bluuebunny/crossref_metadata_2025 huggingface dataset:
Non-Markovian closure kinetics of flexible polymers with hydrodynamic interactions
Authors: Levernier N. , Dolgushev M. , Bénichou O. , Blumen A. , Guérin T. , Voituriez R.
Published: November 2015

This paper presents a theoretical analysis of the closure kinetics of a polymer with hydrodynamic interactions. This analysis, which takes into account the non-Markovian dynamics of the end-to-end vector and relies on the preaveraging of the mobility tensor (Zimm dynamics), is shown to reproduce very accurately the results of numerical simulations of the complete nonlinear dynamics. It is found that Markovian treatments based on a Wilemski-Fixman approximation significantly overestimate cyclization times (up to a factor 2), showing the importance of memory effects in the dynamics. In addition, this analysis provides scaling laws of the mean first cyclization time (MFCT) with the polymer size N and capture radius b, which are identical in both Markovian and non-Markovian approaches. In particular, it is found that the scaling of the MFCT for large N is given by T ∼ N3/2ln(N/b2), which differs from the case of the Rouse dynamics where T ∼ N2. The extension to the case of the reaction kinetics of a monomer of a Zimm polymer with an external target in a confined volume is also presented.
Spectrometer for shot-to-shot photon energy characterization in the multi-bunch mode of the free electron laser at Hamburg
Authors: Palutke S. , Gerken N. C. , Mertens K. , Klumpp S. , Mozzanica A. , Schmitt B. , Wunderer C. , Graafsma H. , Meiwes-Broer K.-H. , Wurth W. , Martins M.
Published: November 2015

The setup and first results from commissioning of a fast online photon energy spectrometer for the vacuum ultraviolet free electron laser at Hamburg (FLASH) at DESY are presented. With the use of the latest advances in detector development, the presented spectrometer reaches readout frequencies up to 1 MHz. In this paper, we demonstrate the ability to record online photon energy spectra on a shot-to-shot base in the multi-bunch mode of FLASH. Clearly resolved shifts in the mean wavelength over the pulse train as well as shot-to-shot wavelength fluctuations arising from the statistical nature of the photon generating self-amplified spontaneous emission process have been observed. In addition to an online tool for beam calibration and photon diagnostics, the spectrometer enables the determination and selection of spectral data taken with a transparent experiment up front over the photon energy of every shot. This leads to higher spectral resolutions without the loss of efficiency or photon flux by using single-bunch mode or monochromators.
Nonlinear eigenvalue approximation for compact operators
Authors: Moskow Shari
Published: November 2015

In the work of Osborn [Math. Comput. 29, 712–725 (1975)], a general spectral approximation theory was developed for compact operators on a Banach space which does not require that the operators be self-adjoint and also provides a first order correction term. Here, we extend some of the results of that paper to nonlinear eigenvalue problems. We present examples of its application that arise in electromagnetics and numerical analysis.
Prediction of transmittance spectra for transparent composite electrodes with ultra-thin metal layers
Authors: Zhao Zhao , Khorasani Arash Elhami , Theodore N. D. , Dhar A. , Alford T. L.
Published: November 2015

Recent interest in indium-free transparent composite-electrodes (TCEs) has motivated theoretical and experimental efforts to better understand and enhance their electrical and optical properties. Various tools have been developed to calculate the optical transmittance of multilayer thin-film structures based on the transfer-matrix method. However, the factors that affect the accuracy of these calculations have not been investigated very much. In this study, two sets of TCEs, TiO2/Au/TiO2 and TiO2/Ag/TiO2, were fabricated to study the factors that affect the accuracy of transmittance predictions. We found that the predicted transmittance can deviate significantly from measured transmittance for TCEs that have ultra-thin plasmonic metal layers. The ultrathin metal layer in the TCE is typically discontinuous. When light interacts with the metallic islands in this discontinuous layer, localized surface plasmons are generated. This causes extra light absorption, which then leads to the actual transmittance being lower than the predicted transmittance.
Photo-controllable thermal diffusivity and thermal conductivity driven by the orientation change of nematic liquid crystal with azo-dendrimers
Authors: Ryu Meguya , Takezoe Hideo , Haba Osamu , Yonetake Koichiro , Morikawa Junko
Published: November 2015

We measured the temperature dependences of anisotropic thermal properties, i.e., thermal diffusivity, thermal effusivity, thermal conductivity, and heat capacity per unit volume, of a nematogen 4′-n-pentyloxybiphenyl-4-carbonitrile (5OCB) containing a small amount (0.02 wt. %) of dendritic azobenzene derivatives (azo-dendrimer), using a temperature wave method. The azo-dendrimers spontaneously adsorb on cell surfaces and act as a command surface, i.e., photo-induced planar/homeotropic alignment by ultraviolet/visible light illumination. By using this effect, we demonstrated thermal property changes except for the heat capacity by almost two times within a few tens of seconds. The phenomenon can be applied to a sheet with photo-controllable thermal diffusivity or thermal conductivity.
In-situ evolution of helium bubbles in SiC under irradiation
Authors: Beaufort M.-F. , Vallet M. , Nicolaï J. , Oliviero E. , Barbot J.-F.
Published: November 2015

