bluuebunny/crossref_metadata_2025 huggingface dataset:
The smallest man‐made jet engine
Authors: Sanchez Samuel , Solovev Alexander A. , Harazim Stefan M. , Deneke Christoph , Feng Mei Yong , Schmidt Oliver G.
Published: September 2011

The design of catalytic engines powered by chemical fuels is an exciting and emerging field in multidisciplinary scientific communities. Recent progress in nanotechnology has enabled scientists to shrink the size of macroengines down to microscopic, but yet powerful, engines. Since a couple of years ago, we have reported our progress towards the control and application of catalytic microtubular engines powered by the breakdown of hydrogen peroxide fuel which produces a thrust of oxygen bubbles. Efforts were undertaken in our group to prove whether the fabrication of nanoscale jets is possible. Indeed, the smallest jet engine (600 nm in diameter and 1 picogram of weight) was synthesized based on heteroepitaxially grown layers. These nanojets are able to self‐propel in hydrogen peroxide solutions and are promising for the realisation of multiple tasks. DOI 10.1002/tcr.201100010
Human equilibrative nucleoside transporter 1 expression is a strong independent prognostic factor in UICC T3—T4 pancreatic cancer patients treated with preoperative gemcitabine‐based chemoradiotherapy
Authors: Murata Yasuhiro , Hamada Takashi , Kishiwada Masashi , Ohsawa Ichiro , Mizuno Shugo , Usui Masanobu , Sakurai Hiroyuki , Tabata Masami , Ii Noriko , Inoue Hiroyuki , Shiraishi Taizo , Isaji Shuji
Published: September 2011

Background/purpose

We aimed to determine the relationship between the intratumoral expression of human equilibrative nucleoside transporter (hENT1), the main gemcitabine transporter into cells, and the outcome of gemcitabine‐based chemoradiotherapy (Gem‐CRT) in patients with International Union Against Cancer (UICC) T3—T4 pancreatic adenocarcinoma.

Methods

The expressions of hENT1, thymidylate synthase (TS), and dihydropyrimidine dehydrogenase were immunohistochemically analyzed using the resected specimens from 55 patients (T3, 38 and T4, 17) who had received curative‐intent resection after Gem‐CRT.

Results

The status of hENT1 expression (positive in 39 and negative in 16) was significantly associated with “clinical efficacy” (defined as more than 50% reduction of the serum carbohydrate antigen [CA] 19‐9 level with stable disease [SD] or partial response [PR] according to the Response Evaluation Criteria in Solid Tumors [RECIST]) for Gem‐CRT. The 1‐ and 3‐year overall survival (OS) rates were significantly higher in the positive hENT1 expression group (82.9, 39.5%) than in the negative expression group (42.9, 14.3%) (p = 0.0037). According to combination analysis of hENT1 and TS expressions, the 1‐ and 3‐year OS rates were significantly higher in the positive‐low combination (89.1, 51.0%) group than in the negative‐high group (66.7, 0%) (p = 0.023). Multivariate analysis revealed that positive hENT1 expression and R0 resection were significant prognostic factors for OS.

Conclusions

The hENT1 expression in pancreatic adenocarcinoma strongly influences the outcome of preoperative Gem‐CRT treatment. This biomarker could become a useful predictor of therapeutic effect for gemcitabine‐based therapy in pancreatic cancer patients.
Pregnancy and its management in women with GSD type III ‐ a single centre experience
Authors: Ramachandran Radha , Wedatilake Yehani , Coats Caroline , Walker Fiona , Elliott Perry , Lee Philip J , Lachmann Robin H , Murphy Elaine
Published: September 2011

We present a review of our experience and pregnancy outcome in patients with GSD III managed by our centre. Between 1997 and 2010 there were 15 pregnancies in seven women with GSD III. Four women had GSD IIIb (nine pregnancies) and three GSD IIIa (six pregnancies). There was a successful outcome in all 15 pregnancies with delivery of 15 liveborn infants. Four infants were of low birthweight (<2nd centile) but all have developed normally apart from one with behavioural/psychiatric problems. Three women had pre‐existing cardiomyopathy prior to pregnancy. One of these women had deterioration of her cardiomyopathy during pregnancy and again in the post‐partum period. Women with GSD III do not seem to have any issues with fertility. Overall the outcome of pregnancy for both mother and child is good. Care needs to be taken to avoid maternal hypoglycemia which may be associated with intrauterine growth restriction and low birth weight. Cardiac function should be monitored carefully particularly in those with pre‐existing cardiomyopathy.
Family Physicians’ Awareness and Knowledge of the Genetic Information Non‐Discrimination Act (GINA)
Authors: Laedtke Amanda L. , O'Neill Suzanne M. , Rubinstein Wendy S. , Vogel Kristen J.
Published: September 2011

