bluuebunny/crossref_metadata_2025 huggingface dataset:
An Overview of Atomic Spectrometric Techniques
Authors: Sanz‐Medel Alfredo , Pereiro Rosario , Manuel Costa‐Fernández José
Published: June 2013

The principles, instrumentation, and analytical performance of most common quantitative atomic techniques based on optical spectrometry (absorption, emission or fluorescence) and mass spectrometry for the analysis of liquid samples and for direct solid analysis are outlined. Emphasis is given to conceptual explanations aiming to stress the advantages and disadvantages of each technique, the increase in the complexity of the data they generate and how this can be addressed. Powerful quantification strategies such as isotope dilution analysis are also discussed. Moreover, considering that on‐line liquid sample introduction systems such as flow injection manifolds and chromatography have become commonplace in most laboratories, a section is dedicated to the combination of flow systems with spectrometric detection techniques; in this context, special attention is paid to modern issues related to detection of fast transient signals. Finally, a brief introduction to quality assurance control guidelines, instrument maintenance and troubleshooting is provided.
Performance estimation of two‐sliding mode controllers for chatter reduction in linear systems
Authors: O'Toole Michael D. , Bouazza‐Marouf Kaddour , Kerr David
Published: June 2013

Sliding mode control is a simple and powerful technique for the robust control of uncertain systems. However, despite theoretical promise, real systems using sliding mode controllers have a tendency to chatter at higher frequencies. Second order or two‐sliding mode controllers, can be used to suppress chatter while retaining the desirable properties of a classical sliding mode controller. These more complex controllers increase the number of parameters in the system. The affect of these new parameters on system performance is unclear, and this can make it difficult to tune the controllers to meet a desired performance criteria. This study addresses the problem of estimating the performance of a system controlled by two‐sliding mode controllers. Describing functions are proposed to estimate chattering amplitude and settling time, and a new method is presented, based on invariant ellipsoid sets, to predict the maximum output bound of the system. The aim is assist in producing a systematic approach for practitioners wishing to directly apply sliding mode controllers with chatter suppressing properties to real applications.
Design and performance evaluation of a bidirectional isolated dc–dc converter with extended dual‐phase‐shift scheme
Authors: Wen Huiqing , Su Bin , Xiao Weidong
Published: June 2013

This study describes the design and performance evaluation of a bidirectional isolated dc–dc converter with an extended dual‐phase‐shift (EDPS) scheme. The operation principle and equivalent circuits with consideration of the deadband are presented. The deadband effect with EDPS is different from the conventional phase‐shift (CPS) scheme, and the corresponding compensation coefficient is determined. Different operation modes are identified with respect to phase‐shift angles of EDPS and load conditions. The safe operational area is also analysed with the comparison of different operation modes. The output voltage and output power characteristics with open‐loop or closed‐loop operation are discussed. The average theoretical 48.5% reduction in the output voltage ripple using EDPS has been achieved. The average reduction in inductor peak and rms with EDPS are statistically calculated as 37.8 and 26.8%. The measured efficiency has improved from 68.1% using CPS to 81.9% using EDPS for low‐power application.
Improved power quality bridgeless Cuk converter fed brushless DC motor drive for air conditioning system
Authors: Singh Bhim , Bist Vashist
Published: June 2013

This study presents a bridgeless Cuk converter‐fed brushless DC (BLDC) motor drive for an air conditioning system. A new approach of speed control of BLDC motor is proposed by controlling the voltage at DC bus using a single voltage sensor. The proposed drive utilises a bridgeless Cuk converter operating in discontinuous inductor current mode (DICM) for the power factor correction (PFC) and improved power quality (PQ) at the AC mains for a wide range of speed control. The bridgeless Cuk converter operating in a DICM gives an inherent PFC and requires a simple voltage follower approach for the voltage control. The bridgeless converter topology is designed for obtaining the low conduction losses and requirement of low size of heat sink for the switches. The proposed system is designed and its performance is simulated for an air conditioning system to operate over a wide range of speed control with near unity power factor at AC mains. Finally, the performance of the proposed drive obtained in simulation is validated with test results on a developed drive for its operation over a wide range of speed control with improved PQ at AC mains.
Performance improvement for IEEE 802.15.4 CSMA/CA scheme in large‐scale wireless multi‐hop sensor networks
Authors: Zhu Jianping , Tao Zhengsu , Lv Chunfeng
Published: June 2013

The hidden‐terminal problem and routing establishment or maintenance bring about a tremendous amount of energy consumption in multi‐hop wireless sensor networks (WSNs). In this study, the authors propose a carrier sense multiple access with collision avoidance (CSMA/CA) scheme MultiCSMA for multi‐hop WSNs adopting two strategies which refer to a novel hidden‐terminal list algorithm to avoid the impact of hidden terminals and a parallel access scheme to dispense with taking the routing overhead into account. The accurate statistical performance metrics of throughput and delay of unsaturated, unacknowledged IEEE 802.15.4 beacon enabled networks for one‐hop and two‐hop scenarios are predicted based on Markov models adopting these two improved strategies, in which nodes are assumed to locate randomly over a circle plane according to Poisson distribution. Comprehensive simulations demonstrate that the analysis results match well with the simulation results, and delay performance of the authors schemes is superior to those of other schemes, whereas throughput is superior to others for relative higher node density.
Mundgesundheit von berufstätigen und nicht berufstätigen Frauen – Ergebnisse einer regionalen Untersuchung und Umfrage
Authors: Ehlers V. , Willershausen I. , Weyer V. , Leskov-Hamza T. , Lampe F. , Willershausen B.
Published: June 2013

In der vorliegenden Studie sollte der Mundgesundheitszustand sowie Mundhygienemaßnahmen bei berufstätigen und nichtberufstätigen Frauen untersucht und miteinander verglichen werden. Neben einer zahnärztlichen Untersuchung wurden mittels Fragebogen sowohl Mundhygienemaßnahmen als auch soziodemografische Daten erhoben.

