bluuebunny/crossref_metadata_2025 huggingface dataset:
Exploring potential crossing seams in periodic systems: Intersystem crossing pathways in the benzene crystal
Authors: Saita Kenichiro , Takagi Makito , Harabuchi Yu , Okada Haruki , Maeda Satoshi
Published: July 2018

The intersystem crossing (ISC) pathways of triplet benzene molecules in a benzene crystal were investigated theoretically. A combination of the gradient projection (GP) method, which is a standard method for optimizing the crossing seam of two potential energy surfaces, and the single-component artificial-force-induced reaction (SC-AFIR) method (GP/SC-AFIR) was used. This is the first reported use of a GP/SC-AFIR calculation using a density functional theory calculation with periodic boundary conditions. A systematic search for the minimum-energy structures in the seams of crossing of the singlet (S0) and triplet (T1) potential energy surfaces (S0/T1-MESX structures) found 39 independent S0/T1-MESX structures. Energy barriers between the S0/T1-MESX and the stationary structure of the triplet state (T1-MIN) were computed, and then two competing ISC pathways were extracted; the calculated overall energy barrier to the intermolecular C–C-bonded type (SX3) and the out-of-plane bent C–H type (SX15) S0/T1-MESX structures from T1-MIN were 0.26 and 0.27 eV, respectively. The rate constants for SX3 and SX15 formation were estimated to be 5.07 × 108 and 2.17 × 108 s−1 (at 273 K), respectively, or 9.73 × 10−5 and 4.78 × 10−6 s−1 (at 77 K), respectively. At 273 K, which is close to the melting point of the benzene crystal (278.5 K), SX3 and SX15 are easily accessible from T1-MIN, and ISC could occur through the S0/T1-MESX points. By contrast, at 77 K, T1-MIN survives long enough for phosphorescence to compete with ISC.
Resistive switching study in HfO2 based resistive memories by conductive atomic force microscopy in vacuum
Authors: Singh A. K. , Blonkowski S. , Kogelschatz M.
Published: July 2018

This study aims to characterize the oxide based Resistive Random Access Memory memory cell at the nanoscale. Resistive memory stacks were characterized by conductive atomic force microscopy (C-AFM) under vacuum. The AFM tips served as the top electrode. The effect of different tip materials, polarities, bottom electrodes, and compliance currents on resistive switching is described and compared with the results obtained for devices at the micrometric scale. The experimental results are then interpreted by a filament based model. An interpretation in terms of conductive filament geometry is finally given.
Frequency domain thermoreflectance technique for measuring the thermal conductivity of individual micro-particles
Authors: Goni Miguel , Patelka Maciej , Ikeda Sho , Sato Toshiyuki , Schmidt Aaron J.
Published: July 2018

The thermal properties of micron scale particles are an important factor in the design of composite materials and other applications. Here we present an optical technique based on frequency domain thermoreflectance (FDTR) that is capable of measuring the thermal conductivity of individual particles a few microns across. In addition, the technique can provide values for a particle’s effective volume which is a new capability compared to conventional FDTR applied to multilayer samples. We also show and explain the response of systems that constrain heat flow along the in-plane direction due to a boundary. We tested this technique with natural diamond and doped silicon particles of different sizes. For the diamond particles, the thermal conductivity values obtained were within the range of reported literature values, while for the silicon particles, the thermal conductivities were slightly lower than the bulk sample they were fabricated from, possibly due to defects introduced during the fabrication process.
A discharge jump induced by external triggering in inductively coupled millimeter-sized plasma jet at atmospheric pressure
Authors: Yang K. , Zhang Y. C. , Li H. , Liu H. X. , Zhu M. L. , Zhu X. D.
Published: July 2018

We report an inductively coupled millimeter-sized plasma jet driven by the very high frequency of 150 MHz at atmospheric pressure. A phenomenon is observed that the discharge jump is induced by external triggering. The plasma near room temperature ejects out from the exit of quartz tube as the plasma is generated through one-time triggering by a spark igniter under an applied input voltage, and its length varies with the input voltage. With the further increase in the input voltage, the plasma plume becomes stable. By applying second-triggering, the plasma changes to be full of the quartz tube, and a slight change is observed in the shape of plasma plume with the input voltage. Meanwhile, the jet temperature rises suddenly to more than 500 K. The coil current is measured to present different dependences on the input voltage for discharging with and without second-triggering. It is considered that the E-H mode transition happens in the discharge jump due to the external triggering. The application of the strongly electric field through the second-triggering results in a sudden variation of the electron density and resulting plasma impedance, which is responsible for the discharge jump observed.
The MBE growth of arbitrarily thick SrTiO3/LaAlO3 quantum well heterostructures for use in next-generation optoelectronic devices
Authors: Ortmann J. Elliott , Posadas Agham B. , Demkov Alexander A.
Published: July 2018

While the SrTiO3/LaAlO3 (STO/LAO) materials system has been widely studied in the hopes of integrating it into transition metal oxide (TMO) electronic devices, recent reports have focused on its optical properties. Electronic confinement in STO quantum wells (QWs) and the optical modulation of confined charge carriers have recently been demonstrated, suggesting the feasibility of producing TMO-based QW optoelectronic devices. However, before these devices can be realized, it is necessary to develop the capability to grow such structures arbitrarily thick while maintaining high crystalline quality. We report on the fabrication of STO/LAO QW heterostructures and demonstrate via reflection high-energy electron diffraction, X-ray diffraction, reciprocal space mapping, and X-ray reflectivity measurements that these heterostructures can be grown arbitrarily thick while maintaining a high crystalline quality and uniform periodicity, in contrast to previous reports. While we focus primarily on the STO/LAO system in this report, we believe the growth and design principles contained herein can inform the growth of a multitude of different TMO QW heterostructures, paving the way for the next generation of TMO-based QW optoelectronic devices.
Autocorrelation pulse-duration measurement of relativistic femtosecond laser
Authors: Guo Zhao , Shen Baifei , Zhang Xiaomei , Ji Liangliang , Zhang Lingang , Liu Chen
Published: July 2018

