bluuebunny/crossref_metadata_2025 huggingface dataset:
The focusing effect in backward Raman amplification in plasma
Authors: Li Zhaoli , Peng Hao , Zuo Yanlei , Su Jingxin , Yang Suhui
Published: April 2018

In this paper, the focusing effect on backward Raman amplification in plasma is investigated. A fluid model, used to simulate the backward Raman amplification and including the relativistic, ponderomotive, and thermal self-focusing and the mutual-focusing effect simultaneously, is proposed and investigated. The focusing effect is shown to severely distort the profile of the seed when the seed intensity was as high as 1017 W/cm2. Reducing the plasma density can relax the focusing effect, but at the cost of decreasing the amplification efficiency. Changing the profile of the seed has a limited effect on mitigating the focusing effect. A Gaussian profile of the pump and a defocusing shape of the plasma density seem to be an effective way to mitigate the focusing effect without decreasing the amplification efficiency.
Concept of a tunable source of coherent THz radiation driven by a plasma modulated electron beam
Authors: Zhang H. , Konoplev I. V. , Doucas G. , Smith J.
Published: April 2018

We have carried out numerical studies which consider the modulation of a picosecond long relativistic electron beam in a plasma channel and the generation of a micro-bunched train. The subsequent propagation of the micro-bunched beam in the vacuum area was also investigated. The same numerical model was then used to simulate the radiation arising from the interaction of the micro-bunched beam with a metallic grating. The dependence of the radiation spectrum on the parameters of the micro-bunched beam has been studied and the tunability of the radiation by the variation of the micro-bunch spacing has been demonstrated. The micro-bunch spacing can be changed easily by altering the plasma density without changing the beam energy or current. Using the results of these studies, we develop a conceptual design of a tunable source of coherent terahertz (THz) radiation driven by a plasma modulated beam. Such a source would be a potential and useful alternative to conventional vacuum THz tubes and THz free-electron laser sources.
TiN/Al2O3/ZnO gate stack engineering for top-gate thin film transistors by combination of post oxidation and annealing
Authors: Kato Kimihiko , Matsui Hiroaki , Tabata Hitoshi , Takenaka Mitsuru , Takagi Shinichi
Published: April 2018

Control of fabrication processes for a gate stack structure with a ZnO thin channel layer and an Al2O3 gate insulator has been examined for enhancing the performance of a top-gate ZnO thin film transistor (TFT). The Al2O3/ZnO interface and the ZnO layer are defective just after the Al2O3 layer formation by atomic layer deposition. Post treatments such as plasma oxidation, annealing after the Al2O3 deposition, and gate metal formation (PMA) are promising to improve the interfacial and channel layer qualities drastically. Post-plasma oxidation effectively reduces the interfacial defect density and eliminates Fermi level pinning at the Al2O3/ZnO interface, which is essential for improving the cut-off of the drain current of TFTs. A thermal effect of post-Al2O3 deposition annealing at 350 °C can improve the crystalline quality of the ZnO layer, enhancing the mobility. On the other hand, impacts of post-Al2O3 deposition annealing and PMA need to be optimized because the annealing can also accompany the increase in the shallow-level defect density and the resulting electron concentration, in addition to the reduction in the deep-level defect density. The development of the interfacial control technique has realized the excellent TFT performance with a large ON/OFF ratio, steep subthreshold characteristics, and high field-effect mobility.
Hole patterns in ultrathin vanadium oxide layers on a Rh(111) surface during catalytic oxidation reactions with NO
Authors: von Boehn Bernhard , Mehrwald Sarah , Imbihl Ronald
Published: April 2018

Various oxidation reactions with NO as oxidant have been investigated on a partially VOx covered Rh(111) surface (θV = 0.3 MLE) in the 10−4 mbar range, using photoelectron emission microscopy (PEEM) as spatially resolving method. The PEEM studies are complemented by rate measurements and by low-energy electron diffraction. In catalytic methanol oxidation with NO and in the NH3 + NO reaction, we observe that starting from a homogeneous surface with increasing temperature first a stripe pattern develops, followed by a pattern in which macroscopic holes of nearly bare metal surface are surrounded by a VOx film. These hole patterns represent just the inverse of the VOx distribution patterns seen if O2 instead of NO is used as oxidant.
Ultrafast endothermic transfer of non-radiative exciplex state to radiative excitons in polyfluorene random copolymer for blue electroluminescence
Authors: Moghe Dhanashree A. , Dey Amrita , Johnson Kerr , Lu L.-P. , Friend Richard H. , Kabra Dinesh
Published: April 2018

We report a blue-emitting random copolymer (termed modified Aryl-F8) consisting of three repeat units of polydioctylfluorene (F8), Aryl-polydioctylfluorene (Aryl-F8), and an aromatic amine comonomer unit, poly(bis-N,Ν′-(4-butylphenyl)-bis-N,N′-phenyl-1,4 phenylenediamine) chemically linked to get an improved charge carrier balance without compromising on the photoluminescence (PL) quantum yield with respect to the Aryl-F8 homo-polymer. The measured photoluminescence quantum efficiency (∼70%) of the blue-emitting polymer is comparable to or greater than the individual monomer units. The time resolved PL spectra from the modified Aryl-F8 are similar to those of Arylated-poly(9,9′-dioctylfluorene-co-bis-N,N′-(4-butylphenyl)-bis-N,N′-phenyl-1,4 phenylenediamine) (PFB) even at a time scale of 100–250 ps, indicating an ultrafast energy transfer from the (Aryl-F8 or F8):Arylated-PFB interface to Arylated-PFB, i.e., endothermic transfer of non-radiative exciplex to a radiative molecular exciton. Furthermore, the presence of non-radiative exciplex is confirmed by the photoluminescence decay profile and temperature dependent PL spectra. The luminance efficiency achieved for the modified Aryl-F8 polymer light-emitting diodes is ∼11 cd A−1 with an external quantum efficiency (EQE) of ∼4.5%, whereas it is 0.05 cd/A with an EQE of ∼0.025% for Aryl-F8. Almost two orders of higher efficiency is achieved due to the improved charge carrier balance from the random copolymer without compromising on the photoluminescence yield.
Machine learning approaches to evaluate correlation patterns in allosteric signaling: A case study of the PDZ2 domain
Authors: Botlani Mohsen , Siddiqui Ahnaf , Varma Sameer
Published: April 2018

