bluuebunny/crossref_metadata_2025 huggingface dataset:
Riddled basins of attraction in systems exhibiting extreme events
Authors: Saha Arindam , Feudel Ulrike
Published: March 2018

Using a system of two FitzHugh-Nagumo units, we demonstrate the occurrence of riddled basins of attraction in delay-coupled systems as the coupling between the units is increased. We characterize riddled basins using the uncertainty exponent which is a measure of the dimensions of the basin boundary. Additionally, we show that the phase space can be partitioned into pure and mixed regions, where initial conditions in the pure regions certainly avoid the generation of extreme events, while initial conditions in the mixed region may or may not exhibit such events. This implies that any tiny perturbation of initial conditions in the mixed region could yield the emergence of extreme events because the latter state possesses a riddled basin of attraction.
Experiments of a 100 kV-level pulse generator based on metal-oxide varistor
Authors: Cui Yan-cheng , Wu Qi-lin , Yang Han-wu , Gao Jing-ming , Li Song , Shi Cheng-yu
Published: March 2018

This paper introduces the development and experiments of a 100 kV-level pulse generator based on a metal-oxide varistor (MOV). MOV has a high energy handling capacity and nonlinear voltage-current (V-I) characteristics, which makes it useful for high voltage pulse shaping. Circuit simulations based on the measured voltage-current characteristics of MOV verified the shaping concept and showed that a circuit containing a two-section pulse forming network (PFN) will result in better defined square pulse than a simple L-C discharging circuit. A reduced-scale experiment was carried out and the result agreed well with simulation prediction. Then a 100 kV-level pulse generator with multiple MOVs in a stack and a two-section pulse forming network (PFN) was experimented. A pulse with a voltage amplitude of 90 kV, rise time of about 50 ns, pulse width of 500 ns, and flat top of about 400 ns was obtained with a water dummy load of 50 Ω. The results reveal that the combination of PFN and MOV is a practical way to generate high voltage pulses with better flat top waveforms, and the load voltage is stable even if the load’s impedance varies. Such pulse generator can be applied in many fields such as surface treatment, corona plasma generation, industrial dedusting, and medical disinfection.
Variable convergence liquid layer implosions on the National Ignition Facility
Authors: Zylstra A. B. , Yi S. A. , Haines B. M. , Olson R. E. , Leeper R. J. , Braun T. , Biener J. , Kline J. L. , Batha S. H. , Berzak Hopkins L. , Bhandarkar S. , Bradley P. A. , Crippen J. , Farrell M. , Fittinghoff D. , Herrmann H. W. , Huang H. , Khan S. , Kong C. , Kozioziemski B. J. , Kyrala G. A. , Ma T. , Meezan N. B. , Merrill F. , Nikroo A. , Peterson R. R. , Rice N. , Sater J. D. , Shah R. C. , Stadermann M. , Volegov P. , Walters C. , Wilson D. C.
Published: March 2018

Liquid layer implosions using the “wetted foam” technique, where the liquid fuel is wicked into a supporting foam, have been recently conducted on the National Ignition Facility for the first time [Olson et al., Phys. Rev. Lett. 117, 245001 (2016)]. We report on a series of wetted foam implosions where the convergence ratio was varied between 12 and 20. Reduced nuclear performance is observed as convergence ratio increases. 2-D radiation-hydrodynamics simulations accurately capture the performance at convergence ratios (CR) ∼ 12, but we observe a significant discrepancy at CR ∼ 20. This may be due to suppressed hot-spot formation or an anomalous energy loss mechanism.
Particle shape effect on erosion of optical glass substrates due to microparticles
Authors: Waxman Rachel , Gray Perry , Guven Ibrahim
Published: March 2018

Impact experiments using sand particles and soda lime glass spheres were performed on four distinct glass substrates. Sand particles were characterized using optical and scanning electron microscopy. High-speed video footage from impact tests was used to calculate incoming and rebound velocities of the individual impact events, as well as the particle volume and two-dimensional sphericity. Furthermore, video analysis was used in conjunction with optical and scanning electron microscopy to relate the incoming velocity and particle shape to subsequent fractures, including both radial and lateral cracks. Indentation theory [Marshall et al., J. Am. Ceram. Soc. 65, 561–566 (1982)] was applied and correlated with lateral crack lengths. Multi-variable power law regression was performed, incorporating the particle shape into the model and was shown to have better fit to damage data than the previous indentation model.
Structure prediction of boron-doped graphene by machine learning
Authors: M. Dieb Thaer , Hou Zhufeng , Tsuda Koji
Published: March 2018

Heteroatom doping has endowed graphene with manifold aspects of material properties and boosted its applications. The atomic structure determination of doped graphene is vital to understand its material properties. Motivated by the recently synthesized boron-doped graphene with relatively high concentration, here we employ machine learning methods to search the most stable structures of doped boron atoms in graphene, in conjunction with the atomistic simulations. From the determined stable structures, we find that in the free-standing pristine graphene, the doped boron atoms energetically prefer to substitute for the carbon atoms at different sublattice sites and that the para configuration of boron-boron pair is dominant in the cases of high boron concentrations. The boron doping can increase the work function of graphene by 0.7 eV for a boron content higher than 3.1%.
Floating potential of emitting surfaces in plasmas with respect to the space potential
Authors: Kraus B. F. , Raitses Y.
Published: March 2018

