bluuebunny/crossref_metadata_2025 huggingface dataset:
Bandgap bowing in Ta-W-O system for efficient solar energy conversion: Insights from density functional theory and X-ray diffraction
Authors: Nashed Ramy , Alamgir Faisal M. , Soon Jang Seung , Ismail Yehea , El-Sayed Mostafa A. , Allam Nageh K.
Published: September 2013

The electronic properties of Ta-W-O system have been studied using density functional theory with PBE0 hybrid functional. The bandgap calculations showed a large and composition-dependent bowing parameter. While the large bowing parameter at low W content (<25%) is related to the charge exchange between the localized W 5d state and the extended states in the conduction band, the volume change is considered the main reason for the large bowing parameter at high W content (>25%). The electron excitation from the Ta2O5 valence band to WO3 conduction band at high W content may contribute to the pronounced decrease in the conduction band energy. The staggered bandgap type between Ta2O5 and WO3, as revealed from the energy band diagram, resulted in efficient charge carriers' separation. The minimum hole effective mass occurs along the y-direction and decreases monotonically with increasing W content. Combining the wide tunability of bandgap with the small effective mass, it is suggested that Ta-W-O alloys can replace the various III-V materials for high efficiency solar cells as well as other optoelectronic devices.
Chemical analysis of exhaled human breath using a terahertz spectroscopic approach
Authors: Fosnight Alyssa M. , Moran Benjamin L. , Medvedev Ivan R.
Published: September 2013

As many as 3500 chemicals are reported in exhaled human breath. Many of these chemicals are linked to certain health conditions and environmental exposures. This experiment demonstrated a method of breath analysis utilizing a high resolution spectroscopic technique for the detection of ethanol, methanol, and acetone in the exhaled breath of a person who consumed alcohol. This technique is applicable to a wide range of polar molecules. For select species, unambiguous detection in a part per trillion dilution range with a total sample size in a femtomol range is feasible. It compares favorably with other methods of breath analysis.
Significantly enhanced performance of an InGaN/GaN nanostructure based photo-electrode for solar power hydrogen generation
Authors: Benton J. , Bai J. , Wang T.
Published: September 2013

A significant reduction in photo-electrochemical etching effects has been achieved on an InGaN/GaN nanorod array structure used as a photoelectrode in NaOH electrolyte by means of depositing transparent nickel oxide nano-particles on the nanorod array structure. Alongside this, the addition of the nickel oxide nano-particles has also led to an increase in photocurrent, thus, enhancing energy conversion efficiency. The enhanced performance is attributed to the discontinuities in both conduction band and valence band formed between the nickel oxide and the GaN, which promote the photo-generated electrons to move to a counter electrode and also lead to an enhanced diffusion of the photo-generated holes from the GaN into the NiO. This effect reduces the recombination of the electrons and the holes due to an increased separation between them and also significantly decreases the photo-electrochemical etching as a result of a sizeable reduction in the number of the photo-generated holes accumulated at the GaN/electrolyte interface.
Domain structures and switching properties in ferroelectric nanocomposites
Authors: Artemev A.
Published: September 2013

The phase field method was used to study the domain structure and switching in nanocomposites consisting of ferroelectric nanorods and a dielectric matrix. The results demonstrate that the domain structure and hysteresis loop shape are controlled by the nanocomposite structure and by the misfit between the nanorods and matrix. Hysteresis loops consisting of triangular offset loops and a narrow central part with a low remnant polarization and coercive field can be obtained as well as rectangular loops with a large remnant polarization and coercive field. The possibility of the switching behaviour control through the misfit control is discussed.
Formation of amorphous structure in Sn3.5Ag droplet by in situ fast scanning calorimetry controllable quenching
Authors: Zhao Bingge , Li Linfang , Zhai Qijie , Gao Yulai
Published: September 2013

Attributing to sensitive fast scanning calorimetry, combined with focused ion beam and high resolution transmission electron microscopy, we observed the solidification structure of single Sn3.5Ag droplet quenched at controllable rate. Amorphous layers in nanometer adjacent to some Ag3Sn crystals were directly detected. Based on solid state amorphization, a nano diffusion couple between primary formed β-Sn matrix and Ag3Sn intermetallic was put forward. Quenched at 15 000 K/s, the concentration gradient in this diffusion area was up to 109 m−1, which could seriously suppress the growth and further homogeneous nucleation of Ag3Sn, leading to the formation of amorphous structure.
Temperature-dependent tunneling electroresistance in Pt/BaTiO3/SrRuO3 ferroelectric tunnel junctions
Authors: Wen Zheng , You Lu , Wang Junling , Li Aidong , Wu Di
Published: September 2013

Tunneling electroresistance of Pt/BaTiO3/SrRuO3 ferroelectric tunnel junctions is investigated as a function of temperature. Two distinct resistance states that are dependent on polarization direction in the BaTiO3 barrier layer and bipolar resistance switching are observed at various temperatures from 10 to 290 K. The ON/OFF current ratio of Pt/BaTiO3/SrRuO3 tunnel junctions increases monotonically with decreasing temperature above 50 K and saturates below 50 K. The enhanced tunneling electroresistance at low temperatures can be ascribed to the suppression of thermally assisted indirect tunneling, which is less sensitive to the polarization reversal of BaTiO3 compared to the direct tunneling.
Near-field investigation of spatial variations of (202¯1¯) InGaN quantum well emission spectra
Authors: Marcinkevičius S. , Zhao Y. , Kelchner K. M. , Nakamura S. , DenBaars S. P. , Speck J. S.
Published: September 2013