Many proteins are regulated by dynamic allostery wherein regulator-induced changes in structure are comparable with thermal fluctuations. Consequently, understanding their mechanisms requires assessment of relationships between and within conformational ensembles of different states. Here we show how machine learning based approaches can be used to simplify this high-dimensional data mining task and also obtain mechanistic insight. In particular, we use these approaches to investigate two fundamental questions in dynamic allostery. First, how do regulators modify inter-site correlations in conformational fluctuations (Cij)? Second, how are regulator-induced shifts in conformational ensembles at two different sites in a protein related to each other? We address these questions in the context of the human protein tyrosine phosphatase 1E’s PDZ2 domain, which is a model protein for studying dynamic allostery. We use molecular dynamics to generate conformational ensembles of the PDZ2 domain in both the regulator-bound and regulator-free states. The employed protocol reproduces methyl deuterium order parameters from NMR. Results from unsupervised clustering of Cij combined with flow analyses of weighted graphs of Cij show that regulator binding significantly alters the global signaling network in the protein; however, not by altering the spatial arrangement of strongly interacting amino acid clusters but by modifying the connectivity between clusters. Additionally, we find that regulator-induced shifts in conformational ensembles, which we evaluate by repartitioning ensembles using supervised learning, are, in fact, correlated. This correlation Δij is less extensive compared to Cij, but in contrast to Cij, Δij depends inversely on the distance from the regulator binding site. Assuming that Δij is an indicator of the transduction of the regulatory signal leads to the conclusion that the regulatory signal weakens with distance from the regulatory site. Overall, this work provides new approaches to analyze high-dimensional molecular simulation data and also presents applications that yield new insight into dynamic allostery.
Numerical analysis of deposition frequency for successive droplets coalescence dynamics
Authors: Cheng Xiaoding , Zhu Yunlong , Zhang Lei , Zhang Dingyi , Ku Tao
Published: April 2018

A pseudopotential based multi-relaxation-time lattice Boltzmann model is employed to investigate the dynamic behaviors of successive droplets’ impact and coalescence on a solid surface. The effects of deposition frequency on the morphology of the formed line are investigated with a zero receding contact angle by analyzing the droplet-to-droplet coalescence dynamics. Two collision modes (in-phase mode and out-of-phase mode) between the pre-deposited bead and the subsequent droplet are identified depending on the deposition frequency. A uniform line can be obtained at the optimal droplet spacing in the in-phase mode (Δt* < 1.875). However, a scalloped line pattern is formed in the out-of-phase mode (Δt* > 1.875). It is found that decreasing the droplet spacing or advancing contact angle can improve the smoothness of line in the out-of-phase mode. Furthermore, the effects of deposition frequency on the morphology of the formed lines are validated to be applicable to cases with a finite receding contact angle.
D2O clusters isolated in rare-gas solids: Dependence of infrared spectrum on concentration, deposition rate, heating temperature, and matrix material
Authors: Shimazaki Yoichi , Arakawa Ichiro , Yamakawa Koichiro
Published: April 2018

The infrared absorption spectra of D2O monomers and clusters isolated in rare-gas matrices were systematically reinvestigated under the control of the following factors: the D2O concentration, deposition rate, heating temperature, and rare-gas species. We clearly show that the cluster-size distribution is dependent on not only the D2O concentration but also the deposition rate of a sample; as the rate got higher, smaller clusters were preferentially formed. Under the heating procedures at different temperatures, the cluster-size growth was successfully observed. Since the monomer diffusion was not enough to balance the changes in the column densities of the clusters, the dimer diffusion was likely to contribute the cluster growth. The frequencies of the bonded-OD stretches of (D2O)k with k = 2-6 were almost linearly correlated with the square root of the critical temperature of the matrix material. Additional absorption peaks of (D2O)2 and (D2O)3 in a Xe matrix were assigned to the species trapped in tight accommodation sites.
Isomorph theory of physical aging
Authors: Dyre Jeppe C.
Published: April 2018

This paper derives and discusses the configuration-space Langevin equation describing a physically aging R-simple system and the corresponding Smoluchowski equation. Externally controlled thermodynamic variables like temperature, density, and pressure enter the description via the single parameter Ts/T, in which T is the bath temperature and Ts is the “systemic” temperature defined at any time t as the thermodynamic equilibrium temperature of the state point with density ρ(t) and potential energy U(t). In equilibrium, Ts ≅ T with fluctuations that vanish in the thermodynamic limit. In contrast to Tool’s fictive temperature and other effective temperatures in glass science, the systemic temperature is defined for any configuration with a well-defined density, even if it is not close to equilibrium. Density and systemic temperature define an aging phase diagram, in which the aging system traces out a curve. Predictions are discussed for aging following various density-temperature and pressure-temperature jumps from one equilibrium state to another, as well as for a few other scenarios. The proposed theory implies that R-simple glass-forming liquids are characterized by the dynamic Prigogine-Defay ratio being equal to unity.
New Products
Authors: Mandelis Andreas
Published: April 2018

