bluuebunny/crossref_metadata_2025 huggingface dataset:
A statistical analysis of properties of small transients in the solar wind 2007–2009: STEREO and Wind observations
Authors: Yu W. , Farrugia C. J. , Lugaz N. , Galvin A. B. , J. Kilpua E. K. , Kucharek H. , Möstl C. , Leitner M. , Torbert R. B. , C. Simunac K. D. , Luhmann J. G. , Szabo A. , Wilson L. B. , Ogilvie K. W. , Sauvaud J.‐A.
Published: December 2013

We present a comprehensive statistical analysis of small solar wind transients (STs) in 2007–2009. Extending work on STs by Kilpua et al. (2009) to a 3 year period, we arrive at the following identification criteria: (i) a duration < 12 h, (ii) a low proton temperature and/or a low proton beta, and (iii) enhanced field strength relative to the 3 year average. In addition, it must have at least one of the following: (a) decreased magnetic field variability, (b) large, coherent rotation of the field vector, (c) low Alfvén Mach number, and (d) Te/Tp higher than the 3 year average. These criteria include magnetic flux ropes. We searched for STs using Wind and STEREO data. We exclude Alfvénic fluctuations. Case studies illustrate features of these configurations. In total, we find 126 examples, ∼81% of which lie in the slow solar wind (≤ 450 km s−1). Many start or end with sharp field and flow gradients/discontinuities. Year 2009 had the largest number of STs. The average ST duration is ∼4.3 h, 75%<6 h. Comparing with interplanetary coronal mass ejections (ICMEs) in the same solar minimum, we find the major difference to be that Tp in STs is not significantly less than the expected Tp. Thus, whereas a low Tp is generally considered a very reliable signature of ICMEs, it is not a robust signature of STs. Finally, since plasma β∼1, force‐free modeling of STs having a magnetic flux rope geometry may be inappropriate.
Reconstruction of an evolving magnetic flux rope in the solar wind: Decomposing spatial and temporal variations from single‐spacecraft data
Authors: Hasegawa Hiroshi , Sonnerup Bengt U. Ö. , Hu Qiang , Nakamura Takuma
Published: December 2013

We present a novel single‐spacecraft method for decomposing spatial and temporal variations of physical quantities at points along the path of a spacecraft in space‐time. The method is designed for use in the reconstruction of evolving two‐dimensional, approximately magnetohydrostatic structures in a space plasma. It is an extension of the one developed by Sonnerup and Hasegawa (2010) and Hasegawa et al. (2010), in which it was assumed that variations in the time series of data, recorded as the structures move past the spacecraft, are all due to spatial effects. In reality, some of the observed variations are usually caused by temporal evolution of the structure during the time it moves past the observing spacecraft; the information in the data about the spatial structure is aliased by temporal effects. The purpose here is to remove this time aliasing from the reconstructed maps of field and plasma properties. Benchmark tests are performed by use of synthetic data taken by a virtual spacecraft as it traverses, at a constant velocity, a magnetic flux rope growing sufficiently slowly (relative to the Alfvén speed) in a two‐dimensional magnetohydrodynamic simulation of magnetic reconnection. These tests show that the new method can better recover the space‐time behavior of the flux rope than does the original version, in which time‐aliasing effects had not been removed. An application of the new method to a solar wind flux rope, observed by the ACE spacecraft, suggests that the cross‐sectional shape of the core part of the flux rope was varying.
Properties of terrestrial gamma ray flashes detected by AGILE MCAL below 30 MeV
Authors: Marisaldi M. , Fuschino F. , Tavani M. , Dietrich S. , Price C. , Galli M. , Pittori C. , Verrecchia F. , Mereghetti S. , Cattaneo P. W. , Colafrancesco S. , Argan A. , Labanti C. , Longo F. , Del Monte E. , Barbiellini G. , Giuliani A. , Bulgarelli A. , Campana R. , Chen A. , Gianotti F. , Giommi P. , Lazzarotto F. , Morselli A. , Rapisarda M. , Rappoldi A. , Trifoglio M. , Trois A. , Vercellone S.
Published: December 2013

We present the characteristics of 308 terrestrial gamma ray flashes (TGFs) detected by the Minicalorimeter (MCAL) instrument on board the AGILE satellite during the period March 2009–July 2012 in the ±2.5° latitude band and selected to have the maximum photon energy up to 30 MeV. The characteristics of the AGILE events are analyzed and compared to the observational framework established by the two other currently active missions capable of detecting TGFs from space, RHESSI and Fermi. A detailed model of the MCAL dead time is presented, which is fundamental to properly interpret our observations. The most significant contribution to dead time is due to the anticoincidence shield in its current configuration and not to the MCAL detector itself. Longitude and local time distributions are compatible with previous observations, while the duration distribution is biased toward longer values because of dead time. The intensity distribution is compatible with previous observations, when dead time is taken into account. The TGFs cumulative spectrum supports a low production altitude, in agreement with previous measurements. We also compare our sample to lightning sferics detected by the World Wide Lightning Location Network and suggest a new method to assess quantitatively the consistency of two TGF populations based on the comparison of the associated lightning activity. According to this method, AGILE and RHESSI samples are compatible with the same parent population. The AGILE TGF catalog below 30 MeV is accessible online at the website of the ASI Science Data Center http://www.asdc.asi.it/mcaltgfcat/.
Transmission of large‐amplitude ULF waves through a quasi‐parallel shock at Venus
Authors: Shan Lican , Lu Quanming , Wu Mingyu , Gao Xinliang , Huang Can , Zhang Tielong , Wang Shui
Published: December 2013