The potential difference between a floating emitting surface and the plasma surrounding it has been described by several sheath models, including the space-charge-limited sheath, the electron sheath with high emission current, and the inverse sheath produced by charge-exchange ion trapping. Our measurements reveal that each of these models has its own regime of validity. We determine the potential of an emissive filament relative to the plasma potential, emphasizing variations in emitted current density and neutral particle density. The potential of a filament in a diffuse plasma is first shown to vanish, consistent with the electron sheath model and increasing electron emission. In a denser plasma with ample neutral pressure, the floating filament potential is positive, as predicted by a derived ion trapping condition. Lastly, the filament floated negatively in a third plasma, where flowing ions and electrons and nonnegligible electric fields may have disrupted ion trapping. Depending on the regime chosen, emitting surfaces can float positively or negatively with respect to the plasma potential.
Microstructures, magnetic properties and coercivity mechanisms of Nd-Ce-Fe-B based alloys by Zr substitution
Authors: Wang Lei , Quan Qichen , Zhang Lili , Hu Xianjun , Ur Rehman Sajjad , Jiang Qingzheng , Du Junfeng , Zhong Zhenchen
Published: March 2018

In this paper, the effects of Zr addition on microstructures, magnetic properties, exchange coupling, and coercivity mechanisms of Nd-Ce-Fe-B alloys fabricated by melt-spinning technique are investigated. It is found that the coercivity Hcj is enhanced significantly by Zr substitution in the (Nd0.8Ce0.2)13Fe82-xZrxB5 alloys, while the remanence Jr is reduced slightly. The Hcj increases from 12.2 to 13.7 kOe by adding Zr up to 1.5 at. %, whereas Hcj is decreased with a further increase in Zr content. The larger lattice constants and unit cell volumes of the matrix phase indicate that Zr atoms enter into the hard magnetic phase by substituting Fe sites. The reduction of Tc implies the attenuation of the exchange interaction in the 2:14:1 phase with Zr occupying the Fe sites. The weakened intergranular exchange coupling of the Zr added alloy may be attributed to the formation of a non-magnetic intergranular phase. It is worth noting that the coercivity is dominated by the pinning of domain walls at defect positions even though the nucleation of reversal domains still exists. The synergistic function between the pinning effect and the exchange coupling leads to improved magnetic properties.
Specific heat characteristics of Ce70Ga8.5Cu18.5Ni3 metallic glass at low temperatures
Authors: Liu Rentao , Zhong Langxiang , Zhang Bo
Published: March 2018

Specific heat behaviors have been studied in Ce70Ga8.5Cu18.5Ni3 bulk metallic glass (BMG) from 2 K to 50 K. The low-temperature specific heat of the Ce-based metallic glass is a combined action of the Fermi liquids term, Debye oscillator term, and Einstein oscillator term as well as excess term. We also observed an intense boson peak around 15 K and attributed it to a harmonic localized Einstein mode influenced by the dense-packed atomic cluster structure. It is also demonstrated that Ce70Ga8.5Cu18.5Ni3 BMG belongs to the strongly correlated heavy-fermion system with a great electron specific heat coefficient and a high Wilson ratio. It exhibits a typical Fermi-Liquid feature when the temperature is above 10 K, while it exhibits a Non-Fermi-Liquid feature when the temperature is below 3.5 K.
Effect of equation of state on laser imprinting by comparing diamond and polystyrene foils
Authors: Kato H. , Shigemori K. , Nagatomo H. , Nakai M. , Sakaiya T. , Ueda T. , Terasaki H. , Hironaka Y. , Shimizu K. , Azechi H.
Published: March 2018

We present herein a comprehensive study of how the equation of state affects laser imprinting by nonuniform laser irradiation of an inertial fusion target. It has been suggested that a stiffer and denser material would reduce laser imprinting based on the equation of motion with pressure perturbation. We examine the detailed temporal evolution of the imprint amplitude by using the two-dimensional radiation hydrodynamic simulation PINOCO-2D for diamond, which is a candidate stiff-ablator material for inertial fusion targets. The simulated laser imprinting amplitude is compared with experimental measurements of areal-density perturbations obtained by using face-on x-ray backlighting for diamond and polystyrene (PS) (the latter as a reference). The experimental results are well reproduced by the results of the PINOCO-2D simulation, which indicates that the imprinting amplitude due to nonuniform irradiation (average intensity, 4.0 × 1012 to 5.0 × 1013) differs by a factor of two to three between diamond and PS. The difference in laser imprinting is mainly related to the material density and compressibility. These parameters are key factors that determine the laser imprinting amplitude.
Switching dynamics of TaOx-based threshold switching devices
Authors: Goodwill Jonathan M. , Gala Darshil K. , Bain James A. , Skowronski Marek
Published: March 2018

Bi-stable volatile switching devices are being used as access devices in solid-state memory arrays and as the active part of compact oscillators. Such structures exhibit two stable states of resistance and switch between them at a critical value of voltage or current. A typical resistance transient under a constant amplitude voltage pulse starts with a slow decrease followed by a rapid drop and leveling off at a low steady state value. This behavior prompted the interpretation of initial delay and fast transition as due to two different processes. Here, we show that the entire transient including incubation time, transition time, and the final resistance values in TaOx-based switching can be explained by one process, namely, Joule heating with the rapid transition due to the thermal runaway. The time, which is required for the device in the conducting state to relax back to the stable high resistance one, is also consistent with the proposed mechanism.
Weak antilocalization and low-temperature characterization of sputtered polycrystalline bismuth selenide
Authors: Sahu Protyush , Chen Jun-Yang , Myers Jason C. , Wang Jian-Ping
Published: March 2018