Historically, physicians have expressed concern about their patients’ risk of genetic discrimination, which has acted as a barrier to uptake of genetic services. The Genetic Information Nondiscrimination Act of 2008 (GINA) is intended to protect patients against employer and health insurance discrimination. Physicians’ awareness and knowledge of GINA has yet to be evaluated. In 2009, we mailed surveys to 1500 randomly selected members of the American Academy of Family Physicians. Questions measured physicians’ current knowledge of GINA and their level of concern for genetic discrimination. In total, 401 physicians completed the survey (response rate 26.9%). Approximately half (54.5%) of physicians had no awareness of GINA. Of physicians who reported basic knowledge of GINA, the majority were aware of the protections offered for group health insurance (92.7%), private health insurance (82.9%), and employment (70.7%). Fewer physicians were aware of GINA's limitations regarding life insurance (53.7%) and long‐term care insurance (58.8%). Physicians demonstrated highest levels of concern for health insurance, life insurance, and long‐term care insurance discrimination, with less concern for employer and family/social discrimination. Level of concern for the risk of genetic discrimination did not correlate significantly with awareness of GINA. Approximately 17 months after GINA was signed into federal law, physicians’ knowledge remained limited regarding the existence of this legislation and relevant details. Physicians who are aware of GINA continue to have significant concerns regarding the risk of genetic discrimination. This study reveals the need to further educate physicians about the existence of GINA and the protections offered.
Improving Acid Number Testing of Biodiesel Feedstock and Product
Authors: Kovács A. , Czinkota I. , Tóth J.
Published: September 2011

The acidity of low and high free fatty acid containing feedstock varieties and biodiesel production intermediary products were tested using a variety of standard methods by the use of manual and automatic titration apparatus. The objective was to select the optimal test method for intermediary products in biodiesel processing and to optimize the selected technique by reducing the extent of bias. We found that there are two major reasons for variations in electrode potential readings. Colloid chemistry has an impact on the initial phase of titration by breakage and reformulation of the partially disperse system. Electric and magnetic fields in the titration beaker were the main reasons for sensitive fluctuations in electrode potentials in the potential range of interest for acid number readings. Refluxing the analyte with the diluting solvent proved to be an efficient technique to offset the influence of colloid processes. Addition of a filter electrolyte to the titration solvent allowed the filter fluctuations to be related to changes in uniformity of electric and magnetic fields in the titration beaker. Addition of filter electrolyte improved signal reliability than shading the external noises by wrapping the titration beaker in aluminium foil. Mathematical interpretation of potential readings revealed the extent of improvement in electrode potential fluctuation by the techniques employed. Both the aqueous and non‐aqueous titration are suitable for accurate testing the acid number of biodiesel feedstock and intermediary products.
Synthesis of Animal Fats Ethylolamides, Ethylolamide Phosphates and Their Petroleum‐Collecting and Dispersing Properties
Authors: Asadov Ziyafaddin H. , Rahimov Ravan A. , Salamova Nargiz V.
Published: September 2011

Ethylolamides of animal (beef and mutton) fats have been synthesized and modified with H3PO4. The identity of these products was confirmed by IR and NMR spectroscopy. The physical properties of the synthesized surfactants including interfacial tension and critical micelle concentration (CMC) were studied. From these measurements, the maximum surface excess concentration and the minimum area per molecule at the kerosene solution/water interface, the surface pressure at the CMC, and the standard thermodynamic parameters of adsorption and micellization were calculated. Ethylolamides and ethylolamide phosphates were obtained and tested as petroleum‐collecting and petroleum‐dispersing reagents. Some correlations between these parameters of the ethylol units and their ability to collect thin petroleum films from the water surface were revealed.
Lubricity‐Enhancing Low‐Temperature Diesel Fuel Additives
Authors: Wang Sunmin , Shen Jianheng , Reaney Martin J. T.
Published: September 2011

Branched chain alkyl esters have lower crystallization temperatures than those with straight chain headgroups. We investigated the effect of branched chain headgroups on the cold flow properties and lubricity of alkyl esters. Commercial grade canola methyl ester was transformed into branched chain alkyl esters through a two or three‐stage base‐catalyzed transesterification reaction with 1‐methoxy‐2‐propanol and 3‐methyl‐1‐butanol. Conversion rates between 85 and 95% were achieved. The alkyl esters exhibited improved cold flow properties. The pour points were reduced from −12 to −27 °C as a result of incorporating branched headgroups. Addition of 0.1 or 0.2% (v/v) 1‐methoxy‐2‐propyl alkyl ester improved the lubricity of a commercial pre‐production ultra low sulfur diesel (ULSD) fuel, as determined by increased lubricity number and reduced wear scar diameter. The inclusion of methyl‐tert butyl ether or ethanolamides additives to ULSD containing alkyl esters had an antagonistic effect on lubricity. The branched‐chain alkyl esters have the potential to be used as lubricity‐enhancing and low‐temperature fuel additives.
INHOMOGENEOUS PERIODIC PARABOLIC PROBLEMS WITH INDEFINITE DATA
Authors: GODOY T. , KAUFMANN U.
Published: September 2011

Let Ω⊂ℝNbe a smooth bounded domain and letf⁄≡0 be a possibly discontinuous and unbounded function. We give a necessary and sufficient condition onffor the existence of positive solutions for allλ>0 of Dirichlet periodic parabolic problems of the formLu=h(x,t,u)+λf(x,t), wherehis a nonnegative Carathéodory function that is sublinear at infinity. When this condition is not fulfilled, under some additional assumptions onhwe characterize the set ofλs for which the aforementioned problem possesses some positive solution. All results remain true for the corresponding elliptic problems.
RATIONAL POINTS ON THREE SUPERELLIPTIC CURVES
Authors: SHEN ZHONGYAN , CAI TIANXIN
Published: September 2011

In this paper, we obtain all rational points (x,y) on the superelliptic curves
Dissociation mediates the relationship between childhood trauma and hallucination-proneness
Authors: Varese F. , Barkus E. , Bentall R. P.
Published: September 2011

Background

It has been proposed that the relationship between childhood trauma and hallucinations can be explained by dissociative processes. The present study examined whether the effect of childhood trauma on hallucination-proneness is mediated by dissociative tendencies. In addition, the influence of dissociative symptoms on a cognitive process believed to underlie hallucinatory experiences (i.e. reality discrimination; the capacity to discriminate between internal and external cognitive events) was also investigated.