There exist large‐amplitude ultralow frequency (ULF) waves in the upstream region of a quasi‐parallel shock, which are excited due to the reflected ions by the shock. These waves are then brought back to the shock by the solar wind, and at last they coalesce and merge with the shock. In this paper, with the magnetic field measurements from Venus Express, for the first time we observe the transmission of large‐amplitude ULF waves from the upstream region to the downstream under quasi‐parallel shock conditions. These waves exist in both the upstream and downstream regions of the Venusian bow shock, which have the similar characteristics: their peak frequencies are 0.04–0.05 Hz in the spacecraft frame, their propagation angles do not change greatly, they have left‐hand polarization with respect to the mean magnetic field in the spacecraft frame, and they also have a large compressibility. We conclude that they are magnetosonic waves. The generation mechanism of such waves at the Venusian bow shock is also discussed in the paper.
Three‐dimensional simulation of the electromagnetic fields induced by the 2011 Tohoku tsunami
Authors: Zhang Luolei , Utada Hisashi , Shimizu Hisayoshi , Baba Kiyoshi , Maeda Takuto
Published: December 2013

The motion of seawater induces electromotive force of significant intensity due to Faraday's law, and the resulting electromagnetic (EM) field can be recorded by instruments installed on land or on the ocean bottom. However, few studies have successfully made a quantitative interpretation to obtain geophysical information from observations of tsunami‐induced EM signals by an exact and accurate application of Maxwell equations. We built a scheme for three‐dimensional numerical simulation to calculate EM fields due to ocean tidal flow and tested the system's accuracy by using the source currents in the ocean as expected from a Tohoku tsunami simulation. Here we show examples of a comparison of data from one land observatory in the Tohoku district, one island observatory in the Izu‐Bonin arc, and one seafloor station in the northwest Pacific Ocean. The water motion that generates source current in the sea consists of both the primary poloidal and toroidal magnetic modes. Our numerical simulation shows that the field of the primary toroidal magnetic mode can be effective for seafloor observations but only when the seafloor is highly conductive. We examined how the conductivity of the shallower part of the seabed, composed of sediments, can be constrained by the tsunami‐induced EM field observations, which is difficult in case of using ordinary seafloor magnetotelluric signals. We also defined the motional impedance just as the case of ordinary magnetotellurics and showed that both modeled and observed impedances approximately indicate the phase velocity of the long wave as predicted by a simple theory.
A new bubble dynamics model to study bubble growth, deformation, and coalescence
Authors: Huber C. , Su Y. , Nguyen C. T. , Parmigiani A. , Gonnermann H. M. , Dufek J.
Published: December 2013

We propose a new bubble dynamics model to study the evolution of a suspension of bubbles over a wide range of vesicularity, and that accounts for hydrodynamical interactions between bubbles while they grow, deform under shear flow conditions, and exchange mass by diffusion coarsening. The model is based on a lattice Boltzmann method for free surface flows. As such, it assumes an infinite viscosity contrast between the exsolved volatiles and the melt. Our model allows for coalescence when two bubbles approach each other because of growth or deformation. The parameter (disjoining pressure) that controls the coalescence efficiency, i.e., drainage time for the fluid film between the bubbles, can be set arbitrarily in our calculations. We calibrated this parameter by matching the measured time for the drainage of the melt film across a range of Bond numbers (ratio of buoyancy to surface tension stresses) with laboratory experiments of a bubble rising to a free surface. The model is then used successfully to model Ostwald ripening and bubble deformation under simple shear flow conditions. The results we obtain for the deformation of a single bubble are in excellent agreement with previous experimental and theoretical studies. For a suspension, we observe that the collective effect of bubbles is different depending on the relative magnitude of viscous and interfacial stresses (capillary number). At low capillary number, we find that bubbles deform more readily in a suspension than for the case of a single bubble, whereas the opposite is observed at high capillary number.
Physical state of Himalayan crust and uppermost mantle: Constraints from seismic attenuation and velocity tomography
Authors: Sheehan Anne F. , de la Torre Thomas L. , Monsalve Gaspar , Abers Geoffrey A. , Hacker Bradley R.
Published: December 2013

We jointly interpret P and S wave seismic attenuation (1/Q) along with previously published seismic velocity results for the crust and uppermost mantle of eastern Nepal and the southern Tibetan Plateau. Seismic attenuation measurements can provide information complementary to seismic velocity estimates and can help distinguish between compositional and thermal mechanisms for observed anomalies. In addition to a dramatic change in seismic velocity observed between the crust of Nepal and southern Tibet, we find a large increase in seismic attenuation from high Q (low attenuation) in eastern Nepal to low Q (high attenuation) in the crust beneath southern Tibet for both P waves and S waves. We interpret the broad zone of low Q values in the southern Tibetan crust as thermal in origin, requiring an elevated geotherm (warm) relative to Nepal, with low VP/VS corresponding to a dominantly felsic middle and upper crust beneath southern Tibet. We find a sharply bounded region with enhanced low Q and high VP/VS at 45–50 km depth beneath southern Tibet, which we suggest may be due to trapped fluid beneath an impermeable cap associated with the crustal alpha‐beta quartz transition. Using calibrations from mineral physics, the alpha‐beta quartz transition suggests a temperature of 930–960°C at 45 km depth (50 km beneath the surface) beneath the southern Tibetan Plateau. High values of QP and QS throughout the uppermost mantle in the region are consistent with cool temperatures in the underthrusting Indian Plate, contributing to brittle conditions and earthquakes in the uppermost mantle.
Dehumanization in children: The link with moral disengagement in bullying and victimization
Authors: van Noorden Tirza H.J. , Haselager Gerbert J.T. , Cillessen Antonius H.N. , Bukowski William M.
Published: December 2013

