bluuebunny/crossref_metadata_2025 huggingface dataset:
Aspect ratio effects on neoclassical tearing modes from comparison between DIII-D and National Spherical Torus Experiment
Authors: La Haye R. J. , Buttery R. J. , Gerhardt S. P. , Sabbagh S. A. , Brennan D. P.
Published: June 2012

Neoclassical tearing mode islands are sustained by helically perturbed bootstrap currents arising at finite beta from toroidal effects that trap a fraction of the particles in non-circulating orbits. DIII-D and NSTX are here operated with similar shape and cross-sectional area but almost a factor of two difference in inverse aspect ratio a/R. In these experiments, destabilized n=1 tearing modes were self-stabilized (reached the “marginal point”) by reducing neutral-beam power and thus beta. The measure of the marginal island gives information on the small-island stabilizing physics that in part (with seeding) governs onset. The marginal island width on NSTX is found to be about three times the ion banana width and agrees with that measured in DIII-D, except for DIII-D modes closer to the magnetic axis, which are about two times the ion banana width. There is a balance of the helically perturbed bootstrap term with small island effects with the sum of the classical and curvature terms in the modified Rutherford equation for tearing-mode stability at the experimental marginal point. Empirical evaluation of this sum indicates that while the stabilizing effect of the curvature term is negligible in DIII-D, it is important in NSTX. The mode temporal behavior from the start of neutral-beam injection reduction also suggests that NSTX operates closer to marginal classical tearing stability; this explains why there is little hysteresis in beta between mode onset, saturation, and self-stabilization (while DIII-D has large hysteresis in beta). NIMROD code module component calculations based on DIII-D and NSTX reconstructed experimental equilibria are used to diagnose and confirm the relative importance of the stabilizing curvature effect, an advantage for low aspect ratio; the relatively greater curvature effect makes for less susceptibility to NTM onset even if the classical tearing stability index is near marginal.
Changes in magnetic properties of Co/Pd multilayers induced by hydrogen absorption
Authors: Munbodh Kineshma , Perez Felio A. , Lederman David
Published: June 2012

The saturation magnetization (MS) and perpendicular anisotropy energy (KP) of Co/Pd multilayers were studied when the samples were exposed to 1 atm of H2 at room temperature. The samples had fixed Co nominal thicknesses of 2.5 Å and 4.5 Å and Pd thickness values ranging from 0 Å to 25 Å. The interface structure was determined from the x-ray scattering length density (SLD) profile. When the Pd thickness was less than 10 Å, there was a large amount of interface disorder which resulted in no change in MS and KP. As the Pd thickness increased, the SLD contrast between the Co and Pd layers also increased, leading to a decrease in MS and KP after H2 absorption. This can be explained by a decrease in H2 solubility as interface alloying became more dominant for thinner layers, which resulted from a smaller hydrogen electron transfer to the Pd 4d band. The changes in MS and KP in the less interdiffused samples also resulted from this electron transfer. Magnetic changes were reversible with characteristic absorption and desorption times of approximately 40 s for 1 atm of H2.
Imaging ambipolar diffusion of photocarriers in GaAs thin films
Authors: Paget D. , Cadiz F. , Rowe A. C. H. , Moreau F. , Arscott S. , Peytavit E.
Published: June 2012

Images of the steady-state luminescence of passivated GaAs self-standing films under excitation by a tightly focussed laser are analyzed as a function of light excitation power. While unipolar diffusion of photoelectrons is dominant at very low light excitation power, an increased power results in a decrease of the diffusion constant near the center of the image due to the onset of ambipolar diffusion. The results are in agreement with a numerical solution of the diffusion equations and with a physical analysis of the luminescence intensity at the centre of the image, which permits the determination of the ambipolar diffusion constant as a function of electron concentration.
Tunable coupled surface acoustic cavities
Authors: de Lima M. M. , Santos P. V. , Kosevich Yu. A. , Cantarero A.
Published: June 2012

We demonstrate the electric tuning of the acoustic field in acoustic microcavities (MCs) defined by a periodic arrangement of metal stripes within a surface acoustic delay line on LiNbO3 substrate. Interferometric measurements show the enhancement of the acoustic field distribution within a single MC, the presence of a “bonding” and “anti-bonding” modes for two strongly coupled MCs, as well as the positive dispersion of the “mini-bands” formed by five coupled MCs. The frequency and amplitude of the resonances can be controlled by the potential applied to the metal stripes.
Synchrotron x-ray nano-tomography characterization of the sintering of multilayered systems
Authors: Yan Zilin , Guillon Olivier , Wang Steve , Martin Christophe L. , Lee Chul-Seung , Bouvard Didier
Published: June 2012

Synchrotron x-ray nano-tomography was used to characterize the microstructures of multi-layer ceramic capacitors before and after sintering. 3D microstructures of the same sample were reconstructed and quantitatively analyzed. The discontinuities observed in inner electrodes were found to originate from initial heterogeneities of nickel powders in the electrodes. They are supposed to grow due to the constraint of adjacent dielectric layers. Dielectric layers show anisotropic shrinkage with a decrease in density as function of layer position in the multilayer.
Assessment of the roles of various inactivation agents in an argon-based direct current atmospheric pressure cold plasma jet
Authors: Zhang Qian , Sun Peng , Feng Hongqing , Wang Ruixue , Liang Yongdong , Zhu Weidong , Becker Kurt H. , Zhang Jue , Fang Jing
Published: June 2012

