bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of measured and computed radial trajectories of plasma focus devices UMDPF1 and UMDPF0
Authors: Lim L. H. , Yap S. L. , Lim L. K. , Lee M. C. , Poh H. S. , Ma J. , Yap S. S. , Lee S.
Published: September 2015

In published literature, there has been scant data on radial trajectory of the plasma focus and no comparison of computed with measured radial trajectory. This paper provides the first such comparative study. We compute the trajectories of the inward-moving radial shock and magnetic piston of UMDPF1 plasma focus and compare these with measured data taken from a streak photograph. The comparison shows agreement with the measured radial trajectory in terms of average speeds and general shape of trajectory. This paper also presents the measured trajectory of the radially compressing piston in another machine, the UMDPF0 plasma focus, confirming that the computed radial trajectory also shows similar general agreement. Features of divergence between the computed and measured trajectories, towards the end of the radial compression, are discussed. From the measured radial trajectories, an inference is made that the neutron yield mechanism could not be thermonuclear. A second inference is made regarding the speeds of axial post-pinch shocks, which are recently considered as a useful tool for damage testing of fusion-related wall materials.
Quick scanning monochromator for millisecond in situ and in operando X-ray absorption spectroscopy
Authors: Müller O. , Lützenkirchen-Hecht D. , Frahm R.
Published: September 2015

The design and capabilities of a novel Quick scanning Extended X-ray Absorption Fine Structure (QEXAFS) monochromator are presented. The oscillatory movement of the crystal stage is realized by means of a unique open-loop driving scheme operating a direct drive torque motor. The entire drive mechanics are installed inside of a goniometer located on the atmospheric side of the vacuum chamber. This design allows remote adjustment of the oscillation frequency and spectral range, giving complete control of QEXAFS measurements. It also features a real step-scanning mode, which operates without a control loop to prevent induced vibrations. Equipped with Si(111) and Si(311) crystals on a single stage, it facilitates an energy range from 4.0 keV to 43 keV. Extended X-ray absorption fine structure spectra up to k = 14.4 Å−1 have been acquired within 17 ms and X-ray absorption near edge structure spectra covering more than 200 eV within 10 ms. The achieved data quality is excellent as shown by the presented measurements.
Photoinduced electrical response in quantum dots/graphene hybrid structure
Authors: Gromova Yu. , Alaferdov A. , Rackauskas S. , Ermakov V. , Orlova A. , Maslov V. , Moshkalev S. , Baranov A. , Fedorov A.
Published: September 2015

We report on the enhancement of the electrical photoresponse in a hybrid structure composed of multi-layer graphene flakes covered by a layer of CdSe/ZnS quantum dots (QDs) and placed between metal electrodes. The rate of the photoexcitation energy transfer from QDs to graphene, (0.5–2)×109 s−1 which controls the photoelectrical response of the structure, was found from the analysis of photoluminescence intensities and decay times for QDs in solution, on a bare glass substrate and on the surface of multilayer graphene, and in the presence of ammonia vapors.
Intramolecular competition between n-pair and π-pair hydrogen bonding: Microwave spectrum and internal dynamics of the pyridine–acetylene hydrogen-bonded complex
Authors: Mackenzie Rebecca B. , Dewberry Christopher T. , Coulston Emma , Cole George C. , Legon Anthony C. , Tew David P. , Leopold Kenneth R.
Published: September 2015

a-type rotational spectra of the hydrogen-bonded complex formed from pyridine and acetylene are reported. Rotational and 14N hyperfine constants indicate that the complex is planar with an acetylenic hydrogen directed toward the nitrogen. However, unlike the complexes of pyridine with HCl and HBr, the acetylene moiety in HCCH—NC5H5 does not lie along the symmetry axis of the nitrogen lone pair, but rather, forms an average angle of 46° with the C2 axis of the pyridine. The a-type spectra of HCCH—NC5H5 and DCCD—NC5H5 are doubled, suggesting the existence of a low lying pair of tunneling states. This doubling persists in the spectra of HCCD—NC5H5, DCCH—NC5H5, indicating that the underlying motion does not involve interchange of the two hydrogens of the acetylene. Single 13C substitution in either the ortho- or meta-position of the pyridine eliminates the doubling and gives rise to separate sets of spectra that are well predicted by a bent geometry with the 13C on either the same side (“inner”) or the opposite side (“outer”) as the acetylene. High level ab initio calculations are presented which indicate a binding energy of 1.2 kcal/mol and a potential energy barrier of 44 cm−1 in the C2v configuration. Taken together, these results reveal a complex with a bent hydrogen bond and large amplitude rocking of the acetylene moiety. It is likely that the bent equilibrium structure arises from a competition between a weak hydrogen bond to the nitrogen (an n-pair hydrogen bond) and a secondary interaction between the ortho-hydrogens of the pyridine and the π electron density of the acetylene.
Efficient calculation of nuclear spin-rotation constants from auxiliary density functional theory
Authors: Zuniga-Gutierrez Bernardo , Camacho-Gonzalez Monica , Bendana-Castillo Alfonso , Simon-Bastida Patricia , Calaminici Patrizia , Köster Andreas M.
Published: September 2015

