bluuebunny/crossref_metadata_2025 huggingface dataset:
A path to scaling helium-3 spin-exchange optical pumping
Authors: Anderson S. J. , Ruset I. C. , Watt D. W. , Ketel J. , Ketel S. , Distelbrink J. H. , Hersman F. W.
Published: June 2020

Polarized 3He has contributed to breakthroughs in particle physics, neutron scattering, and lung imaging, mostly by optical pumping of liter quantities in valved cells or in sealed cells pumped in situ. Only metastability exchange optical pumping currently meets the demand for delivering large quantities of highly polarized 3He to external volumes. Our development program is under way to achieve medium to large-scale spin-exchange optical pumping of 3He. Thin-walled aluminosilicate cells placed in contact with thermal reservoirs inside a pressure vessel were optically pumped with kilowatt-scale lasers spectrally narrowed to match pressure-broadened absorption linewidths. We report here the key elements of this program and significant milestones: multi-liter volume valved cells that provide long longitudinal lifetimes that reached polarization as high as 85% inside a thermally stable and pressurized environment.
Rate-induced transitions and advanced takeoff in power systems
Authors: Suchithra K. S. , Gopalakrishnan E. A. , Surovyatkina Elena , Kurths Jürgen
Published: June 2020

One of the most common causes of failures in complex systems in nature or engineering is an abrupt transition from a stable to an alternate stable state. Such transitions cause failures in the dynamic power systems. We focus on this transition from a stable to an unstable manifold for a rate-dependent mechanical power input via a numerical investigation in a theoretical power system model. Our studies uncover early transitions that depend on the rate of variation of mechanical input. Furthermore, we determine the dependency of a critical rate on initial conditions of the system. Accordingly, this knowledge of the critical rate can be used in devising an effective control strategy based on artificial intelligence (AI).
All-optical nanophotonic resonant element for switching and routing applications exploiting graphene saturable absorption
Authors: Christopoulos Thomas , Ataloglou Vasileios G. , Kriezis Emmanouil E.
Published: June 2020

A silicon disk resonator overlaid with a uniform graphene layer in an add-drop configuration is proposed as an all-optical routing element. Operation is based on the saturable absorption effect provided by the graphene layer. The element is thoroughly analyzed as a two-channel device in the context of an appropriate nonlinear framework combining perturbation theory and temporal coupled-mode theory. Taking into consideration the primary nonlinear effect, which is graphene saturable absorption, a design path is carefully developed that eventually leads to a traveling-wave resonant element with low-power requirements, low insertion loss, high extinction ratio, and sufficient bandwidth. In a subsequent step, other important nonlinear effects originating from graphene and the silicon disk, including the Kerr effect and free-carrier effects, are considered and means for counterbalancing their action are demonstrated. A low control power of 9mW together with a bandwidth of 20GHz is shown possible, with the insertion loss of almost 3dB and an extinction ratio over 10dB in both ports (add and drop).
A rapid-quench technique for multi-anvil high-pressure-temperature experiments
Authors: Bondar Dmitry , Fei Hongzhan , Withers Anthony C. , Katsura Tomoo
Published: June 2020

In order to extend the pressure and compositional range where silicate melts can be quenched to form glass in a multi-anvil high-pressure and high-temperature apparatus, a rapid-quench technique, which includes an external cooling system and a low thermal-inertia assembly, was developed. This technique allows much higher cooling rates (6000–7000 °C/s) than regular piston-cylinder (130 °C/s) apparatus and multi-anvil (650 °C/s) apparatus, which are widely used in solid Earth science. Such high cooling rates are critical to avoid unwanted changes in a sample, such as melt crystallization and volatile loss, during quenching.
X-ray detection of ultrashort spin current pulses in synthetic antiferromagnets
Authors: Stamm C. , Murer C. , Wörnle M. S. , Acremann Y. , Gort R. , Däster S. , Reid A. H. , Higley D. J. , Wandel S. F. , Schlotter W. F. , Gambardella P.
Published: June 2020

We explore the ultrafast generation of spin currents in magnetic multilayer samples by applying fs laser pulses to one layer and measuring the magnetic response in the other layer by element-resolved x-ray spectroscopy. In Ni(5 nm)/Ru(2 nm)/Fe(4 nm), the Ni and Fe magnetization directions couple antiferromagnetically due to the Ruderman–Kittel–Kasuya–Yosida interaction but may be oriented parallel through an applied magnetic field. After exciting the top Ni layer with a fs laser pulse, we also find that the Fe layer underneath demagnetizes, with a 4.1±1.9% amplitude difference between parallel and antiparallel orientation of the Ni and Fe magnetizations. We attribute this difference to the influence of a spin current generated by the fs laser pulse that transfers angular momentum from the Ni into the Fe layer. Our results confirm that superdiffusive spin transport plays a role in determining the sub-ps demagnetization dynamics of synthetic antiferromagnetic layers, but also evidence large depolarization effects due to hot electron dynamics, which are independent of the relative alignment of the magnetization in Ni and Fe.
Study of detailed balance between excitons and free carriers in diamond using broadband terahertz time-domain spectroscopy
Authors: Ichii T. , Hazama Y. , Naka N. , Tanaka K.
Published: June 2020