Three types of gases, pure argon (99.999%), argon with 2% oxygen, and argon with 2% oxygen and 10% nitrogen were used as operating gases of a direct current atmospheric pressure cold plasma jet to inactivate Staphylococcus aureus (S. aureus) suspended in a liquid. The inactivation efficacies for the plasma jets operating in the three gases decrease from Ar/O2(2%) to Ar/O2(2%)/N2(10%) to pure Ar. Optical emission spectroscopy, electron spin resonance spectroscopy, high performance liquid chromatography, and atomic absorption spectrophotometry were employed to identify and monitor the reactive species in the plasma-liquid system for the three operating gases and revealed the presence of O, 1O2, OH, NO, H2O2, O3, and NO3−/NO2− as well as Cu+/Cu2+. The S. aureus inactivation results indicate that atomic oxygen (O) is the key inactivation agent, while other species play a lesser role in the inactivation progress studied here.
Magnetic pulser and sample holder for time- and spin-resolved photoemission spectroscopy on magnetic materials
Authors: Fognini A. , Michlmayr T. U. , Bähler T. , Wetli C. , Vaterlaus A. , Acremann Y.
Published: June 2012

A compact coil setup, in conjunction with a high power current pulser, is presented; developed especially for time- and spin-resolved photoemission spectroscopy measuring the sample in magnetic remanence at room temperature. A novel approach is presented where the sample is switched in the stray field of a coil pair. This enables the electrical biasing of the sample without altering the electron trajectories due to field gradients introduced by the coils. The pulser driving the coils reaches a peak power of 1 MW at 1 kA with a switching frequency up to 10 kHz suitable for experiments, for example, with state of the art repetition rates of femtosecond laser systems.
Effect of “dipolar-biasing” on the tunability of tunneling magnetoresistance in transition metal oxide systems
Authors: Anil Kumar P. , Sarma D. D.
Published: June 2012

We observe an unusual tunneling magnetoresistance (TMR) phenomenon in a composite of La2/3Sr1/3MnO3 with CoFe2O4 where the TMR versus applied magnetic field loop suggests a “negative coercive field.” Tracing its origin back to a “dipolar-biasing” of La2/3Sr1/3MnO3 by CoFe2O4, we show that the TMR of even a single composite can be tuned continuously so that the resistance peak or the highest sensitivity of the TMR can be positioned anywhere on the magnetic field axis with a suitable magnetic history of the sample. This phenomenon of an unprecedented tunability of the TMR should be present in general in all such composites.
Infrared absorbance of silicene and germanene
Authors: Bechstedt Friedhelm , Matthes Lars , Gori Paola , Pulci Olivia
Published: June 2012

Calculating the complex dielectric function for optical interband transitions we show that the two-dimensional crystals silicene and germanene possess the same low-frequency absorbance as graphene. It is determined by the Sommerfeld finestructure constant. Deviations occur for higher frequencies when the first interband transitions outside K or K′ contribute. The low-frequency results are a consequence of the honeycomb geometry but do not depend on the group-IV atom, the sheet buckling, and the orbital hybridization. The two-dimensional crystals may be useful as absorption normals in silicon technology.
Non-equilibrium spatial distribution of Rashba spin torque in ferromagnetic metal layer
Authors: Chung N. L. , Jalil M. B. A. , Tan S. G.
Published: June 2012

We study the spatial distribution of spin torque induced by a strong Rashba spin-orbit coupling (RSOC) in a ferromagnetic (FM) metal layer, using the Keldysh non-equilibrium Green's function method. In the presence of the s-d interaction between the non-equilibrium conduction electrons and the local magnetic moments, the RSOC effect induces a torque on the moments, which we term the Rashba spin torque. A correlation between the Rashba spin torque and the spatial spin current is presented in this work, clearly mapping the spatial distribution of Rashba spin torque in a nano-sized ferromagnetic device. When local magnetism is turned on, the out-of-plane (Sz) Spin Hall effect (SHE) is disrupted, but rather unexpectedly an in-plane (Sy) SHE is detected. We also study the effect of Rashba strength (αR) and splitting exchange (Δ) on the non-equilibrium Rashba spin torque averaged over the device. Rashba spin torque allows an efficient transfer of spin momentum such that a typical switching field of 20 mT can be attained with a low current density of less than 107A/cm2.
Enhancement of glass-forming ability of Fe-based bulk metallic glasses with high saturation magnetic flux density
Authors: Zhang Mingxiao , Wang Anding , Shen Baolong
Published: June 2012

The effects of substituting Fe with Ni on thermal properties, glass-forming ability (GFA) and magnetic properties of Fe76-xNixMo3.5P10C4B4Si2.5 (x = 0−30 at.%) alloys were investigated in detail. The breadth of the supercooled liquid region was found to gradually increase from 42 to 55 K with increasing Ni content to 30 at.%. When x = 5 at.%, the alloy composition approached a eutectic point, resulting in an increase in GFA. As a result, FeNiMoPCBSi bulk metallic glasses with critical diameters up to 5.5 mm were successfully synthesized by copper mold casting. These glassy alloys exhibit a high saturation magnetic flux density of 0.75−1.21 T and excellent soft magnetic properties, i.e., low coercive force of 1.1−2.0 A/m, and high effective permeability of 14400−19700 at 1 kHz under a field of 1 A/m. The reasons for the high stability of the supercooled liquid, and the high GFA as well as excellent soft magnetic properties are discussed in this article.
“Saving the Phenomena” Today
Authors: Teller Paul
Published: June 2012