Scanning near-field optical spectroscopy was applied to semipolar (202¯1¯) InGaN/GaN quantum wells (QWs) to evaluate spatial homogeneity of QW band gap and its dependence on the growth conditions. In the most uniform QW, photoluminescence (PL) spectra were found to be narrow with small peak wavelength and spectral width variations. A QW grown at reduced temperature showed sub-micrometer size PL features aligned along the a axis and caused by nonuniform In incorporation at surface undulations. At extended defects, complex and strongly varying near-field spectra were observed and tentatively assigned to QW segments of different orientations around these defects.
Magnetic behavior of layered perovskite Sr2CoO4 thin film
Authors: Pandey Pankaj K. , Choudhary R. J. , Phase D. M.
Published: September 2013

We have studied the magnetic properties of Sr2CoO4 (SCO) thin film. Magnetic hysteresis loops of the film divulge two-phase-like magnetic behavior consisting of hard and soft magnetic phases. Temperature dependent magnetization measurements and time evolution of thermo-remanent magnetization relaxation indicate the possibility of spin-glass dynamics in SCO. The Arrott plots (M2 vs. H/M) exhibit the convex behavior, while the M4 vs. H/M plots show the linear relation near Curie temperature signifying itinerant ferromagnetism in the material, consistent with the calculated Rhodes-Wohlfarth ratio for the film. It is suggested that SCO has electrons with localized character as well as itinerant character.
An ultra-low leakage current single carbon nanotube diode with split-gate and asymmetric contact geometry
Authors: Hughes M. A. , Homewood K. P. , Curry R. J. , Ohno Y. , Mizutani T.
Published: September 2013

A single carbon nanotube diode is reported, with Ti and Pd contacts, and split gates. Without gate bias the device displays strong rectification, with a leakage current (I0) of 6 × 10−16 A, and an ideality factor (η) of 1.38. When the gate above the Ti contact is biased negatively the diode inverts. When positive bias is then applied to the gate above the Pd contact minority carrier injection is suppressed. Configured such I0 and η were 2 × 10−14 A and 2.01, respectively. Electrical characterization indicates that the Schottky barrier height for electrons is lower for the Pd contact than the Ti contact.
Observations of soft X-ray emission and plasma dynamics of a compact capillary discharge operated in xenon
Authors: Valenzuela J. C. , Wyndham E. S. , Favre M. , Chuaqui H.
Published: September 2013

We report observations of a low stored energy, low inductance compact capillary discharge operated in xenon. Even though the stored electrical energy is less than 1 J, significant output in the optical windows at 110 and 135 Å is measured. The soft X-ray emission is time-resolved and the conversion energy of the source is obtained. A lower bound to the conversion efficiency at 110 Å ± 2% and 135 Å ± 1% of 3.6% and 1.6% is obtained, respectively. The use of moiré-schlieren optical diagnostic allows the evolution of the line electron density. In particular, we observe a significant degree of compression in a tight on axis pinch as well as radial compression waves. The temporal evolution of the X-ray emission, which occurs during the current reversal and later, is discussed in relation to work in argon discharges and in relation to model calculations.
Specific characteristics of negative corona currents generated in short point-plane gap
Authors: Li Zhen , Zhang Bo , He Jinliang
Published: September 2013

The Trichel pulse is a typical kind of negative corona current observed in electronegative gases with a highly regular form. The characteristics of the Trichel pulse, such as the repetition frequency, the amplitude of each pulse, and the mean current, are dependent on different discharge conditions. Quite many scholars have studied the mean current and the current-voltage characteristic of Trichel pulses, yet the specific characteristics of the pulses have barely been investigated. In this paper, a series of experiments were carried out in a short point-to-plane discharge gap to investigate the detailed characteristics of Trichel pulses. After numerical fitting of the experiment results was performed, a new set of empirical formulas were derived to predict the specific characteristics of the negative corona current under different conditions. Different from existing literature, this paper uses as variables the average electric field intensity and the corona inception field intensity which is independent of the gap spacing in the empirical formulas. In the experiments, an inverse correlation between amplitude and repetition frequency of the pulses was observed. Based on the investigation of the remaining space charge in the discharge gap, this correlation is theoretically proved to be caused by the influence of space charges.
The modified equation for spinless particles and superalgebra
Authors: Sadeghi J. , Rostami M. , Sadeghi Z.
Published: September 2013

