bluuebunny/crossref_metadata_2025 huggingface dataset:
Asteroseismology with SuperWASP
Authors: Smalley Barry
Published: February 2014

The highly successful SuperWASP planetary transit finding programme has surveyed a large fraction of both the northern and southern skies. There now exists in its archive over 420 billion photometric measurements for more than 31 million stars. SuperWASP provides good quality photometry with a precision exceeding 1% per observation in the approximate magnitude range 9 < V < 12. The archive enables long-baseline, high-cadence studies of stellar variability to be undertaken. An overview of the SuperWASP project is presented, along with results which demonstrate the survey's asteroseismic capabilities.
On the necessity of a new interpretation of the stellar light curves
Authors: Pascual-Granado J. , Garrido R. , Suárez J. C.
Published: February 2014

The power of asteroseismology relies on the ability to infer the stellar structure from the unambiguous frequency identification of the corresponding pulsation mode. Hence, the use of a Fourier transform is in the basis of asteroseismic studies. Nevertheless, the difficulties with the interpretation of the frequencies found in many stars lead us to reconsider whether Fourier analysis is the most appropriate technique to identify pulsation modes. We have found that the data, usually analyzed using Fourier techniques, present a non-analyticity originating from the lack of connectivity of the underlying function describing the physical phenomena. Therefore, the conditions for the Fourier series to converge are not fulfilled. In the light of these results, we examine in this talk some stellar light curves from different asteroseismology space missions (CoRoT, Kepler and SoHO) in which the interpretation of the data in terms of Fourier frequencies becomes difficult. We emphasize the necessity of a new interpretation of the stellar light curves in order to identify the correct frequencies of the pulsation modes.
Blazhko effect in Cepheids and RR Lyrae stars
Authors: Szabó Róbert
Published: February 2014

The Blazhko effect is the conspicuous amplitude and phase modulation of the pulsation of RR Lyrae stars that was discovered in the early 20th century. The field of study of this mysterious modulation has recently been invigorated thanks to the space photometric missions providing long, uninterrupted, ultra-precise time-series data. In this paper I give a brief overview of the new observational findings related to the Blazhko effect, such as extreme modulations, irregular modulation cycles and additional periodicities. I argue that these findings together with dedicated ground-based efforts provide us now with a fairly complete picture and a good starting point to theoretical investigations. Indeed, new, unpredicted dynamical phenomena have been discovered in Blazhko RR Lyrae stars, such as period doubling, high-order resonances, three-mode pulsation and low-dimensional chaos. These led to the proposal of a new explanation to this century-old enigma, namely a high-order resonance between radial modes. Along these lines I present the latest efforts and advances from the theoretical point of view. Lastly, amplitude variations in Cepheids are discussed.
Bisector analysis of RR Lyrae: atmosphere dynamics at different phases
Authors: Guggenberger Elisabeth , Shulyak Denis , Tsymbal Vadim , Kolenberg Katrien
Published: February 2014

This article reports some preliminary results on an analysis of line bisectors of metal absorption lines of RR Lyrae, the prototype of its class of pulsators. The extensive data set used for this study consists of a time series of spectra obtained at various pulsation phases as well as different Blazhko phases. This setup should allow a comparison of the atmospheric behaviour, especially of the function of radial velocity versus depth at differing Blazhko phases, but (almost) identical pulsation phase, making it possible to investigate whether the modulation causes a change in the atmospheric motion of RR Lyrae. While the nature of the Blazhko modulation has often been investigated photometrically and described as a change in the light curve, studies on time series of high resolution spectra are rare. We present for the first time work on line bisectors at different phases of RR Lyr.
Seismic studies of planet-harbouring stars
Authors: Vauclair Sylvie
Published: February 2014

During the past decades, stellar oscillations and exoplanet searches were developed in parallel, and the observations were done with the same instruments: radial velocity method, essentially with ground-based instruments, and photometric methods (light curves) from space. The same observational data on one star could lead to planet discoveries at large time scales (days to years) and to the detection of stellar oscillations at small time scales (minutes), such as for the star μ Arae. Since the beginning, it seemed interesting to investigate the differences between stars with and without observed planets. Also, a precise determination of the stellar parameters is important to characterize the detected exoplanets. With the thousands of exoplanet candidates discovered by Kepler, automatic procedures and pipelines are needed with large data bases to characterize the central stars. However, precise asteroseismic studies of well-chosen stars are still important for a deeper insight.
Concluding remarks
Authors: Christensen-Dalsgaard Jørgen , Kawaler Steven D.
Published: February 2014

We cannot presume to summarize all of the science we've discussed in the talks, posters, and informal discussions. Here, we discuss a few of the themes that emerged, concentrating on the theoretical basis that Wojtek Dziembowiski and his colleagues have developed and explored over the past 40+ years. We connect those with observational results – especially those from recent ground-based surveys and space-based missions that have revolutionized the study of stellar variability.
Analysis of γ Doradus and δ Scuti stars observed by Kepler
Authors: Bradley Paul A. , Guzik Joyce A. , Miles Lillian F. , Jackiewicz Jason , Uytterhoeven Katrien , Kinemuchi Karen
Published: February 2014

