bluuebunny/crossref_metadata_2025 huggingface dataset:
Transcriptional response of Prochlorococcus to co-culture with a marine Alteromonas: differences between strains and the involvement of putative infochemicals
Authors: Aharonovich Dikla , Sher Daniel
Published: April 2016

Interactions between marine microorganisms may determine the dynamics of microbial communities. Here, we show that two strains of the globally abundant marine cyanobacterium Prochlorococcus, MED4 and MIT9313, which belong to two different ecotypes, differ markedly in their response to co-culture with a marine heterotrophic bacterium, Alteromonas macleodii strain HOT1A3. HOT1A3 enhanced the growth of MIT9313 at low cell densities, yet inhibited it at a higher concentration, whereas it had no effect on MED4 growth. The early transcriptomic responses of Prochlorococcus cells after 20 h in co-culture showed no evidence of nutrient starvation, whereas the expression of genes involved in photosynthesis, protein synthesis and stress responses typically decreased in MED4 and increased in MIT313. Differential expression of genes involved in outer membrane modification, efflux transporters and, in MIT9313, lanthipeptides (prochlorosins) suggests that Prochlorococcus mount a specific response to the presence of the heterotroph in the cultures. Intriguingly, many of the differentially-expressed genes encoded short proteins, including two new families of co-culture responsive genes: CCRG-1, which is found across the Prochlorococcus lineage and CCRG-2, which contains a sequence motif involved in the export of prochlorosins and other bacteriocin-like peptides, and are indeed released from the cells into the media.
Mode engineering for realistic quantum-enhanced interferometry
Authors: Jachura Michał , Chrapkiewicz Radosław , Demkowicz-Dobrzański Rafał , Wasilewski Wojciech , Banaszek Konrad
Published: April 2016

Quantum metrology overcomes standard precision limits by exploiting collective quantum superpositions of physical systems used for sensing, with the prominent example of non-classical multiphoton states improving interferometric techniques. Practical quantum-enhanced interferometry is, however, vulnerable to imperfections such as partial distinguishability of interfering photons. Here we introduce a method where appropriate design of the modal structure of input photons can alleviate deleterious effects caused by another, experimentally inaccessible degree of freedom. This result is accompanied by a laboratory demonstration that a suitable choice of spatial modes combined with position-resolved coincidence detection restores entanglement-enhanced precision in the full operating range of a realistic two-photon Mach–Zehnder interferometer, specifically around a point which otherwise does not even attain the shot-noise limit due to the presence of residual distinguishing information in the spectral degree of freedom. Our method highlights the potential of engineering multimode physical systems in metrologic applications.
Correction: Corrigendum: Integration of Metabolic Modeling with Gene Co-expression Reveals Transcriptionally Programmed Reactions Explaining Robustness in Mycobacterium tuberculosis
Authors: Puniya Bhanwar Lal , Kulshreshtha Deepika , Mittal Inna , Mobeen Ahmed , Ramachandran Srinivasan
Published: April 2016

Scientific Reports 6: Article number: 23440; Published online: 22 March 2016; Updated: 29 April 2016 The Acknowledgements section in this Article was omitted. The Acknowledgements should read: “We thank Dr. Kausik Chakraborty for thought provoking discussion. BSC0121 is duly acknowledged for providing support for this work.
Improvement of surface ECG recording in adult zebrafish reveals that the value of this model exceeds our expectation
Authors: Liu Chi Chi , Li Li , Lam Yun Wah , Siu Chung Wah , Cheng Shuk Han
Published: April 2016

The adult zebrafish has been used to model the electrocardiogram (ECG) for human cardiovascular studies. Nonetheless huge variations are observed among studies probably because of the lack of a reliable and reproducible recording method. In our study, an adult zebrafish surface ECG recording technique was improved using a multi-electrode method and by pre-opening the pericardial sac. A convenient ECG data analysis method without wavelet transform was also established. Intraperitoneal injection of KCl in zebrafish induced an arrhythmia similar to that of humans, and the arrhythmia was partially rescued by calcium gluconate. Amputation and cryoinjury of the zebrafish heart induced ST segment depression and affected QRS duration after injury. Only cryoinjury decelerated the heart rate. Different changes were also observed in the QT interval during heart regeneration in these two injury models. We also characterized the electrocardiophysiology of breakdance zebrafish mutant with a prolonged QT interval, that has not been well described in previous studies. Our study provided a reliable and reproducible means to record zebrafish ECG and analyse data. The detailed characterization of the cardiac electrophysiology of zebrafish and its mutant revealed that the potential of the zebrafish in modeling the human cardiovascular system exceeds expectations.
Maternal fructose drives placental uric acid production leading to adverse fetal outcomes
Authors: Asghar Zeenat A. , Thompson Alysha , Chi Maggie , Cusumano Andrew , Scheaffer Suzanne , Al-Hammadi Noor , Saben Jessica L. , Moley Kelle H.
Published: April 2016

