bluuebunny/crossref_metadata_2025 huggingface dataset:
A quantum chemistry study of the free‐radical copolymerization propagation kinetics of styrene and 2‐hydroxyethyl acrylate
Authors: Dossi Marco , Storti Giuseppe , Moscatelli Davide
Published: July 2011

Several difficulties are reported in literature about the experimental analysis of polymerizations involving 2‐hydroxyethyl acrylate (HEA), mainly due to transfer reactions that characterize the system. In particular, major problems are emerged in the study of free radical copolymerization kinetics of HEA. In this work, free‐radical copolymerization propagation kinetics of HEA and styrene (ST) are investigated through a computational approach based on density functional theory. Monomer reactivity ratios for HEA/ST copolymerization are calculated at 50°C and 125°C, obtaining values that exhibit a weak dependence on temperature. In particular, HEA reactivity ratio, rHEA, equal to 0.14 and ST reactivity ratio, rST, equal to 0.31 at 50°C, whereas rHEA = 0.17 and rST = 0.29 at 125°C. Moreover, the reliability of such parameters has been tested by analyzing copolymer composition data as a function of monomer feed composition, at the same temperatures indicated above. Experimental values proposed in literature are well predicted by the terminal copolymerization model using the kinetic parameters computationally determined. POLYM. ENG. SCI., 2011. © 2011 Society of Plastics Engineers
Synthesis and characterization of styrene modified vinylester resin‐clay nanocomposites
Authors: Abdelwahab Mohamed , Agag Tarek , Akelah Ahmed , Takeichi Tsutomu
Published: July 2011

The influence of styrene as a reactive diluent on the morphology of vinylester resin‐clay hybrids has been studied. Two mixtures of diglycidylether of bisphenol‐A diacrylate as vinyl ester resin and styrene (20 and 40%) were prepared. Various weight ratios of styryl‐functional organoclay were added to vinylester resin/styrene mixture, followed by polymerization of the mixture up to 160°C. The morphology of the hybrids studied by X‐ray diffraction and Scanning Electron Microscope revealed that the dispersion of organoclay increased with the increase of styrene content. The inclusion of styrene to the system gave ordered intercalated nanocomposites. The surface hardness of the hybrid films decreased with adding a higher content of styrene. Thermogravimetric analysis indicates that clay is effective in promoting char‐forming reaction of vinylester resin/styrene clay nanocomposites. POLYM. ENG. SCI., 2012. © 2011 Society of Plastics Engineers
Personality, Punishment and Public Goods: Strategic Shifts towards Cooperation as a Matter of Dispositional Honesty–Humility
Authors: Hilbig Benjamin E. , Zettler Ingo , Heydasch Timo
Published: July 2011

Contributions in the public goods game—a classical social dilemma situation—have been shown to depend strongly on the presence versus absence of punishment or sanctions for free riders. Also, there appear to be noteworthy individual differences in the degree to which decision makers cooperate. Herein, we aimed to bring these two lines of research together. Firstly, we predicted that both presence of punishment and high dispositional Honesty–Humility (as conceptualized in the Honesty–Humility, Emotionality, eXtraversion, Agreeableness, Conscientiousness, Openness to experience model of personality) should yield higher contributions. Secondly, and more importantly, we expected an interaction, such that only those low in Honesty–Humility would condition their behaviour on the presence versus absence of punishment, thus employing cooperation strategically. In line with the hypothesis, the results of two experiments (one of which comprised a longitudinal design) corroborated that the degree to which decision makers shift towards higher contributions when punishment is introduced depends on their dispositional level of Honesty–Humility. Copyright © 2011 John Wiley & Sons, Ltd.
Higher Extraversion and Lower Conscientiousness in Humans Infected with Toxoplasma
Authors: Lindová Jitka , Příplatová Lenka , Flegr Jaroslav
Published: July 2011

Toxoplasmosis is associated with specific differences in the personality of infected subjects relative to non–infected subjects. These differences are usually considered to be a side effect of the manipulative activity of the parasite aimed to increase the probability of its transmission from the intermediate host to the definitive host by predation. The personality of infected subjects was studied mostly using the Cattell's questionnaire. However, this questionnaire is now considered outdated and has been mostly substituted with the Neuroticism–Extraversion–Openness Personality Inventory—Revised (NEO–PI–R) questionnaire in clinical practice. Here, we searched for the association between toxoplasmosis and the personality by screening a population of students with the NEO–PI–R questionnaire. We found that Toxoplasma–infected male and female students had significantly higher extraversion and lower conscientiousness. The conscientiousness negatively correlated with the length of infection in men, which suggested that the toxoplasmosis associated differences were more probably the result of slow cumulative changes induced by latent toxoplasmosis, rather than transient side effect of acute Toxoplasma infection. The existence of this correlation also supported (but of course not proved) the hypothesis that Toxoplasma infection influenced the personality, rather than the hypothesis that the personality influenced the probability of the infection. Copyright © 2011 John Wiley & Sons, Ltd.
Proteomic analysis of larval integument, trachea and adult scale from the silkworm, Bombyx mori
Authors: Fu Qiang , Li Peng , Xu Yunmin , Zhang Sai , Jia Ling , Zha Xingfu , Xiang Zhonghuai , He Ningjia
Published: July 2011