Für die Studie konnten insgesamt 415 Frauen (210 berufstätige und 205 nicht berufstätige Frauen) der Altersgruppe 25–65 Jahre erfasst werden. Bei allen Frauen erfolgte eine zahnärztliche Untersuchung einschließlich einer radiologischen Befundung (Panoramaschichtaufnahme). Die zahnärztliche Untersuchung beinhaltete Anzahl der Zähne, Karieshäufigkeit (DMFT-Wert), Art und Häufigkeit von Restaurationen, Mundhygienemaßnahmen (API), Entzündungsgrad der Gingiva (SBI), Sondierungstiefen und das Vorliegen von Rezessionen. Des weiteren wurde ein Fragebogen ausgefüllt, der Informationen zu anamnestischen Daten, Familiensituation, Bildungsstand und Berufstätigkeit beinhaltete. Für die Studie lag das positive Votum der Ethikkommission (Rheinland-Pfalz) vor.

Die nicht erwerbstätigen Frauen/Hausfrauen (Alter: 38,1±9,7 Jahre) waren zu 90% verheiratet, nur zu 3% starke Raucherinnen und nur 2% hatten einen Hochschulabschluss. Berufstätige Frauen (Alter: 43,2±11 Jahre) waren zu 73% verheiratet, 17% waren starke Raucherinnen (>20 Zigaretten/Tag) und 10% hatten einen Hochschulabschluss. Die Mundhygienemaßnahmen der Berufstätigen waren im Vergleich zu den nicht erwerbstätigen Frauen tendenziell besser, jedoch hatten die berufstätigen Frauen vermehrt aggressive Parodontalerkrankungen (15% vs. 3,3%; p<0,027). In der logistischen Regression wiesen berufstätige Frauen im Gegensatz zu nicht Erwerbstätigen ein 4-fach erhöhtes Risiko auf, eine aggressive Parodontitis zu entwickeln (Odds Ratio 4,23; 95% KI: 0,77–23,17).

Die Mundgesundheit von berufstätigen Frauen und Frauen ohne Erwerbstätigkeit zeigte leichte Unterschiede. Diese Untersuchungen legen den Schluss nahe, dass Berufstätigkeit, Bildungsstand und Lebensstil der Frauen sowohl die oralen Pflegemaßnahmen als auch die Mundgesundheit beeinflussen.
On the analytical representation of free energy profiles with a Morse/long-range model: Application to the water dimer
Authors: Tritzant-Martinez Yalina , Zeng Tao , Broom Aron , Meiering Elizabeth , Le Roy Robert J. , Roy Pierre-Nicholas
Published: June 2013

We investigate the analytical representation of potentials of mean force (pmf) using the Morse/long-range (MLR) potential approach. The MLR method had previously been used to represent potential energy surfaces, and we assess its validity for representing free-energies. The advantage of the approach is that the potential of mean force data only needs to be calculated in the short to medium range region of the reaction coordinate while the long range can be handled analytically. This can result in significant savings in terms of computational effort since one does not need to cover the whole range of the reaction coordinate during simulations. The water dimer with rigid monomers whose interactions are described by the commonly used TIP4P model [W. Jorgensen and J. Madura, Mol. Phys. 56, 1381 (1985)]10.1080/00268978500103111 is used as a test case. We first calculate an “exact” pmf using direct Monte Carlo (MC) integration and term such a calculation as our gold standard (GS). Second, we compare this GS with several MLR fits to the GS to test the validity of the fitting procedure. We then obtain the water dimer pmf using metadynamics simulations in a limited range of the reaction coordinate and show how the MLR treatment allows the accurate generation of the full pmf. We finally calculate the transition state theory rate constant for the water dimer dissociation process using the GS, the GS MLR fits, and the metadynamics MLR fits. Our approach can yield a compact, smooth, and accurate analytical representation of pmf data with reduced computational cost.
Dynamics of two-dimensional and quasi-two-dimensional polymers
Authors: Sung Bong June , Yethiraj Arun
Published: June 2013

The dynamic properties of dense two-dimensional (2D) polymer melts are studied using discontinuous molecular dynamics simulations. Both strictly 2D and quasi-2D systems are investigated. The strictly 2D model system consists of a fluid of freely jointed tangent hard disc chains. The translational diffusion coefficient, D, is strongly system size dependent with D ∼ ln L where L is the linear dimension of the square simulation cell. The rotational correlation time, τrot, is, however, independent of system size. The dynamics is consistent with Rouse behavior with D/ln L ∼ N−1 and τrot ∼ N2 for all area fractions. Analysis of the intermediate scattering function, Fs(k, t), shows that the dynamics becomes slow for N = 256 and the area fraction of 0.454 and that there might be a glass transition for long polymers at sufficiently high area fractions. The polymer mobility is not correlated with the conformation of the molecules. In the quasi-2D system hard sphere chains are confined between corrugated surfaces so that chains cannot go over each other or into the surfaces. The conformational properties are identical to the 2D case, but D and τrot are independent of system size. The scaling of D and τrot with N is similar to that of strictly 2D systems. The simulations suggest that 2D polymers are never entangled and follow Rouse dynamics at all densities.
The role of cold work on the shock response of tantalum
Authors: Millett J. C. F. , Whiteman G. , Park N. T. , Case S. , Bourne N. K.
Published: June 2013