Bogen and Woodward argued the indirect connection between data and theory in terms of their conception of “phenomena.” I outline and elaborate on their presentation. To illuminate the connection with contemporary thinking in terms of models, I distinguish between phenomena tokens, representations of which can be identified with data models, and phenomena types that can be identified with relatively low-lying models or aspects of models in the model hierarchy. Throughout I stress the role of idealization in these considerations.
Are Stellar Kinds Natural Kinds? A Challenging Newcomer in the Monism/Pluralism and Realism/Antirealism Debates
Authors: Ruphy Stéphanie
Published: June 2012

Stars are remarkably absent from reflections on natural kinds and classifications, with gold, tiger, jade, and water getting all the philosophical attention. It is a pity, for interesting philosophical lessons can be drawn from stellar taxonomy as regards two central debates about natural kinds, to wit, the monism/pluralism debate and the realism/antirealism debate. I show in particular that stellar kinds will not please the essentialist monist, nor will it please the pluralist embracing promiscuous realism à la Dupré. I conclude on a more general note by questioning the relationship between taxonomic scientific practice and philosophical doctrines of natural kinds.
Mathematics, Science, and Confirmation Theory
Authors: Pincock Christopher
Published: June 2012

This article begins by distinguishing intrinsic and extrinsic contributions of mathematics to scientific representation. This leads to two investigations into how these different sorts of contributions relate to confirmation. I present a way of accommodating both contributions that complicates the traditional assumptions of confirmation theory. In particular, I argue that subjective Bayesianism does best in accounting for extrinsic contributions, while objective Bayesianism is more promising for intrinsic contributions.
Comparative Process Tracing and Climate Change Fingerprints
Authors: Parker Wendy S.
Published: June 2012

Climate change fingerprint studies investigate the causes of recent climate change. I argue that these studies have much in common with Steel's streamlined comparative process tracing, illustrating a mechanisms-based approach to extrapolation in which the mechanisms of interest are simulated rather than physically instantiated. I then explain why robustness and variety-of-evidence considerations turn out to be important for understanding the evidential value of climate change fingerprint studies.
Confirmation and Robustness of Climate Models
Authors: Lloyd Elisabeth A.
Published: June 2012

Recent philosophical attention to climate models has highlighted their weaknesses and uncertainties. Here I address the ways that models gain support through observational data. I review examples of model fit, variety of evidence, and independent support for aspects of the models, contrasting my analysis with that of other philosophers. I also investigate model robustness, which often emerges when comparing climate models simulating the same time period or set of conditions. Starting from Michael Weisberg's analysis of robustness, I conclude that his approach involves a version of reasoning from variety of evidence, enabling this robustness to be a confirmatory virtue
Effective equidistribution of the real part of orbits on hyperbolic surfaces
Authors: Truelsen Jimi
Published: June 2012

For non-cocompact Fuchsian groups with finite covolume we prove that the real part of the orbit of a point in the upper half-plane is equidistributed with an effective error term. This extends previous results by A. Good, M. Risager, and Z. Rudnick. We use the equidistribution result to generalize a theorem by F. Chamizo.
Live-cell monitoring of periodic gene expression in synchronous human cells identifies Forkhead genes involved in cell cycle control
Authors: Grant Gavin D. , Gamsby Joshua , Martyanov Viktor , Brooks Lionel , George Lacy K. , Mahoney J. Matthew , Loros Jennifer J. , Dunlap Jay C. , Whitfield Michael L.
Published: June 2012

We developed a system to monitor periodic luciferase activity from cell cycle–regulated promoters in synchronous cells. Reporters were driven by a minimal human E2F1 promoter with peak expression in G1/S or a basal promoter with six Forkhead DNA-binding sites with peak expression at G2/M. After cell cycle synchronization, luciferase activity was measured in live cells at 10-min intervals across three to four synchronous cell cycles, allowing unprecedented resolution of cell cycle–regulated gene expression. We used this assay to screen Forkhead transcription factors for control of periodic gene expression. We confirmed a role for FOXM1 and identified two novel cell cycle regulators, FOXJ3 and FOXK1. Knockdown of FOXJ3 and FOXK1 eliminated cell cycle–dependent oscillations and resulted in decreased cell proliferation rates. Analysis of genes regulated by FOXJ3 and FOXK1 showed that FOXJ3 may regulate a network of zinc finger proteins and that FOXK1 binds to the promoter and regulates DHFR, TYMS, GSDMD, and the E2F binding partner TFDP1. Chromatin immunoprecipitation followed by high-throughput sequencing analysis identified 4329 genomic loci bound by FOXK1, 83% of which contained a FOXK1-binding motif. We verified that a subset of these loci are activated by wild-type FOXK1 but not by a FOXK1 (H355A) DNA-binding mutant.
Pentraxin‐3 in chronic heart failure: the CORONA and GISSI‐HF trials
Authors: Latini Roberto , Gullestad Lars , Masson Serge , Nymo Ståle Haugset , Ueland Thor , Cuccovillo Ivan , Vårdal Mari , Bottazzi Barbara , Mantovani Alberto , Lucci Donata , Masuda Nobuhito , Sudo Yukio , Wikstrand John , Tognoni Gianni , Aukrust Pål , Tavazzi Luigi ,   on behalf of the Investigators of the Controlled Rosuvastatin Multinational Trial in Heart Failure (CORONA) and GISSI‐Heart Failure (GISSI‐HF) trials
Published: June 2012

Aims

Pentraxin‐3 (PTX3) is a component of the humoral arm of innate immunity which can regulate inflammatory processes. Since the role of inflammation in the progression of chronic heart failure (HF) is debated, we investigated the prognostic value of PTX3 and the effect of a statin in two large populations of patients with HF.