A fundamental understanding of the photoexcited carrier system in diamond is crucial to facilitate its application in photonic and electronic devices. Here, we report the detailed balance between free carriers and excitons in intrinsic diamond by using a deep-ultraviolet pump in combination with broadband terahertz (THz) probe spectroscopy. We investigated the transformation of photoexcited carriers to excitons by using an internal transition of excitons, which is found to occur at a frequency of 16 THz. We determined the equilibrium constant in the Saha equation from the temperature dependence of the free-carrier density measured at chemical equilibrium. The derived exciton binding energy is larger than the conventional value, which indicates an energy shift due to the fine-structure splitting of the exciton states.
Linear array of charge sensitive infrared phototransistors for long wavelength infrared detection
Authors: Wang Hengliang , Zhu Yidi , Huang Shenyang , Zhang Lijian , Zhu Liping , Xu Hongtao , Chen Pingping , Lu Wei , An Zhenghua
Published: June 2020

Infrared has been deeply involved in frontier research, modern technologies, and human society, which requires sensitive infrared detection and sensing, in particular, array imaging. A charge-sensitive infrared phototransistor (CSIP) device is made of a GaAs/AlGaAs double quantum well and has been shown to exhibit much larger infrared photoresponsivity than conventional infrared photodetectors, attributable to its built-in amplification mechanism of large transconductance. In this work, we propose and demonstrate a linear array architecture of long wavelength CSIPs with each pixel directly addressable via its reset gate. The performance of a prototype 1×8 linear array of CSIPs is studied at 5 K, and each pixel shows a large photoresponsivity of >50 A/W at the peak wavelength of λ=11 μm, nearly two orders higher than conventional detectors. Using a home-made multi-channel pulse generator, the array is operated at a typical frame rate of ∼5 ms, without the necessity of using cryogenic readout circuits. Besides, the fabrication of the proposed CSIP array requires only state-of-the-art planar technology; our work, therefore, provides a promising solution to realize very sensitive and small-scale array infrared imaging for sensitive long-wavelength infrared applications.
Superconducting quantum many-body circuits for quantum simulation and computing
Authors: Wilkinson Samuel A. , Hartmann Michael J.
Published: June 2020

Quantum simulators are attractive as a means to study many-body quantum systems that are not amenable to classical numerical treatment. A versatile framework for quantum simulation is offered by superconducting circuits. In this perspective, we discuss how superconducting circuits allow the engineering of a wide variety of interactions, which, in turn, allows the simulation of a wide variety of model Hamiltonians. In particular, we focus on strong photon–photon interactions mediated by nonlinear elements. This includes on-site, nearest-neighbor, and four-body interactions in lattice models, allowing the implementation of extended Bose–Hubbard models and the toric code. We discuss not only the present state in analog quantum simulation but also future perspectives of superconducting quantum simulation, which open up when concatenating quantum gates in emerging quantum computing platforms.
A feasibility study of zebrafish embryo irradiation with laser-accelerated protons
Authors: Rösch Thomas F. , Szabó Zoltán , Haffa Daniel , Bin Jianhui , Brunner Szilvia , Englbrecht Franz S. , Friedl Anna A. , Gao Ying , Hartmann Jens , Hilz Peter , Kreuzer Christian , Lindner Florian H. , Ostermayr Tobias M. , Polanek Róbert , Speicher Martin , Szabó Emília R. , Taray Derya , Tőkés Tünde , Würl Matthias , Parodi Katia , Hideghéty Katalin , Schreiber Jörg
Published: June 2020

The development from single shot basic laser plasma interaction research toward experiments in which repetition rated laser-driven ion sources can be applied requires technological improvements. For example, in the case of radio-biological experiments, irradiation duration and reproducible controlled conditions are important for performing studies with a large number of samples. We present important technological advancements of recent years at the ATLAS 300 laser in Garching near Munich since our last radiation biology experiment. Improvements range from target positioning over proton transport and diagnostics to specimen handling. Exemplarily, we show the current capabilities by performing an application oriented experiment employing the zebrafish embryo model as a living vertebrate organism for laser-driven proton irradiation. The size, intensity, and energy of the laser-driven proton bunches resulted in evaluable partial body changes in the small (<1 mm) embryos, confirming the feasibility of the experimental system. The outcomes of this first study show both the appropriateness of the current capabilities and the required improvements of our laser-driven proton source for in vivo biological experiments, in particular the need for accurate, spatially resolved single bunch dosimetry and image guidance.
Relay and complete synchronization in heterogeneous multiplex networks of chaotic maps
Authors: Rybalova E. , Strelkova G. , Schöll E. , Anishchenko V.
Published: June 2020

We study relay and complete synchronization in a heterogeneous triplex network of discrete-time chaotic oscillators. A relay layer and two outer layers, which are not directly coupled but interact via the relay layer, represent rings of nonlocally coupled two-dimensional maps. We consider for the first time the case when the spatiotemporal dynamics of the relay layer is completely different from that of the outer layers. Two different configurations of the triplex network are explored: when the relay layer consists of Lozi maps while the outer layers are given by Henon maps and vice versa. Phase and amplitude chimera states are observed in the uncoupled Henon map ring, while solitary state regimes are typical for the isolated Lozi map ring. We show for the first time relay synchronization of amplitude and phase chimeras, a solitary state chimera, and solitary state regimes in the outer layers. We reveal regimes of complete synchronization for the chimera structures and solitary state modes in all the three layers. We also analyze how the synchronization effects depend on the spatiotemporal dynamics of the relay layer and construct phase diagrams in the parameter plane of inter-layer vs intra-layer coupling strength of the relay layer.
Requirements of epitaxially grown InGaAs channel layers for tunnel field-effect transistors
Authors: Yokoyama Masafumi , Yamamoto Taketsugu , Ahn Dae-Hwan , Takenaka Mitsuru , Takagi Shinichi
Published: June 2020

