bluuebunny/crossref_metadata_2025 huggingface dataset:
On cat's eyes and multiple disjoint cells natural convection flow in tall tilted cavities
Authors: Báez Elsa , Nicolás Alfredo
Published: October 2014

Natural convection fluid flow in air-filled tall tilted cavities is studied numerically with a direct projection method applied on the unsteady Boussinesq approximation in primitive variables. The study is focused on the so called cat's eyes and multiple disjoint cells as the aspect ratio A and the angle of inclination ϕ of the cavity vary. Results have already been reported with primitive and stream function-vorticity variables. The former are validated with the latter ones, which in turn were validated through mesh size and time-step independence studies. The new results complemented with the previous ones lead to find out the fluid motion and heat transfer invariant properties of this thermal phenomenon, which is the novelty here.
Exact stochastic unraveling of an optical coherence dynamics by cumulant expansion
Authors: Olšina Jan , Kramer Tobias , Kreisbeck Christoph , Mančal Tomáš
Published: October 2014

A numerically exact Monte Carlo scheme for calculation of open quantum system dynamics is proposed and implemented. The method consists of a Monte Carlo summation of a perturbation expansion in terms of trajectories in Liouville phase-space with respect to the coupling between the excited states of the molecule. The trajectories are weighted by a complex decoherence factor based on the second-order cumulant expansion of the environmental evolution. The method can be used with an arbitrary environment characterized by a general correlation function and arbitrary coupling strength. It is formally exact for harmonic environments, and it can be used with arbitrary temperature. Time evolution of an optically excited Frenkel exciton dimer representing a molecular exciton interacting with a charge transfer state is calculated by the proposed method. We calculate the evolution of the optical coherence elements of the density matrix and linear absorption spectrum, and compare them with the predictions of standard simulation methods.
Research Update: A hafnium-based metal-organic framework as a catalyst for regioselective ring-opening of epoxides with a mild hydride source
Authors: Stephenson Casey J. , Hassan Beyzavi M. , Klet Rachel C. , Hupp Joseph T. , Farha Omar K.
Published: October 2014

Reaction of styrene oxide with sodium cyanoborohydride and a catalytic amount of Hf-NU-1000 yields the anti-Markovnikov product, 2-phenylethanol, with over 98% regioselectivity. On the other hand, propylene oxide is ring opened in a Markovnikov fashion to form 2-propanol with 95% regioselectivity. Both styrene oxide and propylene oxide failed to react with sodium cyanoborohydride without the addition of Hf-NU-1000 indicative of the crucial role of Hf-NU-1000 as a catalyst in this reaction. To the best of our knowledge, this is the first report of the use of a metal-organic framework material as a catalyst for ring-opening of epoxides with hydrides.
Phase separation during freezing upon warming of aqueous solutions
Authors: Bogdan A. , Loerting T.
Published: October 2014

Using differential scanning calorimetry, we show that the addition of solute(s) to emulsified water lowers the freezing temperature to <231 K, the homogeneous nucleation temperature of pure bulk water, or even completely suppresses freezing. In the latter case, freezing upon warming occurs above TX ≈ 150 K and leads to a phase separation into pure ice and a freeze-concentrated solution (FCS) which crystallizes upon further warming. We also show that emulsified 20–21.5 wt. % HCl solutions and the FCS of HCl/H2O solutions transform to glass at Tg ≈ 127–128 K, i.e., lower than Tg ≈ 136 K of water. We suggest that water nanodrops adsorbed on fumed silica resemble bulk water more than water confined in nanoscaled confinement and also more than nanoscaled water domains in aqueous solution.
Explicit spatial description of fluid inclusions in porous matrices in terms of an inhomogeneous integral equation
Authors: Lomba Enrique , Bores Cecilia , Kahl Gerhard
Published: October 2014

We study the fluid inclusion of both Lennard-Jones (LJ) particles and particles with competing interaction ranges – short range attractive and long range repulsive (SALR) – in a disordered porous medium constructed as a controlled pore glass in two dimensions. With the aid of a full two-dimensional Ornstein-Zernike approach, complemented by a Replica Ornstein-Zernike integral equation, we explicitly obtain the spatial density distribution of the fluid adsorbed in the porous matrix and a good approximation for the average fluid-matrix correlations. The results illustrate the remarkable differences between the adsorbed LJ and SALR systems. In the latter instance, particles tend to aggregate in clusters which occupy pockets and bays in the porous structure, whereas the LJ fluid uniformly wets the porous walls. A comparison with Molecular Dynamics simulations shows that the two-dimensional Ornstein-Zernike approach with a Hypernetted Chain closure together with a sensible approximation for the fluid-fluid correlations can provide an accurate picture of the spatial distribution of adsorbed fluids for a given configuration of porous material.
Quantization of systems with temporally varying discretization. II. Local evolution moves
Authors: Höhn Philipp A.
Published: October 2014

