bluuebunny/crossref_metadata_2025 huggingface dataset:
The magnitude of the effect of air pollution on sunshine hours in China
Authors: Wang Yawen , Yang Yonghui , Zhao Na , Liu Chen , Wang Qinxue
Published: April 2012

This study investigates the changes in sunshine hours in relation to API (Air Pollution Index) across China. Data were collected from a total of 38 cities over the period of 1960–2009. Sunshine hours in over 84% of the cities significantly (p < 0.05) decline with an average of 16.7% for the 1960s–2000s. This decline is mainly prevalent over Sichuan Basin (22.4%), North China Plain (18.8%), and Yangtze River Delta (18.2%). While the sunshine hour decline is largely in the 20th century (with the strongest drop in the 1980s and the least in the 1990s), it rebounds by 0.3% after 2000. For especially in winter seasons and the North China region, API is negatively related with sunshine hours. For days with API > 80, sunshine hours are on the average 0.7 h d−1 (8.4%) shorter than for days with API ≤ 80 under clear‐sky condition for 2001–2005. In cities with average daily API ≤ 80 and >80 for the 2000s, sunshine hour decline for the 1960s–2000s is 0.8 h d−1 (13.4%) and 1.0 h d−1 (15.9%) respectively. Winter seasons with high API (90) exhibit the highest sunshine hour decline (21.5%). The study shows that spatiotemporal changes in sunshine hours in China could largely be explained in terms of API.
Application of the CALIOP layer product to evaluate the vertical distribution of aerosols estimated by global models: AeroCom phase I results
Authors: Koffi Brigitte , Schulz Michael , Bréon Francois‐Marie , Griesfeller Jan , Winker David , Balkanski Yves , Bauer Susanne , Berntsen Terje , Chin Mian , Collins William D. , Dentener Frank , Diehl Thomas , Easter Richard , Ghan Steven , Ginoux Paul , Gong Sunling , Horowitz Larry W. , Iversen Trond , Kirkevåg Alf , Koch Dorothy , Krol Maarten , Myhre Gunnar , Stier Philip , Takemura Toshihiko
Published: April 2012

The CALIOP (Cloud‐Aerosol Lidar with Orthogonal Polarization) layer product is used for a multimodel evaluation of the vertical distribution of aerosols. Annual and seasonal aerosol extinction profiles are analyzed over 13 sub‐continental regions representative of industrial, dust, and biomass burning pollution, from CALIOP 2007–2009 observations and from AeroCom (Aerosol Comparisons between Observations and Models) 2000 simulations. An extinction mean height diagnostic (Zα) is defined to quantitatively assess the models' performance. It is calculated over the 0–6 km and 0–10 km altitude ranges by weighting the altitude of each 100 m altitude layer by its aerosol extinction coefficient. The mean extinction profiles derived from CALIOP layer products provide consistent regional and seasonal specificities and a low inter‐annual variability. While the outputs from most models are significantly correlated with the observed Zα climatologies, some do better than others, and 2 of the 12 models perform particularly well in all seasons. Over industrial and maritime regions, most models show higher Zα than observed by CALIOP, whereas over the African and Chinese dust source regions, Zα is underestimated during Northern Hemisphere Spring and Summer. The positive model bias in Zα is mainly due to an overestimate of the extinction above 6 km. Potential CALIOP and model limitations, and methodological factors that might contribute to the differences are discussed.
New measurements of lightning electric fields in Florida: Waveform characteristics, interaction with the ionosphere, and peak current estimates
Authors: Haddad Michael A. , Rakov Vladimir A. , Cummer Steven A.
Published: April 2012

We analyzed wideband electric field waveforms of 265 first and 349 subsequent return strokes in negative natural lightning. The distances ranged from 10 to 330 km. Evolution of first‐ and subsequent‐stroke field waveforms as a function of distance is examined. Statistics on the following field waveform parameters are given: initial electric field peak, opposite‐polarity overshoot, ratio of the initial electric field peak to the opposite polarity overshoot, zero‐to‐peak risetime, initial half‐cycle duration, and opposite polarity overshoot duration. The overwhelming majority of both first and subsequent return‐stroke field waveforms at 50 to 330 km exhibit an opposite polarity overshoot. At distances greater than 100 km, electric field waveforms, recorded under primarily daytime conditions, tend to be oscillatory. Using finite difference time domain modeling, we interpreted the initial positive half‐cycle and the opposite‐polarity overshoot as the ground wave and the second positive half‐cycle as the one‐hop ionospheric reflection. The observed difference in arrival times of these two waves for subsequent strokes is considerably smaller than for first strokes, suggesting that the first‐stroke electromagnetic field caused a descent of the ionospheric D‐layer. We speculate that there may be cumulative effect of multiple strokes in lowering the ionospheric reflection height. Return‐stroke peak currents estimated from the empirical formula, I = 1.5–0.037DE (where I is considered negative and in kA, E is the electric field peak considered positive and in V/m, and D is distance in km), are compared to those reported by the NLDN.
A detailed paleomagnetic record between 2.1 and 2.75 Ma at IODP Site U1314 in the North Atlantic: Geomagnetic excursions and the Gauss‐Matuyama transition
Authors: Ohno Masao , Hayashi Tatsuya , Komatsu Fumiki , Murakami Fumi , Zhao Meng , Guyodo Yohan , Acton Gary , Evans Helen F. , Kanamatsu Toshiya
Published: April 2012