The evolution of individual He bubbles in 4H-SiC thin foils during irradiation with 1.5 MeV Au ions has been studied by in-situ transmission electron microscopy. During irradiation, individual He-bubbles under displacement damage were observed to gradually decrease in size at different rates due to their position within the thin foil. In the bulk, slow bubble shrinkage at a constant rate can be explained by a competition between direct displacement of He out of the bubble and re-trapping, while the bubble remains at equilibrium pressure. A 1D-model proved that half of the ejected-He is re-trapped during the displacing irradiation. At high irradiation dose, the excess of vacancies due to bubble shrinkage and the vacancies provided by the irradiation itself leads to the formation of small satellite bubbles. The system thus evolves toward a steady state of bubble size with all the helium atoms in the matrix. In thin parts, bubbles showed a faster shrinkage rate with little or no re-trapping before quick disappearance.
Effect of surface roughness and size of beam on squeeze-film damping—Molecular dynamics simulation study
Authors: Kim Hojin , Strachan Alejandro
Published: November 2015

We use large-scale molecular dynamics (MD) to characterize fluid damping between a substrate and an approaching beam. We focus on the near contact regime where squeeze film (where fluid gap is comparable to the mean free path of the gas molecules) and many-body effects in the fluid become dominant. The MD simulations provide explicit description of many-body and non-equilibrium processes in the fluid as well as the surface topography. We study how surface roughness and beam width increases the damping coefficient due to their effect on fluid mobility. We find that the explicit simulations are in good agreement with prior direct simulation Monte Carlo results except at near-contact conditions where many-body effects in the compressed fluid lead the increased damping and weaker dependence on beam width. We also show that velocity distributions near the beam edges and for short gaps deviate from the Boltzmann distribution indicating a degree of local non-equilibrium. These results will be useful to parameterize compact models used for microsystem device-level simulations and provide insight into mesoscale simulations of near-contact damping.
Multicolor lasing prints
Authors: Ta Van Duong , Yang Shancheng , Wang Yue , Gao Yuan , He Tingchao , Chen Rui , Demir Hilmi Volkan , Sun Handong
Published: November 2015

This work demonstrates mass production of printable multi-color lasing microarrays based on uniform hemispherical microcavities on a distributed Bragg reflector using inkjet technique. By embedding two different organic dyes into these prints, optically pumped whispering gallery mode microlasers with lasing wavelengths in green and red spectral ranges are realized. The spectral linewidth of the lasing modes is found as narrow as 0.11 nm. Interestingly, dual-color lasing emission in the ranges of 515–535 nm and 585–605 nm is simultaneously achieved by using two different dyes with certain ratios. Spectroscopic measurements elucidate the energy transfer process from the green dye (donor) to the red one (acceptor) with an energy transfer efficiency up to 80% in which the nonradiative Förster resonance energy transfer dominates. As such, the acceptor lasing in the presence of donor exhibits a significantly lower (∼2.5-fold) threshold compared with that of the pure acceptor lasing with the same concentration.
Quartz-enhanced conductance spectroscopy for nanomechanical analysis of polymer wire
Authors: Zheng Huadan , Yin Xukun , Zhang Guofeng , Dong Lei , Wu Hongpeng , Liu Xiaoli , Ma Weiguang , Zhang Lei , Yin Wangbao , Xiao Liantuan , Jia Suotang , Tittel Frank K.
Published: November 2015

Quartz-enhanced conductance spectroscopy is developed as an analytical tool to investigate dynamic nanomechanical behaviors of polymer wires, in order to determine the glass transition temperature (Tg). A polymethyl methacrylate (PMMA) microwire with a diameter of 10 μm was bridged across the prongs of a quartz tuning fork (QTF). With the advantage of QTF self-sensing as compared with micro-cantilevers or other resonators, the resonance frequency and Q factor can be directly determined by means of its electrical conductance spectra with respect to the frequency of the external excitation source (dI/dV vs f), and therefore, no optical beam is required. The Tg of the PMMA microwire was determined by the maximum loss modulus of the QTF, calculated from the resonance frequency and the Q factor as a function of temperature. The measured Tg of the PMMA is 103 °C with an error of ±2 °C. Both heating/cooling and physical aging experiments were carried out, demonstrating that the technique is both reversible and reproducible.
Molecular dynamics simulations of cascades in strained carbide inclusions embedded in α-iron
Authors: Henriksson K. O. E. , Nordlund K.
Published: November 2015

The effect of strain on the amount of point defects created in Fe and Cr carbide inclusions embedded in ferrite has been investigated. The spherical carbide inclusions consisted of either Fe3C or Cr23C6. Recoil energies from 100 eV to 3 keV and strains from −0.15 (compressive) to 0.01 (tensile) were used. The overall tendency is that the number of point defects — such as antisites, vacancy and interstitials — inside the carbide is lowered when the strain grows more negative (compressive). Outside the carbides, the number of defects is markedly higher for strongly compressive strains than for e.g. zero strain, especially at high energies.
The effect of burnt soils on growth of Xanthorrhoea glauca subsp. angustifolia (Xanthorrhoeaceae) seedlings in box-ironbark ecosystems, northern central Victoria
Authors: Bellette Marc P. , Lawrence Ruth E. , Enright Neal J.
Published: November 2015

