bluuebunny/crossref_metadata_2025 huggingface dataset:
A comprehensive study on the leakage current mechanisms of Pt/SrTiO3/Pt capacitor
Authors: Mojarad Shahin A. , Kwa Kelvin S. K. , Goss Jonathan P. , Zhou Zhiyong , Ponon Nikhil K. , Appleby Daniel J. R. , Al-Hamadany Raied A. S. , O’Neill Anthony
Published: January 2012

The leakage current characteristics of SrTiO3 MIM capacitors, fabricated using atomic layer deposition, are investigated. The characteristics are highly sensitive to the polarity and magnitude of applied voltage bias, punctuated by sharp increases at high field. The characteristics are also asymmetric with bias and the negative to positive current crossover point always occurs at a negative voltage bias. In this work, a model comprising thermionic field emission and tunneling phenomena is proposed to explain the dependence of leakage current upon the device parameters quantitatively.
Resonant carrier scattering by core-shell nanoparticles for thermoelectric power factor enhancement
Authors: Bahk Je-Hyeong , Santhanam Parthiban , Bian Zhixi , Ram Rajeev , Shakouri Ali
Published: January 2012

We theoretically investigate the use of energetically sharp resonances of core-shell nanoparticles embedded in semiconductors to selectively scatter carriers and thereby enhance the thermoelectric power factor and figure of merit. Appropriate selection of materials for the core-shell band structure can lead to the formation of quasi-bound states inside the nanoparticles, which strongly scatter carriers near these energy levels, making sharp features in the energy-dependent electron relaxation time. We find that the power factor of PbTe at 80 K is enhanced by more than 80% when core-shell nanoparticles of 3 nm core diameter and 1.5 nm shell width are introduced with density 1 × 1018 cm−3.
Investigation of a high spatial resolution method based on polar coordinate maximum entropy method for analyzing electron density fluctuation data measured by laser phase contrast
Authors: Matsuo K. , Iguchi H. , Okamura S. , Matsuoka K.
Published: January 2012

Laser phase contrast is a powerful diagnostic method to determine the spatial distribution of electron density fluctuations in magnetically confined plasmas, although its applicability depends on magnetic field configurations. The spatial resolution of fluctuations is linked with the resolution of the propagation direction that is derived from the two-dimensional spectral analysis of the wavenumber for the fluctuations. The method was applied to fluctuation measurements in a compact helical system. In order to improve the resolution of the propagation direction with a relatively small number of data points, the maximum entropy method with polar coordinates was employed. A spatial resolution of the order of 1 cm was obtained, which is satisfactory in a plasma with a 20 cm minor radius.
Role of coexisting tetragonal regions in the rhombohedral phase of Na0.5Bi0.5TiO3-xat.%BaTiO3 crystals on enhanced piezoelectric properties on approaching the morphotropic phase boundary
Authors: Yao Jianjun , Monsegue Niven , Murayama Mitsuhiro , Leng Weinan , Reynolds William T. , Zhang Qinhui , Luo Haosu , Li Jiefang , Ge Wenwei , Viehland D.
Published: January 2012

The ferroelectric domain and local structures of Na0.5Bi0.5TiO3-xat.%BaTiO3 (NBT-x%BT) crystals for x = 0, 4.5, and 5.5 have been investigated by transmission electron microscopy. The results show that the size of polar nano-regions was refined with increasing xat. %BT. The tetragonal phase volume fraction, as identified by in-phase octahedral tilting, was found to be increased with BT. The findings indicate that the large electric field induced strains in morphotropic phase boundary compositions of NBT-x%BT originate not only from polarization rotation but also polarization extension.
Effects of Cu diffusion-doping on structural, optical, and magnetic properties of ZnO nanorod arrays grown by vapor phase transport method
Authors: Yılmaz S. , McGlynn E. , Bacaksız E. , Özcan Ş. , Byrne D. , Henry M. O. , Chellappan R. K.
Published: January 2012

Well-aligned ZnO nanorods were prepared by the vapor phase transport method on Si covered with a ZnO buffer layer. After the nanostructure growth, Cu was doped into the ZnO nanorods by diffusion at three different temperatures and for different times. Undoped and Cu diffusion-doped ZnO samples are highly textured, with the c axis of the wurtzite structure along the growth direction. The incorporation of Cu caused some slight changes in the nanorod alignment, although the wurtzite crystal structure was maintained. X-ray photoelectron spectroscopy measurements revealed that Cu ions were in a divalent state and substituted for the Zn2+ ions of the ZnO matrix. Photoluminescence results at 10 K indicate that the incorporation of copper leads to a relative increase of Cu-related structured green band deep level intensity. Magnetic measurements revealed that both undoped and Cu diffusion-doped ZnO samples exhibited room temperature ferromagnetism. It was also found that bound magnetic polarons play an important role in the appearance of room temperature ferromagnetism in Cu diffusion-doped ZnO nanorods.
Feasibility study of broadband efficient “water window” source
Authors: Higashiguchi Takeshi , Otsuka Takamitsu , Yugami Noboru , Jiang Weihua , Endo Akira , Li Bowen , Dunne Padraig , O’Sullivan Gerry
Published: January 2012

