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  • Oxford University Press  (21,336)
  • Hindawi  (19,371)
  • International Union of Crystallography (IUC)
  • 2010-2014  (42,038)
  • 1935-1939
  • 2014  (42,038)
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  • 2010-2014  (42,038)
  • 1935-1939
Year
  • 1
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    The Sensible Heat Flux in the Course of the Year at Ny-Ålesund, Svalbard: Characteristics of Eddy Covariance Data and Corresponding Model Results (2014)
    Hindawi
    In:  EPIC3Advances in Meteorology, Hindawi, pp. Article ID 852108, ISSN: 1687-9309
    Details
    Publication Date: 2020-03-05
    Description: In this paper we present one year of meteorological and flux measurements obtained near Ny-Ålesund, Spitsbergen. Fluxes are derived by the eddy covariance method and by a hydrodynamic model approach (HMA) as well. Both methods are compared and analyzed with respect to season and mean wind direction. Concerning the wind field we find a clear distinction between 3 prevailing regimes (which have influence on the flux behavior) mainly caused by the topography at the measurement site. Concerning the fluxes we find a good agreement between the HMA and the eddy covariance method in cases of turbulent mixing in summer but deviations at stable conditions, when the HMA almost always shows negative fluxes. Part of the deviation is based on a dependence of HMA fluxes on friction velocity and the influence of the molecular boundary layer. Moreover, the flagging system of the eddy covariance software package TK3 is briefly revised. A new quality criterion for the use of fluxes obtained by the eddy covariance method, which is based on integral turbulence characteristics, is proposed.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 2
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    Post-seismic viscoelastic deformation and stress transfer after the 1960 M9.5 Valdivia, Chile earthquake : effects on the 2010 M8.8 Maule, Chile earthquake (2014)
    Oxford University Press
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © The Authors, 2014. This article is posted here by permission of The Royal Astronomical Society for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 197 (2014): 697-704, doi:10.1093/gji/ggu048.
    Description: After the 1960 M9.5 Valdivia, Chile earthquake, three types of geodetic observations were made during four time periods at nearby locations. These post-seismic observations were previously explained by post-seismic afterslip on the downdip extension of the 1960 rupture plane. In this study, we demonstrate that the post-seismic observations can be explained alternatively by volumetric viscoelastic relaxation of the asthenosphere mantle. In searching for the best-fitting viscosity model, we invert for two variables, the thickness of the elastic lithosphere, He, and the effective Maxwell decay time of the asthenosphere mantle, TM, assuming a 100-km-thick asthenosphere mantle. The best solutions to fit the observations in four sequential time periods, 1960–1964, 1960–1968, 1965–1973 and 1980–2010, each yield a similar He value of about 65 km but significantly increasing TM values of 0.7, 6, 10 and 80 yr, respectively. We calculate the corresponding viscoelastic Coulomb stress increase since 1960 on the future rupture plane of the 2010 M8.8 Maule, Chile earthquake. The calculated viscoelastic stress increase on the 2010 rupture plane varies gradually from 13.1 bars at the southern end to 0.1 bars at the northern end. In contrast, the stress increase caused by an afterslip model has a similar spatial distribution but slightly smaller values of 0.1–3.2 bars on the 2010 rupture plane.
    Description: This work was supported by a MIT/WHOI Joint Program Student Fellowship and a Graduate Student Fellowship from the WHOI Deep Ocean Exploration Institute (MD), as well as NSF Grant OCE-1141785 and a Deerbrook Foundation Award (JL).
    Keywords: Seismic cycle ; Transient deformation ; Seismicity and tectonics ; Subduction zone processes ; Dynamics: seismotectonics ; South America
    Repository Name: Woods Hole Open Access Server
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  • 3
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    Horizontal gene transfer is a significant driver of gene innovation in dinoflagellates (2014)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Genome Biology and Evolution 5 (2013): 2368-2381, doi:10.1093/gbe/evt179.
    Description: The dinoflagellates are an evolutionarily and ecologically important group of microbial eukaryotes. Previous work suggests that horizontal gene transfer (HGT) is an important source of gene innovation in these organisms. However, dinoflagellate genomes are notoriously large and complex, making genomic investigation of this phenomenon impractical with currently available sequencing technology. Fortunately, de novo transcriptome sequencing and assembly provides an alternative approach for investigating HGT. We sequenced the transcriptome of the dinoflagellate Alexandrium tamarense Group IV to investigate how HGT has contributed to gene innovation in this group. Our comprehensive A. tamarense Group IV gene set was compared with those of 16 other eukaryotic genomes. Ancestral gene content reconstruction of ortholog groups shows that A. tamarense Group IV has the largest number of gene families gained (314–1,563 depending on inference method) relative to all other organisms in the analysis (0–782). Phylogenomic analysis indicates that genes horizontally acquired from bacteria are a significant proportion of this gene influx, as are genes transferred from other eukaryotes either through HGT or endosymbiosis. The dinoflagellates also display curious cases of gene loss associated with mitochondrial metabolism including the entire Complex I of oxidative phosphorylation. Some of these missing genes have been functionally replaced by bacterial and eukaryotic xenologs. The transcriptome of A. tamarense Group IV lends strong support to a growing body of evidence that dinoflagellate genomes are extraordinarily impacted by HGT.
    Description: J.H.W. was supported by the NSF IGERT Program in Comparative Genomics at the University of Arizona (grant number DGE-0654435). This work was supported by grants from the National Science Foundation (grant numbers OCE-0723498, EF-0732440) and funding provided by the BIO5 Institute at the University of Arizona to J.D.H.
    Keywords: Gene innovation ; Alexandrium tamarense Group IV ; Phylogenetic profile ; Phylogenomics ; De novo transcriptome assembly ; Mitochondrial metabolism
    Repository Name: Woods Hole Open Access Server
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  • 4
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    Magnetotelluric data, stable distributions and impropriety: an existential combination (2014)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © Author, 2014. This article is posted here by permission of The Royal Astronomical Society for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 198 (2014): 622-636, doi: 10.1093/gji/ggu121.
    Description: The robust statistical model of a Gaussian core contaminated by outlying data that underlies robust estimation of the magnetotelluric (MT) response function has been re-examined. The residuals from robust estimators are systematically long tailed compared to a distribution based on the Gaussian, and hence are inconsistent with the robust model. Instead, MT data are pervasively described by the alpha stable distribution family whose variance and sometimes mean are undefined. A maximum likelihood estimator (MLE) that exploits the stable nature of MT data is formulated, and its two-stage implementation in which stable parameters are first fit to the data and then the MT responses are solved for is described. The MLE is shown to be inherently robust, but differs from the conventional robust estimator because it is based on a model derived from the data, while robust estimators are ad hoc, being based on the robust model that is inconsistent with actual data. Propriety versus impropriety of the complex MT response was investigated, and a likelihood ratio test for propriety and its null distribution was established. The Cramér-Rao lower bounds for the covariance matrix of proper and improper MT responses were specified. The MLE was applied to exemplar long period and broad-band data sets from South Africa. Both are shown to be significantly stably distributed using the Kolmogorov–Smirnov goodness of fit and Ansari-Bradley non-parametric dispersion tests. Impropriety of the MT responses at both sites is pervasive, hence the improper Cramér-Rao bound was used to estimate the MLE covariance. The MLE is shown to be nearly unbiased and well described by a Gaussian distribution based on bootstrap simulation. The MLE was compared to a conventional robust estimator, establishing that the standard errors of the former are systematically smaller than for the latter and that the standardized differences between them exhibit excursions that are both too frequent and too large to be described by a Gaussian model. This is ascribed to pervasive bias of the robust estimator that is to some degree obscured by their systematically large confidence bounds. Finally, a series of topics for further investigation is proposed.
    Description: This work was supported by NSF grant EAR0809074.
    Keywords: Time series analysis ; Numerical approximations and analysis ; Fractals and multifractals ; Probability distributions ; Magnetotellurics
    Repository Name: Woods Hole Open Access Server
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  • 5
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    Virus infection of Haptolina ericina and Phaeocystis pouchetii implicates evolutionary conservation of programmed cell death induction in marine haptophyte–virus interactions (2014)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Journal of Plankton Research 36 (2014): 943-955, doi:10.1093/plankt/fbu029.
    Description: The mechanisms by which phytoplankton cope with stressors in the marine environment are neither fully characterized nor understood. As viruses are the most abundant entities in the global ocean and represent a strong top-down regulator of phytoplankton abundance and diversity, we sought to characterize the cellular response of two marine haptophytes to virus infection in order to gain more knowledge about the nature and diversity of microalgal responses to this chronic biotic stressor. We infected laboratory cultures of the haptophytes Haptolina ericina and Phaeocystis pouchetii with CeV-01B or PpV-01B dsDNA viruses, respectively, and assessed the extent to which host cellular responses resemble programmed cell death (PCD) through the activation of diagnostic molecular and biochemical markers. Pronounced DNA fragmentation and activation of cysteine aspartate-specific proteases (caspases) were only detected in virus-infected cultures of these phytoplankton. Inhibition of host caspase activity by addition of the pan-caspase inhibitor z-VAD-fmk did not impair virus production in either host–virus system, differentiating it from the Emiliania huxleyi-Coccolithovirus model of haptophyte–virus interactions. Nonetheless, our findings point to a general conservation of PCD-like activation during virus infection in ecologically diverse haptophytes, with the subtle heterogeneity of cell death biochemical responses possibly exerting differential regulation on phytoplankton abundance and diversity.
    Description: Funding to J.L.R, R.-A.S. and A.L. was provided by the Norwegian Research Council for the “VIPMAP” (nr. 186142) and “HAPTODIV” (nr. 190307) projects, and by the European Research Council Advanced Grant ERC-AG-LS8 “Microbial Network Organisation” (MINOS, project number 250254). J.L.R. received a FRIBIO overseas research fellowship from the Norwegian Research Council. K.D.B. and B.V.M. were supported by funding from the United States National Science Foundation (OCE-1061883).
    Keywords: Caspase ; DNA fragmentation ; IETD ; Phycodnaviridae ; z-VAD-fmk ; Haptophyte
    Repository Name: Woods Hole Open Access Server
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  • 6
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    The evolution of the four subunits of voltage-gated calcium channels : ancient roots, increasing complexity, and multiple losses (2014)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Genome Biology and Evolution 6 (2014): 2210-2217, doi:10.1093/gbe/evu177.
    Description: The alpha subunits of voltage-gated calcium channels (Cavs) are large transmembrane proteins responsible for crucial physiological processes in excitable cells. They are assisted by three auxiliary subunits that can modulate their electrical behavior. Little is known about the evolution and roles of the various subunits of Cavs in nonbilaterian animals and in nonanimal lineages. For this reason, we mapped the phyletic distribution of the four channel subunits and reconstructed their phylogeny. Although alpha subunits have deep evolutionary roots as ancient as the split between plants and opistokonths, beta subunits appeared in the last common ancestor of animals and their close-relatives choanoflagellates, gamma subunits are a bilaterian novelty and alpha2/delta subunits appeared in the lineage of Placozoa, Cnidaria, and Bilateria. We note that gene losses were extremely common in the evolution of Cavs, with noticeable losses in multiple clades of subfamilies and also of whole Cav families. As in vertebrates, but not protostomes, Cav channel genes duplicated in Cnidaria. We characterized by in situ hybridization the tissue distribution of alpha subunits in the sea anemone Nematostella vectensis, a nonbilaterian animal possessing all three Cav subfamilies common to Bilateria. We find that some of the alpha subunit subtypes exhibit distinct spatiotemporal expression patterns. Further, all six sea anemone alpha subunit subtypes are conserved in stony corals, which separated from anemones 500 MA. This unexpected conservation together with the expression patterns strongly supports the notion that these subtypes carry unique functional roles.
    Keywords: Voltage-gated calcium channel ; Ion channel ; Cnidaria ; Nematostella vectensis ; Evolution of nervous system
    Repository Name: Woods Hole Open Access Server
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  • 7
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    Multi-events earthquake early warning algorithm using a Bayesian approach (2014)
    Oxford University Press
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    Publication Date: 2014-12-13
    Description: Current earthquake early warning (EEW) systems lack the ability to appropriately handle multiple concurrent earthquakes, which led to many false alarms during the 2011 Tohoku earthquake sequence in Japan. This paper uses a Bayesian probabilistic approach to handle multiple concurrent events for EEW. We implement the theory using a two-step algorithm. First, an efficient approximate Bayesian model class selection scheme is used to estimate the number of concurrent events. Then, the Rao-Blackwellized Importance Sampling method with a sequential proposal probability density function is used to estimate the earthquake parameters, that is hypocentre location, origin time, magnitude and local seismic intensity. A real data example based on 2 months data (2011 March 9–April 30) around the time of the 2011 M 9 Tohoku earthquake is studied to verify the proposed algorithm. Our algorithm results in over 90 per cent reduction in the number of incorrect warnings compared to the existing EEW system operating in Japan.
    Keywords: Seismology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 8
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    Extensive Copy Number Variations in Admixed Indian Population of African Ancestry: Potential Involvement in Adaptation (2014)
    Oxford University Press
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    Publication Date: 2014-12-13
    Description: Admixture mapping has been enormously resourceful in identifying genetic variations linked to phenotypes, adaptation, and diseases. In this study through analysis of copy number variable regions (CNVRs), we report extensive restructuring in the genomes of the recently admixed African-Indian population (OG-W-IP) that inhabits a highly saline environment in Western India. The study included subjects from OG-W-IP (OG), five different Indian and three HapMap populations that were genotyped using Affymetrix version 6.0 arrays. Copy number variations (CNVs) detected using Birdsuite were used to define CNVRs. Population structure with respect to CNVRs was delineated using random forest approach. OG genomes have a surprising excess of CNVs in comparison to other studied populations. Individual ancestry proportions computed using STRUCTURE also reveals a unique genetic component in OGs. Population structure analysis with CNV genotypes indicates OG to be distant from both the African and Indian ancestral populations. Interestingly, it shows genetic proximity with respect to CNVs to only one Indian population IE-W-LP4, which also happens to reside in the same geographical region. We also observe a significant enrichment of molecular processes related to ion binding and receptor activity in genes encompassing OG-specific CNVRs. Our results suggest that retention of CNVRs from ancestral natives and de novo acquisition of CNVRs could accelerate the process of adaptation especially in an extreme environment. Additionally, this population would be enormously useful for dissecting genes and delineating the involvement of CNVs in salt adaptation.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    A catalogue of 2D photometric decompositions in the SDSS-DR7 spectroscopic main galaxy sample: preferred models and systematics (2014)
    Oxford University Press
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    Publication Date: 2014-12-12
    Description: We present a catalogue of 2D, point spread function-corrected de Vacouleurs, Sérsic, de Vacouleurs+Exponential, and Sérsic+Exponential fits of ~7 x 10 5 spectroscopically selected galaxies drawn from the Sloan Digital Sky Survey (SDSS) Data Release 7. Fits are performed for the SDSS r band utilizing the fitting routine galfit and analysis pipeline pymorph . We compare these fits to prior catalogues. Fits are analysed using a physically motivated flagging system. The flags suggest that more than 90 per cent of two-component fits can be used for analysis. We show that the fits follow the expected behaviour for early and late galaxy types. The catalogues provide a robust set of structural and photometric parameters for future galaxy studies. We show that some biases remain in the measurements, e.g. the presence of bars significantly affect the bulge measurements although the bulge ellipticity may be used to separate barred and non-barred galaxies, and about 15 per cent of bulges of two-component fits are also affected by resolution. The catalogues are available in electronic format. We also provide an interface for generating postage stamp images of the 2D model and residual as well as the 1D profile. These images can be generated for a user-uploaded list of galaxies on demand.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 10
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    Bio-Optical Characteristics of the Northern Gulf of California during June 2008 (2014)
    Hindawi
    Details
    Publication Date: 2014-12-08
    Description: Bio-optical variables in the Northern Gulf of California were analyzed using in situ and satellite data obtained during a cruise in June 2008. The study area was divided into three bio-optical regions: Upper Gulf (UG), Northern Gulf (NG), and Great Isles (GI). Each region was characterized according to phytoplankton pigment concentration, phytoplankton and nonpigmented material spectral absorption coefficients, and spectral reflectance. Observed patterns were an indication of the shift in bio-optical conditions from north to south going from turbid and eutrophic waters to mesotrophic ones. Although there was a good agreement between satellite and in situ Chla (RMSE ±33%), an overestimation of in situ Chla was observed. This was partly explained by the presence of nonalgal particles, as well as the influence of desert and continental aerosols, which is generally overcorrected in the standard processing. The UG and NG could be considered as Case  2 waters, but they did exhibit different bio-optical characteristics. This implies that both biological and optical properties should be invoked to better understand water reflectance variability in the study region and its implications for the remote sensing of Chla and biogeochemical processes.
