bluuebunny/crossref_metadata_2025 huggingface dataset:
Gut microbiota Modulated by Probiotics and Garcinia cambogia Extract Correlate with Weight Gain and Adipocyte Sizes in High Fat-Fed Mice
Authors: Heo Jaeyoung , Seo Minseok , Park Hwanhee , Lee Woon Kyu , Guan Le Luo , Yoon Joon , Caetano-Anolles Kelsey , Ahn Hyeonju , Kim Se-Young , Kang Yoon-Mo , Cho Seoae , Kim Heebal
Published: September 2016

Results of recent studies on gut microbiota have suggested that obesogenic bacteria exacerbate obesity and metabolic dysfunction in the host when fed a high fat diet (HFD). In order to explore obesity-associated bacterial candidates and their response to diet, the composition of faecal bacterial communities was investigated by analyzing 16S rRNA gene sequences in mice. Dietary intervention with probiotics and Garcinia cambogia extract attenuated weight gain and adipocyte size in HFD-fed mice. To identify obesity-causative microbiota, two statistical analyses were performed. Forty-eight bacterial species were found to overlap between the two analyses, indicating the commonly identified species as diet-driven and obesity-associated, which would make them strong candidates for host-microbiome interaction on obesity. Finally, correlation based network analysis between diet, microbe, and host revealed that Clostridium aminophilum, a hyper-ammonia-producing bacterium, was highly correlated with obesity phenotypes and other associated bacteria, and shown to be suppressed by the combination of probiotics and Garcinia cambogia extract. Results of the present study suggest that probiotics and Garcinia cambogia extract alleviate weight gain and adiposity, in part via differentially modulating the composition of gut microbiota in HFD fed mice.
Predator-prey interactions in the plankton: larval fish feeding on evasive copepods
Authors: Jackson James M. , Lenz Petra H.
Published: September 2016

Capture success and prey selectivity were investigated in clownfish Amphiprion ocellaris larvae using videography. Three prey types were tested using developmental stages (nauplii, copepodites and adults) of the copepod Parvocalanus crassirostris. Predatory abilities improved rapidly between days 1 and 14 post-hatch. Initially, capture success was limited to nauplii with few attacks on larger stages. Captures of copepodites were first observed at 3 dph, and of adults at 8 dph. Consistent strikes at the larger prey were observed on the day prior to successful captures (2 dph for copepodites, 7 dph for adults). Difference in capture success between nauplii and adults at 8 dph was an order of magnitude. Differences in capture success among prey types persisted but decreased to three-fold by 14 dph. Younger A. ocellaris attacked nauplii preferentially and avoided adult prey. Strike selectivity declined with age, and no selectivity was observed after 10 dph. However, numerically 50% of the ingested prey were still nauplii at 14 dph under the experimental conditions.
Using an Artificial Neural Bypass to Restore Cortical Control of Rhythmic Movements in a Human with Quadriplegia
Authors: Sharma Gaurav , Friedenberg David A. , Annetta Nicholas , Glenn Bradley , Bockbrader Marcie , Majstorovic Connor , Domas Stephanie , Mysiw W. Jerry , Rezai Ali , Bouton Chad
Published: September 2016

Neuroprosthetic technology has been used to restore cortical control of discrete (non-rhythmic) hand movements in a paralyzed person. However, cortical control of rhythmic movements which originate in the brain but are coordinated by Central Pattern Generator (CPG) neural networks in the spinal cord has not been demonstrated previously. Here we show a demonstration of an artificial neural bypass technology that decodes cortical activity and emulates spinal cord CPG function allowing volitional rhythmic hand movement. The technology uses a combination of signals recorded from the brain, machine-learning algorithms to decode the signals, a numerical model of CPG network, and a neuromuscular electrical stimulation system to evoke rhythmic movements. Using the neural bypass, a quadriplegic participant was able to initiate, sustain, and switch between rhythmic and discrete finger movements, using his thoughts alone. These results have implications in advancing neuroprosthetic technology to restore complex movements in people living with paralysis.
Female Adult Aedes albopictus Suppression by Wolbachia-Infected Male Mosquitoes
Authors: Mains James W. , Brelsfoard Corey L. , Rose Robert I. , Dobson Stephen L.
Published: September 2016

Dengue, chikungunya and zika viruses are pathogens with an increasing global impact. In the absence of an approved vaccine or therapy, their management relies on controlling the mosquito vectors. But traditional controls are inadequate and the range of invasive species such as Aedes albopictus (Asian Tiger Mosquito) is expanding. Genetically modified mosquitoes are being tested, but their use has encountered regulatory barriers and public opposition in some countries. Wolbachia bacteria can cause a form of conditional sterility, which can provide an alternative to genetic modification or irradiation. It is unknown however, whether openly released, artificially infected male Ae. albopictus can competitively mate and sterilize females at a level adequate to suppress a field population. Also, the unintended establishment of Wolbachia at the introduction site could result from horizontal transmission or inadvertent female release. In 2014, an Experimental Use Permit from the United States Environmental Protection Agency approved a pilot field trial in Lexington, Kentucky, USA. Here, we present data showing localized reduction of both egg hatch and adult female numbers. The artificial Wolbachia type was not observed to establish in the field. The results are discussed in relation to the applied use of Wolbachia-infected males as a biopesticide to suppress field populations of Ae. albopictus.
Growth and development of Arabidopsis thaliana under single-wavelength red and blue laser light
Authors: Ooi Amanda , Wong Aloysius , Ng Tien Khee , Marondedze Claudius , Gehring Christoph , Ooi Boon S.
Published: September 2016

