). By considering the related uncertainties, the DERs can maximise their expected payoff or profit by undertaking strategies through the price bidding strategy, based on the proposed structure, considering Nash equilibrium. The results show the effectiveness and accuracy of the proposed framework in determining the optimal power set‐points of players participating in the market to achieve the objectives.
Noise analysis in distributed amplifiers with feedback‐active load
Authors: Terán Jose Vicente , de la Fuente Maria Luisa , Limiti Ernesto , Aja Beatriz , Artal Eduardo
Published: June 2016

This study presents the noise analysis of amplifiers when the input line termination is implemented via an active load. The noise figure (NF) of distributed amplifiers is analysed to determine the effect of the gate and drain terminations. The noise of a transistor configured as a one‐port device has been analysed and a lower noise temperature has been achieved as compared with a conventional resistor. In order to improve the noise performance of the overall amplifier, a parallel feedback has been added to the active load, and its effects are analysed in terms of noise. A distributed amplifier has been designed as a test vehicle of the analysis and characterised with a resistor as input line termination and with an active load to demonstrate the improvement in NF at frequencies below 2 GHz. The resulting amplifier exhibits 10.9 dB of small signal gain from 1 to 5 GHz, with a reduction of 0.6 dB in NF below 2 GHz when the input line termination is replaced by an active load.
Analysis of inductance calculation of coaxial circular filamentary coils, thin‐wall solenoids, and disk coils using inverse hyperbolic functions
Authors: Liang Sizhuang
Published: June 2016

This study presents a method using inverse hyperbolic functions to calculate the mutual and self‐inductance inductance of coaxial circular filamentary coils, thin‐wall solenoids, disk coils, and coils with rectangular cross‐section in air. A generalised expression is given for any combination of these coils, which only requires numerical integration with one variable. Singularities are fully analysed and methods to resolve the singularities are presented in this study. When calculating the self‐inductance of a disk coil or a thin‐wall solenoid, the proposed method involves an improper integral, and the accuracy of the proposed method is limited unless a quadrature rule applicable to improper integrals is applied. For other situations, results by the proposed method were compared with those in the literature, and they were in excellent agreement.
Biosynthesis and antibacterial activity of gold nanoparticles coated with reductase enzymes
Authors: Hosseini Mansoure , Mashreghi Mansour , Eshghi Hossein
Published: June 2016

Potential of luminescent bacteria in production of metal nanoparticles (NPs) has not been well evaluated up until now. These bacteria contain lux operon which is included of reductase enzymes, by increasing bacterial cell density, the expression of aldehyde synthetic enzymes elevate and enhance the yields of NPs synthesis. Therefore, extracellular synthesis of gold NPs (AuNPs) using natural occurring luminescent bacteria, VLA, VLB, VLC and genetically engineered luminescent bacteria, Pseudomonas putida KT2440 and Pseudomonas fluorescence OS8 have been successfully conducted. NPs were characterised and their antibacterial activity evaluated using microtitre plates at different concentrations against some hospital pathogenic bacteria. Biosynthetic AuNPs produced had maximum absorption at the ranges of 500–550 nanometre wavelengths. Transmission electron microscopy images showed particle sizes between 10 and 50 nanometres and confirmed the success of purification process. The NPs were spherical and the FTIR analysis showed the existence of biomolecules on surface of purified NPs that could be most probably related to reductase enzymes that are stabilised on NPs surfaces. Further investigation on antibacterial properties of these novel NPs which coated by reductase enzymes showed that any increase or decrease in antibacterial activity is dependent on NPs concentration.
Fredholm and Wronskian representations of solutions to the KPI equation and multi-rogue waves
Authors: Gaillard Pierre
Published: June 2016