The effect of prior cold work on the shock response of tantalum has been investigated via plate impact. As-received and 50% cold-rolled material has been studied to determine the Hugoniot Elastic Limit (HEL), shear strength evolution behind the shock front, and spall strength. Results show that there is a significant drop in both HEL and shear strength due to cold-rolling, but as the thickness of the target (or time) increases, results converge between the two states. Results suggest that this is due to the cold-rolling process moving dislocations away from the surrounding interstitial solute atoms that collect there, thus reducing the initial stress to initiate yield. In other words, the main contribution of cold-rolling is to increase the population of mobile dislocations within the microstructure rather that just increase the dislocation density as a whole. In contrast, the spall strength in both states appears almost identical. It is suggested that the high Peierls stress prevents a large increase in dislocation density during rolling and hence reduces any post rolling strengthening that might be observed in the spallation response. Finally, we observe a significant change in spall response below a pulse width of 150 ns. We believe that this represents a change from a nucleation and growth of ductile voids type mechanism to one based on ductile fracture of atomic planes. The fact that at these low pulse durations, results appear to trend towards the theoretical strength of tantalum would lend support to this hypothesis.
Strong luminescence induced by elastic deformation of piezoelectric crystals
Authors: Chandra V. K. , Chandra B. P. , Jha Piyush
Published: June 2013

The luminescence induced by elastic deformation of solids, called the phenomenon of elastico-mechanoluminescence (EML), is observed in several materials. For applied pressure in the range of 17 MPa, certain crystals emit intense EML, which can be seen in day light with naked eye. In the present paper, we explore that, as the piezoelectric constant near the photo-generated electric dipoles formed by trapping of charge carriers in crystals is several times higher as compared to that at normal sites, the piezoelectrically induced detrapping of charge carriers and EML emission may take place for less value of the pressure applied onto the crystals.
Multiferroic perovskite (Pb0.845Sm0.08Fe0.035)(Ti0.98Mn0.02)O3 with ferroelectric and weak ferromagnetic properties
Authors: Craciun F. , Dimitriu E. , Grigoras M. , Lupu N.
Published: June 2013

We have investigated the multiferroic properties of PbTiO3 substituted on the A-site with Sm3+ and Fe2+ magnetic ions. We show that the ceramic material with composition (Pb0.845Sm0.08Fe0.035)(Ti0.98Mn0.02)O3 has a spontaneous ferroelectric polarization of about 14 μC/cm2 and weak ferromagnetism (remanent magnetization ∼2.3 emu/g) which persists even at room temperature. The dielectric constant is 190, tan δ ∼ 0.005, and the piezoelectric g33 constant is 25 mV × m/N. Temperature dependence of dielectric permittivity shows a strong anomaly at 662 K, at the paraelectric-ferroelectric transition, and a broader anomaly below 140 K where magnetization also increases, probably due to magnetoelectric coupling between ferroelectric and magnetic states.
Fano effects in electron transport through an armchair graphene nanoribbon with one line defect
Authors: Han Yu , Sui Xiao-Yan , Gong Wei-Jiang
Published: June 2013

Electron transport in an armchair graphene nanoribbon is theoretically investigated by considering the presence of one line defect. It is found that different-property Fano effects occur in electron transport through such a structure, which are determined by the nanoribbon width and the coupling manner between the line defect and the nanoribbon. The spectra of the density of electron states show that the line defect induces some localized quantum states around the Dirac point, and that the different localizations of these states lead to the abundant transport results. By analyzing the influence of the structure parameters, the Fano effects are described in detail. With the obtained results, we consider such a structure to be a promising candidate for nanoswitch.
Multi-technique x-ray and optical characterization of crystalline phase, texture, and electronic structure of atomic layer deposited Hf1−xZrxO2 gate dielectrics deposited by a cyclical deposition and annealing scheme
Authors: Vasić Relja , Consiglio Steven , Clark Robert D. , Tapily Kandabara , Sallis Shawn , Chen Bo , Newby David , Medikonda Manasa , Raja Muthinti Gangadhara , Bersch Eric , Jordan-Sweet Jean , Lavoie Christian , Leusink Gert J. , Diebold Alain C.
Published: June 2013

A multi-technique approach was used to determine the crystalline phase, texture, and electronic structure of Hf1−xZrxO2 (x = 0–1) high-k gate dielectric thin films grown by atomic layer deposition using a cyclical deposition and annealing method. X-ray diffraction (XRD) analysis performed in both grazing incidence and pole figure configurations identified the tetragonal phase for Zr/(Zr + Hf)% = 58% and a concomitant increase in tetragonal phase for further increase in Zr content. X-ray absorption spectroscopy (XAS) was used to determine the local atomic structure and metal oxide bond orientation. Polarization dependent XAS in normal and grazing incidence showed preferential metal-oxygen bond orientation consistent with the texturing observed by XRD. X-ray photoemission spectroscopy (XPS) and spectroscopic ellipsometry (SE) were also performed with special focus on spectral features which arise as a consequence of atomic ordering and specific crystalline phase. The combination of XAS, XPS, SE, and XRD enabled the determination of the effects of the deposition scheme and compositional alloying on the electronic structure, crystal field effects, optical properties, crystal phase, and texture for the mixed oxide alloy series. The multi-technique approach revealed the martensitic-like transformation of crystalline phase from monoclinic to tetragonal as the majority metal oxide concentration in the alloy mixture changed from HfO2 to ZrO2.
Nucleation and growth of Nb nanoclusters during plasma gas condensation
Authors: Bray K. R. , Jiao C. Q. , DeCerbo J. N.
Published: June 2013