We demonstrate a table-top broadband emission water window source based on laser-produced high-Z plasmas. Resonance emission from multiply charged ions merges to produce intense unresolved transition arrays (UTAs) in the 2–4 nm region, extending below the carbon K edge (4.37 nm). Arrays resulting from n=4-n=4 transitions are overlaid with n=4-n=5 emission and shift to shorter wavelength with increasing atomic number. An outline of a microscope design for single-shot live cell imaging is proposed based on a bismuth plasma UTA source, coupled to multilayer mirror optics.
Relaxation dynamics and residual strain in metamorphic AlSb on GaAs
Authors: Ripalda J. M. , Sanchez A. M. , Taboada A. G. , Rivera A. , Alén B. , González Y. , González L. , Briones F. , Rotter T. J. , Balakrishnan G.
Published: January 2012

We have observed the evolution of the accumulated stress during heteroepitaxial growth of highly lattice mismatched AlSb on GaAs by measuring the deformation of the substrate as a function of time. High resolution transmission electron microscopy images show almost all of the plastic relaxation is accommodated by an array of 90° misfit dislocations at the interface. The in-plane lattice parameter of the resulting metamorphic AlSb is slightly smaller (0.3%) than the bulk value and perfectly matches the lattice parameter of bulk GaSb. It is, therefore, possible to grow nearly stress-free GaSb on GaAs using a metamorphic AlSb buffer layer.
First-principles study of the transport behavior of zigzag graphene nanoribbons tailored by strain
Authors: Wang Jinying , Liu Zhongfan , Liu Zhirong
Published: January 2012

The charge transport properties of zigzag graphene nanoribbons (ZGNRs) under uniaxial and shear strains are theoretically studied. Although all strained ZGNRs have similar metallic band structures, they show four types of transport behavior under bias voltages that depend on the type of strain and the mirror symmetry of the ZGNR. Under an applied uniaxial strain, the current of symmetric ZGNRs is consistently small, while for asymmetric ZGNRs it is large. In contrast, the current increases with increasing shear strain for symmetric ZGNRs while it decreases for asymmetric ZGNRs. The current properties merge when the shear strain exceeds a critical value, and the two systems then show similar behavior. Our results suggest that strained ZGNRs with an appropriate applied shear are ideal conducting wires.
A first glimpse of possibly primordial intergalactic gas
Authors: Schwarzschild Bertram M.
Published: January 2012

Before the first stars, there were presumably no nuclei heavier than lithium. But pristine gas without a trace of stellar contamination has been elusive.
Chief scientist Ellen Williams seeks to bring new energy to BP
Authors: Matthews Jermey N. A.
Published: January 2012

After spending three decades in academia conducting nanotechnology research, the chemist-turned-physicist is now tackling the energy problem in the faster-paced industrial environment.
Chile aims to better exploit role as telescope host
Authors: Feder Toni
Published: January 2012

The country’s scientists and engineers are starting to take part in the design and construction of telescopes, a trend that could boost other industries and the economy.
Quantum coherence spectroscopy reveals complex dynamics in bacterial light-harvesting complex 2 (LH2)
Authors: Harel Elad , Engel Gregory S.
Published: January 2012

Light-harvesting antenna complexes transfer energy from sunlight to photosynthetic reaction centers where charge separation drives cellular metabolism. The process through which pigments transfer excitation energy involves a complex choreography of coherent and incoherent processes mediated by the surrounding protein and solvent environment. The recent discovery of coherent dynamics in photosynthetic light-harvesting antennae has motivated many theoretical models exploring effects of interference in energy transfer phenomena. In this work, we provide experimental evidence of long-lived quantum coherence between the spectrally separated B800 and B850 rings of the light-harvesting complex 2 (LH2) of purple bacteria. Spectrally resolved maps of the detuning, dephasing, and the amplitude of electronic coupling between excitons reveal that different relaxation pathways act in concert for optimal transfer efficiency. Furthermore, maps of the phase of the signal suggest that quantum mechanical interference between different energy transfer pathways may be important even at ambient temperature. Such interference at a product state has already been shown to enhance the quantum efficiency of transfer in theoretical models of closed loop systems such as LH2.
Evidence for the extraterrestrial origin of a natural quasicrystal
Authors: Bindi Luca , Eiler John M. , Guan Yunbin , Hollister Lincoln S. , MacPherson Glenn , Steinhardt Paul J. , Yao Nan
Published: January 2012

We present evidence that a rock sample found in the Koryak Mountains in Russia and containing icosahedrite, an icosahedral quasicrystalline phase with composition Al
63
Cu
24
Fe
13
, is part of a meteorite, likely formed in the early solar system about 4.5 Gya. The quasicrystal grains are intergrown with diopside, forsterite, stishovite, and additional metallic phases [khatyrkite (CuAl
2
), cupalite (CuAl), and β-phase (AlCuFe)]. This assemblage, in turn, is enclosed in a white rind consisting of diopside, hedenbergite, spinel (MgAl
2
O
4
), nepheline, and forsterite. Particularly notable is a grain of stishovite (from the interior), a tetragonal polymorph of silica that only occurs at ultrahigh pressures (≥10 Gpa), that contains an inclusion of quasicrystal. An extraterrestrial origin is inferred from secondary ion mass spectrometry
18
O/
16
O and
17
O/
16
O measurements of the pyroxene and olivine intergrown with the metal that show them to have isotopic compositions unlike any terrestrial minerals and instead overlap those of anhydrous phases in carbonaceous chondrite meteorites. The spinel from the white rind has an isotopic composition suggesting that it was part of a calcium-aluminum-rich inclusion similar to those found in CV3 chondrites. The mechanism that produced this exotic assemblage is not yet understood. The assemblage (metallic copper-aluminum alloy) is extremely reduced, and the close association of aluminum (high temperature refractory lithophile) with copper (low temperature chalcophile) is unexpected. Nevertheless, our evidence indicates that quasicrystals can form naturally under astrophysical conditions and remain stable over cosmic timescales, giving unique insights on their existence in nature and stability.
Bivalent recognition of nucleosomes by the tandem PHD fingers of the CHD4 ATPase is required for CHD4-mediated repression
Authors: Musselman Catherine A. , Ramírez Julita , Sims Jennifer K. , Mansfield Robyn E. , Oliver Samuel S. , Denu John M. , Mackay Joel P. , Wade Paul A. , Hagman James , Kutateladze Tatiana G.
Published: January 2012

