bluuebunny/crossref_metadata_2025 huggingface dataset:
Exchange functionals based on finite uniform electron gases
Authors: Loos Pierre-François
Published: March 2017

We show how one can construct a simple exchange functional by extending the well-know local-density approximation (LDA) to finite uniform electron gases. This new generalized local-density approximation functional uses only two quantities: the electron density ρ and the curvature of the Fermi hole α. This alternative “rung 2” functional can be easily coupled with generalized-gradient approximation (GGA) functionals to form a new family of “rung 3” meta-GGA (MGGA) functionals that we have named factorizable MGGAs. Comparisons are made with various LDA, GGA, and MGGA functionals for atoms and molecules.
Effect of rotation on Jeans instability of magnetized radiative quantum plasma
Authors: Joshi H. , Pensia R. K.
Published: March 2017

The influence of rotation on the Jeans instability of homogeneous magnetized radiative quantum plasma is investigated. The basic equations of the problem are constructed and linearized by using the Quantum Magnetohydrodynamics (QMHD) model. The general dispersion relation is obtained by using the normal mode analysis technique, which is reduced for both the transverse and the longitudinal mode of propagations and further it is reduced for the axis of rotation parallel and perpendicular to the magnetic field. We found that the stabilizing effects of rotation are decreases for a strong magnetic field which is shown in the graphical representation. We also found that the quantum correction modified the condition of Jeans instability in both modes of propagation. The stabilizing effect of rotation is more increased in the presence of quantum correction.
Wetting at the nanoscale: A molecular dynamics study
Authors: Khalkhali Mohammad , Kazemi Nasser , Zhang Hao , Liu Qingxia
Published: March 2017

A novel method to calculate the solid-liquid contact angle is introduced in this study. Using the 3D configuration of a liquid droplet on a solid surface, this method calculates the contact angle along the contact line and provides an angular distribution. Although this method uses the 3D configuration of liquid droplets, it does not require the calculation of the 3D density profile to identify the boundaries of the droplet. This decreases the computational cost of the contact angle calculation greatly. Moreover, no presumption about the shape of the liquid droplet is needed when using the method introduced in this study. Using this method, the relationship between the size and the contact angle of water nano-droplets on a graphite substrate was studied. It is shown that the contact angle generally decreases by increasing the size of the nano-droplet. The microscopic contact angle of 83.0° was obtained for water on graphite which is in a good agreement with previous experimental and numerical studies. Neglecting other nanoscale effects which may influence the contact angle, the line tension of SPC/E (extended simple point charge model) water was calculated to be 3.6×10−11 N, which is also in good agreement with the previously calculated values.
Communication: Vibrational relaxation of CO(1Σ) in collision with Ar(1S) at temperatures relevant to the hypersonic flight regime
Authors: Denis-Alpizar Otoniel , Bemish Raymond J. , Meuwly Markus
Published: March 2017

Vibrational energy relaxation (VER) of diatomics following collisions with the surrounding medium is an important elementary process for modeling high-temperature gas flow. VER is characterized by two parameters: the vibrational relaxation time τvib and the state relaxation rates. Here the vibrational relaxation of CO(ν=0←ν=1) in Ar is considered for validating a computational approach to determine the vibrational relaxation time parameter (pτvib) using an accurate, fully dimensional potential energy surface. For lower temperatures, comparison with experimental data shows very good agreement whereas at higher temperatures (up to 25 000 K), comparisons with an empirically modified model due to Park confirm its validity for CO in Ar. Additionally, the calculations provide insight into the importance of Δν>1 transitions that are ignored in typical applications of the Landau–Teller framework.
Molecular weight dependence of the intrinsic size effect on Tg in AAO template-supported polymer nanorods: A DSC study
Authors: Askar Shadid , Wei Tong , Tan Anthony W. , Torkelson John M.
Published: March 2017

Many studies have established a major effect of nanoscale confinement on the glass transition temperature (Tg) of polystyrene (PS), most commonly in thin films with one or two free surfaces. Here, we characterize smaller yet significant intrinsic size effects (in the absence of free surfaces or significant attractive polymer-substrate interactions) on the Tg and fragility of PS. Melt infiltration of various molecular weights (MWs) of PS into anodic aluminum oxide (AAO) templates is used to create nanorods supported on AAO with rod diameter (d) ranging from 24 to 210 nm. The Tg (both as Tg,onset and fictive temperature) and fragility values are characterized by differential scanning calorimetry. No intrinsic size effect is observed for 30 kg/mol PS in template-supported nanorods with d = 24 nm. However, effects on Tg are present for PS nanorods with Mn and Mw ≥ ∼175 kg/mol, with effects increasing in magnitude with increasing MW. For example, in 24-nm-diameter template-supported nanorods, Tg, rod − Tg, bulk = −2.0 to −2.5 °C for PS with Mn = 175 kg/mol and Mw = 182 kg/mol, and Tg, rod − Tg, bulk = ∼−8 °C for PS with Mn = 929 kg/mol and Mw = 1420 kg/mol. In general, reductions in Tg occur when d ≤ ∼2Rg, where Rg is the bulk polymer radius of gyration. Thus, intrinsic size effects are significant when the rod diameter is smaller than the diameter (2Rg) associated with the spherical volume pervaded by coils in bulk. We hypothesize that the Tg reduction occurs when chain segment packing frustration is sufficiently perturbed by confinement in the nanorods. This explanation is supported by observed reductions in fragility with the increasing extent of confinement. We also explain why these small intrinsic size effects do not contradict reports that the Tg-confinement effect in supported PS films with one free surface exhibits little or no MW dependence.
Copropagation of coupled laser pulses in magnetized plasmas: Modulational instability and coupled solitons
Authors: Borhanian Jafar , Aghaei Golijan Hassan
Published: March 2017

