WorldWideScience

Sample records for molecular evidence constrain

  1. An algorithm for mass matrix calculation of internally constrained molecular geometries.

    Science.gov (United States)

    Aryanpour, Masoud; Dhanda, Abhishek; Pitsch, Heinz

    2008-01-28

    Dynamic models for molecular systems require the determination of corresponding mass matrix. For constrained geometries, these computations are often not trivial but need special considerations. Here, assembling the mass matrix of internally constrained molecular structures is formulated as an optimization problem. Analytical expressions are derived for the solution of the different possible cases depending on the rank of the constraint matrix. Geometrical interpretations are further used to enhance the solution concept. As an application, we evaluate the mass matrix for a constrained molecule undergoing an electron-transfer reaction. The preexponential factor for this reaction is computed based on the harmonic model.

  2. An algorithm for mass matrix calculation of internally constrained molecular geometries

    International Nuclear Information System (INIS)

    Aryanpour, Masoud; Dhanda, Abhishek; Pitsch, Heinz

    2008-01-01

    Dynamic models for molecular systems require the determination of corresponding mass matrix. For constrained geometries, these computations are often not trivial but need special considerations. Here, assembling the mass matrix of internally constrained molecular structures is formulated as an optimization problem. Analytical expressions are derived for the solution of the different possible cases depending on the rank of the constraint matrix. Geometrical interpretations are further used to enhance the solution concept. As an application, we evaluate the mass matrix for a constrained molecule undergoing an electron-transfer reaction. The preexponential factor for this reaction is computed based on the harmonic model

  3. X-ray Constrained Extremely Localized Molecular Orbitals: Theory and Critical Assessment of the New Technique.

    Science.gov (United States)

    Genoni, Alessandro

    2013-07-09

    Following the X-ray constrained wave function approach proposed by Jayatilaka, we have devised a new technique that allows to extract molecular orbitals strictly localized on small molecular fragments from sets of experimental X-ray structure factors amplitudes. Since the novel strategy enables to obtain electron distributions that have quantum mechanical features and that can be easily interpreted in terms of traditional chemical concepts, the method can be also considered as a new useful tool for the determination and the analysis of charge densities from high-resolution X-ray experiments. In this paper, we describe in detail the theory of the new technique, which, in comparison to our preliminary work, has been improved both treating the effects of isotropic secondary extinctions and introducing a new protocol to halt the fitting procedure against the experimental X-ray scattering data. The performances of the novel strategy have been studied both in function of the basis-sets flexibility and in function of the quality of the considered crystallographic data. The tests performed on four different systems (α-glycine, l-cysteine, (aminomethyl)phosphonic acid and N-(trifluoromethyl)formamide) have shown that the achievement of good statistical agreements with the experimental measures mainly depends on the quality of the crystal structures (i.e., geometry positions and thermal parameters) used in the X-ray constrained calculations. Finally, given the reliable transferability of the obtained Extremely Localized Molecular Orbitals (ELMOs), we envisage to exploit the novel approach to construct new ELMOs databases suited to the development of linear-scaling methods for the refinement of macromolecular crystal structures.

  4. CONSTRAINING DUST AND MOLECULAR GAS PROPERTIES IN Lyα BLOBS AT z ∼ 3

    International Nuclear Information System (INIS)

    Yang Yujin; Decarli, Roberto; Walter, Fabian; Leipski, Christian; Dannerbauer, Helmut; Le Floc'h, Emeric; Weiss, Axel; Menten, Karl M.; Dey, Arjun; Chapman, Scott C.; Prescott, Moire K. M.; Neri, Roberto; Borys, Colin; Matsuda, Yuichi; Yamada, Toru; Hayashino, Tomoki; Tapken, Christian

    2012-01-01

    In order to constrain the bolometric luminosities, dust properties, and molecular gas content of giant Lyα nebulae, the so-called Lyα blobs, we have carried out a study of dust continuum and CO line emission in two well-studied representatives of this population at z ∼ 3: an Lyα blob discovered by its strong Spitzer Multiband Infrared Photometer 24 μm detection (LABd05) and the Steidel blob 1 (SSA22-LAB01). We find that the spectral energy distribution of LABd05 is well described by an active-galactic-nucleus-starburst composite template with L FIR = (4.0 ± 0.5) × 10 12 L ☉ , comparable to high-z submillimeter galaxies and ultraluminous infrared galaxies. New Large APEX Bolometer Camera 870 μm measurements rule out the reported Submillimeter Common-User Bolometer Array detection of the SSA22-LAB01 (S 850μm = 16.8 mJy) at the >4σ level. Consistent with this, ultradeep Plateau de Bure Interferometer observations with ∼2'' spatial resolution also fail to detect any 1.2 mm continuum source down to ≈0.45 mJy beam –1 (3σ). Combined with the existing (sub)millimeter observations in the literature, we conclude that the FIR luminosity of SSA22-LAB01 remains uncertain. No CO line is detected in either case down to integrated flux limits of S ν ΔV ∼ –1 , indicating a modest molecular gas reservoir, M(H 2 ) 10 M ☉ . The non-detections exclude, with high significance (12σ), the previous tentative detection of a CO J = 4-3 line in the SSA22-LAB01. The increased sensitivity afforded by the Atacama Large Millimeter/submillimeter Array will be critical in studying molecular gas and dust in these interesting systems.

  5. Overcoming potential energy distortions in constrained internal coordinate molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Kandel, Saugat; Salomon-Ferrer, Romelia; Larsen, Adrien B.; Vaidehi, Nagarajan, E-mail: nvaidehi@coh.org [Division of Immunology, Beckman Research Institute of the City of Hope, Duarte, California 91010 (United States); Jain, Abhinandan, E-mail: Abhi.Jain@jpl.nasa.gov [Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, California 91109 (United States)

    2016-01-28

    The Internal Coordinate Molecular Dynamics (ICMD) method is an attractive molecular dynamics (MD) method for studying the dynamics of bonded systems such as proteins and polymers. It offers a simple venue for coarsening the dynamics model of a system at multiple hierarchical levels. For example, large scale protein dynamics can be studied using torsional dynamics, where large domains or helical structures can be treated as rigid bodies and the loops connecting them as flexible torsions. ICMD with such a dynamic model of the protein, combined with enhanced conformational sampling method such as temperature replica exchange, allows the sampling of large scale domain motion involving high energy barrier transitions. Once these large scale conformational transitions are sampled, all-torsion, or even all-atom, MD simulations can be carried out for the low energy conformations sampled via coarse grained ICMD to calculate the energetics of distinct conformations. Such hierarchical MD simulations can be carried out with standard all-atom forcefields without the need for compromising on the accuracy of the forces. Using constraints to treat bond lengths and bond angles as rigid can, however, distort the potential energy landscape of the system and reduce the number of dihedral transitions as well as conformational sampling. We present here a two-part solution to overcome such distortions of the potential energy landscape with ICMD models. To alleviate the intrinsic distortion that stems from the reduced phase space in torsional MD, we use the Fixman compensating potential. To additionally alleviate the extrinsic distortion that arises from the coupling between the dihedral angles and bond angles within a force field, we propose a hybrid ICMD method that allows the selective relaxing of bond angles. This hybrid ICMD method bridges the gap between all-atom MD and torsional MD. We demonstrate with examples that these methods together offer a solution to eliminate the potential

  6. CONSTRAINING DUST AND MOLECULAR GAS PROPERTIES IN Ly{alpha} BLOBS AT z {approx} 3

    Energy Technology Data Exchange (ETDEWEB)

    Yang Yujin; Decarli, Roberto; Walter, Fabian; Leipski, Christian [Max-Planck-Institut fuer Astronomie, Koenigstuhl 17, Heidelberg (Germany); Dannerbauer, Helmut; Le Floc' h, Emeric [Laboratoire AIM, CEA/DSM-CNRS-Universite Paris Diderot, Irfu/Service d' Astrophysique, CEA-Saclay, Orme des Merisiers, 91191 Gif-sur-Yvette Cedex (France); Weiss, Axel; Menten, Karl M. [Max-Planck-Insitut fuer Radioastronomie, Auf dem Huegel 69, D-53121 Bonn (Germany); Dey, Arjun [National Optical Astronomy Observatory, 950 North Cherry Avenue, Tucson, AZ 85719 (United States); Chapman, Scott C. [Institute of Astronomy, University of Cambridge, Madingley Road, Cambridge CB3 0HA (United Kingdom); Prescott, Moire K. M. [Department of Physics, Broida Hall, Mail Code 9530, University of California, Santa Barbara, CA 93106 (United States); Neri, Roberto [IRAM-Institut de Radio Astronomie Millimetrique, 300 rue de la Piscine, 38406 Saint-Martin d' Heres (France); Borys, Colin [IPAC, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125 (United States); Matsuda, Yuichi [Department of Physics, Durham University, South Road, Durham DH1 3LE (United Kingdom); Yamada, Toru [Astronomical Institute, Tohoku University, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578 (Japan); Hayashino, Tomoki [Research Center for Neutrino Science, Graduate School of Science, Tohoku University, Sendai 980-8578 (Japan); Tapken, Christian [Leibnitz-Institut fuer Astrophysik Potsdam (AIP), An der Sternwarte 16, 14482 Potsdam (Germany)

    2012-01-10

    In order to constrain the bolometric luminosities, dust properties, and molecular gas content of giant Ly{alpha} nebulae, the so-called Ly{alpha} blobs, we have carried out a study of dust continuum and CO line emission in two well-studied representatives of this population at z {approx} 3: an Ly{alpha} blob discovered by its strong Spitzer Multiband Infrared Photometer 24 {mu}m detection (LABd05) and the Steidel blob 1 (SSA22-LAB01). We find that the spectral energy distribution of LABd05 is well described by an active-galactic-nucleus-starburst composite template with L{sub FIR} = (4.0 {+-} 0.5) Multiplication-Sign 10{sup 12} L{sub Sun }, comparable to high-z submillimeter galaxies and ultraluminous infrared galaxies. New Large APEX Bolometer Camera 870 {mu}m measurements rule out the reported Submillimeter Common-User Bolometer Array detection of the SSA22-LAB01 (S{sub 850{mu}m} = 16.8 mJy) at the >4{sigma} level. Consistent with this, ultradeep Plateau de Bure Interferometer observations with {approx}2'' spatial resolution also fail to detect any 1.2 mm continuum source down to Almost-Equal-To 0.45 mJy beam{sup -1} (3{sigma}). Combined with the existing (sub)millimeter observations in the literature, we conclude that the FIR luminosity of SSA22-LAB01 remains uncertain. No CO line is detected in either case down to integrated flux limits of S{sub {nu}}{Delta}V {approx}< 0.25-1.0 Jy km s{sup -1}, indicating a modest molecular gas reservoir, M(H{sub 2}) < (1-3) Multiplication-Sign 10{sup 10} M{sub Sun }. The non-detections exclude, with high significance (12{sigma}), the previous tentative detection of a CO J = 4-3 line in the SSA22-LAB01. The increased sensitivity afforded by the Atacama Large Millimeter/submillimeter Array will be critical in studying molecular gas and dust in these interesting systems.

  7. Robust and Efficient Constrained DFT Molecular Dynamics Approach for Biochemical Modeling

    Czech Academy of Sciences Publication Activity Database

    Řezáč, Jan; Levy, B.; Demachy, I.; de la Lande, A.

    2012-01-01

    Roč. 8, č. 2 (2012), s. 418-427 ISSN 1549-9618 Institutional research plan: CEZ:AV0Z40550506 Keywords : constrained density functional the ory * electron transfer * density fitting Subject RIV: CF - Physical ; The oretical Chemistry Impact factor: 5.389, year: 2012

  8. Constraining the Dust Opacity Law in Three Small and Isolated Molecular Clouds

    Energy Technology Data Exchange (ETDEWEB)

    Webb, K. A.; Thanjavur, K. [Department of Physics and Astronomy, 3800 Finnerty Road, University of Victoria, Victoria, BC, V8P 5C2 (Canada); Di Francesco, J. [National Research Council of Canada, Herzberg Institute of Astrophysics, 5071 West Saanich Road, Victoria, BC, V9E 2E7 (Canada); Sadavoy, S. [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Launhardt, R.; Vicente, J. Abreu; Kainulainen, J. [Max-Planck-Institut für Astronomy, Königstuhl 17, D-69117, Heidelberg (Germany); Shirley, Y. [Steward Observatory, 933 North Cherry Avenue, Tucson, AZ 85721 (United States); Stutz, A., E-mail: kawebb@uvic.ca [Departmento de Astronomìa, Facultad Ciencias Físicas y Matemáticas, Universidad de Concepción, Av. Esteban Iturra s/n Barro Universitario, Casilla 160-C, Concepción (Chile)

    2017-11-01

    Density profiles of isolated cores derived from thermal dust continuum emission rely on models of dust properties, such as mass opacity, that are poorly constrained. With complementary measures from near-infrared extinction maps, we can assess the reliability of commonly used dust models. In this work, we compare Herschel -derived maps of the optical depth with equivalent maps derived from CFHT WIRCAM near-infrared observations for three isolated cores: CB 68, L 429, and L 1552. We assess the dust opacities provided from four models: OH1a, OH5a, Orm1, and Orm4. Although the consistency of the models differs between the three sources, the results suggest that the optical properties of dust in the envelopes of the cores are best described by either silicate and bare graphite grains (e.g., Orm1) or carbonaceous grains with some coagulation and either thin or no ice mantles (e.g., OH5a). None of the models, however, individually produced the most consistent optical depth maps for every source. The results suggest that either the dust in the cores is not well-described by any one dust property model, the application of the dust models cannot be extended beyond the very center of the cores, or more complex SED fitting functions are necessary.

  9. Extended Lagrangian formulation of charge-constrained tight-binding molecular dynamics.

    Science.gov (United States)

    Cawkwell, M J; Coe, J D; Yadav, S K; Liu, X-Y; Niklasson, A M N

    2015-06-09

    The extended Lagrangian Born-Oppenheimer molecular dynamics formalism [Niklasson, Phys. Rev. Lett., 2008, 100, 123004] has been applied to a tight-binding model under the constraint of local charge neutrality to yield microcanonical trajectories with both precise, long-term energy conservation and a reduced number of self-consistent field optimizations at each time step. The extended Lagrangian molecular dynamics formalism restores time reversal symmetry in the propagation of the electronic degrees of freedom, and it enables the efficient and accurate self-consistent optimization of the chemical potential and atomwise potential energy shifts in the on-site elements of the tight-binding Hamiltonian that are required when enforcing local charge neutrality. These capabilities are illustrated with microcanonical molecular dynamics simulations of a small metallic cluster using an sd-valent tight-binding model for titanium. The effects of weak dissipation on the propagation of the auxiliary degrees of freedom for the chemical potential and on-site Hamiltonian matrix elements that is used to counteract the accumulation of numerical noise during trajectories was also investigated.

  10. Constraining the potential temperature of the Archaean mantle: A review of the evidence from komatiites

    Science.gov (United States)

    Nisbet, E. G.; Cheadle, M. J.; Arndt, N. T.; Bickle, M. J.

    1993-09-01

    The maximum potential temperature of the Archaean mantle is poorly known, and is best constrained by the MgO contents of komatiitic liquids, which are directly related to eruptive temperatures. However, most Archaean komatiites are significantly altered and it is difficult to assess the composition of the erupted liquid. Relatively fresh lavas from the SASKMAR suite, Belingwe Greenstone Belt, Zimbabwe (2.7 Ga) include chills of 25.6 wt.% MgO, and olivines ranging to Fo 93.6, implying eruption at around 1520°C. A chill sample from Alexo Township, Ontario (also 2.7 Ga) is 28 wt.% MgO, and associated olivines range to Fo 94.1, implying eruption at 1560°C. However, inferences of erupted liquids containing 32-33 wt.% MgO, from lavas in the Barberton Greenstone Belt, South Africa (3.45 Ga) and from the Perseverance Complex, Western Australia (2.7 Ga) may be challenged on the grounds that they contain excess (cumulate) olivine, or were enriched in Mg during alteration or metamorphism. Re-interpretation of olivine compositions from these rocks shows that they most likely contained a maximum of 29 wt.% MgO corresponding to an eruption temperature of 1580°C. This composition is the highest liquid MgO content of an erupted lava that can be supported with any confidence. The hottest modern magma, on Gorgona Island (0.155 Ga) contained 18-20% MgO and erupted at circa 1400°C. If 1580°C is taken as the temperature of the most magnesian known eruption, then the source mantle from which the liquids rose would have been at up to 2200°C at pressures of 18 GPa corresponding to a mantle potential temperature of 1900°C. These temperatures are in excess of the mantle temperatures predicted by secular cooling models, and thus komatiites can only be formed in hot rising convective jets in the mantle. This result requires that Archaean mantle jets may have been 300°C hotter than the Archaean ambient mantle temperature. This temperature difference is similar to the 200-300

  11. Spectral shifting strongly constrains molecular cloud disruption by radiation pressure on dust

    Science.gov (United States)

    Reissl, Stefan; Klessen, Ralf S.; Mac Low, Mordecai-Mark; Pellegrini, Eric W.

    2018-03-01

    Aim. We aim to test the hypothesis that radiation pressure from young star clusters acting on dust is the dominant feedback agent disrupting the largest star-forming molecular clouds and thus regulating the star-formation process. Methods: We performed multi-frequency, 3D, radiative transfer calculations including both scattering and absorption and re-emission to longer wavelengths for model clouds with masses of 104-107 M⊙, containing embedded clusters with star formation efficiencies of 0.009-91%, and varying maximum grain sizes up to 200 μm. We calculated the ratio between radiative and gravitational forces to determine whether radiation pressure can disrupt clouds. Results: We find that radiation pressure acting on dust almost never disrupts star-forming clouds. Ultraviolet and optical photons from young stars to which the cloud is optically thick do not scatter much. Instead, they quickly get absorbed and re-emitted by the dust at thermal wavelengths. As the cloud is typically optically thin to far-infrared radiation, it promptly escapes, depositing little momentum in the cloud. The resulting spectrum is more narrowly peaked than the corresponding Planck function, and exhibits an extended tail at longer wavelengths. As the opacity drops significantly across the sub-mm and mm wavelength regime, the resulting radiative force is even smaller than for the corresponding single-temperature blackbody. We find that the force from radiation pressure falls below the strength of gravitational attraction by an order of magnitude or more for either Milky Way or moderate starbust conditions. Only for unrealistically large maximum grain sizes, and star formation efficiencies far exceeding 50% do we find that the strength of radiation pressure can exceed gravity. Conclusions: We conclude that radiation pressure acting on dust does not disrupt star-forming molecular clouds in any Local Group galaxies. Radiation pressure thus appears unlikely to regulate the star

  12. Molecular characterization of Wilms tumor from a resource-constrained region of sub-Saharan Africa

    Science.gov (United States)

    Murphy, Andrew J.; Axt, Jason R.; de Caestecker, Christian; Pierce, Janene; Correa, Hernan; Seeley, Erin H.; Caprioli, Richard M.; Newton, Mark W.; de Caestecker, Mark P.; Lovvorn, Harold N.

    2012-01-01

    Sub-Saharan African children have an increased incidence of Wilms tumor (WT) and experience alarmingly poor outcomes. Although these outcomes are largely due to inadequate therapy, we hypothesized that WT from this region exhibit features of biologic aggressiveness that may warrant broader implementation of high-risk therapeutic protocols. We evaluated 15 Kenyan WT (KWT) for features of aggressive disease (blastemal predominance, Ki67/cellular proliferation) and treatment resistance (anaplasia, p53 immunopositivity). To explore additional biologic features of KWT, we determined the mutational status of the CTNNB1/β-catenin and WT1 genes and performed immunostaining for markers of Wnt pathway activation (β-catenin) and nephronic progenitor cell self-renewal (WT1, CITED1, SIX2). We characterized the proteome of KWT using imaging mass spectrometry (IMS). Results were compared to histology and age-matched North American WT (NAWT) controls. For KWT patients, blastemal predominance was noted in 53.3% and anaplasia in 13%. We detected increased loss to follow up (p=0.028), disease relapse (p=0.044), mortality (p=0.001), and nuclear unrest (p=0.001) in KWT patients compared to controls. KWT and NAWT showed similar Ki67/cellular proliferation. We detected an increased proportion of epithelial nuclear β-catenin in KWT (p=0.013). All 15 KWT were found to harbor wild-type β-catenin, and 1 contained a WT1 nonsense mutation. WT1 was detected by immunostaining in 100% of KWT, CITED1 in 80%, and SIX2 in 80%. IMS revealed a molecular signature unique to KWT that was distinct from NAWT. African WTs appear to express markers of adverse clinical behavior and treatment resistance and may require alternative therapies or implementation of high-risk treatment protocols. PMID:22437966

  13. Is handwriting constrained by phonology? Evidence from Stroop tasks with written responses and Chinese characters

    Directory of Open Access Journals (Sweden)

    Markus eDamian

    2013-10-01

    Full Text Available To what extent is handwritten word production based on phonological codes? A few studies conducted in Western languages have recently provided evidence showing that phonology contributes to the retrieval of graphemic properties in written output tasks. Less is known about how orthographic production works in languages with non-alphabetic scripts such as written Chinese. We report a Stroop study in which Chinese participants wrote the colour of characters on a digital graphic tablet; characters were either neutral, or homophonic to the target (congruent, or homophonic to an alternative (incongruent. Facilitation was found from congruent homophonic distractors, but only when the homophone shared the same tone with the target. This finding suggests a contribution of phonology to written word production. A second experiment served as a control experiment to exclude the possibility that the effect in Experiment 1 had an exclusively semantic locus. Overall, the findings offer new insight into the relative contribution of phonology to handwriting, particularly in non-Western languages.

  14. Lignin biodegradation: experimental evidence, molecular, biochemical and physiological mechanisms

    Energy Technology Data Exchange (ETDEWEB)

    Monties, B

    1985-01-01

    A critical review is presented of English, French and some German language literature, mainly from 1983 onwards. It examines experimental evidence on the behaviour as barriers to biodegradation of lignins and phenolic polymers such as tannins and suberins. The different molecular mechanisms of lignolysis by fungi (mainly), actinomycetes and bacteria are examined. A new biochemical approach to the physiological mechanism of regulation of lignolytic activities is suggested based on the discoveries of ligniolytic enzymes: effects of nitrogen, oxygen and substrate are discussed. It is concluded that a better knowledge of the structure and reactivity of phenolic barriers is needed in order to control the process of lignolysis.

  15. Vitamin D and Colorectal Cancer: Molecular, Epidemiological, and Clinical Evidence

    Science.gov (United States)

    Dou, Ruoxu; Ng, Kimmie; Giovannucci, Edward L.; Manson, JoAnn E.; Qian, Zhi Rong; Ogino, Shuji

    2016-01-01

    In many cells throughout the body, vitamin D is converted into its active form calcitriol, and binds to vitamin D receptor (VDR), which functions as a transcription factor to regulate various biological processes including cellular differentiation and immune response. Vitamin D metabolizing enzymes (including CYP24A1 and CYP27B1) and VDR play major roles in exerting and regulating effects of vitamin D. Preclinical and epidemiological studies provide evidence for anticancer effects of vitamin D (in particular, against colorectal cancer), though clinical trials have yet to prove its benefit. Additionally, molecular pathological epidemiology research can provide insights into the interaction of vitamin D with tumour molecular and immunity status. Other future research directions include genome-wide research on VDR transcriptional targets, gene-environment interaction analyses, and clinical trials on vitamin D efficacy in colorectal cancer patients. Here we review the literature on vitamin D and colorectal cancer from both mechanistic and population studies, and discuss the links and controversies within and between the two parts of evidence. PMID:27245104

  16. Vitamin D and colorectal cancer: molecular, epidemiological and clinical evidence.

    Science.gov (United States)

    Dou, Ruoxu; Ng, Kimmie; Giovannucci, Edward L; Manson, JoAnn E; Qian, Zhi Rong; Ogino, Shuji

    2016-05-01

    In many cells throughout the body, vitamin D is converted into its active form calcitriol and binds to the vitamin D receptor (VDR), which functions as a transcription factor to regulate various biological processes including cellular differentiation and immune response. Vitamin D-metabolising enzymes (including CYP24A1 and CYP27B1) and VDR play major roles in exerting and regulating the effects of vitamin D. Preclinical and epidemiological studies have provided evidence for anti-cancer effects of vitamin D (particularly against colorectal cancer), although clinical trials have yet to prove its benefit. In addition, molecular pathological epidemiology research can provide insights into the interaction of vitamin D with tumour molecular and immunity status. Other future research directions include genome-wide research on VDR transcriptional targets, gene-environment interaction analyses and clinical trials on vitamin D efficacy in colorectal cancer patients. In this study, we review the literature on vitamin D and colorectal cancer from both mechanistic and population studies and discuss the links and controversies within and between the two parts of evidence.

  17. Evidence for systems-level molecular mechanisms of tumorigenesis

    Directory of Open Access Journals (Sweden)

    Capellá Gabriel

    2007-06-01

    Full Text Available Abstract Background Cancer arises from the consecutive acquisition of genetic alterations. Increasing evidence suggests that as a consequence of these alterations, molecular interactions are reprogrammed in the context of highly connected and regulated cellular networks. Coordinated reprogramming would allow the cell to acquire the capabilities for malignant growth. Results Here, we determine the coordinated function of cancer gene products (i.e., proteins encoded by differentially expressed genes in tumors relative to healthy tissue counterparts, hereafter referred to as "CGPs" defined as their topological properties and organization in the interactome network. We show that CGPs are central to information exchange and propagation and that they are specifically organized to promote tumorigenesis. Centrality is identified by both local (degree and global (betweenness and closeness measures, and systematically appears in down-regulated CGPs. Up-regulated CGPs do not consistently exhibit centrality, but both types of cancer products determine the overall integrity of the network structure. In addition to centrality, down-regulated CGPs show topological association that correlates with common biological processes and pathways involved in tumorigenesis. Conclusion Given the current limited coverage of the human interactome, this study proposes that tumorigenesis takes place in a specific and organized way at the molecular systems-level and suggests a model that comprises the precise down-regulation of groups of topologically-associated proteins involved in particular functions, orchestrated with the up-regulation of specific proteins.

  18. Molecular evidence for the early history of living amphibians.

    Science.gov (United States)

    Feller, A E; Hedges, S B

    1998-06-01

    The evolutionary relationships of the three orders of living amphibians (lissamphibians) has been difficult to resolve, partly because of their specialized morphologies. Traditionally, frogs and salamanders are considered to be closest relatives, and all three orders are thought to have arisen in the Paleozoic (>250 myr). Here, we present evidence from the DNA sequences of four mitochondrial genes (2.7 kilobases) that challenges the conventional hypothesis and supports a salamander-caecilian relationship. This, in light of the fossil record and distribution of the families, suggests a more recent (Mesozoic) origin for salamanders and caecilians directly linked to the initial breakup of the supercontinent Pangaea. We propose that this single geologic event isolated salamanders and archaeobatrachian frogs on the northern continents (Laurasia) and the caecilians and neobatrachian frogs on the southern continents (Gondwana). Among the neobatrachian frog families, molecular evidence supports a South American clade and an African clade, inferred here to be the result of mid-Cretaceous vicariance. Copyright 1998 Academic Press.

  19. Curcumin and insulin resistance-Molecular targets and clinical evidences.

    Science.gov (United States)

    Jiménez-Osorio, Angélica Saraí; Monroy, Adriana; Alavez, Silvestre

    2016-11-12

    Curcumin ((1E,6E)-1,7-bis(4-hydroxy-3-methoxyphenyl)-1,6-heptadiene-3,5-dione), the main component of the Indian spice turmeric, has been used in traditional medicine to improve diabetes and its comorbidities. Since the last two decades, scientific research has shown that in addition to its antioxidant properties, curcumin could also work as protein homeostasis regulator and it is able to modulate other intracellular pathways. Curcumin supplementation has been proposed to improve insulin resistance (IR) through the activation of the insulin receptor and its downstream pathways in several experimental models, pointing out that its clinical use may be a good and innocuous strategy to improve IR-related diseases. IR is associated with many diseases and syndromes like carbohydrate intolerance, diabetes, metabolic syndrome, and cardiovascular disease. Therefore, it is imperative to identify safe therapeutic interventions aimed to reduce side effects that could lead the patient to leave the treatment. To date, many clinical trials have been carried out using turmeric and curcumin to improve metabolic syndrome, carbohydrate intolerance, diabetes, and obesity in individuals with IR. Results so far are inconclusive because dose, time of treatment, and type of curcumin can change the study outcome significantly. However, there is some clinical evidence suggesting a beneficial effect of curcumin on IR. In this review, we discuss the factors that could influence curcumin effects in clinical trials aimed to improve IR and related diseases, and the conclusions that can be drawn from results obtained so far. © 2016 BioFactors, 42(6):561-580, 2016. © 2016 International Union of Biochemistry and Molecular Biology.

  20. Molecular Evidence for the Hybrid Origin of Ilex dabieshanensis (Aquifoliaceae.

    Directory of Open Access Journals (Sweden)

    Lin Shi

    Full Text Available Ilex, the largest genus of dioecious woody plants, is a good study system to assess the role of hybridization in speciation and evolution. Ilex dabieshanensis, a tree endemic to Dabieshan Mountains region, was initially described as a new species. Based on morphological intermediacy and sympatric distribution with its putative parental species, I. cornuta and I. latifolia, we proposed it as a natural hybrid between them. In this study, we sequenced one chloroplast intergenic spacer (trnH-psbA and two nuclear genes (gapC and nepGS in I. dabieshanensis and its putative parental species to test the hybrid origin hypothesis. Our results showed that there were one to two differentially fixed sequence differences between I. cornuta and I. latifolia at the two nuclear genes. Twelve of the 14 individuals of I. dabieshanensis exhibited additivity in chromatograms on these differentially fixed sites at both nuclear genes, and the remaining two exhibited additivity in chromatograms on the fixed site at only the nepGS gene. Except one haplotype of I. cornuta at the nepGS gene, all of the haplotypes of I. cornuta at the two nuclear genes were well separated from those of I. latifolia, and most haplotypes of I. dabieshanensis were shared with those of I. cornuta and I. latifolia. Phylogenetic analysis of these haplotypes was largely consistent with haplotype network analysis. I. cornuta and I. latifolia differed by two nucleotide substitutions in the chloroplast intergenic spacer, and 12 individuals of I. dabieshanensis had the same sequences as I. latifolia, while the remaining two were identical with I. cornuta. The molecular data provide convincing evidence for the hybrid origin of I. dabieshanensis and asymmetrical direction of hybridization. One haplotype of I. cornuta at the nepGS gene was nested with those of I. latifolia, indicating introgression to I. cornuta.