An approach is proposed to directly measure the relativistic laser pulse duration. In the scheme, two identical high-intensity laser pulses are irradiated on a thin plasma target symmetrically in V-shape. High order harmonics carrying the information of two incident pulses are generated in different directions during the nonlinear interaction process. The direction of the third harmonic can be predicted from the theoretical analysis and its intensity in this direction can be recorded as an autocorrelation function of the delay time between the incident pulses. Then, the pulse duration which is 70% of the full width at half maximum of the autocorrelation curve can be obtained. This approach has been verified by particle-in-cell simulations and the error is 3.7% for a 30 fs relativistic laser pulse as an example.
Computational simulation of atmospheric pressure discharges with the needle-array electrode
Authors: Zhang Jiao , Wang Yanhui , Wang Dezhen
Published: July 2018

Needle-electrode discharge with the advantage of high flexibility and low broken-down voltage, etc., is desirable for many plasma applications. However, such applications are limited by its small treatment scale. Arranging needles together in parallel provides a feasible way to enlarge the treatment area. The interaction among the needles, however, cannot be ignored and is desirable to be discussed. In this paper, a 2-D self-consistent fluid model is developed to study the atmospheric pressure discharge with single-needle and needle-array electrodes. It is observed that the streamer generated by surrounding needle tends to propagate with a curving trajectory, i.e., it is initially repulsive by the central streamer and then bends towards the central axis. Additionally, the central needle discharge is restricted by adjacent needle discharge, if the distance between needles is relatively small. Several ways are put forward to improve the discharge spatial uniformity in the needle-array electrode.
Orbitronic effect on the magnetic reconstruction of monocell SrMnO3 on ferroelectric BaTiO3 substrate
Authors: Huang Xiaokun , Li Guannan , Hu Jingsan , Zhang Weiyi
Published: July 2018

The magnetic reconstruction of doped LaMnO3 on the ferroelectric substrate intrinsically involves sizeable carrier inhomogeneity on the scale of one-unit cell due to the charge screening effect at the interface. The small variation in Mn-d valence caused by the inhomogeneity may be responsible for the conflicting magnetic patterns predicted for thick magnetic films. To avoid the complexity resulting from the carrier inhomogeneity, we consider in this paper the magnetic reconstruction of a rigorously carrier homogeneous monocell SrMnO3 film on a BaTiO3 substrate. Stoichiometric SrMnO3 is used to further prevent the film from structural defects and associated Anderson's localization. Our study showed that magnetic reconstruction takes place between nearest-neighbor antiferromagnetic to ferromagnetic structures during polarization reversal of the substrate even if the ground state of bulk SrMnO3 is far away from the magnetic phase boundary. Furthermore, the estimated effective magnetoelectric coupling coefficient is 6.1 × 10−2 Oe cm V−1. It is more than doubled than those values obtained for thick magnetic films. Our detailed analysis suggested that the magnetic reconstruction is dictated by the modulated double-exchange ferromagnetic coupling mediated by Mn-d(eg)-orbitals against the superexchange antiferromagnetic coupling mediated by d(t2g)-orbitals. The nearest-chain antiferromagnetic structure also appears during the polarization reversal process.
Density functional theory—projected local density of states—based estimation of Schottky barrier for monolayer MoS2
Authors: Gao Junsen , Nandi Dipanjan , Gupta Manisha
Published: July 2018

One of the biggest challenges so far in implementing 2D materials in device applications is the formation of a high quality Schottky barrier. Here, we have conducted density functional theory simulations and employed the projected local density of states technique to study the Schottky contact formation between monolayer (ML) MoS2 with different metal electrodes (Mo, W, and Au). Electrode formation on ML MoS2 changes it from intrinsic to a doped material due to metallization, which creates issues in the formation of a good Schottky contact. Amongst the metals studied here, we observe that Mo tends to form the best Schottky barrier with ML MoS2 based on both the vertical and lateral Schottky barrier heights (0.13 eV for the vertical Schottky barrier and 0.1915 eV for the lateral Schottky barrier) and the built-in potential (0.0793 eV). As compared to Mo, Au forms a high-resistance ohmic contact with a much larger vertical barrier height of 0.63 ± 0.075 eV and a negligible built-in potential. It is thus observed that ML MoS2 is very susceptible to strain and pinning of the Fermi level due to metal junction formation. Thus, understanding both the vertical and horizontal Schottky barrier heights along with the built-in potential is critical for designing high performance 2D semiconductor devices.
Stretching our understanding of C3: Experimental and theoretical spectroscopy of highly excited nν1 + mν3 states (n ≤ 7 and m ≤ 3)
Authors: Schröder Benjamin , Doney Kirstin D. , Sebald Peter , Zhao Dongfeng , Linnartz Harold
Published: July 2018