Several quantum gravity approaches and field theory on an evolving lattice involve a discretization changing dynamics generated by evolution moves. Local evolution moves in variational discrete systems (1) are a generalization of the Pachner evolution moves of simplicial gravity models, (2) update only a small subset of the dynamical data, (3) change the number of kinematical and physical degrees of freedom, and (4) generate a dynamical (or canonical) coarse graining or refining of the underlying discretization. To systematically explore such local moves and their implications in the quantum theory, this article suitably expands the quantum formalism for global evolution moves, constructed in Paper I [P. A. Höhn, “Quantization of systems with temporally varying discretization. I. Evolving Hilbert spaces,” J. Math. Phys. 55, 083508 (2014); e-print arXiv:1401.6062 [gr-qc]], by employing that global moves can be decomposed into sequences of local moves. This formalism is spelled out for systems with Euclidean configuration spaces. Various types of local moves, the different kinds of constraints generated by them, the constraint preservation, and possible divergences in resulting state sums are discussed. It is shown that non-trivial local coarse graining moves entail a non-unitary projection of (physical) Hilbert spaces and “fine grained” Dirac observables defined on them. Identities for undoing a local evolution move with its (time reversed) inverse are derived. Finally, the implications of these results for a Pachner move generated dynamics in simplicial quantum gravity models are commented on.
Improved production of Br atoms near zero speed by photodissociating laser aligned Br2 molecules
Authors: Deng L. Z. , Yin J. P.
Published: October 2014

We theoretically investigated the improvement on the production rate of the decelerated bromine (Br) atoms near zero speed by photodissociating laser aligned Br2 precursors. Adiabatic alignment of Br2 precursors exposed to long laser pulses with duration on the order of nanoseconds was investigated by solving the time-dependent Schrödinger equation. The dynamical fragmentation of adiabatically aligned Br2 precursors was simulated and velocity distribution of the Br atoms produced was analyzed. Our study shows that the larger the degree of the precursor alignment, ⟨cos2 θ⟩, the higher the production rate of the decelerated Br atoms near zero speed. For Br2 molecules with an initial rotational temperature of ∼1 K, a ⟨cos2 θ⟩ value of ∼0.88 can result in an improvement factor of over ∼20 on the production rate of the decelerated Br atoms near zero speed, requiring a laser intensity of only ∼1 × 1012 W/cm2 for alignment.
Anisotropic energy transfers in quasi-static magnetohydrodynamic turbulence
Authors: Reddy K. Sandeep , Kumar Raghwendra , Verma Mahendra K.
Published: October 2014

We perform direct numerical simulations of quasi-static magnetohydrodynamic turbulence and compute various energy transfers including the ring-to-ring and conical energy transfers, and the energy fluxes of the perpendicular and parallel components of the velocity field. We show that the rings with higher polar angles transfer energy to ones with lower polar angles. For large interaction parameters, the dominant energy transfer takes place near the equator (polar angle θ≈π2). The energy transfers are local both in wavenumbers and angles. The energy flux of the perpendicular component is predominantly from higher to lower wavenumbers (inverse cascade of energy), while that of the parallel component is from lower to higher wavenumbers (forward cascade of energy). Our results are consistent with earlier results, which indicate quasi two-dimensionalization of quasi-static magnetohydrodynamic flows at high interaction parameters.
Effect of quantum well non-uniformities on lasing threshold, linewidth, and lateral near field filamentation in violet (Al,In)GaN laser diodes
Authors: Jeschke J. , Zeimer U. , Redaelli L. , Einfeldt S. , Kneissl M. , Weyers M.
Published: October 2014

The lateral near field patterns and filamentation effects of gain guided broad area (Al,In)GaN-based laser diodes emitting around 415 nm have been investigated. Diodes from the same laser bar, which are close to each other, show nearly the same number and widths of filaments. Comparison of different bars, which are from the same wafer but further apart from each other, reveals that a higher number of filaments correlates with a higher laser threshold and broader spectral linewidth. Cathodoluminescence mappings at 80 K show strong variations of the quantum well band gap and hence of the emission wavelength for the bars with strong filamentation. These observations confirm previous theoretical predictions stating that large band gap fluctuations increase the threshold current and spectral linewidth. Furthermore, filamentation is enhanced as well because of a reduction of the carrier diffusion length.
Joint contributions of Ag ions and oxygen vacancies to conducting filament evolution of Ag/TaOx/Pt memory device
Authors: Chung Yu-Lung , Cheng Wen-Hui , Jeng Jiann-Shing , Chen Wei-Chih , Jhan Sheng-An , Chen Jen-Sue
Published: October 2014

The electroforming and resistive switching behaviors in the Ag/TaOx/Pt trilayer structure are investigated under a continual change of temperatures between 300 K and 100 K to distinguish the contributions of Ag ions and oxygen vacancies in developing of conducting filaments. For either electroforming or resistive switching, a significantly higher forming/set voltages is needed as the device is operated at 100 K, as compared to that observed when operating at 300 K. The disparity in forming/set voltages of Ag/TaOx/Pt operating at 300 K and 100 K is attributed to the contribution of oxygen vacancies, in addition to Ag atoms, in formation of conducting filament at 100 K since the mobilities of oxygen vacancies and Ag ions become comparable at low temperature. The presence of oxygen vacancy segment in the conducting filament also modifies the reset current from a gradually descending behavior (at 300 K) to a sharp drop (at 100 K). Furthermore, the characteristic set voltage and reset current are irreversible as the operation temperature is brought from 100 K back to 300 K, indicating the critical role of filament constituents on the switching behaviors of Ag/oxide/Pt system.
Tunable electronic structure in dilute magnetic semiconductor Sr3SnO/c-YSZ/Si (001) epitaxial heterostructures
Authors: Lee Y. F. , Narayan J. , Schwartz J.
Published: October 2014