The current study explored subtle dehumanization—the denial of full humanness—in children, using distinctions of forms (i.e., animalistic vs. mechanistic) and social targets (i.e., friends vs. non‐friends). In addition, the link between dehumanization and moral disengagement in bullying and victimization was investigated. Participants were 800 children (7–12 years old) from third to fifth grade classrooms. Subtle animalistic and mechanistic dehumanization toward friends and non‐friends were measured with the new Juvenile Dehumanization Measure. Results showed that animalistic dehumanization was more common than mechanistic dehumanization and that non‐friends were dehumanized more than friends. The highest levels of dehumanization were found in animalistic form toward non‐friends and the lowest levels in mechanistic form toward friends. Both moral disengagement and animalistic dehumanization toward friends were positively associated with bullying. However, moral disengagement was negatively associated with victimization, whereas both animalistic and mechanistic dehumanization toward non‐friends were positively associated with victimization. The current findings indicate that children are able to distinguish different forms and targets of dehumanization and that dehumanization plays a distinct role from moral disengagement in bullying and victimization. Aggr. Behav. 40:320–328, 2014. © 2013 Wiley Periodicals, Inc.
A novel adaptive control approach for nonlinearly parameterized systems
Authors: Chen Zhiyong
Published: December 2013

Nonlinearly parameterized systems are commonly encountered in control of practical systems. However, the conventional adaptive estimation and control strategies, based on the essential assumption of linear parameterization, are incapable of dealing with this class of systems. This incapability in turn becomes a bottleneck for prevalent applications of adaptive control. In literature, there have been some attempts to break through this bottleneck by investigating the characteristics of nonlinearities. However, it is still open for an implementable strategy that is powerful for nonlinearly parameterized systems as the certainty equivalence principle for linearly parameterized systems. This paper aims to contribute an attempt to this open problem by proposing a novel adaptive control approach. On the one hand, the controller is conceptually simple, and it does not explicitly rely on the expression of system nonlinearities. On the other hand, the controller is able to achieve system stability and parameter convergence. Copyright © 2013 John Wiley & Sons, Ltd.
Enhancing the Mechanical Properties of AE42 Magnesium Alloy through Friction Stir Processing
Authors: Arora Harpreet Singh , Grewal Harpreet Singh , Singh Harpreet , Dhindaw Brij Kumar , Mukherjee Sundeep
Published: December 2013

Friction stir processing (FSP) was carried out for AE42 Mg alloy resulting in significant grain refinement and uniform dispersion of fine in situ precipitates. The average grain size was 20 μm for the as‐cast AE42 alloy, which was refined to 1.5 μm after FSP. Tensile testing revealed significantly higher modulus and yield strength for the friction stir processed (FSPed) specimen with some improvement in ductility. The fractured surface of the as‐cast alloy showed ridges, grooves and cracks indicating brittle failure. In contrast, the fractured surface of FSPed specimen showed fine dimples, characteristic of ductile failure. Nano‐indentation was used to analyze the variation of hardness and modulus across the nugget zone of the FSPed specimen. FSPed specimen demonstrated greater strain‐hardening tendency compared to the as‐cast alloy. Enhancing the mechanical properties of Mg alloys can result in substantial cost savings across a number of industries and have wide economic impact.
Structural Determination and Imaging of Charge Ordering and Oxygen Vacancies of the Multifunctional Oxides REBaMn2O6‐χ (RE = Gd, Tb)
Authors: Ávila‐Brande David , King Graham , Urones‐Garrote Esteban , Subakti  , Llobet Anna , García‐Martín Susana
Published: December 2013

Charge ordering and oxygen vacancy ordering are revealed in REBaMn2O6‐δ (RE = Gd, Tb) oxides with perovskite‐related structures. Electron diffraction and transmission electron microscopy results indicate a modulation of the crystal structure. The average oxidation state of Mn and the oxygen stoichiometry are determined by means of electron energy‐loss spectroscopy, giving a REBaMn2O5.75 general formula. A 1:3 Mn4+:Mn3+ charge ordering model is confirmed by neutron powder diffraction, and oxygen vacancies‐Mn3+ association is suggested by pair distribution function analysis. Direct imaging of the oxygen sublattice is obtained by phase image reconstruction. Location of the oxygen vacancies in the anion sublattice is achieved by analysis of the intensity of the averaged phase image. Both ionic conduction and multiferroic behavior are predicted from the crystal structures of these oxides.
Mitochondrial DNA and Y‐chromosome structure at the mediterranean and atlantic façades of the iberian peninsula
Authors: Santos Cristina , Fregel Rosa , Cabrera Vicente M. , Álvarez Luis , Larruga Jose M. , Ramos Amanda , López Miguel A. , Pilar Aluja María , González Ana M.
Published: December 2013

Objectives

The aim of this study is to analyze mitochondrial DNA and Y‐chromosome lineages in a range of Atlantic and Mediterranean populations of the Iberian Peninsula in search of genetic differences between both façades and to uncover the most probable geographic origin and coalescence ages of lineages.

Methods

The control region of mitochondrial DNA and haplogroup diagnostic positions were analyzed in 575 subjects and Y‐chromosome markers were typed in 260 unrelated males. Moreover, previously published data were compiled and used in the analyses.