In this paper we consider modified wave equations for spinless particles in an external magnetic field. We consider 4-potentials which guarantee Lorentz' and Coulomb's conditions. The new variable for modified wave equation leads us to consider the associated Laguerre differential equation. We take advantage of the factorization method in Laguerre differential equation and solve the modified equation. In order to obtain the wave function, energy spectrum and its quantization, we will establish conditions for the orbital quantum number. We account such orbital quantum number and obtain the raising and lowering operators. If we want to have supersymmetry partners, we need to apply the shape invariance condition. This condition for the partner potential will help us find the limit of ρ as \documentclass[12pt]{minimal}\begin{document}$\rho =\pm {\sqrt{l}}$\end{document}ρ=±l.
Hard x-ray photoelectron spectroscopy study on valence band structure of semiconducting BaSi2
Authors: Baba Masakazu , Ito Keita , Du Weijie , Sanai Tatsunori , Okamoto Kazuaki , Toko Kaoru , Ueda Shigenori , Imai Yoji , Kimura Akio , Suemasu Takashi
Published: September 2013

The valence band structures of a 35-nm-thick BaSi2 epitaxial film on Si(111) have been explored at room temperature by hard x-ray photoelectron spectroscopy (HAXPES). The experimentally obtained photoelectron spectrum is well reproduced by first-principles calculations based on the pseudopotential method. The top of the valence band consists mainly of Si 3s and 3p states in BaSi2, suggesting that the effective mass of holes is small in BaSi2. This is favorable from the viewpoint of solar cell applications. The observed spectrum shifted slightly to the lower energy side due to n-type conductivity of BaSi2. The valence band top was observed at about 0.8 eV below the Fermi level in the HAXPES spectrum.
Comment on “Nano-particle magnetism with a dispersion of particle sizes” [J. Appl. Phys. 112, 103915 (2012)]
Authors: Tournus F. , Tamion A.
Published: September 2013

A recent paper1 examines zero field-cooled/field-cooled (ZFC/FC) susceptibility curves for nanoparticle assemblies with a size distribution. It is explained that the “volume and number weighted distribution are equally valid for the representation of distribution functions in nanoparticle magnetic systems” and the usual modelling approach (abrupt transition from a blocked to a superparamagnetic regime, at a given temperature) is compared to the more elaborate one (the “progressive crossover model (PCM)”) introduced in our previous articles.2–4 The importance of the f0 value is also stressed. In this article, several statements are made in opposition to some of our previously published results. Because we like to believe that these words were driven by a simple “misunderstanding” of our models and analysis, we would like to clarify some points in the present comment.
Calcium-doping effects on photovoltaic response and structure in multiferroic BiFeO3 ceramics
Authors: Tu C. S. , Hung C.-M. , Xu Z.-R. , Schmidt V. H. , Ting Y. , Chien R. R. , Peng Y.-T. , Anthoninappen J.
Published: September 2013

Photovoltaic (PV) effects, power-conversion efficiencies, and structures have been systematically measured in (Bi1−xCax)FeO3−δ ceramics for x = 0.05, 0.10, and 0.15. The heterostructures of indium tin oxide (ITO) film/(Bi1−xCax)FeO3−δ ceramics/Au film exhibit significant PV effects under illumination of λ = 405 nm. The maximum power-conversion efficiency in the ITO/(Bi0.90Ca0.10)FeO2.95 (BFO10C)/Au can reach 0.0072%, which is larger than 0.0025% observed in the graphene/polycrystalline BFO/Pt films [Zang et al., Appl. Phys. Lett. 99, 132904 (2011)]. A theoretical model based on optically excited current in the depletion region between ITO film and Ca-doped BFO ceramics is used to describe the I-V characteristic, open-circuit voltage, and short-circuit current density as a function of illumination intensity. This work suggests that the Ca-substitution can reduce the rhombohedral distortion and stabilize the single-phase structure.
Bounded population sizes, fluctuating selection and the tempo and mode of coexistence
Authors: Yi Xiao , Dean Antony M.
Published: September 2013

Significance

Habitats vary over time, but the influence of temporal variability on biodiversity is largely unknown. We develop a simple theory that shows temporal fluctuations in the direction of selection alone can promote biodiversity, and we confirm this prediction by direct experiment. Our work provides fundamental insights into the structure of competition and lays a conceptual foundation unifying competition theory in population genetics and ecology.
Re-reading August Wilson’s Fences
Authors: Ogoanah Felix Nwabeze
Published: September 2013

August Wilson’s Fences is perhaps the most controversial in his ten-play chronicle of the African American experience in the 20th century. The play’s conflict centres on Troy’s alleged highhandedness against his son and his extra-marital affair. The morality behind these issues has been the subject of debate since the play debuted in 1987, and the protagonist is generally believed to be a villain. This paper challenges this negative perspective, which is largely based on Western socio-cultural paradigms and logic, and provides an alternative reading of the play by reasserting the influence of the Black Aesthetic on Wilson, and by linking it to a specific African pre-text: Chinua Achebe’s Things Fall Apart. Keywords: August Wilson’s Fences; African world view; Black Aesthetic; Chinua Achebe’s Things Fall Apart; intertextuality
Competing for coverage
Authors: Caple Helen
Published: September 2013

This paper reports on findings from a research project conducted on behalf of the Australian Sports Commission (ASC) examining the portrayal of female athletes in the Australian news media. While the project as a whole includes analyses of both print and broadcast news media, we focus here on findings concerning the reporting on sportswomen in print newspapers. Using social semiotic tools for investigating ideational/representational and interpersonal/interactional meanings in language and images, qualitative analyses of both the headlines and photographs are reported on. The findings suggest that Australian sportswomen are now treated both verbally and visually as serious athletes who are very much in control of their emotions. However, the extent of this coverage remains greatly impoverished in comparison to that for male athletes. Keywords: Australian sports reporting; text-image relations; female athletes; multimodality; evaluation
The empirical trend
Authors: Sampson Geoffrey
Published: September 2013