We construct solutions to the Kadomtsev-Petviashvili equation (KPI) in terms of Fredholm determinants. We deduce solutions written as a quotient of Wronskians of order 2N. These solutions, called solutions of order N, depend on 2N − 1 parameters. When one of these parameters tends to zero, we obtain N order rational solutions expressed as a quotient of two polynomials of degree 2N(N + 1) in x, y, and t depending on 2N − 2 parameters. So we get with this method an infinite hierarchy of solutions to the KPI equation.
First-principles thermodynamics and defect kinetics guidelines for engineering a tailored RRAM device
Authors: Clima Sergiu , Chen Yang Yin , Chen Chao Yang , Goux Ludovic , Govoreanu Bogdan , Degraeve Robin , Fantini Andrea , Jurczak Malgorzata , Pourtois Geoffrey
Published: June 2016

Resistive Random Access Memories are among the most promising candidates for the next generation of non-volatile memory. Transition metal oxides such as HfOx and TaOx attracted a lot of attention due to their CMOS compatibility. Furthermore, these materials do not require the inclusion of extrinsic conducting defects since their operation is based on intrinsic ones (oxygen vacancies). Using Density Functional Theory, we evaluated the thermodynamics of the defects formation and the kinetics of diffusion of the conducting species active in transition metal oxide RRAM materials. The gained insights based on the thermodynamics in the Top Electrode, Insulating Matrix and Bottom Electrode and at the interfaces are used to design a proper defect reservoir, which is needed for a low-energy reliable switching device. The defect reservoir has also a direct impact on the retention of the Low Resistance State due to the resulting thermodynamic driving forces. The kinetics of the diffusing conducting defects in the Insulating Matrix determine the switching dynamics and resistance retention. The interface at the Bottom Electrode has a significant impact on the low-current operation and long endurance of the memory cell. Our first-principles findings are confirmed by experimental measurements on fabricated RRAM devices.
Current transport mechanism in graphene/AlGaN/GaN heterostructures with various Al mole fractions
Authors: Pandit Bhishma , Seo Tae Hoon , Ryu Beo Deul , Cho Jaehee
Published: June 2016

The current transport mechanism of graphene formed on AlxGa1−xN/GaN heterostructures with various Al mole fractions (x = 0.15, 0.20, 0.30, and 0.40) is investigated. The current–voltage measurement from graphene to AlGaN/GaN shows an excellent rectifying property. The extracted Schottky barrier height of the graphene/AlGaN/GaN contacts increases with the Al mole fraction in AlGaN. However, the current transport mechanism deviates from the Schottky-Mott theory owing to the deterioration of AlGaN crystal quality at high Al mole fractions confirmed by reverse leakage current measurement.
A semi-continuum model on vibration frequency of silicon nanowires in <111> orientation
Authors: Yu Hong , Chen Hong-Bo
Published: June 2016

In this article, a new semi-continuum model is built to describe the fundamental vibration frequency of the silicon nanowires in <111> orientation. The Keating potential model and the discrete nature in the width and the thickness direction of the silicon nanowires in <111> orientation are applied in the new semi-continuum model. Based on the Keating model and the principle of conservation of energy, the vibration frequency of the silicon nanowires with the triangle, the rhombus, and the hexagon cross sections are derived. It is indicated that the calculation results based on this new model are accordant with the simulation results of the software based on molecular dynamics (MD).
A closer look into concept of strategy and its implications for translation training
Authors: Heydarian Seyed Hossein
Published: June 2016

The significance of the concept ofstrategy, broadly defined as a solution for a translation problem, has increasingly been recognised in Translation Studies. It has widely been referred to in descriptive studies of translation and its most practical considerations. This article aims at providing a closer perspective of the term and the area of debates in its practicality in order to draw a plan for its application in translation training. It could ideally been assumed that by finding common strategies applicable in different translation classrooms with different SL-TL pairs, we could find a way towards the general model of translation and translation training. Translation strategies, therefore from this standpoint, could be of assistance to improve translation competence at academia and thereby, to increase translation quality in a global context.
Football and netball in women’s struggle against HIV/AIDS in Africa
Authors: DeLancey Mark W.
Published: June 2016

The HIV/AIDS problem has improved in recent years. The number of newly infected persons is declining year after year (2.1 million new cases in 2013). However, the news is still grim and especially so for young women. Why does HIV seem to discriminate against women, especially younger women? Women are physiologically more susceptible than men, but among the most significant causes are gender inequity and related poverty and human rights issues.