The Kepler spacecraft observed over 2000 faint stars that were part of our Guest Observer proposals. The stars were selected from the Kepler Input Catalog (KIC) to be in or near the γ Doradus or δ Scuti instability strips (8300 K > Teff > 6200 K and 3.6 < log g < 4.7). The Kepler magnitude was <16 and the contamination factor was < 10−2. The goal was to extend the search for “hybrid” δ Sct-γ Dor pulsators to fainter magnitudes. By inspecting the light curves and Fourier transforms, we find 42 δ Sct candidate stars, 299 γ Dor candidates, and 36 “hybrid” candidate stars showing both types of variations.
Pysca – Automated frequency extraction from photometric time series
Authors: Herzberg Wiebke , Glogowski Kolja
Published: February 2014

Pysca, a Python software package for automated extraction of frequencies, amplitudes and phases from non-equally sampled photometric time series, is presented.
Rapidly varying A-type stars in the SuperWASP archive
Authors: Holdsworth Daniel L. , Smalley Barry
Published: February 2014

The searches for transiting exoplanets have produced a vast amount of time-resolved photometric data of many millions of stars. One of the leading ground-based surveys is the SuperWASP project. We present the initial results of a survey of over 1.5 million A-type stars in the search for high frequency pulsations using SuperWASP photometry. We are able to detect pulsations down to the 0.5 mmag level in the broad-band photometry. This has enabled the discovery of several rapidly oscillating Ap stars and over 200 δ Scuti stars with frequencies above 50 d−1, and at least one pulsating sdB star. Such a large number of results allows us to statistically study the frequency overlap between roAp and δ Scuti stars and probe to higher frequency regimes with existing data.
Pulsation in extremely low-mass helium stars
Authors: Jeffery C. S. , Saio H.
Published: February 2014

We explore the stability of extremely low-mass stars (M < 0.25 M⊙) across a wide range of composition, effective temperature, and luminosity. We identify the instability boundaries associated with radial oscillations. These are a strong function of both composition and radial order (0 ≤ n ≤ 13). The classical blue edge shifts to higher effective temperature and luminosity with decreasing hydrogen abundance. Higher-order modes are more easily excited, and small islands of instability develop. Short-period oscillations have been discovered in the low-mass pre-white dwarf component of the eclipsing binary J0247–25. If its envelope is depleted in hydrogen, J0247–25B is unstable to intermediate-order p modes. Driving is by the classical κ mechanism operating in the second helium ionization zone. The observed periods, temperature and luminosity of J0247–25B require an envelope hydrogen abundance 0.2 ≤ X ≤ 0.3.
Photometry using Kepler “superstamps” of open clusters NGC 6791 & NGC 6819
Authors: Kuehn Charles A. , Drury Jason , Stello Dennis , Bedding Timothy R.
Published: February 2014

The Kepler space telescope has proven to be a gold mine for the study of variable stars. Unfortunately, Kepler only returns a handful of pixels surrounding each star on the target list, which omits a large number of stars in the Kepler field. For the open clusters NGC 6791 and NGC 6819, Kepler also reads out larger superstamps which contain complete images of the central region of each cluster. These cluster images can potentially be used to study additional stars in the open clusters. We present preliminary results from using traditional photometric techniques to identify and analyze additional variable stars from these images.
Asteroseismology of fast-rotating stars: the example of α Ophiuchi
Authors: Mirouh Giovanni M. , Reese Daniel R. , Lara Francisco Espinosa , Ballot Jérôme , Rieutord Michel
Published: February 2014

Many early-type stars have been measured with high angular velocities. In such stars, mode identification is difficult as the effects of fast and differential rotation are not well known. Using fundamental parameters measured by interferometry, the ESTER structure code and the TOP oscillation code, we investigate the oscillation spectrum of α Ophiuchi, for which observations by the MOST satellite found 57 oscillations frequencies. Results do not show a clear identification of the modes and highlight the difficulties of asteroseismology for such stars with a very complex oscillation spectrum.
New analysis of ZZ Ceti star PG 2303+243
Authors: Pakštienė E. , Laugalys V. , Qvam J. , Boyle R. P.
Published: February 2014

The new photometric observations of PG 2303+243 were obtained in 2012 during a campaign carried out with three telescopes. The analysis of these observations is presented in this paper. We identified l = 1 and l = 2 pulsation modes. The pulsation periods were compared with theoretical ones for models of ZZ Ceti stars. This allowed us to estimate the physical parameters of PG 2303+243. The star seems to be cooler and has thicker hydrogen layer than it was thought before. We have derived M*/M⊙ = 0.66, Teff = 11014 K and log(MH/M*)=−4.246 for this star.
Review of the ultrafast time resolution photopolarimeters based on SPADs
Authors: Słowikowska Aga , Kanbach Gottfried , Goździewski Krzysztof , Krzeszowski Krzysztof , Rau Arne
Published: February 2014

We review photopolarimeters that are based on the Single Photon Avalanche Diodes (SPADs) and were designed, built, developed, and extensively used for high time resolution studies of astrophysical sources. Examples of such detectors are OPTIMA, GASP, AquEYE, and IquEYE which can measure the time of arrival of single optical photons with an accuracy of down to 50 picoseconds. We describe the most exciting results obtained with the SPADs detectors starting from the best existing optical polarimetric measurements of the Crab pulsar, the discovery of the first optical magnetar and its quasi-periodic oscillations, as well as a verification of exoplanets around eclipsing cataclysmic variables. Additionally, we discuss possible applications of such detectors for asteroseismology.
Extensive spectroscopic and photometric study of HD 25558, a long orbital-period binary with two SPB components
Authors: Sódor Á. , De Cat P. , Wright D. J. , Neiner C. , Briquet M. , Dukes R. J. , Fekel F. C. , Henry G. W. , Williamson M. H. , Muterspaugh M. W. , Brunsden E. , Pollard K. R. , Cottrell P. L. , Maisonneuve F. , Kilmartin P. M. , Matthews J. M. , Kallinger T. , Beck P. G. , Kambe E. , Engelbrecht C. A. , Czanik R. J. , Yang S. , Hashimoto O. , Honda S. , Fu J.-N. , Castanheira B. , Lehmann H. , Behara N. , Van Winckel H. , Scaringi S. , Menu J. , Lobel A. , Lampens P. , Mathias P.
Published: February 2014

