bluuebunny/crossref_metadata_2025 huggingface dataset:
An extreme ultraviolet Michelson interferometer for experiments at free-electron lasers
Authors: Hilbert Vinzenz , Blinne Alexander , Fuchs Silvio , Feigl Torsten , Kämpfer Tino , Rödel Christian , Uschmann Ingo , Wünsche Martin , Paulus Gerhard G. , Förster Eckhart , Zastrau Ulf
Published: September 2013

We present a Michelson interferometer for 13.5 nm soft x-ray radiation. It is characterized in a proof-of-principle experiment using synchrotron radiation, where the temporal coherence is measured to be 13 fs. The curvature of the thin-film beam splitter membrane is derived from the observed fringe pattern. The applicability of this Michelson interferometer at intense free-electron lasers is investigated, particularly with respect to radiation damage. This study highlights the potential role of such Michelson interferometers in solid density plasma investigations using, for instance, extreme soft x-ray free-electron lasers. A setup using the Michelson interferometer for pseudo-Nomarski-interferometry is proposed.
Revisiting a many-body model for water based on a single polarizable site: From gas phase clusters to liquid and air/liquid water systems
Authors: Réal Florent , Vallet Valérie , Flament Jean-Pierre , Masella Michel
Published: September 2013

We present a revised version of the water many-body model TCPE [M. Masella and J.-P. Flament, J. Chem. Phys. 107, 9105 (1997)], which is based on a static three charge sites and a single polarizable site to model the molecular electrostatic properties of water, and on an anisotropic short range many-body energy term specially designed to accurately model hydrogen bonding in water. The parameters of the revised model, denoted TCPE/2013, are here developed to reproduce the ab initio energetic and geometrical properties of small water clusters (up to hexamers) and the repulsive water interactions occurring in cation first hydration shells. The model parameters have also been refined to reproduce two liquid water properties at ambient conditions, the density and the vaporization enthalpy. Thanks to its computational efficiency, the new model range of applicability was validated by performing simulations of liquid water over a wide range of temperatures and pressures, as well as by investigating water liquid/vapor interfaces over a large range of temperatures. It is shown to reproduce several important water properties at an accurate enough level of precision, such as the existence liquid water density maxima up to a pressure of 1000 atm, the water boiling temperature, the properties of the water critical point (temperature, pressure, and density), and the existence of a “singularity” temperature at about 225 K in the supercooled regime. This model appears thus to be particularly well-suited for characterizing ion hydration properties under different temperature and pressure conditions, as well as in different phases and interfaces.
Interface investigation of the alcohol-/water-soluble conjugated polymer PFN as cathode interfacial layer in organic solar cells
Authors: Zhong Shu , Wang Rui , Ying Mao Hong , He Zhicai , Wu Hongbin , Chen Wei , Cao Yong
Published: September 2013

In this work, in situ ultraviolet photoelectron spectroscopy measurements were used to investigate the working mechanism of an alcohol-/water-soluble conjugated polymer poly [(9,9-bis(3′-(N,N-dimethylamino)propyl)-2,7-fluorene)-alt-2,7-(9,9–dioctylfluorene)] (PFN) as the cathode interfacial layer in organic solar cells from the view of interfacial energy level alignment. Fullerene (C60) was chosen as the model acceptor material in contact with PFN as well as two other cathode interfacial layers ZnO and TiO2 in the configuration of an inverted solar cell structure. Significant charge transfer between PFN modified ITO (indium tin oxide) electrode and C60 is observed due to the low work function of PFN. This results in the Fermi level of the substrate pinned very close to the lowest unoccupied molecular orbital of C60 as well as an additional electric field at the cathode/acceptor interface. Both of them facilitate the electron extraction from the acceptor C60 to the ITO cathode, as confirmed by the electrical measurements of the electron-only devices with PFN modification. The better electron extraction originated from the Fermi level pinning and the additional interface electric field are believed to contribute to the efficiency enhancement of the inverted organic solar cells employing PFN as cathode interfacial layer.
Tunable Schottky barrier height and surface potential by using hydrogen ions
Authors: Hsu J. K. , Lin T. Y. , Lai C. Y. , Chien T. C. , Song J. H. , Yeh P. H.
Published: September 2013

In this research work, hydrogen ion can be used for Schottky barrier height and surface potential tuning with specific power. The current output of Ohmic and Schottky contacted device would be enhanced from 8.25 μA to 171 μA and 2.84 pA to 1.3 μA (hydrogen plasma power was increased from 0 to 60 W), respectively. With adequate hydrogen plasma power, the transport mechanism (variation of Schottky barrier height and surface potential) can be studied in vacuum and atmosphere environment. In this work, we not only improve the current output but also provide the transport mechanism in vacuum and atmosphere environment. The enhancement and intension of ZnO nanowires device can be achieved by using hydrogen plasma treatment for extensive application.
Observation of a new cryogenic temperature dielectric relaxation in multiferroic Bi7Fe3Ti3O21
Authors: Patwe S. J. , Achary S. N. , Manjanna J. , Tyagi A. K. , Deshpande S. K. , Mishra S. K. , Krishna P. S. R. , Shinde A. B.
Published: September 2013