  1. A massively parallel algorithm for the solution of constrained equations of motion with applications to large-scale, long-time molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Fijany, A. [Jet Propulsion Lab., Pasadena, CA (United States); Coley, T.R. [Virtual Chemistry, Inc., San Diego, CA (United States); Cagin, T.; Goddard, W.A. III [California Institute of Technology, Pasadena, CA (United States)

    1997-12-31

    Successful molecular dynamics (MD) simulation of large systems (> million atoms) for long times (> nanoseconds) requires the integration of constrained equations of motion (CEOM). Constraints are used to eliminate high frequency degrees of freedom (DOF) and to allow the use of rigid bodies. Solving the CEOM allows for larger integration time-steps and helps focus the simulation on the important collective dynamics of chemical, biological, and materials systems. We explore advances in multibody dynamics which have resulted in O(N) algorithms for propagating the CEOM. However, because of their strictly sequential nature, the computational time required by these algorithms does not scale down with increased numbers of processors. We then present the new constraint force algorithm for solving the CEOM and show that this algorithm is fully parallelizable, leading to a computational cost of O(N/P+IogP) for N DOF on P processors.

  2. Achievable Strength-Based Signal Detection in Quantity-Constrained PAM OOK Concentration-Encoded Molecular Communication.

    Science.gov (United States)

    Mahfuz, Mohammad Upal

    2016-10-01

    In this paper, the expressions of achievable strength-based detection probabilities of concentration-encoded molecular communication (CEMC) system have been derived based on finite pulsewidth (FP) pulse-amplitude modulated (PAM) on-off keying (OOK) modulation scheme and strength threshold. An FP-PAM system is characterized by its duty cycle α that indicates the fraction of the entire symbol duration the transmitter remains on and transmits the signal. Results show that the detection performance of an FP-PAM OOK CEMC system significantly depends on the statistical distribution parameters of diffusion-based propagation noise and intersymbol interference (ISI). Analytical detection performance of an FP-PAM OOK CEMC system under ISI scenario has been explained and compared based on receiver operating characteristics (ROC) for impulse (i.e., spike)-modulated (IM) and FP-PAM CEMC schemes. It is shown that the effects of diffusion noise and ISI on ROC can be explained separately based on their communication range-dependent statistics. With full duty cycle, an FP-PAM scheme provides significantly worse performance than an IM scheme. The paper also analyzes the performance of the system when duty cycle, transmission data rate, and quantity of molecules vary.

  3. Affinities of the family Sollasellidae (Porifera, Demospongiae). II. Molecular evidence

    NARCIS (Netherlands)

    Erpenbeck, D.; Hooper, J.N.A.; List-Armitage, S.E.; Degnan, B.M.; Wörheide, G.; Soest, van R.W.M.

    2007-01-01

    This is the second part of a revision and re-classification of the demosponge family Sollasellidae, and an example of a successful use of combined morphological and molecular data. Sollasella had been a poorly known, long forgotten taxon, placed incertae sedis in the order Hadromerida in the last

  4. Choosing health, constrained choices.

    Science.gov (United States)

    Chee Khoon Chan

    2009-12-01

    In parallel with the neo-liberal retrenchment of the welfarist state, an increasing emphasis on the responsibility of individuals in managing their own affairs and their well-being has been evident. In the health arena for instance, this was a major theme permeating the UK government's White Paper Choosing Health: Making Healthy Choices Easier (2004), which appealed to an ethos of autonomy and self-actualization through activity and consumption which merited esteem. As a counterpoint to this growing trend of informed responsibilization, constrained choices (constrained agency) provides a useful framework for a judicious balance and sense of proportion between an individual behavioural focus and a focus on societal, systemic, and structural determinants of health and well-being. Constrained choices is also a conceptual bridge between responsibilization and population health which could be further developed within an integrative biosocial perspective one might refer to as the social ecology of health and disease.

  5. Constrained consequence

    CSIR Research Space (South Africa)

    Britz, K

    2011-09-01

    Full Text Available their basic properties and relationship. In Section 3 we present a modal instance of these constructions which also illustrates with an example how to reason abductively with constrained entailment in a causal or action oriented context. In Section 4 we... of models with the former approach, whereas in Section 3.3 we give an example illustrating ways in which C can be de ned with both. Here we employ the following versions of local consequence: De nition 3.4. Given a model M = hW;R;Vi and formulas...

  6. Molecular Evidence for Species-Level Distinctions in Clouded Leopards

    OpenAIRE

    Buckley-Beason, Valerie A.; Johnson, Warren E.; Nash, Willliam G.; Stanyon, Roscoe; Menninger, Joan C.; Driscoll, Carlos A.; Howard, JoGayle; Bush, Mitch; Page, John E.; Roelke, Melody E.; Stone, Gary; Martelli, Paolo P.; Wen, Ci; Ling, Lin; Duraisingam, Ratna K.

    2006-01-01

    Among the 37 living species of Felidae, the clouded leopard (Neofelis nebulosa) is generally classified as a monotypic genus basal to the Panthera lineage of great cats [1–5]. This secretive, mid-sized (16–23 kg) carnivore, now severely endangered, is traditionally subdivided into four southeast Asian subspecies (Figure 1A) [4–8]. We used molecular genetic methods to re-evaluate subspecies partitions and to quantify patterns of population genetic variation among 109 clouded leopards of known ...

  7. Affinities of the family Sollasellidae (Porifera, Demospongiae). II. Molecular evidence.

    OpenAIRE

    Erpenbeck, D.J.G.; Hooper, J.N.A.; List-Armitage, S.E.; Degman, B.M.; Wördheide, G.; van Soest, R.W.M.

    2007-01-01

    This is the second part of a revision and re-classification of the demosponge family Sollasellidae, and an example of a successful use of combined morphological and molecular data. Sollasella had been a poorly known, long forgotten taxon, placed incertae sedis in the order Hadromerida in the last major revision of the demosponges. It has recently been suggested to belong to Raspailiidae in the order Poecilosclerida due to striking morphological similarities. The present analysis verified this...

  8. Constraining the Molecular Complexity in the Interstellar Medium—The Formation of Ethyl Methyl Ether (CH3OCH2CH3) in Star-forming Regions

    Science.gov (United States)

    Bergantini, Alexandre; Frigge, Robert; Kaiser, Ralf I.

    2018-05-01

    We report the first confirmed synthesis of ethyl methyl ether (EME, CH3CH2OCH3) within astrophysical model ices containing water (H2O) and methane (CH4) exposed to ionizing radiation at ultra-low temperatures of 5 K. EME (also known as methoxyethane), was recently observed toward Orion KL and currently is the largest confirmed oxygen-bearing molecule found in the interstellar medium. Exploiting isomer-selective photoionization (PI) of the subliming molecules in the temperature-programmed desorption phase at 10.49, 9.92, and 9.70 eV, coupled with reflectron time-of-flight mass spectrometry and isotopic substitution experiments (H2 18O–CH4), the detection of fragment ions of EME at m/z = 45 (C2H5O+) and m/z = 59 (C3H7O+), and probing the proton transfer in subliming ethanol–EME complexes via m/z = 61 (C3H9O+), the present study reveals that EME can be formed from suprathermal reactions initiated by cosmic rays and secondary electrons generated within astrophysical ices. The detection of EME in our experiments represents a significant advance in the understanding of formation pathways of complex organic molecules present in hot cores and helps to constrain astrochemical models on the formation of such species within molecular clouds.

  9. Little evidence for dynamic divergences in ultraviscous molecular liquids

    DEFF Research Database (Denmark)

    Hecksher, Tina; Nielsen, Albena; Olsen, Niels Boye

    2008-01-01

    The physics of the ultraviscous liquid phase preceding glass formation continues to pose major problems that remain unsolved. It is actively debated, for instance, whether the marked increase of the relaxation time reflects an underlying phase transition to a state of infinite relaxation time....... To elucidate the empirical evidence for this intriguing scenario, some of the most accurate relaxationtime data available for any class of ultraviscous liquids-those obtained by dielectric relaxation experiments on organic liquids just above the glass transition-were compiled. Analysis of data for 42 liquids...... shows that there is no compelling evidence for the Vogel-Fulcher-Tammann (VFT) prediction that the relaxation time diverges at a finite temperature.We conclude that theories with a dynamic divergence of the VFT formlack a direct experimental basis....

  10. Molecular Evidence of Drug Resistance in Asymptomatic Malaria Infections, Myanmar, 2015.

    Science.gov (United States)

    Nyunt, Myat Htut; Shein, Thinzar; Zaw, Ni Ni; Han, Soe Soe; Muh, Fauzi; Lee, Seong-Kyun; Han, Jin-Hee; Thant, Kyaw Zin; Han, Eun-Taek; Kyaw, Myat Phone

    2017-03-01

    Artemisinin resistance containment in Myanmar was initiated in 2011 after artemisinin-resistant Plasmodium falciparum malaria was reported. Molecular evidence suggests that asymptomatic malaria infections harboring drug resistance genes are present among residents of the Myanmar artemisinin resistance containment zone. This evidence supports efforts to eliminate these hidden infections.

  11. Molecular evidence for species-level distinctions in clouded leopards.

    Science.gov (United States)

    Buckley-Beason, Valerie A; Johnson, Warren E; Nash, Willliam G; Stanyon, Roscoe; Menninger, Joan C; Driscoll, Carlos A; Howard, JoGayle; Bush, Mitch; Page, John E; Roelke, Melody E; Stone, Gary; Martelli, Paolo P; Wen, Ci; Ling, Lin; Duraisingam, Ratna K; Lam, Phan V; O'Brien, Stephen J

    2006-12-05

    Among the 37 living species of Felidae, the clouded leopard (Neofelis nebulosa) is generally classified as a monotypic genus basal to the Panthera lineage of great cats. This secretive, mid-sized (16-23 kg) carnivore, now severely endangered, is traditionally subdivided into four southeast Asian subspecies (Figure 1A). We used molecular genetic methods to re-evaluate subspecies partitions and to quantify patterns of population genetic variation among 109 clouded leopards of known geographic origin (Figure 1A, Tables S1 ans S2 in the Supplemental Data available online). We found strong phylogeographic monophyly and large genetic distances between N. n. nebulosa (mainland) and N. n. diardi (Borneo; n = 3 individuals) with mtDNA (771 bp), nuclear DNA (3100 bp), and 51 microsatellite loci. Thirty-six fixed mitochondrial and nuclear nucleotide differences and 20 microsatellite loci with nonoverlapping allele-size ranges distinguished N. n. nebulosa from N. n. diardi. Along with fixed subspecies-specific chromosomal differences, this degree of differentiation is equivalent to, or greater than, comparable measures among five recognized Panthera species (lion, tiger, leopard, jaguar, and snow leopard). These distinctions increase the urgency of clouded leopard conservation efforts, and if affirmed by morphological analysis and wider sampling of N. n. diardi in Borneo and Sumatra, would support reclassification of N. n. diardi as a new species (Neofelis diardi).

  12. Molecular evidence of Chlamydophila pneumoniae infection in reptiles in Argentina.

    Science.gov (United States)

    Frutos, María C; Monetti, Marina S; Ré, Viviana E; Cuffini, Cecilia G

    2014-01-01

    In the central area of Argentina, the epidemiological and molecular characteristics of Chlamydophila pneumoniae infections in reptiles are still unknown. A nested polymerase chain reaction of the rpoB gene was used to detect C. pneumoniae in cloacal swab samples from 19 reptiles at a recreational area. Eleven (57.89%) reptiles were positive; the sequencing and phylogenetic analysis confirmed the presence of this bacterium. Neither C. pneumoniae DNA in the caregivers pharynges nor IgM antibodies anti-C. pneumoniae in their serum samples were detected; however, caregivers presented very high titers of IgG anti-C. pneumoniae. The detection of C. pneumoniae DNA in reptiles demonstrated the circulation of this agent in the recreational area and could be responsible for the exacerbated immune response of the personnel handling the reptiles, which suggests a potential zoonotic cycle. This is the first report of the detection of C. pneumoniae in reptiles in Argentina. Copyright © 2014 Asociación Colombiana de Psiquiatría. Publicado por Elsevier España. All rights reserved.

  13. Molecular Evidence of Different Rickettsia Species in Villeta, Colombia.

    Science.gov (United States)

    Faccini-Martínez, Álvaro A; Ramírez-Hernández, Alejandro; Forero-Becerra, Elkin; Cortés-Vecino, Jesús A; Escandón, Patricia; Rodas, Juan D; Palomar, Ana M; Portillo, Aránzazu; Oteo, José A; Hidalgo, Marylin

    2016-02-01

    The aim of this work was to detect and identify Rickettsia species in ticks collected in rural areas of Villeta, Colombia. Tick specimens were collected from domestic animals and walls of houses in five rural villages of Villeta town and from humans in Naranjal village (same town). Moreover, a flea collected from the same area was also processed. DNA was extracted and tested by conventional, semi-nested, and nested PCR reactions targeting rickettsial genes. In the ticks collected from humans from Naranjal village, a nymph of Amblyomma cajennense sensu lato was amplified using primers for ompA and sequenced (100% identity with "Candidatus Rickettsia amblyommii"). Last, three amplicons from the Ctenocephalides felis flea, corresponding to gltA, ompB, and 16S rRNA genes, showed high identity with R. felis (98.5%, 97.3%, and 99.2%, respectively) and "Candidatus Rickettsia asemboensis" (99.7% and 100%, respectively). To our knowledge, these results correspond to the first molecular detection in Colombia of "Candidatus Rickettsia amblyommii" and "Ca. Rickettsia asemboensis" in fleas.

  14. Evidence for Dynamic Chemical Kinetics at Individual Molecular Ruthenium Catalysts.

    Science.gov (United States)

    Easter, Quinn T; Blum, Suzanne A

    2018-02-05

    Catalytic cycles are typically depicted as possessing time-invariant steps with fixed rates. Yet the true behavior of individual catalysts with respect to time is unknown, hidden by the ensemble averaging inherent to bulk measurements. Evidence is presented for variable chemical kinetics at individual catalysts, with a focus on ring-opening metathesis polymerization catalyzed by the second-generation Grubbs' ruthenium catalyst. Fluorescence microscopy is used to probe the chemical kinetics of the reaction because the technique possesses sufficient sensitivity for the detection of single chemical reactions. Insertion reactions in submicron regions likely occur at groups of many (not single) catalysts, yet not so many that their unique kinetic behavior is ensemble averaged. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. DNA fingerprinting of sugarcane for detecting molecular evidence of somaclonal variation

    International Nuclear Information System (INIS)

    Ramos Leal, M.; Canales, E.; Michel, R.; Coto, O.; Cornide, M.T.

    1998-01-01

    Molecular characterisation of eight sugarcane mutants which tolerate 1% NaCl, was performed by means of restriction fragment length polymorphism (RFLP) analysis at the genomic level, using a group of molecular probes for ribosomal DNAs and two others, Δ-pyrroline-5-carboxylate reductase (ΔP5CR) and ATPase, probably related to salinity stress tolerance. Results showed the molecular evidence of genetic changes in comparison to the susceptible donor variety and the possible presence of more that one mechanism to tolerate salt stress. (author)

  16. New circumscription of freshwater fish parasites Monobothrium diesing, 1863 and Promonobothrium mackiewicz, 1968 (Cestoda: Caryophyllidea) using morphological and molecular evidence.

    Science.gov (United States)

    Scholz, Tomáš; Oros, Mikuláš; Choudhury, Anindo; Brabec, Jan; Waeschenbach, Andrea

    2015-02-01

    Two genera of caryophyllidean cestodes, Monobothrium Diesing, 1863 and Promonobothrium Mackiewicz, 1968 , from cypriniform fishes (cyprinids and suckers) in the Holarctic Region, are revised using morphological and molecular evidence. Monobothrium, which includes morphologically distinct species that occur in European cyprinids (Cyprinidae) and North American suckers (Catostomidae), is separated into 3 genera. Monobothrium becomes monotypic and is represented by its type species, Monobothrium wageneri Nybelin, 1922 , which occurs in European tench, Tinca tinca (Cyprinidae). Monobothrium auriculatum Kulakovskaya, 1961 from Leuciscus danilevskii (Cyprinidae) in the Ukraine, is tentatively transferred to Caryophyllaeus Gmelin, 1790 as Caryophyllaeus auriculatus ( Kulakovskaya, 1961 ) n. comb. because it possesses morphological characteristics considered to be typical of Caryophyllaeus but which are absent in Monobothrium (shape of the scolex, presence of a seminal receptacle, short neck, and absence of a large, muscular papilla surrounding the large gonopores). The 5 remaining Monobothrium species from suckers in North America are transferred to Promonobothrium based on shared morphological features and molecular data. Species of Promonobothrium differ from M. wageneri by having an external seminal vesicle (absent in M. wageneri), the absence of postovarian vitelline follicles in North American species (present in M. wageneri), and a scolex that is digitiform papillate, loculopapillate, or loculotruncate, i.e., equipped with weak loculi and a terminal introvert (vs. claviform, bluntly ended, with 6 weak, shallow, longitudinal grooves in M. wageneri). Phylogenetic analysis of nuclear ribosomal RNA genes ssr- and lsrDNA placed Promonobothrium minytremi within a clade of 3 of the 5 North American Monobothrium species. The position of M. wageneri, although distinct from the remaining Monobothrium species, is unresolved within the Caryophyllidea. This study further

  17. Coherent and incoherent giant dipole resonance γ-ray emission induced by heavy ion collisions: Study of the 40Ca+48Ca system by means of the constrained molecular dynamics model

    International Nuclear Information System (INIS)

    Papa, Massimo; Cardella, Giuseppe; Bonanno, Antonio; Pappalardo, Giuseppe; Rizzo, Francesca; Amorini, Francesca; Bonasera, Aldo; Di Pietro, Alessia; Figuera, Pier Paolo; Tudisco, Salvatore; Maruyama, Toshiki

    2003-01-01

    Coherent and incoherent dipolar γ-ray emission is studied in a fully dynamical approach by means of the constrained molecular dynamics model. The study is focused on the system 40 Ca+ 48 Ca for which recently experimental data have been collected at 25 MeV/nucleon. The approach allows us to explain the experimental results in a self-consistent way without using statistical or hybrid models. Moreover, calculations performed at higher energy show interesting correlations between the fragment formation process, the degree of collectivity, and the coherence degree of the γ-ray emission process

  18. Molecular evidence on the evolutionary and biogeographical patterns of European cyprinids.

    Science.gov (United States)

    Zardoya, R; Doadrio, I

    1999-08-01

    The phylogenetic relationships of 106 European cyprinid taxa were determined based on the complete nucleotide sequence (1140 bp) of the mitochondrial cytochrome b gene. The molecular phylogeny was used (1) to revise the current systematics of European cyprinids, (2) to establish the phylogenetic utility of traditional morphological characters that are widely used in Cyprinidae systematics, and (3) to discuss alternative hypotheses on the biogeography of the family in Europe. The age of the major lineages within European cyprinids was tentatively estimated with a molecular clock and showed full agreement with the fossil record of the group. Moreover, the results provided unambiguous evidence for a close phylogenetic affinity of some Caucasian and Greek endemic cyprinid taxa (e.g., B. capito and B. brachycephalus and Leuciscus keadicus, Barbus graecus, and B. albanicus, respectively) to Iberian and North African, but not Central European, cyprinids. The existence of such unexpected phylogenetic relationships refutes the classical hypothesis on the biogeography of European cyprinids, which assumes a dispersal of the cyprinid fauna from central Europe to southern Europe and northern Africa during the Miocene (and, hence, predicts a close phylogenetic relationship of all Caucasian, Greek, Iberian, and North African cyprinids to central European taxa). Instead, the existence of a Mediterranean realm independent of the central European route seems plausible based on the molecular evidence. It is likely that the new biogeographical scenario proposed here might apply to other primary freshwater European animals with low dispersal abilities, including fish, amphibians, and invertebrates.

  19. Neurobiology of Chronic Stress-Related Psychiatric Disorders: Evidence from Molecular Imaging Studies

    Science.gov (United States)

    Davis, Margaret T.; Holmes, Sophie E.; Pietrzak, Robert H.; Esterlis, Irina

    2018-01-01

    Chronic stress accounts for billions of dollars of economic loss annually in the United States alone, and is recognized as a major source of disability and mortality worldwide. Robust evidence suggests that chronic stress plays a significant role in the onset of severe and impairing psychiatric conditions, including major depressive disorder, bipolar disorder, and posttraumatic stress disorder. Application of molecular imaging techniques such as positron emission tomography and single photon emission computed tomography in recent years has begun to provide insight into the molecular mechanisms by which chronic stress confers risk for these disorders. The present paper provides a comprehensive review and synthesis of all positron emission tomography and single photon emission computed tomography imaging publications focused on the examination of molecular targets in individuals with major depressive disorder, posttraumatic stress disorder, or bipolar disorder to date. Critical discussion of discrepant findings and broad strengths and weaknesses of the current body of literature is provided. Recommended future directions for the field of molecular imaging to further elucidate the neurobiological substrates of chronic stress-related disorders are also discussed. This article is part of the inaugural issue for the journal focused on various aspects of chronic stress. PMID:29862379

  20. Frames of scientific evidence: How journalists represent the (un)certainty of molecular medicine in science television programs.

    Science.gov (United States)

    Ruhrmann, Georg; Guenther, Lars; Kessler, Sabrina Heike; Milde, Jutta

    2015-08-01

    For laypeople, media coverage of science on television is a gateway to scientific issues. Defining scientific evidence is central to the field of science, but there are still questions if news coverage of science represents scientific research findings as certain or uncertain. The framing approach is a suitable framework to classify different media representations; it is applied here to investigate the frames of scientific evidence in film clips (n=207) taken from science television programs. Molecular medicine is the domain of interest for this analysis, due to its high proportion of uncertain and conflicting research findings and risks. The results indicate that television clips vary in their coverage of scientific evidence of molecular medicine. Four frames were found: Scientific Uncertainty and Controversy, Scientifically Certain Data, Everyday Medical Risks, and Conflicting Scientific Evidence. They differ in their way of framing scientific evidence and risks of molecular medicine. © The Author(s) 2013.

  1. Cell phone use and parotid salivary gland alterations: no molecular evidence.

    Science.gov (United States)

    de Souza, Fabrício T A; Correia-Silva, Jeane F; Ferreira, Efigênia F; Siqueira, Elisa C; Duarte, Alessandra P; Gomez, Marcus Vinícius; Gomez, Ricardo S; Gomes, Carolina C

    2014-07-01

    The association between cell phone use and the development of parotid tumors is controversial. Because there is unequivocal evidence that the microenvironment is important for tumor formation, we investigated in the parotid glands whether cell phone use alters the expression of gene products related to cellular stress. We used the saliva produced by the parotid glands of 62 individuals to assess molecular alterations compatible with cellular stress, comparing the saliva from the gland exposed to cell phone radiation (ipsilateral) to the saliva from the opposite, unexposed parotid gland (contralateral) of each individual. We compared salivary flow, total protein concentration, p53, p21, reactive oxygen species (ROS), and salivary levels of glutathione (GSH), heat shock proteins 27 and 70, and IgA between the ipsilateral and contralateral parotids. No difference was found for any of these parameters, even when grouping individuals by period of cell phone use in years or by monthly average calls in minutes. We provide molecular evidence that the exposure of parotid glands to cell phone use does not alter parotid salivary flow, protein concentration, or levels of proteins of genes that are directly or indirectly affected by heat-induced cellular stress. ©2014 American Association for Cancer Research.

  2. Evidence of clinical utility: an unmet need in molecular diagnostics for patients with cancer.

    Science.gov (United States)

    Parkinson, David R; McCormack, Robert T; Keating, Susan M; Gutman, Steven I; Hamilton, Stanley R; Mansfield, Elizabeth A; Piper, Margaret A; Deverka, Patricia; Frueh, Felix W; Jessup, J Milburn; McShane, Lisa M; Tunis, Sean R; Sigman, Caroline C; Kelloff, Gary J

    2014-03-15

    This article defines and describes best practices for the academic and business community to generate evidence of clinical utility for cancer molecular diagnostic assays. Beyond analytical and clinical validation, successful demonstration of clinical utility involves developing sufficient evidence to demonstrate that a diagnostic test results in an improvement in patient outcomes. This discussion is complementary to theoretical frameworks described in previously published guidance and literature reports by the U.S. Food and Drug Administration, Centers for Disease Control and Prevention, Institute of Medicine, and Center for Medical Technology Policy, among others. These reports are comprehensive and specifically clarify appropriate clinical use, adoption, and payer reimbursement for assay manufacturers, as well as Clinical Laboratory Improvement Amendments-certified laboratories, including those that develop assays (laboratory developed tests). Practical criteria and steps for establishing clinical utility are crucial to subsequent decisions for reimbursement without which high-performing molecular diagnostics will have limited availability to patients with cancer and fail to translate scientific advances into high-quality and cost-effective cancer care. See all articles in this CCR Focus section, "The Precision Medicine Conundrum: Approaches to Companion Diagnostic Co-development." ©2014 AACR.

  3. Serological and molecular evidence of hepadnavirus infection in swine

    Directory of Open Access Journals (Sweden)

    Yasmine R Vieira

    2015-02-01

    Full Text Available [b]Introduction and objective[/b]. Recently, investigations in a swine herd identified evidence of the existence of a novel member of the Hepadnavirus family endemic in swine. The aim of this study was to investigate the serological and molecular markers of Hepadnavirus circulation in Brazilian domestic swine and wild boar herds, and to evaluate the identity with HBV and other Hepadnaviruses reported previously. [b]Materials and methods[/b]. For the study, 376 swine were screened for hepatitis B virus serological markers. Analyses were performed in serum samples using commercial enzyme-linked immunosorbent assay (ELISA kits (DiaSorin® for anti-HBc, HBsAg and anti-HBs. Reactive and undetermined swine serum samples were selected to perform DNA viral extraction (QIAamp DNA Mini Kit, Qiagen®, partial genome amplification and genome sequencing. [b]Results[/b]. From 376 swine samples analysed, 28 (7.45% were reactive to anti-HBc, 3 (0.80% to HBsAg and 6 (1.6% to anti-HBs. Besides, more 17 (4.52% swine samples analyzed were classified in the grey zone of the EIA test to anti-HBc and 2 (0.53% to HBsAg. From 49 samples molecularly analyzed after serological trial, 4 samples showed a positive result for the qualitative PCR for Hepadnavirus. Phylogenetic reconstruction using partial genome sequencing (360 bp of 3 samples showed similarity with HBV with 90.8–96.3% of identity. [b]Conclusions.[/b] Serological and molecular data showed evidence of the circulation of a virus similar to hepatitis B virus in swine.

  4. Hard x-ray Morphological and Spectral Studies of the Galactic Center Molecular Cloud SGR B2: Constraining Past SGR A* Flaring Activity

    DEFF Research Database (Denmark)

    Zhang, Shuo; Hailey, Charles J.; Mori, Kaya

    2015-01-01

    In 2013, NuSTAR observed the Sgr B2 region and for the first time resolved its hard X-ray emission on subarcminute scales. Two prominent features are detected above 10 keV:. a newly emerging cloud, G0.66-0.13, and the central 90 '' radius region containing two compact cores, Sgr B2(M) and Sgr B2(N......), surrounded by diffuse emission. It is inconclusive whether the remaining level of Sgr. B2 emission is still decreasing or has reached a constant background level. A decreasing X-ray emission can be best explained by the X-ray reflection nebula scenario, where the cloud reprocesses a past giant outburst from...... Sgr A*. In the X-ray reflection nebula (XRN) scenario, the 3-79 keV Sgr. B2 spectrum allows us to self-consistently test the XRN model using both the Fe K alpha line and the continuum emission. The peak luminosity of the past Sgr A* outburst is constrained to L3-79keV∼5 x 1038 ergs s-1. A newly...

  5. First molecular evidence of Toxoplasma gondii in opossums (Didelphis virginiana from Yucatan, Mexico

    Directory of Open Access Journals (Sweden)

    M. Torres-Castro

    2016-03-01

    Full Text Available Toxoplasma gondii is an obligate intracellular parasite recognized as a causal agent of toxoplasmosis; zoonotic disease endemic in many countries worldwide, including Mexico. Different species of animals participate in the wild cycle infection, including opossums of the species Didelphis virginiana. Thirteen D. virginiana were captured in Yucatan, Mexico. Detection of T. gondii was achieved by Polymerase Chain Reaction, which determined an infection of 76.9% (10/13 in brains. Positive amplicons were sequenced for analysis, this produced results similar to T. gondii with identity and coverage values of 98% and 96-100%, respectively. This study presents the first molecular evidence of the circulation of T. gondii in D. virginiana from Mexico.

  6. First molecular evidence of Toxoplasma gondii in opossums (Didelphis virginiana) from Yucatan, Mexico.

    Science.gov (United States)

    Torres-Castro, M; Noh-Pech, H; Puerto-Hernández, R; Reyes-Hernández, B; Panti-May, A; Hernández-Betancourt, S; Yeh-Gorocica, A; González-Herrera, L; Zavala-Castro, J; Puerto, F I

    2016-01-01

    Toxoplasma gondii is an obligate intracellular parasite recognized as a causal agent of toxoplasmosis; zoonotic disease endemic in many countries worldwide, including Mexico. Different species of animals participate in the wild cycle infection, including opossums of the species Didelphis virginiana. Thirteen D. virginiana were captured in Yucatan, Mexico. Detection of T. gondii was achieved by Polymerase Chain Reaction, which determined an infection of 76.9% (10/13) in brains. Positive amplicons were sequenced for analysis, this produced results similar to T. gondii with identity and coverage values of 98% and 96-100%, respectively. This study presents the first molecular evidence of the circulation of T. gondii in D. virginiana from Mexico.

  7. Fuzzy method of recognition of high molecular substances in evidence-based biology

    Science.gov (United States)

    Olevskyi, V. I.; Smetanin, V. T.; Olevska, Yu. B.