The requirements of the epitaxially grown InGaAs channel layers for tunnel field-effect transistors (TFETs) have been studied by a comparison between the experimental results and technology computer-aided design (TCAD) simulations. It is observed that the threshold voltage (Vth) of InGaAs TFETs with high In contents is shifted more toward the negative bias direction and the off-characteristics are degraded more than that expected in simulation results. These results are attributable to the increase in n-type effective carrier concentration (Nch) in the InGaAs and InAs channels, which can be caused by lattice relaxation because of the large lattice mismatch between the epitaxial layer and the substrate. The use of a thin channel layer with high In content InGaAs and/or InAs can be a solution for achieving high on-current and low off-current simultaneously. It is found that p-type doping in the InGaAs and InAs channels can mitigate the degradation of the cut-off properties. Moreover, it is observed that increased Nch by unintentional Si impurity atoms at the epitaxial layer and the substrate interface can affect the performance of TFETs with thin InGaAs channels, which can be suppressed by introducing an insertional undoped buffer layer. The impact of Nch is also studied for the short channel devices by TCAD simulations. The p-type doping in InGaAs channels can also mitigate short channel effects in comparison to the n-type doping. The carefully controlled epitaxial growth of InGaAs and InAs channel layers with Nch <1 × 1017 cm−3 is required to realize superior performance InGaAs TFETs.
Injection of a heavy fluid into a light fluid in a closed-end pipe
Authors: Akbari S. , Taghavi S. M.
Published: June 2020

We report experimental results on the injection of a heavy fluid into a light one in a closed-end pipe, inclined at intermediate angles. The injection of the heavy fluid is made using an inner duct with a smaller diameter than that of the pipe in which the light fluid is placed. The fluids used are miscible and Newtonian, and they have the same viscosity. Our observation shows that, during the removal/replacement of the light fluid by the heavy fluid, at least four distinct flow stages can be identified: (i) initial buoyant jet of the heavy fluid, (ii) development of a mixing region, (iii) slumping flow of the heavy fluid, and (iv) heavy fluid front reaching the pipe end and returning toward the mixing region. Using high-speed camera images along with the ultrasound Doppler velocimetry and laser induced fluorescence data, the flow characteristics in these flow stages are quantified, and they are described in detail vs the dimensionless groups that govern the flow dynamics, namely, the Froude number (Fr), the Reynolds number (Re), the Archimedes number (Ar), and the pipe inclination angle (β). While our findings are of fundamental importance, they can also be used to provide a fluid mechanics understanding of the dump bailing method in the plug and abandonment (P&A) of oil and gas wells.
Time-resolved emission and scattering imaging of plume dynamics and nanoparticle ejection in femtosecond laser ablation of silver thin films
Authors: Park Minok , Jeun Jinhong , Han Gyoowan , Grigoropoulos Costas P.
Published: June 2020

Time-resolved emission and scattering imaging are employed to analyze the ablation mechanisms of silver thin films induced by femtosecond laser irradiation of Gaussian intensity profile under different laser fluences and gas background pressures. At fluences near the ablation threshold, nanoparticles (NPs) of 40 nm–100 nm in size are ejected in the vertical direction from the target sample. The average ejection speed of these NPs increases with the laser fluence and also as the background gas pressure drops from ambient atmospheric to ∼10−5 Torr. At higher fluences, a plume is formed at the center of the laser beam and NPs are released in oblique trajectories from the peripheral area of the laser-irradiated spot.
Intense microsecond electron pulses from a Schottky emitter
Authors: Bongiovanni Gabriele , Olshin Pavel K. , Drabbels Marcel , Lorenz Ulrich J.
Published: June 2020

Thanks to their high brightness, field emitters are the electron sources of choice in most high-end electron microscopes. Under typical operating conditions, the available emission current from these emitters is largely limited by practical considerations, and extracting significantly larger currents is usually not possible without reducing the lifetime of the emitter or even damaging it. Such limitations may, however, not apply if the emitter is only briefly subjected to extreme operating conditions so that damage can be outrun. Here, we demonstrate that it is possible to temporarily operate a Schottky emitter far outside its stable operating regime and significantly increase its emission current. We do so by locally heating the tip of the emitter with a microsecond laser pulse, which boosts the emission current by a factor of 3.7 to nearly 450 μA. We believe that the generation of intense microsecond electron pulses from a field emitter will particularly benefit the atomic-resolution imaging of fast processes that occur on the microsecond timescale.
Finite-temperature coupled cluster: Efficient implementation and application to prototypical systems
Authors: White Alec F. , Kin-Lic Chan Garnet
Published: June 2020