In this communication, we report details of structural, magnetic, and dielectric properties of multiferroic Bi7Fe3Ti3O21 at cryogenic temperatures. The low temperature impedance spectroscopic studies showed a relaxor-like dielectric anomaly which follows Vogel-Fulcher relation with freezing temperature (TVF) of 33 K. Temperature and field dependent magnetization indicate the onset of a possible antiferromagnetic ordering below 150 K. Variable temperature powder neutron diffraction studies indicate no structural change down to 22 K. The appearance of the low temperature dielectric anomaly along with evidence of magnetic ordering at low temperatures suggests the presence of magnetic domains of mesoscopic scale within the bulk matrix.
Phonon transmission and thermal conductance across graphene/Cu interface
Authors: Chen Liang , Huang Zhen , Kumar Satish
Published: September 2013

We investigate phonon transmission and thermal boundary conductance (TBC) across graphene/Cu interface using density functional theory and atomistic Green's function method. The analysis of phonon dispersions and density of states of single layer graphene (SLG) shows that even weak SLG/Cu interaction can soften the transverse optical and longitudinal optical modes and suppress low frequency out-of-plane acoustic (ZA) modes. Our calculations predict that a small stretching of the SLG lattice (∼1.6%) significantly enhances the SLG/Cu interaction which is reflected in larger band-gap for ZA/ZO phonon mode and a remarkable increase in TBC (∼59%).
Mechanical double loop behavior in BaTiO3: Stress induced paraelastic to ferroelastic phase transformation
Authors: Daniels John E. , Picht Gunnar , Kimber Simon , Webber Kyle G.
Published: September 2013

The structural origin of the mechanical double loop behavior of polycrystalline BaTiO3 at temperatures just above the Curie point has been investigated using in situ high-energy synchrotron x-ray diffraction during uniaxial compressive mechanical loading. The results show a stress-induced transition from the high temperature paraelastic cubic phase to a ferroelastic tetragonal phase with a domain texture close to the saturated state. The nature of the observed stress-induced phase transition was influenced by the proximity of the temperature to the Curie point. With increasing temperature above the Curie point, the transition stress increased while the rate of the transition decreased.
Plasma density measurements using chirped pulse broad-band Raman amplification
Authors: Vieux G. , Ersfeld B. , Farmer J. P. , Hur M. S. , Issac R. C. , Jaroszynski D. A.
Published: September 2013

Stimulated Raman backscattering is used as a non-destructive method to determine the density of plasma media at localized positions in space and time. By colliding two counter-propagating, ultra-short laser pulses with a spectral bandwidth larger than twice the plasma frequency, amplification occurs at the Stokes wavelengths, which results in regions of gain and loss separated by twice the plasma frequency, from which the plasma density can be deduced. By varying the relative delay between the laser pulses, and therefore the position and timing of the interaction, the spatio-temporal distribution of the plasma density can be mapped out.
Simulation study of wakefield generation by two color laser pulses propagating in homogeneous plasma
Authors: Kumar Mishra Rohit , Saroch Akanksha , Jha Pallavi
Published: September 2013

This paper deals with a two-dimensional simulation of electric wakefields generated by two color laser pulses propagating in homogeneous plasma, using VORPAL simulation code. The laser pulses are assumed to have a frequency difference equal to the plasma frequency. Simulation studies are performed for two similarly as well as oppositely polarized laser pulses and the respective amplitudes of the generated longitudinal wakefields for the two cases are compared. Enhancement of wake amplitude for the latter case is reported. This simulation study validates the analytical results presented by Jha et al. [Phys. Plasmas 20, 053102 (2013)].
Wheat genotypes with high early vigour accumulate more nitrogen and have higher photosynthetic nitrogen use efficiency during early growth
Authors: Pang Jiayin , Palta Jairo A. , Rebetzke Gregory J. , Milroy Stephen P.
Published: September 2013

Genotypic differences in early growth and nitrogen (N) uptake among 24 wheat (Triticum aestivum L.) genotypes were assessed in a field trial. At late tillering, large genetic variation was observed for shoot biomass (23–56 g m–2 ground area) and N uptake (1.1–1.8 g m–2 ground area). A strong correlation between aboveground biomass and N uptake was observed. Variation around this relationship was also found, with some genotypes having similar N uptake but large differences in aboveground biomass. A controlled environment experiment was conducted to investigate the underlying mechanisms for this variation in aboveground biomass using three vigorous genotypes (38–19, 92–11 and CV97) and a non-vigorous commercial cultivar (Janz). Vigorous genotypes had lower specific leaf N in the youngest fully expanded leaf than Janz. However, there was no difference in chlorophyll content, maximum Rubisco activity or the rate of electron transport per unit area. This suggests that Janz invested more N in non-photosynthetic components than the vigorous lines, which could explain the higher photosynthetic N use efficiency of the vigorous genotypes. The results suggest that the utilisation of wheat genotypes with high early vigour could improve the efficiency of N use for biomass production in addition to improving N uptake during early growth.
Phosphorus dynamics in sediments of a eutrophic lake derived from 31P nuclear magnetic resonance spectroscopy
Authors: Özkundakci Deniz , Hamilton David P. , McDowell Richard , Hill Stefan
Published: September 2013