The nonlinear propagation of two circularly polarized strong laser pulses in a magnetized plasma is considered. In a weakly relativistic regime, it is shown that the evolution of amplitudes of the laser pulses is governed by two coupled cubic nonlinear Schrödinger (NLS) equations. The modulational instability of coupled plane wave solutions is investigated based on coupled NLS equations. The dependence of the growth rate on relevant parameters of the system is addressed. The possibility of formation of various kinds of coupled solitary wave solutions in magnetized and unmagnetized cases is considered, and the variation of the profile of these solutions with different parameters is explored.
Cooperative enhancement of the nonlinear optical response in conjugated energetic materials: A TD-DFT study
Authors: Sifain Andrew E. , Tadesse Loza F. , Bjorgaard Josiah A. , Chavez David E. , Prezhdo Oleg V. , Scharff R. Jason , Tretiak Sergei
Published: March 2017

Conjugated energetic molecules (CEMs) are a class of explosives with high nitrogen content that posses both enhanced safety and energetic performance properties and are ideal for direct optical initiation. As isolated molecules, they absorb within the range of conventional lasers. Crystalline CEMs are used in practice, however, and their properties can differ due to intermolecular interaction. Herein, time-dependent density functional theory was used to investigate one-photon absorption (OPA) and two-photon absorption (TPA) of monomers and dimers obtained from experimentally determined crystal structures of CEMs. OPA scales linearly with the number of chromophore units, while TPA scales nonlinearly, where a more than 3-fold enhancement in peak intensity, per chromophore unit, is calculated. Cooperative enhancement depends on electronic delocalization spanning both chromophore units. An increase in sensitivity to nonlinear laser initiation makes these materials suitable for practical use. This is the first study predicting a cooperative enhancement of the nonlinear optical response in energetic materials composed of relatively small molecules. The proposed model quantum chemistry is validated by comparison to crystal structure geometries and the optical absorption of these materials dissolved in solution.
On the non-exponentiality of the dielectric Debye-like relaxation of monoalcohols
Authors: Arrese-Igor S. , Alegría A. , Colmenero J.
Published: March 2017

We have investigated the Debye-like relaxation in a series of monoalcohols (MAs) by broadband dielectric spectroscopy and thermally stimulated depolarization current techniques in order to get further insight on the time dispersion of this intriguing relaxation. Results indicate that the Debye-like relaxation of MAs is not always of exponential type and conforms well to a dispersion of Cole-Davidson type. Apart from the already reported non-exponentiality of the Debye-like relaxation in 2-hexyl-1-decanol and 2-butyl-1-octanol, a detailed analysis of the dielectric permittivity of 5-methyl-3-heptanol shows that this MA also presents some extent of dispersion on its Debye-like relaxation which strongly depends on the temperature. Results suggest that the non-exponential character of the Debye-like relaxation might be a general characteristic in the case of not so intense Debye-like relaxations relative to the α relaxation. Finally, we briefly discuss on the T-dependence and possible origin for the observed dispersion.
Detection of current induced spin polarization in epitaxial Bi2Te3 thin film
Authors: Dey Rik , Roy Anupam , Pramanik Tanmoy , Rai Amritesh , Heon Shin Seung , Majumder Sarmita , Register Leonard F. , Banerjee Sanjay K.
Published: March 2017

We electrically detect charge current induced spin polarization on the surface of a molecular beam epitaxy grown Bi2Te3 thin film in a two-terminal device with a ferromagnetic MgO/Fe contact and a nonmagnetic Ti/Au contact. The two-point resistance, measured in an applied magnetic field, shows a hysteresis tracking the magnetization of Fe. A theoretical estimate is obtained for the change in resistance on reversing the magnetization direction of Fe from coupled spin-charge transport equations based on the quantum kinetic theory. The order of magnitude and the sign of the hysteresis are consistent with the spin-polarized surface state of Bi2Te3.
Charge state switching of Cu acceptors in ZnO nanorods
Authors: Rahman M. Azizar , Westerhausen Mika T. , Nenstiel Christian , Choi Sumin , Hoffmann Axel , Gentle Angus , Phillips Matthew R. , Ton-That Cuong
Published: March 2017

Undoped and Ga-doped ZnO nanorods both exhibit an intense green luminescence (GL) band centered at ∼2.4 eV. Unlike the defect-related GL in undoped nanorods, the GL band in Ga-doped nanorods displays a periodic fine structure separated by 72 meV, which consists of doublets with an energy spacing of 30 ± 3 meV. The emergence of the structured GL is due to the Cu+ state being stabilized by the rise in the Fermi level above the 0/- (Cu2+/Cu+) charge transfer level as a result of Ga donor incorporation. From a combination of optical characterization and simulation using the Brownian oscillator model, the doublet fine structures are shown to originate from two hole transitions with the Cu+ state located at 390 meV above the valence band.
Analysis and experimental verification of neutron-activated LiF as a stable matrix for tritium beta sources
Authors: Nullmeyer Bradley R. , Kwon Jae W. , Gahl John M. , Dobey Ronald J. , Gunn Gregory , Flagg Michael , Herbold Carl
Published: March 2017