Indoor horticulture offers a sensible solution for sustainable food production and is becoming increasingly widespread. However, it incurs high energy and cost due to the use of artificial lighting such as high-pressure sodium lamps, fluorescent light or increasingly, the light-emitting diodes (LEDs). The energy efficiency and light quality of currently available horticultural lighting is suboptimal, and therefore less than ideal for sustainable and cost-effective large-scale plant production. Here, we demonstrate the use of high-powered single-wavelength lasers for indoor horticulture. They are highly energy-efficient and can be remotely guided to the site of plant growth, thus reducing on-site heat accumulation. Furthermore, laser beams can be tailored to match the absorption profiles of different plant species. We have developed a prototype laser growth chamber and demonstrate that plants grown under laser illumination can complete a full growth cycle from seed to seed with phenotypes resembling those of plants grown under LEDs reported previously. Importantly, the plants have lower expression of proteins diagnostic for light and radiation stress. The phenotypical, biochemical and proteome data show that the single-wavelength laser light is suitable for plant growth and therefore, potentially able to unlock the advantages of this next generation lighting technology for highly energy-efficient horticulture.
Mitigation of indomethacin-induced gastrointestinal damages in fat-1 transgenic mice via gate-keeper action of ω-3-polyunsaturated fatty acids
Authors: Han Young-Min , Park Jong-Min , Kang Jing X. , Cha Ji-Young , Lee Ho-Jae , Jeong Migeyong , Go Eun-Jin , Hahm Ki Baik
Published: September 2016

Non-steroidal anti-inflammatory drugs (NSAIDs) damage the gastrointestinal (GI) epithelial cell membranes by inducing several signals through lipid raft organization after membrane incorporation, whereas ω-3 polyunsaturated fatty acids (PUFAs) relieve inflammation, reduce oxidative stress, and provide cytoprotection, consequent to lipid raft disorganization. Therefore, we hypothesized that ω-3 PUFAs can protect the GI from NSAID-induced damages by initiating the gatekeeper action of cell membranes, subsequent to anti-inflammatory and anti-oxidative actions. Administration of indomethacin (IND) leads to the formation of lipid rafts and activation of caveolin-1; however, no such observations were made upon co-administration of eicosapentaenoic acid (EPA) and IND. In addition, the EPA-induced lipid raft disorganization, caveolin-1 inactivation, and cellular cytotoxicity were inhibited when target cells were knocked-out using G-protein coupled receptor 120 (GPR 120). EPA significantly attenuated IND-induced oxidative damage and apoptosis. IND administration induced significant ulceration, bleeding, and oedema in the stomach or small intestine of wild-type (WT) mice; however, such severe damages to the GI significantly decreased in fat-1 transgenic (TG) mice (P < 0.001), which exhibited decreased cyclooxygenase-2 expression and apoptosis, decreased interleukin-1β and FAS concentrations, and increased heme oxygenase-1 concentration. Our study indicates that the gatekeeper function of ω-3 PUFAs improves GI safety when administered with NSAID.
Elemental characterisation of melanin in feathers via synchrotron X-ray imaging and absorption spectroscopy
Authors: Edwards Nicholas P. , van Veelen Arjen , Anné Jennifer , Manning Phillip L. , Bergmann Uwe , Sellers William I. , Egerton Victoria M. , Sokaras Dimosthenis , Alonso-Mori Roberto , Wakamatsu Kazumasa , Ito Shosuke , Wogelius Roy A.
Published: September 2016

Melanin is a critical component of biological systems, but the exact chemistry of melanin is still imprecisely known. This is partly due to melanin’s complex heterogeneous nature and partly because many studies use synthetic analogues and/or pigments extracted from their natural biological setting, which may display important differences from endogenous pigments. Here we demonstrate how synchrotron X-ray analyses can non-destructively characterise the elements associated with melanin pigment in situ within extant feathers. Elemental imaging shows that the distributions of Ca, Cu and Zn are almost exclusively controlled by melanin pigment distribution. X-ray absorption spectroscopy demonstrates that the atomic coordination of zinc and sulfur is different within eumelanised regions compared to pheomelanised regions. This not only impacts our fundamental understanding of pigmentation in extant organisms but also provides a significant contribution to the evidence-based colour palette available for reconstructing the appearance of fossil organisms.
Efficacy of extracorporeal cardiopulmonary resuscitation compared to conventional cardiopulmonary resuscitation for adult cardiac arrest patients: a systematic review and meta-analysis
Authors: Ahn Chiwon , Kim Wonhee , Cho Youngsuk , Choi Kyu-Sun , Jang Bo-Hyoung , Lim Tae Ho
Published: September 2016

We performed a meta-analysis to compare the impact of extracorporeal cardiopulmonary resuscitation (ECPR) to that of conventional cardiopulmonary resuscitation (CCPR) in adult patients who experience cardiac arrest of cardiac origin. A literature search was performed using criteria set forth in a predefined protocol. Report inclusion criteria were that ECPR was compared to CCPR in adult patients with cardiac arrest of cardiac origin, and that survival and neurological outcome data were available. Exclusion criteria were reports describing non-cardiac origin arrest, review articles, editorials, and nonhuman studies. The efficacies of ECPR and CCPR were compared in terms of survival and neurological outcome. A total of 38,160 patients from 7 studies were ultimately included. ECPR showed similar survival (odds ratio [OR] 2.26, 95% confidence interval [CI] 0.45–11.20) and neurologic outcomes (OR 3.14, 95% CI 0.66–14.85) to CCPR in out-of-hospital cardiac arrest patients. For in-hospital cardiac arrest (IHCA) patients, however, ECPR was associated with significantly better survival (OR 2.40, 95% CI 1.44–3.98) and neurologic outcomes (OR 2.63, 95% CI 1.38–5.02) than CCPR. Hence, ECPR may be more effective than CCPR as an adjuvant therapy for survival and neurologic outcome in cardiac-origin IHCA patients.
Resonant excitation energy transfer from carbon dots to different sized silver nanoparticles
Authors: Prajapati Roopali , Bhattacharya Arpan , Mukherjee Tushar Kanti
Published: September 2016