We report a systematic study of the structural, physical, and chemical properties of epitaxial thin films of emerging dilute magnetic semiconductor (DMS) Sr3SnO (SSO) integrated with Si (100) prepared by various post-growth annealing treatments. The transport properties of these films are primarily governed by oxygen vacancies and the results are explained with the variable-range hopping model. The increased oxygen vacancy concentration generated by post-growth vacuum annealing results in a shorter hopping distance and reduced hopping energy and Coulomb gap, leading to lower resistivity; oxygen annealing shows the opposite effects. The work function ranges from 4.54 to 4.02 eV and shows a negative linear relationship with oxygen vacancy concentration, accompanied by a 0.42 eV shift in the surface Fermi level. The transport and ultraviolet photoelectron spectroscopy probes agree quantitatively on measurement of the resistivity and surface electronic structure. The results provide a direct and consistent explanation that the property changes in the bulk and at the surface are primarily attributed to oxygen vacancies, which are believed to be the carriers in the SSO thin films. The ability to manipulate the work function and oxygen vacancy concentration in epitaxial DMS SSO thin films offers great potential for the development of spintronic devices.
The superionic phase transitions in (NH4)3H(SeO4)2 under hydrostatic pressure up to 400 MPa
Authors: Lindner Ł. , Zdanowska-Frączek M. , Pawłowski A. , Frączek Z. J.
Published: October 2014

The effect of hydrostatic pressure on proton conductivity of (NH4)3H(SeO4)2 superionic crystal was studied in a wide temperature range and different isobaric conditions by means of impedance spectroscopy method. The measurements were performed along the trigonal c axis of the crystal, i.e., along the direction perpendicular to the plane in which, in the superionic phases, a dynamically disordered H-bond network is formed. The obtained pressure-temperature phase diagram is linear with increasing pressure. The triple point, which is the point of coexistence of the three phases: ferroelastic phase IV, ferroelastic phase III, and superionic phase II was found at p = 116.3 MPa and T = 287.3 K. High pressure leads to increase in the temperature range of stability of both superionic phases and to a drastic decrease in the temperature width of the ferroelastic phase III. With increasing pressure, the range of the superionic phase II expands at the expense of the range of the ferroelastic phase III, which is unstable and vanishes at the triple point.
Collapse of ferromagnetism in itinerant-electron system: A magnetic, transport properties, and high pressure study of (Hf,Ta)Fe2 compounds
Authors: Diop L. V. B. , Kastil J. , Isnard O. , Arnold Z. , Kamarad J.
Published: October 2014

The magnetism and transport properties were studied for Laves (Hf,Ta)Fe2 itinerant-electron compounds, which exhibit a temperature-induced first-order transition from the ferromagnetic (FM) to the antiferromagnetic (AFM) state upon heating. At finite temperatures, the field-induced metamagnetic phase transition between the AFM and FM has considerable effects on the transport properties of these model metamagnetic compounds. A large negative magnetoresistance of about 14% is observed in accordance with the metamagnetic transition. The magnetic phase diagram is determined for the Laves Hf1−xTaxFe2 series and its Ta concentration dependence discussed. An unusual behavior is revealed in the paramagnetic state of intermediate compositions, it gives rise to the rapid increase and saturation of the local spin fluctuations of the 3d electrons. This new result is analysed in the frame of the theory of Moriya. For a chosen composition Hf0.825Ta0.175Fe2, exhibiting such remarkable features, a detailed investigation is carried out under hydrostatic pressure up to 1 GPa in order to investigate the volume effect on the magnetic properties. With increasing pressure, the magnetic transition temperature TFM-AFM from ferromagnetic to antiferromagnetic order decreases strongly non-linearly and disappears at a critical pressure of 0.75 GPa. In the pressure-induced AFM state, the field-induced first-order AFM-FM transition appears and the complex temperature dependence of the AFM-FM transition field is explained by the contribution from both the magnetic and elastic energies caused by the significant temperature variation of the amplitude of the local Fe magnetic moment. The application of an external pressure leads also to the progressive decrease of the Néel temperature TN. In addition, a large pressure effect on the spontaneous magnetization MS for pressures below 0.45 GPa, dln(Ms)/dP = −6.3 × 10−2 GPa−1 was discovered. The presented results are consistent with Moriya's theoretical predictions and can significantly help to better understand the underlying physics of itinerant electron magnetic systems nowadays widely investigated for both fundamental and applications purposes.
Ultra-fast selective sensing of ethanol and petrol using microwave-range metamaterial complementary split-ring resonators
Authors: Rawat Vaishali , Dhobale Sandip , Kale S. N.
Published: October 2014