Multidimensional LC‐tandem MS was used to investigate the protein compositions of three tissues of silkworm, Bombyx mori. A total of 162, 259, and 175 peptides from silkworm larval integument and trachea, and adult scale obtained by database search were matched to 48, 51, and 40 proteins, respectively. Forty‐one cuticular proteins were identified from three tissues and covered all five cuticular protein families of silkworm. In the adult scale, all seven cuticular proteins were identified for the first time in the final pellet after SDS extraction. The majority of cuticular proteins were found in each tissue differentially, suggesting that tissue‐specific cuticular proteins were involved in the building of the specialized tissues. Seventy‐three non‐cuticular proteins were also identified in this analysis mainly including muscular proteins, proteinases, inhibitors, transport proteins, and redox‐related proteins.
Modulation of septin and molecular motor recruitment in the microtubule environment of the Taxol‐resistant human breast cancer cell line MDA‐MB‐231
Authors: Froidevaux‐Klipfel Laurence , Poirier Florence , Boursier Céline , Crépin Ronan , Poüs Christian , Baudin Bruno , Baillet Anita
Published: July 2011

Cell resistance to low doses of paclitaxel (Taxol) involves a modulation of microtubule (MT) dynamics. We applied a proteomic approach based on 2‐DE coupled with MS to identify changes in the MT environment of Taxol‐resistant breast cancer cells. Having established a proteomic pattern of the microtubular proteins extracted from MDA‐MB‐231 cells, we verified by Western blotting that in resistant cells, α‐ and β‐tubulins (more specifically the βIII and βIV isotypes) increased. Interestingly, four septins (SEPT2, 8, 9 and 11), which are GTPases involved in cytokinesis and in MT/actin cytoskeleton organization, were overexpressed and enriched in the MT environment of Taxol‐resistant cells compared to their sensitive counterpart. Changes in the MT proteome of resistant cells also comprised increased kinesin‐1 heavy chain expression and recruitment on MTs while dynein light chain‐1 was downregulated. Modulation of motor protein recruitment around MTs might reflect their important role in controlling MT dynamics via the organization of signaling pathways. The identification of proteins previously unknown to be linked to taxane‐resistance could also be valuable to identify new biological markers of resistance.
Differential expression profile of membrane proteins in zebrafish (Danio rerio) brain exposed to methyl parathion
Authors: Huang Qing‐Yu , Huang He‐Qing
Published: July 2011

Methyl parathion (MP) is a widely used organophosphorus pesticide, which has been related to a broad spectrum of toxic effects on environmental organisms. The present study investigated the changes in the protein profile of enriched membrane fraction from zebrafish (Danio rerio) brain exposed to three concentrations (0.5, 1 and 2 mg/L) of MP. 2‐DE revealed that the abundance of 21 protein spots was significantly changed by MP stress. By matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry and database search, 16 protein spots were identified as membrane proteins, among which 8 were down‐regulated, while 8 were up‐regulated. These proteins are mainly involved in oxidative stress response, signal transduction, metabolism, protein synthesis and degradation, neuroplasticity and regeneration as well as synaptic transmission. These results may aid our understanding of the mechanism of MP‐induced neurotoxicity and provide the possibility of the establishment of candidate biomarkers of MP.
Identifying differentially expressed genes in cancer patients using a non‐parameter Ising model
Authors: Li Xumeng , Feltus Frank A. , Sun Xiaoqian , Wang James Z. , Luo Feng
Published: July 2011

Identification of genes and pathways involved in diseases and physiological conditions is a major task in systems biology. In this study, we developed a novel non‐parameter Ising model to integrate protein–protein interaction network and microarray data for identifying differentially expressed (DE) genes. We also proposed a simulated annealing algorithm to find the optimal configuration of the Ising model. The Ising model was applied to two breast cancer microarray data sets. The results showed that more cancer‐related DE sub‐networks and genes were identified by the Ising model than those by the Markov random field model. Furthermore, cross‐validation experiments showed that DE genes identified by Ising model can improve classification performance compared with DE genes identified by Markov random field model.
QSE: A new 3‐D solvent exposure measure for the analysis of protein structure
Authors: Li Peipei , Pok Gouchol , Jung Kwang Su , Shon Ho Sun , Ryu Keun Ho
Published: July 2011

Solvent exposure of amino acids measures how deep residues are buried in tertiary structure of proteins, and hence it provides important information for analyzing and predicting protein structure and functions. Existing methods of calculating solvent exposure such as accessible surface area, relative accessible surface area, residue depth, contact number, and half‐sphere exposure still have some limitations. In this article, we propose a novel solvent exposure measure named quadrant‐sphere exposure (QSE) based on eight quadrants derived from spherical neighborhood. The proposed measure forms a microenvironment around Cα atom as a sphere with a radius of 13 Å, and subdivides it into eight quadrants according to a rectangular coordinate system constructed based on geometric relationships of backbone atoms. The number of neighboring Cα atoms whose labels are the same is given as the QSE value of the center Cα atom at hand. As evidenced by histograms that show very different distributions for different structure configurations, the proposed measure captures local properties that are characteristic for a residue's eight‐directional neighborhood within a sphere. Compared with other measures, QSE provides a different view of solvent exposure, and provides information that is specific for different tertiary structure. As the experimental results show, QSE measure can potentially be used in protein structure analysis and predictions.
Replacing the Equations of Fano and Fisher for Cased Charge Blast Equivalence – I Ductile Casings
Authors: Hutchinson Mike D.
Published: July 2011

