bluuebunny/crossref_metadata_2025 huggingface dataset:
Radionuclides released to the environment following nuclear events
Authors: Salbu Brit
Published: May 2011

The accident at the Fukushima Daiichi nuclear power plant, precipitated by the devastating earthquake and subsequent tsunami that struck the northeastern coast of Japan in March 2011, has raised concerns about the fate of radioactive particles released into the environment. Radioactive particles with different composition, size, shape, structures, and colors have been identified throughout the world in different biotic and abiotic media. This article briefly summarizes what is currently understood about the fate of, and risks posed by, these materials in the environment. Integr Environ Assess Manag 2011;7:362–364. © 2011 SETAC
Overview of exposure to and effects from radionuclides in terrestrial and marine environments
Authors: Sample Bradley E.
Published: May 2011

The accident at the Fukushima Daiichi nuclear power plant, precipitated by the devastating earthquake and subsequent tsunami that struck the northeastern coast of Japan in March 2011, has raised concerns about potential impacts to terrestrial and marine environments from radionuclides released into the environment. A preliminary understanding of the potential ecological impacts from radionuclides can be ascertained from observations and data developed following previous environmental incidents elsewhere in the world. This article briefly summarizes how biota experience exposure to ionizing radiation, what effects may be produced, and how they may differ among taxa and habitats. Integr Environ Assess Manag 2011;7:368–370. © 2011 SETAC
Technology and the forces of nature: A lesson of humility calling for ecocentrism
Authors: Bréchignac Francois
Published: May 2011

The incident at the Fukushima Daiichi nuclear power plant, resulting from the powerful earthquake and tsunami that struck the northeastern coast of Japan in March 2011, reminds humankind of the powerful natural forces that shape our world. This article calls for a new ecocentric approach to human interaction with the environment, with particular reference to the environmental consequences of radiation. Integr Environ Assess Manag 2011;7:409–410. © 2011 SETAC
Yogurt consumption and risk of colorectal cancer in the Italian European prospective investigation into cancer and nutrition cohort
Authors: Pala Valeria , Sieri Sabina , Berrino Franco , Vineis Paolo , Sacerdote Carlotta , Palli Domenico , Masala Giovanna , Panico Salvatore , Mattiello Amalia , Tumino Rosario , Giurdanella Maria C. , Agnoli Claudia , Grioni Sara , Krogh Vittorio
Published: May 2011

Fermented dairy products like yogurt have been suggested to protect against colorectal cancer (CRC). We conducted a prospective study on 45,241 (14,178 men; 31,063 women) volunteers of the EPIC‐Italy cohort who completed a dietary questionnaire including specific questions on yogurt intake. During 12 years of follow‐up, 289 volunteers were diagnosed with CRC. Hazard ratios (HRs) for the disease and 95% confidence intervals (CIs) were estimated by Cox proportional hazard models, stratified by dietary questionnaire and adjusted for energy intake and other potential confounders. Yogurt intake was inversely associated with CRC risk. For the energy‐adjusted model, HR for CRC in the highest versus lowest tertile of yogurt intake was 0.62 (95% CI, 0.46–0.83). In the full model adjusted for energy, simple sugar, calcium, fiber, animal fat, alcohol and red meat intake, as well as body mass index, smoking, education and physical activity, HR was 0.65 (95% CI, 0.48–0.89) in the highest versus lowest tertile. The protective effect of yogurt was evident in the entire cohort, but was stronger in men, although there was no interaction of sex with the yogurt–CRC association (pinteraction 0.20, fully adjusted model). In our prospective study, high yogurt intake was significantly associated with decreased CRC risk, suggesting that yogurt should be part of a diet to prevent the disease. Investigation of larger cohorts is necessary to reveal any residual confounding of the association of yogurt intake with CRC risk.
Cd modifies hepatic Zn deposition and modulates δ‐ALA‐D activity and MT levels by distinct mechanisms
Authors: Braga Marcos Martins , Dick Tuiskon , de Oliveira Diogo Losch , Guerra Adriele Scopel , Leite Marina Concli , Ardais Ana Paula , Souza Diogo Onofre , Rocha João B.T.
Published: May 2011

Cadmium (Cd) is a pollutant that is harmful to human and animals. The liver is a target for Cd accumulation and it can disrupt Zn homeostasis. Here we examined the interaction of Zn and Cd to determine how these two metals could affect δ‐aminolevulinate‐dehydratase (δ‐ALA‐D) and metallothionein (MT), two potential molecular endpoints for Cd hepatotoxicity. Cd exposure (0.25 and 1 mg kg1 body weight, i.p., for 10 days) caused a marked increase in hepatic Zn deposition, which was not modified by treatment with Zn (2 mg kg1, i.p.). Cd caused a dose‐dependent increase in hepatic Cd content that was not modified by Zn. Zn and/or Cd treatment increased hepatic δ‐ALA‐D activity, although the increase caused by Cd was less marked. Reactivation index of δ‐ALA‐D by DTT was decreased by Zn and Cd exposure, which indicates that Zn protects enzyme from oxidation. Hepatic MT was increased only after exposure to 1 mg kg−1 Cd and Zn reduced the stimulation of MT synthesis. The results presented here indicate that Cd can redistribute Zn from non‐hepatic tissues to liver and the increase in hepatic Zn deposition can account for the increase in hepatic δ‐ALA‐D activity after Cd exposure. However, Zn blocked the increase in hepatic MT levels caused by Cd. Thus, the modulation of the two molecular endpoints of Cd toxicity used here was distinct, which indicates that the mechanism(s) involved in Zn and Cd distribution, δ‐ALA‐D and MT regulation are not coincident. Copyright © 2011 John Wiley & Sons, Ltd.
Catalytic organosolv fractionation of willow wood and wheat straw as pretreatment for enzymatic cellulose hydrolysis
Authors: Huijgen Wouter J. J. , Smit Arjan T. , Reith Johannes H. , Uil Herman den
Published: May 2011

BACKGROUND: Ethanol‐based organosolv fractionation of lignocellulosic biomass is an effective pretreatment technology for enzymatic cellulose hydrolysis to produce sugars and lignin within a biorefinery. This study focuses on the catalytic effect of H2SO4, HCl, and MgCl2 on organosolv pretreatment of willow wood and wheat straw.