In the present study we have demonstrated the size-dependent resonant nanometal surface energy transfer (NSET) from carbon dots (CDs) to silver nanoparticles (Ag NPs) using photoluminescence spectroscopy.
Ultrafast excited states dynamics of [Ru(bpy)3]2+ dissolved in ionic liquids
Authors: Borgwardt Mario , Wilke Martin , Kiyan Igor Yu. , Aziz Emad F.
Published: September 2016

In this work, we demonstrate the potential of room-temperature ionic liquids as solvents to investigate the excited states dynamics of [Ru(bpy)3]2+ by means of time-resolved photoelectron spectroscopy.
Synthesis and characterization of chiral smectic side-chain liquid crystalline elastomers containing nematic and chiral mesogens
Authors: Jiang Ying , Cong Yuehua , Zhang Baoyan
Published: September 2016

A novel series of siloxane-based chiral smectic side-chain liquid crystalline elastomers containing nematic and chiral mesogens were fabricated through synthesis involving a one-step hydrosilication reaction via a liquid crystalline crosslinking agent containing smectic and nematic phases.
Tunable luminescence of lanthanide (Ln = Sm, Eu, Tb) hydrophilic ionic polymers based on poly(N-methyl-4-vinylpyridinium-co-styrene) cations
Authors: Zhao Ying , He Ling , Qin Song , Tao Guo-Hong
Published: September 2016

Hydrophilic luminescent lanthanide-containing ionic polymers poly-[MVPS]2[Ln(NO3)5] were prepared, which can be utilized as reversible colorimetric water-responsive sensors.
Structural and micro-Raman studies of DyMnO3 with potassium substitution at the Dy site
Authors: Yadagiri K. , Nithya R.
Published: September 2016

We synthesize a new series of compounds, Dy1−xKxMnO3 (x = 0.1, 0.2 & 0.3) and report the structural and spectroscopic properties of the new compounds in comparison to DyMnO3.
Surfactant directed polyaniline nanostructures for high performance sulphur dioxide chemiresistors: effect of morphologies, chemical structure and porosity
Authors: Chaudhary Vishal , Kaur Amarjeet
Published: September 2016

The present investigation explores the effect of the type of surfactant on the sulphur dioxide sensing behaviour of high surface area polyaniline nanostructures (HSPAN).
Mosaic structure effect and superior catalytic performance of AgBr/Ag2MoO4 composite materials
Authors: Zhang Jing-Yu , Lu Yi , Liu Jin-Ku , Jiang Hao
Published: September 2016

The research focused on mosaic style AgBr–Ag2MoO4 composite materials prepared by in situ composite method. The catalytic efficiency enhanced 149 times compared to pure Ag2MoO4. The success of instant catalysis owed to the mosaic structure effect.
Separation of carbon dioxide and nitrogen gases through modified boron nitride nanosheets as a membrane: insights from molecular dynamics simulations
Authors: Azamat Jafar , Khataee Alireza , Sadikoglu Fahreddin
Published: September 2016

The progress of gas propagating through the pores of BNNSs was simulated using MD simulations. During a simulation time of 50 ns at 298 K, there is no CO2 propagating through, meaning a high selectivity of pore 4 for CO2/N2 separation.
Metabolic engineering of TiO2 nanoparticles in Nitzschia palea to form diatom nanotubes: an ingredient for solar cells to produce electricity and biofuel
Authors: Gautam Shristy , Kashyap Mrinal , Gupta Shradhey , Kumar Vikas , Schoefs Benoit , Gordon Richard , Jeffryes Clayton , Joshi Khashti Ballabh , Vinayak Vandana
Published: September 2016

Diatoms are nature's nanobot because they can be described as cells in a glass house.
Copper(ii) carboxymethylcellulose (CMC-CuII) as an efficient catalyst for aldehyde–alkyne–amine coupling under solvent-free conditions
Authors: Liu Xiaoping , Lin Bijin , Zhang Zhuan , Lei Hao , Li Yiqun
Published: September 2016

A novel heterogeneous Cu(ii) carboxymethylcellulose catalyst was prepared and successfully employed in the A3 coupling without using any co-catalyst, other additives, bases under solvent-free conditions.
Fabrication of a versatile chitosan nanocomposite hydrogel impregnated with biosynthesized silver nanoparticles using Sapindus mukorossi: characterization and applications
Authors: V. Porchezhiyan , S. E. Noorjahan
Published: September 2016

A biological and eco-friendly method has been adopted for the synthesis of silver nanoparticles, which can be used for a number of applications.
Pyramidalization/twisting of the amide functional group via remote steric congestion triggered by metal coordination
Authors: Adachi Shinya , Kumagai Naoya , Shibasaki Masakatsu
Published: September 2016