The determination of organic phosphorus (P) compounds in lake sediments can provide information on the potential for internal P loading. Settling seston and vertical sediment core samples from highly eutrophic Lake Okaro, New Zealand, were collected during a mixed winter and stratified summer period, representing, respectively, when the water column was well oxygenated and when the bottom waters were anoxic. Samples were analysed with 31P nuclear magnetic resonance (31P NMR) spectroscopy, which showed that both bottom sediments and settling seston contained orthophosphate, orthophosphate monoesters and diesters, pyrophosphates, polyphosphates and phosphonates. Phosphorus concentration in settling seston increased ~2.5-fold in winter as a result of seasonally induced changes in phytoplankton biomass, with a marked increase in the concentration of orthophosphate. Several potentially bioavailable P compounds in the bottom sediments were identified that were likely to contribute to recycling of P from the sediment to the water column. An ‘apparent half-life’ was used to quantify the time scales on which these compounds were recycled to the overlying water column. Orthophosphate monoesters that include inositol phosphates were the most persistent P compound. On the basis of half-lives, high internal P loadings may persist for more than 20 years, potentially hindering restoration efforts in Lake Okaro.
LAPS-FSH: a new and effective long-acting follicle-stimulating hormone analogue for the treatment of infertility
Authors: Jung Sunyoung , Park Youngjin , Kim YoungHoon , Kim Yu Yon , Choi Hyun-Ji , Son Woo-Chan , Kwon SeChang
Published: September 2013

Although several long-acting follicle-stimulating hormone (FSH) therapies have been developed to enhance the ovarian response, a disadvantage of FSH therapy is its relatively short half-life, which requires women to receive one to two injections per day for almost 2 weeks. In the present study, we developed a novel FSH analogue by conjugating recombinant human FSH (rhFSH) and the constant region of the human immunoglobulin G4 fragment via non-peptidyl linkers. The efficacy of the FSH analogue was evaluated in vitro by cAMP level assessments, pharmacokinetic studies and a determination of ovarian weight and by comparing these findings with the results from other FSH analogues. In addition, the total number of antral and Graafian follicles was determined after 7 days of treatment with control, 6 µg kg–1 follitropin β, 6, 12 or 42 µg kg–1 corifollitropin α or 3, 6 or 12 µg kg–1 long acting protein/peptide discovery-follicle-stimulating hormone (LAPS-FSH). As a result, the animals treated with 12 µg kg–1 LAPS-FSH produced additional and larger healthy follicles. These data demonstrate that LAPS-FSH promotes growth and inhibits atresia of the ovarian follicle compared with other available drugs, suggesting that our new drug enhances the efficacy and duration of treatment. It is expected that our new FSH analogue will result in a higher chance of pregnancy in patients who are unresponsive to other drugs.
Targeted delivery of proapoptotic peptides to tumor-associated macrophages improves survival
Authors: Cieslewicz Maryelise , Tang Jingjing , Yu Jonathan L. , Cao Hua , Zavaljevski Maja , Motoyama Koka , Lieber Andre , Raines Elaine W. , Pun Suzie H.
Published: September 2013

Significance

Tumor-associated macrophages (TAMs) are cells of our innate immune system that have been associated with poor prognosis in many types of cancers. When polarized toward the anti-inflammatory state, TAMs promote immune evasion and angiogenesis, thereby driving tumor growth. Using a peptide library selection strategy, we identified a sequence, called M2pep, that preferentially binds to anti-inflammatory murine macrophages. We then used M2pep to carry a proapoptotic peptide to TAMs by i.v. delivery and demonstrated that selective reduction of TAMs resulted in improved survival in tumor-bearing mice. These results suggest that a molecular-targeting approach for TAM depletion is a promising adjunct strategy to add to the arsenal of anticancer therapies.
Cell motility and drug gradients in the emergence of resistance to chemotherapy
Authors: Wu Amy , Loutherback Kevin , Lambert Guillaume , Estévez-Salmerón Luis , Tlsty Thea D. , Austin Robert H. , Sturm James C.
Published: September 2013

Significance

Ultimately, chemotherapy often fails because of the emergence of cancer cells resistant to the chemotherapy. We show that this emergence can be driven by the presence of chemotherapy drug gradients and motility of the cancer cells within the gradient.
Constrained optimization framework for joint inversion of geophysical data sets
Authors: Sosa A. , Velasco A. A. , Velazquez L. , Argaez M. , Romero R.
Published: September 2013

Many experimental techniques in geophysics advance the understanding of Earth processes by estimating and interpreting Earth structure (e.g. velocity and/or density structure). Different types of geophysical data can be collected and analysed separately, sometimes resulting in inconsistent models of the Earth depending on the data used. We present a constrained optimization approach for a joint inversion least-squares (LSQ) algorithm to characterize 1-D Earth's structure. We use two geophysical data sets sensitive to shear velocities: receiver function and surface wave dispersion velocity observations. We study the use of bound constraints on the regularized inverse problem, which are more physical than the regularization parameters required by conventional unconstrained formulations. Specifically, we develop a constrained optimization formulation that is solved with a primal-dual interior-point (PDIP) method, and validate our results with a traditional, unconstrained formulation that is solved with a truncated singular value decomposition (TSVD) for a set of numerical experiments with synthetic crustal velocity models. We conclude that the PDIP results are as accurate as those from the regularized TSVD approach, are less affected by noise, and honour the geophysical constraints.
Weighing the Local Group in the presence of dark energy
Authors: Partridge C. , Lahav O. , Hoffman Y.
Published: September 2013