Seedlings of Xanthorrhoea glauca subsp. angustifolia D.J.Bedford (Xanthorrhoeaceae) were grown in burnt, unburnt and ash-rich soils from the box-ironbark ecosystem, northern central Victoria. Analysis of root architecture and the chemistry of leaves and roots demonstrate that burning improves seedling biomass development and acquisition of nutrients. An increased uptake of zinc by seedlings after fire is thought to be ecologically important and may infer vesicular-arbuscular mycorrhizal associations. The early development of a secondary root system is likely to contribute to seedling survivorship. Given the observed high adult mortality after managed fuel-reduction fires, the importance of understanding and manipulating recruitment dynamics through an adaptive and strategic fire management of the remaining populations is likely to define the long-term survival of the species in Victoria.
Temperature affects the dormancy and germination of sympatric annual (Oryza meridionalis) and perennial (O. rufipogon) native Australian rices (Poaceae) and influences their emergence in introduced para grass (Urochloa mutica) swards
Authors: Bellairs Sean M. , Wurm Penelope A. S. , Kernich Beckie
Published: November 2015

The seed biology of two ecologically and genetically important sympatric wild rice species from northern Australia was compared – perennial Oryza rufipogon Griff. and annual Oryza meridionalis N.Q.Ng. The aim was to determine mechanisms of dormancy exhibited at seed shed and to identify factors that trigger or inhibit germination. This information was used to investigate the ecology of in situ Oryza populations in introduced para grass swards (Urochloa mutica (Forssk.) T.Q. Nguyen) and to understand interactions between the two sympatric Oryza species. Primary dormancy in the two species is similar, namely, non-deep physiological dormancy, determined by external maternal structures and broken by warm temperature treatments equivalent to dry season soil temperatures. Light quality, smoke water, gibberellic acid and nitric acid treatments had minor influences on germination. Changes to the soil profile and aboveground biomass structure due to swards of U. mutica significantly affected emergence of O. meridionalis. Thus the influence of soil temperature explains the results of previous field studies in which biomass or litter on the soil surface prevented germination. This has implications for biodiversity management on monsoonal floodplains of northern Australia, where introduced pasture species produce greater biomass than native grasslands, reduce soil temperatures and are displacing native rices. There were differences between the Oryza species – dormancy was more quickly broken in annual O. meridionalis, reflecting the reduced need for investment in seed bank persistence for annual species in annually inundated and climatically reliable wetlands.
Study on Pyrrole 4-Pyrazoline Derivatives: Experimental and Quantum Chemical Approaches
Authors: Singh R. N. , Rawat Poonam , Baboo Vikas
Published: November 2015

As part of a study on pyrrole derivatives we report here a combined experimental and quantum chemical study of pyrrole 4-pyrazoline biheterocyclic derivatives. The structure of the synthesised compounds have been studied using experimental IR, UV, 1H and 13C NMR spectroscopic analyses along with density functional theory (DFT) calculations using the B3LYP functional with 6–311+G (d,p) basis set. The global, local reactivity, and thermodynamic parameters support the analysis. All the experimental vibrational bands have been discussed and assigned to normal modes on the basis of our calculations. In addition, the computed 1H and 13C NMR data, obtained by DFT calculations, are found to be in good agreement with the experimental data and serve as valuable tools in identifying the products. The vibrational analysis shows red shifts in vN–H and vC=O stretching vibrations as a result of dimer formation. The theoretical electronic absorption spectra have been calculated by using time dependent-DFT methods. The static first hyperpolarizability (β0) values for the synthesized pyrrole–pyrazoline derivatives 4A–D are calculated as 16.97 × 10–30, 47.64 × 10–30, 65.40 × 10–30, 65.39 × 10–30 esu, respectively, and increase from 4A to 4C as a result of the addition of an –NO2 acceptor in 4B and two –NO2 group acceptors in 4C. However, an additional –Cl group in 4D on the phenyl ring attached to the pyrazoline moiety does not result in a clear change from 4C. The calculated static and dynamic hyperpolarizability results show that the investigated molecules might be used as non-linear optical materials.
Characterization of a new Lactobacillus salivarius strain engineered to express IBV multi-epitope antigens by chromosomal integration
Authors: Ma Bing-cun , Yang Xin , Wang Hong-ning , Cao Hai-peng , Xu Peng-wei , Ding Meng-die , Liu Hui
Published: November 2015

To obtain adhesive and safe lactic acid bacteria (LAB) strains for expressing heterologous antigens, we screened LAB inhabitants in intestine of Tibetan chickens by analyzing their adhesion and safety properties and the selected LAB was engineered to express heterologous antigen (UTEpi C-A) based on chromosomal integration strategy. We demonstrated that a new Lactobacillu salivarius TCMM17 strain is strongly adhesive to chicken intestinal epithelial cells, contains no endogenous plasmids, is susceptible to tested antimicrobials, and shows no toxicities. In order to examine the potential of TCMM17 strain as heterogenous antigen delivering vehicle, we introduced a UTEpi C-A expression cassette in its chromosome by constructing a non-replicative plasmid (pORI280-UUTEpi C-AD). The recombinant TCMM17 strain (∆TCMM17) stably was found to keep the gene cassette through 50 generations, and successfully displayed EpiC encoded by the cassette on its surface. This work provides a universal platform for development of novel oral vaccines and expression of further antigens of avian pathogens.
20-hydroxyecdysone accumulation and regulation in Ajuga lobata D. Don suspension culture
Authors: Qian Jingjing , Yang Yueyue , Li Xin , Chi Defu
Published: November 2015