We discuss the theory and implementation of the finite temperature coupled cluster singles and doubles (FT-CCSD) method including the equations necessary for an efficient implementation of response properties. Numerical aspects of the method including the truncation of the orbital space and integration of the amplitude equations are tested on some simple systems, and we provide some guidelines for applying the method in practice. The method is then applied to the 1D Hubbard model, the uniform electron gas (UEG) at warm, dense conditions, and some simple materials. The performance of model systems at high temperatures is encouraging: for the one-dimensional Hubbard model, FT-CCSD provides a qualitatively accurate description of finite-temperature correlation effects even at U = 8, and it allows for the computation of systematically improvable exchange–correlation energies of the warm, dense UEG over a wide range of conditions. We highlight the obstacles that remain in using the method for realistic ab initio calculations on materials.
Using simultaneous x-ray diffraction and velocity interferometry to determine material strength in shock-compressed diamond
Authors: MacDonald M. J. , McBride E. E. , Galtier E. , Gauthier M. , Granados E. , Kraus D. , Krygier A. , Levitan A. L. , MacKinnon A. J. , Nam I. , Schumaker W. , Sun P. , van Driel T. B. , Vorberger J. , Xing Z. , Drake R. P. , Glenzer S. H. , Fletcher L. B.
Published: June 2020

We determine the strength of laser shock-compressed polycrystalline diamond at stresses above the Hugoniot elastic limit using a technique combining x-ray diffraction from the Linac Coherent Light Source with velocity interferometry. X-ray diffraction is used to measure lattice strains, and velocity interferometry is used to infer shock and particle velocities. These measurements, combined with density-dependent elastic constants calculated using density functional theory, enable determination of material strength above the Hugoniot elastic limit. Our results indicate that diamond retains approximately 20 GPa of strength at longitudinal stresses of 150–300 GPa under shock compression.
Coupling of Ca
2+
and voltage activation in BK channels through the αB helix/voltage sensor interface
Authors: Geng Yanyan , Deng Zengqin , Zhang Guohui , Budelli Gonzalo , Butler Alice , Yuan Peng , Cui Jianmin , Salkoff Lawrence , Magleby Karl L.
Published: June 2020

Large-conductance Ca
2+
and voltage-activated K
+
(BK) channels control membrane excitability in many cell types. BK channels are tetrameric. Each subunit is composed of a voltage sensor domain (VSD), a central pore-gate domain, and a large cytoplasmic domain (CTD) that contains the Ca
2+
sensors. While it is known that BK channels are activated by voltage and Ca
2+
, and that voltage and Ca
2+
activations interact, less is known about the mechanisms involved. We explore here these mechanisms by examining the gating contribution of an interface formed between the VSDs and the αB helices located at the top of the CTDs. Proline mutations in the αB helix greatly decreased voltage activation while having negligible effects on gating currents. Analysis with the Horrigan, Cui, and Aldrich model indicated a decreased coupling between voltage sensors and pore gate. Proline mutations decreased Ca
2+
activation for both Ca
2+
bowl and RCK1 Ca
2+
sites, suggesting that both high-affinity Ca
2+
sites transduce their effect, at least in part, through the αB helix. Mg
2+
activation also decreased. The crystal structure of the CTD with proline mutation L390P showed a flattening of the first helical turn in the αB helix compared to wild type, without other notable differences in the CTD, indicating that structural changes from the mutation were confined to the αB helix. These findings indicate that an intact αB helix/VSD interface is required for effective coupling of Ca
2+
binding and voltage depolarization to pore opening and that shared Ca
2+
and voltage transduction pathways involving the αB helix may be involved.
Consistent scaling of inbreeding depression in space and time in a house sparrow metapopulation
Authors: Niskanen Alina K. , Billing Anna M. , Holand Håkon , Hagen Ingerid J. , Araya-Ajoy Yimen G. , Husby Arild , Rønning Bernt , Myhre Ane Marlene , Ranke Peter Sjolte , Kvalnes Thomas , Pärn Henrik , Ringsby Thor Harald , Lien Sigbjørn , Sæther Bernt-Erik , Muff Stefanie , Jensen Henrik
Published: June 2020

Inbreeding may increase the extinction risk of small populations. Yet, studies using modern genomic tools to investigate inbreeding depression in nature have been limited to single populations, and little is known about the dynamics of inbreeding depression in subdivided populations over time. Natural populations often experience different environmental conditions and differ in demographic history and genetic composition, characteristics that can affect the severity of inbreeding depression. We utilized extensive long-term data on more than 3,100 individuals from eight islands in an insular house sparrow metapopulation to examine the generality of inbreeding effects. Using genomic estimates of realized inbreeding, we discovered that inbred individuals had lower survival probabilities and produced fewer recruiting offspring than noninbred individuals. Inbreeding depression, measured as the decline in fitness-related traits per unit inbreeding, did not vary appreciably among populations or with time. As a consequence, populations with more resident inbreeding (due to their demographic history) paid a higher total fitness cost, evidenced by a larger variance in fitness explained by inbreeding within these populations. Our results are in contrast to the idea that effects of inbreeding generally depend on ecological factors and genetic differences among populations, and expand the understanding of inbreeding depression in natural subdivided populations.
Using gross ecosystem product (GEP) to value nature in decision making
Authors: Ouyang Zhiyun , Song Changsu , Zheng Hua , Polasky Stephen , Xiao Yi , Bateman Ian J. , Liu Jianguo , Ruckelshaus Mary , Shi Faqi , Xiao Yang , Xu Weihua , Zou Ziying , Daily Gretchen C.
Published: June 2020