An extremely compact metamaterial microstrip sensor based on complementary split-ring-resonators (CSRRs) has been fabricated for chemical sensing. This device exhibits a resonance with high rejection at 4.5 GHz, which demonstrates concomitant variations when exposed to liquids of various permittivity values. The resonance frequency of CSRR is sensitive to the change in nearby dielectric material. The sensing of petrol shows a shift in frequency with a sharp dip in transmission, while, with ethanol, the frequency shift is accompanied with increase in the power of the signal. The ultra-fast reversibility and repeatability offers good headway towards hybrid fuel sensing applications.
Circuit model optimization of a nano split ring resonator dimer antenna operating in infrared spectral range
Authors: Gneiding N. , Zhuromskyy O. , Shamonina E. , Peschel U.
Published: October 2014

Metamaterials are comprised of metallic structures with a strong response to incident electromagnetic radiation, like, for example, split ring resonators. The interaction of resonator ensembles with electromagnetic waves can be simulated with finite difference or finite elements algorithms, however, above a certain ensemble size simulations become inadmissibly time or memory consuming. Alternatively a circuit description of metamaterials, a well developed modelling tool at radio and microwave frequencies, allows to significantly increase the simulated ensemble size. This approach can be extended to the IR spectral range with an appropriate set of circuit element parameters accounting for physical effects such as electron inertia and finite conductivity. The model is verified by comparing the coupling coefficients with the ones obtained from the full wave numerical simulations, and used to optimize the nano-antenna design with improved radiation characteristics.
On-wafer magnetically tunable millimeter wave notch filter using M-phase Ba hexagonal ferrite/Pt thin films on Si
Authors: Harward I. , Camley R. E. , Celinski Z.
Published: October 2014

A prototype of a fully integrated on-wafer, magnetically tunable band-stop filter operating at millimeter wave frequencies is demonstrated on a Si substrate. In contrast to earlier studies, the filter uses a very thin barium hexagonal ferrite film incorporated into the dielectric layer of a microstrip transmission line to filter the signal. The zero-field operational frequency is about 34 GHz, increasing linearly with the strength of a static, perpendicularly applied magnetic field at a rate of about 2.7 GHz/kOe. Experimentally, high signal attenuation (33–67 dB/cm) at the resonance frequency and insertion losses as low as 4.5 dB were simultaneously observed, while the 3 dB device bandwidths were generally below 1 GHz. Our calculations are in quantitative agreement with the experimental results. We also find an important result that the thickness and conductivity of the Pt ground plane plays a key role in insertion losses, indicating directions for further improvements.
Interplay of light transmission and catalytic exchange current in photoelectrochemical systems
Authors: Fountaine Katherine T. , Lewerenz Hans J. , Atwater Harry A.
Published: October 2014

We develop an analytic current-voltage expression for a variable junction photoelectrochemical (PEC) cell and use it to investigate and illustrate the influence of the optical and electrical properties of catalysts on the optoelectronic performance of PEC devices. Specifically, the model enables a simple, yet accurate accounting of nanostructured catalyst optical and electrical properties through incorporation of an optical transmission factor and active catalytic area factor. We demonstrate the utility of this model via the output power characteristics of an exemplary dual tandem solar cell with indium gallium phosphide and indium gallium arsenide absorbers with varying rhodium catalyst nanoparticle loading. The approach highlights the importance of considering interactions between independently optimized components for optimal PEC device design.
Fano resonance of an asymmetric dielectric wire pair
Authors: Zhang Fuli , Huang XinChao , Zhao Qian , Chen Lei , Wang Ying , Li Qiang , He Xuan , Li Chang , Chen Ke
Published: October 2014

We experimentally demonstrate Fano resonance in a metamaterial composed of an asymmetric ferroelectric wire pair. By assembling two parallel ceramic wires of different lengths, sharp Fano-type transmission spectra emerge as a result of interference between the quadrupole and dipole modes. A rapid increase in group delay is observed as a result of a steep variation in transmission phase. The location of the Fano resonance peak depends on the wire separation and degree of asymmetry. Furthermore, Fano resonance can be thermally modulated from 9.8 GHz to 10.5 GHz as the ambient temperature varies from 10 °C to 50 °C, as a consequence of the temperature dependence of the permittivity of the ceramic material.
Homing and orientation of Palinurus elephas (Fabricius) in three no-take areas of the central-western Mediterranean: implications for marine reserve design
Authors: Follesa Maria Cristina , Cannas Rita , Cau Alessandro , Cuccu Danila , Mulas Antonello , Porcu Cristina , Saba Silvia , Cau Angelo
Published: October 2014

The homing and orientation skills of Palinurus elephas were investigated in three no-take areas of the central-western Mediterranean in order to inform future reserve design. In general, P. elephas did not show a particular ability to orient homeward. A considerable portion of tagged lobsters were recaptured in the same direction as the capture point but, the points of capture and recapture were at such a distance from each other as to exclude any possible return to the original den. Homing ability seemed to be constrained to where lobsters were only displaced a short distance. For distances longer than 0.5km, the lobster movements seem to become nomadic, without a particular direction. The movement pattern suggests that it will be important that any restocking of marine reserves must be performed with lobsters collected in adjacent zones at distance more than 0.5km. Lobsters captured in a fishing zone <0.5km outside the reserve will return to the point of capture whilethose collected from further away will not go back to their original place. Our results indicate that, for species like P. elephas, small reserves can protect most small subpopulations with a consequent benefit for the surrounding commercial areas.
Assessing surf-zone fish assemblage variability in southern Brazil
Authors: Rodrigues Fábio L. , Cabral Henrique N. , Vieira João P.
Published: October 2014