We present the high resolution infrared detection of fifteen highly vibrationally excited nν1 + mν3 combination bands (n ≤ 7 and m ≤ 3) of C3 produced in a supersonically expanding propyne plasma, of which fourteen are reported for the first time. The fully resolved spectrum, around 3 μm, is recorded using continuous wave cavity ring-down spectroscopy. A detailed analysis of the resulting spectra is provided by ro-vibrational calculations based on an accurate local ab initio potential energy surface for C3 (X̃1Σg+). The experimental results not only offer a significant extension of the available data set, extending the observed number of quanta v1 to 7 and v3 to 3, but also a vital test to the fundamental understanding of this benchmark molecule. The present variational calculations give remarkable agreement compared to experimental values with typical accuracies of ∼0.01% for the vibrational frequencies and ∼0.001% for the rotational parameters, even for high energy levels around 10 000 cm−1.
Thermal tuning of silicon terahertz whispering-gallery mode resonators
Authors: Vogt Dominik Walter , Jones Angus Harvey , Leonhardt Rainer
Published: July 2018

We investigate thermal tuning of an ultra-high quality (Q) terahertz (THz) whispering-gallery mode resonator (WGMR) made of low loss silicon. The Si THz WGMR can be continuously tuned with a rate of about 29 MHz/K in the frequency range from 650 GHz to 666 GHz. Furthermore, we utilize the Si WGMR to extract the thermo-optic coefficient of Si at 459 GHz and 659 GHz in the temperature range from 295 K to 363 K.
A high-precision and fast-sampling frequency measurement method based on FPGA carry chain for airborne optically pumped cesium magnetometer
Authors: Dong Haobin , Hu Shuting , Ge Jian , Liu Huan , Luo Wang , Yuan Zhiwen , Zhu Jun , Zhang Haiyang
Published: July 2018

Improving the precision and sampling rate of the resonance frequency of cesium atoms is the key to enhancing the same factors of an airborne optically pumped cesium magnetometer (AOPCM). Aiming at the existed problems of AOPCM and characteristics of resonance signal, this paper proposes a high-precision and fast-sampling frequency measurement method based on carry chains of Field-Programmable Gate Array (FPGA). In order to achieve a fast-sampling rate, an improved equal precision frequency measurement method is proposed to measure the standard signal and the resonance signal continuously. Besides, by using the serial full adder to connect FPGA carry chains to a delay line, the delay line is used to compensate the unsynchronized clock edge, so the counting error can be reduced, and the precision of frequency measurement can be improved greatly. Experiments show that the frequency resolution is 0.014 nT and the relative error is lower than 2 × 10−6 when the sampling rate is 500 Hz. The experimental result indicates that the proposed method improves the precision and sampling rate of resonance frequency measurement greatly. Consequently, the precision and sampling rate of AOPCM can be improved.
Thermal sensing in fluid at the micro-nano-scales
Authors: Yang Fan , Yang Nana , Huo Xiaoye , Xu Shengyong
Published: July 2018

Temperature is one of the most fundamental parameters for the characterization of a physical system. With rapid development of lab-on-a-chip and biology at single cell level, a great demand has risen for the temperature sensors with high spatial, temporal, and thermal resolution. Nevertheless, measuring temperature in liquid environment is always a technical challenge. Various factors may affect the sensing results, such as the fabrication parameters of built-in sensors, thermal property of electrical insulating layer, and stability of fluorescent thermometers in liquid environment. In this review, we focused on different kinds of micro/nano-thermometers applied in the thermal sensing for microfluidic systems and cultured cells. We discussed the advantages and limitations of these thermometers in specific applications and the challenges and possible solutions for more accurate temperature measurements in further studies.
Optical near-field mapping with a superconducting nanowire detector
Authors: Luszcz Karol , Bonvin Eric , Novotny Lukas
Published: July 2018

Optical near-fields are interesting from a theoretical perspective and of importance for practical applications, such as high-resolution imaging, sensing, and antenna-coupled quantum light sources. In this work, we use a custom-designed superconducting nanowire single-photon detector to directly read out the near-field interaction between a source and a detector. We use a subwavelength-sized aperture at the end of an optical fiber to record spatial near-field maps and to measure the distance dependence of the optical near-field interaction. Our measurements can be well described by a superposition of evanescent source fields with no noticeable probe-sample coupling. Our approach is a first step towards the development of near-field imaging techniques with single quantum sensitivity.
Electronically nonadiabatic mechanism of the vibrational relaxation of NO in Ar: Rate coefficients from ab initio potentials and asymptotic coupling
Authors: Dashevskaya E. I. , Litvin I. , Nikitin E. E. , Troe J.
Published: July 2018

In this paper, the electronically nonadiabatic Landau-Zener (LZ) mechanism for the vibrational relaxation v = 1 → v = 0 of NO(X2Π) in collisions with Ar(S01) is discussed. It corresponds to nonadiabatic transitions between two crossing vibronic potential energy surfaces (PESs) originating from vibrational states of the collision complex and supported by two coupled electronic PESs. The LZ rate coefficients k10LZ are calculated within the uniform Airy approach in the reaction coordinate approximation with parameters derived from ab initio PESs and an asymptotic estimation of the Franck–Condon factor in the nonadiabatic coupling region. The rate coefficients are close to the experimental rate coefficients available over the range of 900–2500 K, where the electronically adiabatic Landau-Teller (LT) mechanism with the rate coefficients k10LT does not make a noticeable contribution to the total relaxation rate. The ratio k10LZ/k10LT increases with temperature and the LZ and LT mechanisms have comparable rates at about 4000 K.
Modelled impacts of extreme heat and drought on maize yield in South Africa
Authors: Mangani Robert , Tesfamariam Eyob , Bellocchi Gianni , Hassen Abubeker
Published: July 2018