Maternal metabolic diseases increase offspring risk for low birth weight and cardiometabolic diseases in adulthood. Excess fructose consumption may confer metabolic risks for both women and their offspring. However, the direct consequences of fructose intake per se are unknown. We assessed the impact of a maternal high-fructose diet on the fetal-placental unit in mice in the absence of metabolic syndrome and determined the association between maternal serum fructose and placental uric acid levels in humans. In mice, maternal fructose consumption led to placental inefficiency, fetal growth restriction, elevated fetal serum glucose and triglyceride levels. In the placenta, fructose induced de novo uric acid synthesis by activating the activities of the enzymes AMP deaminase and xanthine oxidase. Moreover, the placentas had increased lipids and altered expression of genes that control oxidative stress. Treatment of mothers with the xanthine oxidase inhibitor allopurinol reduced placental uric acid levels, prevented placental inefficiency and improved fetal weights and serum triglycerides. Finally, in 18 women delivering at term, maternal serum fructose levels significantly correlated with placental uric acid levels. These findings suggest that in mice, excess maternal fructose consumption impairs placental function via a xanthine oxidase/uric acid-dependent mechanism and similar effects may occur in humans.
Immunoglubolin dynamics and cancer prevalence in Tasmanian devils (Sarcophilus harrisii)
Authors: Ujvari Beata , Hamede Rodrigo , Peck Sarah , Pemberton David , Jones Menna , Belov Katherine , Madsen Thomas
Published: April 2016

Immunoglobulins such as IgG and IgM have been shown to induce anti-tumour cytotoxic activity. In the present study we therefore explore total serum IgG and IgM expression dynamics in 23 known-aged Tasmanian devils (Sarcophilus harrisii) of which 9 where affected by Devil Facial Tumour Disease (DFTD). DFTD is clonally transmissible cancer that has caused massive declines in devil numbers. Our analyses revealed that IgM and IgG expression levels as well as IgM/IgG ratios decreased with increasing devil age. Neither age, sex, IgM nor IgG expression levels affected devil DFTD status in our analyses. However, devils with increased IgM relative to IgG expression levels had significantly lower DFTD prevalence. Our results therefore suggest that IgM/IgG ratios may play an important role in determining devil susceptibility to DFTD. We consequently propose that our findings warrant further studies to elucidate the underpinning(s) of devil IgM/IgG ratios and DFTD status.
Targeting EZH2-mediated methylation of H3K27 inhibits proliferation and migration of Synovial Sarcoma in vitro
Authors: Shen Jacson K. , Cote Gregory M. , Gao Yan , Choy Edwin , Mankin Henry J. , Hornicek Francis J. , Duan Zhenfeng
Published: April 2016

Synovial sarcoma is an aggressive soft tissue sarcoma genetically defined by the fusion oncogene SS18-SSX. It is hypothesized that either SS18-SSX disrupts SWI/SNF complex inhibition of the polycomb complex 2 (PRC2) methyltransferase Enhancer of Zeste Homologue 2 (EZH2), or that SS18-SSX is able to directly recruit PRC2 to aberrantly silence target genes. This is of potential therapeutic value as several EZH2 small molecule inhibitors are entering early phase clinical trials. In this study, we first confirmed EZH2 expression in the 76% of human synovial sarcoma samples. We subsequently investigated EZH2 as a therapeutic target in synovial sarcomain vitro. Knockdown of EZH2 by shRNA or siRNA resulted in inhibition of cell growth and migration across a series of synovial sarcoma cell lines. The EZH2 selective small-molecule inhibitor EPZ005687 similarly suppressed cell proliferation and migration. These data support the hypothesis that targeting EZH2 may be a promising therapeutic strategy in the treatment of synovial sarcoma; clinical trials are initiating enrollment currently.
Cellulose and hemicellulose decomposition by forest soil bacteria proceeds by the action of structurally variable enzymatic systems
Authors: López-Mondéjar Rubén , Zühlke Daniela , Becher Dörte , Riedel Katharina , Baldrian Petr
Published: April 2016

Evidence shows that bacteria contribute actively to the decomposition of cellulose and hemicellulose in forest soil; however, their role in this process is still unclear. Here we performed the screening and identification of bacteria showing potential cellulolytic activity from litter and organic soil of a temperate oak forest. The genomes of three cellulolytic isolates previously described as abundant in this ecosystem were sequenced and their proteomes were characterized during the growth on plant biomass and on microcrystalline cellulose. Pedobacter and Mucilaginibacter showed complex enzymatic systems containing highly diverse carbohydrate-active enzymes for the degradation of cellulose and hemicellulose, which were functionally redundant for endoglucanases, β-glucosidases, endoxylanases, β-xylosidases, mannosidases and carbohydrate-binding modules. Luteibacter did not express any glycosyl hydrolases traditionally recognized as cellulases. Instead, cellulose decomposition was likely performed by an expressed GH23 family protein containing a cellulose-binding domain. Interestingly, the presence of plant lignocellulose as well as crystalline cellulose both trigger the production of a wide set of hydrolytic proteins including cellulases, hemicellulases and other glycosyl hydrolases. Our findings highlight the extensive and unexplored structural diversity of enzymatic systems in cellulolytic soil bacteria and indicate the roles of multiple abundant bacterial taxa in the decomposition of cellulose and other plant polysaccharides.
Pumping Electron-Positron Pairs from a Well Potential
Authors: Wang Qiang , Liu Jie , Fu Li-bin
Published: April 2016

In the presence of very deep well potential, electrons will spontaneously occupy the empty embedded bound states and electron-positron pairs are created by means of a non-perturbative tunneling process. In this work, by slowly oscillating the width or depth, the population transfer channels are opened and closed periodically. We find and clearly show that by the non-synchronous ejections of particles, the saturation of pair number in a static super-critical well can be broken and electrons and positrons can be pumped inexhaustibly from vacuum with a constant production rate. In the adiabatic limit, final pair number after a single cycle has quantized values as a function of the upper boundary of the oscillating and the critical upper boundaries indicate the diving points of the bound states.
Bufexamac ameliorates LPS-induced acute lung injury in mice by targeting LTA4H
Authors: Xiao Qiang , Dong Ningning , Yao Xue , Wu Dang , Lu Yanli , Mao Fei , Zhu Jin , Li Jian , Huang Jin , Chen Aifang , Huang Lu , Wang Xuehai , Yang Guangxiao , He Guangyuan , Xu Yong , Lu Weiqiang
Published: April 2016