Niobium nanoclusters were produced using a plasma gas condensation process. The influence of gas flow rate, aggregation length, and source current on the nanocluster nucleation and growth were analyzed. Nanoclusters with an average diameter from 4 nm to 10 nm were produced. Cluster size and concentration were tuned by controlling the process inputs. The effects of each parameter on the nucleation zone, growth length, and residence time was examined. The parameters do not affect the cluster formation and growth independently; their influence on cluster formation can be either cumulative or competing. Examining the nucleation and growth over a wide combination of parameters provided insight into their interactions and the impact on the growth process. These results provide the opportunity for a broader understanding into the nucleation and growth of nanoclusters and some insights into how process parameters interact during deposition. This knowledge will enhance the ability to create nanoclusters with desired size dispersions.
Optoelectronic properties of single-layer, double-layer, and bulk tin sulfide: A theoretical study
Authors: Tritsaris Georgios A. , Malone Brad D. , Kaxiras Efthimios
Published: June 2013

SnS is a metal monochalcogenide suitable for use as absorber material in thin film photovoltaic cells. Its structure is an orthorhombic crystal of weakly coupled layers, each layer consisting of strongly bonded Sn-S units. We use first-principles calculations to study model single-layer, double-layer, and bulk structures of SnS in order to elucidate its electronic structure. We find that the optoelectronic properties of the material can vary significantly with respect to the number of layers and the separation between them: the calculated band gap is wider for fewer layers (2.72 eV, 1.57 eV, and 1.07 eV for single-layer, double-layer, and bulk SnS, respectively) and increases with tensile strain along the layer stacking direction (by ∼55 meV/1% strain).
Excitation and propagation of electromagnetic fluctuations with ion-cyclotron range of frequency in magnetic reconnection laboratory experiment
Authors: Inomoto Michiaki , Kuwahata Akihiro , Tanabe Hiroshi , Ono Yasushi ,   TS Group
Published: June 2013

Large-amplitude electromagnetic fluctuations of ion-cyclotron-frequency range are detected in a laboratory experiment inside the diffusion region of a magnetic reconnection with a guide field. The fluctuations have properties similar to kinetic Alfvén waves propagating obliquely to the guide field. Temporary enhancement of the reconnection rate is observed during the occurrence of the fluctuations, suggesting a relationship between the modification in the local magnetic structure given by these fluctuations and the intermittent fast magnetic reconnection.
Room temperature electrically tunable terahertz Faraday effect
Authors: Shuvaev A. , Pimenov A. , Astakhov G. V. , Mühlbauer M. , Brüne C. , Buhmann H. , Molenkamp L. W.
Published: June 2013

We demonstrate electrical control of the room temperature Faraday effect in a 100-nm-thick film of strained HgTe, which is a topological insulator. The terahertz (THz) response of our device is dominated by the Drude response of carriers with high mobility. The electrical control is achieved by gating the carrier density in a static magnetic field, opening new perspectives for applications like high-speed amplitude and phase modulators in the THz frequency range.
Electrical linear control of the electronic structure of graphene quantum dots
Authors: Dong Qing-Rui
Published: June 2013

The tight-binding method is employed to investigate the single-electron electronic structure of triangular graphene quantum dots subject to non-uniform electric fields. The specially designed non-uniform electric fields can provide the equal or opposite electrostatic potentials for all edge carbon atoms. The low-energy eigenstates do not vary significantly with the non-uniform electric fields, which allows electrical linear control of the low-energy states. Moreover, the levels of degenerate zero-energy states can be adjusted electrically independently while the levels of nonzero-energy states almost do not vary. This linear control by non-uniform electric fields can be a more efficient way to tune the degenerate zero-energy states. Our findings may be useful for the application of graphene quantum dots to electronic and photovoltaic devices.
Interrupted interface growth and periodic boundary layer trapping in dendrite growth of steel
Authors: Ma Xiaoping , Li Dianzhong
Published: June 2013

The time continuity, spatial continuity, and segregation are investigated in the directional solidified columnar dendrite with pulling velocity 40 μm/s and quenching solidified columnar dendrite of 20SiMn and 20SiMnMo steel. The results show that the growth of columnar dendrite is a dynamic discrete process with interrupted interface growth and periodic trapping of solute enriched boundary layer in growing austenite dendrite matrix. Theoretical analysis shows that the non-equilibrium solute partition at the growing interface and actual temperature gradient accounts for above phenomena. Such growth style results in the segregationless dendrite in the mesoscale.
Understanding ecosystem dynamics in South Australia’s arid lands: a framework to assist biodiversity conservation
Authors: McIlwee Allen P. , Rogers Daniel , Pisanu Phil , Brandle Robert , McDonald John
Published: June 2013