The computation of the spin-rotation tensor within the framework of auxiliary density functional theory (ADFT) in combination with the gauge including atomic orbital (GIAO) scheme, to treat the gauge origin problem, is presented. For the spin-rotation tensor, the calculation of the magnetic shielding tensor represents the most demanding computational task. Employing the ADFT-GIAO methodology, the central processing unit time for the magnetic shielding tensor calculation can be dramatically reduced. In this work, the quality of spin-rotation constants obtained with the ADFT-GIAO methodology is compared with available experimental data as well as with other theoretical results at the Hartree-Fock and coupled-cluster level of theory. It is found that the agreement between the ADFT-GIAO results and the experiment is good and very similar to the ones obtained by the coupled-cluster single-doubles-perturbative triples-GIAO methodology. With the improved computational performance achieved, the computation of the spin-rotation tensors of large systems or along Born-Oppenheimer molecular dynamics trajectories becomes feasible in reasonable times. Three models of carbon fullerenes containing hundreds of atoms and thousands of basis functions are used for benchmarking the performance. Furthermore, a theoretical study of temperature effects on the structure and spin-rotation tensor of the H12C–12CH–DF complex is presented. Here, the temperature dependency of the spin-rotation tensor of the fluorine nucleus can be used to identify experimentally the so far unknown bent isomer of this complex. To the best of our knowledge this is the first time that temperature effects on the spin-rotation tensor are investigated.
Large-scale analysis of unconfined self-similar Rayleigh–Taylor turbulence
Authors: Soulard Olivier , Griffond Jérôme , Gréa Benoît-Joseph
Published: September 2015

The large-scale properties of unconfined Rayleigh–Taylor turbulence are investigated using an eddy-damped quasi-normal markovianized approximation. Within this framework, turbulent spectra are shown to undergo at late times and at large scales, an evolution dominated by non-linear backscattering processes. As a result, the analysis predicts that large scale initial conditions are eventually forgotten: there is no large scale invariant and no equivalent of a principle of permanence of large eddies. Additional properties of Rayleigh–Taylor large scales are also discussed. In particular, their scaling and anisotropy are examined, with an emphasis put on the combined influence of buoyancy production and non-linearities. The different assumptions and predictions of this work are verified by performing an implicit large eddy simulation of a Rayleigh–Taylor configuration.
Moderation and diffusion of positrons in tungsten meshes and foils
Authors: Williams A. I. , Murtagh D. J. , Fayer S. E. , Andersen S. L. , Chevallier J. , Kövér Á. , Van Reeth P. , Humberston J. W. , Laricchia G.
Published: September 2015

The efficiency of tungsten meshes and thin foils for moderation of fast positrons from 22Na has been investigated in transmission geometry and a fair agreement has been found with previous experimental results where directly comparable. For foils, the dependence on material thickness is found to be similar to the prediction of the Vehanen-Mäkinen diffusion model; however, the magnitude is 5–10 times lower. A broad consensus is observed between experiment and the results of a three-dimensional model developed in this work. For a given thickness, meshes are found to be generally better than foils by around a factor of 10 with a maximum efficiency (∼10−3) comparable to that achieved with thin single crystal foils, in accord with previous measurements and the results of the present model.
Cryogenic micro-calorimeters for mass spectrometric identification of neutral molecules and molecular fragments
Authors: Novotný O. , Allgeier S. , Enss C. , Fleischmann A. , Gamer L. , Hengstler D. , Kempf S. , Krantz C. , Pabinger A. , Pies C. , Savin D. W. , Schwalm D. , Wolf A.
Published: September 2015

We have systematically investigated the energy resolution of a magnetic micro-calorimeter (MMC) for atomic and molecular projectiles at impact energies ranging from E≈13 to 150 keV. For atoms we obtained absolute energy resolutions down to ΔE≈120 eV and relative energy resolutions down to ΔE/E≈10−3. We also studied in detail the MMC energy-response function to molecular projectiles of up to mass 56 u. We have demonstrated the capability of identifying neutral fragmentation products of these molecules by calorimetric mass spectrometry. We have modeled the MMC energy-response function for molecular projectiles and concluded that backscattering is the dominant source of the energy spread at the impact energies investigated. We have successfully demonstrated the use of a detector absorber coating to suppress such spreads. We briefly outline the use of MMC detectors in experiments on gas-phase collision reactions with neutral products. Our findings are of general interest for mass spectrometric techniques, particularly for those desiring to make neutral-particle mass measurements.
Wetting properties of molecularly rough surfaces
Authors: Svoboda Martin , Malijevský Alexandr , Lísal Martin
Published: September 2015

We employ molecular dynamics simulations to study the wettability of nanoscale rough surfaces in systems governed by Lennard-Jones (LJ) interactions. We consider both smooth and molecularly rough planar surfaces. Solid substrates are modeled as a static collection of LJ particles arranged in a face-centered cubic lattice with the (100) surface exposed to the LJ fluid. Molecularly rough solid surfaces are prepared by removing several strips of LJ atoms from the external layers of the substrate, i.e., forming parallel nanogrooves on the surface. We vary the solid-fluid interactions to investigate strongly and weakly wettable surfaces. We determine the wetting properties by measuring the equilibrium droplet profiles that are in turn used to evaluate the contact angles. Macroscopic arguments, such as those leading to Wenzel’s law, suggest that surface roughness always amplifies the wetting properties of a lyophilic surface. However, our results indicate the opposite effect from roughness for microscopically corrugated surfaces, i.e., surface roughness deteriorates the substrate wettability. Adding the roughness to a strongly wettable surface shrinks the surface area wet with the liquid, and it either increases or only marginally affects the contact angle, depending on the degree of liquid adsorption into the nanogrooves. For a weakly wettable surface, the roughness changes the surface character from lyophilic to lyophobic due to a weakening of the solid-fluid interactions by the presence of the nanogrooves and the weaker adsorption of the liquid into the nanogrooves.
Robustness, efficiency, and optimality in the Fenna-Matthews-Olson photosynthetic pigment-protein complex
Authors: Baker Lewis A. , Habershon Scott
Published: September 2015