CHD4 is a catalytic subunit of the NuRD (nucleosome remodeling and deacetylase) complex essential in transcriptional regulation, chromatin assembly and DNA damage repair. CHD4 contains tandem plant homeodomain (PHD) fingers connected by a short linker, the biological function of which remains unclear. Here we explore the combinatorial action of the CHD4 PHD1/2 fingers and detail the molecular basis for their association with chromatin. We found that PHD1/2 targets nucleosomes in a multivalent manner, concomitantly engaging two histone H3 tails. This robust synergistic interaction displaces HP1
γ
from pericentric sites, inducing changes in chromatin structure and leading to the dispersion of the heterochromatic mark H3K9me3. We demonstrate that recognition of the histone H3 tails by the PHD fingers is required for repressive activity of the CHD4/NuRD complex. Together, our data elucidate the molecular mechanism of multivalent association of the PHD fingers with chromatin and reveal their critical role in the regulation of CHD4 functions.
Life motion signals lengthen perceived temporal duration
Authors: Wang Li , Jiang Yi
Published: January 2012

Point-light biological motions, conveying various different attributes of biological entities, have particular spatiotemporal properties that enable them to be processed with remarkable efficiency in the human visual system. Here we demonstrate that such signals automatically lengthen their perceived temporal duration independent of global configuration and without observers’ subjective awareness of their biological nature. By using a duration discrimination paradigm, we showed that an upright biological motion sequence was perceived significantly longer than an inverted but otherwise identical sequence of the same duration. Furthermore, this temporal dilation effect could be extended to spatially scrambled biological motion signals, whose global configurations were completely disrupted, regardless of whether observers were aware of the nature of the stimuli. However, such an effect completely disappeared when critical biological characteristics were removed. Taken together, our findings suggest a special mechanism of time perception tuned to life motion signals and shed new light on the temporal encoding of biological motion.
Spiral chain O
4
form of dense oxygen
Authors: Zhu Li , Wang Ziwei , Wang Yanchao , Zou Guangtian , Mao Ho-kwang , Ma Yanming
Published: January 2012

Oxygen is in many ways a unique element: It is the only known diatomic molecular magnet, and it exhibits an unusual O
8
cluster in its high-pressure solid phase. Pressure-induced molecular dissociation as one of the fundamental problems in physical sciences has been reported from theoretical or experimental studies of diatomic solids H
2
, N
2
, F
2
, Cl
2
, Br
2
, and I
2
but remains elusive for molecular oxygen. We report here the prediction of the dissociation of molecular oxygen into a polymeric spiral chain O
4
structure (space group
I
4
1
/
acd
,
θ
-O
4
) above 1.92-TPa pressure using the particle-swarm search method. The
θ
-O
4
phase has a similar structure as the high-pressure phase III of sulfur. The molecular bonding in the insulating
ε
-O
8
phase or the isostructural superconducting
ζ
-O
8
phase remains remarkably stable over a large pressure range of 0.008–1.92 TPa. The pressure-induced softening of a transverse acoustic phonon mode at the zone boundary
V
point of O
8
phase might be the ultimate driving force for the formation of
θ
-O
4
. Stabilization of
θ
-O
4
turns oxygen from a superconductor into an insulator by opening a wide band gap (approximately 5.9 eV) that originates from the
sp
3
-like hybridized orbitals of oxygen and the localization of valence electrons.
The spread of a transposon insertion in
Rec8
is associated with obligate asexuality in
Daphnia
Authors: Eads Brian D. , Tsuchiya Dai , Andrews Justen , Lynch Michael , Zolan Miriam E.
Published: January 2012

Although transitions from sexual to asexual reproduction are thought to have important evolutionary consequences, little is known about the mechanistic underpinnings of these changes. The cyclical parthenogen
Daphnia pulex
is a powerful model in which to address these issues because female-limited meiosis suppression can be transmitted to sexual individuals via males, providing the opportunity for genetic dissection of the trait. A previous study identified genomic regions differentiating obligately asexual females from their sexual counterparts, and a candidate gene within one such region, encoding the meiotic cohesin Rec8, is the subject of this investigation. The
D. pulex
genome contains three Rec8 loci, all of which are quite polymorphic. However, at one of the loci, all obligately asexual clones carry an allele containing an identical upstream insertion of a transposable element as well as a frameshift mutation, both of which are completely absent from sexual lineages. The low level of variation within the insertion allele across all asexual lineages suggests that this element may be in the process of spreading through the species, and abrogation or modification of Rec8 function is possibly responsible for converting meiotically reproducing lineages into obligate asexuals.
Evaluating bacterial gene-finding HMM structures as probabilistic logic programs
Authors: Mørk Søren , Holmes Ian
Published: January 2012

Motivation: Probabilistic logic programming offers a powerful way to describe and evaluate structured statistical models. To investigate the practicality of probabilistic logic programming for structure learning in bioinformatics, we undertook a simplified bacterial gene-finding benchmark in PRISM, a probabilistic dialect of Prolog.