Neutrophils play an important role in the occurrence and development of acute lung injury (ALI). Leukotriene B4 (LTB4), a hydrolysis product of epoxide leukotriene A4 (LTA4) catalyzed by LTA4 hydrolase (LTA4H), is one of the most potent chemoattractants for neutrophil. Bufexamac is a drug widely used as an anti-inflammatory agent on the skin, however, the mechanism of action is still not fully understood. In this study, we found bufexamac was capable of specifically inhibiting LTA4H enzymatic activity and revealed the mode of interaction of bufexamac and LTA4H using X-ray crystallography. Moreover, bufexamac significantly prevented the production of LTB4 in neutrophil and inhibited the fMLP-induced neutrophil migration through inhibition of LTA4H. Finally, bufexamac significantly attenuated lung inflammation as reflected by reduced LTB4 levels and weakened neutrophil infiltration in bronchoalveolar lavage fluid from a lipopolysaccharide-induced ALI mouse model. In summary, our study indicates that bufexamac acts as an inhibitor of LTB4 biosynthesis and may have potential clinical applications for the treatment of ALI.
D–A–D-type narrow-bandgap small-molecule photovoltaic donors: pre-synthesis virtual screening using density functional theory
Authors: Gim Yeongrok , Kim Daekyeom , Kyeong Minkyu , Byun Seunghwan , Park Yuri , Kwon Sooncheol , Kim Heejoo , Hong Sukwon , Lansac Yves , Jang Yun Hee
Published: April 2016

A new series of D–A–D-type small-molecule photovoltaic donors are designed and screened before synthesis using time-dependent density functional theory calculations.
Application of molecularly imprinted polymers for the solid-phase extraction of hexanitrohexaazaisowurtzitane (CL-20) from soil samples
Authors: Wang Jian , Xue Min , Meng Zihui , Xu Zhibin , Luo Jun
Published: April 2016

Eight molecularly imprinted polymers (MIPs) for CL-20 were synthesized by precipitation polymerization in acetonitrile.
A dual-site two-photon fluorescent probe for visualizing lysosomes and tracking lysosomal hydrogen sulfide with two different sets of fluorescence signals in the living cells and mouse liver tissues
Authors: Liu Yong , Meng Fangfang , He Longwei , Liu Keyin , Lin Weiying
Published: April 2016

We have firstly developed a fluorescent probe TP-PMVC, which can monitor lysosomes and lysosomal H2S with dual signal.
The first synthesis and X-ray crystallographic analysis of an oxygen-bridged planarized triphenylborane
Authors: Kitamoto Yuichi , Suzuki Takatsugu , Miyata Yasuo , Kita Hiroshi , Funaki Kenji , Oi Shuichi
Published: April 2016

An oxygen-bridged planarized triphenylborane has been successfully synthesized.
Impact of the coordination environment on the magnetic properties of single-molecule magnets based on homo- and hetero-dinuclear terbium(iii) heteroleptic tris(crownphthalocyaninate)
Authors: Holmberg Rebecca J. , Polovkova Marina A. , Martynov Alexander G. , Gorbunova Yulia G. , Murugesu Muralee
Published: April 2016

Homonuclear and novel heteronuclear TbIII/YIII triple-decker heteroleptic crownphthalocyaninate complexes have been synthesized and studied for their SMM properties.
Three-dimensional models for studying development and disease: moving on from organisms to organs-on-a-chip and organoids
Authors: Jackson E. L. , Lu H.
Published: April 2016

Organ-on-a-chip and organoid culture models present complementary approaches in studying development and disease by balancing experimental tractability and the ability to mimic physiological complexity.
Dynamics of nanocubes embedding into polymer films investigated via spatially resolved plasmon modes
Authors: Bottomley Adam , Prezgot Daniel , Coyle Jason P. , Ianoul Anatoli
Published: April 2016

In this work spatially resolved hybrid plasmon modes are used to monitor precisely the integration of nanoparticles into thin films.
Ultrafast SET-LRP of hydrophobic acrylates in multiphase alcohol–water mixtures
Authors: Enayati Mojtaba , Jezorek Ryan L. , Monteiro Michael J. , Percec Virgil
Published: April 2016

A multiphase SET-LRP system using thein situgenerated Cu(0) by reduction of Cu(ii)Br2with NaBH4in various alcohols containing water was developed and used for SET-LRP of hydrophobic acrylates. From left to right: a solution of methanol/water containing Cu(ii)Br2, the same solution after addition of BA and its SET-LRP.
Fixation of carbon dioxide concurrently or in tandem with free radical polymerization for highly transparent polyacrylates with specific UV absorption
Authors: Liu Bin , Zhang Ying-Ying , Zhang Xing-Hong , Du Bin-Yang , Fan Zhi-Qiang
Published: April 2016

Highly transparent CO2-based polyacrylates with nearly 100% UV absorption in a wavelength range of 200–313 nm are prepared.
New alkaloids from Daphniphyllum himalense
Authors: Zhang Hua , Zhang Dong-Dong , Li Jing-Ya , Shyaula Sajan L. , Li Jia , Yue Jian-Min
Published: April 2016