Linguistic science of the past half-century has often been distorted through neglect of normal scientific standards of empirical falsifiability. An earlier paper in this journal used a quantitative literature survey to examine how far in practice the newer trend towards use by linguists of corpora and other empirical data sources had progressed. The result was ambiguous: a trend towards greater empiricism had occurred since about 1970, but around the turn of the century it appeared to have reversed, and the end of the period surveyed (2002) fell so soon thereafter that it was hard to guess whether this reversal was a blip or a long-term change. With a further decade of linguistic literature to examine, the present paper repeats the survey using a more systematic sampling technique, and this yields results that are much more clearcut than those of the earlier paper.
Event-construal in press reports of violence in two recent political protests
Authors: Hart Christopher
Published: September 2013

In this paper I extend the scope of the Cognitive Linguistic Approach to Critical Discourse Analysis (CDA) by incorporating Langacker’s model of Cognitive Grammar in a critical analysis of press reports of violence in two political protests. In doing so, I address issues recently raised against CDA concerning cognitive equivalence. The paper presents an analysis of the alternative conceptualisations of violence invoked in online reports fromThe Telegraphvs.The Guardianof two recent political protests. Systematic differences in construal are found across several parameters of conceptualisation, including schematisation and various ‘focal adjustments’, which, it is suggested, represent potential sites of ideological reproduction.
The meanings of “war”
Authors: Lukin Annabelle
Published: September 2013

In this paper I interpret findings from a project investigating media coverage of the 2003 “Coalition” invasion of Iraq, drawing on a corpus of news reports from the Australian Broadcasting Corporation TV news. The findings reported are evidence of a consistency that reflects the unconscious working of an ideology about “war”, with ideology considered in linguistic terms as a “configurative rapport” (Whorf 1956). To trace some dimensions of this ideology, I explore the meanings of “war”, its linguistic reactances, and its consequences for the creation of text with respect to registers of news discourse. I consider “war” from the point of view of lexis: its referential meaning, its relation to other related signs, (Saussure 1974), its denotative and connotative meanings (Hasan 2003) and its collocation and colligational potentials (Firth 1937[1964], 1962). I then consider it from the point of view of text-in-context (e.g. Halliday & Hasan 1985). The paper extends the 30 year interest in the relations of language, mind and society that have characterised studies of ideology in critical linguistics/CDA.
Citizenship, community, and counter-terrorism
Authors: MacDonald Malcolm N. , Hunter Duncan , O'Regan John P.
Published: September 2013

This paper analyses a corpus of UK policy documents which sets out national security policy as an exemplar of the contemporary discourse of counter-terrorism in Europe, the USA and worldwide. A corpus of 148 documents (c. 2.8 million words) was assembled to reflect the security discourse produced by the UK government before and after the 7/7 attacks on the London Transport system. To enable a chronological comparison, the two sub-corpora were defined: one relating to a discourse of citizenship and community cohesion (2001–2006); and one relating to the ‘Preventing Violent Extremism’ discourse (2007–2011). Wordsmith Tools (Scott 2008) was used to investigate keywords and patterns of collocation. The results present themes emerging from a comparative analysis of the 100 strongest keywords in each sub-corpus; as well as a qualitative analysis of related patterns of the collocation, focusing in particular on features of connotation and semantic prosody.
The second digital transition: to the mobile space — an analysis of Europeana
Authors: NICHOLAS David , CLARK David
Published: September 2013

According to industry estimates the mobile device (smartphone and tablet) will soon be the main platform for searching the Web and yet our knowledge of how mobile consumers use information – especially scholarly information, and how that differs from desktop or ‘tethered’ users – is imperfect to say the very least. This article aims to correct this through an analysis of the usage logs of a major cultural, multimedia website, Europeana.eu, which started tackling the mobile challenge in 2011. The challenges of identifying mobile use – no easy matter – are described. The information behaviour of 150,000 mobile users is examined and compared with that for desktop users. The main findings are that mobile users are the fastest‐growing user community and that their visits are very different in the aggregate from those arising from desktops. Mobile visits are information ‘lite‘: typically shorter, less interactive, and with less content viewed per visit. Use takes on a social rather than office rhythm, with use peaking at nights and weekends.
Medical research charities and open access
Authors: PINFIELD Stephen
Published: September 2013

This paper provides an analysis of the attitudes and activities of UK medical research charities in relation to open access (OA). Both quantitative and qualitative data are presented derived from a recent survey of charities covering areas such as policy development, funding arrangements, and business process design for OA. Positions on key issues including green and gold OA, funding article‐processing charges (APCs), and publication licences are assessed. Modelling of potential APCs as a percentage of overall annual research spend is undertaken to show possible costs of a charged‐for gold system. Medical research charities clearly regard OA as important and some see it as an opportunity to further their mission. However, many expressed significant concerns particularly about the costs and expertise required to support OA. Further co‐ordination of policy development and action across the sector and with other stakeholders is recommended in order to help ensure optimal implementation of OA.
DockAFM: benchmarking protein structures by docking under AFM topographs
Authors: Chaves Rui C. , Pellequer Jean-Luc
Published: September 2013

Summary: Proteins can adopt a variety of conformations. We present a simple server for scoring the agreement between 3D atomic structures and experimental envelopes obtained by atomic force microscopy. Three different structures of immunoglobulins (IgG) or blood coagulation factor V activated were tested and their agreement with several topographical surfaces was computed. This approach can be used to test structural variability within a family of proteins.