This study investigated the detailed geomagnetic field variation between 2.1 and 2.75 Ma from a sediment core (IODP Site U1314) with high sedimentation rate (≥10 cm/kyr) and good age control. Characteristic remanent magnetization directions were well resolved by stepwise alternating field demagnetization. As a proxy of relative paleointensity, natural remanent magnetization (NRM) normalized by anhysteretic remanent magnetization (ARM) was used after testing that the influence of magnetic interaction in ARM is negligible. As a result, the following features of the geomagnetic field in the studied period have been revealed. During the transition of the Gauss‐Matuyama (G‐M) reversal and the Réunion Subchron, the paleointensity decreased to the value lower than 20% of the average intensity in the whole studied interval. In addition to these lows, eight paleointensity lows were found associated with large directional changes that satisfy the definition of a geomagnetic excursion. Four of these have ages close to ages reported for geomagnetic excursions in prior studies, whereas the other four excursions have not previously been observed. In our results, we confirm that the G‐M transition occurred in marine isotope stage 103 even if we consider the shift in depth due to the lock‐in process of magnetic particles. The temporal variation in paleointensity showed asymmetric behavior associated with the G‐M transition, with a gradual decrease prior to the transition and a rapid recovery after the transition.
Lithospheric flexure in the Sichuan Basin and Longmen Shan at the eastern edge of Tibet
Authors: Fielding Eric J. , McKenzie Dan
Published: April 2012

The mountain range at the steep eastern edge of the Tibetan Plateau, the Longmen Shan, was deformed by a Mw7.9 earthquake with oblique thrust and strike‐slip motion in 2008. The tectonic processes and structure of the lithosphere beneath this range have been controversial. Gravity measurements reflect the distribution of mass within the Earth, including the large load of rock above the geoid in mountain ranges. We investigate the response of the lithosphere to the load of the Longmen Shan and estimate the flexural rigidity or effective elastic thicknessTeusing new gravity data acquired by recent satellites and the combined GOCO2S and EIGEN‐6c datasets. The free‐air gravity anomalies over the Longmen Shan show that its mass is supported by flexure of the adjacent Sichuan Basin lithosphere, similar to the flexural support of the Himalayas. Analysis of a stacked profile of the free‐air anomalies shows that the effective elastic thickness of the basin lithosphere is greater than 10 km, but has a broad minimum misfit function with no upper limit on the thickness. Two‐dimensional admittance analysis shows theTe of easternmost Tibet is very low, approximately 7 km.
Sensitivity of an Earth system climate model to idealized radiative forcing
Authors: Andrews Timothy , Ringer Mark A. , Doutriaux‐Boucher Marie , Webb Mark J. , Collins William J.
Published: April 2012

We diagnose forcing and climate feedbacks in benchmark sensitivity experiments with the new Met Office Hadley Centre Earth system climate model HadGEM2‐ES. To identify the impact of newly‐included biogeophysical and chemical processes, results are compared to a parallel set of experiments performed with these processes switched off, and different couplings with the biogeochemistry. In abrupt carbon dioxide quadrupling experiments we find that the inclusion of these processes does not alter the global climate sensitivity of the model. However, when the change in carbon dioxide is uncoupled from the vegetation, or when the model is forced with a non‐carbon dioxide forcing – an increase in solar constant – new feedbacks emerge that make the climate system less sensitive to external perturbations. We identify a strong negative dust‐vegetation feedback on climate change that is small in standard carbon dioxide sensitivity experiments due to the physiological/fertilization effects of carbon dioxide on plants in this model.
How well do we know recent climate trends at the tropical tropopause?
Authors: Wang James S. , Seidel Dian J. , Free Melissa
Published: April 2012

The tropical tropopause is a transition layer between the troposphere and stratosphere that influences global climate and atmospheric chemistry. Several studies have reported multidecadal tropical tropopause cooling and have suggested a correlation between observed tropopause temperature and stratospheric water vapor. Our more rigorous examination of the observations shows tropopause trends have greater uncertainty than previously suggested and the cooling may not be statistically significant. We used two approaches to remove time‐varying bias effects from cold‐point tropopause trends estimated from radiosonde observations. Our results are consistent with expectations from a conceptual model of tropopause changes and could resolve discrepancies between complex climate models and observations.
The influence of changes in synoptic regimes on north Australian wet season rainfall trends
Authors: Catto J. L. , Jakob C. , Nicholls N.
Published: April 2012