Tritium (3H) has long been considered a useful radioisotope for many purposes due to its low-energy and pure beta decay. However, due to its aggressive migration, solid-state retention of tritium for use as a beta radiation source is challenging. Bulk-level infusion of tritium in a solid is often employed as a solution to effusion and outgassing but limits the beta radiation output due to the use of high-Z materials. This letter presents experimental and simulated analysis regarding the production and efficacy of a low-Z, solid-state tritium beta source. Single-crystal lithium fluoride (LiF) is used as a host matrix for tritium radionuclides, which are generated by the 6Li(n,α)3H reaction when the crystal is exposed to thermal neutron irradiation. The experimental findings present negligible outgassing of tritium from the material, while the simulation results suggest thickness optimization of the LiF/3H beta source. Moreover, the simulation results indicate significantly enhanced beta output efficiency compared to palladium tritide, which is a state-of-the-art tritium host. With proper thickness, the tritium-filled LiF matrix is a stable low energy beta source, which can be easily produced and incorporated into a variety of applications.
Stress control of heterogeneous nanocrystalline diamond sphere through pressure-temperature tuning
Authors: Ding Wei , Han Jingjing , Hu Qiwei , Chen Yang , Liu Fangming , Liu Yinjuan , Gou Li , He Duanwei , Zhan Guodong
Published: March 2017

The hollow nanocrystalline diamond (NCD) sphere, a promising ablator material for inertial confinement fusion capsule, is generally fabricated by the chemical vapor deposition method. Herein, we report on a method to transform hydrogenated tetrahedral amorphous carbon coatings on spherical molybdenum (Mo) substrates into nanocrystalline diamond films via a designed high pressure high temperature (HPHT) treatment that balances the mismatch in the thermal expansion coefficient between a diamond coating and the Mo substrate through the difference in the bulk modulus. The results show that the density and strength of the diamond shell increase significantly and the residual stress is eliminated as well. The methodology of the designed HPHT treatment can not only provide an alternative way to fabricate NCD spheres but also can apply to other heterogeneous material stress control applications.
Design and analysis on fume exhaust system of blackbody cavity sensor for continuously measuring molten steel temperature
Authors: Mei Guohui , Zhang Jiu , Zhao Shumao , Xie Zhi
Published: March 2017

Fume exhaust system is the main component of the novel blackbody cavity sensor with a single layer tube, which removes the fume by gas flow along the exhaust pipe to keep the light path clean. However, the gas flow may break the conditions of blackbody cavity and results in the poor measurement accuracy. In this paper, we analyzed the influence of the gas flow on the temperature distribution of the measuring cavity, and then calculated the integrated effective emissivity of the non-isothermal cavity based on Monte-Carlo method, accordingly evaluated the sensor measurement accuracy, finally obtained the maximum allowable flow rate for various length of the exhaust pipe to meet the measurement accuracy. These results will help optimize the novel blackbody cavity sensor design and use it better for measuring the temperature of molten steel.
A modification of the arcsine–log calibration curve for analysing soil test value–relative yield relationships
Authors: Correndo Adrián A. , Salvagiotti Fernando , García Fernando O. , Gutiérrez-Boem Flavio H.
Published: March 2017

This article aims to discuss the arcsine–log calibration curve (ALCC) method designed for the Better Fertiliser Decisions for Cropping Systems (BFDC) to calibrate relationships between relative yield (RY) and soil test value (STV). Its main advantage lies in estimating confidence limits of the critical value (CSTV). Nevertheless, intervals for 95% confidence level are often too wide, and authors suggest a reduction in the confidence level to 70% in order to achieve narrower estimates. Still, this method can be further improved by modifying specific procedures. For this purpose, several datasets belonging to the BFDC were used. For any confidence level, estimates with the modified ALCC procedures were always more accurate than the original ALCC. The overestimation of confidence limits with the original ALCC was inversely related to the correlation coefficient of the dataset, which might allow a relatively simple and reliable correction of previous estimates. In addition, because the method is based on the correlation between STV and RY, the importance to test it for significance is emphasised in order to support the hypothesis of a relationship. Then, the modified ALCC approach could also allow a more reliable comparison of datasets by slopes of the bivariate linear relationship between transformed variables.
Predators and genetic fitness: key threatening factors for the conservation of a bettong species
Authors: Pacioni Carlo , Williams Matthew R. , Lacy Robert C. , Spencer Peter B. S. , Wayne Adrian F.
Published: March 2017