A number of strategies and tactics are used in the struggle with HIV/AIDS. Some are old ideas, found successful in campaigns against other diseases. Others are of more recent origin. Among the latter has been the use of sport. In this essay, we discuss some of the ways in which sport is used to assist women in the struggle against HIV/AIDS.

A survey of problems associated with the spread and the prevention of HIV/AIDS is indicative of the difficulties faced. Of the many strategies and tactics, is there a role for sport? Sport has been able to assist with some of the associated problems. Although in some instances a sport activity is aimed at a single issue, more often the purposes are multiple. Often, events and programmes are not specifically aimed at a female audience, though frequently separate activities are used for each gender.
Co-current toroidal rotation-driven and turbulent stresses with resonant magnetic perturbations in the edge plasmas of the J-TEXT tokamak
Authors: Zhao K.J. , Shi Yuejiang , Liu H. , Diamond P.H. , Li F.M. , Cheng J. , Chen Z.P. , Nie L. , Ding Y.H. , Wu Y.F. , Chen Z.Y. , Rao B. , Cheng Z.F. , Gao L. , Zhang X.Q. , Yang Z.J. , Wang N.C. , Wang L. , Jin W. , Xu J.Q. , Yan L.W. , Dong J.Q. , Zhuang G.
Published: June 2016

The acceleration of the co-current toroidal rotations around resonant surfaces by resonant magnetic perturbations (RMPs) through turbulence is presented. These experiments were performed using a Langmuir probe array in the edge plasmas of the J-TEXT tokamak. This study aims at understanding the RMP effects on edge toroidal rotations and exploring its control method. With RMPs, the flat electron temperature T
e profile, due to magnetic islands, appears around resonant surfaces (Zhao et al 2015 Nucl. Fusion
55 073022). When the resonant surface is closer to the last closed flux surface, the flat T
e profile vanishes with RMPs. In both cases, the toroidal rotations significantly increase in the direction of the plasma current around the resonant surfaces with RMPs. The characteristics of turbulence are significantly affected by RMPs around the resonant surfaces. The turbulence intensity profile changes and the poloidal wave vector k

θ
increases with RMPs. The power fraction of the turbulence components in the ion diamagnetic drift direction increases with RMPs. The measurements of turbulent Reynolds stresses are consistent with the toroidal flows that can be driven by turbulence. The estimations of the energy transfer between the turbulence and toroidal flows suggest that turbulence energy transfers into toroidal flows. The result has the implication of the intrinsic rotation being driven by RMPs via turbulence.
Finite cyclicity of slow-fast Darboux systems with a two-saddle loop
Authors: Bobieński Marcin , Gavrilov Lubomir
Published: June 2016

We prove that the cyclicity of a slow-fast integrable system of Darboux type with a double heteroclinic loop is finite and uniformly bounded.
Psychological Responses to Scarcity
Authors: Zhao Jiaying , Tomm Brandon M.
Published: June 2016