Methods and results

Plasma levels of PTX3 were measured at randomization and after 3 months in 1457 patients enrolled in the Controlled Rosuvastatin Multinational Trial in HF (CORONA) and 1233 patients enrolled in the GISSI‐Heart Failure trial (GISSI‐HF). The relationships between baseline PTX3 levels or their changes over time and mortality were evaluated with multivariable Cox proportional hazard models including clinical factors, high sensitivity C‐reactive protein (hsCRP), and N‐terminal pro brain natriuretic peptide (NT‐proBNP). PTX3 concentration [median (Q1–Q3) = 5.34 (3.55–7.64) ng/mL, n = 2690] was higher in females, in older patients, and those with lower body mass index. Baseline elevated PTX3 was associated with a higher risk of all‐cause mortality [759 events, hazard ratio (HR) for 1 SD increase 1.20, 95% confidence interval (CI) 1.12–1.30, P < 0.0001], cardiovascular mortality (587 events, HR 1.27, 95% CI 1.17–1.38, P < 0.0001), or hospitalization for worsening HF (720 events, HR 1.21, 95% CI 1.12–1.30, P < 0.0001), and marginally improved discrimination. Three‐month changes in PTX3 were associated with fatal events after adjustment for hsCRP or NT‐proBNP. Rosuvastatin lowered hsCRP levels but significantly raised PTX3.

Conclusion

In two independent clinical trials that enrolled patients with chronic HF, PTX3 was consistently associated with outcomes. The opposite effects of a statin on hsCRP and PTX3 call for further investigation.

Trial registration

NCT00336336 (GISSI‐HF), NCT00206310 (CORONA).
The High-Affinity Phosphate Transporter GmPT5 Regulates Phosphate Transport to Nodules and Nodulation in Soybean
Authors: Qin Lu , Zhao Jing , Tian Jiang , Chen Liyu , Sun Zhaoan , Guo Yongxiang , Lu Xing , Gu Mian , Xu Guohua , Liao Hong
Published: June 2012

Legume biological nitrogen (N) fixation is the most important N source in agroecosystems, but it is also a process requiring a considerable amount of phosphorus (P). Therefore, developing legume varieties with effective N2 fixation under P-limited conditions could have profound significance for improving agricultural sustainability. We show here that inoculation with effective rhizobial strains enhanced soybean (Glycine max) N2 fixation and P nutrition in the field as well as in hydroponics. Furthermore, we identified and characterized a nodule high-affinity phosphate (Pi) transporter gene, GmPT5, whose expression was elevated in response to low P. Yeast heterologous expression verified that GmPT5 was indeed a high-affinity Pi transporter. Localization of GmPT5 expression based on β-glucuronidase staining in soybean composite plants with transgenic roots and nodules showed that GmPT5 expression occurred principally in the junction area between roots and young nodules and in the nodule vascular bundles for juvenile and mature nodules, implying that GmPT5 might function in transporting Pi from the root vascular system into nodules. Overexpression or knockdown of GmPT5 in transgenic composite soybean plants altered nodulation and plant growth performance, which was partially dependent on P supply. Through both in situ and in vitro 33P uptake assays using transgenic soybean roots and nodules, we demonstrated that GmPT5 mainly functions in transporting Pi from roots to nodules, especially under P-limited conditions. We conclude that the high-affinity Pi transporter, GmPT5, controls Pi entry from roots to nodules, is critical for maintaining Pi homeostasis in nodules, and subsequently regulates soybean nodulation and growth performance.
Inducible Repression of Multiple Expansin Genes Leads to Growth Suppression during Leaf Development
Authors: Goh Hoe-Han , Sloan Jennifer , Dorca-Fornell Carmen , Fleming Andrew
Published: June 2012

Expansins are cell wall proteins implicated in the control of plant growth via loosening of the extracellular matrix. They are encoded by a large gene family, and data linked to loss of single gene function to support a role of expansins in leaf growth remain limited. Here, we provide a quantitative growth analysis of transgenics containing an inducible artificial microRNA construct designed to down-regulate the expression of a number of expansin genes that an expression analysis indicated are expressed during the development of Arabidopsis (Arabidopsis thaliana) leaf 6. The results support the hypothesis that expansins are required for leaf growth and show that decreased expansin gene expression leads to a more marked repression of growth during the later stage of leaf development. In addition, a histological analysis of leaves in which expansin gene expression was suppressed indicates that, despite smaller leaves, mean cell size was increased. These data provide functional evidence for a role of expansins in leaf growth, indicate the importance of tissue/organ developmental context for the outcome of altered expansin gene expression, and highlight the separation of the outcome of expansin gene expression at the cellular and organ levels.
Structure refinement and superspace description of the system Bi2(n + 2)Mo
n
O6(n + 1) (n = 3, 4, 5 and 6)
Authors: Bereciartua P. J. , Zuñiga F. J. , Perez-Mato J. M. , Petříček V. , Vila E. , Castro A. , Rodríguez-Carvajal J. , Doyle S.
Published: June 2012

The system Bi2(n + 2)Mo
n
O6(n + 1) is described within the superspace formalism. Two superspace models are proposed for the different members of this family, depending on the parity of the parameter n. The superspace model for the odd members is constructed through the embedding of the cationic distribution of the member with n = 3, and the modification of a superspace model previously proposed for the compound Bi2MoO6. However, this model cannot be applied to the even members of the family. Performing the appropriate transformations, a suitable superspace model for the even members is obtained. The atomic structure of the different compounds of the family have been refined through the Rietveld method combining synchrotron X-ray and neutron powder diffraction data.
Unified (3 + 1)-dimensional superspace description of the 2212-type stair-like [Bi2Sr3Fe2O9]
m
[Bi4Sr6Fe2O16] family of compounds
Authors: Elcoro Luis , Pérez Olivier , Perez-Mato J. M. , Petříček Václav
Published: June 2012