A series ofDaphniphyllumalkaloids with selective kinase inhibitory activity were isolated and structurally characterized fromDaphniphyllum himalense.
Mechanically strong, flexible and thermally stable graphene oxide/nanocellulosic films with enhanced dielectric properties
Authors: Beeran P. T. Yasir , Bobnar Vid , Gorgieva Selestina , Grohens Yves , Finšgar Matjaž , Thomas Sabu , Kokol Vanja
Published: April 2016

Mechanically strong and flexible films with dielectric properties and energy storage ability have been fabricated from ammonia-functionalized graphene oxide (NGO) nanoplatelets and cellulose nanofibrils (CNFs) vs. TEMPO pre-oxidized CNFs (TCNFs).
Hydrophobization of silver nanoparticles through surface-initiated atom transfer radical polymerization
Authors: Quinsaat Jose Enrico Q. , Nüesch Frank A. , Hofmann Heinrich , Opris Dorina M.
Published: April 2016

Poly(methyl methacrylate) (PMMA)-coated Ag@SiO2core–shell particles with enhanced dispersibility in non-polar solvents were synthesized by surface-initiated atom transfer radical polymerization.
D–A–D type chromophores with aggregation-induced emission and two-photon absorption: synthesis, optical characteristics and cell imaging
Authors: Ding Ai-Xiang , Hao Hu-Jun , Gao Yong-Guang , Shi You-Di , Tang Quan , Lu Zhong-Lin
Published: April 2016

Substituent tuned D–A–D type chromophores with good AIE and TPA properties were successfully applied as OPEF and TPEF cellular stains.
Phase based 2D passive source localisation using receiver networks
Authors: Berdanier Charles , Wicks Michael , Baker Christopher , Wu Zhiqiang
Published: April 2016

In this study the authors introduce a novel method for passive source localisation that exploits phase variance. This method performs phase detection and estimation without relying on precise antenna geometry. The method uses a network of coherent receivers to estimate a continuous wave transmitter source in a two‐dimensional plane with a network of statically and arbitrarily placed receivers with known positions. First the authors develop the mathematical formulation of the method. Next they establish the relationship between knowledge of the transmitter phase at arbitrarily placed receiver locations and a countable number of ambiguous transmitter locations. The authors then develop a more realistic scenario involving multi‐path, noise and other signals in the receiver bandwidth and present numerical results for three different geometries. Finally, the authors compare the numerical results with those achieved with traditional phase difference of arrival.
Clairvoyant radar sea clutter covariance matrix modelling
Authors: McDonald Michael Kenneth , Cerutti‐Maori Delphine
Published: April 2016

Closed form expressions are derived for the calculation of the clairvoyant covariance matrix for radar sea clutter arising from individual clutter components with Gaussian spectra. Two forms are presented corresponding to a power series expansion of a sinc2 antenna gain pattern and a Gaussian approximation to the mainlobe of the antenna pattern. The variation of covariance matrix eigenvalues due to factors such as coherent processing interval, spectra bandwidth, centre frequency and relative power is examined.
First-principles prediction of solar radiation shielding performance for transparent windows of GdB6
Authors: Xiao Lihua , Su Yuchang , Ran Jingyu , Liu Yike , Qiu Wei , Wu Jianming , Lu Fanghai , Shao Fang , Tang Dongsheng , Peng Ping
Published: April 2016

The structural, electronic, magnetic, and optical properties of GdB6 are studied using the first-principles calculations. Calculated values for magnetic and optical properties and lattice constant are found to be consistent with previously reported experimental results. The calculated results show that GdB6 is a perfect near-infrared absorption/reflectance material that could serve as a solar radiation shielding material for windows with high visible light transmittance, similar to LaB6, which is assigned to its plasma oscillation and a collective oscillation (volume plasmon) of carrier electrons. It was found that the magnetic 4f electrons of Gd are not relevant to the important optical properties of GdB6. These theoretical studies serve as a reference for future studies.
Effect of ethanol concentrations on temperature driven structural changes of chymotrypsin inhibitor 2
Authors: Mohanta Dayanidhi , Jana Madhurima
Published: April 2016

A series of atomistic molecular dynamics (MD) simulations of a small enzymatic protein Chymotrypsin Inhibitor 2 (CI2) in water-ethanol mixed solutions were carried out to explore the underlying mechanism of ethanol driven conformational changes of the protein. Efforts have been made to probe the influence of ethanol concentrations ranging from 0% to 75% (v/v) at ambient condition (300 K (T1)) and at elevated temperatures (375 K (T2) and 450 K (T3)) to investigate the temperature induced conformational changes of the protein further. Our study showed that the effect of varying ethanol concentrations on protein’s structure is almost insignificant at T1 and T2 temperatures whereas at T3 temperature, partial unfolding of CI2 in 10% ethanol solution followed by full unfolding of the protein at ethanol concentrations above 25% occurs. However, interestingly, at T3 temperature CI2’s native structure was found to be retained in pure water (0% ethanol solution) indicating that the cosolvent ethanol do play an important role in thermal denaturation of CI2. Such observations were quantified in the light of root-mean-square deviations (RMSDs) and radius of gyration. Although higher RMSD values of β-sheet over α-helix indicate complete destruction of the β-structure of CI2 at high ethanol concentrations, the associated time scale showed that the faster melting of α-helix happens over β-sheet. Around 60%-80% of initial native contacts of the protein were found broken with the separation of hydrophobic core consisting eleven residues at ethanol concentrations greater than 25%. This leads protein to expand with the increase in solvent accessible surface area. The interactions between protein and solvent molecules showed that protein’s solvation shell preferred to accommodate ethanol molecules as compared to water thereby excluded water molecules from CI2’s surface. Further, concentration dependent differential self-aggregation behavior of ethanol is likely to regulate the replacement of relatively fast diffused water by low diffused ethanol molecules from protein’s surface during the unfolding process.
Effect of mass and density of ambient gas on the interaction of laser-blow-off plasma plumes propagating in close proximity
Authors: Kumar Bhupesh , Singh R. K. , Kumar Ajai
Published: April 2016