Suspension culture of Ajuga lobata D. Don cells provides a method of synthesis of the phytoecdysteroid 20-hydroxyecdysone (20E) which can regulate the molting process of larvae. We characterized the culture conditions to optimize 20E production. Growth of A. lobata D. Don cells fits the logistic equation curve with a growth cycle of 19 days. Medium conductivity was negatively correlated with dry cell weight and 20E accumulation, thus could be used to determine the optimal time for cell harvest. Continuous subculture reduced 20E synthesis, but supplementing medium with 20E precursors mevalonic (MVA), α-Pinene, and nitric oxide (NO) can significantly promote cell growth and influence 20E accumulation. Combination of α-Pinene, MVA, and SNP significantly elevated 20E accumulation, thus may synergistically enhance 20E synthesis in A. lobata D. Don. The optimal concentrations of α-Pinene, MVA, and NO donor SNP in suspension culture were 50 μL L−1, 10 mg L−1, and 80 μmol L−1.
Modulation of the slow/common gating of CLC channels by intracellular cadmium
Authors: Yu Yawei , Tsai Ming-Feng , Yu Wei-Ping , Chen Tsung-Yu
Published: November 2015

Members of the CLC family of Cl− channels and transporters are homodimeric integral membrane proteins. Two gating mechanisms control the opening and closing of Cl− channels in this family: fast gating, which regulates opening and closing of the individual pores in each subunit, and slow (or common) gating, which simultaneously controls gating of both subunits. Here, we found that intracellularly applied Cd2+ reduces the current of CLC-0 because of its inhibition on the slow gating. We identified CLC-0 residues C229 and H231, located at the intracellular end of the transmembrane domain near the dimer interface, as the Cd2+-coordinating residues. The inhibition of the current of CLC-0 by Cd2+ was greatly enhanced by mutation of I225W and V490W at the dimer interface. Biochemical experiments revealed that formation of a disulfide bond within this Cd2+-binding site is also affected by mutation of I225W and V490W, indicating that these two mutations alter the structure of the Cd2+-binding site. Kinetic studies showed that Cd2+ inhibition appears to be state dependent, suggesting that structural rearrangements may occur in the CLC dimer interface during Cd2+ modulation. Mutations of I290 and I556 of CLC-1, which correspond to I225 and V490 of CLC-0, respectively, have been shown previously to cause malfunction of CLC-1 Cl− channel by altering the common gating. Our experimental results suggest that mutations of the corresponding residues in CLC-0 change the subunit interaction and alter the slow gating of CLC-0. The effect of these mutations on modulations of slow gating of CLC channels by intracellular Cd2+ likely depends on their alteration of subunit interactions.
Key comparison BIPM.RI(I)-K7 of the air-kerma standards of the ENEA-INMRI, Italy and the BIPM in mammography x-rays
Authors: Kessler C , Burns D , Roger P , Toni M P , Pinto M , Bovi M , Cappadozzi G , Silvestri C
Published: November 2015

A first key comparison has been made between the air-kerma standards of the ENEA-INMRI, Italy and the BIPM in mammography x-ray beams. The results show the standards to be in agreement at the level of the standard uncertainty for the comparison of 4.8 parts in 103. The results are analysed and presented in terms of degrees of equivalence, suitable for entry in the BIPM key comparison database.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.

The final report has been peer-reviewed and approved for publication by the CCRI, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Temporal and spatial variation in size at maturity of the common whelk (Buccinum undatum)
Authors: Haig Jodie A. , Pantin Julia R. , Salomonsen Harriet , Murray Lee G. , Kaiser Michel J.
Published: November 2015

There is little common rationale for the 45 to 75 mm total shell length (TSL) minimum landing sizes (MLS) for Buccinum undatum among countries in the Northeast Atlantic. Size at maturity and length frequency of B. undatum populations vary over small spatial scales; however, the driving mechanism for this is unknown. Size at maturity research for B. undatum dates back to the late 1980s; since then, there has been little consensus on laboratory methods or in which season to undertake the research. Here, we assess small-scale spatial variation in size at maturity over a year to identify the seasons that increase error in visual maturity estimates. We compare and contrast results from methods used in the literature to estimate maturity for B. undatum. Monthly, B. undatum samples were obtained from Welsh fishers between May 2013 and May 2014 from eight sites at four locations (n = 5080). All whelks were sexed, weighed, and measured, and up to 60 whelks from each location were assessed for maturity (n = 1659). Mature whelks were found in all months, with a peak in reproductive activity through summer and early autumn, followed by the onset of spawning in November. Size at maturity varied between sexes and sites, and ranged from 51 to 76 mm TSL. Whelks caught in shallow waters (0–10 m) matured at a smaller size than those from deeper waters (up to 60 m). Length frequency varied at each site suggesting that a single increase in MLS would impact fishers disproportionately. No methodology trialled was found without inherent errors when used in isolation, though a combination of methods proved ideal. The seasonal variation in maturity estimates suggested that assigning maturity is increasingly difficult outside annual reproductive periods and that prespawning is the ideal time to undertake visual gonad assessments for whelks.
Interaction of the hepatitis B virus X protein with the lysine methyltransferase SET and MYND domain‐containing 3 induces activator protein 1 activation
Authors: Hayashi Miwako , Deng Lin , Chen Ming , Gan Xiang , Shinozaki Kenta , Shoji Ikuo , Hotta Hak
Published: November 2015