The distortion of the planar structure of amides is manifested by taking advantage of the temporary increase of the peripheral steric factor.
Convenient synthesis of EDOT-based dyes by CH-activation and their application as dyes in dye-sensitized solar cells
Authors: Abdalhadi S. M. , Connell A. , Zhang X. , Wiles A. A. , Davies M. L. , Holliman P. J. , Cooke G.
Published: September 2016

Precursors to three new 3,4-ethylenedioxythiophene (EDOT) incorportaing dyes have been synthesisedviaa one-pot C–H activation route usingN,N-dimethylaniline as a donor group.
Enhancing the performance of lithium–sulfur batteries by anchoring polar polymers on the surface of sulfur host materials
Authors: Chen Manfang , Wang Xianyou , Cai Siyu , Ma Zhongyun , Song Peng , Fisher Adrian C.
Published: September 2016

Through anchoring polar polymer Triton X-100 on carbon materials, the MAC/S manifests excellent electrochemical performance as the cathode for Li–S batteries.
Fabrication of hydroxyapatite/chitosan composite hydrogels loaded with exosomes derived from miR-126-3p overexpressed synovial mesenchymal stem cells for diabetic chronic wound healing
Authors: Li Min , Ke Qin-Fei , Tao Shi-Cong , Guo Shang-Chun , Rui Bi-Yu , Guo Ya-Ping
Published: September 2016

Hydroxyapatite/chitosan composite hydrogels loaded with exosomes was fabricated for promoting wound surface re-epithelialization, angiogenesis, collagen maturity and diabetic chronic wound healing.
Formation mechanism and cytocompatibility of nano-shaped calcium silicate hydrate/calcium titanium silicate/TiO2 composite coatings on titanium
Authors: Zhang Lan , Huang Xiaoyan , Han Yong
Published: September 2016

Compared with as-MAOed TiO2, the triple-layered coating (HT2h) comprised of an outer layer of nanoleaf Ca3Si6O15(H2O)7, a middle layer of nanograined Ca(Si1.9Ti0.1)O5 and an inner layer of microporous TiO2 can significantly improve the behaviors of osteoblasts.
Full-band UV shielding and highly daylight luminescent silane-functionalized graphene quantum dot nanofluids and their arbitrary polymerized hybrid gel glasses
Authors: Xie Zheng , Du Qingqing , Wu Yongzhong , Hao Xiaopeng , Liu Chunyan
Published: September 2016

A facile and efficient approach for the preparation of silane-functionalized graphene quantum dot (SiGQD) nanofluids is described.
Asymmetric-triazine-cored triads as thermally activated delayed fluorescence emitters for high-efficiency yellow OLEDs with slow efficiency roll-off
Authors: Xiang Yepeng , Gong Shaolong , Zhao Yongbiao , Yin Xiaojun , Luo Jiajia , Wu Kailong , Lu Zheng-Hong , Yang Chuluo
Published: September 2016

Two asymmetric-triazine triads are demonstrated for the first time as yellow TADF emitters exhibiting a peak external quantum efficiency of 13.0% and an ultra-slow efficiency roll-off of 11.5% at high luminance.
A vivid example of turning waste into treasure: persistent luminescence of Ca2Ga2(Si,Ge)O7:Pr3+,Yb3+ phosphor tailored by band gap engineering
Authors: Zou Zehua , Zhou Hui , Wang Wenxiang , Zhang Jiachi , Cao Cheng , Zhang Teng , Ci Zhipeng , Zhao Zhengyan , Wang Yuhua
Published: September 2016

We exhibit a vivid example of turning waste into treasure for the development of persistent luminescence (PersL) phosphor.
Direct silicon–nitrogen bonded host materials with enhanced σ–π conjugation for blue phosphorescent organic light-emitting diodes
Authors: Li Huanhuan , Xu Lijia , Tang Yuting , Tao Ye , Xu Shen , Zheng Chao , Xing Guichuan , Zhou Xinhui , Huang Wei , Chen Runfeng
Published: September 2016

High-performance host materials have been designed in the π–σ–π molecular architecture via N–Si–N bonding with increased d-orbital participation of silicon for enhanced σ–π conjugation and improved optoelectronic properties.
CPW‐fed octagonal super‐wideband fractal antenna with defected ground structure
Authors: Singhal Sarthak , Singh Amit Kumar
Published: September 2016

A coplanar waveguide (CPW)‐fed octagonal super‐wideband fractal antenna is presented. It comprises four iterations of an octagonal slot‐loaded octagonal radiating patch, CPW feedline, and modified ground plane loaded with a pair of rectangular notches. An impedance bandwidth of 3.8–68GHz (179%) – i.e. a17.89:1 ratio bandwidth – is achieved. Desirable radiation performance characteristics, including relatively stable and omnidirectional radiation patterns, are obtained over this range. The experimental and simulation results are found to be in good agreement. The designed antenna has the advantages of wider bandwidth and miniaturised size over the previously reported structures.
Miniaturisation of UWB triangular slot antenna by the use of DRAF
Authors: Orazi Homayoon , Soleiman Hadi
Published: September 2016

In this study, the dual‐reverse‐arrow fractal (DRAF) geometry is applied to the sides of a slotted microstrip triangular patch to design ultra‐wideband (UWB) antenna with a coplanar waveguide (CPW) feed with and without notch bands. It is shown that the proposed DRAF geometry has the capability of both reducing the antenna size, but without decreasing its bandwidth and also maintaining the other antenna radiation characteristics. It is shown that the antenna is miniaturised by 40% compared with the simple triangular patch. Furthermore, in order to prevent any interference of the proposed antenna with the wireless system of high performance radio LAN (HiperLAN)/2, a notch band is created by cutting two similar slots in the T‐shaped CPW‐feed. Such an antenna has applications in UWB systems. Two prototype DRAF antennas are fabricated and measured, which verify its desirable features.
How should spin-weighted spherical functions be defined?
Authors: Boyle Michael
Published: September 2016

