bluuebunny/crossref_metadata_2025 huggingface dataset:
Ion aggregation in high salt solutions. VI. Spectral graph analysis of chaotropic ion aggregates
Authors: Choi Jun-Ho , Cho Minhaeng
Published: November 2016

Carrying out molecular dynamics simulations and graph theoretical analyses of high salt solutions, and comparing numerically calculated vibrational spectroscopic properties of water with femtosecond IR pump-probe experimental data, we have recently found that ions in high salt solutions can form two morphologically different ion aggregate structures. In the cases of NaCl solutions, Na+ and Cl− tend to form compact cluster-like ion aggregate in high NaCl solutions. In contrast, K+ and SCN− form spatially extended network-like ion aggregates that also exhibit a percolating network behavior. Interestingly, a variety of graph theoretical properties of ion network in high KSCN solutions were found to be very similar to those of water H-bonding network. It was shown that spatially extended ion networks in high KSCN solutions are completely intertwined with water H-bonding networks, which might be the key to understand the high solubility of thiocyanate salts in water. Here, we further consider two salts that have been extensively studied experimentally by using femtosecond IR pump-probe technique, which are NaClO4 and NaBF4. Note that ClO4− and BF4− are well-known chaotropic ions that have been believed to behave as water structure breaker. To understand how such chaotropic ions affect water H-bonding structure, we carried out spectral graph analyses of molecular dynamics simulation data of these aqueous solutions. Graph spectra and degree distribution of ion aggregates formed in high NaBF4 and NaClO4 solutions show that these chaotropic anions also have a strong propensity to form ion networks. The fact that salts containing chaotropic ions like SCN−, BF4−, and ClO4− have very high solubility limits in water could then be related to our observation that these chaotropic anions with counter cations in high salt solutions are capable of forming intricate ion networks intertwined with water H-bonding networks. We anticipate that the present graph theoretical analysis method would be of use in further studying both various anomalous behaviors of interfacial water and fundamental physical chemistry of mixing and salt solubility in water.
Design and experiments of a linear piezoelectric motor driven by a single mode
Authors: Liu Zhen , Yao Zhiyuan , Li Xiang , Fu Qianwei
Published: November 2016

In this contribution, we propose a novel linear piezoelectric motor with a compact stator that is driven by a single mode. The linear piezoelectric motor can realize bidirectional motion by changing the vibration modes of the stator. Finite element analysis is performed to determine the required vibration mode of the stator and obtain the optimal stator structure and dimensions. Furthermore, the trajectories of the driving foot are analyzed with and without consideration of the mechanical contact with the slider. It is shown that the trajectory of the driving foot is an oblique line when disregarding the contact, and the trajectory becomes an oblique ellipse while taking into account the contact. Finally, a prototype of the motor is fabricated based on the results of finite element analysis. The optimization results show that the motor reaches its maximum thrust force of 4.0 kg, maximum thrust–weight ratio of 33.3, maximum unloaded velocity of 385 mm/s under the excitation of Mode-B, and maximum unloaded velocity of 315 mm/s under the excitation of Mode-L.
Braid group representations from a deformation of the harmonic oscillator algebra
Authors: Tarlini M.
Published: November 2016

We describe a new technique to obtain representations of the braid group Bn from the ℜ–matrix of a quantum deformed algebra of the one dimensional harmonic oscillator. We consider the action of the ℜ–matrix not on the tensor product of representations of the algebra, that in the harmonic oscillator case are infinite dimensional, but on the subspace of the tensor product corresponding to the lowest weight vectors.
High current density 2D/3D MoS2/GaN Esaki tunnel diodes
Authors: Krishnamoorthy Sriram , Lee Edwin W. , Lee Choong Hee , Zhang Yuewei , McCulloch William D. , Johnson Jared M. , Hwang Jinwoo , Wu Yiying , Rajan Siddharth
Published: November 2016

The integration of two-dimensional materials such as transition metal dichalcogenides with bulk semiconductors offer interesting opportunities for 2D/3D heterojunction-based device structures without any constraints of lattice matching. By exploiting the favorable band alignment at the GaN/MoS2 heterojunction, an Esaki interband tunnel diode is demonstrated by transferring large area Nb-doped, p-type MoS2 onto heavily n-doped GaN. A peak current density of 446 A/cm2 with repeatable room temperature negative differential resistance, peak to valley current ratio of 1.2, and minimal hysteresis was measured in the MoS2/GaN non-epitaxial tunnel diode. A high current density of 1 kA/cm2 was measured in the Zener mode (reverse bias) at −1 V bias. The GaN/MoS2 tunnel junction was also modeled by treating MoS2 as a bulk semiconductor, and the electrostatics at the 2D/3D interface was found to be crucial in explaining the experimentally observed device characteristics.
Thermometry of plasmonic nanostructures by anti-Stokes electronic Raman scattering
Authors: Xie Xu , Cahill David G.
Published: November 2016

Measurements of temperature of optically excited plasmonic nanostructures are needed to evaluate their functionality and thermal stability. Here, we describe a simple, accurate, and non-invasive thermometry based on anti-Stokes electronic Raman scattering. We validate the approach using an array of uniformly heated Au nanodisks and perform experiments on the heating of individual nanodisk by a focused laser beam. The steady-state temperature rise of an individual nanodisk has comparable contributions from the thermal conductance of the Au/quartz interface and heat spreading in the quartz substrate. The temperature measurements have an accuracy of 3% of the absolute temperature in the range of temperatures 300 < T < 700 K.
Giant many-body effects in liquid ammonia absorption spectrum
Authors: Ziaei Vafa , Bredow Thomas
Published: November 2016

