bluuebunny/crossref_metadata_2025 huggingface dataset:
Generalist predators disrupt parasitoid aphid control by direct and coincidental intraguild predation
Authors: Traugott M. , Bell J.R. , Raso L. , Sint D. , Symondson W.O.C.
Published: October 2011

Generalist predators and parasitoids are considered to be important regulators of aphids. The former not only feed on these pests, but might also consume parasitoids at all stages of development. This direct or coincidental interference affects the natural control of aphids, the scale of which is largely unknown, and it has rarely been examined under natural conditions. Here, molecular diagnostics were used to track trophic interactions in an aphid-parasitoid-generalist predator community during the build-up of a cereal aphid population. We found that generalist predators, principally carabid and staphylinid beetles as well as linyphiid spiders, had strong trophic links to both parasitoids and aphids. Remarkably, more than 50% of the parasitoid DNA detected in predators stems from direct predation on adult parasitoids. The data also suggest that coincidental intraguild predation is common too. Generalist predators, hence, disrupt parasitoid aphid control, although the levels at which the predators feed on pests and parasitoids seem to vary significantly between predator taxa. Our results suggest that taxon-specific trophic interactions between natural enemies need to be considered to obtain a more complete understanding of the route to effective conservation biological control.
More than just a simple abscess: could it be caused by Panton–Valentine leukocidin positive Staphylococcus aureus?
Authors: Manara J , Shears P
Published: October 2011

Objective:

A 33-year-old woman presented with a three-day history of an abscess in the left alar region, four weeks after drainage of a breast abscess. The later infection was confirmed to be due to Panton–Valentine leukocidin positive, methicillin-resistant Staphylococcus aureus. This report aims to raise awareness of such infections, and to advise when Panton–Valentine leukocidin toxin testing is appropriate.

Method:

Case report and discussion.

Results:

Although superficial Panton–Valentine leukocidin positive Staphylococcus aureus infections are relatively benign, more serious infections can be potentially life-threatening. Clinicians should be able to identify the features of potential Panton–Valentine leukocidin positive Staphylococcus aureus infection, in order to implement appropriate therapy.

Conclusion:

Clinicians need to be aware of Panton–Valentine leukocidin positive Staphylococcus aureus infections, and should ask specific questions when investigating the clinical history of patients with recurrent abscesses, as this bacterial strain is not routinely assessed by microbiology departments. If such an infection is suspected, clinicians should be aware of local protocols regarding toxin testing, antibiotic choice and decolonisation agents.
TRUTH, LOGICAL VALIDITY AND DETERMINATENESS: A COMMENTARY ON FIELD’SSAVING TRUTH FROM PARADOX
Authors: WELCH P. D.
Published: October 2011

We consider notions oftruthandlogical validitydefined in various recent constructions of Hartry Field. We try to explicate his notion ofdeterminate truthby clarifying thepath-dependent hierarchiesof hisdeterminateness operator.
Fine particle deposition to porous beds
Authors: Hamm Nathan T. , Dade W. Brian , Renshaw Carl E.
Published: October 2011

We summarize the results of flume experiments examining the transport behavior of dilute suspensions of silt‐sized particles carried in an open channel flow over three separate bed types including porous open mesh, glass beads, and small cobbles. In these experiments the time‐varying concentration of particles in suspension transport was measured as a function of suspended‐particle size and bed shear stress, and analyzed using a 1‐D model incorporating simultaneous deposition and entrainment. Rates of fine‐particle deposition to the bed are found to approach Stoke's settling velocity in slow flows, but diminish systematically with increasing bed shear stress and mean flow speed. No discernible re‐entrainment from the porous beds was observed, indicating that such beds act as an effective sink for fine particles. When our new results are compared to those of related, previously reported experiments examining fine‐particle transport over smooth impermeable beds, silt‐sized particles display similar behavior with regard to systematic reduction in deposition velocity independent of suspended‐silt‐particle size or bed porosity. This behavior is tentatively interpreted to reflect the effects of lift in a linear shear flow in excess of submerged weight of individual particles. Our findings compare favorably with values of effective settling velocity of fine particulate organic matter in natural channel flows reported elsewhere.
Strong shaking in recent New Zealand earthquakes
Authors: Fry Bill , Benites Rafael , Reyners Martin , Holden Caroline , Kaiser Anna , Bannister Stephen , Gerstenberger Matt , Williams Charles , Ristau John , Beavan John
Published: October 2011

