bluuebunny/crossref_metadata_2025 huggingface dataset:
Diversity, abundance and expression of nitrite reductase (nirK)-like genes in marine thaumarchaea
Authors: Lund Marie B , Smith Jason M , Francis Christopher A
Published: May 2012

Ammonia-oxidizing archaea (AOA) are widespread and abundant in aquatic and terrestrial habitats and appear to have a significant impact on the global nitrogen cycle. Like the ammonia-oxidizing bacteria, AOA encode a gene homologous to copper-containing nitrite reductases (nirK), which has been studied very little to date. In this study, the diversity, abundance and expression of thaumarchaeal nirK genes from coastal and marine environments were investigated using two mutually excluding primer pairs, which amplify the nirK variants designated as AnirKa and AnirKb. Only the AnirKa variant could be detected in sediment samples from San Francisco Bay and these sequences grouped with the nirK from Candidatus Nitrosopumilus maritimus and Candidatus Nitrosoarchaeum limnia. The two nirK variants had contrasting distributions in the water column in Monterey Bay and the California Current. AnirKa was more abundant in the epi- to mesopelagic Monterey Bay water column, whereas AnirKb was more abundant in the meso- to bathypelagic California Current water. The abundance and community composition of AnirKb, but not AnirKa, followed that of thaumarchaeal amoA, suggesting that either AnirKa is not exclusively associated with AOA or that commonly used amoA primers may be missing a significant fraction of AOA diversity in the epipelagic. Interestingly, thaumarchaeal nirK was expressed 10–100-fold more than amoA in Monterey Bay. Overall, this study provides valuable new insights into the distribution, diversity, abundance and expression of this alternative molecular marker for AOA in the ocean.
Nitrification of archaeal ammonia oxidizers in acid soils is supported by hydrolysis of urea
Authors: Lu Lu , Han Wenyan , Zhang Jinbo , Wu Yucheng , Wang Baozhan , Lin Xiangui , Zhu Jianguo , Cai Zucong , Jia Zhongjun
Published: May 2012

The hydrolysis of urea as a source of ammonia has been proposed as a mechanism for the nitrification of ammonia-oxidizing bacteria (AOB) in acidic soil. The growth of Nitrososphaera viennensis on urea suggests that the ureolysis of ammonia-oxidizing archaea (AOA) might occur in natural environments. In this study, 15N isotope tracing indicates that ammonia oxidation occurred upon the addition of urea at a concentration similar to the in situ ammonium content of tea orchard soil (pH 3.75) and forest soil (pH 5.4) and was inhibited by acetylene. Nitrification activity was significantly stimulated by urea fertilization and coupled well with abundance changes in archaeal amoA genes in acidic soils. Pyrosequencing of 16S rRNA genes at whole microbial community level demonstrates the active growth of AOA in urea-amended soils. Molecular fingerprinting further shows that changes in denaturing gradient gel electrophoresis fingerprint patterns of archaeal amoA genes are paralleled by nitrification activity changes. However, bacterial amoA and 16S rRNA genes of AOB were not detected. The results strongly suggest that archaeal ammonia oxidation is supported by hydrolysis of urea and that AOA, from the marine Group 1.1a-associated lineage, dominate nitrification in two acidic soils tested.
Metabolic specialization and the assembly of microbial communities
Authors: Johnson David R , Goldschmidt Felix , Lilja Elin E , Ackermann Martin
Published: May 2012

Metabolic specialization is a general biological principle that shapes the assembly of microbial communities. Individual cell types rarely metabolize a wide range of substrates within their environment. Instead, different cell types often specialize at metabolizing only subsets of the available substrates. What is the advantage of metabolizing subsets of the available substrates rather than all of them? In this perspective piece, we argue that biochemical conflicts between different metabolic processes can promote metabolic specialization and that a better understanding of these conflicts is therefore important for revealing the general principles and rules that govern the assembly of microbial communities. We first discuss three types of biochemical conflicts that could promote metabolic specialization. Next, we demonstrate how knowledge about the consequences of biochemical conflicts can be used to predict whether different metabolic processes are likely to be performed by the same cell type or by different cell types. We then discuss the major challenges in identifying and assessing biochemical conflicts between different metabolic processes and propose several approaches for their measurement. Finally, we argue that a deeper understanding of the biochemical causes of metabolic specialization could serve as a foundation for the field of synthetic ecology, where the objective would be to rationally engineer the assembly of a microbial community to perform a desired biotransformation.
Renal stem cells: fact or science fiction?
Authors: McCampbell Kristen K. , Wingert Rebecca A.
Published: May 2012

The kidney is widely regarded as an organ without regenerative abilities. However, in recent years this dogma has been challenged on the basis of observations of kidney recovery following acute injury, and the identification of renal populations that demonstrate stem cell characteristics in various species. It is currently speculated that the human kidney can regenerate in some contexts, but the mechanisms of renal regeneration remain poorly understood. Numerous controversies surround the potency, behaviour and origins of the cell types that are proposed to perform kidney regeneration. The present review explores the current understanding of renal stem cells and kidney regeneration events, and examines the future challenges in using these insights to create new clinical treatments for kidney disease.
Regulation of synaptic functions in central nervous system by endocrine hormones and the maintenance of energy homoeostasis
Authors: Pang Zhiping P. , Han Weiping
Published: May 2012