The effects of mass and pressure of ambient gas on the propagation dynamics of two laser-blow-off plasma plumes created in close proximity are investigated. A time gated fast imaging technique is used for recording the images of the laterally colliding plumes under different experimental conditions. Pressure is varied from 0.1 to 3 mbar in three ambient, i.e., helium, neon, and argon. Emphasis is given on the nature of shock-shock interaction under different ambient conditions. It has been observed that the shock-velocity, shape, strength, and their interactions are strongly dependent on the mass and density of the ambient gases. The role of the interacting shocks and their subsequent reflections on the formation and geometrical shape of the interaction region in different ambient conditions is briefly described.
The unified ballooning theory with weak up-down asymmetric mode structure and the numerical studies
Authors: Xie T. , Qin H. , Zhang Y. Z. , Mahajan S. M.
Published: April 2016

A unified ballooning theory, constructed on the basis of two special theories [Zhang et al., Phys. Fluids B 4, 2729 (1992); Y. Z. Zhang and T. Xie, Nucl. Fusion Plasma Phys. 33, 193 (2013)], shows that a weak up-down asymmetric mode structure is normally formed in an up-down symmetric equilibrium; the weak up-down asymmetry in mode structure is the manifestation of non-trivial higher order effects beyond the standard ballooning equation. It is shown that the asymmetric mode may have even higher growth rate than symmetric modes. The salient features of the theory are illustrated by investigating a fluid model for the ion temperature gradient (ITG) mode. The two dimensional (2D) analytical form of the ITG mode, solved in ballooning representation, is then converted into the radial-poloidal space to provide the natural boundary condition for solving the 2D mathematical local eigenmode problem. We find that the analytical expression of the mode structure is in a good agreement with finite difference solution. This sets a reliable framework for quasi-linear computation.
Comparisons between global and local gyrokinetic simulations of an ASDEX Upgrade H-mode plasma
Authors: Navarro Alejandro Bañón , Told Daniel , Jenko Frank , Görler Tobias , Happel Tim ,   ASDEX Upgrade Team
Published: April 2016

We investigate by means of local and global nonlinear gyrokinetic GENE simulations an ASDEX Upgrade H-mode plasma. We find that for the outer core positions (i.e., ρtor≈0.5−0.7), nonlocal effects are important. For nominal input parameters local simulations over-predict the experimental heat fluxes by a large factor, while a good agreement is found with global simulations. This was a priori not expected, since the values of 1/ρ⋆ were large enough that global and local simulations should have been in accordance. Nevertheless, due to the high sensitivity of the heat fluxes with respect to the input parameters, it is still possible to match the heat fluxes in local simulations with the experimental and global results by varying the ion temperature gradient within the experimental uncertainties. In addition to that, once an agreement in the transport quantities between local (flux-matched) and global simulations is achieved, an agreement for other quantities, such as density and temperature fluctuations, is also found. The case presented here clearly shows that even in the presence of global size-effects, the local simulation approach is still a valid and accurate approach.
Investigation of dopant clustering and segregation to defects in semiconductors using atom probe tomography
Authors: Blavette D. , Duguay S.
Published: April 2016

The role of atom probe tomography in the investigation of clustering and segregation of dopants to lattice defects in semiconductors is highlighted on the basis of some selected salient illustrations obtained at the Groupe de Physique des Matériaux of Rouen (France). The instrument is shown to be able to map out the 3D distribution of chemical species in the three dimensions of space at the ultimate scale. Results related to clustering, segregation of dopants (As, B, and P) to grain boundaries, dislocation loops, and extended defects in silicon are discussed.
Electron temperature measurements inside the ablating plasma of gas-filled hohlraums at the National Ignition Facility
Authors: Barrios M. A. , Liedahl D. A. , Schneider M. B. , Jones O. , Brown G. V. , Regan S. P. , Fournier K. B. , Moore A. S. , Ross J. S. , Landen O. , Kauffman R. L. , Nikroo A. , Kroll J. , Jaquez J. , Huang H. , Hansen S. B. , Callahan D. A. , Hinkel D. E. , Bradley D. , Moody J. D.
Published: April 2016

The first measurement of the electron temperature (Te) inside a National Ignition Facility hohlraum is obtained using temporally resolved K-shell X-ray spectroscopy of a mid-Z tracer dot. Both isoelectronic- and interstage-line ratios are used to calculate the local Te via the collisional–radiative atomic physics code SCRAM [Hansen et al., High Energy Density Phys 3, 109 (2007)]. The trajectory of the mid-Z dot as it is ablated from the capsule surface and moves toward the laser entrance hole (LEH) is measured using side-on x-ray imaging, characterizing the plasma flow of the ablating capsule. Data show that the measured dot location is farther away from the LEH in comparison to the radiation-hydrodynamics simulation prediction using HYDRA [Marinak et al., Phys. Plasmas 3, 2070 (1996)]. To account for this discrepancy, the predicted simulation Te is evaluated at the measured dot trajectory. The peak Te, measured to be 4.2 keV ± 0.2 keV, is ∼0.5 keV hotter than the simulation prediction.
Particle acceleration during magnetic reconnection in a low-beta pair plasma
Authors: Guo Fan , Li Hui , Daughton William , Li Xiaocan , Liu Yi-Hsin
Published: April 2016