Spin-weighted spherical functions provide a useful tool for analyzing tensor-valued functions on the sphere. A tensor field can be decomposed into complex-valued functions by taking contractions with tangent vectors on the sphere and the normal to the sphere. These component functions are usually presented as functions on the sphere itself, but this requires an implicit choice of distinguished tangent vectors with which to contract. Thus, we may more accurately say that spin-weighted spherical functions are functions of both a point on the sphere and a choice of frame in the tangent space at that point. The distinction becomes extremely important when transforming the coordinates in which these functions are expressed, because the implicit choice of frame will also transform. Here, it is proposed that spin-weighted spherical functions should be treated as functions on the spin or rotation groups, which simultaneously tracks the point on the sphere and the choice of tangent frame by rotating elements of an orthonormal basis. In practice, the functions simply take a quaternion argument and produce a complex value. This approach more cleanly reflects the geometry involved, and allows for a more elegant description of the behavior of spin-weighted functions. In this form, the spin-weighted spherical harmonics have simple expressions as elements of the Wigner 𝔇 representations, and transformations under rotation are simple. Two variants of the angular-momentum operator are defined directly in terms of the spin group; one is the standard angular-momentum operator L, while the other is shown to be related to the spin-raising operator ð.
Fast, hot electron production and ion acceleration in a helicon inductive plasma
Authors: Sung Yung-Ta , Li Yan , Scharer John E.
Published: September 2016

A large, time-averaged, double layer-like plasma potential drop of 80 V over several hundred Debye lengths has been observed in the magnetic expansion region on the Madison Helicon eXperiment. It is operated in an inductive mode at 900 W and low argon operating pressures (0.12–0.20 mTorr) in the collisionless regime. The plasma space potential drop is due to the formation of a double layer-like structure in the magnetic expansion region and is much higher than the potential drop caused by a Boltzmann expansion. With the plasma potential drop, a locally negative potential ion hole region at lower pressures with a higher electron density than ion density has been observed just the downstream of the potential drop region. Two-temperature Maxwellian electron distributions with a warm (Te≈15 eV) and bulk (Te≈5 eV) components are observed just upstream of the double layer validated through a RF compensated Langmuir probe and an optical emission spectroscopy (OES) diagnostics. In the expansion chamber downstream of the double layer-like potential drop, a single warm (Te≈15 eV) Maxwellian electron distribution is observed via both the Langmuir probe and OES diagnostics. Ion beam energies of 65 eV are also observed downstream of the potential drop.
Role of neutral gas in scrape-off layer of tokamak plasma in the presence of finite electron temperature and its gradient
Authors: Bisai N. , Kaw P. K.
Published: September 2016

The role of neutral gas molecules in the Scrape-off Layer (SOL) region of tokamak plasma is important as it is expected to modify the plasma turbulence. Two-dimensional model has been used that consists of electron continuity, molecular ion continuity, quasi-neutrality, electron energy, and neutral molecular gas continuity equations in the presence of electron impact molecular ionizations and other non-ionizing collisions. The growth rate obtained from these equations has been presented using linear theory. It is observed that the growth rate increases with the neutral gas ionization coefficients. The nonlinear equations are solved numerically in the presence and absence of the neutral gas molecules. Radial profiles of plasma density, electron temperature, and electric field have been obtained. It is found that the neutral gas reduces electric fields. More significant reduction of the poloidal electric field has been found by the neutral gas. Time series obtained from the numerical data has been analyzed. A strong decrease in fluctuation of the plasma density, electron temperature, and potential has been found at the outer region the SOL plasma in the presence of the gas molecules.
A comparison between HfO2/Al2O3 nano-laminates and ternary HfxAlyO compound as the dielectric material in InGaAs based metal-oxide-semiconductor (MOS) capacitors
Authors: Krylov Igor , Pokroy Boaz , Eizenberg Moshe , Ritter Dan
Published: September 2016

We compare the electrical properties of HfO2/Al2O3 nano-laminates with those of the ternary HfxAlyO compound in metal oxide semiconductor (MOS) capacitors. The dielectrics were deposited by atomic layer deposition on InGaAs. Water, ozone, and oxygen plasma were tested as oxygen precursors, and best results were obtained using water. The total dielectric thickness was kept constant in our experiments. It was found that the effective dielectric constant increased and the leakage current decreased with the number of periods. Best results were obtained for the ternary compound. The effect of the sublayer thicknesses on the electrical properties of the interface was carefully investigated, as well as the role of post-metallization annealing. Possible explanations for the observed trends are provided. We conclude that the ternary HfxAlyO compound is more favorable than the nano-laminates approach for InGaAs based MOS transistor applications.
TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field
Authors: Dziedzic Jacek , Mao Yuezhi , Shao Yihan , Ponder Jay , Head-Gordon Teresa , Head-Gordon Martin , Skylaris Chris-Kriton
Published: September 2016