Hepatitis B virus (HBV) is a widespread human pathogen that often causes chronic hepatitis, liver cirrhosis and hepatocellular carcinoma. The detailed mechanisms underlying HBV pathogenesis remain poorly understood. The HBV X protein (HBx) is a multifunctional regulator that modulates viral replication and host cell functions, such as cell cycle progression, apoptosis and protein degradation through interaction with a variety of host factors. Recently, the nonstructural protein 5A (NS5A) of hepatitis C virus has been reported to interact with methyltransferase SET and MYND domain‐containing 3 (SMYD3), which is implicated in chromatin modification and development of cancer. Because HBx shares fundamental regulatory functions concerning viral replication and pathogenesis with NS5A, it was decided to examine whether HBx interacts with SMYD3. In the present study, it was demonstrated by co‐immunoprecipitation analysis that HBx interacts with both ectopically and endogenously expressed SMYD3 in Huh‐7.5 cells. Deletion mutation analysis revealed that the C‐terminal region of HBx (amino acids [aa] 131–154) and an internal region of SMYD3 (aa 269–288) are responsible for their interaction. Immunofluorescence and proximity ligation assays showed that HBx and SMYD3 co‐localize predominantly in the cytoplasm. Luciferase reporter assay demonstrated that the interaction between HBx and SMYD3 activates activator protein 1 (AP‐1) signaling, but not that of nuclear factor‐kappa B (NF‐κB). On the other hand, neither overexpression nor knockdown of SMYD3 altered production of HBV transcripts and HBV surface antigen (HBsAg). In conclusion, a novel HBx‐interacting protein, SMYD3, was identified, leading to proposal of a novel mechanism of AP‐1 activation in HBV‐infected cells.
Elective induction of labour and maternal request: a national population‐based study
Authors: Coulm B , Blondel B , Alexander S , Boulvain M , Le Ray C
Published: November 2015

Objective

To estimate the rate of elective inductions in France and the proportion of them that were maternally requested, and to study the factors associated with elective inductions that were or were not requested by women.

Design

Cross‐sectional population‐based study.

Setting

All maternity units in France.

Population

About 14 681 women from the 2010 French National Perinatal Survey of a representative sample of births.

Methods

Inductions were classified as elective based on their indications and maternal and fetal characteristics, collected from medical records. Elective inductions requested by women were identified from the mother's postpartum interviews. Polytomous logistic regression analysis was used to study the determinants of inductions that were or were not maternally requested. Women with spontaneous labour served as the comparison group.

Main outcome measure

Rate of elective inductions.

Results

The induction rate was 22.6, 13.9% elective. Among elective inductions, 47.3% were requested by women. The characteristics of mothers, pregnancies, and maternity units were similar in both groups of elective inductions. The main associated factors were parity 2 or more [adjusted odds ratio (OR) 4.7, 95% confidence interval (CI) 3.1–7.2 for maternally requested inductions and aOR of 1.8 (95% CI1.2–2.7) for unrequested inductions, compared with parity 0] and private hospital status [aOR 4.5 95% (CI 3.3–6.0) for maternally requested inductions and aOR 3.7 (95% CI 2.8–4.9) for inductions not requested by the mother]. We found no association between maternal social characteristics and type of elective induction.

Conclusion

Parity and organisational factors appear to influence the decision about elective inductions. It would be interesting to determine how obstetricians and women make this decision and for what reasons.

Tweetable abstract

About 13.9% of inductions of labour were elective in France, 47.3% of these requested by women.
Comparison of differential gene expression to water stress among bacteria with relevant pollutant‐degradation properties
Authors: Moreno‐Forero Silvia K. , Rojas Edward , Beggah Siham , van der Meer Jan R.
Published: November 2015

Resistance to semi‐dry environments has been considered a crucial trait for superior growth and survival of strains used for bioaugmentation in contaminated soils. In order to compare water stress programmes, we analyse differential gene expression among three phylogenetically different strains capable of aromatic compound degradation: Arthrobacter chlorophenolicus A6, Sphingomonas wittichii RW1 and Pseudomonas veronii 1YdBTEX2. Standardized laboratory‐induced water stress was imposed by shock exposure of liquid cultures to water potential decrease, induced either by addition of solutes (NaCl, solute stress) or by addition of polyethylene glycol (matric stress), both at absolute similar stress magnitudes and at those causing approximately similar decrease of growth rates. Genome‐wide differential gene expression was recorded by micro‐array hybridizations. Growth of P. veronii 1YdBTEX2 was the most sensitive to water potential decrease, followed by S. wittichii RW1 and A. chlorophenolicus A6. The number of genes differentially expressed under decreasing water potential was lowest for A. chlorophenolicus A6, increasing with increasing magnitude of the stress, followed by S. wittichii RW1 and P. veronii 1YdBTEX2. Gene inspection and gene ontology analysis under stress conditions causing similar growth rate reduction indicated that common reactions among the three strains included diminished expression of flagellar motility and increased expression of compatible solutes (which were strain‐specific). Furthermore, a set of common genes with ill‐defined function was found between all strains, including ABC transporters and aldehyde dehydrogenases, which may constitute a core conserved response to water stress. The data further suggest that stronger reduction of growth rate of P. veronii 1YdBTEX2 under water stress may be an indirect result of the response demanding heavy NADPH investment, rather than the presence or absence of a suitable stress defence mechanism per se.
A temperate river estuary is a sink for methanotrophs adapted to extremes of pH, temperature and salinity
Authors: Sherry Angela , Osborne Kate A. , Sidgwick Frances R. , Gray Neil D. , Talbot Helen M.
Published: November 2015