Scarcity is the condition of having insufficient resources to cope with demands. This condition presents significant challenges to the human cognitive system. For example, having limited financial resources requires the meticulous calculation of expenses with respect to a budget. Likewise, having limited time requires the stringent management of schedules with respect to a deadline. As such, scarcity consumes cognitive resources such as attention, working memory, and executive control and elicits a range of systematic and even counter-productive cognitive and behavioral responses as a result. Specifically, scarcity induces an attentional focus on the problem at hand, which facilitates performance by enhancing cognitive processing of information relevant to the problem, increasing the efficiency of resource use, and stabilizing the perception of value. Such prioritization of the problem at hand may seem advantageous, but it can produce undesirable consequences. For example, scarcity causes myopic and impulsive behavior, prioritizing short-term gains over long-term gains. Ironically, scarcity can also result in a failure to notice beneficial information in the environment that alleviates the condition of scarcity. More detrimentally, scarcity directly impairs cognitive function, which can lead to suboptimal decisions and choices that exacerbate the condition of scarcity. Thus, scarcity means not only a shortage of physical resources (e.g., money or time) but also a deficit of cognitive resources (e.g., attention, executive control). The cognitive deficits under scarcity are particularly problematic because they impair performance and lead to counter-productive behaviors that deepen the cycle of scarcity. In addition, people under financial scarcity suffer from stigmas and stereotypes associated with poverty. These social perceptions of poverty further burden the mind by consuming cognitive resources, weakening performance in the poor. Understanding the cognitive and behavioral responses to scarcity provides new insights into why the poor remain poor, identifying the psychological causes of scarcity, and illuminating potential interventions to stop the cycle of scarcity. These insights have important implications for the design and the implementation of policies and services targeting the populations under scarcity.
pong: fast analysis and visualization of latent clusters in population genetic data
Authors: Behr Aaron A. , Liu Katherine Z. , Liu-Fang Gracie , Nakka Priyanka , Ramachandran Sohini
Published: June 2016

Motivation: A series of methods in population genetics use multilocus genotype data to assign individuals membership in latent clusters. These methods belong to a broad class of mixed-membership models, such as latent Dirichlet allocation used to analyze text corpora. Inference from mixed-membership models can produce different output matrices when repeatedly applied to the same inputs, and the number of latent clusters is a parameter that is often varied in the analysis pipeline. For these reasons, quantifying, visualizing, and annotating the output from mixed-membership models are bottlenecks for investigators across multiple disciplines from ecology to text data mining.

Results: We introduce pong, a network-graphical approach for analyzing and visualizing membership in latent clusters with a native interactive D3.js visualization. pong leverages efficient algorithms for solving the Assignment Problem to dramatically reduce runtime while increasing accuracy compared with other methods that process output from mixed-membership models. We apply pong to 225 705 unlinked genome-wide single-nucleotide variants from 2426 unrelated individuals in the 1000 Genomes Project, and identify previously overlooked aspects of global human population structure. We show that pong outpaces current solutions by more than an order of magnitude in runtime while providing a customizable and interactive visualization of population structure that is more accurate than those produced by current tools.

Availability and Implementation: pong is freely available and can be installed using the Python package management system pip. pong’s source code is available at https://github.com/abehr/pong.

Contact:  aaron_behr@alumni.brown.edu or sramachandran@brown.edu

Supplementary Information: Supplementary data are available at Bioinformatics online.
compendiumdb: an R package for retrieval and storage of functional genomics data
Authors: Nandal Umesh K. , van Kampen Antoine H. C. , Moerland Perry D.
Published: June 2016

Summary: Currently, the Gene Expression Omnibus (GEO) contains public data of over 1 million samples from more than 40 000 microarray-based functional genomics experiments. This provides a rich source of information for novel biological discoveries. However, unlocking this potential often requires retrieving and storing a large number of expression profiles from a wide range of different studies and platforms. The compendiumdb R package provides an environment for downloading functional genomics data from GEO, parsing the information into a local or remote database and interacting with the database using dedicated R functions, thus enabling seamless integration with other tools available in R/Bioconductor.

Availability and Implementation: The compendiumdb package is written in R, MySQL and Perl. Source code and binaries are available from CRAN (http://cran.r-project.org/web/packages/compendiumdb/) for all major platforms (Linux, MS Windows and OS X) under the GPLv3 license.

Contact:  p.d.moerland@amc.uva.nl

Supplementary information:  Supplementary data are available at Bioinformatics online.
KCMBT: a k-mer Counter based on Multiple Burst Trees
Authors: Mamun Abdullah-Al , Pal Soumitra , Rajasekaran Sanguthevar
Published: June 2016

Motivation: A massive number of bioinformatics applications require counting of k-length substrings in genetically important long strings. A k-mer counter generates the frequencies of each k-length substring in genome sequences. Genome assembly, repeat detection, multiple sequence alignment, error detection and many other related applications use a k-mer counter as a building block. Very fast and efficient algorithms are necessary to count k-mers in large data sets to be useful in such applications.

