bluuebunny/crossref_metadata_2025 huggingface dataset:
Arabidopsis thalianaresistance to insects, mediated by an earthworm‐produced organic soil amendment
Authors: Cardoza Yasmin J
Published: November 2010

BACKGROUND:Vermicompost is an organic soil amendment produced by earthworm digestion of organic waste. Studies show that plants grown in soil amended with vermicompost grow faster, are more productive and are less susceptible to a number of arthropod pests. In light of these studies, the present study was designed to determine the type of insect resistance (antixenosis or antibiosis) present in plants grown in vermicompost‐amended potting soil. Additionally, the potential role of microarthropods, entomopathogenic organisms and non‐pathogenic microbial flora found in vermicompost on insect resistance induction was investigated.

RESULTS:Findings show that vermicompost from two different sources (Raleigh, North Carolina, and Portland, Oregon) were both effective in causingArabidopsisplants to be resistant to the generalist herbivoreHelicoverpa zea(Boddie). However, while the Raleigh (Ral) vermicompost plant resistance was expressed as both non‐preference (antixenosis) and milder (lower weight and slower development) toxic effect (antibiosis) resistance, Oregon (OSC) vermicompost plant resistance was expressed as acute antibiosis, resulting in lower weights and higher mortality rates.

CONCLUSION:Vermicompost causes plants to have non‐preference (antixenosis) and toxic (antibiosis) effects on insects. This resistance affects insect development and survival on plants grown in vermicompost‐amended soil. Microarthropods and entomopathogens do not appear to have a role in the resistance, but it is likely that resistance is due to interactions between the microbial communities in vermicompost with plant roots, as is evident from vermicompost sterilization assays conducted in this study. Copyright © 2010 Society of Chemical Industry
Stimulation of osteoblastic differentiation and mineralization in MC3T3‐E1 cells by yeast hydrolysate
Authors: Lee Hyun‐Sun , Jung Eun‐Young , Bae Song Hwan , Kwon Ki Han , Kim Jin‐Man , Suh Hyung Joo
Published: November 2010

In a previous study, it was reported that yeast hydrolysate (YH) was effective in promoting bone growth in Sprague‐Dawley (SD) rats. To further clarify the mechanism of YH, the effects of YH on proliferation, differentiation and gene expression in vitro were investigated using osteoblastic cell lines (MC3T3‐E1). Cell proliferation increased significantly as much as 110% of the basal value when cells were treated with 100 µg/mL of YH. Alkaline phosphatase (ALP) activity increased significantly with a YH concentration of 25–100 µg/mL, and the activity increased 152% that of the control at 100 µg/mL. The calcium content increased as much as 129% at 100 µg/mL YH. The gene expression levels of ALP and collagen type II (COL II) significantly increased approximately 1.3‐fold and 1.7‐fold of control, respectively, at 100 µg/mL. YH increased significantly the mRNA level of bone sialoprotein (BSP) but not in a dose‐dependent manner. The mRNA levels of bone morphogenetic proteins (BMP)‐2, BMP‐4, collagen type I (COL I) and osteonectin (ON) did not increase. In summary, YH increased the proliferation of osteoblasts and directly stimulated ALP and bone matrix proteins (e.g. BSP, COL II), and these increases trigger osteoblastic differentiation (e.g. mineralized nodule formation). Copyright © 2010 John Wiley & Sons, Ltd.
Evaluation of Turkish seaweeds for antiprotozoal, antimycobacterial and cytotoxic activities
Authors: Süzgeç‐Selçuk Sevda , Meriçli Ali H. , Güven Kasım C. , Kaiser Marcel , Casey Rosalyn , Hingley‐Wilson Suzie , Lalvani Ajit , Tasdemir Deniz
Published: November 2010

As part of our continuing research on seaweeds, crude MeOH extracts of two green, three brown and six red algae collected from Marmara, Black, Aegean and Mediterranean Seas were screened. Four parasitic protozoa, i.e. Plasmodium falciparum, Trypanosoma brucei rhodesiense, T. cruzi, Leishmania donovani and the tubercle bacillus Mycobacterium tuberculosis were used as test organisms for the in vitro assays. The selective toxicity of the extracts was also determined against mammalian L6 cells. All seaweed extracts were active against T. brucei rhodesiense; the Dasya pedicellata extract was the most potent (IC50 value 0.37 µg/mL). The same extract also weakly inhibited the growth of T. cruzi (IC50 62.02 µg/mL). All seaweed extracts also showed leishmanicidal activity (IC50 values 16.76–69.98 µg/mL). The majority of the extracts also exhibited antiplasmodial potential and the most potent extracts were those from D. pedicellata (IC50 0.38 µg/mL), Codium bursa (IC50 1.38 µg/mL) and Caulerpa rasemosa (IC50 3.12 µg/mL). One brown and two red algal extracts showed some weak activity against Mycobacterium tuberculosis (MIC values 125–256 µg/mL). Except for the extract of Dasya pedicellata, none of the extracts displayed any cytotoxicity. This is the second study investigating the antiprotozoal activities of Turkish marine algae and identifies Dasya pedicellata, an understudied algal species, as a candidate for further studies. Copyright © 2010 John Wiley & Sons, Ltd.
Oligomerized grape seed proanthocyanidins ameliorates isoproterenol‐induced cardiac remodeling in rats: role of oxidative stress
Authors: Zuo You‐mei , Wang Xing‐hui , Gao Shan , Zhang Ye
Published: November 2010