The initial velocity of casing fragments from bombs, shells etc. was first calculated by R. W. Gurney in 1943 [1]. Subsequent to this derivation by Gurney, which was based on a reasonable simplification of the case and gas dynamics, his wartime co‐worker, U. Fano [2], claimed to have calculated the proportion of kinetic energy remaining with the explosive gases following energy partition with the casing. This paper shows that both Fano’s equation for cased charge blast equivalence and a further derivation by Fisher in 1953 [3], based on Fano’s, are in fact inconsistent with Gurney’s reasonable physical model. Neither of these two reports has ever been the subject of independent peer‐review, despite having been extensively cited. This paper identifies the error made by Fano and copied by Fisher and draws attention to an alternate equation recently published by the author which gives similar predictions to that of Fisher, while being consistent with Gurney’s original derivation. Also, this paper establishes for the first time that the use of such equations for cased charge blast impulse equivalence is valid.
Determination of protein fold class from Raman or Raman optical activity spectra using random forests
Authors: Kinalwa Myra , Blanch Ewan W. , Doig Andrew J.
Published: July 2011

Knowledge of the fold class of a protein is valuable because fold class gives an indication of protein function and evolution. Fold class can be accurately determined from a crystal structure or NMR structure, though these methods are expensive, time‐consuming, and inapplicable to all proteins. In contrast, vibrational spectra [infra‐red, Raman, or Raman optical activity (ROA)] are rapidly obtained for proteins under wide range of biological molecules under diverse experimental and physiological conditions. Here, we show that the fold class of a protein can be determined from Raman or ROA spectra by converting a spectrum into data of 10 cm−1 bin widths and applying the random forest machine learning algorithm. Spectral data from 605 and 1785 cm−1 were analyzed, as well as the amide I, II, and III regions in isolation and in combination. ROA amide II and III data gave the best performance, with 33 of 44 proteins assigned to one of the correct four top‐level structural classification of proteins (SCOP) fold class (all α, all β, α and β, and disordered). The method also shows which spectral regions are most valuable in assigning fold class.
Structural analysis of CPF_2247, a novel α‐amylase from Clostridium perfringens
Authors: Ficko‐Blean Elizabeth , Stuart Christopher P. , Boraston Alisdair B.
Published: July 2011

CPF_2247 from Clostridium perfringens ATCC 13124 was identified as a putative carbohydrate‐active enzyme by its low sequence identity to endo‐β‐1,4‐glucanases belonging to family 8 of the glycoside hydrolase classification. The X‐ray crystal structure of CPF_2247 determined to 2.0 Å resolution by single‐wavelength anomalous dispersion using seleno‐methionine‐substituted protein revealed an (α/α)6 barrel fold. A large cleft on the surface of the protein contains residues that are structurally conserved with key elements of the catalytic machinery in clan GH‐M glycoside hydrolases. Assessment of CPF_2247 as a carbohydrate‐active enzyme disclosed α‐glucanase activity on amylose, glycogen, and malto‐oligosaccharides. Proteins 2011;. © 2011 Wiley‐Liss, Inc.
Three ways in, one way out: Water dynamics in the trans‐membrane domains of the inner membrane translocase AcrB
Authors: Fischer Nadine , Kandt Christian
Published: July 2011

Powered by proton‐motive force, the inner membrane translocase AcrB is the engine of the AcrAB‐TolC efflux pump in Escherichia coli. As proton conduction in proteins occurs along hydrogen‐bonded networks of polar residues and water molecules, knowledge of the protein‐internal water distribution and water‐interacting residues allows drawing conclusions to possible pathways of proton conduction. Here, we report a series of 6× 50 ns independent molecular dynamics simulations of asymmetric AcrB embedded in a phospholipid/water environment. Simulating each monomer in its proposed protonation state, we calculated for each trans‐membrane domain the average water distribution, identified residues interacting with these waters and quantified each residue's frequency of water hydrogen bond contact. Combining this information we find three possible routes of proton transfer connecting a continuously hydrated region of known key residues in the TMD interior to bulk water by one cytoplasmic and up to three periplasm water channels in monomer B and A. We find that water access of the trans‐membrane domains is regulated by four groups of residues in a combination of side chain re‐orientations and shifts of trans‐membrane helices. Our findings support a proton release event via Arg971 during the C intermediate or in the transition to A, and proton uptake occurring in the A or B state or during a so far unknown intermediate in between B and C where cytoplasmic water access is still possible. Our simulations suggest experimentally testable hypotheses, which have not been investigated so far. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Prechemistry versus preorganization in DNA replication fidelity
Authors: Ram Prasad B. , Warshel Arieh
Published: July 2011