Precipitation over the north of Australia mainly falls during the wet season and is associated with the Australian monsoon. Recent studies have shown that precipitation in the north and northwest of Australia during the wet season has increased over the past 50 years. In previous work, daily radiosonde data at a single site (Darwin) were used to identify five distinct wet season regimes, each associated with a characteristic synoptic circulation pattern and rainfall probability distribution. Here the five regimes are used to decompose the 50‐year precipitation trend at Darwin from 1957/1958–2007/2008 into two contributions; that due to changes in the regime relative frequency of occurrence, and that due to changes in the within‐regime precipitation. Over the entire wet season from September to April, the within‐regime precipitation does not change significantly for any of the regimes. However, the relative frequency of occurrence decreases significantly for the driest regimes, and increases significantly for one of the wettest regimes, suggesting that changes in the large‐scale circulation are a more important contributor to the precipitation trends than are thermodynamic changes. During December to March, the largest contributions to the total precipitation trend come from changes in all three of the wettest regimes. During November and April, when the average precipitation is lower, there is a large relative contribution to the precipitation trend from the increase in frequency of a wet regime and a decrease in frequency of the dry regimes. This contributes to the significant lengthening of the north Australian wet season.
Aeolian transport in the field: A comparison of the effects of different surface treatments
Authors: Dong Zhibao , Lv Ping , Zhang Zhengcai , Qian Guangqiang , Luo Wanyin
Published: April 2012

Aeolian transport represents the result of wind–surface interactions, and therefore depends strongly on variations in the characteristics of the sediment surface. We conducted field observations of aeolian transport of typical dune sand in three 80 m × 80 m plots with different surface treatments: gravel‐covered sand, enclosed shifting sand, and open (unprotected) shifting sand. The study was performed at the Shapotou Aeolian Experiment Site in the southeastern part of China's Tengger Desert to compare the effects of these different surface treatments on aeolian transport. To do so, we analyzed the flux density profiles and transport rates above each surface. The flux density profiles for all three treatments followed the exponential decay law that was proposed by most previous researchers to describe the saltation flux density profiles. Coefficients of the exponential decay function were defined as a function of the surface and the wind velocity. The enclosed and open plots with shifting sand had similar flux density profiles, but the flux density above gravel‐covered plots showed that transport decayed more slowly with increasing height, producing flux density profiles with a higher average saltation height. The transport rate above the three treatment plots tended to increase proportionally with the cube of the mean wind velocity and with the maximum wind velocity during the observation period, but was more strongly correlated with the square of drift potential. Transport rates above the plot with open shifting sand were greater than those above the plots with enclosed shifting sand and the gravel‐covered plot.
AKT‐dependent phosphorylation of Niban regulates nucleophosmin‐ and MDM2‐mediated p53 stability and cell apoptosis
Authors: Ji Haitao , Ding Zhiyong , Hawke David , Xing Dongming , Jiang Bing‐Hua , Mills Gordon B , Lu Zhimin
Published: April 2012

Although Niban is highly expressed in human cancer cells, the cellular functions of Niban remain largely unknown. We demonstrate here that ultraviolet irradiation induces phosphorylation of Niban at S602 by AKT, which increases the association of Niban with nucleophosmin and disassociation of nucleophosmin from the MDM2 complex. This leads to the promotion of MDM2–p53 interaction and subsequent p53 degradation, thereby providing an antiapoptotic effect. Conversely, depletion of or deficiency in Niban expression promotes stabilization of p53 with increased cell apoptosis. Our findings illustrate a pivotal role for AKT‐mediated phosphorylation of Niban in protecting cells from genotoxic stress–induced cell apoptosis.
Tailored ramp-loading via shock release of stepped-density reservoirs
Authors: Prisbrey Shon T. , Park Hye-Sook , Remington Bruce A. , Cavallo Robert , May Mark , Pollaine Stephen M. , Rudd Robert , Maddox Brian , Comley Andrew , Fried Larry , Blobaum Kerri , Wallace Russ , Wilson Mike , Swift David , Satcher Joe , Kalantar Dan , Perry Ted , Giraldez Emilio , Farrell Michael , Nikroo Abbas
Published: April 2012

The concept of a gradient piston drive has been extended from that of a single component reservoir, such as a high explosive, to that of a multi-component reservoir that utilizes low density foams and large shocks to achieve high pressures (∼3.5 mbar) and controlled pressure vs. time profiles on a driven sample. Simulated and experimental drives shaped through the use of multiple component (including carbonized resorcinol formaldehyde and SiO2 foam) reservoirs are compared. Individual density layers in a multiple component reservoir are shown to correlate with velocity features in the measured drive which enables the ability to tune a pressure drive by adjusting the components of the reservoir. Pre-shot simulations are shown to be in rough agreement with the data, but post-shot simulations involving the use of simulated plasma drives were needed to achieve an exact match. Results from a multiple component reservoir shot (∼3.5 mbar) at the National Ignition Facility are shown.
Massless, string localized quantum fields for any helicity
Authors: Plaschke M. , Yngvason J.
Published: April 2012

For any massless, irreducible representation of the covering of the proper, orthochronous Poincaré group we construct covariant, free quantum fields that generate the representation space from the vacuum and are localized in semi-infinite strings in the sense of commutation or anti-commutation of the field operators at space-like separation of the strings. Besides the space-like string direction the field operators carry a spinor or tensor index for one of the finite dimensional representations \documentclass[12pt]{minimal}\begin{document}$D^{(\frac{j}{2},\frac{k}{2})}$\end{document}D(j2,k2) of \documentclass[12pt]{minimal}\begin{document}$SL(2,\mathbb C)$\end{document}SL(2,C). For given (j, k) the possible integer or half-integer values that the helicity h can take are for string fields only restricted by the condition \documentclass[12pt]{minimal}\begin{document}$|h|\le \frac{j+k}{2}$\end{document}|h|≤j+k2, in contrast to the case of point localized fields where \documentclass[12pt]{minimal}\begin{document}$h=\frac{k}{2}-\frac{j}{2}$\end{document}h=k2−j2 must hold. For infinite helicity no additional index on the string-field is needed in the Bose case while in the Fermi case the fields carry an additional spinor index. For finite helicity we consider in particular string-localized fields that are generalized potentials for point localized fields. The short distance behavior of their two-point functions is independent of the helicity.
Non-integer flux: Why it does not work
Authors: Smilga A. V.
Published: April 2012