Energy homoeostasis, a co-ordinated balance of food intake and energy expenditure, is regulated by the CNS (central nervous system). The past decade has witnessed significant advances in our understanding of metabolic processes and brain circuitry which responds to a broad range of neural, nutrient and hormonal signals. Accumulating evidence demonstrates altered synaptic plasticity in the CNS in response to hormone signals. Moreover, emerging observations suggest that synaptic plasticity underlies all brain functions, including the physiological regulation of energy homoeostasis, and that impaired synaptic constellation and plasticity may lead to pathological development and conditions. Here, we summarize the current knowledge on the regulation of postsynaptic receptors such as AMPA (α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid), NMDA (N-methyl-D-aspartate) and GABA (γ-aminobutyric acid) receptors, and the presynaptic components by hormone signals. A detailed understanding of the neurobiological mechanisms by which hormones regulate energy homoeostasis may lead to novel strategies in treating metabolic disorders.
Genes expression profiling of peripheral blood cells of patients with hepatocellular carcinoma
Authors: Zhang Peng‐jun , Wei Run , Wen Xin‐yu , Ping Liang , Wang Cheng‐bin , Dong Zhen‐nan , Deng Xin‐xin , Bo Wang , Bin Chen , Tian Ya‐ping
Published: May 2012

HCC (hepatocellular carcinoma) is often diagnosed at an advanced stage with poor prognosis. Peripheral blood may be useful in cancer classification, and therefore we investigated the gene expression found by Affymetrix HG‐U133 Plus2.0 microarray, with samples from nine HCC patients and five healthy NC (normal controls). A total of 726 probe sets showed significant differences based on the criteria of P<0.05 and absolute fold change >2. The genes were related to many biological functions, including immune response, transcription regulation and metabolism processes. Ten genes [IL‐8 (interleukin 8), GOS2 (G0/G1 switch gene 2), CXCR4 (CXC chemokine receptor 4), FOS, RPS24 (40S ribosomal protein S24), HAP90AA1, PFDN5, RPL27, GZMA and PFN1] showing significant differences were confirmed by real‐time PCR in 54 HCC patients and 56 healthy NC. Seven genes [IL‐8, GOS2, CXCR4, FOS, RPS24, HSP90AA1 (heat shock protein 90AA1) and PFN1] showed significant difference both in RT—PCR (reverse transcription—PCR) and microarray. Expression of IL‐8 and FOS proteins was up‐regulated in HCC compared with healthy controls. A gene signature in peripheral blood which can distinguish HCC patients and healthy controls may have been identified.
Acceleration of cone-produced electrons by double-line Ti-sapphire laser beating
Authors: Mori Y. , Kitagawa Y.
Published: May 2012

Acceleration of electrons is demonstrated in a beat wave scheme by using a prepulse-free short-pulse (150 fs) double-line Ti-sapphire laser. To inject electrons, we used a hybrid target composed of a cone-drilled plate and a gas jet, where the cone-produced electrons were accelerated via the forced plasma wave excited in the gas jet that was situated behind the plate. This resulted in an increase in slope temperature from 0.05 to 0.15 MeV. We find a correlation between the slope temperature and forced relativistic plasma wave. The wake amplitude is 15 GV/m at the resonant density of 2.5×1018 cm-3 in a hydrogen plasma. The wake acceleration models can explain the increase in slope temperature.
Translation representations and scattering by two intervals
Authors: Jorgensen Palle , Pedersen Steen , Tian Feng
Published: May 2012

Studying unitary one-parameter groups in Hilbert space \documentclass[12pt]{minimal}\begin{document}$(U(t),\mathscr{H})$\end{document}(U(t),H), we show that a model for obstacle scattering can be built, up to unitary equivalence, with the use of translation representations for L2-functions in the complement of two finite and disjoint intervals. The model encompasses a family of systems \documentclass[12pt]{minimal}\begin{document}$(U(t),\mathscr{H})$\end{document}(U(t),H). For each, we obtain a detailed spectral representation, and we compute the scattering operator and scattering matrix. We illustrate our results in the Lax-Phillips model where \documentclass[12pt]{minimal}\begin{document}$(U(t),\mathscr{H})$\end{document}(U(t),H) represents an acoustic wave equation in an exterior domain; and in quantum tunneling for dynamics of quantum states.
The use of optical microscopy to examine crystallite nucleation and growth in thermally annealed plasma enhanced chemical vapor deposition and hot wire chemical vapor deposition a-Si:H films
Authors: Mahan A. H. , Dabney M. S. , Reedy R. C. , Molina D. , Ginley D. S.
Published: May 2012

We report a simple method to investigate crystallite nucleation and growth in stepwise, thermally annealed plasma enhanced chemical vapor deposition and hot wire chemical vapor deposition a-Si:H films. By confining film thicknesses to the range 500–4000 Å, optical microscopy in the reflection mode can be used to readily detect crystallites in the thermally annealed a-Si:H lattice. Measurements of the crystallite density versus annealing time for identically prepared films of different thickness show that the crystallite nucleation rate is smaller for thinner films, suggesting that crystallite nucleation is homogeneous, in agreement with previous results. A comparison of film nucleation rates with those obtained by other methods on identically prepared films shows excellent agreement, thus establishing the validity of the current technique. The potential effect of impurity (oxygen) incorporation during the stepwise annealing in air is shown not to affect crystallite nucleation and growth, in that SIMS oxygen profiles for stepwise versus continuous annealing show not only similar impurity profiles but also similar bulk impurity densities.
Tripolar vortex formation in dense quantum plasma with ion-temperature-gradients
Authors: Qamar Anisa , Ata-ur-Rahman  , Mirza Arshad M.
Published: May 2012