The molecular origin of nucleotide insertion catalysis and fidelity of DNA polymerases is explored by means of computational simulations. Special attention is paid to the examination of the validity of proposals that invoke prechemistry effects, checkpoints concepts, and dynamical effects. The simulations reproduce the observed fidelity in Pol β, starting with the relevant observed X‐ray structures of the complex with the right (R) and wrong (W) nucleotides. The generation of free energy surfaces for the R and W systems also allowed us to analyze different proposals about the origin of the fidelity and to reach several important conclusions. It is found that the potential of mean force (PMF) obtained by proper sampling does not support QM/MM‐based proposals of a large barrier before the prechemistry state. Furthermore, examination of dynamical proposals by the renormalization approach indicates that the motions from open to close configurations do not contribute to catalysis or fidelity. Finally we discuss and analyze the induced fit concept and show that, despite its importance, it does not explain fidelity. That is, the fidelity is apparently due to the change in the preorganization of the chemical site, as a result of the relaxation of the binding site upon binding of the incorrect nucleotide. Finally and importantly, since the issue is the barrier associated with the enzyme–substrate (ES)/DNA complex at the chemical transition state and not the path to this complex formation (unless this path involves rate determining steps), it is also not useful to invoke checkpoints while discussing fidelity. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Integrate plant reliability efforts with mechanical integrity
Authors: Vaughen Bruce K. , Nagel John F. , Allen Matthew J.
Published: July 2011

Maintenance ensures the reliability of the equipment to meet operation's demands. Operations ensure the production of sufficient and high quality product. Engineering designs and installs equipment that minimizes risk. Safety ensures that the engineering and administrative controls are in place to minimize that risk. This article presents a concept that combines these reliability and safety efforts, such that the maintenance, operations, engineering and safety groups speak the same language to minimize the overall business risk.

This proposed approach combines existing plant reliability efforts with several Process Safety Management elements. The basic steps include identifying safety‐critical equipment, ensuring accurate and up‐to‐date Process Safety Information (PSI), establishing the mechanical integrity (MI) Program, establishing Planned Maintenance (PM) programs, and creating equipment‐specific maintenance procedures.

The resultant mechanical integrity quality assurance (MI QA) program combines equipment reliability and operational integrity efforts to ensure that the equipment is properly designed (via PSI), fabricated as designed (via PSI and MI), and installed as designed (via Pre‐Start‐up Safety Reviews). The MI QA program also ensures that the equipment is operated and maintained as designed by trained personnel. Some benefits include being able to: (1) share and document best MI and PM practices between different sites; (2) focus limited PM‐related resources on the process safety‐critical equipment; and (3) help monitor the essential reliability efforts to ensure continued safe operation. © 2011 American Institute of Chemical Engineers Process Saf Prog, 2011
Staggered InGaAs/GaAsP strained layer superlattices for use in optical devices
Authors: Colter P. C. , Carlin C. Z. , Samberg J. P. , Bradshaw G. K. , Bedair S. M.
Published: July 2011

Strained layer superlattice (SLS) structures lattice matched to GaAs, such as InGaAs/GaAsP, use thin films to meet both the strain balance and critical layer thickness (CLT) conditions. Optical absorption in the InGaAs layers will be shifted to higher energies relative to thick films due to both the quantum size effect (QSE) and compressive strain, which is an undesirable restriction. We report on a new concept for a strain balance superlattice that will allow for thicker InGaAs films and reduce the cutoff energy. The staggered strain balanced superlattice structure can improve the performance of optical detectors and solar cells.
A new estimate on the indirect Coulomb energy
Authors: Benguria Rafael D. , Bley Gonzalo A. , Loss Michael
Published: July 2011

Here we prove a new lower bound on the indirect Coulomb energy in quantum mechanics, in terms of the single particle density of the system. The new universal lower bound is an alternative to the classical Lieb–Oxford bound (with a smaller constant, C = 1.45 < CLO = 1.68) but involving an additive kinetic energy term of the single particle density as well. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
Off‐center shallow donors in a spherical Si quantum dot with dielectric border
Authors: Cristea M. , Niculescu E. C.
Published: July 2011

Within the effective mass approximation and using a finite element method, the ground state energy and electron cloud localization of the shallow donors in a Si quantum dot (QD) with dielectric border are calculated. Simultaneous effects of dielectric mismatch (DM) at the core–shell interface, the impurity radial position, and the external electric field on the electronic properties are investigated. We found that (i) for a freestanding QD, the binding energy is strongly enhanced due to the additional interactions of the electron with the polarization charges; (ii) the electron cloud distribution can be easily modulated by varying the impurity position; (iii) the electric field‐induced shift in energy levels increases with the DM. Therefore, the electronic energy levels of the nanocrystal could be tuned by properly tailoring the heterostructure parameters (DM with the surrounding matrix, impurity location) as well as by varying the electric field strength. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
The Importance of the DFT method on the computation of the second hyperpolarizability of semiconductor clusters of increasing size: A critical analysis on prolate aluminum phosphide clusters
Authors: Karamanis Panaghiotis
Published: July 2011