    Print ISSN: 1687-9406
    Electronic ISSN: 1687-9414
    Topics: Geosciences
    Published by Hindawi
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  • 11
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    Stochastic Consensus of Single-Integrator Multiagent Systems with Inherent Nonlinear Dynamics and Measurement Noises in Directed Fixed Topologies (2014)
    Hindawi
    Details
    Publication Date: 2014-12-08
    Description: Consensus of continuous-time single-integrator multiagent systems with inherent nonlinear dynamics and measurement noises is addressed in this paper. The consensus controller is developed for directed interaction topologies. Each agent’s control input is constructed based on its own state and its neighbors’ states corrupted by noises. The control input contains a time-varying consensus gain in order to attenuate the noises. Conditions for ensuring mean square convergence under noisy measurement and asymptotic convergence in the noise-free case are derived. Finally, some simulations were carried out to show the effectiveness of our control law and how it can solve the consensus problem.
    Print ISSN: 1024-123X
    Electronic ISSN: 1563-5147
    Topics: Mathematics , Technology
    Published by Hindawi
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  • 12
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    Phantom Eye Syndrome: A Review of the Literature (2014)
    Hindawi
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    Publication Date: 2014-12-08
    Description: The purpose of this literature review was to describe the main features of phantom eye syndrome in relation to their possible causes, symptoms, treatments, and influence of eye amputation on quality of life of anophthalmic patients. For this, a bibliographical research was performed in Pubmed database using the following terms: “eye amputation,” “eye trauma,” “phantom eye syndrome,” “phantom pain,” and “quality of life,” associated or not. Thirteen studies were selected, besides some relevant references contained in the selected manuscripts and other studies hallowed in the literature. Thus, 56 articles were included in this review. The phantom eye syndrome is defined as any sensation reported by the patient with anophthalmia, originated anophthalmic cavity. In phantom eye syndrome, at least one of these three symptoms has to be present: phantom vision, phantom pain, and phantom sensations. This syndrome has a direct influence on the quality of life of the patients, and psychological support is recommended before and after the amputation of the eyeball as well as aid in the treatment of the syndrome. Therefore, it is suggested that, for more effective treatment of phantom eye syndrome, drug therapy should be associated with psychological approach.
    Electronic ISSN: 1537-744X
    Topics: Natural Sciences in General
    Published by Hindawi
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  • 13
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    Crystal structure of (±)-(4RS,5RS,7SR)-4-[(1RS,2RS,3RS,6RS)-3-benzoyloxy-2-(2-hydroxyethyl)-6-methoxymethoxy-2-methylcyclohexyl]-8,10,10-trimethyl-2-oxo-1,3-dioxaspiro[4.5]dec-8-en-7-yl benzoate benzene monosolvate (2014)
    International Union of Crystallography (IUC)
    Details
    Publication Date: 2014-12-14
    Description: In the title compound, C36H44O10·C6H6, the dioxolane ring adopts an envelope conformation with the C atom bonded to the H atom as the flap, while the cyclohexene and cyclohexane rings are in half-chair and chair conformations, respectively. In the crystal, a pair of O—H...O hydrogen bonds with an R22(26) graph-set motif connect the benzoate molecules into an inversion dimer. The dimers are linked by a weak C—H...O interaction into a tape structure along [01-1]. The benzene molecule links the tapes through C—H...O and C—H...π interactions, forming a sheet parallel to (100).
    Keywords: crystal structurehydrogen bondstaxane skeletonpaclitaxel
    Electronic ISSN: 1600-5368
    Topics: Chemistry and Pharmacology , Geosciences
    Published by International Union of Crystallography (IUC)
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  • 14
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    Crystal structures of isoquinoline–3-chloro-2-nitrobenzoic acid (1/1) and isoquinolinium 4-chloro-2-nitrobenzoate (2014)
    International Union of Crystallography (IUC)
    Details
    Publication Date: 2014-12-14
    Description: In each of the title isomeric compounds, C9H7.3N·C7H3.7ClNO4, (I), and C9H8N·C7H3ClNO4, (II), of isoquinoline with 3-chloro-2-nitrobenzoic acid and 4-chloro-2-nitrobenzoic acid, the two components are linked by a short hydrogen bond between a base N atom and a carboxy O atom. In the hydrogen-bonded unit of (I), the H atom is disordered over two positions with N and O site occupancies of 0.30 (3) and 0.70 (3), respectively, while in (II), an acid–base interaction involving H-atom transfer occurs and the H atom is located at the N site. In the crystal of (I), the acid–base units are connected through C—H...O hydrogen bonds into a tape structure along the b-axis direction. Inversion-related adjacent tapes are further linked through π–π interactions [centroid–centroid distances = 3.6389 (7)–3.7501 (7) Å], forming a layer parallel to (001). In the crystal of (II), the acid–base units are connected through C—H...O hydrogen bonds into a ladder structure along the a-axis direction. The ladders are further linked by another C—H...O hydrogen bond into a layer parallel to (001).
    Keywords: crystal structureshort hydrogen bondchloro- and nitro-substituted benzoic acidisoquinoline
    Electronic ISSN: 1600-5368
    Topics: Chemistry and Pharmacology , Geosciences
    Published by International Union of Crystallography (IUC)
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  • 15
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    Crystal structure of (Z)-2-[(E)-2-benzylidenehydrazin-1-ylidene]-1,2-diphenylethanone (2014)
    International Union of Crystallography (IUC)
    Details
    Publication Date: 2014-12-14
    Description: The title compound, C21H16N2O, has an almost planar (r.m.s. deviation = 0.0074 Å) 1,2-dibenzylidenehydrazine backbone with an approximately orthogonal almost planar (r.m.s. deviation = 0.0368 Å) phenylethanone substituent on one of the imine C atoms. The dihedral angle between the two mean planes is 76.99 (4)°. In the crystal, molecules are linked via C—H...O hydrogen bonds and C—H...π contacts, forming a three-dimensional structure with molecules stacked along the a-axis direction.
    Keywords: crystal structureSchiff baseazinesdimersC—H...π contacts
    Electronic ISSN: 1600-5368
    Topics: Chemistry and Pharmacology , Geosciences
    Published by International Union of Crystallography (IUC)
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  • 16
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    Crystal structure of 5-(4-benzyloxyphenyl)-3-(4-methoxyphenyl)-6-methylcyclohex-2-en-1-one (2014)
    International Union of Crystallography (IUC)
    Details
    Publication Date: 2014-12-14
    Description: The title compound, C27H26O3, crystallized with two independent molecules (A and B) in the asymmetric unit. In molecule A, the plane of the central benzene ring forms dihedral angles of 75.78 (14) and 52.75 (16)° with that of the terminal benzene rings, and the dihedral angle between the planes of the terminal benzene rings is 51.49 (17)°. The corresponding values for molecule B are 75.18 (14), 58.11 (16) and 47.91 (16)°, respectively. The cyclohexene ring adopts an envelope conformation in both molecules, with the C atom to which is attached the central benzene ring as the flap. The crystal packing, is stabilized by C—H...π interactions.
    Keywords: crystal structurecyclohexenecyclcohexen-1-one
    Electronic ISSN: 1600-5368
    Topics: Chemistry and Pharmacology , Geosciences
    Published by International Union of Crystallography (IUC)
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  • 17
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    Crystal structure of 8-[7,8-bis(4-chlorobenzoyl)-7H-cyclopenta[a]acenaphthylen-9-yl]naphthalene-1-carboxylic acid (2014)
    International Union of Crystallography (IUC)
    Details
    Publication Date: 2014-12-14
    Description: The title compound, C40H22Cl2O4, was formed by a Michael–Aldol domino reaction sequence, which coupled acenaphthenequinone with 4-chloroacetophenone in the presence of KOH in methanol. The dihedral angles between the central cyclopenta[a]acenaphthylene fused-ring system (r.m.s. deviation = 0.066 Å) and the 4-chlorobenzoyl rings are 62.25 (10) and 70.19 (10)°. The dihedral angle between the central ring system and the naphthoic acid grouping is 62.46 (7)°. This twisting of the pendant rings facilitates the formation of an intramolecular aromatic π–π stacking interaction between the 4-chlorobenzoyl and naphthoic acid rings, with centroid–centroid distances of 3.4533 (16) and 3.5311 (16) Å, and a C—H...π interaction between one of the H atoms of the central moiety and the 4-chlorobenzoyl ring with an H...π distance of 2.57 Å. In the crystal, carboxylic acid inversion dimers generate R22(8) loops. The dimers are linked by weak C—H...O and C—H...Cl hydrogen bonds and C—H...π interactions, generating a three-dimensional architecture.
    Keywords: crystal structuredomino reactionacenaphthenequinone4-chloroacetophenonehydrogen bonding
    Electronic ISSN: 1600-5368
    Topics: Chemistry and Pharmacology , Geosciences
    Published by International Union of Crystallography (IUC)
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  • 18
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    Crystal structure of (E)-1-(4′-methoxy-[1,1′-biphenyl]-4-yl)-3-(3-nitrophenyl)prop-2-en-1-one (2014)
    International Union of Crystallography (IUC)
    Details
    Publication Date: 2014-12-14
    Description: The title compound, C22H17NO4, crystallizes with two independent molecules (A and B) in the asymmetric unit. Each molecule exists as an E isomer with C—C=C—C torsion angles of −175.69 (17) and −178.41 (17)° in A and B, respectively. In molecule A, the planes of the terminal benzene rings are twisted by an angle of 26.67 (10)°, while the biphenyl unit is non-planar, the dihedral angle between the rings being 30.81 (10)°. The dihedral angle between the nitrophenyl ring and the inner phenyl ring is 6.50 (9)°. The corresponding values in molecule B are 60.61 (9), 31.07 (8) and 31.05 (9)°. In the crystal, molecules are arranged in a head-to-head manner, with the 3-nitrophenyl groups nearly parallel to one another. The A and B molecules are linked to one another via C—H...O hydrogen bonds, forming chains lying parallel to (-320) and enclosing R22(10) and R22(12) ring motifs. The methoxy group in both molecules is positionally disordered with a refined occupancy ratio of 0.979 (4):0.021 (4) for molecule A and 0.55 (4):0.45 (4) for molecule B.
    Keywords: crystal structurechalconesC—H...O hydrogen bondingmain-residue disorder
    Electronic ISSN: 1600-5368
    Topics: Chemistry and Pharmacology , Geosciences
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  • 19
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    Crystal structure of dioxidobis(pentane-2,4-dionato-κ2O,O′)[1-phenyl-3-(pyridin-4-yl)propane-κN]uranium(VI) (2014)
    International Union of Crystallography (IUC)
    Details
    Publication Date: 2014-12-14
    Description: In the title compound, [UO2(C5H7O2)2(C14H15N)], the uranyl(VI) unit ([O=U=O]2+) is coordinated to two acetylacetonate (acac) anions and one 1-phenyl-3-(pyridin-4-yl)propane (ppp) molecule. The geometry around the U atom is UNO6 pentagonal–bipyramidal; two uranyl(VI) O atoms are located at the axial positions, whereas four O atoms from two chelating bidentate acac ligands and one N atom of a ppp ligand form the equatorial plane.
    Keywords: crystal structurepentane-2,4-dionate1-phenyl-3-(pyridin-4-yl)propaneuranium(VI) complex
    Electronic ISSN: 1600-5368
    Topics: Chemistry and Pharmacology , Geosciences
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  • 20
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    Coordination of bis(pyrazol-1-yl)amine to palladium(II): influence of the co-ligands and counter-ions on the molecular and crystal structures (2014)
    International Union of Crystallography (IUC)
    Details
    Publication Date: 2014-12-14
    Description: The structures of a series of complexes with general formula n[Pd(pza)X]Y·mH2O (n = 1, 2; X = Cl, Br, I, N3, NCS; Y = NO3, I, N3, [Pd(SCN)4]; m = 0, 0.5, 1) have been determined, where pza is the tridentate ligand bis[2-(3,5-dimethylpyrazol-1-yl)ethyl]amine, C14H23N5. In all complexes, {bis[2-(3,5-dimethylpyrazol-1-yl-κN2)ethyl]amine-κN}chloridopalladium nitrate, [Pd(pza)Cl]NO3, (1), {bis[2-(3,5-dimethylpyrazol-1-yl-κN2)ethyl]amine-κN}bromidopalladium nitrate, [Pd(pza)Br]NO3, (2), {bis[2-(3,5-dimethylpyrazol-1-yl-κN2)ethyl]amine-κN}iodidopalladium iodide hemihydrate, [Pd(pza)I]I·0.5H2O, (3), azido{bis[2-(3,5-dimethylpyrazol-1-yl-κN2)ethyl]amine-κN}palladium azide monohydrate, [Pd(pza)N3]N3·H2O, (4), and bis[{bis[2-(3,5-dimethylpyrazol-1-yl-κN2)ethyl]amine-κN}(thiocyanato-κN)palladium] tetrakis(thiocyanato-κS)palladate, [Pd(pza)NCS]2[Pd(SCN)4], (5), the [Pd(pza)X]+ complex cation displays a square-planar coordination geometry, and the pza ligand is twisted, approximating twofold rotation symmetry. Although the pza ligand is found with the same conformation along the series, the dihedral angle between pyrazole rings depends on the co-ligand X. This angle span the range 79.0 (3)–88.6 (1)° for the studied complexes. In (3), two complex cations, two I− anions and one water molecule of crystallization are present in the asymmetric unit. In (5), the central amine group of pza is disordered over two positions [occupancy ratio 0.770 (18):0.230 (18)]. The complex [Pd(SCN)4]2− anion of this compound exhibits inversion symmetry and shows the Pd2+ transition metal cation likewise in a square-planar coordination environment. Compound (5) is also a rare occurrence of a non-polymeric compound in which the pseudohalide ligand NCS− behaves both as thiocyanate and isothiocyanate, i.e. is coordinating either through the N atom (in the cation) or the S atom (in the anion).