Globally, many wildlife species are declining and an increasing number are threatened by extinction or are extinct. Active management is generally required to mitigate these trends and population viability analysis (PVA) enables different scenarios to be evaluated and informs management decisions. Based on population parameters obtained from a threatened bettong, the woylie (Bettongia penicillata ogilbyi), we developed and validated a PVA model. We identified the demographic and genetic responses to different threatening factors and developed a general framework that would facilitate similar work in other bettong species. The two main threatening processes are predation by introduced animals and its interaction with reduced fitness (e.g. due to inbreeding depression or a disease). Although predation alone can drive a decline in certain circumstances (e.g. when predation success is independent from prey population density), synergistically, predation and reduced fitness can be particularly relevant, especially for small populations. The minimum viable population size was estimated at 1000–2000 individuals. In addition, the models identified that research into age-specific mortality rates and predation rates by introduced animals should be the focus of future work. The PVA model created here provides a basis to investigate threatening processes and management strategies in woylie populations and other extant bettong species, given the ecological and physiological similarities among these threatened species.
Numerosity representation is encoded in human subcortex
Authors: Collins Elliot , Park Joonkoo , Behrmann Marlene
Published: March 2017

Significance

Despite major neuroanatomical differences, adults, infants, nonhuman primates, and invertebrates possess the ability to evaluate relative quantities. Humans’ ability starts with coarse granularity (distinguishing ratios of numerical quantities of 3:1 or larger), but this becomes increasingly precise over development. This series of experiments demonstrates a role of the subcortex in discriminating numerosities in larger (4:1 or 3:1), but not in smaller ratios. These findings map onto the precision with which newborns evaluate number. Combined with evidence from the development of numerical skills, this study implicates the human subcortex as a possible source of core number knowledge that is both related to phylogenetic numerical competence and serves as the foundation on which more complex ontogenetic numerical skills may be built.
Potent neuroprotection after stroke afforded by a double-knot spider-venom peptide that inhibits acid-sensing ion channel 1a
Authors: Chassagnon Irène R. , McCarthy Claudia A. , Chin Yanni K.-Y. , Pineda Sandy S. , Keramidas Angelo , Mobli Mehdi , Pham Vi , De Silva T. Michael , Lynch Joseph W. , Widdop Robert E. , Rash Lachlan D. , King Glenn F.
Published: March 2017

Significance

Six million people die each year from stroke, and 5 million survivors are left with a permanent disability. Moreover, the neuronal damage caused by stroke often triggers a progressive decline in cognitive function that doubles the risk of dementia for stroke survivors. Despite this massive global disease burden, there are no approved drugs for treating the neuronal injury caused to the brain by the oxygen deprivation occurring during an ischemic stroke. The precipitous drop in brain pH resulting from stroke activates acid-sensing ion channel 1a. We show that inhibition of these channels using a “double-knot” spider venom peptide massively attenuates brain damage after stroke and improves behavioral outcomes, even when the peptide is administered 8 h after stroke onset.
Structure of a headful DNA-packaging bacterial virus at 2.9 Å resolution by electron cryo-microscopy
Authors: Zhao Haiyan , Li Kunpeng , Lynn Anna Y. , Aron Keith E. , Yu Guimei , Jiang Wen , Tang Liang
Published: March 2017

Significance

The enormous prevalence of tailed double-stranded DNA bacteriophages on this planet is made possible by highly efficient self-assembly of usually hundreds of protein subunits into highly stable capsids. These capsids must stand with an internal pressure as a result of the phage DNA-packaging process. Here we report the complete atomic model of the headful DNA-packaging bacteriophage Sf6 at 2.9 Å resolution determined by electron cryo-microscopy. The structure reveals the DNA-inflated, tensed state of a robust yet flexible protein shell assembled via noncovalent interactions, enabled by remarkable global conformational polymorphism of capsid proteins, a network formed by extended N arms, and abundant β-sheet–like mainchain:mainchain intermolecular interactions. The assembly mechanism may be common among tailed DNA phages and herpesviruses.
Neuroendocrine androgen action is a key extraovarian mediator in the development of polycystic ovary syndrome
Authors: Caldwell Aimee S. L. , Edwards Melissa C. , Desai Reena , Jimenez Mark , Gilchrist Robert B. , Handelsman David J. , Walters Kirsty A.
Published: March 2017

Significance

The cause of polycystic ovary syndrome (PCOS) is unknown, but androgen excess is a key feature. We combined a hyperandrogenized PCOS mouse model with global and tissue- and cell-specific androgen-resistant mouse lines to uncover the sites of androgen action that initiate PCOS. We demonstrate that direct androgen actions, particularly in neurons but less so in granulosa cells, are required for the development of key reproductive and metabolic PCOS features. These data highlight the previously overlooked importance of extraovarian neuroendocrine androgen action in the origins of PCOS. Targeting androgen-driven mechanisms may represent new options for developing a mechanism-based treatment of PCOS.
Molecular interactions and inhibition of the staphylococcal biofilm-forming protein SdrC
Authors: Feuillie Cécile , Formosa-Dague Cécile , Hays Leanne M. C. , Vervaeck Ophélie , Derclaye Sylvie , Brennan Marian P. , Foster Timothy J. , Geoghegan Joan A. , Dufrêne Yves F.
Published: March 2017