In the present work, we accurately calculate the absorption spectrum of liquid ammonia up to 13 eV using many-body perturbation approach. The electronic bandgap of liquid NH3 is perfectly described as the combination of density functional theory, Coulomb-hole screened exchange, and G0W0 approximation to the electronic self-energy, yielding a direct gap (Γ → Γ) of 7.71 eV, fully consistent with the experimentally measured gap from photo-emission spectroscopy. With respect to the NH3 optical properties, the entire spectrum in particular the low lying first absorption band is extremely affected by electron-hole interactions, leading to a fundamental redistribution of spectral weights of the independent-particle spectrum. Three well separated but broad main peaks are identified at 7.0, 9.8, and 11.8 eV with steadily increasing intensities in excellent agreement with the experimental data. Furthermore, we observe a giant net blue-shift of the first absorption peak of about 1.4 eV from gaseous to liquid phase as the direct consequence of many-body effects, allowing the associated liquid ammonia absorption band exciton to delocalize and feel more effectively the repulsion effects imposed by the surrounding solvent shells. Further, the spectrum is insensitive to the coupling of resonant and anti-resonant contributions. Concerning electronic response structure of liquid NH3, it is most sensitive to excitations at energies lower than its electronic gap.
Regularization of Kepler problem in κ-spacetime
Authors: Guha Partha , Harikumar E. , Zuhair N. S.
Published: November 2016

In this paper, we regularize the Kepler problem on κ-spacetime in several different ways. First, we perform a Moser-type regularization and then we proceed for the Ligon-Schaaf regularization to our problem. In particular, generalizing Heckman and de Laat [J. Symplectic Geom. 10, 463-473 (2012)] in the noncommutative context, we show that the Ligon-Schaaf regularization map following from an adaptation of the Moser regularization can be generalized to the Kepler problem on κ-spacetime.
Intermolecular interactions of oligothienoacenes: Do S⋯S interactions positively contribute to crystal structures of sulfur-containing aromatic molecules?
Authors: Tsuzuki Seiji , Orita Hideo , Sato Naoki
Published: November 2016

Intermolecular interactions in the crystals of tetra- and penta-thienoacene were studied using ab initio molecular orbital calculations for evaluating the magnitude of characteristic S⋯S interactions with great attention paid to their origin. The interactions between the π-stacked neighboring molecules are significantly greater than those between the neighboring molecules exhibiting the S⋯S contact, although it has sometimes been claimed that the S⋯S interactions play important roles in adjusting the molecular arrangement of sulfur-containing polycyclic aromatic molecules in the crystals owing to short S⋯S contacts. The coupled cluster calculations with single and double substitutions with noniterative triple excitation interaction energies at the basis set limit estimated for the π-stacked and S⋯S contacted neighboring molecules in the tetrathienoacene crystal are −11.17 and −4.27 kcal/mol, respectively. Those for π-stacked molecules in the pentathienoacene crystal is −14.38 kcal/mol, while those for S⋯S contacted molecules are −7.02 and −6.74 kcal/mol. The dispersion interaction is the major source of the attraction between the π-stacked and S⋯S contacted molecules, while the orbital-orbital interactions are repulsive: The orbital-orbital interactions, which are significant for charge carrier transport properties, are not much more than the results of the short S⋯S contact caused by the strong dispersion interactions. Besides, the intermolecular interaction energy calculated for a trithienoacene dimer has strong orientation dependence.
A first-principles study of the SnO2 monolayer with hexagonal structure
Authors: Xiao Wen-Zhi , Xiao Gang , Wang Ling-Ling
Published: November 2016

We report the structural, electronic, magnetic, and elastic properties of a two-dimensional (2D) honeycomb stannic oxide (SnO2) monolayer based on comprehensive first-principles calculations. The free-standing and well-ordered 2D centered honeycomb SnO2 (T-SnO2) monolayer with D3d point-group symmetry has good dynamical stability, as well as thermal stability at 500 K. The T-SnO2 monolayer is a nonmagnetic wide-bandgap semiconductor with an indirect bandgap of 2.55/4.13 eV obtained by the generalized gradient approximation with the Perdew–Burke–Ernzerhof/Heyd–Scuseria–Ernzerhof hybrid functional, but it acquires a net magnetic moment upon creation of a Sn vacancy defect. The elastic constants obtained from the relaxed ion model show that the T-SnO2 monolayer is much softer than MoS2. The bandgap monotonically decreases with increasing strain from −8% to 15%. An indirect-to-direct bandgap transition occurs upon applying biaxial strain below −8%. Synthesis of the T-SnO2 monolayer is proposed. We identify the Zr(0001) surface as being suitable to grow and stabilize the T-SnO2 monolayer. The unique structure and electronic properties mean that the T-SnO2 monolayer has promising applications in nanoelectronics. We hope that the present study on the stable free-standing SnO2 monolayer will inspire researchers to further explore its importance both experimentally and theoretically.
Polymer translocation through nanopore into active bath
Authors: Pu Mingfeng , Jiang Huijun , Hou Zhonghuai
Published: November 2016