    Keywords: crystal structurecoordination compoundsbis[2-(3,5-dimethylpyrazol-1-yl)ethyl]amine (pza) ligandbis(pyrazol-1-yl)aminepalladium(II)
    Electronic ISSN: 1600-5368
    Topics: Chemistry and Pharmacology , Geosciences
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  • 21
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    Crystal structure of 1,3-bis(4-methylbenzyl)-1H-1,3-benzimidazol-3-ium bromide monohydrate (2014)
    International Union of Crystallography (IUC)
    Details
    Publication Date: 2014-12-14
    Description: In the title hydrated symetrically substituted 1,3-bis(4-methylbenzyl)benzimidazolium salt, C23H23N2+·Br−·H2O, the dihedral angles between the benzimidazole ring system (r.m.s. deviation = 0.003 Å) and the pendant benzene rings are 73.18 (16) and 77.52 (16)°. Both benzene rings lie to the same side of the benzimidazole ring system, giving the cation an overall U-shape. In the crystal, the cation is linked to the water molecule by a short C—H...O hydrogen bond and the water molecule forms O—H...Br hydrogen bonds. Together, these interactions lead to [010] chains. The packing is consolidated by C—H...Br hydrogen bonds and aromatic π–π stacking interactions [centroid–centroid distances = 3.5401 (17) and 3.8815 (18) Å], generating a three-dimensional network.
    Keywords: crystal structure1,3-bis(4-methylbenzyl)-1H-3,1-benzimidazol-3-ium bromide monohydratebenzimidazolium saltsN-heterocyclic carbeneshydrogen bondsaromatic π–π stacking interactions
    Electronic ISSN: 1600-5368
    Topics: Chemistry and Pharmacology , Geosciences
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  • 22
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    Crystal structure of 6,9-dimethyl-7H-[1,2,4]triazolo[4,3-b][1,2,4]triazepin-8(9H)-one 0.40-hydrate (2014)
    International Union of Crystallography (IUC)
    Details
    Publication Date: 2014-12-14
    Description: In the molecule of the title compound, C7H9N5O·0.40H2O, the seven-membered heterocyclic ring exhibits a boat conformation, whereas the five-membered triazole ring is almost planar (r.m.s. deviation = 0.005 Å). In the crystal, centrosymmetric dimers are linked by pairs of C—H...O hydrogen bonds into dimers, which are further connected via O—H...N and C—H...N hydrogen bonds, forming a three-dimensional network. The structure contains a partially occupied water molecule lying on a twofold axis with an occupancy factor of 0.4.
    Keywords: crystal structure1,2,4-triazepin-8(9H)-onepharmacological and biological activitieshydrogen bonding
    Electronic ISSN: 1600-5368
    Topics: Chemistry and Pharmacology , Geosciences
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  • 23
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    Crystal structure of bis(η5-cyclopentadienyl)(2,3-diethylbutane-1,4-diyl)hafnium(IV) (2014)
    International Union of Crystallography (IUC)
    Details
    Publication Date: 2014-12-14
    Description: The title compound, [Hf(C5H5)2(C8H16)], proves a structural motif of hafnacyclopentane besides the coordination of two cyclopentadienyl ligands in an η5-fashion. The hafnacyclopentane ring has a twist conformation and is substituted by two ethyl groups in the β,β′-positions, which are trans orientated to each other. One cyclopentadienyl ring and one ethyl group are each disordered over two positions with site-occupancy ratios of 0.679 (15):0.321 (15) and 0.702 (18):0.298 (18), respectively.
    Keywords: crystal structurehafnocenefive-membered metallacycle
    Electronic ISSN: 1600-5368
    Topics: Chemistry and Pharmacology , Geosciences
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  • 24
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    Crystal structure of 2-azaniumyl-3-bromo-6-oxo-5,6-dihydropyrido[1,2-a]quinoxalin-11-ium dibromide (2014)
    International Union of Crystallography (IUC)
    Details
    Publication Date: 2014-12-14
    Description: The title salt, C12H10BrN3O2+·2Br−, was synthesized from the reaction of N1,N4-bis(pyridin-2-ylmethylidene)benzene-1,4-diamine and bromine in a methanol solution. All non-H atoms of the 2-azaniumyl-3-bromo-6-oxo-5,6-dihydropyrido[1,2-a]quinoxalin-11-ium cation are nearly coplanar, the maximum deviation being 0.114 (4) Å. In the crystal, the cations and anions are linked through N—H...Br hydrogen bonds and weak C—H...Br interactions, forming a three-dimensional supramolecular architecture. A short Br...Br contact [3.3088 (9) Å] is observed in the crystal.
    Keywords: crystal structurebromidepyrido[1,2-a]quinoxalin-11-iumC—H...Br interactions
    Electronic ISSN: 1600-5368
    Topics: Chemistry and Pharmacology , Geosciences
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  • 25
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    Crystal structure of ethyl 2-[2-((1E)-{(1E)-2-[2-(2-ethoxy-2-oxoethoxy)benzylidene]hydrazin-1-ylidene}methyl)phenoxy]acetate (2014)
    International Union of Crystallography (IUC)
    Details
    Publication Date: 2014-12-14
    Description: The complete molecule of the title compound, C22H24N2O6, is generated by crystallographic inversion symmetry and is approximately planar (r.m.s. deviation of the non-H atoms = 0.134 Å). The packing consists of inter-digitated sheets inclined at 25.9 (4)° to one another and linked by short C—H...O hydrogen bonds.
    Keywords: crystal structureazomethenesbis-phenoxy carboxylate
    Electronic ISSN: 1600-5368
    Topics: Chemistry and Pharmacology , Geosciences
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  • 26
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    Crystal structure of 2,2-dichloro-1-(piperidin-1-yl)butane-1,3-dione (2014)
    International Union of Crystallography (IUC)
    Details
    Publication Date: 2014-12-14
    Description: In the title compound, C9H13Cl2NO2, the piperidine ring shows a chair conformation and the O—C—C—O torsion angle between the carbonyl groups is 183.6 (4)°. In the crystal, molecules are linked into an infinite layer along the ab plane by a bifurcated C—H...O hydrogen bond between the carbonyl O atom adjacent to the methyl group and one of the methylene groups next to nitrogen and an additional hydrogen bond of the C—H...Cl type. These layers are connected into a three-dimensional supramolecular arrangement by O...Cl contacts [2.8979 (12) and 3.1300 (12) Å].
    Keywords: crystal structure2,2-dichloro-1-(piperidin-1-yl)butane-1,3-dionehydrogen bondingO...Cl contacts
    Electronic ISSN: 1600-5368
    Topics: Chemistry and Pharmacology , Geosciences
    Published by International Union of Crystallography (IUC)
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  • 27
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    Crystal structure of (E)-N-(3,4-dimethoxybenzylidene)morpholin-4-amine. Corrigendum (2014)
    International Union of Crystallography (IUC)
    Details
    Publication Date: 2014-12-14
    Description: The list of authors in the paper by Çelikesir et al. [Acta Cryst. (2014), E70, o935] is corrected.
    Electronic ISSN: 1600-5368
    Topics: Chemistry and Pharmacology , Geosciences
    Published by International Union of Crystallography (IUC)
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  • 28
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    Crystal structure of (E)-4-{1-[2-(carbamothioyl)hydrazin-1-ylidene]ethyl}phenyl 4-methylbenzoate (2014)
    International Union of Crystallography (IUC)
    Details
    Publication Date: 2014-12-14
    Description: The asymmetric unit of the title compound, C17H17N3O2S, consists of two independent molecules, A and B, with different conformations: in molecule A, the dihedral angles between the central benzene ring and the pendant tolyl and carbamothioylhydrazono groups are 71.12 (9) and 5.95 (8)°, respectively. The corresponding angles in molecule B are 50.56 (12) and 26.43 (11)°, respectively. Both molecules feature an intramolecular N—H...N hydrogen bond, which closes an S(5) ring. In the crystal, molecules are linked by N—H...O, N—H...S and C—H...O hydrogen bonds, generating a three-dimensional network.
    Keywords: crystal structurethiosemicarbazones derivativesbiological activityhydrogen bondingester
    Electronic ISSN: 1600-5368
    Topics: Chemistry and Pharmacology , Geosciences
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  • 29
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    Crystal structure of (E)-2-[1-(benzo[d][1,3]dioxol-5-yl)ethylidene]-N-methylhydrazine-1-carbothioamide (2014)
    International Union of Crystallography (IUC)
    Details
    Publication Date: 2014-12-14
    Description: In the title compound, C11H13N3O2S, there is a short intramolecular N—H...N contact. The benzo[d][1,3]dioxole ring system is approximately planar (r.m.s. deviation = 0.025 Å) and makes a dihedral angle of 56.83 (6)° with the mean plane of the methylthiosemicarbazone fragment [–N—N—C(=S)—N—C; maximum deviation = 0.1111 (14) Å for the imino N atom]. In the crystal, molecules are linked via pairs of N—H...S hydrogen bonds, forming inversion dimers. The dimers are connected by N—H...S hydrogen bonds into layers parallel to (100). The H atoms of both methyl groups are disordered over two sets of sites and were refined with occupancy ratios of 0.5:0.5 and 0.75:0.25.
    Keywords: crystal structurethiosemiarbazone3′,4′-(methylenedioxy)acetophenone4-methylthiosemicarbazonehydrogen bondingtwo-dimensional network
    Electronic ISSN: 1600-5368
    Topics: Chemistry and Pharmacology , Geosciences
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  • 30
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    The H I-dominated low-surface-brightness galaxy KKR 17 (2014)
    Oxford University Press
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    Publication Date: 2014-12-13
    Description: We present new narrow-band (Hα and [O  iii ]) images and optical spectrophotometry of H  ii regions for a gas-rich low-surface-brightness irregular galaxy, KKR 17. The central surface brightness of the galaxy is μ 0 ( B ) = 24.15 ± 0.03 mag s –2 . The galaxy was detected by the Arecibo Legacy Fast ALFA survey (ALFALFA). Its mass is dominated by neutral hydrogen (H  i ) gas. In contrast, both the stellar masses of the bright H  ii and diffuse stellar regions are small. In addition, the fit to the spectral energy distribution to each region shows the stellar populations of H  ii and diffuse regions are different. The bright H  ii region contains a large fraction of O-type stars, revealing recent strong star formation, whereas the diffuse region is dominated by median age stars with a typical age of ~600 Myr. Using McGaugh's abundance model, we found that the average metallicity of KKR 17 is 12 + (O/H) = 8.0 ± 0.1. The star-formation rate of KKR 17 is 0.21 ± 0.04 M  yr –1 , which is ~1/5 of our Milky Way's. Based on the analysis results for young stellar clusters in the H  ii region, the bright H  ii region has two sub-components with different velocities and metallicities. This may be caused by the outflow of massive stars or merging events. However, the mechanism triggering star formation in the H  ii region is still uncertain.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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    A multiwavelength study of the M dwarf binary YY Geminorum (2014)
    Oxford University Press
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    Publication Date: 2014-12-13
    Description: We review the results of the 1988 multiwavelength campaign on the late-type eclipsing binary YY Geminorum. Observations include: broad-band optical and near-infrared photometry, simultaneous optical and ultraviolet ( IUE ) spectroscopy, X-ray ( Ginga ) and radio (VLA) data. From models fitted to the optical light curves, fundamental physical parameters have been determined together with evidence for transient maculations (spots) located near quadrature longitudes and intermediate latitudes. Eclipses were observed at optical, ultraviolet and radio wavelengths. Significant drops in 6 cm radio emission near the phases of both primary and secondary eclipse indicate relatively compact radio emitting volumes that may lie between the binary components. IUE observations during secondary eclipse are indicative of a uniform chromosphere saturated with Mg  ii emission and an extended volume of Lyα emission. Profile fitting of high-dispersion Hα spectra confirms the chromospheric saturation and indicates significant Hα opacity to heights of a few per cent of the photospheric radius. There is evidence for an enhanced Hα emission region visible near phase 0.25–0.35 which may be associated with a large spot on the primary and with two small optical flares which were also observed at other wavelengths: one in microwave radiation and the other in X-rays. For both flares, L X / L opt is consistent with energy release in closed magnetic structures.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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    How Do Metal Ion Levels Change over Time in Hip Resurfacing Patients? A Cohort Study (2014)
    Hindawi
    Details
    Publication Date: 2014-12-15
    Description: Metal-on-metal hip resurfacing (MOM-HR) is offered as an alternative to traditional hip arthroplasty for young, active adults with advanced osteoarthritis. Nevertheless, concerns remain regarding wear and corrosion of the bearing surfaces and the resulting increase in metal ion levels. We evaluated three cohorts of patients with Birmingham hip resurfacing (BHR) at an average follow-up of 2, 5, and 9 years. We asked whether there would be differences in ion levels between the cohorts and inside the gender. Nineteen patients were prospectively analyzed. The correlation with clinical-radiographic data was also performed. Chromium, cobalt, nickel, and molybdenum concentrations were measured by atomic absorption spectrophotometry. Chromium and cobalt levels demonstrated a tendency to decrease over time. Such tendency was present only in females. An inverse correlation between chromium, implant size, and Harris hip score was present at short term; it disappeared over time together with the decreased ion levels. The prospective analysis showed that, although metal ion levels remained fairly constant within each patient, there was a relatively large variation between subjects, so mean data in this scenario must be interpreted with caution. The chronic high exposure should be carefully considered during implant selection, particularly in young subjects, and a stricter monitoring is mandatory.