In order to supplement manufacturers’ information, this Department will welcome the submission by our readers of brief communications reporting measurements on the physical properties of materials which supersede earlier data or suggest new research applications.
A semi-discrete modified KdV equation
Authors: Sun Jianqing , Hu Xingbiao , Zhang Yingnan
Published: April 2018

In this paper, we present an integrable semi-discretization of the modified Korteweg-deVries (mKdV) equation. We discretize the “time” variable of the mKdV equation and get an integrable differential-difference system. Under a standard limit, the differential-difference system converges to the continuous mKdV equation. By Hirota’s bilinear method, we find some explicit solutions including solitons and breather solutions. From the semi-discrete system, we design a numerical scheme to the mKdV equation and carry out several numerical experiments with the 3-soliton solution and breather solution.
In vitro digestion of tropical legume starch is influenced by the combination of heating and soaking treatments
Authors: Torres Julieta , Muñoz Luz S. , Peters Michael , Montoya Carlos A.
Published: April 2018

Raw legumes have in general low starch digestion, which limits their use in animal nutrition. This study aimed to determine the effect of different thermal (raw, autoclaving and boiling for 5 and 20 min) and soaking (without or with) treatments on the in vitro degree of hydrolysis (DH) of starch for selected grains of tropical legumes (Canavalia brasiliensis, CB; Lablab purpureus, LP; pink, red and white colour hulls Vigna unguiculata, PVU, RVU and WVU). Indigested residues collected after in vitro sequential pepsin-pancreatin (120–240 min) digestion were used to determine the starch DH and the estimated digestible starch content. The starch content was in general higher when the legumes were treated (e.g. autoclaving increased 28% the starch content of CB). Autoclaving and boiling for 5 min increased the DH for both unsoaked and soaked CB and RVU (+6–16% units), whereas they reduced the DH for unsoaked boiled LP, PVU, WVU and unsoaked autoclaved LP (P < 0.05). Extending the boiling from 5 to 20 min reduced the DH for CB, PVU, RVU and WVU (–8–22% units), whereas it increased 17% units the DH of LP (P < 0.05). In contrast, extending the autoclaving increased DH for soaked LP, PVU and WVU (+4–13% units) (P < 0.05), but did not affect the other legumes (P > 0.05). Similar trends were observed for the estimated digestible starch content, despite the changes in starch content. In conclusion, the effect of soaking and heating treatment combinations on the DH of starch and estimated digestible starch content varied among legumes. Conditions for starch determination may be adapted for legumes.
Carbon pools in China’s terrestrial ecosystems: New estimates based on an intensive field survey
Authors: Tang Xuli , Zhao Xia , Bai Yongfei , Tang Zhiyao , Wang Wantong , Zhao Yongcun , Wan Hongwei , Xie Zongqiang , Shi Xuezheng , Wu Bingfang , Wang Gengxu , Yan Junhua , Ma Keping , Du Sheng , Li Shenggong , Han Shijie , Ma Youxin , Hu Huifeng , He Nianpeng , Yang Yuanhe , Han Wenxuan , He Hongling , Yu Guirui , Fang Jingyun , Zhou Guoyi
Published: April 2018

Significance

Previous estimations of carbon budgets in China’s terrestrial ecosystems varied greatly because of the multiplicity of data sources and the inconsistency of methodologies. By conducting a methodologically consistent field campaign across the country, we estimated that the total carbon pool in China’s forests, shrublands, grasslands, and croplands was 79.24 ± 2.42 Pg C. The carbon density exhibited a strong dependence on climate regime: it decreased with temperature but increased with precipitation. The country’s forests have a large potential of biomass carbon sequestration of 1.9–3.4 Pg C in the next 10 to 20 years assuming no removals. Our findings provide a benchmark to identify the effectiveness of the government’s natural protection policies.
Effects of national ecological restoration projects on carbon sequestration in China from 2001 to 2010
Authors: Lu Fei , Hu Huifeng , Sun Wenjuan , Zhu Jiaojun , Liu Guobin , Zhou Wangming , Zhang Quanfa , Shi Peili , Liu Xiuping , Wu Xing , Zhang Lu , Wei Xiaohua , Dai Limin , Zhang Kerong , Sun Yirong , Xue Sha , Zhang Wanjun , Xiong Dingpeng , Deng Lei , Liu Bojie , Zhou Li , Zhang Chao , Zheng Xiao , Cao Jiansheng , Huang Yao , He Nianpeng , Zhou Guoyi , Bai Yongfei , Xie Zongqiang , Tang Zhiyao , Wu Bingfang , Fang Jingyun , Liu Guohua , Yu Guirui
Published: April 2018