We have derived system of nonlinear equations governing the dynamics of low-frequency electrostatic toroidal ion-temperature-gradient mode for dense quantum magnetoplasma. For some specific profiles of the equilibrium density, temperature, and ion velocity gradients, the nonlinear equations admit a stationary solution in the form of a tripolar vortex. These results are relevant to understand nonlinear structure formation in dense quantum plasmas in the presence of equilibrium ion-temperature and density gradients.
Fe doped ZnO thin film for mediator-less biosensing application
Authors: Saha Shibu , Tomar Monika , Gupta Vinay
Published: May 2012

Fe doped ZnO (FZO) thin film is prepared by pulsed laser deposition for its application as mediator-less biosensing matrix. Fe doping introduces redox centre in ZnO along with shallow donor level and promotes the electron transfer capability due to substitution of Fe at Zn sites. Glucose oxidase (GOx), chosen as model enzyme, was immobilized on surface of the prepared matrix. Cyclic voltammetry and photometric assay show that the developed bio-electrode, GOx/FZO/indium tin oxide/Glass is sensitive to glucose concentration with enhanced response (0.2 µA mM−1 cm−2) and low Km (3.01 mM). The results show promising application of Fe doped ZnO thin film as an attractive matrix for mediator-less biosensing.
Threshold resistive and capacitive switching behavior in binary amorphous GeSe
Authors: Jeong Doo Seok , Lim Hyungkwang , Park Goon-Ho , Hwang Cheol Seong , Lee Suyoun , Cheong Byung-ki
Published: May 2012

A threshold switching (TS) event in a binary amorphous GeSe film placed between Pt top and bottom electrodes was examined. This GeSe film exhibits fast (<40 ns) TS behavior. The observed TS of the resistance was found to be accompanied with the TS of the capacitance. A mechanism for the TS of the GeSe film was suggested by revisiting the previous controversy about the thermal versus non-thermal electronic mechanism. The non-thermal electronic mechanism envisaging the double-injection of electronic carriers can qualitatively account for the measured threshold resistive and capacitive switching, whereas the TS behavior simulated using the thermal mechanism is inconsistent with the experimental observation.
Hamiltonian magnetohydrodynamics: Helically symmetric formulation, Casimir invariants, and equilibrium variational principles
Authors: Andreussi T. , Morrison P. J. , Pegoraro F.
Published: May 2012

The noncanonical Hamiltonian formulation of magnetohydrodynamics (MHD) is used to construct variational principles for continuously symmetric equilibrium configurations of magnetized plasma, including flow. In particular, helical symmetry is considered, and results on axial and translational symmetries are retrieved as special cases of the helical configurations. The symmetry condition, which allows the description in terms of a magnetic flux function, is exploited to deduce a symmetric form of the noncanonical Poisson bracket of MHD. Casimir invariants are then obtained directly from the Poisson bracket. Equilibria are obtained from an energy-Casimir principle and reduced forms of this variational principle are obtained by the elimination of algebraic constraints.
Suspension flow and sedimentation in self-affine fractures
Authors: Shing Lo Tak , Koplik Joel
Published: May 2012

The transport and gravitational sedimentation of a particulate suspension in fracture joints with self-affinely rough walls is studied by lattice Boltzmann numerical simulations. We consider either homogeneous or bidisperse distributions of non-Brownian spheres in a Newtonian fluid, driven through a fracture by a pressure gradient, and acted upon by gravity. Most results concern the case of open fractures, in which the two walls of the channel do not approach closely enough to block the flow. We present profiles of particle density and profiles of particle and fluid velocities, along with total flow rates and characterizations of the sediment, for three values of particle concentration and a range of buoyancy and Reynolds numbers, principally in the inertial regime. We systematically study the effects of increasing the pressure gradient and the strength of sedimentation and compare the results to those for channel bounded by flat surfaces. We find that both the flow rate and the average particle velocity for flows through an open fracture, when suitably normalized, depend only on the volume fraction of the particles and the buoyancy number in the steady state regardless of the pressure drop, and observe interesting scaling laws in the large buoyancy number limit. We also investigate the possibility for correlations between the surface morphology of the sediment region and the geometry of the underlying fracture surface in the strong sedimentation limit, but no evidence for correlation is found.
Layer-by-layer thermal conductivities of the Group III nitride films in blue/green light emitting diodes
Authors: Su Zonghui , Huang Li , Liu Fang , Freedman Justin P. , Porter Lisa M. , Davis Robert F. , Malen Jonathan A.
Published: May 2012

Thermal conductivities (k) of the individual layers of a GaN-based light emitting diode (LED) were measured along [0001] using the 3-omega method from 100-400 K. Base layers of AlN, GaN, and InGaN, grown by organometallic vapor phase epitaxy on SiC, have effective k much lower than bulk values. The 100 nm thick AlN layer has k = 0.93 ± 0.16 W/mK at 300 K, which is suppressed >100 times relative to bulk AlN. Transmission electron microscope images revealed high dislocation densities (4 × 1010 cm−2) within AlN and a severely defective AlN-SiC interface that cause additional phonon scattering. Resultant thermal resistances degrade LED performance and lifetime making layer-by-layer k, a critical design metric for LEDs.
Interfacial interaction of gas molecules and single-walled carbon nanotubes
Authors: Zhong Jun , Chiou Jauwern , Dong Chungli , Glans Per-Anders , Pong Way-Faung , Chang Chinglin , Wu Ziyu , Guo Jinghua
Published: May 2012