We revise the mass estimate of the Local Group (LG) when dark energy (in the form of the cosmological constant) is incorporated into the timing argument (TA) mass estimator for the LG. Assuming the age of the Universe and the cosmological constant according to the recent values from the Planck cosmic microwave background experiment, we find the mass of the LG to be MTAΛ = (4.73 ± 1.03) × 1012 M⊙ which is 13 per cent higher than the classical TA mass estimate. This partly explains the discrepancy between earlier results from Lambda cold dark matter simulations and the classical TA. When a similar analysis is performed on 16 LG-like galaxy pairs from the Constrained Local Universe Simulations, we find that the scatter in the ratio of the virial to the TA estimated mass is given by Mvir/MTAΛ = 1.04 ± 0.16. Applying it to the LG mass estimation we find a calibrated Mvir = (4.92 ± 1.08(obs.) ± 0.79(sys.)) × 1012 M⊙.
Sodium Reduction in Bread Using Low‐Sodium Sea Salt
Authors: Miller Rebecca A. , Jeong Juhui
Published: September 2013

Yeast bread is a major contributor of sodium in the American diet. Because of its functional impact on dough rheology and the quality of the final baked product, simply reducing the level of sodium chloride (salt) in the formula or replacing it with salt substitutes has found minimal success. The objective of this study was to determine the effect of sea salt containing 57 or 64% less sodium than common sea salt on the breadmaking properties and consumer acceptability of bread. The sodium content of the salt had no effect on dough strength, mixing time, gas production, loaf volume, or crumb grain. The flavor and overall liking of breads containing sea salt with 57 and 64% less sodium content were scored only slightly lower than bread containing the control salt by an untrained panel of 118 consumers. No difference in texture and no unacceptable flavor notes in the bread made with reduced‐sodium salts were reported. Thus, it appears that use of reduced‐sodium sea salt is a satisfactory alternative to reduce the sodium content of bread.
Control of Fusarium Wilt of Watermelon by Grafting onto Bottlegourd or Interspecific Hybrid Squash Despite Colonization of Rootstocks by Fusarium
Authors: Keinath A. P. , Hassell R. L.
Published: September 2013

Grafting watermelon (Citrullus lanatus var. lanatus) onto rootstocks of interspecific hybrid squash (Cucurbita moschata × C. maxima), bottle gourd (Lagenaria siceraria), or citron (Citrullus lanatus var. citroides) has been used in Asia and Israel to mange Fusarium wilt of watermelon caused by Fusarium oxysporum f. sp. niveum. The objectives of this study were to determine the frequency of infection of six rootstocks by F. oxysporum f. sp. niveum races 1 and 2 and the field performance of grafted rootstocks in Charleston, SC. Grafted and nongrafted watermelon and rootstock plants were inoculated in the greenhouse with race 1, race 2, or water (the control treatment). With both races, the frequency of recovery of F. oxysporum from scion and rootstock portions of inoculated watermelon plants grafted onto ‘Ojakkyo’ citron was greater than from watermelon plants grafted onto ‘Shintosa Camel’ and ‘Strong Tosa’ interspecific hybrid squash, and from plants grafted onto ‘Emphasis’, ‘Macis’, and ‘WMXP 3945’ bottlegourd. For nongrafted plants inoculated with race 1, percent recovery also was greater from Ojakkyo than from interspecific hybrid squash and bottlegourd. For nongrafted plants inoculated with race 2, F. oxysporum was recovered from the base of ≥79% of all inoculated plants. More than two-thirds (15) of 21 isolates recovered from the tops or scions of inoculated plants were pathogenic on watermelon. In spring 2010 and 2011, the six rootstocks were grafted with seedless watermelon ‘Tri-X 313’, which is susceptible to both races, and transplanted in a field infested with races 1 and 2 of F. oxysporum f. sp. niveum. Disease incidence for nongrafted and self-grafted Tri-X 313 (the control treatments) and Tri-X 313 grafted onto Ojakkyo citron did not differ significantly. Grafted watermelon plants produced greater weights and numbers of fruit than plants of the two control treatments. Nonpathogenic isolates of F. oxysporum and isolates of F. oxysporum f. sp. niveum colonized interspecific hybrid squash, bottlegourd, and grafted watermelon. The rootstocks evaluated, however, restricted movement of F. oxysporum f. sp. niveum into the watermelon scion, suppressed wilt symptoms, and increased fruit yields in an infested field.
Differential Susceptibility of Nine Cucurbit Species to the Foliar Blight and Crown Canker Phases of Gummy Stem Blight
Authors: Keinath Anthony P.
Published: September 2013

Eighteen cucurbit cultivars representing five genera, nine species, and 17 horticultural types were inoculated with Didymella bryoniae in field plots in Charleston, SC, in autumn 2008, autumn 2009, and spring 2011 to determine susceptibility to gummy stem blight. In each year, gummy stem blight cankers occurred more frequently on crowns or main stems of ‘Athena’ muskmelon (Cucumis melo) and ‘Green Striped Cushaw’ squash (Cucurbita argyrosperma) than on all other cultivars except ‘Rocio’ honeydew (Cucumis melo) in 2009, and bottle gourd (Lagenaria siceraria) and Ojakkyo citron (Citrullus lanatus var. citroides) in 2011. Cucurbita moschata was highly resistant to stem cankers. Severity of gummy stem blight on foliage was moderate to severe in autumn 2009, mild to severe in autumn 2008, and very mild in spring 2011 (due to unusually dry weather). Watermelon (Citrullus lanatus var. lanatus) and melon were the most susceptible to foliar blight in 2008 and 2009. In all 3 years, ‘Cheese’ and ‘Bugle’ squash (both Cucurbita moschata), and ‘Judgment III’ and ‘Lioness’ summer squash (C. pepo) were among the cultivars with the least diseased leaf area. C. moschata, C. pepo, C. maxima, and Luffa cylindrica (smooth loofah) were significantly less susceptible to foliar blight than Cucumis melo and three Citrullus lanatus cultivars in 2008 and 2009. This study also is the first documentation of susceptibility of Cucurbita argyrosperma to gummy stem blight.
Infection Caused by Phaeomoniella chlamydospora Associated with Esca-like Symptoms in Grapevine in Chile
Authors: Díaz Gonzalo A. , Latorre Bernardo A.
Published: September 2013