Pigment-protein complexes (PPCs) play a central role in facilitating excitation energy transfer (EET) from light-harvesting antenna complexes to reaction centres in photosynthetic systems; understanding molecular organisation in these biological networks is key to developing better artificial light-harvesting systems. In this article, we combine quantum-mechanical simulations and a network-based picture of transport to investigate how chromophore organization and protein environment in PPCs impacts on EET efficiency and robustness. In a prototypical PPC model, the Fenna-Matthews-Olson (FMO) complex, we consider the impact on EET efficiency of both disrupting the chromophore network and changing the influence of (local and global) environmental dephasing. Surprisingly, we find a large degree of resilience to changes in both chromophore network and protein environmental dephasing, the extent of which is greater than previously observed; for example, FMO maintains EET when 50% of the constituent chromophores are removed, or when environmental dephasing fluctuations vary over two orders-of-magnitude relative to the in vivo system. We also highlight the fact that the influence of local dephasing can be strongly dependent on the characteristics of the EET network and the initial excitation; for example, initial excitations resulting in rapid coherent decay are generally insensitive to the environment, whereas the incoherent population decay observed following excitation at weakly coupled chromophores demonstrates a more pronounced dependence on dephasing rate as a result of the greater possibility of local exciton trapping. Finally, we show that the FMO electronic Hamiltonian is not particularly optimised for EET; instead, it is just one of many possible chromophore organisations which demonstrate a good level of EET transport efficiency following excitation at different chromophores. Overall, these robustness and efficiency characteristics are attributed to the highly connected nature of the chromophore network and the presence of multiple EET pathways, features which might easily be built into artificial photosynthetic systems.
Efficiency droop improvement in InGaN light-emitting diodes with graded InGaN barriers of increasing indium composition
Authors: Cheng Liwen , Wu Shudong , Xia Changquan , Chen Haitao
Published: September 2015

In this work, graded barrier InGaN light-emitting diodes with increasing indium composition barriers are proposed and investigated numerically. When the conventional GaN barriers are replaced by this unique graded InGaN barrier design, the forward voltage at 100 mA is reduced from 3.32 V to 3.27 V, and the efficiency droop is improved from 46.6% to 7.5%. The simulation results observed in this work indicate that these improvements can be attributed to increased electron confinement and enhanced hole injection efficiency caused by the modified energy band diagram.
Observation of increased space-charge limited thermionic electron emission current by neutral gas ionization in a weakly-ionized deuterium plasma
Authors: Hollmann E. M. , Yu J. H. , Doerner R. P. , Nishijima D. , Seraydarian R. P.
Published: September 2015

The thermionic electron emission current emitted from a laser-produced hot spot on a tungsten target in weakly-ionized deuterium plasma is measured. It is found to be one to two orders of magnitude larger than expected for bipolar space charge limited thermionic emission current assuming an unperturbed background plasma. This difference is attributed to the plasma being modified by ionization of background neutrals by the emitted electrons. This result indicates that the allowable level of emitted thermionic electron current can be significantly enhanced in weakly-ionized plasmas due to the presence of large neutral densities.
The osmotic virial formulation of the free energy of polymer mixing
Authors: Bosse August W. , Douglas Jack F.
Published: September 2015

We derive an alternative formulation of the free energy of polymer mixing in terms of an osmotic virial expansion. Starting from a generalized free energy of mixing, and the assumption that the internal energy of mixing is analytic in the polymer composition variable, we demonstrate that the free energy of mixing can be represented as an infinite series in the osmotic virial coefficients. This osmotic virial formulation is consistent with, but more general than, a relationship derived for polymer blends with structured monomers by Dudowicz, Freed, and Douglas [J. Chem. Phys. 116, 9983 (2002)] and Douglas, Dudowicz, and Freed [J. Chem. Phys. 127, 224901 (2007)].
On the representation of many-body interactions in water
Authors: Medders Gregory R. , Götz Andreas W. , Morales Miguel A. , Bajaj Pushp , Paesani Francesco
Published: September 2015

Recent work has shown that the many-body expansion of the interaction energy can be used to develop analytical representations of global potential energy surfaces (PESs) for water. In this study, the role of short- and long-range interactions at different orders is investigated by analyzing water potentials that treat the leading terms of the many-body expansion through implicit (i.e., TTM3-F and TTM4-F PESs) and explicit (i.e., WHBB and MB-pol PESs) representations. It is found that explicit short-range representations of 2-body and 3-body interactions along with a physically correct incorporation of short- and long-range contributions are necessary for an accurate representation of the water interactions from the gas to the condensed phase. Similarly, a complete many-body representation of the dipole moment surface is found to be crucial to reproducing the correct intensities of the infrared spectrum of liquid water.
Post-recombination early Universe cooling by translation–internal inter-conversion: The role of minor constituents
Authors: McCaffery Anthony J.
Published: September 2015