On 4 September 2010 a surface‐rupturing crustal earthquake (Mw 7.1) struck the Canterbury Plains region of New Zealand's South Island [Gledhill et al., 2011]. The Canterbury Plains is a region of relatively low seismicity in New Zealand, and the structure that ruptured was a previously unmapped fault (Figure 1a). Fortunately, even though parts of the region experienced liquefaction of unconsolidated sediments and sands—including neighborhoods of the city of Christchurch (population 377,000)—no fatalities occurred. Compared to the average New Zealand aftershock decay model, the aftershock sequence for the 2010 earthquake was relatively underproductive for the first 5 months. But on 22 February 2011 anMw 6.2 aftershock (teleseismic and regional estimates range from (Mw 6.1 to (Mw 6.3 with regional inversions favoring higher values) occurred within kilometers of the center of Christchurch (A. E. Kaiser et al., The (Mw 6.2 Christchurch earthquake of February 2011: Preliminary report, submitted to New Zealand Journal of Geology and Geophysics, 2011). The event increased the productivity of other aftershocks (Figure 1b). This particular aftershock was devastating, generating much more destruction than theMw 7.1 event, including more than 180 fatalities. Recorded peak ground acceleration (PGA) in the city was more than double the acceleration of gravity (g). Many of the poorly consolidated, low‐shear‐wave‐velocity soils liquefied during the shaking. Damage estimates reached approximately US$15 billion, making the aftershock New Zealand's costliest natural disaster.
New polar studies database
Authors: Showstack Randy
Published: October 2011

The Polar Graduate Programmes Database is a new resource to help young researchers looking for graduate programs related to polar and cryospheric research as well as to help graduate programs recruit new students. The database was announced at the end of September by the Association of Polar Early Career Scientists, the University of the Arctic, and the International Antarctic Institute. The database can be accessed at http://apecs.is/graduate‐programmes.
Honors
Authors: Anonymous
Published: October 2011

More than a dozen AGU members are among 94 researchers announced by U.S. president Barack Obama on 26 September as recipients of the Presidential Early Career Award for Scientists and Engineers. The award, which is coordinated by the Office of Science and Technology Policy within the Executive Office of the President, is considered the highest honor bestowed by the U.S. government on science and engineering professionals in the early stages of their independent research careers. This year's recipients includeJeffrey Book, Naval Research Laboratory; Jonathan Cirtain, NASA Marshall Space Flight Center; Fotini Katopodes Chow, University of California, Berkeley; Elizabeth Cochran, U.S. Geological Survey (USGS);Ian Howat, Ohio State University; Christiane Jablonowski, University of Michigan; Justin Kasper, Smithsonian Astrophysical Observatory;Elena Litchman, Michigan State University; James A. Morris Jr., National Oceanic and Atmospheric Administration (NOAA); Erin M. Oleson, NOAA; Victoria Orphan, California Institute of Technology;Sasha Reed, USGS; David Shelly, USGS; and Feng Wang, University of California, Berkeley. Five AGU members are among 10 U.S. representatives recently selected for International Arctic Science Committee working groups. The AGU members, chosen as representatives through the U.S. National Academies review process, are Atmosphere Working Group member James Overland, Pacific Marine Environmental Laboratory, NOAA; Cryosphere Working Group members Walter Meier, University of Colorado at Boulder, and Elizabeth Hunke, Los Alamos National Laboratory; Marine Working Group member Mary‐Louise Timmermans, Yale University; and Terrestrial Working Group member Vanessa Lougheed, University of Texas at El Paso.
Sources and sinks of methane in Lake Kivu
Authors: Balcerak Ernie
Published: October 2011

Africa's Lake Kivu, which borders Rwanda and the Republic of the Congo, contains huge amounts of methane (an estimated 60 cubic kilometers) and carbon dioxide (an estimated 300 cubic kilometers). Although the methane could provide a source of energy if it could be tapped, the high concentrations of gases pose a risk of dangerous gas eruptions, threatening the local population. Furthermore, it has been reported that concentrations of methane have risen by as much as 15% in the past 30 years. Scientists need to learn more about the sources and sinks of methane in Lake Kivu to better assess the risk of catastrophic outgassing and sustainability of methane harvesting.
Arctic air may become cleaner as temperatures rise
Authors: Balcerak Ernie
Published: October 2011

The air in the Arctic is cleaner during summer than during winter. Previous studies have shown that for light‐scattering pollutants, this seasonal cycle is due mainly to summer precipitation removing pollutants from the air during atmospheric transport from midlatitude industrial and agricultural sources. With new measurements from Barrow, Alaska, and Alert, Nunavut, Canada, Garrett et al. extended previous research to show that light‐absorbing aerosols such as black carbon are also efficiently removed by seasonal precipitation. Precipitation removes these particles from the air most efficiently at high humidities and relatively warm temperatures, suggesting that as the Arctic gets warmer and wetter in the future, the air and snow might also become cleaner.
A semianalytical three‐dimensional process‐based model for hyporheic nitrogen dynamics in gravel bed rivers
Authors: Marzadri Alessandra , Tonina Daniele , Bellin Alberto
Published: October 2011