The interfacial interaction between single-walled carbon nanotubes (SWNTs) and various gas molecules (H2, He, and N2) at different pressures has been probed by in situ x-ray absorption near-edge structure (XANES) spectroscopy. Experimental results reveal the different strength of interfacial interaction (involving external and internal collisions) between SWNTs and various gas molecules under different pressures. At gas pressures higher than 5 Torr, the unoccupied states of SWNTs show some features corresponding to the structure deformation with a reversible behavior when cycling under vacuum and gas conditions. The XANES study for different gases (H2, He, and N2) shows a strong dependence of gas molecular weight, which provides experimental evidence to the gas scattering mechanism.
Total instantaneous energy transport in polychromatic fluid gravity waves at finite depth
Authors: Engström J. , Isberg J. , Eriksson M. , Leijon M.
Published: May 2012

The total instantaneous energy transport can be found for polychromatic waves when using the deep water approximation. Expanding this theory to waves in waters of finite depth, we derive an expression for the total instantaneous energy transport for polychromatic fluid gravity waves based on potential theory with linearized free surface boundary conditions. We present the results for time series of wave elevation measured at the Uppsala University wave energy research test site. We show that a significant proportion of the total instantaneous energy transport is not accounted for when using the deep water theory. This is important since many wave energy conversion devices under development will operate in waters that do not fulfil the deep water criteria.
Water uptake dynamics under progressive drought stress in diverse accessions of the OryzaSNP panel of rice (Oryza sativa)
Authors: Gowda Veeresh R. P. , Henry Amelia , Vadez Vincent , Shashidhar H. E. , Serraj Rachid
Published: May 2012

In addition to characterising root architecture, evaluating root water uptake ability is important for understanding drought response. A series of three lysimeter studies were conducted using the OryzaSNP panel, which consists of 20 diverse rice (Oryza sativa L.) genotypes. Large genotypic differences in drought response were observed in this genotype panel in terms of plant growth and water uptake. Total water uptake and daily water uptake rates in the drought-stress treatment were correlated with root length density, especially at depths below 30 cm. Patterns of water uptake among genotypes remained consistent throughout the stress treatments: genotypes that initially extracted more water were the same genotypes that extracted more water at the end of the study. These results suggest that response to drought by deep root growth, rather than a conservative soil water pattern, seems to be important for lowland rice. Genotypes in the O. sativa type aus group showed some of the greatest water uptake and root growth values. Since the OryzaSNP panel has been genotyped in detail with SNP markers, we expect that these results will be useful for understanding the genetics of rice root growth and function for water uptake in response to drought.
Alterations in RNA processing during immune-mediated programmed cell death
Authors: Rajani Danielle K. , Walch Michael , Martinvalet Denis , Thomas Marshall P. , Lieberman Judy
Published: May 2012

During immune-mediated death, death-inducing granzyme (Gzm) proteases concentrate in the nucleus of cells targeted for immune elimination, suggesting that nuclear processes are important targets. Here we used differential 2D proteomics of GzmA-treated nuclei to identify potential GzmA substrates. Of 44 candidates, 33 were RNA-binding proteins important in posttranscriptional RNA processing, including 14 heterogeneous nuclear ribonucleoproteins (hnRNP). Multiple hnRNPs were degraded in cells undergoing GzmA-, GzmB-, or caspase-mediated death. GzmA and caspase activation impaired nuclear export of newly synthesized RNA and disrupted pre-mRNA splicing. Expressing GzmA-resistant hnRNP A1 inhibited GzmA-mediated cell death and rescued pre-mRNA splicing, suggesting that hnRNP A1 is an important GzmA substrate. Cellular stresses are known to inhibit initiation of cap-dependent translation. Disrupting pre-mRNA processing should block further new protein synthesis and promote death by interfering with pathways induced to protect cells from death.
Development of experimental autoimmune encephalomyelitis (EAE) in mice requires vitamin D and the vitamin D receptor
Authors: Wang Yanping , Marling Steven J. , Zhu Jinge G. , Severson Kyle S. , DeLuca Hector F.
Published: May 2012

The development of experimental autoimmune encephalomyelitis (EAE), a model of multiple sclerosis, has been studied in mice that were (i) vitamin D-deficient, (ii) minus the vitamin D receptor, (iii) minus a vitamin D 25-hydroxylase, and (iv) minus the vitamin D 25-hydroxyvitamin D-1α-hydroxylase. EAE development was markedly suppressed in mice lacking the vitamin D receptor and partially suppressed in vitamin D-insufficient mice. However, the absence of either of the two key hydroxylases (i.e., 25-hydroxylase and 1α-hydroxylase) neither inhibits nor enhances the development of EAE. These results indicate that vitamin D and the vitamin D receptor are required for the development of EAE. The results also suggest that 1,25-dihydroxyvitamin D3may not play a role in this autoimmune response.
High-throughput, high-fidelity HLA genotyping with deep sequencing
Authors: Wang Chunlin , Krishnakumar Sujatha , Wilhelmy Julie , Babrzadeh Farbod , Stepanyan Lilit , Su Laura F. , Levinson Douglas , Fernandez-Viña Marcelo A. , Davis Ronald W. , Davis Mark M. , Mindrinos Michael
Published: May 2012