We consider the Dirac operator on S2 without one point in the case of non-integer magnetic flux. We show that the spectral problem for \documentclass[12pt]{minimal}\begin{document}$H = \big/\!\!\!\!{\cal D}^2$\end{document}H=D̸2 can be well defined, if including in the Hilbert space \documentclass[12pt]{minimal}\begin{document}${\cal H}$\end{document}H only nonsingular on S2 wave functions. However, this Hilbert space is not invariant under the action of \documentclass[12pt]{minimal}\begin{document}$\big/\!\!\!\!{\cal D}$\end{document}D̸ — for certain \documentclass[12pt]{minimal}\begin{document}$\psi \in {\cal H}$\end{document}ψ∈H, \documentclass[12pt]{minimal}\begin{document}$\big/\!\!\!\!{\cal D} \psi$\end{document}D̸ψ does not belong to \documentclass[12pt]{minimal}\begin{document}${\cal H}$\end{document}H anymore. This breaks explicitly the supersymmetry of the spectrum. In the integer flux case, supersymmetry can be restored if extending the Hilbert space to include locally regular sections of the corresponding fiber bundle. For non-integer fluxes, such an extension is not possible.
The influence of the ionizer geometry on the absolute density calibration of reactive neutral species in a molecular beam mass spectrometry
Authors: Krähling Tobias , Ellerweg Dirk , Benedikt Jan
Published: April 2012

Molecular beam mass spectrometry is a powerful diagnostic technique, which can be used for the measurement of absolute number densities of reactive species in non-equilibrium reactive plasmas. However, the calibration of absolute number densities is susceptible to systematic errors. Critical issues are the proper design of the sampling system and the correction of the background signal. Here we discuss the effect of reflections of particles from the molecular beam in an ionizer, formation of additional background particle density in the ionizer, and its effect on the density calibration of reactive particle densities. A Monte Carlo simulation of particle trajectories in the ionizer is used to estimate the detection probability of a beam particle after the collision with the ionizer wall. The simulation shows that as much as two-third of the signal can be due to scattered particles in the commercially available mass spectrometers. This effect leads to systematic underestimation of densities of reactive particles, which are reactive at the surface and, therefore, do not have any background density. A simple change in the ionizer geometry is suggested, which can significantly reduce this problem.
Formation of shock waves in a cold dusty plasma
Authors: Das G. C. , Choudhury Balen , Bora M. P.
Published: April 2012

In this brief report, we present our calculations leading to formation of coherent structures through shock waves, which is studied with the help of the Burger wave equation, in certain space plasmas contaminated by the massive cold dust grains. Burger equation, in an ideal Maxwellian complex plasma, is derived and results are reported, which could be relevant in case of different space and astrophysical plasmas including Saturn’s spokes, F-ring, planetary nebulae, etc.
Entropic estimate of cooperative binding of substrate on a single oligomeric enzyme: An index of cooperativity
Authors: Banerjee Kinshuk , Das Biswajit , Gangopadhyay Gautam
Published: April 2012

Here we have systematically studied the cooperative binding of substrate molecules on the active sites of a single oligomeric enzyme in a chemiostatic condition. The average number of bound substrate and the net velocity of the enzyme catalyzed reaction are studied by the formulation of stochastic master equation for the cooperative binding classified here as spatial and temporal. We have estimated the entropy production for the cooperative binding schemes based on single trajectory analysis using a kinetic Monte Carlo technique. It is found that the total as well as the medium entropy production shows the same generic diagnostic signature for detecting the cooperativity, usually characterized in terms of the net velocity of the reaction. This feature is also found to be valid for the total entropy production rate at the non-equilibrium steady state. We have introduced an index of cooperativity, C, defined in terms of the ratio of the surprisals or equivalently, the stochastic system entropy associated with the fully bound state of the cooperative and non-cooperative cases. The criteria of cooperativity in terms of C is compared with that of the Hill coefficient of some relevant experimental result and gives a microscopic insight on the mechanism of cooperative binding of substrate on a single oligomeric enzyme which is usually estimated from the macroscopic reaction rate.
Thermal boundary resistance for gold and CoFe alloy on silicon nitride films
Authors: Jeong Taehee , Zhu Jian-Gang , Chung Suk , Gibbons Matthew R.
Published: April 2012