We present a novel quantum mechanical/molecular mechanics (QM/MM) approach in which a quantum subsystem is coupled to a classical subsystem described by the AMOEBA polarizable force field. Our approach permits mutual polarization between the QM and MM subsystems, effected through multipolar electrostatics. Self-consistency is achieved for both the QM and MM subsystems through a total energy minimization scheme. We provide an expression for the Hamiltonian of the coupled QM/MM system, which we minimize using gradient methods. The QM subsystem is described by the onetep linear-scaling DFT approach, which makes use of strictly localized orbitals expressed in a set of periodic sinc basis functions equivalent to plane waves. The MM subsystem is described by the multipolar, polarizable force field AMOEBA, as implemented in tinker. Distributed multipole analysis is used to obtain, on the fly, a classical representation of the QM subsystem in terms of atom-centered multipoles. This auxiliary representation is used for all polarization interactions between QM and MM, allowing us to treat them on the same footing as in AMOEBA. We validate our method in tests of solute-solvent interaction energies, for neutral and charged molecules, demonstrating the simultaneous optimization of the quantum and classical degrees of freedom. Encouragingly, we find that the inclusion of explicit polarization in the MM part of QM/MM improves the agreement with fully QM calculations.
Non-linear interactions in a boundary layer developing over an array of cubes using stochastic estimation
Authors: Blackman Karin , Perret Laurent
Published: September 2016

In the present work, a boundary layer developing over a rough-wall consisting of staggered cubes with a plan area packing density, λp = 25%, is studied within a wind tunnel using combined particle image velocimetry and hot-wire anemometry to investigate the non-linear interactions between large-scale momentum regions and small-scale structures induced by the presence of the roughness. Due to the highly turbulent nature of the roughness sub-layer and measurement equipment limitations, temporally resolved flow measurements are not feasible, making the conventional filtering methods used for triple decomposition unsuitable for the present work. Thus, multi-time delay linear stochastic estimation is used to decompose the flow into large-scales and small-scales. Analysis of the scale-decomposed skewness of the turbulent velocity (u′) shows a significant contribution of the non-linear term uL′uS′2¯, which represents the influence of the large-scales (uL′) onto the small-scales (uS′). It is shown that this non-linear influence of the large-scale momentum regions occurs with all three components of velocity in a similar manner. Finally, through two-point spatio-temporal correlation analysis, it is shown quantitatively that large-scale momentum regions influence small-scale structures throughout the boundary layer through a non-linear top-down mechanism.
Transient thermal camouflage and heat signature control
Authors: Yang Tian-Zhi , Su Yishu , Xu Weikai , Yang Xiao-Dong
Published: September 2016

Thermal metamaterials have been proposed to manipulate heat flux as a new way to cloak or camouflage objects in the infrared world. To date, however, thermal metamaterials only operate in the steady-state and exhibit detectable, transient heat signatures. In this letter, the theoretical basis for a thermal camouflaging technique with controlled transient diffusion is presented. This technique renders an object invisible in real time. More importantly, the thermal camouflaging device instantaneously generates a pre-designed heat signature and behaves as a perfect thermal illusion device. A metamaterial coating with homogeneous and isotropic thermal conductivity, density, and volumetric heat capacity was fabricated and very good camouflaging performance was achieved.
Remark on higher-derivative mechanics with l-conformal Galilei symmetry
Authors: Masterov Ivan
Published: September 2016

Based on the results in [A. Galajinsky and I. Masterov, Nucl. Phys. B 866, 212 (2013)], we consider a way to construct a higher-derivative mechanical model which possesses the l-conformal Galilei symmetry. The dynamical system describes generalized Pais-Uhlenbeck oscillator in the presence of an effective external field.
Particle manipulation with acoustic vortex beam induced by a brass plate with spiral shape structure
Authors: Wang Tian , Ke Manzhu , Li Weiping , Yang Qian , Qiu Chunyin , Liu Zhengyou
Published: September 2016

In this work, we give direct demonstration of acoustic radiation force and acoustic torque on particles exerted by an acoustic vortex beam, which is realized by an acoustic artificial structure plate instead of traditional transducer arrays. First, the first order acoustic vortex beam, which has the distinctive features of a linear and continuous phase variation from −π to π around its propagation axis and a magnitude null at its core, is obtained through one single acoustic source incident upon a structured brass plate with Archimedean spiral grating engraved on the back surface. Second, annular self-patterning of polystyrene particles with a radius of 90 μm is realized in the gradient field of this acoustic vortex beam. In addition, we further exhibit acoustic angular momentum transfer to an acoustic absorptive matter, which is verified by a millimeter-sized polylactic acid disk self-rotating in water in the acoustic field of the generated vortex beam.
The electrical properties of n-ZnO/p-SnO heterojunction diodes
Authors: Javaid K. , Xie Y. F. , Luo H. , Wang M. , Zhang H. L. , Gao J. H. , Zhuge F. , Liang L. Y. , Cao H. T.
Published: September 2016

In the present work, n-type zinc oxide (ZnO) and p-type tin monoxide (SnO) based heterostructure diodes were fabricated on an indium-tin-oxide glass using the radio frequency magnetron sputtering technique. The prepared ZnO/SnO diodes exhibited a typical rectifying behavior, with a forward to reverse current ratio about 500 ± 5 at 2 V and turn on voltage around 1.6 V. The built-in voltage of the diode was extracted to be 0.5 V based on the capacitance-voltage (C–V) measurement. The valence and conduction band offsets were deliberated through the band energy diagram of ZnO/SnO heterojunction, as 1.08 eV and 0.41 eV, respectively. The potential barrier-dependent carrier transportation mechanism across the space charge region was also investigated.
Mixture interlayer for high performance organic-inorganic perovskite photodetectors
Authors: Tang Feng , Chen Qi , Chen Lei , Ye Fengye , Cai Jinhua , Chen Liwei
Published: September 2016