The effects of oligomerized grape seed proanthocyanidins (GSP) on haemodynamics, cardiac hypertrophy and fibrosis as well as apoptosis signal‐regulating kinase 1 (ASK1) and nuclear factor‐κB (NF‐κB) cascades in isoproterenol (Iso)‐induced cardiac remodelling (CR) rat model were investigated, in addition, the serum SOD activities and MDA content were assayed. Rats were treated with Iso to induce CR and were given distilled water or GSP for 1 week. Control rats received vehicle instead of Iso. Administration of GSP markedly alleviated the elevation of the left ventricle weight (LVW)/body weight (BW), heart weight (HW)/body weight (BW) ratio and cross‐sectional area of cardiomyocytes, decreased collagen deposition in the heart, and improved the haemodynamic index. Meanwhile, treatment with GSP significantly ameliorated oxidative stress by improving SOD activities and decreasing MDA formation. Moreover, GSP apparently inhibited the expression ASK1, NF‐κB and its targeted gene – COX‐2. These findings suggest that administration of GSP has the potential to attenuate Iso‐induced CR by repressing oxidative stress and inhibiting the activation of the cellular signaling cascades involving the ASK1 and NF‐κB pathways, at least in part, providing a molecular mechanism for the cardioprotective effect of GSP. Copyright © 2010 John Wiley & Sons, Ltd.
Using viscous and variable friction dampers for improving structural seismic response
Authors: Ribakov Y.
Published: November 2010

Using supplemental dampers is known as an efficient way for improving structural seismic response. Viscous, friction, yielding steel and other types of dampers were developed in the last few decades for this reason and are produced by the industry and used in modern structures and in retrofitted buildings all over the world. This paper is focused on investigating a damping system including viscous and variable friction dampers. Numerical analysis of a multi‐storey structure was carried out. At the first stage, the structure was provided by optimal viscous dampers and its response to a white noise was obtained. According to this response, appropriate parameters of variable friction dampers were obtained using an equivalent energy dissipation hypothesis. At the second stage, dynamic response of the structure under real seismic motions was studied. It was shown that using a hybrid damping system including viscous and variable friction dampers yields essential improvement in structural response and looks attractive for practical implementations. Copyright © 2010 John Wiley & Sons, Ltd.
Investigating the reliability of RC beams of tall buildings designed based on the new ACI 318‐05/ASCE 7‐05
Authors: Baji H. , Ronagh H. R.
Published: November 2010

The level of safety achievable in reinforced concrete (RC) beams designed based on the new ACI 318‐05/ASCE 7‐05 is investigated in this study. The study makes use of the more recent statistical data on flexure and shear provided by Szerszen and Nowak. Due to the importance of using real ratios of lateral/gravity loads in any such reliability analysis, a set of RC buildings was chosen, loaded and designed and the actual nominal wind‐to‐dead load ratios were derived. Using these and the statistical data mentioned above, reliability indices for moment and shear were calculated. The resulting reliability indices for moment and shear are then presented in comparison. In addition, the reliability index variations along the beam at the controlling stations are compared to each other. The results of the study indicate that reliability indices at the controlling stations obtained for different limit states are not consistent for low values of nominal wind‐to‐dead load ratios, but converge consistently for high ratios. It seems that the use of older shear strength factors provides a reliable safety margin and that the use of the more recent statistical data for material combined with the older shear strength factors leads to more consistency. Copyright © 2010 John Wiley & Sons, Ltd.
First word
Authors: Kirby Roger
Published: November 2010

Welcome to the first issue of Trends in Urology and Men's Health, an exciting new project that builds on the success of Trends in Urology, Gynaecology and Sexual Health and takes it several steps into the future. The journal has been redesigned as a visually ground‐breaking sister journal to the British Journal of Urology International (BJUI), aimed at a multidisciplinary audience of healthcare professionals who care for men's health. The central campaigning message will be to ‘reduce premature deaths in men, and improve quality of life for all’. The new journal will provide high‐quality articles from leading specialists in the areas of prostate disease, erectile dysfunction, incontinence and genitourinary medicine. In addition, its broad remit will include other areas that affect men's health, including cardiovascular disease and diabetes. Copyright © 2010 Wiley Interface Ltd
The statins: a drug class to celebrate
Authors: Betteridge John
Published: November 2010

Part 1 of this article provides an overview of the statins – safe and effective lipid‐lowering drugs for preventing major cardiovascular events. Part 2 will look at the trials that have provided the evidence base for their use. Copyright © 2010 Wiley Interface Ltd
Where are we now with prostate cancer diagnosis?
Authors: Wong Lih‐Ming , Neal David E.
Published: November 2010

A question‐and‐answer review of the current issues in prostate cancer diagnosis. Copyright © 2010 Wiley Interface Ltd
Sexual dysfunction: the importance of involving the partner
Authors: Edwards David
Published: November 2010

The partner of a man with sexual problems has a vital role in encouraging him to seek help. Copyright © 2010 Wiley Interface Ltd
Simultaneous real‐time imaging of four‐chamber and left ventricular outflow tract views using xPlane imaging capability of a matrix array probe
Authors: Yuan Y. , Leung K. Y. , Ouyang Y. S. , Yang F. , Tang M. H. Y. , Chau A. K. T. , Dai Q.
Published: November 2010

Objectives

To determine the feasibility and reliability of using xPlane imaging to examine simultaneously the four‐chamber and left ventricular outflow tract (LVOT) views in real time, to assess rotation angles from the four‐chamber view to the LVOT view, and to investigate factors affecting the angles.