River Tyne (UK) estuarine sediments harbour a genetically and functionally diverse community of methane‐oxidizing bacteria (methanotrophs), the composition and activity of which were directly influenced by imposed environmental conditions (pH, salinity, temperature) that extended far beyond those found in situ. In aerobic sediment slurries methane oxidation rates were monitored together with the diversity of a functional gene marker for methanotrophs (pmoA). Under near in situ conditions (4–30°C, pH 6–8, 1–15 g l−1 NaCl), communities were enriched by sequences affiliated with Methylobacter and Methylomonas spp. and specifically a Methylobacter psychrophilus‐related species at 4–21°C. More extreme conditions, namely high temperatures ≥ 40°C, high ≥ 9 and low ≤ 5 pH, and high salinities ≥ 35 g l−1 selected for putative thermophiles (Methylocaldum), acidophiles (Methylosoma) and haloalkaliphiles (Methylomicrobium). The presence of these extreme methanotrophs (unlikely to be part of the active community in situ) indicates passive dispersal from surrounding environments into the estuary.
A simple approach for maximizing the overlap of phylogenetic and comparative data
Authors: Pennell Matthew W. , FitzJohn Richard G. , Cornwell William K.
Published: November 2015

Biologists are increasingly using curated, public data sets to conduct phylogenetic comparative analyses. Unfortunately, there is often a mismatch between species for which there is phylogenetic data and those for which other data are available. As a result, researchers are commonly forced to either drop species from analyses entirely or else impute the missing data.

A simple strategy to improve the overlap of phylogenetic and comparative data is to swap species in the tree that lack data with ‘phylogenetically equivalent’ species that have data. While this procedure is logically straightforward, it quickly becomes very challenging to do by hand. Here, we present algorithms that use topological and taxonomic information to maximize the number of swaps without altering the structure of the phylogeny.

We have implemented our method in a new R package phyndr, which will allow researchers to apply our algorithm to empirical data sets. It is relatively efficient such that taxon swaps can be quickly computed, even for large trees. To facilitate the use of taxonomic knowledge, we created a separate data package taxonlookup; it contains a curated, versioned taxonomic lookup for land plants and is interoperable with phyndr.

Emerging online data bases and statistical advances are making it possible for researchers to investigate evolutionary questions at unprecedented scales. However, in this effort species mismatch among data sources will increasingly be a problem; evolutionary informatics tools, such as phyndr and taxonlookup, can help alleviate this issue.
Herding behaviour in the Australian loan market and its impact on bank loan quality
Authors: Tran Vuong Thao , Nguyen Hoa , Lin Chien Ting
Published: November 2015

We examine the effect of herding behaviour on the credit quality of bank loans in Australia. We find that bank herding varies with different types of loans. It tends to be more prevalent in owner‐occupied housing loans and credit cards than other types of loans. During the global financial crisis period, herding in owner‐occupied housing loans was most pronounced due to the flight‐to‐quality phenomenon in the housing sector. Furthermore, we find that the big four banks tend to herd more than smaller and regional banks. Bank herding behaviour is countercyclical, as it is negatively related to real GDP growth and the cost of funding but is positively related to market risk. Regulatory capital requirements may also encourage herding as banks are required to hold less risk‐weighted capital for residential loans. Most importantly, bank herding is related to higher impaired assets and therefore lower loan quality. Our findings may have implications for policymakers and bank regulators.
Lessons from Praxis: Autonomy and Spatiality in Contemporary Latin American Social Movements
Authors: Lopes de Souza Marcelo
Published: November 2015

In the course of the 20th century, left‐libertarian thought and praxis never ceased to be present in Latin America, even during the most difficult years of competition with Marxism‐Leninism and of military repression. But it was above all from the 1990s onwards that particularly original kinds of libertarian thought and praxis began to flourish there. Alongside more or less renewed versions of classical anarchism, new forms of praxis and analysis emerged at the end of the 20th and beginning of the 21st century; from Mexican neo‐Zapatism to a part of Argentina's piqueteros to some expressions of Brazil's sem‐teto movement, many new movements and ideas have developed in the last two decades. These new movements are at the same time remarkably libertarian and by no means reducible to the very honourable but somewhat too restrictive label “anarchism”. In fact, many of them are clearly “hybrid”, in the sense that they are products of both left‐libertarian and Marxist influences.

Typically, these Latin American movements share a commitment to principles such as horizontality, self‐management and decentralism (which have never been part of Marxism's typical repertoire of practices and principles); moreover, autonomy is a key notion for most of them. Furthermore, spatial practices, territorialisation among them, are proving decisive for many movements and protest actions.

The concept of territory is one of those “geographical” concepts that have been intensely subjected, in recent decades, to strong attempts of redefinition and debugging. In this paper, the territory is fundamentally seen (as a first approximation) as a space defined and delimited by and through power relations, and it is important to see that power (both heteronomous and autonomous power) is exerted only with reference to a territory and, very often, by means of a territory. The kind of power exerted by emancipatory social movements does not constitute an exception to this rule.
The effect of antenatal dietary and lifestyle advice for women who are overweight or obese on emotional well‐being: the LIMIT randomized trial
Authors: Dodd Jodie M. , Newman Angela , Moran Lisa J. , Deussen Andrea R. , Grivell Rosalie M. , Yelland Lisa N. , Crowther Caroline A. , McPhee Andrew J. , Wittert Gary , Owens Julie A. , Turnbull Deborah , Robinson Jeffrey S. ,   the LIMIT Randomised Trial Group
Published: November 2015

Introduction

Our aim was to evaluate the effect of dietary and lifestyle advice given to women who were overweight or obese during pregnancy on maternal quality of life, anxiety and risk of depression, and satisfaction with care.