    Electronic ISSN: 1537-744X
    Topics: Natural Sciences in General
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    Adsorption of Polyanion onto Large Alpha Alumina Beads with Variably Charged Surface (2014)
    Hindawi
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    Publication Date: 2014-12-16
    Description: Adsorption of strong polyelectrolyte, poly(styrenesulfonate), PSS, of different molecular weights onto large α-Al2O3 beads was systematically investigated as functions of pH and NaCl concentrations. The ultraviolet (UV) absorption spectra of PSS at different pH and salt concentrations confirmed that the structure of PSS is independent of pH. With the change of molecular weight from 70 kg/mol (PSS 70) to 1000 kg/mol (PSS 1000), adsorption amount of PSS increases and proton coadsorption on the surface of α-Al2O3 decreases at given pH and salt concentration. It suggests that higher molecular weight of PSS was less flat conformation than lower one. The adsorption density of PSS 70 and PSS 1000 decreases with decreasing salt concentrations, indicating that both electrostatic and nonelectrostatic interactions are involved. Experimental results of both PSS 70 and PSS 1000 adsorption isotherms onto α-Al2O3 at different pH and salt concentrations can be represented well by two-step adsorption model. The effects of molecular weight and salt concentration are explained by structure of adsorbed PSS onto α-Al2O3. The influence of added SDS on the isotherms is evaluated from the sequential adsorption. The SDS uptake onto α-Al2O3 in the presence of hemimicelles can prevent the adsorption of PSS at low concentration so that adsorption of PSS reduces with preadsorbed SDS.
    Print ISSN: 1687-7985
    Electronic ISSN: 1687-7993
    Topics: Chemistry and Pharmacology , Physics
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    An efficient radiative cooling approximation for use in hydrodynamic simulations (2014)
    Oxford University Press
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    Publication Date: 2014-12-14
    Description: To make relevant predictions about observable emission, hydrodynamical simulation codes must employ schemes that account for radiative losses, but the large dimensionality of accurate radiative transfer schemes is often prohibitive. Stamatellos and collaborators introduced a scheme for smoothed particle hydrodynamics (SPH) simulations based on the notion of polytropic pseudo-clouds that uses only local quantities to estimate cooling rates. The computational approach is extremely efficient and works well in cases close to spherical symmetry, such as in star formation problems. Unfortunately, the method, which takes the local gravitational potential as an input, can be inaccurate when applied to non-spherical configurations, limiting its usefulness when studying discs or stellar collisions, among other situations of interest. Here, we introduce the ‘pressure scale height method,’ which incorporates the fluid pressure scaleheight into the determination of column densities and cooling rates, and show that it produces more accurate results across a wide range of physical scenarios while retaining the computational efficiency of the original method. The tested models include spherical polytropes as well as discs with specified density and temperature profiles. We focus on applying our techniques within an SPH code, although our method can be implemented within any particle-based Lagrangian or grid-based Eulerian hydrodynamic scheme. Our new method may be applied in a broad range of situations, including within the realm of stellar interactions, collisions, and mergers.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 35
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    Massive Conformal Gravity (2014)
    Hindawi
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    Publication Date: 2014-12-15
    Description: We construct a massive theory of gravity that is invariant under conformal transformations. The massive action of the theory depends on the metric tensor and a scalar field, which are considered the only field variables. We find the vacuum field equations of the theory and analyze its weak-field approximation and Newtonian limit.
    Print ISSN: 1687-7357
    Electronic ISSN: 1687-7365
    Topics: Physics
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    Critical Blow-Up and Global Existence for Discrete Nonlinear p-Laplacian Parabolic Equations (2014)
    Hindawi
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    Publication Date: 2014-12-15
    Description: The goal of this paper is to investigate the blow-up and the global existence of the solutions to the discrete p-Laplacian parabolic equation , , , , , depending on the parameters and . Besides, we provide several types of the comparison principles to this equation, which play a key role in the proof of the main theorems. In addition, we finally give some numerical examples which exploit the main results.
    Print ISSN: 1026-0226
    Electronic ISSN: 1607-887X
    Topics: Mathematics
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    A Complex Dynamical Analysis of the Indian Stock Market (2014)
    Hindawi
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    Publication Date: 2014-12-15
    Description: This paper seeks to analyze the dynamical structure of the Indian stock market by considering two major Indian stock market indices, namely, BSE Sensex and CNX Nifty. The recurrence quantification analysis (RQA) is applied on the daily closing data of the two series during the period from January 2, 2002, to October 10, 2013. A Rolling Window of 100 and step size 21 are applied in order to see how both the series behave over time. The analysis based on three RQA measures, namely, % determinism (DET), laminarity (LAM), and trapping time (TT), provides conclusive evidence that the Indian equity market is chaotic in nature. Evidences for phase transition in the Indian equity market around the time of financial crisis are also found.
    Print ISSN: 2090-2123
    Electronic ISSN: 2090-2131
    Topics: Economics
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    Magnetic resonance tomography using elongated transmitter and in-loop receiver arrays for time-efficient 2-D imaging of subsurface aquifer structures (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: Surface nuclear magnetic resonance (surface-NMR) is a promising technique for exploring shallow subsurface aquifer structures. Surface-NMR can be applied in environments that are characterized as a 1-D layered Earth. The technique utilizes a single loop and is referred to as magnetic resonance sounding. The technique referred to as magnetic resonance tomography (MRT) allows complex 2-D aquifer structures to be explored. Currently, MRT requires multiple loops and a roll along measurement scheme, which causes long survey time. We propose a loop layout using an elongated transmitter and an in-loop receiver arrays (ETRA) to conduct a 2-D survey with just one measurement. We present a comprehensive comparison between the new layout and the common approaches based on sensitivity and resolution analyses and show synthetic and field data. The results show that ETRA generates subsurface images at sufficient resolution with significantly lower survey times than other loop layouts.
    Keywords: Geomagnetism, Rock Magnetism and Palaeomagnetism
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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    Integrated velocity field from ground and satellite geodetic techniques: application to Arenal volcano (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-17
    Description: Measurements of ground deformation can be used to identify and interpret geophysical processes occurring at volcanoes. Most studies rely on a single geodetic technique, or fit a geophysical model to the results of multiple geodetic techniques. Here we present a methodology that combines GPS, Total Station measurements and InSAR into a single reference frame to produce an integrated 3-D geodetic velocity surface without any prior geophysical assumptions. The methodology consists of five steps: design of the network, acquisition and processing of the data, spatial integration of the measurements, time series computation and finally the integration of spatial and temporal measurements. The most significant improvements of this method are (1) the reduction of the required field time, (2) the unambiguous detection of outliers, (3) an increased measurement accuracy and (4) the construction of a 3-D geodetic velocity field. We apply this methodology to ongoing motion on Arenal's western flank. Integration of multiple measurement techniques at Arenal volcano revealed a deformation field that is more complex than that described by individual geodetic techniques, yet remains consistent with previous studies. This approach can be applied to volcano monitoring worldwide and has the potential to be extended to incorporate other geodetic techniques and to study transient deformation.
    Keywords: Gravity, Geodesy and Tides
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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    Review of Polymer, Dye-Sensitized, and Hybrid Solar Cells (2014)
    Hindawi
    Details
    Publication Date: 2014-12-15
    Description: The combination of inorganic nanoparticles semiconductor, conjugated polymer, and dye-sensitized in a layer of solar cell is now recognized as potential application in developing flexible, large area, and low cost photovoltaic devices. Several conjugated low bandgap polymers, dyes, and underlayer materials based on the previous studies are quoted in this paper, which can provide guidelines in designing low cost photovoltaic solar cells. All of these materials are designed to help harvest more sunlight in a wider range of the solar spectrum besides enhancing the rate of charge transfer in a device structure. This review focuses on developing solid-state dye-synthesized, polymer, and hybrid solar cells.
    Print ISSN: 1110-662X
    Electronic ISSN: 1687-529X
    Topics: Electrical Engineering, Measurement and Control Technology , Energy, Environment Protection, Nuclear Power Engineering
    Published by Hindawi
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    A Middleware for the Integration of Smart Grid Elements with WSN Based Solutions (2014)
    Hindawi
    Details
    Publication Date: 2014-12-17
    Description: Currently, electricity distributors make use of various types of equipment divided into levels of automation. This automation enables the integration of elements such as Intelligent Electronic Devices (IEDs) to the supervision of the distribution electrical system, but there is not an appropriate environment to increase the scale of these elements. In this context, the smart grid comes with specifications that allow adding new elements to the intelligence of the power grid operation. However, the cost of communication is still an impediment to the scalability of the integration of these elements into the current structure. In this paper, we propose a middleware that optimizes the communication of this integration using wireless sensor networks (WSN). The goal is to ensure a gradual integration of new elements taking advantage of the increase in the number of sensor nodes in the network due to the scalability of the system itself. The conversion solutions have been used to allow easy communication between the WSN and the smart grid system, and we also have used data aggregation and compression techniques to increase the lifetime of the wireless sensor network.
    Print ISSN: 1550-1329
    Electronic ISSN: 1550-1477
    Topics: Electrical Engineering, Measurement and Control Technology
    Published by Hindawi
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    EOQ Model for Deteriorating Items with Stock-Level-Dependent Demand Rate and Order-Quantity-Dependent Trade Credit (2014)
    Hindawi
    Details
    Publication Date: 2014-12-17
    Description: This paper develops a generalized inventory model for exponentially deteriorating items with current-stock-dependent demand rate and permissible delay in payments. In the model, the payment for the item must be made immediately if the order quantity is less than the predetermined quantity; otherwise, a fixed trade credit period is permitted. The maximization of the average profit per unit of time is taken as the inventory system’s objective. The necessary and sufficient conditions and some properties of the optimal solution to the model are developed. Simple solution procedures are proposed to efficiently determine the optimal ordering policies of the considered problem. Numerical example is also presented to illustrate the solution procedures obtained.
    Print ISSN: 1024-123X
    Electronic ISSN: 1563-5147
    Topics: Mathematics , Technology
    Published by Hindawi
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    Galactic outflow and diffuse gas properties at z 〉= 1 using different baryonic feedback models (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-17
    Description: We measure and quantify properties of galactic outflows and diffuse gas at z ≥ 1 in cosmological hydrodynamical simulations. Our novel subresolution model, Multi-Phase Particle Integrator (MUPPI), implements supernova feedback using fully local gas properties, where the wind velocity and mass loading are not given as input. We find the following trends at z  = 2 by analysing central galaxies having a stellar mass higher than 10 9 M . The outflow velocity and mass outflow rate ( $\dot{M}_{\rm out}$ ) exhibit positive correlations with galaxy mass and with the star formation rate (SFR). However, most of the relations present a large scatter. The outflow mass loading factor () is between 0.2 and 10. The comparison effective model generates a constant outflow velocity, and a negative correlation of with halo mass. The number fraction of galaxies where outflow is detected decreases at lower redshifts, but remains more than 80 per cent over z  = 1–5. The outflow velocity correlation with SFR becomes flatter at z  = 1, and displays a negative correlation with halo mass in massive galaxies. Our study demonstrates that both the MUPPI and effective models produce significant outflows at ~1/10 of the virial radius; at the same time shows that the properties of outflows generated can be different from the input speed and mass loading in the effective model. Our MUPPI model, using local properties of gas in the subresolution recipe, is able to develop galactic outflows whose properties correlate with global galaxy properties , and consistent with observations.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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    Multiplex sequencing of pooled mitochondrial genomes--a crucial step toward biodiversity analysis using mito-metagenomics (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-17
    Description: The advent in high-throughput-sequencing (HTS) technologies has revolutionized conventional biodiversity research by enabling parallel capture of DNA sequences possessing species-level diagnosis. However, polymerase chain reaction (PCR)-based implementation is biased by the efficiency of primer binding across lineages of organisms. A PCR-free HTS approach will alleviate this artefact and significantly improve upon the multi-locus method utilizing full mitogenomes. Here we developed a novel multiplex sequencing and assembly pipeline allowing for simultaneous acquisition of full mitogenomes from pooled animals without DNA enrichment or amplification. By concatenating assemblies from three de novo assemblers, we obtained high-quality mitogenomes for all 49 pooled taxa, with 36 species 〉15 kb and the remaining 〉10 kb, including 20 complete mitogenomes and nearly all protein coding genes (99.6%). The assembly quality was carefully validated with Sanger sequences, reference genomes and conservativeness of protein coding genes across taxa. The new method was effective even for closely related taxa, e.g. three Drosophila spp., demonstrating its broad utility for biodiversity research and mito-phylogenomics. Finally, the in silico simulation showed that by recruiting multiple mito-loci, taxon detection was improved at a fixed sequencing depth. Combined, these results demonstrate the plausibility of a multi-locus mito-metagenomics approach as the next phase of the current single-locus metabarcoding method.
    Keywords: Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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    Easy quantitative assessment of genome editing by sequence trace decomposition (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-17
    Description: The efficacy and the mutation spectrum of genome editing methods can vary substantially depending on the targeted sequence. A simple, quick assay to accurately characterize and quantify the induced mutations is therefore needed. Here we present TIDE, a method for this purpose that requires only a pair of PCR reactions and two standard capillary sequencing runs. The sequence traces are then analyzed by a specially developed decomposition algorithm that identifies the major induced mutations in the projected editing site and accurately determines their frequency in a cell population. This method is cost-effective and quick, and it provides much more detailed information than current enzyme-based assays. An interactive web tool for automated decomposition of the sequence traces is available. TIDE greatly facilitates the testing and rational design of genome editing strategies.
    Keywords: Targeted gene modification
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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    Accurate ab initio prediction of NMR chemical shifts of nucleic acids and nucleic acids/protein complexes (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-17
    Description: NMR chemical shift predictions based on empirical methods are nowadays indispensable tools during resonance assignment and 3D structure calculation of proteins. However, owing to the very limited statistical data basis, such methods are still in their infancy in the field of nucleic acids, especially when non-canonical structures and nucleic acid complexes are considered. Here, we present an ab initio approach for predicting proton chemical shifts of arbitrary nucleic acid structures based on state-of-the-art fragment-based quantum chemical calculations. We tested our prediction method on a diverse set of nucleic acid structures including double-stranded DNA, hairpins, DNA/protein complexes and chemically-modified DNA. Overall, our quantum chemical calculations yield highly/very accurate predictions with mean absolute deviations of 0.3–0.6 ppm and correlation coefficients ( r 2 ) usually above 0.9. This will allow for identifying misassignments and validating 3D structures. Furthermore, our calculations reveal that chemical shifts of protons involved in hydrogen bonding are predicted significantly less accurately. This is in part caused by insufficient inclusion of solvation effects. However, it also points toward shortcomings of current force fields used for structure determination of nucleic acids. Our quantum chemical calculations could therefore provide input for force field optimization.