Methods

In 145 fetuses at 11–37 weeks' gestation, we visualized the four‐chamber view in one of three cardiac positions: a subcostal view with the apex at the 3 or 9 o'clock position; an apical view with the apex at the 12 or 6 o'clock position; or a view with the fetal heart apex midway between these two positions. We then used the rotation function of xPlane imaging, using the four‐chamber view as the reference plane, to visualize the LVOT view simultaneously in real time on the secondary image plane, on the right side of the split screen, by rotating a reference line from 0° with a rotation step of 5°. The rotation angle necessary for the first appearance of LVOT was recorded as the first rotation angle. The reference line was then rotated until the LVOT was just out of view, and this last rotation angle was recorded as the second rotation angle. The difference between these two angles was recorded as the angle span of the LVOT display. Reliability was assessed by intraclass correlation coefficient (ICC).

Results

Of the 145 fetuses examined, 29 had cardiac defects. Using xPlane imaging, the LVOT was visualized successfully after 14 weeks in 95.1% of cases. The first and second rotation angles varied significantly with cardiac position (P < 0.001); when the fetal heart was examined using a subcostal approach with the apex at the 3 or 9 o'clock position, the first rotation angle was smaller than that at the apical view for normal hearts (20° vs. 50°, P < 0.001). There was also a significant difference for the second rotation angle and for the angle span, between fetuses with and without normal LVOT (P = 0.038 and 0.006, respectively). Regarding intra‐ and interobserver reliability for measurement of first and second rotation angles, the ICCs were high (range, 0.847–0.980).

Conclusion

Using xPlane imaging, it is feasible to examine simultaneously the four‐chamber and LVOT views in real time, and measurement of the rotation angles between these two views is reproducible. The rotation angles depend on the position of the fetal heart, and the normality of the LVOT. Proposed algorithms for examination of the fetal heart with three‐/four‐dimensional ultrasonography may need to be adapted to optimize visualization of the standard planes. Copyright © 2011 ISUOG. Published by John Wiley & Sons, Ltd.
Being Extreme in the classroom: Experiences teaching XP
Authors: Goldman Alfredo , Kon Fabio , Silva Paulo J. S. , Yoder Joseph W.
Published: November 2010

Agile Methods propose a new way of looking at software development that questions many of the beliefs of conventional Software Engineering. Agile methods such as Extreme Programming (XP) have been very effective in producing high-quality software in real-world projects with strict time constraints.

Nevertheless, most university courses and industrial training programs are still based on old-style heavyweight methods. This article, based on our experiences teaching XP in academic and industrial environments, presents effective ways of teaching students and professionals on how to develop high-quality software following the principles of agile software development. We also discuss related work in the area, describe real-world cases, and discuss open problems not yet resolved.
Advances in perfusion magnetic resonance imaging in Alzheimer's disease
Authors: Chen Wei , Song Xiaowei , Beyea Steven , D'Arcy Ryan , Zhang Yunting , Rockwood Kenneth
Published: November 2010

Recent research has demonstrated that brain circulation abnormalities, either during task‐induced neural activity or at rest, are more commonly associated with Alzheimer's disease (AD) than was previously thought. This is consistent with the increasing attention to the early involvement of vascular risk factors in the development of AD, in addition to the dominating neurodegenerative pathology. Early detection of cerebral perfusion changes could help advance diagnosis and intervention therapies. The present article reviews advances in perfusion magnetic resonance imaging in the study of AD. In general, there are consistent accounts of cerebral hypoperfusion in the temporal and parietal lobes in people with clinically diagnosed AD. In the early stages of the disease, transient hyperperfusion may occur particularly in the prefrontal cortex, possibly as a compensatory effect. Nevertheless, significant variability in the details of perfusion patterns is present in the early phases, making the use of these methods in early diagnosis difficult. Noninvasive perfusion‐weighted magnetic resonance imaging methods have advantages over nuclear medicine imaging, especially for safe usage in long‐term follow‐up studies. Optimization of perfusion‐weighted imaging techniques is crucial for any future clinical application. Additional studies are needed with optimization likely to come with 3T and higher field strength magnets.
Latitudinal gradient in the taxonomic composition of parasite communities
Authors: Poulin R. , Leung T.L.F
Published: November 2010

Although latitudinal gradients in diversity have been well studied, latitudinal variation in the taxonomic composition of communities has received less attention. Here, we use a large dataset including 950 surveys of helminth endoparasite communities in 650 species of vertebrate hosts to test for latitudinal changes in the relative contributions of trematodes, cestodes, nematodes and acanthocephalans to parasite assemblages. Although the species richness of helminth communities showed no consistent latitudinal variation, their taxonomic composition varied as a function of both host type and latitude. First, trematodes and acanthocephalans accounted for a higher proportion of species in helminth communities of fish, whereas nematodes achieved a higher proportion of the species in communities of bird and especially mammal hosts. Second, the proportion of trematodes in helminth communities of birds and mammals increased toward higher latitudes. Finally, the proportion of nematodes per community increased toward lower latitudes regardless of the type of host. We present tentative explanations for these patterns, and argue that new insights in parasite community ecology can be gained by searching for latitudinal gradients not only in parasite species richness, but also in the taxonomic composition of parasite assemblages.
Mortality Projections using Generalized Additive Models with applications to annuity values for the Irish population
Authors: Hall M. , Friel N.
Published: November 2010