Results: We evaluate Hidden Markov Model structures for bacterial protein-coding gene potential, including a simple null model structure, three structures based on existing bacterial gene finders and two novel model structures. We test standard versions as well as ADPH length modeling and three-state versions of the five model structures. The models are all represented as probabilistic logic programs and evaluated using the PRISM machine learning system in terms of statistical information criteria and gene-finding prediction accuracy, in two bacterial genomes. Neither of our implementations of the two currently most used model structures are best performing in terms of statistical information criteria or prediction performances, suggesting that better-fitting models might be achievable.

Availability: The source code of all PRISM models, data and additional scripts are freely available for download at: http://github.com/somork/codonhmm.

Contact:  soer@ruc.dk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Osteoarthritis
Authors: Brion Paul H. , Kalunian Kenneth C.
Published: January 2012

Osteoarthritis is the commonest form of arthritis, detectable radiographically in 80% of patients over the age of 55 and accounting for more dependency in walking and stair-climbing than any other disease. In clinical practice it is defined by the presence of joint symptoms (pain, aching, stiffness) plus evidence of structural change (including crepitus on active joint motion, bony enlargement, radiographic changes of joint space narrowing or osteophytes)....
Design and analysis of DNA strand displacement devices using probabilistic model checking
Authors: Lakin Matthew R. , Parker David , Cardelli Luca , Kwiatkowska Marta , Phillips Andrew
Published: January 2012

Designing correct, robust DNA devices is difficult because of the many possibilities for unwanted interference between molecules in the system. DNA strand displacement has been proposed as a design paradigm for DNA devices, and the DNA strand displacement (DSD) programming language has been developed as a means of formally programming and analysing these devices to check for unwanted interference. We demonstrate, for the first time, the use of probabilistic verification techniques to analyse the correctness, reliability and performance of DNA devices during the design phase. We use the probabilistic model checker
prism
, in combination with the DSD language, to design and debug DNA strand displacement components and to investigate their kinetics. We show how our techniques can be used to identify design flaws and to evaluate the merits of contrasting design decisions, even on devices comprising relatively few inputs. We then demonstrate the use of these components to construct a DNA strand displacement device for approximate majority voting. Finally, we discuss some of the challenges and possible directions for applying these methods to more complex designs.
John Tweedie and Charles Darwin in Buenos Aires
Authors: Ollerton Jeff , Chancellor Gordon , van Wyhe John
Published: January 2012

The journey of exploration undertaken by Charles Darwin FRS during the voyage of HMS
Beagle
has a central place within the historical development of evolutionary theory and has been intensively studied. Despite this, new facts continue to emerge about some of the details of Darwin's activities. Drawing on recently published Darwin material and unpublished letters in the archives of the Royal Botanic Gardens, Kew, we document a hitherto unexamined link between Darwin and John Tweedie (1775–1862), a relatively obscure Scottish gardener turned South American plant collector. All of the available evidence points to a meeting between the two men in Buenos Aires in 1832. Tweedie provided Darwin with information about the geography of the Rio Paraná, including the locality of fossilized wood eroding from the river bank. It also seems likely that Tweedie supplied Darwin with seeds that he later shipped back to John Stevens Henslow in Cambridge. Although this brief meeting was at the time relatively unimportant to either man, echoes of that encounter have resonated with Tweedie's descendants to the present day and have formed the basis for a family story about a written correspondence between Darwin and Tweedie. Local information supplied to Darwin by residents such as Tweedie was clearly important and deserves further attention.
Critical thresholds in sea lice epidemics: evidence, sensitivity and subcritical estimation
Authors: Frazer L. Neil , Morton Alexandra , Krkošek Martin
Published: January 2012

Host density thresholds are a fundamental component of the population dynamics of pathogens, but empirical evidence and estimates are lacking. We studied host density thresholds in the dynamics of ectoparasitic sea lice (Lepeophtheirus salmonis) on salmon farms. Empirical examples include a 1994 epidemic in Atlantic Canada and a 2001 epidemic in Pacific Canada. A mathematical model suggests dynamics of lice are governed by a stable endemic equilibrium until the critical host density threshold drops owing to environmental change, or is exceeded by stocking, causing epidemics that require rapid harvest or treatment. Sensitivity analysis of the critical threshold suggests variation in dependence on biotic parameters and high sensitivity to temperature and salinity. We provide a method for estimating the critical threshold from parasite abundances at subcritical host densities and estimate the critical threshold and transmission coefficient for the two epidemics. Host density thresholds may be a fundamental component of disease dynamics in coastal seas where salmon farming occurs.
Frequency-dependent payoffs and sequential decision-making favour consistent tactic use
Authors: Dubois Frédérique , Giraldeau Luc-Alain , Réale Denis
Published: January 2012