Results: We propose a novel trie-based algorithm for this k-mer counting problem. We compare our devised algorithm k-mer Counter based on Multiple Burst Trees (KCMBT) with available all well-known algorithms. Our experimental results show that KCMBT is around 30% faster than the previous best-performing algorithm KMC2 for human genome dataset. As another example, our algorithm is around six times faster than Jellyfish2. Overall, KCMBT is 20–30% faster than KMC2 on five benchmark data sets when both the algorithms were run using multiple threads.

Availability and Implementation: KCMBT is freely available on GitHub: (https://github.com/abdullah009/kcmbt_mt).

Contact:  rajasek@engr.uconn.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Understanding the mechanisms in accelerated drug reactions
Authors: Torres María J. , Salas Maria , Ariza Adriana , Fernández Tahia D.
Published: June 2016

Purpose of review

The purpose is to understand the underlying mechanisms of accelerated allergic reactions to drugs, defined here as reactions occurring between 1 and 24 h after drug intake.

Recent findings

Recent publications have shown that accelerated reactions are T cell-mediated, although an IgE mechanism cannot be ruled out in some cases.

Classification of allergic reactions to drugs is complex. Based on the time interval between drug administration and appearance of the clinical reaction, as well as the type of clinical symptoms, they can be classified as: immediate, typically appearing from less than 1 to 6 h after the last drug administration and nonimmediate, occurring at any time from 1 h after drug administration. Therefore, overlap exists in what the Levine classification defined as accelerated reactions, where clinical symptoms are mainly urticaria and less often exanthema and serum sickness-like reactions. The immunological mechanisms involved suggest that they are T cell-mediated reactions with a Th1 pattern, comprising increased production of IFNγ, TNFα, the chemokine CXCL9 and its corresponding receptor CXCR3. In most cases an IgE-mediated response is ruled out because of negative immediate skin test results, no detection of serum-specific IgE antibodies or tryptase, and no skin-secreted tryptase. However, an IgE-mediated response can be demonstrated in exceptional situations. Finally, serum sickness-like reactions have been reported as an immune complex-mediated accelerated reaction. However, the exact mechanism has not been confirmed.
Longitudinal Analysis of Gender Differences in Academic Productivity Among Medical Faculty Across 24 Medical Schools in the United States
Authors: Raj Anita , Carr Phyllis L. , Kaplan Samantha E. , Terrin Norma , Breeze Janis L. , Freund Karen M.
Published: June 2016

Purpose

To examine gender differences in academic productivity, as indicated by publications and federal grant funding acquisition, among a longitudinal cohort of medical faculty from 24 U.S. medical schools, 1995 to 2012–2013.

Method

Data for this research were taken from the National Faculty Survey involving a survey with medical faculty recruited from medical schools in 1995, and followed up in 2012–2013. Data included surveys and publication and grant funding databases. Outcomes were number of publications, h-index, and principal investigator on a federal grant in the prior two years. Gender differences were assessed using negative binomial regression models for publication and h-index outcomes, and logistic regression for the grant funding outcome; analyses adjusted for race/ethnicity, rank, specialty area, and years since first academic appointment.

Results

Data were available for 1,244 of the 1,275 (98%) subjects eligible for the follow-up study. Men were significantly more likely than women to be married/partnered, have children, and hold the rank of professor (P < .0001). Adjusted regression models documented that women had a lower rate of publication (relative number = 0.71; 95% CI = 0.63, 0.81; P < .0001) and h-index (relative number = 0.81; 95% CI = 0.73, 0.90; P < .0001) relative to men, but there was no gender difference in grant funding.

Conclusions

Women faculty acquired federal funding at similar rates as male faculty, yet lagged behind in terms of publications and their impact. Medical academia must consider how to help address ongoing gender disparities in publication records.