Generalized Additive Models (GAMs) with age, period and cohort as possible covariates are used to predict future mortality improvements for the Irish population. The GAMs considered are the 1-dimensional age + period and age + cohort models and the 2-dimensional age-period and age-cohort models. In each case thin plate regression splines are used as the smoothing functions. The generalized additive models are compared with the P-Spline (Currie et al., 2004) and Lee-Carter (Lee & Carter, 1992) models included in version 1.0 of the Continuous Mortality Investigation (CMI) library of mortality projections. Using the Root Mean Square Error to assess the accuracy of future predictions, the GAMs outperform the P-Spline and Lee-Carter models over intervals of 25 and 35 years in the age range 60 to 90. The GAMs allow intuitively simple models of mortality to be specified whilst also providing the flexibility to model complex relationships between the covariates. The majority of morality improvements derived from the projections of future Irish mortality yield annuity values at ages 60, 65, 70 and 80 in 2007 in the range of annuity values calculated, assuming a 2 to 4 percent annual compound improvement in mortality rates for both males and females.
A nonhydrostatic version of FVCOM: 1. Validation experiments
Authors: Lai Zhigang , Chen Changsheng , Cowles Geoffrey W. , Beardsley Robert C.
Published: November 2010

The unstructured grid finite volume coastal ocean model (FVCOM) system has been expanded to include nonhydrostatic dynamics. This addition uses the factional step method with both split mode explicit and semi‐implicit schemes. The unstructured grid finite volume method, combined with a correction of the final free surface from its intermediate value with inclusion of nonhydrostatic effects, efficiently reduces numerical damping and thus ensures second‐order accuracy of the solutions with local/global volume conservation. Numerical experiments have been made to fully validate the nonhydrostatic FVCOM, including surface standing and solitary waves in idealized flat‐ and sloping‐bottomed channels in homogeneous conditions, the density adjustment problem for lock exchange flow in a flat‐bottomed channel, and two‐layer internal solitary wave breaking on a sloping shelf. The model results agree well with the relevant analytical solutions and laboratory data. These validation experiments demonstrate that the nonhydrostatic FVCOM is capable of resolving complex nonhydrostatic dynamics in coastal and estuarine regions.
Hybrid simulations of the termination shock: Suprathermal ion velocity distributions in the heliosheath
Authors: Wu Pin , Liu Kaijun , Winske Dan , Gary S. Peter , Schwadron Nathan A. , Funsten Herbert O.
Published: November 2010

The Los Alamos hybrid simulation code is used to examine kinetic properties of pickup ions at the heliospheric termination shock and in the downstream heliosheath. All simulations are one‐dimensional in spatial variations, represent the electrons as a zero‐mass fluid, and address only perpendicular shocks. Interpretation of measurements from the IBEX and Voyager spacecraft depend sensitively on the properties of the suprathermal ions downstream of the termination shock, so this research addresses three topics concerning such ions. First, a careful examination of pickup ion trajectories shows that their initial acceleration does not require specular reflection at the shock, as is sometimes assumed, but is the consequence of gyromotion by selected ions at the shock. The primary factor in this energy gain is a gyro‐phase‐dependent interaction with the motional electric field upstream of, and the magnetic field at, the shock. Second, shock simulations are carried out in which the upstream pickup ions are assumed to have four different types of velocity distributions. The downstream ion perpendicular velocity distributions f(v⊥) are similar in each of the runs and may be approximately characterized as a thermal Maxwellian and a suprathermal distribution. The only significant difference among the four downstream distributions is in the tails of the suprathermal component. Third, simulations are carried out for three different upstream Mach numbers; the results show that faster solar wind flows lead to increased fluxes of ions in the tails of the suprathermal component and are generally consistent with energetic neutral atom observations by the IBEX spacecraft.
Observations of the eruption of the Sarychev volcano and simulations using the HadGEM2 climate model
Authors: Haywood James M. , Jones Andy , Clarisse Lieven , Bourassa Adam , Barnes John , Telford Paul , Bellouin Nicolas , Boucher Olivier , Agnew Paul , Clerbaux Cathy , Coheur Pierre , Degenstein Doug , Braesicke Peter
Published: November 2010