Determining what level of investment is required, and where and how it is used, to maintain biodiversity across vast areas is difficult. In response to this challenge, the South Australian Department of Environment, Water and Natural Resources has developed an information framework known as the ‘Aridlands Landscape Assessment Framework’ (ALAF) to provide a systematic basis for identifying landscape-specific, coarse-filter priorities for conservation investment across the arid zone. The ALAF is an analytical and conceptual framework that seeks to define ecosystem components and ecological processes operating at a landscape level, and understand where these processes are not meeting the requirements of extant biodiversity. This requires a systematic process to identify plant communities that occur in distinct biophysical settings. The next step is to document the dynamic processes that drive change within these communities in space and time. When coupled with knowledge of the requirements of indicator flora and fauna, this understanding will allow identification of those components that are at greatest risk, where, and for what reasons. This paper provides an overview of each step in the ALAF process and outlines how the framework has been used thus far to inform conservation planning across Witjira National Park.
Impact of a toxic invasive species on freshwater crocodile (Crocodylus johnstoni) populations in upstream escarpments
Authors: Britton Adam R. C. , Britton Erin K. , McMahon Clive R.
Published: June 2013

Context
Spread of the invasive cane toad (Rhinella marina) across northern Australia is of concern. Predator species, including the freshwater crocodile (Crocodylus johnstoni), are susceptible to cane toad toxins when ingested. Upstream populations of freshwater crocodiles are smaller than downstream counterparts because of limited resources. We measured the impact of cane toad arrival on densities of these upstream populations.

Aims
Our aim was to determine whether the influx of cane toads had a negative impact on populations of upstream ‘stunted’ freshwater crocodiles.

Methods
Population surveys for crocodiles were conducted in three upstream creek systems, using day- and night-based survey methods, before the arrival of cane toads in the area. These surveys were repeated under similar conditions following the arrival of cane toads, to compare the distribution and densities of freshwater crocodiles and, hence, measure the impact of cane toads.

Key results
There were significant declines in crocodile density at two survey sites following the arrival of cane toads, and we found dead crocodiles and cane toad carcasses with crocodile bite marks. The third site showed no change in density. There was a decline in mean density across all sites from 3.0 crocodiles km–1 to 1.1 crocodiles km–1 following the arrival of cane toads.

Conclusions
There was an overall decrease in crocodile densities and a reduction in distribution following the arrival of cane toads into the survey area. Dead crocodiles and evidence of their having eaten cane toads strongly suggest that these declines were caused directly by the arrival of cane toads into the area. One site showed no apparent change other than an increase in wariness, which may reflect the distribution of available feeding and shelter resources among the three sites.

Implications
These results suggest that upstream freshwater crocodile populations are highly susceptible to cane toad toxins, and that impacts on their population can include local extirpation. Considering their morphological and possibly genetic distinctiveness, the loss of these unique populations is of conservation concern.
Reversion of a fungal genetic code alteration links proteome instability with genomic and phenotypic diversification
Authors: Bezerra Ana R. , Simões João , Lee Wanseon , Rung Johan , Weil Tobias , Gut Ivo G. , Gut Marta , Bayés Mónica , Rizzetto Lisa , Cavalieri Duccio , Giovannini Gloria , Bozza Silvia , Romani Luigina , Kapushesky Misha , Moura Gabriela R. , Santos Manuel A. S.
Published: June 2013

Many fungi restructured their proteomes through incorporation of serine (Ser) at thousands of protein sites coded by the leucine (Leu) CUG codon. How these fungi survived this potentially lethal genetic code alteration and its relevance for their biology are not understood. Interestingly, the human pathogen
Candida albicans
maintains variable Ser and Leu incorporation levels at CUG sites, suggesting that this atypical codon assignment flexibility provided an effective mechanism to alter the genetic code. To test this hypothesis, we have engineered
C. albicans
strains to misincorporate increasing levels of Leu at protein CUG sites. Tolerance to the misincorporations was very high, and one strain accommodated the complete reversion of CUG identity from Ser back to Leu. Increasing levels of Leu misincorporation decreased growth rate, but production of phenotypic diversity on a phenotypic array probing various metabolic networks, drug resistance, and host immune cell responses was impressive. Genome resequencing revealed an increasing number of genotype changes at polymorphic sites compared with the control strain, and 80% of Leu misincorporation resulted in complete loss of heterozygosity in a large region of chromosome V. The data unveil unanticipated links between gene translational fidelity, proteome instability and variability, genome diversification, and adaptive phenotypic diversity. They also explain the high heterozygosity of the
C. albicans
genome and open the door to produce microorganisms with genetic code alterations for basic and applied research.
Heritage-culture images disrupt immigrants’ second-language processing through triggering first-language interference
Authors: Zhang Shu , Morris Michael W. , Cheng Chi-Ying , Yap Andy J.
Published: June 2013

For bicultural individuals, visual cues of a setting’s cultural expectations can activate associated representations, switching the frames that guide their judgments. Research suggests that cultural cues may affect judgments through automatic priming, but has yet to investigate consequences for linguistic performance. The present studies investigate the proposal that heritage-culture cues hinder immigrants’ second-language processing by priming first-language structures. For Chinese immigrants in the United States, speaking to a Chinese (vs. Caucasian) face reduced their English fluency, but at the same time increased their social comfort, effects that did not occur for a comparison group of European Americans (study 1). Similarly, exposure to iconic symbols of Chinese (vs. American) culture hindered Chinese immigrants’ English fluency, when speaking about both culture-laden and culture-neutral topics (study 2). Finally, in both recognition (study 3) and naming tasks (study 4), Chinese icon priming increased accessibility of anomalous literal translations, indicating the intrusion of Chinese lexical structures into English processing. We discuss conceptual implications for the automaticity and adaptiveness of cultural priming and practical implications for immigrant acculturation and second-language learning.
Trophic cascade alters ecosystem carbon exchange
Authors: Strickland Michael S. , Hawlena Dror , Reese Aspen , Bradford Mark A. , Schmitz Oswald J.
Published: June 2013