Method

Patients with schizophrenia spectrum disorders (n=45) and healthy controls (with no history of hallucinations;n=20) completed questionnaire measures of hallucination-proneness, dissociative tendencies and childhood trauma, as well as performing an auditory signal detection task.

Results

Compared to both healthy and non-hallucinating clinical controls, hallucinating patients reported both significantly higher dissociative tendencies and childhood sexual abuse. Dissociation positively mediated the effect of childhood trauma on hallucination-proneness. This mediational role was particularly robust for sexual abuse over other types of trauma. Signal detection abnormalities were evident in hallucinating patients and patients with a history of hallucinations, but were not associated with pathological dissociative symptoms.

Conclusions

These results are consistent with dissociative accounts of the trauma-hallucinations link. Dissociation, however, does not affect reality discrimination. Future research should examine whether other cognitive processes associated with both dissociative states and hallucinations (e.g. deficits in cognitive inhibition) may explain the relationship between dissociation and hallucinatory experiences.
COMBINE - What it is, what it could be
Authors: Le Novere Nicolas
Published: September 2011

The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields. By doing so, it is expected that the federated projects will develop a set of interoperable and non-overlapping standards covering all the aspects of modeling in biology.Building on the experience of mature projects, which already have stable specifications, software support, user-base and community governance, COMBINE will help foster or support fledging efforts aimed at filling gaps or new needs. As those efforts mature, they may become part of the core set of COMBINE standards.One of the initial activities of COMBINE is to coordinate the organization of scientific and technical events common to several standards.
General updates about SBML and SBML Team activities
Authors: Hucka Michael
Published: September 2011

In this presentation, I summarize very briefly some recent updates to SBML.org, SBML development, and software from the SBML Team.
Towards a web-based simulation experiment description repository
Authors: Guravage Michael , Merks Roeland
Published: September 2011

Modellers are producing more and more complex models. Unless these models are sufficiently characterised and made available to the research community their reuse will be minimal, and reproducing simulation experiments incorporating them will prove problematic. Consensus on the content and form of experiment recipes that combine models and simulations will encourage model sharing and facilitate reuse.A set of guidelines specifying the 'Minimum Information About a Simulation Experiment'(MIASE) proposes a common set of information necessary to reproduce simulation experiments that incorporate quantitative models.We have instantiated these guidelines in a web-based content management system. With our system you can create Simulation and Experiment Descriptions, enrich them with experimental data and annotate them with domain meta-information to facilitate classification, searching and cross referencing - all with the goal of reusing your models and reproducing your experimental results.
SBRML- A Markup Language for Encoding Systems Biology Results
Authors: Dada Joseph
Published: September 2011

Background:

The wide acceptance of Systems Biology Markup Language (SBML) as standard format for models of biochemical systems makes it possible to build, share, evaluate and develop biochemical models cooperatively. However, there is currently no standard format for encoding the results of computational analyses of systems biology models. To address this issue, we present here the Systems Biology Results Markup Language (SBRML), an XML-based format for representing systems biology results. SBRML provides a means of representing computational simulation results as well as encoding experimental data in the context of a particular model.

Methods & Results:

SBRML is based on XML and is specified through the XML Schema language. SBRML Object Model (SBRML-OM) was first developed using the Universal Modelling Language (UML), and a Model-Driven Architecture (MDA) approach was then used to derive the corresponding XML Schema semi-automatically with the help of mapping rules for classes and associations. SBRML can be used to describe any type of systems biology results, the model that is used to generate the results, the ontology terms that link all the terms/vocabularies used to an external ontology sources, the operation (e.g. time course, steady state etc.) that is performed on the model and a flexible means for encoding the results of the operation. SBRML associates a model with several data sets. Each data set consists of a series of values associated with model variables, and their corresponding parameter values. It provides a flexible way of indexing both simulation results and experimental data to model parameter values which supports both spreadsheet-like data or multidimensional data cubes. Some of its major uses are: associating experimental results with models for passing to analysis tools, sharing and archiving of model simulations and recording the results of analysis for validation, archiving or comparison.