This study assessed two versions of the crop model CropSyst (i.e. EMS, existing; MMS, modified) for their ability to simulate maize (Zea mays L.) yield in South Africa. MMS algorithms explicitly account for the impact of extreme weather events (droughts, heat waves, cold shocks, frost) on leaf development and yield formation. The case study of this research was at an experimental station near Johannesburg where both versions of the model were calibrated and validated by using field data collected from 2004 to 2008. The comparison of EMS and MMS showed considerable difference between the two model versions during extreme drought and heat events. MMS improved grain-yield prediction by ~30% compared with EMS, demonstrating a better ability to capture the behaviour of stressed crops under a range of conditions. MMS also showed a greater variability in response when both versions were forced with scenarios of projected climate change, with increased severity of drought and increased temperature conditions at the horizons 2030 and 2050, which could drive decreased maize yield. Yield was even lower with MMS (8 v. 11 t ha–1 for EMS) at the horizon 2050, relative to the baseline scenario (~13 t ha–1 at the horizon 2000). Modelling solutions accounting for the impact of extreme weather events can be seen as a promising tool for supporting agricultural management strategies and policy decisions in South Africa and globally.
How does long-term drought acclimation modify structure-function relationships? A quantitative approach to leaf phenotypic plasticity of barley
Authors: Bresta P. , Nikolopoulos D. , Stavroulaki V. , Vahamidis P. , Economou G. , Karabourniotis G.
Published: July 2018

Under drought conditions the growth and survival of a plant depend on its adaptive characteristics and acclimation ability. Adaptation refers to inherent morpho-physiological characters providing protection against water losses. Acclimation, however, is a special case of phenotypic plasticity: environment-dependent phenotypic expression resulting to a ‘new’ phenotype through drought-induced modulations in leaf morphology, anatomy and physiology. Given that phenotypic plasticity influences environmental tolerance, a multi-trait plasticity index could be of great importance. Therefore, we examined the acclimation processes of three different barley genotypes using a multi-trait plasticity assessment with emphasis on the leaf water economy-related traits. Our results showed that (i) the structure–function co-ordination during long-term drought acclimation follows the trade-off between carbon gain and water saving as well as the competition between investments in photosynthesis vs synthesis of protective compounds; (ii) the genotypes with smaller leaf area, narrower and denser veins, as well as smaller and denser stomata i.e. traits providing tolerance, exhibited less drastic adjustments under stress conditions, suggesting a trade-off between acclimation and tolerance-adaptation; and (iii) the slope values of a multi-trait ‘reaction norm’ based on regression analysis of PCA scores were indicative of the degree of plasticity for each genotype, providing an accurate representation of a complex set of data with single numeric results easily comparable.
Optimising the linear electron transport rate measured by chlorophyll a fluorescence to empirically match the gross rate of oxygen evolution in white light: towards improved estimation of the cyclic electron flux around photosystem I in leaves
Authors: Zhang Meng-Meng , Fan Da-Yong , Sun Guang-Yu , Chow Wah Soon
Published: July 2018

The cyclic electron flux (CEF) around photosystem I (PSI) was discovered in isolated chloroplasts more than six decades ago, but its quantification has been hampered by the absence of net formation of a product or net consumption of a substrate. We estimated in vivo CEF in leaves as the difference (ΔFlux) between the total electron flux through PSI (ETR1) measured by a near infrared signal, and the linear electron flux through both photosystems by optimised measurement of chlorophyll a fluorescence (LEFfl). Chlorophyll fluorescence was excited by modulated green light from a light-emitting diode at an optimal average irradiance, and the fluorescence was detected at wavelengths >710 nm. In this way, LEFfl matched the gross rate of oxygen evolution multiplied by 4 (LEFO2) in broad-spectrum white actinic irradiance up to half (spinach, poplar and rice) or one third (cotton) of full sunlight irradiance. This technique of estimating CEF can be applied to leaves attached to a plant.
More than just the animals: opportunities and costs of reintroducing threatened black-footed rock-wallabies to remote Indigenous land
Authors: Ireland Luke , Zabek Magdalena , Galindez-Silva Carolina , Weir Sara , West Rebecca , Olds Liberty , Backhouse Brett , Copley Peter , Read John
Published: July 2018

Conservation activities, including translocations of threatened species, are increasingly important priorities for conserving biodiversity and culture on Indigenous-managed lands, which occupy over 20% of the Australian landmass. In the Anangu Pitjantjatjara Yankunytjatjara (APY) Lands of north-western South Australia, the Warru Recovery Team reintroduced the threatened black-footed rock-wallaby (warru) to Wamitjara in May 2018. We outline the unique planning and logistical issues inherent in securing support and involvement of Traditional Owners and Indigenous rangers for predator, weed and fire management, cross-fostering, captive breeding, monitoring and translocation of the rock-wallabies. Altogether, the project cost AU$3.86 million (actual – AU$1.86 million, in kind – AU$2.00 million) over 10 years of preparation and one year of post-translocation monitoring. This consisted of AU$1.18 million for cross-fostering and captive breeding at Monarto Zoo and a further AU$0.55 million for the construction and maintenance of a fenced exclosure in the APY Lands. It is estimated that AU$0.51 million of the total costs were directly attributed to working remote and Indigenous-owned land, with most of the remaining costs typical of other reintroduction programs. Large-scale reintroduction opportunities on Indigenous-managed land can provide considerable conservation outcomes as well as delivering cultural objectives and supporting employment.
Ethological observations of social behavior in the operating room
Authors: Jones Laura K. , Jennings Bonnie Mowinski , Higgins Melinda K. , de Waal Frans B. M.
Published: July 2018