Material and methods

We conducted a randomized trial, involving pregnant women with body mass index ≥25 kg/m2, recruited from maternity units in South Australia. Women were randomized to Lifestyle Advice or Standard Care, and completed questionnaires assessing risk of depression (Edinburgh Postnatal Depression Scale), anxiety (Spielberger State‐Trait Anxiety Inventory), and quality of life (SF‐36) at trial entry, 28 and 36 weeks' gestation, and 4 months postpartum. Secondary trial outcomes assessed for this analysis were risk of depression, anxiety, maternal quality of life, and satisfaction with care.

Results

One or more questionnaires were completed by 976 of 1108 (90.8%) women receiving Lifestyle Advice and 957 of 1104 (89.7%) women receiving Standard Care. The risk of depression [adjusted risk ratio 1.01; 95% confidence interval (CI) 0.82–1.24; p = 0.95], anxiety (adjusted risk ratio 1.09; 95% CI 0.93–1.27; p = 0.31), and health‐related quality of life were similar between the two groups. Women receiving Lifestyle Advice reported improved healthy food choice [Lifestyle Advice 404 (68.9%) vs. Standard Care 323 (51.8%); p < 0.0001], and exercise knowledge [Lifestyle Advice 444 (75.8%) vs. Standard Care 367 (58.8%); p < 0.0001], and reassurance about their health [Lifestyle Advice 499 (85.3%) vs. Standard Care 485 (77.9%); p = 0.0112], and health of their baby [Lifestyle Advice 527 (90.2%) vs. Standard Care 545 (87.6%); p = 0.0143].

Conclusion

Lifestyle advice in pregnancy improved knowledge and provided reassurance without negatively impacting well‐being.
Review article: the antimicrobial effects of rifaximin on the gut microbiota
Authors: DuPont H. L.
Published: November 2015

Background

Disruption of the gut microbiota through use of systemic antimicrobials or activation of the mucosal inflammatory response by pathogens can cause dysregulation of the intestinal mucosa.

Aim

To explore the mechanisms of action of rifaximin that may underlie its clinical benefits in travellers’ diarrhoea (TD).

Methods

A literature search was performed using the terms ‘rifaximin’ and ‘L/105’ in combination with the terms ‘in vitro activity’, ‘diarrhea’, ‘microbiota’ and ‘gut flora’.

Results

Rifaximin has been traditionally identified as a nonsystemic, broad‐spectrum, bactericidal antibiotic. Evidence shows that the activity of rifaximin against enteropathogens in this setting is likely enhanced by its increased solubility in the presence of bile acids in the small intestine. Results of clinical studies show that although rifaximin is efficacious in TD, a clinical cure often occurs without apparent bacterial eradication and with minimal effect on the gut microbiota, suggesting an effect of rifaximin other than direct antibiotic activity.

Conclusions

Although definitive studies on the effect of rifaximin on the gut microbiota in large cohorts of healthy volunteers or patients have not been published, pre‐clinical studies provide some insight. These studies have shown that rifaximin may have effects on both the pathogen and host, including direct effects on pathogenic bacteria (such as reducing the expression of bacterial virulence factors) and indirect effects on the host (such as inhibiting bacterial attachment and internalisation at the intestinal mucosa and reducing mucosal inflammation).
Review article: the potential mechanisms of action of rifaximin in the management of inflammatory bowel diseases
Authors: Sartor R. B.
Published: November 2015

Background

Gut microbiota dysbiosis contributes to the pathogenesis of inflammatory bowel diseases (IBD). Although the microbiota's role in IBD pathogenesis, specifically Crohn's disease (CD), provides a rationale for antibiotic treatment, antibiotic use in CD remains controversial. Rifaximin, traditionally identified as a nonsystemic bactericidal antibiotic, may be therapeutically beneficial for inducing CD remission.

Aim

To examine the role of rifaximin in the management of IBD and its potential mechanisms of action.

Methods

A literature search using the following strategy: (‘inflammatory bowel disease’ OR ‘Crohn's’ OR ‘ulcerative’), ‘rifaximin’ AND (‘barrier’ OR ‘translocation’ OR ‘adhesion’ OR ‘internalization’ OR ‘pregnane X’), AND ‘pregnane X’ AND (‘Crohn's’ OR ‘ulcerative colitis’ OR ‘inflammatory bowel disease’).

Results

In vitro data suggest rifaximin mediates changes in epithelial cell physiology and reduces bacterial attachment and internalisation. In experimental colitis models, rifaximin antagonised the effects of tumour necrosis factor‐α on intestinal epithelial cells by activating pregnane X receptor, which inhibits nuclear factor‐κB–mediated proinflammatory mediators and induces detoxification genes (e.g. multidrug resistance 1 and cytochrome P450 3A4). Rifaximin also inhibits bacterial translocation into the mesenteric lymph nodes.