RESULTS: The use of catalysts improved fractionation of both feedstocks. The maximum enzymatic cellulose digestibility obtained was 87% for willow wood (using 0.01 mol L−1 H2SO4 as catalyst) and 99% for wheat straw (0.02 mol L−1 HCl). Non‐catalytic organosolv fractionation at identical conditions resulted in 74% (willow wood) and 44% (wheat straw) glucose yield by enzymatic hydrolysis. Application of catalysts in organosolv pretreatment was particularly effective for wheat straw. The influence of the acid catalysts was found to be primarily due to their effect on the pH of the organosolv liquor. Acid catalysts particularly promoted xylan hydrolysis. MgCl2 was less effective than the acid catalysts, but it seemed to more selectively improve delignification of willow wood.

CONCLUSION: Application of catalysts in organosolv pretreatment of willow wood and wheat straw was found to substantially improve fractionation and enzymatic digestibility. The use of catalysts can contribute to achieving maximum utilization of lignocellulosic biomass in organosolv‐based biorefineries. Copyright © 2011 Society of Chemical Industry
Reproducibility analysis of diffusion tensor indices and fiber architecture of human calf muscles in vivo at 1.5 Tesla in neutral and plantarflexed ankle positions at rest
Authors: Sinha Shantanu , Sinha Usha
Published: May 2011

Purpose:

To investigate the reproducibility of diffusion tensor imaging (DTI) ‐derived indices and fiber architecture of calf muscles at 1.5 Tesla (T), to establish an imaging based method to confirm ankle position, and to compare fiber architecture at different ankle positions.

Materials and Methods:

Six subjects were imaged at 1.5T with the foot in neutral and plantarflexed positions. DTI indices were calculated in four muscle compartments (medial and lateral gastrocnemius [MG, LG], superficial and deep anterior tibialis [AT‐S, AT‐D]). Two subjects were scanned on 3 days to calculate the coefficient of variability (CV) and the repeatability coefficient (RC).

Results:

DTI indices were close to the values obtained in earlier 3T and 1.5T studies. Fractional anisotropy decreased significantly in the MG and increased significantly in the AT‐S and AT‐D compartments while fiber orientation with respect to the magnet Z‐axis increased significantly in the MG and decreased significantly in the AT‐S compartment with plantarflexion. The CV and RC for the DTI indices and fiber orientations were comparable to 3T studies. Fiber lengths and orientation angles in the MG matched corresponding measures from ultrasound studies.

Conclusion:

DTI at 1.5T provides reproducible measures of diffusion indices and fiber architecture of calf muscle at different muscle lengths. J. Magn. Reson. Imaging 2011;. © 2011 Wiley‐Liss, Inc.
Exercise training increases myocardial perfusion in residual viable myocardium within infarct zone
Authors: Su Mao‐Yuan M. , Lee Bai‐Chin , Yu Hsi‐Yu , Wu Yen‐Wen , Chu Woei‐Chyn , Tseng Wen‐Yih I
Published: May 2011

Purpose:

To study the effect of exercise training on the myocardial perfusion in the postinfarct myocardium.

Materials and Methods:

Twenty‐nine patients with stable chronic myocardial infarction were randomly assigned to either a training group (N = 17) or a control group (N = 12). The training group received a 3‐month exercise program. Cardiovascular MR was first performed before the training to establish a baseline, and subsequently performed once again upon conclusion of the program. Late gadolinium enhancement was used both to define the infarct and remote zones and to quantify the ratio of the residual viable myocardium (VMR) within the infarct zone. The myocardium was divided into subendocardial and subepicardial layers with equal thickness. The interval change of myocardial perfusion reserve (MPR) was computed for each zone and layer. The association between the exercise‐induced perfusion change and VMR was analyzed for layers of the infarct zone.

Results:

In the training group, the remote zone showed significantly increased MPR. The infarct zone showed no perfusion change in the subendocardial layer, but it demonstrated significantly increased MPR in the subepicardial layer. In the infarct zone, the change in MPR was associated with VMR.

Conclusion:

In chronic myocardial infarction, the exercise‐induced perfusion change in the infarct zone is proportional to the amount of residual viable myocardium. J. Magn. Reson. Imaging 2011;. © 2011 Wiley‐Liss, Inc.
Outcome of hypovascular hepatic nodules revealing no gadoxetic acid uptake in patients with chronic liver disease
Authors: Motosugi Utaroh , Ichikawa Tomoaki , Sano Katsuhiro , Sou Hironobu , Onohara Kojiro , Muhi Ali , Amemiya Fumitake , Enomoto Nobuyuki , Matsuda Masanori , Fujii Hideki , Araki Tsutomu
Published: May 2011

Purpose:

To elucidate the natural history of hypovascular nodules that appear hypointense on hepatocyte‐phase gadoxetic acid‐enhanced MR images by focusing on hypervascularization over time.