Trunk diseases such as esca have been recognized as an economically important problem of grapevine worldwide. A study was conducted to characterize the distribution of Phaeomoniella chlamydospora in Chile. A field survey of young and mature grapevines from 67 vineyards located along a 1,315-km north-south axis demonstrated that P. chlamydospora was present in 94.9% of the grapevine samples showing the black-wood streaking symptom (BWS) but not the characteristic foliar symptoms of esca. Phylogenetic analysis of the ribosomal DNA internal transcribed spacer (ITS) combined with β-tubulin (BT) genes grouped Chilean isolates together with reference isolates from South Africa and the United States, whereas Spanish isolates were clustered separately. Chilean isolates differed by only 2 to 3 bp for BT and ITS, respectively. Conidia germinated at 5 to 35°C, with an optimal temperature of 25 to 30°C. Isolates were pathogenic, and Koch's postulates were fulfilled in separate sets of inoculations of axenic plantlets, cuttings, 2-year-old plants, spurs, and shoots of V. vinifera. This study showed that P. chlamydospora was associated consistently with BWS and no other apparent symptom in young and mature grapevines, including nursery plants, in Chile. Inoculum was absent from the soil, grapevine pruning debris, sap samples, and herbaceous weeds, which is in contrast to past studies. At this time, Vitis spp. are the only known hosts of P. chlamydospora in Chile.
Systemic Resistance to Gray Mold Induced in Tomato by Benzothiadiazole and Trichoderma harzianum T39
Authors: Harel Yael Meller , Mehari Zeraye Haile , Rav-David Dalia , Elad Yigal
Published: September 2013

Gray mold (Botrytis cinerea) is an important disease of tomato (Solanum lycopersicum). This study examined defense-related gene expression involved in the resistance to B. cinerea that is induced in tomato plants by benzothiadiazole and Trichoderma harzianum T39 soil drench. In whole plants, transcriptional changes related to salicylic acid and ethylene were induced by the application of a 0.01% benzothiadiazole solution, whereas changes related to jasmonic acid were induced by the application of a 0.4% T39 suspension. On detached leaves, soil treatment by T39 led to enhanced resistance to B. cinerea infection that was proportional to the concentration of the T39 suspension. By 5 days after pathogen inoculation, the plants that had received the 0.04% T39 drench exhibited 62% less severe disease than the untreated plants. The 0.4% T39 drench led to an 84% reduction in disease severity. Observations of B. cinerea infection in leaves harvested from plants grown in the treated soils revealed that drenching with a T39 suspension induces systemic resistance against B. cinerea and primes salicylic acid- and ethylene-related gene expression in a manner proportional to the concentration of the biocontrol agent. Benzothiadiazole treatment induced resistance to gray mold independently of salicylic acid and led to strong priming of two genes known to be involved in defense against B. cinerea, Pti5 and PI2.
Southern rice black-streaked dwarf virus Alters Insect Vectors' Host Orientation Preferences to Enhance Spread and Increase Rice ragged stunt virus Co-Infection
Authors: Wang Han , Xu Donglin , Pu Lingling , Zhou Guohui
Published: September 2013

In recent years, Southern rice black-streaked dwarf virus (SRBSDV), a tentative species in the genus Fijivirus (family Reoviridae), has spread rapidly and caused serious rice losses in eastern and southeastern Asia. With this virus spread, Rice ragged stunt virus (RRSV, genus Oryzavirus, family Reoviridae) became more common in southern China, usually in co-infection with the former. SRBSDV and RRSV are transmitted by two different species of planthoppers, white-backed planthopper (WBPH, Sogatella furcifera) and brown planthopper (BPH, Nilaparvata lugens), respectively, in a persistent, circulative, propagative manner. In this study, using a Y-shape olfactometer-based device, we tested the host preference of three types of macropterous WBPH adults for healthy or SRBSDV-infected rice plants. The results showed that virus-free WBPHs significantly preferred infected rice plants to healthy plants, whereas both the viruliferous and nonviruliferous WBPHs preferred healthy plants to infected plants. In additional tests, we found that the BPHs significantly preferred healthy plants when they were virus free, whereas RRSV-carrying BPHs preferred SRBSDV-infected rice plants. From these findings, we propose that plant viruses may alter host selection preference of vectors to enhance their spread and that of insects vectoring another virus to result in co-infection with more than one virus.
Warmer ambient temperatures depress liver function in a mammalian herbivore
Authors: Kurnath Patrice , Dearing M. Denise
Published: September 2013