We report a thorough crystal and transport characterization of sputtered polycrystalline BixSe1−x (20 nm), grown on a thermally oxidized silicon substrate. The crystal and grain structures of the sample are characterized by transmission electron microscopy. Selected-area electron diffraction shows a highly polycrystalline structure. Transport measurements suggest semiconducting behavior of the BixSe1−x film with a very high carrier concentration (∼1020 cm3) and low mobility [∼8 cm2/(V s)]. High-field magnetoresistance measurements reveal weak antilocalization, to which both the low mobility and the angular dependence suggest an impurity-dominated contribution. Fitting parameters are obtained from 2D magnetoconductivity using the Hikami-Larkin-Nagaoka equation. The variation of the phase coherence length with temperature suggests electron–electron scattering for phase decoherence. Electron–electron interaction theory is used to analyze the low-temperature conductivity.
Gate-tunable quantum dot in a high quality single layer MoS2 van der Waals heterostructure
Authors: Pisoni Riccardo , Lei Zijin , Back Patrick , Eich Marius , Overweg Hiske , Lee Yongjin , Watanabe Kenji , Taniguchi Takashi , Ihn Thomas , Ensslin Klaus
Published: March 2018

We have fabricated an encapsulated monolayer MoS2 device with metallic ohmic contacts through a pre-patterned hexagonal boron nitride (hBN) layer. In the bulk, we observe an electron mobility as high as 3000 cm2/Vs at a density of 7 × 1012 cm−2 at a temperature of 1.7 K. Shubnikov-de Haas oscillations start at magnetic fields as low as 3.3 T. By realizing a single quantum dot gate structure on top of hBN, we are able to confine electrons in MoS2 and observe the Coulomb blockade effect. By tuning the middle gate voltage, we reach a double dot regime where we observe the standard honeycomb pattern in the charge stability diagram.
PIV study of non-Marangoni surface flows in thin liquid films induced by single- and multi-point thermodes
Authors: Cui Nai-Yi , Wang Song-Po
Published: March 2018

The non-Marangoni directional flows, which can occur in only very thin liquid films, have been studied using particle image velocimetry techniques. Single- and multi-point thermodes have been used in this study for generating the flows. The results show that the direction of these flows is governed by the variation trend of the thickness of the film and the shape of the temperature profile. A hot thermode always drives a thick-to-thin flow, whereas a cold thermode always drives a flow in the opposite direction. Increasing the temperature difference between the thermode and the ambience, or decreasing the thickness of the liquid film, can accelerate the flow speed. However, the flow speed cannot exceed an upper limit. When more than one thermode was used, different flow patterns, including thick-to-thin streams driven by hot thermodes and thin-to-thick streams driven by cold thermodes, could be formed. The experimental results strongly suggest that these flows were not driven by thermo-capillary forces but by a newly proposed thermo-dynamic mechanism.
Optical absorption and oxygen passivation of surface states in III-nitride photonic devices
Authors: Rousseau Ian , Callsen Gordon , Jacopin Gwénolé , Carlin Jean-François , Butté Raphaël , Grandjean Nicolas
Published: March 2018

III-nitride surface states are expected to impact high surface-to-volume ratio devices, such as nano- and micro-wire light-emitting diodes, transistors, and photonic integrated circuits. In this work, reversible photoinduced oxygen desorption from III-nitride microdisk resonator surfaces is shown to increase optical attenuation of whispering gallery modes by 100 cm−1 at λ = 450 nm. Comparison of photoinduced oxygen desorption in unintentionally and n+-doped microdisks suggests that the spectral changes originate from the unpinning of the surface Fermi level, likely taking place at etched nonpolar III-nitride sidewalls. An oxygen-rich surface prepared by thermal annealing results in a broadband Q improvement to state-of-the-art values exceeding 1 × 104 at 2.6 eV. Such findings emphasize the importance of optically active surface states and their passivation for future nanoscale III-nitride optoelectronic and photonic devices.
Ecological responses of Stipa steppe in Inner Mongolia to experimentally increased temperature and precipitation. 3. Soil respiration
Authors: Wang Xuexia , Chen Yali , Yan Yulong , Wan Zhiqiang , Chao Ran , Gu Rui , Yang Jie , Gao Qingzhu
Published: March 2018

The response of soil respiration to simulated climatic warming and increased precipitation was evaluated on the arid–semi-arid Stipa steppe of Inner Mongolia. Soil respiration rate had a single peak during the growing season, reaching a maximum in July under all treatments. Soil temperature, soil moisture and their interaction influenced the soil respiration rate. Relative to the control, warming alone reduced the soil respiration rate by 15.6 ± 7.0%, whereas increased precipitation alone increased the soil respiration rate by 52.6 ± 42.1%. The combination of warming and increased precipitation increased the soil respiration rate by 22.4 ± 11.2%. When temperature was increased, soil respiration rate was more sensitive to soil moisture than to soil temperature, although the reverse applied when precipitation was increased. Under the experimental precipitation (20% above natural rainfall) applied in the experiment, soil moisture was the primary factor limiting soil respiration, but soil temperature may become limiting under higher soil moisture levels.
Dimeric sorting code for concentrative cargo selection by the COPII coat
Authors: Nie Chao , Wang Huimin , Wang Rui , Ginsburg David , Chen Xiao-Wei
Published: March 2018