We carried out an extensive photometric and spectroscopic investigation of the SPB binary, HD 25558 (see Fig. 1 for the time and geographic distribution of the observations). The ~2000 spectra obtained at 13 observatories during 5 observing seasons, the ground-based multi-colour light curves and the photometric data from the MOST satellite revealed that this object is a double-lined spectroscopic binary with a very long orbital period of about 9 years. We determined the physical parameters of the components, and have found that both lie within the SPB instability strip. Accordingly, both components show line-profile variations consistent with stellar pulsations. Altogether, 11 independent frequencies and one harmonic frequency were identified in the data. The observational data do not allow the inference of a reliable orbital solution, thus, disentangling cannot be performed on the spectra. Since the lines of the two components are never completely separated, the analysis is very complicated. Nevertheless, pixel-by-pixel variability analysis of the cross-correlated line profiles was successful, and we were able to attribute all the frequencies to the primary or secondary component. Spectroscopic and photometric mode-identification was also performed for several of these frequencies of both binary components. The spectroscopic mode-identification results suggest that the inclination and rotation of the two components are rather different. While the primary is a slow rotator with ~6 d rotation period, seen at ~60° inclination, the secondary rotates fast with ~1.2 d rotation period, and is seen at ~20° inclination. Our spectropolarimetric measurements revealed that the secondary component has a magnetic field with at least a few hundred Gauss strength, while no magnetic field was detected in the primary.

The detailed analysis and results of this study will be published elsewhere.
Seismic investigation of the γ Dor star KIC 6462033: The first results of Kepler and ground-based follow up observations
Authors: Ulusoy C. , Ulaş B. , Damasso M. , Carbognani A. , Cenadelli D. , Stateva I. , Iliev I. Kh. , Dimitrov D.
Published: February 2014

Preliminary results on the analysis of the Kepler light curve and photometric ground-based time series of γ Dor star KIC 6462033 (TYC 3144-646-1, V = 10.83, P = 0.69686 d) are presented in order to determine pulsation frequencies.
Receding mechanism of NLO response of polyanion [M8O26]4− (M = Cr, Mo, W) and the closed loops theory analysis
Authors: Li Fujun , Hu Xiaojun , Sa Rongjian , Feng Jing
Published: February 2014

The second hyperpolarizability of six octa-poly-oxo anions [M8O26]4− (M = Cr, Mo, W) were studied by DFT/TDDFT method.
‘Turn-on’ coordination based detection of Pd2+and bioimaging applications
Authors: Kaur Paramjit , Kaur Navdeep , Kaur Mandeep , Dhuna Vikram , Singh Jatinder , Singh Kamaljit
Published: February 2014

A BODIPY based molecular probe recognises Pd2+via off–ontype fluorescence enhancement which could be correlated to the restricted PET on the basis of DFT/TD-DFT calculations.
Formal hydrogenation of arynes with silyl Cβ–H bonds as an active hydride source
Authors: Mamidipalli Phani , Yun Sang Young , Wang Kung-Pern , Zhou Tao , Xia Yuanzhi , Lee Daesung
Published: February 2014

In stark contrast to the effective 1°, 2°, and 3° C–H bond insertion of alkyl groups tethered to arynes, the 2° and 3° C–H bonds on the β-carbon of silyl groups show high tendency for hydride transfer rather than C–H insertion, whereas the corresponding 1° C–H bonds exclusively undergo C–H insertion.
Linear and nonlinear optical properties for AA and AB stacking of carbon nitride polymorph (C3N4)
Authors: Reshak A. H. , Khan Saleem Ayaz , Auluck S.
Published: February 2014

The linear and nonlinear optical susceptibilities of AA and AB stacking of the carbon nitride polymorph were calculated using the all electron full potential linear augmented plane wave method based on density functional theory.
Two-dimensional ferromagnetic iron crystals constrained by graphene edges: a first principles study
Authors: Wang Peng , Wang Hongtao , Yang Wei
Published: February 2014

Graphene edges, the thinnest and strongest support, may provide necessary constraint in preventing the collapse of two-dimensional (2D) crystals into 3D clusters, as studied by density functional theory (DFT).
Differential transmission lines with surface plasmon polaritons at low frequencies
Authors: Wu J.J. , Hou D.J. , Shen J.Q. , Chiueh H.L. , Yang T.J. , Wu C.‐J.
Published: February 2014