    2017-10-01

    Nowadays modern requirements to achieving reliable results along with high quality of researches put mathematical analysis methods of results at the forefront. Because of this, evidence-based methods of processing experimental data have become increasingly popular in the biological sciences and medicine. Their basis is meta-analysis, a method of quantitative generalization of a large number of randomized trails contributing to a same special problem, which are often contradictory and performed by different authors. It allows identifying the most important trends and quantitative indicators of the data, verification of advanced hypotheses and discovering new effects in the population genotype. The existing methods of recognizing high molecular substances by gel electrophoresis of proteins under denaturing conditions are based on approximate methods for comparing the contrast of electrophoregrams with a standard solution of known substances. We propose a fuzzy method for modeling experimental data to increase the accuracy and validity of the findings of the detection of new proteins.

  8. Topical use of sucralfate in epithelial wound healing: clinical evidences and molecular mechanisms of action.

    Science.gov (United States)

    Masuelli, Laura; Tumino, Giovanni; Turriziani, Mario; Modesti, Andrea; Bei, Roberto

    2010-01-01

    Sucralfate is a basic aluminium salt of sucrose octasulphate which was orally employed for prevention and treatment of several gastrointestinal diseases including gastroesophageal reflux, gastric and duodenal ulcer. Recent studies have employed sucralfate as a topical drug for the healing of several types of epithelial wounds such as ulcers, inflammatory dermatitis, mucositis and burn wounds. Epithelial wound healing is a well orchestrated process involving hemostasis, inflammatory reaction, cell proliferation and tissue remodelling which leads to granulation tissue development and filling of the wound space. This report will review clinical evidences on the use of topical sucralfate for the management of epithelial lesions and deal with the current knowledge on the molecular mechanisms of action of this compound towards the epithelial wound healing process and will also discuss relevant patents.

  9. Study of gene expression alteration in male androgenetic alopecia: evidence of predominant molecular signalling pathways.

    Science.gov (United States)

    Michel, L; Reygagne, P; Benech, P; Jean-Louis, F; Scalvino, S; Ly Ka So, S; Hamidou, Z; Bianovici, S; Pouch, J; Ducos, B; Bonnet, M; Bensussan, A; Patatian, A; Lati, E; Wdzieczak-Bakala, J; Choulot, J-C; Loing, E; Hocquaux, M

    2017-11-01

    Male androgenetic alopecia (AGA) is the most common form of hair loss in men. It is characterized by a distinct pattern of progressive hair loss starting from the frontal area and the vertex of the scalp. Although several genetic risk loci have been identified, relevant genes for AGA remain to be defined. To identify biomarkers associated with AGA. Molecular biomarkers associated with premature AGA were identified through gene expression analysis using cDNA generated from scalp vertex biopsies of hairless or bald men with premature AGA, and healthy volunteers. This monocentric study reveals that genes encoding mast cell granule enzymes, inflammatory mediators and immunoglobulin-associated immune mediators were significantly overexpressed in AGA. In contrast, underexpressed genes appear to be associated with the Wnt/β-catenin and bone morphogenic protein/transforming growth factor-β signalling pathways. Although involvement of these pathways in hair follicle regeneration is well described, functional interpretation of the transcriptomic data highlights different events that account for their inhibition. In particular, one of these events depends on the dysregulated expression of proopiomelanocortin, as confirmed by polymerase chain reaction and immunohistochemistry. In addition, lower expression of CYP27B1 in patients with AGA supports the notion that changes in vitamin D metabolism contributes to hair loss. This study provides compelling evidence for distinct molecular events contributing to alopecia that may pave the way for new therapeutic approaches. © 2017 British Association of Dermatologists.

  10. The Roles of recognition processes and look-ahead search in time-constrained expert problem solving: Evidence from grandmaster level chess.

    OpenAIRE

    Gobet, F; Simon, H A

    1996-01-01

    Chess has long served as an important standard task environment for research on human memory and problem-solving abilities and processes. In this paper, we report evidence on the relative importance of recognition processes and planning (look-ahead) processes in very high level expert performance in chess. The data show that the rated skill of a top-level grandmaster is only slightly lower when he is playing simultaneously against a half dozen grandmaster opponents than under tournament con...

  11. Molecular evidence for lignin degradation in sulfate-reducing mangrove sediments (Amazônia, Brazil)

    Science.gov (United States)

    Dittmar, Thorsten; Lara, Rubén José

    2001-05-01

    - Molecular lignin analyses have become a powerful quantitative approach for estimating flux and fate of vascular plant organic matter in coastal and marine environments. The use of a specific molecular biomarker requires detailed knowledge of its decomposition rates relative to the associated organic matter and its structural diagenetic changes. To gain insight into the poorly known processes of anaerobic lignin diagenesis, molecular analyses were performed in the sulfate-reducing sediment of a north Brazilian mangrove. Organic matter in samples representing different diagenetic stages (i.e., fresh litter, a sediment core, and percolating water) was characterized by alkaline CuO oxidation for lignin composition, element (C, N), and stable carbon isotope analyses. On the basis of these results and on a balance model, long-term in situ decomposition rates of lignin in sulfate-reducing sediments were estimated for the first time. The half-life ( T1/2) of lignin derived from mangrove leaf litter (mainly Rhizophora mangle) was ˜150 yr in the upper 1.5 m of the sediment. Associated organic carbon from leaf tissue was depleted to ˜75% within weeks, followed by a slow mineralization in the sediment ( T1/2 ≈ 300 yr). Unlike the known pathways of lignin diagenesis, even highly degraded lignin did not show any alterations of the propyl or methoxyl side chains, as evident from stable acid to aldehyde ratios and the proportion of methoxylated phenols (vanillyl and syringyl phenols). Aromatic ring cleavage is probably the principal mechanism for lignin decay in the studied environment. Cinnamyl phenols were highly abundant in mangrove leaves and were rapidly depleted during early diagenesis. Thus, the cinnamyl to vanillyl ratio could be used as a tracer for early diagenesis even under the sulfate-reducing conditions. Syringyl phenols were removed from dissolved organic matter in interstitial water, probably by sorption onto the sediment. Suspended organic matter in a

  12. Clinical translation of photobiomodulation therapy using evidences from precision molecular pathway analyses (Conference Presentation)

    Science.gov (United States)

    Arany, Praveen

    2017-02-01

    Can `light' be a Drug? To satisfy this definition as a pharmaceutical agent, light must be absorbed and change bodily function. Much evidence from our understanding of our visual cycle and Vitamin D metabolism have all noted this phenomenon. Advances in optophotonic technologies along with a better understanding of light-tissue interactions, especially in in vivo optical imaging and optogenetics, are spearheading the popularity of biophotonics in biology and medicine. The use of lasers and light devices at high doses in dermatology, ophthalmology, oncology and dentistry are now considered mainstream for certain clinical applications such as surgery, skin rejuvenation, ocular and soft tissue recontouring, anti-tumor and anti-microbial photodynamic therapy. In contrast, therapeutic use of low dose biophotonics devices is called Low Level Light / Laser Therapy (LLLT), now termed Photobiomodulation (PBM) Therapy. This therapy is defined as a non-thermal use of non-ionizing forms of electromagnetic radiation to alleviate pain, inflammation, modulating the immune responses and promoting wound healing and tissue regeneration. Surprisingly, despite vast volumes of scientific literature from both clinical and laboratory studies noting the phenomenological evidences for this innovative therapy, limited mechanistic insights have prevented the development of rigorous, reproducible clinical protocols. This presentation will outline our current efforts at ongoing efforts in our group to assess molecular pathways and precisely define clinical treatment variables to enable clinical translation with PBM therapies.

  13. Three Molecular Markers Show No Evidence of Population Genetic Structure in the Gouldian Finch (Erythrura gouldiae.

    Directory of Open Access Journals (Sweden)

    Peri E Bolton

    Full Text Available Assessment of genetic diversity and connectivity between regions can inform conservation managers about risk of inbreeding, potential for adaptation and where population boundaries lie. The Gouldian finch (Erythrura gouldiae is a threatened species in northern Australia, occupying the savannah woodlands of the biogeographically complex monsoon tropics. We present the most comprehensive population genetic analysis of diversity and structure the Gouldian finch using 16 microsatellite markers, mitochondrial control region and 3,389 SNPs from genotyping-by-sequencing. Mitochondrial diversity is compared across three related, co-distributed finches with different conservation threat-statuses. There was no evidence of genetic differentiation across the western part of the range in any of the molecular markers, and haplotype diversity but not richness was lower than a common co-distributed species. Individuals within the panmictic population in the west may be highly dispersive within this wide area, and we urge caution when interpreting anecdotal observations of changes to the distribution and/or flock sizes of Gouldian finch populations as evidence of overall changes to the population size of this species.

  14. Applying Unique Molecular Identifiers in Next Generation Sequencing Reveals a Constrained Viral Quasispecies Evolution under Cross-Reactive Antibody Pressure Targeting Long Alpha Helix of Hemagglutinin

    Science.gov (United States)

    Hauck, Nastasja C.; Kirpach, Josiane; Kiefer, Christina; Farinelle, Sophie; Morris, Stephen A.; Muller, Claude P.; Lu, I-Na

    2018-01-01

    To overcome yearly efforts and costs for the production of seasonal influenza vaccines, new approaches for the induction of broadly protective and long-lasting immune responses have been developed in the past decade. To warrant safety and efficacy of the emerging crossreactive vaccine candidates, it is critical to understand the evolution of influenza viruses in response to these new immune pressures. Here we applied unique molecular identifiers in next generation sequencing to analyze the evolution of influenza quasispecies under in vivo antibody pressure targeting the hemagglutinin (HA) long alpha helix (LAH). Our vaccine targeting LAH of hemagglutinin elicited significant seroconversion and protection against homologous and heterologous influenza virus strains in mice. The vaccine not only significantly reduced lung viral titers, but also induced a well-known bottleneck effect by decreasing virus diversity. In contrast to the classical bottleneck effect, here we showed a significant increase in the frequency of viruses with amino acid sequences identical to that of vaccine targeting LAH domain. No escape mutant emerged after vaccination. These results not only support the potential of a universal influenza vaccine targeting the conserved LAH domains, but also clearly demonstrate that the well-established bottleneck effect on viral quasispecies evolution does not necessarily generate escape mutants. PMID:29587397

  15. "Invisible" conformers of an antifungal disulfide protein revealed by constrained cold and heat unfolding, CEST-NMR experiments, and molecular dynamics calculations.

    Science.gov (United States)

    Fizil, Ádám; Gáspári, Zoltán; Barna, Terézia; Marx, Florentine; Batta, Gyula

    2015-03-23

    Transition between conformational states in proteins is being recognized as a possible key factor of function. In support of this, hidden dynamic NMR structures were detected in several cases up to populations of a few percent. Here, we show by two- and three-state analysis of thermal unfolding, that the population of hidden states may weight 20-40 % at 298 K in a disulfide-rich protein. In addition, sensitive (15) N-CEST NMR experiments identified a low populated (0.15 %) state that was in slow exchange with the folded PAF protein. Remarkably, other techniques failed to identify the rest of the NMR "dark matter". Comparison of the temperature dependence of chemical shifts from experiments and molecular dynamics calculations suggests that hidden conformers of PAF differ in the loop and terminal regions and are most similar in the evolutionary conserved core. Our observations point to the existence of a complex conformational landscape with multiple conformational states in dynamic equilibrium, with diverse exchange rates presumably responsible for the completely hidden nature of a considerable fraction. © 2015 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

  16. “Invisible” Conformers of an Antifungal Disulfide Protein Revealed by Constrained Cold and Heat Unfolding, CEST-NMR Experiments, and Molecular Dynamics Calculations

    Science.gov (United States)

    Fizil, Ádám; Gáspári, Zoltán; Barna, Terézia; Marx, Florentine; Batta, Gyula

    2015-01-01

    Transition between conformational states in proteins is being recognized as a possible key factor of function. In support of this, hidden dynamic NMR structures were detected in several cases up to populations of a few percent. Here, we show by two- and three-state analysis of thermal unfolding, that the population of hidden states may weight 20–40 % at 298 K in a disulfide-rich protein. In addition, sensitive 15N-CEST NMR experiments identified a low populated (0.15 %) state that was in slow exchange with the folded PAF protein. Remarkably, other techniques failed to identify the rest of the NMR “dark matter”. Comparison of the temperature dependence of chemical shifts from experiments and molecular dynamics calculations suggests that hidden conformers of PAF differ in the loop and terminal regions and are most similar in the evolutionary conserved core. Our observations point to the existence of a complex conformational landscape with multiple conformational states in dynamic equilibrium, with diverse exchange rates presumably responsible for the completely hidden nature of a considerable fraction. PMID:25676351

  17. Applying Unique Molecular Identifiers in Next Generation Sequencing Reveals a Constrained Viral Quasispecies Evolution under Cross-Reactive Antibody Pressure Targeting Long Alpha Helix of Hemagglutinin

    Directory of Open Access Journals (Sweden)

    Nastasja C. Hauck

    2018-03-01

    Full Text Available To overcome yearly efforts and costs for the production of seasonal influenza vaccines, new approaches for the induction of broadly protective and long-lasting immune responses have been developed in the past decade. To warrant safety and efficacy of the emerging crossreactive vaccine candidates, it is critical to understand the evolution of influenza viruses in response to these new immune pressures. Here we applied unique molecular identifiers in next generation sequencing to analyze the evolution of influenza quasispecies under in vivo antibody pressure targeting the hemagglutinin (HA long alpha helix (LAH. Our vaccine targeting LAH of hemagglutinin elicited significant seroconversion and protection against homologous and heterologous influenza virus strains in mice. The vaccine not only significantly reduced lung viral titers, but also induced a well-known bottleneck effect by decreasing virus diversity. In contrast to the classical bottleneck effect, here we showed a significant increase in the frequency of viruses with amino acid sequences identical to that of vaccine targeting LAH domain. No escape mutant emerged after vaccination. These results not only support the potential of a universal influenza vaccine targeting the conserved LAH domains, but also clearly demonstrate that the well-established bottleneck effect on viral quasispecies evolution does not necessarily generate escape mutants.

  18. Evolutionary constrained optimization

    CERN Document Server

    Deb, Kalyanmoy

    2015-01-01

    This book makes available a self-contained collection of modern research addressing the general constrained optimization problems using evolutionary algorithms. Broadly the topics covered include constraint handling for single and multi-objective optimizations; penalty function based methodology; multi-objective based methodology; new constraint handling mechanism; hybrid methodology; scaling issues in constrained optimization; design of scalable test problems; parameter adaptation in constrained optimization; handling of integer, discrete and mix variables in addition to continuous variables; application of constraint handling techniques to real-world problems; and constrained optimization in dynamic environment. There is also a separate chapter on hybrid optimization, which is gaining lots of popularity nowadays due to its capability of bridging the gap between evolutionary and classical optimization. The material in the book is useful to researchers, novice, and experts alike. The book will also be useful...

  19. Hybridization improved bacteria resistance in abalone: Evidence from physiological and molecular responses.

    Science.gov (United States)

    Liang, Shuang; Luo, Xuan; You, Weiwei; Ke, Caihuan

    2018-01-01

    are more active or efficient in immune system function, hence they could effectively defense against a bacterial invasion, leading to higher survival rates after challenge. This study provides physiological and molecular evidences for interpreting the disease resistant heterosis in this abalone hybrid system, which could help us in a better understanding and utilization of heterosis in abalone aquaculture. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. The evidence base for the use of internal dosimetry in the clinical practice of molecular radiotherapy

    Energy Technology Data Exchange (ETDEWEB)

    Strigari, Lidia [Regina Elena National Cancer Institute, Laboratory of Medical Physics and Expert Systems, Rome (Italy); Konijnenberg, Mark [Erasmus MC, Department of Nuclear Medicine, Rotterdam (Netherlands); Chiesa, Carlo [Instituto Nazionale Tumori, Department of Nuclear Medicine, Milan (Italy); Bardies, Manuel [UMR 1037 INSERM / Universite Paul Sabatier, Centre de Recherche en Cancerologie de Toulouse, Toulouse (France); Du, Yong [Royal Marsden NHS Foundation Trust, Department of Nuclear Medicine and PET/CT, Sutton, London (United Kingdom); Gleisner, Katarina Sjoegreen [Medical Radiation Physics, Clinical Sciences, Lund (Sweden); Lassmann, Michael [University of Wuerzburg, Department of Nuclear Medicine, Wuerzburg (Germany); Flux, Glenn [Royal Marsden NHS Foundation Trust and Institute of Cancer Research, Joint Department of Physics, Sutton (United Kingdom)

    2014-10-15

    Molecular radiotherapy (MRT) has demonstrated unique therapeutic advantages in the treatment of an increasing number of cancers. As with other treatment modalities, there is related toxicity to a number of organs at risk. Despite the large number of clinical trials over the past several decades, considerable uncertainties still remain regarding the optimization of this therapeutic approach and one of the vital issues to be answered is whether an absorbed radiation dose-response exists that could be used to guide personalized treatment. There are only limited and sporadic data investigating MRT dosimetry. The determination of dose-effect relationships for MRT has yet to be the explicit aim of a clinical trial. The aim of this article was to collate and discuss the available evidence for an absorbed radiation dose-effect relationships in MRT through a review of published data. Based on a PubMed search, 92 papers were found. Out of 79 studies investigating dosimetry, an absorbed dose-effect correlation was found in 48. The application of radiobiological modelling to clinical data is of increasing importance and the limited published data on absorbed dose-effect relationships based on these models are also reviewed. Based on National Cancer Institute guideline definition, the studies had a moderate or low rate of clinical relevance due to the limited number of studies investigating overall survival and absorbed dose. Nevertheless, the evidence strongly implies a correlation between the absorbed doses delivered and the response and toxicity, indicating that dosimetry-based personalized treatments would improve outcome and increase survival. (orig.)

  1. Morphological and molecular evidence for a stepwise evolutionary transition from teeth to baleen in mysticete whales.

    Science.gov (United States)

    Deméré, Thomas A; McGowen, Michael R; Berta, Annalisa; Gatesy, John

    2008-02-01

    The origin of baleen in mysticete whales represents a major transition in the phylogenetic history of Cetacea. This key specialization, a keratinous sieve that enables filter-feeding, permitted exploitation of a new ecological niche and heralded the evolution of modern baleen-bearing whales, the largest animals on Earth. To date, all formally described mysticete fossils conform to two types: toothed species from Oligocene-age rocks ( approximately 24 to 34 million years old) and toothless species that presumably utilized baleen to feed (Recent to approximately 30 million years old). Here, we show that several Oligocene toothed mysticetes have nutrient foramina and associated sulci on the lateral portions of their palates, homologous structures in extant mysticetes house vessels that nourish baleen. The simultaneous occurrence of teeth and nutrient foramina implies that both teeth and baleen were present in these early mysticetes. Phylogenetic analyses of a supermatrix that includes extinct taxa and new data for 11 nuclear genes consistently resolve relationships at the base of Mysticeti. The combined data set of 27,340 characters supports a stepwise transition from a toothed ancestor, to a mosaic intermediate with both teeth and baleen, to modern baleen whales that lack an adult dentition but retain developmental and genetic evidence of their ancestral toothed heritage. Comparative sequence data for ENAM (enamelin) and AMBN (ameloblastin) indicate that enamel-specific loci are present in Mysticeti but have degraded to pseudogenes in this group. The dramatic transformation in mysticete feeding anatomy documents an apparently rare, stepwise mode of evolution in which a composite phenotype bridged the gap between primitive and derived morphologies; a combination of fossil and molecular evidence provides a multifaceted record of this macroevolutionary pattern.

  2. Deciphering spreading mechanisms in amyotrophic lateral sclerosis: clinical evidence and potential molecular processes.

    Science.gov (United States)

    Pradat, Pierre-François; Kabashi, Edor; Desnuelle, Claude

    2015-10-01

    The aim of this review is to refer to recent arguments supporting the existence of specific propagation mechanisms associated with spreading of neuron injury in amyotrophic lateral sclerosis (ALS). Misfolded ALS-linked protein accumulation can induce aggregation of their native equivalent isoforms through a mechanism analogous to the infectious prion proteins initiation and its propagation. Although ALS is clinically heterogeneous, a shared characteristic is the focal onset and the progressive extension to all body regions. Being viewed until now as just summation of the increased number of affected neurons, dispersion is now rather considered as the result of a seeded self-propagating process. A sequential regional spreading pattern is supported by the distribution of TDP-43 aggregates in ALS autopsy cases. Electrophysiology and advanced neuroimaging methods also recently provided some evidence for propagation of lesions both in the brain and spinal cord, more longitudinal studies being still needed. Lesions are supposed to spread cell-to-cell regionally or through connected neuronal pathway. At the molecular level, the prion-like spreading is an emerging mechanism hypothesis, but other machineries such as those that are in charge of dealing with misfolded proteins and secretion of deleterious peptides may be involved in the propagation of neuron loss. Deciphering the mechanisms underlying spreading of ALS symptoms is of crucial importance to better understand this neurodegenerative disease, build new and appropriate animal models and to define novel therapeutic targets.

  3. Molecular evidence of sorbitol dehydrogenase in tomato, a non-Rosaceae plant.

    Science.gov (United States)

    Ohta, Kazuhiro; Moriguchi, Ryo; Kanahama, Koki; Yamaki, Shohei; Kanayama, Yoshinori

    2005-12-01

    The enzyme NAD-dependent sorbitol dehydrogenase (SDH) is well characterized in the Rosaceae family of fruit trees, which synthesizes sorbitol as a translocatable photosynthate. Expressed sequence tags of SDH-like sequences have also been generated from various non-Rosaceae species that do not synthesize sorbitol as a primary photosynthetic product, but the physiological roles of the encoded proteins in non-Rosaceae plants are unknown. Therefore, we isolated an SDH-like cDNA (SDL) from tomato (Lycopersicon esculentum Mill.). Genomic Southern blot analysis suggested that SDL exists in the tomato genome as a single-copy gene. Northern blot analysis showed that SDL is ubiquitously expressed in tomato plants. Recombinant SDL protein was produced and purified for enzymatic characterization. SDL catalyzed the interconversion of sorbitol and fructose with NAD (H). SDL showed highest activity for sorbitol among the several substrates tested. SDL showed no activity with NADP+. Thus, SDL was identified as a SDH, although the Km values and substrate specificity of SDL were significantly different from those of SDH purified from the Japanese pear (Pyrus pyrifolia), a Rosaceae fruit tree. In addition, tomato was transformed with antisense SDL to evaluate the contribution of SDL to SDH activity in tomato. The transformation decreased SDH activity to approximately 50% on average. Taken together, these results provide molecular evidence of SDH in tomato, and SDL was renamed LeSDH.

  4. Speciation in ancient cryptic species complexes: evidence from the molecular phylogeny of Brachionus plicatilis (Rotifera).

    Science.gov (United States)

    Gómez, Africa; Serra, Manuel; Carvalho, Gary R; Lunt, David H

    2002-07-01

    Continental lake-dwelling zooplanktonic organisms have long been considered cosmopolitan species with little geographic variation in spite of the isolation of their habitats. Evidence of morphological cohesiveness and high dispersal capabilities support this interpretation. However, this view has been challenged recently as many such species have been shown either to comprise cryptic species complexes or to exhibit marked population genetic differentiation and strong phylogeographic structuring at a regional scale. Here we investigate the molecular phylogeny of the cosmopolitan passively dispersing rotifer Brachionus plicatilis (Rotifera: Monogononta) species complex using nucleotide sequence variation from both nuclear (ribosomal internal transcribed spacer 1, ITS1) and mitochondrial (cytochrome c oxidase subunit I, COI) genes. Analysis of rotifer resting eggs from 27 salt lakes in the Iberian Peninsula plus lakes from four continents revealed nine genetically divergent lineages. The high level of sequence divergence, absence of hybridization, and extensive sympatry observed support the specific status of these lineages. Sequence divergence estimates indicate that the B. plicatilis complex began diversifying many millions of years ago, yet has showed relatively high levels of morphological stasis. We discuss these results in relation to the ecology and genetics of aquatic invertebrates possessing dispersive resting propagules and address the apparent contradiction between zooplanktonic population structure and their morphological stasis.

  5. Molecular genetic evidence for the place of origin of the Pacific rat, Rattus exulans.

    Directory of Open Access Journals (Sweden)

    Vicki Thomson

    Full Text Available Commensal plants and animals have long been used to track human migrations, with Rattus exulans (the Pacific rat a common organism for reconstructing Polynesian dispersal in the Pacific. However, with no knowledge of the homeland of R. exulans, the place of origin of this human-commensal relationship is unknown. We conducted a mitochondrial DNA phylogeographic survey of R. exulans diversity across the potential natural range in mainland and Island Southeast Asia in order to establish the origin of this human-commensal dyad. We also conducted allozyme electrophoresis on samples from ISEA to obtain a perspective on patterns of genetic diversity in this critical region. Finally, we compared molecular genetic evidence with knowledge of prehistoric rodent faunas in mainland and ISEA. We find that ISEA populations of R. exulans contain the highest mtDNA lineage diversity including significant haplotype diversity not represented elsewhere in the species range. Within ISEA, the island of Flores in the Lesser Sunda group contains the highest diversity in ISEA (across all loci and also has a deep fossil record of small mammals that appears to include R. exulans. Therefore, in addition to Flores harboring unusual diversity in the form of Homo floresiensis, dwarfed stegodons and giant rats, this island appears to be the homeland of R. exulans.

  6. Molecular imaging of tumor photoimmunotherapy: Evidence of photosensitized tumor necrosis and hemodynamic changes

    DEFF Research Database (Denmark)

    Kishimoto, Shun; Oshima, Nobu; Yamamoto, Kazutoshi

    2018-01-01

    Near-infrared photoimmunotherapy (NIR PIT) employs the photoabsorbing dye IR700 conjugated to antibodies specific for cell surface epidermal growth factor receptor (EGFR). NIR PIT has shown highly selective cytotoxicity in vitro and in vivo. Cell necrosis is thought to be the main mode of cytotox......Near-infrared photoimmunotherapy (NIR PIT) employs the photoabsorbing dye IR700 conjugated to antibodies specific for cell surface epidermal growth factor receptor (EGFR). NIR PIT has shown highly selective cytotoxicity in vitro and in vivo. Cell necrosis is thought to be the main mode...... of cytotoxicity based mainly on in vitro studies. To better understand the acute effects of NIR PIT, molecular imaging studies were performed to assess its cellular and vascular effects.In addition to in vitro studies for cytotoxicity of NIR PIT, the in vivo tumoricidal effects and hemodynamic changes induced....... Following NIR PIT, metabolic MRI using hyperpolarized fumarate showed the production of malate in EGFR-expressing A431 tumor xenografts, providing direct evidence for photosensitized tumor necrosis induced by NIR PIT. R2* mapping studies showed temporal changes in oxygenation, with an accompanying increase...

  7. Diversification and the rate of molecular evolution: no evidence of a link in mammals

    Directory of Open Access Journals (Sweden)

    Bromham Lindell

    2011-10-01

    Full Text Available Abstract Background Recent research has indicated a positive association between rates of molecular evolution and diversification in a number of taxa. However debate continues concerning the universality and cause of this relationship. Here, we present the first systematic investigation of this relationship within the mammals. We use phylogenetically independent sister-pair comparisons to test for a relationship between substitution rates and clade size at a number of taxonomic levels. Total, non-synonymous and synonymous substitution rates were estimated from mitochondrial and nuclear DNA sequences. Results We found no evidence for an association between clade size and substitution rates in mammals, for either the nuclear or the mitochondrial sequences. We found significant associations between body size and substitution rates, as previously reported. Conclusions Our results present a contrast to previous research, which has reported significant positive associations between substitution rates and diversification for birds, angiosperms and reptiles. There are three possible reasons for the differences between the observed results in mammals versus other clades. First, there may be no link between substitution rates and diversification in mammals. Second, this link may exist, but may be much weaker in mammals than in other clades. Third, the link between substitution rates and diversification may exist in mammals, but may be confounded by other variables.

  8. Diversification and the rate of molecular evolution: no evidence of a link in mammals.

    Science.gov (United States)

    Goldie, Xavier; Lanfear, Robert; Bromham, Lindell

    2011-10-04

    Recent research has indicated a positive association between rates of molecular evolution and diversification in a number of taxa. However debate continues concerning the universality and cause of this relationship. Here, we present the first systematic investigation of this relationship within the mammals. We use phylogenetically independent sister-pair comparisons to test for a relationship between substitution rates and clade size at a number of taxonomic levels. Total, non-synonymous and synonymous substitution rates were estimated from mitochondrial and nuclear DNA sequences. We found no evidence for an association between clade size and substitution rates in mammals, for either the nuclear or the mitochondrial sequences. We found significant associations between body size and substitution rates, as previously reported. Our results present a contrast to previous research, which has reported significant positive associations between substitution rates and diversification for birds, angiosperms and reptiles. There are three possible reasons for the differences between the observed results in mammals versus other clades. First, there may be no link between substitution rates and diversification in mammals. Second, this link may exist, but may be much weaker in mammals than in other clades. Third, the link between substitution rates and diversification may exist in mammals, but may be confounded by other variables.