In June 2009 the Sarychev volcano located in the Kuril Islands to the northeast of Japan erupted explosively, injecting ash and an estimated 1.2 ± 0.2 Tg of sulfur dioxide into the upper troposphere and lower stratosphere, making it arguably one of the 10 largest stratospheric injections in the last 50 years. During the period immediately after the eruption, we show that the sulfur dioxide (SO2) cloud was clearly detected by retrievals developed for the Infrared Atmospheric Sounding Interferometer (IASI) satellite instrument and that the resultant stratospheric sulfate aerosol was detected by the Optical Spectrograph and Infrared Imaging System (OSIRIS) limb sounder and CALIPSO lidar. Additional surface‐based instrumentation allows assessment of the impact of the eruption on the stratospheric aerosol optical depth. We use a nudged version of the HadGEM2 climate model to investigate how well this state‐of‐the‐science climate model can replicate the distributions of SO2 and sulfate aerosol. The model simulations and OSIRIS measurements suggest that in the Northern Hemisphere the stratospheric aerosol optical depth was enhanced by around a factor of 3 (0.01 at 550 nm), with resultant impacts upon the radiation budget. The simulations indicate that, in the Northern Hemisphere for July 2009, the magnitude of the mean radiative impact from the volcanic aerosols is more than 60% of the direct radiative forcing of all anthropogenic aerosols put together. While the cooling induced by the eruption will likely not be detectable in the observational record, the combination of modeling and measurements would provide an ideal framework for simulating future larger volcanic eruptions.
Simple and stereospecific homologation of urethane‐protected α‐amino acids to their higher homologs using HBTU1
Authors: Vasanthakumar G.‐R. , Babu V.V.S.
Published: November 2010

Abstract: A simple, efficient and stereospecific approach for the homologation of urethane‐protected α‐amino acids to β‐amino acids by the Arndt–Eistert method employing Fmoc‐/Boc‐α‐amino acid and 2‐(1H‐benzotriazole‐1‐yl)‐1,1,3,3‐tetramethyl‐uronium hexafluorophosphate mixture for the acylation of diazomethane synthesizing the key intermediates Fmoc‐/Boc‐α‐aminodiazomethanes as crystalline solids is described.
Fermenting knowledge: the history of winemaking, science and yeast research
Authors: Chambers Paul J , Pretorius Isak S
Published: November 2010

In the second article of the ‘Food and Science’ series, Paul Chambers and Isak Pretorius explain the central role of yeast in wine making and how biotechnology can contribute to improving the quality of wine.
Poring over exosome structure
Authors: Tsanova Borislava , van Hoof Ambro
Published: November 2010

The authors analyse the eukaryotic exosome structure, published in EMBO reports, in light of the known archaeal and prokaryotic exosomes, and discuss its striking flexibility and the conservation of the RNA channelling mechanism.
Fire history, fire regimes, and climate change – integrating information for management and planning
Authors: Sommers William
Published: November 2010

Background/Question/Methods

Federal and other natural resource managers in the United States are now required to consider climate change in their planning. Wildland fire is a major component included in many of these planning efforts. Fire is a widespread ecosystem disturbance process that is global in scope with local to regional, event driven, resource and societal impacts. The frequency, severity and extent of Wildland fires are largely a function of interactions between vegetation and atmospheric processes. Fire activity and management costs have increased significantly over the last few decades. There is growing evidence that these increases relate to measured changes in climate variables. Our understanding of fire history, fire regimes, and past interactions between fire and climate has grown substantially in recent years. Fire regimes provide a context for interpreting fire history to facilitate our understanding of fire in relation to climate and other factors, and provide a bridge between ecosystem characteristics and climate change projections. The challenge is to provide managers with placed-based information about fire and climate change, involving multiple scales of atmospheric and ecosystem process interaction, that they can use for planning and communication purposes.

Results/Conclusions

We present results of an on going study that integrates fire history, fire regime, and climate change information in formats designed for use by managers in their climate change planning efforts. A representative group of land managers reviewed our proposed information structure in an interactive workshop setting, and provided recommendations for how to make this information accessible and useful to them. We characterize atmospheric scales of importance to fire as the climate change, climate variability, and event scales. These relate to long-term evolution of vegetation, seasonal to decadal drought, and fire events. We use Bailey's vegetation classification at various ecosystem scales to organize the fire history and fire regime information. Bailey classifications also serve as a bridge to LANDFIRE components, such as the Fire Regime Condition Class (FRCC), and as a link to GCM-based climate projections. In addition to reporting overall findings, we present examples of specific place-based information for representative ecosystems in different areas of the United States.
Structural analysis of fertilinβ cyclic peptide mimics that are ligands for α6β1 integrin
Authors: Li H. , Sampson N.
Published: November 2010

Abstract: The NMR structural analysis of two fertilinβ mimics cyclo(EC2DC1)YNH2,1, and cyclo(D2EC2D1C1)YNH2,2 is described. Both of these mimics are moderate inhibitors of sperm−egg binding with IC50 values of 500 µm in a mouse in vitro fertilization assay. For peptide 1, the optimized conformations that best match the NMR data have a pseudo‐type II′β‐turn with the linker and Glu at the i+1 and i+2 positions, respectively. The EC2D1C1 sequence is in a nonclassical (type IV) β‐turn. For peptide 2, the conformation that best matches the NMR data has two turns: a pseudo‐type II′β‐turn in the D2EC2D1 sequence followed by a nonclassical β‐turn in the EC2D1C1 sequence. The Cβ−Cβ distance between E and D1 in peptide 1 is 9.1 Å, in peptide 2, it is 7.7 Å. Thus, one possibility for the high IC50 values of these cyclic peptides is that the acidic residues are not constrained to a sufficiently tight turn, and thus much entropy must still be lost upon binding to the α6β1 integrin. This explains why the cyclic peptides are the same as linear peptides at inhibiting sperm−egg binding.
Double dimer peptide constructs are immunogenic and protective against Plasmodium falciparum in the experimental Aotus monkey model
Authors: Rivera Z. , Granados G. , Pinto M. , Varón D. , Carvajal C. , Chaves F. , Calvo J. , Rodríguez R. , Guzmán F. , Patarroyo M.E.
Published: November 2010