Materials and Methods:

In this study, 135 hypovascular nodules revealing no gadoxetic acid uptake in 53 patients were examined. All nodules were retrospectively examined using serial follow‐up computed tomography (CT) and MRI examinations until hypervascularity was observed on arterial‐phase dynamic CT or gadoxetic acid‐enhanced MR images, or on CT during hepatic arteriography. Logistic regression analysis was used to investigate the association between hypervascularization and MR findings including a presence of fat assessed by a signal drop on opposed‐phase T1‐weighted images.

Results:

Of the 135 nodules, 16 underwent hypervascularization. The size of the nodules and the presence of fat in the nodules were independent indicators of hypervascularization. The 1‐year cumulative risk of hypervascularization was 15.6%. This risk was significantly increased in the case of nodules >10 mm (37.6%, P < 0.01) and fat‐containing nodules (26.5%, P < 0.01).

Conclusion:

Hypovascular nodules that appear hypointense on hepatocyte‐phase gadoxetic acid‐enhanced MR images may progress to conventional hypervascular hepatocellular carcinoma. Nodules more than 10 mm in diameter and containing fat are at high risk for developing hypervascularization. J. Magn. Reson. Imaging 2011;. © 2011 Wiley‐Liss, Inc.
Macroporous monolithic supports for affinity chromatography
Authors: Arrua Ruben Dario , Alvarez Igarzabal Cecilia Inés
Published: May 2011

In the early 1990s, three research groups simultaneously developed continuous macroporous rod‐shaped polymeric systems to eliminate the problem of flow through the interparticle spaces generally presented by the chromatography columns that use particles as filler. The great advantage of those materials, forming a continuous phase rod, is to increase the mass transfer by convective transport, as the mobile phase is forced to go through all means of separation, in contrast to particulate media where the mobile phase flows through the interparticle spaces. Due to their special characteristics, the monolithic polymers are used as base‐supports in different separation techniques, those chromatographic processes being the most important and, to a greater extent, those involving the separation of biomolecules as in the case of affinity chromatography. This mini‐review reports the contributions of several groups to the development of macroporous monoliths and their modification by immobilization of specific ligands on the products for their application in affinity chromatography.
Computational Insights into Ligand Selectivity of Estrogen Receptors from Pharmacophore Modeling
Authors: Fang Jing , Shen Jie , Cheng Feixiong , Xu Zhejun , Liu Guixia , Tang Yun
Published: May 2011

Estrogen receptors (ERs) belong to the nuclear receptor superfamily, which play crucial roles in the human body. To date, two subtypes, ERα and ERβ, have been identified. The function and expression of both subtypes are various, stimulating the interest for discovering subtype selective ligands. However, ERα and ERβ are highly homologous. They share 56 % sequence identity in the ligand binding domain and only two pairs of residues differ in the ligand binding pocket. In this study, pharmacophore models were built for both subtypes based on 23 ERα and 24 ERβ selective ligands, respectively. It was found from these pharmacophore models that hydrophobic and hydrogen bonding interactions were essential for the subtype selectivity. The hydrogen bond donor feature in the phenol part was a favorable contribution to ERβ selectivity, whereas the one in the benzopyran part of the ligand was important for ERα selectivity. Furthermore, simulated virtual screening was performed with both subtype specific pharmacophore models. The results confirmed the reliability and discrimination ability of both models. These findings could not only be helpful for the understanding of a possible mechanism underlying ligand selectivity of ERs, but could also pave a new avenue for the discovery of novel selective ER ligands.
Characterization of paramagnetic effects of molecular oxygen on blood oxygenation level‐dependent‐modulated hyperoxic contrast studies of the human brain
Authors: Pilkinton David T. , Gaddam Santosh R. , Reddy Ravinder
Published: May 2011

In hyperoxic contrast studies modulated by the blood oxygenation level‐dependent effect, it is often assumed that hyperoxia is a purely intravascular, positive contrast agent in T‐weighted images, and the effects that are not due to blood oxygenation level‐dependent contrast are small enough to be ignored. In this study, this assumption is re‐evaluated and non‐blood oxygenation level‐dependent effects in T‐weighted hyperoxic contrast studies of the human brain were characterized. We observed significant negative signal changes in T‐weighted images in the frontal lobes; B0 maps suggest that this effect was primarily due to increased intravoxel dephasing from increased static field inhomogeneity due to susceptibility changes from oxygen in and around the upper airway. These static field effects were shown to scale with magnetic field strength. Signal changes observed around the brain periphery and in the ventricles suggest the effect of image distortions from oxygen‐induced bulk B0 shifts, along with a possible contribution from decreased T due to oxygen dissolved in the cerebrospinal fluid. Reducing the concentration of inhaled oxygen was shown to mitigate negative contrast of molecular oxygen due to these effects, while still maintaining sufficient blood oxygenation level‐dependent contrast to produce accurate measurements of cerebral blood volume. Magn Reson Med, 2011. © 2011 Wiley‐Liss, Inc.
B0 mapping with multi‐channel RF coils at high field
Authors: Robinson Simon , Jovicich Jorge
Published: May 2011