Gross domestic product (GDP) summarizes a vast amount of economic information in a single monetary metric that is widely used by decision makers around the world. However, GDP fails to capture fully the contributions of nature to economic activity and human well-being. To address this critical omission, we develop a measure of gross ecosystem product (GEP) that summarizes the value of ecosystem services in a single monetary metric. We illustrate the measurement of GEP through an application to the Chinese province of Qinghai, showing that the approach is tractable using available data. Known as the “water tower of Asia,” Qinghai is the source of the Mekong, Yangtze, and Yellow Rivers, and indeed, we find that water-related ecosystem services make up nearly two-thirds of the value of GEP for Qinghai. Importantly most of these benefits accrue downstream. In Qinghai, GEP was greater than GDP in 2000 and three-fourths as large as GDP in 2015 as its market economy grew. Large-scale investment in restoration resulted in improvements in the flows of ecosystem services measured in GEP (127.5%) over this period. Going forward, China is using GEP in decision making in multiple ways, as part of a transformation to inclusive, green growth. This includes investing in conservation of ecosystem assets to secure provision of ecosystem services through transregional compensation payments.
O
-GlcNAcylation on LATS2 disrupts the Hippo pathway by inhibiting its activity
Authors: Kim Eunah , Kang Jeong Gu , Kang Min Jueng , Park Jae Hyung , Kim Yeon Jung , Kweon Tae Hyun , Lee Han-Woong , Jho Eek‐hoon , Lee Yong-ho , Kim Seung-Il , Yi Eugene C. , Park Hyun Woo , Yang Won Ho , Cho Jin Won
Published: June 2020

Significance

The Hippo pathway plays a crucial role in maintaining tissue homeostasis. Generally, activated Hippo pathway effectors, YAP/TAZ, induce the transcription of their negative regulators, NF2 and LATS2, and this negative feedback loop maintains homeostasis of the Hippo pathway. However, YAP and TAZ are consistently hyperactivated in various cancer cells, enhancing tumor growth. Our study found that LATS2, a direct-inhibiting kinase of YAP/TAZ and a core component of the negative feedback loop in the Hippo pathway, is modified with
O
-GlcNAc. LATS2
O
-GlcNAcylation inhibited its activity by interrupting the interaction with the MOB1 adaptor protein, thereby activating YAP and TAZ to promote cell proliferation. Thus, our study suggests that LATS2
O
-GlcNAcylation is deeply involved in Hippo pathway dysregulation in cancer cells.
Massive formation of early diagenetic dolomite in the Ediacaran ocean: Constraints on the “dolomite problem”
Authors: Chang Biao , Li Chao , Liu Deng , Foster Ian , Tripati Aradhna , Lloyd Max K. , Maradiaga Ingrid , Luo Genming , An Zhihui , She Zhenbing , Xie Shucheng , Tong Jinnan , Huang Junhua , Algeo Thomas J. , Lyons Timothy W. , Immenhauser Adrian
Published: June 2020

Significance

Massive Paleozoic and Precambrian dolostone successions have long puzzled geologists in light of the kinetic barriers that inhibit low-temperature dolomite nucleation and precipitation (i.e., the “dolomite problem”). Significantly, the widely accepted hypothesis that such massive dolomites are the product of burial–hydrothermal dolomitization challenges their validity as archives of Earth surface environments. Here, we place constraints on the formation of massive dolomicrite deposits of the Ediacaran Doushantuo Formation (South China), demonstrating their syndepositional (i.e., early diagenetic) formation over a >63-My interval. Our findings suggest that the “dolomite problem” may be a product of specific conditions common if not persistent in Paleozoic and Precambrian oceans, and that massive dolostone successions may be faithful recorders of environmental conditions in the early oceans.
Multi-omics analysis on an agroecosystem reveals the significant role of organic nitrogen to increase agricultural crop yield
Authors: Ichihashi Yasunori , Date Yasuhiro , Shino Amiu , Shimizu Tomoko , Shibata Arisa , Kumaishi Kie , Funahashi Fumiaki , Wakayama Kenji , Yamazaki Kohei , Umezawa Akio , Sato Takumi , Kobayashi Makoto , Kamimura Mayu , Kusano Miyako , Che Fang-Sik , O`Brien Martin , Tanoi Keitaro , Hayashi Makoto , Nakamura Ryuhei , Shirasu Ken , Kikuchi Jun , Nihei Naoto
Published: June 2020