Abstract: Multiple antigen peptide constructs (MAPs) have been used to obtain defined multimeric peptide molecules useful in the development of possible synthetic malaria vaccines. In this context, a method was developed, named double dimer constructs (DDCs), involving the direct synthesis of a dimeric peptide with a C‐terminal cysteine. A tetrameric molecule was then obtained by oxidation of sulfhydryl groups. Dimer synthesis was optimized using a Fmoc/tBu strategy, dimers were purified by HPLC, oxidized with DMSO and characterized by HPLC and MALDI‐TOF‐MS. The tetramers or DDCs obtained by this method were used as immunogens in the search for a possible malaria vaccine. It was found that they were immunogenic in the experimental Aotus monkey model, and were able to induce protective immunity when challenged experimentally with a highly infective Plasmodium falciparum malaria strain.
Multireference general-model-space state-universal and state-specific coupled-cluster approaches to excited states
Authors: Li Xiangzhu , Paldus Josef
Published: November 2010

The concept of C-conditions, originally introduced in the framework of the multireference (MR), general-model-space (GMS), state-universal (SU), coupled-cluster (CC) approach with singles and doubles (GMS-SU-CCSD) to account for the internal amplitudes that vanish in the case of a complete model space, is applied to a state-selective or state-specific Mukherjee MR-CC method (MkCCSD). In contrast to the existing applications, the emphasis is on the description of excited states, particularly those belonging to the same symmetry species. The applicability of the C-conditions in all MR-SU-CC approaches is emphasized. Convergence problems encountered in the MkCCSD method when handling higher-lying states are pointed out. The performance of the GMS-SU-CCSD and MkCCSD methods is illustrated by considering low-lying vertical excitation energies of the ethylene molecule and para-benzyne diradical. A comparison with the equation-of-motion CCSD results, as well as with the available experimental data and recent multireference configuration interaction theoretical results, is also provided.
Point vortices in two dimensional-plasma hydrodynamics
Authors: Tur Anatoly , Yanovsky Vladimir
Published: November 2010

An exact theory of point vortices in two dimensional (2D) electron-ion plasma hydrodynamics is presented. This theory is a logical generalization of the classical theory of point vortices in a 2D Euler equation. The existence of two types of point vortices is shown: ion and electron, and their structure is described in detail. Ion vortices interact over long distances, while electron vortices interact over short distances. A dynamic system is obtained, which describes the common motion of an arbitrary number of electron and ion vortices. The proposed theory can be used to construct finite dimensional dynamical models of plasma motion, as well as for the construction of finite dimensional statistical models of turbulence, transport processes and filaments.
Improvement of the intrinsic time resolving power of the Cologne iron-free orange type electron spectrometers
Authors: Régis J.-M. , Materna Th. , Pascovici G. , Christen S. , Dewald A. , Fransen C. , Jolie J. , Petkov P. , Zell K. O.
Published: November 2010

Conversion electron spectroscopy represents an important tool for nuclear structure analysis of medium and heavy nuclei. Two iron-free magnetic electron spectrometers of the orange type have been installed at the Institute for Nuclear Physics of the University of Cologne. The very large transmission of 15% and the very good energy resolution of 1% makes the iron-free orange spectrometer a powerful instrument. By means of fast timing techniques, lifetimes of nuclear excited states can be measured with an accuracy better than 20 ps. For the first time, the energy dependent centroid position of prompt events yielding the time-walk characteristics (the prompt curve) of the orange spectrometer fast timing setup has been measured using prompt secondary δ-electrons generated in a pulsed beam experiment. The prompt curve calibrated as a function of energy allows precise lifetime determination down to a few tens of picoseconds by the use of the centroid shift method.
Reflections of ions in electrostatic analyzers: A case study with New Horizons/Solar Wind Around Pluto
Authors: Randol B. M. , Ebert R. W. , Allegrini F. , McComas D. J. , Schwadron N. A.
Published: November 2010

Electrostatic analyzers (ESAs), in various forms, are used to measure plasma in a range of applications. In this article, we describe how ions reflect from the interior surfaces of an ESA, the detection of which constitutes a fundamentally nonideal response of ESAs. We demonstrate this effect by comparing laboratory data from a real ESA-based space instrument, the Solar Wind Around Pluto (SWAP) instrument, aboard the NASA New Horizons spacecraft, to results from a model based on quantum mechanical simulations of particles reflected from the instrument’s surfaces combined with simulations of particle trajectories through the instrument’s applied electrostatic fields. Thus, we show, for the first time, how reflected ions in ESAs lead to nonideal effects that have important implications for understanding the data returned by these instruments, as well as for designing new low-background ESA-based instruments. Specifically, we show that the response of SWAP widens considerably below a level of 10−3 of the peak response. Thus, a direct measurement of a plasma distribution with SWAP will have an energy-dependent background on the order of ≤10−3 of the peak of the signal due to that distribution. We predict that this order of magnitude estimate for the background applies to a large number of ESA-based instruments because ESAs operate using a common principle. However, the exact shape of the energy-dependent response will be different for different instruments. The principle of operation is that ions outside the ideal range of energy-per-charge are deflected into the walls of the ESA. Therefore, we propose that a new design paradigm is necessary to mitigate the effect of ion reflections and thus accurately and directly measure the energy spectrum of a plasma using ESAs. In this article, we build a framework for minimizing the effect of ion reflections in the design of new ESAs. Through the use of existing computer simulation software, a design team can use our method to quantify the amount of reflections in their instrument and iteratively change design parameters before fabrication, conserving resources. A possible direction for the new design paradigm is having nonsolid walls of the ESA, already used in some applications.
Thermal boundary resistance from mode energy relaxation times: Case study of argon-like crystals by molecular dynamics
Authors: Rajabpour Ali , Volz Sebastian
Published: November 2010