Advances in microelectronics technology strongly depend on the thermal optimization of metal/dielectric interfaces, which requires precise modeling and thermal characterization of metal/dielectric structures. This work experimentally investigated the influence of metallic layers on the thermal boundary resistance of silicon nitride dielectric material. The results reveal that the thermal boundary resistance of silicon nitride thin films depends on the metallic layers. The thermal boundary resistance at the interface between Au and SiNx is larger than that between Co0.9Fe0.1 and SiNx. The reasons to cause this difference are discussed with phonon transmission probability and the ratio of the Debye temperature between metals and dielectrics.
Classical helium atom with radiation reaction
Authors: Camelio G. , Carati A. , Galgani L.
Published: April 2012

We study a classical model of helium atom in which, in addition to the Coulomb forces, the radiation reaction forces are taken into account. This modification brings in the model a new qualitative feature of a global character. Indeed, as pointed out by Dirac, in any model of classical electrodynamics of point particles involving radiation reaction one has to eliminate, from the a priori conceivable solutions of the problem, those corresponding to the emission of an infinite amount of energy. We show that the Dirac prescription solves a problem of inconsistency plaguing all available models which neglect radiation reaction, namely, the fact that in all such models, most initial data lead to a spontaneous breakdown of the atom. A further modification is that the system thus acquires a peculiar form of dissipation. In particular, this makes attractive an invariant manifold of special physical interest, the zero-dipole manifold that corresponds to motions in which no energy is radiated away (in the dipole approximation). We finally study numerically the invariant measure naturally induced by the time-evolution on such a manifold, and this corresponds to studying the formation process of the atom. Indications are given that such a measure may be singular with respect to that of Lebesgue.
Source of slow lithium atoms from Ne or H2 matrix isolation sublimation
Authors: Sacramento R. L. , Alves B. X. , Almeida D. T. , Wolff W. , Li M. S. , Cesar C. L.
Published: April 2012

We have studied, via laser absorption spectroscopy, the velocity distribution of 7Li atoms released from cryogenic matrices of solid neon or molecular hydrogen. The Li atoms are implanted into the Ne or H2 matrices – grown onto a sapphire substrate – by laser ablation of a solid Li or LiH precursor. A heat pulse is then applied to the sapphire substrate sublimating the matrix together with the isolated atoms. With a NiCr film resistor deposited directly onto the sapphire substrate we are able to transfer high instantaneous power to the matrix, thus reaching a fast sublimation regime. In this regime the Li atoms can get entrained in the released matrix gas, and we were also able to achieve matrix sublimation times down to 10 μs for both H2 or Ne matrix, enabling us to proceed with the trapping of the species of our interest such as atomic hydrogen, lithium, and molecules. The sublimation of the H2 matrix, with its large center-of-mass velocity, provides evidence for a new regime of one-dimensional thermalization. The laser ablated Li seems to penetrate the H2 matrix deeper than it does in Ne.
Ge atom distribution in buried dome islands
Authors: Portavoce A. , Hoummada K. , Berbezier I. , Ronda A. , Mangelinck D.
Published: April 2012

Laser-assisted atom probe tomography microscopy is used to provide direct and quantitative compositional measurements of tri-dimensional Ge distribution in Ge dome islands buried by Si. Sub-nanometer spatial resolution 3D imaging shows that islands keep their facets after deposition of the Si cap, and that the island/substrate/Si cap interfaces are abrupt. The core of the domes contains 55% of Ge, while the island shell exhibits a constant composition of 15% of Ge. The {113} facets of the islands present a Ge enrichment up to 35%. The wetting layer composition is not homogeneous, varying from 9.5% to 30% of Ge.
Perspective on density functional theory
Authors: Burke Kieron
Published: April 2012

Density functional theory (DFT) is an incredible success story. The low computational cost, combined with useful (but not yet chemical) accuracy, has made DFT a standard technique in most branches of chemistry and materials science. Electronic structure problems in a dazzling variety of fields are currently being tackled. However, DFT has many limitations in its present form: too many approximations, failures for strongly correlated systems, too slow for liquids, etc. This perspective reviews some recent progress and ongoing challenges.
Visualization of hybridization states with atomic resolution using electron energy loss spectroscopy mapping
Authors: Haruta M. , Kurashima K. , Nagai T. , Komatsu H. , Shimakawa Y. , Kurata H. , Kimoto K.
Published: April 2012

Hybridization state mapping with atomic resolution was demonstrated using electron energy loss spectroscopy combined with scanning transmission electron microscopy. The O 2p states hybridized with Sn 5s and Cu 3d in a layered double perovskite La2CuSnO6 were individually distinguished by significant contrast differences in the oxygen K-edge energy-loss near-edge structure. The anisotropic oxygen intensity in the distorted CuO6 octahedron resulting from the Jahn-Teller effect could also be observed. The localized Cu 3d hole in the bc plane was indirectly imaged in real space using two-dimensional oxygen mapping.
Evidence for giant piezoresistance effect in n-type silicon nanowire field-effect transistors
Authors: Kang Ting-Kuo
Published: April 2012

Experimental evidence for the giant piezoresistance (PZR) effect in n-type silicon nanowires (SiNWs) on silicon-on-insulator wafers, also called SiNW field-effect transistors (SiNWFETs), is demonstrated. While an external mechanical strain is applied to SiNWFETs depleted by a back-gate bias, a marked increase in the subthreshold drain current is found, thus supporting the widely reported giant piezoresistance effect. This increase can be attributed to the change in Si/SiO2 interface states, further suggesting interface trap-induced giant piezoresistance. Furthermore, through repeated cycles of tensile and released strain, the electromechanical response of the subthreshold drain current with time offers a potential for creating strain-gated SiNWFETs.
Note: Adhesive stamp electrodes using spider silk masks for electronic transport measurements of supra-micron sized samples
Authors: Steven E. , Jobiliong E. , Eugenio P. M. , Brooks J. S.
Published: April 2012