Conclusions:

SBRML is a software-neutral language intended to allow any type of systems biology results to be represented. Standardization of systems biology results format will bring obvious benefits in terms of storage and retrieval, but will also benefit any program that needs to read data in the context of a biochemical model. Application areas are enzyme kinetics data, microarray gene expression data, and various types of simulation results. We will soon release a library (in various programming languages) for reading and writing SBRML documents.
Plant regulation of microbial enzyme production in situ
Authors: Averill Colin , Finzi Adrien
Published: September 2011

Soil extracellular enzymes regulate the rate at which complex organic forms of nitrogen (N) become bio-available. Much research has focused on the limitations to heterotrophic enzyme production via lab incubations, but little has been done to understand the limitations to enzyme production in situ. We created root and symbiotic mycelia exclusion treatments using mesh in-growth bags in the field to isolate the effect of roots and other portions of the microbial community on enzyme production. When fertilized with complex protein N we found increases in N-degrading enzyme concentrations only when root in-growth was allowed. No response was observed when complex N was added to root-free treatments. Expanding on economic rules of microbial element limitation theory developed from lab incubation data, we suggest this is due to active transport of labile carbon (C) from roots to associated microbial communities in root bags. Roots alleviate C-limitation of microbial enzyme synthesis, representing a trade off between plants and microbes- plant C for microbial derived N.
Neurotrophin-4 modulates the mechanotransducer Cav3.2 T-type calcium current in mice down-hair neurons
Authors: Hilaire Cécile , Lucas Olivier , Valmier Jean , Scamps Frédérique
Published: September 2011

The T-type Ca2+ channel Cav3.2 is expressed in nociceptive and mechanosensitive sensory neurons. The mechanosensitive D-hair (down-hair) neurons, which innervate hair follicles, are characterized by a large-amplitude Cav3.2 T-current involved in the amplification of slow-moving stimuli. The molecules and signalling pathways that regulate T-current expression in mechanoreceptors are unknown. In the present study, we investigated the effects of NT-4 (neurotrophin-4) on Cav3.2 T-current expression in D-hair neurons in vitro. Interruption of the supply of NT-4 with peripheral nerve axotomy induced a non-transcriptional decrease in the T-current amplitude of fluorogold-labelled axotomized sensory neurons. The T-current amplitude was restored by incubation with NT-4. Deletion of NT-4 through genetic ablation resulted in a similar selective loss of the large-amplitude T-current in NT-4−/− sensory neurons, which was rescued by the addition of NT-4. NT-4 had no effect on the T-current in Cav3.2−/− D-hair neurons. Neither the biophysical properties of the T-current nor the transcript expression of Cav3.2 were modified by NT-4. Pharmacological screening of signalling pathways activated under the high-affinity NT-4 receptor TrkB (tropomyosin receptor kinase B) identified a role for PI3K (phosphoinositide 3-kinase) in the potentiation of T-current. The results of the present study demonstrate the post-transcriptional up-regulation of the Cav3.2 T-current through TrkB activation and identify NT-4 as a target-derived factor that regulates the mechanosensitive function of D-hair neurons through expression of the T-current.
Accurate low dimensional models for deterministic fluid systems driven by uncertain forcing
Authors: Dergham G. , Sipp D. , Robinet J.-C.
Published: September 2011

This paper addresses the model reduction of high-order linear systems within the framework of the incompressible Navier-Stokes equations. We look for reduced-order models that capture the response of some specific sensor whatever the initial flow condition and in the presence of any time-dependent external forcing. Namely, this work deals with the accurate modeling of the input-output dynamics of a fluid system when considering each degree of freedom of the system as an input, and the given measurement as the output. In the case of complex or realistic flows, the number of inputs is too large to apply the standard balanced truncation procedure. To alleviate this problem, we introduce a method called input projection. Input projection is shown to be analogous to the output projection procedure introduced by Rowley, Int. J. Bifurcation. Chaos Appl. Sci. Eng. 15, 997 (2005). To illustrate the model reduction, we consider the dynamics of a globally stable flow over a rounded backward-facing step. Reduced-order models are obtained by projecting the full original system onto: (i) the basis of the leading balanced modes computed from the input-projected systems and (ii) the most observable modes. The balanced models are observed to accurately capture the transient growths along the separated flow whatever the input while outperforming the models based on the most observable modes.
Evidence for a resonant cyclotron interaction between runaway electrons and MHD modes in the experimental advanced superconducting tokamak
Authors: Li Erzhong , Zhou Ruijie , Hu Liqun
Published: September 2011

In the past, the resonant cyclotron interaction between runaway electrons and lower hybrid waves via anomalous Doppler broadening was experimentally investigated, and it was shown to be able to create a barrier to the energy that could be reached by the runaway electrons [E. Li et al., Nucl. Instrum. Methods Phys. Res. A 621, 566 (2010)]. In this paper, to our knowledge for the first time, experimental evidence will be provided for a resonant cyclotron interaction between runaway electrons and magnetohydrodynamics modes in a stochastic magnetic field in the experimental advanced superconducting tokamak (EAST), which has been theoretically proposed as a mechanism able to limit the maximum attainable energy by runaway electrons in tokamak plasmas [J. R. Martín-Solís and R. Sánchez, Phys. Plasmas 15, 112505 (2008)].
Intuitive approach to magnetic reconnection
Authors: Kulsrud Russell M.
Published: September 2011