Surf-zone fish assemblage was investigated to assess its patterns of variability for two sandy beaches in southern Brazil. Fish were collected monthly (July 2009–June 2011), and the hauls were conducted with two different beach seine nets. Generalized linear models were used in the following two different approaches: (1) a Poisson model was used to assess and compare fish species richness; and (2) a logistic and gamma models were used to explain the occurrence and variability in abundance of Mugil liza and Trachinotus marginatus (dominant species). A set of nine explanatory variables was used to explain the patterns of ecological variability. At a large scale, seven variables explain 24.8% of the variance in species richness; and season (16.2%) and beach seine (3.0%) were the most important. The presence of M. liza was associated with beach seine (20.4%), whereas the abundance was associated with beach seine (12.1%) and five other explanatory variables. The presence and abundance of T. marginatus was associated with season (18.6% and 22.3%, respectively). Species richness seems to be strongly related to season, although the choice of net used can play an important role. Warmer months are richer in number of species, and the larger net is able to catch more species than the smaller one.
Use of underwater video to assess freshwater fish populations in dense submersed aquatic vegetation
Authors: Wilson Kyle L. , Allen Micheal S. , Ahrens Robert N. M. , Netherland Michael D.
Published: October 2014

Underwater video cameras (UVC) provide a non-lethal technique to sample fish in dense submersed aquatic vegetation. Fish often inhabit densely vegetated areas, but deficiencies of most sampling gears bias relative abundance estimates that inform fisheries management. This study developed methods using UVC to estimate relative abundance in dense vegetation using three experimental ponds covered with surface-matted hydrilla (Hydrilla verticillata) stocked at different densities of Lepomis spp. and largemouth bass (Micropterus salmoides). We conducted UVC point counts over 13 weeks to measure relative fish abundance and occurrence from video analysis. Ponds were then drained to obtain true fish densities. In total, fish were detected in 55% of all counts and juvenile and adult Lepomis spp. and largemouth bass were enumerated. End-of-season true fish densities ranged across ponds (from 52 to 37000 fishha–1). Additionally, pond 2’s true density changed substantially from 370 to 12300 fishha–1. True population size was accurately reflected in differences in estimated relative abundances obtained from fish counts, as in pond 2 where mean fish counts increased from 0.10 in week 1 to 2.33 by week 13. Underwater video accurately and precisely quantified relative abundance at naturally-occurring fish densities, but this success was reduced at low densities.
How long does it take to pay back rangeland improvement investments? A case study from Erzurum Province in Turkey
Authors: Kara Abdurrahman , Kadıoğlu Sibel , Dumlu S. Emre , Aksakal Erdal , Özgöz M. Merve , Uzun Mustafa , Çakal Şerafettin , Şimşek Uğur
Published: October 2014

The aim of the study was to estimate the payback period of rangeland improvement investments made under the coordination of the Eastern Anatolia Agricultural Research Institute (EAARI) in the Eastern Anatolia region, Turkey. Farm data were collected from randomly selected rangeland-dependent dairy cattle farms through face-to-face interviews, which resulted in 99 completed questionnaires. Additionally, the data for rangeland improvement studies were obtained from the EAARI. The villages of study were selected from those for which rangeland condition had been determined previously. The data collected by structured questionnaires were for the 2004–05 production year. The farms were studied under three farm size groups of 0–12, 12.1–25 and 25+ ha. Gross margins were calculated for each studied farm. In the analysis of the data, stepwise regression, multiple linear regression and descriptive statistical methods were used. Of the 17 variables considered, only four variables entered to the log-linear livestock gross margin model. These were the type of building used by livestock in winter, cattle and sheep numbers and rangeland condition. Using estimates of the average values of the unit costs of rangeland improvement and additional incomes due to the improvements, it was estimated that on average each Turkish lira invested in rangeland improvement studies could be amortised in three grazing seasons.
Scaling laws governing stochastic growth and division of single bacterial cells
Authors: Iyer-Biswas Srividya , Wright Charles S. , Henry Jonathan T. , Lo Klevin , Burov Stanislav , Lin Yihan , Crooks Gavin E. , Crosson Sean , Dinner Aaron R. , Scherer Norbert F.
Published: October 2014

Significance

Growth and division of individual cells are the fundamental events underlying many biological processes, including the development of organisms, the growth of tumors, and pathogen–host interactions. Quantitative studies of bacteria can provide insights into single-cell growth and division but are challenging owing to the intrinsic noise in these processes. Now, by using a unique combination of measurement and analysis technologies, together with mathematical modeling, we discover quantitative features that are conserved across physiological conditions. These universal behaviors reflect the physical principle that a single timescale governs noisy bacterial growth and division despite the complexity of underlying molecular mechanisms.
Unconscious information changes decision accuracy but not confidence
Authors: Vlassova Alexandra , Donkin Chris , Pearson Joel
Published: October 2014