A new kind of differential microstrip lines by introducing periodic subwavelength corrugation in the edge, which is able to support low‐frequency spoof surface plasmon polaritions, is proposed. The surface current distribution of the subwavelength periodic corrugated microstrip is numerically analysed. A kind of differential to single‐ended microstrip coupling circuit is designed to investigate the ability of suppressing the crosstalk of such a subwavelength periodic corrugated differential pair. Experimental results show that such a structure can be utilised to effectively suppress crosstalk, and to reduce the transformation between differential‐mode and common‐mode signals.
Electrical addressing of polymer stabilized hyper-twisted chiral nematic liquid crystals with interdigitated electrodes: Experiment and model
Authors: Lorenz A. , Gardiner D. J. , Morris S. M. , Castles F. , Qasim M. M. , Choi S. S. , Kim W.-S. , Coles H. J. , Wilkinson T. D.
Published: February 2014

Electro-optic switching in short-pitch polymer stabilized chiral nematic liquid crystals was studied and the relative contributions of flexoelectric and dielectric coupling were investigated: polymer stabilization was found to effectively suppress unwanted textural transitions of the chiral nematic liquid crystal and thereby enhance the electro-optical performance (high optical contrast for visible light, a near ideal optical hysteresis, fast electro-optic response). Test cells were studied that possessed interdigitated electrodes to electrically address the liquid crystal. Based on simulations, a well-fitted phenomenological description of the electro-optic response was derived considering both flexoelectro-optic and Kerr-effect based electro-optic response.
Equilibrium Cu-Ag nanoalloy structure formation revealed by in situ scanning transmission electron microscopy heating experiments
Authors: Lu Ping , Chandross Michael , Boyle Timothy J. , Clark Blythe G. , Vianco Paul
Published: February 2014

Using in situ scanning transmission electron microscopy heating experiments, we observed the formation of a 3-dimensional (3D) epitaxial Cu-core and Ag-shell equilibrium structure of a Cu-Ag nanoalloy. The structure was formed during the thermal interaction of Cu(∼12 nm) and Ag NPs(∼6 nm) at elevated temperatures (150–300 °C) by the Ag NPs initially wetting the Cu NP along its {111} surfaces at one or multiple locations forming epitaxial Ag/Cu (111) interfaces, followed by Ag atoms diffusing along the Cu surface. This phenomenon was confirmed through Monte Carlo simulations to be a nanoscale effect related to the large surface-to-volume ratio of the NPs.
Season and reproductive status rather than genetic factors influence change in ewe weight and fat over time 2. Spline analysis of crossbred ewes
Authors: Walkom S. F. , Brien F. D. , Hebart M. L. , Fogarty N. M. , Hatcher S. , Pitchford W. S.
Published: February 2014

The success of slaughter lamb enterprises is heavily influenced by the ability of the breeding ewe to produce a lamb annually across variable environments. It has been shown that by maintaining heavier weight and condition across the annual production cycle producers can make significant improvements in maternal performance. This paper follows on from a previous analysis of crossbred ewes within the Maternal Central Progeny Test and examines the potential to select for reduced fluctuation in weight and fat across the production cycle. A cubic spline model was fitted to the weight and fat score data from the first three parities of 2688 first-cross ewes. The analysis partitioned the influence of environment, reproduction and genetic effects on the shape of the weight and fat score splines across three parities. Yearly and seasonal variation in feed supply and the demands of raising a lamb are the major influences on fluctuations in the weight and fat score of the breeding ewe. The genetic effects were constant across time with 98 and 92% of the genetic variation for weight and fat, respectively, associated with the spline’s intercept. In agreement with the findings of the first paper of the series it can be concluded that genetic lines do not re-rank for weight or fat score over time. The influence of sire breed on weight and fat score was constant across time with sire breeds fluctuating in parallel across time. As a result it is concluded that to avoid low fat reserves and the subsequent low fertility during the ‘tough’ periods, selection to improve ewe body condition could be made at any time and under any environmental conditions.
Oocyte expression, secretion and somatic cell interaction of mouse bone morphogenetic protein 15 during the peri-ovulatory period
Authors: Mester Brigitta , Ritter Lesley J. , Pitman Janet L. , Bibby Adrian H. , Gilchrist Robert B. , McNatty Kenneth P. , Juengel Jennifer L. , McIntosh C. Joy
Published: February 2014

Bone morphogenetic protein 15 (BMP15) is a key intraovarian growth factor regulating mammalian fertility, yet expression and localisation of different BMP15 protein forms within ovarian follicles around the time of the preovulatory LH surge remains unclear. Using immunoblotting and immunocytochemistry, the present study identified that post-translationally processed BMP15 proregion and mature proteins are increasingly expressed and localised with cumulus and granulosa cells from mice treated with pregnant mare’s serum gonadotropin (PMSG) + human chorionic gonadotrophin (hCG). However, this increased expression was absent in cumulus–oocyte complexes matured in vitro. Pull-down assays further revealed that the recombinant BMP15 proregion is capable of specific interaction with isolated granulosa cells. To verify an oocyte, and not somatic cell, origin of Bmp15 mRNA and coregulated growth differentiation factor 9 (Gdf9), in situ hybridisation and quantitative polymerase chain reaction results confirmed the exclusive oocyte localisation of Bmp15 and Gdf9, regardless of treatment or assay method. Relative oocyte expression levels of Bmp15 and Gdf9 decreased significantly after PMSG + hCG treatment; nevertheless, throughout all treatments, the Bmp15 : Gdf9 mRNA expression ratio remained unchanged. Together, these data provide evidence that the preovulatory LH surge leads to upregulation of several forms of BMP15 protein secreted by the oocyte for putative sequestration and/or interaction with ovarian follicular somatic cells.
Opposing actions of IL-2 and IL-21 on Th9 differentiation correlate with their differential regulation of BCL6 expression
Authors: Liao Wei , Spolski Rosanne , Li Peng , Du Ning , West Erin E. , Ren Min , Mitra Suman , Leonard Warren J.
Published: February 2014