Significance

Hierarchy and gender composition affect the balance of cooperation and conflict on surgical teams. In this investigation, behavior was quantified with methods traditionally used to study nonhuman primate groups. Observers used an ethogram to timestamp 6,348 spontaneous social interactions from 200 surgical procedures. Conflict and cooperation in the operating room showed a significant interaction effect with regard to professional roles (e.g., conflict was initiated mostly down the hierarchy between individuals several ranks apart) and by gender interaction (e.g., cooperation was better if the attending surgeon’s gender differed from that of the team majority). These findings may inform ongoing and future interventions designed to improve team performance and patient safety.
Confinement generates single-crystal aragonite rods at room temperature
Authors: Zeng Muling , Kim Yi-Yeoun , Anduix-Canto Clara , Frontera Carlos , Laundy David , Kapur Nikil , Christenson Hugo K. , Meldrum Fiona C.
Published: July 2018

Significance

Calcium carbonate is a widespread compound whose two common crystalline forms, calcite and aragonite, are important biominerals. Although aragonite is only marginally less stable than calcite under ambient conditions, it usually only crystallizes from solution at high temperatures or in the presence of magnesium ions. However, organisms readily form both calcite and aragonite biominerals, a capacity usually attributed to the action of specific organic macromolecules. By investigating calcium carbonate precipitation in submicron pores we here show that aragonite is promoted in confinement and that pure aragonite crystallizes in nanoscale pores in the absence of any additives. This is of great significance to biomineralization processes, which invariably occur in small volumes, and suggests that organisms may exploit confinement effects to control polymorph.
Origins of equine dentistry
Authors: Taylor William Timothy Treal , Bayarsaikhan Jamsranjav , Tuvshinjargal Tumurbaatar , Bender Scott , Tromp Monica , Clark Julia , Lowry K. Bryce , Houle Jean-Luc , Staszewski Dimitri , Whitworth Jocelyn , Fitzhugh William , Boivin Nicole
Published: July 2018

Significance

The domestication of horses and adoption of horse riding were critical processes that culminated in the emergence of mounted warriors and nomadic empires that shaped world history. The constraints of horse biology and riding equipment meant that equine veterinary care, particularly of teeth, was a core component of the success of the human–horse relationship. We report the earliest evidence of equine dentistry, from the Mongolian Steppe, at 1150 BCE. Key shifts in equine dentistry practice through time can be linked first to the emergence of horseback riding and later to the use of metal bits that enabled better control of horses. The maintenance of horse health through dentistry underwrote the key role of horses in cultures and economies around the world.
Decoding on the ribosome depends on the structure of the mRNA phosphodiester backbone
Authors: Keedy Hannah E. , Thomas Erica N. , Zaher Hani S.
Published: July 2018

Significance

Reading of the genetic code is an intricate process in which the ribosome plays an active role in ensuring that translation proceeds rapidly and accurately. Studies have revealed that the mRNA adopts an unusual structure between the P and A sites of the small ribosomal subunit, where it is significantly kinked. In this work we probed the role of the kink structure in decoding. Substitutions that disrupt this structure were found to increase the accuracy of decoding. Conversely, peptide-bond formation on difficult-to-decode codons was severely reduced when this kink structure was perturbed. Our data suggest that the rigid nature of the mRNA backbone is important for ensuring efficient codon–anticodon interactions under suboptimal conditions.
Repression of human and mouse brain inflammaging transcriptome by broad gene-body histone hyperacetylation
Authors: Cheng Hao , Xuan Hongwen , Green Christopher D. , Han Yixing , Sun Na , Shen Hongjie , McDermott Joseph , Bennett David A. , Lan Fei , Han Jing-Dong J.
Published: July 2018

Significance

Brain aging and neural degenerative diseases are characterized by chronic low-degree inflammation, also known as “inflammaging.” Histone acetylation is a classical mark for active gene expression. Here, using H3K27ac ChIP-seq and RNA-seq of human and mouse brain samples, we found that, during aging, overactivated inflammation-related genes are marked by decreased broad gene-body hyperacetylation. Restoring the gene-body hyper H3K27ac by histone deacetylase inhibitors suppressed such overactivation, implying a potential fine-tuning function of broad gene-body H3K27ac on these inflammaging genes. Our study uncovered a mode of epigenetic regulation of the brain inflammaging genes, suggesting the reversibility of the inflammaging process and a potential angle for intervention of aging-related brain function decline and neural degenerative diseases.
Costs and benefits of provocation in bacterial warfare
Authors: Gonzalez Diego , Sabnis Akshay , Foster Kevin R. , Mavridou Despoina A. I.
Published: July 2018