Significance

One of the more intriguing but controversial ideas in psychology is that unconscious information can influence our decisions without us even knowing it. Here, we explicitly tested these controversial ideas with a novel behavioral task and computational models of decision-making. We report that unconscious information can be accumulated in a similar manner but less effectively than conscious information. However, unlike conscious information, unconscious information does not seem to boost decision confidence. Our findings cannot be accounted for using existing models of priming or adaptation.
Benchmarking all-atom simulations using hydrogen exchange
Authors: Skinner John J. , Yu Wookyung , Gichana Elizabeth K. , Baxa Michael C. , Hinshaw James R. , Freed Karl F. , Sosnick Tobin R.
Published: October 2014

Significance

Molecular dynamics simulations have recently become capable of observing multiple protein unfolding and refolding events in a single-millisecond–long trajectory. This major advance produces atomic-level information with nanosecond resolution, a feat unmatched by experimental methods. Such simulations are being extensively analyzed to assess their description of protein folding, yet the results remain difficult to validate experimentally. We apply a combination of hydrogen exchange, NMR, and other techniques to test the simulations with a resolution of single H-bonds. Several significant discrepancies between the simulations and experimental data were uncovered for regions of the energy surface outside of the native basin. This comparison yields suggestions for improving the force fields and provides a general method for experimentally validating folding simulations.
DLK1/PREF1 regulates nutrient metabolism and protects from steatosis
Authors: Charalambous Marika , Da Rocha Simao Teixeira , Radford Elizabeth Jane , Medina-Gomez Gema , Curran Scott , Pinnock Scarlett B. , Ferrón Sacri R. , Vidal-Puig Antonio , Ferguson-Smith Anne C.
Published: October 2014

Significance

Hepatosteatosis or nonalcoholic fatty liver disease (NAFLD) is an important health problem affecting approximately 20% of the population of the United States and is associated with cardiovascular risk factors such as insulin resistance and obesity. Using a Delta-like homologue (Dlk1) [also known as preadipocyte factor 1 (Pref1)] transgenic model, we identified a new player in the growth hormone (GH) signaling pathway that, when overexpressed, is protective against obesity and hepatosteatosis. Because the dosage of circulating DLK1 is naturally elevated in early life and during pregnancy, we believe that our transgenic model mimics endogenous mechanisms of DLK1-mediated GH signaling modulation that are used during periods of metabolic stress to protect from steatosis and alter fuel utilization in the whole organism.
Sensing nerve injury at the axonal ER: Activated Luman/CREB3 serves as a novel axonally synthesized retrograde regeneration signal
Authors: Ying Zhengxin , Misra Vikram , Verge Valerie M. K.
Published: October 2014

Significance

Peripheral nerve injury often occurs at axonal sites remote from the neuronal cell bodies. Information about these remote injuries must be accurately relayed back to the cell body as part of the reprogramming that occurs to transition the neuron to a regenerating state. We provide new insights into how the axonal endoplasmic reticulum (ER) proximal to the injury site generates a critical regeneration signal in sensory neurons. This involves injury-triggered activation and synthesis of an intraaxonal, ER transmembrane transcription factor, Luman/cAMP response element binding protein 3, that is retrogradely transported back into the nucleus. Manipulation of axon-derived Luman expression in injured sensory neurons reveals an important role for Luman in regulation of the intrinsic elongating form of axonal growth associated with the regeneration state.
p100/IκBδ sequesters and inhibits NF-κB through kappaBsome formation
Authors: Tao Zhihua , Fusco Amanda , Huang De-Bin , Gupta Kushol , Young Kim Daniel , Ware Carl F. , Van Duyne Gregory D. , Ghosh Gourisankar
Published: October 2014

Significance

NF-κB activation pathways program cells to induce various activities including survival and inflammation. NF-κB activation requires inhibitor IκB degradation. Two of the IκB proteins, p100 and p105, are also the precursors of two NF-κB proteins, p52 and p50. The mechanism by which the p100 inhibits NF-κB remains elusive. The X-ray structure of the C-terminal domain of p100 reveals tetrameric organization and an essential function of tetramerization in sequestering four NF-κB molecules in a subunit-independent manner. Such broader nonspecific NF-κB inhibition by p100 contrasts with the functions of other IκB proteins. A host of genetic mutations linked to excessive p100 processing derail homeostatic NF-κB activity. Our work provides a molecular framework to understand homeostatic regulation of p100 function.
Self-assembled MmsF proteinosomes control magnetite nanoparticle formation in vitro
Authors: Rawlings Andrea E. , Bramble Jonathan P. , Walker Robyn , Bain Jennifer , Galloway Johanna M. , Staniland Sarah S.
Published: October 2014

Significance

Magnetotactic bacteria produce morphologically precise magnetite nanoparticles within organelles termed “magnetosomes.” Biomineralization proteins tightly regulate crystallization of these nanoparticles. A master protein regulator of particle morphology in vivo, magnetosome membrane specific F (MmsF), has recently been discovered. In this study, we purified MmsF and two homologous proteins from
Magnetospirillum magneticum
strain AMB-1. MmsF imposes strict control over the formation of magnetite nanoparticles when added to chemical precipitation reactions, whereas the highly similar homologues produce alternative iron oxides with less desirable magnetic properties. Remarkably, these intrinsic membrane proteins with three membrane-spanning regions are water-soluble and self-assemble in vitro into nanoscale “proteinosomes.” We speculate that self-assembly exists in vivo and might be required for the activity of the protein.
Membrane-enabled dimerization of the intrinsically disordered cytoplasmic domain of ADAM10
Authors: Deng Wei , Cho Sungyun , Su Pin-Chuan , Berger Bryan W. , Li Renhao
Published: October 2014