Polymer translocation through nanopores into a crowded environment is of ubiquitous importance in many biological processes. Here we investigate polymer translocation through a nanopore into an active bath of self-propelled particles in two-dimensional space using Langevin dynamics simulations. Interestingly, we find that the mean translocation time τ can show a bell-shape dependence on the particle activity Fa at a fixed volume fraction ϕ, indicating that the translocation process may become slower for small activity compared to the case of the passive media, and only when the particle activity becomes large enough can the translocation process be accelerated. In addition, we also find that τ can show a minimum as a function of ϕ if the particle activity is large enough, implying that an intermediate volume fraction of active particles is most favorable for the polymer translocation. Detailed analysis reveals that such nontrivial behaviors result from the two-fold effect of active bath: one that active particles tend to accumulate near the pore, providing an extra pressure hindering the translocation, and the other that they also aggregate along the polymer chain, generating an effective pulling force accelerating the translocation. Such results demonstrate that active bath plays rather subtle roles on the polymer translocation process.
Discriminating between surface and bulk recombination in organic solar cells by studying the thickness dependence of the open-circuit voltage
Authors: Zonno Irene , Krogmeier Benedikt , Katte Verena , Lübke Dana , Martinez-Otero Alberto , Kirchartz Thomas
Published: November 2016

In case of thin-film solar cells, it is often rather difficult to determine what the dominant recombination mechanism is. In particular, it is difficult to distinguish recombination at the interface between the absorber layer and the electrodes (typically called surface recombination) from recombination in the bulk of the absorber—or in case of organic solar cells at the internal donor-acceptor interfaces. Here, we suggest a method to distinguish surface and bulk recombination in thin-film solar cells based on the thickness dependence of the saturation current density, which we derive from the open-circuit voltage and the photocurrent at short circuit or reverse bias. By means of numerical simulations, we show that surface and bulk recombination currents scale differently with thickness assuming the material properties to be unchanged. We test our predictions on a range of organic solar cell data from our laboratory and from literature and show that in the field of organic photovoltaics the whole range of cases, from mostly surface limited to purely bulk limited, is observed.
Non-invasive charge detection in surface-acoustic-wave-defined dynamic quantum dots
Authors: Astley M. R. , Kataoka M. , Ford C. J. B. , Barnes C. H. W. , Anderson D. , Jones G. A. C. , Farrer I. , Ritchie D. A. , Pepper M.
Published: November 2016

Using a non-invasive charge detection method, we detect a flow of electrons trapped in dynamic quantum dots. The dynamic quantum dots are defined by surface acoustic waves (SAWs) and move through a long depleted one-dimensional channel. A one-dimensional constriction is placed next to the SAW channel but in a separate circuit; the current induced by the SAWs through this detector constriction is sensitive to the number of electrons trapped in the SAW minima. We observe steps in the detector acoustoelectric current as the number of electrons carried by SAWs are varied as 1,2,3….
The study of origin of interfacial perpendicular magnetic anisotropy in ultra-thin CoFeB layer on the top of MgO based magnetic tunnel junction
Authors: Li Zhi-Peng , Li Shaoping , Zheng Yuankai , Fang Jason , Chen Lifan , Hong Liang , Wang Haifeng
Published: November 2016

A comprehensive microstructure study has been conducted experimentally for identifying the origin or mechanism of perpendicular magnetic anisotropy (PMA) in the ultra-thin (10 Å) CoFeB layer on the top of magnetic tunnel junction (MTJ). The high resolution transmission electron microscopy reveals that the feature of crystal structure in 10 Å-CoFeB layer is localized in nature at the CoFeB-MgO interface. On the other hand, the strain-relaxed crystalline structure is observed in the thick CoFeB (20 Å) layer at the CoFeB-MgO interface, associated with a series of dislocation formations. The electron energy loss spectroscopy further suggests that the local chemical stoichiometry of the ultra-thin 10 Å-CoFeB layer is notably changed at the CoFeB-MgO interface, compared with an atomic stoichiometry in a thick 20 Å-CoFeB layer. The origin of PMA mechanism is therefore identified experimentally as an interface effect, which can be attributed to a change of local atom bonding or lattice constant of the transition metal at the CoFeB-MgO based MTJ interface. Furthermore, such a local interfacial atom bonding change is seemly induced by the localized anisotropic strain and consistent with previous theoretical speculations and calculations. The observed experimental findings provide some perspective on microstructure and chemistry on PMA in ultra-thin CoFeB film at the MTJ interface, then deepening our understanding of the mechanism of PMA within MTJ stack and thus facilitating advancement for emerging spintronics technology.
The continuum state in photoluminescence of type-II In0.46Al0.54As/Al0.54Ga0.46As quantum dots
Authors: Su Linlin , Liang Baolai , Wang Ying , Guo Qinglin , Li Xiaowei , Wang Shufang , Fu Guangsheng , Mazur Yuriy I. , Ware Morgan E. , Salamo Gregory J.
Published: November 2016

The continuum state associated with type-II In0.46Al0.54As/Al0.54Ga0.46As quantum dots (QDs) is investigated. Emission from the continuum states of the QDs is directly observed in photoluminescence (PL) spectra. The PL excitation and time-resolved PL spectra reveal an efficient carrier relaxation from the AlGaAs barrier into the InAlAs QD ground state via the continuum states. The temperature dependence of the PL spectra shows a decreasing PL linewidth and a strong redshift of the peak energy at low temperature, indicating that carriers are redistributed through the continuum states by thermal activation and lateral transfer.
A monolayer graphene/GaAs nanowire array Schottky junction self-powered photodetector
Authors: Wu Yao , Yan Xin , Zhang Xia , Ren Xiaomin
Published: November 2016