Mapping the static magnetic field via the phase evolution over gradient echo scans acquired at two or more echo times is an established method. A number of possibilities exist, however, for combining phase data from multi‐channel coils, denoising and thresholding field maps for high field applications. Three methods for combining phase images when no body/volume coil is available are tested: (i) Hermitian product, (ii) phase‐matching over channels, and (iii) a new approach based on calculating separate field maps for each channel. The separate channel method is shown to yield field maps with higher signal‐to‐noise ratio than the Hermitian product and phase‐matching methods and fewer unwrapping errors at low signal‐to‐noise ratio. Separate channel combination also allows unreliable voxels to be identified via the standard deviation over channels, which is found to be the most effective means of denoising field maps. Tests were performed using multichannel coils with between 8 and 32 channels at 3 T, 4 T, and 7 T. For application in the correction of distortions in echo‐planar images, a formulation is proposed for reducing the local gradient of field maps to eliminate signal pile‐up or swapping artifacts. Field maps calculated using these techniques, implemented in a freely available MATLAB toolbox, provide the basis for an effective correction for echo‐planar imaging distortions at high fields. Magn Reson Med, 2011. © 2011 Wiley‐Liss, Inc.
Sparse‐CAPR: Highly accelerated 4D CE‐MRA with parallel imaging and nonconvex compressive sensing
Authors: Trzasko Joshua D. , Haider Clifton R. , Borisch Eric A. , Campeau Norbert G. , Glockner James F. , Riederer Stephen J. , Manduca Armando
Published: May 2011

Cartesian Acquisition with Projection‐Reconstruction‐like sampling is a SENSE‐type parallel 3DFT acquisition paradigm for 4D contrast‐enhanced magnetic resonance angiography that has been demonstrated capable of providing high spatial and temporal resolution, diagnostic‐quality images at very high acceleration rates. However, Cartesian Acquisition with Projection–Reconstruction‐like sampling images are typically reconstructed online using Tikhonov regularization and partial Fourier methods, which are prone to exhibit noise amplification and undersampling artifacts when operating at very high acceleration rates. In this work, a sparsity‐driven offline reconstruction framework for Cartesian Acquisition with Projection‐Reconstruction‐like sampling is developed and demonstrated to consistently provide improvements over the currently‐employed reconstruction strategy against these ill‐effects. Moreover, the proposed reconstruction strategy requires no changes to the existing Cartesian Acquisition with Projection–Reconstruction‐like sampling acquisition protocol, and an efficient numerical optimization and hardware system are described that allow for a 256 × 160 × 80 volume contrast‐enhanced magnetic resonance angiography volume to be reconstructed from an eight‐channel data set in less than 2 min. Magn Reson Med, 2011. © 2011 Wiley‐Liss, Inc.
Amide proton transfer imaging with improved robustness to magnetic field inhomogeneity and magnetization transfer asymmetry using saturation with frequency alternating RF irradiation
Authors: Scheidegger Rachel , Vinogradov Elena , Alsop David C.
Published: May 2011

Amide proton transfer (APT) imaging has shown promise as an indicator of tissue pH and as a marker for brain tumors. Sources of error in APT measurements include direct water saturation, and magnetization transfer (MT) from membranes and macromolecules. These are typically suppressed by postprocessing asymmetry analysis. However, this approach is strongly dependent on B0 homogeneity and can introduce additional errors due to intrinsic MT asymmetry, aliphatic proton features opposite the amide peak and radiation damping‐induced asymmetry. Although several methods exist to correct for B0 inhomogeneity, they tremendously increase scan times and do not address errors induced by asymmetry of the z‐spectrum. In this article, a novel saturation scheme—saturation with frequency alternating RF irradiation (SAFARI)—is proposed in combination with a new magnetization transfer ratio (MTR) parameter designed to generate APT images insensitive to direct water saturation and MT, even in the presence of B0 inhomogeneity. The feasibility of the SAFARI technique is demonstrated in phantoms and in the human brain. Experimental results show that SAFARI successfully removes direct water saturation and MT contamination from APT images. It is insensitive to B0 offsets up to 180 Hz without using additional B0 correction, thereby dramatically reducing scanning time. Magn Reson Med, 2011. © 2011 Wiley Periodicals, Inc.
2H2O incorporation into hepatic acetyl‐CoA and de novo lipogenesis as measured by Krebs cycle‐mediated 2H‐enrichment of glutamate and glutamine
Authors: Silva Ana Maria , Martins Fatima , Jones John G. , Carvalho Rui
Published: May 2011

Deuterated water is widely used for measuring de novo lipogenesis on the basis of quantifying lipid 2H‐enrichment relative to that of body water. However, incorporation of 2H‐enrichment from body water into newly synthesized lipid molecules is incomplete therefore the true lipid precursor enrichment differs from that of body water. We describe a novel measurement of de novo lipogenesis that is based on a true precursor‐product analysis of hepatic acetyl‐CoA and triglyceride methyl enrichments from deuterated water. After deuterated water administration to seven in situ and seven perfused livers, acetyl‐CoA methyl enrichment was inferred from 2H nuclear magnetic resonance analysis of hepatic glutamate/glutamine (Glx) enrichment and triglyceride methyl enrichment was directly determined by 2H nuclear magnetic resonance of triglycerides. Acetyl‐CoA 2H‐enrichment was 71% ± 1% that of body water for in situ livers and 53% ± 2% of perfusate water for perfused livers. From the ratio of triglyceride‐methyl/acetyl‐CoA enrichments, fractional de novo lipogenesis rates of 0.97% ± 0.09%/2 hr and 7.92% ± 1.47%/48 hr were obtained for perfused and in situ liver triglycerides, respectively. Our method reveals that acetyl‐CoA enrichment is significantly less than body water both for in situ and perfused livers. Furthermore, the difference between acetyl‐CoA and body water enrichments is sensitive to the experimental setting. Magn Reson Med, 2011. © 2011 Wiley Periodicals, Inc.
Discrete differential operators on irregular nodes (DDIN)
Authors: Isshiki H.
Published: May 2011