Significance

China has launched six key ecological restoration projects since the late 1970s, but the contribution of these projects to terrestrial C sequestration remains unknown. In this study we examined the ecosystem C sink in the project area (∼16% of the country’s land area) and evaluated the project-induced C sequestration. The total annual C sink in the project area between 2001 and 2010 was estimated to be 132 Tg C per y, over half of which (74 Tg C per y, 56%) was caused by the implementation of the six projects. This finding indicates that the implementation of the ecological restoration projects in China has significantly increased ecosystem C sequestration across the country.
Plant diversity enhances productivity and soil carbon storage
Authors: Chen Shiping , Wang Wantong , Xu Wenting , Wang Yang , Wan Hongwei , Chen Dima , Tang Zhiyao , Tang Xuli , Zhou Guoyi , Xie Zongqiang , Zhou Daowei , Shangguan Zhouping , Huang Jianhui , He Jin-Sheng , Wang Yanfen , Sheng Jiandong , Tang Lisong , Li Xinrong , Dong Ming , Wu Yan , Wang Qiufeng , Wang Zhiheng , Wu Jianguo , Chapin F. Stuart , Bai Yongfei
Published: April 2018

Significance

Soil carbon sequestration plays an important role in mitigating anthropogenic increases in atmospheric CO
2
concentrations. Recent studies have shown that biodiversity increases soil organic carbon (SOC) storage in experimental grasslands. However, the effects of species diversity on SOC storage in natural ecosystems have rarely been studied, and the potential mechanisms are yet to be understood. The results presented here show that favorable climate conditions, particularly high precipitation, tend to increase both species richness and belowground biomass, which had a consistent positive effect on SOC storage in forests, shrublands, and grasslands. Nitrogen deposition and soil pH generally have a direct negative effect on SOC storage. Ecosystem management that maintains high levels of plant diversity can enhance SOC storage and other ecosystem services that depend on plant diversity.
Shifting plant species composition in response to climate change stabilizes grassland primary production
Authors: Liu Huiying , Mi Zhaorong , Lin Li , Wang Yonghui , Zhang Zhenhua , Zhang Fawei , Wang Hao , Liu Lingli , Zhu Biao , Cao Guangmin , Zhao Xinquan , Sanders Nathan J. , Classen Aimée T. , Reich Peter B. , He Jin-Sheng
Published: April 2018

Significance

Climate change is altering the structure and function of high-elevation ecosystems. Combining long-term observations with manipulative experiments is a powerful, yet rarely used way to test the sensitivity of such ecosystems to climatic change. Here, experimental evidence and meta-analysis confirm long-term observations that demonstrate climate warming and associated drying did not change net primary production, but did lead to a shift of allocation belowground. This observed shift was caused by a change in community composition. Although alpine grassland productivity appears to be resistant to warming, deeper root systems in response to warming could alter the amount of soil organic carbon stored in the subsoil, indicating that rooting depth should be taken into account when predicting soil organic carbon stocks under warming.
Mass and heat transfer between evaporation and condensation surfaces: Atomistic simulation and solution of Boltzmann kinetic equation
Authors: Zhakhovsky Vasily V. , Kryukov Alexei P. , Levashov Vladimir Yu. , Shishkova Irina N. , Anisimov Sergey I.
Published: April 2018

Boundary conditions required for numerical solution of the Boltzmann kinetic equation (BKE) for mass/heat transfer between evaporation and condensation surfaces are analyzed by comparison of BKE results with molecular dynamics (MD) simulations. Lennard–Jones potential with parameters corresponding to solid argon is used to simulate evaporation from the hot side, nonequilibrium vapor flow with a Knudsen number of about 0.02, and condensation on the cold side of the condensed phase. The equilibrium density of vapor obtained in MD simulation of phase coexistence is used in BKE calculations for consistency of BKE results with MD data. The collision cross-section is also adjusted to provide a thermal flux in vapor identical to that in MD. Our MD simulations of evaporation toward a nonreflective absorbing boundary show that the velocity distribution function (VDF) of evaporated atoms has the nearly semi-Maxwellian shape because the binding energy of atoms evaporated from the interphase layer between bulk phase and vapor is much smaller than the cohesive energy in the condensed phase. Indeed, the calculated temperature and density profiles within the interphase layer indicate that the averaged kinetic energy of atoms remains near-constant with decreasing density almost until the interphase edge. Using consistent BKE and MD methods, the profiles of gas density, mass velocity, and temperatures together with VDFs in a gap of many mean free paths between the evaporation and condensation surfaces are obtained and compared. We demonstrate that the best fit of BKE results with MD simulations can be achieved with the evaporation and condensation coefficients both close to unity.
Disparate binding kinetics by an intrinsically disordered domain enables temporal regulation of transcriptional complex formation
Authors: Robertson Neil O. , Smith Ngaio C. , Manakas Athina , Mahjoub Mahiar , McDonald Gordon , Kwan Ann H. , Matthews Jacqueline M.
Published: April 2018

Significance

Different combinations and permutations of transcription factors work together to regulate the expression of target genes. These proteins often contain high levels of intrinsically disordered regions, which are important mediators of protein–protein interactions. We show that unusual binding kinetics associated with an intrinsically disordered region in a transcriptional coregulator can regulate the formation of transcriptional complexes that lead to the specification of neuronal cell subtypes. Notably, a single intrinsically disordered region shows selective differences in binding kinetics for proteins of the same family, which have implications for how intrinsic disorder contributes to regulatory processes and complexity in higher organisms.
Rapid acquisition and model-based analysis of cell-free transcription–translation reactions from nonmodel bacteria
Authors: Moore Simon J. , MacDonald James T. , Wienecke Sarah , Ishwarbhai Alka , Tsipa Argyro , Aw Rochelle , Kylilis Nicolas , Bell David J. , McClymont David W. , Jensen Kirsten , Polizzi Karen M. , Biedendieck Rebekka , Freemont Paul S.
Published: April 2018