Significance

One-third of the mammalian genome encodes proteins that are transported by the secretory pathway. Coat protein complexes such as COPII generate carrier vesicles and recruit cargos, orchestrated by cognate small GTPases as “molecular switches.” How coat complexes select specific cargos remains incompletely understood. Here we applied proximity-dependent biotinylation, fusing the promiscuous biotin ligase BirA* with the SAR1B GTPase, to track the dynamics of COPII-mediated export from the endoplasmic reticulum. LMAN1, a cargo receptor for COPII, is transiently enriched and released by the coat complex. The enrichment requires a dimeric sorting signal, formed by two copies of LMAN1. Hence, the COPII coat undergoes a dynamic engaging–disengaging cycle to select unique sets of secretory cargos.
Earliest isotopic evidence in the Maya region for animal management and long-distance trade at the site of Ceibal, Guatemala
Authors: Sharpe Ashley E. , Emery Kitty F. , Inomata Takeshi , Triadan Daniela , Kamenov George D. , Krigbaum John
Published: March 2018

Significance

The nature of animal management in Mesoamerica is not as well understood compared with other state-level societies around the world. In this study, isotope analysis of animal remains from Ceibal, Guatemala, provides the earliest direct evidence of live animal trade and possible captive animal rearing in the Maya region. Carbon, nitrogen, and oxygen isotopes show that domesticated and possibly even wild animals were raised in or around Ceibal and were deposited in the ceremonial core. Strontium isotope analysis reveals the Maya brought dogs to Ceibal from the distant Guatemalan highlands. The possible ceremonial contexts of these captive-reared and imported taxa suggests animal management played an important role in the symbolic development of political power.
Facial color is an efficient mechanism to visually transmit emotion
Authors: Benitez-Quiroz Carlos F. , Srinivasan Ramprakash , Martinez Aleix M.
Published: March 2018

Significance

Emotions correspond to the execution of a number of computations by the central nervous system. Previous research has studied the hypothesis that some of these computations yield visually identifiable facial muscle movements. Here, we study the supplemental hypothesis that some of these computations yield facial blood flow changes unique to the category and valence of each emotion. These blood flow changes are visible as specific facial color patterns to observers, who can then successfully decode the emotion. We present converging computational and behavioral evidence in favor of this hypothesis. Our studies demonstrate that people identify the correct emotion category and valence from these facial colors, even in the absence of any facial muscle movement.
Subdiffusive and superdiffusive transport in plane steady viscous flows
Authors: Zaks Michael A. , Nepomnyashchy Alexander
Published: March 2018

Significance

Anomalous transport is usually regarded as a manifestation of a spatiotemporal disorder. We predict a persistent anomalous dispersion of tracers in time-independent spatially periodic viscous flows, in the absence of either a Lagrangian chaos or a Brownian motion. The origin of transport anomalies is the slowdown near stagnation points and solid surfaces, responsible for singularities of the particle passage time. Remarkably, both subdiffusive and superdiffusive dispersion of tracers can be achieved by an appropriate choice of the flow geometry.
Microscopic dynamics and failure precursors of a gel under mechanical load
Authors: Aime Stefano , Ramos Laurence , Cipelletti Luca
Published: March 2018

Significance

The sudden, catastrophic failure of materials under a constant mechanical load is widespread, occurring from geological scales, as in earthquakes, to biological and soft-matter systems, as in protein, polymer, and colloidal gels. Failure is often preceded by a long induction time, with little if any macroscopic signs of weakening, making it unpredictable. Here, we investigate the failure of a model colloidal gel under a constant load, measuring simultaneously its mechanical response and microscopic dynamics. We show that the gel undergoes a burst of microscopic plastic rearrangements that largely precede failure, undetectable by monitoring conventional structural quantities. The notion of a dynamic precursor thus emerges as a powerful tool to understand and predict the sudden failure of solids.
Division-independent differentiation mandates proliferative competition among stem cells
Authors: Reilein Amy , Melamed David , Tavaré Simon , Kalderon Daniel
Published: March 2018

Significance

Adult stem cells support tissue maintenance throughout life, but they also can be cells of origin for cancer, allowing clonal expansion and long-term maintenance of the first oncogenic mutations. We considered how a mutation that increases the proliferation rate of a stem cell would affect the probability of its competitive survival and amplification for different potential organizations of stem cells. Quantitative modeling showed that the key characteristic predicting the impact of relative proliferation rate on competition is whether differentiation of a stem cell is coupled to its division. We then usedDrosophilafollicle stem cells to provide definitive experimental evidence for the general prediction that relative proliferation rates dictate stem cell competition specifically for stem cells that exhibit division-independent differentiation.
Haemophilus influenzae
genome evolution during persistence in the human airways in chronic obstructive pulmonary disease
Authors: Pettigrew Melinda M. , Ahearn Christian P. , Gent Janneane F. , Kong Yong , Gallo Mary C. , Munro James B. , D’Mello Adonis , Sethi Sanjay , Tettelin Hervé , Murphy Timothy F.
Published: March 2018