A previous research made an integral mathematical contribution for obtaining local function interpolation using neighboring nodal values of the solution function. Subsequent researchers developed mesh‐free methods for Finite Element Method (FEM). This principle can also be used to obtain discrete differential operators on irregular nodes. They may be successfully applied to Finite Difference method, Moving Particle Semi‐implicit (MPS) method and Random Collocation Method (RCM). In this paper, we obtain discrete differential operators on irregular nodes and successfully apply them to solve differential equations using the RCM. We also discuss mathematical aspects of the MPS method. Copyright © 2011 John Wiley & Sons, Ltd.
The dynamic protein partnership of RNA polymerase inBacillus subtilis
Authors: Delumeau Olivier , Lecointe François , Muntel Jan , Guillot Alain , Guédon Eric , Monnet Véronique , Hecker Michael , Becher Dörte , Polard Patrice , Noirot Philippe
Published: May 2011

In prokaryotes, transcription results from the activity of a 400 kDa RNA polymerase (RNAP) protein complex composed of at least five subunits (2α, β, β′, ω). To ensure adequate responses to changing environmental cues, RNAP activity is tightly controlled by means of interacting regulatory proteins. Here, we report the affinity‐purification of the Bacillus subtilis RNAP complexes from cells in different growth states and stress conditions, and the quantitative assessment by mass spectrometry of the dynamic changes in the composition of the RNAP complex. The stoichiometry of RNA polymerase was determined by a comparison of two mass spectrometry‐based quantification methods: a label‐based and a label‐free method. The validated label‐free method was then used to quantify the proteins associated with RNAP. The levels of sigma factors bound to RNAP varied during growth and exposure to stress. Elongation factors, helicases such as HelD and PcrA, and novel unknown proteins were also associated with RNAP complexes. The content in 6S RNAs of purified RNAP complexes increased at the onset of the stationary phase. These quantitative variations in the protein and RNA composition of the RNAP complexes well correlate with the known physiology of B. subtilis cells under different conditions.
Combined proteomic and transcriptomic analysis of the response of Bacillus anthracis to oxidative stress
Authors: Pohl Susanne , Tu Wang Y. , Aldridge Phillip D. , Gillespie Colin , Hahne Hannes , Mäder Ulrike , Read Timothy D. , Harwood Colin R.
Published: May 2011

The endospore‐forming Gram‐positive pathogen Bacillus anthracis is responsible for the usually fatal disease, inhalational anthrax. The success of this pathogen is dependent on its ability to subvert elements of the innate immune system of its animal hosts. B. anthracis spores, which are the main infective agent, are engulfed and germinate in patrolling alveolar macrophages. In order for the infection to progress, the resulting vegetative cells must resist the antimicrobial oxidative burst mounted by the host NADPH oxidase complex. The response of B. anthracis to this and other macrophage‐related stresses is therefore of major importance to the success of this pathogen, and consequently we have analysed the superoxide and peroxide stress stimulons of B. anthracis strain UM23C1‐2 by means of a combined transcriptomics and proteomics approach. The results show distinct patterns of expression in response to paraquat (endogenous superoxide) and hydrogen peroxide stress. While the main response to paraquat is the induction of iron uptake pathways, the response to peroxide predominantly involves the induction of protection and repair mechanisms. Comparisons between the responses of B. anthracis and related soil bacterium, B. subtilis, reveal differences that are likely to be relevant to their respective habitats.
Synthesis and properties of mesogen‐jacketed liquid crystalline polymers containing biphenyl mesogen with asymmetric substitutions
Authors: Zhang Lanying , Wu Hongliang , Shen Zhihao , Fan Xinghe , Zhou Qifeng
Published: May 2011

This work focuses on the design, synthesis, and characterization of a series of mesogen‐jacketed liquid crystalline polymers (MJLCPs), poly(alkyl 4′‐(octyloxy)‐2‐vinylbiphenyl‐4‐carboxylate) (pVBP(m,8), m = 1, 2, 4, 6, 8, 10, 12). For the first time, we realized asymmetric substitutions in the mesogens of MJLCPs. The polymers obtained by conventional free radical polymerization were investigated in detail by a combination of various techniques, such as differential scanning calorimetry, wide‐angle X‐ray diffraction, and polarized light microscopy. Our results showed that all the polymers were thermally stable, and their glass transition temperatures decreased when m increased. The liquid crystalline (LC) phases that developed at high temperatures and disappeared at low temperatures were strongly dependent on the difference in lengths of alkyl groups on the 4 and 4′ substitution positions of the side‐chain biphenyl. While polymer pVBP(1,8) was not liquid crystalline, columnar liquid crystalline phases were observed for all other pVBP(m,8) (m = 2, 4, 6, 8, 10, 12) polymers. Polymer pVBP(8,8) showed a tetragonal columnar nematic liquid crystalline phase, and the other LC polymers exhibited columnar nematic phases. In additions, the smaller the difference in the lengths of the terminal alkyls, the easier the development of the liquid crystalline phase. Birefringence measurements showed that solution‐cast polymer films exhibited moderately high positive birefringence values, indicating potential applications as optical compensation films for liquid crystal displays. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011
Synthesis strategies to incorporate acrylic acid into N‐vinylcaprolactam‐based microgels
Authors: Imaz Ainara , Forcada Jacqueline
Published: May 2011