Although natural selection should have favoured individuals capable of adjusting the weight they give to personal and social information according to circumstances, individuals generally differ consistently in their individual weighting of both types of information. Such individual differences are correlated with personality traits, suggesting that personality could directly affect individuals’ ability to collect personal or social information. Alternatively, the link between personality and information use could simply emerge as a by-product of the sequential decision-making process in a frequency-dependent context. Indeed, when the gains associated with behavioural options depend on the choices of others, an individual's sequence of arrival could constrain its choice of options leading to the emergence of correlated behaviours. Any factor such as personality that affects decision order could thus be correlated with information use. To test this new explanation, we developed an individual-based model that simulates a group of animals engaged in a game of sequential frequency-dependent decision: a producer–scrounger game. Our results confirm that the sequence of decision, in this case enforced by the order in which animals enter a foraging area, consistently influences their mean tactic use and their individual plasticity, an outcome reminiscent of the correlation reported between personality and social information use.
On a collision course: competition and dispersal differences create no-analogue communities and cause extinctions during climate change
Authors: Urban Mark C. , Tewksbury Josh J. , Sheldon Kimberly S.
Published: January 2012

Most climate change predictions omit species interactions and interspecific variation in dispersal. Here, we develop a model of multiple competing species along a warming climatic gradient that includes temperature-dependent competition, differences in niche breadth and interspecific differences in dispersal ability. Competition and dispersal differences decreased diversity and produced so-called ‘no-analogue’ communities, defined as a novel combination of species that does not currently co-occur. Climate change altered community richness the most when species had narrow niches, when mean community-wide dispersal rates were low and when species differed in dispersal abilities. With high interspecific dispersal variance, the best dispersers tracked climate change, out-competed slower dispersers and caused their extinction. Overall, competition slowed the advance of colonists into newly suitable habitats, creating lags in climate tracking. We predict that climate change will most threaten communities of species that have narrow niches (e.g. tropics), vary in dispersal (most communities) and compete strongly. Current forecasts probably underestimate climate change impacts on biodiversity by neglecting competition and dispersal differences.
The sound of one-hand clapping: handedness and perisylvian neural correlates of a communicative gesture in chimpanzees
Authors: Meguerditchian Adrien , Gardner Molly J. , Schapiro Steven J. , Hopkins William D.
Published: January 2012

Whether lateralization of communicative signalling in non-human primates might constitute prerequisites of hemispheric specialization for language is unclear. In the present study, we examined (i) hand preference for a communicative gesture (clapping in 94 captive chimpanzees from two research facilities) and (ii) the
in vivo
magnetic resonance imaging brain scans of 40 of these individuals. The preferred hand for clapping was defined as the one in the upper position when the two hands came together. Using computer manual tracing of regions of interest, we measured the neuroanatomical asymmetries for the homologues of key language areas, including the inferior frontal gyrus (IFG) and planum temporale (PT). When considering the entire sample, there was a predominance of right-handedness for clapping and the distribution of right- and left-handed individuals did not differ between the two facilities. The direction of hand preference (right- versus left-handed subjects) for clapping explained a significant portion of variability in asymmetries of the PT and IFG. The results are consistent with the view that gestural communication in the common ancestor may have been a precursor of language and its cerebral substrates in modern humans.
NtSCP1 from Tobacco Is an Extracellular Serine Carboxypeptidase III That Has an Impact on Cell Elongation
Authors: Bienert Manuela Désirée , Delannoy Mélanie , Navarre Catherine , Boutry Marc
Published: January 2012

The leaf extracellular space contains several peptidases, most of which are of unknown function. We isolated cDNAs for two extracellular serine carboxypeptidase III genes from tobacco (Nicotiana tabacum), NtSCP1 and NtSCP2, belonging to a phylogenetic clade not yet functionally characterized in plants. NtSCP1 and NtSCP2 are orthologs derived from the two ancestors of tobacco. Reverse transcription-polymerase chain reaction analysis showed that NtSCP1 and NtSCP2 are expressed in root, stem, leaf, and flower tissues. Expression analysis of the β-glucuronidase reporter gene fused to the NtSCP1 transcription promoter region confirmed this expression profile. Western blotting of NtSCP1 and expression of an NtSCP1-green fluorescent protein fusion protein showed that the protein is located in the extracellular space of tobacco leaves and culture cells. Purified His-tagged NtSCP1 had carboxypeptidase activity in vitro. Transgenic tobacco plants overexpressing NtSCP1 showed a reduced flower length due to a decrease in cell size. Etiolated seedlings of these transgenic plants had shorter hypocotyls. These data provide support for a role of an extracellular type III carboxypeptidase in the control of cell elongation.
It was the best of times, it was the worst of times: A psychophysiologist's view of cognitive aging
Authors: Fabiani Monica
Published: January 2012

This paper reviews research on age‐related changes in working memory and attention control. This work is interpreted within a framework labeled “GOLDEN aging” (growing of lifelong differences explains normal aging), which is based on the idea that normal aging (as opposed to pathological aging) represents maturational processes causing progressive shifts in the distributions of mental abilities over the lifespan. As such, brain phenomena observed in normal aging are already apparent, under appropriate conditions, in younger adults. Among the phenomena that can be interpreted according to the GOLDEN aging framework are reductions in working memory capacity, impairments of inhibitory processes, increases in frontal lobe activation, and lack of suppression of responses as a function of repetition.
Are phonological representations in bilinguals language specific? An ERP study on interlingual homophones
Authors: Carrasco‐Ortiz Haydee , Midgley Katherine J. , Frenck‐Mestre Cheryl
Published: January 2012