Little is known of the mechanism by which H and H2, the principal constituents of the post-re-combination early Universe, cooled sufficiently to permit cluster formation, nucleosynthesis, and, eventually, the formation of structured objects. Radiative decay primarily cools the internal modes of H2, as Δj = − 2 jumps accompany quadrupolar emission. This, however, would be a self-limiting mechanism. In this work, a translational energy cooling mechanism based on collision-induced, translation-to-internal mode conversion, is extended, following an earlier study [A. J. McCaffery and R. J. Marsh, J. Chem. Phys. 139, 234310 (2013)] of ensembles comprising H2 in a H atom bath gas. Here, the possible influence of minor species, such as HD, on this cooling mechanism is investigated. Results suggest that the influence of HD is small but not insignificant. Conversion is very rapid and an overall translation-to-internal energy conversion efficiency of some 5% could be expected. This finding may be of use in the further development of models of this complex phase of early Universe evolution. An unexpected finding in this study was that H2 + HD ensembles are capable of very rapid translation-to-internal conversion with efficiencies of >40% and relaxation rates that appear to be relatively slow. This may have potential as an energy storage mechanism.
Blow-up phenomena for the weakly dissipative Dullin-Gottwald-Holm equation revisited
Authors: Zhang Zaiyun , Huang Jianhua , Sun Mingbao
Published: September 2015

In this paper, we investigate the Cauchy problem for the weakly dissipative Dullin-Gottwald-Holm equation. We first establish the local well-posedness result by Kato’s semigroup theory. Then, we obtain the precise blow-up scenario and present some blow-up results for strong solutions to the equation. Finally, we discuss the blow-up rate of the wave-breaking solutions. This result complements the early one in the literature, such as Novruzov [J. Math. Phys. 54, 092703 (2013)].
Rare-earth doped transparent ceramics for spectral filtering and quantum information processing
Authors: Kunkel Nathalie , Ferrier Alban , Thiel Charles W. , Ramírez Mariola O. , Bausá Luisa E. , Cone Rufus L. , Ikesue Akio , Goldner Philippe
Published: September 2015

Homogeneous linewidths below 10 kHz are reported for the first time in high-quality Eu3+ doped Y 2O3 transparent ceramics. This result is obtained on the 7F0→5D0 transition in Eu3+ doped Y 2O3 ceramics and corresponds to an improvement of nearly one order of magnitude compared to previously reported values in transparent ceramics. Furthermore, we observed spectral hole lifetimes of ∼15 min that are long enough to enable efficient optical pumping of the nuclear hyperfine levels. Additionally, different Eu3+ concentrations (up to 1.0%) were studied, resulting in an increase of up to a factor of three in the peak absorption coefficient. These results suggest that transparent ceramics can be useful in applications where narrow and deep spectral holes can be burned into highly absorbing lines, such as quantum information processing and spectral filtering.
Graphene-hexagonal boron nitride resonant tunneling diodes as high-frequency oscillators
Authors: Gaskell J. , Eaves L. , Novoselov K. S. , Mishchenko A. , Geim A. K. , Fromhold T. M. , Greenaway M. T.
Published: September 2015

We assess the potential of two-terminal graphene-hexagonal boron nitride-graphene resonant tunneling diodes as high-frequency oscillators, using self-consistent quantum transport and electrostatic simulations to determine the time-dependent response of the diodes in a resonant circuit. We quantify how the frequency and power of the current oscillations depend on the diode and circuit parameters including the doping of the graphene electrodes, device geometry, alignment of the graphene lattices, and the circuit impedances. Our results indicate that current oscillations with frequencies of up to several hundred GHz should be achievable.
Note: A small roll angle measurement method with enhanced resolution based on a heterodyne interferometer
Authors: Tang S. , Wang Z. , Li M. , Zhang W. , Yang F. , Zhang X.
Published: September 2015

Small roll angle is hard to be measured directly by commercial interferometer instruments due to their low sensitivities in axial direction. A method for its measurement based on a heterodyne interferometer is presented, which adopts accessories including a half wave plate, a multiple-reflector, and a phase meter to achieve test by detecting phase differences between the measurement and reference arms. Mathematical model reveals the resolution will be improved by increasing pass times through the half wave plate. The theoretical resolution is up to 0.19 in. when the pass times increase to three and the phase meter resolution is 0.01°. The proposed method is proved by the experiment.
Communication: Coherences observed in vivo in photosynthetic bacteria using two-dimensional electronic spectroscopy
Authors: Dahlberg Peter D. , Norris Graham J. , Wang Cheng , Viswanathan Subha , Singh Ved P. , Engel Gregory S.
Published: September 2015

Energy transfer through large disordered antenna networks in photosynthetic organisms can occur with a quantum efficiency of nearly 100%. This energy transfer is facilitated by the electronic structure of the photosynthetic antennae as well as interactions between electronic states and the surrounding environment. Coherences in time-domain spectroscopy provide a fine probe of how a system interacts with its surroundings. In two-dimensional electronic spectroscopy, coherences can appear on both the ground and excited state surfaces revealing detailed information regarding electronic structure, system-bath coupling, energy transfer, and energetic coupling in complex chemical systems. Numerous studies have revealed coherences in isolated photosynthetic pigment-protein complexes, but these coherences have not been observed in vivo due to the small amplitude of these signals and the intense scatter from whole cells. Here, we present data acquired using ultrafast video-acquisition gradient-assisted photon echo spectroscopy to observe quantum beating signals from coherences in vivo. Experiments were conducted on isolated light harvesting complex II (LH2) from Rhodobacter sphaeroides, whole cells of R. sphaeroides, and whole cells of R. sphaeroides grown in 30% deuterated media. A vibronic coherence was observed following laser excitation at ambient temperature between the B850 and the B850∗ states of LH2 in each of the 3 samples with a lifetime of ∼40-60 fs.
The kinetic friction between a nanowire and a flat substrate measured using nanomanipulation with optical microscopy
Authors: Wang Shiliang , Hou Lizhen , Xie Hongtao , Huang Han
Published: September 2015