Availability and implementation: DockAFM is available at http://biodev.cea.fr/dockafm.

Contact:  chaves.rui.c@gmail.com or jlpellequer@cea.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
INVEX—a web-based tool for integrative visualization of expression data
Authors: Xia Jianguo , Lyle Ngan H. , Mayer Matthew L. , Pena Olga M. , Hancock Robert E. W.
Published: September 2013

Summary: Gene expression or metabolomics data generated from clinical settings are often associated with multiple metadata (i.e. diagnosis, genotype, gender, etc.). It is of great interest to analyze and to visualize the data in these contexts. Here, we introduce INVEX—a novel web-based tool that integrates the server-side capabilities for data analysis with the browse-based technology for data visualization. INVEX has two key features: (i) flexible differential expression analysis for a wide variety of experimental designs; and (ii) interactive visualization within the context of metadata and biological annotations. INVEX has built-in support for gene/metabolite annotation and a fully functional heatmap builder.

Availability and implementation: Freely available at http://www.invex.ca.

Contact:  bob@hancocklab.ubc.ca
Lep-MAP: fast and accurate linkage map construction for large SNP datasets
Authors: Rastas Pasi , Paulin Lars , Hanski Ilkka , Lehtonen Rainer , Auvinen Petri
Published: September 2013

Motivation: Current high-throughput sequencing technologies allow cost-efficient genotyping of millions of single nucleotide polymorphisms (SNPs) for hundreds of samples. However, the tools that are currently available for constructing linkage maps are not well suited for large datasets. Linkage maps of large datasets would be helpful in de novo genome assembly by facilitating comprehensive genome validation and refinement by enabling chimeric scaffold detection, as well as in family-based linkage and association studies, quantitative trait locus mapping, analysis of genome synteny and other complex genomic data analyses.

Results: We describe a novel tool, called Lepidoptera-MAP (Lep-MAP), for constructing accurate linkage maps with ultradense genome-wide SNP data. Lep-MAP is fast and memory efficient and largely automated, requiring minimal user interaction. It uses simultaneously data on multiple outbred families and can increase linkage map accuracy by taking into account achiasmatic meiosis, a special feature of Lepidoptera and some other taxa with no recombination in one sex (no recombination in females in Lepidoptera). We demonstrate that Lep-MAP outperforms other methods on real and simulated data. We construct a genome-wide linkage map of the Glanville fritillary butterfly (Melitaea cinxia) with over 40 000 SNPs. The data were generated with a novel in-house SOLiD restriction site-associated DNA tag sequencing protocol, which is described in the online supplementary material.

Availability and implementation: Java source code under GNU general public license with the compiled classes and the datasets are available from http://sourceforge.net/users/lep-map.

Contact:  pasi.rastas@helsinki.fi

Supplementary information:  Supplementary data are available at Bioinformatics online.
A quasi-periodic oscillation in the blazar J1359+4011
Authors: King O. G. , Hovatta T. , Max-Moerbeck W. , Meier D. L. , Pearson T. J. , Readhead A. C. S. , Reeves R. , Richards J. L. , Shepherd M. C.
Published: September 2013

The Owens Valley Radio Observatory 40-m telescope has been monitoring the 15-GHz radio flux density of over 1200 blazars since 2008. The 15-GHz light curve of the flat spectrum radio quasar J1359+4011 shows a strong and persistent quasi-periodic oscillation. The time-scale of the oscillation varies between 120 and 150 d over an ∼4 year time span. We interpret this as the active galactic nucleus mass-scaled analogue of low-frequency quasi-periodic oscillations from Galactic microquasars or as evidence of modulation of the accretion flow by thermal instabilities in the ‘inner’ accretion disc.
Valuing the Vote: The Redistribution of Voting Rights and State Funds following the Voting Rights Act of 1965 *
Authors: Cascio Elizabeth U. , Washington Ebonya
Published: September 2013

The Voting Rights Act of 1965, called one of the most effective pieces of civil rights legislation in U.S. history, generated dramatic increases in black voter registration across the South. We ask whether the increase in black voting rights was accompanied by an increase in blacks’ share of public spending. We exploit a key provision of the act—removal of literacy tests at registration—for identification. Employing a triple-difference framework over a 20-year period, we find that counties with higher black population shares in former literacy test states saw greater increases in both voter turnout and state transfers than comparison counties in non–literacy test states, a finding that is consistent with models of distributive politics.
High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genome
Authors: Hajjoul Houssam , Mathon Julien , Ranchon Hubert , Goiffon Isabelle , Mozziconacci Julien , Albert Benjamin , Carrivain Pascal , Victor Jean-Marc , Gadal Olivier , Bystricky Kerstin , Bancaud Aurélien
Published: September 2013