We present a three‐dimensional semianalytical process‐based model of dissolved oxygen and dissolved inorganic nitrogen (DIN) transformation within the hyporheic zone of gravel bed rivers. Oxygen and multispecies solute transport is solved within a Lagrangian framework with transformation of DIN species modeled by linearized Monod's kinetics, with temperature‐dependent reaction rate coefficients derived from field experiments. Our solutions, which are obtained under the assumptions of sediments with uniform hydraulic properties and negligible local dispersion, highlight the importance of morphological characteristics of the streambed on DIN transformations within the hyporheic zone. By means of this model we explore the effects of streambed topography and relative abundance of ammonium and nitrate in stream waters on the reactive nitrogen cycle in the hyporheic zone of gravel bed rivers with a pool and riffle morphology. Our model shows complex concentration dynamics within the hyporheic zone that may act as a source or a sink of nitrogen depending on the residence time distribution, which can be parameterized in terms of streambed morphology, and the ratio between the in‐stream concentrations of ammonium and nitrate. Application of the model to seven natural streams shows good agreement between predicted and measured nitrous oxide emissions from their hyporheic zone.
Nitrate pollution in intensively farmed regions: What are the prospects for sustaining high‐quality groundwater?
Authors: Howden Nicholas J. K. , Burt Tim P. , Worrall Fred , Mathias Simon , Whelan Mick J.
Published: October 2011

Widespread pollution of groundwater by nutrients due to 20th century agricultural intensification has been of major concern in the developed world for several decades. This paper considers the River Thames catchment (UK), where water‐quality monitoring at Hampton (just upstream of London) has produced continuous records for nitrate for the last 140 years, the longest continuous record of water chemistry anywhere in the world. For the same period, data are available to characterize changes in both land use and land management at an annual scale. A modeling approach is used that combines two elements: an estimate of nitrate available for leaching due to land use and land management; and, an algorithm to route this leachable nitrate through to surface or groundwaters. Prior to agricultural intensification at the start of World War II, annual average inputs were around 50 kg ha−1, and river concentrations were stable at 1 to 2 mg l−1, suggesting in‐stream denitrification capable of removing 35 (±15) kt N yr−1. Postintensification data suggest an accumulation of 100 (±40) kt N yr−1 in the catchment, most of which is stored in the aquifer. This build up of reactive N species within the catchments means that restoration of surface nitrate concentrations typical of the preintensification period would require massive basin‐wide changes in land use and management that would compromise food security and take decades to be effective. Policy solutions need to embrace long‐term management strategies as an urgent priority.
Directed evolution of a temperature-, peroxide- and alkaline pH-tolerant versatile peroxidase
Authors: Garcia-Ruiz Eva , Gonzalez-Perez David , Ruiz-Dueñas Francisco J. , Martínez Angel T. , Alcalde Miguel
Published: October 2011

The VPs (versatile peroxidases) secreted by white-rot fungi are involved in the natural decay of lignin. In the present study, a fusion gene containing the VP from Pleurotus eryngii was subjected to six rounds of directed evolution, achieving a level of secretion in Saccharomyces cerevisiae (21 mg/l) as yet unseen for any ligninolytic peroxidase. The evolved variant for expression harboured four mutations and increased its total VP activity 129-fold. The signal leader processing by the STE13 protease at the Golgi compartment changed as a consequence of overexpression, retaining the additional N-terminal sequence Glu-Ala-Glu-Ala that enhanced secretion. The engineered N-terminally truncated variant displayed similar biochemical properties to those of the non-truncated counterpart in terms of kinetics, stability and spectroscopic features. Additional cycles of evolution raised the T50 8°C and significantly increased the enzyme's stability at alkaline pHs. In addition, the Km for H2O2 was enhanced up to 15-fold while the catalytic efficiency was maintained, and there was an improvement in peroxide stability (with half-lives for H2O2 of 43 min at a H2O2/enzyme molar ratio of 4000:1). Overall, the directed evolution approach described provides a set of strategies for selecting VPs with improvements in secretion, activity and stability.
Atomistic simulations of the solid-liquid transition of 1-ethyl-3-methyl imidazolium bromide ionic liquid
Authors: Feng Haijun , Zhou Jian , Qian Yu
Published: October 2011

Achieving melting point around room temperature is important for applications of ionic liquids. In this work, molecular dynamics simulations are carried out to investigate the solid-liquid transition of ionic liquid 1-ethyl-3-methyl imidazolium bromide ([emim]Br) by direct heating, hysteresis, void-nucleation, sandwich, and microcanonical ensemble approaches. Variations of the non-bonded energy, density, diffusion coefficient, and translational order parameter of [emim]Br are analyzed as a function of temperature, and a coexisting solid-liquid system is achieved in the microcanonical ensemble method. The melting points obtained from the first three methods are 547 ± 8 K, 429 ± 8 K, and 370 ± 6 K; while for the sandwich method, the melting points are 403 ± 4 K when merging along the x-axis by anisotropic isothermal-isobaric (NPT) ensemble, 393 ± 4 K when along the y-axis by anisotropic NPT ensemble, and 375 ± 4 K when along the y-axis by isotropic NPT ensemble. For microcanonical ensemble method, when the slabs are merging along different directions (x-axis, y-axis, and z-axis), the melting points are 364 ± 3 K, 365 ± 3 K, and 367 ± 3 K, respectively, the melting points we get by different methods are approximately 55.4%, 21.9%, 5.1%, 14.5%, 11.6%, 6.5%, 3.4%, 3.7%, and 4.3% higher than the experimental value of 352 K. The advantages and disadvantages of each method are discussed. The void-nucleation and microcanonical ensemble methods are most favorable for predicting the solid-liquid transition.
Multiple state transition interface sampling of alanine dipeptide in explicit solvent
Authors: Du Wei-Na , Marino Kristen A. , Bolhuis Peter G.
Published: October 2011