Both inorganic fertilizer inputs and crop yields have increased globally, with the concurrent increase in the pollution of water bodies due to nitrogen leaching from soils. Designing agroecosystems that are environmentally friendly is urgently required. Since agroecosystems are highly complex and consist of entangled webs of interactions between plants, microbes, and soils, identifying critical components in crop production remain elusive. To understand the network structure in agroecosystems engineered by several farming methods, including environmentally friendly soil solarization, we utilized a multiomics approach on a field planted withBrassica rapa. We found that the soil solarization increased plant shoot biomass irrespective of the type of fertilizer applied. Our multiomics and integrated informatics revealed complex interactions in the agroecosystem showing multiple network modules represented by plant traits heterogeneously associated with soil metabolites, minerals, and microbes. Unexpectedly, we identified soil organic nitrogen induced by soil solarization as one of the key components to increase crop yield. A germ-free plant in vitro assay and a pot experiment using arable soils confirmed that specific organic nitrogen, namely alanine and choline, directly increased plant biomass by acting as a nitrogen source and a biologically active compound. Thus, our study provides evidence at the agroecosystem level that organic nitrogen plays a key role in plant growth.
Predicting optical spectra for optoelectronic polymers using coarse-grained models and recurrent neural networks
Authors: Simine Lena , Allen Thomas C. , Rossky Peter J.
Published: June 2020

Coarse-grained modeling of conjugated polymers has become an increasingly popular route to investigate the physics of organic optoelectronic materials. While ultraviolet (UV)-vis spectroscopy remains one of the key experimental methods for the interrogation of these materials, a rigorous bridge between simulated coarse-grained structures and spectroscopy has not been established. Here, we address this challenge by developing a method that can predict spectra of conjugated polymers directly from coarse-grained representations while avoiding repetitive procedures such as
ad hoc
back-mapping from coarse-grained to atomistic representations followed by spectral computation using quantum chemistry. Our approach is based on a generative deep-learning model: the long-short-term memory recurrent neural network (LSTM-RNN). The latter is suggested by the apparent similarity between natural languages and the mathematical structure of perturbative expansions of, in our case, excited-state energies perturbed by conformational fluctuations. We also use this model to explore the level of sensitivity of spectra to the coarse-grained representation back-mapping protocol. Our approach presents a tool uniquely suited for improving postsimulation analysis protocols, as well as, potentially, for including spectral data as input in the refinement of coarse-grained potentials.
Hypothalamic tanycytes generate acute hyperphagia through activation of the arcuate neuronal network
Authors: Bolborea Matei , Pollatzek Eric , Benford Heather , Sotelo-Hitschfeld Tamara , Dale Nicholas
Published: June 2020

Significance

Tanycytes are nutrient-sensing cells that line the third ventricle within the hypothalamus. The role of tanycytes in the regulation of food intake has not been documented. Indeed, the mechanistic link between nutrient concentrations in the CSF and activation of neurons responsible for the regulation of food intake, such as orexigenic (NPY/AgRP) or anorexigenic (POMC) cells, is not yet clear. Here, we demonstrate that tanycytes, engineered to express channelrhodopsin, can activate arcuate neurons to induce acute hyperphagia when activated by light. These data provide further evidence that tanycytes are an integral link between CSF nutrients and the hypothalamic neuronal networks that regulate appetite and energy balance.
The limits of color awareness during active, real-world vision
Authors: Cohen Michael A. , Botch Thomas L. , Robertson Caroline E.
Published: June 2020

Significance

Color is a foundational aspect of visual experience that aids in segmenting objects, identifying food sources, and signaling emotions. Intuitively, it feels that we are immersed in a colorful world that extends to the farthest limits of our periphery. How accurate is our intuition? Here, we used gaze-contingent rendering in immersive VR to reveal the limits of color awareness during naturalistic viewing. Observers explored 360° real-world environments, which we altered so that only the regions where observers looked were in color, while their periphery was black-and-white. Overall, we found that observers routinely failed to notice when color vanished from the majority of their visual world. These results show that our intuitive sense of a rich, colorful world is largely incorrect.
The
Legionella
kinase LegK7 exploits the Hippo pathway scaffold protein MOB1A for allostery and substrate phosphorylation
Authors: Lee Pei-Chung , Beyrakhova Ksenia , Xu Caishuang , Boniecki Michal T. , Lee Mitchell H. , Onu Chisom J. , Grishin Andrey M. , Machner Matthias P. , Cygler Miroslaw
Published: June 2020

During infection, the bacterial pathogen
Legionella pneumophila
manipulates a variety of host cell signaling pathways, including the Hippo pathway which controls cell proliferation and differentiation in eukaryotes. Our previous studies revealed that
L. pneumophila
encodes the effector kinase LegK7 which phosphorylates MOB1A, a highly conserved scaffold protein of the Hippo pathway. Here, we show that MOB1A, in addition to being a substrate of LegK7, also functions as an allosteric activator of its kinase activity. A crystallographic analysis of the LegK7–MOB1A complex revealed that the N-terminal half of LegK7 is structurally similar to eukaryotic protein kinases, and that MOB1A directly binds to the LegK7 kinase domain. Substitution of interface residues critical for complex formation abrogated allosteric activation of LegK7 both in vitro and within cells and diminished MOB1A phosphorylation. Importantly, the N-terminal extension (NTE) of MOB1A not only regulated complex formation with LegK7 but also served as a docking site for downstream substrates such as the transcriptional coregulator YAP1. Deletion of the NTE from MOB1A or addition of NTE peptides as binding competitors attenuated YAP1 recruitment to and phosphorylation by LegK7. By providing mechanistic insight into the formation and regulation of the LegK7–MOB1A complex, our study unravels a sophisticated molecular mimicry strategy that is used by
L. pneumophila
to take control of the host cell Hippo pathway.
Peripheral myelin protein 22 preferentially partitions into ordered phase membrane domains
Authors: Marinko Justin T. , Kenworthy Anne K. , Sanders Charles R.
Published: June 2020