Two different synthesis strategies were used to synthesize N‐vinylcaprolactam (VCL)‐acrylic acid (AA)‐based temperature‐ and pH‐sensitive microgels under the adequate conditions to avoid possible hydrolysis of VCL due to the presence of carboxylic groups provided by AA. Polymeric and colloidal features of the microgels were analyzed: the partial conversion evolutions of each comonomer were determined by 1H NMR and the swelling/deswelling behavior by means of Photon Correlation Spectroscopy. Considering that microgels are porous soft nanoparticles, conductimetric titrations at the swollen state were carried out to calculate the volumetric charge density. The results indicate that the addition of AA after 30 minutes of reaction time helped to incorporate higher amounts of AA into microgels and as a result, to obtain both temperature‐ and pH‐sensitive nanoparticles. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011
Influence of polymer backbone branching on liquid crystal mesomorphous in nonequimolar complexes of poly(ethyleneimine) and dendritic amphiphiles
Authors: Cheng Zhiyu , Ren Biye , Li Chongqing , Liu Xinxing , Tong Zhen
Published: May 2011

Two kinds of ionic self‐assembled complexes of linear or branched poly(ethyleneimine) (lPEI or bPEI) with Percec‐type dendrons [(3,4,5)16G1‐COOH] were prepared as lPEI‐(3,4,5)16G1‐x and bPEI‐(3,4,5)16G1‐x, where x is the mole ratio of the carboxyl groups of the dendritic amphiphile to the amino groups at the PEI chain. The crystal and mesomorphous structures and thermal properties of these complexes were investigated with X‐ray diffraction (XRD), Fourier transform infrared (FTIR), differential scanning calorimetry (DSC), and polarized optical microscope (POM). Both the lPEI and bPEI complexes exhibited the same αH crystal phase and similar lamellar mesomorphous phase, irrespective of the branching of the polymer backbone and the binding degree. The lPEI series complexes lPEI‐(3,4,5)16G1‐x, however, had more ordered lamellar stacking than that of the bPEI‐(3,4,5)16G1‐x complexes, so the thermotropic liquid crystal phase SmA was formed only in the lPEI‐(3,4,5)16G1‐x complexes beyond the melting point of the tail crystal of the dendritic amphiphile. No liquid crystalline phase was found from the bPEI‐(3,4,5)16G1‐x complexes. The results suggest that the branching of polymer backbone plays a key role to the formation of thermotropic liquid crystal in the polymer–dendritic amphiphile complex. The present finding is significant for the design of functional nanostructures based on the ionic complexation of polymers and amphiphiles. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2011
Biochemical and structural studies on the high affinity of Hsp70 for ADP
Authors: Arakawa Akihiko , Handa Noriko , Shirouzu Mikako , Yokoyama Shigeyuki
Published: May 2011

The molecular chaperone 70‐kDa heat shock protein (Hsp70) is driven by ATP hydrolysis and ADP–ATP exchange. ADP dissociation from Hsp70 is reportedly slow in the presence of inorganic phosphate (Pi). In this study, we investigated the interaction of Hsp70 and its nucleotide‐binding domain (NBD) with ADP in detail, by isothermal titration calorimetry measurements and found that Mg2+ ion dramatically elevates the affinity of Hsp70 for ADP. On the other hand, Pi increased the affinity in the presence of Mg2+ ion, but not in its absence. Thus, Pi enhances the effect of the Mg2+ ion on the ADP binding. Next, we determined the crystal structures of the ADP‐bound NBD with and without Mg2+ ion. As compared with the Mg2+ ion‐free structure, the ADP‐ and Mg2+ ion‐bound NBD contains one Mg2+ ion, which is coordinated with the β‐phosphate group of ADP and associates with Asp10, Glu175, and Asp199, through four water molecules. The Mg2+ ion is also coordinated with one Pi molecule, which interacts with Lys71, Glu175, and Thr204. In fact, the mutations of Asp10 and Asp199 reduced the affinity of the NBD for ADP, in both the presence and the absence of Pi. Therefore, the Mg2+ ion‐mediated network, including the Pi and water molecules, increases the affinity of Hsp70 for ADP, and thus the dissociation of ADP is slow. In ADP–ATP exchange, the slow ADP dissociation might be rate‐limiting. However, the nucleotide‐exchange factors actually enhance ADP release by disrupting the Mg2+ ion‐mediated network.
Micro‐machined fluidic devices for terahertz time‐domain spectroscopy
Authors: Baragwanath Adam J. , Swift G. Peter , Dai DeChang , Zeze Dagou , Gallant Andrew J. , Chamberlain J. Martyn
Published: May 2011

Here we present a silicon based, micro‐machined fluidic device for terahertz frequencies, fabricated using standard lithographic and micro‐machining processes in a cleanroom environment. Designed for use in a conventional transmission terahertz time‐domain spectroscopy (THz‐TDS) arrangement, we present a possible solution to the ‘water problem’ currently hampering the analysis of aqueous and biological systems at THz frequencies. We detail results from a range of experiments, highlighting the device sensitivity and potential, wide‐ranging applications. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Spectral features of specular reflection from nanoparticle films
Authors: Fokine M. , Jang Hoon , Gouvêa P. M. P. , Braga A. M. B. , Carvalho I. C. S.
Published: May 2011