    Keywords: Nucleic acid structure, Protein-nucleic acid interaction
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    Topics: Biology
    Published by Oxford University Press
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    Synthesis, biophysical properties and biological activity of second generation antisense oligonucleotides containing chiral phosphorothioate linkages (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-17
    Description: Bicyclic oxazaphospholidine monomers were used to prepare a series of phosphorothioate (PS)-modified gapmer antisense oligonucleotides (ASOs) with control of the chirality of each of the PS linkages within the 10-base gap. The stereoselectivity was determined to be 98% for each coupling. The objective of this work was to study how PS chirality influences biophysical and biological properties of the ASO including binding affinity ( T m ), nuclease stability, activity in vitro and in vivo , RNase H activation and cleavage patterns (both human and E. coli ) in a gapmer context. Compounds that had nine or more Sp-linkages in the gap were found to be poorly active in vitro , while compounds with uniform Rp-gaps exhibited activity very similar to that of the stereo-random parent ASOs. Conversely, when tested in vivo , the full Rp-gap compound was found to be quickly metabolized resulting in low activity. A total of 31 ASOs were prepared with control of the PS chirally of each linkage within the gap in an attempt to identify favorable Rp/Sp positions. We conclude that a mix of Rp and Sp is required to achieve a balance between good activity and nuclease stability.
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    Topics: Biology
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    qDNAmod: a statistical model-based tool to reveal intercellular heterogeneity of DNA modification from SMRT sequencing data (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-17
    Description: In an isogenic cell population, phenotypic heterogeneity among individual cells is common and critical for survival of the population under different environment conditions. DNA modification is an important epigenetic factor that can regulate phenotypic heterogeneity. The single molecule real-time (SMRT) sequencing technology provides a unique platform for detecting a wide range of DNA modifications, including N6-methyladenine (6-mA), N4-methylcytosine (4-mC) and 5-methylcytosine (5-mC). Here we present qDNAmod, a novel bioinformatic tool for genome-wide quantitative profiling of intercellular heterogeneity of DNA modification from SMRT sequencing data. It is capable of estimating proportion of isogenic haploid cells, in which the same loci of the genome are differentially modified. We tested the reliability of qDNAmod with the SMRT sequencing data of Streptococcus pneumoniae strain ST556. qDNAmod detected extensive intercellular heterogeneity of DNA methylation (6-mA) in a clonal population of ST556. Subsequent biochemical analyses revealed that the recognition sequences of two type I restriction–modification (R-M) systems are responsible for the intercellular heterogeneity of DNA methylation initially identified by qDNAmod. qDNAmod thus represents a valuable tool for studying intercellular phenotypic heterogeneity from genome-wide DNA modification.
    Keywords: Nucleic acid modification, Computational Methods
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    Topics: Biology
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    Constrained transcription factor spacing is prevalent and important for transcriptional control of mouse blood cells (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-17
    Description: Combinatorial transcription factor (TF) binding is essential for cell-type-specific gene regulation. However, much remains to be learned about the mechanisms of TF interactions, including to what extent constrained spacing and orientation of interacting TFs are critical for regulatory element activity. To examine the relative prevalence of the ‘enhanceosome’ versus the ‘TF collective’ model of combinatorial TF binding, a comprehensive analysis of TF binding site sequences in large scale datasets is necessary. We developed a motif-pair discovery pipeline to identify motif co-occurrences with preferential distance(s) between motifs in TF-bound regions. Utilizing a compendium of 289 mouse haematopoietic TF ChIP-seq datasets, we demonstrate that haematopoietic-related motif-pairs commonly occur with highly conserved constrained spacing and orientation between motifs. Furthermore, motif clustering revealed specific associations for both heterotypic and homotypic motif-pairs with particular haematopoietic cell types. We also showed that disrupting the spacing between motif-pairs significantly affects transcriptional activity in a well-known motif-pair—E-box and GATA, and in two previously unknown motif-pairs with constrained spacing—Ets and Homeobox as well as Ets and E-box. In this study, we provide evidence for widespread sequence-specific TF pair interaction with DNA that conforms to the ‘enhanceosome’ model, and furthermore identify associations between specific haematopoietic cell-types and motif-pairs.
    Keywords: Computational Methods
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    Topics: Biology
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    In silico prediction of splice-altering single nucleotide variants in the human genome (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-17
    Description: In silico tools have been developed to predict variants that may have an impact on pre-mRNA splicing. The major limitation of the application of these tools to basic research and clinical practice is the difficulty in interpreting the output. Most tools only predict potential splice sites given a DNA sequence without measuring splicing signal changes caused by a variant. Another limitation is the lack of large-scale evaluation studies of these tools. We compared eight in silico tools on 2959 single nucleotide variants within splicing consensus regions (scSNVs) using receiver operating characteristic analysis. The Position Weight Matrix model and MaxEntScan outperformed other methods. Two ensemble learning methods, adaptive boosting and random forests, were used to construct models that take advantage of individual methods. Both models further improved prediction, with outputs of directly interpretable prediction scores. We applied our ensemble scores to scSNVs from the Catalogue of Somatic Mutations in Cancer database. Analysis showed that predicted splice-altering scSNVs are enriched in recurrent scSNVs and known cancer genes. We pre-computed our ensemble scores for all potential scSNVs across the human genome, providing a whole genome level resource for identifying splice-altering scSNVs discovered from large-scale sequencing studies.
    Keywords: RNA characterisation and manipulation, Computational Methods
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    Topics: Biology
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    AGO2 and SETDB1 cooperate in promoter-targeted transcriptional silencing of the androgen receptor gene (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: In mammals, RNA interference is primarily a post-transcriptional mechanism. Evidence has accumulated for additional role in transcriptional gene silencing (TGS) but the question for a good paradigm for small interfering antigene RNA (agRNA)-induced chromatin modification remains unanswered. Here, we show that SETDB1, a histone H3-lysine 9 (H3K9)-specific methyltransferase, cooperates with Argonaute-2 (AGO2) and plays an essential role in agRNA-induced TGS. The androgen receptor ( AR ) gene was transcriptionally silenced by agRNA targeted to its promoter, and we show that this repression was mitigated by knockdown of SETDB1 or AGO2 . Chromatin immunoprecipitation demonstrated that agRNA-driven AGO2 was first targeted to the AR promoter, followed by SETDB1. SIN3A and HDAC1/2, the components of the SIN3-HDAC complex, immunoprecipitated with SETDB1, and localized at the agRNA-targeted promoter. Agreeing with the presence of SETDB1, trimethyl-H3K9 was enriched in the AR promoter. Both EZH2 and trimethyl-H3K27 were also present in the targeted locus; accordingly, EZH2 immunoprecipitated with SETDB1. DNA methylation level was not significantly changed, suggesting the absence of de novo methylating activity in agRNA-induced AR promoter. Our results demonstrate that SETDB1, together with AGO2, plays an essential role in TGS through recruiting chromatin remodeler and/or other modifiers, consequently creating a repressive chromatin milieu at the targeted promoter.
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    Topics: Biology
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    The TCF C-clamp DNA binding domain expands the Wnt transcriptome via alternative target recognition (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: LEF/TCFs direct the final step in Wnt/β-catenin signalling by recruiting β-catenin to genes for activation of transcription. Ancient, non-vertebrate TCFs contain two DNA binding domains, a High Mobility Group box for recognition of the Wnt Response Element (WRE; 5'-CTTTGWWS-3') and the C-clamp domain for recognition of the GC-rich Helper motif (5'-RCCGCC-3'). Two vertebrate TCFs (TCF-1/TCF7 and TCF-4/TCF7L2) use the C-clamp as an alternatively spliced domain to regulate cell-cycle progression, but how the C-clamp influences TCF binding and activity genome-wide is not known. Here, we used a doxycycline inducible system with ChIP-seq to assess how the C-clamp influences human TCF1 binding genome-wide. Metabolic pulse-labeling of nascent RNA with 4'Thiouridine was used with RNA-seq to connect binding to the Wnt transcriptome. We find that the C-clamp enables targeting to a greater number of gene loci for stronger occupancy and transcription regulation. The C-clamp uses Helper sites concurrently with WREs for gene targeting, but it also targets TCF1 to sites that do not have readily identifiable canonical WREs. The coupled ChIP-seq/4'Thiouridine-seq analysis identified new Wnt target genes, including additional regulators of cell proliferation. Thus, C-clamp containing isoforms of TCFs are potent transcriptional regulators with an expanded transcriptome directed by C-clamp-Helper site interactions.
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    Inference of interactions between chromatin modifiers and histone modifications: from ChIP-Seq data to chromatin-signaling (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: Chromatin modifiers and histone modifications are components of a chromatin-signaling network involved in transcription and its regulation. The interactions between chromatin modifiers and histone modifications are often unknown, are based on the analysis of few genes or are studied in vitro . Here, we apply computational methods to recover interactions between chromatin modifiers and histone modifications from genome-wide ChIP-Seq data. These interactions provide a high-confidence backbone of the chromatin-signaling network. Many recovered interactions have literature support; others provide hypotheses about yet unknown interactions. We experimentally verified two of these predicted interactions, leading to a link between H4K20me1 and members of the Polycomb Repressive Complexes 1 and 2. Our results suggest that our computationally derived interactions are likely to lead to novel biological insights required to establish the connectivity of the chromatin-signaling network involved in transcription and its regulation.
    Keywords: Genomics
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    Profiling small RNA reveals multimodal substructural signals in a Boltzmann ensemble (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: As the biomedical impact of small RNAs grows, so does the need to understand competing structural alternatives for regions of functional interest. Suboptimal structure analysis provides significantly more RNA base pairing information than a single minimum free energy prediction. Yet computational enhancements like Boltzmann sampling have not been fully adopted by experimentalists since identifying meaningful patterns in this data can be challenging. Profiling is a novel approach to mining RNA suboptimal structure data which makes the power of ensemble-based analysis accessible in a stable and reliable way. Balancing abstraction and specificity, profiling identifies significant combinations of base pairs which dominate low-energy RNA secondary structures. By design, critical similarities and differences are highlighted, yielding crucial information for molecular biologists. The code is freely available via http://gtfold.sourceforge.net/profiling.html .
    Keywords: Nucleic acid structure, Computational Methods
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    EDITORIAL: NAR AWARDS 2014 (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
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    DNA cleavage by CgII and NgoAVII requires interaction between N- and R-proteins and extensive nucleotide hydrolysis (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: The stress-sensitive restriction-modification (RM) system CglI from Corynebacterium glutamicum and the homologous NgoAVII RM system from Neisseria gonorrhoeae FA1090 are composed of three genes: a DNA methyltransferase (M.CglI and M.NgoAVII), a putative restriction endonuclease (R.CglI and R.NgoAVII, or R-proteins) and a predicted DEAD-family helicase/ATPase (N.CglI and N.NgoAVII or N-proteins). Here we report a biochemical characterization of the R- and N-proteins. Size-exclusion chromatography and SAXS experiments reveal that the isolated R.CglI, R.NgoAVII and N.CglI proteins form homodimers, while N.NgoAVII is a monomer in solution. Moreover, the R.CglI and N.CglI proteins assemble in a complex with R 2 N 2 stoichiometry. Next, we show that N-proteins have ATPase activity that is dependent on double-stranded DNA and is stimulated by the R-proteins. Functional ATPase activity and extensive ATP hydrolysis (~170 ATP/s/monomer) are required for site-specific DNA cleavage by R-proteins. We show that ATP-dependent DNA cleavage by R-proteins occurs at fixed positions (6–7 nucleotides) downstream of the asymmetric recognition sequence 5'-GCCGC-3'. Despite similarities to both Type I and II restriction endonucleases, the CglI and NgoAVII enzymes may employ a unique catalytic mechanism for DNA cleavage.
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    Diverse cell stresses induce unique patterns of tRNA up- and down-regulation: tRNA-seq for quantifying changes in tRNA copy number (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: Emerging evidence points to roles for tRNA modifications and tRNA abundance in cellular stress responses. While isolated instances of stress-induced tRNA degradation have been reported, we sought to assess the effects of stress on tRNA levels at a systems level. To this end, we developed a next-generation sequencing method that exploits the paucity of ribonucleoside modifications at the 3'-end of tRNAs to quantify changes in all cellular tRNA molecules. Application of this tRNA-seq method to Saccharomyces cerevisiae identified all 76 expressed unique tRNA species out of 295 coded in the yeast genome, including all isoacceptor variants, with highly precise relative (fold-change) quantification of tRNAs. In studies of stress-induced changes in tRNA levels, we found that oxidation (H 2 O 2 ) and alkylation (methylmethane sulfonate, MMS) stresses induced nearly identical patterns of up- and down-regulation for 58 tRNAs. However, 18 tRNAs showed opposing changes for the stresses, which parallels our observation of signature reprogramming of tRNA modifications caused by H 2 O 2 and MMS. Further, stress-induced degradation was limited to only a small proportion of a few tRNA species. With tRNA-seq applicable to any organism, these results suggest that translational control of stress response involves a contribution from tRNA abundance.
    Keywords: Nucleic acid modification, Transcriptome Mapping - Monitoring Gene Expression
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    Rad51/Dmc1 paralogs and mediators oppose DNA helicases to limit hybrid DNA formation and promote crossovers during meiotic recombination (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: During meiosis programmed DNA double-strand breaks (DSBs) are repaired by homologous recombination using the sister chromatid or the homologous chromosome (homolog) as a template. This repair results in crossover (CO) and non-crossover (NCO) recombinants. Only CO formation between homologs provides the physical linkages guiding correct chromosome segregation, which are essential to produce healthy gametes. The factors that determine the CO/NCO decision are still poorly understood. Using Schizosaccharomyces pombe as a model we show that the Rad51/Dmc1-paralog complexes Rad55-Rad57 and Rdl1-Rlp1-Sws1 together with Swi5-Sfr1 play a major role in antagonizing both the FANCM-family DNA helicase/translocase Fml1 and the RecQ-type DNA helicase Rqh1 to limit hybrid DNA formation and promote Mus81-Eme1-dependent COs. A common attribute of these protein complexes is an ability to stabilize the Rad51/Dmc1 nucleoprotein filament, and we propose that it is this property that imposes constraints on which enzymes gain access to the recombination intermediate, thereby controlling the manner in which it is processed and resolved.
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    Landscape of target:guide homology effects on Cas9-mediated cleavage (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: To study target sequence specificity, selectivity, and reaction kinetics of Streptococcus pyogenes Cas9 activity, we challenged libraries of random variant targets with purified Cas9::guide RNA complexes in vitro . Cleavage kinetics were nonlinear, with a burst of initial activity followed by slower sustained cleavage. Consistent with other recent analyses of Cas9 sequence specificity, we observe considerable (albeit incomplete) impairment of cleavage for targets mutated in the PAM sequence or in ‘seed’ sequences matching the proximal 8 bp of the guide. A second target region requiring close homology was located at the other end of the guide::target duplex (positions 13–18 relative to the PAM). Sequences flanking the guide+PAM region had measurable (albeit modest) effects on cleavage. In addition, the first-base Guanine constraint commonly imposed by gRNA expression systems has little effect on overall cleavage efficiency. Taken together, these studies provide an in vitro understanding of the complexities of Cas9–gRNA interaction and cleavage beyond the general paradigm of site determination based on the ‘seed’ sequence and PAM.