Significance

Nontypeable
Haemophilus influenzae
(NTHi) exclusively colonize and infect humans and play an important role in the course and pathogenesis of chronic obstructive pulmonary disease (COPD). We conducted whole-genome sequencing of 269 NTHi isolates from a 15-y prospective study of COPD to assess in vivo adaption of NTHi. NTHi uses slipped-strand mispairing in simple sequence repeats to regulate critical virulence functions as the primary mechanism to adapt to survival in the human airways. Analyses of changes in 12 candidate vaccine antigens during persistence provided data with important implications for guiding vaccine development. These results advance understanding of how an exclusively human pathogen alters its genome to adapt to survival in the hostile environment of the human respiratory tract.
Land use strategies to mitigate climate change in carbon dense temperate forests
Authors: Law Beverly E. , Hudiburg Tara W. , Berner Logan T. , Kent Jeffrey J. , Buotte Polly C. , Harmon Mark E.
Published: March 2018

Significance

Regional quantification of feasibility and effectiveness of forest strategies to mitigate climate change should integrate observations and mechanistic ecosystem process models with future climate, CO
2
, disturbances from fire, and management. Here, we demonstrate this approach in a high biomass region, and found that reforestation, afforestation, lengthened harvest cycles on private lands, and restricting harvest on public lands increased net ecosystem carbon balance by 56% by 2100, with the latter two actions contributing the most. Forest sector emissions tracked with our life cycle assessment model decreased by 17%, partially meeting emissions reduction goals. Harvest residue bioenergy use did not reduce short-term emissions. Cobenefits include increased water availability and biodiversity of forest species. Our improved analysis framework can be used in other temperate regions.
LHCSR1-dependent fluorescence quenching is mediated by excitation energy transfer from LHCII to photosystem I in
Chlamydomonas reinhardtii
Authors: Kosuge Kotaro , Tokutsu Ryutaro , Kim Eunchul , Akimoto Seiji , Yokono Makio , Ueno Yoshifumi , Minagawa Jun
Published: March 2018

Significance

Unlike another effector protein for algal nonphotochemical quenching (NPQ)—LIGHT HARVESTING COMPLEX II STRESS RELATED PROTEIN 3 (LHCSR3)—the role of LHCSR1 in NPQ has been very limited. In this report, we studied the fluorescence quenching event occurring in the presence and the absence of LHCSR1 and demonstrated that there is a significant excitation energy transfer from Light-harvesting complex II (LHCII) to Photosystem I (PSI), and not only to Photosystem II, upon activation of LHCSR1 by low pH. The results suggest another layer of photoprotection mechanism based on this UV-inducible protein LHCSR1.
Biofilm Lithography enables high-resolution cell patterning via optogenetic adhesin expression
Authors: Jin Xiaofan , Riedel-Kruse Ingmar H.
Published: March 2018

Significance

Bacteria live in surface-attached communities known as biofilms, where spatial structure is tightly linked to community function. We have developed a genetically encoded biofilm patterning tool (“Biofilm Lithography”) by engineering bacteria such that the expression of membrane adhesion proteins responsible for surface attachment is optically regulated. Accordingly, these bacteria only form biofilm on illuminated surface regions. With this tool, we are able to use blue light to patternEscherichia colibiofilms with 25 μm spatial resolution. We present an accompanying biophysical model to understand the mechanism behind light-regulated biofilm formation and to provide insight on related natural biofilm processes. Overall, this biofilm patterning tool can be applied to study natural microbial communities as well as to engineer living biomaterials.
Xio is a component of the
Drosophila
sex determination pathway and RNA
N
6
-methyladenosine methyltransferase complex
Authors: Guo Jian , Tang Hong-Wen , Li Jing , Perrimon Norbert , Yan Dong
Published: March 2018

Significance

RNAs contain over 100 types of chemical modifications, and
N
6
-methyladenosine (m
6
A) is the most common internal modification in eukaryotic mRNA. m
6
A is involved in a variety of important biological processes, including sex determination in
Drosophila
, by modifying
Sxl
pre-mRNA and regulating its alternative splicing. m
6
A is installed by a large methyltransferase complex called the m
6
A “writer.” We have identified
xio
as a component of the
Drosophila
sex determination pathway based on its female-to-male transformation phenotypes. Xio interacts with other m
6
A writer subunits, and its loss of function shows typical phenotypes associated with other m
6
A factors, such as
Sxl
splicing misregulation, adult defects, and reduced m
6
A levels. Therefore, we conclude that Xio is a member of the m
6
A writer complex.
Sensorineural hearing loss degrades behavioral and physiological measures of human spatial selective auditory attention
Authors: Dai Lengshi , Best Virginia , Shinn-Cunningham Barbara G.
Published: March 2018

Significance

Listeners with hearing loss have trouble communicating in many social settings. In such situations, listeners with normal hearing suppress the neural representation of competing sounds, a process known as auditory selective attention. We compared hearing-impaired (HI) and normal-hearing (NH) listeners on a spatial selective attention task while measuring neural responses using electroencephalography. Compared with NH listeners, HI listeners have poorer sensitivity to spatial cues, perform more poorly on the selective attention task, and show weaker neural suppression of competing sounds. Moreover, these different measures are correlated both for HI and for NH listeners. These results suggest that poor spatial acuity produces problems with selective attention. These findings have implications both for basic science and for development of next-generation hearing aids.
A
pex1
missense mutation improves peroxisome function in a subset of
Arabidopsis pex6
mutants without restoring PEX5 recycling
Authors: Gonzalez Kim L. , Ratzel Sarah E. , Burks Kendall H. , Danan Charles H. , Wages Jeanne M. , Zolman Bethany K. , Bartel Bonnie
Published: March 2018