Event‐related potentials (ERPs) served to investigate whether phonological representations from both the first (L1) and second (L2) language of bilinguals are activated during silent reading of L2 words. French‐English late bilinguals and control monolingual English speakers read interlingual homophones (e.g., “knee” in English, which has substantial phonological overlap with the French word “nid,” meaning “nest”) and matched control words. Results showed a reduction in N400 amplitude in response to interlingual homophones in comparison to control words for bilinguals, but not for English monolinguals. The reduced N400 response to homophones in bilinguals suggests facilitation of word recognition. These results suggest parallel activation of both L1 and L2 phonological representations when reading silently in the L2. These findings point to a language nonspecific model for bilinguals at the phonological level of representation.
Finding the missing stimulus mismatch negativity (MMN): Emitted MMN to violations of an auditory gestalt
Authors: Salisbury Dean F.
Published: January 2012

Deviations from repetitive auditory stimuli evoke a mismatch negativity (MMN). Counterintuitively, omissions of repetitive stimuli do not. Violations of patterns reflecting complex rules also evoke MMN. To detect a MMN to missing stimuli, we developed an auditory gestalt task using one stimulus. Groups of six pips (50 ms duration, 330 ms stimulus onset asynchrony [SOA], 400 trials), were presented with an intertrial interval (ITI) of 750 ms while subjects (n = 16) watched a silent video. Occasional deviant groups had missing 4th or 6th tones (50 trials each). Missing stimuli evoked a MMN (p < .05). The missing 4th (−0.8 µV, p <.01) and the missing 6th stimuli (−1.1 µV, p < .05) were more negative than standard 6th stimuli (0.3 µV). MMN can be elicited by a missing stimulus at long SOAs by violation of a gestalt grouping rule. Patterned stimuli appear more sensitive to omissions and ITI than homogenous streams.
Hepatitis C Virus RNA Elimination and Development of Resistance in Replicon Cells Treated with BMS-790052
Authors: Wang Chunfu , Huang Haichang , Valera Lourdes , Sun Jin-Hua , O'Boyle Donald R. , Nower Peter T. , Jia Lingling , Qiu Dike , Huang Xin , Altaf Aneela , Gao Min , Fridell Robert A.
Published: January 2012

BMS-790052, a first-in-class hepatitis C virus (HCV) replication complex inhibitor, targeting nonstructural protein 5A (NS5A), displays picomolar to nanomolar potency against genotypes 1 to 5. This exceptional potency translated into robust anti-HCV activity in clinical studies with HCV genotype 1-infected subjects. To date, all BMS-790052-associated resistance mutations have mapped to the N-terminal region of NS5A. To further characterize the antiviral activity of BMS-790052, HCV replicon elimination and colony formation assays were performed. Replicon was cleared from genotype 1a and 1b replicon cells in a time- and dose-dependent manner. Elimination of the genotype 1a replicon required longer treatment durations and higher concentrations of BMS-790052 than those for the genotype1b replicon. Single amino acid substitutions that conferred relatively low levels of resistance were observed at early time points and at low doses. Higher doses and longer treatment durations yielded mutations that conferred greater levels of resistance, including linked amino acid substitutions. Replicon cells that survived inhibitor treatment remained fully sensitivity to pegylated alpha interferon (pegIFN-α) and other HCV inhibitors. Moreover, genotype 1a replicon elimination was markedly enhanced when pegIFN-α and BMS-790052 were combined. Resistant variants observed in this study were very similar to those observed in a multiple ascending dose (MAD) monotherapy trial of BMS-790052, validating replicon elimination studies as a model to predict clinical resistance. Insights gained from the
in vitro
anti-HCV activity and resistance profiles of BMS-790052 will be used to help guide the clinical development of this novel HCV inhibitor.
Transferable Multidrug Resistance Plasmid Carrying
cfr
Associated with
tet
(L),
ant(4
′
)-Ia
, and
dfrK
Genes from a Clinical Methicillin-Resistant Staphylococcus aureus ST125 Strain
Authors: Ruiz de Gopegui Enrique , Juan Carlos , Zamorano Laura , Pérez José L. , Oliver Antonio
Published: January 2012

A multidrug resistance (MDR) conjugative plasmid of ca. 50 kb (designated pERGB) was detected in a linezolid and methicillin-resistant
Staphylococcus aureus
strain with sequence type 125 (ST125-MRSA-IVc). This strain was detected in two patients with chronic obstructive pulmonary disease, previously treated with multiple antimicrobials, including linezolid. pERGB was transferable by conjugation and carried the resistance genes
cfr
(oxazolidinones, phenicols, lincosamides, pleuromutilins, and streptogramin A),
ant(4
′
)-Ia
(tobramycin),
tet
(L) (tetracycline), and
dfrK
(trimethoprim). A novel genetic structure, linking all of these resistance genes for the first time, was elucidated through sequencing of a 15,259-bp fragment from pERGB. Active surveillance to prevent the dissemination of such highly concerning MDR transferable elements is needed.
MpeR Regulates the
mtr
Efflux Locus in Neisseria gonorrhoeae and Modulates Antimicrobial Resistance by an Iron-Responsive Mechanism
Authors: Mercante Alexandra Dubon , Jackson Lydgia , Johnson Paul J. T. , Stringer Virginia A. , Dyer David W. , Shafer William M.
Published: January 2012