The kinetic frictional force between a nanowire and its supporting flat substrate was measured using nanomanipulation with optical microscopy at ambient atmosphere. During testing, the nanowire was pushed at its center point by a sharp tip and thus exhibited an arc shape held by the frictional shear stress (kinetic friction per area). The arc-shaped nanowire slid along the supporting substrate with further pushing. The frictional shear stress was derived from the arc shape of the nanowire based on the theory of elasticity. The frictional shear stresses of Al2O3 nanowires on the Si and SiN substrates were measured to be 2.0 ± 0.2 and 1.5 ± 0.2 MPa, respectively. It was found that the lengths of the nanowires and their angular orientations with the substrate, the arc shapes being formed and the driving mode of the tip had insignificant effects on the measured frictional shear stress.
Microfluidic chemical processing with on-chip washing by deterministic lateral displacement arrays with separator walls
Authors: Chen Yu , D'Silva Joseph , Austin Robert H. , Sturm James C.
Published: September 2015

We describe a microfluidic device for on-chip chemical processing, such as staining, and subsequent washing of cells. The paper introduces “separator walls” to increase the on-chip incubation time and to improve the quality of washing. Cells of interest are concentrated into a treatment stream of chemical reagents at the first separator wall for extended on-chip incubation without causing excess contamination at the output due to diffusion of the unreacted treatment chemicals, and then are directed to the washing stream before final collections. The second separator wall further reduces the output contamination from diffusion to the washing stream. With this approach, we demonstrate on-chip leukocyte staining with Rhodamine 6G and washing. The results suggest that other conventional biological and analytical processes could be replaced by the proposed device.
Skyrmion stability in nanocontact spin-transfer oscillators
Authors: Chui C. P. , Zhou Yan
Published: September 2015

We investigate the conditions for nanocontact spin-transfer oscillators (NC-STOs) that allow for stabilization of a skyrmion. Emphasis is made on the breathing mode, which can be regarded as a source of microwave generation. Micromagnetic simulations of NC-STOs with varying parameters have been performed, with the resulting magnetization plotted in the form of phase diagrams. It is found that control of spin wave mode in conventional STOs can be applied to skyrmion-based STOs.
Using site-occupancy models to prepare for the spread of chytridiomyosis and identify factors affecting detectability of a cryptic susceptible species, the Tasmanian tree frog
Authors: Cashins Scott D. , Philips Annie , Skerratt Lee F.
Published: September 2015

Context
The global reduction of amphibian biodiversity as a result of the disease chytridiomycosis (caused by the fungus Batrachochytrium dendrobatidis; Bd) has highlighted the need to accurately detect local population declines in association with Bd presence. Although Bd has spread globally, some remote regions such as the Tasmanian Wilderness World Heritage Area (1.40 million ha; TWWHA) in Australia, remain largely, but not entirely, disease free. The Tasmanian tree frog (Litoria burrowsae) resides primarily within TWWHA boundaries, and is believed to be susceptible to chytridiomycosis.

Aims
In the absence of historical abundance data, we used a single-season multi-state site-occupancy model to investigate the impact of Bd on L. burrowsae populations, on factors affecting species detection and to inform ongoing surveillance and conservation.

Methods
We recorded frog detection and ranked call intensity (estimation of population size) from repeated independent surveys within a season to estimate the role of covariates, such as presence of Bd and environmental variables, on species occupancy and detection probability.

Key results
Modelling revealed large frog populations are more likely to be present at naturally formed than human-formed ponds, strong winds negatively affect detection of populations, and time after sunset affects detection of large populations. Large frog populations were more likely to be Bd-negative; however, models including Bd presence were not well supported, in part a result of the small number of Bd-positive sites recorded.

Conclusions and Implications
The utility of site-occupancy modelling in understanding the impact of disease on populations is little known, but has the potential to improve the accuracy and efficiency of many conservation programs.
Emergence of electron coherence and two-color all-optical switching in MoS
2
based on spatial self-phase modulation
Authors: Wu Yanling , Wu Qiong , Sun Fei , Cheng Cai , Meng Sheng , Zhao Jimin
Published: September 2015

Significance

Generating electron coherence is nontrivial in that most sophisticated electronic experimental methods are noncoherent or cannot be used to induce and detect collective states. By using coherent spatial self-phase modulation (SSPM) (a nonlinear optical property) we observed the emergence of electron coherence in a gapped quantum material, MoS
2
. By observing gap-dependent SSPM we discovered that it is a ubiquitous property of two-dimensional layered quantum materials. Furthermore, we demonstrate that this ac electron coherence can be harnessed to realize two-color all-optical switching with superb performance.
Loop recognition and copper-mediated disulfide reduction underpin metal site assembly of Cu
A
in human cytochrome oxidase
Authors: Morgada Marcos N. , Abriata Luciano A. , Cefaro Chiara , Gajda Karolina , Banci Lucia , Vila Alejandro J.
Published: September 2015