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    Identification of tri-phosphatase activity in the biogenesis of retroviral microRNAs and RNAP III-generated shRNAs (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-17
    Description: Transcripts possessing a 5'-triphosphate are a hallmark of viral transcription and can trigger the host antiviral response. 5'-triphosphates are also found on common host transcripts transcribed by RNA polymerase III (RNAP III), yet how these transcripts remain non-immunostimulatory is incompletely understood. Most microRNAs (miRNAs) are 5'-monophosphorylated as a result of sequential endonucleolytic processing by Drosha and Dicer from longer RNA polymerase II (RNAP II)-transcribed primary transcripts. In contrast, bovine leukemia virus (BLV) expresses subgenomic RNAP III transcripts that give rise to miRNAs independent of Drosha processing. Here, we demonstrate that each BLV pre-miRNA is directly transcribed by RNAP III from individual, compact RNAP III type II genes. Thus, similar to manmade RNAP III-generated short hairpin RNAs (shRNAs), the BLV pre-miRNAs are initially 5'-triphosphorylated. Nonetheless, the derivative 5p miRNAs and shRNA-generated 5p small RNAs (sRNAs) possess a 5'-monophosphate. Our enzymatic characterization and small RNA sequencing data demonstrate that BLV 5p miRNAs are co-terminal with 5'-triphosphorylated miRNA precursors (pre-miRNAs). Thus, these results identify a 5'-tri-phosphatase activity that is involved in the biogenesis of BLV miRNAs and shRNA-generated sRNAs. This work advances our understanding of retroviral miRNA and shRNA biogenesis and may have implications regarding the immunostimulatory capacity of RNAP III transcripts.
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    A bottom-up characterization of transfer functions for synthetic biology designs: lessons from enzymology (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: Within the field of synthetic biology, a rational design of genetic parts should include a causal understanding of their input-output responses—the so-called transfer function—and how to tune them. However, a commonly adopted strategy is to fit data to Hill-shaped curves without considering the underlying molecular mechanisms. Here we provide a novel mathematical formalization that allows prediction of the global behavior of a synthetic device by considering the actual information from the involved biological parts. This is achieved by adopting an enzymology-like framework, where transfer functions are described in terms of their input affinity constant and maximal response. As a proof of concept, we characterize a set of Lux homoserine-lactone-inducible genetic devices with different levels of Lux receptor and signal molecule. Our model fits the experimental results and predicts the impact of the receptor's ribosome-binding site strength, as a tunable parameter that affects gene expression. The evolutionary implications are outlined.
    Keywords: Synthetic Biology and Assembly Cloning, Computational Methods
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    Crystal structure of the R-protein of the multisubunit ATP-dependent restriction endonuclease NgoAVII (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: The restriction endonuclease (REase) NgoAVII is composed of two proteins, R.NgoAVII and N.NgoAVII, and shares features of both Type II restriction enzymes and Type I/III ATP-dependent restriction enzymes (see accompanying paper Zaremba et al. , 2014). Here we present crystal structures of the R.NgoAVII apo-protein and the R.NgoAVII C-terminal domain bound to a specific DNA. R.NgoAVII is composed of two domains: an N-terminal nucleolytic PLD domain; and a C-terminal B3-like DNA-binding domain identified previously in BfiI and EcoRII REases, and in plant transcription factors. Structural comparison of the B3-like domains of R.NgoAVII, EcoRII, BfiI and the plant transcription factors revealed a conserved DNA-binding surface comprised of N- and C-arms that together grip the DNA. The C-arms of R.NgoAVII, EcoRII, BfiI and plant B3 domains are similar in size, but the R.NgoAVII N-arm which makes the majority of the contacts to the target site is much longer. The overall structures of R.NgoAVII and BfiI are similar; however, whilst BfiI has stand-alone catalytic activity, R.NgoAVII requires an auxiliary cognate N.NgoAVII protein and ATP hydrolysis in order to cleave DNA at the target site. The structures we present will help formulate future experiments to explore the molecular mechanisms of intersubunit crosstalk that control DNA cleavage by R.NgoAVII and related endonucleases.
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    Synergetic regulation of translational reading-frame switch by ligand-responsive RNAs in mammalian cells (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: Distinct translational initiation mechanisms between prokaryotes and eukaryotes limit the exploitation of prokaryotic riboswitch repertoire for regulatory RNA circuit construction in mammalian application. Here, we explored programmed ribosomal frameshifting (PRF) as the regulatory gene expression platform for engineered ligand-responsive RNA devices in higher eukaryotes. Regulation was enabled by designed ligand-dependent conformational rearrangements of the two cis-acting RNA motifs of opposite activity in -1 PRF. Particularly, RNA elements responsive to trans-acting ligands can be tailored to modify co-translational RNA refolding dynamics of a hairpin upstream of frameshifting site to achieve reversible and adjustable -1 PRF attenuating activity. Combined with a ligand-responsive stimulator, synthetic RNA devices for synergetic translational-elongation control of gene expression can be constructed. Due to the similarity between co-transcriptional RNA hairpin folding and co-translational RNA hairpin refolding, the RNA-responsive ligand repertoire provided in prokaryotic systems thus becomes accessible to gene-regulatory circuit construction for synthetic biology application in mammalian cells.
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    DNA repair inhibition by UVA photoactivated fluoroquinolones and vemurafenib (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: Cutaneous photosensitization is a common side effect of drug treatment and can be associated with an increased skin cancer risk. The immunosuppressant azathioprine, the fluoroquinolone antibiotics and vemurafenib—a BRAF inhibitor used to treat metastatic melanoma—are all recognized clinical photosensitizers. We have compared the effects of UVA radiation on cultured human cells treated with 6-thioguanine (6-TG, a DNA-embedded azathioprine surrogate), the fluoroquinolones ciprofloxacin and ofloxacin and vemurafenib. Despite widely different structures and modes of action, each of these drugs potentiated UVA cytotoxicity. UVA photoactivation of 6-TG, ciprofloxacin and ofloxacin was associated with the generation of singlet oxygen that caused extensive protein oxidation. In particular, these treatments were associated with damage to DNA repair proteins that reduced the efficiency of nucleotide excision repair. Although vemurafenib was also highly phototoxic to cultured cells, its effects were less dependent on singlet oxygen. Highly toxic combinations of vemurafenib and UVA caused little protein carbonylation but were nevertheless inhibitory to nucleotide excision repair. Thus, for three different classes of drugs, photosensitization by at least two distinct mechanisms is associated with reduced protection against potentially mutagenic and carcinogenic DNA damage.
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    Replication-guided nucleosome packing and nucleosome breathing expedite the formation of dense arrays (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: The first level of genome packaging in eukaryotic cells involves the formation of dense nucleosome arrays, with DNA coverage near 90% in yeasts. How cells achieve such high coverage within a short time, e.g. after DNA replication, remains poorly understood. It is known that random sequential adsorption of impenetrable particles on a line reaches high density extremely slowly, due to a jamming phenomenon. The nucleosome-shifting action of remodeling enzymes has been proposed as a mechanism to resolve such jams. Here, we suggest two biophysical mechanisms which assist rapid filling of DNA with nucleosomes, and we quantitatively characterize these mechanisms within mathematical models. First, we show that the ‘softness’ of nucleosomes, due to nucleosome breathing and stepwise nucleosome assembly, significantly alters the filling behavior, speeding up the process relative to ‘hard’ particles with fixed, mutually exclusive DNA footprints. Second, we explore model scenarios in which the progression of the replication fork could eliminate nucleosome jamming, either by rapid filling in its wake or via memory of the parental nucleosome positions. Taken together, our results suggest that biophysical effects promote rapid nucleosome filling, making the reassembly of densely packed nucleosomes after DNA replication a simpler task for cells than was previously thought.
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    Loss of loop adenines alters human telomere d[AG3(TTAG3)3] quadruplex folding (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: Abasic (AP) lesions are the most frequent type of damages occurring in cellular DNA. Here we describe the conformational effects of AP sites substituted for 2'-deoxyadenosine in the first ( ap7 ), second ( ap13 ) or third ( ap19 ) loop of the quadruplex formed in K + by the human telomere DNA 5'-d[AG 3 (TTAG 3 ) 3 ]. CD spectra and electrophoresis reveal that the presence of AP sites does not hinder the formation of intramolecular quadruplexes. NMR spectra show that the structural heterogeneity is substantially reduced in ap7 and ap19 as compared to that in the wild-type. These two ( ap7 and ap19 ) sequences are shown to adopt the hybrid-1 and hybrid-2 quadruplex topology, respectively, with AP site located in a propeller-like loop. All three studied sequences transform easily into parallel quadruplex in dehydrating ethanol solution. Thus, the AP site in any loop region facilitates the formation of the propeller loop. Substitution of all adenines by AP sites stabilizes the parallel quadruplex even in the absence of ethanol. Whereas guanines are the major determinants of quadruplex stability, the presence or absence of loop adenines substantially influences quadruplex folding. The naturally occurring adenine-lacking sites in the human telomere DNA can change the quadruplex topology in vivo with potentially vital biological consequences.
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    Specific minor groove solvation is a crucial determinant of DNA binding site recognition (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: The DNA sequence preferences of nearly all sequence specific DNA binding proteins are influenced by the identities of bases that are not directly contacted by protein. Discrimination between non-contacted base sequences is commonly based on the differential abilities of DNA sequences to allow narrowing of the DNA minor groove. However, the factors that govern the propensity of minor groove narrowing are not completely understood. Here we show that the differential abilities of various DNA sequences to support formation of a highly ordered and stable minor groove solvation network are a key determinant of non-contacted base recognition by a sequence-specific binding protein. In addition, disrupting the solvent network in the non-contacted region of the binding site alters the protein's ability to recognize contacted base sequences at positions 5–6 bases away. This observation suggests that DNA solvent interactions link contacted and non-contacted base recognition by the protein.
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    The topology of Stein fillable manifolds in high dimensions I (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: We give a bordism-theoretic characterization of those closed almost contact $(2q{+ }1)$ -manifolds (with $q\geq 2$ ) that admit a Stein fillable contact structure. Our method is to apply Eliashberg's $h$ -principle for Stein manifolds in the setting of Kreck's modified surgery. As an application, we show that any simply connected almost contact 7-manifold with torsion-free second homotopy group is Stein fillable. We also discuss the Stein fillability of exotic spheres and examine subcritical Stein fillability.
    Print ISSN: 0024-6115
    Electronic ISSN: 1460-244X
    Topics: Mathematics
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    A vanishing result for a Casson-type instanton invariant (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: Casson-type invariants emerging from Donaldson theory over certain negative-definite four-manifolds were recently suggested by Teleman. These are defined by an algebraic count of points in a zero-dimensional moduli space of flat instantons. Motivated by the cobordism programme of proving Witten's conjecture, we use a moduli space of ${\rm PU}(2)$ Seiberg–Witten monopoles to exhibit an oriented one-dimensional cobordism of the instanton moduli space to the empty space. The Casson-type invariant must therefore vanish.
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    A fourth-order model for MEMS with clamped boundary conditions (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: The dynamical and stationary behaviors of a fourth-order equation in the unit ball with clamped boundary conditions and a singular reaction term are investigated. The equation arises in the modeling of microelectromechanical systems and includes a positive voltage parameter $\lambda$ . It is shown that there is a threshold value $\lambda _* 〉 0$ of the voltage parameter such that no radially symmetric stationary solution exists for $\lambda 〉 \lambda _* $ , while at least two such solutions exist for $\lambda \in (0,\lambda _* )$ . Local and global well-posedness results are obtained for the corresponding hyperbolic and parabolic evolution problems as well as the occurrence of finite time singularities when $\lambda 〉 \lambda _* $ .
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    Topics: Mathematics
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    Methods, Diagnostic Criteria, Cutoff Points, and Prevalence of Sarcopenia among Older People (2014)
    Hindawi
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    Publication Date: 2014-12-17
    Description: Aim. To identify methods, index, diagnostic criteria, and corresponding cutoff points used to estimate the prevalence of sarcopenia in older people in different countries. Methods. A systematic review was carried out in accordance with PRISMA Statement. The search encompassed the MEDLINE and LILACS databases and was executed during March 2012 using the keyword sarcopenia. Results. A total of 671 studies were identified by the search strategy, and 30 meet all inclusion criteria. Specifically for dual-X-ray absorptiometry, prevalence ranged from 2.2% to 95% in men and from 0.1% to 33.9% in women. For bioelectrical impedance analysis, the range was from 6.2% to 85.4% in men and 2.8% to 23.6% in women. Regarding anthropometric and computed tomography, prevalence rates were, respectively, 14.1% and 55.9%. Conclusions. Heterogeneity in prevalence of sarcopenia was identified, due to diagnostic method choice, cutoff points, and, characteristics of the population as well as reference population. These factors should be considered in research designs to enable comparison and validation of results. Despite the limitations of most studies that indicated high prevalence rates, the results indicate the need for early detection of this syndrome.
    Electronic ISSN: 1537-744X
    Topics: Natural Sciences in General
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    Development, Characterization, and Pharmacodynamic Evaluation of Hydrochlorothiazide Loaded Self-Nanoemulsifying Drug Delivery Systems (2014)
    Hindawi
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    Publication Date: 2014-12-17
    Description: The objective of the current work was to develop optimized self-nanoemulsifying drug delivery systems (SNEDDS) and evaluate their in vitro and in vivo performance. The research comprised various studies which includes solubility studies in various vehicles, pseudoternary phase diagram construction, and preparation and characterization of SNEDDS along with in vitro dissolution and in vivo pharmacodynamic profiling. Based on dissolution profile, a remarkable increase in rate of dissolution was observed in comparison with plain drug and marketed formulation. Optimized SNEDDS formulation was composed of Capmul MCM (19.17% w/w), Tween 80 (57.5% w/w), Transcutol P (12.7% w/w), and HCT (4.17% w/w). In vivo pharmacodynamic evaluation in Wistar rats showed considerable increase in pharmacological effect of HCT by SNEDDS formulation as compared with plain HCT.
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    Evolutionary Optimization Algorithms for Sunlight-Based Positioning Sensor Networks (2014)
    Hindawi
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    Publication Date: 2014-12-18
    Description: The sunlight intensity-based global positioning system (SGPS) is able to geolocate outdoor objects by means of the sunlight intensity detection. This paper presents the integration of SGPS into a sensor network in order to improve the overall accuracy using evolutionary algorithms. Another contribution of the paper is to theoretically solve both global and relative positioning of the sensors composing the network within the same framework without satellite-based GPS technology. Results show that this approach is promising and has potential to be improved further.