Previous studies have shown that the MpeR transcriptional regulator produced by
Neisseria gonorrhoeae
represses the expression of
mtrF
, which encodes a putative inner membrane protein (MtrF). MtrF works as an accessory protein with the Mtr efflux pump, helping gonococci to resist high levels of diverse hydrophobic antimicrobials. Regulation of
mpeR
has been reported to occur by an iron-dependent mechanism involving Fur (ferric uptake regulator). Collectively, these observations suggest the presence of an interconnected regulatory system in gonococci that modulates the expression of efflux pump protein-encoding genes in an iron-responsive manner. Herein, we describe this connection and report that levels of gonococcal resistance to a substrate of the
mtrCDE
-encoded efflux pump can be modulated by MpeR and the availability of free iron. Using microarray analysis, we found that the
mtrR
gene, which encodes a direct repressor (MtrR) of
mtrCDE
, is an MpeR-repressed determinant in the late logarithmic phase of growth when free iron levels would be reduced due to bacterial consumption. This repression was enhanced under conditions of iron limitation and resulted in increased expression of the
mtrCDE
efflux pump operon. Furthermore, as judged by DNA-binding analysis, MpeR-mediated repression of
mtrR
was direct. Collectively, our results indicate that both genetic and physiologic parameters (e.g., iron availability) can influence the expression of the
mtr
efflux system and modulate levels of gonococcal susceptibility to efflux pump substrates.
Flotillin-1 (Reggie-2) Contributes to Chlamydia pneumoniae Growth and Is Associated with Bacterial Inclusion
Authors: Korhonen Juha T. , Puolakkainen Mirja , Häivälä Reetta , Penttilä Tuula , Haveri Anu , Markkula Eveliina , Lahesmaa Riitta
Published: January 2012

Chlamydiae
are obligate intracellular pathogens replicating only inside the eukaryotic host. Here, we studied the effect of human flotillin-1 protein on
Chlamydia pneumoniae
growth in human line (HL) and A549 epithelial cell lines. RNA interference was applied to disrupt flotillin-1-mediated endocytosis. Host-associated bacteria were detected by quantitative PCR, and
C. pneumoniae
growth was evaluated by inclusion counts.
C. pneumoniae
attachment to host cells was unaffected, but bacterial intracellular growth was attenuated in the flotillin-1-silenced cells. By using confocal microscopy, we detected flotillin-1 colocalized with the inclusion membrane protein A (IncA) in the
C. pneumoniae
inclusion membranes. In addition, flotillin-1 was associated with IncA in detergent-resistant membrane microdomains (DRMs) in biochemical fractioning. These results suggest that flotillin-1 localizes to the
C. pneumoniae
inclusion membrane and plays an important role for intracellular growth of
C. pneumoniae
.
Failure To Recruit Anti-Inflammatory CD103+Dendritic Cells and a Diminished CD4+Foxp3+Regulatory T Cell Pool in Mice That Display Excessive Lung Inflammation and Increased Susceptibility to Mycobacterium tuberculosis
Authors: Leepiyasakulchai Chaniya , Ignatowicz Lech , Pawlowski Andrzej , Källenius Gunilla , Sköld Markus
Published: January 2012

Susceptibility toMycobacterium tuberculosisis characterized by excessive lung inflammation, tissue damage, and failure to control bacterial growth. To increase our understanding of mechanisms that may regulate the host immune response in the lungs, we characterized dendritic cells expressing CD103 (αEintegrin) (αE-DCs) and CD4+Foxp3+regulatory T (Treg) cells duringM. tuberculosisinfection. In resistant C57BL/6 and BALB/c mice, the number of lung αE-DCs increased dramatically duringM. tuberculosisinfection. In contrast, highly susceptible DBA/2 mice failed to recruit αE-DCs even during chronic infection. Even though tumor necrosis factor alpha (TNF-α) is produced by multiple DCs and macrophage subsets and is required for control of bacterial growth, αE-DCs remained TNF-α negative. Instead, αE-DCs contained a high number of transforming growth factor beta-producing cells in infected mice. Further, we show that Tregcells in C57BL/6 and DBA/2 mice induce gamma interferon during pulmonary tuberculosis. In contrast to resistant mice, the Tregcell population was diminished in the lungs, but not in the draining pulmonary lymph nodes (PLN), of highly susceptible mice during chronic infection. Tregcells have been reported to inhibitM. tuberculosis-specific T cell immunity, leading to increased bacterial growth. Still, despite the reduced number of lung Tregcells in DBA/2 mice, the bacterial load in the lungs was increased compared to resistant animals. Our results show that αE-DCs and Tregcells that may regulate the host immune response are increased inM. tuberculosis-infected lungs of resistant mice but diminished in infected lungs of susceptible mice.
Delivery of Large Heterologous Polypeptides across the Cytoplasmic Membrane of Antigen-Presenting Cells by the Bordetella RTX Hemolysin Moiety Lacking the Adenylyl Cyclase Domain
Authors: Holubova Jana , Kamanova Jana , Jelinek Jiri , Tomala Jakub , Masin Jiri , Kosova Martina , Stanek Ondrej , Bumba Ladislav , Michalek Jaroslav , Kovar Marek , Sebo Peter
Published: January 2012