Human leukocyte antigen (HLA) genes are the most polymorphic in the human genome. They play a pivotal role in the immune response and have been implicated in numerous human pathologies, especially autoimmunity and infectious diseases. Despite their importance, however, they are rarely characterized comprehensively because of the prohibitive cost of standard technologies and the technical challenges of accurately discriminating between these highly related genes and their many allelles. Here we demonstrate a high-resolution, and cost-effective methodology to type HLA genes by sequencing, which combines the advantage of long-range amplification, the power of high-throughput sequencing platforms, and a unique genotyping algorithm. We calibrated our method for HLA-A, -B, -C, and -DRB1 genes with both reference cell lines and clinical samples and identified several previously undescribed alleles with mismatches, insertions, and deletions. We have further demonstrated the utility of this method in a clinical setting by typing five clinical samples in an Illumina MiSeq instrument with a 5-d turnaround. Overall, this technology has the capacity to deliver low-cost, high-throughput, and accurate HLA typing by multiplexing thousands of samples in a single sequencing run, which will enable comprehensive disease-association studies with large cohorts. Furthermore, this approach can also be extended to include other polymorphic genes.
Seasonal Patterns in White Crappies' Consumption and Growth: Influences of Varying Water Temperatures and Prey Availability
Authors: Michaletz Paul H. , Bajer Przemyslaw G. , Hayward Robert S.
Published: May 2012

Crappies Pomoxis spp. are popular sport fishes but often fail to achieve sizes that are acceptable to anglers. While many factors may contribute to episodes of suboptimal growth in crappies, insufficient densities of prey fish and high summer water temperatures (>27°C) have been considered to be key underlying causes. We examined the influences of prey fish size, prey availability, and water temperature on the consumption and growth of white crappies P. annularis (ages 1–3) in three Missouri reservoirs over five successive years. Monthly growth rates were estimated using aging analyses, while consumption was estimated using a bioenergetics model. All age‐groups grew fastest in the reservoir that was warmest but in which prey fish availability was the highest. Diet analyses coupled with bioenergetics modeling suggested that white crappies were able to maintain positive growth rates at temperatures exceeding 27°C by maximizing consumption rates when adequate prey fish resources were available. When sufficient prey fish resources were unavailable, white crappies fed on invertebrates and often ceased growing or lost weight, even during periods with suitable water temperatures. Our study documents the importance of adequate prey fish resources for maintaining positive growth rates of white crappies, especially during periods of adverse temperature conditions.
Effect of rapid thermal annealing on the structural and electrical properties of solid ZnO/NiO heterojunctions prepared by a chemical solution process
Authors: Lee Yi-Mu , Yang Hsi-Wen , Huang Chao-Ming
Published: May 2012

Transparent pn-heterojunction electrodes composed of n-type zinc oxide (ZnO) nanorod arrays and p-type NiO are fabricated by a chemical solution route combined with rapid thermal annealing (RTA). The effects of RTA treatment (450 °C, 1 min) in reducing atmosphere on the structural properties and alignment of the ZnO nanorods are investigated. SEM images and XRD patterns show that the average diameter and length are increased, and the alignment and crystal quality of the nanorod arrays are significantly improved. The RTA-treated ZnO shows uniform and well-aligned nanorod arrays with a high aspect ratio of ∼12.4. The structural improvements associated with ZnO crystalline and defect reduction are further verified from the enhanced UV to visible emission ratio by a photoluminescence analysis. Moreover, the effect of RTA on the I–V characteristics of the ZnO/NiO heterojunction electrodes is also investigated; the electrical parameters of the junction are determined from the forward-bias I–V characteristics using Cheung's method. The results reveal that the series resistance is significantly reduced from 784.4 to 114.8 Ω, which leads to better rectifying behaviour with rectifying slope increased to ∼6.67 mA V−1. The RTA-processed ZnO/NiO heterojunctions with excellent optoelectronic properties may find wide applications in sensors and solid-state oxide junction-based devices.
A statistical methodology to derive the scaling law for the H-mode power threshold using a large multi-machine database
Authors: Murari A. , Lupelli I. , Gaudio P. , Gelfusa M. , Vega J.
Published: May 2012

In this paper, a refined set of statistical techniques is developed and then applied to the problem of deriving the scaling law for the threshold power to access the H-mode of confinement in tokamaks. This statistical methodology is applied to the 2010 version of the ITPA International Global Threshold Data Base v6b(IGDBTHv6b). To increase the engineering and operative relevance of the results, only macroscopic physical quantities, measured in the vast majority of experiments, have been considered as candidate variables in the models. Different principled methods, such as agglomerative hierarchical variables clustering, without assumption about the functional form of the scaling, and nonlinear regression, are implemented to select the best subset of candidate independent variables and to improve the regression model accuracy. Two independent model selection criteria, based on the classical (Akaike information criterion) and Bayesian formalism (Bayesian information criterion), are then used to identify the most efficient scaling law from candidate models. The results derived from the full multi-machine database confirm the results of previous analysis but emphasize the importance of shaping quantities, elongation and triangularity. On the other hand, the scaling laws for the different machines and at different currents are different from each other at the level of confidence well above 95%, suggesting caution in the use of the global scaling laws for both interpretation and extrapolation purposes.
Tension-dependent nucleosome remodeling at the pericentromere in yeast
Authors: Verdaasdonk Jolien S. , Gardner Ryan , Stephens Andrew D. , Yeh Elaine , Bloom Kerry
Published: May 2012