Results

The level of genetic structure deduced from uniparental markers for the Iberian Peninsula was weak, with stronger Atlantic versus Mediterranean than North to South differentiation and larger diversities in the South. In general, mitochondrial DNA haplogroups had mainly Paleolithic and Mesolithic coalescences in Europe, although some of them, ruling out drift effects, seem to have younger implantation in Central Europe and the Atlantic areas than in the Mediterranean (I, J, J2a, T1, and W) while others as N1 and X could have reached the Iberian Peninsula at the Neolithic transition. On the other hand, younger coalescence ages are being proposed for the arriving or spread of the bulk of Y‐chromosome lineages in Europe.

Conclusions

The major haplotypic affinities found for all the Iberian Peninsula regions were always with North Africa and the Atlantic Islands. These results draw an Atlantic network that clearly resembles those of the Megalithic Copper and Bronze cultures at this part of Europe. Am. J. Hum. Biol. 26:130–141, 2014. © 2013 Wiley Periodicals, Inc.
Possible Intervention of Prototropic and Silatropic Ene‐type Mechanisms in Asymmetric Catalytic Mukaiyama Aldol Reactions
Authors: Honda Kazuya , Mikami Koichi
Published: December 2013

Prototropic and silatropic ene mechanisms were analyzed in the BINOL‐TiIV, bisoxazoline (box)‐CuII, and BINAP‐PdII complex‐catalyzed asymmetric Mukaiyama aldol reaction of methyl glyoxylate and acetone‐derived 2‐trimethylsiloxypropene. Our ab initio calculations indicate that the BINOL‐TiIV‐catalyzed Mukaiyama aldol reaction proceeds through the concerted prototropic or silatropic ene pathways and that box‐CuII‐ and BINAP‐PdII‐catalyzed reactions proceed through the stepwise prototropic ene pathways. The transition‐state conformations are thus syn‐clinal with hydrogen and silane as the migratory groups aligned to the formyl oxygen atom in close syn‐clinal proximity, respectively.
Quasi All‐Silica Zeolite Obtained by Isomorphous Degermanation of an As‐Made Germanium‐Containing Precursor
Authors: Burel Laurence , Kasian Nataliia , Tuel Alain
Published: December 2013

Ge‐containing ITQ‐22 zeolites have been almost completely degermanated under strong acidic conditions without modifications of the framework topology. Simultaneous to Ge extraction, the framework was partially dissolved; mesopores were formed but the structure was maintained through the re‐incorporation of some of silicon species at vacant sites. The presence of many defects in the degermanated framework enabled the incorporation of tetrahedral aluminum, opening the way to the preparation of new and stable acid catalysts with original topologies.
Janus Nanoparticles: Preparation, Characterization, and Applications
Authors: Song Yang , Chen Shaowei
Published: December 2013

In chemical functionalization of colloidal particles, the functional moieties are generally distributed rather homogeneously on the particle surface. Recently, a variety of synthetic protocols have been developed in which particle functionalization may be carried out in a spatially controlled fashion, leading to the production of structurally asymmetrical particles. Janus particles represent the first example in which the two hemispheres exhibit distinctly different chemical and physical properties, which is analogous to the dual‐faced Roman god, Janus. Whereas a variety of methods have been reported for the preparation of (sub)micron‐sized polymeric Janus particles, it has remained challenging for the synthesis and (unambiguous) structural characterization of much smaller nanometer‐sized Janus particles. Herein, several leading methods for the preparation of nanometer‐sized Janus particles are discussed and the important properties and applications of these Janus nanoparticles in electrochemistry, sensing, and catalysis are highlighted. Some perspectives on research into functional patchy nanoparticles are also given.
The Many Roles of Quantum Chemical Predictions in Synthetic Organic Chemistry
Authors: Nguyen Quynh Nhu N. , Tantillo Dean J.
Published: December 2013

This account discusses representative case studies for various applications of quantum chemical calculations in synthetic organic chemistry. These include confirmation of target structures, methodology development, and catalyst design. These examples demonstrate how predictions from quantum chemical calculations can be utilized to streamline synthetic efforts.
Thermochemical biorefineries with multiproduction using a platform chemical
Authors: Haro Pedro , Villanueva Perales Ángel Luis , Arjona Ricardo , Ollero Pedro
Published: December 2013

Multiproduction is a promising option for thermochemical biorefineries in order to reduce the risk of investment. It promotes the diversification of revenue, allows a better material and energy integration, and enhances profitability, which could improve the future development of thermochemical biorefineries. However, the design of thermochemical biorefineries with multiproduction requires of new tools and new perspectives that differ from those that have been used in the design of biomass‐to‐liquid/gas (BTL/G) processes, which are single‐product orientated. The use of a platform chemical has revealed a new field of promising possibilities for multiproduction. Nonetheless, the consideration of several kinds of final products makes difficult the calculation of the energy efficiency and the assessment of both sustainability and profitability. In the case of sustainability, it is necessary to know how to allocate the greenhouse gas (GHG) emissions of each product (including electricity) and the potential impact of the production of chemicals, which are not combusted in their final use and bring a net retention of carbon. The incorporation of bioenergy with carbon capture and storage (BECCS) is assessed as a potential income for this kind of biorefinery, which could also achieve a larger saving of GHG emissions than that regulated by European administration. The design of thermochemical biorefineries with multiproduction, in the case of using a platform chemical, are able to co‐produce low‐value high‐volume products like fuels along with high‐value low‐volume products like solvents and chemicals, which have been demonstrated by conventional oil refineries to be highly profitable. © 2013 Society of Chemical Industry and John Wiley & Sons, Ltd
Molecular dynamics simulation study on the interaction of collagen‐like peptides with gelatinase‐A (MMP‐2)
Authors: Azhagiya Singam E. R. , Rajapandian V. , Subramanian V.
Published: December 2013