TheBordetellaadenylate cyclase toxin-hemolysin (CyaA; also called ACT or AC-Hly) targets CD11b-expressing phagocytes and translocates into their cytosol an adenylyl cyclase (AC) that hijacks cellular signaling by conversion of ATP to cyclic AMP (cAMP). Intriguingly, insertion of large passenger peptides removes the enzymatic activity but not the cell-invasive capacity of the AC domain. This has repeatedly been exploited for delivery of heterologous antigens into the cytosolic pathway of CD11b-expressing dendritic cells by CyaA/AC−toxoids, thus enabling their processing and presentation on major histocompatibility complex (MHC) class I molecules to cytotoxic CD8+T lymphocytes (CTLs). We produced a set of toxoids with overlapping deletions within the first 371 residues of CyaA and showed that the structure of the AC enzyme does not contain any sequences indispensable for its translocation across target cell membrane. Moreover, replacement of the AC domain (residues 1 to 371) with heterologous polypeptides of 40, 146, or 203 residues yielded CyaAΔAC constructs that delivered passenger CTL epitopes into antigen-presenting cells (APCs) and induced strong antigen-specific CD8+CTL responsesin vivoin mice andex vivoin human peripheral blood mononuclear cell cultures. This shows that the RTX (repeats intoxin) hemolysin moiety, consisting of residues 374 to 1706 of CyaA, harbors all structural information involved in translocation of the N-terminal AC domain across target cell membranes. These results decipher the extraordinary capacity of the AC domain of CyaA to transport large heterologous cargo polypeptides into the cytosol of CD11b+target cells and pave the way for the construction of CyaAΔAC-based polyvalent immunotherapeutic T cell vaccines.
Leukocyte Inflammatory Responses Provoked by Pneumococcal Sialidase
Authors: Chang Yung-Chi , Uchiyama Satoshi , Varki Ajit , Nizet Victor
Published: January 2012

Cell surface expression of sialic acid has been reported to decrease during immune cell activation, but the significance and regulation of this phenomenon are still being investigated. The major human bacterial pathogen
Streptococcus pneumoniae
causes pneumonia, sepsis and meningitis, often accompanied by strong inflammatory responses.
S. pneumoniae
expresses a sialidase (NanA) that contributes to mucosal colonization, platelet clearance, and blood-brain barrier penetration. Using wild-type and isogenic NanA-deficient mutant strains, we showed that
S. pneumoniae
NanA can desialylate the surface of human THP-1 monocytes, leading to increased ERK phosphorylation, NF-κB activation, and proinflammatory cytokine release.
S. pneumoniae
NanA expression also stimulates interleukin-8 release and extracellular trap formation from human neutrophils. A mechanistic contribution of unmasking of inhibitory Siglec-5 from
cis
sialic acid interactions to the proinflammatory effect of NanA is suggested by decreased SHP-2 recruitment to the Siglec-5 intracellular domain and RNA interference studies. Finally, NanA increased production of proinflammatory cytokines in a murine intranasal challenge model of
S. pneumoniae
pneumonia.

IMPORTANCE
Sialic acids decorate the surface of all mammalian cells and play important roles in physiology, development, and evolution. Siglecs are sialic acid-binding receptors on the surface of immune cells, many of which engage in
cis
interactions with host sialoglycan ligands and dampen inflammatory responses through transduction of inhibitory signals. Recently, certain bacterial pathogens have been shown to suppress leukocyte innate immune responses by molecular mimicry of host sialic acid structures and engagement of inhibitory Siglecs. Our present work shows that the converse can be true, i.e., that a microbial sialic acid-cleaving enzyme can induce proinflammatory responses, which are in part mediated by unmasking of an inhibitory Siglec. We conclude that host leukocytes are poised to detect and respond to microbial sialidase activity with exaggerated inflammatory responses, which could be beneficial or detrimental to the host depending on the site, stage and magnitude of infection.
Electrolytes in sick neonates – which sodium is the right answer?
Authors: King Richard I , Mackay Richard J , Florkowski Christopher M , Lynn Adrienne M
Published: January 2012

Introduction

Hypoproteinaemia leads to spuriously high-sodium values when measured by indirect ion-selective electrodes (ISE) as used in main laboratory analysers compared with direct ISE employed in point-of-care analysers (POCT). The authors, therefore, investigated the occurrence of hypoalbuminaemia and its effect on measured sodium from POCT and the main laboratory analyser of neonatal intensive-care samples.

Method

Sodium, in paired retrospective samples, measured by the main laboratory and neonatal unit blood-gas (POCT) analysers were compared.

Results

Hypoalbuminaemia (<30 g/l) was present in 1400/2420 paired results. Sodium was higher when measured by laboratory analyser, the difference increased with decreasing albumin; sodium (laboratory – POCT)=7.6 (±1.1)–0.22 (±0.04)×albumin. A difference >3 mmol/l was present in 31% and consequently underestimated (9.4%) hyponatraemia and overestimated (3.8%) hypernatraemia.

Conclusion

Hypoalbuminaemia is common in sick neonates and monitoring electrolytes using POCT and laboratory analysers frequently yield significantly different results with consequent misclassification. In these patients, measurement of electrolytes by direct ISE (blood-gas analyser) may be more accurate.