Organic-inorganic perovskites are promising light absorbing active materials for photodetectors; however, the performance of current organic-inorganic perovskite-based photodetectors are limited by the high dark current due to hole injection at the cathode interlayer typically composed of fullerene derivatives. We have developed a mixture interlayer by simply blending polymethyl methacrylate (PMMA) with [6,6]-phenyl-C61-butyric acidmethyl ester (PCBM). Scanning Kelvin probe microscopy imaging reveals that the presence of PMMA reduced the work function of the PCBM:PMMA interlayer, which leads to increased energy barrier for hole injection and better hole-blocking property. Optimized perovskite photodetector with PCBM:PMMA hole-blocking interlayer exhibits a high detectivity of 1.1 × 1013 Jones, a broad linear dynamic range of 112 dB, and a fast response time of 2.2 μs.
Socioeconomic status as a factor in Indigenous and non-Indigenous children with hearing loss: analysis of national survey data
Authors: Simpson Andrea , Enticott Joanne C. , Douglas Jacinta
Published: September 2016

In this paper, the association between socioeconomic status and speech, language and communication outcomes for primary-school-going children with hearing loss using population survey data was analysed. The dataset used for analysis consisted of 289973 children in total, of which 3174 children had hearing loss. For all children, higher socioeconomic status was positively correlated with better speech, language and communication outcomes. A hearing loss was indicated for 1% of non-Indigenous children and 4.3% of Indigenous children. Non-Indigenous children with hearing loss were found to be fairly evenly distributed by socioeconomic status, whereas Indigenous children with hearing loss were found to be statistically significantly more likely to be living in the most disadvantaged socioeconomic areas. Socioeconomic status was found to affect developmental outcomes for all children, regardless of Indigenous and hearing loss status.
Symplastic signaling instructs cell division, cell expansion, and cell polarity in the ground tissue of
Arabidopsis thaliana
roots
Authors: Wu Shuang , O’Lexy Ruthsabel , Xu Meizhi , Sang Yi , Chen Xu , Yu Qiaozhi , Gallagher Kimberly L.
Published: September 2016

Significance

Cell-to-cell communication is critical for the coordination of developmental processes between cells and tissues within an organism. Mechanical signals, secreted peptides, and hormones can all convey information between cells. In plants, neighboring cells can directly communicate with each other via plasmodesmata (PD). It has long been assumed that the exchange of proteins and RNAs via PD is important for the regulation of plant development. However, the tools for large-scale testing of this hypothesis have been lacking. Here we exploit a tool that effectively blocks movement of proteins and small RNAs between cells to show that PD-dependent cell-to-cell signaling is important for the coordination of cell divisions, cell polarity, and cell expansion between cell layers in the
Arabidopsis
root.
Elevated ERK/p90 ribosomal S6 kinase activity underlies audiogenic seizure susceptibility in fragile X mice
Authors: Sawicka Kirsty , Pyronneau Alexander , Chao Miranda , Bennett Michael V. L. , Zukin R. Suzanne
Published: September 2016

Significance

Fragile X syndrome is the most common heritable cause of intellectual disability and autism. Elevated protein synthesis is considered a major contributor to the pathophysiology of fragile X. ERK (extracellular signal-regulated kinase) and mTOR (mechanistic target of rapamycin) are key signaling molecules in two prominent pathways that regulate protein synthesis. A major finding of this study is that ERK (but not mTOR) signaling is elevated in the neocortex of fragile X mice. Elevated ERK activity causes overactivation of p90-ribosomal S6 kinase (RSK) and hyperphosphorylation of ribosomal protein S6. Audiogenic seizures in fragile X mice, which mimic sensory hypersensitivity in fragile X humans, are prevented by RSK inhibition. Thus, RSK is a potential therapeutic target for treatment of fragile X.
Recruitment of Juvenile Atlantic Sturgeon in the Savannah River, Georgia
Authors: Bahr Derek L. , Peterson Douglas L.
Published: September 2016

Atlantic Sturgeon Acipenser oxyrinchus oxyrinchus were once abundant along the Atlantic coast of North America from the Saint Lawrence River, Canada, to the St. Johns River, Florida. Severe overfishing, coupled with habitat losses during the 1900s, resulted in major population declines that eventually led to the subspecies’ listing under the U.S. Endangered Species Act in 2012. Despite this listing, quantified recruitment data are largely lacking for most Atlantic Sturgeon populations, particularly those within the South Atlantic distinct population segment. The objective of this study was to quantify annual recruitment of Atlantic Sturgeon in the Savannah River, Georgia, by estimating annual abundance of age‐1, river‐resident juveniles. During the summers of 2013–2015, we used anchored gill nets and trammel nets to sample juvenile Atlantic Sturgeon throughout the Savannah River estuary. Ages of captured juveniles were determined by using length‐frequency analysis, and abundance of each juvenile age‐class was estimated with Huggins closed‐capture models in RMark. We estimated the Savannah River to contain 528 age‐1 juveniles in 2013, 589 in 2014, and 597 in 2015. The results from this study indicate that the Savannah River population is likely the second largest within the South Atlantic distinct population segment. Future studies are needed to determine the relative importance of the Savannah River as a natural source of recruitment for smaller, more imperiled populations in adjacent rivers. Consequently, we suggest that management efforts continue to prioritize the protection of both the population and the associated critical habitats within the Savannah River estuary.