Although several models have been proposed for the interaction of collagen with gelatinase‐A (matrix metalloproteinases‐2 (MMP‐2)), the extensive role of each domain of gelatinase A in hydrolyzing the collagens with and without interruptions is still elusive. Molecular docking, molecular dynamics (MD) simulation, normal mode analysis (NMA) and framework rigidity optimized dynamics algorithm (FRODAN) based analysis were carried out to understand the function of various domains of MMP‐2 upon interaction with collagen like peptides. The results reveal that the collagen binding domain (CBD) binds to the C‐terminal of collagen like peptide with interruption. CBD helps in unwinding the loosely packed interrupted region of triple helical structure to a greater extent. It can be possible to speculate that the role of hemopexin (HPX) domain is to prevent further unwinding of collagen like peptide by binding to the other end of the collagen like peptide. The catalytic (CAT) domain then reorients itself to interact with the part of the unwound region of collagen like peptide for further hydrolysis. In conclusion the CBD of MMP‐2 recognizes the collagen and aids in unwinding the collagen like peptide with interruptions, and the HPX domain of MMP‐2 binds to the other end of the collagen allowing CAT domain to access the cleavage site. This study provides a comprehensive understanding of the structural basis of collagenolysis by MMP‐2. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 779–794, 2014.
Genome scale metabolic modeling of the riboflavin overproducer Ashbya gossypii
Authors: Ledesma‐Amaro Rodrigo , Kerkhoven Eduard J. , Revuelta José Luis , Nielsen Jens
Published: December 2013

Ashbya gossypii is a filamentous fungus that naturally overproduces riboflavin, or vitamin B2. Advances in genetic and metabolic engineering of A. gossypii have permitted the switch from industrial chemical synthesis to the current biotechnological production of this vitamin. Additionally, A. gossypii is a model organism with one of the smallest eukaryote genomes being phylogenetically close to Saccharomyces cerevisiae. It has therefore been used to study evolutionary aspects of bakers' yeast. We here reconstructed the first genome scale metabolic model of A. gossypii, iRL766. The model was validated by biomass growth, riboflavin production and substrate utilization predictions. Gene essentiality analysis of the A. gossypii model in comparison with the S. cerevisiae model demonstrated how the whole‐genome duplication event that separates the two species has led to an even spread of paralogs among all metabolic pathways. Additionally, iRL766 was used to integrate transcriptomics data from two different growth stages of A. gossypii, comparing exponential growth to riboflavin production stages. Both reporter metabolite analysis and in silico identification of transcriptionally regulated enzymes demonstrated the important involvement of beta‐oxidation and the glyoxylate cycle in riboflavin production. Biotechnol. Bioeng. 2014;111: 1191–1199. © 2013 Wiley Periodicals, Inc.
Bone marrow levels of 25 hydroxy vitamin D are not depressed in cases of hip fracture compared with controls
Authors: Power J. , Taggart J. , Parker M. , Berry J. L. , Reeve J.
Published: December 2013

There is little information on tissue as distinct from plasma levels of vitamin D metabolites in cases of hip fracture compared with controls. Femoral neck fractures in the elderly are associated with increased cortical remodelling and endosteal resorption, leading to regional increases in porosity and reduced cortical thickness. Vitamin D metabolites play a central role in the maintenance of normal serum calcium levels and may, through interactions with parathyroid hormone, exert an important influence on bone structure. To investigate whether hip fracture might be associated with tissue vitamin D deficiency, we have measured by radioimmunoassay the levels of 25 hydroxy vitamin D (25 (OH)D) in bone marrow samples extracted from the proximal femurs of 16 female subjects who had suffered fracture (mean age = 82.1 years, standard error (se) 1.9) and nine sex matched post mortem controls (mean age = 83.8 years, se 2.5). Twenty five (OH)D concentrations were significantly greater in the fracture cases (median = 3.7, IQR = 2.5–3.9 ng/g) than in the control group (median = 1.5, IQR = 0.9–2.3 ng/g; P = 0.0007, non‐parametric Wilcoxon/Kruskal–Wallis test). It was suggested in the 1970s that bone loss and hip fracture risk in the UK were driven by vitamin D deficiency. Our results suggest that the alterations in femoral neck bone microstructure and remodelling in hip fracture cannot be assigned to the single cause of relative deficiency of vitamin D. Vitamin D deficiency or insufficiency may nevertheless increase remodelling and loss of bone tissue and contribute causally to a minority of hip fractures. Copyright © 2013 John Wiley & Sons, Ltd.
DNA‐Directed Assembly of Antibody–Fluorophore Conjugates for Quantitative Multiparametric Flow Cytometry
Authors: Flor Amy C. , Williams Jimmy H. , Blaine Kelly M. , Duggan Ryan C. , Sperling Anne I. , Schwartz David A. , Kron Stephen J.
Published: December 2013