Significance

Transmembrane receptors often dimerize to facilitate signaling across the cell membrane. Here we show that the intrinsically disordered cytoplasmic domain of a disintegrin and metalloprotease (ADAM)10, an important transmembrane protease, can acquire structure and dimerize when it is adjoined to a transmembrane helix and thus placed near the membrane surface. This study is, to our knowledge, the first report of a transmembrane helix enabling dimerization of an adjacent intrinsically disordered sequence, which not only advances our understanding of the activation mechanism of ADAM protease, but also provides novel insights on the principles of membrane–protein interactions and their roles in transmembrane signaling.
Stretch-activated ion channel Piezo1 directs lineage choice in human neural stem cells
Authors: Pathak Medha M. , Nourse Jamison L. , Tran Truc , Hwe Jennifer , Arulmoli Janahan , Le Dai Trang T. , Bernardis Elena , Flanagan Lisa A. , Tombola Francesco
Published: October 2014

Significance

Stem cells make lineage-choice decisions based on a combination of internal and external signals, including mechanical cues from the surrounding environment. Here we show that Piezo1, an ion channel opened by membrane tension, plays an important role in transducing matrix mechanical information to intracellular pathways affecting differentiation in neural stem cells. Piezo1 activity influences whether neural stem cells differentiate along a neuronal or astrocytic lineage. One of the barriers to successful neural stem cell transplantation therapy for neurological disorders lies in directing the fate of transplanted cells. Pharmacological agents aimed at modulating Piezo1 activity may be useful in directing the fate of transplanted neural stem cells toward the desired lineage.
Preservation of viral genomes in 700-y-old caribou feces from a subarctic ice patch
Authors: Ng Terry Fei Fan , Chen Li-Fang , Zhou Yanchen , Shapiro Beth , Stiller Mathias , Heintzman Peter D. , Varsani Arvind , Kondov Nikola O. , Wong Walt , Deng Xutao , Andrews Thomas D. , Moorman Brian J. , Meulendyk Thomas , MacKay Glen , Gilbertson Robert L. , Delwart Eric
Published: October 2014

Significance

Knowledge of ancient viruses is limited due to their low concentration and poor preservation in ancient specimens. Using a viral particle-associated nucleic acid enrichment approach, we genetically characterized one complete DNA and one partial RNA viral genome from a 700-y-old fecal sample preserved in ice. Using reverse genetics, we reconstituted the DNA virus, which replicated and systemically spread in a model plant species. Under constant freezing conditions, encapsidated viral nucleic acids may therefore be preserved for centuries. Our finding indicates that cryogenically preserved materials can be repositories of ancient viral nucleic acids, which in turn allow molecular genetics to regenerate viruses to study their biology.
Human population reduction is not a quick fix for environmental problems
Authors: Bradshaw Corey J. A. , Brook Barry W.
Published: October 2014

Significance

The planet’s large, growing, and overconsuming human population, especially the increasing affluent component, is rapidly eroding many of the Earth’s natural ecosystems. However, society’s only real policy lever to reduce the human population humanely is to encourage lower per capita fertility. How long might fertility reduction take to make a meaningful impact? We examined various scenarios for global human population change to the year 2100 by adjusting fertility and mortality rates (both chronic and short-term interventions) to determine the plausible range of outcomes. Even one-child policies imposed worldwide and catastrophic mortality events would still likely result in 5–10 billion people by 2100. Because of this demographic momentum, there are no easy ways to change the broad trends of human population size this century.
Unconscious discrimination of social cues from eye whites in infants
Authors: Jessen Sarah , Grossmann Tobias
Published: October 2014

Significance

The human eye with its prominent white sclera is thought to facilitate social and cooperative interactions among humans. While there is evidence for brain mechanisms that allow for the unconscious detection of eye cues in adults, it is not known whether this ability of the human brain emerges early in ontogeny and can therefore be considered a key feature of human social functioning. The current study provides neural evidence for the unconscious detection of emotion and gaze cues from the sclera in 7-mo-old infants. Our findings demonstrate the existence of fast, efficient, and reliable social cue detection mechanisms in the human infant brain that likely provide a vital foundation for the development of social interactive skills.
Size limits of self-assembled colloidal structures made using specific interactions
Authors: Zeravcic Zorana , Manoharan Vinothan N. , Brenner Michael P.
Published: October 2014

Significance

Nature uses hierarchical assembly to make complex structures such as biomolecules, virus shells, and microtubules with high fidelity. Today a key challenge is to translate this process to artificial systems, which hinges on understanding the fundamental questions of efficiency and scalability of self-assembly. Although self-assembly has been studied for decades, the principles behind it and its fundamental and practical limits are still largely unknown. In this paper we establish size limitations for assembling structures of controlled size and shape out of colloidal particles with specific interactions. Inspired by simulations of structures with highly variable shapes and sizes, we develop an understanding of yield through a general theory of excited states that compete with the desired structure in assembly.
Timing and heterogeneity of mutations associated with drug resistance in metastatic cancers
Authors: Bozic Ivana , Nowak Martin A.
Published: October 2014