Chromosome dynamics are recognized to be intimately linked to genomic transactions, yet the physical principles governing spatial fluctuations of chromatin are still a matter of debate. Using high-throughput single-particle tracking, we recorded the movements of nine fluorescently labeled chromosome loci located on chromosomes III, IV, XII, and XIV of Saccharomyces cerevisiae over an extended temporal range spanning more than four orders of magnitude (10−2–103 sec). Spatial fluctuations appear to be characterized by an anomalous diffusive behavior, which is homogeneous in the time domain, for all sites analyzed. We show that this response is consistent with the Rouse polymer model, and we confirm the relevance of the model with Brownian dynamics simulations and the analysis of the statistical properties of the trajectories. Moreover, the analysis of the amplitude of fluctuations by the Rouse model shows that yeast chromatin is highly flexible, its persistence length being qualitatively estimated to <30 nm. Finally, we show that the Rouse model is also relevant to analyze chromosome motion in mutant cells depleted of proteins that bind to or assemble chromatin, and suggest that it provides a consistent framework to study chromatin dynamics. We discuss the implications of our findings for yeast genome architecture and for target search mechanisms in the nucleus.
A Novel Rickettsia Species Detected in Vole Ticks (Ixodes angustus) from Western Canada
Authors: Anstead Clare A. , Chilton Neil B.
Published: September 2013

The genomic DNA of ixodid ticks from western Canada was tested by PCR for the presence ofRickettsia. No rickettsiae were detected inIxodes sculptus, whereas 18% of theI. angustusand 42% of theDermacentor andersoniorganisms examined were PCR positive forRickettsia. The rickettsiae from each tick species were characterized genetically using multiple genes. Rickettsiae within theD. andersoniorganisms had sequences at four genes that matched those ofR. peacockii. In contrast, theRickettsiapresent within the larvae, nymphs, and adults ofI. angustushad novel DNA sequences at four of the genes characterized compared to the sequences available from GenBank for all recognized species ofRickettsiaand all other putative species within the genus. Phylogenetic analyses of the sequence data revealed that the rickettsiae inI. angustusdo not belong to the spotted fever, transitional, or typhus groups of rickettsiae but are most closely related to “CandidatusRickettsia kingi” and belong to a clade that also includesR. canadensis, “CandidatusRickettsia tarasevichiae,” and “CandidatusRickettsia monteiroi.”
Effect of Incubation Temperature on the Detection of Thermophilic Campylobacter Species from Freshwater Beaches, Nearby Wastewater Effluents, and Bird Fecal Droppings
Authors: Khan Izhar U. H. , Hill Stephen , Nowak Eva , Edge Thomas A.
Published: September 2013

This large-scale study compared incubation temperatures (37°C versus 42°C) to study the detection of thermophilic
Campylobacter
species, including
Campylobacter jejuni
,
C. coli
, and
C. lari
, in various surface water samples and bird fecal droppings around Hamilton Harbor, Lake Ontario. The putative culture isolates obtained from incubation temperatures of 37 and 42°C were confirmed by
Campylobacter
genus- and species-specific triplex PCR assays targeting the 16S rRNA gene and the 16S-23S rRNA gene internal transcribed spacer (ITS) region. A total of 759 water, wastewater, and bird fecal dropping samples were tested. Positive amplification reactions for the genus
Campylobacter
were found for 454 (60%) samples incubated at 37°C, compared to 258 (34%) samples incubated at 42°C.
C. jejuni
(16%) and
C. lari
(12%) were detected significantly more frequently at the 42°C incubation temperature than at 37°C (8% and 5%, respectively). In contrast, significantly higher rates of
C. coli
(14%) and other
Campylobacter
spp. (36%) were detected at the 37°C incubation temperature than at 42°C (8% and 7%, respectively). These results were consistent across surface water, wastewater, and bird fecal dropping samples. At times,
Campylobacter
spp. were recovered and detected at 37°C (3% for
C. jejuni
, 10% for
C. coli
, and 3% for
C. lari
) when the same samples incubated at 42°C were negative. A significantly higher rate of other
Campylobacter
spp. was detected only at 37°C (32%) than only at 42°C (3%). These results indicate that incubation temperature can significantly influence the culturability and detection of thermophilic and other fastidious
Campylobacter
spp. and that a comprehensive characterization of the
Campylobacter
spp. in surface water, wastewaters, or bird fecal droppings will require incubation at both 37 and 42°C.
Depth-Related Changes in Community Structure of Culturable Mineral Weathering Bacteria and in Weathering Patterns Caused by Them along Two Contrasting Soil Profiles
Authors: Huang Jing , Sheng Xia-Fang , Xi Jun , He Lin-Yan , Huang Zhi , Wang Qi , Zhang Zhen-Dong
Published: September 2013