The (3 + 1)-dimensional superspace approach is applied to describe and refine a series of sheared compounds related to layered high T
c superconducting oxides. Two commensurate members (m = 4, 5) of the 2212 stair-like [Bi2Sr3Fe2O9]
m
[Bi4Sr6Fe2O16] family of compounds, previously studied using single-crystal diffraction data, are analyzed. A common average unit cell has been identified and a composition-dependent modulation wavevector is proposed. The model is built using only three independent atomic domains, one for the metal atoms and two for the O atoms. The three Sr, Bi and Fe species are described using close-connected crenel-like functions forming a continuous atomic domain along the internal space. The two oxygen domains are represented by crenel functions and the displacive modulation functions are built up by Legendre polynomials recently implemented in the program JANA2006. Surprisingly, the results of the refinements show a striking similarity of the displacive modulations for the two compounds analyzed, indicating that a unique model can be used to describe the correlations between the atomic displacements of the 2212 stair-like series. This final model is then applied to predict the structure of new members of the family.
Increase in incidence of adult T‐cell leukemia/lymphoma in non‐endemic areas of Japan and the United States
Authors: Chihara Dai , Ito Hidemi , Katanoda Kota , Shibata Akiko , Matsuda Tomohiro , Tajima Kazuo , Sobue Tomotaka , Matsuo Keitaro
Published: June 2012

Adult T‐cell leukemia/lymphoma (ATLL) is a peripheral T cell neoplasm that is associated with infection by the human T‐cell leukemia virus type I (HTLV‐1). Although the high incidence of ATLL in HTLV‐1‐endemic areas is well known, population‐based evidence concerning the incidence of ATLL in non‐endemic areas is scarce. To answer this, we estimated the age‐standardized incidence of ATLL from 1993 to 2006 for Japan and 1993 to 2008 for the US and assessed its trend using data from a population‐based cancer registry in Japan and Surveillance Epidemiology and End Results (SEER) in the US. The Japanese data were collected from 15 prefectures. A total of 2055 patients in the three prefectures in Kyushu and 1380 patients in the 12 prefectures in Honshu were diagnosed with ATLL in the study period. In the US, a total of 140 patients were diagnosed with ATLL. The results showed that the age‐standardized incidence in non‐endemic areas in Japan and in the US significantly increased during this period (annual percent change [95%CI]; Japan‐Honshu: +4.6% [1.1, 8.2]; US: +6.2% [1.5, 11.1]), while in the endemic areas of Japan there was no change (annual percent change [95%CI]; Japan‐Kyushu: 0.0% [−1.6, 1.7]). This result indicates that the disease has been spread by carriers to non‐endemic areas, and suggests the necessity of establishing a standard preventive strategy.
Prosaposin, a regulator of estrogen receptor alpha, promotes breast cancer growth
Authors: Wu Yihong , Sun Linlin , Zou Weiying , Xu Jiejie , Liu Haiou , Wang Wenzhong , Yun Xiaojing , Gu Jianxin
Published: June 2012

Prosaposin, a secreted protein, is a well‐known pleiotropic growth factor. Although a previous report has indicated that prosaposin is overexpressed in breast cancer cell lines, the role of prosaposin in the development of breast cancer remains to be identified. Here, we first revealed that prosaposin upregulated estrogen receptor alpha expression, nuclear translocation and transcriptional activity by western blot, immunofluorescence assay and dual luciferase reporter gene assay, respectively. Furthermore, we demonstrated prosaposin upregulated estrogen receptor alpha expression through MAPK‐signaling pathway using MAPK inhibitor. Proliferation assay and tumor xenograft experiments in nude mice (n = 6 per group) further confirmed prosaposin could promote breast cancer growth significantly in vitro and in vivo. These findings suggested that prosaposin might enhance estrogen receptor alpha‐mediated signaling axis and play a role in breast cancer development and progression.
Temporal and spatial Bean pod mottle virus‐induced gene silencing in soybean
Authors: Juvale Parijat S. , Hewezi Tarek , Zhang Chunquan , Kandoth Pramod Kaitheri , Mitchum Melissa G. , Hill John H. , Whitham Steven A. , Baum Thomas J.
Published: June 2012

Virus‐induced gene silencing (VIGS) is a powerful reverse genetics tool in plant science. In this study, we investigated the temporal and spatial silencing patterns achieved by Bean pod mottle virus (BPMV)‐based VIGS in soybean using virus constructs targeting green fluorescence protein (GFP). Silencing GFP enabled an in‐depth analysis of silencing in soybean tissues over time in a transgenic line constitutively expressing GFP. We discovered evidence for variable GFP silencing based on insert orientation and targeted region in the coding sequence. A 3′ sequence in reverse orientation produced the strongest silencing phenotypes. Furthermore, we documented that BPMV VIGS can achieve widespread silencing in a broad range of tissues, including leaves, stems, flowers and roots. Near‐complete silencing was attained in leaves and flowers. Although weaker than in shoots, the observed gene silencing in soybean roots will also allow reverse genetics studies in this tissue. When GFP fluorescence was assayed in cross‐sections of stems and leaf petioles, near‐complete and uniform silencing was observed in all cell types. Silencing was observed from as early as 2 weeks post‐virus inoculation in leaves to 7 weeks post‐virus inoculation in flowers, suggesting that this system can induce and maintain silencing for significant durations.
Acidovorax citrulli: generating basic and applied knowledge to tackle a global threat to the cucurbit industry
Authors: BURDMAN SAUL , WALCOTT RON
Published: June 2012

Acidovorax citrulli is the causal agent of bacterial fruit blotch (BFB) of cucurbit plants. In recent years, the disease has spread to many parts of the world, mainly via the inadvertent distribution of contaminated commercial seeds. Because of the costly lawsuits filed by growers against seed companies and the lack of efficient management methods, BFB represents a serious threat to the cucurbit industry, and primarily to watermelons and melons. Despite the economic importance of the disease, little is known about the basic aspects of A. citrulli pathogenesis. Nevertheless, the release of the genome of one A. citrulli strain, as well as the optimization of molecular manipulation and inoculation methods, has prompted basic studies and allowed advances towards an understanding of A. citrulli pathogenicity. In this article, we summarize the current knowledge about this important pathogen, with emphasis on its epidemiology and the factors involved in its pathogenicity and virulence.