  9. Molecular, cellular and physiological evidences for the anorexigenic actions of nesfatin-1 in goldfish.

    Directory of Open Access Journals (Sweden)

    Ronald Gonzalez

    2010-12-01

    Full Text Available Nesfatin-1 is a recently discovered anorexigen encoded in the precursor peptide, nucleobindin-2 (NUCB2 in mammals. To date, nesfatin-1 has not been described in any non-mammalian species, although some information is available in the sequenced genomes of several species. Our objective was to characterize nesfatin-1 in fish.In the present study, we employed molecular, immunohistochemical, and physiological studies to characterize the structure, distribution, and appetite regulatory effects of nesfatin-1 in a non-mammalian vertebrate. A very high conservation in NUCB2 sequences, especially in the nesfatin-1 region was found in lower vertebrates. Abundant expression of NUCB2 mRNA was detected in several tissues including the brain and liver of goldfish. Nesfatin-1-like immunoreactive cells are present in the feeding regulatory nucleus of the hypothalamus and in the gastrointestinal tract of goldfish. Approximately 6-fold increase in NUCB2 mRNA levels was found in the liver after 7-day food-deprivation, and a similar increase was also found after short-term fasting. This points toward a possible liver specific role for NUCB2 in the control of metabolism during food-deprivation. Meanwhile, ∼2-fold increase at 1 and 3 h post-feeding and an ∼3-fold reduction after a 7-day food-deprivation was observed in NUCB2 mRNA in the goldfish hypothalamus. In vivo, a single intraperitoneal injection of the full-length native (goldfish; gf nesfatin-1 at a dose of 50 ng/g body weight induced a 23% reduction of food intake one hour post-injection in goldfish. Furthermore, intracerebroventricular injection of gfnesfatin-1 at a dose of 5 ng/g body weight resulted in ∼50% reduction in food intake.Our results provide molecular, anatomical and functional evidences to support potential anorectic and metabolic roles for endogenous nesfatin-1 in goldfish. Collectively, we provide novel information on NUCB2 in non-mammals and an anorexigenic role for nesfatin-1 in

  10. Exploring Constrained Creative Communication

    DEFF Research Database (Denmark)

    Sørensen, Jannick Kirk

    2017-01-01

    Creative collaboration via online tools offers a less ‘media rich’ exchange of information between participants than face-to-face collaboration. The participants’ freedom to communicate is restricted in means of communication, and rectified in terms of possibilities offered in the interface. How do...... these constrains influence the creative process and the outcome? In order to isolate the communication problem from the interface- and technology problem, we examine via a design game the creative communication on an open-ended task in a highly constrained setting, a design game. Via an experiment the relation...... between communicative constrains and participants’ perception of dialogue and creativity is examined. Four batches of students preparing for forming semester project groups were conducted and documented. Students were asked to create an unspecified object without any exchange of communication except...

  11. Evident?

    DEFF Research Database (Denmark)

    Plant, Peter

    2012-01-01

    Quality assurance and evidence in career guidance in Europe are often seen as self-evident approaches, but particular interests lie behind......Quality assurance and evidence in career guidance in Europe are often seen as self-evident approaches, but particular interests lie behind...

  12. Mixed signals? Morphological and molecular evidence suggest a color polymorphism in some neotropical polythore damselflies.

    Directory of Open Access Journals (Sweden)

    Melissa Sánchez Herrera

    Full Text Available The study of color polymorphisms (CP has provided profound insights into the maintenance of genetic variation in natural populations. We here offer the first evidence for an elaborate wing polymorphism in the Neotropical damselfly genus Polythore, which consists of 21 described species, distributed along the eastern slopes of the Andes in South America. These damselflies display highly complex wing colors and patterning, incorporating black, white, yellow, and orange in multiple wing bands. Wing colors, along with some components of the male genitalia, have been the primary characters used in species description; few other morphological traits vary within the group, and so there are few useful diagnostic characters. Previous research has indicated the possibility of a cryptic species existing in P. procera in Colombia, despite there being no significant differences in wing color and pattern between the populations of the two putative species. Here we analyze the complexity and diversity of wing color patterns of individuals from five described Polythore species in the Central Amazon Basin of Peru using a novel suite of morphological analyses to quantify wing color and pattern: geometric morphometrics, chromaticity analysis, and Gabor wavelet transformation. We then test whether these color patterns are good predictors of species by recovering the phylogenetic relationships among the 5 species using the barcode gene (COI. Our results suggest that, while highly distinct and discrete wing patterns exist in Polythore, these "wingforms" do not represent monophyletic clades in the recovered topology. The wingforms identified as P. victoria and P. ornata are both involved in a polymorphism with P. neopicta; also, cryptic speciation may have taking place among individuals with the P. victoria wingform. Only P. aurora and P. spateri represent monophyletic species with a single wingform in our molecular phylogeny. We discuss the implications of this

  13. Mixed signals? Morphological and molecular evidence suggest a color polymorphism in some neotropical polythore damselflies.

    Science.gov (United States)

    Sánchez Herrera, Melissa; Kuhn, William R; Lorenzo-Carballa, Maria Olalla; Harding, Kathleen M; Ankrom, Nikole; Sherratt, Thomas N; Hoffmann, Joachim; Van Gossum, Hans; Ware, Jessica L; Cordero-Rivera, Adolfo; Beatty, Christopher D

    2015-01-01

    The study of color polymorphisms (CP) has provided profound insights into the maintenance of genetic variation in natural populations. We here offer the first evidence for an elaborate wing polymorphism in the Neotropical damselfly genus Polythore, which consists of 21 described species, distributed along the eastern slopes of the Andes in South America. These damselflies display highly complex wing colors and patterning, incorporating black, white, yellow, and orange in multiple wing bands. Wing colors, along with some components of the male genitalia, have been the primary characters used in species description; few other morphological traits vary within the group, and so there are few useful diagnostic characters. Previous research has indicated the possibility of a cryptic species existing in P. procera in Colombia, despite there being no significant differences in wing color and pattern between the populations of the two putative species. Here we analyze the complexity and diversity of wing color patterns of individuals from five described Polythore species in the Central Amazon Basin of Peru using a novel suite of morphological analyses to quantify wing color and pattern: geometric morphometrics, chromaticity analysis, and Gabor wavelet transformation. We then test whether these color patterns are good predictors of species by recovering the phylogenetic relationships among the 5 species using the barcode gene (COI). Our results suggest that, while highly distinct and discrete wing patterns exist in Polythore, these "wingforms" do not represent monophyletic clades in the recovered topology. The wingforms identified as P. victoria and P. ornata are both involved in a polymorphism with P. neopicta; also, cryptic speciation may have taking place among individuals with the P. victoria wingform. Only P. aurora and P. spateri represent monophyletic species with a single wingform in our molecular phylogeny. We discuss the implications of this polymorphism, and the

  14. First molecular evidence of Hepatozoon canis infection in red foxes and golden jackals from Hungary.

    Science.gov (United States)

    Farkas, Róbert; Solymosi, Norbert; Takács, Nóra; Hornyák, Ákos; Hornok, Sándor; Nachum-Biala, Yaarit; Baneth, Gad

    2014-07-02

    Recently, Hepatozoon canis infection has been detected among shepherd, hunting and stray dogs in the southern part of Hungary, which is considered to be free of Rhipicephalus sanguineus sensu lato and close to the border with Croatia. The aim of this study was to acquire information on the possibility that red foxes and/or golden jackals could play a role in the appearance and spread of H. canis in Hungary. A conventional PCR was used to amplify a 666 bp long fragment of the Hepatozoon 18S rRNA gene from blood samples collected from 334 foxes shot in 231 locations in 16 counties and 15 golden jackals shot in 9 locations in two southwestern counties close to Croatia. A second PCR assay was performed in some of the samples positive by the first PCR to amplify a larger segment (approximately 1500 bp) of the 18S rRNA gene of Hepatozoon spp. for further phylogenetic analysis. Hepatozoon infection was detected in canids shot in 30 locations and 9 counties. Altogether 26 foxes (8.0%, 95% CI: 5-11%) and 9 jackals (60%, 95% CI: 33-81%) were PCR positive. Hepatozoon canis sequences were obtained from 12 foxes and 7 jackals. DNA sequences from 16 animals were 99-100% similar to H. canis from Croatian foxes or dogs while two of the sequences were 99% similar to an Italian fox. Half (13/26) of the infected red foxes and all golden jackals were shot in the two southwestern counties. This is the first report on molecular evidence of H. canis in red foxes (Vulpes vulpes) and golden jackals (Canis aureus) from Hungary, which is considered free from the tick vector of H. canis, R. sanguineus. Although no R. sanguineus sensu lato had been found on infected or non-infected wild canids, the detection of authochnous canine hepatozoonosis in Hungary might imply that the range of R. sanguineus sensu lato has reached this country.

  15. Molecular evidence of the toxic effects of diatom diets on gene expression patterns in copepods.

    Directory of Open Access Journals (Sweden)

    Chiara Lauritano

    Full Text Available Diatoms are dominant photosynthetic organisms in the world's oceans and are considered essential in the transfer of energy through marine food chains. However, these unicellular plants at times produce secondary metabolites such as polyunsaturated aldehydes and other products deriving from the oxidation of fatty acids that are collectively termed oxylipins. These cytotoxic compounds are responsible for growth inhibition and teratogenic activity, potentially sabotaging future generations of grazers by inducing poor recruitment in marine organisms such as crustacean copepods.Here we show that two days of feeding on a strong oxylipin-producing diatom (Skeletonema marinoi is sufficient to inhibit a series of genes involved in aldehyde detoxification, apoptosis, cytoskeleton structure and stress response in the copepod Calanus helgolandicus. Of the 18 transcripts analyzed by RT-qPCR at least 50% were strongly down-regulated (aldehyde dehydrogenase 9, 8 and 6, cellular apoptosis susceptibility and inhibitor of apoptosis IAP proteins, heat shock protein 40, alpha- and beta-tubulins compared to animals fed on a weak oxylipin-producing diet (Chaetoceros socialis which showed no changes in gene expression profiles.Our results provide molecular evidence of the toxic effects of strong oxylipin-producing diatoms on grazers, showing that primary defense systems that should be activated to protect copepods against toxic algae can be inhibited. On the other hand other classical detoxification genes (glutathione S-transferase, superoxide dismutase, catalase, cytochrome P450 were not affected possibly due to short exposure times. Given the importance of diatom blooms in nutrient-rich aquatic environments these results offer a plausible explanation for the inefficient use of a potentially valuable food resource, the spring diatom bloom, by some copepod species.

  16. Molecular evidence for Lessepsian invasion of soritids (larger symbiont bearing benthic foraminifera.

    Directory of Open Access Journals (Sweden)

    Gily Merkado

    Full Text Available The Mediterranean Sea is considered as one of the hotspots of marine bioinvasions, largely due to the influx of tropical species migrating through the Suez Canal, so-called Lessepsian migrants. Several cases of Lessepsian migration have been documented recently, however, little is known about the ecological characteristics of the migrating species and their aptitude to colonize the new areas. This study focused on Red Sea soritids, larger symbiont-bearing benthic foraminifera (LBF that are indicative of tropical and subtropical environments and were recently found in the Israeli coast of the Eastern Mediterranean. We combined molecular phylogenetic analyses of soritids and their algal symbionts as well as network analysis of Sorites orbiculus Forskål to compare populations from the Gulf of Elat (northern Red Sea and from a known hotspot in Shikmona (northern Israel that consists of a single population of S. orbiculus. Our phylogenetic analyses show that all specimens found in Shikmona are genetically identical to a population of S. orbiculus living on a similar shallow water pebbles habitat in the Gulf of Elat. Our analyses also show that the symbionts found in Shikmona and Elat soritids belong to the Symbiodinium clade F5, which is common in the Red Sea and also present in the Indian Ocean and Caribbean Sea. Our study therefore provides the first genetic and ecological evidences that indicate that modern population of soritids found on the Mediterranean coast of Israel is probably Lessepsian, and is less likely the descendant of a native ancient Mediterranean species.

  17. Molecular evidence for an involvement of organic anion transporters (OATs) in aristolochic acid nephropathy

    International Nuclear Information System (INIS)

    Bakhiya, Nadiya; Arlt, Volker M.; Bahn, Andrew; Burckhardt, Gerhard; Phillips, David H.; Glatt, Hansruedi

    2009-01-01

    Aristolochic acid (AA), present in Aristolochia species, is the major causative agent in the development of severe renal failure and urothelial cancers in patients with AA nephropathy. It may also be a cause of Balkan endemic nephropathy. Epithelial cells of the proximal tubule are the primary cellular target of AA. To study whether organic anion transporters (OATs) expressed in proximal tubule cells are involved in uptake of AA, we used human epithelial kidney (HEK293) cells stably expressing human (h) OAT1, OAT3 or OAT4. AA potently inhibited the uptake of characteristic substrates, p-aminohippurate for hOAT1 and estrone sulfate for hOAT3 and hOAT4. Aristolochic acid I (AAI), the more cytotoxic and genotoxic AA congener, exhibited high affinity for hOAT1 (K i = 0.6 μM) as well as hOAT3 (K i = 0.5 μM), and lower affinity for hOAT4 (K i = 20.6 μM). Subsequently, AAI-DNA adduct formation (investigated by 32 P-postlabelling) was used as a measure of AAI uptake. Significantly higher levels of adducts occurred in hOAT-expressing cells than in control cells: this effect was abolished in the presence of the OAT inhibitor probenecid. In Xenopus laevis oocytes hOAT-mediated efflux of p-aminohippurate was trans-stimulated by extracellular AA, providing further molecular evidence for AA translocation by hOATs. Our study indicates that OATs can mediate the uptake of AA into proximal tubule cells and thereby participate in kidney cell damage by this toxin.

  18. Isotopic evidence for primordial molecular cloud material in metal-rich carbonaceous chondrites

    DEFF Research Database (Denmark)

    van Kooten, Elishevah M. M. E.; Wielandt, Daniel Kim Peel; Schiller, Martin

    2016-01-01

    product of (26)Al. This correlation is interpreted as reflecting progressive thermal processing of in-falling (26)Al-rich molecular cloud material in the inner Solar System. The thermally unprocessed molecular cloud matter reflecting the nucleosynthetic makeup of the molecular cloud before the last......)Mg*-depleted and (54)Cr-enriched component. This composition is consistent with that expected for thermally unprocessed primordial molecular cloud material before its pollution by stellar-derived (26)Al. The (26)Mg* and (54)Cr compositions of bulk metal-rich chondrites require significant amounts (25......-50%) of primordial molecular cloud matter in their precursor material. Given that such high fractions of primordial molecular cloud material are expected to survive only in the outer Solar System, we infer that, similarly to cometary bodies, metal-rich carbonaceous chondrites are samples of planetesimals...

  19. Constrained superfields in supergravity

    Energy Technology Data Exchange (ETDEWEB)

    Dall’Agata, Gianguido; Farakos, Fotis [Dipartimento di Fisica ed Astronomia “Galileo Galilei”, Università di Padova,Via Marzolo 8, 35131 Padova (Italy); INFN, Sezione di Padova,Via Marzolo 8, 35131 Padova (Italy)

    2016-02-16

    We analyze constrained superfields in supergravity. We investigate the consistency and solve all known constraints, presenting a new class that may have interesting applications in the construction of inflationary models. We provide the superspace Lagrangians for minimal supergravity models based on them and write the corresponding theories in component form using a simplifying gauge for the goldstino couplings.

  20. Minimal constrained supergravity

    Energy Technology Data Exchange (ETDEWEB)

    Cribiori, N. [Dipartimento di Fisica e Astronomia “Galileo Galilei”, Università di Padova, Via Marzolo 8, 35131 Padova (Italy); INFN, Sezione di Padova, Via Marzolo 8, 35131 Padova (Italy); Dall' Agata, G., E-mail: dallagat@pd.infn.it [Dipartimento di Fisica e Astronomia “Galileo Galilei”, Università di Padova, Via Marzolo 8, 35131 Padova (Italy); INFN, Sezione di Padova, Via Marzolo 8, 35131 Padova (Italy); Farakos, F. [Dipartimento di Fisica e Astronomia “Galileo Galilei”, Università di Padova, Via Marzolo 8, 35131 Padova (Italy); INFN, Sezione di Padova, Via Marzolo 8, 35131 Padova (Italy); Porrati, M. [Center for Cosmology and Particle Physics, Department of Physics, New York University, 4 Washington Place, New York, NY 10003 (United States)

    2017-01-10

    We describe minimal supergravity models where supersymmetry is non-linearly realized via constrained superfields. We show that the resulting actions differ from the so called “de Sitter” supergravities because we consider constraints eliminating directly the auxiliary fields of the gravity multiplet.

  1. Minimal constrained supergravity

    Directory of Open Access Journals (Sweden)

    N. Cribiori

    2017-01-01

    Full Text Available We describe minimal supergravity models where supersymmetry is non-linearly realized via constrained superfields. We show that the resulting actions differ from the so called “de Sitter” supergravities because we consider constraints eliminating directly the auxiliary fields of the gravity multiplet.

  2. Minimal constrained supergravity

    International Nuclear Information System (INIS)

    Cribiori, N.; Dall'Agata, G.; Farakos, F.; Porrati, M.

    2017-01-01

    We describe minimal supergravity models where supersymmetry is non-linearly realized via constrained superfields. We show that the resulting actions differ from the so called “de Sitter” supergravities because we consider constraints eliminating directly the auxiliary fields of the gravity multiplet.

  3. Role of creatine kinase isoenzymes on muscular and cardiorespiratory endurance: genetic and molecular evidence.

    Science.gov (United States)

    Echegaray, M; Rivera, M A

    2001-01-01

    polymorphism, distinguished by the NcoI restriction enzyme, and an increase in cardiorespiratory endurance as indexed by maximal oxygen uptake following 20 weeks of training. In conclusion, there is now evidence at the tissue, cell and molecular level indicating that the CK-PCr system plays an important role in determining the phenotypes of muscular and cardiorespiratory endurance. It is envisioned that newer technologies will help determine how the genetic variability of these genes (and many others) impact on performance and health-related phenotypes.

  4. Fast Molecular Outflows in Luminous Galaxy Mergers: Evidence for Quasar Feedback from Herschel

    Science.gov (United States)

    Veilleux, S.; Melendez, M.; Sturm, E.; Garcia-Carpio, J.; Fischer, J.; Gonzalez-Alfonso, E.; Contursi, A.; Lutz, D.; Poglitsch, A.; Davies, R.; hide

    2013-01-01

    We report the results from a systematic search for molecular (OH 119 micron) outflows with Herschel/PACS in a sample of 43 nearby (z 11.8 +/- 0.3]. The quasars in these systems play a dominant role in driving the molecular outflows. However, the most AGN dominated systems, where OH is seen purely in emission, show relatively modest OH line widths, despite their large AGN luminosities, perhaps indicating that molecular outflows subside once the quasar has cleared a path through the obscuring material.

  5. Constrained Vapor Bubble Experiment

    Science.gov (United States)

    Gokhale, Shripad; Plawsky, Joel; Wayner, Peter C., Jr.; Zheng, Ling; Wang, Ying-Xi

    2002-11-01

    Microgravity experiments on the Constrained Vapor Bubble Heat Exchanger, CVB, are being developed for the International Space Station. In particular, we present results of a precursory experimental and theoretical study of the vertical Constrained Vapor Bubble in the Earth's environment. A novel non-isothermal experimental setup was designed and built to study the transport processes in an ethanol/quartz vertical CVB system. Temperature profiles were measured using an in situ PC (personal computer)-based LabView data acquisition system via thermocouples. Film thickness profiles were measured using interferometry. A theoretical model was developed to predict the curvature profile of the stable film in the evaporator. The concept of the total amount of evaporation, which can be obtained directly by integrating the experimental temperature profile, was introduced. Experimentally measured curvature profiles are in good agreement with modeling results. For microgravity conditions, an analytical expression, which reveals an inherent relation between temperature and curvature profiles, was derived.

  6. Constrained noninformative priors

    International Nuclear Information System (INIS)

    Atwood, C.L.

    1994-10-01

    The Jeffreys noninformative prior distribution for a single unknown parameter is the distribution corresponding to a uniform distribution in the transformed model where the unknown parameter is approximately a location parameter. To obtain a prior distribution with a specified mean but with diffusion reflecting great uncertainty, a natural generalization of the noninformative prior is the distribution corresponding to the constrained maximum entropy distribution in the transformed model. Examples are given

  7. Molecular Evidence for Differential Long-term Outcomes of Early Life Severe Acute Malnutrition

    Directory of Open Access Journals (Sweden)

    Allan Sheppard

    2017-04-01

    Implications of All the Available Evidence: These data are compatible with the different clinical responses to SAM arising from developmentally-induced epigenetic changes laid down largely before birth and provide evidence for the predictive adaptive response model operating in human development.

  8. Breast cancer in Ethiopia: evidence for geographic difference in the distribution of molecular subtypes in Africa.

    Science.gov (United States)

    Hadgu, Endale; Seifu, Daniel; Tigneh, Wondemagegnhu; Bokretsion, Yonas; Bekele, Abebe; Abebe, Markos; Sollie, Thomas; Merajver, Sofia D; Karlsson, Christina; Karlsson, Mats G

    2018-02-14

    Breast cancer is a heterogeneous disease with several morphological and molecular subtypes. Widely accepted molecular classification system uses assessment of estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2) and proliferation marker Ki67. Few studies have been conducted on the incidence and molecular types of breast cancer in Sub-Saharan Africa. Previous studies mainly from Western and Central Africa, showed breast cancer to occur at younger ages and to present with aggressive features, such as high-grade, advanced stage and triple-negative phenotype (negative for ER, PR and HER2). Limited data from East Africa including Ethiopia however shows hormone receptor negative tumors to account for a lower proportion of all breast cancers than has been reported from elsewhere in Africa. In this study from Tikur Anbessa Specialized Hospital, 114 breast cancer patients diagnosed between 2012 and 2015 were enrolled. ER, PR, Ki67 and HER2 receptor status were assessed using immunohistochemistry from tissue microarrays. FISH was used for assessment of gene amplification in all equivocal tumor samples and for confirmation in HER2-enriched cases. The distribution of molecular subtypes was: Luminal A: 40%; Luminal B: 26%; HER2-enriched: 10%; TNBC: 23%. ER were positive in 65% of all tumors and 43% the cases were positive for PR. There was statistically significant difference in median age at diagnosis between the molecular subtypes (P molecular subtypes in different age ranges with Luminal B subtype being more common at younger ages (median = 36) and Luminal A subtype more prevalent at older ages (median = 42). There were no statistically significant differences in tumor grade, histology, and stage between the molecular subtypes of breast cancer. The present study detected Luminal A breast cancer to be the most common subtype and reveals a relatively low rate of hormone receptor negative and TNBC. Our findings and

  9. Molecular evidence for polyphyletic origin of the primary symbionts of sucking lice (Phthiraptera, Anoplura)

    Czech Academy of Sciences Publication Activity Database

    Hypša, Václav; Křížek, J.

    2007-01-01

    Roč. 54, č. 2 (2007), s. 242-251 ISSN 0095-3628 Grant - others:GA ČR(CZ) GA206/04/0520 Institutional research plan: CEZ:AV0Z60220518 Keywords : Anoplura * endosymbionts * coevolution * molecular phylogeny Subject RIV: EE - Microbiology, Virology Impact factor: 2.558, year: 2007

  10. Molecular evidence of cryptic speciation in the "cosmopolitan" excavating sponge Cliona celata (Porifera, Clionaidae)

    NARCIS (Netherlands)

    Xavier, J.R.; Rachello-Dolmen, P.G.; Parra-Velandia, F.; Schönberg, C.H.L.; Breeuwer, J.A.J.; van Soest, R.W.M.

    2010-01-01

    Over the past several decades molecular tools have shown an enormous potential to aid in the clarification of species boundaries in the marine realm, particularly in morphologically simple groups. In this paper we report a case of cryptic speciation in an allegedly cosmopolitan and ecologically

  11. H2 emission and CO absorption in Centaurus A : Evidence for a circumnuclear molecular disk

    NARCIS (Netherlands)

    Israel, F.P.; Dishoeck, van E.F.; Baas, F.; Koornneef, J.; Black, J.H.; Graauw, de Th.

    1990-01-01

    Emission and absorption lines of H2 and CO in nuclei of several galaxies with strong NIR emission, including Centaurus A (NGC 5128), were studied at the La Silla observatory to obtain constraints on the physical parameters of molecular material close to the nucleus of the NGC 5128 galaxy. Results

  12. Molecular diagnosis of cattle trypanosomes in Venezuela: evidences of Trypanosoma evansi and Trypanosoma vivax infections.

    Science.gov (United States)

    Ramírez-Iglesias, J R; Eleizalde, M C; Reyna-Bello, A; Mendoza, M

    2017-06-01

    In South America Trypanosoma evansi has been determined by molecular methods in cattle from Bolivia, Brazil, Colombia and Peru, reason for which the presence of this parasite is not excluded in Venezuelan livestock. Therefore, the aim of this study was to perform parasitological and molecular diagnosis of cattle trypanosomosis in small livestock units from two regions in this country. The parasitological diagnosis was carried out by MHCT and the molecular by PCR using genus-specific ITS1 primers that differentiate T. vivax and T. evansi infections. 47 cattle were evaluated in the "Laguneta de la Montaña" sector, Miranda State, where 3 animals were diagnosed as positive (6.4 %) by MHCT and 14 (30 %) by PCR as Trypanosoma spp., out of which 9 animals resulted positive for T. vivax , 3 for T. evansi and 2 with double infections. Whilst in the "San Casimiro" sector, State of Aragua, out of the 38 cattle evaluated 7 animals were diagnosed as positive (18.4 %) by MHCT and 19 (50 %) by PCR, determining only the presence of T. evansi in this locality. The molecular diagnosis by PCR using ITS1 primers allowed T. evansi detection in cattle field populations, which suggests the possible role of these animals as reservoirs in the epidemiology of the disease caused by T. evansi in Venezuela.

  13. Ring-constrained Join

    DEFF Research Database (Denmark)

    Yiu, Man Lung; Karras, Panagiotis; Mamoulis, Nikos

    2008-01-01

    . This new operation has important applications in decision support, e.g., placing recycling stations at fair locations between restaurants and residential complexes. Clearly, RCJ is defined based on a geometric constraint but not on distances between points. Thus, our operation is fundamentally different......We introduce a novel spatial join operator, the ring-constrained join (RCJ). Given two sets P and Q of spatial points, the result of RCJ consists of pairs (p, q) (where p ε P, q ε Q) satisfying an intuitive geometric constraint: the smallest circle enclosing p and q contains no other points in P, Q...

  14. Direct evidence for coastal iodine particles from Laminaria macroalgae – linkage to emissions of molecular iodine

    Directory of Open Access Journals (Sweden)

    G. McFiggans

    2004-01-01

    Full Text Available Renewal of ultrafine aerosols in the marine boundary layer may lead to repopulation of the marine distribution and ultimately determine the concentration of cloud condensation nuclei (CCN. Thus the formation of nanometre-scale particles can lead to enhanced scattering of incoming radiation and a net cooling of the atmosphere. The recent demonstration of the chamber formation of new particles from the photolytic production of condensable iodine-containing compounds from diiodomethane (CH2I2, (O'Dowd et al., 2002; Kolb, 2002; Jimenez et al., 2003a; Burkholder and Ravishankara, 2003, provides an additional mechanism to the gas-to-particle conversion of sulphuric acid formed in the photo-oxidation of dimethylsulphide for marine aerosol repopulation. CH2I2 is emitted from seaweeds (Carpenter et al., 1999, 2000 and has been suggested as an initiator of particle formation. We demonstrate here for the first time that ultrafine iodine-containing particles are produced by intertidal macroalgae exposed to ambient levels of ozone. The particle composition is very similar both to those formed in the chamber photo-oxidation of diiodomethane and in the oxidation of molecular iodine by ozone. The particles formed in all three systems are similarly aspherical. When small, those formed in the molecular iodine system swell only moderately when exposed to increased humidity environments, and swell progressively less with increasing size; this behaviour occurs whether they are formed in dry or humid environments, in contrast to those in the CH2I2 system. Direct coastal boundary layer observations of molecular iodine, ultrafine particle production and iodocarbons are reported. Using a newly measured molecular iodine photolysis rate, it is shown that, if atomic iodine is involved in the observed particle bursts, it is of the order of at least 1000 times more likely to result from molecular iodine photolysis than diiodomethane photolysis. A hypothesis for molecular

  15. Experimental evidence of the role of viscosity in the molecular kinetic theory of dynamic wetting.

    Science.gov (United States)

    Duvivier, D; Seveno, D; Rioboo, R; Blake, T D; De Coninck, J

    2011-11-01

    We report an experimental study of the dynamics of spontaneous spreading of aqueous glycerol drops on glass. For a range of glycerol concentrations, we follow the evolution of the radius and contact angle over several decades of time and investigate the influence of solution viscosity. The application of the molecular kinetic theory to the resulting data allows us to extract the coefficient of contact-line friction ζ, the molecular jump frequency κ(0), and the jump length λ for each solution. Our results show that the modified theory, which explicitly accounts for the effect of viscosity, can successfully be applied to droplet spreading. The viscosity affects the jump frequency but not the jump length. In combining these data, we confirm that the contact-line friction of the solution/air interface against the glass is proportional to the viscosity and exponentially dependent on the work of adhesion.

  16. First molecular evidence of potentially zoonotic Babesia microti and Babesia sp. EU1 in Ixodes ricinus ticks in Belgium

    OpenAIRE

    Lempereur, L.; De Cat, A.; Caron, Y.; Madder, M.; Claerebout, E.; Saegerman, C.; Losson, B.

    2011-01-01

    We report the first molecular evidence of the presence of Babesia sp. EU1 and Babesia microti in Ixodes ricinus ticks in Belgium. A 1-year national survey collected 1005 ticks from cats and dogs. A polymerase chain reaction technique amplifying a part of the 18S rRNA gene detected Babesia spp. in 11 out of 841 selected and validated tick extracts. Subsequent sequencing identified Ba. microti (n = 3) and Babesia sp. EU1 (n = 6). This study has demonstrated a low infection rate (1.31% with 95% ...

  17. Pathophysiology of Adipocyte Defects and Dyslipidemia in HIV Lipodystrophy: New Evidence from Metabolic and Molecular Studies

    OpenAIRE

    Ashok Balasubramanyam; Rajagopal V. Sekhar; Farook Jahoor; Henry J. Pownall; Dorothy Lewis

    2006-01-01

    Despite a burgeoning mass of descriptive information regarding the epidemiology, clinical features, body composition changes, hormonal alterations and dyslipidemic patterns in patients with HIV lipodystrophy syndrome (HLS), the specific biochemical pathways that are dysregulated in the condition and the molecular mechanisms that lead to their dysfunction, remain relatively unexplored. In this paper, we review studies that detail the metabolic basis of the dyslipidemia - specifically, the hype...

  18. A molecular perspective on a complex polymorphic inversion system with cytological evidence of multiply reused breakpoints.