Significance

Nonmodel bacteria have essential roles to play in the future development of biotechnology by providing new sources of biocatalysts, antibiotics, hosts for bioproduction, and engineered “living therapies.” The characterization of such hosts can be challenging, as many are not tractable to standard molecular biology techniques. This paper presents a rapid and automated methodology for characterizing new DNA parts from a nonmodel bacterium using cell-free transcription–translation. Data analysis was performed with Bayesian parameter inference to provide an understanding of gene-expression dynamics and resource sharing. We suggest that our integrated approach is expandable to a whole range of nonmodel bacteria for the characterization of new DNA parts within a native cell-free background for new biotechnology applications.
Mechanisms of sampling interstitial fluid from skin using a microneedle patch
Authors: Samant Pradnya P. , Prausnitz Mark R.
Published: April 2018

Significance

Diagnosis and monitoring of disease is often done by measuring biomarkers found in blood, urine, saliva, and other bodily fluids. Another rich source of biomarkers is the interstitial fluid that surrounds cells and tissues in the body, but difficulty in accessing this fluid has limited its use in research and medicine. Here, we conducted experimental studies coupled with theoretical modeling to design a patch containing microscopic needles that puncture into superficial layers of skin and thereby enable withdrawal of interstitial fluid through micropores in a simple, minimally invasive manner. This patch can help researchers access interstitial fluid to advance discovery of novel biomarkers and enable doctors to use interstitial fluid for possible future diagnosis and monitoring of disease.
Human
N
-acetylglucosaminyltransferase II substrate recognition uses a modular architecture that includes a convergent exosite
Authors: Kadirvelraj Renuka , Yang Jeong-Yeh , Sanders Justin H. , Liu Lin , Ramiah Annapoorani , Prabhakar Pradeep Kumar , Boons Geert-Jan , Wood Zachary A. , Moremen Kelley W.
Published: April 2018

Significance

Cell-surface and secreted glycoproteins are initially synthesized and glycosylated in the endoplasmic reticulum. Glycan structures are trimmed and remodeled as they transit the secretory pathway, resulting in multi-branched complex-type structures. The enzymes that remodel these structures have precise linkage and branch specificities, with the product of one reaction being specifically recognized as the substrate for the following reaction. These reactions include
N
-acetylglucosaminyltransferase II (MGAT2), an enzyme that initiates complex branch extension by precise recognition of its glycan substrate. The structural basis for MGAT2 substrate recognition is the subject of the present study. Structures of MGAT2-substrate complexes reveal both modular and convergent mechanisms for selective substrate recognition and catalysis and provide a generalized model for template-based synthesis of glycan structures by glycosyltransferases.
Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria
Authors: Xu Ling , Naylor Dan , Dong Zhaobin , Simmons Tuesday , Pierroz Grady , Hixson Kim K. , Kim Young-Mo , Zink Erika M. , Engbrecht Kristin M. , Wang Yi , Gao Cheng , DeGraaf Stephanie , Madera Mary A. , Sievert Julie A. , Hollingsworth Joy , Birdseye Devon , Scheller Henrik V. , Hutmacher Robert , Dahlberg Jeffery , Jansson Christer , Taylor John W. , Lemaux Peggy G. , Coleman-Derr Devin
Published: April 2018

Significance

Drought remains a critical obstacle to meeting the food demands of the coming century. Understanding the interplay between drought stress, plant development, and the plant microbiome is central to meeting this challenge. Here, we demonstrate that drought causes enrichment of a distinct set of microbes in roots, composed almost entirely of monoderms, which lack outer membranes and have thick cell walls. We demonstrate that under drought, roots increase the production of many metabolites, and that monoderms inhabiting the drought-treated rhizosphere exhibit increased activity of transporters connected with some of these same compounds. The discovery of this drought-induced enrichment and associated shifts in metabolite exchange between plant and microbe reveal a potential blueprint for manipulating plant microbiomes for improved crop fitness.
Individuals, institutions, and innovation in the debates of the French Revolution
Authors: Barron Alexander T. J. , Huang Jenny , Spang Rebecca L. , DeDeo Simon
Published: April 2018

Significance

How do democracies make decisions? We can read transcripts from parliament houses and legislative halls to see how particular ideas are introduced and debated, but we understand very little about the general principles of how these systems deal with information, or the origins of those principles. Here we study the parliamentary assembly of the first 2 years of the French Revolution, a model for democracies and revolutions across the globe, and show how patterns of speaking are created, picked up, and ignored or propagated. Political ideology, top–down rules, and individual charisma all affect how word patterns survive and thrive or, conversely, disappear and drop away.
Integrating effects of species composition and soil properties to predict shifts in montane forest carbon–water relations
Authors: Maxwell Toby M. , Silva Lucas C. R. , Horwath William R.
Published: April 2018

Significance

This research focuses on how species composition and soil properties interact to control carbon fixation and water loss in California’s montane forests. Two conclusions arise: (
i
) The amount of carbon fixed per unit of water lost via transpiration varies widely among forest stands depending on dominant tree species and their inherent leaf characteristics, and (
ii
) different parent materials and stages of soil development regulate the effect of climate on water-use efficiency and productivity of trees across altitudinal gradients. Taken together, dynamic biological processes related to species composition and relatively inert physicochemical properties that characterize soil development can be combined to anticipate changes in forest carbon and water balances.
MinE conformational switching confers robustness on self-organized Min protein patterns
Authors: Denk Jonas , Kretschmer Simon , Halatek Jacob , Hartl Caroline , Schwille Petra , Frey Erwin
Published: April 2018