Multiparametric flow cytometry offers a powerful approach to single‐cell analysis with broad applications in research and diagnostics. Despite advances in instrumentation, progress in methodology has lagged. Currently there is no simple and efficient method for antibody labeling or quantifying the number of antibodies bound per cell. Herein, we describe a DNA‐directed assembly approach to fluorescent labeling that overcomes these barriers. Oligonucleotide‐tagged antibodies and microparticles can be annealed to complementary oligonucleotides bearing fluorophores to create assay‐specific labeling probes and controls, respectively. The ratio of the fluorescence intensity of labeled cells to the control particles allows direct conversion of qualitative data to quantitative units of antibody binding per cell. Importantly, a single antibody can be labeled with any fluorophore by using a simple mix‐and‐match labeling strategy. Thus, any antibody can provide a quantitative probe in any fluorescent channel, thus overcoming major barriers to the use of flow cytometry as a technique for systems biology and clinical diagnostics.
High Selectivity Higher Alcohols Synthesis from Syngas over Three‐Dimensionally Ordered Macroporous Cu‐Fe Catalysts
Authors: Lu Yongwu , Cao Baobao , Yu Fei , Liu Jian , Bao Zhenghong , Gao Jinsen
Published: December 2013

We show that higher alcohols can be produced with high selectivity from syngas over three‐dimensionally ordered macroporous Cu–Fe catalyst. The catalyst was developed by using a glyoxylate route colloidal crystal template method. The high intrinsic activity was ascribed to three factors. First, the unique ordered structure has a large pore size and interconnected macroporous tunnels of the catalyst with a large accessible surface area improves the catalytic activity. Second, a high density of uniformly distributed defective Cu0 and χ‐Fe5C2 nanoparticles derived from the glyoxylate route helps to provide abundant, active, stable dual sites. Third, atomic steps on the Cu surface, induced by planar defects and lattice strain, serve as high‐activity oxygenation sites; and active χ‐Fe5C2 chain‐growth sites surrounds the defective and strained form of Cu surface intimately, which results in a synergetic effect between the active and stable Cu–FexCy dual sites for higher alcohols synthesis.
Activation of a Carbon Support Through a Two‐Step Wet Oxidation and Highly Active Ruthenium–Activated Carbon Catalysts for the Hydrogenation of Benzene
Authors: Li Ying , Lan Guojun , Feng Guoquan , Jiang Wei , Han Wenfeng , Tang Haodong , Liu Huazhang
Published: December 2013

A two‐step liquid oxidation approach was developed for the activation of carbon materials. Following nitric acid treatment and subsequent liquid oxidation by a mild oxidant such as H2O2, the number of surface acidic functional groups was increased without destroying the physical structures of the carbon materials. Ruthenium catalysts supported on activated carbon prepared by this two‐step liquid oxidation method show significantly improved Ru dispersion and excellent catalytic performance in the hydrogenation of benzene. The dispersion of ruthenium and the catalytic performance of Ru/activated carbon increases monotonically with the amount of surface functional groups.
The study of the RASMS method on the QSAR of three kinds of drugs
Authors: Tong Jianbo , Zhong Li , Liu Shuling , Zhao Xiang , Chang Jia
Published: December 2013

Random sampling analysis on molecular surface (RASMS) method was applied to three series of drugs' quantitative structure–activity relationship that were molded by multiple linear regression. The correlation coefficients () and cross‐validation correlation coefficients () obtained by the models built were 0.834 and 0.748 for the 44 anti‐tuberculotic derivatives, 0.961 and 0.781 for the 41 HIV‐1 reverse transcriptase inhibitors, and 0.824 and 0.773 for the 38 phosphodiesterase inhibitors, respectively. Satisfactory results showed that information related to biological activity can be systemically expressed by RASMS. Copyright © 2013 John Wiley & Sons, Ltd.
Removal of Total Dissolved Solids in Spent Caustic Using Biochar: Pretreatment for Subsequent Biological Treatment
Authors: Oh Seok‐Young , Shin Dong‐Sik
Published: December 2013

Biological oxidative treatment of spent caustic, a liquid waste generated from a refinery plant, is limited due to high concentrations of total dissolved solids (TDS). In this study, we investigated the possibility of using biochar as a sorbent to remove TDS in spent caustic to enhance the subsequent biological treatment. Compared to inefficient removal of TDS with granular activated carbon, biochar can effectively remove TDS from spent caustic, resulting in up to 65% removal of TDS as biochar dosage was increased in batch reactors. With 51.8 min of retention time, 59% of TDS was removed in a column reactor. After TDS removal, chemical oxygen demand removal in biological reactors was markedly enhanced. Our results suggest that biochar may have potential as a sorbent to remove TDS from spent caustic before biological treatment.
The Effect of Various Zinc Binding Groups on Inhibition of Histone Deacetylases 1–11
Authors: Madsen Andreas S. , Kristensen Helle M. E. , Lanz Gyrithe , Olsen Christian A.
Published: December 2013

Histone deacetylases (HDACs) have the ability to cleave the acetyl groups of ε‐N‐acetylated lysine residues in a variety of proteins. Given that human cells contain thousands of different acetylated lysine residues, HDACS may regulate a wide variety of processes including some implicated in conditions such as cancer and neurodegenerative disorders. Herein we report the synthesis and in vitro biochemical profiling of a series of compounds, including known inhibitors as well as novel chemotypes, that incorporate putative new zinc binding domains. By evaluating the compound collection against all 11 recombinant human HDACs, we found that the trifluoromethyl ketone functionality provides potent inhibition of all four subclasses of the Zn2+‐dependent HDACs. Potent inhibition was observed with two different scaffolds, demonstrating the efficiency of the trifluoromethyl ketone moiety as a zinc binding motif. Interestingly, we also identified silanediol as a zinc binding group with potential for future development of non‐hydroxamate class I and class IIb HDAC inhibitors.
N‐Cinnamoylation of Antimalarial Classics: Quinacrine Analogues with Decreased Toxicity and Dual‐Stage Activity
Authors: Gomes Ana , Pérez Bianca , Albuquerque Inês , Machado Marta , Prudêncio Miguel , Nogueira Fátima , Teixeira Cátia , Gomes Paula
Published: December 2013