Significance

ATPases have diverse cellular roles, including extracting proteins from membranes to maintain organellar function. The PEX1–PEX6 heterohexameric ATPases are thought to retrotranslocate PEX5 from the peroxisome membrane, and PEX1–PEX6 dysfunction impairs peroxisome biogenesis in humans and plants. We implemented a
pex6
suppressor screen in
Arabidopsis
and recovered a compensatory
pex1
allele that rescues several
pex6
defects. Preventing autophagy also improved
pex6
peroxisome function, and combining the
pex1
and autophagy lesions delivered synergistic benefits. Surprisingly, these different alterations ameliorated
pex6
symptoms without notably restoring the sole known function of PEX6, suggesting that PEX1–PEX6 has unexplored functions. Because the
pex6
mutations ameliorated by
pex1
are analogous to those in human
pex6
patients, this study informs research on peroxisome dysfunction in other eukaryotes.
Converting
Escherichia coli
into an archaebacterium with a hybrid heterochiral membrane
Authors: Caforio Antonella , Siliakus Melvin F. , Exterkate Marten , Jain Samta , Jumde Varsha R. , Andringa Ruben L. H. , Kengen Servé W. M. , Minnaard Adriaan J. , Driessen Arnold J. M. , van der Oost John
Published: March 2018

Significance

Escherichia coli
has been engineered toward an archaebacterium with an unprecedented high level of archaeal ether phospholipids. The obtained cells stably maintain a mixed heterochiral membrane. This finding challenges theories that assume that intrinsic instability of mixed membranes led to the “lipid divide” and the subsequent differentiation of bacteria and archaea. Furthermore, this study paves the way for future membrane engineering of industrial production organisms with improved robustness.
Monoclonal antibody targeting the β-barrel assembly machine of
Escherichia coli
is bactericidal
Authors: Storek Kelly M. , Auerbach Marcy R. , Shi Handuo , Garcia Natalie K. , Sun Dawei , Nickerson Nicholas N. , Vij Rajesh , Lin Zhonghua , Chiang Nancy , Schneider Kellen , Wecksler Aaron T. , Skippington Elizabeth , Nakamura Gerald , Seshasayee Dhaya , Koerber James T. , Payandeh Jian , Smith Peter A. , Rutherford Steven T.
Published: March 2018

Significance

The outer membrane of Gram-negative bacteria presents a formidable barrier to the discovery of new antibiotics needed to combat infections by multidrug-resistant bacteria. Targeting essential proteins or processes directly exposed to the environment could bypass this obstacle. Here, we describe a monoclonal antibody that selectively and potently antagonizes BamA, which folds and inserts integral outer membrane β-barrel proteins, by binding to a surface-exposed BamA epitope and, as a result, inhibits bacterial cell growth. Mechanisms of resistance to the antibody reveal that membrane fluidity affects BamA activity. This antibody validates the potential therapeutic strategy of targeting essential, exposed functions and provides a powerful tool for dissecting the fundamental process of folding integral membrane β-barrel proteins in vivo.
Agricultural origins on the Anatolian plateau
Authors: Baird Douglas , Fairbairn Andrew , Jenkins Emma , Martin Louise , Middleton Caroline , Pearson Jessica , Asouti Eleni , Edwards Yvonne , Kabukcu Ceren , Mustafaoğlu Gökhan , Russell Nerissa , Bar-Yosef Ofer , Jacobsen Geraldine , Wu Xiaohong , Baker Ambroise , Elliott Sarah
Published: March 2018

Significance

We demonstrate that the initial spread of farming outside of the area of its first appearance in the Fertile Crescent of Southwest Asia, into Central Anatolia, involved adoption of cultivars by indigenous foragers and contemporary experimentation in animal herding of local species. This represents a rare clear-cut instance of forager adoption and sustained low-level food production. We have also demonstrated that farming uptake was not uniform, with some forager communities rejecting it despite proximity to early farming communities. We also show that adoption of small-scale cultivation could still have significant social consequences for the communities concerned. The evidence suggests forager adoption of cultivation and initiation of herding was not necessarily motivated by simple economic concerns of increasing levels of food production and security.
Frictional lubricity enhanced by quantum mechanics
Authors: Zanca Tommaso , Pellegrini Franco , Santoro Giuseppe E. , Tosatti Erio
Published: March 2018

Significance

Sliding friction, a corner of physics still under debate after centuries, is currently studied in nanosystems such as optical lattice emulators, where parameters are easy to control but where applicability of classical mechanics is no longer guaranteed. The quantum effects on friction being largely unexplored, we show here that even a basic theoretical model predicts important novelties. For a particle dragged over large barriers, whose classical stick–slip friction would be large, Landau–Zener tunneling through the barrier can avert stick–slip, with an increase of lubricity. This and related forms of quantum lubricity should be observable for cold ions sliding in optical lattices.
Construction and evolution of an
Escherichia coli
strain relying on nonoxidative glycolysis for sugar catabolism
Authors: Lin Paul P. , Jaeger Alec J. , Wu Tung-Yun , Xu Sharon C. , Lee Abraxa S. , Gao Fanke , Chen Po-Wei , Liao James C.
Published: March 2018