Significance

Interleukin-9 (IL-9) is a γc-family cytokine produced by Th9 cells that regulates a range of immune responses, including allergic inflammation. We show that IL-2 via STAT5 is required for Th9 differentiation. IL-2 inhibits B cell lymphoma 6 (BCL6), which inhibits Th9 differentiation, whereas IL-21 induces BCL6. BCL6 bound near STAT5 and STAT6 binding sites, including at theIl9(gene encoding IL-9) promoter, and BCL6 binding increased and STAT binding decreased after treatment with anti–IL-2/IL-2R. Thus, IL-2 and IL-21 have opposing actions on BCL6 expression, which inversely correlates with Th9 differentiation and IL-9 production, with implications for controlling Th9 differentiation and potentially allergic inflammation.
Distance to health services affects local-level vaccine efficacy for pneumococcal conjugate vaccine (PCV) among rural Filipino children
Authors: Root Elisabeth Dowling , Lucero Marilla , Nohynek Hanna , Anthamatten Peter , Thomas Deborah S. K. , Tallo Veronica , Tanskanen Antti , Quiambao Beatriz P. , Puumalainen Taneli , Lupisan Socorro P. , Ruutu Petri , Ladesma Erma , Williams Gail M. , Riley Ian , Simões Eric A. F.
Published: February 2014

Significance

Although pneumococcal conjugate vaccines (PCVs) are widely available in industrialized nations, the cost of these vaccines and the strategy of universal vaccination of infants, as endorsed by the World Health Organization, are daunting obstacles to the adoption of these vaccines in developing countries. Using spatial epidemiological methods to examine the spatial variation in vaccine efficacy (VE) in an 11-valent PCV trial in Bohol, Philippines, we suggest an alternative strategy to universal vaccination. Our main finding suggests that areas with poor access to healthcare have the highest VE. An alternative vaccination strategy could target vaccination to areas where children are most likely to benefit, rather than focus on nationwide immunization.
Rapid upslope shifts in New Guinean birds illustrate strong distributional responses of tropical montane species to global warming
Authors: Freeman Benjamin G. , Class Freeman Alexandra M.
Published: February 2014

Significance

Montane species may respond to global warming by shifting their distributions upslope in response to warming temperatures. Such shifts are well documented in the temperate zone, but the situation in the tropics, where species are predicted to be more sensitive to altered temperatures, remains unclear. We found strong upslope shifts in the bird species found on two independent New Guinean mountains originally surveyed in the 1960s. Moreover, we incorporated our results into a metaanalysis that suggests tropical montane species are responding more strongly to climate change than temperate-zone species. Though the magnitude of climate change is higher in the temperate zone, both overall biodiversity and distributional shifts due to warming temperatures are greater in the tropics.
Chromosome 3p loss of heterozygosity is associated with a unique metabolic network in clear cell renal carcinoma
Authors: Gatto Francesco , Nookaew Intawat , Nielsen Jens
Published: February 2014

Significance

It is suggested that regulation of metabolism is a point of convergence of many different cancer-associated pathways. Here we challenged the validity of this assertion and verified that a transversal metabolic signature in cancer emerges chiefly in the regulation of nucleotide metabolism. However, the most common form of renal cancer deviates from this behavior and presents some defects in its metabolic network not present in the normal kidney and unseen in other tumors. Notably, reduced copy number in key metabolic genes located adjacent to
VHL
(a tumor suppressor gene frequently deleted in this cancer) recapitulates these defects. These results are suggestive that recurrent chromosomal loss of heterozygosity in cancer may uniquely shape the metabolic network.
Small-angle X-ray scattering-derived structure of the HIV-1 5′ UTR reveals 3D tRNA mimicry
Authors: Jones Christopher P. , Cantara William A. , Olson Erik D. , Musier-Forsyth Karin
Published: February 2014

Significance

A highly conserved region of the HIV-1 RNA genome is responsible for regulating numerous steps of the retroviral life cycle, including initiation of reverse transcription. A complete understanding of the mechanisms controlling HIV-1 replication requires structural characterization of this RNA; unfortunately, however, its large size and conformational flexibility makes common methods of solving structures, such as X-ray crystallography and NMR, exceedingly difficult. The present study uses a solution technique, small-angle X-ray scattering coupled with computational molecular modeling, to characterize three ∼100-nucleotide RNAs that play central roles in HIV-1 replication. One of these domains mimics the L-shaped fold of tRNA, providing a structural basis for understanding how this genomic RNA coordinates interactions with a tRNA-binding host factor to facilitate initiation of reverse transcription.
Analysis of the tumor-initiating and metastatic capacity of PDX1-positive cells from the adult pancreas
Authors: Ischenko Irene , Petrenko Oleksi , Hayman Michael J.
Published: February 2014