Significance

Many fundamental cellular processes are spatially regulated by self-organized protein patterns, which are often based on nucleotide-binding proteins that switch their nucleotide state upon interaction with a second, activating protein. For reliable function, these protein patterns must be robust against parameter changes, although the basis for such robustness is generally elusive. Here we take a combined theoretical and experimental approach to the
Escherichia coli
Min system, a paradigmatic system for protein self-organization. By mathematical modeling and in vitro reconstitution of mutant proteins, we demonstrate that the robustness of pattern formation is dramatically enhanced by an interlinked functional switching of both proteins, rather than one. Such interlinked functional switching could be a generic means of obtaining robustness in biological pattern-forming systems.
GoAmazon2014/5 campaign points to deep-inflow approach to deep convection across scales
Authors: Schiro Kathleen A. , Ahmed Fiaz , Giangrande Scott E. , Neelin J. David
Published: April 2018

Significance

Representations of strongly precipitating deep-convective systems in climate models are among the most important factors in their simulation. Parameterizations of these motions face the dual challenge of unclear pathways to including mesoscale organization and high sensitivity of convection to approximations of turbulent entrainment of environmental air. Ill-constrained entrainment processes can even affect global average climate sensitivity under global warming. Multiinstrument observations from the Department of Energy GoAmazon2014/5 field campaign suggest that an alternative formulation from radar-derived dominant updraft structure yields a strong relationship of precipitation to buoyancy in both mesoscale and smaller-scale convective systems. This simultaneously provides a key step toward representing the influence of mesoscale convection in climate models and sidesteps a problematic dependence on traditional entrainment rates.
Developmentally inspired programming of adult human mesenchymal stromal cells toward stable chondrogenesis
Authors: Occhetta Paola , Pigeot Sebastien , Rasponi Marco , Dasen Boris , Mehrkens Arne , Ullrich Thomas , Kramer Ina , Guth-Gundel Sabine , Barbero Andrea , Martin Ivan
Published: April 2018

Significance

The study offers a pharmacological solution to the challenging target of inducing stable chondrogenesis by human mesenchymal stromal cells (hMSCs), including protection against vascularization. Cells were reversed from the tendency to follow the default differentiation pathway, namely endochondral ossification and osteogenesis. Our findings open perspectives in articular cartilage regeneration, as well as in the establishment of hMSC-based models of cartilage development, physiology, and possibly pathology. Importantly, the results were achieved by mimicking molecular processes occurring during embryonic cartilage formation. This indicates that adult hMSCs share similarities with embryonic mesenchyme and validates the relevance to engineer developmental processes (“developmental engineering”) to control fate specification by adult stem/progenitor cell systems.
Plasmodium-associated changes in human odor attract mosquitoes
Authors: Robinson Ailie , Busula Annette O. , Voets Mirjam A. , Beshir Khalid B. , Caulfield John C. , Powers Stephen J. , Verhulst Niels O. , Winskill Peter , Muwanguzi Julian , Birkett Michael A. , Smallegange Renate C. , Masiga Daniel K. , Mukabana W. Richard , Sauerwein Robert W. , Sutherland Colin J. , Bousema Teun , Pickett John A. , Takken Willem , Logan James G. , de Boer Jetske G.
Published: April 2018

Significance

In vector-borne disease systems, there is mounting evidence that vertebrate hosts become more attractive to disease vectors during infection, yet in human malaria, the underlying mechanism has not been studied. We identified compounds, including aldehydes, that are produced in relatively greater amounts in the skin odor of individuals with malaria, thus demonstrating a basis for this phenomenon in the cues used during mosquito host location. By establishing the attractiveness of these compounds to malaria mosquito vectors in laboratory bioassays, we characterize a process by whichPlasmodiuminfection of humans could lead to increased mosquito biting. These compounds may serve as biomarkers of malaria or be used to enhance the efficacy of chemical lures used to trap mosquitoes.
Digitizing omics profiles by divergence from a baseline
Authors: Dinalankara Wikum , Ke Qian , Xu Yiran , Ji Lanlan , Pagane Nicole , Lien Anching , Matam Tejasvi , Fertig Elana J. , Price Nathan D. , Younes Laurent , Marchionni Luigi , Geman Donald
Published: April 2018

Significance

Technological advances enable increasingly comprehensive profiling of the molecular landscapes of cells, and these data can inform the personalized treatment of complex diseases. Two major obstacles are the complexity of these data and the high degree of person-to-person heterogeneity. We develop a highly simplified, personalized data representation by comparing the profile of an individual to the range of landscapes in a baseline population, thereby mimicking basic clinical diagnostic testing for departures of selected variables from normal levels. Moreover, our method can be applied to any data modality and at any level of granularity, from single features to any subset of features treated as a single entity, for example the gene expression levels in a pathway. Experiments involve both healthy human tissues and various cancer subtypes.
Spatial and temporal heterogeneity of neural responses in human posteromedial cortex
Authors: Daitch Amy L. , Parvizi Josef
Published: April 2018