We report a self-powered photodetector based on the graphene/GaAs nanowire Schottky junctions. The device is fabricated by transferring a monolayer graphene onto an n-doped GaAs nanowire array. The nanowires are grown by Au-catalyzed metal organic chemical vapor deposition, and the Au particles are subsequently removed by wet etching to achieve close contact between graphene and GaAs. The device exhibits a responsivity of 1.54 mA/W at zero bias and a short response/recover time of 71/194 μs at room temperature, showing a strong possibility for high-speed near-infrared applications.
Communication: Constant uncertainty molecular dynamics: A simple and efficient algorithm to incorporate quantum nature into a real-time molecular dynamics simulation
Authors: Hasegawa Taisuke
Published: November 2016

We propose a novel molecular dynamics (MD) algorithm for approximately dealing with a nuclear quantum dynamics in a real-time MD simulation. We have found that real-time dynamics of the ensemble of classical particles acquires quantum nature by introducing a constant quantum mechanical uncertainty constraint on its classical dynamics. The constant uncertainty constraint is handled by the Lagrange multiplier method and implemented into a conventional MD algorithm. The resulting constant uncertainty molecular dynamics (CUMD) is applied to the calculation of quantum position autocorrelation functions on quartic and Morse potentials. The test calculations show that CUMD gives better performance than ring-polymer MD because of the inclusion of the quantum zero-point energy during real-time evolution as well as the quantum imaginary-time statistical effect stored in an initial condition. The CUMD approach will be a possible starting point for new real-time quantum dynamics simulation in condensed phase.
Fracture-resistant thin-film metallic glass: Ultra-high plasticity at room temperature
Authors: Yu Chia-Chi , Lee C. M. , Chu Jinn P. , Greene J. E. , Liaw Peter K.
Published: November 2016

We report the first example of room-temperature rubber-like deformation in thin-film metallic glasses (TFMGs), 260-nm-thick Zr60Cu24Al11Ni5 layers, under ultra-high shear strain. The TFMGs were deposited, with no external heating, on Zr-based bulk metallic glass (BMG) and Si(001) substrates by rf magnetron sputtering in a 3 mTorr Ar plasma. Cross-sectional transmission electron microscopy (XTEM) analyses and nanoindentation results reveal that the TFMGs undergo an incredibly large shear strain, estimated to be ∼4000%, during fatigue tests, and thickness reductions of up to 61.5%, with no shear-banding or cracking, during extreme nanoindentation experiments extending through the film and into the substrate. TFMG/BMG samples also exhibit film/substrate diffusion bonding during deformation as shown by high-resolution XTEM.
Electronic properties of a new structured Sin/O superlattice
Authors: Yu S. , Zhang L. , Xu Y. X. , Wu S. Q. , Zhu Z. Z.
Published: November 2016

Silicon is a material which dominants the semiconductor industry and has a well-established processing technology based on it. However, silicon has an indirect-bandgap and is not efficient in light emitting. This limits its applications in optoelectronics. In this paper, we proposed a new structural model for the silicon-based superlattice, i.e., the Sin/O one. The model consists of alternating films of n-layers of Si and a monolayer of oxygen along z-direction, together with a surface cell of Si(001) (2×1) reconstruction in the x-y plane. The importance of employing such a Si(001) (2×1) reconstruction is that all the electrons at interface can be strongly bonded. Our results showed interesting electronic properties, e.g., the band folding and large band gap of bulk Si, when the thickness of the silicon layers was increased (but still thin). Our structure might also offer other interesting properties.
Ocean spray: An outsized influence on weather and climate
Authors: Richter David H. , Veron Fabrice
Published: November 2016

Because the production, behavior, and life span of seawater droplets are complex, measuring and modeling them require a wide range of interdisciplinary techniques.
SARS-CoV 3CL protease cleaves its C-terminal autoprocessing site by novel subsite cooperativity
Authors: Muramatsu Tomonari , Takemoto Chie , Kim Yong-Tae , Wang Hongfei , Nishii Wataru , Terada Takaho , Shirouzu Mikako , Yokoyama Shigeyuki
Published: November 2016

Significance

The SARS-CoV protease (3CL
pro
) has “noncanonical” substrate specificity for its C-terminal autoprocessing. Phe is required at both the second position upstream of the cleavage point (P2) and the third downstream position (P3′). This finding is surprising, given that 3CL
pro
reportedly requires Leu at the P2 position with no preference at the P3′ position. The conventional “consensus sequence” cannot explain this noncanonical specificity. Crystallography revealed that Phe at the P2 position changes the conformation of the substrate-binding pocket, and thereby creates the subsite for Phe at the P3′ position. This noncanonical specificity avoids the autoinhibition due to the mature C-terminal sequence of 3CL
pro
, which should be serious if Leu exists at the P2 position.
Cilia have high cAMP levels that are inhibited by Sonic Hedgehog-regulated calcium dynamics
Authors: Moore Bryn S. , Stepanchick Ann N. , Tewson Paul H. , Hartle Cassandra M. , Zhang Jin , Quinn Anne Marie , Hughes Thomas E. , Mirshahi Tooraj
Published: November 2016