Significance

Bacteria live in dense environments where competition for space and resources is fierce. For this reason, they often use diffusible toxins to eliminate closely related strains. Some toxins trigger systematic retaliation, raising the question of the role of provocation in bacterial warfare. We combine mathematical modeling and experiments to study the costs and benefits of provocation. In one-to-one encounters, provocation is costly as it leads to strong counterattacks. However, with three or more strains present, provocation can provide benefits via a “divide-and-conquer” effect, whereby a strain forces its opponents to wipe each other out. This effect could be harnessed as a targeted antibacterial approach; adding low levels of certain antibiotics to communities can promote warfare and cross-elimination between strains.
Conservation of mRNA quality control factor Ski7 and its diversification through changes in alternative splicing and gene duplication
Authors: Marshall Alexandra N. , Han Jaeil , Kim Minseon , van Hoof Ambro
Published: July 2018

Significance

The rapid degradation of mRNAs that lack a stop codon is critical to fidelity of gene expression and in yeast, it requires Ski7. Ski7 function is not fully understood and
SKI7
-like genes are not apparent in other organisms. We show that in most eukaryotes Ski7 is expressed as an alternative splice isoform from the
HBS1
gene. This most conserved example of alternative splicing probably arose in the common ancestor of animals, fungi, and plants. However, in six taxa alternative splicing was replaced by duplicated genes. After each duplication the
SKI7
-like gene has undergone several changes that we analyzed experimentally. The results clarify how duplicated genes diversify, identify novel
SKI7
-like genes, and reveal changes in nonstop mRNA decay.
Role for fatty acid amide hydrolase (FAAH) in the leptin-mediated effects on feeding and energy balance
Authors: Balsevich Georgia , Sticht Martin , Bowles Nicole P. , Singh Arashdeep , Lee Tiffany T. Y. , Li Zhiying , Chelikani Prasanth K. , Lee Francis S. , Borgland Stephanie L. , Hillard Cecilia J. , McEwen Bruce S. , Hill Matthew N.
Published: July 2018

Significance

We present evidence that an endocannabinoid-dependent signaling mechanism contributes to the hypophagic actions of leptin. Specifically, leptin increases fatty acid amide hydrolase (FAAH) activity and reduces
N
-arachidonoylethanolamine (anandamide; AEA) signaling, particularly within the hypothalamus, to promote a suppression of food intake. This mechanism is lost in diet-induced obesity and is furthermore modulated by a human genetic variant (C385A) of the
FAAH
gene. As such, reduced sensitivity to leptin in
FAAH
385A-allele carriers may contribute to their higher risk to develop obesity and related metabolic complications.
Synthetic far-red light-mediated CRISPR-dCas9 device for inducing functional neuronal differentiation
Authors: Shao Jiawei , Wang Meiyan , Yu Guiling , Zhu Sucheng , Yu Yuanhuan , Heng Boon Chin , Wu Jiali , Ye Haifeng
Published: July 2018

Significance

We have developed an optogenetic far-red light (FRL)-activated CRISPR-dCas9 system (FACE) that is orthogonal, fine-tunable, reversible, and has robust endogenous gene-activation profiles upon stimulation with FRL, with deep tissue penetration capacity, low brightness, short illumination time, and negligible phototoxicity. The FACE device is biocompatible and meets the criteria for safe medical application in humans, providing a robust differentiation strategy for mass production of functional neural cells from induced pluripotent stem cells simply by utilizing a beam of FRL. This optogenetic device has expanded the optogenetic toolkit for precise mammalian genome engineering in many areas of basic and translational research that require precise spatiotemporal control of cellular behavior, which may in turn boost the clinical progress of optogenetics-based precision therapy.
Sinking particles promote vertical connectivity in the ocean microbiome
Authors: Mestre Mireia , Ruiz-González Clara , Logares Ramiro , Duarte Carlos M. , Gasol Josep M. , Sala M. Montserrat
Published: July 2018

Significance

Prokaryotes dominate the living biomass and the biological diversity of the ocean, one of the largest ecosystems on earth. The sinking of particles is a widespread mechanism that transports materials to the deep ocean, with a significant role in the global carbon cycle. Whether this process constitutes a global dispersal pathway for prokaryotic diversity connecting surface communities to those in the dark ocean has never been tested. Here we show that surface and deep-sea prokaryotic communities are strongly connected, constituting a vast oceanic metacommunity where local assemblages are linked through the transport of sinking particles. This vertical dispersal, mediated mainly by the largest sinking particles, emerges as a fundamental process shaping the assembly and biogeography of deep ocean prokaryotic communities.
Two polymorphic cholesterol monohydrate crystal structures form in macrophage culture models of atherosclerosis
Authors: Varsano Neta , Beghi Fabio , Elad Nadav , Pereiro Eva , Dadosh Tali , Pinkas Iddo , Perez-Berna Ana J. , Jin Xueting , Kruth Howard S. , Leiserowitz Leslie , Addadi Lia
Published: July 2018

Significance

Atherosclerosis causes heart attack and stroke and is a major fatal disease in the Western world. Cholesterol crystal rods and plates are the hallmark of developed atherosclerotic plaques and are associated with plaque rupture and thrombus formation. We show here that the elongated rod-shaped crystals that form inside macrophage cells enriched with cholesterol have a crystal structure different from the thin plates associated with the cell plasma membrane. The two crystal structures are induced by the different biological environment where they form. Besides identifying the structure of cholesterol crystals in pathological plaques, this work may thus provide information on cellular crystal growth mechanisms, once the factors that favor the formation of the different structures are understood.
Redundancy in synaptic connections enables neurons to learn optimally
Authors: Hiratani Naoki , Fukai Tomoki
Published: July 2018