    Print ISSN: 1550-1329
    Electronic ISSN: 1550-1477
    Topics: Electrical Engineering, Measurement and Control Technology
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    5 G WiFi Signal-Based Indoor Localization System Using Cluster -Nearest Neighbor Algorithm (2014)
    Hindawi
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    Publication Date: 2014-12-18
    Description: Indoor localization based on existent WiFi signal strength is becoming more and more prevalent and ubiquitous. Unfortunately, the WiFi received signal strength (RSS) is susceptible by multipath, signal attenuation, and environmental changes, which is the major challenge for accurate indoor localization. To overcome these limitations, we propose the cluster -nearest neighbor (KNN) algorithm with 5 G WiFi signal to reduce the environmental interference and improve the localization performance without additional equipment. In this paper, we propose three approaches to improve the performance of localization algorithm. For one thing, we reduce the computation effort based on the coarse localization algorithm. For another, according to the detailed analysis of the 2.4 G and 5 G signal fluctuation, we expand the real-time measurement RSS before matching the fingerprint map. More importantly, we select the optimal nearest neighbor points based on the proposed cluster KNN algorithm. We have implemented the proposed algorithm and evaluated the performance with existent popular algorithms. Experimental results demonstrate that the proposed algorithm can effectively improve localization accuracy and exhibit superior performance in terms of localization stabilization and computation effort.
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    Topics: Electrical Engineering, Measurement and Control Technology
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    Magnetic flux of progenitor stars sets gamma-ray burst luminosity and variability (2014)
    Oxford University Press
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    Publication Date: 2014-12-18
    Description: Long-duration gamma-ray bursts (GRBs) are thought to come from the core collapse of Wolf–Rayet stars. Whereas their stellar masses M * have a rather narrow distribution, the population of GRBs is very diverse, with gamma-ray luminosities L spanning several orders of magnitude. This suggests the existence of a ‘hidden’ stellar variable whose burst-to-burst variation leads to a spread in L . Whatever this hidden variable is, its variation should not noticeably affect the shape of GRB light curves, which display a constant luminosity (in a time-average sense) followed by a sharp drop at the end of the burst seen with Swift /XRT. We argue that such a hidden variable is progenitor star's large-scale magnetic flux. Shortly after the core collapse, most of stellar magnetic flux accumulates near the black hole (BH) and remains there. The flux extracts BH rotational energy and powers jets of roughly a constant luminosity, L j . However, once BH mass accretion rate $\dot{M}$ falls below ~ L j / c 2 , the flux becomes dynamically important and diffuses outwards, with the jet luminosity set by the rapidly declining mass accretion rate, $L_{\rm j}\sim \dot{M}c^2$ . This provides a potential explanation for the sharp end of GRBs and the universal shape of their light curves. During the GRB, gas infall translates spatial variation of stellar magnetic flux into temporal variation of L j . We make use of the deviations from constancy in L j to perform stellar magnetic flux ‘tomography’. Using this method, we infer the presence of magnetized tori in the outer layers of progenitor stars for GRB 920513 and GRB 940210.
    Print ISSN: 0035-8711
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    Stability Analysis of a Car-Following Model on Two Lanes (2014)
    Hindawi
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    Publication Date: 2014-12-18
    Description: Considering lateral influence from adjacent lane, an improved car-following model is developed in this paper. Then linear and nonlinear stability analyses are carried out. The modified Korteweg-de Vries (MKdV) equation is derived with the kink-antikink soliton solution. Numerical simulations are implemented and the result shows good consistency with theoretical study.
    Print ISSN: 1024-123X
    Electronic ISSN: 1563-5147
    Topics: Mathematics , Technology
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    The Improved Kriging Interpolation Algorithm for Local Underwater Terrain Based on Fractal Compensation (2014)
    Hindawi
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    Publication Date: 2014-12-18
    Description: The interpolation-reconstruction of local underwater terrain using the underwater digital terrain map (UDTM) is an important step for building an underwater terrain matching unit and directly affects the accuracy of underwater terrain matching navigation. The Kriging method is often used in terrain interpolation, but, with this method, the local terrain features are often lost. Therefore, the accuracy cannot meet the requirements of practical application. Analysis of the geographical features is performed on the basis of the randomness and self-similarity of underwater terrain. We extract the fractal features of local underwater terrain with the fractal Brownian motion model, compensating for the possible errors of the Kriging method with fractal theory. We then put forward an improved Kriging interpolation method based on this fractal compensation. Interpolation-reconstruction tests show that the method can simulate the real underwater terrain features well and that it has good usability.
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    Blind foreground subtraction for intensity mapping experiments (2014)
    Oxford University Press
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    Publication Date: 2014-12-18
    Description: We make use of a large set of fast simulations of an intensity mapping experiment with characteristics similar to those expected of the Square Kilometre Array in order to study the viability and limits of blind foreground subtraction techniques. In particular, we consider three different approaches: polynomial fitting, principal component analysis (PCA) and independent component analysis (ICA). We review the motivations and algorithms for the three methods, and show that they can all be described, using the same mathematical framework, as different approaches to the blind source separation problem. We study the efficiency of foreground subtraction both in the angular and radial (frequency) directions, as well as the dependence of this efficiency on different instrumental and modelling parameters. For well-behaved foregrounds and instrumental effects, we find that foreground subtraction can be successful to a reasonable level on most scales of interest. We also quantify the effect that the cleaning has on the recovered signal and power spectra. Interestingly, we find that the three methods yield quantitatively similar results, with PCA and ICA being almost equivalent.
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    Hot gas in massive haloes drives both mass quenching and environment quenching (2014)
    Oxford University Press
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    Publication Date: 2014-12-18
    Description: Observed galaxies with high stellar masses or in dense environments have low specific star formation rates, i.e. they are quenched. Based on cosmological hydrodynamic simulations that include a prescription where quenching occurs in regions dominated by hot (〉10 5.4  K) gas, we argue that this hot gas quenching in haloes 〉10 12 M drives both mass quenching (i.e. central quenching) and environment quenching (i.e. satellite quenching). These simulations reproduce a broad range of locally observed trends among quenching, halo mass, stellar mass, environment, and distance to halo centre. Mass quenching is independent of environment because ~10 12 –10 13 M ‘mass quenching haloes’ inhabit a large range of environments. On the other hand, environment quenching is independent of stellar mass because galaxies of all stellar masses may live in dense environments as satellites of groups and clusters. As in observations, the quenched fraction of satellites increases with halo mass and decreases with distance to the centre of the group or cluster. We investigate pre-processing in group haloes, ejected former satellites, and hot gas that extends beyond the virial radius. The agreement of our model with key observational trends suggests that hot gas in massive haloes plays a leading role in quenching low-redshift galaxies.
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    Observations of hydroxyl in early-type galaxies (2014)
    Oxford University Press
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    Publication Date: 2014-12-18
    Description: We used Arecibo Observatory and the Green Bank Telescope to observe OH in 12 early-type galaxies with known reservoirs of dense gas. We present three new detections of OH in absorption in the 1667 MHz line. One objective of our survey was to find evidence of molecular outflows, but our sensitivity and the strength of the OH absorption were insufficient to detect outflows. The detected sources have infrared luminosities and dust temperatures among the lowest of any galaxy detected in OH absorption. The ratio L HCN / L CO , a measure of the dense gas fraction in galaxies, is a powerful selector of OH megamasers for galaxies with high infrared luminosity. In early-type galaxies, which have much lower infrared luminosities, L HCN / L CO is also a promising tool for discovering OH, but in absorption rather than in maser emission. In addition to dense molecular gas, a radio continuum source and a favourable line of sight to the observer are likely key factors in detecting OH absorbers.
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    Low-end mass function of the arches cluster (2014)
    Oxford University Press
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    Publication Date: 2014-12-18
    Description: The initial mass function (IMF) of the Arches cluster, which was formed a few million years ago in the harsh environment of the Galactic Centre (GC), has long been a target of interest to those who study the GC and the theory of star formation. The distinct star-forming conditions in the GC might have caused the cluster to have a shallower slope or an elevated lower mass cutoff in its IMF. But its mass function (MF) has been revealed only down to 1–2 M (the lower limit of resolved stars), and the low-end MF of the Arches is still unknown. To estimate the unresolved part of the Arches MF, we have devised a novel photometric method that involves the histogram of pixel intensities in the observed image, which contains information on the unresolved, faint stars. By comparing the pixel intensity histograms (PIHs) of numerous artificial images constructed from model IMFs with the observed PIH, we find that the best-fitting model IMF for the Arches cluster has a cutoff mass less than or similar to 0.1 M and a shape very close to that of the Kroupa MF. Our findings imply that the IMF of the Arches cluster is similar to those found in the Galactic disc.
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    Development and Characterization of Poly(1-vinylpyrrolidone-co-vinyl acetate) Copolymer Based Polymer Electrolytes (2014)
    Hindawi
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    Publication Date: 2014-11-06
    Description: Gel polymer electrolytes (GPEs) are developed using poly(1-vinylpyrrolidone-co-vinyl acetate) [P(VP-co-VAc)] as the host polymer, lithium bis(trifluoromethane) sulfonimide [LiTFSI] as the lithium salt and ionic liquid, and 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide [EMImTFSI] by using solution casting technique. The effect of ionic liquid on ionic conductivity is studied and the optimum ionic conductivity at room temperature is found to be 2.14 × 10−6 S cm−1 for sample containing 25 wt% of EMImTFSI. The temperature dependence of ionic conductivity from 303 K to 353 K exhibits Arrhenius plot behaviour. The thermal stability of the polymer electrolyte system is studied by using thermogravimetric analysis (TGA) while the structural and morphological properties of the polymer electrolyte is studied by using Fourier transform infrared (FTIR) spectroscopy and X-ray diffraction analysis (XRD), respectively.
    Electronic ISSN: 1537-744X
    Topics: Natural Sciences in General
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    Antimetastatic and Anti-Inflammatory Potentials of Essential Oil from Edible Ocimum sanctum Leaves (2014)
    Hindawi
    Details
    Publication Date: 2014-11-06
    Description: Antimetastatic and anti-inflammatory activities of Ocimum sanctum essential oil (OSEO) have been assessed in this study. OSEO at the concentration of 250 μg/mL and above showed a significant () decrease in the number of migrated cancer cells. In addition, OSEO at concentration of 250 μg/mL and above suppressed MMP-9 activity in lipopolysaccharide (LPS) induced inflammatory cells. A dose-dependent downregulation of MMP-9 expression was observed with the treatment of OSEO compared to the control. Our findings indicate that OSEO has both antimetastatic and anti-inflammatory potentials, advocating further investigation for clinical applications in the treatment of inflammation associated cancer.
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    Topics: Natural Sciences in General
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    Implant-Related Infection in the Tibia: Surgical Revision Strategy with Vancomycin Cement (2014)
    Hindawi
    Details
    Publication Date: 2014-11-06
    Description: The development of a deep wound infection in the presence of internal hardware presents a clinical dilemma. The purpose of the present study was to evaluate the treatment outcomes of vancomycin cement with other advances of surgical techniques for implant-related infection (IRI) in the tibia. This study included 217 consecutive patients who had sustained IRI of the tibia. Of them, 152 patients had soft tissue defects and the internal hardware was exposed. Repeated debridement and negative pressure assisted closure were used. All the infected internal hardware was removed. External fixations and flaps were used. Custom-made vancomycin cement was inserted into the dead space of the wounds and left in site for a month. The follow-up was from 12 months to 108 months, averaging 37.5 months. For all the 217 patients, the general osteomyelitis healing rate and bone union rate were 86.6% and 97.2%, respectively. This study shows high rates of healing of IRI in the tibia if the new advances of surgery could be effectively combined into the treatment strategy with vancomycin cement as an important treatment.
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    Antioxidative Activities and Active Compounds of Extracts from Catalpa Plant Leaves (2014)
    Hindawi
    Details
    Publication Date: 2014-11-06
    Description: In order to screen the Catalpa plant with high antioxidant activity and confirm the corresponding active fractions from Catalpa ovata G. Don, C. fargesii Bur., and C. bungei C. A. Mey., total flavonoid contents and antioxidant activities of the extracts/fractions of Catalpa plant leaves were determined. The determined total flavonoid content and antioxidant activity were used as assessment criteria. Those compounds with antioxidant activity were isolated with silica gel column chromatography and ODS column chromatography. Our results showed that the total flavonoid content in C. bungei C. A. Mey. (30.07 mg/g·DW) was the highest, followed by those in C. fargesii Bur. (25.55 mg/g·DW) and C. ovata G. Don (24.96 mg/g·DW). According to the determination results of total flavonoid content and antioxidant activity in 3 clones of leaves of C. bungei C. A. Mey., the total flavonoid content and antioxidant activity in crude extracts from C. bungei C. A. Mey. 6 (CA6) leaves were the highest. Moreover, the results showed that the total flavonoid content and antioxidant activities of ethyl acetate (EA) fraction in ethanol crude extracts in CA6 leaves were the highest, followed by n-butanol, petroleum ether (PE), and water fractions. Two flavonoid compounds with antioxidant activity were firstly isolated based on EA fraction. The two compounds were luteolin (1) and apigenin (2), respectively.
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    A Lectin from Dioclea violacea Interacts with Midgut Surface of Lutzomyia migonei, Unlike Its Homologues, Cratylia floribunda Lectin and Canavalia gladiata Lectin (2014)
    Hindawi
    Details
    Publication Date: 2014-11-06
    Description: Leishmaniasis is a vector-borne disease transmitted by phlebotomine sand fly. Susceptibility and refractoriness to Leishmania depend on the outcome of multiple interactions that take place within the sand fly gut. Promastigote attachment to sand fly midgut epithelium is essential to avoid being excreted together with the digested blood meal. Promastigote and gut sand fly surface glycans are important ligands in this attachment. The purpose of the present study was to evaluate the interaction of three lectins isolated from leguminous seeds (Diocleinae subtribe), D-glucose and D-mannose-binding, with glycans on Lutzomyia migonei midgut. To study this interaction the lectins were labeled with FITC and a fluorescence assay was performed. The results showed that only Dioclea violacea lectin (DVL) was able to interact with midgut glycans, unlike Cratylia floribunda lectin (CFL) and Canavalia gladiata lectin (CGL). Furthermore, when DVL was blocked with D-mannose the interaction was inhibited. Differences of spatial arrangement of residues and volume of carbohydrate recognition domain (CRD) may be the cause of the fine specificity of DVL for glycans in the surface on Lu. migonei midgut. The findings in this study showed the presence of glycans in the midgut with glucose/mannose residues in its composition and these residues may be important in interaction between Lu. migonei midgut and Leishmania.