Bacteria play important roles in mineral weathering and soil formation. However, few reports of mineral weathering bacteria inhabiting subsurfaces of soil profiles have been published, raising the question of whether the subsurface weathering bacteria are fundamentally distinct from those in surface communities. To address this question, we isolated and characterized mineral weathering bacteria from two contrasting soil profiles with respect to their role in the weathering pattern evolution, their place in the community structure, and their depth-related changes in these two soil profiles. The effectiveness and pattern of bacterial mineral weathering were different in the two profiles and among the horizons within the respective profiles. The abundance of highly effective mineral weathering bacteria in the Changshu profile was significantly greater in the deepest horizon than in the upper horizons, whereas in the Yanting profile it was significantly greater in the upper horizons than in the deeper horizons. Most of the mineral weathering bacteria from the upper horizons of the Changshu profile and from the deeper horizons of the Yanting profile significantly acidified the culture media in the mineral weathering process. The proportion of siderophore-producing bacteria in the Changshu profile was similar in all horizons except in the Bg2 horizon, whereas the proportion of siderophore-producing bacteria in the Yanting profile was higher in the upper horizons than in the deeper horizons. Both profiles existed in different highly depth-specific culturable mineral weathering community structures. The depth-related changes in culturable weathering communities were primarily attributable to minor bacterial groups rather than to a change in the major population structure.
Cooperative Degradation of Chitin by Extracellular and Cell Surface-Expressed Chitinases from Paenibacillus sp. Strain FPU-7
Authors: Itoh Takafumi , Hibi Takao , Fujii Yutaka , Sugimoto Ikumi , Fujiwara Akihiro , Suzuki Fumiko , Iwasaki Yukimoto , Kim Jin-Kyung , Taketo Akira , Kimoto Hisashi
Published: September 2013

Chitin, a major component of fungal cell walls and invertebrate cuticles, is an exceedingly abundant polysaccharide, ranking next to cellulose. Industrial demand for chitin and its degradation products as raw materials for fine chemical products is increasing. A bacterium with high chitin-decomposing activity,
Paenibacillus
sp. strain FPU-7, was isolated from soil by using a screening medium containing α-chitin powder. Although FPU-7 secreted several extracellular chitinases and thoroughly digested the powder, the extracellular fluid alone broke them down incompletely. Based on expression cloning and phylogenetic analysis, at least seven family 18 chitinase genes were found in the FPU-7 genome. Interestingly, the product of only one gene (
chiW
) was identified as possessing three S-layer homology (SLH) domains and two glycosyl hydrolase family 18 catalytic domains. Since SLH domains are known to function as anchors to the Gram-positive bacterial cell surface, ChiW was suggested to be a novel multimodular surface-expressed enzyme and to play an important role in the complete degradation of chitin. Indeed, the ChiW protein was localized on the cell surface. Each of the seven chitinase genes (
chiA
to
chiF
and
chiW
) was cloned and expressed in
Escherichia coli
cells for biochemical characterization of their products. In particular, ChiE and ChiW showed high activity for insoluble chitin. The high chitinolytic activity of strain FPU-7 and the chitinases may be useful for environmentally friendly processing of chitin in the manufacture of food and/or medicine.
Effect of Bacteriophage Application on Campylobacter jejuni Loads in Commercial Broiler Flocks
Authors: Kittler Sophie , Fischer Samuel , Abdulmawjood Amir , Glünder Gerhard , Klein Günter
Published: September 2013

Campylobacteriosis is the most frequent food-borne human enteritis. The major source for infection with
Campylobacter
spp. is broiler meat. Risk assessments consider the reduction of
Campylobacter
in primary production to be most beneficial for human health. The aim of this study was to test the efficacy of a bacteriophage application under commercial conditions which had proved to be effective in previous noncommercial studies under controlled experimental conditions. A phage cocktail for
Campylobacter
reduction was tested on three commercial broiler farms each with a control and an experimental group. Colonization of
Campylobacter
was confirmed prior to phage application in fecal samples. Subsequently, a phage cocktail was applied via drinking water in the experimental group (log
10
5.8 to 7.5 PFU/bird). One day after phage application,
Campylobacter
counts of one experimental group were reduced under the detection limit (<50 CFU/g,
P
= 0.0140) in fecal samples. At slaughter, a significant reduction of >log
10
3.2 CFU/g cecal content compared to the control was still detected (
P
= 0.0011). No significant reduction was observed in the experimental groups of the other trials. However, a significant drop in cecal
Campylobacter
counts occurred in a phage-contaminated control. These results suggest that maximum reduction of
Campylobacter
at the slaughterhouse might be achieved by phage application 1 to 4 days prior to slaughter.
The Taz1p Transacylase Is Imported and Sorted into the Outer Mitochondrial Membrane via a Membrane Anchor Domain
Authors: Herndon Jenny D. , Claypool Steven M. , Koehler Carla M.
Published: September 2013

Mutations in the mitochondrial transacylase tafazzin, Taz1p, in
Saccharomyces cerevisiae
cause Barth syndrome, a disease of defective cardiolipin remodeling. Taz1p is an interfacial membrane protein that localizes to both the outer and inner membranes, lining the intermembrane space. Pathogenic point mutations in Taz1p that alter import and membrane insertion result in accumulation of monolysocardiolipin. In this study, we used yeast as a model to investigate the biogenesis of Taz1p. We show that to achieve this unique topology in mitochondria, Taz1p follows a novel import pathway in which it crosses the outer membrane via the translocase of the outer membrane and then uses the Tim9p-Tim10p complex of the intermembrane space to insert into the mitochondrial outer membrane. Taz1p is then transported to membranes of an intermediate density to reach a location in the inner membrane. Moreover, a pathogenic mutation within the membrane anchor (V224R) alters Taz1p import so that it bypasses the Tim9p-Tim10p complex and interacts with the translocase of the inner membrane, TIM23, to reach the matrix. Critical targeting information for Taz1p resides in the membrane anchor and flanking sequences, which are often mutated in Barth syndrome patients. These studies suggest that altering the mitochondrial import pathway of Taz1p may be important in understanding the molecular basis of Barth syndrome.
Tetracycline-Related Transcriptional Regulation of the CTnDOT Mobilization Region
Authors: Waters Jillian L. , Wang Gui-Rong , Salyers Abigail A.
Published: September 2013