Significance

The bacterial pathogenStaphylococcus aureusshows a remarkable ability to aggregate, thereby contributing to the formation of cellular communities that are difficult to eradicate. In this study, we dissect the homophilic interactions at play duringS. aureuscell–cell adhesion, focusing on the key surface protein SdrC. We discover that SdrC is engaged in low-affinity homophilic bonds that promote intercellular adhesion, and that it also favors strong hydrophobic interactions with surfaces, emphasizing that this protein is a multifunctional adhesin. We also show that SdrC-dependent cell-surface attachment, cell–cell adhesion, and biofilm formation can be efficiently blocked by a peptide, thus suggesting this approach could be used for antibiofilm therapy.
Recurrent rewiring and emergence of RNA regulatory networks
Authors: Wilinski Daniel , Buter Natascha , Klocko Andrew D. , Lapointe Christopher P. , Selker Eric U. , Gasch Audrey P. , Wickens Marvin
Published: March 2017

Significance

Regulatory networks change during evolution. A protein that controls many genes in one species may control a different set of genes in another. We examined how mRNA networks evolve, focusing on the PUF (Pumilio and FBF) family of RNA-binding proteins. These govern stability and translation of hundreds of mRNAs and enable coordinate regulation of discrete biological outcomes. To understand how RNA networks evolve, we used knowledge of the RNA specificity of each PUF protein to predict its mRNA targets and directly identified mRNAs bound to each protein in divergent fungi via biochemical methods. We find networks controlled by one protein switch during evolution to be controlled by another and that proteins with different specificities can share, gain, or lose batteries of mRNAs.
Structure of the infectious salmon anemia virus receptor complex illustrates a unique binding strategy for attachment
Authors: Cook Jonathan D. , Sultana Azmiri , Lee Jeffrey E.
Published: March 2017

Significance

The infectious salmon anemia virus (ISAV), an aquatic pathogen with lethal hemorrhagic potential, decimates farmed and freshwater fish populations globally. Here, we determined the crystallographic structures of the hemagglutinin-esterase (HE) viral glycoprotein responsible for the dynamic attachment of the virus to its receptor in Atlantic salmon. We identified surface features of ISAV HE that are conserved across isolates known to cause significant economic burden to fisheries worldwide. This provides a molecular blueprint for the design of a broadly protective vaccine. Furthermore, we showed that ISAV HE has a distinct receptor recognition strategy from those of other influenza-like viruses and coronaviral HE proteins, contributing to our understanding of the diversity of viral entry mechanisms.
Identification of a putative binding site critical for general anesthetic activation of TRPA1
Authors: Ton Hoai T. , Phan Thieu X. , Abramyan Ara M. , Shi Lei , Ahern Gerard P.
Published: March 2017

Significance

General anesthetics are an important class of drugs that suppress the activity of neurons in the brain to produce reversible unconsciousness. In addition, several general anesthetics, including the intravenous drug, propofol, and the inhaled gas, isoflurane, cause pain/irritation upon administration and a reduction in blood pressure. These side effects arise from activation of the transient receptor potential ankyrin repeat 1 (TRPA1) ion channel but the underlying mechanisms are unknown. In this study we identify a potential binding pocket for propofol and isoflurane, including several critical amino acid residues, located in the channel pore region of TRPA1. These results confirm an important role for the pore region in regulating channel activity. Further, the information may be useful in designing drugs to counter anesthetic-mediated activation of TRPA1.
Three-dimensional culture system identifies a new mode of cetuximab resistance and disease-relevant genes in colorectal cancer
Authors: Li Cunxi , Singh Bhuminder , Graves-Deal Ramona , Ma Haiting , Starchenko Alina , Fry William H. , Lu Yuanyuan , Wang Yang , Bogatcheva Galina , Khan Mohseen P. , Milne Ginger L. , Zhao Shilin , Ayers Gregory Daniel , Li Nenggan , Hu Huaying , Washington Mary Kay , Yeatman Timothy J. , McDonald Oliver G. , Liu Qi , Coffey Robert J.
Published: March 2017

Significance

By culturing a human colorectal cancer (CRC) cell line (HCA-7) in 3D, we have generated two cell lines (CC and SC) with distinct morphological, genetic, biochemical, and functional properties. Using this 3D system, we have discovered that increased tyrosine phosphorylation of MET and RON results in cetuximab resistance in the SC cell line that can be overcome by addition of the dual MET/RON tyrosine kinase inhibitor, crizotinib. We have also identified that increased epithelial, but not stromal, versican staining correlates with reduced survival in a clinically annotated CRC tissue microarray.
High-capacity, low-tortuosity, and channel-guided lithium metal anode
Authors: Zhang Ying , Luo Wei , Wang Chengwei , Li Yiju , Chen Chaoji , Song Jianwei , Dai Jiaqi , Hitz Emily M. , Xu Shaomao , Yang Chunpeng , Wang Yanbin , Hu Liangbing
Published: March 2017

Significance

Li metal is considered as the “Holy Grail” anode for Li batteries due to its highest theoretical capacity and lowest electrochemical potential. However, the infinite volume change during the Li stripping/plating process would lead to issues like solid electrolyte interphase cracks and Li dendrites. This work describes a high-capacity and low-tortuosity Li metal anode, which was prepared by infusing molten Li into carbonized wood channels. The straight channels of carbonized wood acting as an ideal host can effectively accommodate the Li volume change, which delivered a lower overpotential and better cycling performance compared with bare Li metal. This work demonstrated the importance of structure design, especially low-tortuosity Li metal structure, for enabling Li metal anode in high-energy batteries.
Discovery of
scmR
as a global regulator of secondary metabolism and virulence in
Burkholderia thailandensis
E264
Authors: Mao Dainan , Bushin Leah B. , Moon Kyuho , Wu Yihan , Seyedsayamdost Mohammad R.
Published: March 2017