Plasmodium falciparum, the causative agent of the most lethal form of malaria, is becoming increasingly resistant to most available drugs. A convenient approach to combat parasite resistance is the development of analogues of classical antimalarial agents, appropriately modified in order to restore their relevance in antimalarial chemotherapy. Following this line of thought, the design, synthesis and in vitro evaluation of N‐cinnamoylated quinacrine surrogates, 9‐(N‐cinnamoylaminobutyl)‐amino‐6‐chloro‐2‐methoxyacridines, is reported. The compounds were found to be highly potent against both blood‐stage P. falciparum, chloroquine‐sensitive 3D7 (IC50=17.0–39.0 nM) and chloroquine‐resistant W2 and Dd2 strains (IC50=3.2–41.2 and 27.1–131.0 nM, respectively), and liver‐stage P. berghei (IC50=1.6–4.9 μM) parasites. These findings bring new hope for the possible future “rise of a fallen angel” in antimalarial chemotherapy, with a potential resurgence of quinacrine‐related compounds as dual‐stage antimalarial leads.
Gd loading by hypotonic swelling: an efficient and safe route for cellular labeling
Authors: Di Gregorio Enza , Ferrauto Giuseppe , Gianolio Eliana , Aime Silvio
Published: December 2013

Cells incubated in hypo‐osmotic media swell and their membranes become leaky. The flow of water that enters the cells results in the net transport of molecules present in the incubation medium directly into the cell cytoplasm. This phenomenon has been exploited to label cells with MRI Gd‐containing contrast agents. It has been found that, in the presence of 100 mm Gd–HPDO3A in an incubation medium characterized by an overall osmolarity of 160 mOsm l−1, each cell is loaded with amounts of paramagnetic complex ranging from 2 × 109 to 2 × 1010 depending on the cell type. To obtain more insight into the determinants of cellular labeling by the ‘hypo‐osmotic shock’ methodology, a study on cell viability, proliferation rate and cell morphology was carried out on J774A.1 and K562 cells as representative of cells grown in adhesion and suspended ones, respectively. Moreover a comparison of the efficiency of the proposed method with established cell labeling procedures such as pinocytosis and electroporation was carried out. Finally, the effects of the residual electric charge, the size and some structural features of the metal complex were investigated. In summary, the ‘hypotonic shock’ methodology appears to be an efficient and promising tool to pursue cellular labeling with paramagnetic complexes. Its implementation is straightforward and one may foresee that it will be largely applied in in vitro cellular labeling of many cell types. Copyright © 2013 John Wiley & Sons, Ltd.
Studying the influence of hydrogel injections into the infarcted left ventricle using the element‐free Galerkin method
Authors: Legner D. , Skatulla S. , MBewu J. , Rama R. R. , Reddy B. D. , Sansour C. , Davies N. H. , Franz T.
Published: December 2013

Myocardial infarction is an increasing health problem worldwide. Because of an under‐supply of blood, the cardiomyocytes in the affected region permanently lose their ability to contract. This in turn gradually weakens the overall heart function. A new therapeutic approach based on the injection of a gel into the infarcted area aims to support the healing and to inhibit adverse remodelling that can lead to heart failure. A computational model is the basis for obtaining a better understanding of the heart mechanics, in particular, how myocardial infarction and gel injections affect its pumping performance. A strain invariant‐based stored energy function is proposed to account for the passive mechanical behaviour of the model, which also makes provision for active contraction. To incorporate injections an additive homogenization approach is introduced. The numerical framework is developed using an in‐house code based on the element‐free Galerkin method. The main focus of this contribution is to investigate the influence of gel injections on the mechanics of the left ventricle during the diastolic filling and systolic isovolumetric (isochoric) contraction phases. It is found that gel injections are able to reduce the elevated fibre stresses caused by an infarct. Copyright © 2013 John Wiley & Sons, Ltd.
Design and performance characterization of electronic structure calculations on massively parallel supercomputers: a case study of GPAW on the Blue Gene/P architecture
Authors: Romero N.A. , Glinsvad C. , Larsen A.H. , Enkovaara J. , Shende S. , Morozov V.A. , Mortensen J.J.
Published: December 2013

Density function theory (DFT) is the most widely employed electronic structure method because of its favorable scaling with system size and accuracy for a broad range of molecular and condensed‐phase systems. The advent of massively parallel supercomputers has enhanced the scientific community's ability to study larger system sizes. Ground‐state DFT calculations on ∼ 103 valence electrons using traditional algorithms can be routinely performed on present‐day supercomputers. The performance characteristics of these massively parallel DFT codes on > 104 computer cores are not well understood. The GPAW code was ported an optimized for the Blue Gene/P architecture. We present our algorithmic parallelization strategy and interpret the results for a number of benchmark test cases.Copyright © 2013 John Wiley & Sons, Ltd.
Tunable Surface‐Enhanced Raman Scattering from High‐Density Gold Semishell Arrays with Controllable Dimensions
Authors: Lang Xianzhong , Li Jiaqi , Luo Xiaoguang , Zhang Yan , Yin Yin , Qiu Teng
Published: December 2013