Diet selection in mammalian herbivores is thought to be mainly influenced by intrinsic factors such as nutrients and plant secondary compounds, yet extrinsic factors like ambient temperature may also play a role. In particular, warmer ambient temperatures could enhance the toxicity of plant defence compounds through decreased liver metabolism of herbivores. Temperature-dependent toxicity has been documented in pharmacology and agriculture science but not in wild mammalian herbivores. Here, we investigated how ambient temperature affects liver metabolism in the desert woodrat,Neotoma lepida. Woodrats (n= 21) were acclimated for 30 days to two ambient temperatures (cool = 21°C, warm = 29°C). In a second experiment, the temperature exposure was reduced to 3.5 h. After temperature treatments, animals were given a hypnotic agent and clearance time of the agent was estimated from the duration of the hypnotic state. The average clearance time of the agent in the long acclimation experiment was 45% longer for animals acclimated to 29°C compared with 21°C. Similarly, after the short exposure experiment, woodrats at 29°C had clearance times 26% longer compared with 21°C. Our results are consistent with the hypothesis that liver function is reduced at warmer environmental temperatures and may provide a physiological mechanism through which climate change affects herbivorous mammals.
The role of ECL2 in CGRP receptor activation: a combined modelling and experimental approach
Authors: Woolley Michael. J. , Watkins Harriet A. , Taddese Bruck , Karakullukcu Z. Gamze , Barwell James , Smith Kevin J. , Hay Debbie L. , Poyner David R. , Reynolds Christopher A. , Conner Alex C.
Published: September 2013

The calcitonin gene-related peptide (CGRP) receptor is a complex of a calcitonin receptor-like receptor (CLR), which is a family B G-protein-coupled receptor (GPCR) and receptor activity modifying protein 1. The role of the second extracellular loop (ECL2) of CLR in binding CGRP and coupling to Gs was investigated using a combination of mutagenesis and modelling. An alanine scan of residues 271–294 of CLR showed that the ability of CGRP to produce cAMP was impaired by point mutations at 13 residues; most of these also impaired the response to adrenomedullin (AM). These data were used to select probable ECL2-modelled conformations that are involved in agonist binding, allowing the identification of the likely contacts between the peptide and receptor. The implications of the most likely structures for receptor activation are discussed.
Modelling and inference reveal nonlinear length-dependent suppression of somatic instability for small disease associated alleles in myotonic dystrophy type 1 and Huntington disease
Authors: Higham Catherine F. , Monckton Darren G.
Published: September 2013

More than 20 human genetic diseases are associated with inheriting an unstable expanded DNA simple sequence tandem repeat, for example, CTG (cytosine–thymine–guanine) repeats in myotonic dystrophy type 1 (DM1) and CAG (cytosine–adenine–guanine) repeats in Huntington disease (HD). These sequences mutate by changing the number of repeats not just between generations, but also during the lifetime of affected individuals. Levels of somatic instability contribute to disease onset and progression but as changes are tissue-specific, age- and repeat length-dependent, interpretation of the level of somatic instability in an individual is confounded by these considerations. Mathematical models, fitted to CTG repeat length distributions derived from blood DNA, from a large cohort of DM1-affected or at risk individuals, have recently been used to quantify inherited repeat lengths and mutation rates. Taking into account age, the estimated mutation rates are lower than predicted among individuals with small alleles (inherited repeat lengths less than 100 CTGs), suggesting that these rates may be suppressed at the lower end of the disease-causing range. In this study, we propose that a length-specific effect operates within this range and tested this hypothesis using a model comparison approach. To calibrate the extended model, we used data derived from blood DNA from DM1 individuals and, for the first time, buccal DNA from HD individuals. In a novel application of this extended model, we identified individuals whose effective repeat length, with regards to somatic instability, is less than their actual repeat length. A plausible explanation for this distinction is that the expanded repeat tract is compromised by interruptions or other unusual features. We quantified effective length for a large cohort of DM1 individuals and showed that effective length better predicts age of onset than inherited repeat length, thus improving the genotype–phenotype correlation. Under the extended model, we removed some of the bias in mutation rates making them less length-dependent. Consequently, rates adjusted in this way will be better suited as quantitative traits to investigate
cis-
or
trans
-acting modifiers of somatic mosaicism, disease onset and progression.
Contact inhibition of locomotion probabilities drive solitary versus collective cell migration
Authors: Desai Ravi A. , Gopal Smitha B. , Chen Sophia , Chen Christopher S.
Published: September 2013

Contact inhibition of locomotion (CIL) is the process whereby cells collide, cease migrating in the direction of the collision, and repolarize their migration machinery away from the collision. Quantitative analysis of CIL has remained elusive because cell-to-cell collisions are infrequent in traditional cell culture. Moreover, whereas CIL predicts mutual cell repulsion and ‘scattering’ of cells, the same cellsin vivoare observed to undergo CIL at some developmental times and collective cell migration at others. It remains unclear whether CIL is simply absent during collective cell migration, or if the two processes coexist and are perhaps even related. Here, we used micropatterned stripes of extracellular matrix to restrict cell migration to linear paths such that cells polarized in one of two directions and collisions between cells occurred frequently and consistently, permitting quantitative and unbiased analysis of CIL. Observing repolarization events in different contexts, including head-to-head collision, head-to-tail collision, collision with an inert barrier, or no collision, and describing polarization as a two-state transition indicated that CIL occurs probabilistically, and most strongly upon head-to-head collisions. In addition to strong CIL, we also observed ‘trains’ of cells moving collectively with high persistence that appeared to emerge from single cells. To reconcile these seemingly conflicting observations of CIL and collective cell migration, we constructed an agent-based model to simulate our experiments. Our model quantitatively predicted the emergence of collective migration, and demonstrated the sensitivity of such emergence to the probability of CIL. Thus CIL and collective migration can coexist, and in fact a shift in CIL probabilities may underlie transitions between solitary cell migration and collective cell migration. Taken together, our data demonstrate the emergence of persistently polarized, collective cell movement arising from CIL between colliding cells.
The relationship between modularity and robustness in signalling networks
Authors: Tran Tien-Dzung , Kwon Yung-Keun
Published: September 2013