    Science.gov (United States)

    Orengo, D J; Puerma, E; Papaceit, M; Segarra, C; Aguadé, M

    2015-06-01

    Genome sequence comparison across the Drosophila genus revealed that some fixed inversion breakpoints had been multiply reused at this long timescale. Cytological studies of Drosophila inversion polymorphism had previously shown that, also at this shorter timescale, some breakpoints had been multiply reused. The paucity of molecularly characterized polymorphic inversion breakpoints has so far precluded contrasting whether cytologically shared breakpoints of these relatively young inversions are actually reused at the molecular level. The E chromosome of Drosophila subobscura stands out because it presents several inversion complexes. This is the case of the E1+2+9+3 arrangement that originated from the ancestral Est arrangement through the sequential accumulation of four inversions (E1, E2, E9 and E3) sharing some breakpoints. We recently identified the breakpoints of inversions E1 and E2, which allowed establishing reuse at the molecular level of the cytologically shared breakpoint of these inversions. Here, we identified and sequenced the breakpoints of inversions E9 and E3, because they share breakpoints at sections 58D and 64C with those of inversions E1 and E2. This has allowed establishing that E9 and E3 originated through the staggered-break mechanism. Most importantly, sequence comparison has revealed the multiple reuse at the molecular level of the proximal breakpoint (section 58D), which would have been used at least by inversions E2, E9 and E3. In contrast, the distal breakpoint (section 64C) might have been only reused once by inversions E1 and E2, because the distal E3 breakpoint is displaced >70 kb from the other breakpoint limits.

  19. Massive Molecular Outflows and Evidence for AGN Feedback from CO Observations

    Science.gov (United States)

    2014-01-01

    outflows of the molecular phase out of which stars form, which in most galaxies also represents the bulk of the ISM; moreover the spectro -imaging...method for estimating the integrated flux and the spa- tial extension of the CO(1–0) wings relies almost exclusively on the analysis of the uv ...the 3 mm continuum emission from the line-free frequency ranges in our wide-band (WideX) observations, and then subtract it directly from the uv data

  20. Molecular evidence for the existence of cryptic species assemblages of several myxosporeans (Myxozoa)

    Czech Academy of Sciences Publication Activity Database

    Bartošová, Pavla; Fiala, Ivan

    2011-01-01

    Roč. 108, č. 3 (2011), s. 573-583 ISSN 0932-0113 R&D Project s: GA AV ČR KJB600960701; GA ČR GD524/03/H133; GA MŠk LC522 Institutional research plan: CEZ:AV0Z60220518 Keywords : SUBUNIT RIBOSOMAL-RNA * RUTILUS-RUTILUS LINNAEUS * LIFE -CYCLE * PHYLOGENY Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.149, year: 2011

  1. Lack of Evidence for Molecular Mimicry in HIV-Infected Subjects.

    Directory of Open Access Journals (Sweden)

    Peter D Burbelo

    Full Text Available Previous studies in HIV patients have reported autoantibodies to several human proteins, including erythropoietin (EPO, interferon-α (IFN-α, interleukin-2 (IL-2, and HLA-DR, as potential mediators of anemia or immunosuppression. The etiology of these autoantibodies has been attributed to molecular mimicry between HIV epitopes and self-proteins. Here, the Luciferase Immunoprecipitation System (LIPS was used to investigate the presence of such autoantibodies in HIV-infected adults. High levels of antibodies to HIV proteins such as capsid (p24, matrix (p17, envelope (gp41, and reverse transcriptase (RT were detected using LIPS in both untreated and anti-retroviral-treated HIV-infected individuals but not in uninfected controls. LIPS readily detected anti-EPO autoantibodies in serum samples from subjects with presumptive pure red cell aplasia but not in any of the samples from HIV-infected or uninfected individuals. Similarly, subjects with HIV lacked autoantibodies to IFN-α, IL-2, HLA-DR and the immunoglobulin lambda light chain; all purported targets of molecular mimicry. While molecular mimicry between pathogen proteins and self-proteins is a commonly proposed mechanism for autoantibody production, the findings presented here indicate such a process is not common in HIV disease.

  2. Tryptophan as an evolutionarily conserved signal to brain serotonin : Molecular evidence and psychiatric implications

    NARCIS (Netherlands)

    Russo, Sascha; Kema, Ido P.; Bosker, Fokko; Haavik, Jan; Korf, Jakob

    2009-01-01

    The role of serotonin (5-HT) in psychopathology has been investigated for decades. Among others, symptoms of depression, panic, aggression and suicidality have been associated with serotonergic dysfunction. Here we summarize the evidence that low brain 5-HT signals a metabolic imbalance that is

  3. Ghost supernova remnants : evidence for pulsar reactivation in dusty molecular clouds

    International Nuclear Information System (INIS)

    Heintzmann, H.; Novello, M.

    1983-01-01

    An evidence in favour of a new model for pulsar evolution is discussed, according to which pulsars may only function as regularly pulsed emitters if an accretion disc provides a sufficiently continuous return-current to the radio pulsar (neutron star). (L.C.) [pt

  4. Morphological and molecular evidence for functional organization along the rostrocaudal axis of the adult zebrafish intestine

    Directory of Open Access Journals (Sweden)

    Lam Siew

    2010-06-01

    Full Text Available Abstract Background The zebrafish intestine is a simple tapered tube that is folded into three sections. However, whether the intestine is functionally similar along its length remains unknown. Thus, a systematic structural and functional characterization of the zebrafish intestine is desirable for future studies of the digestive tract and the intestinal biology and development. Results To characterize the structure and function of the adult zebrafish intestine, we divided the intestine into seven roughly equal-length segments, S1-S7, and systematically examined the morphology of the mucosal lining, histology of the epithelium, and molecular signatures from transcriptome analysis. Prominent morphological features are circumferentially-oriented villar ridges in segments S1-S6 and the absence of crypts. Molecular characterization of the transcriptome from each segment shows that segments S1-S5 are very similar while S6 and S7 unique. Gene ontology analyses reveal that S1-S5 express genes whose functions involve metabolism of carbohydrates, transport of lipids and energy generation, while the last two segments display relatively limited function. Based on comparative Gene Set Enrichment Analysis, the first five segments share strong similarity with human and mouse small intestine while S6 shows similarity with human cecum and rectum, and S7 with human rectum. The intestinal tract does not display the anatomical, morphological, and molecular signatures of a stomach and thus we conclude that this organ is absent from the zebrafish digestive system. Conclusions Our genome-wide gene expression data indicate that, despite the lack of crypts, the rostral, mid, and caudal portions of the zebrafish intestine have distinct functions analogous to the mammalian small and large intestine, respectively. Organization of ridge structures represents a unique feature of zebrafish intestine, though they produce similar cross sections to mammalian intestines

  5. Molecular evidence of Rickettsia felis infection in dogs from northern territory, Australia

    Directory of Open Access Journals (Sweden)

    Rees Robert L

    2011-10-01

    Full Text Available Abstract The prevalence of spotted fever group rickettsial infection in dogs from a remote indigenous community in the Northern Territory (NT was determined using molecular tools. Blood samples collected from 130 dogs in the community of Maningrida were subjected to a spotted fever group (SFG-specific PCR targeting the ompB gene followed by a Rickettsia felis-specific PCR targeting the gltA gene of R. felis. Rickettsia felis ompB and gltA genes were amplified from the blood of 3 dogs. This study is the first report of R. felis infection in indigenous community dogs in NT.

  6. Sharp spatially constrained inversion

    DEFF Research Database (Denmark)

    Vignoli, Giulio G.; Fiandaca, Gianluca G.; Christiansen, Anders Vest C A.V.C.

    2013-01-01

    We present sharp reconstruction of multi-layer models using a spatially constrained inversion with minimum gradient support regularization. In particular, its application to airborne electromagnetic data is discussed. Airborne surveys produce extremely large datasets, traditionally inverted...... by using smoothly varying 1D models. Smoothness is a result of the regularization constraints applied to address the inversion ill-posedness. The standard Occam-type regularized multi-layer inversion produces results where boundaries between layers are smeared. The sharp regularization overcomes...... inversions are compared against classical smooth results and available boreholes. With the focusing approach, the obtained blocky results agree with the underlying geology and allow for easier interpretation by the end-user....

  7. Phylogeny and systematics of the brake fern genus Pteris (Pteridaceae) based on molecular (plastid and nuclear) and morphological evidence.

    Science.gov (United States)

    Zhang, Liang; Zhang, Li-Bing

    2018-01-01

    The brake fern genus Pteris belongs to Pteridaceae subfamily Pteridoideae. It is one of the largest fern genera and has been estimated to contain 200-250 species distributed on all continents except Antarctica. Previous studies were either based on plastid data only or based on both plastid and nuclear data but the sampling was small. In addition, an infrageneric classification of Pteris based on morphological and molecular evidence has not been available yet. In the present study, based on molecular data of eight plastid markers and one nuclear marker (gapCp) of 256 accessions representing ca. 178 species of Pteris, we reconstruct a global phylogeny of Pteris. The 15 major clades identified earlier are recovered here and we further identified a new major clade. Our nuclear phylogeny recovered 11 of these 16 major clades, seven of which are strongly supported. The inclusion of Schizostege in Pteris is confirmed for the first time. Based on the newly reconstructed phylogeny and evidence from morphology, distribution and/or ecology, we classify Pteris into three subgenera: P. subg. Pteris, P. subg. Campteria, and P. subg. Platyzoma. The former two are further divided into three and 12 sections, respectively. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. The Molecular Immunology of Mucositis: Implications for Evidence-Based Research in Alternative and Complementary Palliative Treatments

    Directory of Open Access Journals (Sweden)

    Francesco Chiappelli

    2005-01-01

    Full Text Available The terms ‘mucositis’ and ‘stomatitis’ are often used interchangeably. Mucositis, however, pertains to pharyngeal-esophago-gastrointestinal inflammation that manifests as red, burn-like sores or ulcerations throughout the mouth. Stomatitis is an inflammation of the oral tissues proper, which can present with or without sores, and is made worse by poor dental hygiene. Mucositis is observed in a variety of immunosuppressed patients, but is most often consequential to cancer therapy. It appears as early as the third day of intervention, and is usually established by Day 7 of treatment. Mucositis increases mortality and morbidity and contributes to rising health care costs. The precise immune components involved in the etiology of mucositis are unclear, but evidence-based research (EBR data has shown that applications of granulocyte–macrophage-colony stimulating factor prevent the onset or the exacerbation of oropharyngeal mucositis. The molecular implications of this observation are discussed from the perspective of future developments of complementary and alternative treatments for this condition. It must be emphasized that this article is meant to be neither a review on mucositis and the various treatments for it, nor a discussion paper on its underlying molecular immunology. It is a statement of the implications of EBR for CAM-based interventions for mucositis. It explores and discusses the specific domain of molecular immunology in the context of mucositis and its direct implications for EBR research in CAM-based treatments for mucositis.

  9. Biochemical and molecular evidences for the antitumor potential of Ginkgo biloba leaves extract in rodents.

    Science.gov (United States)

    Ahmed, Hanaa H; Shousha, Wafaa Gh; El-Mezayen, Hatem A; El-Toumy, Sayed A; Sayed, Alaa H; Ramadan, Aesha R

    2017-01-01

    Hepatocellular carcinoma (HCC) is one of the deadliest primary cancers, with a 5-year survival rate of 10% or less. This study was undertaken to elucidate the underlying biochemical and molecular mechanisms in favor of N-nitrosodiethylamine-induced hepatocellular carcinoma. Furthermore, the aim of this work was extended to explore the efficacy of Ginkgo biloba leaves extract in deterioration of HCC in rats. In the current study, HCC group experienced significant downregulation of ING-3 gene expression and upregulation of Foxp-1 gene expression in liver. Treatment of HCC groups with Ginkgo biloba leaves extract resulted in upregulation of ING-3 and downregulation of Foxp-1 gene expression in liver. In addition, there was significant increase in serum alpha-fetoprotein (AFP), carcinoembryonic antigen (CEA) and glypican-3 (GPC-3) levels in HCC group versus the negative control group. In contrast, the groups with HCC subjected to either high or low dose of Ginkgo biloba leaves extract elicited significant reduction (Panaplasia. Interestingly, treatment with Ginkgo biloba leaves extract elicited marked improvement in the histological feature of liver tissue in HCC groups. In conclusion, this research indicated that the carcinogenic potency of N-nitrosodiethylamine targeted multiple systems on the cellular and molecular levels. In addition, the results of the current study shed light on the promising anticancer activity of Ginkgo biloba leaves extract in treatment of hepatocellular carcinoma induced chemically in the experimental model through its apoptotic and antiproliferative properties.

  10. Molecular evidence of keratin and melanosomes in feathers of the Early Cretaceous bird Eoconfuciusornis.

    Science.gov (United States)

    Pan, Yanhong; Zheng, Wenxia; Moyer, Alison E; O'Connor, Jingmai K; Wang, Min; Zheng, Xiaoting; Wang, Xiaoli; Schroeter, Elena R; Zhou, Zhonghe; Schweitzer, Mary H

    2016-12-06

    Microbodies associated with feathers of both nonavian dinosaurs and early birds were first identified as bacteria but have been reinterpreted as melanosomes. Whereas melanosomes in modern feathers are always surrounded by and embedded in keratin, melanosomes embedded in keratin in fossils has not been demonstrated. Here we provide multiple independent molecular analyses of both microbodies and the associated matrix recovered from feathers of a new specimen of the basal bird Eoconfuciusornis from the Early Cretaceous Jehol Biota of China. Our work represents the oldest ultrastructural and immunological recognition of avian beta-keratin from an Early Cretaceous (∼130-Ma) bird. We apply immunogold to identify protein epitopes at high resolution, by localizing antibody-antigen complexes to specific fossil ultrastructures. Retention of original keratinous proteins in the matrix surrounding electron-opaque microbodies supports their assignment as melanosomes and adds to the criteria employable to distinguish melanosomes from microbial bodies. Our work sheds new light on molecular preservation within normally labile tissues preserved in fossils.

  11. Molecular evidence of Ureaplasma urealyticum and Ureaplasma parvum colonization in preterm infants during respiratory distress syndrome

    Directory of Open Access Journals (Sweden)

    Germani Rossella

    2006-11-01

    Full Text Available Abstract Background Ureaplasma urealyticum and U. parvum have been associated with respiratory diseases in premature newborns, but their role in the pathogenesis of the respiratory distress syndrome (RDS is unclear. The aim of this study was to detect, using molecular techniques, the role of Mycoplasma spp. and Ureaplasma spp. in respiratory secretion and blood specimens of preterm newborns with or without RDS and to evaluate the prevalence of perinatal U. urealyticum or U. parvum infection. The influence of chemotherapy on the clinical course was also evaluated. Methods Tracheal aspirate or nasopharingeal fluid samples from 50 preterm babies with (24 or without RDS (26 were analysed for detection of U. urealyticum and U. parvum by culture identification assay and PCR. Sequencing analysis of amplicons allowed us to verify the specificity of methods. Clarithromycin (10 mg kg-1 twice a day was administered in ureaplasma-positive patients who presented clinical signs of RDS. Results 15/24 neonates with RDS (p U. urealyticum or U. parvum. Culture identification assay was positive in 5/50 newborns, three of which with RDS. Sequencing analyses confirmed the specificity of these methods. Association of patent ductus arteriosus with ureaplasma colonization was more statistically significant (p = 0.0004 in patients with RDS than in those without RDS. Conclusion Colonization of the lower respiratory tract by Ureaplasma spp. and particularly by U. parvum in preterm newborns was related to RDS. The routine use of molecular methods could be useful to screen candidate babies for etiologic therapy.

  12. Molecular phylogeny of Pompilinae (Hymenoptera: Pompilidae): Evidence for rapid diversification and host shifts in spider wasps.

    Science.gov (United States)

    Rodriguez, Juanita; Pitts, James P; Florez, Jaime A; Bond, Jason E; von Dohlen, Carol D

    2016-01-01

    Pompilinae is one of the largest subfamilies of spider wasps (Pompilidae). Most pompilines are generalist spider predators at the family level, but some taxa exhibit ecological specificity (i.e., to spider-host guild). Here we present the first molecular phylogenetic analysis of Pompilinae, toward the aim of evaluating the monophyly of tribes and genera. We further test whether changes in the rate of diversification are associated with host-guild shifts. Molecular data were collected from five nuclear loci (28S, EF1-F2, LWRh, Wg, Pol2) for 76 taxa in 39 genera. Data were analyzed using maximum likelihood (ML) and Bayesian inference (BI). The phylogenetic results were compared with previous hypotheses of subfamilial and tribal classification, as well as generic relationships in the subfamily. The classification of Pompilus and Agenioideus is also discussed. A Bayesian relaxed molecular clock analysis was used to examine divergence times. Diversification rate-shift tests accounted for taxon-sampling bias using ML and BI approaches. Ancestral host family and host guild were reconstructed using MP and ML methods. Ancestral host guild for all Pompilinae, for the ancestor at the node where a diversification rate-shift was detected, and two more nodes back in time was inferred using BI. In the resulting phylogenies, Aporini was the only previously proposed monophyletic tribe. Several genera (e.g., Pompilus, Microphadnus and Schistonyx) are also not monophyletic. Dating analyses produced a well-supported chronogram consistent with topologies from BI and ML results. The BI ancestral host-use reconstruction inferred the use of spiders belonging to the guild "other hunters" (frequenting the ground and vegetation) as the ancestral state for Pompilinae. This guild had the highest probability for the ML reconstruction and was equivocal for the MP reconstruction; various switching events to other guilds occurred throughout the evolution of the group. The diversification of

  13. [Low-grade systemic inflammation and the development of metabolic diseases: from the molecular evidence to the clinical practice].

    Science.gov (United States)

    León-Pedroza, José Israel; González-Tapia, Luis Alonso; del Olmo-Gil, Esteban; Castellanos-Rodríguez, Diana; Escobedo, Galileo; González-Chávez, Antonio

    2015-01-01

    Systemic inflammation is characterised by high circulating levels of inflammatory cytokines and increased macrophage infiltration in peripheral tissues. Most importantly, this inflammatory state does not involve damage or loss of function of the infiltrated tissue, which is a distinctive feature of the low-grade systemic inflammation. The term "meta-inflammation" has also been used to refer to the low-grade systemic inflammation due to its strong relationship with the development of cardio-metabolic diseases in obesity. A review is presented on the recent clinical and experimental evidence concerning the role of adipose tissue inflammation as a key mediator of low-grade systemic inflammation. Furthermore, the main molecular mechanisms involved in the inflammatory polarization of macrophages with the ability to infiltrate both the adipose tissue and the vascular endothelium via activation of toll-like receptors by metabolic damage-associated molecular patterns, such as advanced glycation-end products and oxidized lipoproteins, is discussed. Finally, a review is made of the pathogenic mechanisms through which the low-grade systemic inflammation contributes to develop insulin resistance, dyslipidaemia, atherogenesis, type 2 diabetes, and hypertension in obese individuals. A better understanding of the molecular mechanisms of low-grade systemic inflammation in promoting cardio-metabolic diseases is necessary, in order to further design novel anti-inflammatory therapies that take into consideration clinical data, as well as the circulating levels of cytokines, immune cells, and metabolic damage-associated molecular patterns in each patient. Copyright © 2015 Academia Mexicana de Cirugía A.C. Published by Masson Doyma México S.A. All rights reserved.

  14. Oxygen isotope evidence for sorption of molecular oxygen to pyrite surface sites and incorporation into sulfate in oxidation experiments

    International Nuclear Information System (INIS)

    Tichomirowa, Marion; Junghans, Manuela

    2009-01-01

    Experiments were conducted to investigate (i) the rate of O-isotope exchange between SO 4 and water molecules at low pH and surface temperatures typical for conditions of acid mine drainage (AMD) and (ii) the O- and S-isotope composition of sulfates produced by pyrite oxidation under closed and open conditions (limited and free access of atmospheric O 2 ) to identify the O source/s in sulfide oxidation (water or atmospheric molecular O 2 ) and to better understand the pyrite oxidation pathway. An O-isotope exchange between SO 4 and water was observed over a pH range of 0-2 only at 50 deg. C, whereas no exchange occurred at lower temperatures over a period of 8 a. The calculated half-time of the exchange rate for 50 deg. C (pH = 0 and 1) is in good agreement with former experimental data for higher and lower temperatures and excludes the possibility of isotope exchange for typical AMD conditions (T ≤ 25 deg. C, pH ≥ 3) for decades. Pyrite oxidation experiments revealed two dependencies of the O-isotope composition of dissolved sulfates: O-isotope values decreased with longer duration of experiments and increasing grain size of pyrite. Both changes are interpreted as evidence for chemisorption of molecular O 2 to pyrite surface sites. The sorption of molecular O 2 is important at initial oxidation stages and more abundant in finer grained pyrite fractions and leads to its incorporation in the produced SO 4 . The calculated bulk contribution of atmospheric O 2 in the dissolved SO 4 reached up to 50% during initial oxidation stages (first 5 days, pH 2, fine-grained pyrite fraction) and decreased to less than 20% after about 100 days. Based on the direct incorporation of molecular O 2 in the early-formed sulfates, chemisorption and electron transfer of molecular O 2 on S sites of the pyrite surface are proposed, in addition to chemisorption on Fe sites. After about 10 days, the O of all newly-formed sulfates originates only from water, indicating direct interaction

  15. Evidence for nucleosynthetic enrichment of the protosolar molecular cloud core by multiple supernova events

    DEFF Research Database (Denmark)

    Schiller, Martin; Paton, Chad; Bizzarro, Martin

    2015-01-01

    The presence of isotope heterogeneity of nucleosynthetic origin amongst meteorites and their components provides a record of the diverse stars that contributed matter to the protosolar molecular cloud core. Understanding how and when the solar system's nucleosynthetic heterogeneity was established...... and preserved within the solar protoplanetary disk is critical for unraveling the earliest formative stages of the solar system. Here, we report calcium and magnesium isotope measurements of primitive and differentiated meteorites as well as various types of refractory inclusions, including refractory...... and differentiated meteorites along with canonical and FUN-CAIs define correlated, mass-independent variations in 43Ca, 46Ca and 48Ca. Moreover, sequential dissolution experiments of the Ivuna carbonaceous chondrite aimed at identifying the nature and number of presolar carriers of isotope anomalies within primitive...

  16. Molecular evidence and high genetic diversity of shrew-borne Seewis virus in Slovenia.

    Science.gov (United States)

    Resman, Katarina; Korva, Miša; Fajs, Luka; Zidarič, Tanja; Trilar, Tomi; Zupanc, Tatjana Avšič

    2013-10-01

    Seewis virus, the shrew-borne hantavirus from Sorex araneus, has been molecularly detected in reservoir hosts in many different central European countries and Russia. Slovenia is a known endemic country for rodent-borne hantaviruses, therefore the aim of the study was to investigate the presence of shrew-borne hantaviruses in insectivores. Viral L, S and M segment have been recovered only from tissue samples of 7 S. araneus, despite several shrew species were tested. Phylogenetic analysis showed high genetic diversity of SWSV in Slovenia, ranging from 3 to 19.4% for different viral segments. The most divergent were M segment sequences, with 19.4% nucleotide divergence among Slovenian strains. Above that, different SWSV strains from Slovenia do not group into separate geographic clusters. While three separate genetic clades were determined, two of them were simultaneously present in one location at the same time. Copyright © 2013 Elsevier B.V. All rights reserved.

  17. Evidence of a double-lid movement in Pseudomonas aeruginosa lipase: insights from molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Subbulakshmi Latha Cherukuvada

    2005-08-01

    Full Text Available Pseudomonas aeruginosa lipase is a 29-kDa protein that, following the determination of its crystal structure, was postulated to have a lid that stretched between residues 125 and 148. In this paper, using molecular dynamics simulations, we propose that there exists, in addition to the above-mentioned lid, a novel second lid in this lipase. We further show that the second lid, covering residues 210-222, acts as a triggering lid for the movement of the first. We also investigate the role of hydrophobicity in the movement of the lids and show that two residues, Phe214 and Ala217, play important roles in lid movement. To our knowledge, this is the first time that a double-lid movement of the type described in our manuscript has been presented to the scientific community. This work also elucidates the interplay of hydrophobic interactions in the dynamics, and hence the function, of an enzyme.

  18. Epidemiological-molecular evidence of metabolic reprogramming on proliferation, autophagy and cell signaling in pancreas cancer.

    Science.gov (United States)

    Søreide, Kjetil; Sund, Malin

    2015-01-28

    Pancreatic cancer remains one of the deadliest human cancers with little progress made in survival over the past decades, and 5-year survival usually below 5%. Despite this dismal scenario, progresses have been made in understanding of the underlying tumor biology through among other definition of precursor lesions, delineation of molecular pathways, and advances in genome-wide technology. Further, exploring the relationship between epidemiological risk factors involving metabolic features to that of an altered cancer metabolism may provide the foundation for new therapies. Here we explore how nutrients and caloric intake may influence the KRAS-driven ductal carcinogenesis through mediators of metabolic stress, including autophagy in presence of TP53, advanced glycation end products (AGE) and the receptors (RAGE) and ligands (HMGB1), as well as glutamine pathways, among others. Effective understanding the cancer metabolism mechanisms in pancreatic cancer may propose new ways of prevention and treatment. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  19. Evidence-based efficacy of adaptogens in fatigue, and molecular mechanisms related to their stress-protective activity.

    Science.gov (United States)

    Panossian, Alexander; Wikman, Georg

    2009-09-01

    The aim of this review article is to assess the level of scientific evidence presented by clinical trials of adaptogens in fatigue, and to provide a rationale at the molecular level for verified effects. Strong scientific evidence is available for Rhodiola rosea SHR-5 extract, which improved attention, cognitive function and mental performance in fatigue and in chronic fatigue syndrome. Good scientific evidence has been documented in trails in which Schisandra chinensis and Eleutherococcus senticosus increased endurance and mental performance in patients with mild fatigue and weakness. Based on their efficacy in clinical studies, adaptogens can be defined as a pharmacological group of herbal preparations that increase tolerance to mental exhaustion and enhance attention and mental endurance in situations of decreased performance. The beneficial stress-protective effect of adaptogens is related to regulation of homeostasis via several mechanisms of action associated with the hypothalamic-pituitary-adrenal axis and the control of key mediators of stress response such as molecular chaperons (e.g. Hsp70), stress-activated c-Jun N-terminal protein kinase (JNK1), Forkhead Box O transcription factor DAF-16, cortisol and nitric oxide (NO). The key point of action of phytoadaptogens appears to be their up-regulating and stress-mimetic effects on the "stress-sensor" protein Hsp70, which plays an important role in cell survival and apoptosis. Hsp70 inhibits the expression of NO synthase II gene and interacts with glucocorticoid receptors directly and via the JNK pathway, thus affecting the levels of circulating cortisol and NO. Prevention of stress-induced increase in NO, and the associated decrease in ATP production, results in increased performance and endurance. Adaptogen-induced up-regulation of Hsp70 triggers stress-induced JNK-1 and DAF-16-mediated pathways regulating the resistance to stress and resulting in enhanced mental and physical performance and, possibly

  20. Molecular evidence for gender differences in the migratory behaviour of a small seabird.

    Directory of Open Access Journals (Sweden)

    Renata J Medeiros

    Full Text Available Molecular sexing revealed an unexpectedly strong female bias in the sex ratio of pre-breeding European Storm Petrels (Hydrobates pelagicus, attracted to playback of conspecific calls during their northwards migration past SW Europe. This bias was consistent across seven years, ranging from 80.8% to 89.7% female (mean annual sex ratio ± SD = 85.5% female ±4.1%. The sex ratio did not differ significantly from unity (i.e., 50% female among (i Storm Petrel chicks at a breeding colony in NW France, (ii adults found dead on beaches in Southern Portugal, (iii breeding birds attending nest burrows in the UK, captured by hand, and (iv adults captured near a breeding colony in the UK using copies of the same sound recordings as used in Southern Europe, indicating that females are not inherently more strongly attracted to playback calls than males. A morphological discriminant function analysis failed to provide a good separation of the sexes, showing the importance of molecular sexing for this species. We found no sex difference in the seasonal or nocturnal timing of migration past Southern Europe, but there was a significant tendency for birds to be caught in sex-specific aggregations. The preponderance of females captured in Southern Europe suggests that the sexes may differ in migration route or in their colony-prospecting behaviour during migration, at sites far away from their natal colonies. Such differences in migration behaviour between males and females are poorly understood but have implications for the vulnerability of seabirds to pollution and environmental change at sea during the non-breeding season.

  1. Evidence-based nanoscopic and molecular framework for excipient functionality in compressed orally disintegrating tablets.

    Directory of Open Access Journals (Sweden)

    Ali Al-Khattawi

    Full Text Available The work investigates the adhesive/cohesive molecular and physical interactions together with nanoscopic features of commonly used orally disintegrating tablet (ODT excipients microcrystalline cellulose (MCC and D-mannitol. This helps to elucidate the underlying physico-chemical and mechanical mechanisms responsible for powder densification and optimum product functionality. Atomic force microscopy (AFM contact mode analysis was performed to measure nano-adhesion forces and surface energies between excipient-drug particles (6-10 different particles per each pair. Moreover, surface topography images (100 nm2-10 µm2 and roughness data were acquired from AFM tapping mode. AFM data were related to ODT macro/microscopic properties obtained from SEM, FTIR, XRD, thermal analysis using DSC and TGA, disintegration testing, Heckel and tabletability profiles. The study results showed a good association between the adhesive molecular and physical forces of paired particles and the resultant densification mechanisms responsible for mechanical strength of tablets. MCC micro roughness was 3 times that of D-mannitol which explains the high hardness of MCC ODTs due to mechanical interlocking. Hydrogen bonding between MCC particles could not be established from both AFM and FTIR solid state investigation. On the contrary, D-mannitol produced fragile ODTs due to fragmentation of surface crystallites during compression attained from its weak crystal structure. Furthermore, AFM analysis has shown the presence of extensive micro fibril structures inhabiting nano pores which further supports the use of MCC as a disintegrant. Overall, excipients (and model drugs showed mechanistic behaviour on the nano/micro scale that could be related to the functionality of materials on the macro scale.