Significance

The preferential partitioning of single-span membrane proteins for ordered phase domains in phase-separated membranes is now reasonably well understood, but little is known about this phase preference for multispan helical membrane proteins. Here, it is shown that the disease-linked tetraspan membrane protein, PMP22, displays a pronounced preference to partition into the ordered phase, a preference that is reversed by disease mutations. This phase preference may be related to the role of PMP22 in cholesterol homeostasis in myelinating Schwann cells, a role that is also known to be disrupted under conditions of Charcot–Marie–Tooth disease (CMTD) peripheral neuropathy caused by
pmp22
mutations.
Non-Hermitian doping of epsilon-near-zero media
Authors: Coppolaro Marino , Moccia Massimo , Castaldi Giuseppe , Engheta Nader , Galdi Vincenzo
Published: June 2020

Significance

The recently introduced concept of photonic doping in epsilon-near-zero media enables the tailoring and control of the effective magnetic response over broad regions of the parameter space, by resorting to a limited number of arbitrarily placed, nonmagnetic doping particles. Here, we theoretically extend this idea to non-Hermitian scenarios with either doping particles or host media characterized by tailored distributions of gain and loss. This considerably enlarges the attainable effective permeability parameter space, granting access to the entire complex plane. In this extended vision, losses are not considered as second-order, detrimental effects, and their interplay with gain is instrumental to enabling several intriguing effects of potential interest in reconfigurable nanophotonics and optical sensing, whose practical implementation is deferred to future studies.
Epigenetic competition reveals density-dependent regulation and target site plasticity of phosphorothioate epigenetics in bacteria
Authors: Wu Xiaolin , Cao Bo , Aquino Patricia , Chiu Tsu-Pei , Chen Chao , Jiang Susu , Deng Zixin , Chen Shi , Rohs Remo , Wang Lianrong , Galagan James E. , Dedon Peter C.
Published: June 2020

Phosphorothioate (PT) DNA modifications—in which a nonbonding phosphate oxygen is replaced with sulfur—represent a widespread, horizontally transferred epigenetic system in prokaryotes and have a highly unusual property of occupying only a small fraction of available consensus sequences in a genome. Using
Salmonella enterica
as a model, we asked a question of fundamental importance: How do the PT-modifying DndA-E proteins select their G
PS
AAC/G
PS
TTC targets? Here, we applied innovative analytical, sequencing, and computational tools to discover a novel behavior for DNA-binding proteins: The Dnd proteins are “parked” at the G
6m
ATC Dam methyltransferase consensus sequence instead of the expected GAAC/GTTC motif, with removal of the
6m
A permitting extensive PT modification of GATC sites. This shift in modification sites further revealed a surprising constancy in the density of PT modifications across the genome. Computational analysis showed that GAAC, GTTC, and GATC share common features of DNA shape, which suggests that PT epigenetics are regulated in a density-dependent manner partly by DNA shape-driven target selection in the genome.
Mirrored brain organization: Statistical anomaly or reversal of hemispheric functional segregation bias?
Authors: Gerrits Robin , Verhelst Helena , Vingerhoets Guy
Published: June 2020

Humans demonstrate a prototypical hemispheric functional segregation pattern, with language and praxis lateralizing to the left hemisphere and spatial attention, face recognition, and emotional prosody to the right hemisphere. In this study, we used fMRI to determine laterality for all five functions in each participant. Crucially, we recruited a sample of left-handers preselected for atypical (right) language dominance (
n
= 24), which allowed us to characterize hemispheric asymmetry of the other functions and compare their functional segregation pattern with that of left-handers showing typical language dominance (
n
= 39). Our results revealed that most participants with left language dominance display the prototypical pattern of functional hemispheric segregation (44%) or deviate from this pattern in only one function (35%). Similarly, the vast majority of right language dominant participants demonstrated a completely mirrored brain organization (50%) or a reversal for all but one cognitive function (32%). Participants deviating by more than one function from the standard segregation pattern showed poorer cognitive performance, in line with an oft-presumed biological advantage of hemispheric functional segregation.
Amorphous polymer dynamics and free volume element size distributions from ultrafast IR spectroscopy
Authors: Hoffman David J. , Fica-Contreras Sebastian M. , Fayer Michael D.
Published: June 2020

Significance

The free volume content of polymers has immense importance for polymer properties. However, it is extremely difficult to measure the properties of the free volume elements (FVEs) that make up the free volume. Here we employ ultrafast infrared (IR) pump–probe spectroscopy to measure the properties of the nanoscopic FVEs in polymers using small-molecule IR probes. With this new method, the size and size distribution of the FVEs in polymers are measured and found to agree with previous measurements. The IR measurements also show that the FVEs undergo ultrafast structural fluctuations and provide a way to measure the distribution of local electric fields in the FVEs, which are correlated with the size of the FVEs.
Inequality in socially permissible consumption
Authors: Hagerty Serena F. , Barasz Kate
Published: June 2020