Significance

Silent biosynthetic gene clusters represent fertile grounds for the discovery of new small molecules, and a number of approaches have been developed for activating them. Their regulation, however, has received far less attention, especially in Gram-negative bacteria. Here, we show that a LysR-type transcriptional regulator, which we name
scmR
, acts as a gatekeeper of secondary metabolism and virulence in the model organism
Burkholderia thailandensis
E264. Specifically, genetic, chemical, and “omics”-based approaches unveil ScmR as a master regulator that interacts with pathway-specific transcriptional regulators to control, and primarily suppress, secondary metabolism. Because this gene is conserved in other
Burkholderia
species, our results suggest that
scmR
-mediated control of secondary metabolism and virulence may be common within this genus and the
Pseudomallei
-group pathogens.
In vivo optophysiology reveals that G-protein activation triggers osmotic swelling and increased light scattering of rod photoreceptors
Authors: Zhang Pengfei , Zawadzki Robert J. , Goswami Mayank , Nguyen Phuong T. , Yarov-Yarovoy Vladimir , Burns Marie E. , Pugh Edward N.
Published: March 2017

Significance

Complete activation of the phototransduction G-protein cascade of dark-adapted rod photoreceptors causes outer segments to undergo 10% elongation and large local increases in backscattering, as measured in vivo with noninvasive, high-resolution optical coherence tomography. Maximal elongation is caused by a potentially harmful 20% increase in internal osmotic pressure generated by excess osmolytes arising from phototransduction. The light-stimulated elongation and backscattering responses can be explained by an osmo-elastic model of cytoplasmic swelling, combined with changes in refractive index consequent to the swelling and translocation of the G-protein subunits into the cytosol. Disease conditions that affect the structural integrity of rods may cause them to be especially vulnerable to osmotic stress caused by bright light.
Genetic disruption of oncogenic Kras sensitizes lung cancer cells to Fas receptor-mediated apoptosis
Authors: Mou Haiwei , Moore Jill , Malonia Sunil K. , Li Yingxiang , Ozata Deniz M. , Hough Soren , Song Chun-Qing , Smith Jordan L. , Fischer Andrew , Weng Zhiping , Green Michael R. , Xue Wen
Published: March 2017

Significance

Oncogenic
KRAS
underlies 30–90% of lung, colon, and pancreatic cancers, but despite more than 30 y of research, clinical inhibitors of KRAS—and potential resistance mechanisms—remain elusive. Using CRISPR-mediated genome editing of oncogenic
Kras
, we show that some lung cancer cells can survive
Kras
knockout, indicating the existence of mechanisms that allow tumors to escape Kras oncogene addiction. We identify genes highly expressed in Kras knockout cells, including the Fas receptor gene. Antibodies that activate Fas receptor selectively induced apoptosis in Kras-independent lung cancer cells, suggesting a potential strategy for combinatorial therapies against Kras-driven tumors. These findings have direct translational implications for the treatment of lung cancer and other KRAS mutant cancer types.
Self-identity reprogrammed by a single residue switch in a cell surface receptor of a social bacterium
Authors: Cao Pengbo , Wall Daniel
Published: March 2017

Significance

How individuals identify self (clonemates) in heterogeneous populations is a fundamental biological question. Here, we propose a mechanism by which
Myxococcus xanthus
, an aggregative multicellular bacterium, uses a cell surface adhesin to recognize clonemates. Cells selectively bind to other individuals that bear identical or nearly identical receptors. The social outcome of recognition includes bulk sharing of private cellular goods between cells. We reveal the malleable nature of this receptor that provides recognition selectivity among wild populations of myxobacteria. This is an example where single residue substitution can govern the decision for how microbes physically and socially interact.
Triad of human cellular proteins, IRF2, FAM111A, and RFC3, restrict replication of orthopoxvirus SPI-1 host-range mutants
Authors: Panda Debasis , Fernandez Daniel J. , Lal Madhu , Buehler Eugen , Moss Bernard
Published: March 2017

Significance

Viruses are important causes of human disease and provide tools for understanding host immune defense mechanisms. Poxviruses are good models for probing the immune system because many replicate well in human cells, some cause severe disease, and nearly half of the 200 viral genes are devoted to host interactions. The virus/host equilibrium can be perturbed by mutating a viral gene and restored by suppressing the opposing host genes. To find relevant host genes for one such poxvirus mutation, we used a high-throughput human genome-wide RNAi screen and monitored virus spread. Three proteins were identified: Two participate in processive DNA replication and another activates transcription of one of the DNA replication proteins to form a putative antiviral network.
Species richness alone does not predict cultural ecosystem service value
Authors: Graves Rose A. , Pearson Scott M. , Turner Monica G.
Published: March 2017