  2. Lack of evidence of rotavirus-dependent molecular mimicry as a trigger of coeliac disease.

    Science.gov (United States)

    Ziberna, F; De Lorenzo, G; Schiavon, V; Arnoldi, F; Quaglia, S; De Leo, L; Vatta, S; Martelossi, S; Burrone, O R; Ventura, A; Not, T

    2016-12-01

    New data suggest the involvement of rotavirus (RV) in triggering autoimmunity in coeliac disease (CD) by molecular mimicry between the human-transglutaminase protein and the dodecapeptide (260-271 aa) of the RV protein VP7 (pVP7). To assess the role of RV in the onset of CD, we measured anti-pVP7 antibodies in the sera of children with CD and of control groups. We analysed serum samples of 118 biopsy-proven CD patients and 46 patients with potential CD; 32 children with other gastrointestinal diseases; 107 no-CD children and 107 blood donors. Using enzyme-linked immunosorbent assay (ELISA) assay, we measured immunoglobulin (Ig)A-IgG antibodies against the synthetic peptides pVP7, the human transglutaminase-derived peptide (476-487 aa) which shows a homology with VP7 protein and a control peptide. The triple-layered RV particles (TLPs) containing the VP7 protein and the double-layered RV-particles (DLPs) lacking the VP7 protein were also used as antigens in ELISA assay. Antibody reactivity to the RV-TLPs was positive in 22 of 118 (18%) CD patients and in both paediatric (17 of 107, 16%) and adult (29 of 107, 27%) control groups, without showing a statistically significant difference among them (P = 0·6, P = 0·1). Biopsy-proven CD patients as well as the adult control group demonstrated a high positive antibody reactivity against both pVP7 (34 of 118, 29% CD patients; 66 of 107, 62% adult controls) and control synthetic peptides (35 of 118, 30% CD patients; 56 of 107, 52% adult controls), suggesting a non-specific response against RV pVP7. We show that children with CD do not have higher immune reactivity to RV, thus questioning the molecular mimicry mechanism as a triggering factor of CD. © 2016 British Society for Immunology.

  3. Evidence-Based Nanoscopic and Molecular Framework for Excipient Functionality in Compressed Orally Disintegrating Tablets

    Science.gov (United States)

    Al-khattawi, Ali; Alyami, Hamad; Townsend, Bill; Ma, Xianghong; Mohammed, Afzal R.

    2014-01-01

    The work investigates the adhesive/cohesive molecular and physical interactions together with nanoscopic features of commonly used orally disintegrating tablet (ODT) excipients microcrystalline cellulose (MCC) and D-mannitol. This helps to elucidate the underlying physico-chemical and mechanical mechanisms responsible for powder densification and optimum product functionality. Atomic force microscopy (AFM) contact mode analysis was performed to measure nano-adhesion forces and surface energies between excipient-drug particles (6-10 different particles per each pair). Moreover, surface topography images (100 nm2–10 µm2) and roughness data were acquired from AFM tapping mode. AFM data were related to ODT macro/microscopic properties obtained from SEM, FTIR, XRD, thermal analysis using DSC and TGA, disintegration testing, Heckel and tabletability profiles. The study results showed a good association between the adhesive molecular and physical forces of paired particles and the resultant densification mechanisms responsible for mechanical strength of tablets. MCC micro roughness was 3 times that of D-mannitol which explains the high hardness of MCC ODTs due to mechanical interlocking. Hydrogen bonding between MCC particles could not be established from both AFM and FTIR solid state investigation. On the contrary, D-mannitol produced fragile ODTs due to fragmentation of surface crystallites during compression attained from its weak crystal structure. Furthermore, AFM analysis has shown the presence of extensive micro fibril structures inhabiting nano pores which further supports the use of MCC as a disintegrant. Overall, excipients (and model drugs) showed mechanistic behaviour on the nano/micro scale that could be related to the functionality of materials on the macro scale. PMID:25025427

  4. Early cosmology constrained

    Energy Technology Data Exchange (ETDEWEB)

    Verde, Licia; Jimenez, Raul [Institute of Cosmos Sciences, University of Barcelona, IEEC-UB, Martí Franquès, 1, E08028 Barcelona (Spain); Bellini, Emilio [University of Oxford, Denys Wilkinson Building, Keble Road, Oxford, OX1 3RH (United Kingdom); Pigozzo, Cassio [Instituto de Física, Universidade Federal da Bahia, Salvador, BA (Brazil); Heavens, Alan F., E-mail: liciaverde@icc.ub.edu, E-mail: emilio.bellini@physics.ox.ac.uk, E-mail: cpigozzo@ufba.br, E-mail: a.heavens@imperial.ac.uk, E-mail: raul.jimenez@icc.ub.edu [Imperial Centre for Inference and Cosmology (ICIC), Imperial College, Blackett Laboratory, Prince Consort Road, London SW7 2AZ (United Kingdom)

    2017-04-01

    We investigate our knowledge of early universe cosmology by exploring how much additional energy density can be placed in different components beyond those in the ΛCDM model. To do this we use a method to separate early- and late-universe information enclosed in observational data, thus markedly reducing the model-dependency of the conclusions. We find that the 95% credibility regions for extra energy components of the early universe at recombination are: non-accelerating additional fluid density parameter Ω{sub MR} < 0.006 and extra radiation parameterised as extra effective neutrino species 2.3 < N {sub eff} < 3.2 when imposing flatness. Our constraints thus show that even when analyzing the data in this largely model-independent way, the possibility of hiding extra energy components beyond ΛCDM in the early universe is seriously constrained by current observations. We also find that the standard ruler, the sound horizon at radiation drag, can be well determined in a way that does not depend on late-time Universe assumptions, but depends strongly on early-time physics and in particular on additional components that behave like radiation. We find that the standard ruler length determined in this way is r {sub s} = 147.4 ± 0.7 Mpc if the radiation and neutrino components are standard, but the uncertainty increases by an order of magnitude when non-standard dark radiation components are allowed, to r {sub s} = 150 ± 5 Mpc.

  5. Sporulation environment influences spore properties in Bacillus: evidence and insights on underlying molecular and physiological mechanisms.

    Science.gov (United States)

    Bressuire-Isoard, Christelle; Broussolle, Véronique; Carlin, Frédéric

    2018-05-17

    Bacterial spores are resistant to physical and chemical insults, which make them a major concern for public health and for industry. Spores help bacteria to survive extreme environmental conditions that vegetative cells cannot tolerate. Spore resistance and dormancy are important properties for applications in medicine, veterinary health, food safety, crop protection, and other domains. The resistance of bacterial spores results from a protective multilayered structure and from the unique composition of the spore core. The mechanisms of sporulation and germination, the first stage after breaking of dormancy, and organization of spore structure have been extensively studied in Bacillus species. This review aims to illustrate how far the structure, composition and properties of spores are shaped by the environmental conditions in which spores form. We look at the physiological and molecular mechanisms underpinning how sporulation media and environment deeply affect spore yield, spore properties like resistance to wet heat and physical and chemical agents, germination, and further growth. For example, spore core water content decreases as sporulation temperature increases, and resistance to wet heat increases. Controlling the fate of Bacillus spores is pivotal to controlling bacterial risks and process efficiencies in, for example, the food industry, and better control hinges on better understanding how sporulation conditions influence spore properties.

  6. Intense Pulsed Light: Friend or Foe? Molecular Evidence to Clarify Doubts.

    Science.gov (United States)

    Ferreira, Liliana; Vitorino, Rui; Neuparth, Maria João; Rodrigues, David; Gama, Adelina; Faustino-Rocha, Ana I; Ferreira, Rita; Oliveira, Paula A

    2018-02-01

    Intense pulsed light (IPL) has been extensively applied in the field of dermatology and aesthetics; however, the long-term consequences of its use are poorly unknown, and to the best of our knowledge there is no study on the effect of IPL in neoplastic lesions. In order to better understand the molecular mechanisms underlying IPL application in the skin, we used an animal model of carcinogenesis obtained by chemical induction with 12-dimethylbenz(a)anthracene (DMBA) and 12-O-tetradecanoylphorbol-13-acetate (TPA). Institute of Cancer Research (ICR) mice were administered DMBA and/or TPA and treated with IPL. Skin was evaluated by histopathology and 2DE-blot-MS/MS analysis. Our data evidenced an inflammatory response and a metabolic remodeling of skin towards a glycolytic phenotype after chronic exposure to IPL, which was accomplished by increased oxidative stress and susceptibility to apoptosis. These alterations induced by IPL were more notorious in the DMBA sensitized skin. Keratins and metabolic proteins seem to be the more susceptible to oxidative modifications that might result in loss of function, contributing for the histological changes observed in treated skin. Data highlight the deleterious impact of IPL on skin phenotype, which justifies the need for more experimental studies in order to increase our understanding of the IPL long-term safety. Copyright© 2018, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

  7. Cas9-catalyzed DNA Cleavage Generates Staggered Ends: Evidence from Molecular Dynamics Simulations

    Science.gov (United States)

    Zuo, Zhicheng; Liu, Jin

    2016-11-01

    The CRISPR-associated endonuclease Cas9 from Streptococcus pyogenes (spCas9) along with a single guide RNA (sgRNA) has emerged as a versatile toolbox for genome editing. Despite recent advances in the mechanism studies on spCas9-sgRNA-mediated double-stranded DNA (dsDNA) recognition and cleavage, it is still unclear how the catalytic Mg2+ ions induce the conformation changes toward the catalytic active state. It also remains controversial whether Cas9 generates blunt-ended or staggered-ended breaks with overhangs in the DNA. To investigate these issues, here we performed the first all-atom molecular dynamics simulations of the spCas9-sgRNA-dsDNA system with and without Mg2+ bound. The simulation results showed that binding of two Mg2+ ions at the RuvC domain active site could lead to structurally and energetically favorable coordination ready for the non-target DNA strand cleavage. Importantly, we demonstrated with our simulations that Cas9-catalyzed DNA cleavage produces 1-bp staggered ends rather than generally assumed blunt ends.

  8. Global patterns of insect diversification: towards a reconciliation of fossil and molecular evidence?

    Science.gov (United States)

    Condamine, Fabien L; Clapham, Matthew E; Kergoat, Gael J

    2016-01-18

    Macroevolutionary studies of insects at diverse taxonomic scales often reveal dynamic evolutionary patterns, with multiple inferred diversification rate shifts. Responses to major past environmental changes, such as the Cretaceous Terrestrial Revolution, or the development of major key innovations, such as wings or complete metamorphosis are usually invoked as potential evolutionary triggers. However this view is partially contradicted by studies on the family-level fossil record showing that insect diversification was relatively constant through time. In an attempt to reconcile both views, we investigate large-scale insect diversification dynamics at family level using two distinct types of diversification analyses on a molecular timetree representing ca. 82% of the extant families, and reassess the insect fossil diversity using up-to-date records. Analyses focusing on the fossil record recovered an early burst of diversification, declining to low and steady rates through time, interrupted by extinction events. Phylogenetic analyses showed that major shifts of diversification rates only occurred in the four richest holometabolous orders. Both suggest that neither the development of flight or complete metamorphosis nor the Cretaceous Terrestrial Revolution environmental changes induced immediate changes in diversification regimes; instead clade-specific innovations likely promoted the diversification of major insect orders.

  9. Biochemical characterization and molecular evidence of a laccase from the bird's nest fungus Cyathus bulleri.

    Science.gov (United States)

    Vasdev, Kavita; Dhawan, Shikha; Kapoor, Rajeev Kumar; Kuhad, Ramesh Chander

    2005-08-01

    Cyathus bulleri, a bird's nest fungus, known to decolorize polymeric dye Poly R-478, was found to produce 8 U ml(-1) of laccase in malt extract broth. Laccase activity appeared as a single band on non-denaturing gel. Laccase was purified to homogeneity by anion exchange chromatography and gel filtration. The enzyme was a monomer with an apparent molecular mass of 60 kD, pI of 3.7 and was stable in the pH range of 2-6 with an optimum pH of 5.2. The optimal reaction temperature was 45 degrees C and the enzyme lost its activity above 70 degrees C. Enzyme could oxidize a broad range of various phenolic substrates. K(m) values for ABTS, 2,6-dimethoxyphenol, guaiacol, and ferulic acid were found to be 48.6, 56, 22, and 14 mM while K(cat) values were 204, 180, 95.6, and 5.2, respectively. It was completely inhibited by KCN, NaN(3), beta-mercaptoethanol, HgCl(2), and SDS, while EDTA had no effect on enzyme activity. The N-terminal amino acid sequence of C. bulleri laccase showed close homology to N-terminal sequences of laccase from other white-rot fungi. A 150 bp gene sequence encoding copper-binding domains I and II was most similar to the sequence encoding a laccase from Pycnoporus cinnabarinus with 74.8% level of similarity.

  10. Resveratrol for breast cancer prevention and therapy: Preclinical evidence and molecular mechanisms.

    Science.gov (United States)

    Sinha, Dona; Sarkar, Nivedita; Biswas, Jaydip; Bishayee, Anupam

    2016-10-01

    Globally, breast cancer is the most frequently diagnosed cancer among women. The major unresolved problems with metastatic breast cancer is recurrence after receiving objective response to chemotherapy, drug-induced side effects of first line chemotherapy and delayed response to second line of treatment. Unfortunately, very few options are available as third line treatment. It is clear that under such circumstances there is an urgent need for new and effective drugs. Phytochemicals are among the most promising chemopreventive treatment options for the management of cancer. Resveratrol (3,5,4'-trihydroxy-trans-stilbene), a non-flavonoid polyphenol present in several dietary sources, including grapes, berries, soy beans, pomegranate and peanuts, has been shown to possess a wide range of health benefits through its effect on a plethora of molecular targets.The present review encompasses the role of resveratrol and its natural/synthetic analogue in the light of their efficacy against tumor cell proliferation, metastasis, epigenetic alterations and for induction of apoptosis as well as sensitization toward chemotherapeutic drugs in various in vitro and in vivo models of breast cancer. The roles of resveratrol as a phytoestrogen, an aromatase inhibitor and in stem cell therapy as well as adjuvent treatment are also discussed. This review explores the full potential of resveratrol in breast cancer prevention and treatment with current limitations, challenges and future directions of research. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. Molecular evidence for high frequency of multiple paternity in a freshwater shrimp species Caridina ensifera.

    Directory of Open Access Journals (Sweden)

    Gen Hua Yue

    2010-09-01

    Full Text Available Molecular genetic analyses of parentage provide insights into mating systems. Although there are 22,000 members in Malacostraca, not much has been known about mating systems in Malacostraca. The freshwater shrimp Caridina ensifera blue, is a new species belonging to Malacostraca which was discovered recently in Sulawesi, Indonesia. Due to its small body size and low fecundity, this species is an ideal species to study the occurrence and frequency of multiple paternity and to understand of how the low fecundity species persist and evolve.In this study, we developed four polymorphic microsatellites from C. ensifera and applied them to investigate the occurrence and frequency of multiple paternity in 20 C. ensifera broods caught from Lake Matano, Sulawesi. By genotyping the mother and all offspring from each brood we discovered multiple paternity in all 20 broods. In most of the 20 broods, fathers contributed skewed numbers of offspring and there was an apparent inverse correlation between reproductive success of sires and their relatedness to mothers.Our results in combination with recent reports on multiple paternity in crayfish, crab and lobster species suggests that multiple paternity is common in Malacostraca. Skewed contribution of fathers to the numbers of offspring and inverse correlation between reproductive success of sires and their relatedness to mothers suggest that sperm competition occurred and/or pre- and postcopulatory female choice happen, which may be important for avoiding the occurrence of inbreeding and optimize genetic variation in offspring and for persistence and evolution of low fecundity species.

  12. Molecular evidence for a recent demographic expansion in the puma (Puma concolor) (Mammalia, Felidae)

    Science.gov (United States)

    Matte, Eunice M.; Castilho, Camila S.; Miotto, Renata A.; Sana, Denis A.; Johnson, Warren E.; O’Brien, Stephen J.; de Freitas, Thales R. O.; Eizirik, Eduardo

    2013-01-01

    The puma is an iconic predator that ranges throughout the Americas, occupying diverse habitats. Previous phylogeographic analyses have revealed that it exhibits moderate levels of genetic structure across its range, with few of the classically recognized subspecies being supported as distinct demographic units. Moreover, most of the species’ molecular diversity was found to be in South America. To further investigate the phylogeographic structure and demographic history of pumas we analyzed mtDNA sequences from 186 individuals sampled throughout their range, with emphasis on South America. Our objectives were to refine the phylogeographic assessment within South America and to investigate the demographic history of pumas using a coalescent approach. Our results extend previous phylogeographic findings, reassessing the delimitation of historical population units in South America and demonstrating that this species experienced a considerable demographic expansion in the Holocene, ca. 8,000 years ago. Our analyses indicate that this expansion occurred in South America, prior to the hypothesized re-colonization of North America, which was therefore inferred to be even more recent. The estimated demographic history supports the interpretation that pumas suffered a severe demographic decline in the Late Pleistocene throughout their distribution, followed by population expansion and re-colonization of the range, initiating from South America. PMID:24385863

  13. Molecular evidence for a recent demographic expansion in the puma (Puma concolor (Mammalia, Felidae

    Directory of Open Access Journals (Sweden)

    Eunice M. Matte

    2013-01-01

    Full Text Available The puma is an iconic predator that ranges throughout the Americas, occupying diverse habitats. Previous phylogeographic analyses have revealed that it exhibits moderate levels of genetic structure across its range, with few of the classically recognized subspecies being supported as distinct demographic units. Moreover, most of the species' molecular diversity was found to be in South America. To further investigate the phylogeographic structure and demographic history of pumas we analyzed mtDNA sequences from 186 individuals sampled throughout their range, with emphasis on South America. Our objectives were to refine the phylogeographic assessment within South America and to investigate the demographic history of pumas using a coalescent approach. Our results extend previous phylogeographic findings, reassessing the delimitation of historical population units in South America and demonstrating that this species experienced a considerable demographic expansion in the Holocene, ca. 8,000 years ago. Our analyses indicate that this expansion occurred in South America, prior to the hypothesized re-colonization of North America, which was therefore inferred to be even more recent. The estimated demographic history supports the interpretation that pumas suffered a severe demographic decline in the Late Pleistocene throughout their distribution, followed by population expansion and re-colonization of the range, initiating from South America.

  14. Molecular evidence for the first records of facultative parthenogenesis in elapid snakes.

    Science.gov (United States)

    Allen, L; Sanders, K L; Thomson, V A

    2018-02-01

    Parthenogenesis is a form of asexual reproduction by which embryos develop from unfertilized eggs. Parthenogenesis occurs in reptiles; however, it is not yet known to occur in the widespread elapid snakes (Elapidae), which include well-known taxa such as cobras, mambas, taipans and sea snakes. Here, we describe the production of viable parthenogens in two species of Australo-Papuan elapids with divergent reproductive modes: the oviparous coastal/Papuan taipan ( Oxyuranus scutellatus ) and the viviparous southern death adder ( Acanthophis antarcticus ). Analyses of nuclear SNP data excluded paternity for putative fathers and convincingly demonstrated asexual reproduction, thus representing the first evidence of facultative parthenogenesis in Elapidae. Our finding has broad implications for understanding the evolution of reproductive diversity in snakes, as well as managing the conservation of genetic diversity in wild and captive populations.

  15. Constraining neutrinoless double beta decay

    International Nuclear Information System (INIS)

    Dorame, L.; Meloni, D.; Morisi, S.; Peinado, E.; Valle, J.W.F.

    2012-01-01

    A class of discrete flavor-symmetry-based models predicts constrained neutrino mass matrix schemes that lead to specific neutrino mass sum-rules (MSR). We show how these theories may constrain the absolute scale of neutrino mass, leading in most of the cases to a lower bound on the neutrinoless double beta decay effective amplitude.

  16. Molecular evidence of cryptic speciation in the "cosmopolitan" excavating sponge Cliona celata (Porifera, Clionaidae).

    Science.gov (United States)

    Xavier, J R; Rachello-Dolmen, P G; Parra-Velandia, F; Schönberg, C H L; Breeuwer, J A J; van Soest, R W M

    2010-07-01

    Over the past several decades molecular tools have shown an enormous potential to aid in the clarification of species boundaries in the marine realm, particularly in morphologically simple groups. In this paper we report a case of cryptic speciation in an allegedly cosmopolitan and ecologically important species-the excavating sponge Cliona celata (Clionaidae, Hadromerida). In the Northeast Atlantic and Mediterranean C. celata displays a discontinuous distribution of its putative growth stages (boring, encrusting, and massive) leading us to investigate its specific status. Phylogenetic reconstructions of mitochondrial (COI, Atp8) and nuclear (28S) gene fragments revealed levels of genetic diversity and divergence compatible with interspecific relationships. We therefore demonstrate C. celata as constituting a species complex comprised of at least four morphologically indistinct species, each showing a far more restricted distribution: two species on the Atlantic European coasts and two on the Mediterranean and adjacent Atlantic coasts (Macaronesian islands). Our results provide further confirmation that the different morphotypes do indeed constitute either growth stages or ecologically adapted phenotypes as boring and massive forms were found in two of the four uncovered species. We additionally provide an overview of the cases of cryptic speciation which have been reported to date within the Porifera, and highlight how taxonomic crypsis may confound scientific interpretation and hamper biotechnological advancement. Our work together with previous studies suggests that overconservative systematic traditions but also morphological stasis have led to genetic complexity going undetected and that a DNA-assisted taxonomy may play a key role in uncovering the hidden diversity in this taxonomic group. Copyright 2010 Elsevier Inc. All rights reserved.

  17. Reconsolidation and extinction are dissociable and mutually exclusive processes: behavioral and molecular evidence.

    Science.gov (United States)

    Merlo, Emiliano; Milton, Amy L; Goozée, Zara Y; Theobald, David E; Everitt, Barry J

    2014-02-12

    Memory persistence is critically influenced by retrieval. In rats, a single presentation of a conditioned fear stimulus induces memory reconsolidation and fear memory persistence, while repeated fear cue presentations result in loss of fear through extinction. These two opposite behavioral outcomes are operationally linked by the number of cue presentations at memory retrieval. However, the behavioral properties and mechanistic determinants of the transition have not yet been explored; in particular, whether reconsolidation and extinction processes coexist or are mutually exclusive, depending on the exposure to non-reinforced retrieval events. We characterized both behaviorally and molecularly the transition from reconsolidation to extinction of conditioned fear and showed that an increase in calcineurin (CaN) in the basolateral amygdala (BLA) supports the shift from fear maintenance to fear inhibition. Gradually increasing the extent of retrieval induces a gradual decrease in freezing responses to the conditioned stimulus and a gradual increase in amygdala CaN level. This newly synthesized CaN is required for the extinction, but not the reconsolidation, of conditioned fear. During the transition from reconsolidation to extinction, we have revealed an insensitive state of the fear memory where NMDA-type glutamate receptor agonist and antagonist drugs are unable either to modulate CaN levels in the BLA or alter the reconsolidation or extinction processes. Together, our data indicate both that reconsolidation and extinction are mutually exclusive processes and also reveal the presence of a transitional, or "limbo," state of the original memory between these two alternative outcomes of fear memory retrieval, when neither process is engaged.

  18. Searching for speciation genes: molecular evidence for selection associated with colour morphotypes in the Caribbean reef fish genus Hypoplectrus.

    Directory of Open Access Journals (Sweden)

    Ben G Holt

    Full Text Available Closely related species that show clear phenotypic divergence, but without obvious geographic barriers, can provide opportunities to study how diversification can occur when opportunities for allopatric speciation are limited. We examined genetic divergence in the coral reef fish genus Hypoplectrus (family: Serranidae, which comprises of 10-14 morphotypes that are distinguished solely by their distinct colour patterns, but which show little genetic differentiation. Our goal was to detect loci that show clear disequilibrium between morphotypes and across geographical locations. We conducted Amplified Fragment Length Polymorphism molecular analysis to quantify genetic differentiation among, and selection between, morphotypes. Three loci were consistently divergent beyond neutral expectations in repeated pair-wise morphotype comparisons using two different methods. These loci provide the first evidence for genes that may be associated with colour morphotype in the genus Hypoplectrus.

  19. First molecular evidence of potentially zoonotic Babesia microti and Babesia sp. EU1 in Ixodes ricinus ticks in Belgium.

    Science.gov (United States)

    Lempereur, Laetitia; De Cat, Ann; Caron, Yannick; Madder, Maxime; Claerebout, Edwin; Saegerman, Claude; Losson, Bertrand

    2011-02-01

    We report the first molecular evidence of the presence of Babesia sp. EU1 and Babesia microti in Ixodes ricinus ticks in Belgium. A 1-year national survey collected 1005 ticks from cats and dogs. A polymerase chain reaction technique amplifying a part of the 18S rRNA gene detected Babesia spp. in 11 out of 841 selected and validated tick extracts. Subsequent sequencing identified Ba. microti (n=3) and Babesia sp. EU1 (n=6). This study has demonstrated a low infection rate (1.31% with 95% CI: 0.65-2.33) of Babesia spp. carriage in I. ricinus ticks in Belgium but, for the first time, reports two potentially zoonotic species belonging to this genus. Coinfection with Ba. microti and Borrelia burgdorferi sensu stricto also was demonstrated. In addition, this study clearly demonstrates that inhibitors of polymerase chain reaction amplification are present in engorged ticks.

  20. Molecular structure stability of short-chain chlorinated paraffins (SCCPs): Evidence from lattice compatibility and Simha-Somcynsky theories

    Science.gov (United States)

    Yumak, A.; Boubaker, K.; Petkova, P.; Yahsi, U.

    2015-10-01

    In is known that short-chain chlorinated paraffins (SCCPs) are highly complex technical mixtures of polychlorinated n-alkanes with single chlorine content. Due to their physical properties (viscosity, flame resistance) they are used in many different applications, such as lubricant additives, metal processing, leather fat-liquoring, plastics softening, PVC plasticizing and flame retardants in paints, adhesives and sealants. SCCPs are studied here in terms of processing-linked molecular structure stability, under Simha and Somcynsky-EOS theory calculations and elements from Simha-Somcynsky-related Lattice Compatibility Theory. Analyses were carried out on 1-chloropropane, 2-chloropropane, 1-chlorobutane, 2-chlorobutane, 1-chloro 2-methylane, and 2-chloro 2-methylane as (SCCPs) universal representatives. This paper gives evidence to this stability and reviews the current state of knowledge and highlights the need for further research in order to improve future (SCCPs) monitoring efforts.

  1. Molecular evidence for ongoing complementarity and horizontal gene transfer in endosymbiotic systems of mealybugs

    Directory of Open Access Journals (Sweden)

    Sergio eLópez-Madrigal

    2014-08-01

    Full Text Available Intracellular bacterial supply of essential amino acids is common among sap-feeding insects, thus complementing the scarcity of nitrogenous compounds in plant phloem. This is also the role of the two mealybug endosymbiotic systems whose genomes have been sequenced. In the nested endosymbiotic system from Planococcus citri (Pseudococcinae, Candidatus Tremblaya princeps and Candidatus Moranella endobia cooperate to synthesize essential amino acids, while in Phenacoccus avenae (Phenacoccinae this function is performed by its single endosymbiont Candidatus Tremblaya phenacola. However, little is known regarding the evolution of essential amino acid supplementation strategies in other mealybug systems. To address this knowledge gap, we screened for the presence of six selected loci involved in essential amino acid biosynthesis in five additional mealybug species. We found evidence of ongoing complementarity among endosymbionts from insects of subfamily Pseudococcinae, as well as horizontal gene transfer affecting endosymbionts from insects of family Phenacoccinae, providing a more comprehensive picture of the evolutionary history of these endosymbiotic systems. Additionally, we report two diagnostic motifs to help identify invasive mealybug species.

  2. Escitalopram—translating molecular properties into clinical benefit: reviewing the evidence in major depression

    Science.gov (United States)

    Leonard, Brian; Taylor, David

    2010-01-01

    The majority of currently marketed drugs contain a mixture of enantiomers; however, recent evidence suggests that individual enantiomers can have pharmacological properties that differ importantly from enantiomer mixtures. Escitalopram, the S-enantiomer of citalopram, displays markedly different pharmacological activity to the R-enantiomer. This review aims to evaluate whether these differences confer any significant clinical advantage for escitalopram over either citalopram or other frequently used antidepressants. Searches were conducted using PubMed and EMBASE (up to January 2009). Abstracts of the retrieved studies were reviewed independently by both authors for inclusion. Only those studies relating to depression or major depressive disorder were included. The search identified over 250 citations, of which 21 studies and 18 pooled or meta-analyses studies were deemed suitable for inclusion. These studies reveal that escitalopram has some efficacy advantage over citalopram and paroxetine, but no consistent advantage over other selective serotonin reuptake inhibitors. Escitalopram has at least comparable efficacy to available serotonin-norepinephrine reuptake inhibitors, venlafaxine XR and duloxetine, and may offer some tolerability advantages over these agents. This review suggests that the mechanistic advantages of escitalopram over citalopram translate into clinical efficacy advantages. Escitalopram may have a favourable benefit-risk ratio compared with citalopram and possibly with several other antidepressant agents. PMID:20147575

  3. Escitalopram--translating molecular properties into clinical benefit: reviewing the evidence in major depression.

    LENUS (Irish Health Repository)

    Leonard, Brian

    2010-08-01

    The majority of currently marketed drugs contain a mixture of enantiomers; however, recent evidence suggests that individual enantiomers can have pharmacological properties that differ importantly from enantiomer mixtures. Escitalopram, the S-enantiomer of citalopram, displays markedly different pharmacological activity to the R-enantiomer. This review aims to evaluate whether these differences confer any significant clinical advantage for escitalopram over either citalopram or other frequently used antidepressants. Searches were conducted using PubMed and EMBASE (up to January 2009). Abstracts of the retrieved studies were reviewed independently by both authors for inclusion. Only those studies relating to depression or major depressive disorder were included. The search identified over 250 citations, of which 21 studies and 18 pooled or meta-analyses studies were deemed suitable for inclusion. These studies reveal that escitalopram has some efficacy advantage over citalopram and paroxetine, but no consistent advantage over other selective serotonin reuptake inhibitors. Escitalopram has at least comparable efficacy to available serotonin-norepinephrine reuptake inhibitors, venlafaxine XR and duloxetine, and may offer some tolerability advantages over these agents. This review suggests that the mechanistic advantages of escitalopram over citalopram translate into clinical efficacy advantages. Escitalopram may have a favourable benefit-risk ratio compared with citalopram and possibly with several other antidepressant agents.