We have applied the recently developed multiple state transition interface sampling approach to alanine dipeptide in explicit water. We extract the rate constant matrix for configurational changes between each pair of metastable states. The results are comparable with values from previous literature and show that the method is applicable to biomolecular systems.
Effects of heavy ion temperature on low-frequency kinetic Alfvén waves
Authors: Yang L. , Wu D. J.
Published: October 2011

Heavy ion-electron (or proton) temperature ratio varies in a wide range in the solar and space environment. In this paper, proton and heavy ion temperatures are included in a three-fluid plasma model. For the specified parameters, low-frequency (≪ heavy ion gyrofrequency) kinetic Alfvén waves (KAWs) with sub- and super-Alfvénic speeds are found to coexist in the same plasma environment. Our results show that the temperature ratio of heavy ions to electrons can considerably affect the dispersion, propagation, and electromagnetic polarizations of the KAWs. In particular, the temperature ratio can increase the ratio of parallel to perpendicular electric fields and the normalized electric to magnetic field ratio, the variations of which are greatly different in regions with a high heavy ion temperature and with a low one. The results may help to understand the physical mechanism of some energization processes of heavy ions in the solar and space plasma environment. Effects of the ratio of electron thermal to Alfvén speeds and the heavy ion abundance on these parameters are also discussed.
Emission properties of explosive field emission cathodes
Authors: Roy Amitava , Patel Ankur , Menon Rakhee , Sharma Archana , Chakravarthy D. P. , Patil D. S.
Published: October 2011

The research results of the explosive field emission cathode plasma expansion velocity and the initial emission area in the planar diode configuration with cathodes made of graphite, stainless steel, polymer velvet, carbon coated, and carbon fiber (needle type) cathodes are presented. The experiments have been performed at the electron accelerator LIA-200 (200 kV, 100 ns, and 4 kA). The diode voltage has been varied from 28–225 kV, whereas the current density has been varied from 86–928 A/cm2 with 100 ns pulse duration. The experimentally obtained electron beam diode perveance has been compared with the 1 dimensional Child-Langmuir- law. It was found that initially only a part of the cathode take part in the emission process. The plasma expands at 1.7–5.2 cm/μs for 4 mm anode-cathode gap for various cathode materials. It was found that the plasma expansion velocity increases with the decrease in the cathode diameter. At the beginning of the accelerating pulse, the entire cathode area participates in the electron emission process only for the multiple needle type carbon fiber cathode.
Direct imaging of intrinsic molecular orbitals using two-dimensional, epitaxially-grown, nanostructured graphene for study of single molecule and interactions
Authors: Zhou H. T. , Mao J. H. , Li G. , Wang Y. L. , Feng X. L. , Du S. X. , Müllen K. , Gao H.-J.
Published: October 2011

Using epitaxially grown graphene on Ru(0001) as a buffer layer, the intrinsic molecular orbitals of perylene-3,4,9,10-tetracarboxylic dianhydride, pentacene, and C60 molecules were imaged by means of scanning tunneling microscope (STM). Combined with density functional theory calculations, our high resolution STM images of the molecules reveal that the graphene layer decouples the individual molecules electronically from the metallic substrate. Our results show that graphene-based moiré pattern can be used as a unique way to probe the intrinsic electronic structures of molecular adsorbates and their interactions.
The hierarchical expansion of the kinetic energy operator in curvilinear coordinates extended to the vibrational configuration interaction method
Authors: Strobusch D. , Scheurer Ch.
Published: October 2011

The hierarchical expansion of the kinetic energy operator in curvilinear coordinates presented earlier for the vibrational self-consistent field technique is extended to the vibrational configuration interaction (VCI) method. The high accuracy of the modified VCI method is demonstrated by computing first excitation energies of the H2O2 molecule using an analytic potential (PCPSDE) and showing convergence to accurate results from full dimensional discrete variable representation calculations.
Reduced auger recombination in mid-infrared semiconductor lasers
Authors: Bedford Robert G. , Triplett Gregory , Tomich David H. , W. Koch Stephan , Moloney Jerome , Hader Jörg
Published: October 2011

A quantum-design approach to reduce the Auger losses in λ = 2 μm InGaSb type-I quantum well edge-emitting lasers is reported. Experimentally realized structures show a ∼3 × reduction in the threshold, which results in 4.6 × lower Auger current loss at room temperature. This is equivalent to a carrier lifetime improvement of 5.7 × and represents about a 19-fold reduction in the equivalent “Auger coefficient.”
Electron-phonon interaction effects on the direct gap transitions of nanoscale Si films
Authors: Kamineni V. K. , Diebold A. C.
Published: October 2011