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    Burden and Depressive Symptoms Associated with Adult-Child Caregiving for Individuals with Heart Failure (2014)
    Hindawi
    Details
    Publication Date: 2014-11-06
    Description: Background. The primary purpose of this study was to investigate adult-child caregiver burden in heart failure (HF) patients. Secondary purpose of the study was to identify the possible influencing factors for caregiver burden and depressive symptoms in a young adult-child caregiver group. Methods. A total of 138 adult-child caregivers and 138 patients with HF participated in this study. Caregivers’ burden, depressive symptoms, and anxiety levels were assessed by using Zarit Caregiver Burden Scale (ZCBS), Beck Depression Inventory, and State-Trait Anxiety Inventory, respectively. Results. The mean ZCBS scores of the female caregivers were significantly higher than male caregivers. Approximately one-third of the adult-child caregivers had at least mild depressive symptoms. Caregivers with higher depressive symptoms had higher levels of caregiver burden. There were positive correlations between caregiving time, severity of depressive symptoms, and perceived caregiver burden. There was a negative correlation between education level of caregivers and perceived caregiver burden. Age, socioeconomic level, and marital status of patients were affecting factors for depressive symptoms in caregivers. Among caregiver characteristics, gender, marital status, and ZCBS scores seem to influence the depression in caregivers. Conclusions. The study findings suggest significant levels of burden and depressive symptoms even in adult-child caregivers of HF patients.
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    Intrinsic Apoptosis Pathway in Fallopian Tube Epithelial Cells Induced by Cladribine (2014)
    Hindawi
    Details
    Publication Date: 2014-11-06
    Description: Cladribine is a purine nucleoside analog which initiates the apoptotic mechanism within cells. Moreover, the available data confirms that cladribine, with the participation of the p53 protein, as well as the proapoptotic proteins from the Bcl-2 family, also induces the activation of the intrinsic apoptosis pathway. However, while there has been a lot of research devoted to the effect of cladribine on lymphatic system cells, little is known about the impact of cladribine on the reproductive system. The aim of our study was to evaluate apoptosis in oviduct epithelial cells sourced from 15 different female rats. In so doing, the sections were stained with caspases 3, 9, and 8. Results suggest that cladribine also induces apoptosis in the oviduct epithelial cells by way of the intrinsic pathway. Indeed, the discontinuing of the administration of cladribine leads to a reduction in the amount of apoptotic cells in the oviduct epithelium.
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    Consequences of Lethal-Whole-Body Gamma Radiation and Possible Ameliorative Role of Melatonin (2014)
    Hindawi
    Details
    Publication Date: 2014-11-06
    Description: Gamma radiation induces the generation of free radicals, leading to serious cellular damages in biological systems. Radioprotectors act as prophylactic agents that are administered to shield normal cells and tissues from the deleterious effects of radiation. Melatonin synergistically acts as an immune-stimulator and antioxidant. We investigated the possible radioprotective role of melatonin (100 mg/kg i.p.) against lethal-whole-body radiation- (10 Gy) induced sickness, body weight loss, and mortality in rats. Results of the present study suggest that exposure to lethal-whole-body radiation incurred mortality, body weight loss, and apoptosis and it also depleted the immunity and the antioxidant status of the rats. Our results show that melatonin pretreatment provides protection against radiation induced mortality, oxidative stress, and immune-suppression. The melatonin pretreated irradiated rats showed less change in body weight as compared to radiation only group. On the other hand, melatonin appeared to have another radioprotective role, suggesting that melatonin may reduce apoptosis through a caspase-3-mediated pathway by blocking caspase-3 activity.
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    BitPAl: a bit-parallel, general integer-scoring sequence alignment algorithm (2014)
    Oxford University Press
    Details
    Publication Date: 2014-11-07
    Description: Motivation: Mapping of high-throughput sequencing data and other bulk sequence comparison applications have motivated a search for high-efficiency sequence alignment algorithms. The bit-parallel approach represents individual cells in an alignment scoring matrix as bits in computer words and emulates the calculation of scores by a series of logic operations composed of AND, OR, XOR, complement, shift and addition. Bit-parallelism has been successfully applied to the longest common subsequence (LCS) and edit-distance problems, producing fast algorithms in practice. Results: We have developed BitPAl, a bit-parallel algorithm for general, integer-scoring global alignment. Integer-scoring schemes assign integer weights for match, mismatch and insertion/deletion. The BitPAl method uses structural properties in the relationship between adjacent scores in the scoring matrix to construct classes of efficient algorithms, each designed for a particular set of weights. In timed tests, we show that BitPAl runs 7–25 times faster than a standard iterative algorithm. Availability and implementation: Source code is freely available for download at http://lobstah.bu.edu/BitPAl/BitPAl.html . BitPAl is implemented in C and runs on all major operating systems. Contact : jloving@bu.edu or yhernand@bu.edu or gbenson@bu.edu Supplementary information : Supplementary data are available at Bioinformatics online.
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    gCUP: rapid GPU-based HIV-1 co-receptor usage prediction for next-generation sequencing (2014)
    Oxford University Press
    Details
    Publication Date: 2014-11-07
    Description: : Next-generation sequencing (NGS) has a large potential in HIV diagnostics, and genotypic prediction models have been developed and successfully tested in the recent years. However, albeit being highly accurate, these computational models lack computational efficiency to reach their full potential. In this study, we demonstrate the use of graphics processing units (GPUs) in combination with a computational prediction model for HIV tropism. Our new model named gCUP, parallelized and optimized for GPU, is highly accurate and can classify 〉175 000 sequences per second on an NVIDIA GeForce GTX 460. The computational efficiency of our new model is the next step to enable NGS technologies to reach clinical significance in HIV diagnostics. Moreover, our approach is not limited to HIV tropism prediction, but can also be easily adapted to other settings, e.g. drug resistance prediction. Availability and implementation: The source code can be downloaded at http://www.heiderlab.de Contact: d.heider@wz-straubing.de
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    Fast construction of FM-index for long sequence reads (2014)
    Oxford University Press
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    Publication Date: 2014-11-07
    Description: : We present a new method to incrementally construct the FM-index for both short and long sequence reads, up to the size of a genome. It is the first algorithm that can build the index while implicitly sorting the sequences in the reverse (complement) lexicographical order without a separate sorting step. The implementation is among the fastest for indexing short reads and the only one that practically works for reads of averaged kilobases in length. Availability and implementation: https://github.com/lh3/ropebwt2 Contact: hengli@broadinstitute.org
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    AliView: a fast and lightweight alignment viewer and editor for large datasets (2014)
    Oxford University Press
    Details
    Publication Date: 2014-11-07
    Description: : AliView is an alignment viewer and editor designed to meet the requirements of next-generation sequencing era phylogenetic datasets. AliView handles alignments of unlimited size in the formats most commonly used, i.e. FASTA, Phylip, Nexus, Clustal and MSF. The intuitive graphical interface makes it easy to inspect, sort, delete, merge and realign sequences as part of the manual filtering process of large datasets. AliView also works as an easy-to-use alignment editor for small as well as large datasets. Availability and implementation: AliView is released as open-source software under the GNU General Public License, version 3.0 (GPLv3), and is available at GitHub ( www.github.com/AliView ). The program is cross-platform and extensively tested on Linux, Mac OS X and Windows systems. Downloads and help are available at http://ormbunkar.se/aliview Contact: anders.larsson@ebc.uu.se Supplementary information: Supplementary data are available at Bioinformatics online.
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    Trowel: a fast and accurate error correction module for Illumina sequencing reads (2014)
    Oxford University Press
    Details
    Publication Date: 2014-11-07
    Description: Motivation: The ability to accurately read the order of nucleotides in DNA and RNA is fundamental for modern biology. Errors in next-generation sequencing can lead to many artifacts, from erroneous genome assemblies to mistaken inferences about RNA editing. Uneven coverage in datasets also contributes to false corrections. Result: We introduce Trowel, a massively parallelized and highly efficient error correction module for Illumina read data. Trowel both corrects erroneous base calls and boosts base qualities based on the k -mer spectrum. With high-quality k -mers and relevant base information, Trowel achieves high accuracy for different short read sequencing applications.The latency in the data path has been significantly reduced because of efficient data access and data structures. In performance evaluations, Trowel was highly competitive with other tools regardless of coverage, genome size read length and fragment size. Availability and implementation: Trowel is written in C++ and is provided under the General Public License v3.0 (GPLv3). It is available at http://trowel-ec.sourceforge.net . Contact: euncheon.lim@tue.mpg.de or weigel@tue.mpg.de Supplementary information: Supplementary data are available at Bioinformatics online.
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    MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers (2014)
    Oxford University Press
    Details
    Publication Date: 2014-11-07
    Description: : The application of protein–protein docking in large-scale interactome analysis is a major challenge in structural bioinformatics and requires huge computing resources. In this work, we present MEGADOCK 4.0, an FFT-based docking software that makes extensive use of recent heterogeneous supercomputers and shows powerful, scalable performance of 〉97% strong scaling. Availability and Implementation: MEGADOCK 4.0 is written in C++ with OpenMPI and NVIDIA CUDA 5.0 (or later) and is freely available to all academic and non-profit users at: http://www.bi.cs.titech.ac.jp/megadock . Contact: akiyama@cs.titech.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online
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    Detection of active transcription factor binding sites with the combination of DNase hypersensitivity and histone modifications (2014)
    Oxford University Press
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    Publication Date: 2014-11-07
    Description: Motivation: The identification of active transcriptional regulatory elements is crucial to understand regulatory networks driving cellular processes such as cell development and the onset of diseases. It has recently been shown that chromatin structure information, such as DNase I hypersensitivity (DHS) or histone modifications, significantly improves cell-specific predictions of transcription factor binding sites. However, no method has so far successfully combined both DHS and histone modification data to perform active binding site prediction. Results: We propose here a method based on hidden Markov models to integrate DHS and histone modifications occupancy for the detection of open chromatin regions and active binding sites. We have created a framework that includes treatment of genomic signals, model training and genome-wide application. In a comparative analysis, our method obtained a good trade-off between sensitivity versus specificity and superior area under the curve statistics than competing methods. Moreover, our technique does not require further training or sequence information to generate binding location predictions. Therefore, the method can be easily applied on new cell types and allow flexible downstream analysis such as de novo motif finding. Availability and implementation: Our framework is available as part of the Regulatory Genomics Toolbox. The software information and all benchmarking data are available at http://costalab.org/wp/dh-hmm . Contact: ivan.costa@rwth-aachen.de or eduardo.gusmao@rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
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    A method for de novo nucleic acid diagnostic target discovery (2014)
    Oxford University Press
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    Publication Date: 2014-11-07
    Description: Motivation: A proper target or marker is essential in any diagnosis (e.g. an infection or cancer). An ideal diagnostic target should be both conserved in and unique to the pathogen. Currently, these targets can only be identified manually, which is time-consuming and usually error-prone. Because of the increasingly frequent occurrences of emerging epidemics and multidrug-resistant ‘superbugs’, a rapid diagnostic target identification process is needed. Results: A new method that can identify uniquely conserved regions (UCRs) as candidate diagnostic targets for a selected group of organisms solely from their genomic sequences has been developed and successfully tested. Using a sequence-indexing algorithm to identify UCRs and a k -mer integer-mapping model for computational efficiency, this method has successfully identified UCRs within the bacteria domain for 15 test groups, including pathogenic, probiotic, commensal and extremophilic bacterial species or strains. Based on the identified UCRs, new diagnostic primer sets were designed, and their specificity and efficiency were tested by polymerase chain reaction amplifications from both pure isolates and samples containing mixed cultures. Availability and implementation: The UCRs identified for the 15 bacterial species are now freely available at http://ucr.synblex.com . The source code of the programs used in this study is accessible at http://ucr.synblex.com/bacterialIdSourceCode.d.zip Contact: yazhousun@synblex.com Supplementary Information: Supplementary data are available at Bioinformatics online.
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    Quantitative method for the assignment of hinge and shear mechanism in protein domain movements (2014)
    Oxford University Press
    Details
    Publication Date: 2014-11-07
    Description: Motivation: A popular method for classification of protein domain movements apportions them into two main types: those with a ‘hinge’ mechanism and those with a ‘shear’ mechanism. The intuitive assignment of domain movements to these classes has limited the number of domain movements that can be classified in this way. Furthermore, whether intended or not, the term ‘shear’ is often interpreted to mean a relative translation of the domains. Results: Numbers of occurrences of four different types of residue contact changes between domains were optimally combined by logistic regression using the training set of domain movements intuitively classified as hinge and shear to produce a predictor for hinge and shear. This predictor was applied to give a 10-fold increase in the number of examples over the number previously available with a high degree of precision. It is shown that overall a relative translation of domains is rare, and that there is no difference between hinge and shear mechanisms in this respect. However, the shear set contains significantly more examples of domains having a relative twisting movement than the hinge set. The angle of rotation is also shown to be a good discriminator between the two mechanisms. Availability and implementation: Results are free to browse at http://www.cmp.uea.ac.uk/dyndom/interface/ . Contact: sjh@cmp.uea.ac.uk . Supplementary information: Supplementary data are available at Bioinformatics online.
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    Network-based analysis of genotype-phenotype correlations between different inheritance modes (2014)
    Oxford University Press
    Details
    Publication Date: 2014-11-07
    Description: Motivation: Recent studies on human disease have revealed that aberrant interaction between proteins probably underlies a substantial number of human genetic diseases. This suggests a need to investigate disease inheritance mode using interaction, and based on which to refresh our conceptual understanding of a series of properties regarding inheritance mode of human disease. Results: We observed a strong correlation between the number of protein interactions and the likelihood of a gene causing any dominant diseases or multiple dominant diseases, whereas no correlation was observed between protein interaction and the likelihood of a gene causing recessive diseases. We found that dominant diseases are more likely to be associated with disruption of important interactions. These suggest inheritance mode should be understood using protein interaction. We therefore reviewed the previous studies and refined an interaction model of inheritance mode, and then confirmed that this model is largely reasonable using new evidences. With these findings, we found that the inheritance mode of human genetic diseases can be predicted using protein interaction. By integrating the systems biology perspectives with the classical disease genetics paradigm, our study provides some new insights into genotype–phenotype correlations. Contact: haodapeng@ems.hrbmu.edu.cn or biofomeng@hotmail.com Supplementary information: Supplementary data are available at Bioinformatics online.
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    Drug/Cell-line Browser: interactive canvas visualization of cancer drug/cell-line viability assay datasets (2014)
    Oxford University Press
    Details
    Publication Date: 2014-11-07
    Description: : Recently, several high profile studies collected cell viability data from panels of cancer cell lines treated with many drugs applied at different concentrations. Such drug sensitivity data for cancer cell lines provide suggestive treatments for different types and subtypes of cancer. Visualization of these datasets can reveal patterns that may not be obvious by examining the data without such efforts. Here we introduce Drug/Cell-line Browser (DCB), an online interactive HTML5 data visualization tool for interacting with three of the recently published datasets of cancer cell lines/drug-viability studies. DCB uses clustering and canvas visualization of the drugs and the cell lines, as well as a bar graph that summarizes drug effectiveness for the tissue of origin or the cancer subtypes for single or multiple drugs. DCB can help in understanding drug response patterns and prioritizing drug/cancer cell line interactions by tissue of origin or cancer subtype. Availability and implementation: DCB is an open source Web-based tool that is freely available at: http://www.maayanlab.net/LINCS/DCB Contact: avi.maayan@mssm.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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