Plasma energization through magnetic reconnection in the magnetically dominated regime featured by low plasma beta (β=8πnkT0/B2≪1) and/or high magnetization (σ=B2/(4πnmc2)≫1) is important in a series of astrophysical systems such as solar flares, pulsar wind nebula, and relativistic jets from black holes. In this paper, we review the recent progress on kinetic simulations of this process and further discuss plasma dynamics and particle acceleration in a low-β reconnection layer that consists of electron–positron pairs. We also examine the effect of different initial thermal temperatures on the resulting particle energy spectra. While earlier papers have concluded that the spectral index is smaller for higher σ, our simulations show that the spectral index approaches p = 1 for sufficiently low plasma β, even if σ∼1. Since this predicted spectral index in the idealized limit is harder than most observations, it is important to consider effects that can lead to a softer spectrum such as open boundary simulations. We also remark that the effects of three-dimensional reconnection physics and turbulence on reconnection need to be addressed in the future.
Asymmetric quantum-well structures for AlGaN/GaN/AlGaN resonant tunneling diodes
Authors: Yang Lin'an , Li Yue , Wang Ying , Xu Shengrui , Hao Yue
Published: April 2016

Asymmetric quantum-well (QW) structures including the asymmetric potential-barrier and the asymmetric potential-well are proposed for AlGaN/GaN/AlGaN resonant tunneling diodes (RTDs). Theoretical investigation gives that an appropriate decrease in Al composition and thickness for emitter barrier as well as an appropriate increase of both for collector barrier can evidently improve the negative-differential-resistance characteristic of RTD. Numerical simulation shows that RTD with a 1.5-nm-thick GaN well sandwiched by a 1.3-nm-thick Al0.15Ga0.85N emitter barrier and a 1.7-nm-thick Al0.25Ga0.75N collector barrier can yield the I-V characteristic having the peak current (Ip) and the peak-to-valley current ratio (PVCR) of 0.39 A and 3.6, respectively, about double that of RTD with a 1.5-nm-thick Al0.2Ga0.8N for both barriers. It is also found that an introduction of InGaN sub-QW into the diode can change the tunneling mode and achieve higher transmission coefficient of electron. The simulation demonstrates that RTD with a 2.8-nm-thick In0.03Ga0.97N sub-well in front of a 2.0-nm-thick GaN main-well can exhibit the I-V characteristic having Ip and PVCR of 0.07 A and 11.6, about 7 times and double the value of RTD without sub-QW, respectively. The purpose of improving the structure of GaN-based QW is to solve apparent contradiction between the device structure and the device manufacturability of new generation RTDs for sub-millimeter and terahertz applications.
Flux-creep activation energy for a BaFe1.9Ni0.1As2 single crystal derived from alternating current susceptibility measurements
Authors: Ge Jun-Yi , Li Lin-Jun , Xu Zhu-An , Moshchalkov Victor V.
Published: April 2016

Systematic ac susceptibility measurements have been performed to investigate the vortex dynamics in a BaFe1.9Ni0.1As2 single crystal as a function of temperature, frequency, ac field amplitude, and dc magnetic field. The complex activation energy U(T,B,j) is derived in the framework of thermally activated flux creep theory and can be expressed in one simple formula. A power law dependence of U∼Bα with α = −0.46 is observed. The activation energy reaches 104 K at low fields, suggesting strong pinning in the material. The nonlinear function of the activation energy vs. the current density is determined, which has the expression of U∝j−0.1.
Bioacoustic cues and their relations to dominance rank in Père David’s deer stags
Authors: Liu Ni , Jiang Zhigang , Zhang Linyuan , Zhong Zhenyu , Ping Xiaoge , Xu Huailiang , Li Chunwang
Published: April 2016

The vocal display of male animals during the breeding season has received particular attention. To find out whether male acoustic signals could be a quality-assessment cue of callers, we conducted a study on Père David’s deer (Elaphurus davidianus) characterised by a polygynous mating system and high male–male competition during the rutting season. We investigated the relationship between the stag’s acoustic properties and the dominance rank as an indication of quality. Results showed that (1) there were two types of calls, the common roar and the chasing bark, (2) there was no significant difference between the call duration of the common roar and the chasing bark among different dominance ranks, (3) in the common roar, the value of the fundamental frequency, formant frequencies and formant spacing decreased significantly with the rise of dominance ranks and (4) vocal intensity of the common roar differed significantly among the three dominance ranks such as the harem master, the challengers and the bachelors. Our results suggested that some acoustic features, such as formant frequencies, formant spacing and vocal intensity of the common roar were closely related to the dominance rank and could be effective indicators of male competitive ability.
Palaeoecology to inform wetland conservation and management: some experiences and prospects
Authors: Clarke Stewart J. , Lynch A. Jasmyn J.
Published: April 2016