Many biological networks tend to have a high modularity structural property and the dynamic characteristic of high robustness against perturbations. However, the relationship between modularity and robustness is not well understood. To investigate this relationship, we examined real signalling networks and conducted simulations using a random Boolean network model. As a result, we first observed that the network robustness is negatively correlated with the network modularity. In particular, this negative correlation becomes more apparent as the network density becomes sparser. Even more interesting is that, the negative relationship between the network robustness and the network modularity occurs mainly because nodes in the same module with the perturbed node tend to be more sensitive to the perturbation than those in other modules. This result implies that dynamically similar nodes tend to be located in the same module of a network. To support this, we show that a pair of genes associated with the same disease or a pair of functionally similar genes is likely to belong to the same module in a human signalling network.
Complex environmental drivers of immunity and resistance in malaria mosquitoes
Authors: Murdock Courtney C. , Moller-Jacobs Lillian L. , Thomas Matthew B.
Published: September 2013

Considerable research effort has been directed at understanding the genetic and molecular basis of mosquito innate immune mechanisms. Whether environmental factors interact with these mechanisms to shape overall resistance remains largely unexplored. Here, we examine how changes in mean ambient temperature, diurnal temperature fluctuation and time of day of infection affected the immunity and resistance of
Anopheles stephensi
to infection with
Escherichia coli
. We used quantitative PCR to estimate the gene expression of three immune genes in response to challenge with heat-killed
E. coli
. We also infected mosquitoes with live
E. coli
and ran bacterial growth assays to quantify host resistance. Both mosquito immune parameters and resistance were directly affected by mean temperature, diurnal temperature fluctuation and time of day of infection. Furthermore, there was a suite of complex two- and three-way interactions yielding idiosyncratic phenotypic variation under different environmental conditions. The results demonstrate mosquito immunity and resistance to be strongly influenced by a complex interplay of environmental variables, challenging the interpretation of the very many mosquito immune studies conducted under standard laboratory conditions.
Role of the line probe assay INNO-LiPA HBV DR and ultradeep pyrosequencing in detecting resistance mutations to nucleoside/nucleotide analogues in viral samples isolated from chronic hepatitis B patients
Authors: Mese Sevim , Arikan Muzaffer , Cakiris Aris , Abaci Neslihan , Gumus Ergun , Kursun Olcay , Onel Derya , Ustek Duran , Kaymakoglu Sabahattin , Badur Selim , Yenen Osman Sadi , Bozkaya Emel
Published: September 2013

Despite the effectiveness of nucleoside/nucleotide analogues in the treatment of chronic hepatitis B (CHB), their long-term administration is associated with the emergence of resistant hepatitis B virus (HBV) mutants. In this study, mutations resulting in antiviral resistance in HBV DNA samples isolated from 23 CHB patients (nine treatment naïve and 14 treated previously) were studied using a line probe assay (INNO-LiPA HBV DR; Innogenetics) and ultradeep pyrosequencing (UDPS) methods. Whilst the INNO-LiPA HBV DR showed no resistance mutations in HBV DNA samples from treatment-naive patients, mutations mediating lamivudine resistance were detected in three samples by UDPS. Among patients who were treated previously, 19 mutations were detected in eight samples using the INNO-LiPA HBV DR and 29 mutations were detected in 12 samples using UDPS. All mutations detected by the INNO-LiPA HBV DR were also detected by UDPS. There were no mutations that could be detected by INNO-LiPA HBV DR but not by UDPS. A total of ten mutations were detected by UDPS but not by INNO-LiPA HBV DR, and the mean frequency of these mutations was 14.7 %. It was concluded that, although INNO-LiPA HBV DR is a sensitive and practical method commonly used for the detection of resistance mutations in HBV infection, UDPS may significantly increase the detection rate of genotypic resistance in HBV at an early stage.
Perturbation of biogenesis and targeting of Epstein–Barr virus-encoded miR-BART3 microRNA by adenosine-to-inosine editing
Authors: Lei Ting , Yuen Kit-San , Tsao Sai Wah , Chen Honglin , Kok Kin-Hang , Jin Dong-Yan
Published: September 2013

Epstein–Barr virus (EBV) encodes at least 44 mature microRNAs (miRNAs), some of which are abundantly expressed in nasopharyngeal carcinoma cells. EBV-encoded miR-BART6 miRNA is known to undergo adenosine-to-inosine (A-to-I) RNA editing, which impacts on processing and function. Whether additional EBV miRNAs might be A-to-I edited remains to be determined. In this study, we have reported on A-to-I editing of EBV miR-BART3. The A-to-I editing enzyme was expressed abundantly in EBV-infected epithelial carcinoma cells. pri-miR-BART3 was found to be edited at four sites in these cells and in nasopharyngeal carcinoma samples. Whereas editing of the second site located within the seed region prevented the targeting of DICE1 mRNA, editing of the third site effectively crippled the biogenesis of mature miR-BART3. Thus, A-to-I editing perturbs biogenesis and targeting of miR-BART3 and may contribute to its differential expression and function in EBV-infected epithelial cells.
Histone H3 lysine methylation in cognition and intellectual disability disorders
Authors: Parkel Sven , Lopez-Atalaya Jose P. , Barco Angel
Published: September 2013