Significance

Sustaining biodiversity and ecosystem services are common conservation goals. However, understanding relationships between biodiversity and cultural ecosystem services (CES) and determining the best indicators to represent CES remain crucial challenges. We combined ecological and social data to compare CES value of wildflower communities based on observed species richness versus revealed social preferences. Using a discrete-choice experiment with images of wildflower communities, we analyzed which aspects of biodiversity were associated with the aesthetic preferences of forest visitors. Although commonly used to indicate biodiversity-based CES, species richness did not predict aesthetic preference. This study suggests that successful management of CES requires understanding stakeholders’ preferences to determine conservation priorities.
“Contesting the Cynicism of Neoliberalism”
Authors: Liu Ming
Published: March 2017

This article aims to expose the hegemony of neoliberalism in media discourse through a corpus-assisted discourse study of the representations of the Sino-US currency dispute in two newspapers –China Daily(CD) from China andThe New York Times(NYT) from the US. The findings suggest that while neoliberal ideology can be identified in both CD and NYT, it is articulated and appropriated differently in the two newspapers to construct their respective stance towards the issue. Neoliberal beliefs are found pervading different levels of discourse (i.e., thematic, lexical and grammatical) in NYT to construct a combative stance towards China’s exchange rate policies. However, the hegemony of neoliberalism can also be detected through CD’s ambivalent stance towards change and the seemingly contradictory evaluation of the impact of exchange rate changes.
Uzbek re-modeled
Authors: Catedral Lydia
Published: March 2017

This study investigates the relationship between Russian language use and language planning in the context of newly independent, post-soviet Uzbekistan (1991–1992). It is guided by the question:In what ways does the use of Russian loanwords in Uzbek language newspapers accomplish language planning in newly independent Uzbekistan?The main finding from this analysis is that post-independence use of Russian loanwords from particular semantic classes in particular contexts reinforce overtly stated ideologies about Russian and construct difference between soviet Uzbekistan and independent Uzbekistan. These findings demonstrate the need to reexamine the role of Russian language in post-soviet contexts, and they contribute a unique approach to analyzing links between lexical items and ideology in language planning.
Democratic peace as global errand
Authors: Dunmire Patricia L.
Published: March 2017

Focusing on the foreign policy discourse of George H. W. Bush and William Clinton, I examine the role the American jeremiad played in conceptualizing the geopolitical change initiated by the ending of the Cold War. I identify “extending the democratic peace” as the nation’s post-Cold War “errand” and argue that this global mission represented the contemporary “re-dedication” of American policy to the nation’s “divine cause.” I demonstrate that a key issue facing the nation was whether the U.S. would reap the benefits of its Cold War victory by extending its political-economic system globally or whether it would turn inward and, thereby, give rein of the future to the forces of “anarchy” and chaos.” As with earlier renditions of the jeremiad, the post-Cold War variant turned this liminal moment into a “mode of socialization” (Bercovitch 2012, 25) by deploying the concept of democratic peace to legitimate an interventionist foreign policy.
Reduction in hydroxyhydroquinone from coffee increases postprandial fat utilization in healthy humans: a randomized double-blind, cross-over trial
Authors: Soga Satoko , Ota Noriyasu , Shimotoyodome Akira
Published: March 2017

The present study aimed to clarify the effect of reduction in hydroxyhydroquinone (HHQ) from roasted coffee on energy utilization in humans. Indirect calorimetry showed that one-week ingestion of HHQ-reduced coffee led to significantly higher postprandial fat utilization than that of HHQ-containing coffee. This finding indicates that reduction in HHQ from coffee increases postprandial fat utilization.
The preferred viewing location in top-to-bottom sentence reading
Authors: Johnson Rebecca L , Starr Emma L
Published: March 2017

The preferred viewing location (PVL) is a robust finding in research on reading that when fixating on a word during normal sentence reading, readers tend to land slightly to the left of the center of the word. This is in contrast to the optimal viewing location in single word recognition, which falls at the center of the word. This study outlines the history of the PVL in eye tracking since Rayner’s 1979 original study, documenting the origins of the conflicting theoretical explanations. In addition, a new study is reported examining whether the PVL can be attributed solely to oculomotor error or a processing advantage by using an experimental manipulation that separates tracking direction (left-to-right reading) and landing position (left-to-right within a word). Sentences were presented to participants from the top to the bottom of a computer screen with one word per line while eye movements were recorded. In this presentation format, readers continued to land to the left of center, suggesting that the PVL in normal reading is not solely due to oculomotor error.
The Rab7 effector PLEKHM1 binds Arl8b to promote cargo traffic to lysosomes
Authors: Marwaha Rituraj , Arya Subhash B. , Jagga Divya , Kaur Harmeet , Tuli Amit , Sharma Mahak
Published: March 2017

Endocytic, autophagic, and phagocytic vesicles move on microtubule tracks to fuse with lysosomes. Small GTPases, such as Rab7 and Arl8b, recruit their downstream effectors to mediate this transport and fusion. However, the potential cross talk between these two GTPases is unclear. Here, we show that the Rab7 effector PLEKHM1 simultaneously binds Rab7 and Arl8b, bringing about clustering and fusion of late endosomes and lysosomes. We show that the N-terminal RUN domain of PLEKHM1 is necessary and sufficient for interaction with Arl8b and its subsequent localization to lysosomes. Notably, we also demonstrate that Arl8b mediates recruitment of HOPS complex to PLEKHM1-positive vesicle contact sites. Consequently, Arl8b binding to PLEKHM1 is required for its function in delivery and, therefore, degradation of endocytic and autophagic cargo in lysosomes. Finally, we also show that PLEKHM1 competes with SKIP for Arl8b binding, which dictates lysosome positioning. These findings suggest that Arl8b, along with its effectors, orchestrates lysosomal transport and fusion.
Tensin links energy metabolism to extracellular matrix assembly
Authors: Dornier Emmanuel , Norman Jim C.
Published: March 2017