Significance

Cellular respiration in humans depends on the correct assembly of a copper site (Cu
A
) in cytochrome oxidases. Because copper is toxic at high levels, cells require specific mechanisms to regulate copper transport and delivery. Two proteins from the Sco family are involved in this mechanism in human mitochondria, and mutations on any of these proteins jeopardize the assembly of the Cu
A
site, leading to lethal pathologies in newborns. We show that Sco1 is a protein responsible for delivering the copper ions to the oxidase, with a high degree of selectivity. Sco2, instead, provides electrons to reduce the nonmetallated site of the oxidase. This evidence allow us to propose a mechanism for assembly of the Cu
A
site in eukaryotes.
Spatiotemporal distribution of Holocene populations in North America
Authors: Chaput Michelle A. , Kriesche Björn , Betts Matthew , Martindale Andrew , Kulik Rafal , Schmidt Volker , Gajewski Konrad
Published: September 2015

Significance

We provide the first maps to our knowledge of spatiotemporal paleodemographic growth following human migration into the Americas for the past 13,000 y, using a statistical approach that simultaneously addresses sampling and taphonomic biases. The Canadian Archaeological Radiocarbon Database is sufficiently complete in many areas, demonstrating high correspondence between continental-scale
14
C-inferred population estimates and generally accepted archaeological history. Increases in population density seem robust for eastern and western North America, as well as central Alaska and the region surrounding Cahokia. These results are the first step toward being able to understand continental-scale human impacts on the North American ecosystem during the Holocene as well as demographic growth and migrations in relation to environmental changes.
MINCR is a MYC-induced lncRNA able to modulate MYC’s transcriptional network in Burkitt lymphoma cells
Authors: Doose Gero , Haake Andrea , Bernhart Stephan H. , López Cristina , Duggimpudi Sujitha , Wojciech Franziska , Bergmann Anke K. , Borkhardt Arndt , Burkhardt Birgit , Claviez Alexander , Dimitrova Lora , Haas Siegfried , Hoell Jessica I. , Hummel Michael , Karsch Dennis , Klapper Wolfram , Kleo Karsten , Kretzmer Helene , Kreuz Markus , Küppers Ralf , Lawerenz Chris , Lenze Dido , Loeffler Markus , Mantovani-Löffler Luisa , Möller Peter , Ott German , Richter Julia , Rohde Marius , Rosenstiel Philip , Rosenwald Andreas , Schilhabel Markus , Schneider Markus , Scholz Ingrid , Stilgenbauer Stephan , Stunnenberg Hendrik G. , Szczepanowski Monika , Trümper Lorenz , Weniger Marc A. ,   ICGC MMML-Seq Consortium, Hoffmann Steve , Siebert Reiner , Iaccarino Ingram , Richter Gesine , Siebert Reiner , Wagner Susanne , Haake Andrea , Richter Julia , Eils Roland , Lawerenz Chris , Radomski Sylwester , Scholz Ingrid , Borst Christoph , Burkhardt Birgit , Claviez Alexander , Dreyling Martin , Eberth Sonja , Einsele Hermann , Frickhofen Norbert , Haas Siegfried , Hansmann Martin-Leo , Karsch Dennis , Kneba Michael , Lisfeld Jasmin , Mantovani-Löffler Luisa , Rohde Marius , Stadler Christina , Staib Peter , Stilgenbauer Stephan , Ott German , Trümper Lorenz , Zenz Thorsen , Hansmann Martin-Leo , Kube Dieter , Küppers Ralf , Weniger Marc , Haas Siegfried , Hummel Michael , Klapper Wolfram , Kostezka Ulrike , Lenze Dido , Möller Peter , Rosenwald Andreas , Szczepanowski Monika , Ammerpohl Ole , Aukema Sietse , Binder Vera , Borkhardt Arndt , Haake Andrea , Hezaveh Kebria , Hoell Jessica , Leich Ellen , Lichter Peter , Lopez Christina , Nagel Inga , Pischimariov Jordan , Radlwimmer Bernhard , Richter Julia , Rosenstiel Philip , Rosenwald Andreas , Schilhabel Markus , Schreiber Stefan , Vater Inga , Wagner Rabea , Siebert Reiner , Bernhart Stephan H. , Binder Hans , Brors Benedikt , Doose Gero , Eils Jürgen , Eils Roland , Hoffmann Steve , Hopp Lydia , Kretzmer Helene , Kreuz Markus , Korbel Jan , Langenberger David , Loeffler Markus , Radomski Sylwester , Rosolowski Maciej , Schlesner Matthias , Stadler Peter F. , Sungalee Stefanie
Published: September 2015

Significance

Gains of the MYC gene are the most common imbalances in cancer and are associated with poor prognosis, particularly in B-cell lymphoma. Recent advances in DNA sequencing have revealed the existence of thousands of long noncoding RNAs (lncRNAs) with unknown functional relevance. We have here identified a MYC-regulated lncRNA that we named MYC-induced long noncoding RNA (MINCR) that has a strong correlation with MYC expression in cancer. We show that MINCR is functional and controls cell cycle progression by influencing the expression of MYC-regulated cell cycle genes. MINCR is, therefore, a novel player in MYC’s transcriptional network, with the potential to open new therapeutic windows in the fight against malignant lymphoma and, possibly, all cancers that rely on MYC expression.
Mercury offloaded in Northern elephant seal hair affects coastal seawater surrounding rookery
Authors: Cossaboon Jennifer M. , Ganguli Priya M. , Flegal A. Russell
Published: September 2015