Significance

Humans and animals are capable of rapid learning from a small dataset, which is still difficult for artificial neural networks. Recent studies further suggest that our learning speed is nearly optimal given a stream of information, but its underlying mechanism remains elusive. Here, we hypothesized that the elaborate connection structure between presynaptic axons and postsynaptic dendrites is the key element for this near-optimal learning and derived a data-efficient rule for dendritic synaptic plasticity and rewiring from Bayesian theory. We implemented this rule in a detailed neuron model of visual perceptual learning and found that the model well reproduces various known properties of dendritic plasticity and synaptic organization in cortical neurons.
Ablation of PM20D1 reveals
N
-acyl amino acid control of metabolism and nociception
Authors: Long Jonathan Z. , Roche Alexander M. , Berdan Charles A. , Louie Sharon M. , Roberts Amanda J. , Svensson Katrin J. , Dou Florence Y. , Bateman Leslie A. , Mina Amir I. , Deng Zhaoming , Jedrychowski Mark P. , Lin Hua , Kamenecka Theodore M. , Asara John M. , Griffin Patrick R. , Banks Alexander S. , Nomura Daniel K. , Spiegelman Bruce M.
Published: July 2018

Significance

Bioactive lipids control a wide variety of physiologic processes. We have recently identified a branch of bioactive lipid signaling mediated by
N
-acyl amino acids (NAAs) and the circulating enzyme peptidase M20 domain-containing 1 (PM20D1). Here we generate and characterize mice globally deficient in PM20D1. These PM20D1-KO mice have bidirectional changes in NAA levels in blood and tissues and exhibit a variety of metabolic and nociceptive phenotypes. Our findings elucidate the endogenous physiologic functions for NAA signaling in vivo and suggest PM20D1 inhibitors might be useful for the treatment of pain.
Vulnerability of Arctic marine mammals to vessel traffic in the increasingly ice-free Northwest Passage and Northern Sea Route
Authors: Hauser Donna D. W. , Laidre Kristin L. , Stern Harry L.
Published: July 2018

Significance

The Arctic is experiencing unprecedented rates of sea ice loss in concert with expanding anthropogenic activities that may have compounding effects on marine ecosystems. The Northwest Passage and Northern Sea Route have recently seen the advent of commercial traffic, raising questions of how to juggle economic development and conservation. Here we show the vulnerability of 80 subpopulations of seven endemic Arctic marine mammal species to vessel traffic across the Northwest Passage and Northern Sea Route during the open-water season, accompanied by estimates of uncertainty that highlight additional research needs. As global, national, and local organizations sharpen their focus on the Arctic, our results provide a framework to evaluate environmental impacts to the region’s most iconic and sensitive species.
Traceless synthesis of ceramides in living cells reveals saturation-dependent apoptotic effects
Authors: Rudd Andrew K. , Devaraj Neal K.
Published: July 2018

Significance

Ceramides are a chemically diverse class of sphingolipids that have critical roles in a wide range of biological pathways. Despite their high biological interest, ceramides have been difficult to study because of their impermeability to the cell membrane. We overcome the principal issues with ceramide delivery by chemoselectively ligating lipid precursors in vivo. Our method employs a proximity-induced ligation which allows for the in situ synthesis of several different natural ceramide species within live cells. Using this approach, we directly confirm the proapoptotic effects of C16:0 ceramide in vivo and observe that ceramide saturation plays a determinant role in ceramide-driven apoptosis.
An aryl-homoserine lactone quorum-sensing signal produced by a dimorphic prosthecate bacterium
Authors: Liao Lisheng , Schaefer Amy L. , Coutinho Bruna G. , Brown Pamela J. B. , Greenberg E. Peter
Published: July 2018

Significance

Acyl-homoserine lactone (AHL) quorum sensing (QS) has received interest as a possible target for controlling microbial activities and as a model for communication involved in coordinating activities of bacteria. Recent advances show there are two related families of AHL QS signal synthesis enzymes, which differ in whether they acquire the organic acid reaction substrate from biosynthetic or primarily catabolic pathways. Most known AHL synthases utilize fatty acids activated with an acyl carrier protein from fatty acid biosynthesis. Some AHL synthases use coenzyme-A–activated organic acids. We describe a coenzyme-A–dependent AHL synthase QS system. We also set forth an experimental approach for discovering new signals that will allow further expansion of our understanding of the diversity of AHL signaling.
Protein-restricted maternal diet during lactation decreases type I and type III tropocollagen synthesis in the skin of mice offspring
Authors: Yamane Takumi , Konno Ryosuke , Iwatsuki Ken , Oishi Yuichi
Published: July 2018

We investigated the effects of a low protein (LP) maternal diet during lactation on type I and III tropocollagen synthesis in infant mouse skin. The LP diet decreased the levels of type I and III tropocollagen proteins and COL1A1 and COL3A1 mRNA. Thus, the protein composition of the maternal perinatal diet may influence the skin health of offspring.
Genetic variation within endolysosomal system is associated with late-onset Alzheimer’s disease
Authors: Gao Song , Casey Aaron E , Sargeant Tim J , Mäkinen Ville-Petteri
Published: July 2018