A procedure for fabricating adhesive stamp electrodes based on gold coated adhesive tape used to measure electronic transport properties of supra-micron samples in the lateral range 10–100 μm and thickness >1 μm is described. The electrodes can be patterned with a ∼4 μm separation by metal deposition through a mask using Nephila clavipes spider dragline silk fibers. Ohmic contact is made by adhesive lamination of a sample onto the patterned electrodes. The performance of the electrodes with temperature and magnetic field is demonstrated for the quasi-one-dimensional organic conductor (TMTSF)2PF6 and single crystal graphite, respectively.
Transformational adaptation when incremental adaptations to climate change are insufficient
Authors: Kates Robert W. , Travis William R. , Wilbanks Thomas J.
Published: April 2012

All human–environment systems adapt to climate and its natural variation. Adaptation to human-induced change in climate has largely been envisioned as increments of these adaptations intended to avoid disruptions of systems at their current locations. In some places, for some systems, however, vulnerabilities and risks may be so sizeable that they require transformational rather than incremental adaptations. Three classes of transformational adaptations are those that are adopted at a much larger scale, that are truly new to a particular region or resource system, and that transform places and shift locations. We illustrate these with examples drawn from Africa, Europe, and North America. Two conditions set the stage for transformational adaptation to climate change: large vulnerability in certain regions, populations, or resource systems; and severe climate change that overwhelms even robust human use systems. However, anticipatory transformational adaptation may be difficult to implement because of uncertainties about climate change risks and adaptation benefits, the high costs of transformational actions, and institutional and behavioral actions that tend to maintain existing resource systems and policies. Implementing transformational adaptation requires effort to initiate it and then to sustain the effort over time. In initiating transformational adaptation focusing events and multiple stresses are important, combined with local leadership. In sustaining transformational adaptation, it seems likely that supportive social contexts and the availability of acceptable options and resources for actions are key enabling factors. Early steps would include incorporating transformation adaptation into risk management and initiating research to expand the menu of innovative transformational adaptations.
Induction of microRNA-155 is TLR- and type IV secretion system-dependent in macrophages and inhibits DNA-damage induced apoptosis
Authors: Koch Manuel , Mollenkopf Hans-Joachim , Klemm Uwe , Meyer Thomas F.
Published: April 2012

Helicobacter pyloriis a gastric pathogen responsible for a high disease burden worldwide. Deregulated inflammatory responses, possibly involving macrophages, are implicated inH.pylori-induced pathology, and microRNAs, such as miR-155, have recently emerged as crucial regulators of innate immunity and inflammatory responses. miR-155 is regulated by Toll-like receptor (TLR) ligands in monocyte-derived cells and has been shown to be induced in macrophages duringH.pyloriinfection. Here, we investigated the regulation of miR-155 expression in primary murine bone marrow-derived macrophages (BMMs) duringH.pyloriinfection and examined the downstream mRNA targets of this microRNA using microarray analysis. We report TLR2/4- and NOD1/2-independent up-regulation of miR-155, which was found to be dependent on the majorH.pyloripathogenicity determinant, the type IV secretion system (T4SS). miR-155 expression was dependent on NF-κB signaling but was independent of CagA. Microarray analysis identified known gene targets of miR-155 in BMMs duringH.pyloriinfection that are proapoptotic. We also identified and validated miR-155 binding sites in the 3′ UTRs of the targets,Tspan14,Lpin1, andPmaip1. We observed thatH.pylori-infected miR-155−/−BMMs were significantly more susceptible to cisplatin DNA damage-induced apoptosis than were wild-type BMMs. Thus, our data suggest a function for the prototypicalH.pyloripathogenicity factor, the T4SS, in the up-regulation of miR-155 in BMMs. We propose the antiapoptotic effects of miR-155 could enhance macrophage resistance to apoptosis induced by DNA damage duringH.pyloriinfection.
Global changes in diets and the consequences for land requirements for food
Authors: Kastner Thomas , Rivas Maria Jose Ibarrola , Koch Wolfgang , Nonhebel Sanderine
Published: April 2012

Provision of food is a prerequisite for the functioning of human society. Cropland where food and feed are grown is the central, limiting resource for food production. The amount of cropland needed depends on population numbers, average food consumption patterns, and output per unit of land. Around the globe, these factors show large differences. We use data from the Food and Agriculture Organization to consistently assess subcontinental dynamics of how much land was needed to supply the prevailing diets during a span of 46 y, from 1961 to 2007. We find that, in most regions, diets became richer while the land needed to feed one person decreased. A decomposition approach is used to quantify the contributions of the main drivers of cropland requirements for food: changes in population, agricultural technology, and diet. We compare the impact of these drivers for different subcontinents and find that potential land savings through yield increases were offset by a combination of population growth and dietary change. The dynamics of the three factors were the largest in developing regions and emerging economies. The results indicate an inverse relationship between the two main drivers behind increased land requirements for food: with socioeconomic development, population growth decreases and, at the same time, diets become richer. In many regions, dietary change may override population growth as major driver behind land requirements for food in the near future.
Intrinsic disorder modulates protein self-assembly and aggregation
Authors: De Simone Alfonso , Kitchen Craig , Kwan Ann H. , Sunde Margaret , Dobson Christopher M. , Frenkel Daan
Published: April 2012