Significance

Mercury is a potent neurotoxin that accumulates in food webs, posing a global threat to environmental health. Marine mammals are common sentinel species for studying marine pollution; however, their potential role as vectors of contaminants to local ecosystems has rarely been addressed. By quantifying the concentration and chemical form of mercury in seawater affected by Northern elephant seal (
Mirounga angustirostris
) colonization, we demonstrated here that marine mammal behavioral ecology can substantially influence nearshore mercury cycling. Elevated methylmercury (MeHg) levels in seawater adjacent to the rookery during the molting season may become bioavailable to lower trophic levels, indicating that large marine mammal assemblages represent an important source of MeHg to nearshore food chains and coastal marine fisheries, thereby threatening ecosystem health.
Caenorhabditis elegans
ALG-1 antimorphic mutations uncover functions for Argonaute in microRNA guide strand selection and passenger strand disposal
Authors: Zinovyeva Anna Y. , Veksler-Lublinsky Isana , Vashisht Ajay A. , Wohlschlegel James A. , Ambros Victor R.
Published: September 2015

Significance

Loading of Argonautes with the correct strand of the pre-miRNA duplex and disposal of the other strand are essential steps in microRNA biogenesis. Here we report characterization of the protein and microRNA populations associated with mutant ALG-1 Argonautes that are defective in transitioning from microRNA processing to target repression. We show that mutant Argonaute erroneously associates with the normally discarded microRNA* strands, signifying a role for Argonaute ALG-1 in microRNA strand selection. Accumulation of microRNA* is dependent on the microRNA identity, suggesting that specific microRNA features allow wild-type Argonautes to distinguish among different microRNAs. These findings are relevant to understanding Argonaute roles in microRNA biogenesis and, more broadly, to the functions of microRNAs in development and disease.
TNF-α–stimulated fibroblasts secrete lumican to promote fibrocyte differentiation
Authors: Pilling Darrell , Vakil Varsha , Cox Nehemiah , Gomer Richard H.
Published: September 2015

Significance

Fibrosis is involved in 30–45% of deaths in the U.S. The disease may involve a runaway positive feedback loop between fibroblasts and monocyte-derived fibrocytes. The signals from fibrocytes to fibroblasts include inflammatory cytokines such as TNF-α, but the signals from TNF-α-stimulated fibroblasts to fibrocytes are unknown. We find that one of these signals is the protein lumican, and show that lumican levels are increased in fibrotic lesions. The identification of lumican as a signal in fibrotic tissues that promotes fibrocyte differentiation represents a major advance in our understanding of the regulation of the innate immune system, supports the positive feedback loop model of fibrosis, and indicates that lumican-inhibiting drugs may be beneficial in regulating fibrosis.
Design and structure of two HIV-1 clade C SOSIP.664 trimers that increase the arsenal of native-like Env immunogens
Authors: Julien Jean-Philippe , Lee Jeong Hyun , Ozorowski Gabriel , Hua Yuanzi , Torrents de la Peña Alba , de Taeye Steven W. , Nieusma Travis , Cupo Albert , Yasmeen Anila , Golabek Michael , Pugach Pavel , Klasse P. J. , Moore John P. , Sanders Rogier W. , Ward Andrew B. , Wilson Ian A.
Published: September 2015

Significance

A successful HIV-1 vaccine should generate an immune response capable of neutralizing the enormous diversity of globally circulating viruses. Here, we report the discovery and characterization of two clade C recombinant envelope glycoprotein trimers with native-like structural and antigenic properties, including epitopes for all known classes of broadly neutralizing antibodies (bnAbs). Together with previously described trimers from other clades, these two new trimers will aid in immunization strategies designed to induce bnAbs to HIV-1.
Long-term litter decomposition controlled by manganese redox cycling
Authors: Keiluweit Marco , Nico Peter , Harmon Mark E. , Mao Jingdong , Pett-Ridge Jennifer , Kleber Markus
Published: September 2015

Significance

The rate-controlling mechanisms of litter decomposition are of fundamental importance for ecosystem nutrient cycling, productivity, and net carbon (C) balance. Current C cycling models rely primarily on climatic factors and lignin content as the main predictors of litter decomposition rates. Here, we show how the ability of the integrated plant–soil system to promote active redox cycling of manganese (Mn) regulates litter decomposition. Our work suggests that incorporating the coupling of litter decomposition and other elemental cycles, such as the Mn cycle, into conceptual and numerical models may significantly improve our mechanistic understanding and predictions of C cycling in terrestrial ecosystems.
Fibroblast growth factor 9 is a novel modulator of negative affect
Authors: Aurbach Elyse L. , Inui Edny Gula , Turner Cortney A. , Hagenauer Megan H. , Prater Katherine E. , Li Jun Z. , Absher Devin , Shah Najmul , Blandino Peter , Bunney William E. , Myers Richard M. , Barchas Jack D. , Schatzberg Alan F. , Watson Stanley J. , Akil Huda
Published: September 2015

Significance

Molecular mechanisms mediating negative emotion and contributing to major depression remain elusive: here, we present evidence implicating fibroblast growth factor 9 (FGF9) as a key mediator. We use whole-transcriptome studies of postmortem human tissue to demonstrate that FGF9 is elevated in depression. Reverse translation animal studies demonstrate that both endogenous and exogenous FGF9 promotes anxiety- and depression-like behavior. Conversely, localized blockade of endogenous FGF9 expression decreases anxiety behavior. To our knowledge, this paper is the first description of hippocampal FGF9 function and the first evidence implicating FGF9 in negative affect. Thus, FGF9 represents a novel target for treating affective disorders. Moreover, our findings suggest that FGF2 and FGF9 work in functional opposition; we hypothesize that the balance between FGF factors may prove critical for optimal regulation of mood.
Caspase 3 cleavage of Pax7 inhibits self-renewal of satellite cells
Authors: Dick Sarah A. , Chang Natasha C. , Dumont Nicolas A. , Bell Ryan A. V. , Putinski Charis , Kawabe Yoichi , Litchfield David W. , Rudnicki Michael A. , Megeney Lynn A.
Published: September 2015