Significance

Primary cilia are immotile organelles composed of specialized structural and signaling proteins that are essential for Hedgehog (HH) signaling. cAMP-dependent protein kinase (PKA) critically regulates HH signaling, maintaining transcriptional repression. Ciliary PKA activity is critical for HH regulation; however, the signaling steps regulating PKA activity within cilia remain unclear/unexplored. Targeted sensors were used to measure signaling molecules specifically within cilia. We found that cilia have basally high cAMP and PKA activity, controlled by phosphatidylinositol (3,4,5)-trisphosphate, not G proteins. Sonic Hedgehog stimulation reduces ciliary cAMP and PKA activity, which is dependent on Ca
2+
dynamics.
Membrane protein structure determination by SAD, SIR, or SIRAS phasing in serial femtosecond crystallography using an iododetergent
Authors: Nakane Takanori , Hanashima Shinya , Suzuki Mamoru , Saiki Haruka , Hayashi Taichi , Kakinouchi Keisuke , Sugiyama Shigeru , Kawatake Satoshi , Matsuoka Shigeru , Matsumori Nobuaki , Nango Eriko , Kobayashi Jun , Shimamura Tatsuro , Kimura Kanako , Mori Chihiro , Kunishima Naoki , Sugahara Michihiro , Takakyu Yoko , Inoue Shigeyuki , Masuda Tetsuya , Hosaka Toshiaki , Tono Kensuke , Joti Yasumasa , Kameshima Takashi , Hatsui Takaki , Yabashi Makina , Inoue Tsuyoshi , Nureki Osamu , Iwata So , Murata Michio , Mizohata Eiichi
Published: November 2016

Significance

This study shows successful experimental phasing methods (single-wavelength anomalous diffraction, single isomorphous replacement, and single isomorphous replacement with anomalous scattering) for crystal structure determination of a membrane protein by serial femtosecond crystallography with X-ray free electron lasers. Our iodine-containing detergent provided strong anomalous and isomorphous difference signals, which enabled experimental phasing using lower-resolution reflections (worse than 3 Å) from fewer indexed images than phasing attempts reported previously. The findings of this study will be applicable to a wide range of target proteins in structural biology, especially membrane proteins that often diffract to low resolution.
Cardiac electrical defects in progeroid mice and Hutchinson–Gilford progeria syndrome patients with nuclear lamina alterations
Authors: Rivera-Torres José , Calvo Conrado J. , Llach Anna , Guzmán-Martínez Gabriela , Caballero Ricardo , González-Gómez Cristina , Jiménez-Borreguero Luis J. , Guadix Juan A. , Osorio Fernando G. , López-Otín Carlos , Herraiz-Martínez Adela , Cabello Nuria , Vallmitjana Alex , Benítez Raul , Gordon Leslie B. , Jalife José , Pérez-Pomares José M. , Tamargo Juan , Delpón Eva , Hove-Madsen Leif , Filgueiras-Rama David , Andrés Vicente
Published: November 2016

Significance

Defective prelamin A processing causes cardiovascular alterations and premature death in Hutchinson–Gilford progeria syndrome (HGPS) patients and also occurs during physiological aging. We found overt repolarization abnormalities in HGPS patients at advanced disease stages. Similar alterations were present in progeroid
Zmpste24

−/−

mice, which had cardiomyocytes that exhibited prolonged calcium transient duration and reduced sarcoplasmic reticulum calcium loading capacity and release, consistent with absence of isoproterenol-induced ventricular arrhythmias.
Zmpste24

−/−

mice developed age-dependent bradycardia and PQ interval/QRS complex prolongation, likely contributing to premature death. These defects correlated with mislocalization of connexin43, which was also noted in heart tissue from HGPS patients. These results reveal molecular alterations that might cause cardiac rhythm alterations and premature death in HGPS.
Reducing uncertainties in decadal variability of the global carbon budget with multiple datasets
Authors: Li Wei , Ciais Philippe , Wang Yilong , Peng Shushi , Broquet Grégoire , Ballantyne Ashley P. , Canadell Josep G. , Cooper Leila , Friedlingstein Pierre , Le Quéré Corinne , Myneni Ranga B. , Peters Glen P. , Piao Shilong , Pongratz Julia
Published: November 2016

Significance

The conventional approach of calculating the global carbon budget makes the land sink the most uncertain of all budget terms. This is because, rather than being constrained by observations, it is inferred as a residual in the budget equation. Here, we overcome this limitation by performing a Bayesian fusion of different available observation-based estimates of decadal carbon fluxes. This approach reduces the uncertainty in the land sink by 41% and in the ocean sink by 46%. These results are significant because they give unprecedented confidence in the role of the increasing land sink in regulating atmospheric CO
2
, and shed light on the past decadal trend.
Whales, science, and scientific whaling in the International Court of Justice
Authors: Mangel Marc
Published: November 2016

I provide a brief review of the origins of the International Convention on the Regulation of Whaling and the failure to successfully regulate whaling that led to the commercial moratorium in 1986. I then describe the Japanese Whale Research Programs Under Special Permit in the Antarctica (JARPA I, JARPA II) and the origins of the caseWhaling in the Antarctic (Australia v. Japan: New Zealand Intervening)in the International Court of Justice. I explain that the International Court of Justice chose to conduct an objective review of JARPA II, the standard that it used for the review, and the pathway that it took to adjudicate the case without providing a definition of science to be used in international law. I conclude with a brief discussion of the implications of the Judgment for the International Convention on the Regulation of Whaling, and the International Whaling Commission in particular, for other international treaties, and for the interaction of science and law more generally.
Piperine’s mitigation of obesity and diabetes can be explained by its up-regulation of the metabolic rate of resting muscle
Authors: Nogara Leonardo , Naber Nariman , Pate Edward , Canton Marcella , Reggiani Carlo , Cooke Roger
Published: November 2016