Late-onset Alzheimer’s disease is the most common dementia type, yet no treatment exists to stop the neurodegeneration. Evidence from monogenic lysosomal diseases, neuronal pathology and experimental models suggest that autophagic and endolysosomal dysfunction may contribute to neurodegeneration by disrupting the degradation of potentially neurotoxic molecules such as amyloid-β and tau. However, it is uncertain how well the evidence from rare disorders and experimental models capture causal processes in common forms of dementia, including late-onset Alzheimer’s disease. For this reason, we set out to investigate if autophagic and endolysosomal genes were enriched for genetic variants that convey increased risk of Alzheimer’s disease; such a finding would provide population-based support for the endolysosomal hypothesis of neurodegeneration. We quantified the collective genetic associations between the endolysosomal system and Alzheimer’s disease in three genome-wide associations studies (combined n = 62 415). We used the Mergeomics pathway enrichment algorithm that incorporates permutations of the full hierarchical cascade of SNP-gene-pathway to estimate enrichment. We used a previously published collection of 891 autophagic and endolysosomal genes (denoted as AphagEndoLyso, and derived from the Lysoplex sequencing platform) as a proxy for cellular processes related to autophagy, endocytosis and lysosomal function. We also investigated a subset of 142 genes of the 891 that have been implicated in Mendelian diseases (MenDisLyso). We found that both gene sets were enriched for genetic Alzheimer’s associations: an enrichment score 3.67 standard deviations from the null model (P = 0.00012) was detected for AphagEndoLyso, and a score 3.36 standard deviations from the null model (P = 0.00039) was detected for MenDisLyso. The high enrichment score was specific to the AphagEndoLyso gene set (stronger than 99.7% of other tested pathways) and to Alzheimer’s disease (stronger than all other tested diseases). The APOE locus explained most of the MenDisLyso signal (1.16 standard deviations after APOE removal, P = 0.12), but the AphagEndoLyso signal was less affected (3.35 standard deviations after APOE removal, P = 0.00040). Additional sensitivity analyses further indicated that the AphagEndoLyso Gene Set contained an aggregate genetic association that comprised a combination of subtle genetic signals in multiple genes. We also observed an enrichment of Parkinson’s disease signals for MenDisLyso (3.25 standard deviations) and for AphagEndoLyso (3.95 standard deviations from the null model), and a brain-specific pattern of gene expression for AphagEndoLyso in the Gene Tissue Expression Project dataset. These results provide evidence that a diffuse aggregation of genetic perturbations to the autophagy and endolysosomal system may mediate late-onset Alzheimer’s risk in human populations.
The formulation and analysis of energy-preserving schemes for solving high-dimensional nonlinear Klein–Gordon equations
Authors: Wang Bin , Wu Xinyuan
Published: July 2018

In this paper we focus on the analysis of energy-preserving schemes for solving high-dimensional nonlinear Klein–Gordon equations. A novel energy-preserving scheme is developed based on the discrete gradient method and the Duhamel principle. The local error, global convergence and nonlinear stability of the new scheme are analysed in detail. Numerical experiments are implemented to compare with existing numerical methods in the literature, and the numerical results show the remarkable efficiency of the new energy-preserving scheme presented in this paper.
Postpartum Group A Streptococcus Case Series: Reach Out to Infection Prevention!
Authors: Alexander Andrew J , Myers Carol , Beres Stephen B , Olsen Randall J , Musser James M , Mangino Julie E
Published: July 2018

A series of postpartum Streptococcus pyogenes infections prompted an investigation to rule out potential transmission by a health care worker. None of the hospital staff screened were colonized. All isolates were determined to be unrelated by molecular methods, including whole-genome sequencing. Thus, nosocomial transmission was considered unlikely.
Loss of Pelvic Incidence Correction After Long Fusion Using Iliac Screws for Adult Spinal Deformity
Authors: Oba Hiroki , Ebata Shigeto , Takahashi Jun , Ikegami Shota , Koyama Kensuke , Haro Hirotaka , Kato Hiroyuki , Ohba Tetsuro
Published: July 2018

Study Design.

Retrospective observational cohort study.

Objective.

To determine change in pelvic incidence (PI) and loss of correction after long fusion with iliac screws, the effect of iliac screw loosening, and global alignment according to postoperative PI.

Summary of Background Data.

Posterior long fixation and fusion of the thoracic to the ilium is one of the most common surgical treatments for adult spinal deformity (ASD). Long fusion to the sacrum with iliac screws decreases the PI by 3.9° after surgery. PI decreases once by long fusion with iliac screws. However, if the iliac screw loosens, PI may cause correction loss and return to the preoperative PI.

Methods.

We retrospectively reviewed the cases of 69 consecutive patients with ASD. Their mean age (SD) was 70.5 (7.3) years, 12% were male. PI was evaluated preoperatively, early- and 1-year postoperatively. We compared change in PI with and without loosening of iliac screws, spinopelvic parameters according to 1-year-postoperative PI.

Results.

PI decreased significantly from 51.8° (9.3°) to 48.1° (9.5°) early postoperatively (P < 0.01). PI increased significantly from 48.1° (9.5°) to 49.6° (9.7°) within a year postoperatively (P < 0.01). Significant loss of PI correction (2.3°, P < 0.01) occurred within a year after surgery in patients with iliac screw loosening and was significantly different from the PI loss in those without screw loosening (53.9°, 48.2°, P = 0.03). Pelvic tilt, sacral slope, C7 sagittal vertical axis, global tilt, and T1 pelvic angle were significantly smaller in the group with PI <50° postoperatively at 1 year compared with the group with PI >50°.

Conclusion.

Although PI decreases after long fusion surgery with iliac screws, significant correction loss appears within a year. Loosening of iliac screws may exacerbate this loss. Patients with PI <50° postoperatively were able to maintain better global alignment.

Level of Evidence: 3