Trophic cascades—the indirect effects of carnivores on plants mediated by herbivores—are common across ecosystems, but their influence on biogeochemical cycles, particularly the terrestrial carbon cycle, are largely unexplored. Here, using a
13
C pulse-chase experiment, we demonstrate how trophic structure influences ecosystem carbon dynamics in a meadow system. By manipulating the presence of herbivores and predators, we show that even without an initial change in total plant or herbivore biomass, the cascading effects of predators in this system begin to affect carbon cycling through enhanced carbon fixation by plants. Prolonged cascading effects on plant biomass lead to slowing of carbon loss via ecosystem respiration and reallocation of carbon among plant aboveground and belowground tissues. Consequently, up to 1.4-fold more carbon is retained in plant biomass when carnivores are present compared with when they are absent, owing primarily to greater carbon storage in grass and belowground plant biomass driven largely by predator nonconsumptive (fear) effects on herbivores. Our data highlight the influence that the mere presence of predators, as opposed to direct consumption of herbivores, can have on carbon uptake, allocation, and retention in terrestrial ecosystems.
Primary endosymbiosis events date to the later Proterozoic with cross-calibrated phylogenetic dating of duplicated ATPase proteins
Authors: Shih Patrick M. , Matzke Nicholas J.
Published: June 2013

Chloroplasts and mitochondria descended from bacterial ancestors, but the dating of these primary endosymbiosis events remains very uncertain, despite their importance for our understanding of the evolution of both bacteria and eukaryotes. All phylogenetic dating in the Proterozoic and before is difficult: Significant debates surround potential fossil calibration points based on the interpretation of the Precambrian microbial fossil record, and strict molecular clock methods cannot be expected to yield accurate dates over such vast timescales because of strong heterogeneity in rates. Even with more sophisticated relaxed-clock analyses, nodes that are distant from fossil calibrations will have a very high uncertainty in dating. However, endosymbiosis events and gene duplications provide some additional information that has never been exploited in dating; namely, that certain nodes on a gene tree must represent the same events, and thus must have the same or very similar dates, even if the exact date is uncertain. We devised techniques to exploit this information: cross-calibration, in which node date calibrations are reused across a phylogeny, and cross-bracing, in which node date calibrations are formally linked in a hierarchical Bayesian model. We apply these methods to proteins with ancient duplications that have remained associated and originated from plastid and mitochondrial endosymbionts: the α and β subunits of ATP synthase and its relatives, and the elongation factor thermo unstable. The methods yield reductions in dating uncertainty of 14–26% while only using date calibrations derived from phylogenetically unambiguous Phanerozoic fossils of multicellular plants and animals. Our results suggest that primary plastid endosymbiosis occurred ∼900 Mya and mitochondrial endosymbiosis occurred ∼1,200 Mya.
Experimental evidence for the thermophilicity of ancestral life
Authors: Akanuma Satoshi , Nakajima Yoshiki , Yokobori Shin-ichi , Kimura Mitsuo , Nemoto Naoki , Mase Tomoko , Miyazono Ken-ichi , Tanokura Masaru , Yamagishi Akihiko
Published: June 2013

Theoretical studies have focused on the environmental temperature of the universal common ancestor of life with conflicting conclusions. Here we provide experimental support for the existence of a thermophilic universal common ancestor. We present the thermal stabilities and catalytic efficiencies of nucleoside diphosphate kinases (NDK), designed using the information contained in predictive phylogenetic trees, that seem to represent the last common ancestors of Archaea and of Bacteria. These enzymes display extreme thermal stabilities, suggesting thermophilic ancestries for Archaea and Bacteria. The results are robust to the uncertainties associated with the sequence predictions and to the tree topologies used to infer the ancestral sequences. Moreover, mutagenesis experiments suggest that the universal ancestor also possessed a very thermostable NDK. Because, as we show, the stability of an NDK is directly related to the environmental temperature of its host organism, our results indicate that the last common ancestor of extant life was a thermophile that flourished at a very high temperature.
Quantitative phosphoproteomics identifies SnRK2 protein kinase substrates and reveals the effectors of abscisic acid action
Authors: Wang Pengcheng , Xue Liang , Batelli Giorgia , Lee Shinyoung , Hou Yueh-Ju , Van Oosten Michael J. , Zhang Huiming , Tao W. Andy , Zhu Jian-Kang
Published: June 2013

Sucrose nonfermenting 1 (SNF1)-related protein kinase 2s (SnRK2s) are central components of abscisic acid (ABA) signaling pathways. The
snrk2.2/2.3/2.6
triple-mutant plants are nearly completely insensitive to ABA, suggesting that most of the molecular actions of ABA are triggered by the SnRK2s-mediated phosphorylation of substrate proteins. Only a few substrate proteins of the SnRK2s are known. To identify additional substrate proteins of the SnRK2s and provide insight into the molecular actions of ABA, we used quantitative phosphoproteomics to compare the global changes in phosphopeptides in WT and
snrk2.2/2.3/2.6
triple mutant seedlings in response to ABA treatment. Among the 5,386 unique phosphorylated peptides identified in this study, we found that ABA can increase the phosphorylation of 166 peptides and decrease the phosphorylation of 117 peptides in WT seedlings. In the
snrk2.2/2.3/2.6
triple mutant, 84 of the 166 peptides, representing 58 proteins, could not be phosphorylated, or phosphorylation was not increased under ABA treatment. In vitro kinase assays suggest that most of the 58 proteins can serve as substrates of the SnRK2s. The SnRK2 substrates include proteins involved in flowering time regulation, RNA and DNA binding, miRNA and epigenetic regulation, signal transduction, chloroplast function, and many other cellular processes. Consistent with the SnRK2 phosphorylation of flowering time regulators, the
snrk2.2/2.3/2.6
triple mutant flowered significantly earlier than WT. These results shed new light on the role of the SnRK2 protein kinases and on the downstream effectors of ABA action, and improve our understanding of plant responses to adverse environments.
Architecture of respiratory syncytial virus revealed by electron cryotomography
Authors: Liljeroos Lassi , Krzyzaniak Magdalena Anna , Helenius Ari , Butcher Sarah Jane
Published: June 2013