Significance

The default mode network (DMN) is active both during the resting state and during internally directed cognition (e.g., remembering a past event) but is suppressed during focused attention to the external environment. However, it is currently unknown to what extent memory- and rest-related activity in the DMN originate from the same neuronal populations or exhibit similar temporal dynamics. Using direct intracranial recordings in human subjects, we observed at least three distinct, yet anatomically close, classes of sites within the posteromedial cortex, a hub of the DMN; one is active when recalling an autobiographical event and suppressed during externally directed cognition, one is active during rest, and one is active during the transition from a task to rest.
O
6
-methylguanine–induced transcriptional mutagenesis reduces p53 tumor-suppressor function
Authors: Ezerskyte Monika , Paredes João A. , Malvezzi Stefano , Burns John A. , Margison Geoffrey P. , Olsson Magnus , Scicchitano David A. , Dreij Kristian
Published: April 2018

Significance

The impact of DNA lesions on replication and mutagenesis is of high relevance for human health; however, the role of lesion-induced transcriptional mutagenesis (TM) in disease development is unknown. Here, the impact of
O
6
-methylguanine–induced TM on p53 function as a tumor suppressor was investigated in human cells. Results showed that TM in 15% of the transcripts resulted in a reduced ability of p53 protein to transactivate genes that regulate cell-cycle arrest and induction of apoptosis. This resulted in the loss of functional cell-cycle checkpoints and in impaired activation of apoptosis, both canonical p53 tumor-suppressor functions. This work provides evidence that TM can induce phenotypic changes in mammalian cells that have important implications for its role in tumorigenesis.
MK2 contributes to tumor progression by promoting M2 macrophage polarization and tumor angiogenesis
Authors: Suarez-Lopez Lucia , Sriram Ganapathy , Kong Yi Wen , Morandell Sandra , Merrick Karl A. , Hernandez Yuliana , Haigis Kevin M. , Yaffe Michael B.
Published: April 2018

Significance

Colon cancer is the third most common cancer type and the second leading cause of cancer-related death. Chronic inflammation is a major contributor to colon cancer development and progression, but the molecular details of how inflammation contributes to colon cancer remain unclear. The p38MAPK/MAPKAP Kinase 2 (MK2) pathway is a central mediator of cell stress and inflammation. Here, we examine the importance of this pathway in an inflammation-driven model of colon cancer using whole-body and tissue-specific MK2 knockouts, in combination with measurements of macrophage polarization, endothelial proliferation, and morphogenesis. We demonstrate that the MK2 pathway promotes colon tumor development by regulating the polarization of macrophages into an M2 tumor-promoting state that modulates the tumor microenvironment and enhances tumor angiogenesis.
Interaction instability of localization in quasiperiodic systems
Authors: Žnidarič Marko , Ljubotina Marko
Published: April 2018

Significance

Understanding how small imperfections affect a system’s dynamics is one of the central questions of theoretical physics—namely, do properties change in a smooth way, such that small perturbation leads to small changes, or do they change discontinuously? Localization in disordered many-particle quantum systems has been shown to be stable to interactions. On a single-particle level, one can also achieve localization with a quasiperiodic potential—a system without disorder but with rich properties. It is believed that localization in disordered as well as in quasiperiodic potentials behaves in essentially the same way, in particular, that both are stable against interactions. We show that this is not so. A quasiperiodic localized system discontinuously changes from localization to diffusion upon introducing interactions.
Study of protein folding under native conditions by rapidly switching the hydrostatic pressure inside an NMR sample cell
Authors: Charlier Cyril , Alderson T. Reid , Courtney Joseph M. , Ying Jinfa , Anfinrud Philip , Bax Adriaan
Published: April 2018

Significance

Development of specialized instrumentation enables rapid switching of the hydrostatic pressure inside an operating NMR spectrometer. This technology allows observation of protein signals during the repeated folding process. Applied to ubiquitin, a previously extensively studied model of protein folding, the methodology reveals an initially highly dynamic state that deviates relatively little from random coil behavior but also provides evidence for numerous repeatedly failed folding events, previously only observed in computer simulations. Above room temperature, direct NMR evidence shows a ∼50% fraction of proteins folding through an on-pathway kinetic intermediate, thereby revealing two equally efficient parallel folding pathways.
A Note on Selected Craft Beer Brand Names
Authors: Nuessel Frank
Published: April 2018

This note addresses selectively the names of craft beers produced by U.S. microbreweries. It considers the following points: (1) a brief history of beer, (2) the rise of the microbrewery in the U.S., (3) a definition of microbrewery, (4) a brief discussion of beer and craft beer in popular culture (film, television, collecting beer paraphernalia), and (5) a selected list of craft beer brand names to illustrate their referents.
Deformation and fracture in (0001) and (10-10) GaN single crystals
Authors: Kavouras P. , Ratschinski I. , Dimitrakopulos G.P. , Leipner H.S. , Komninou Ph. , Leibiger G. , Habel F.
Published: April 2018

Indentation techniques were utilised to induce deformation on polar (0001) c-plane and non-polar [Formula: see text] m-plane GaN single crystal. Cracking was more sensitively dependent on the orientation of the indenter tip, compared to hardness. The indentation-induced plastic deformation and fracture sequences were studied by cathodoluminescence imaging and optical microscopy, respectively. Polar GaN was harder than non-polar, while pop-in discontinuities occurred at lower loads in polar than non-polar GaN. Dislocation arrangements were more isotropic at the polar than the non-polar orientation. Polar GaN was more susceptible to cracking compared to non-polar. Indentation at the high load regime fostered radial and lateral crack formation at both indenter orientations in polar GaN. Post-indentation lateral crack propagation was observed in situ in polar GaN.