Nucleosome positioning is important for the structural integrity of chromosomes. During metaphase the mitotic spindle exerts physical force on pericentromeric chromatin. The cell must adjust the pericentromeric chromatin to accommodate the changing tension resulting from microtubule dynamics to maintain a stable metaphase spindle. Here we examine the effects of spindle-based tension on nucleosome dynamics by measuring the histone turnover of the chromosome arm and the pericentromere during metaphase in the budding yeast Saccharomyces cerevisiae. We find that both histones H2B and H4 exhibit greater turnover in the pericentromere during metaphase. Loss of spindle-based tension by treatment with the microtubule-depolymerizing drug nocodazole or compromising kinetochore function results in reduced histone turnover in the pericentromere. Pericentromeric histone dynamics are influenced by the chromatin-remodeling activities of STH1/NPS1 and ISW2. Sth1p is the ATPase component of the Remodels the Structure of Chromatin (RSC) complex, and Isw2p is an ATP-dependent DNA translocase member of the Imitation Switch (ISWI) subfamily of chromatin-remodeling factors. The balance between displacement and insertion of pericentromeric histones provides a mechanism to accommodate spindle-based tension while maintaining proper chromatin packaging during mitosis.
The inositol 5-phosphatase SHIP2 is an effector of RhoA and is involved in cell polarity and migration
Authors: Kato Katsuhiro , Yazawa Tsubasa , Taki Kentaro , Mori Kazutaka , Wang Shujie , Nishioka Tomoki , Hamaguchi Tomonari , Itoh Toshiki , Takenawa Tadaomi , Kataoka Chikako , Matsuura Yoshiharu , Amano Mutsuki , Murohara Toyoaki , Kaibuchi Kozo
Published: May 2012

Cell migration is essential for various physiological and pathological processes. Polarization in motile cells requires the coordination of several key signaling molecules, including RhoA small GTPases and phosphoinositides. Although RhoA participates in a front–rear polarization in migrating cells, little is known about the functional interaction between RhoA and lipid turnover. We find here that src-homology 2–containing inositol-5-phosphatase 2 (SHIP2) interacts with RhoA in a GTP-dependent manner. The association between SHIP2 and RhoA is observed in spreading and migrating U251 glioma cells. The depletion of SHIP2 attenuates cell polarization and migration, which is rescued by wild-type SHIP2 but not by a mutant defective in RhoA binding. In addition, the depletion of SHIP2 impairs the proper localization of phosphatidylinositol 3,4,5-trisphosphate, which is not restored by a mutant defective in RhoA binding. These results suggest that RhoA associates with SHIP2 to regulate cell polarization and migration.
Endoglin regulates PI3-kinase/Akt trafficking and signaling to alter endothelial capillary stability during angiogenesis
Authors: Lee Nam Y. , Golzio Christelle , Gatza Catherine E. , Sharma Arun , Katsanis Nicholas , Blobe Gerard C.
Published: May 2012

Endoglin (CD105) is an endothelial-specific transforming growth factor β (TGF-β) coreceptor essential for angiogenesis and vascular homeostasis. Although endoglin dysfunction contributes to numerous vascular conditions, the mechanism of endoglin action remains poorly understood. Here we report a novel mechanism in which endoglin and Gα-interacting protein C-terminus–interacting protein (GIPC)–mediated trafficking of phosphatidylinositol 3-kinase (PI3K) regulates endothelial signaling and function. We demonstrate that endoglin interacts with the PI3K subunits p110α and p85 via GIPC to recruit and activate PI3K and Akt at the cell membrane. Opposing ligand-induced effects are observed in which TGF-β1 attenuates, whereas bone morphogenetic protein-9 enhances, endoglin/GIPC-mediated membrane scaffolding of PI3K and Akt to alter endothelial capillary tube stability in vitro. Moreover, we employ the first transgenic zebrafish model for endoglin to demonstrate that GIPC is a critical component of endoglin function during developmental angiogenesis in vivo. These studies define a novel non-Smad function for endoglin and GIPC in regulating endothelial cell function during angiogenesis.
R-Ras controls axon branching through afadin in cortical neurons
Authors: Iwasawa Nariaki , Negishi Manabu , Oinuma Izumi
Published: May 2012

Regulation of axon growth, guidance, and branching is essential for constructing a correct neuronal network. R-Ras, a Ras-family small GTPase, has essential roles in axon formation and guidance. During axon formation, R-Ras activates a series of phosphatidylinositol 3-kinase signaling, inducing activation of a microtubule-assembly promoter—collapsin response mediator protein-2. However, signaling molecules linking R-Ras to actin cytoskeleton–regulating axonal morphology remain obscure. Here we identify afadin, an actin-binding protein harboring Ras association (RA) domains, as an effector of R-Ras inducing axon branching through F-actin reorganization. We observe endogenous interaction of afadin with R-Ras in cortical neurons during the stage of axonal development. Ectopic expression of afadin increases axon branch number, and the RA domains and the carboxyl-terminal F-actin binding domain are required for this action. RNA interference knockdown experiments reveal that knockdown of endogenous afadin suppressed both basal and R-Ras–mediated axon branching in cultured cortical neurons. Subcellular localization analysis shows that active R-Ras–induced translocation of afadin and its RA domains is responsible for afadin localizing to the membrane and inducing neurite development in Neuro2a cells. Overall, our findings demonstrate a novel signaling pathway downstream of R-Ras that controls axon branching.
Tailored telemonitoring in patients with heart failure: results of a multicentre randomized controlled trial
Authors: Boyne Josiane J.J. , Vrijhoef Hubertus J.M. , Crijns Harry J.G.M. , De Weerd Gerjan , Kragten Johannes , Gorgels Anton P.M. ,   on behalf of the TEHAF investigators
Published: May 2012

Aims

Recent increases in heart failure tend to overload the healthcare system. Consequently, there is a need for innovative strategies to reduce heart failure hospitalizations.