Taxonomy

Bacteria; Betaproteobacteria; order Burkholderiales; family C
omamonadaceae; genus Acidovorax; species citrulli.

Microbiological properties

Gram‐negative, strictly aerobic, rod‐shaped; average dimensions of 0.5 μm × 1.7 μm; motile by means of an ∼5.0‐μm‐long polar flagellum; colonies on King's medium B are round, smooth, transparent and nonpigmented; optimal temperatures for growth around 27–30 °C; induces a hypersensitive response on nonhost tobacco and tomato leaves.

Host range

Acidovorax citrulli strains are pathogenic to various species of the Cucurbitaceae family, including watermelon, melon, squash, pumpkin and cucumber. Significant economic losses have been reported in watermelon and melon.

Disease symptoms

Watermelon and melon seedlings and fruits are highly susceptible to A. citrulli. Typical seedling symptoms include water‐soaked lesions on cotyledons that are often adjacent to the veins and later become necrotic, lesions on the hypocotyl, and seedling collapse and death. On watermelon fruits, symptoms begin as small, irregular, water‐soaked lesions which later extend through the rind, turn brown and crack. On melon fruits, symptoms are characterized by small, often sunken rind lesions and internal fruit decay. Symptoms on the leaves of mature plants are difficult to diagnose because they are often inconspicuous or similar to those caused by other biotic or abiotic stresses. When they occur, leaf lesions can spread along the midrib and main veins. Lesions appear dark‐brown to black on watermelon and light to reddish‐brown on melon.

Useful websites

Bacterial fruit blotch of cucurbits at APSnet, http://www.apsnet.org/edcenter/intropp/lessons/prokaryotes/Pages/BacterialBlotch.aspx; bacterial fruit blotch guide from ASTA, http://www.amseed.com/pdfs/DiseaseGuide‐BFB‐English.pdf; Acidovorax citrulli AAC00‐1 genome at JGI, http://genome.jgi‐psf.org/aciav/aciav.info.html.
The effects of sitagliptin on gastric emptying in healthy humans – a randomised, controlled study
Authors: Stevens J. E. , Horowitz M. , Deacon C. F. , Nauck M. , Rayner C. K. , Jones K. L.
Published: June 2012

Background

The rate of gastric emptying (GE) and subsequent release of the incretin hormones, glucagon‐like peptide‐1 (GLP‐1) and glucose‐dependent insulinotropic peptide (GIP) are critical determinants of postprandial glycaemia in health and type 2 diabetes. Slowing of GE may be the dominant mechanism by which exogenous GLP‐1, and some GLP‐1 analogues, improve postprandial glycaemia.

Aim

To determine the effect of sitagliptin on GE in healthy subjects, and the relationships between GE with glycaemia and incretin hormone secretion.

Methods

Fifteen volunteers (22.8 ± 0.7 years) were studied on two occasions following 2 days dosing with sitagliptin (100 mg/day) or placebo. GE (scintigraphy), glycaemia and plasma GLP‐1 and GIP (total and intact), insulin and glucagon were measured for 240 min following a mashed potato meal (1808 kJ).

Results

There was no difference in GE between sitgaliptin and placebo [50% emptying time (T50): P = 0.4]. Mean blood glucose was slightly less (P = 0.02) on sitagliptin. Sitagliptin reduced plasma glucagon between 75 and 120 min (P < 0.05), and increased intact GLP‐1 (P = 0.0002) and intact GIP (P = 0.0001) by approximately twofold, but reduced total GIP (P = 0.0003) and had no effect on total GLP‐1 (P = 0.16) or insulin (P = 0.75). On sitagliptin the initial rise in blood glucose (r = −0.66, P = 0.008) and the intact GIP response (r = −0.66, P = 0.007) were inversely related, whereas the intact GLP‐1 response was related directly (r = 0.52, P = 0.05) to the T50.

Conclusions

While the effects of sitagliptin on glycaemic control are unlikely to relate to slowing of GE in healthy humans, the rate of GE is a significant determinant of postprandial glycaemia on sitagliptin (Clinical Trial:NCT00501657).
A whole genome scan for QTL affecting milk protein percentage in Italian Holstein cattle, applying selective milk DNA pooling and multiple marker mapping in a daughter design
Authors: Russo V. , Fontanesi L. , Dolezal M. , Lipkin E. , Scotti E. , Zambonelli P. , Dall'Olio S. , Bigi D. , Davoli R. , Canavesi F. , Medugorac I. , Föster M. , Sölkner J. , Schiavini F. , Bagnato A. , Soller M.
Published: June 2012