Conclusion

Accumulating evidence suggests that mechanisms of action of rifaximin in IBD may not be limited to direct bactericidal activity; therefore, rifaximin could potentially be redefined as a gut environment modulator.
Effect of Statin Treatment on Plasma 4β‐Hydroxycholesterol Concentrations
Authors: Björkhem‐Bergman Linda , Nylén Hanna , Eriksson Mats , Parini Paolo , Diczfalusy Ulf
Published: November 2015

The endogenous oxysterol 4β‐hydroxycholesterol may be used as a marker for the drug‐metabolizing enzymes cytochrome P450 3A (CYP3A). The primary aim of this study was to investigate the effect of statin treatment on plasma 4β‐hydroxycholesterol concentrations. Plasma samples from a previously performed clinical study where gallstone patients had been treated with placebo (n = 6), 20 mg fluvastatin (n = 9) or 80 mg atorvastatin (n = 9) daily for 4 weeks were analysed. Hepatic CYP3A mRNA levels had previously been shown to be unchanged in all three treatment groups. Plasma 4β‐hydroxycholesterol did not change significantly (p = 0.92) in the placebo group, but treatment with low‐dose fluvastatin or high‐dose atorvastatin resulted in reductions in plasma concentration of 10.7% (p < 0.05) and 36.5% (p < 0.01), respectively. However, the 4β‐hydroxycholesterol/cholesterol ratio did not change significantly for the patients receiving placebo or patients receiving low‐dose fluvastatin. The ratio for patients receiving high‐dose atorvastatin increased by 12% (p < 0.05). In conclusion, the total plasma cholesterol level is an important determinant for the plasma 4β‐hydroxycholesterol level.
Nebivolol Ameliorates Cisplatin‐Induced Nephrotoxicity in Rats
Authors: Morsy Mohamed A. , Heeba Gehan H.
Published: November 2015

Treatment with cisplatin is associated with dose‐limiting side effects, mainly nephrotoxicity. On the other hand, nebivolol, a β1‐adrenoceptor antagonist, exhibits vasodilatory and antioxidative properties. This study aimed to determine whether nebivolol possesses a protective effect against cisplatin nephrotoxicity and explore many mechanisms underlying this potential effect. Nephrotoxicity was induced in Wistar rats by a single intraperitoneal injection of cisplatin (6 mg/kg) on day 2. Nebivolol (10 mg/kg) was administered orally for 7 consecutive days. Nebivolol showed a nephroprotective effect as demonstrated by the significant reduction in the elevated levels of serum creatinine and urea as well as renal levels of malondialdehyde, nitric oxide products (nitrite/nitrate), inducible nitric oxide synthase, tumour necrosis factor‐alpha, caspase‐3, angiotensin II and endothelin‐1 with a concurrent increase in renal levels of reduced glutathione and endothelial nitric oxide synthase compared to untreated rats. Histopathological examination confirmed the nephroprotective effect of nebivolol. Pre‐treatment with Nω‐nitro‐L‐arginine methyl ester, the non‐specific nitric oxide synthase inhibitor, partially altered the protection afforded by nebivolol. In conclusion, nebivolol protects rats against cisplatin‐induced nephrotoxicity that is most likely through its antioxidant, anti‐inflammatory and antiapoptotic effects as well as by abrogation of the augmented angiotensin II and endothelin‐1 levels.
Recurrence rate of lentigo maligna after micrographically controlled staged surgical excision
Authors: de Vries K. , Greveling K. , Prens L.M. , Munte K. , Koljenović S. , van Doorn M.B.A. , Prens E.P.
Published: November 2015

Background

Lentigo maligna is a slowly growing melanoma in situ. Current guidelines advise wide local excision with a margin of 5 mm as the treatment of first choice, which has recurrence rates ranging from 6% to 20%.

Objectives

To determine retrospectively the recurrence rate of lentigo maligna after staged surgical excision.

Methods

Records of all patients with lentigo maligna treated with our method of staged surgical excision between 2002 and 2011 were retrieved. To identify recurrences we used the computer program Sympathy, which is linked to PALGA, a nationwide network and registry of histo- and cytopathology in the Netherlands.

Results

We identified 100 patients, who were treated with staged surgical excision with 100% immunohistopathological control of lateral margins. Digital pictures were used to facilitate orientation during the several stages of surgery. After a mean follow-up of 60 months, four patients had a recurrence, after 37, 58, 74 and 77 months of follow-up.

Conclusions

Staged surgical excision is superior in clearance and recurrence rates to wide local excision for lentigo maligna and should be considered as the treatment of first choice in national and international guidelines.
Cool and hot executive function as predictors of aggression in early childhood: Differentiating between the function and form of aggression
Authors: Poland Sarah E. , Monks Claire P. , Tsermentseli Stella
Published: November 2015

Executive function (EF) has been implicated in childhood aggression. Understanding of the role of EF in aggression has been hindered, however, by the lack of research taking into account the function and form of aggression and the almost exclusive focus on cool EF. This study examined the role of cool and hot EF in teacher reported aggression, differentiating between reactive and proactive as well as physical and relational aggression. Children (N = 106) completed laboratory tasks measuring cool (inhibition, planning, working memory) and hot EF (affective decision‐making, delay of gratification). Cool, but not hot, EF significantly contributed to understanding of childhood aggression. Inhibition was a central predictor of childhood aggression. Planning and working memory, in contrast, were significant independent predictors of proactive relational aggression only. Added to this, prosocial behaviour moderated the relationship between working memory and reactive relational aggression. This study therefore suggests that cool EF, particularly inhibition, is associated with childhood aggression across the different functions and forms.