CTnDOT is a 65-kb conjugative transposon (CTn) in
Bacteroides
spp. that confers resistance to the antibiotics erythromycin and tetracycline (Tc). Conjugative transfer of CTnDOT is regulated upon exposure of cells to Tc. In the absence of Tc, no transfer is detectable; however, a cascade of regulatory events results in the conjugative transfer of CTnDOT upon Tc induction. Previous studies addressing regulation of CTnDOT conjugative transfer focused primarily on the 13-kb transfer (
tra
) operon, which encodes the proteins required for assembly of the mating apparatus. We report here that the
mob
operon that encodes the relaxase and coupling proteins required for mobilization of CTnDOT are regulated at the transcriptional level upon Tc induction. The Xis2d and Exc excision proteins are required for the upregulation of
mob
transcription upon Tc induction, and yet a deletion of
xis2c
has no effect. We also show preliminary evidence suggesting that the integrase, IntDOT, may play a regulatory role, as pLYL72 transfer is not detectable when
intDOT
is provided in
trans
.
Phenotypic Profiling of Mycobacterium tuberculosis EspA Point Mutants Reveals that Blockage of ESAT-6 and CFP-10 Secretion
In Vitro
Does Not Always Correlate with Attenuation of Virulence
Authors: Chen Jeffrey M. , Zhang Ming , Rybniker Jan , Basterra Laetitia , Dhar Neeraj , Tischler Anna D. , Pojer Florence , Cole Stewart T.
Published: September 2013

The EspA protein of
Mycobacterium tuberculosis
is essential for the type VII ESX-1 protein secretion apparatus, which delivers the principal virulence factors ESAT-6 and CFP-10. In this study, site-directed mutagenesis of EspA was performed to elucidate its influence on the ESX-1 system. Replacing Trp
55
(W55) or Gly
57
(G57) residues in the putative W-X-G motif of EspA with arginines impaired ESAT-6 and CFP-10 secretion
in vitro
and attenuated
M. tuberculosis
. Replacing the Phe
50
(F50) and Lys
62
(K62) residues, which flank the W-X-G motif, with arginine and alanine, respectively, destabilized EspA, abolished ESAT-6 and CFP-10 secretion
in vitro
, and attenuated
M. tuberculosis
. Likewise, replacing the Phe
5
(F5) and Lys
41
(K41) residues with arginine and alanine, respectively, also destabilized EspA and blocked ESAT-6 and CFP-10 secretion
in vitro
. However, these two particular mutations did not attenuate
M. tuberculosis
in cellular models of infection or during acute infection in mice. We have thus identified amino acid residues in EspA that are important for facilitating ESAT-6 and CFP-10 secretion and virulence. However, our data also indicate for the first time that blockage of
M. tuberculosis
ESAT-6 and CFP-10 secretion
in vitro
and attenuation are mutually exclusive.
Paramedic Initiated Lisinopril For Acute Stroke Treatment (PIL-FAST): results from the pilot randomised controlled trial
Authors: Shaw Lisa , Price Christopher , McLure Sally , Howel Denise , McColl Elaine , Younger Paul , Ford Gary A
Published: September 2013

Background

High blood pressure (BP) during acute stroke is associated with poorer stroke outcome. Trials of treatments to lower BP have not resulted in improved outcome, but this may be because treatment commenced too late. Emergency medical service staff (paramedics) are uniquely placed to administer early treatment; however, experience of prehospital randomised controlled trials (RCTs) is very limited.

Methods

We conducted a pilot RCT to determine the feasibility of a definitive prehospital BP-lowering RCT in acute stroke. Paramedics were trained to identify, consent and deliver a first dose of lisinopril or placebo to adults with suspected stroke and hypertension while responding to the emergency call. Further treatment continued in hospital. Study eligibility, recruitment rate, completeness of receipt of study medication and clinical data (eg, BP) were collected to inform the design of a definitive RCT.

Results

In 14 months, 14 participants (median age=73 years, median National Institute of Health Stroke Scale=4) were recruited and received the prehospital dose of medication. Median time from stroke onset (as assessed by paramedic) to treatment was 70 min. Four participants completed 7 days of study treatment. Of ambulance transported suspected stroke patients, 1% were both study eligible and attended by a PIL-FAST paramedic.

Conclusions

It is possible to conduct a paramedic initiated double-blind RCT of a treatment for acute stroke. However, to perform a definitive RCT in a reasonable timescale, a large number of trained paramedics across several ambulance services would be needed to recruit the number of patients likely to be required.

Clinical trial registration

http://www.clinicaltrials.gov. Unique identifier:NCT01066572.