Two reconnection problems are considered. The first problem concerns global physics. The plasma in the global reconnection region is in magnetostatic equilibrium. It is shown that this equilibrium can be uniquely characterized by a set of constraints. During reconnection and independently of the local reconnection physics, these constraints can be uniquely evolved from any initial state. The second problem concerns Petschek reconnection. Petschek’s model for fast reconnection, which is governed by resistive MHD equations with constant resistivity is not validated by numerical simulations. Malyshkin et al. [Phys. Plasmas 12, 102920 (2005)], showed that the reason for the discrepancy is that Petschek did not employ Ohm’s law throughout the local diffusion region, but only at the X-point. A derivation of Petschek reconnection, including Ohm’s law throughout the entire diffusion region, removes the discrepancy. This derivation is based largely on Petschek’s original 1964 calculation [in AAS-NASA Symposium on Solar Flares (National Aeronautics and Space Administration, Washington, D.C., 1964), NASA SP50, p. 425]. A useful physical interpretation of the role which Ohm’s law plays in the diffusion region is presented.
Experimental demonstration of tokamak inductive flux saving by transient coaxial helicity injection on national spherical torus experiment
Authors: Raman R. , Mueller D. , Jarboe T. R. , Nelson B. A. , Bell M. G. , Gerhardt S. , LeBlanc B. , Menard J. , Ono M. , Roquemore L. , Soukhanovskii V.
Published: September 2011

Discharges initiated by transient coaxial helicity injection in National Spherical Torus Experiment have attained peak toroidal plasma currents up to 300 kA. When induction from the central solenoid is then applied, these discharges develop up to 300 kA additional current compared to discharges initiated by induction only. CHI initiated discharges in NSTX have achieved 1 MA of plasma current using only 258 mWb of solenoid flux whereas standard induction-only discharges require about 50% more solenoid flux to reach 1 MA. In addition, the CHI-initiated discharge has lower plasma density and a low normalized internal plasma inductance of 0.35, as needed for achieving advanced scenarios in NSTX.
Phase transition of a single star polymer: A Wang-Landau sampling study
Authors: Wang Zilu , He Xuehao
Published: September 2011

Star polymers, as an important class of nonlinear macromolecules, process special thermodynamic properties for the existence of a common connecting point. The thermodynamic transitions of a single star polymer are systematically studied with the bond fluctuation model using Wang-Landau sampling techniques. A new analysis method employing the shape factor is proposed to locate the coil-globule (CG) and liquid-crystal (LC) transitions, which shows a higher efficiency and accuracy than the canonical specific heat function. The LC transition temperature is found to obey the identical scaling law as the linear polymers. However, the CG transition temperature shifts towards the LC transition with the increasing of the arm number. The reason is that for the star polymer a lower temperature is needed for the attractive force to overcome the excluded volume effect of the polymer chain because of its high arm density. This work clearly proves the structural distinction of the linear and star polymers can only affect the CG transition while has no influence on the LC transition.
Multiwavelength fabrication of vertical-cavity surface-emitting lasers based on asymmetric one-dimensional photonic crystal
Authors: Guan B. L. , Guo X. , Ren X. J. , Li S. , Shen G. D.
Published: September 2011

A dual-wavelength vertical-cavity surface-emitting laser with an asymmetric one-dimensional photonic crystal structure was demonstrated based on the band-gap theory. The wavelengths of the VCSEL can be located at 979.7 and 943 nm with the aid of the Al0.8Ga0.2As defect layer. Particularly, the lasing of the dual-wavelength VCSEL was in the same light propagation direction for both the wavelengths with a high Q factor. Furthermore, the relative peaks position of the two wavelengths can be tuned from ∼33 to ∼50 nm by adjusting the refractive index contrast of the asymmetric photonic crystal structure, which will promote the formation of multidefect mode states.
Late-time particle emission from laser-produced graphite plasma
Authors: Harilal S. S. , Hassanein A. , Polek M.
Published: September 2011

We report a late-time “fireworks-like” particle emission from laser-produced graphite plasma during its evolution. Plasmas were produced using graphite targets excited with 1064 nm Nd: yttrium aluminum garnet (YAG) laser in vacuum. The time evolution of graphite plasma was investigated using fast gated imaging and visible emission spectroscopy. The emission dynamics of plasma is rapidly changing with time and the delayed firework-like emission from the graphite target followed a black-body curve. Our studies indicated that such firework-like emission is strongly depended on target material properties and explained due to material spallation caused by overheating the trapped gases through thermal diffusion along the layer structures of graphite.
Non-collinear magnetization configuration in interlayer exchange coupled magnetic thin films
Authors: Choi J. , Min B.-C. , Kim J.-Y. , Park B.-G. , Park J. H. , Lee Y. S. , Shin K.-H.
Published: September 2011

Element specific magnetic hysteresis loops of the interlayer exchange coupled CoFeB/Ru/[Co/Ni]4 structure were measured utilizing x-ray magnetic circular dichroism. It was found that the Co/Ni multilayer and the CoFeB layer have Ru thickness dependent oscillatory interlayer coupling. Due to its interlayer coupling with the perpendicularly magnetized Co/Ni multilayer, the CoFeB magnetization direction is slightly tilted out-of-plane from its in-plane magnetic easy axis. Quantitative measurements show that the tilting angle is small (<12°) and that a small in-plane magnetic field (∼50 Oe) applied to this structure will result in a completely in-plane CoFeB magnetization.
Communication: Theoretical exploration of Au++H2, D2, and HD reactive collisions
Authors: Dorta-Urra Anaís , Zanchet Alexandre , Roncero Octavio , Aguado Alfredo , Armentrout P. B.
Published: September 2011