This study shows that the dielectric function of crystalline Si quantum wells (c-Si QW) is influenced by both carrier confinement and electron-phonon interactions. The energy shifts and lifetime broadening of the excitonic E1 direct gap transition of c-Si QWs from 2 to 10 nm are found to have a significant dimensional and temperature dependence that can be traced to changes in the phonon dispersion of nanoscale films. The influence of electron-phonon interactions on the dielectric function was verified by altering the phonon dispersion using different dielectric layers above a 5 nm c-Si QW.
Q-factor control of a microcantilever by mechanical sideband excitation
Authors: Venstra Warner J. , Westra Hidde J. R. , van der Zant Herre S. J.
Published: October 2011

We demonstrate the coupling between the fundamental and second flexural modes of a microcantilever. A mechanical analogue of cavity-optomechanics is then employed, where the mechanical cavity is formed by the second vibrational mode of the same cantilever, coupled to the fundamental mode via the geometric nonlinearity. By exciting the cantilever at the sum and difference frequencies between fundamental and second flexural modes, the motion of the fundamental mode of the cantilever is damped and amplified. This concept makes it possible to enhance or suppress the Q-factor over a wide range.
Communication: Multicanonical entropy-like solution of statistical temperature weighted histogram analysis method
Authors: Rizzi Leandro G. , Alves Nelson A.
Published: October 2011

A multicanonical update relation for calculation of the microcanonical entropy Smicro(E) by means of the estimates of the inverse statistical temperature βS, is proposed. This inverse temperature is obtained from the recently proposed statistical temperature weighted histogram analysis method (ST-WHAM). The performance of ST-WHAM concerning the computation of Smicro(E) from canonical measures, in a model with strong free-energy barriers, is also discussed on the basis of comparison with the multicanonical simulation estimates.
Communication: Enhancement of dopant dependent x-ray photoelectron spectroscopy peak shifts of Si by surface photovoltage
Authors: Sezen Hikmet , Suzer Sefik
Published: October 2011

Binding energies measured by x-ray photoelectron spectroscopy (XPS) are influenced by doping, since electrons are transferred to (p-type) and from (n-type) samples when they are introduced into the spectrometer, or brought into contact with each other (p-n junction). We show that the barely measurable Si2p binding energy difference between moderately doped n- and p-Si samples can be enhanced by photoillumination, due to reduction in surface band-bending, which otherwise screens this difference. Similar effects are also measured for samples containing oxide layers, since the band-bending at the buried oxide-Si interfaces is manifest as photovoltage shifts, although XPS does not probe the interface directly. The corresponding shift for the oxide layer of the p-Si is almost twice that of without the oxide, whereas no measurable shifts are observable for the oxide of the n-Si. These results are all related to band-bending effects and are vital in design and performance of photovoltaics and other related systems.
Genetic diversity and biogeographic history inform future conservation management strategies for the rare sunset frog (Spicospina flammocaerulea)
Authors: Edwards D. L. , Roberts J. D.
Published: October 2011

Outlining the distribution of genetic variation, patterns of gene flow and clarifying the biogeographic processes underlying population history are critical components of a comprehensive conservation strategy for endangered or vulnerable species. We provide this information for the vulnerable sunset frog (Spicospina flammocaerulea) using a comprehensive genetic dataset (ND2) with samples from 17 of 22 geographic localities where this species has been found. From genetic, biogeographic and coalescent-based analyses, we document the existing genetic variation, likely movement patterns and explore the biogeographic history of S. flammocaerulea. While catchment-based genetic variation is well documented in other high-rainfall taxa in south-western Australia, a much more complex scenario including dispersal across ridge lines between catchments better explains the distribution of genetic variation and observed patterns of gene flow in S. flammocaerulea. The population history of S. flammocaerulea is strongly indicative of recent population contraction and expansion, which may be related to late Pleistocene climate fluctuations. This suggests that this species can adapt or move in response to fluctuating climates provided suitable habitats or expansion areas are available. However, like many other endemic taxa with limited geographic ranges in south-western Australia, the potential to shift distributions is hampered by being land-locked within an agricultural landscape, limiting management options in the face of climate change.
Urinary corticosterone responses and haematological stress indicators in the endangered Fijian ground frog (Platymantis vitiana) during transportation and captivity
Authors: Narayan Edward , Hero Jean-Marc
Published: October 2011

Physiological stress assessment is important for in-situ conservation and captive management of threatened wildlife. Leukocyte (white blood cell) evaluation, especially the neutrophil : lymphocyte (N : L) ratio, provides a logical representation of experimentally elevated corticosterone (stress hormone) in amphibians. Urinary corticosterone enzyme-immunoassay (EIA) is a rapid non-invasive tool for assessing stress responses in amphibians. To our knowledge, no one has explored the relationship between N : L ratio and urinary corticosterone in wild amphibians in a non-experimental way. This study provides a comparative assessment of relative leukocyte numbers, N : L ratios and urinary corticosterone responses of the endangered Fijian ground frog (Platymantis vitiana) during transportation and captivity. Adult frogs (n = 40) were collected from Viwa, Fiji Island for captive breeding. Frogs showed significant changes in leukocyte proportions during transportation and captivity. N : L ratios were higher 6 h after transportation and over 5 and 15 days in captivity. Urinary corticosterone responses of the frogs were also higher 6 h after transportation and after 5 and 15 days in captivity. All leukocyte proportions, N : L ratios and urinary corticosterone concentrations of the frogs returned near baseline levels after the frogs were kept in an environmentally enriched outdoor enclosure for over 25 days. These results highlight the value of leukocyte evaluation and urinary corticosterone EIAs as physiological tools for evaluating stress in amphibians.
Worker heterozygosity and immune response in feral and managed honeybees (Apis mellifera)
Authors: Lowe E. C. , Simmons L. W. , Baer B.
Published: October 2011