  4. Transcriptional activity of the giant barrel sponge, Xestospongia muta Holobiont: Molecular Evidence for Metabolic Interchange

    Directory of Open Access Journals (Sweden)

    Cara L Fiore

    2015-04-01

    Full Text Available Compared to our understanding of the taxonomic composition of the symbiotic microbes in marine sponges, the functional diversity of these symbionts is largely unknown. Furthermore, the application of genomic, transcriptomic, and proteomic techniques to functional questions on sponge host-symbiont interactions is in its infancy. In this study, we generated a transcriptome for the host and a metatranscriptome of its microbial symbionts for the giant barrel sponge, Xestospongia muta, from the Caribbean. In combination with a gene-specific approach, our goals were to 1 characterize genetic evidence for nitrogen cycling in X. muta, an important limiting nutrient on coral reefs 2 identify which prokaryotic symbiont lineages are metabolically active and, 3 characterize the metabolic potential of the prokaryotic community. Xestospongia muta expresses genes from multiple nitrogen transformation pathways that when combined with the abundance of this sponge, and previous data on dissolved inorganic nitrogen fluxes, shows that this sponge is an important contributor to nitrogen cycling on coral reefs. Additionally, we observed significant differences in gene expression of the archaeal amoA gene, which is involved in ammonia oxidation, between coral reef locations consistent with differences in the fluxes of dissolved inorganic nitrogen previously reported. In regards to symbiont metabolic potential, the genes in the biosynthetic pathways of several amino acids were present in the prokaryotic metatranscriptome dataset but in the host-derived transcripts only the catabolic reactions for these amino acids were present. A similar pattern was observed for the B vitamins (riboflavin, biotin, thiamin, cobalamin. These results expand our understanding of biogeochemical cycling in sponges, and the metabolic interchange highlighted here advances the field of symbiont physiology by elucidating specific metabolic pathways where there is high potential for host

  5. Molecular Evidence of Adenosine Deaminase Linking Adenosine A2A Receptor and CD26 Proteins.

    Science.gov (United States)

    Moreno, Estefanía; Canet, Júlia; Gracia, Eduard; Lluís, Carme; Mallol, Josefa; Canela, Enric I; Cortés, Antoni; Casadó, Vicent

    2018-01-01

    Adenosine is an endogenous purine nucleoside that acts in all living systems as a homeostatic network regulator through many pathways, which are adenosine receptor (AR)-dependent and -independent. From a metabolic point of view, adenosine deaminase (ADA) is an essential protein in the regulation of the total intracellular and extracellular adenosine in a tissue. In addition to its cytosolic localization, ADA is also expressed as an ecto-enzyme on the surface of different cells. Dipeptidyl peptidase IV (CD26) and some ARs act as binding proteins for extracellular ADA in humans. Since CD26 and ARs interact with ADA at opposite sites, we have investigated if ADA can function as a cell-to-cell communication molecule by bridging the anchoring molecules CD26 and A 2A R present on the surfaces of the interacting cells. By combining site-directed mutagenesis of ADA amino acids involved in binding to A 2A R and a modification of the bioluminescence resonance energy transfer (BRET) technique that allows detection of interactions between two proteins expressed in different cell populations with low steric hindrance (NanoBRET), we show direct evidence of the specific formation of trimeric complexes CD26-ADA-A 2A R involving two cells. By dynamic mass redistribution assays and ligand binding experiments, we also demonstrate that A 2A R-NanoLuc fusion proteins are functional. The existence of this ternary complex is in good agreement with the hypothesis that ADA could bridge T-cells (expressing CD26) and dendritic cells (expressing A 2A R). This is a new metabolic function for ecto-ADA that, being a single chain protein, it has been considered as an example of moonlighting protein, because it performs more than one functional role (as a catalyst, a costimulator, an allosteric modulator and a cell-to-cell connector) without partitioning these functions in different subunits.

  6. Molecular Evidence of Adenosine Deaminase Linking Adenosine A2A Receptor and CD26 Proteins

    Directory of Open Access Journals (Sweden)

    Estefanía Moreno

    2018-02-01

    Full Text Available Adenosine is an endogenous purine nucleoside that acts in all living systems as a homeostatic network regulator through many pathways, which are adenosine receptor (AR-dependent and -independent. From a metabolic point of view, adenosine deaminase (ADA is an essential protein in the regulation of the total intracellular and extracellular adenosine in a tissue. In addition to its cytosolic localization, ADA is also expressed as an ecto-enzyme on the surface of different cells. Dipeptidyl peptidase IV (CD26 and some ARs act as binding proteins for extracellular ADA in humans. Since CD26 and ARs interact with ADA at opposite sites, we have investigated if ADA can function as a cell-to-cell communication molecule by bridging the anchoring molecules CD26 and A2AR present on the surfaces of the interacting cells. By combining site-directed mutagenesis of ADA amino acids involved in binding to A2AR and a modification of the bioluminescence resonance energy transfer (BRET technique that allows detection of interactions between two proteins expressed in different cell populations with low steric hindrance (NanoBRET, we show direct evidence of the specific formation of trimeric complexes CD26-ADA-A2AR involving two cells. By dynamic mass redistribution assays and ligand binding experiments, we also demonstrate that A2AR-NanoLuc fusion proteins are functional. The existence of this ternary complex is in good agreement with the hypothesis that ADA could bridge T-cells (expressing CD26 and dendritic cells (expressing A2AR. This is a new metabolic function for ecto-ADA that, being a single chain protein, it has been considered as an example of moonlighting protein, because it performs more than one functional role (as a catalyst, a costimulator, an allosteric modulator and a cell-to-cell connector without partitioning these functions in different subunits.

  7. Molecular and biochemical evidence for the involvement of calcium/calmodulin in auxin action

    Science.gov (United States)

    Yang, T.; Poovaiah, B. W.

    2000-01-01

    -dependent manner suggests that calcium/CaM regulate ZmSAUR1 at the post-translational level. Our data provide the first direct evidence for the involvement of calcium/CaM-mediated signaling in auxin-mediated signal transduction.

  8. Molecular Evidence for Natural Hybridization between Cotoneaster dielsianus and C. glaucophyllus

    Directory of Open Access Journals (Sweden)

    Mingwan Li

    2017-05-01

    Full Text Available Hybridization accompanied by polyploidization and apomixis has been demonstrated as a driving force in the evolution and speciation of many plants. A good example to study the evolutionary process of hybridization associated with polyploidy and apomixis is the genus Cotoneaster (Rosaceae, which includes approximately 150 species, most of which are polyploid apomicts. In this study, we investigated all Cotoneaster taxa distributed in a small region of Malipo, Yunnan, China. Based on the morphological characteristics, four Cotoneaster taxa were identified and sampled: C. dielsianus, C. glaucophyllus, C. franchetii, and a putative hybrid. Flow cytometry analyses showed that C. glaucophyllus was diploid, while the other three taxa were tetraploid. A total of five low-copy nuclear genes and six chloroplast regions were sequenced to validate the status of the putative hybrid. Sequence analyses showed that C. dielsianus and C. glaucophyllus are distantly related and they could be well separated using totally 50 fixed nucleotide substitutions and four fixed indels at the 11 investigated genes. All individuals of the putative hybrid harbored identical sequences: they showed chromatogram additivity for all fixed differences between C. dielsianus and C. glaucophyllus at the five nuclear genes, and were identical with C. glaucophyllus at the six chloroplast regions. Haplotype analysis revealed that C. dielsianus possessed nine haplotypes for the 11 genes, while C. glaucophyllus had ten, and there were no shared haplotypes between the two species. The putative hybrid harbored two haplotypes for each nuclear gene: one shared with C. dielsianus and the other with C. glaucophyllus. They possessed the same chloroplast haplotype with C. glaucophyllus. Our study provided convincing evidence for natural hybridization between C. dielsianus and C. glaucophyllus, and revealed that all hybrid individuals were derivatives of one initial F1 via apomixes. C. glaucophyllus

  9. Constrained evolution in numerical relativity

    Science.gov (United States)

    Anderson, Matthew William

    The strongest potential source of gravitational radiation for current and future detectors is the merger of binary black holes. Full numerical simulation of such mergers can provide realistic signal predictions and enhance the probability of detection. Numerical simulation of the Einstein equations, however, is fraught with difficulty. Stability even in static test cases of single black holes has proven elusive. Common to unstable simulations is the growth of constraint violations. This work examines the effect of controlling the growth of constraint violations by solving the constraints periodically during a simulation, an approach called constrained evolution. The effects of constrained evolution are contrasted with the results of unconstrained evolution, evolution where the constraints are not solved during the course of a simulation. Two different formulations of the Einstein equations are examined: the standard ADM formulation and the generalized Frittelli-Reula formulation. In most cases constrained evolution vastly improves the stability of a simulation at minimal computational cost when compared with unconstrained evolution. However, in the more demanding test cases examined, constrained evolution fails to produce simulations with long-term stability in spite of producing improvements in simulation lifetime when compared with unconstrained evolution. Constrained evolution is also examined in conjunction with a wide variety of promising numerical techniques, including mesh refinement and overlapping Cartesian and spherical computational grids. Constrained evolution in boosted black hole spacetimes is investigated using overlapping grids. Constrained evolution proves to be central to the host of innovations required in carrying out such intensive simulations.

  10. Evidência molecular da ocorrência de um fitoplasma associado ao lenho mole da macieira Molecular evidence for an association of a phytoplasma with apple rubbery wood

    Directory of Open Access Journals (Sweden)

    Luiz Fernando Caldeira Ribeiro

    2007-03-01

    Full Text Available O lenho mole da macieira é uma doença relevante em diversas partes do mundo. Sintomas típicos desta doença têm sido observados em pomares instalados em estados do sul do território brasileiro desde a década de oitenta. Enxertia tem revelado a natureza infecciosa da doença e a observação de corpúsculos filamentosos no floema tem evidenciado possível associação com fitoplasma. No presente trabalho plantas com sintomas de lenho mole foram coletadas em pomar comercial, visando demonstrar a presença de fitoplasma em tecido doente, bem como identificar molecularmente este fitoplasma. Através do emprego de duplo PCR com iniciadores universais R16mF2/R1 e R16F2n/R2, fitoplasma foi consistentemente detectado em plantas sintomáticas. A identificação conduzida com duplo PCR usando-se iniciadores específicos R16(IIIF2/R demonstrou que o fitoplasma detectado pertencia ao grupo 16SrIII. Análises de RFLP conduzidas com as endonucleases AluI, KpnI, HinfI, HpaII, MseI, RsaI e SauIIIA confirmaram que o fitoplasma era um representante típico do grupo 16SrIII. A detecção e identificação molecular se constitui numa forte evidência que um fitoplasma está associado ao lenho mole da macieira no Brasil, complementando os trabalhos realizados anteriormente com transmissão por enxertia e observação por microscopia eletrônica .Apple rubbery wood is an important disease occurring worldwide. Typical symptoms have been observed since 80' decade in orchards located in the South part of Brazil. In previous studies, grafting has evidenciated that the disease had infeccious etiology and visualization of filamentous bodies inside phloem had indicated that a phytoplasma could be associated with the disease. In the present study, plants with symptoms of rubbery wood were sampled in a commercial orchard in order to demonstrate the presence of phytoplasma in infected tissue and to identify molecularly that the organism. Using nested PCR with universal

  11. Lightweight cryptography for constrained devices

    DEFF Research Database (Denmark)

    Alippi, Cesare; Bogdanov, Andrey; Regazzoni, Francesco

    2014-01-01

    Lightweight cryptography is a rapidly evolving research field that responds to the request for security in resource constrained devices. This need arises from crucial pervasive IT applications, such as those based on RFID tags where cost and energy constraints drastically limit the solution...... complexity, with the consequence that traditional cryptography solutions become too costly to be implemented. In this paper, we survey design strategies and techniques suitable for implementing security primitives in constrained devices....

  12. Flying lemurs – The 'flying tree shrews'? Molecular cytogenetic evidence for a Scandentia-Dermoptera sister clade

    Directory of Open Access Journals (Sweden)

    Volobouev Vitaly

    2008-05-01

    Full Text Available Abstract Background Flying lemurs or Colugos (order Dermoptera represent an ancient mammalian lineage that contains only two extant species. Although molecular evidence strongly supports that the orders Dermoptera, Scandentia, Lagomorpha, Rodentia and Primates form a superordinal clade called Supraprimates (or Euarchontoglires, the phylogenetic placement of Dermoptera within Supraprimates remains ambiguous. Results To search for cytogenetic signatures that could help to clarify the evolutionary affinities within this superordinal group, we have established a genome-wide comparative map between human and the Malayan flying lemur (Galeopterus variegatus by reciprocal chromosome painting using both human and G. variegatus chromosome-specific probes. The 22 human autosomal paints and the X chromosome paint defined 44 homologous segments in the G. variegatus genome. A putative inversion on GVA 11 was revealed by the hybridization patterns of human chromosome probes 16 and 19. Fifteen associations of human chromosome segments (HSA were detected in the G. variegatus genome: HSA1/3, 1/10, 2/21, 3/21, 4/8, 4/18, 7/15, 7/16, 7/19, 10/16, 12/22 (twice, 14/15, 16/19 (twice. Reverse painting of G. variegatus chromosome-specific paints onto human chromosomes confirmed the above results, and defined the origin of the homologous human chromosomal segments in these associations. In total, G. variegatus paints revealed 49 homologous chromosomal segments in the HSA genome. Conclusion Comparative analysis of our map with published maps from representative species of other placental orders, including Scandentia, Primates, Lagomorpha and Rodentia, suggests a signature rearrangement (HSA2q/21 association that links Scandentia and Dermoptera to one sister clade. Our results thus provide new evidence for the hypothesis that Scandentia and Dermoptera have a closer phylogenetic relationship to each other than either of them has to Primates.

  13. Molecular and genealogical evidence for a founder effect in Fanconi anemia families of the Afrikaner population of South Africa

    Science.gov (United States)

    Tipping, A. J.; Pearson, T.; Morgan, N. V.; Gibson, R. A.; Kuyt, L. P.; Havenga, C.; Gluckman, E.; Joenje, H.; de Ravel, T.; Jansen, S.; Mathew, C. G.

    2001-01-01

    Fanconi anemia (FA) is a rare, genetically heterogeneous autosomal recessive disorder associated with progressive aplastic anemia, congenital abnormalities, and cancer. FA has a very high incidence in the Afrikaner population of South Africa, possibly due to a founder effect. Previously we observed allelic association between polymorphic markers flanking the FA group A gene (FANCA) and disease chromosomes in Afrikaners. We genotyped 26 FA families with microsatellite and single nucleotide polymorphic markers and detected five FANCA haplotypes. Mutation scanning of the FANCA gene revealed association of these haplotypes with four different mutations. The most common was an intragenic deletion of exons 12–31, accounting for 60% of FA chromosomes in 46 unrelated Afrikaner FA patients, while two other mutations accounted for an additional 20%. Screening for these mutations in the European populations ancestral to the Afrikaners detected one patient from the Western Ruhr region of Germany who was heterozygous for the major deletion. The mutation was associated with the same unique FANCA haplotype as in Afrikaner patients. Genealogical investigation of 12 Afrikaner families with FA revealed that all were descended from a French Huguenot couple who arrived at the Cape on June 5, 1688, whereas mutation analysis showed that the carriers of the major mutation were descendants of this same couple. The molecular and genealogical evidence is consistent with transmission of the major mutation to Western Germany and the Cape near the end of the 17th century, confirming the existence of a founder effect for FA in South Africa. PMID:11344308

  14. Serologic and molecular evidence for testudinid herpesvirus 2 infection in wild Agassiz’s desert tortoise, Gopherus agassizii

    Science.gov (United States)

    Jacobson, Elliott R.; Berry, Kristin H.; Wellehan, James F. X.; Origgi, Francesco; Childress, April L.; Braun, Josephine; Schrenzel, Mark; Yee, Julie; Rideout, Bruce

    2012-01-01

    Following field observations of wild Agassiz’s desert tortoises (Gopherus agassizii) with oral lesions similar to those seen in captive tortoises with herpesvirus infection, we measured the prevalence of antibodies to Testudinid herpesvirus (TeHV) 3 in wild populations of desert tortoises in California. The survey revealed 30.9% antibody prevalence. In 2009 and 2010, two wild adult male desert tortoises, with gross lesions consistent with trauma and puncture wounds, respectively, were necropsied. Tortoise 1 was from the central Mojave Desert and tortoise 2 was from the northeastern Mojave Desert. We extracted DNA from the tongue of tortoise 1 and from the tongue and nasal mucosa of tortoise 2. Sequencing of polymerase chain reaction products of the herpesviral DNA-dependent DNA polymerase gene and the UL39 gene respectively showed 100% nucleotide identity with TeHV2, which was previously detected in an ill captive desert tortoise in California. Although several cases of herpesvirus infection have been described in captive desert tortoises, our findings represent the first conclusive molecular evidence of TeHV2 infection in wild desert tortoises. The serologic findings support cross-reactivity between TeHV2 and TeHV3. Further studies to determine the ecology, prevalence, and clinical significance of this virus in tortoise populations are needed.

  15. The Potential Role of Lycopene for the Prevention and Therapy of Prostate Cancer: From Molecular Mechanisms to Clinical Evidence

    Science.gov (United States)

    Holzapfel, Nina Pauline; Holzapfel, Boris Michael; Champ, Simon; Feldthusen, Jesper; Clements, Judith; Hutmacher, Dietmar Werner

    2013-01-01

    Lycopene is a phytochemical that belongs to a group of pigments known as carotenoids. It is red, lipophilic and naturally occurring in many fruits and vegetables, with tomatoes and tomato-based products containing the highest concentrations of bioavailable lycopene. Several epidemiological studies have linked increased lycopene consumption with decreased prostate cancer risk. These findings are supported by in vitro and in vivo experiments showing that lycopene not only enhances the antioxidant response of prostate cells, but that it is even able to inhibit proliferation, induce apoptosis and decrease the metastatic capacity of prostate cancer cells. However, there is still no clearly proven clinical evidence supporting the use of lycopene in the prevention or treatment of prostate cancer, due to the only limited number of published randomized clinical trials and the varying quality of existing studies. The scope of this article is to discuss the potential impact of lycopene on prostate cancer by giving an overview about its molecular mechanisms and clinical effects. PMID:23857058

  16. Molecular characterization of Newcastle disease viruses in Ostriches (Struthio camelus L.): further evidences of recombination within avian paramyxovirus type 1.

    Science.gov (United States)

    Yin, Yanbo; Cortey, Martí; Zhang, Yi; Cui, Shangjin; Dolz, Roser; Wang, Jianlin; Gong, Zhenhua

    2011-05-05

    Newcastle disease virus (NDV) strains isolated from ostriches have been genotyped for the first time by partial sequencing of the F gene to determine the epidemiologic role that this species can play within ND outbreaks. Fifteen additional NDV strains, mostly isolated from chickens but also from pigeons and penguins, were also included in the study to determine genetic relationships with ostriches NDV isolates. High genetic diversity was demonstrated in ostrich NDV isolates, as the 10 isolates were grouped in four distinct NDV genotypes. In agreement with the results obtained when chicken isolates have been molecularly characterized, the predominant genotype in ostriches was the genotype VII. More interestingly, evidences of recombination between genotype II and VII were observed in one ostrich isolate and in two further chicken isolates. Therefore, it seems that ostriches may play a relevant role in the ecology and epidemiology of ND particularly in those regions where they have an increasing farming importance as minor poultry species. Copyright © 2010 Elsevier B.V. All rights reserved.

  17. Molecular evolution of glutamine synthetase II: Phylogenetic evidence of a non-endosymbiotic gene transfer event early in plant evolution

    Directory of Open Access Journals (Sweden)

    Tartar Aurélien

    2010-06-01

    Full Text Available Abstract Background Glutamine synthetase (GS is essential for ammonium assimilation and the biosynthesis of glutamine. The three GS gene families (GSI, GSII, and GSIII are represented in both prokaryotic and eukaryotic organisms. In this study, we examined the evolutionary relationship of GSII from eubacterial and eukaryotic lineages and present robust phylogenetic evidence that GSII was transferred from γ-Proteobacteria (Eubacteria to the Chloroplastida. Results GSII sequences were isolated from four species of green algae (Trebouxiophyceae, and additional green algal (Chlorophyceae and Prasinophytae and streptophyte (Charales, Desmidiales, Bryophyta, Marchantiophyta, Lycopodiophyta and Tracheophyta sequences were obtained from public databases. In Bayesian and maximum likelihood analyses, eubacterial (GSIIB and eukaryotic (GSIIE GSII sequences formed distinct clades. Both GSIIB and GSIIE were found in chlorophytes and early-diverging streptophytes. The GSIIB enzymes from these groups formed a well-supported sister clade with the γ-Proteobacteria, providing evidence that GSIIB in the Chloroplastida arose by horizontal gene transfer (HGT. Bayesian relaxed molecular clock analyses suggest that GSIIB and GSIIE coexisted for an extended period of time but it is unclear whether the proposed HGT happened prior to or after the divergence of the primary endosymbiotic lineages (the Archaeplastida. However, GSIIB genes have not been identified in glaucophytes or red algae, favoring the hypothesis that GSIIB was gained after the divergence of the primary endosymbiotic lineages. Duplicate copies of the GSIIB gene were present in Chlamydomonas reinhardtii, Volvox carteri f. nagariensis, and Physcomitrella patens. Both GSIIB proteins in C. reinhardtii and V. carteri f. nagariensis had N-terminal transit sequences, indicating they are targeted to the chloroplast or mitochondrion. In contrast, GSIIB proteins of P. patens lacked transit sequences, suggesting

  18. Molecular evidence for historical presence of knock-down resistance in Anopheles albimanus, a key malaria vector in Latin America.

    Science.gov (United States)

    Lol, Juan C; Castellanos, María E; Liebman, Kelly A; Lenhart, Audrey; Pennington, Pamela M; Padilla, Norma R

    2013-09-18

    Anopheles albimanus is a key malaria vector in the northern neotropics. Current vector control measures in the region are based on mass distributions of long-lasting insecticidal nets (LLINs) and focal indoor residual spraying (IRS) with pyrethroids. Resistance to pyrethroid insecticides can be mediated by increased esterase and/or multi-function oxidase activity and/or mutations in the voltage-gated sodium channel gene. The aim of this work was to characterize the homologous kdr region of the voltage-gated sodium channel gene in An. albimanus and to conduct a preliminary retrospective analysis of field samples collected in the 1990's, coinciding with a time of intense pyrethroid application related to agricultural and public health insect control in the region. Degenerate primers were designed to amplify the homologous kdr region in a pyrethroid-susceptible laboratory strain (Sanarate) of An. albimanus. Subsequently, a more specific primer pair was used to amplify and sequence the region that contains the 1014 codon associated with pyrethroid resistance in other Anopheles spp. (L1014F, L1014S or L1014C). Direct sequencing of the PCR products confirmed the presence of the susceptible kdr allele in the Sanarate strain (L1014) and the presence of homozygous-resistant kdr alleles in field-collected individuals from Mexico (L1014F), Nicaragua (L1014C) and Costa Rica (L1014C). For the first time, the kdr region in An. albimanus is described. Furthermore, molecular evidence suggests the presence of kdr-type resistance in field-collected An. albimanus in Mesoamerica in the 1990s. Further research is needed to conclusively determine an association between the genotypes and resistant phenotypes, and to what extent they may compromise current vector control efforts.

  19. Constraining walking and custodial technicolor

    DEFF Research Database (Denmark)

    Foadi, Roshan; Frandsen, Mads Toudal; Sannino, Francesco

    2008-01-01

    We show how to constrain the physical spectrum of walking technicolor models via precision measurements and modified Weinberg sum rules. We also study models possessing a custodial symmetry for the S parameter at the effective Lagrangian level-custodial technicolor-and argue that these models...

  20. Trends in PDE constrained optimization

    CERN Document Server

    Benner, Peter; Engell, Sebastian; Griewank, Andreas; Harbrecht, Helmut; Hinze, Michael; Rannacher, Rolf; Ulbrich, Stefan

    2014-01-01

    Optimization problems subject to constraints governed by partial differential equations (PDEs) are among the most challenging problems in the context of industrial, economical and medical applications. Almost the entire range of problems in this field of research was studied and further explored as part of the Deutsche Forschungsgemeinschaft (DFG) priority program 1253 on “Optimization with Partial Differential Equations” from 2006 to 2013. The investigations were motivated by the fascinating potential applications and challenging mathematical problems that arise in the field of PDE constrained optimization. New analytic and algorithmic paradigms have been developed, implemented and validated in the context of real-world applications. In this special volume, contributions from more than fifteen German universities combine the results of this interdisciplinary program with a focus on applied mathematics.   The book is divided into five sections on “Constrained Optimization, Identification and Control”...

  1. Constrained Photophysics of 5,7-dimethoxy-2,3,4,9-tetrahydro-1H-carbazol-1-one in the Bioenvironment of Serum Albumins: A Spectroscopic Endeavour Supported by Molecular Docking Analysis.

    Science.gov (United States)

    Mitra, Amrit Krishna; Sau, Abhishek; Pal, Uttam; Saha, Chandan; Basu, Samita

    2017-07-01

    This paper vividly indicates that steady state as well as time-resolved fluorescence techniques can serve as highly sensitive monitors to explore the interactions of 5,7-dimethoxy-2,3,4,9-tetrahydro-1H-carbazol-1-one with model transport proteins, bovine serum albumin (BSA) and human serum albumin (HSA). Besides these, we have used fluorescence anisotropy study to assess the degree of restrictions imparted by the micro-environments of serum albumins. Again, to speculate the triplet excited state interaction between such fluorophore and albumin proteins (BSA& HSA), laser flash-photolysis experiments have been carried out. Molecular docking experiments have also been performed to support the conclusions obtained from steady state experiments.

  2. How many Pygmy Marmoset (Cebuella Gray, 1870) species are there? A taxonomic re-appraisal based on new molecular evidence

    OpenAIRE

    Boubli, JP; da Silva, MNF; Rylands, AB; Nash, SD; Bertuol, F; Nunes, M; Mittermeier, RA; Byrne, H; da Silva, FE; Röhe, F; Sampaio, I; Schneider, H; Farias, IP; Hrbek, T

    2017-01-01

    The pygmy marmoset, Cebuella pygmaea, the smallest of the New World monkeys, has one of the largest geographical distributions of the Amazonian primates. Two forms have been recognized: Cebuella pygmaea pygmaea (Spix, 1823), and C. p. niveiventris Lönnberg, 1940. In this study, we investigated if the separation of pygmy marmosets into these two clades can be corroborated by molecular data. We also examine and compare coloration of the pelage in light of the new molecular results. We analyzed ...

  3. Constraining the dark side with observations

    International Nuclear Information System (INIS)

    Diez-Tejedor, Alberto

    2007-01-01

    The main purpose of this talk is to use the observational evidences pointing out to the existence of a dark side in the universe in order to infer some of the properties of the unseen material. We will work within the Unified Dark Matter models, in which both, Dark Matter and Dark Energy appear as the result of one unknown component. By modeling effectively this component with a classical scalar field minimally coupled to gravity, we will use the observations to constrain the form of the dark action. Using the flat rotation curves of spiral galaxies we will see that we are restringed to the use of purely kinetic actions, previously studied in cosmology by Scherrer. Finally we arrive to a simple action which fits both cosmological and astrophysical observations

  4. Constraining the dark side with observations

    Energy Technology Data Exchange (ETDEWEB)

    Diez-Tejedor, Alberto [Dpto. de Fisica Teorica, Universidad del PaIs Vasco, Apdo. 644, 48080, Bilbao (Spain)

    2007-05-15

    The main purpose of this talk is to use the observational evidences pointing out to the existence of a dark side in the universe in order to infer some of the properties of the unseen material. We will work within the Unified Dark Matter models, in which both, Dark Matter and Dark Energy appear as the result of one unknown component. By modeling effectively this component with a classical scalar field minimally coupled to gravity, we will use the observations to constrain the form of the dark action. Using the flat rotation curves of spiral galaxies we will see that we are restringed to the use of purely kinetic actions, previously studied in cosmology by Scherrer. Finally we arrive to a simple action which fits both cosmological and astrophysical observations.

  5. An evidence-based update on the pharmacological activities and possible molecular targets of Lycium barbarum polysaccharides

    Directory of Open Access Journals (Sweden)

    Cheng J

    2014-12-01

    Full Text Available Jiang Cheng,1,2 Zhi-Wei Zhou,2 Hui-Ping Sheng,3 Lan-Jie He,4 Xue-Wen Fan,1 Zhi-Xu He,5 Tao Sun,6 Xueji Zhang,7 Ruan Jin Zhao,8 Ling Gu,9 Chuanhai Cao,2 Shu-Feng Zhou2,5 1Department of Neurology, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, People’s Republic of China; 2Department of Pharmaceutical Science, College of Pharmacy, University of South Florida, Tampa, FL, USA; 3Department of Infectious Diseases, 4Department of Endocrinology, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, 5Guizhou Provincial Key Laboratory for Regenerative Medicine, Stem Cell and Tissue Engineering Research Center and Sino-US Joint Laboratory for Medical Sciences, Guiyang Medical University, Guiyang, Guizhou, 6Key Laboratory of Craniocerebral Diseases of Ningxia Hui Autonomous Region, Ningxia Medical University, Yinchuan, Ningxia, 7Research Center for Bioengineering and Sensing Technology, University of Science and Technology Beijing, Beijing, People’s Republic of China; 8Center for Traditional Chinese Medicine, Sarasota, FL, USA; 9School of Biology and Chemistry, University of Pu’er, Pu’er, Yunnan, People’s Republic of China Abstract: Lycium barbarum berries, also named wolfberry, Fructus lycii, and Goji berries, have been used in the People’s Republic of China and other Asian countries for more than 2,000 years as a traditional medicinal herb and food supplement. L. barbarum polysaccharides (LBPs are the primary active components of L. barbarum berries and have been reported to possess a wide array of pharmacological activities. Herein, we update our knowledge on the main pharmacological activities and possible molecular targets of LBPs. Several clinical studies in healthy subjects show that consumption of wolfberry juice improves general wellbeing and immune functions. LBPs are reported to have antioxidative and antiaging properties in different models. LBPs show antitumor activities against various types of

  6. Nested Sampling with Constrained Hamiltonian Monte Carlo

    OpenAIRE

    Betancourt, M. J.