A quasi-classical study of the endoergic Au+(1S) + \documentclass[12pt]{minimal}\begin{document}${\rm H}_2(X^1 \Sigma _g^+$\end{document}H2(X1Σg+) → AuH+ (2Σ+) + H(2S) reaction, and isotopic variants, is performed to compare with recent experimental results [F. Li, C. S. Hinton, M. Citir, F. Liu, and P. B. Armentrout, J. Chem. Phys. 134, 024310 (2011)].10.1063/1.3514899 For this purpose, a new global potential energy surface has been developed based on multi-reference configuration interaction ab initio calculations. The quasi-classical trajectory results show a very good agreement with the experiments, showing the same trends for the different isotopic variants of the hydrogen molecule. It is also found that the total dissociation into three fragments, Au++H+H, is the dominant reaction channel for energies above the H2 dissociation energy. This results from a well in the entrance channel of the potential energy surface, which enhances the probability of H–Au–H insertion.
Population dynamics, diet and pest status of the grassland melomys (Melomys burtoni) in northern Queensland sugarcane crops
Authors: Dyer Brendan C. , Clarke Anthony R. , Fuller Susan J.
Published: September 2011

Context In far-northern Queensland, Melomys burtoni and M. cervinipes occur within sugarcane crops and adjacent habitats and are potentially damaging to sugarcane. Aims To examine the population dynamics and diet of Melomys spp. within sugarcane crops so that, in conjunction with cane-stalk damage assessments, their pest status could be determined and information provided relevant to the development of sustainable pest-management tools. Methods Eight sites within sugarcane fields, four adjacent to grassland and four adjacent to closed forest, were established around Tully in far-northern Queensland. We examined demographic characteristics of all rodents (the two Melomys spp. and Rattus sordidus) within the crops by capture–release studies. Snap-trapping and dissection studies, along with weed-biomass surveys, were conducted for diet analysis, whereas damaged stalk counts were undertaken to understand the damage process. Fieldwork commenced within a fully developed crop, then continued through the annual harvest period and all subsequent crop growth stages to the next harvest. Sampling was undertaken monthly from February 2005 to April 2006. Key results Melomys cervinipes was rarely caught in sugarcane and should not be regarded as a pest. In contrast, M. burtoni feeds on sugarcane and was responsible for damage to ~6% of stalks. In sites adjacent to closed forest, R. sordidus was found in higher numbers than was M. burtoni in Crop stages 2–4. However, at sites adjacent to grassland, numbers of M. burtoni increased in Crop stage 4, and before crop harvest, M. burtoni was found in higher numbers than was R. sordidus. M. burtoni colonised sugarcane at later stages of crop development than did R. sordidus. Although the level of M. burtoni reproduction was lower than that of R. sordidus, the highest proportion of pregnant M. burtoni individuals occurred during the later stages of crop development, corresponding directly with the highest proportion of juvenile recruitment. Conclusions Of the two Melomys species found in northern Queensland sugarcane crops, only M. burtoni should be regarded as a pest. This rodent breeds and feeds within the crop, primarily after canopy closure. M. burtoni captures were roughly equivalent irrespective of adjacent habitat type, whereas R. sordidus, the traditionally recognised major pest of sugarcane crops, was found in significantly higher numbers in sugarcane adjacent to closed forest. Implications The integrated pest-management (IPM) strategy developed for R. sordidus is centred on the early stages of crop development and includes population monitoring, in-crop weed control, harbourage management and strategic use of permitted rodenticides. The late colonisation and lower breeding potential of M. burtoni mean that the IPM strategy for R. sordidus will not be directly transferable to M. burtoni.
Pulsed IR laser ablation of organic polymers in air: shielding effects and plasma pipe formation
Authors: Panchenko A N , Shulepov M A , Tel'minov A E , Zakharov L A , Paletsky A A , Bulgakova N M
Published: September 2011

We report the effect of ‘plasma pipe’ formation on pulsed laser ablation of organic polymers in air under normal conditions. Ablation of polymers (PMMA, polyimide) is carried out in a wide range of CO2 laser fluences with special attention to plasma formation in the ablation products. Evolution of laser ablation plumes in air under different pressures is investigated with simultaneous registration of radiation spectra of the ablation products. An analysis based on thermo-chemical modelling is performed to elucidate the effects of laser light attenuation upon ablation, including plasma and chemical processes in a near-target space. The analysis has shown that the experimental observations of plume development in air can be explained by a combination of processes including formation of a pre-ionized channel along the laser beam propagation, laser-supported detonation wave and effective combustion of the polymer ablation products. A scenario of a streamer-like polymer plasma flow within an air plasma pipe created via laser-induced breakdown is proposed.
Influence of temperature on the glow regime of a discharge in air at atmospheric pressure between two point electrodes
Authors: Tholin Fabien , Bourdon Anne
Published: September 2011