Protein molecules have evolved to adopt distinctive and well-defined functional and soluble states under physiological conditions. In some circumstances, however, proteins can self-assemble into fibrillar aggregates designated as amyloid fibrils. In vivo these processes are normally associated with severe pathological conditions but can sometimes have functional relevance. One such example is the hydrophobins, whose aggregation at air–water interfaces serves to create robust protein coats that help fungal spores to resist wetting and thus facilitate their dispersal in the air. We have performed multiscale simulations to address the molecular determinants governing the formation of functional amyloids by the class I fungal hydrophobin EAS. Extensive samplings of full-atom replica-exchange molecular dynamics and coarse-grained simulations have allowed us to identify factors that distinguish aggregation-prone from highly soluble states of EAS. As a result of unfavourable entropic terms, highly dynamical regions are shown to exert a crucial influence on the propensity of the protein to aggregate under different conditions. More generally, our findings suggest a key role that specific flexible structural elements can play to ensure the existence of soluble and functional states of proteins under physiological conditions.
Promiscuous restriction is a cellular defense strategy that confers fitness advantage to bacteria
Authors: Vasu Kommireddy , Nagamalleswari Easa , Nagaraja Valakunja
Published: April 2012

Most bacterial genomes harbor restriction–modification systems, encoding a REase and its cognate MTase. On attack by a foreign DNA, the REase recognizes it as nonself and subjects it to restriction. Should REases be highly specific for targeting the invading foreign DNA? It is often considered to be the case. However, when bacteria harboring a promiscuous or high-fidelity variant of the REase were challenged with bacteriophages, fitness was maximal under conditions of catalytic promiscuity. We also delineate possible mechanisms by which the REase recognizes the chromosome as self at the noncanonical sites, thereby preventing lethal dsDNA breaks. This study provides a fundamental understanding of how bacteria exploit an existing defense system to gain fitness advantage during a host–parasite coevolutionary “arms race.”
Designing biomimetic pores based on carbon nanotubes
Authors: García-Fandiño Rebeca , Sansom Mark S. P.
Published: April 2012

Biomimetic nanopores based on membrane-spanning single-walled carbon nanotubes have been designed to include selectivity filters based on combinations of anionic and cationic groups mimicking those present in bacterial porins and in voltage-gated sodium and calcium channels. The ion permeation and selectivity properties of these nanopores when embedded in a phospholipid bilayer have been explored by molecular dynamics simulations and free energy profile calculations. The interactions of the nanopores with sodium, potassium, calcium, and chloride ions have been explored as a function of the number of anionic and cationic groups within the selectivity filter. Unbiased molecular dynamics simulations show that the overall selectivity is largely determined by the net charge of the filter. Analysis of distribution functions reveals considerable structuring of the distribution of ions and water within the nanopores. The distributions of ions along the pore axis reveal local selectivity for cations around filter, even in those nanopores (C0) where the net filter charge is zero. Single ion free energy profiles also reveal clear evidence for cation selectivity, even in the C0 nanopores. Detailed analysis of the interactions of the C0 nanopore with Ca
2+
ions reveals that local interactions with the anionic (carboxylate) groups of the selectivity filter lead to (partial) replacement of solvating water as the ion passes through the pore. These studies suggest that a computational biomimetic approach can be used to evaluate our understanding of the design principles of nanopores and channels.
Pressure tunes electrical resistivity by four orders of magnitude in amorphous Ge
2
Sb
2
Te
5
phase-change memory alloy
Authors: Xu M. , Cheng Y. Q. , Wang L. , Sheng H. W. , Meng Y. , Yang W. G. , Han X. D. , Ma E.
Published: April 2012

Ge-Sb-Te-based phase-change memory is one of the most promising candidates to succeed the current flash memories. The application of phase-change materials for data storage and memory devices takes advantage of the fast phase transition (on the order of nanoseconds) and the large property contrasts (e.g., several orders of magnitude difference in electrical resistivity) between the amorphous and the crystalline states. Despite the importance of Ge-Sb-Te alloys and the intense research they have received, the possible phases in the temperature–pressure diagram, as well as the corresponding structure–property correlations, remain to be systematically explored. In this study, by subjecting the amorphous Ge
2
Sb
2
Te
5
(
a
-GST) to hydrostatic-like pressure (
P
), the thermodynamic variable alternative to temperature, we are able to tune its electrical resistivity by several orders of magnitude, similar to the resistivity contrast corresponding to the usually investigated amorphous-to-crystalline (
a
-GST to rock-salt GST) transition used in current phase-change memories. In particular, the electrical resistivity drops precipitously in the
P
 = 0 to 8 GPa regime. A prominent structural signature representing the underlying evolution in atomic arrangements and bonding in this pressure regime, as revealed by the ab initio molecular dynamics simulations, is the reduction of low-electron-density regions, which contributes to the narrowing of band gap and delocalization of trapped electrons. At
P
 > 8 GPa, we have observed major changes of the average local structures (bond angle and coordination numbers), gradually transforming the
a
-GST into a high-density, metallic-like state. This high-pressure glass is characterized by local motifs that bear similarities to the body-centered-cubic GST (
bcc
-GST) it eventually crystallizes into at 28 GPa, and hence represents a
bcc
-type polyamorph of
a
-GST.
Snapshot of virus evolution in hypersaline environments from the characterization of a membrane-containing
Salisaeta
icosahedral phage 1
Authors: Aalto Antti P. , Bitto David , Ravantti Janne J. , Bamford Dennis H. , Huiskonen Juha T. , Oksanen Hanna M.
Published: April 2012