Significance

Pancreatic cancer is characterized by aggressive growth and a high propensity for metastatic spread. Despite growing understanding of the genetic causes of pancreatic cancer, the mechanism and timing of cancer metastasis, the main cause of deaths in pancreatic cancer patients, remain relatively unexplored. In this study, we used experimental mouse models of pancreatic carcinogenesis to show that hyperactivation of the Ras/MAPK/ERK pathway and stabilization of the MYC protein are the two main driving forces behind the development of pancreatic cancer cells with high metastatic potential. Our results suggest that pancreatic cells bearing Kras mutation can be induced to differentiate into quasi-normal cells with suppressed tumorigenicity by selective inhibition of the MAPK/ERK/MYC signaling cascade. These findings may have important therapeutic implications.
Itk-mediated integration of T cell receptor and cytokine signaling regulates the balance between Th17 and regulatory T cells
Authors: Gomez-Rodriguez Julio , Wohlfert Elizabeth A. , Handon Robin , Meylan Françoise , Wu Julie Z. , Anderson Stacie M. , Kirby Martha R. , Belkaid Yasmine , Schwartzberg Pamela L.
Published: February 2014

A proper balance between Th17 and T regulatory cells (Treg cells) is critical for generating protective immune responses while minimizing autoimmunity. We show that the Tec family kinase Itk (IL2-inducible T cell kinase), a component of T cell receptor (TCR) signaling pathways, influences this balance by regulating cross talk between TCR and cytokine signaling. Under both Th17 and Treg cell differentiation conditions, Itk−/− CD4+ T cells develop higher percentages of functional FoxP3+ cells, associated with increased sensitivity to IL-2. Itk−/− CD4+ T cells also preferentially develop into Treg cells in vivo. We find that Itk-deficient T cells exhibit reduced TCR-induced phosphorylation of mammalian target of rapamycin (mTOR) targets, accompanied by downstream metabolic alterations. Surprisingly, Itk−/− cells also exhibit reduced IL-2–induced mTOR activation, despite increased STAT5 phosphorylation. We demonstrate that in wild-type CD4+ T cells, TCR stimulation leads to a dose-dependent repression of Pten. However, at low TCR stimulation or in the absence of Itk, Pten is not effectively repressed, thereby uncoupling STAT5 phosphorylation and phosphoinositide-3-kinase (PI3K) pathways. Moreover, Itk-deficient CD4+ T cells show impaired TCR-mediated induction of Myc and miR-19b, known repressors of Pten. Our results demonstrate that Itk helps orchestrate positive feedback loops integrating multiple T cell signaling pathways, suggesting Itk as a potential target for altering the balance between Th17 and Treg cells.
SeqGSEA: a Bioconductor package for gene set enrichment analysis of RNA-Seq data integrating differential expression and splicing
Authors: Wang Xi , Cairns Murray J.
Published: February 2014

Summary: SeqGSEA is an open-source Bioconductor package for the functional integration of differential expression and splicing analysis in RNA-Seq data. SeqGSEA implements an analysis pipeline, which first computes differential splicing and differential expression scores, followed by integrating them into a per-gene score that quantifies each gene’s association with a phenotype of interest, and finally executes gene set enrichment analysis in a cutoff-free manner to achieve biological insights. SeqGSEA accounts for biological variability and determines the statistical significance of gene pathways and networks using subject permutation, and thus requires at least five samples per group. Real applications show that SeqGSEA detects more biologically meaningful gene sets without biases toward long or highly expressed genes. SeqGSEA can be set up to run in parallel to reduce the analysis time.

Availability and implementation: The SeqGSEA package with a vignette is available at http://bioconductor.org/packages/release/bioc/html/SeqGSEA.html.

Contact:  Murray.Carins@newcastle.edu.au

Supplementary information:  Supplementary data are available at Bioinformatics online.
First Report of Downy Mildew (Hyaloperonospora lunariae) on White Mustard (Sinapis alba) in Brazil
Authors: Colman A. , Macedo D. M. , Barreto R. W.
Published: February 2014

Sinapis alba (Brassicaceae), white mustard, is broadly cultivated for its seed used as component of table mustard (4). In June 2013, a group of diseased S. alba were observed in a vegetable garden on the campus of the Universidade Federal de Viçosa (municipality of Viçosa, state of Minas Gerais, Brazil). Foliage of diseased plants showed numerous chlorotic areas that developed into severe leaf blight with abundant downy mildew growth abaxially. A dried representative specimen has been deposited in the herbarium at the Universidade Federal de Viçosa (accession no. VIC 39743). The fungus had the following morphology: Sporangiophores arborescent, dichotomously branched, 540 to 840 × 8 to 10 μm hyaline, smooth, branches 105 to 210 μm long; esterigmata subacutate and curved, in pairs, 15 to 42 μm long; sporangia globose, 18 to 24 × 15 to 18 μm, hyaline, smooth. DNA was extracted using a Wizard Promega purification kit. The cytochrome oxidase subunit II (COX2) region was amplified with COX2f and COX2r primers (3). The sequence has been deposited in GenBank (Accession No. KJ396953). DNA sequences representing morphologically similar taxa were downloaded from GenBank nucleotide database, aligned in MEGA 5, and analyzed using Bayesian inference and Markov chain Monte Carlo simulation implemented in MrBayes 3.0 with five repetitions. A sequence of Albugo candida was used as outgroup in the analysis. The morphological characteristics places the fungus on S. alba in the complex of species of Pernosporaceae that attack the Brassicaceae. These are notoriously difficult to discriminate by morphology but our COX2-based phylogenetic analysis places it in Hyaloperonospora lunariae (1). This species was previously only known to cause downy mildew on other species of Brassicaceae (Lunaria annua and Erucastrum nasturtiifolium) in Europe (2). To our knowledge, this is the first report of this pathogen-host association in the world.