Significance

We constructed an
Escherichia coli
strain that does not use glycolysis for sugar catabolism. Instead, it uses the synthetic nonoxidative glycolysis cycle to directly synthesize stoichiometric amounts of the two-carbon building block (acetyl-CoA), which is then converted to three-carbon metabolites to support growth. The resulting strain grows aerobically in glucose minimal medium and can achieve near-complete carbon conservation in the production of acetyl-CoA–derived products during anaerobic fermentation. This strain improves the theoretical carbon yield from 66.7% to 100% in acetyl-CoA–derived product formation.
How to do corpus pragmatics on pragmatically annotated data
Authors: Weisser Martin
Published: March 2018

This book introduces a methodology and research tool (DART) that make it possible to carry out advanced corpus pragmatics research using dialogue corpora enriched with pragmatics-relevant annotations. It first explores the general use of spoken corpora for pragmatics research, as well as issues revolving around their representation and annotation, and then goes on to describe the resources required for such an annotation process. Based on data from three different corpora, ranging from highly constrained, task-oriented, ones (SPAADIA Trainline & Trains 93) to unconstrained dialogues (Switchboard), it next presents an in-depth discussion and illustration of the potential contributions of syntax, semantics, and semantico-pragmatics towards pragmatic force. This is followed by a description of the largely automatic annotation process itself, and finally an analysis of how a set of more than 110 potential speech acts defined in DART contributes towards establishing the specific communicative characteristics of the three corpora.
Interannual variability of significant wave height in the northern South China Sea
Authors: Jiang Lifang , Yin Yi , Cheng Xuhua , Zhang Zhixu
Published: March 2018

Based on the hindcast data from third-generation wave model WAVEWATCH III, this study presents a notable interannual variability of significant wave height in the northern South China Sea. As indicated by the empirical orthogonal function analysis result of the significant wave height during 1976–2005, the first mode of this analysis captures a monopole structure with maximum amplitude in the southwestern Luzon Strait. Power spectrum analysis of the first empirical orthogonal function time series indicates that the significant wave height peaks at 2.67 and 8 year periods in the northern South China Sea. The first-time series had good correlation with El Niño events, with a correlation coefficient of -0.58. By comparing frequency and total duration of the intense tropical cyclones with the significant wave height in the northern South China Sea, it is revealed that the two were associated during 1978–1998 and that the recent increase of the significant wave height is due to the increase in total duration of intense tropical cyclones during 1999–2005. The sea level pressures also support the interannual variability of significant wave height in the northern South China Sea.
Interaction of laser beams with magnetized substance in a strong magnetic field
Authors: Kuzenov V V
Published: March 2018

Laser-driven magneto-inertial fusion assumed plasma and magnetic flux compression by quasisymmetric laser-driven implosion of magnetized target. We develop a 2D radiation magnetohydrodynamic code and a formulation for the one-fluid two-temperature equations for simulating compressible non-equilibrium magnetized target plasma. Laser system with pulse radiation with 10 ns duration is considered for numerical experiments. A numerical study of a scheme of magnetized laser-driven implosion in the external magnetic field is carried out.
What’s New in Pediatric Hip?
Authors: Schmitz Matthew R. , Blumberg Todd J. , Nelson Susan E. , Sees Julieanne P. , Sankar Wudbhav N.
Published: March 2018

Background:

Developmental dysplasia of the hip (DDH), which encompasses a wide spectrum of disease from mild dysplasia to frank dislocation, is one of the most common developmental deformities of the lower extremities and one of the leading causes of future osteoarthritis and hip arthroplasty. Legg-Calvé-Perthes disease (LCPD) results from a vascular insult to the growing femoral epiphysis, which in turn can create permanent morphologic changes to the hip joint. Slipped capital femoral epiphysis (SCFE) occurs when the proximal femoral physis fails allowing the epiphysis to displace in relation to the metaphysis. Infections about the hip also create significant morbidity in the pediatric hip.

Methods:

We searched the PubMed database for all studies related to DDH, LCPD, SCFE, and pediatric hip infections that were published between July 1, 2014 and August 31, 2017. The search was limited to English articles and yielded 839 papers. This project was initiated by the Pediatric Orthopaedic Society of North America Publications Committee and was reviewed and approved by the Pediatric Orthopaedic Society of North America Presidential Line.

Results:

A total of 40 papers were selected for review based upon new and significant findings. Select historical manuscripts are also included to provide sufficient background information.

Conclusions:

DDH, LCPD, SCFE, and infections about the hip continue to be important topics in pediatric orthopaedics and areas of vital research. This manuscript reviews the most important recent literature on the diagnosis and treatment of these pediatric hip conditions.

Level of Evidence:

Level V.
MORPHOLOGIC CHARACTERISTICS OF MACULAR HOLE AND MACULAR HOLE RETINAL DETACHMENT ASSOCIATED WITH EXTREME MYOPIA
Authors: Ohsugi Hideharu , Ikuno Yasushi , Matsuba Shinji , Ohsugi Eiko , Nagasato Daisuke , Shoujou Tomohiro , Tabuchi Hitoshi
Published: March 2018

Purpose:

To investigate the surgical results and morphologic characteristics of macular hole (MH) and macular hole retinal detachment (MHRD) associated with extreme myopia.

Methods:

We retrospectively reviewed consecutive cases with axial length ≥28 mm who were treated with pars plana vitrectomy for MH or MHRD. The choroidal and scleral thickness at the fovea, presence of dome-shaped macula, and the height of posterior staphyloma 3 mm from the fovea were measured from postoperative optical coherence tomography images.