Recent research indicates that epigenetic mechanisms and, in particular, the post-translational modification (PTM) of histones may contribute to memory encoding and storage. Among the dozens of possible histone PTMs, the methylation/demethylation of lysines in the N-terminal tail of histone H3 exhibits particularly strong links with cognitive abilities. First, the persistence and tight association with distinct transcriptional states of the gene make these modifications particularly suitable for being part of the molecular underpinnings of memory storage. Second, correlative evidence indicates that the methylation/demethylation of lysines in histone H3 is actively regulated during memory processes. Third, several enzymes regulating these PTMs are associated with intellectual disability disorders. We review here these three lines of evidence and discuss the potential role of epigenetic mechanisms centered on the methylation of lysine residues on histone H3 in neuroplasticity and neurodevelopmental disorders associated with intellectual disability.
Using a Systematic Approach to Select Flagship Species for Bird Conservation
Authors: VERÍSSIMO DIOGO , PONGILUPPI TATIANA , SANTOS MARIA CINTIA M. , DEVELEY PEDRO F. , FRASER IAIN , SMITH ROBERT J. , MACMILAN DOUGLAS C.
Published: September 2013

Conservation marketing campaigns that focus on flagship species play a vital role in biological diversity conservation because they raise funds and change people's behavior. However, most flagship species are selected without considering the target audience of the campaign, which can hamper the campaign's effectiveness. To address this problem, we used a systematic and stakeholder‐driven approach to select flagship species for a conservation campaign in the Serra do Urubu in northeastern Brazil. We based our techniques on environmental economic and marketing methods. We used choice experiments to examine the species attributes that drive preference and latent‐class models to segment respondents into groups by preferences and socioeconomic characteristics. We used respondent preferences and information on bird species inhabiting the Serra do Urubu to calculate a flagship species suitability score. We also asked respondents to indicate their favorite species from a set list to enable comparison between methods. The species’ traits that drove audience preference were geographic distribution, population size, visibility, attractiveness, and survival in captivity. However, the importance of these factors differed among groups and groups differed in their views on whether species with small populations and the ability to survive in captivity should be prioritized. The popularity rankings of species differed between approaches, a result that was probably related to the different ways in which the 2 methods measured preference. Our new approach is a transparent and evidence‐based method that can be used to refine the way stakeholders are engaged in the design of conservation marketing campaigns.
Global Climate Change Justice: Toward a Risk‐Adjusted Social Floor
Authors: Siegel Paul B. , Jorgensen Steen L.
Published: September 2013

Addressing climate change from social justice and human rights perspectives is a global challenge, and international negotiations dealing with climate change need to incorporate such concerns. This paper reviews existing literature on sustainable development, social justice, human rights, and climate change justice and argues that all approaches lead to a focus on providing everyone a guaranteed social minimum of basic needs, or a social floor. A social floor needs to be dynamic and flexible so that it also includes a risk adjustment (or insurance) component to compensate for the unknown direct and indirect impacts of climate change on households, communities and nations. The proposed globally guaranteed, nationally designed and managed, and locally implemented risk‐adjusted social floor is a forward‐looking approach to climate change justice that focuses on creating resilient economic, social and environmental systems that are equitable and sustainable. The risk‐adjusted social floor is based on UN agreements that guarantee human rights and basic needs, and the security of basic needs. The risk‐adjusted social floor is consistent with principles of the UN Social Protection Floor Initiative and the proposed Global Fund for Social Protection. Implementation of a risk‐adjusted social floor could draw upon existing social protection practices around the world that deliver basic needs (e.g., conditional cash transfers, use of vouchers, fee waivers, feeding programs, micro‐insurance, productive safety nets), along with advances in the use of early warning and rapid response systems to target and deliver emergency assistance. There are also innovations in global insurance instruments and risk pooling methods. The risk‐adjusted social floor integrates key aspects of risk‐based and rights‐based approaches to social protection and poverty reduction.
Taxation and Development: What Have We Learned from Fifty Years of Research?
Authors: Bird Richard M.
Published: September 2013

This paper considers how economic thinking about taxation in developing countries has changed over the last half century. It suggests that three different ‘models’ of development taxation may be discerned over this period. The key element in the first model, which was derived from the dominant public finance literature in the 1950s and 1960s, was the introduction of a comprehensive progressive personal income tax. Experience proved that this approach was not very useful. Fortunately, increased knowledge of the reality of conditions in developing countries, combined with post‐1970 theoretical and empirical studies of taxation, soon led to the emergence of a second model for development taxation, centered on a broad‐based VAT and much lower rate income taxes, both personal and corporate. While there is still much to be said for this model, more recent investigations of the political and administrative as well as economic dimensions of tax systems in developing countries have led to the gradual emergence of a third ‘model’– or, perhaps better, framework – for development taxation. Unlike the earlier approaches, this approach focuses on the need to ‘custom build’ the different components of the tax system as well as the system as a whole and emphasizes the extent to which sustainable reforms must be developed ‘in house’ by countries themselves.