References: (1) O. Constantinescu and J. Fatehi. Nova Hediwigia 74:291, 2002 (2) D. F. Farr and A. Y. Rossman. Fungal Databases, Systematic Mycology and Microbiology Laboratory. Online publication. ARS, USDA, 2013. (3) D. S. S. Hudspeth et al. Mycologia 92:674, 2000. (4) B. B. Simpson and M. C. Ogorzaly. Econonic Botany. McGraw Hill, San Diego, CA, 2001.
Inpatient Falls after Total Knee Arthroplasty
Authors: Memtsoudis Stavros G. , Danninger Thomas , Rasul Rehana , Poeran Jashvant , Gerner Philipp , Stundner Ottokar , Mariano Edward R. , Mazumdar Madhu
Published: February 2014

Background:

Much controversy remains on the role of anesthesia technique and peripheral nerve blocks (PNBs) in inpatient falls (IFs) after orthopedic procedures. The aim of the study is to characterize cases of IFs, identify risk factors, and study the role of PNB and anesthesia technique in IF risk in total knee arthroplasty patients.

Methods:

The authors selected total knee arthroplasty patients from the national Premier Perspective database (Premier Inc., Charlotte, NC; 2006–2010; n = 191,570, >400 acute care hospitals). The primary outcome was IF. Patient- and healthcare system–related characteristics, anesthesia technique, and presence of PNB were determined for IF and non-IF patients. Independent risk factors for IFs were determined by using conventional and multilevel logistic regression.

Results:

Overall, IF incidence was 1.6% (n = 3,042). Distribution of anesthesia technique was 10.9% neuraxial, 12.9% combined neuraxial/general, and 76.2% general anesthesia. PNB was used in 12.1%. Patients suffering IFs were older (average age, 68.9 vs. 66.3 yr), had higher comorbidity burden (average Deyo index, 0.77 vs. 0.66), and had more major complications, including 30-day mortality (0.8 vs. 0.1%; all P < 0.001). Use of neuraxial anesthesia (IF incidence, 1.3%; n = 280) had lower adjusted odds of IF compared with adjusted odds of IF with the use of general anesthesia alone (IF incidence, 1.6%; n = 2,393): odds ratio, 0.70 (95% CI, 0.56–0.87). PNB was not significantly associated with IF (odds ratio, 0.85 [CI, 0.71–1.03]).

Conclusions:

This study identifies several risk factors for IF in total knee arthroplasty patients. Contrary to common concerns, no association was found between PNB and IF. Further studies should determine the role of anesthesia practices in the context of fall-prevention programs.
Indirect multi-trophic interactions mediated by induced plant resistance: impact of caterpillar feeding on aphid parasitoids
Authors: Hagenbucher Steffen , Wäckers Felix L. , Romeis Jörg
Published: February 2014

Cotton produces insecticidal terpenoids that are induced by tissue-feeding herbivores. Damage by
Heliothis virescens
caterpillars increases the terpenoid content, which reduces the abundance of aphids. This effect is not evident in Bt-transgenic cotton, which is resistant to
H. virescens
. We determined whether induction of terpenoids by caterpillars influences the host quality of
Aphis gossypii
for the parasitoid
Lysiphlebus testaceipes
and whether this interaction is influenced by Bt cotton
.
The exposure of parasitoids to terpenoids was determined by quantifying terpenoids in the aphids. We detected several terpenoids in aphids and found a positive relationship between their concentrations in plants and aphids. When
L. testaceipes
was allowed to parasitize aphids on Bt and non-Bt cotton that was infested or uninfested with
H. virescens
, fewer parasitoid mummies were found on infested non-Bt than on Bt cotton. Important parasitoid life-table parameters, however, were not influenced by induced resistance following
H. virescens
infestation, or the Bt trait. Our study provides an example of a tritrophic indirect interaction web, where organisms are indirectly linked through changes in plant metabolites.
Sperm variation within a single ejaculate affects offspring development in Atlantic salmon
Authors: Immler Simone , Hotzy Cosima , Alavioon Ghazal , Petersson Erik , Arnqvist Göran
Published: February 2014

It is generally believed that variation in sperm phenotype within a single ejaculate has no consequences for offspring performance, because sperm phenotypes are thought not to reflect sperm genotypes. We show that variation in individual sperm function within an ejaculate affects the performance of the resulting offspring in the Atlantic salmonSalmo salar. We experimentally manipulated the time between sperm activation and fertilization in order to select for sperm cohorts differing in longevity within single ejaculates of wild caught male salmon. We found that within-ejaculate variation in sperm longevity significantly affected offspring development and hence time until hatching. Whether these effects have a genetic or epigenetic basis needs to be further evaluated. However, our results provide experimental evidence for transgenerational effects of individual sperm function.
Macro- and microscale variables regulate stent haemodynamics, fibrin deposition and thrombomodulin expression
Authors: Jiménez Juan M. , Prasad Varesh , Yu Michael D. , Kampmeyer Christopher P. , Kaakour Abdul-Hadi , Wang Pei-Jiang , Maloney Sean F. , Wright Nathan , Johnston Ian , Jiang Yi-Zhou , Davies Peter F.
Published: February 2014