Genetic diversity in workers influences colony immunity in several species of eusocial insects. Much less work has been conducted to test for comparable effects of worker heterozygosity, a measure of genetic diversity within an individual. Here we present a field study using the honeybee (Apis mellifera) and sampled foraging workers throughout Western Australia. Samples were taken from feral and managed colonies, aiming to maximise the variation in worker and colony heterozygosity. We quantified worker heterozygosity using microsatellites, and tested the idea that individual worker heterozygosity predicts immune response, measured as the enzymatic activity of an antimicrobial peptide phenoloxidase (PO) and encapsulation response. We found substantial variation in worker heterozygosity, but no significant effects of heterozygosity on PO activity or encapsulation response, either on the individual or colony level. Heterozygosity was found to be higher in workers of feral colonies compared with managed colonies. Colonies kept in husbandry, as compared with colonies from the field, had significantly higher levels of PO activity and encapsulation response, providing evidence for substantial environmental effects on individual and colony immunity.
Verbs of visual perception in Italian FrameNet
Authors: Johnson Martina , Lenci Alessandro
Published: October 2011

In this paper, we present a frame semantic analysis of a small group of Italian verbs expressing visual perception, which constitutes the first stage of a project for developing an Italian FrameNet. Our results show a close correspondence between English and Italian perception-related frames. The main element of novelty in our approach is that the creation and annotation of Lexical Units is grounded in distributional information automatically acquired from a large, dependency-parsed corpus, which is balanced against the annotator’s linguistic intuition. We claim that this can help to overcome some of the shortcomings of the classical lexicographic method used to create FrameNet.
Semantic annotation of Italian legal texts
Authors: Venturi Giulia
Published: October 2011

The FrameNet approach to text semantic annotation can be a reliable model to make the linguistic information and semantic content of legal texts explicit. This hypothesis is discussed and empirically demonstrated through a trial of annotating a corpus of Italian legal texts. This study aims to show that FrameNet is particularly appropriate to provide new perspectives for legal language studies and for legal knowledge representation tasks. Moreover, by relying on the output of a statistical dependency parser, the FrameNet-based annotation methodology presented here can be used successfully in the automatic semantic processing of legal texts.
Code-switching
Authors: Bock Zannie
Published: October 2011

This article analyses the function that code-switching plays in selected testimonies given at South Africa’s Truth and Reconciliation Commission which followed the country’s transition to democracy in 1994. In a number of testimonies, victims of human rights abuse under Apartheid code-switched into Afrikaans when recalling particularly offensive uses of language by the police. Within the code-switching literature, it is well recognised that a speaker’s choice of code, particularly for quoted speech, is a strategy for performing different kinds of local identities which index a range of social meanings and relationships (Álvarez-Cáccamo 1996, Koven 2001). Thus code-switching may serve a complex evaluative function although the meanings it generates are very context-dependent. In order to explore this role in the testimonies in this paper, I use the appraisal theory of Systemic Functional Linguistics (Martin & White 2005). I argue that on a number of occasions, code-switching into a particular variety of Afrikaans is used by testifiers as a strategy to invoke negative judgement: it has the effect of associating the police with a particular racist ideology and positioning them for our sanction. Further, it works together with other engagement resources to insert a recognisable historical voice into the text, thereby expanding the heteroglossic nature of the discourse while simultaneously allowing the speakers to signal their rejection of that voice and the ideologies it represents. In the current SFL literature, however, code-switching has not been noted as an appraisal resource. In the light of the examples from the TRC testimonies, I argue that, in multilingual contexts, code-switching has the potential to invoke complex evaluative meanings and should be included in the appraisal framework as an evaluative resource.
Turning speaker meaning on its head
Authors: Dynel Marta
Published: October 2011

This article addresses the issue of non-verbal communication in the light of the Gricean conceptualisation of intentionally conveyed meanings. The first goal is to testify that non-verbal cues can be interpreted as nonnatural meanings and speaker meanings, which partake in intentional communication. Secondly, it is argued that non-verbal signals, exemplified by gestures, are similar to utterances which generate the communicator’s what is said and/or conversational implicatures, together with their different subtypes and manifestations. Both of these objectives necessitate a critical overview of Grice’s work on the focal aspects of meaning and communication, also on the strength of neo-Gricean research.
THIS → is Learning
Authors: Berducci Domenic
Published: October 2011