Significance

We have developed a method for finding pharmaceuticals that would treat obesity and type 2 diabetes by increasing the metabolic rate of resting skeletal muscle. The metabolic rate is increased by shifting the motor protein myosin from a low activity state to a higher activity state. We devised an assay, screened for compounds, and found one molecule, piperine. Piperine increased the metabolic rate of resting muscle fibers. Piperine does not have the properties required to be a pharmaceutical in humans, but it would make a good lead compound for finding compounds that do. Our results provide proof of concept that these metabolic diseases can be treated by future pharmaceuticals that target myosin to increase the metabolism of excess calories.
Global environmental drivers of influenza
Authors: Deyle Ethan R. , Maher M. Cyrus , Hernandez Ryan D. , Basu Sanjay , Sugihara George
Published: November 2016

Significance

Patterns of influenza outbreak are different in the tropics than in temperate regions. Although considerable experimental progress has been made in identifying climate-related drivers of influenza, the apparent latitudinal differences in outbreak patterns raise basic questions as to how potential environmental variables combine and act across the globe. Adopting an empirical dynamic modeling framework, we clarify that absolute humidity drives influenza outbreaks across latitudes, find that the effect of absolute humidity on influenza is U-shaped, and show that this U-shaped pattern is mediated by temperature. These findings offer a unifying synthesis that explains why experiments and analyses disagree on this relationship.
Discovery of selective small-molecule HDAC6 inhibitor for overcoming proteasome inhibitor resistance in multiple myeloma
Authors: Hideshima Teru , Qi Jun , Paranal Ronald M. , Tang Weiping , Greenberg Edward , West Nathan , Colling Meaghan E. , Estiu Guillermina , Mazitschek Ralph , Perry Jennifer A. , Ohguchi Hiroto , Cottini Francesca , Mimura Naoya , Görgün Güllü , Tai Yu-Tzu , Richardson Paul G. , Carrasco Ruben D. , Wiest Olaf , Schreiber Stuart L. , Anderson Kenneth C. , Bradner James E.
Published: November 2016

Significance

Proteasome inhibitors show remarkable anti-multiple myeloma (MM) activity in preclinical and clinical studies. However, resistance develops in the majority of patients, and novel treatments are urgently needed. Histone deacetylase 6 (HDAC6) has been shown to mediate aggresomal protein degradation and could be a potential target for combination treatment to overcome drug resistance. Here we designed and developed an HDAC6-selective small molecule inhibitor, WT161, and used this compound to define mechanisms of anti-MM activity, both alone and in combination with proteasome inhibitors in in vitro and in vivo studies. This study has established the framework for combination treatment of HDAC6 inhibitors with proteasome inhibitors in MM and validates an in vivo quality chemical probe for broad use by the research community.
Intratumoral injection of a CpG oligonucleotide reverts resistance to PD-1 blockade by expanding multifunctional CD8
+
T cells
Authors: Wang Shu , Campos Jose , Gallotta Marilena , Gong Mei , Crain Chad , Naik Edwina , Coffman Robert L. , Guiducci Cristiana
Published: November 2016

Significance

Recent data suggest that patients harboring immunologically incompetent tumors fail to respond to programmed death 1 (PD-1) blockade. We have developed a mouse tumor model that mimics resistance found in human tumors, and we show that intratumoral injections of a high IFN-inducing CpG oligonucleotide, SD-101, can rapidly lead to durable rejection of anti–PD-1 nonresponder tumors and generate systemic immunity to untreated distant-site tumors. The change in tumor microenvironment caused by SD-101 leads to rapid T-cell infiltration and generation of multifunctional CD8
+
T cells. These studies provide significant insights into the synergy between PD-1 blockade and local TLR9 activation and provide the experimental support for clinical studies of combination therapy with PD-1 blockade and intratumoral SD-101.
Enhanced intensity of global tropical cyclones during the mid-Pliocene warm period
Authors: Yan Qing , Wei Ting , Korty Robert L. , Kossin James P. , Zhang Zhongshi , Wang Huijun
Published: November 2016

Significance

To better understand how tropical cyclones (TCs) may respond to future warming, we explore the behavior of TCs during the mid-Pliocene warm period (∼3 Ma), which shares characteristics of projected warmer climate. Our TC-permitting numerical simulations predict enhanced global-average peak TC intensity, longer duration, increased power dissipation, and a poleward migration of the location of peak intensity during the mid-Pliocene, although there are regional differences in the magnitude and statistical power of the climate/TC relationships. Our results share similarities with global TC changes observed during recent global warming and in most future projections and provide a window into the potential TC activity that may be expected in a warmer world.
Lessons from Star Carr on the vulnerability of organic archaeological remains to environmental change
Authors: High Kirsty , Milner Nicky , Panter Ian , Demarchi Beatrice , Penkman Kirsty E. H.
Published: November 2016

Significance

Wetland deposits provide a unique repository of archaeological and environmental information, preserving organic remains rarely found elsewhere. Star Carr is an impressive example, having provided unique evidence for human interactions with the landscape at the end of the last ice age. Tragically, here we provide experimental evidence that human modifications of the local environment are leading to changes in the site’s geochemistry, resulting in the rapid loss of bone and wood artifacts. Our research demands a reassessment of the assumption that sites such as Star Carr should be preserved in situ for the benefit of future researchers and demonstrates that potential changes to the burial environment must be considered before such a policy is pursued.
In vivo nanoparticle imaging of innate immune cells can serve as a marker of disease severity in a model of multiple sclerosis
Authors: Kirschbaum Klara , Sonner Jana K. , Zeller Matthias W. , Deumelandt Katrin , Bode Julia , Sharma Rakesh , Krüwel Thomas , Fischer Manuel , Hoffmann Angelika , Costa da Silva Milene , Muckenthaler Martina U. , Wick Wolfgang , Tews Björn , Chen John W. , Heiland Sabine , Bendszus Martin , Platten Michael , Breckwoldt Michael O.
Published: November 2016