Received April 7, 2016; accepted June 28, 2016 Published online September 23, 2016
Rim15 and Sch9 kinases are involved in induction of autophagic degradation of ribosomes in budding yeast
Authors: Waliullah Talukdar Muhammad , Yeasmin Akter MST , Kaneko Atsuki , Koike Naoki , Terasawa Mashu , Totsuka Takaya , Ushimaru Takashi
Published: September 2016

Autophagic degradation of ribosomes is promoted by nutrient starvation and inactivation of target of rapamycin complex 1 (TORC1). Here we show that selective autophagic degradation of ribosomes (called ribophagy) after TORC1 inactivation requires the specific autophagy receptor Atg11. Rim15 protein kinase upregulated ribophagy, while it downregulated non-selective degradation of ribosomes.
GeneEvolve: a fast and memory efficient forward-time simulator of realistic whole-genome sequence and SNP data
Authors: Tahmasbi Rasool , Keller Matthew C
Published: September 2016

Motivation

Computer simulations are excellent tools for understanding the evolutionary and genetic consequences of complex processes that cannot be analytically predicted and for creating realistic genetic data. There are many software packages that simulate genetic data, but they are typically not fast or memory efficient enough to simulate realistic, individual-level genome-wide SNP/sequence data.

Results

GeneEvolve is a user-friendly and efficient population genetics simulator that handles complex evolutionary and life history scenarios and generates individual-level phenotypes and realistic whole-genome sequence or SNP data. GeneEvolve runs forward-in-time, which allows it to provide a wide range of scenarios for mating systems, selection, population size and structure, migration, recombination and environmental effects. The software is designed to use as input data from real or previously simulated phased haplotypes, allowing it to mimic very closely the properties of real genomic data.

Availability and Implementation

GeneEvolve is freely available at https://github.com/rtahmasbi/GeneEvolve.

Supplementary information

Supplementary data are available at Bioinformatics online.
LD Hub: a centralized database and web interface to perform LD score regression that maximizes the potential of summary level GWAS data for SNP heritability and genetic correlation analysis
Authors: Zheng Jie , Erzurumluoglu A Mesut , Elsworth Benjamin L , Kemp John P , Howe Laurence , Haycock Philip C , Hemani Gibran , Tansey Katherine , Laurin Charles ,   Early Genetics and Lifecourse Epidemiology (EAGLE) Eczema Consortium, Pourcain Beate St , Warrington Nicole M , Finucane Hilary K , Price Alkes L , Bulik-Sullivan Brendan K , Anttila Verneri , Paternoster Lavinia , Gaunt Tom R , Evans David M , Neale Benjamin M
Published: September 2016

Motivation

LD score regression is a reliable and efficient method of using genome-wide association study (GWAS) summary-level results data to estimate the SNP heritability of complex traits and diseases, partition this heritability into functional categories, and estimate the genetic correlation between different phenotypes. Because the method relies on summary level results data, LD score regression is computationally tractable even for very large sample sizes. However, publicly available GWAS summary-level data are typically stored in different databases and have different formats, making it difficult to apply LD score regression to estimate genetic correlations across many different traits simultaneously.

Results

In this manuscript, we describe LD Hub - a centralized database of summary-level GWAS results for 173 diseases/traits from different publicly available resources/consortia and a web interface that automates the LD score regression analysis pipeline. To demonstrate functionality and validate our software, we replicated previously reported LD score regression analyses of 49 traits/diseases using LD Hub; and estimated SNP heritability and the genetic correlation across the different phenotypes. We also present new results obtained by uploading a recent atopic dermatitis GWAS meta-analysis to examine the genetic correlation between the condition and other potentially related traits. In response to the growing availability of publicly accessible GWAS summary-level results data, our database and the accompanying web interface will ensure maximal uptake of the LD score regression methodology, provide a useful database for the public dissemination of GWAS results, and provide a method for easily screening hundreds of traits for overlapping genetic aetiologies.

Availability and Implementation

The web interface and instructions for using LD Hub are available at http://ldsc.broadinstitute.org/

Supplementary information

Supplementary data are available at Bioinformatics online.
Improved methods for multi-trait fine mapping of pleiotropic risk loci
Authors: Kichaev Gleb , Roytman Megan , Johnson Ruth , Eskin Eleazar , Lindström Sara , Kraft Peter , Pasaniuc Bogdan
Published: September 2016

Motivation

Genome-wide association studies (GWAS) have identified thousands of regions in the genome that contain genetic variants that increase risk for complex traits and diseases. However, the variants uncovered in GWAS are typically not biologically causal, but rather, correlated to the true causal variant through linkage disequilibrium (LD). To discern the true causal variant(s), a variety of statistical fine-mapping methods have been proposed to prioritize variants for functional validation.

Results

In this work we introduce a new approach, fastPAINTOR, that leverages evidence across correlated traits, as well as functional annotation data, to improve fine-mapping accuracy at pleiotropic risk loci. To improve computational efficiency, we describe an new importance sampling scheme to perform model inference. First, we demonstrate in simulations that by leveraging functional annotation data, fastPAINTOR increases fine-mapping resolution relative to existing methods. Next, we show that jointly modeling pleiotropic risk regions improves fine-mapping resolution compared to standard single trait and pleiotropic fine mapping strategies. We report a reduction in the number of SNPs required for follow-up in order to capture 90% of the causal variants from 23 SNPs per locus using a single trait to 12 SNPs when fine-mapping two traits simultaneously. Finally, we analyze summary association data from a large-scale GWAS of lipids and show that these improvements are largely sustained in real data.

Availability and Implementation

The fastPAINTOR framework is implemented in the PAINTOR v3.0 package which is publicly available to the research community http://bogdan.bioinformatics.ucla.edu/software/paintor

Supplementary information

Supplementary data are available at Bioinformatics online.