Methods and results

A multicentre randomized controlled trial was carried out to test the hypothesis that telemonitoring reduces heart failure hospitalizations during 1 year follow‐up. The mean age of the 382 participating patients was 71.5 (32–93) years; the mean left ventricular ejection fraction was 0.38, and in 61% it was ≤0.45%. Mean time to first heart failure‐related hospitalization was 161 days for the intervention group and 139 days for the usual‐care group; hospitalizations occurred in 18 (9.1%) compared with 25 (13.5%) patients, with a total number of 24 and 43 hospitalizations, respectively [Kaplan–Meier P = 0.151, hazard ratio (HR) 0.65, 95% confidence interval (CI) 0.35–1.17]. Subgroup analysis of the primary endpoint showed benefits for three subgroups: duration of heart failure, having a pacemaker, and co‐habiting. The combined endpoint of heart failure admission and all‐cause mortality was similar for both groups (Kaplan–Meier P = 0.641, HR 0.89, 95% CI 0.69–1.83). No differences were found regarding secondary endpoints, except for the reduced number of face to face contacts with the heart failure nurse (Mann–Whitney P < 0.001). Mortality was 18 (9.1%) in the intervention group and 12 (6.5%) in the usual‐care group (Mann–Whitney P = 0.34, Cox regression analysis P = 0.82).

Conclusion

No significant differences were found regarding the primary endpoint, possibly caused by a relative underpowering of the population combined with well‐treated study groups. However, telemonitoring tends to reduce heart failure (re)admissions and significantly decreases contacts with specialized nurses. Further research with pre‐specified groups, as found in the subgroup analysis, is needed.

Trial registration: NCT00502255.
The Stress-Activated Protein Kinase FgOS-2 Is a Key Regulator in the Life Cycle of the Cereal Pathogen Fusarium graminearum
Authors: Nguyen Thuat Van , Schäfer Wilhelm , Bormann Jörg
Published: May 2012

Fusarium graminearum is one of the most destructive pathogens of cereals and a threat to food and feed production worldwide. It is an ascomycetous plant pathogen and the causal agent of Fusarium head blight disease in small grain cereals and of cob rot disease in maize. Infection with F. graminearum leads to yield losses and mycotoxin contamination. Zearalenone (ZEA) and deoxynivalenol (DON) are hazardous mycotoxins; the latter is necessary for virulence toward wheat. Deletion mutants of the F. graminearum orthologue of the Saccharomyces cerevisiae Hog1 stress-activated protein kinase, FgOS-2 (ΔFgOS-2), showed drastically reduced in planta DON and ZEA production. However, ΔFgOS-2 produced even more DON than the wild type under in vitro conditions, whereas ZEA production was similar to that of the wild type. These deletion strains are dramatically reduced in pathogenicity toward maize and wheat. We constitutively expressed the fluorescent protein dsRed in the deletion strains and the wild type. Microscopic analysis revealed that ΔFgOS-2 is unable to reach the rachis node at the base of wheat spikelets. During vegetative growth, ΔFgOS-2 strains exhibit increased resistance against the phenylpyrrole fludioxonil. Growth of mutant colonies on agar plates supplemented with NaCl is reduced but conidia formation remained unchanged. However, germination of mutant conidia on osmotic media is severely impaired. Germ tubes are swollen and contain multiple nuclei. The deletion mutants completely fail to produce perithecia and ascospores. Furthermore, FgOS-2 also plays a role in reactive oxygen species (ROS)-related signaling. The transcription and activity of fungal catalases is modulated by FgOS-2. Among the genes regulated by FgOS-2, we found a putative calcium-dependent NADPH-oxidase (noxC) and the transcriptional regulator of ROS metabolism, atf1. The present study describes new aspects of stress-activated protein kinase signaling in F. graminearum.
Influence of Nematicides and Fungicides on Spring Wheat in Fields Infested with Soilborne Pathogens
Authors: Smiley Richard W. , Gourlie Jennifer A. , Rhinhart Karl E. L. , Marshall Juliet M. , Anderson Monte D. , Yan Guiping
Published: May 2012

A complex of fungal soilborne pathogens and plant-parasitic nematodes reduces wheat yields in the Pacific Northwest. On several other crops in nematode-infested soils, seed treatment with abamectin (Avicta) or Bacillus firmus (Votivo) or foliar application of spirotetramat (Movento) reduced root injury and improved yield. These products, along with fungicide seed treatments and aldicarb (Temik), were evaluated in 13 spring wheat trials over 3 years. During 2011, the mean wheat yield at four locations was 419 kg/ha greater (valued at $122/ha) from seed treated with fungicides and insecticide than from untreated seed, due to protection against soilborne fungal pathogens. Aldicarb increased the mean grain yield over the fungicide-plus-insecticide treatment by another 798 kg/ha (valued at $254/ha) and also reduced the density of Heterodera avenae but is not registered for use on wheat. Abamectin and B. firmus had negligible effects on grain yield and postharvest density of Pratylenchus spp. and H. avenae. Spirotetramat reduced density of H. avenae but did not improve grain yield. We conclude that management of fungal pathogens by seed protectants remains essential and that management of nematodes can be achieved through crop rotations and genetic resistance.
Oral Absorbable Fat‐soluble Vitamin Formulation in Pediatric Patients With Cholestasis
Authors: Shen Yu‐Mei , Wu Jia‐Feng , Hsu Hong‐Yuan , Ni Yen‐Hsuan , Chang Mei‐Hwei , Liu Yu‐Wen , Lai Hong‐Shiee , Hsu Wen‐Ming , Weng Hui‐Ling , Chen Huey‐Ling
Published: May 2012