Human respiratory syncytial virus is a human pathogen that causes severe infection of the respiratory tract. Current information about the structure of the virus and its interaction with host cells is limited. We carried out an electron cryotomographic characterization of cell culture-grown human respiratory syncytial virus to determine the architecture of the virion. The particles ranged from 100 nm to 1,000 nm in diameter and were spherical, filamentous, or a combination of the two. The filamentous morphology correlated with the presence of a cylindrical matrix protein layer linked to the inner leaflet of the viral envelope and with local ordering of the glycoprotein spikes. Recombinant viruses with only the fusion protein in their envelope showed that these glycoproteins were predominantly in the postfusion conformation, but some were also in the prefusion form. The ribonucleocapsids were left-handed, randomly oriented, and curved inside the virions. In filamentous particles, they were often adjacent to an intermediate layer of protein assigned to M2-1 (an envelope-associated protein known to mediate association of ribonucleocapsids with the matrix protein). Our results indicate important differences in structure between the
Paramyxovirinae
and
Pneumovirinae
subfamilies within the
Paramyxoviridae
, and provide fresh insights into host cell exit of a serious pathogen.
Identification of a small molecule with activity against drug-resistant and persistent tuberculosis
Authors: Wang Feng , Sambandan Dhinakaran , Halder Rajkumar , Wang Jianing , Batt Sarah M. , Weinrick Brian , Ahmad Insha , Yang Pengyu , Zhang Yong , Kim John , Hassani Morad , Huszar Stanislav , Trefzer Claudia , Ma Zhenkun , Kaneko Takushi , Mdluli Khisi E. , Franzblau Scott , Chatterjee Arnab K. , Johnsson Kai , Mikusova Katarina , Besra Gurdyal S. , Fütterer Klaus , Robbins Scott H. , Barnes S. Whitney , Walker John R. , Jacobs William R. , Schultz Peter G.
Published: June 2013

Significance

The global problem of TB has worsened in recent years with the emergence of drug-resistant organisms, and new drugs are clearly needed. In a cell-based high-throughput screen, a small molecule, TCA1, was discovered that has activity against replicating and nonreplicating
Mycobacterium tuberculosis
. It is also efficacious in acute and chronic rodent models of TB alone or combined with frontline TB drugs. TCA1 functions by a unique mechanism, inhibiting enzymes involved in cell wall and molybdenum cofactor biosynthesis. This discovery represents a significant advance in the search for new agents to treat persistent and drug-resistant TB.
The tumor suppressor CDKN3 controls mitosis
Authors: Nalepa Grzegorz , Barnholtz-Sloan Jill , Enzor Rikki , Dey Dilip , He Ying , Gehlhausen Jeff R. , Lehmann Amalia S. , Park Su-Jung , Yang Yanzhu , Yang Xianlin , Chen Shi , Guan Xiaowei , Chen Yanwen , Renbarger Jamie , Yang Feng-Chun , Parada Luis F. , Clapp Wade
Published: June 2013

Mitosis is controlled by a network of kinases and phosphatases. We screened a library of small interfering RNAs against a genome-wide set of phosphatases to comprehensively evaluate the role of human phosphatases in mitosis. We found four candidate spindle checkpoint phosphatases, including the tumor suppressor CDKN3. We show that CDKN3 is essential for normal mitosis and G1/S transition. We demonstrate that subcellular localization of CDKN3 changes throughout the cell cycle. We show that CDKN3 dephosphorylates threonine-161 of CDC2 during mitotic exit and we visualize CDC2pThr-161 at kinetochores and centrosomes in early mitosis. We performed a phosphokinome-wide mass spectrometry screen to find effectors of the CDKN3-CDC2 signaling axis. We found that one of the identified downstream phosphotargets, CKβ phosphorylated at serine 209, localizes to mitotic centrosomes and controls the spindle checkpoint. Finally, we show that CDKN3 protein is down-regulated in brain tumors. Our findings indicate that CDKN3 controls mitosis through the CDC2 signaling axis. These results have implications for targeted anticancer therapeutics.
The spindle checkpoint, APC/CCdc20, and APC/CCdh1 play distinct roles in connecting mitosis to S phase
Authors: Clijsters Linda , Ogink Janneke , Wolthuis Rob
Published: June 2013