This paper presents simulations of the dynamics of air discharges between two point electrodes at atmospheric pressure for two different gas temperatures 300 and 1000 K. Simulation results show that in the early stages of the glow regime, two streamer discharges propagate in the gap and form after their connection a conducting channel between electrodes. In a recent experimental work on nanosecond repetitively pulsed (NRP) discharges at 1000 K between two point electrodes with an interelectrode gap distance of 5 mm, it was found that a glow regime is obtained if the average electric field in the gap is at least equal to the breakdown field. Simulation results show that for the conditions studied in the experiments, the time of connection of both discharges is close to the 10 ns duration of the voltage pulse if the average electric field in the gap in the conduction phase is equal to the breakdown field. Under these conditions, a glow regime is obtained as a conducting channel has just the time to form between electrodes during the voltage pulse and no significant gas heating may occur. At 300 K, we found that a minimal value of the Laplacian electric field of 8–9 kV cm−1 at atmospheric pressure is necessary to have a stable propagation of the positive streamer without branching in the point-to-point geometry. Then, based on simulation results, we discuss the conditions of existence of the glow regime in NRP discharges at atmospheric pressure and 300 K in a 1 cm interelectrode gap.
SiTaR: a novel tool for transcription factor binding site prediction
Authors: Fazius Eugen , Shelest Vladimir , Shelest Ekaterina
Published: September 2011

Motivation: Prediction of transcription factor binding sites (TFBSs) is crucial for promoter modeling and network inference. Quality of the predictions is spoiled by numerous false positives, which persist as the main problem for all presently available TFBS search methods.

Results: We suggest a novel approach, which is alternative to widely used position weight matrices (PWMs) and Hidden Markov Models. Each motif of the input set is used as a search template to scan a query sequence. Found motifs are assigned scores depending on the non-randomness of the motif's occurrence, the number of matching searching motifs and the number of mismatches. The non-randomness is estimated by comparison of observed numbers of matching motifs with those predicted to occur by chance. The latter can be calculated given the base compositions of the motif and the query sequence. The method does not require preliminary alignment of the input motifs, hence avoiding uncertainties introduced by the alignment procedure. In comparison with PWM-based tools, our method demonstrates higher precision by the same sensitivity and specificity. It also tends to outperform methods combining pattern and PWM search. Most important, it allows reducing the number of false positive predictions significantly.

Availability: The method is implemented in a tool called SiTaR (Site Tracking and Recognition) and is available at http://sbi.hki-jena.de/sitar/index.php.

Contact:  ekaterina.shelest@hki-jena.de

Supplementary Information:  Supplementary data are available at Bioinformatics online.
The microenvironment patterns the pluripotent mouse epiblast through paracrine Furin and Pace4 proteolytic activities
Authors: Mesnard Daniel , Donnison Martyn , Fuerer Christophe , Pfeffer Peter L. , Constam Daniel B.
Published: September 2011

The fate of pluripotent cells in early mouse embryos is controlled by graded Nodal signals that are activated by the endoproteases Furin and Pace4. Soluble forms of Furin and Pace4 cleave proNodal in vitro and after secretion in transfected cells, but direct evidence for paracrine activity in vivo is elusive. Here, we show that Furin and Pace4 are released by the extraembryonic microenvironment, and that they cleave a membrane-bound reporter substrate in adjacent epiblast cells and activate Nodal to maintain pluripotency. Secreted Pace4 and Furin also stimulated mesoderm formation, whereas endoderm was only induced by Pace4, correlating with a difference in the spatiotemporal distribution of these proteolytic activities. Our analysis of paracrine Furin and Pace4 activities and their in vivo functions significantly advances our understanding of how the epiblast is patterned by its microenvironment. Adding cell–cell communication to the pleiotropic portfolio of these proteases provides a new framework to study proprotein processing also in other relevant contexts.
Regulation of the Fanconi anemia pathway by a SUMO-like delivery network
Authors: Yang Kailin , Moldovan George-Lucian , Vinciguerra Patrizia , Murai Junko , Takeda Shunichi , D'Andrea Alan D.
Published: September 2011

The USP1/UAF1 complex deubiquitinates the Fanconi anemia protein FANCD2, thereby promoting homologous recombination and DNA cross-link repair. How USP1/UAF1 is targeted to the FANCD2/FANCI heterodimer has remained unknown. Here we show that UAF1 contains a tandem repeat of SUMO-like domains in its C terminus (SLD1 and SLD2). SLD2 binds directly to a SUMO-like domain-interacting motif (SIM) on FANCI. Deletion of the SLD2 sequence of UAF1 or mutation of the SIM on FANCI disrupts UAF1/FANCI binding and inhibits FANCD2 deubiquitination and DNA repair. The USP1/UAF1 complex also deubiquitinates PCNA-Ub, and deubiquitination requires the PCNA-binding protein hELG1. The SLD2 sequence of UAF1 binds to a SIM on hELG1, thus targeting the USP1/UAF1 complex to its PCNA-Ub substrate. We propose that the regulated targeting of USP1/UAF1 to its DNA repair substrates, FANCD2-Ub and PCNA-Ub, by SLD–SIM interactions coordinates homologous recombination and translesion DNA synthesis.
Wnt signaling meets internal dissent: Figure 1.
Authors: Grove Elizabeth A.
Published: September 2011

In canonical Wnt signaling, β-catenin translocates to the cell nucleus, interacting with Tcf/Lef factors to activate transcription of Wnt target genes. In this issue of Genes & Development, Vacik and colleagues (pp. 1783–1795) report that a highly conserved sequence in intron 5 of Tcf7l2 conceals an internal promoter region that, when activated by Vax2, drives transcription of truncated Tcf7l2 mRNAs. The encoded Tcf7l2 protein binds to DNA, but not β-catenin, and therefore acts as a dominant-negative Wnt antagonist.
The organization of the Bacillus subtilis 168 chromosome region between the spoVA and serA genetic loci, based on sequence data
Authors: Sorokin Alexei , Zumstein Emmanuelle , Azevedo Vasco , Ehrlich S. Dusko , Serror Pascale
Published: September 2011