Wetlands are an important social–ecological resource, being fundamentally important to many natural processes, human wellbeing and livelihoods. They also contain important stores of information in their sediments which are increasingly being used to improve conservation and environmental management outcomes. We describe how palaeoecology can inform understanding of longer-term processes in wetland environments and examples of where it has contributed directly to site-based conservation decisions for wetlands in the UK. Palaeoecological science is being used in partnerships between some scientists and wetland managers, yet there is scope for broadening its use to support more integrated, inclusive forms of management. We discuss this potential of palaeoecology to inform more holistic approaches to conservation through: landscape-scale conservation; a focus on ecosystem services and natural capital; and the interdisciplinary approach of social–ecological systems that frames conservation as being for ‘people and nature’. Realising this potential requires enhanced communication and engagement between scientists and research users about palaeoecological data, their scope for application, and limitations. The need for climate change adaptation, the use of narratives about past environmental changes and future management scenarios, and the need for improved approaches to conservation provide opportunities for bridging the science–policy–practitioner gap and advancing wetland conservation and management.
From ergative to comparee marker
Authors: Jacques Guillaume
Published: April 2016

This article describes the uses of the marker kɯ in Japhug, which presents many distinct functions, including ergative, instrumental, distributive, causal linker, manner linker and comparee marker in the comparative construction. A series of grammaticalization pathways, some of which have never been documented before, are proposed to account for the polyfunctionality of this marker.
Making intelligence more transparent
Authors: Zhang Hui , Di Weichao
Published: April 2016

This paper attempts to make a critical cognitive analysis of US strategic intelligence reports and aims at investigating language strategies and cognitive biases that occur in the reports and how the reports create the “realities” that may influence policymakers’ decisions. The data for analysis include seven reports released by US Intelligence Community which analyze, more or less, the Sino-US relations currently and in the foreseeable future as well as the implications of a rising China on US policies. The analytic framework is built up by integrating Critical Metaphor Analysis, Conceptual Blending Theory and Discourse Space Theory, each of which deal with different aspects of the discourse and on the whole provide a comprehensive analysis of it. The critical cognitive analysis of intelligence reports could disclose the views that analysts hold on particular issues, providing valuable reference for understanding or evaluating their reports’ contents, and reveal the ideology inherent in US strategic thinking, helping to estimate US strategic policies in the long term.
Purification, gene cloning, and characterization of γ-butyrobetainyl CoA synthetase fromAgrobacteriumsp. 525a
Authors: Fujimitsu Hiroshi , Matsumoto Akira , Takubo Sayaka , Fukui Akiko , Okada Kazuma , Mohamed Ahmed Isam A , Arima Jiro , Mori Nobuhiro
Published: April 2016

The report is the first of purification, overproduction, and characterization of a unique γ-butyrobetainyl CoA synthetase from soil-isolated Agrobacterium sp. 525a. The primary structure of the enzyme shares 70–95% identity with those of ATP-dependent microbial acyl-CoA synthetases of the Rhizobiaceae family. As distinctive characteristics of the enzyme of this study, ADP was released in the catalytic reaction process, whereas many acyl CoA synthetases are annotated as an AMP-forming enzyme. The apparent Km values for γ-butyrobetaine, CoA, and ATP were, respectively, 0.69, 0.02, and 0.24 mM.
A shock at the radio relic position in Abell 115
Authors: Botteon A. , Gastaldello F. , Brunetti G. , Dallacasa D.
Published: April 2016

We analysed a deep Chandra observation (334 ks) of the galaxy cluster Abell 115 and detected a shock cospatial with the radio relic. The X-ray surface brightness profile across the shock region presents a discontinuity, corresponding to a density compression factor $\mathcal {C}=2.0\pm 0.1$, leading to a Mach number $\mathcal {M}=1.7\pm 0.1$ ($\mathcal {M}=1.4{\rm -}2$ including systematics). Temperatures measured in the upstream and downstream regions are consistent with what expected for such a shock: $T_{\rm u}=4.3^{+1.0}_{-0.6}\:\rm {keV}$ and $T_{\rm d}=7.9^{+1.4}_{-1.1}\:\rm {keV}$, respectively, implying a Mach number $\mathcal {M}=1.8^{+0.5}_{-0.4}$. So far, only few other shocks discovered in galaxy clusters are consistently detected from both density and temperature jumps. The spatial coincidence between this discontinuity and the radio relic edge strongly supports the view that shocks play a crucial role in powering these synchrotron sources. We suggest that the relic is originated by shock re-acceleration of relativistic electrons rather than acceleration from the thermal pool. The position and curvature of the shock and the associated relic are consistent with an off-axis merger with unequal mass ratio where the shock is expected to bend around the core of the less massive cluster.
The Affordable Care Act, Substance Use Disorders, and Low-Income Clients: Implications for Social Work
Authors: McCabe Heather A. , Wahler Elizabeth A.
Published: April 2016

Social workers are leaders in the substance abuse services field and may often work in substance use disorder (SUD) education, prevention, assessment, treatment, or resource coordination and case management roles. As the Patient Protection and Affordable Care Act (ACA) (2010) drives changes in the fields of health and behavioral health, social workers have an opportunity to lead structural changes at the micro and macro levels that will have a positive impact on low-income clients with SUDs. In this article, authors examine the current state of SUDs and health care access, the impact of the ACA on the field, and implications for social work practice and education. Social workers should seek specialized education and credentialing in SUD services, know how to help clients apply for health care coverage, and advocate for integrated substance abuse treatment and health care programs and an expansion of Medicaid in their local communities. Social workers are well positioned to be a voice for clients to ensure that the current structural changes result in a better, integrated system of care that is able to respond to the needs of low-income clients with SUDs.
Dermatologic complications of anti-PD-1/PD-L1 immune checkpoint antibodies
Authors: Sibaud Vincent , Meyer Nicolas , Lamant Laurence , Vigarios Emmanuelle , Mazieres Julien , Delord Jean Pierre
Published: April 2016

Purpose of review

The therapeutic use of anti-PD-1/PD-L1 antibodies (nivolumab, pembrolizumab) is rapidly increasing. Given their mechanism of action that triggers T-cell activation, these immune checkpoint inhibitors induce specific adverse events that are mostly of immunologic origin. In this way, cutaneous toxicities represent the most frequent immune-related adverse events (irAEs). The purpose of this review is to summarize the most prevalent dermatologic complications induced by PD-1/PD-L1 immune checkpoint-blocking antibodies and to compare their dermatologic safety profile with anti-CTLA-4 ipilimumab.