DNA replication depends on a preceding licensing event by Cdt1 and Cdc6. In animal cells, relicensing after S phase but before mitosis is prevented by the Cdt1 inhibitor geminin and mitotic cyclin activity. Here, we show that geminin, like cyclin B1 and securin, is a bona fide target of the spindle checkpoint and APC/CCdc20. Cyclin B1 and geminin are degraded simultaneously during metaphase, which directs Cdt1 accumulation on segregating sister chromatids. Subsequent activation of APC/CCdh1 leads to degradation of Cdc6 well before Cdt1 becomes unstable in a replication-coupled manner. In mitosis, the spindle checkpoint supports Cdt1 accumulation, which promotes S phase onset. We conclude that the spindle checkpoint, APC/CCdc20, and APC/CCdh1 act successively to ensure that the disappearance of licensing inhibitors coincides exactly with a peak of Cdt1 and Cdc6. Whereas cell cycle entry from quiescence requires Cdc6 resynthesis, our results indicate that proliferating cells use a window of time in mitosis, before Cdc6 is degraded, as an earlier opportunity to direct S phase.
N-ras couples antigen receptor signaling to Eomesodermin and to functional CD8+ T cell memory but not to effector differentiation
Authors: Iborra Salvador , Ramos Manuel , Arana David M. , Lázaro Silvia , Aguilar Francisco , Santos Eugenio , López Daniel , Fernández-Malavé Edgar , Del Val Margarita
Published: June 2013

Signals from the TCR that specifically contribute to effector versus memory CD8+ T cell differentiation are poorly understood. Using mice and adoptively transferred T lymphocytes lacking the small GTPase N-ras, we found that N-ras–deficient CD8+ T cells differentiate efficiently into antiviral primary effectors but have a severe defect in generating protective memory cells. This defect was rescued, although only partly, by rapamycin-mediated inhibition of mammalian target of rapamycin (mTOR) in vivo. The memory defect correlated with a marked impairment in vitro and in vivo of the antigen-mediated early induction of T-box transcription factor Eomesodermin (Eomes), whereas T-bet was unaffected. Besides N-ras, early Eomes induction in vitro required phosphoinositide 3-kinase (PI3K)–AKT but not extracellular signal-regulated kinase (ERK) activation, and it was largely insensitive to rapamycin. Consistent with N-ras coupling Eomes to T cell memory, retrovirally enforced expression of Eomes in N-ras–deficient CD8+ T cells effectively rescued their memory differentiation. Thus, our study identifies a critical role for N-ras as a TCR-proximal regulator of Eomes for early determination of the CD8+ T cell memory fate.
Rhizobial Synthesized Cytokinins Contribute to But Are Not Essential for the Symbiotic Interaction Between Photosynthetic Bradyrhizobia and Aeschynomene Legumes
Authors: Podlešáková Kateřina , Fardoux Joel , Patrel Delphine , Bonaldi Katia , Novák Ondřej , Strnad Miroslav , Giraud Eric , Spíchal Lukáš , Nouwen Nico
Published: June 2013

Cytokinins (CK) play an important role in the formation of nitrogen-fixing root nodules. It has been known for years that rhizobia secrete CK in the extracellular medium but whether they play a role in nodule formation is not known. We have examined this question using the photosynthetic Bradyrhizobium sp. strain ORS285 which is able to nodulate Aeschynomene afraspera and A. indica using a Nod-dependent or Nod-independent symbiotic process, respectively. CK profiling showed that the most abundant CK secreted by Bradyrhizobium sp. strain ORS285 are the 2MeS (2-methylthiol) derivatives of trans-zeatin and isopentenyladenine. In their pure form, these CK can activate legume CK receptors in vitro, and their exogenous addition induced nodule-like structures on host plants. Deletion of the miaA gene showed that transfer RNA degradation is the source of CK production in Bradyrhizobium sp. strain ORS285. In nodulation studies performed with A. indica and A. afraspera, the miaA mutant had a 1-day delay in nodulation and nitrogen fixation. Moreover, A. indica plants formed considerably smaller but more abundant nodules when inoculated with the miaA mutant. These data show that CK produced by Bradyrhizobium sp. strain ORS285 are not the key signal triggering nodule formation during the Nod-independent symbiosis but they contribute positively to nodule development in Aeschynomene plants.
Increased Resistance Against Citrus Canker Mediated by a Citrus Mitogen-Activated Protein Kinase
Authors: de Oliveira Maria Luiza Peixoto , de Lima Silva Caio Cesar , Abe Valéria Yukari , Costa Marcio Gilberto Cardoso , Cernadas Raúl Andrés , Benedetti Celso Eduardo
Published: June 2013

Mitogen-activated protein kinases (MAPK) play crucial roles in plant immunity. We previously identified a citrus MAPK (CsMAPK1) as a differentially expressed protein in response to infection by Xanthomonas aurantifolii, a bacterium that causes citrus canker in Mexican lime but a hypersensitive reaction in sweet oranges. Here, we confirm that, in sweet orange, CsMAPK1 is rapidly and preferentially induced by X. aurantifolii relative to Xanthomonas citri. To investigate the role of CsMAPK1 in citrus canker resistance, we expressed CsMAPK1 in citrus plants under the control of the PR5 gene promoter, which is induced by Xanthomonas infection and wounding. Increased expression of CsMAPK1 correlated with a reduction in canker symptoms and a decrease in bacterial growth. Canker lesions in plants with higher CsMAPK1 levels were smaller and showed fewer signs of epidermal rupture. Transgenic plants also revealed higher transcript levels of defense-related genes and a significant accumulation of hydrogen peroxide in response to wounding or X. citri infection. Accordingly, nontransgenic sweet orange leaves accumulate both CsMAPK1 and hydrogen peroxide in response to X. aurantifolii but not X. citri infection. These data, thus, indicate that CsMAPK1 functions in the citrus canker defense response by inducing defense gene expression and reactive oxygen species accumulation during infection.