Significance

Satellite cells form the resident stem cell population in adult skeletal muscle, providing the foundation for postnatal growth and repair of this tissue. Satellite cell self-renewal is maintained by the paired-box transcription factor Pax7, suggesting that this protein is a key determinant in managing cell fate decisions for this niche. Here, we show activation of caspase 3 protease limits satellite cell self-renewal, through targeted cleavage and inactivation of Pax7 in a casein kinase (CK2)-dependent manner. Temporal regulation of caspase 3 activity may offer a robust mechanism to control the satellite cell compartment and enhance skeletal muscle regeneration.
Structural insight into selectivity and resistance profiles of ROS1 tyrosine kinase inhibitors
Authors: Davare Monika A. , Vellore Nadeem A. , Wagner Jacob P. , Eide Christopher A. , Goodman James R. , Drilon Alexander , Deininger Michael W. , O’Hare Thomas , Druker Brian J.
Published: September 2015

Significance

Targeting oncogenic ROS1 fusion proteins with crizotinib has shown promising clinical outcomes in non-small cell lung cancer (NSCLC) patients, but emergence of resistance to therapy has been reported. By profiling the activity of clinically viable ROS1/anaplastic lymphoma kinase (ALK) inhibitors, we discovered that the Food and Drug Administration (FDA)-approved inhibitor cabozantinib potently inhibits native ROS1 and the crizotinib-resistant ROS1
G2032R
mutant, suggesting potential utility for treatment of ROS1-rearranged lung cancer. Notably, cabozantinib is ineffective against the closely related ALK kinase. Molecular modeling shows specific structural differences between the kinase domains of ROS1 and ALK that explain selective binding of cabozantinib to ROS1. These findings reveal limitations pertaining to the widely presumed inhibitory reciprocity of ROS1 and ALK inhibitors and may facilitate rational design of new ROS1-selective inhibitors.
A mechanically driven form of Kirigami as a route to 3D mesostructures in micro/nanomembranes
Authors: Zhang Yihui , Yan Zheng , Nan Kewang , Xiao Dongqing , Liu Yuhao , Luan Haiwen , Fu Haoran , Wang Xizhu , Yang Qinglin , Wang Jiechen , Ren Wen , Si Hongzhi , Liu Fei , Yang Lihen , Li Hejun , Wang Juntong , Guo Xuelin , Luo Hongying , Wang Liang , Huang Yonggang , Rogers John A.
Published: September 2015

Significance

Existing options in three-dimensional (3D) assembly of micro/nanomaterials are constrained by a narrow accessible range of materials and/or 3D geometries. Here we introduce concepts for a form of Kirigami for the precise, mechanically driven assembly of 3D mesostructures from 2D micro/nanomembranes with strategically designed geometries and patterns of cuts. Theoretical and experimental studies in a broad set of examples demonstrate the applicability across length scales from macro to micro and nano, in materials ranging from monocrystalline silicon to metal and plastic, with levels of topographical complexity that significantly exceed those possible with other schemes. The resulting engineering options in functional 3D mesostructures have important implications for construction of advanced micro/nanosystems technologies.
Nanoscale patterning of STIM1 and Orai1 during store-operated Ca
2+
entry
Authors: Perni Stefano , Dynes Joseph L. , Yeromin Andriy V. , Cahalan Michael D. , Franzini-Armstrong Clara
Published: September 2015

Significance

Almost all cell types rely on calcium signals to maintain homeostasis and trigger specific cell responses. In eukaryotic cells, store-operated Ca
2+
entry (SOCE) is one of the mechanisms used to ensure control over cytosolic Ca
2+
signaling and internal Ca
2+
stores. Mutations in either Orai1 or stromal interaction molecule 1 (STIM1) lead to lethal severe combined immune deficiencies. Using a morphological approach with transmission and freeze–fracture electron microscopy, we describe STIM1-Orai1 interactions and visualize the distribution of individual Orai1 channels on the cell surface. This approach confirms STIM1-Orai1 interaction at specialized endoplasmic reticulum (ER)–plasma membrane junctions following ER depletion and provides new insight on STIM1-Orai1 stoichiometry.
Targeting protein translation, RNA splicing, and degradation by morpholino-based conjugates in
Plasmodium falciparum
Authors: Garg Aprajita , Wesolowski Donna , Alonso Dulce , Deitsch Kirk W. , Ben Mamoun Choukri , Altman Sidney
Published: September 2015

Significance

Malaria remains a major public health issue worldwide and world health organization estimates ∼198 million cases and ∼584,000 deaths in the year of 2013 alone due to malaria. Lack of an effective vaccine and rapid emergence of drug resistance are two major causes of this persistent problem. Understanding the biology of the parasite and studies of its gene function are essential to identify potential drug targets. Here we report a morpholino oligomer (MO)-based approach to alter gene expression via inhibition of post-transcriptional processes or by targeting mRNAs for degradation. The ease in design of the MO molecules presents a possibility for their use in large-scale genome functional analyses and possibly in malaria therapy.