The importance of the density functional theory (DFT) methods on the computation of cluster hyperpolarizabilities is discussed. The performance of the conventional BLYP, BP86, BPW91, B3LYP, B3PW91, and B3P86 functionals in the computation of the second hyperpolarizability of aluminum phosphide prolate clusters up to 60 atoms is compared with the “half and half functionals” BHandH and BHandHLYP and to the long‐range corrected functionals LC‐(BLYP, BP86, BPW91), CAM‐B3LYP, and wB97XD. The presented results demonstrate that when long‐range corrections are incorporated on pure and hybrid functionals their performance is vastly affected. What is more, the obtained DFT results are compared with second‐order Møller–Plesset perturbation theory (MP2) all electron calculations. It is shown that all the long‐range outcomes are bracketed by the MP2 and Hatree–Fock (HF) values. The relative ordering of the obtained longitudinal hyperpolarizabilities follows strictly the trend MP2 > CAM‐B3LYP > wB97XD > LC‐(BLYP, BP86, BPW91) > HF. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
Japanese sentence pattern learning with the use of illustrative examples extracted from the web
Authors: Han Dongli , Song Xin
Published: July 2011

It is quite difficult for a foreigner to compose a Japanese sentence comparing with the case of speaking Japanese. Two main factors are supposed to be leading to this situation. One is the scale of Japanese vocabulary and another is the variousness of Japanese sentence patterns. As most Kanji characters are common in Chinese and Japanese, the more confusing issue for native Chinese‐speaking foreigners is the latter one. There are many sentence patterns in Japanese to express different meanings in various situations. In this paper, we first make a survey on existing strategies to support foreigners to compose Japanese sentences, and then develop a system for native Chinese‐speaking foreigners to learn Japanese sentence patterns with the use of illustrative examples extracted from the Web in a practical and convenient way. Finally, we conduct some experiments to examine the effectiveness of our approach. © 2011 Institute of Electrical Engineers of Japan. Published by John Wiley & Sons, Inc.
Viscoelastic properties, morphology, and thermal stability of rigid and plasticized poly(vinyl chloride)/poly(methyl methacrylate) blends
Authors: Aouachria Kamira , Belhaneche‐Bensemra Naima , Massardier‐Nageotte V.
Published: July 2011

Viscoelastic properties, morphology, and thermal stability of rigid and plasticized poly(vinyl chloride)/poly (methyl methacrylate) (PVC/PMMA) blends were studied. For that purpose, blends of variable composition from 0 to 100 wt% were prepared in the presence (15, 30, and 50 wt%) and in the absence of di(2‐ethylhexyl) phthalate as plasticizer. Their miscibility was investigated by using dynamic mechanical thermal analysis (DMTA) and scanning electron microscopy (SEM). The DMTA and SEM results showed that the two polymers are miscible. Thermogravimetric studies on these blends were carried out in a flowing atmosphere of air from ambient temperature to 550°C. The results showed that the thermal degradation of rigid and plasticized PVC/PMMA in this broad range of temperature is a three‐step process and that PMMA exerted a stabilizing effect on the thermal degradation of PVC during the first step by reducing the rate of dehydrochlorination. J. VINYL ADDIT. TECHNOL., 2011. © 2011 Society of Plastics Engineers
Wavefunction methods for noncovalent interactions
Authors: Hohenstein Edward G. , Sherrill C. David
Published: July 2011

Noncovalent interactions remain poorly understood despite their importance to supramolecular chemistry, biochemistry, and materials science. They are an ideal target for theoretical study, where interactions of interest can be probed directly, free from competing secondary interactions. However, the most popular tools of computational chemistry are not particularly reliable for noncovalent interactions. Here we review recent works in wavefunction‐based quantum chemistry techniques aimed at greater accuracy and faster computations for these systems. We describe recent developments in high‐accuracy benchmarks, a variety of recent wavefunction methods with promise for noncovalent interactions, various approximations to speed up these methods, and recent advances in wavefunction‐based symmetry‐adapted perturbation theory, which provides not only interaction energies but also their decomposition into physically meaningful components. Together, these advances are currently extending robust, accurate computations of noncovalent interactions from systems with around one dozen heavy atoms up to systems with several dozens of heavy atoms. © 2011 John Wiley & Sons, Ltd.

This article is categorized under:

Electronic Structure Theory > Ab Initio Electronic Structure Methods
Alternative in vitro assays in nanomaterial toxicology
Authors: Hartung Thomas , Sabbioni Enrico
Published: July 2011

Nanomaterials are acclaimed for their novel properties, for which broad new uses are being discovered with increasing frequency. It is obvious that, as the properties change, unwanted properties (toxicity) are to be expected as well. Current toxicology, however, is already overwhelmed with the challenge of addressing new chemicals, not to mention the enormous number of old chemicals never properly assessed. Limitations of traditional approaches range from animal welfare issues, which were a strong driving force for alternative approaches (the 3Rs concept) over the last two decades, to aspects of throughput and accuracy of the predicted toxicities. The latter has prompted discussion about a revolutionary change in chemical safety assessment, now known as Toxicology for the 21st Century (Tox‐21c). The multitude of possible formulations of nanomaterials to be assessed for novel toxic properties makes these alternative approaches especially attractive, given the well recognized limitations of traditional animal‐based approaches—limitations that might be even more pronounced for nanomaterials, which have notably altered biokinetics. WIREs Nanomed Nanobiotechnol 2011 3 545–573 DOI: 10.1002/wnan.153