Lower-income individuals are frequently criticized for their consumption decisions; this research examines why. Eleven preregistered studies document systematic differences in permissible consumption
—
interpersonal judgments about what is acceptable (or not) for others to consume—such that lower-income individuals’ decisions are subject to more negative and restrictive evaluations. Indeed, the same consumption decisions may be deemed less permissible for a lower-income individual than for an individual with higher or unknown income (studies 1A and 1B), even when purchased with windfall funds. This gap persists among participants from a large, nationally representative sample (study 2) and when testing a broad array of “everyday” consumption items (study 3). Additional studies investigate why: The same items are often perceived as less necessary for lower- (versus higher-) income individuals (studies 4 and 5). Combining both permissibility and perceived necessity, additional studies (studies 6 and 7) demonstrate a causal link between the two constructs: A purchase decision will be deemed permissible (or not) to the extent that it is perceived as necessary (or not). However, because—for lower-income individuals—fewer items are perceived as necessary, fewer are therefore socially permissible to consume. This finding not only exposes a fraught double standard, but also portends consequential behavioral implications: People prefer to allocate strictly “necessary” items to lower-income recipients (study 8), even if such items are objectively and subjectively less valuable (studies 9A and 9B), which may result in an imbalanced and inefficient provision of resources to the poor.
A long noncoding RNA regulates inflammation resolution by mouse macrophages through fatty acid oxidation activation
Authors: Nakayama Yukiteru , Fujiu Katsuhito , Yuki Ryuzaburo , Oishi Yumiko , Morioka Masaki Suimye , Isagawa Takayuki , Matsuda Jun , Oshima Tsukasa , Matsubara Takumi , Sugita Junichi , Kudo Fujimi , Kaneda Atsushi , Endo Yusuke , Nakayama Toshinori , Nagai Ryozo , Komuro Issei , Manabe Ichiro
Published: June 2020

Proper resolution of inflammation is vital for repair and restoration of homeostasis after tissue damage, and its dysregulation underlies various noncommunicable diseases, such as cardiovascular and metabolic diseases. Macrophages play diverse roles throughout initial inflammation, its resolution, and tissue repair. Differential metabolic reprogramming is reportedly required for induction and support of the various macrophage activation states. Here we show that a long noncoding RNA (lncRNA),lncFAO, contributes to inflammation resolution and tissue repair in mice by promoting fatty acid oxidation (FAO) in macrophages.lncFAOis induced late after lipopolysaccharide (LPS) stimulation of cultured macrophages and in Ly6Chimonocyte-derived macrophages in damaged tissue during the resolution and reparative phases. We found thatlncFAOdirectly interacts with the HADHB subunit of mitochondrial trifunctional protein and activates FAO.lncFAOdeletion impairs resolution of inflammation related to endotoxic shock and delays resolution of inflammation and tissue repair in a skin wound. These results demonstrate that by tuning mitochondrial metabolism,lncFAOacts as a node of immunometabolic control in macrophages during the resolution and repair phases of inflammation.
Local and global structures in discourse and interaction
Authors: Haselow Alexander
Published: June 2020

Based on the relatively broad evidence for the assumption that language structure and linguistic cognition are organized in a dualistic way, this chapter follows proposals for a distinction between microstructures and macrostructures in language. While the first serve the establishment of morphosyntactic and semantic relationships, the latter are responsible for structuration in terms of discourse structure, interaction management and cognitive alignment. Using “extra-clausal” constituents as an example, it will be shown that there are points in spoken discourse that are highly sensitive for the structuration of language on a macrolevel, namely the beginning and the end of turns, and that expressions serving macrostructure, which tend to cluster in these positions, have a syntax of their own.
The Finnish projector phrase se että as a fixed
expression
Authors: Vatanen Anna , Suomalainen Karita , Laury Ritva
Published: June 2020

This chapter shows that the Finnish expression se että ‘it
(is) that’, consisting of a demonstrative followed by a complementizer, is a
fixed projective element in talk-in-interaction both on its own and with
collocating elements. It shares features with projector phrases identified
for other languages: it is used both to prepare the addressee for the nature
of the upcoming and to underline the upcoming as central to the ongoing
interaction. The analysis of se että having grammaticized
into a projector phrase is supported by prosodic evidence: the two elements
are most often produced as one prosodic word. The findings support the idea
that se että emerges in interaction with a fixed form
rather than being generated by a syntactic rule.
“B” aware: Memory lane access is restricted!
Authors: Kennedy Ruth , Klein Ulf
Published: June 2020

Understanding the molecular mechanisms that govern the differentiation of high-affinity germinal center (GC) B cells into memory B cells versus plasma cells is a major quest of adaptive immunity. In this issue, Toboso-Navasa et al. (https://doi.org/10.1084/jem.20191933) provide evidence that the MYC–MIZ1 transcriptional repressor complex restricts the differentiation of GC B cells into MBCs.
Revisiting the heavy vector quarkonium leptonic widths *
Authors: Wang Guo-Li , Wu Xing-Gang
Published: June 2020

We revisit the heavy quarkonium leptonic decays

and

using the Bethe-Salpeter method. The emphasis is on the relativistic corrections. For the

decays, the relativistic effects are

%,

%,

%,

% and

%, respectively. For the

decays, the relativistic effects are

%,

%,

%,

% and

%, respectively. Thus, the relativistic corrections are large and important in heavy quarkonium leptonic decays, especially for the highly excited charmonium. Our results for

are consistent with the experimental data.