Objective:

Fat‐soluble vitamin (FSV) deficiencies are common complications in pediatric patients with chronic cholestasis. The aim of the present study was to evaluate the status of FSV deficiencies in patients under present practice and to test the effect of an oral, absorbable, fat‐soluble vitamin formulation (OAFSV) in these patients.

Methods:

We recruited a total of 23 pediatric patients receiving conventional FSV supplementation in a single medical center, with diagnosis of biliary atresia (10), progressive familial intrahepatic cholestasis (9), Alagille syndrome (2), and other conditions (2). Ten patients switched to OAFSV and continued for 3 months. Plasma levels of vitamins A, D, and E and an international normalized ratio (INR) for prothrombin time (PT), a surrogate marker for vitamin K deficiency, were measured.

Results:

The proportion of patients with FSV A, D, E, and K deficiencies under conventional supplementation was 73.9%, 81.8%, 91.3%, and 20.0%, respectively. In patients with total bilirubin levels ≥3.0 mg/dL, the proportion of at least 1 FSV deficiency was 100%; and the deficiency rates of vitamin A, D, E, and K were 78.6%, 100.0%, 100.0% and 21.4%, respectively. Of the 10 patients receiving standard daily dose of OAFSV for 3 months, no adverse events or overdose effects were found. The rates of vitamin A, D, and E deficiency in the patients receiving OAFSV decreased from 80.0%, 100%, and 100%, respectively, to 70.0%, 60.0%, and 60.0% after 3 months of oral supplementation.

Conclusions:

High rates of FSV deficiency were found in pediatric patients with chronic cholestasis under present follow‐up. OAFSV supplementation is safe and potentially effective in pediatric patients with cholestasis.
More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs
Authors: Crawford Nicholas G. , Faircloth Brant C. , McCormack John E. , Brumfield Robb T. , Winker Kevin , Glenn Travis C.
Published: May 2012

We present the first genomic-scale analysis addressing the phylogenetic position of turtles, using over 1000 loci from representatives of all major reptile lineages including tuatara. Previously, studies of morphological traits positioned turtles either at the base of the reptile tree or with lizards, snakes and tuatara (lepidosaurs), whereas molecular analyses typically allied turtles with crocodiles and birds (archosaurs). A recent analysis of shared microRNA families found that turtles are more closely related to lepidosaurs. To test this hypothesis with data from many single-copy nuclear loci dispersed throughout the genome, we used sequence capture, high-throughput sequencing and published genomes to obtain sequences from 1145 ultraconserved elements (UCEs) and their variable flanking DNA. The resulting phylogeny provides overwhelming support for the hypothesis that turtles evolved from a common ancestor of birds and crocodilians, rejecting the hypothesized relationship between turtles and lepidosaurs.
Nitric oxide transport in an axisymmetric stenosis
Authors: Liu Xiao , Fan Yubo , Xu X. Yun , Deng Xiaoyan
Published: May 2012

To test the hypothesis that disturbed flow can impede the transport of nitric oxide (NO) in the artery and hence induce atherogenesis, we used a lumen–wall model of an idealized arterial stenosis with NO produced at the blood vessel–wall interface to study the transport of NO in the stenosis. Blood flows in the lumen and through the arterial wall were simulated by Navier–Stokes equations and Darcy's Law, respectively. Meanwhile, the transport of NO in the lumen and the transport of NO within the arterial wall were modelled by advection–diffusion reaction equations. Coupling of fluid dynamics at the endothelium was achieved by the Kedem–Katchalsky equations. The results showed that both the hydraulic conductivity of the endothelium and the non-Newtonian viscous behaviour of blood had little effect on the distribution of NO. However, the blood flow rate, stenosis severity, red blood cells (RBCs), RBC-free layer and NO production rate at the blood vessel–wall interface could significantly affect the transport of NO. The theoretical study revealed that the transport of NO was significantly hindered in the disturbed flow region distal to the stenosis. The reduced NO concentration in the disturbed flow region might play an important role in the localized genesis and development of atherosclerosis.
Retention of δ-ferrite in aluminium-alloyed TRIP-assisted steels
Authors: Choi Young Joo , Suh Dong-Woo , Bhadeshia H. K. D. H.
Published: May 2012

There have been significant difficulties in the theoretical justification for the optimization of δ-TRIP steel, since the original concept was invented. In particular, the prediction of phase fractions has been notoriously unreliable using standard thermodynamic methods. New thermodynamic databases have become available and seem to explain the results pertaining to both published and new experiments conducted to probe the data. Solidification experiments are reported in order to test the non-equilibrium retention of excess δ-ferrite in the microstructure observed at an ambient temperature. These provided valuable information for comparison against kinetic simulations that prove that the excess ferrite cannot be attributed to growth phenomena. Instead, evidence is offered to show that it is the difficulty in nucleating austenite that prevents the thermodynamically required transformation of δ-ferrite.