We derive the mode spectrum of the thermal boundary resistance between two bodies having a temperature difference ΔT. A general expression of the time τ that defines the resistance is derived as the equilibrium autocorrelation of ΔT integrated over time. A further decomposition of this autocorrelation yields the resistance spectrum as equal to the mode relaxation time weighted by its energy mean square fluctuation. We then perform molecular dynamics simulations of argon like crystals in equilibrium and nonequilibrium regimes to prove the relevance of our model. This general method allows for deriving the resistance spectrum and therefore can yield key rules to control the exchanged heat flux.
Transport in time-dependent dynamical systems: Finite-time coherent sets
Authors: Froyland Gary , Santitissadeekorn Naratip , Monahan Adam
Published: November 2010

We study the transport properties of nonautonomous chaotic dynamical systems over a finite-time duration. We are particularly interested in those regions that remain coherent and relatively nondispersive over finite periods of time, despite the chaotic nature of the system. We develop a novel probabilistic methodology based upon transfer operators that automatically detect maximally coherent sets. The approach is very simple to implement, requiring only singular vector computations of a matrix of transitions induced by the dynamics. We illustrate our new methodology on an idealized stratospheric flow and in two and three-dimensional analyses of European Centre for Medium Range Weather Forecasting (ECMWF) reanalysis data.
Design and operation of a portable scanner for high performance microchip capillary array electrophoresis
Authors: Scherer James R. , Liu Peng , Mathies Richard A.
Published: November 2010

We have developed a compact, laser-induced fluorescence detection scanner, the multichannel capillary array electrophoresis portable scanner (McCAEPs) as a platform for electrophoretic detection and control of high-throughput, integrated microfluidic devices for genetic and other analyses. The instrument contains a confocal optical system with a rotary objective for detecting four different fluorescence signals, a pneumatic system consisting of two pressure/vacuum pumps and 28 individual addressable solenoid valves for control of on-chip microvalves and micropumps, four Polymerase Chain Reaction (PCR) temperature control systems, and four high voltage power supplies for electrophoresis. The detection limit of the instrument is ∼20 pM for on-chip capillary electrophoresis of fluorescein dyes. To demonstrate the system performance for forensic short tandem repeat (STR) analysis, two experiments were conducted: (i) electrophoretic separation and detection of STR samples on a 96-lane microfabricated capillary array electrophoresis microchip. Fully resolved PowerPlex® 16 STR profiles amplified from 1 ng of 9947A female standard DNA were successfully obtained; (ii) nine-plex STR amplification, sample injection, separation, and fluorescence detection of 100-copy 9948 male standard DNA in a single integrated PCR- capillary electrophoresis microchip. These results demonstrate that the McCAEPs can be used as a versatile control and detection instrument that operates integrated microfluidic devices for high-performance forensic human identification.
Two-dimensional Blasius viscous flow of a power-law fluid over a semi-infinite flat plane
Authors: Van Gorder Robert A.
Published: November 2010

Analytic results are obtained for the similarity equation governing the two-dimensional Blasius viscous flow of a power-law fluid over a semi-infinite flat plane via Taylor series for small values of the independent similarity variable. Then, an analytic perturbative procedure is used to determine an approximate solution that exhibits the correct asymptotic behavior. This perturbation method allows for the computation of the shear stress at the wall, something which is impossible with a Taylor series approach. It is found that the perturbation solutions converge sufficiently rapidly; indeed, a first order approximation gives qualitatively accurate results. Furthermore, we employ the perturbation method to deduce the influence of the power-law index, n, on the obtained similarity solutions.
Bow-wave-like hydraulic jump and horseshoe vortex around an obstacle in a supercritical open channel flow
Authors: Mignot E. , Riviere N.
Published: November 2010

The objective of the present paper is to characterize the interaction of a supercritical open channel flow with an emerged, rectangular shaped obstacle. Upstream from the obstacle, two main flow structures are observed: (i) a hydraulic jump in the near-surface region and (ii) a horseshoe vortex in the near-bed region. Both flow structures are detached upstream from the obstacle and two main flow types occur regarding their relative detachment lengths. For high Reynolds numbers (turbulent regime), the detachment length of the hydraulic jump exceeds the one of the horseshoe vortex; this flow type is named “breaking type.” Oppositely, for lower Reynolds numbers (laminar regime), the detachment length of the horseshoe vortex exceeds the one of the hydraulic jump, and the flow type is named “separation type.” Experimental measurements based on particle deposition and colored streamline deflection are used to detect the location and shape of the detachment curves. We showed that for both flow types, the shape of the hydraulic jump curve is hyperbolic, constrained by two asymptotes following the Froude angle on each side of the obstacle. On the other hand, the shape of the horseshoe vortex curve depends on the flow type; it is hyperbolic in the separation type and elliptic in the breaking type. The dimensional analysis reveals that three parameters can influence the detachment curves: the upstream Froude and Reynolds numbers and the upstream water depth normalized by the obstacle thickness. The influence of these parameters is investigated experimentally on a water table for both flow types.
The eigenfrequency spectrum of linear magnetohydrodynamic perturbations in stationary equilibria: A variational principle
Authors: Andries Jesse
Published: November 2010