In this paper I attempt to dissolve two confused ideas inherent in scientific studies of learning: That the locus of learning processes lies hidden inside the mind/brain, and also that this putatively hidden phenomenon causes learned actions. I attempt this dissolution through conceptual argument and data analysis, first by contrasting the use of the concept ‘learning’ in ordinary and scientific interaction, followed by a Wittgenstein-inspired conversation analysis of a micro-longitudinal case of learning interaction — a biochemist teaching lab techniques to a technician — in order to demonstrate that learning processes are inherently social. I conclude that the scientific view of learning processes as hidden is misconceived through its misuse of the concept “learning”. The empirical results demonstrate that learning processes are indeed public and manifest in an indefinite number of forms, and whatever may be found in the brain associated with learning are concomitant factors, not learning itself.
Spectroscopic study on resistive switching property of perovskite manganite film with controlled oxygen deficient state
Authors: Choi Sun Gyu , Lee Hong-Sub , Choi Hyejung , Chung Sung-Woong , Park Hyung-Ho
Published: October 2011

La0.7Sr0.3MnO3 thin films were prepared on Pt/Ti/SiO2/Si substrates using a radio frequency magnetron sputtering technique under various Ar : O2 flow rates at a substrate temperature of 450 °C. X-ray diffraction results showed that the growth orientation and crystallinity of film were affected by Ar : O2 ratio. Using x-ray photoelectron spectroscopy and near edge x-ray absorption fine structure, the chemical state of La0.7Sr0.3MnO3 film was revealed to have reduced oxygen deficiencies with increasing O2 flow during deposition. The valence band maximum was also shifted to the Fermi edge, and resistive switching properties were decreased with reduced oxygen vacancies from increased oxygen flow rate.
The 2D plasma potential distribution in a HiPIMS discharge
Authors: Mishra A , Kelly P J , Bradley J W
Published: October 2011

Using an emissive probe the spatial-temporal distribution of the plasma potential V
p in a high power impulse magnetron sputtering discharge has been measured. The magnetron (with a planar circular titanium target) was operated in argon gas at a fixed pressure of 0.54 Pa, a pulse frequency of 100 Hz with a 100 µs on-time and average power of 650 W. In the early part of the voltage pulse (∼6–8 µs), V
p attains deep negative values (∼−150 V) at positions close to the target (10 mm) and above the racetrack, diminishing with distance, but never reaching ground potential, even at excursions of 80 mm. In the confined plasma region, extraordinarily high axial and radial electric field components, up to several kV m−1, are calculated from the plasma potential measurements.

As the plasma develops and the discharge current reaches a maximum (at ∼40 µs), V
p is elevated everywhere in the plasma, however, still with deep negative values (down to −40 V) at positions closest to the target. From the derived electric fields and modelled (vacuum) magnetic field, the 2D distribution of E × B electron drift velocities has been determined. During the early discharge phase, a broad drift channel is predicted above the racetrack, with drift speeds up to ∼3 × 105 ms−1 centred ∼30 mm above the target racetrack. As the discharge develops, these speeds reduce by about a factor 3 and the centre of the velocity distribution moves further away from the target and inwards towards the discharge axis, resembling that observed in dc and pulsed-dc magnetron operation.
Nonlinear properties of meta-dimer comprised of coupled ring resonators
Authors: Fan Yuancheng , Wei Zeyong , Han Jin , Liu Xige , Li Hongqiang
Published: October 2011

We experimentally and theoretically investigate the nonlinear electromagnetic properties of an on-chip metamaterial system comprised of two coupled ring resonators (CRRs) as meta-dimer and a varactor loaded in between them as nonlinear medium inclusion. The resonant frequency of the anti-symmetric coupling mode of CRRs is sensitive to the input power and can be tuned to an extremely low frequency as the induced voltage gradient loaded on the varactor is maximized when the mode is excited. Nonlinear responses, including the shift of resonant frequency as well as hysteresis effects, are demonstrated experimentally in distinct ranges of input powers. The findings have potential applications in implementing subwavelength nonlinear components for integrated plasmonic nanocircuits or metactronics.
Effect of negative substrate bias voltage on the structure and properties of CrN films deposited by modulated pulsed power (MPP) magnetron sputtering
Authors: Lin J , Sproul W D , Moore J J , Wu Z L , Lee S L
Published: October 2011

As a variation of high power pulsed magnetron sputtering technique, modulated pulsed power (MPP) magnetron sputtering has shown the capability of maintaining a good deposition rate while achieving a high degree of ionization of the sputtered material with low ion energies. It is critical to usefully utilize the negative substrate bias voltage (V
b) to attract these ions towards the substrate to enhance the ion bombardment on growing films by controlling the kinetic energy and the behaviours of ions and electrons arriving on growing films. In this study, CrN thin films have been deposited by MPP in a closed field unbalanced magnetron sputtering system at different V
b varied from 0 to −150 V. The peak and mean substrate ion current densities were measured during the depositions as a function of V
b. The films were annealed at 450 °C in Ar for 1 hr in an effort to release the defects and residual stress in the as-deposited films. The structure and properties of as-deposited and annealed films were characterized by electron probe micro-analysis, x-ray diffraction, scanning electron microscopy, transmission electron microscopy, nanoindentation, and ball-on-disc wear test. An increase in the Cr/N ratio of the film was observed as the V
b was increased negatively to above −70 V, which resulted in the formation of the hexagonal Cr2N film at V
b = −150 V. A preferred (3 1 1) texture was observed in the CrN films deposited as V
b increased from −50 V to −100 V. The residual stress of the films increased as the V
b was increased from 0 to −100 V and then decreased with further increasing the V
b. The increase in the V
b led to grain refinement and an increase in the hardness of the films, but the wear resistance of the films decreased rapidly as the V
b was increased to −150 V.
Surface stress-induced deflection of a microcantilever with various widths and overall microcantilever sensitivity enhancement via geometry modification
Authors: Zhang Guiming , Zhao Libo , Jiang Zhuangde , Yang Shuming , Zhao Yulong , Huang Enze , Wang Xiaopo , Liu Zhigang
Published: October 2011