Significance

Metastatic dissemination to surgically inaccessible sites is the major cause of death in cancer patients. Targeted therapies, often initially effective against metastatic disease, invariably fail due to resistance. We use mathematical modeling to study heterogeneity of resistance to treatment and describe for the first time, to our knowledge, the entire ensemble of resistant subclones present in metastatic lesions. We show that radiographically detectable metastatic lesions harbor multiple resistant subclones of comparable size and compare our predictions to clinical data on resistance-associated mutations in colorectal cancer patients. Our model provides important information for the development of second-line treatments that aim to inhibit known resistance mutations.
Stochastic nanoroughness modulates neuron–astrocyte interactions and function via mechanosensing cation channels
Authors: Blumenthal Nils R. , Hermanson Ola , Heimrich Bernd , Shastri V. Prasad
Published: October 2014

Significance

The role of soluble signals in neural differentiation and neurodegeneration is well established. However, the impact of nanotopography imposed by macromolecules within brain tissue on neuronal function and pathologies is not fully appreciated. We have discovered that nanoroughness can modulate the function of hippocampal neurons and their relationship with astrocytes. Inhibition of mechanosensing cation channels including Piezo-1, whose distribution is altered by nanotopography, abrogates the effects imposed by nanotopography and the association of neurons with astrocytes. The finding that regions of amyloid plaque buildup in Alzheimer’s involve changes to tissue nanoroughness provides a link between nanoscale physical cues and loss of function in neurons and may have implications in uncovering the factors that promote neurodegenerative diseases.
Direct and indirect punishment among strangers in the field
Authors: Balafoutas Loukas , Nikiforakis Nikos , Rockenbach Bettina
Published: October 2014

Significance

Why do humans cooperate in one-time interactions with strangers? The most prominent explanations for this long-standing puzzle rely on punishment of noncooperators, but differ in the form punishment takes. In models of direct punishment, noncooperators are punished directly at personal cost, whereas indirect reciprocity assumes that punishment is indirect by withholding rewards. To resolve the persistent debate on which model better explains cooperation, we conduct the first field experiment, to our knowledge, on direct and indirect punishment among strangers in real-life interactions. We show that many people punish noncooperators directly but prefer punishing indirectly by withholding help when possible. The occurrence of direct and indirect punishment in the field shows that both are key to understanding the evolution of human cooperation.
Structural basis for translational surveillance by the large ribosomal subunit-associated protein quality control complex
Authors: Lyumkis Dmitry , Oliveira dos Passos Dario , Tahara Erich B. , Webb Kristofor , Bennett Eric J. , Vinterbo Staal , Potter Clinton S. , Carragher Bridget , Joazeiro Claudio A. P.
Published: October 2014

Significance

All organisms have systems in place to ensure that aberrant nascent polypeptide chains are promptly dealt with before being released from ribosomes and posing harm to the cell. The ribosome-associated quality control complex (RQC), composed of the Ltn1 E3 ubiquitin ligase catalytic subunit and cofactors, has become a paradigm for understanding quality control in eukaryotes. However, exactly how RQC functions has remained unknown. Here, we determine the structure of the 60S subunit-bound RQC complex. The data provide critical insights into how RQC is able to selectively target aberrant nascent chains, while ignoring nascent chains in normally translating ribosomes. Furthermore, the structure shows the architecture of a ribosome-bound E3 ligase poised to mark nascent chains for degradation.
Functional conservation despite structural divergence in ligand-responsive RNA switches
Authors: Boerneke Mark A. , Dibrov Sergey M. , Gu Jing , Wyles David L. , Hermann Thomas
Published: October 2014

Significance

RNA viruses, including the human pathogenic hepatitis C virus (HCV), use a structured untranslated region of their genome to hijack host cell ribosomes for the synthesis of viral proteins. These genome regions are termed internal ribosome entry site (IRES) elements and are encoded by distinct sequences in different viruses but share common functional RNA motifs. This study shows that viral IRES elements contain conformationally flexible RNA switches, whose state can be captured by the binding of a common ligand. Conformational switching plays a role in the function of the IRES elements. These new RNA switches are smaller than previously discovered “riboswitches” and may be the simplest form of ligand-responsive mechanical modules in nucleic acids.
Fallout plume of submerged oil from
Deepwater Horizon
Authors: Valentine David L. , Fisher G. Burch , Bagby Sarah C. , Nelson Robert K. , Reddy Christopher M. , Sylva Sean P. , Woo Mary A.
Published: October 2014

Significance

Following the sinking of the
Deepwater Horizon
in the Gulf of Mexico an unprecedented quantity of oil irrupted into the ocean at a depth of 1.5 km. The novelty of this event makes the oil’s subsequent fate in the deep ocean difficult to predict. This work identifies a fallout plume of hydrocarbons from the Macondo Well contaminating the ocean floor over an area of 3,200 km
2
. Our analysis suggests the oil initially was suspended in deep waters and then settled to the underlying sea floor. The spatial distribution of contamination implicates accelerated settling as an important fate for suspended oil, supports a patchwork mosaic model of oil deposition, and frames ongoing attempts to determine the event’s impact on deep-ocean ecology.