Three different lambda phage clones with overlapping inserts of Bacillus subtilis DNA, which cover the region from spoIIAA to serA, have been isolated. The nucleotide sequence of their inserts, starting after spoVAF and ending at serA, has been determined. A contiguous sequence of 35354 bp was established, including previously analysed overlapping adjacent regions. Within the newly determined sequence 31 open reading frames (ORFs) with putative ribosome‐binding sites have been found. Nine of them correspond to previously sequenced and characterized genes: spoVAF, lysA, sipS, ribG, ribB, ribA, ribH, ribTD and dacB. Comparison of the amino acid sequences of the products encoded by the other ORFs to known proteins allowed putative functions to be assigned to seven of these ORFs. Among these are the following: (i) the ppiB gene, encoding a cytoplasmic peptidylprolyl isomerase; (ii) two pairs of signal‐transducers, one homologous to phoR–phoP of B. subtilis, encoding regulators of phosphatase biosynthesis, and the second to the fecI–fecR of Escherichia coli, which is responsible for the regulation of the citrate‐dependent iron (III) transport system; (iii) aroC and serA genes, involved in the biosynthesis of aromatic amino acids and serine, respectively, the function of which has beer: confirmed by constructing corresponding mutants with disrupted ORFs. The organization of putative operons has been postulated on the basis of the sequences of their transcription terminators, promoters and regulatory elements.
Differential metabolic response of barley genotypes, varying in resistance, to trichothecene‐producing and ‐nonproducing (tri5−) isolates of Fusarium graminearum
Authors: Kumaraswamy G. K. , Kushalappa A. C. , Choo T. M. , Dion Y. , Rioux S.
Published: September 2011

Resistance of barley to Fusarium graminearum was studied using a pair each of resistant and susceptible black and yellow barley lines. The spikelets were inoculated with a trichothecene‐producing isolate, a trichothecene‐nonproducing isolate (tri5−), or a mock solution. Spikelets were collected 72 h after inoculation and metabolites were analysed using a LC‐hybrid MS system. Metabolite abundances were used to identify the constitutive (RRC) and induced resistance‐related metabolites (RRI). The pathogen virulence factor, DON, and its plant detoxification product, DON‐3‐O‐glucoside (D3G), were also identified and designated as resistance‐indicator (RI) metabolites. The RRC, RRI and RI metabolites were putatively identified. Jasmonic acid was significantly induced in barley following inoculation with a trichothecene‐producing isolate, but not with a tri5− isolate. The former isolate reduced the induction of both the number and amount of RR metabolites. The metabolites cinnamic acid, sinapoyl alcohol, coniferin, catechin and naringin were identified only in response to the inoculation with a tri5− mutant. The abundances of p‐coumaric acid, coniferaldehyde and sinapaldehyde increased more in response to the tri5− mutant than to the trichothecene‐producing isolate. The total amount of DON synthesized and its conversion to D3G varied greatly between the resistant and susceptible black barley, but not in yellow barley. Interestingly, an increase in the amount of total DON produced was associated with a decrease in the conversion of DON to D3G. The roles of RRC, RRI and RI metabolites in plant defence and their further use as potential biomarkers in screening are discussed.
The Cochrane Library review titles that are important to users of health care, a Cochrane Consumer Network project
Authors: Wale Janet L. , Belizán María , Nadel Jane , Jeffrey Claire , Vij Sita L.
Published: September 2011

Background  The Cochrane Consumer Network is an internet‐based community of international users of health care contributing to the work of The Cochrane Collaboration, whose mission is to inform healthcare decision making through development of systematic reviews of best evidence on healthcare interventions.

Objective  To prioritize existing review titles listed on The Cochrane Library from a healthcare user perspective, with particular emphasis on patients, carers and health consumers.

Design  An online survey was developed and after piloting was made available internationally. The broad dissemination strategy targeted Consumer Network members and Cochrane Review Group editorial staff to identify champions who notified patient support groups and participated in snowballing. The first part of the survey defined criteria that could be applied to review titles and asked survey respondents to rank them. The second part asked respondents to select a health area and prioritize review titles that were of importance to them. Each health area corresponded to a Cochrane Review Group.

Results and discussion  Sufficient responses were obtained from 522 valid responses to prioritize review topics in 19 health areas. A total of 321 respondents completed the titles assessment. The types of prioritized interventions were determined by the health area. An important observation was the emphasis on lifestyle and non‐medication therapies in many of the included health areas. The clearest exception to this broad observation was where acute care is required such as antibiotics for acute respiratory tract and HIV‐associated infections and for cardiac conditions. For some cancers, advanced cancer interventions were prioritized. The most important criteria were for the title to convey a clear meaning and the title conveyed that the review would have an impact on health and well‐being. The least important criteria were that the topic was newsworthy or prioritized in the healthcare system.

Conclusion  This project was able to identify priority Cochrane review topics for users of health care in 19 of the 50 areas of health care covered by The Cochrane Collaboration. Reviews addressing lifestyle and non‐medical interventions were strongly represented in the prioritized review titles. These findings highlight the importance of developing readable, informative lay summaries to support evidence‐based decision making by healthcare users.