In this work we analyze the internal reflection (Fresnel reflection) from Au nanoparticles on the end face of optical fibers. We demonstrate that changes in the refractive index of the surrounding medium can be detected by shifts in the reflection spectra associated with changes in the Localized Surface Plasmon Resonance of the Au‐Nanoparticles. The spectral response is simulated using a model based on the interference in multilayer structures and can be described by transfer‐matrix method. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Optical properties of amorphous hydrogenated and microcrystalline silicon films prepared by plasma enhanced chemical vapor deposition and re‐crystallized at moderate temperatures
Authors: Netrvalova Marie , Prusakova Lucie , Mullerova Jarmila , Sutta Pavol
Published: May 2011

Amorphous hydrogenated silicon films different in thickness (600 – 2400 nm) were deposited by plasma enhanced chemical vapour deposition on Corning glass substrates at 250 °C using silan 10% / argon 90% gas mixture. The samples were consequently isothermally heated in a high temperature vacuum chamber at 0.1 Pa and at temperatures from 580 to 620 °C. In order to evaluate structural and optical properties of the films X‐ray diffraction analysis, Raman spectrometry and optical spectrophotometry were used. Crystalline state (amorphous or microcrystalline), optical band gaps, refractive indices, extinction coefficients, absorption coefficients were determined. X‐ray diffraction analysis indicated that originally deposited films were amorphous with different degree of homogeneity depending on the film thickness. After the heat treatment the films became polycrystalline with crystallite sizes 40‐50 nm without particular dependence on the recrystallization process used. Raman spectrometry confirmed the results obtained from X‐ray diffraction and furthermore revealed the residual amorphous phase 20–25% in volume. Optical spectrophotometry has shown that the values of refractive indices of thermally treated films approach the mono‐crystalline silicon refractive index. Extinction coefficients of the thermally treated films are slightly higher than those for monocrystalline silicon. Absorption coefficients for thermally treated films reached quite high values near the absorption edge of the original amorphous material, which can be advantageous for tandem solar cell technologies. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Efficient second harmonic generation green light in RTP planar waveguides
Authors: Cugat Jaume , Solé Rosa Maria , Pujol Maria Cinta , Carvajal Joan Josep , Mateos Xavier , Díaz Francesc , Aguiló Magdalena
Published: May 2011

In this paper, epitaxial layers of Rb1‐xBaxTi1‐y‐zYbyNbzOPO4 have been successfully grown on (001) oriented RbTiOPO4 substrates. Although the Ba2+ contents in these layers was very low, the contrasts in refractive indices between the epitaxial layer and the substrate were high enough to allow the propagation of one TE and three TM modes, at the wavelength of 632.8 nm, using a 5 μm thickness epilayer. These light propagation modes were first simulated, using the refractive indices of the layer and the substrate measured previously. The TE and TM dark‐mode spectra obtained experimentally, using the prism coupler method and a He‐Ne laser beam, agree well with the simulation results. Finally, type II Second Harmonic Generation experiments were carried out with pumping at 1130 nm and obtaining green light at 565 nm. The experimental efficiency in the Second Harmonic Generation experiments was of 69%/mWcm2. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Tropical cyclone convection: the effects of ambient vertical vorticity
Authors: Wissmeier Ulrike , Smith Roger K.
Published: May 2011

We present idealized numerical model experiments to isolate and quantify the influence of ambient vertical vorticity on the dynamics of deep convection, such as that in the inner‐core region of a tropical depression. The vertical vorticity is represented either by a uniform horizontal shear, a uniform solid‐body rotation, or a combination of both. We show that the growing convective cells amplify locally the ambient rotation at low levels by more than an order of magnitude and that this vorticity, which is produced by the stretching of existing ambient vorticity, persists long after the initial updraught has decayed. Significant amplification of vorticity occurs even for a background rotation rate typical of the undisturbed tropical atmosphere and even for clouds of only moderate vertical extent. This finding has important implications for tropical cyclogenesis and provides a basis for a unified theory of tropical cyclogenesis and tropical cyclone intensification.

The presence of ambient vertical vorticityreducesthe updraught strength, slightly more when the vorticity is associated with horizontal shear than when it is associated with solid‐body rotation on account of enhanced entrainment. The reduction of the updraught strength can be attributed to the reduction of the lateral inflow by the centrifugal and Coriolis forces. Despite the significant amplification of vorticity, the sum of the centrifugal and Coriolis forces is mostly small compared with the lateral pressure gradient. Thus, at the level of background rotation studied, the Rossby elasticity effects in the updraught postulated by Montgomeryet al.are not large, but may be important for higher levels of background rotation. The simulations ignore several processes that are likely to be important in reality, such as ambient vertical shear and surface friction, but they provide important benchmark calculations for interpreting the additional complexity arising from the inclusion of these effects. Copyright © 2011 Royal Meteorological Society
Observation errors in all‐sky data assimilation
Authors: Geer Alan J. , Bauer Peter
Published: May 2011