Significance

Multiple sclerosis is a devastating neurological condition that can affect the entire central nervous system. Innate immune cells mediate the underlying tissue damage, but visualizing these cellular culprits is currently not possible. Diagnosis and treatment monitoring are performed by MRI, but so far imaging markers are unspecific and based on secondary parameters (edema/gliosis; blood–brain barrier disruption). We used a nanoparticle-based approach to image brain-resident and infiltrating innate immune cells in inflammatory lesions. Nanoparticle uptake is specific for innate immune cells and correlates with clinical severity. Thus, targeting innate immunity by molecular imaging may serve as a direct marker of disease activity with the potential of clinical translation to a wide variety of inflammatory conditions for improved diagnosis and treatment monitoring.
Networks of conforming or nonconforming individuals tend to reach satisfactory decisions
Authors: Ramazi Pouria , Riehl James , Cao Ming
Published: November 2016

Significance

Many real-life decisions where one out of two actions must be chosen can be modeled on networks consisting of individuals who are either coordinating, that is, take an action only if sufficient neighbors are also doing so, or anticoordinating, that is, take an action only if too many neighbors are doing the opposite. It is not yet known whether such networks tend to reach a state where every individual is satisfied with his decision. We show that indeed any network of coordinating, and any network of anticoordinating individuals always reaches a satisfactory state, regardless of how they are connected, how different their preferences are, and how many simultaneous decisions are made over time.
Intraspecific genetic variation in hosts affects regulation of obligate heritable symbionts
Authors: Chong Rebecca A. , Moran Nancy A.
Published: November 2016

Significance

Symbiosis between animals and bacteria enables the exploitation of new ecological niches and promotes diversification. Many insects have obligate heritable bacteria that provision nutrients enabling new lifestyles, such as sap-feeding. A model system for obligate symbiosis is the pea aphid and its heritable bacterial symbiont
Buchnera aphidicola
. Using this system, we address the extent of variation in host regulation of symbiont populations and find that pea aphids have extensive genetic variation in the ability to regulate
Buchnera
numbers. In addition, higher abundance of
Buchnera
is associated with lower reproductive rates in aphid hosts. Thus, we provide experimental evidence demonstrating that genetic variation in hosts affects regulation of symbiosis, suggesting fitness costs and potential negative consequences of obligate symbiosis.
Neural correlates of specific musical anhedonia
Authors: Martínez-Molina Noelia , Mas-Herrero Ernest , Rodríguez-Fornells Antoni , Zatorre Robert J. , Marco-Pallarés Josep
Published: November 2016

Significance

This study provides direct evidence supporting the model of reward–auditory cortex interaction as underlying musical pleasure: People who do not experience that pleasure have selectively reduced responses in that system. People who are especially sensitive to musical reward conversely seem to show an enhanced interaction. Our paper offers insights into the neurobiological basis of music-induced pleasure that could also provide the basis for thinking more broadly about other types of aesthetic rewards. Our results also provide an important step toward the understanding of how music may have acquired reward value through evolution.
First genealogy for a wild marine fish population reveals multigenerational philopatry
Authors: Salles Océane C. , Pujol Benoit , Maynard Jeffrey A. , Almany Glenn R. , Berumen Michael L. , Jones Geoffrey P. , Saenz-Agudelo Pablo , Srinivasan Maya , Thorrold Simon R. , Planes Serge
Published: November 2016

Significance

Evidence for natal philopatry, the return of individuals to their natal location for reproduction, is scarce in marine fish populations despite being common in anadromous fishes. The proportion of individuals returning to natal sites is an important metric for estimating the effects of inbreeding and the potential for local adaptation to generate resilience to climate change. Here, we present the first multigenerational pedigree for a wild marine fish. We resolved the genealogical tree of families of orange clownfishAmphiprion perculaspanning up to five generations, using data from a 10-year genetic survey of a population at Kimbe Island, Papua New Guinea. We found that longitudinal philopatry plays a significant role in driving population renewal of the orange clownfish.
Fusion transcriptome profiling provides insights into alveolar rhabdomyosarcoma
Authors: Xie Zhongqiu , Babiceanu Mihaela , Kumar Shailesh , Jia Yuemeng , Qin Fujun , Barr Frederic G. , Li Hui
Published: November 2016

Significance

Here, we propose an approach to study connections between biological samples. By using binary input of fusion RNA expression, samples of same or similar tissue origin were clustered together. The concept was then put into use to gain insights for the pediatric alveolar rhabdomyosarcoma (ARMS). We found that the signature fusion RNA for ARMS,
PAX3
–
FOXO1
(paired box gene 3 fused with forkhead box O1), and all the other chimeric RNAs expressed in ARMS cells are expressed at the same normal myogenic time point(s). Several chimeric RNAs were further confirmed to be specifically expressed in clinical rhabdomyosarcoma tumor cases. These results support the link between at least some ARMS tumors and the
PAX3
–
FOXO1
-expressing myogenic cell. Fusion RNA profiling is a tool to investigate the etiology of fusion-gene-associated cancers.
E3 ubiquitin ligase SP1 regulates peroxisome biogenesis in
Arabidopsis
Authors: Pan Ronghui , Satkovich John , Hu Jianping
Published: November 2016