Recent findings

More than 40% of melanoma patients treated with anti-PD-1 therapy are faced with dermatologic irAEs. However, these cutaneous complications usually remain self-limiting and readily manageable. Nonspecific macular papular rash and pruritus represent the most common manifestations. More characteristic lichenoid dermatitis or psoriasis may also develop. Vitiligo is also frequent in patients with melanoma but has not been reported in other types of solid cancers. Mucosal involvement may also occur, including xerostomia and lichenoid reactions. Although available data remain scarce, anti-PD-L1 antibodies present a similar dermatologic safety profile.

Dermatologic irAEs induced by PD-1 or PD-L1 blockade therapy rarely result in significant morbidity or permanent discontinuation of treatment. However, early recognition and appropriate management are crucial for restricting dose-limiting toxicities.
Ocular and orbital side-effects of checkpoint inhibitors: a review article
Authors: Antoun Joëlle , Titah Cherif , Cochereau Isabelle
Published: April 2016

Purpose of review

Checkpoint inhibitors have been increasingly considered as new targets for cancer therapies. Patients receiving checkpoint inhibitors develop many immune-related adverse events (IRAEs). However, ophthalmic IRAEs are rare and have been reported in less than 1% of patients. To date, few case reports evaluating the ophthalmological side-effects of checkpoint inhibitors have been published. In this review, we plan to report the different ocular and orbital side-effects of the checkpoint inhibitors, and to help guide ophthalmologists and oncologists in their management.

Recent findings

Ocular side-effects of checkpoint inhibitors include peripheral ulcerative keratitis, uveitis, Vogt–Koyanagi–Harada syndrome, choroidal neovascularization and melanoma-associated retinopathy. Both thyroid-associated orbitopathy and idiopathic orbital inflammation have also been reported in association with checkpoint inhibitors. Mild IRAE can be treated with topical steroids, whereas systemic corticosteroids and discontinuation of checkpoint inhibitors are indicated in more severe ocular and orbital inflammation.

Physicians involved in the care of oncologic patients should be aware of the ocular and orbital IRAEs that may develop with checkpoint inhibitors. A strong cooperation between oncologists and ophthalmologists is required in the diagnosis and prompt management of these IRAEs.
Present and future role of surgery in metastatic gastrointestinal malignancies
Authors: Naredi Peter , Olofsson Bagge Roger
Published: April 2016

Purpose of review

Metastases from gastrointestinal malignancies are systemic or abdominal disseminations of cancer cells. From a biological perspective surgical resections are questionable but case series show that for some tumour types, surgery influences survival outcome. This review focuses on management and indications for surgery in recent literature of these metastatic gastrointestinal malignancies.

Recent findings

A few gastrointestinal malignancies have emerged to be candidates for surgery in case of metastatic disease. Surgery can be considered in selected cases with liver metastases or abdominal dissemination of colorectal cancer, metastases from gastrointestinal stromal tumours or neuroendocrine tumours. On the contrary, recent publications do not support surgery for metastatic disease of any other gastrointestinal origin. The literature has ample examples of small series and anecdotal cases of successful surgical interventions for most tumour types but no new evidence has been presented to support broader indications for surgery.

The evidence base for surgery of different metastatic gastrointestinal malignancies is unchanged. There are some clarifications when to perform surgery and the timing of surgery in regard to combined treatments. No new tumour types are added to potential candidates for surgery.
Assessing barriers to a rational chemoprevention trial design in young patients with familial adenomatous polyposis
Authors: Wood Joanna P. , Howells Lynne M. , Brown Karen , Thomas Anne L.
Published: April 2016

Familial adenomatous polyposis coli (FAP) is an autosomal dominant condition caused by a germline mutation in the adenomatous polyposis coli gene. Colonic adenomas form and almost all patients will develop colorectal cancer if they are not managed at an early stage. The safest preventive strategy is surgical resection of the colon, most commonly performed in late teenage years. There is a paucity of trials investigating the use of primary chemoprevention to delay polyp formation in paediatric FAP. There are extensive preclinical and early clinical data demonstrating that curcumin may be a safe and effective chemotherapeutic agent in reducing the polyp burden in this disease. We ultimately proposed to design and conduct a clinical study to assess whether curcumin treatment delays the need for surgery and/or prevents cancer in young patients with FAP. Research into clinical trial protocols has demonstrated that assessing patients’ perceptions at the initial stage leads to better outcomes. We therefore conducted a questionnaire study of patients and parents of children affected by FAP to gain information to aid the protocol design. Results demonstrated that there are some FAP patients for whom this study is relevant and desirable. Those with a personal history of curcumin use reported that it was well tolerated. However, the response rate was poor (25%), indicating that there are potential difficulties ensuring adequate recruitment to the proposed trial. This report draws on lessons learnt from prior trials and the findings from the questionnaire to outline the challenges faced in designing such a study.