We report on a complete genome scan for quantitative trait loci (QTL) affecting milk protein percentage (PP) in the Italian Holstein‐Friesian cattle population, applying a selective DNA pooling strategy in a daughter design. Ten Holstein‐Friesian sires were chosen, and for each sire, about 200 daughters, each from the high and low tails of estimated breeding value for PP, were used to construct milk DNA pools. Sires and pools were genotyped for 181 dinucleotide microsatellites covering all cattle autosomes. Sire marker allele frequencies in the pools were obtained by shadow correction of peak height in the electropherograms. After quality control, pool data from eight sires were used for all subsequent analyses. The QTL heterozygosity estimate was lower than that of similar studies in other cattle populations. Multiple marker mapping identified 19 QTL located on 14 chromosomes (BTA1, 2, 3, 4, 5, 6, 8, 9, 12, 14, 17, 20, 23 and 27). The sires were also genotyped for seven polymorphic sites in six candidate genes (ABCG2, SPP1, casein kappa, DGAT1, GHR and PRLR) located within QTL regions of BTA6, 14 and 20 found in this study. The results confirmed or excluded the involvement of some of the analysed markers as the causative polymorphic sites of the identified QTL. The QTL identified, combined with genotype data of these candidate genes, will help to identify other quantitative trait genes and clarify the complex QTL patterns observed for a few chromosomes. Overall, the results are consistent with the Italian Holstein population having been under long‐term selection for high PP.
First steps: bovine genomics in historical perspective
Authors: Womack James E.
Published: June 2012

The vision of Morris Soller was instrumental in launching the field of bovine genomics. This study is a review of the early years of bovine gene mapping leading up to the sequencing and assembly of the bovine genome in 2009. A historical perspective of parasexual, linkage and physical mapping is provided with a focus on the contribution of these maps to the eventual assignment and orientation of genes and sequence to cattle chromosomes.
Infiltration of a mixture of immune cells may be related to good prognosis in patients with differentiated thyroid carcinoma
Authors: Cunha Lucas L. , Morari Elaine C. , Guihen Ana C. T. , Razolli Daniela , Gerhard Renê , Nonogaki Suely , Soares Fernando A. , Vassallo José , Ward Laura S.
Published: June 2012

Objective

Immune responses against differentiated thyroid carcinomas (DTC) have long been recognized. We aimed to investigate the role of immune cell infiltration in the progression of DTC.

Design

We studied 398 patients – 253 with papillary and 13 with follicular thyroid cancers, as well as 132 with nonmalignant tissues.

Patients and measurements

Immune cell infiltration was identified using CD3, CD4, CD8, CD20, CD68 and FoxP3 immunohistochemical markers. In addition, we assessed colocalization of CD4 and IL‐17 to identify Th17 lymphocytic infiltration and colocalization of CD33 and CD11b to identify infiltration of myeloid‐derived suppressor cells (MDSC).

Results

Immune cells infiltrated malignant tissues more often than benign lesions. The presence of chronic lymphocytic thyroiditis (CLT) concurrent to DTC, CD68+, CD4+, CD8+, CD20+, FoxP3+ and Th17 lymphocytes but not MDSCs was associated with clinical and pathological features of lower tumour aggressiveness and a more favourable patient outcome. A log‐rank test confirmed an association between concurrent CLT, tumour‐associated macrophage infiltration, and CD8+ lymphocytes and an increased in disease‐free survival, suggesting that evidence of these immune reactions is associated with a favourable prognosis.

Conclusion

Our data suggest that the tumour or peri‐tumoural microenvironment may act to modify the observed pattern of immune response. Immune cell infiltration and the presence of concurrent CLT helped characterize specific tumour histotypes associated with favourable prognostic features.
Combining projected changes in species richness and composition reveals climate change impacts on coastal Mediterranean fish assemblages
Authors: Albouy Camille , Guilhaumon François , Araújo Miguel B. , Mouillot David , Leprieur Fabien
Published: June 2012

Species Temporal Turnover (STT) is one of the most familiar metrics to assess changes in assemblage composition as a consequence of climate change. However, STT mixes two components in one metric, changes in assemblage composition caused by a process of species loss or gain (i.e. the nestedness component) and changes in assemblage composition caused by a process of species replacement (i.e. the species replacement component). Drawing on previous studies investigating spatial patterns of beta diversity, we propose measures of STT that allow analysing each component (species replacement vs. nestedness), separately. We also present a mapping strategy to simultaneously visualize changes in species richness and assemblage composition. To illustrate our approach, we used the Mediterranean coastal fish fauna as a case study. Using Bioclimatic Envelope Models (BEMs) we first projected the potential future climatic niches of 288 coastal Mediterranean fish species based on a global warming scenario. We then aggregated geographically the species‐level projections to analyse the projected changes in species richness and composition. Our results show that projected changes in assemblage composition are caused by different processes (species replacement vs. nestedness) in several areas of the Mediterranean Sea. In addition, our mapping strategy highlights that the coastal fish fauna in several regions of the Mediterranean Sea could experience a ‘cul‐de‐sac’ effect if exposed to climate warming. Overall, the joint exploration of changes in species richness and composition coupled with the distinction between species replacement and nestedness bears important information for understanding the nature of climate change impacts on biodiversity. These methodological advances should help decision‐makers in prioritizing action in the areas facing the greatest vulnerability to climate.
Determinants of participation in patients with severe haemophilia
Authors: van Genderen F. R. , van Meeteren N. L. U. , Fischer K. , Helders P. J. M.
Published: June 2012