This article is categorized under:

Toxicology and Regulatory Issues in Nanomedicine > Toxicology of Nanomaterials
Nanoscale thermal analysis for nanomedicine by nanocalorimetry
Authors: Yi Feng , La Van David A.
Published: July 2011

Microfabricated nanocalorimeters sensitively measure the thermal properties of nanomaterials and can be used for biomedical and in vitro measurements. This review examines the capabilities of nanocalorimeters including specific applications to nanomedicine such as measurements of nanomaterial stability, protein crystallization, ligand–protein binding, phase transitions, phase separations, interfacial reactions, and sorption–desorption phenomena. Widespread adoption of nanotechnology into clinical medicine will require a more complete understanding of the basic properties of nanomaterials, the relationship between nanomaterial processing, and physical properties and a deeper understanding of how nanomaterial physical properties control biological interactions. Nanocalorimetry is suitable where high sensitivity and high‐rate thermal and thermodynamic measurements are needed. Because of their small size and rapid measurement speed, nanocalorimeters can be used for single measurements or with high throughput automation. WIREs Nanomed Nanobiotechnol 2012, 4:31–41. doi: 10.1002/wnan.155

This article is categorized under:

Diagnostic Tools > Biosensing

Therapeutic Approaches and Drug Discovery > Emerging Technologies

Nanotechnology Approaches to Biology > Nanoscale Systems in Biology
Potential role of atomic force microscopy in systems biology
Authors: Ramachandran Srinivasan , Teran Arce Fernando , Lal Ratnesh
Published: July 2011

Systems biology is a quantitative approach for understanding a biological system at its global level through systematic perturbation and integrated analysis of all its components. Simultaneous acquisition of information data sets pertaining to the system components (e.g., genome, proteome) is essential to implement this approach. There are limitations to such an approach in measuring gene expression levels and accounting for all proteins in the system. The success of genomic studies is critically dependent on polymerase chain reaction (PCR) for its amplification, but PCR is very uneven in amplifying the samples, ineffective in scarce samples and unreliable in low copy number transcripts. On the other hand, lack of amplifying techniques for proteins critically limits their identification to only a small fraction of high concentration proteins. Atomic force microscopy (AFM), AFM cantilever sensors, and AFM force spectroscopy in particular, could address these issues directly. In this article, we reviewed and assessed their potential role in systems biology. WIREs Syst Biol Med 2011 3 702–716 DOI: 10.1002/wsbm.154

This article is categorized under:

Laboratory Methods and Technologies > Genetic/Genomic Methods

Laboratory Methods and Technologies > Proteomics Methods
Modeling of spatially‐restricted intracellular signaling
Authors: Neves Susana R.
Published: July 2011

Understanding the signaling capabilities of a cell presents a major challenge, not only due to the number of molecules involved, but also because of the complex network connectivity of intracellular signaling. Recently, the proliferation of quantitative imaging techniques has led to the discovery of the vast spatial organization of intracellular signaling. Computational modeling has emerged as a powerful tool for understanding how inhomogeneous signaling originates and is maintained. This article covers the current imaging techniques used to obtain quantitative spatial data and the mathematical approaches used to model spatial cell biology. Modeling‐derived hypotheses have been experimentally tested and the integration of modeling and imaging approaches has led to non‐intuitive mechanistic insights. WIREs Syst Biol Med 2012, 4:103–115. doi: 10.1002/wsbm.155

This article is categorized under:

Models of Systems Properties and Processes > Mechanistic Models
Enriching the Genetic Counseling Recruitment Pipeline: A National Cross‐Sectional Study of Public High School Counselors
Authors: Kumaravel Sharanya N. , Tabangin Meredith E. , Sebera Kerry E. , Warren Nancy Steinberg
Published: July 2011

Early awareness of careers is helpful in recruiting students into a career pipeline. School counselors are among the top resources that students turn to when seeking advice about choosing their career. Studies show that high school is the ideal time to generate interest in the genetic counseling career, especially for minorities. This novel study of 291 high school counselors working in ethnically diverse public school districts in the United States examined to what extent members of this important group discuss genetic counseling as a career option with their students. The findings indicate that the majority of school counselors in this study (83%) did not discuss genetic counseling with their students, citing a lack of resources and lack of student interest as the major barriers. Suggestions of ways to increase high school counselors’ awareness of the genetic counseling career in order to enhance the goal of enriching recruitment of ethnic minorities into the genetic counseling pipeline are presented.
Existence of self-dual non-topological solutions in the Chern–Simons Higgs model
Authors: Choe Kwangseok , Kim Namkwon , Lin Chang-Shou
Published: July 2011

In this paper we investigate the existence of non-topological solutions of the Chern–Simons Higgs model in

\mathbb{R}^{2}

. A long standing problem for this equation is: Given

N

vortex points and

\beta > 8\pi (N + 1)

, does there exist a non-topological solution in

\mathbb{R}^{2}

such that the total magnetic flux is equal to

\beta / 2

? In this paper, we prove the existence of such a solution if

\beta \notin \{8\pi N\frac{k}{k−1}|k = 2,…,N\}

. We apply the bubbling analysis and the Leray–Schauder degree theory to solve this problem.