Significance

Peroxisomes are eukaryotic organelles crucial for development. Peroxisomal matrix proteins are imported by the peroxisome import machinery composed of peroxins (PEX proteins), but how the function of these PEX proteins is regulated is largely unknown. We discovered in
Arabidopsis
that the ubiquitin–proteasome system regulates peroxisome protein import via an E3 ubiquitin ligase, SP1 (suppressor of
ppi1
locus1), which targets PEX13 and possibly several other components of the peroxisome matrix protein import machinery for degradation. Our data demonstrate that the same E3 ubiquitin ligase can be shared by metabolically linked peroxisomes and chloroplasts to promote the destabilization of distinct components of the two import machineries, suggesting that the ubiquitin–proteasome system may represent an important regulatory mechanism coordinating the biogenesis of functionally associated organelles.
Expression of HIV-1 matrix protein p17 and association with B-cell lymphoma in HIV-1 transgenic mice
Authors: Carroll Virginia A. , Lafferty Mark K. , Marchionni Luigi , Bryant Joseph L. , Gallo Robert C. , Garzino-Demo Alfredo
Published: November 2016

Significance

Non-Hodgkin lymphomas are associated with HIV infection. Current hypotheses on lymphomagenesis, based on immunosuppression and/or activation and/or inflammation, are generic and do not provide mechanistic, testable models. Here we show that several HIV proteins are expressed in a HIV transgenic mouse model of lymphoma, but only Matrix/p17 is consistently expressed at high levels even in early disease stages. Microarray analyses of gene expression showed an enrichment of recombination-activating genes (Rag1/2) in mouse lymphoma tissue. When activated human B cells were treated with p17, induction of RAG1 expression was observed in three of seven donors. Taken together, and in the context of the literature, our results point to the involvement of p17 in supporting B-cell growth and genetic instability.
Degradation of cyclic diguanosine monophosphate by a hybrid two-component protein protects
Azoarcus
sp. strain CIB from toluene toxicity
Authors: Martín-Moldes Zaira , Blázquez Blas , Baraquet Claudine , Harwood Caroline S. , Zamarro María T. , Díaz Eduardo
Published: November 2016

Significance

Some bacteria have a remarkable ability to grow on toxic aromatic hydrocarbons under anaerobic conditions. Although bacteria have evolved cellular mechanisms to cope with hydrocarbon toxicity, it was unclear if signal transduction systems might exist to coordinate a protective response. Here we describe a hybrid two-component system, the TolR protein, from the bacterium
Azoarcus
sp. strain CIB that on binding toluene and other aromatic hydrocarbons degrades intracellular cyclic diguanosine monophosphate (c-di-GMP). A drop in c-di-GMP protects cells from toluene toxicity. C-di-GMP, found universally in bacteria, is involved in diverse functions including biofilm formation and virulence. Our finding of hydrocarbon sensing and c-di-GMP degradation by TolR for purposes of modulating hydrocarbon toxicity describes an additional role for c-di-GMP in bacterial physiology.
DNA-relay mechanism is sufficient to explain ParA-dependent intracellular transport and patterning of single and multiple cargos
Authors: Surovtsev Ivan V. , Campos Manuel , Jacobs-Wagner Christine
Published: November 2016

Significance

Although intracellular patterning is crucial for cell function, the mechanisms by which spatial patterns arise often remain elusive. Here, we investigate the mechanism of intracellular patterning by the broadly conserved bacterial ParA/B systems, which drive the transport and partitioning of cellular cargos such as plasmids. We show that a simple model that considers only the known biochemical properties of the ParA and ParB proteins and the stochastic dynamics of chromosomal loci observed in vivo explains the spontaneous formation of propagating protein gradients, cargo oscillations, and equidistant patterns that are characteristic of ParA/B systems. Our study shows that stochastic processes and directionally random forces alone—without cytoskeletal elements or motor proteins—can result in directed motion and complex spatial patterning.
Warm storage for arc magmas
Authors: Barboni Mélanie , Boehnke Patrick , Schmitt Axel K. , Harrison T. Mark , Shane Phil , Bouvier Anne-Sophie , Baumgartner Lukas
Published: November 2016

Significance

The increasingly popular notion that steady-state magma chambers are highly crystallized, and thus only capable of erupting during brief (<1 ka) reheatings, implies that melt detection beneath volcanoes warns of imminent eruption. By integrating the microgeochronology and geochemistry of zircons from lavas with those from components crystallized within the magma chamber and incorporated during eruption, we show that the Soufrière (Saint Lucia) volcanic reservoir was instead eruptible over long (>100 ka) timescales. Together with data from other volcanic complexes, we show that arc magmas may generally be stored warm (are able to erupt for >100 ka). Thus geophysical detection of melt beneath volcanoes represents the normal state of magma storage and holds little potential as an indicator of volcanic hazard.
Calcium sensor regulation of the Ca
V
2.1 Ca
2+
channel contributes to long-term potentiation and spatial learning
Authors: Nanou Evanthia , Scheuer Todd , Catterall William A.
Published: November 2016

Significance

Learning and memory are caused by changes in strength of communication between neurons at synapses. Both brief changes (short-term plasticity) and long-lasting changes (long-term plasticity) are important. Synaptic transmission is initiated by calcium channels, which are regulated by calcium-sensor proteins that induce short-term synaptic plasticity. We studied genetically modified mice with a mutation in the binding site for calcium-sensor proteins on calcium channels, which alters short-term synaptic plasticity. Surprisingly, we found that synapses in the hippocampus of these mice also have impaired long-term potentiation. In addition, these mutant mice have impaired spatial learning and memory. Our results show that disruption of calcium-channel regulation by calcium-sensor proteins alters both short-term and long-term plasticity, and these changes impair spatial learning and memory.