The multifactorial nature of disability makes it difficult to point out a specific cause for limitations in participation. The conceptual framework of the WHO‐ICF (International Classification of Function, Disability and Health) was used to study the determinants participation in patients with severe haemophilia. Outcome was assessed in a single‐centre cohort of 124 patients with severe haemophilia. Joint mobility and muscle strength of the elbows, knees and ankles, in combination with recent X‐ray findings (N = 39 only) and the MPQ‐DLV pain questionnaire were used to assess Body Functions and Structures. Four performance‐based functional tasks and the HAL questionnaire were used to assess Activities. The IPA questionnaire was used to assess Participation. Stepwise and hierarchical regression analysis adjusted for age and psychological health (Dutch‐AIMS 2) was used to associate the various domains of the ICF. Irrespective of age, joint mobility was an important factor in explaining self‐reported and performance‐based activities. Muscle strength had no significant association with participation. Self‐reported activities showed a stronger association with participation than performance‐based activities. Adjusted for age and psychological health, joint mobility and pain explained none of the variation in participation. Self‐reported activities, however, significantly contributed in explaining participation (25%), whereas performance‐based activities (3%) did not. This study adds to the knowledge of determinants of participation in haemophilia. As the currently used instruments on joint status and activities only partially explain differences in participation, this aspect of clinical outcome should be included to fully assess outcome in haemophilia.
Fine‐tuning the fruit‐tracking hypothesis: spatiotemporal links between fruit availability and fruit consumption by birds in Andean mountain forests
Authors: Blendinger Pedro G. , Ruggera Román A. , Núñez Montellano M. Gabriela , Macchi Leandro , Zelaya Patricia V. , Álvarez M. Eva , Martín Eduardo , Acosta Oriana Osinaga , Sánchez Rocío , Haedo Josefina
Published: June 2012

1. The fruit‐tracking hypothesis predicts spatiotemporal links between changes in the abundance of fruit‐eating birds and the abundance of their fleshy‐fruit resources.

2. While the spatial scale of plant–frugivore interactions has been explored to understand mismatches between observed and expected fruit–frugivore patterns, methodological issues such as the consequences of measuring fruit and frugivore abundance rather than fruit availability and fruit consumption have not been evaluated.

3. Here, we explored whether predicted fruit–frugivore spatiotemporal links can be captured with higher accuracy by proximate measurements of interaction strength. We used a 6‐ha grided plot in an Andean subtropical forest to study the link between (i) fruit and fruit‐eating bird abundances; (ii) fruit availability and frequency of fruit consumption; and (iii) covariation between frugivore abundance and frequency of frugivory. We evaluated these links for the entire frugivore assemblage and for the four most important species using data gathered bimonthly along a 2‐year period.

4. Fleshy‐fruit availability and abundance varied sharply temporally and were patchily distributed in mosaics that differed in fruit quantity. Fruit availability and abundance also varied along spatial gradients extended over the whole study plot. We found a strong response of the entire frugivorous bird assemblage to fruit availability over time, and a weakly significant relationship over space at the local scale. The main frugivore species widely differed in their responses to changes in fruit abundance in such a way that response at the assemblage level cannot be seen as the sum of individual responses of each species. Our results suggest that fruit tracking in frugivorous–insectivorous birds may be largely explained by species‐specific responses to changes in the availability of fruits and alternative resources.

5. In agreement with our prediction, more accurate measurements of interaction strength described fruit–frugivore relationships better than traditional measurements. Moreover, we show that covariation between frugivore abundance, frequency of fruit consumption and fruit availability must be included in the fruit‐tracking hypothesis framework to demonstrate (or reject) spatiotemporal fruit tracking. We propose that estimation of nutrient and energy availability in fruits could be a new frontier to understanding the forces driving foraging decisions that lead to fruit tracking.
Effects of Calcium Supplementation During Pregnancy on Maternal, Fetal and Birth Outcomes
Authors: Imdad Aamer , Bhutta Zulfiqar A.
Published: June 2012

Gestational hypertensive disorders are the second leading cause of maternal death worldwide. Epidemiological and clinical studies have shown that an inverse relationship exists between calcium intake and development of hypertension in pregnancy. The purpose of this review was to evaluate preventive effect of calcium supplementation during pregnancy on gestational hypertensive disorders and related maternal and neonatal morbidity and mortality. A literature search was carried out on PubMed, WHOLIS, PAHO and Cochrane Library. Only randomised trials were included in the review. Data were extracted into a standardised Excel sheet. Primary outcomes were pre‐eclampsia, preterm birth and birthweight. Other neonatal outcomes such as neonatal mortality, small‐for‐gestational age and low birthweight were also evaluated. A total of 15 randomised controlled trials were included in this review. Pooled analysis showed that calcium supplementation during pregnancy reduced risk of pre‐eclampsia by 52% [relative risk (RR) 0.48; 95% confidence interval (CI) 0.34, 0.67] and that of severe pre‐eclampsia by 25% (RR 0.75 [95% CI 0.57, 0.98]). There was no effect on incidence of eclampsia (RR 0.73 [95% CI 0.41, 1.27]). There was a significant reduction for risk of maternal mortality/severe morbidity (RR 0.80 [95% CI 0.65, 0.97]). Calcium supplementation during pregnancy was also associated with a significant reduction in risk of pre‐term birth (RR 0.76 [95% CI 0.60, 0.97]). There was an extra gain of 85 g in the intervention group compared with control (mean difference 85 g [95% CI 37, 133]). There was no effect of calcium supplementation on perinatal mortality (RR 0.90 [95% CI 0.74, 1.09]). There was a statistically non‐significant increased risk of urolithiasis in the intervention group compared with control (RR 1.52 [95% CI 0.06, 40.67]). In conclusion, calcium supplementation during pregnancy is associated with a reduction in risk of gestational hypertensive disorders and pre‐term birth and an increase in birthweight. There is no increased risk of kidney stones.