Lʼobjectif de cet article est de prouver lʼexistence de solutions non-topologiques du modèle de Chern–Simons Higgs dans

\mathbb{R}^{2}

. Un problème de longue date existe pour cette équation : Soit

N

points vortex et

\beta > 8\pi (N + 1)

, existe-t-il une solution non-topologique dans

\mathbb{R}^{2}

telle que le flux magnétique total est égal à

\beta / 2

? Dans cet article, nous prouvons lʼexistence dʼune solution pour

\beta \notin \{8\pi N\frac{k}{k−1}|k = 2,…,N\}

. Nous appliquons lʼanalyse par bulles et la theorie de Leray–Schauder pour résoudre ce problème.
Anesthesia in presymptomatic Alzheimer's disease: A study using the triple‐transgenic mouse model
Authors: Tang Junxia X. , Mardini Feras , Caltagarone Breanna M. , Garrity Sean T. , Li Rosie Q. , Bianchi Shannon L. , Gomes Olubusola , Laferla Frank M. , Eckenhoff Roderic G. , Eckenhoff Maryellen F.
Published: July 2011

Background

Experimental evidence suggests that anesthetics accelerate symptomatic neurodegenerative disorders such as Alzheimer's disease (AD). Because AD pathology precedes symptoms, we asked ourselves whether anesthetic exposure in the presymptomatic interval accelerated neuropathology and appearance of symptoms.

Methods

Triple‐transgenic AD mice were exposed to general aesthetics, either halothane or isoflurane, at 2, 4, and 6 months of age, they then underwent water maze cognitive testing 2 months later, and subsequently their brains were analyzed using enzyme‐linked immunosorbent assay, immunoblots, and immunohistochemistry for amyloid and tau pathology and biomarkers.

Results

Learning and memory improved after halothane exposure in the 2‐month‐old group relative to controls, but no changes were noted in the isoflurane group. When gender was examined in all age groups, females exposed to halothane performed better as compared with those exposed to isoflurane or controls. Therefore, improvement in the 2‐month exposure group is most likely because of a gender effect. Level of phospho‐tau in the hippocampus was significantly increased 2 months after anesthesia, especially in the 6‐month exposure group, but changes in amyloid, caspase, microglia, or synaptophysin levels were not detected.

Conclusions

These results indicate that exposure to two different inhalation‐type anesthetics during the presymptomatic phase of AD does not accelerate cognitive decline, after 2 months, and may cause a stress response, marked by hippocampal phosphorylated tau, resulting in preconditioning against the ongoing neuropathology, primarily in female mice.
Turbulent entrainment into inert and reacting multiphase plumes
Authors: McHUGH SEAN T. , CARDOSO SILVANA S. S.
Published: July 2011

Theoretical predictions and experimental results for turbulent entrainment in inert and reacting, multiphase plumes are presented. It is shown that in an inert, pure plume, the entrainment coefficient is approximately constant with downstream distance. In a reacting plume, in which buoyancy is depleted by chemical reaction, the entrainment coefficient decreases strongly with distance from the source owing mainly to a decrease in the Richardson number. The effect on entrainment of the drift in the velocity and buoyancy distributions in the radial direction, i.e. the similarity drift introduced by Kaminski, Tait & Carazzo (J. Fluid Mech., vol. 526, 2005, pp. 361–76), is found to increase with downstream distance and with the reaction rate but, on laboratory-scale experiments, remains small compared to the contribution to entrainment from the turbulent stresses and buoyancy.
Pectin and high-amylose maize starch increase caecal hydrogen production and relieve hepatic ischaemia–reperfusion injury in rats
Authors: Nishimura Naomichi , Tanabe Hiroki , Sasaki Yumi , Makita Yui , Ohata Misako , Yokoyama Saori , Asano Mami , Yamamoto Tatsuro , Kiriyama Shuhachi
Published: July 2011

We investigated whether the feeding of high H2-generating dietary fibre and resistant starch (RS) could suppress hepatic ischaemia–reperfusion (IR) injury, which results from oxidative stress, in rats fed a pectin (Pec) or high-amylose maize starch (HAS) diet. Male Sprague–Dawley rats were fed a control (C) diet, with or without Pec (0–5 % Pec) or HAS (0–30 % HAS) supplementation for 7 d. Portal H2concentration showed a significant dose-dependent increase with the amount of Pec or HAS supplementation. Plasma alanine and aspartate aminotransferase activities remarkably increased in the C rats (5 % cellulose) due to IR treatment, while it decreased significantly or showed tendencies to decrease in 5 % Pec and 20 % HAS diet-fed rats. The hepatic oxidised glutathione (GSSG):total glutathione ratio increased significantly in IR rats maintained on the C diet compared with sham-operated rats. On the other hand, reduced glutathione (GSH):total glutathione and GSH:GSSG ratios decreased significantly. The GSSG:total glutathione ratio that increased due to IR treatment decreased significantly on HAS and Pec intake, while GSH:total glutathione and GSH:GSSG ratios increased significantly. Hepatic sinusoids of IR rats fed the C diet were occluded, but those of IR rats fed the Pec diet were similar to those in the sham-operated rats. In conclusion, we found that Pec or HAS, which enhance H2generation in the large intestine, alleviated hepatic IR injury. The present study demonstrates another physiological significance of dietary fibre and RS.
John Saltmarsh and the Mystery of Redemption
Authors: Parnham David
Published: July 2011