A convenient reproducible technique is reported for the fabrication of large‐area gold semishell arrays by mechanically pressing porous anodic alumina (PAA) stamps into gold/polymer bilayer structures that serve as robust and cost‐efficient surface‐enhanced Raman‐scattering (SERS) substrates. The surface structure can be tuned further to optimize the enhancement factor according to optional PAA fabrication parameters and imprinting pressures. Finite‐difference time‐domain calculations indicate that the structure may possess excellent SERS characteristics due to the high density and abundance of hot spots.
The Non‐Ergodic Nature of Internal Conversion
Authors: Sølling Theis I. , Kuhlman Thomas S. , Stephansen Anne B. , Klein Liv B. , Møller Klaus B.
Published: December 2013

The absorption of light by molecules can induce ultrafast dynamics and coupling of electronic and nuclear vibrational motion. The ultrafast nature in many cases rests on the importance of several potential energy surfaces in guiding the nuclear motion—a concept of central importance in many aspects of chemical reaction dynamics. This Minireview focuses on the non‐ergodic nature of internal conversion, that is, on the concept that the nuclear dynamics only sample a reduced phase space, potentially resulting in localization of the dynamics in real space. A series of results that highlight the nonstatistical nature of the excited‐state deactivation process is presented. The examples are categorized into four groups. 1) Localization of the energy in one degree of freedom in S2→S1 transitions, in which the transition is either determined by the time spent in the S2→S1 coupling region or by the time it takes to reach it. 2) Localization of energy into a single reactive mode, which is dictated by the internal conversion process. 3) Initiation of the internal conversion by activation of a single complex motion, which then specifically couples to a reactive mode. 4) Nonstatistical internal conversion as a tool to accomplish biomolecular stability. Herein, the discussion on nonstatistical internal conversion in DNA as a mechanism to eliminate electronic excitation energy is extended to include molecules with an SS bond as a model of the disulfide bridge in peptides. All of these examples are summed up in Kasha’s rule. For systems with multiple degrees of freedom it will be possible to locate an appropriate motion somewhere in phase space that will take the wavepacket to the coupling region and facilitate an ultrafast transition to S1. Once at S1, the momentum of the wavepacket is lost and the only options left are the statistical processes of reaction or light emission.
Performance analysis of multi‐input multi‐output systems with maximum likelihood detection over shadowed fading channels
Authors: Leib Harry , Lin Wenjing
Published: December 2013

Multiple‐input multiple‐output (MIMO) transmission techniques constitute an important technology in modern wireless communication. Hence, performance analysis methods for such systems are of considerable interest. This paper considers first the average pairwise error probability for uncoded MIMO systems employing maximum likelihood detection over a composite Rayleigh‐Lognormal fading channel with spatial correlation. It provides general results, applicable also to a wider class of shadowing models, concerning asymptotical diversity gains and shows that they are not changed by such shadowing. Then, analytical evaluation techniques for bit‐error‐rate (BER) over composite Rayleigh‐Lognormal fading channels, based on the truncated union bound and the transfer function, are considered. Furthermore, these techniques are modified for applications over spatially correlated channels. This paper shows that such performance evaluation techniques provide good approximations to BER of spatially uncorrelated MIMO systems and also in the presence of moderate spatial correlation, over Rayleigh‐Lognormal fading channels. Copyright © 2013 John Wiley & Sons, Ltd.
Quinic Acid Derivative KZ‐41 Exhibits Radiomitigating Activity in Preclinical Models of Radiation Injury
Authors: Thompson Karin E. , Zeng Kui , Wilson Christy M. , Gaber Mostafa W. , Miller Duane D. , Yates Charles R.
Published: December 2013

Preclinical Research

Acute radiation syndrome is induced when a significant portion of the body receives high‐dose, as well as high‐dose rate, radiation. We have previously identified a quinic acid‐based derivative, KZ‐41, that protects from radiation injury. Further preclinical efficacy studies were conducted to determine the radiomitigating activity of KZ‐41. C57BL/6 mice received total body irradiation (TBI—LD80/30, 137Cs; ∼2 min) followed by either normal saline or KZ‐41 (100 mg/kg sc ∼26 h post‐TBI). KZ‐41 increased 30‐day survival by approximately 45% compared with vehicle controls (P < 0.05). To further investigate the potential radiomodulating mechanisms of KZ‐41, we developed a combined radiation and vascular injury model. C57BL/6 mice surgically fixed with dorsal windows for dermal vasculature imaging received either sham or TBI (137Cs; 6 Gray). Postcapillary venule injury was induced (24, 48, 72, and 96 h post‐TBI) followed by imaging at 5 min and 24 h to assess clot formation and blood flow. Impairment in flow (P < 0.05) and clot formation (P < 0.05) were observed as early as 48 and 72 h, respectively. Thus, vascular injury 72 h post‐TBI was used to evaluate intervention (KZ‐41; 100 mg/kg i.p. at 12, 36, and 60 h post‐TBI) on radiation‐induced changes in both flow and clot formation. KZ‐41, although not improving flow, increased clot formation (P < 0.05). Platelet counts were lower in both irradiated groups compared with sham controls (P < 0.05). In summary, KZ‐41 exerts radiomitigating activity in lethally irradiated mice. Imaging results suggest KZ‐41 exerts radiomitigating activity through mechanisms involving promotion of initial clot formation and vascular flow restoration. The imaging model described herein is useful for further examination of radiation‐induced vascular injury repair mechanisms.