The regulation of integrin function is key to fundamental cellular processes, including cell migration and extracellular matrix (ECM) assembly. In this issue, Georgiadou et al. (2017. J. Cell Biol. https://doi.org/10.1083/jcb.201609066) report that the metabolic sensor adenosine monophosphate–activated protein kinase influences tensin production to regulate α5β1-integrin and fibrillar adhesion assembly and thus reveal an important connection between energy metabolism and ECM assembly.
CMDR based differential evolution identifies the epistatic interaction in genome-wide association studies
Authors: Yang Cheng-Hong , Chuang Li-Yeh , Lin Yu-Da
Published: March 2017

Motivation

Detecting epistatic interactions in genome-wide association studies (GWAS) is a computational challenge. Such huge numbers of single-nucleotide polymorphism (SNP) combinations limit the some of the powerful algorithms to be applied to detect the potential epistasis in large-scale SNP datasets.

Approach

We propose a new algorithm which combines the differential evolution (DE) algorithm with a classification based multifactor-dimensionality reduction (CMDR), termed DECMDR. DECMDR uses the CMDR as a fitness measure to evaluate values of solutions in DE process for scanning the potential statistical epistasis in GWAS.

Results

The results indicated that DECMDR outperforms the existing algorithms in terms of detection success rate by the large simulation and real data obtained from the Wellcome Trust Case Control Consortium. For running time comparison, DECMDR can efficient to apply the CMDR to detect the significant association between cases and controls amongst all possible SNP combinations in GWAS.

Availability and Implementation

DECMDR is freely available at https://goo.gl/p9sLuJ.

Supplementary information

Supplementary data are available at Bioinformatics online.
Inhibition of the P2X7–PANX1 complex suppresses spreading depolarization and neuroinflammation
Authors: Chen Shih-Pin , Qin Tao , Seidel Jessica L. , Zheng Yi , Eikermann Matthias , Ferrari Michel D. , van den Maagdenberg Arn M. J. M. , Moskowitz Michael A. , Ayata Cenk , Eikermann-Haerter Katharina
Published: March 2017

Spreading depolarization is a wave of neuronal and glial depolarization. Within minutes after spreading depolarization, the neuronal hemichannel pannexin 1 (PANX1) opens and forms a pore complex with the ligand-gated cation channel P2X7, allowing the release of excitatory neurotransmitters to sustain spreading depolarization and activate neuroinflammation. Here, we explore the hypothesis that the P2X7–PANX1 pore complex is a critical determinant of spreading depolarization susceptibility with important consequences for neuroinflammation and trigeminovascular activation. We found that genetic loss of function or ablation of the P2x7 gene inhibits spreading depolarization. Moreover, pharmacological suppression of the P2X7–PANX1 pore complex inhibits spreading depolarization in mice carrying the human familial hemiplegic migraine type 1 R192Q missense mutation as well as in wild-type mice and rats. Pore inhibitors elevate the electrical threshold for spreading depolarization, and reduce spreading depolarization frequency and amplitude. Pore inhibitors also suppress downstream consequences of spreading depolarization such as upregulation of interleukin-1 beta, inducible nitric oxide synthase and cyclooxygenase-2 in the cortex after spreading depolarization. In addition, they inhibit surrogates for trigeminovascular activation, including expression of calcitonin gene-related peptide in the trigeminal ganglion and c-Fos in the trigeminal nucleus caudalis. Our results are consistent with the hypothesis that the P2X7–PANX1 pore complex is a critical determinant of spreading depolarization susceptibility and its downstream consequences, of potential relevance to its signature disorders such as migraine.
The commons tragedy in the North Sea brown shrimp fishery: how horizontal institutional interactions inhibit a self-governance structure
Authors: Steenbergen Josien , Trapman Brita K. , Steins Nathalie A. , Poos Jan Jaap
Published: March 2017

Self-regulation is now widely regarded as an effective mechanism for collective action aimed at sustainable management of common pool resources. The brown shrimp (Crangon crangon) fishing industry in the Netherlands has been working on the implementation of a self-management strategy since 2007, as part of its ambition to get certified to the Marine Stewardship Council standard. Part of the self-management strategy is the development of a harvest control rule for reducing fishing effort when catches are low. Until recently, these attempts failed. The failure of the initiatives for self-management is examined within Ostrom’s nested framework for understanding institutions for managing resource use. This framework emphasises the importance of strong vertical embeddedness of institutional arrangements for resource (co)management. Our analysis shows that, despite a strong vertical embeddedness, mismatches between different institutional frameworks at the same level (horizontal interaction) affect the performance of self-management at the organizational level. This inhibits the resource users’ collective actions to self-manage their brown shrimp fishery, leading to a potential commons tragedy.