Early in 1646, an intriguing little book came forth from Giles Calvert's press.Free-Grace, or, The Flowings of Christ's Blood Freely to Sinnersby John Saltmarsh—at that time rector of Brasted in Kent and shortly to assume a chaplaincy at headquarters of the New Model Army—evoked caustic rebuttals from divines of high caliber and prominent profile, each sporting a nose for troublemakers and a willingness to controvert and condemn. This,prima facie, is mildly perplexing. For the demeanor of Saltmarsh's book is not obviously contentious. Rather,Free-Graceis studied in its disinclination to engage argumentatively with specific protagonists; it is neither thunderous nor acidulous, and makes scant effort to situate itself in the to-and-fro of the paper wars conducted in the mangled mid-century terrain of English practical divinity.
Scholasticism, Exegesis, and the Historicization of Mosaic Authorship in Moses Bar Kepha'sOn Paradise
Authors: Moss Yonatan
Published: July 2011

The author of the Pentateuch is famously unknown. There are various ancient speculations about the relative roles of God and Moses in the production of the text,1and there is a plethora of modern investigations into the Bible's constituent documents and the authors responsible for them, but the biblical text itself is silent. The biblical narrator never identifies himself or herself2and never narrates in the first person; rather he or she speaks “out of the void, in an authoritative voice that masks any authorial presence.”3
Charles Thomson and the First American New Testament
Authors: Michaels J. Ramsey
Published: July 2011

Charles Thomson (1729–1824) is best known as the first translator of the Septuagint, or Greek Old Testament, into English—or for that matter into any modern language. He is less well known as the first American translator of the New Testament, for his four volumes included the New Testament as well as the Old.1His achievements are remarkable, for he was no professional scholar but a layman—early American patriot, Secretary to the Continental Congress, and friend of Thomas Jefferson—who taught himself Greek in order to carry out the task. Born in Ireland in 1729, he arrived in America as an orphan at the age of ten, learned Latin, went into business, and became an activist in resisting the repressive measures of the British government, particularly the Stamp Act.
Efficacy of the cyclooctadepsipeptide PF1022A againstHeligmosomoides bakeri in vitroandin vivo
Authors: NWOSU UZOMA , VARGAS MIREILLE , HARDER ACHIM , KEISER JENNIFER
Published: July 2011

The cyclooctadepsipeptide PF1022A derived from the fungus,Mycelia sterilia, is characterized by a broad spectrum of activity against different parasitic gastrointestinal nematodes of livestock. In the present work the anthelmintic activity of PF1022A againstHeligmosomoides bakeri, a widely used laboratory model was studied. Albendazole, ivermectin and levamisole served as reference.In vitro, PF1022A showed low activity on embryonation but significantly inhibited egg hatch (10 and 100μg/ml), whereas albendazole (10 and 100μg/ml) revealed statistically significant inhibitions of both embryonation and egg hatch. PF1022A (1–100μg/ml) completely inhibited larval movement at most examination points. Comparable significant anthelmintic activity on the larval stages ofH. bakeriwas observed with levamisole (48–100%), while slightly lower activities were observed with ivermectin (20–92%) and albendazole (0–87%) at 1–100μg/ml. PF1022A and levamisole significantly inhibited motility and egg release of adult worms, while albendazole and ivermectin failed to demonstrate activity. Significant worm burden reductions were achieved with PF1022A, levamisole and ivermectinin vivo. For example, at 0·125 mg/kg PF1022A a worm burden reduction of 91·8% was observed. The use of drug combinations did not further enhance thein vitroandin vivoactivity of PF1022A. In conclusion, further investigations are warranted with PF1022A, as the drug is characterized by significant larvicidal and nematocidal activityin vitroandin vivo.
Identification of a Nosema bombycis (Microsporidia) spore wall protein corresponding to spore phagocytosis
Authors: CAI SHUNFENG , LU XINGMENG , QIU HAIHONG , LI MINGQIAN , FENG ZHENZHEN
Published: July 2011

Life-cycle stages of the microsporidia Nosema bombycis, the pathogen causing silkworm pebrine, were separated and purified by an improved method of Percoll-gradient centrifugation. Soluble protein fractions of late sporoblasts (spore precursor cells) and mature spores were analysed by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE). Protein spots were recovered from gels and analysed by mass spectrometry. The most abundant differential protein spot was identified by database search to be a hypothetical spore wall protein. Using immunoelectron microscopy, we demonstrated that HSWP5 is localized to the exospore of mature spores and renamed it as spore wall protein 5 (NbSWP5). Further spore phagocytosis assays indicated that NbSWP5 can protect spores from phagocytic uptake by cultured insect cells. This spore wall protein may function both for structural integrity and in modulating host cell invasion.