This article examines the first‐guess (FG) departures of microwave imager radiances assimilated in all‐sky conditions (i.e. clear, cloudy and precipitating). Agreement between FG and observations is good in clear skies, with error standard deviations around 2 K, but in heavy cloud or precipitation errors increase to 20 K. The forecast model is not good at predicting cloud and precipitation with exactly the right intensity or location. This leads to apparently non‐Gaussian behaviour, both heteroscedasticity, i.e. an increase in error with cloud amount, and boundedness, i.e. the size of errors is close to the geophysical range of the observations, which runs from clear to fully cloudy. However, the dependence of FG departure standard deviations on the mean cloud amount is predictable. Using this dependence to normalise the FG departures gives an error distribution that is close to Gaussian. Thus if errors are treated correctly, all‐sky observations can be assimilated successfully under the assumption of Gaussianity on which assimilation systems are based. This ‘symmetric’ error model can be used to provide a robust threshold quality‐control check and to determine the size of observation errors for all‐sky assimilation. In practice, however, this ‘observation’ error is being used to account for the model's difficulty in forecasting cloud, which really comes from errors in the background and in the forecast model. Hence in future it will be necessary to improve the representation of background and model error. Separately, symmetric cloud amount is recommended as a predictor for bias correction schemes, avoiding the sampling problems associated with ‘asymmetric’ predictors like the FG cloud amount. Copyright © 2011 Royal Meteorological Society
Development and application of enhanced sampling techniques to simulate the long‐time scale dynamics of biomolecular systems
Authors: Spiriti Justin , Kamberaj Hiqmet , Van Der Vaart Arjan
Published: May 2011

The behavior of proteins and DNA is largely determined by their dynamics, which involves transitions between various conformational states. Computer simulations can provide detailed insights into these dynamics, but the long‐time scales of the transitions severely complicate such an approach. In this review, we present a few recently developed enhanced sampling techniques for the simulation of conformational changes at atomic resolution. To illustrate the application of these techniques, we discuss the isomerization of a nonprolyl peptide bond in a collagenase and a joint simulation‐experimental study of a DNA‐dye system. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
Modeling of PEG grafting and prediction of interfacial force profile using X‐ray photoelectron spectroscopy
Authors: Damodaran Vinod B. , Fee Conan J. , Popat Ketul C.
Published: May 2011

Poly(ethylene glycol) (PEG)‐grafted Sephadex™ derivatives were prepared by a covalent amine conjugation method and characterized using XPS. PEG‐grafting kinetics were studied using both Langmuir and Langmuir–Freundlich isotherm models by correlating fractional CO intensities obtained from high‐resolution C 1s scans with the grafting period. Theoretical values were compared with experimental results to confirm the reliability of the modeling predictions. Detailed surface characterization of PEG‐grafted Sephadex derivatives was performed using XPS data, and the results were used to predict the interaction free energy and stick force exerted at the matrix interface. Copyright © 2011 John Wiley & Sons, Ltd.
Approximating Pareto optimal compiler optimization sequences—a trade‐off between WCET, ACET and code size
Authors: Lokuciejewski Paul , Plazar Sascha , Falk Heiko , Marwedel Peter , Thiele Lothar
Published: May 2011

With the growing complexity of embedded systems software, high code quality can only be achieved using a compiler. Sophisticated compilers provide a vast spectrum of various optimizations to improve code aggressively w.r.t. different objective functions, e.g. average‐case execution time (ACET) or code size. Owing to the complex interactions between the optimizations, the choice for a promising sequence of code transformations is not trivial. Compiler developers address this problem by proposing standard optimization levels, e.g.O3orOs. However, previous studies have shown that these standard levels often miss optimization potential or might even result in performance degradation. In this paper, we propose the first adaptive worst‐case execution time (WCET)‐aware compiler framework for an automatic search of compiler optimization sequences that yield highly optimized code. Besides the objective functions ACET and code size, we consider the WCET which is a crucial parameter for real‐time systems. To find suitable trade‐offs between these objectives, stochastic evolutionary multi‐objective algorithms identifying Pareto optimal solutions for the objectives 〈WCET, ACET 〉 and 〈WCET, code size 〉 are exploited. A comparison based on statistical performance assessments is performed that helps to determine the most suitable multi‐objective optimizer. The effectiveness of our approach is demonstrated on real‐life benchmarks showing that standard optimization levels can be significantly outperformed. Copyright © 2011 John Wiley & Sons, Ltd.
Non‐functional information transmission patterns for distributed real‐time Java
Authors: Basanta‐Val P. , Garcia‐Valls M. , Estevez‐Ayres I.
Published: May 2011

Many real‐time systems use preemptive priority‐based scheduling in their internals to guarantee certain real‐time performance. This includes technologies that range from The Real‐Time Specification for Java (RTSJ) to middleware like Real‐Time Common Object Request Broker Architecture (RT‐CORBA), which offers additional models and policies that blend client and server information. This decision eases the integration of real‐time admission tests and dispatching policies in these types of infrastructures. In this paper, we analyze different trade‐offs that emerge from the definition of different propagation models for distributed real‐time Java. The paper covers technological integration aspects as impact on interfaces and other practical issues mainly related to the performance that this model offers to a real‐time application and non‐functional overhead. The contribution described in the paper may help in the development of The Distributed Specification for Java (DRTSJ). Copyright © 2011 John Wiley & Sons, Ltd.
Effects of storage conditions and acid solvent types on structural, mechanical and physical properties of kudzu starch (Pueraria lobata)‐chitosan composite films
Authors: Zhong Yu , Li Yunfei
Published: May 2011

Effects of acid solvents (acetic, lactic and malic acid) on properties of kudzu starch‐chitosan composite films were evaluated at −20 or 25°C during storage of 60 days. The yellowness of films enhanced, whereas water content and water vapour permeability of films declined with increasing storage time. Tensile strength of films choosing acetic and lactic acid as solvents, and solubility of all the films increased within 30 days thereafter decreased. Storage temperature had no impact on X‐ray diffraction, water content and solubility. Under the same storage conditions, the film using acetic acid as solvent presented the strongest mechanical property, the smallest solubility and the lightest colour. The film made from lactic acid solution was the most flexible and the yellowiest. The film with malic acid solvent showed the highest ordering degree, the lowest water content and the best water barrier property.