Results:

Significant improvement in visual acuity was obtained postoperatively in both MH (16 eyes; 15 patients) and MHRD (19 eyes; 18 patients) groups (P < 0.05). Final MH closure rate was not significantly different between the groups (MH: 15/16, MHRD: 14/19, P = 0.19). Axial length was not significantly different between the groups (MH: 30.5 ± 1.5 mm, MHRD: 29.6 ± 1.3 mm, P = 0.098). Eyes with MH had significantly greater choroidal thickness (MH: 61.9 ± 66.0 μm, MHRD: 24.1 ± 19.8 μm, P = 0.045), greater scleral thickness (MH: 294 ± 77 μm, MHRD: 232 ± 89 μm, P = 0.008), higher frequency of dome-shaped macula (MH: 6/16, MHRD: 1/19, P = 0.032), and lower staphyloma height (MH: 190 ± 113 μm, MHRD: 401 ± 156 μm, P < 0.001).

Conclusion:

Surgical outcomes were generally favorable. The pathogenetic differences between the two conditions may be attributable to differences with respect to eye morphology.
Rapid Paediatric Sequencing (RaPS): Comprehensive real-life workflow for rapid diagnosis of critically ill children
Authors: Boukhibar Lamia , Clement Emma , Jones Wendy , Drury Suzanne , Ocaka Louise , Gagunashvili Andrey , Le Quesne Stabej Polona , Bacchelli Chiara , Jani Nital , Rahman Shamima , Jenkins Lucy , Hurst Jane , Bitner-Glindzicz Maria , Peters Mark , Beales Philip , Williams Hywel J
Published: March 2018

Background

Rare genetic conditions are frequent risk factors for, or direct causes of, organ failure requiring paediatric intensive care unit (PICU) support. Such conditions are frequently suspected but unidentified at PICU admission. Compassionate and effective care is greatly assisted by definitive diagnostic information. There is therefore a need to provide a rapid genetic diagnosis to inform clinical management.

To date, Whole Genome Sequencing (WGS) approaches have proved successful in diagnosing a proportion of children with rare diseases, but results may take months to report or require the use of equipment and practices not compatible with a clinical diagnostic setting. We describe an end-to-end workflow for the use of rapid WGS for diagnosis in critically ill children in a UK National Health Service (NHS) diagnostic setting.

Methods

We sought to establish a multidisciplinary Rapid Paediatric Sequencing (RaPS) team for case selection, trio WGS, a rapid bioinformatics pipeline for sequence analysis and a phased analysis and reporting system to prioritise genes with a high likelihood of being causal. Our workflow was iteratively developed prospectively during the analysis of the first 10 children and applied to the following 14 to assess its utility.

Findings

Trio WGS in 24 critically ill children led to a molecular diagnosis in ten (42%) through the identification of causative genetic variants. In three of these ten individuals (30%) the diagnostic result had an immediate impact on the individual’s clinical management. For the last 14 trios, the shortest time taken to reach a provisional diagnosis was four days (median 7 days).

Interpretation

Rapid WGS can be used to diagnose and inform management of critically ill children using widely available off the shelf products within the constraints of an NHS clinical diagnostic setting. We provide a robust workflow that will inform and facilitate the rollout of rapid genome sequencing in the NHS and other healthcare systems globally.

Funding

The study was funded by NIHR GOSH/UCL BRC: ormbrc-2012-1
External and Internally Generated Task Predictions are Integrated in Prefrontal Cortex to Jointly Guide Cognitive Control
Authors: Jiang Jiefeng , Wagner Anthony D. , Egner Tobias
Published: March 2018

Cognitive control proactively configures information processing to suit expected task demands. Predictions of forthcoming demand can be driven by explicit external cues or be generated internally, based on past experience (cognitive history). However, it is not known whether and how the brain reconciles these two sources of information to guide control. Pairing a probabilistic task-switching paradigm with computational modeling, we found that external and internally generated predictions jointly guide task preparation, with a bias for internal predictions. Using model-based neuroimaging, we then show that the two sources of task prediction are integrated in dorsolateral prefrontal cortex, and jointly inform a representation of the likelihood of a change in task demand, encoded in frontoparietal cortex. Upon task-stimulus onset, dorsomedial prefrontal cortex encoded the need for reactive task-set adjustment. These data reveal, for the first time, how the human brain integrates external cues and cognitive history to prepare for an upcoming task.
A benchmarking study on virtual ligand screening against homology models of human GPCRs
Authors: Lim Victor Jun Yu , Du Weina , Chen Yu Zong , Fan Hao
Published: March 2018

G-protein-coupled receptor (GPCR) is an important target class of proteins for drug discovery, with over 27% of FDA-approved drugs targeting GPCRs. However, being a membrane protein, it is difficult to obtain the 3D crystal structures of GPCRs for virtual screening of ligands by molecular docking. Thus, we evaluated the virtual screening performance of homology models of human GPCRs with respect to the corresponding crystal structures. Among the 19 GPCRs involved in this study, we observed that 10 GPCRs have homology models that have better or comparable performance with respect to the corresponding X-ray structures, making homology models a viable choice for virtual screening. For a small subset of GPCRs, we also explored how certain methods like consensus enrichment and sidechain perturbation affect the utility of homology models in virtual screening, as well as the selectivity between agonists and antagonists. Most notably, consensus enrichment across multiple homology models often yields results comparable to the best performing model, suggesting that ligand candidates predicted with consensus scores from multiple models can be the optimal option in practical applications where the performance of each model cannot be estimated.