This is part of a thematic issue on Nanoscale Materials Characterisation and Modeling by Advances Microscopy Methods - EUROMAT.
Microstructure, mechanical properties and shape memory effect of Cu–Hf–Al–Ni alloys
Authors: Zhang Xin , Zhao Xu , Wang Fang , Liu Qingsuo , Wang Qian
Published: April 2018

The influence of hafnium element's incorporation on a Cu– xHf–13.0Al–4.0Ni (wt-%) ( x = 0.5, 1.0 and 2.0) high-temperature shape memory alloy was investigated systematically. The results show that the matrix of Cu– xHf–13.0Al–4.0Ni ( x = 0.5, 1.0 and 2.0) alloys is 18R martensite, and an orthorhombic-structured Cu8Hf3 phase is formed and distributed at the grain boundaries. The grain size is significantly reduced with increasing Hf content. The mechanical properties of Cu– xHf–13.0Al–4.0Ni ( x = 0.5, 1.0 and 2.0) alloys are improved by Hf doping due to the combination of refinement strengthening, solid solution strengthening and second phase strengthening. After heating under pre-strain of 10%, the shape memory effect of the Cu–1.0Hf–13.0Al–4.0Ni alloy reaches 5.6%, which is obviously higher than that of the Cu–13.0Al–4.0Ni alloy.
Influence of V content on properties of Ti–W–V–N films
Authors: He Sheng , Yu Lihua , Ju Hongbo , Geng Yaoxiang , Asempah Isaac , Xu Junhua
Published: April 2018

Ti–W–V–N composite films with different vanadium contents were synthesised by multi-target reactive magnetron sputtering. The microstructure, mechanical and tribological properties of Ti–W–V–N films were investigated by X-ray diffraction, scanning electron microscope, high-resolution transmission electron microscopy, nanoindentation and high-temperature ball-on-disc tribometer. The results showed that all the Ti–W–V–N composite films were face-centred cubic (fcc) structure, consisting of fcc-(Ti,W,V)N substitutional solid solution. When the V content ≥21.5 at.-%, the films consisted of fcc-(Ti,W,V)N and fcc-VN. The hardness of the films first increased and then decreased with the maximum value of 32.4 GPa, at 21.5 at.-% V. The test temperature had a significant effect on the tribological properties of Ti–W–V–N film with 21.5 at.-% V, the coefficient of friction (CoF) first increased and then decreased, with a minimum value of 0.304 at 700°C.While the wear rate increased gradually with increasing temperature.
Athletic identity and self‐esteem among active and retired Paralympic athletes
Authors: Marin‐Urquiza Adriana , Ferreira José Pedro , Van Biesen Debbie
Published: April 2018

Athletic identity (AI) has been suggested as a variable that can have an impact on the psychological health of the athletes upon retirement. The aim of this study was to provide more insight on the transition out of elite sport by assessing and comparing the extent of AI and self‐esteem in an active group (AG) and a retired group (RG) of Paralympic athletes. Perceived stress and depressive symptoms were additionally assessed in the AG and RG, respectively. A non‐probability sampling method was used to recruit active and retired Paralympic athletes (AG, n = 43; RG, n = 41, where 35 retired voluntarily and 6 retired involuntarily) with visual or physical impairments, from Dutch‐, English‐, Portuguese‐ and Spanish‐speaking countries. Participants completed an electronic survey with questionnaires to assess the study variables mentioned above. Descriptive analysis, comparisons (Mann–Whitney U test and t‐test) and Spearman's correlation coefficient were performed for the statistical analysis. Scores of AI were significantly lower in the RG (44.6 ± 9.6) compared to the AG (49.4 ± 8.9); t(82) = 2.36, p = .021, d = 0.51. No differences in self‐esteem were found between RG and AG; however, within the RG, athletes who involuntarily retired (21 ± 7.1) had significantly lower self‐esteem scores than those who retired voluntarily (25.2 ± 4.2); t(39) = 2.04, p = .049, d = 0.73. In conclusion, free choice upon retirement can positively influence the athletes’ self‐esteem, whereas a strong AI may negatively influence the retirement process, as it was positively correlated with depressive symptoms (ρ = .409, p = .008). These findings can have practical implications for sport psychologists to better support their athletes.
A flexible MHC class I multimer loading system for large-scale detection of antigen-specific T cells
Authors: Luimstra Jolien J. , Garstka Malgorzata A. , Roex Marthe C.J. , Redeker Anke , Janssen George M.C. , van Veelen Peter A. , Arens Ramon , Falkenburg J.H. Frederik , Neefjes Jacques , Ovaa Huib
Published: April 2018

Adaptive immunity is initiated by T cell recognition of specific antigens presented by major histocompatibility complexes (MHCs). MHC multimer technology has been developed for the detection, isolation, and characterization of T cells in infection, autoimmunity, and cancer. Here, we present a simple, fast, flexible, and efficient method to generate many different MHC class I (MHC I) multimers in parallel using temperature-mediated peptide exchange. We designed conditional peptides for HLA-A*02:01 and H-2Kb that form stable peptide–MHC I complexes at low temperatures, but dissociate when exposed to a defined elevated temperature. The resulting conditional MHC I complexes, either alone or prepared as ready-to-use multimers, can swiftly be loaded with peptides of choice without additional handling and within a short time frame. We demonstrate the ease and flexibility of this approach by monitoring the antiviral immune constitution in an allogeneic stem cell transplant recipient and by analyzing CD8+ T cell responses to viral epitopes in mice infected with lymphocytic choriomeningitis virus or cytomegalovirus.