The issues of surface stress-induced deflection of a microcantilever with various widths and overall microcantilever sensitivity enhancement of microcantilever-based biosensors are investigated in this paper. A remarkably precise and simple analytical formula for calculating surface stress-induced deflection of a microcantilever with various widths is deduced. Particularly, the effect of surface stress on the location of the microcantilever's neutral axis is considered. This explicit analytical formula is validated by the finite element method simulation. An analytical equation for computing the fundamental resonant frequency of a microcantilever with various widths is also derived. This paper explores the deflections and resonant frequencies of the microcantilevers having basic and modified shapes. It is found that minimizing the effective mass near the microcantilever's free end and the clamping width at the fixed end significantly enhances the overall microcantilever sensitivity. A novel microcantilever, which is expected to have much more excellent performance and overall sensitivity than the simple rectangular-shaped microcantilever, is proposed as sensor element in biological detection.
KABOOM! A new suffix array based algorithm for clustering expression data
Authors: Hazelhurst Scott , Lipták Zsuzsanna
Published: October 2011

Motivation: Second-generation sequencing technology has reinvigorated research using expression data, and clustering such data remains a significant challenge, with much larger datasets and with different error profiles. Algorithms that rely on all-versus-all comparison of sequences are not practical for large datasets.

Results: We introduce a new filter for string similarity which has the potential to eliminate the need for all-versus-all comparison in clustering of expression data and other similar tasks. Our filter is based on multiple long exact matches between the two strings, with the additional constraint that these matches must be sufficiently far apart. We give details of its efficient implementation using modified suffix arrays. We demonstrate its efficiency by presenting our new expression clustering tool, wcd-express, which uses this heuristic. We compare it to other current tools and show that it is very competitive both with respect to quality and run time.

Availability: Source code and binaries available under GPL at http://code.google.com/p/wcdest. Runs on Linux and MacOS X.

Contact:  scott.hazelhurst@wits.ac.za; zsuzsa@cebitec.uni-bielefeld.de

Supplementary Information:  Supplementary data are available at Bioinformatics online.
CAMBerVis: visualization software to support comparative analysis of multiple bacterial strains
Authors: Woźniak Michał , Wong Limsoon , Tiuryn Jerzy
Published: October 2011

Motivation: A number of inconsistencies in genome annotations are documented among bacterial strains. Visualization of the differences may help biologists to make correct decisions in spurious cases.

Results: We have developed a visualization tool, CAMBerVis, to support comparative analysis of multiple bacterial strains. The software manages simultaneous visualization of multiple bacterial genomes, enabling visual analysis focused on genome structure annotations.

Availability: The CAMBerVis software is freely available at the project website: http://bioputer.mimuw.edu.pl/camber. Input datasets for Mycobacterium tuberculosis and Staphylocacus aureus are integrated with the software as examples.

Contact:  m.wozniak@mimuw.edu.pl

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Risk Factors for Zaireebolavirus–Specific IgG in Rural Gabonese Populations
Authors: Nkoghe Dieudonne , Padilla Cindy , Becquart Pierre , Wauquier Nadia , Moussavou Ghislain , Akué Jean Paul , Ollomo Benjamin , Pourrut Xavier , Souris Marc , Kazanji Mirdad , Gonzalez Jean-Paul , Leroy Eric
Published: October 2011

Background.  In Gabon, several Ebolavirus outbreaks have occurred exclusively in the northeastern region. We conducted a large serosurvey to identify areas and populations at risk and potential demographic, clinical, and behavioral risk factors.

Methods.  Blood samples and clinical and sociodemographic data were collected from 4349 adults and 362 children in a random sample of 220 villages in the 9 provinces of Gabon. An enzyme-linked immunosorbent assay was used to detect Zaire ebolavirus (ZEBOV)–specific IgG, and thin blood smears were used to detect parasites. Logistic regression was implemented using Stata software (Stata), and a probability level of <.05 was considered to be statistically significant.

Results.  The prevalence of ZEBOV-specific IgG was 15.3% overall, increasing to 32.4% (P< .001) in forest areas. No sociodemographic risk factors were found, but the antibody prevalence increased linearly up to 20 years of age. Chronic arthralgia and amicrofilaremia were the only factors associated with ZEBOV seropositivity.

Conclusions.  These findings confirm the endemicity of ZEBOV in Gabon and its link to the ecosystem. Human antibody positivity would appear to be to the result of exposure to contaminated fruits.