The multitude of archaea and bacteria inhabiting extreme environments has only become evident during the last decades. As viruses apply a significant evolutionary force to their hosts, there is an inherent value in learning about viruses infecting these extremophiles. In this study, we have focused on one such unique virus–host pair isolated from a hypersaline environment: an icosahedral, membrane-containing double-stranded DNA virus—
Salisaeta
icosahedral phage 1 (SSIP-1) and its halophilic host bacterium
Salisaeta
sp. SP9-1 closely related to
Salisaeta longa
. The architectural principles, virion composition, and the proposed functions associated with some of the ORFs of the virus are surprisingly similar to those found in viruses belonging to the PRD1–adenovirus lineage. The virion structure, determined by electron cryomicroscopy, reveals that the bulk of the outer protein capsid is composed of upright standing pseudohexameric capsomers organized on a
T
= 49 icosahedral lattice. Our results give a comprehensive description of a halophilic virus–host system and shed light on the relatedness of viruses based on their virion architecture.
Membrane binding ofEscherichia coliRNase E catalytic domain stabilizes protein structure and increases RNA substrate affinity
Authors: Murashko Oleg N. , Kaberdin Vladimir R. , Lin-Chao Sue
Published: April 2012

RNase E plays an essential role in RNA processing and decay and tethers to the cytoplasmic membrane inEscherichia coli; however, the function of this membrane–protein interaction has remained unclear. Here, we establish a mechanistic role for the RNase E–membrane interaction. The reconstituted highly conserved N-terminal fragment of RNase E (NRne, residues 1–499) binds specifically to anionic phospholipids through electrostatic interactions. The membrane-binding specificity of NRne was confirmed using circular dichroism difference spectroscopy; the dissociation constant (Kd) for NRne binding to anionic liposomes was 298 nM.E.coliRNase G and RNase E/G homologs from phylogenetically distantAquifex aeolicus, Haemophilus influenzaeRd, andSynechocystissp. were found to be membrane-binding proteins. Electrostatic potentials of NRne and its homologs were found to be conserved, highly positive, and spread over a large surface area encompassing four putative membrane-binding regions identified in the “large” domain (amino acids 1–400, consisting of the RNase H, S1, 5′-sensor, and DNase I subdomains) ofE.coliNRne. In vitro cleavage assay using liposome-free and liposome-bound NRne and RNA substrates BR13 and GGG-RNAI showed that NRne membrane binding altered its enzymatic activity. Circular dichroism spectroscopy showed no obvious thermotropic structural changes in membrane-bound NRne between 10 and 60 °C, and membrane-bound NRne retained its normal cleavage activity after cooling. Thus, NRne membrane binding induced changes in secondary protein structure and enzymatic activation by stabilizing the protein-folding state and increasing its binding affinity for its substrate. Our results demonstrate that RNase E–membrane interaction enhances the rate of RNA processing and decay.
Regulation of selective autophagy onset by a Ypt/Rab GTPase module
Authors: Lipatova Zhanna , Belogortseva Natalia , Zhang Xiu Qi , Kim Jane , Taussig David , Segev Nava
Published: April 2012

The key regulators of intracellular trafficking, Ypt/Rab GTPases, are stimulated by specific upstream activators and, when activated, recruit specific downstream effectors to mediate membrane-transport events. The yeast Ypt1 and its human functional homolog hRab1 regulate both endoplasmic reticulum (ER)-to-Golgi transport and autophagy. However, it is not clear whether the mechanism by which these GTPases regulate autophagy depends on their well-documented function in ER-to-Golgi transport. Here, we identify Atg11, the preautophagosomal structure (PAS) organizer, as a downstream effector of Ypt1 and show that the Ypt1–Atg11 interaction is required for PAS assembly under normal growth conditions. Moreover, we show that Ypt1 and Atg11 colocalize with Trs85, a Ypt1 activator subunit, and together they regulate selective autophagy. Finally, we show that Ypt1 and Trs85 interact on Atg9-containing membranes, which serve as a source for the membrane component of the PAS. Together our results define a Ypt/Rab module—comprising an activator, GTPase, and effector—that orchestrates the onset of selective autophagy, a process vital for cell homeostasis. Furthermore, because Atg11 does not play a role in ER-to-Golgi transport, we demonstrate here that Ypt/Rabs can regulate two independent membrane-transport processes by recruiting process-specific effectors.