Drug eluting stents are associated with late stent thrombosis (LST), delayed healing and prolonged exposure of stent struts to blood flow. Using macroscale disturbed and undisturbed fluid flow waveforms, we numerically and experimentally determined the effects of microscale model strut geometries upon the generation of prothrombotic conditions that are mediated by flow perturbations. Rectangular cross-sectional stent strut geometries of varying heights and corresponding streamlined versions were studied in the presence of disturbed and undisturbed bulk fluid flow. Numerical simulations and particle flow visualization experiments demonstrated that the interaction of bulk fluid flow and stent struts regulated the generation, size and dynamics of the peristrut flow recirculation zones. In the absence of endothelial cells, deposition of thrombin-generated fibrin occurred primarily in the recirculation zones. When endothelium was present, peristrut expression of anticoagulant thrombomodulin (TM) was dependent on strut height and geometry. Thinner and streamlined strut geometries reduced peristrut flow recirculation zones decreasing prothrombotic fibrin deposition and increasing endothelial anticoagulant TM expression. The studies define physical and functional consequences of macro- and microscale variables that relate to thrombogenicity associated with the most current stent designs, and particularly to LST.
On the quasi-steady aerodynamics of normal hovering flight part II: model implementation and evaluation
Authors: Nabawy Mostafa R. A. , Crowther William J.
Published: February 2014

This paper introduces a generic, transparent and compact model for the evaluation of the aerodynamic performance of insect-like flapping wings in hovering flight. The model is generic in that it can be applied to wings of arbitrary morphology and kinematics without the use of experimental data, is transparent in that the aerodynamic components of the model are linked directly to morphology and kinematics via physical relationships and is compact in the sense that it can be efficiently evaluated for use within a design optimization environment. An important aspect of the model is the method by which translational force coefficients for the aerodynamic model are obtained from first principles; however important insights are also provided for the morphological and kinematic treatments that improve the clarity and efficiency of the overall model. A thorough analysis of the leading-edge suction analogy model is provided and comparison of the aerodynamic model with results from application of the leading-edge suction analogy shows good agreement. The full model is evaluated against experimental data for revolving wings and good agreement is obtained for lift and drag up to 90° incidence. Comparison of the model output with data from computational fluid dynamics studies on a range of different insect species also shows good agreement with predicted weight support ratio and specific power. The validated model is used to evaluate the relative impact of different contributors to the induced power factor for the hoverfly and fruitfly. It is shown that the assumption of an ideal induced power factor (k= 1) for a normal hovering hoverfly leads to a 23% overestimation of the generated force owing to flapping.
Towards a complete model of soil liquefaction: the importance of fluid flow and grain motion
Authors: Lakeland Daniel L. , Rechenmacher Amy , Ghanem Roger
Published: February 2014

When loosely packed water-saturated granular soils, for example sands, are subjected to strong earthquake shaking, they may liquefy, causing large deformations with great destructive power. The phenomenon is quite general and occurs in any fluid-saturated granular material and is a consequence of the transfer of stress from inter-grain contacts to water pressure. In modern geotechnical practice, soil liquefaction is commonly considered to be an ‘undrained’ phenomenon; pressure is thought to be generated because earthquake deformations are too quick to allow fluid flow, which enables water depressurization. Here, we show via a first principles analysis that liquefaction is not a strictly undrained process; and, in fact, it is the interplay between grain rearrangement, fluid migration and changes in permeability, which causes the loss of strength observed in so many destructive earthquake events around the world. The results call into question many of the common laboratory and field methods of evaluating the liquefaction resistance of soil and indicate new directions for the field, laboratory and scale-model study of this important phenomenon.
Passive sampling devices enable capacity building and characterization of bioavailable pesticide along the Niger, Senegal and Bani Rivers of Africa
Authors: Anderson Kim A. , Seck Dogo , Hobbie Kevin A. , Traore Anna Ndiaye , McCartney Melissa A. , Ndaye Adama , Forsberg Norman D. , Haigh Theodore A. , Sower Gregory J.
Published: February 2014

It is difficult to assess pollution in remote areas of less-developed regions owing to the limited availability of energy, equipment, technology, trained personnel and other key resources. Passive sampling devices (PSDs) are technologically simple analytical tools that sequester and concentrate bioavailable organic contaminants from the environment. Scientists from Oregon State University and the Centre Régional de Recherches en Ecotoxicologie et de Sécurité Environnementale (CERES) in Senegal developed a partnership to build capacity at CERES and to develop a pesticide-monitoring project using PSDs. This engagement resulted in the development of a dynamic training process applicable to capacity-building programmes. The project culminated in a field and laboratory study where paired PSD samples were simultaneously analysed in African and US laboratories with quality control evaluation and traceability. The joint study included sampling from 63 sites across six western African countries, generating a 9000 data point pesticide database with virtual access to all study participants.
(4bS,8aS)-1-Isopropyl-4b,8,8-trimethyl-4b,5,6,7,8,8a,9,10-octahydrophenanthren-2-yl acetate
Authors: Oubabi Radouane , Auhmani Aziz , Ait Itto My Youssef , Auhmani Abdelwahed , Daran Jean-Claude
Published: February 2014

The hemisynthesis of the title compound, C22H32O2, was carried out through direct acetylation reaction of the naturally occurring diterpene totarol [systematic name: (4bS,8aS)-4b,8,8-trimethyl-1-propan-2-yl-5,6,7,8a,9,10-hexahydrophenanthren-2-ol]. The molecule is built up from three fused six membered rings, one saturated and two unsaturated. The central unsaturated ring has a half-chair conformation, whereas the other unsaturated ring displays a chair conformation. The absolute configuration is deduced from the chemical pathway. The value of the Hooft parameter [−0.10 (6)] allowed this absolute configuration to be confirmed.