The frequencies of the normal modes of oscillation of linear magnetohydrodynamic perturbations of a stationary equilibrium are related to the stationary points of a quadratic functional over the Hilbert space of Lagrangian displacement vectors, which is subject to a constraint. In the absence of a background flow (or of a uniform flow), the relation reduces to the well-known Rayleigh–Ritz variational principle. In contrast to the existing variational principles for perturbations of stationary equilibria, the present treatment does neither impose additional symmetry restrictions on the equilibrium, nor does it involve the generalization to bilinear functionals instead of quadratic forms. This allows a more natural interpretation of the quadratic forms as energy functionals.
Internal tests and improvements of the Krook model for nonlocal electron energy transport in laser produced plasmas
Authors: Colombant Denis G. , Manheimer Wallace M.
Published: November 2010

Electron thermal transport in a laser produced plasma cannot be described with a local approximation in many regions of a laser produced plasma because the electron mean free path is longer than the temperature gradient scale length. Since a Krook model for the electron Vlasov equation is analytically solvable in the nonlocal limit, one can find simple expressions for the electron thermal flux in the nonlocal limit, and these can be economically incorporated into fluid simulations. The Krook model provides reasonable descriptions of both preheat and flux limitation. We have analyzed the Krook model in a series of publications. Here we streamline the presentation of the model, show qualitatively just what the model predicts in certain situations, give internal tests to check the validity of the model, and provide more accurate analytic approximations to the integral formulas which the model gives rise to.
Creation of persistent, straight, 2 mm long laser driven channels in underdense plasmas
Authors: Sarri G. , Lancaster K. L. , Trines R. , Clark E. L. , Hassan S. , Jiang J. , Kageiwa N. , Lopes N. , Ramis R. , Rehman A. , Ribeyre X. , Russo C. , Scott R. H. H. , Tanimoto T. , Temporal M. , Borghesi M. , Davies J. R. , Najmudin Z. , Tanaka K. A. , Tatarakis M. , Norreys P. A.
Published: November 2010

The experimental study of the behavior of deuterium plasma with densities between 2×1018 and 2×1020 cm−3, subjected to a 6 TW, 30 ps, 3×1018 W cm−2 laser pulse, is presented. Conclusive experimental proof that a single straight channel is generated when the laser pulse interacts with the lowest densities is provided. This channel shows no small-scale longitudinal density modulations, extends up to 2 mm in length and persists for up to 150 ps after the peak of the interaction. Bifurcation of the channel after 1 mm propagation distance is observed for the first time. For higher density interactions, above the relativistic self-focusing threshold, bubblelike structures are observed to form at late times. These observations have implications for both laser wakefield accelerators and fast ignition inertial fusion studies.
Effect of laser parameters and assist gas on spectral response of silicon fibrous nanostructure
Authors: Mahmood Abdul Salam , Venkatakrishnan Krishnan , Tan Bo , Alubiady M.
Published: November 2010

This article report, for the first time, the influence of laser parameters on the spectral response of weblike silicon fibrous nanostructures. These nanostructures are formed by femtosecond laser irradiation at megahertz pulse frequency under atmosphere and nitrogen ambient. The observed decreasing in reflectance is correlated with the density of fibrous nanostructures and the size of the agglomerated nanoparticles. Compared to bulk silicon, Raman spectra of fibrous nanostructures shows a downward shift and asymmetric broadening at the first order phonon peak. The shift and broadening are attributed to phonon confinement of fibrous nanostructure. Polarization and nitrogen gas modify the morphology of generated nanomaterials but does not have effect on light absorptance. Pulsewidth and pulse frequency do not have significant effect on light absorptance.
The three-dimensional mixed-spin Heisenberg model applied to the magnetic properties of La1−xSrxMnO3 in the random phase approximation
Authors: Hu Ai-Yuan , Chen Yuan , Wang Qin
Published: November 2010

The magnetic properties of the manganese oxide compounds La1−xSrxMnO3 are studied by means of the double-time Green’s function. The phase diagram, magnetization, spin-wave dispersion, and spin-wave stiffness are obtained within the random phase approximation. Our results are in agreement with other theoretical and experimental results.
Light scattering from dislocations in silicon
Authors: Monier Vanessa , Capello Luciana , Kononchuk Oleg , Pichaud Bernard
Published: November 2010

Nondecorated glide dislocations in Czochralski grown silicon have been studied by laser scattering tomography technique. Dependence of intensity of scattered light on polarization of the incident light has been measured for different orientations of the dislocation line and Burgers vector. Detailed theory of light scattering by dislocation in silicon crystals is presented. It is shown that by combination of polarization and tomography measurements it is possible to determine slip system of nondecorated mixed dislocation in Si.