    2010-01-01

    Nested sampling is a powerful approach to Bayesian inference ultimately limited by the computationally demanding task of sampling from a heavily constrained probability distribution. An effective algorithm in its own right, Hamiltonian Monte Carlo is readily adapted to efficiently sample from any smooth, constrained distribution. Utilizing this constrained Hamiltonian Monte Carlo, I introduce a general implementation of the nested sampling algorithm.

  7. NMR evidence for Co-Al-Co molecular groups trapped in cages of Co4Al13

    International Nuclear Information System (INIS)

    Jeglic, P.; Heggen, M.; Feuerbacher, M.; Bauer, B.; Gille, P.; Haarmann, F.

    2009-01-01

    We present the results of 27 Al nuclear magnetic resonance (NMR) experiments on the phase Co 4 Al 13 . These results are compared to a recent structure model [1], which demonstrates a unique bonding for Al atoms in the Co-Al-Co molecular groups. In our measurement, two 27 Al signals were identified. The first one originates from Al atoms forming cages. The second signal corresponds to Al sites with exceptionally large almost axially symmetric quadrupole coupling. This finding is in perfect agreement with isolated Co-Al-Co molecular groups in accordance to Ref. [1].

  8. Constrained minimization in C ++ environment

    International Nuclear Information System (INIS)

    Dymov, S.N.; Kurbatov, V.S.; Silin, I.N.; Yashchenko, S.V.

    1998-01-01

    Based on the ideas, proposed by one of the authors (I.N.Silin), the suitable software was developed for constrained data fitting. Constraints may be of the arbitrary type: equalities and inequalities. The simplest of possible ways was used. Widely known program FUMILI was realized to the C ++ language. Constraints in the form of inequalities φ (θ i ) ≥ a were taken into account by change into equalities φ (θ i ) = t and simple inequalities of type t ≥ a. The equalities were taken into account by means of quadratic penalty functions. The suitable software was tested on the model data of the ANKE setup (COSY accelerator, Forschungszentrum Juelich, Germany)

  9. Coherent states in constrained systems

    International Nuclear Information System (INIS)

    Nakamura, M.; Kojima, K.

    2001-01-01

    When quantizing the constrained systems, there often arise the quantum corrections due to the non-commutativity in the re-ordering of constraint operators in the products of operators. In the bosonic second-class constraints, furthermore, the quantum corrections caused by the uncertainty principle should be taken into account. In order to treat these corrections simultaneously, the alternative projection technique of operators is proposed by introducing the available minimal uncertainty states of the constraint operators. Using this projection technique together with the projection operator method (POM), these two kinds of quantum corrections were investigated

  10. Processes underpinning development and maintenance of diversity in rice in West Africa: Evidence from combining morphological and molecular markers

    NARCIS (Netherlands)

    Mokuwa, G.A.; Nuijten, H.A.C.P.; Okry, F.; Teeken, B.W.E.; Maat, H.; Richards, P.; Struik, P.C.

    2014-01-01

    We assessed the interplay of artificial and natural selection in rice adaptation in low-input farming systems in West Africa. Using 20 morphological traits and 176 molecular markers, 182 farmer varieties of rice (Oryza spp.) from 6 West African countries were characterized. Principal component

  11. Molecular evidence of shared hookworm Ancylostoma tubaeforme haplotypes between the critically endangered Iberian lynx and sympatric domestic cats

    Czech Academy of Sciences Publication Activity Database

    Millán, J.; Blasco-Costa, Maria Isabel

    2012-01-01

    Roč. 186, 3-4 (2012), s. 518-522 ISSN 0304-4017 Institutional support: RVO:60077344 Keywords : Ancylostomiasis * Hookworm * Reservoir * Spain Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.381, year: 2012 http://www.sciencedirect.com/science/article/pii/S030440171100759X#

  12. Formation of molecular bromine from the reaction of ozone with deliquesced NaBr aerosol: Evidence for interface chemistry

    Czech Academy of Sciences Publication Activity Database

    Hunt, S. W.; Roeselová, Martina; Wang, W.; Wingen, L. M.; Knipping, E. M.; Tobias, D. J.; Dabdub, D.; Finlayson-Pitts, B. J.

    2004-01-01

    Roč. 108, - (2004), s. 11559-11572 ISSN 1089-5639 Grant - others:NSF(US) 0209719; NSF(US) 0431512 Institutional research plan: CEZ:AV0Z4055905 Keywords : ozone * sea-salt aerosol * molecular dynamics simulation Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.639, year: 2004

  13. Molecular taxonomy of Plagioscion Heckel (Perciformes, Sciaenidae and evidence from mtDNA RFLP markers for an invasive species in the Paraná river, Southern Brazil Taxonomia molecular de Plagioscion Heckel (Perciformes, Sciaenidae e evidências de marcadores moleculares RFLPs de mtDNA para uma espécie invasora no rio Paraná, Sul do Brasil

    Directory of Open Access Journals (Sweden)

    Rodrigo A. Torres

    2006-12-01

    Full Text Available Mitochondrial RFLP markers were developed to examine whether Plagioscion squamosissimus (Heckel, 1840 is invasive in natural environments of the congener P. ternetzi in the Paraná river, in southern Brazil. Specimens of P. squamosissimus and of the putative P. ternetzi (Boulenger, 1895 were obtained from the Negro river (Manaus, Amazonas, Brazil and from Paraná river, respectively. Fragments of the cytochrome b gene (900bp were amplified by PCR and four restriction enzymes (Eco RI, Mbo I, Bam HI and Alu I yielded the mitochondrial markers. An additional RFLP analysis with a cytochrome b gene sequence of Plagioncion sp. from GeneBank was carried out to validate the prior analysis. No genetic differentiation was found among either sample. While molecular variation in the cytochrome b analysis was no substantial among individuals, the combined analysis was important for demonstrating that there is no evidence for differentiation of the putative sample P. ternetzi from that of P. squamosissimus. The ecological implications of the introduced occurrence of P. squamosissimus, as well as the role of molecular taxonomic approaches for biodiversity studies are discussed.Marcadores RFLPs mitocondriais foram desenvolvidos para verificar se Plagioscion squamosissimus (Heckel, 1840 é invasora nos ambientes naturais da espécie congênere P. ternetzi no rio Paraná, no sul do Brasil. Exemplares de Plagioscion squamosissimus e supostamente de P. ternetzi (Boulenger, 1895 foram obtidos, respectivamente, do rio Negro (Manaus, AM, Brasil e rio Paraná (Foz do Iguaçu, PR, Brasil. Foram amplificados, via PCR, fragmentos de cerca de 900pb do Citocromo b e foram utilizadas quatro enzimas de restrição (Eco RI, Mbo I, Bam HI e Alu I para os fins de geração dos marcadores moleculares. Foi desenvolvida, a partir de uma seqüência de Citocromo b de Plagioscion sp. (genebank, uma análise de RFLP adicional, objetivando validar a primeira análise acima mencionada

  14. How well do different tracers constrain the firn diffusivity profile?

    Directory of Open Access Journals (Sweden)

    C. M. Trudinger

    2013-02-01

    Full Text Available Firn air transport models are used to interpret measurements of the composition of air in firn and bubbles trapped in ice in order to reconstruct past atmospheric composition. The diffusivity profile in the firn is usually calibrated by comparing modelled and measured concentrations for tracers with known atmospheric history. However, in most cases this is an under-determined inverse problem, often with multiple solutions giving an adequate fit to the data (this is known as equifinality. Here we describe a method to estimate the firn diffusivity profile that allows multiple solutions to be identified, in order to quantify the uncertainty in diffusivity due to equifinality. We then look at how well different combinations of tracers constrain the firn diffusivity profile. Tracers with rapid atmospheric variations like CH3CCl3, HFCs and 14CO2 are most useful for constraining molecular diffusivity, while &delta:15N2 is useful for constraining parameters related to convective mixing near the surface. When errors in the observations are small and Gaussian, three carefully selected tracers are able to constrain the molecular diffusivity profile well with minimal equifinality. However, with realistic data errors or additional processes to constrain, there is benefit to including as many tracers as possible to reduce the uncertainties. We calculate CO2 age distributions and their spectral widths with uncertainties for five firn sites (NEEM, DE08-2, DSSW20K, South Pole 1995 and South Pole 2001 with quite different characteristics and tracers available for calibration. We recommend moving away from the use of a firn model with one calibrated parameter set to infer atmospheric histories, and instead suggest using multiple parameter sets, preferably with multiple representations of uncertain processes, to assist in quantification of the uncertainties.

  15. Evidence of low molecular weight components in the organic matrix of the reef building coral, Stylophora pistillata.

    Science.gov (United States)

    Puverel, S; Houlbrèque, F; Tambutté, E; Zoccola, D; Payan, P; Caminiti, N; Tambutté, S; Allemand, D

    2007-08-01

    Biominerals contain both inorganic and organic components. Organic components are collectively termed the organic matrix, and this matrix has been reported to play a crucial role in mineralization. Several matrix proteins have been characterized in vertebrates, but only a few in invertebrates, primarily in Molluscs and Echinoderms. Methods classically used to extract organic matrix proteins eliminate potential low molecular weight matrix components, since cut-offs ranging from 3.5 to 10 kDa are used to desalt matrix extracts. Consequently, the presence of such components remains unknown and these are never subjected to further analyses. In the present study, we have used microcolonies from the Scleractinian coral Stylophora pistillata to study newly synthesized matrix components by labelling them with 14C-labelled amino acids. Radioactive matrix components were investigated by a method in which both total organic matrix and fractions of matrix below and above 5 kDa were analyzed. Using this method and SDS-PAGE analyses, we were able to detect the presence of low molecular mass matrix components (weight molecules, these probably form the bulk of newly synthesized organic matrix components. Our results suggest that these low molecular weight components may be peptides, which can be involved in the regulation of coral skeleton mineralization.

  16. Formal language constrained path problems

    Energy Technology Data Exchange (ETDEWEB)

    Barrett, C.; Jacob, R.; Marathe, M.

    1997-07-08

    In many path finding problems arising in practice, certain patterns of edge/vertex labels in the labeled graph being traversed are allowed/preferred, while others are disallowed. Motivated by such applications as intermodal transportation planning, the authors investigate the complexity of finding feasible paths in a labeled network, where the mode choice for each traveler is specified by a formal language. The main contributions of this paper include the following: (1) the authors show that the problem of finding a shortest path between a source and destination for a traveler whose mode choice is specified as a context free language is solvable efficiently in polynomial time, when the mode choice is specified as a regular language they provide algorithms with improved space and time bounds; (2) in contrast, they show that the problem of finding simple paths between a source and a given destination is NP-hard, even when restricted to very simple regular expressions and/or very simple graphs; (3) for the class of treewidth bounded graphs, they show that (i) the problem of finding a regular language constrained simple path between source and a destination is solvable in polynomial time and (ii) the extension to finding context free language constrained simple paths is NP-complete. Several extensions of these results are presented in the context of finding shortest paths with additional constraints. These results significantly extend the results in [MW95]. As a corollary of the results, they obtain a polynomial time algorithm for the BEST k-SIMILAR PATH problem studied in [SJB97]. The previous best algorithm was given by [SJB97] and takes exponential time in the worst case.

  17. Molecular analysis demonstrates high prevalence of chloroquine resistance but no evidence of artemisinin resistance in Plasmodium falciparum in the Chittagong Hill Tracts of Bangladesh.

    Science.gov (United States)

    Alam, Mohammad Shafiul; Ley, Benedikt; Nima, Maisha Khair; Johora, Fatema Tuj; Hossain, Mohammad Enayet; Thriemer, Kamala; Auburn, Sarah; Marfurt, Jutta; Price, Ric N; Khan, Wasif A

    2017-08-15

    Artemisinin resistance is present in the Greater Mekong region and poses a significant threat for current anti-malarial treatment guidelines in Bangladesh. The aim of this molecular study was to assess the current status of drug resistance in the Chittagong Hill Tracts of Bangladesh near the Myanmar border. Samples were obtained from patients enrolled into a Clinical Trial (NCT02389374) conducted in Alikadam, Bandarban between August 2014 and January 2015. Plasmodium falciparum infections were confirmed by PCR and all P. falciparum positive isolates genotyped for the pfcrt K76T and pfmdr1 N86Y markers. The propeller region of the kelch 13 (k13) gene was sequenced from isolates from patients with delayed parasite clearance. In total, 130 P. falciparum isolates were available for analysis. The pfcrt mutation K76T, associated with chloroquine resistance was found in 81.5% (106/130) of cases and the pfmdr1 mutation N86Y in 13.9% (18/130) cases. No single nucleotide polymorphisms were observed in the k13 propeller region. This study provides molecular evidence for the ongoing presence of chloroquine resistant P. falciparum in Bangladesh, but no evidence of mutations in the k13 propeller domain associated with artemisinin resistance. Monitoring for artemisinin susceptibility in Bangladesh is needed to ensure early detection and containment emerging anti-malarial resistance.

  18. Molecular evidence for the subspecific differentiation of blue sheep (Pseudois nayaur) and polyphyletic origin of dwarf blue sheep (Pseudois schaeferi).

    Science.gov (United States)

    Tan, Shuai; Zou, Dandan; Tang, Lei; Wang, Gaochao; Peng, Quekun; Zeng, Bo; Zhang, Chen; Zou, Fangdong

    2012-06-01

    Blue sheep (Pseudois nayaur), a Central Asian ungulate with restricted geographic distribution, exhibits unclear variation in morphology and phylogeographic structure. The composition of species and subspecies in the genus Pseudois is controversial, particularly with respect to the taxonomic designation of geographically restricted populations. Here, 26 specimens including 5 dwarf blue sheep (Pseudois schaeferi), which were collected from a broad geographic region in China, were analyzed for 2 mitochondrial DNA fragments (cytochrome b and control region sequences). In a pattern consistent with geographically defined subspecies, we found three deeply divergent mitochondrial lineages restricted to different geographic regions. The currently designated two subspecies of blue sheep, Pseudois nayaur nayaur and Pseudois nayaur szechuanensis, were recognized in the phylogenetic trees. In addition, the Helan Mountain population showed distinct genetic characteristics from other geographic populations, and thus should be classified as a new subspecies. In contrast, dwarf blue sheep clustered closely with some blue sheep from Sichuan Province in the phylogenetic trees. Therefore, dwarf blue sheep appear to be a subset of Pseudois nayaur szechuanensis. After considering both population genetic information and molecular clock analysis, we obtained some relevant molecular phylogeographic information concerning the historical biogeography of blue sheep. These results also indicate that western Sichuan was a potential refugium for blue sheep during the Quaternary period.

  19. Functional and Molecular Evidence for Kv7 Channel Subtypes in Human Detrusor from Patients with and without Bladder Outflow Obstruction

    DEFF Research Database (Denmark)

    Svalø, Julie; Sheykhzade, Majid; Nordling, Jørgen

    2015-01-01

    The aim of the study was to investigate whether Kv7 channels and their ancillary β-subunits, KCNE, are functionally expressed in the human urinary bladder. Kv7 channels were examined at the molecular level and by functional studies using RT-qPCR and myography, respectively. We found mRNA expressi...... between Kv7 channels and β-adrenoceptors in the human urinary bladder. The performed gene expression analysis combined with the organ bath studies imply that compounds that activate Kv7 channels could be useful for treatment of overactive bladder syndrome.......The aim of the study was to investigate whether Kv7 channels and their ancillary β-subunits, KCNE, are functionally expressed in the human urinary bladder. Kv7 channels were examined at the molecular level and by functional studies using RT-qPCR and myography, respectively. We found mRNA expression...... (activator of Kv7.1 channels, 10 μM) and ML213 (activator of Kv7.2, Kv7.4, Kv7.4/7.5 and Kv7.5 channels, 10 μM), reduced the tone of 1 μM carbachol pre-constricted bladder strips. XE991 (blocker of Kv7.1-7.5 channels, 10 μM) had opposing effects as it increased contractions achieved with 20 mM KPSS...

  20. Online molecular characterization of fine particulate matter in Port Angeles, WA: Evidence for a major impact from residential wood smoke

    Science.gov (United States)

    Gaston, Cassandra J.; Lopez-Hilfiker, Felipe D.; Whybrew, Lauren E.; Hadley, Odelle; McNair, Fran; Gao, Honglian; Jaffe, Daniel A.; Thornton, Joel A.

    2016-08-01

    We present on-line molecular composition measurements of wintertime particulate matter (PM) during 2014 using an iodide-adduct high-resolution, time-of-flight chemical ionization mass spectrometer (HR-TOF-CIMS) coupled to a Filter Inlet for Gases and AEROsols (FIGAERO). These measurements were part of an intensive effort to characterize PM in the region with a focus on ultrafine particle sources. The technique was used to detect and quantify different classes of wood burning tracers, including levoglucosan, methoxyphenols, and nitrocatechols, among other compounds in near real-time. During the campaign, particulate mass concentrations of compounds with the same molecular composition as levoglucosan ranged from 0.002 to 19 μg/m3 with a median mass concentration of 0.9 μg/m3. Wood burning markers, in general, showed a strong diurnal pattern peaking at night and in the early morning. This diurnal profile combined with cold, stagnant conditions, wind directions from predominantly residential areas, and observations of lower combustion efficiency at night support residential wood burning as a dominant source of wintertime PM in Port Angeles. This finding has implications for improving wintertime air quality in the region by encouraging the use of high efficiency wood-burning stoves or other cleaner home heating options throughout the relevant domain.

  1. Charge Transport in 4 nm Molecular Wires with Interrupted Conjugation: Combined Experimental and Computational Evidence for Thermally Assisted Polaron Tunneling.

    Science.gov (United States)

    Taherinia, Davood; Smith, Christopher E; Ghosh, Soumen; Odoh, Samuel O; Balhorn, Luke; Gagliardi, Laura; Cramer, Christopher J; Frisbie, C Daniel

    2016-04-26

    We report the synthesis, transport measurements, and electronic structure of conjugation-broken oligophenyleneimine (CB-OPI 6) molecular wires with lengths of ∼4 nm. The wires were grown from Au surfaces using stepwise aryl imine condensation reactions between 1,4-diaminobenzene and terephthalaldehyde (1,4-benzenedicarbaldehyde). Saturated spacers (conjugation breakers) were introduced into the molecular backbone by replacing the aromatic diamine with trans-1,4-diaminocyclohexane at specific steps during the growth processes. FT-IR and ellipsometry were used to follow the imination reactions on Au surfaces. Surface coverages (∼4 molecules/nm(2)) and electronic structures of the wires were determined by cyclic voltammetry and UV-vis spectroscopy, respectively. The current-voltage (I-V) characteristics of the wires were acquired using conducting probe atomic force microscopy (CP-AFM) in which an Au-coated AFM probe was brought into contact with the wires to form metal-molecule-metal junctions with contact areas of ∼50 nm(2). The low bias resistance increased with the number of saturated spacers, but was not sensitive to the position of the spacer within the wire. Temperature dependent measurements of resistance were consistent with a localized charge (polaron) hopping mechanism in all of the wires. Activation energies were in the range of 0.18-0.26 eV (4.2-6.0 kcal/mol) with the highest belonging to the fully conjugated OPI 6 wire and the lowest to the CB3,5-OPI 6 wire (the wire with two saturated spacers). For the two other wires with a single conjugation breaker, CB3-OPI 6 and CB5-OPI 6, activation energies of 0.20 eV (4.6 kcal/mol) and 0.21 eV (4.8 kcal/mol) were found, respectively. Computational studies using density functional theory confirmed the polaronic nature of charge carriers but predicted that the semiclassical activation energy of hopping should be higher for CB-OPI molecular wires than for the OPI 6 wire. To reconcile the experimental and

  2. Metschnikowia cf. typographi and other pathogens from the bark beetle Ips sexdentatus - Prevalence, histological and ultrastructural evidence, and molecular characterization

    DEFF Research Database (Denmark)

    Kleespies, Regina G; Lim, Young Woon; Tkaczuk, Cezary

    2017-01-01

    Ips sexdentatus (six-spined engraver beetle) from Austria and Poland were dissected and examined for the presence of pathogens. Specimens collected in Austria were found to contain the ascomycetous fungus Metschnikowia cf. typographi. Infection rates ranged from 3.6% to 26.8% at different...... collection sites. M. cf. typographi infected midguts were investigated by histological, ultrastructural and molecular techniques. Extraordinary ultrastructural details are shown, such as ascospores with bilateral flattened flanks resembling alar rims at both sides of their attenuating tube-like ends....... The eugregarine Gregarina typographi was diagnosed most frequently. Infection rates of all I. sexdentatus specimens ranged from 21.4% to 71.9% in Austria and 54.1% to 68.8% in Poland. Other entomopathogenic protists, bacteria, or viruses were not detected....

  3. First molecular evidence of Anaplasma ovis and Rickettsia spp. in keds (Diptera: Hippoboscidae) of sheep and wild ruminants.

    Science.gov (United States)

    Hornok, Sándor; de la Fuente, José; Biró, Nóra; Fernández de Mera, Isabel G; Meli, Marina L; Elek, Vilmos; Gönczi, Eniko; Meili, Theres; Tánczos, Balázs; Farkas, Róbert; Lutz, Hans; Hofmann-Lehmann, Regina

    2011-10-01

    To evaluate the presence of rickettsial agents in hippoboscid flies with molecular methods, 81 sheep keds (Melophagus ovinus) were collected from 23 sheep, 144 deer keds (Lipoptena cervi) were caught in the environment, and a further 463 and 59 individuals of the latter species were obtained from fresh carcasses of 29 red deer and 17 roe deer, respectively. DNA was extracted individually or in pools. Anaplasma ovis was demonstrated in all examined sheep keds, and from one pool of free-living deer keds. Rickettsia helvetica or other, unidentified rickettsiae were also present in one pool of sheep keds, and in four pools of deer keds from both red deer and roe deer. This is the first account of polymerase chain reaction positivity of hippoboscid flies for A. ovis and rickettsiae. These results raise the possibility that-apart from cattle and roe deer as already reported-sheep and red deer might also play a reservoir role in the epidemiology of rickettsioses.

  4. First Morphological and Molecular Evidence of the Negative Impact of Diatom-Derived Hydroxyacids on the Sea Urchin Paracentrotus lividus

    Science.gov (United States)

    Varrella, Stefano; Romano, Giovanna; Ruocco, Nadia; Ianora, Adrianna; Bentley, Matt G.; Costantini, Maria

    2016-01-01

    Oxylipins (including polyunsaturated aldehydes [PUAs], hydoxyacids, and epoxyalcohols) are the end-products of a lipoxygenase/hydroperoxide lyase metabolic pathway in diatoms. To date, very little information is available on oxylipins other than PUAs, even though they represent the most common oxylipins produced by diatoms. Here, we report, for the first time, on the effects of 2 hydroxyacids, 5- and 15-HEPE, which have never been tested before, using the sea urchin Paracentrotus lividus as a model organism. We show that HEPEs do induce developmental malformations but at concentrations higher when compared with PUAs. Interestingly, HEPEs also induced a marked developmental delay in sea urchin embryos, which has not hitherto been reported for PUAs. Recovery experiments revealed that embryos do not recover following treatment with HEPEs. Finally, we report the expression levels of 35 genes (involved in stress, development, differentiation, skeletogenesis, and detoxification processes) to identify the molecular targets affected by HEPEs. We show that the 2 HEPEs have very few common molecular targets, specifically affecting different classes of genes and at different times of development. In particular, 15-HEPE switched on fewer genes than 5-HEPE, upregulating mainly stress-related genes at a later pluteus stage of development. 5-HEPE was stronger than 15-HEPE, targeting 24 genes, mainly at the earliest stages of embryo development (at the blastula and swimming blastula stages). These findings highlight the differences between HEPEs and PUAs and also have important ecological implications because many diatom species do not produce PUAs, but rather these other chemicals are derived from the oxidation of fatty acids. PMID:26984781

  5. Processes underpinning development and maintenance of diversity in rice in West Africa: evidence from combining morphological and molecular markers.

    Directory of Open Access Journals (Sweden)

    Alfred Mokuwa

    Full Text Available We assessed the interplay of artificial and natural selection in rice adaptation in low-input farming systems in West Africa. Using 20 morphological traits and 176 molecular markers, 182 farmer varieties of rice (Oryza spp. from 6 West African countries were characterized. Principal component analysis showed that the four botanical groups (Oryza sativa ssp. indica, O. sativa ssp. japonica, O. glaberrima, and interspecific farmer hybrids exhibited different patterns of morphological diversity. Regarding O. glaberrima, morphological and molecular data were in greater conformity than for the other botanical groups. A clear difference in morphological features was observed between O. glaberrima rices from the Togo hills and those from the Upper Guinea Coast, and among O. glaberrima rices from the Upper Guinea Coast. For the other three groups such clear patterns were not observed. We argue that this is because genetic diversity is shaped by different environmental and socio-cultural selection pressures. For O. glaberrima, recent socio-cultural selection pressures seemed to restrict genetic diversity while this was not observed for the other botanical groups. We also show that O. glaberrima still plays an important role in the selection practices of farmers and resulting variety development pathways. This is particularly apparent in the case of interspecific farmer hybrids where a relationship was found between pericarp colour, panicle attitude and genetic diversity. Farmer varieties are the product of long and complex trajectories of selection governed by local human agency. In effect, rice varieties have emerged that are adapted to West African farming conditions through genotype × environment × society interactions. The diversity farmers maintain in their rice varieties is understood to be part of a risk-spreading strategy that also facilitates successful and often serendipitous variety innovations. We advocate, therefore, that farmers and

  6. Processes underpinning development and maintenance of diversity in rice in West Africa: evidence from combining morphological and molecular markers.

    Science.gov (United States)

    Mokuwa, Alfred; Nuijten, Edwin; Okry, Florent; Teeken, Béla; Maat, Harro; Richards, Paul; Struik, Paul C

    2014-01-01

    We assessed the interplay of artificial and natural selection in rice adaptation in low-input farming systems in West Africa. Using 20 morphological traits and 176 molecular markers, 182 farmer varieties of rice (Oryza spp.) from 6 West African countries were characterized. Principal component analysis showed that the four botanical groups (Oryza sativa ssp. indica, O. sativa ssp. japonica, O. glaberrima, and interspecific farmer hybrids) exhibited different patterns of morphological diversity. Regarding O. glaberrima, morphological and molecular data were in greater conformity than for the other botanical groups. A clear difference in morphological features was observed between O. glaberrima rices from the Togo hills and those from the Upper Guinea Coast, and among O. glaberrima rices from the Upper Guinea Coast. For the other three groups such clear patterns were not observed. We argue that this is because genetic diversity is shaped by different environmental and socio-cultural selection pressures. For O. glaberrima, recent socio-cultural selection pressures seemed to restrict genetic diversity while this was not observed for the other botanical groups. We also show that O. glaberrima still plays an important role in the selection practices of farmers and resulting variety development pathways. This is particularly apparent in the case of interspecific farmer hybrids where a relationship was found between pericarp colour, panicle attitude and genetic diversity. Farmer varieties are the product of long and complex trajectories of selection governed by local human agency. In effect, rice varieties have emerged that are adapted to West African farming conditions through genotype × environment × society interactions. The diversity farmers maintain in their rice varieties is understood to be part of a risk-spreading strategy that also facilitates successful and often serendipitous variety innovations. We advocate, therefore, that farmers and farmer varieties should

  7. A New Morphological Phylogeny of the Ophiuroidea (Echinodermata Accords with Molecular Evidence and Renders Microfossils Accessible for Cladistics.

    Directory of Open Access Journals (Sweden)

    Ben Thuy

    Full Text Available Ophiuroid systematics is currently in a state of upheaval, with recent molecular estimates fundamentally clashing with traditional, morphology-based classifications. Here, we attempt a long overdue recast of a morphological phylogeny estimate of the Ophiuroidea taking into account latest insights on microstructural features of the arm skeleton. Our final estimate is based on a total of 45 ingroup taxa, including 41 recent species covering the full range of extant ophiuroid higher taxon diversity and 4 fossil species known from exceptionally preserved material, and the Lower Carboniferous Aganaster gregarius as the outgroup. A total of 130 characters were scored directly on specimens. The tree resulting from the Bayesian inference analysis of the full data matrix is reasonably well resolved and well supported, and refutes all previous classifications, with most traditional families discredited as poly- or paraphyletic. In contrast, our tree agrees remarkably well with the latest molecular estimate, thus paving the way towards an integrated new classification of the Ophiuroidea. Among the characters which were qualitatively found to accord best with our tree topology, we selected a list of potential synapomorphies for future formal clade definitions. Furthermore, an analysis with 13 of the ingroup taxa reduced to the lateral arm plate characters produced a tree which was essentially similar to the full dataset tree. This suggests that dissociated lateral arm plates can be analysed in combination with fully known taxa and thus effectively unlocks the extensive record of fossil lateral arm plates for phylogenetic estimates. Finally, the age and position within our tree implies that the ophiuroid crown-group had started to diversify by the Early Triassic.

  8. Preliminary Evidence on the Diagnostic and Molecular Role of Circulating Soluble EGFR in Non-Small Cell Lung Cancer

    Directory of Open Access Journals (Sweden)

    Filippo Lococo

    2015-08-01

    Full Text Available Assessment of biological diagnostic factors providing clinically-relevant information to guide physician decision-making are still needed for diseases with poor outcomes, such as non-small cell lung cancer (NSCLC. Epidermal growth factor receptor (EGFR is a promising molecule in the clinical management of NSCLC. While the EGFR transmembrane form has been extensively investigated in large clinical trials, the soluble, circulating EGFR isoform (sEGFR, which may have a potential clinical use, has rarely been considered. This study investigates the use of sEGFR as a potential diagnostic biomarker for NSCLC and also characterizes the biological function of sEGFR to clarify the molecular mechanisms involved in the course of action of this protein. Plasma sEGFR levels from a heterogeneous cohort of 37 non-advanced NSCLC patients and 54 healthy subjects were analyzed by using an enzyme-linked immunosorbent assay. The biological function of sEGFR was analyzed in vitro using NSCLC cell lines, investigating effects on cell proliferation and migration. We found that plasma sEGFR was significantly decreased in the NSCLC patient group as compared to the control group (median value: 48.6 vs. 55.6 ng/mL respectively; p = 0.0002. Moreover, we demonstrated that sEGFR inhibits growth and migration of NSCLC cells in vitro through molecular mechanisms that included perturbation of EGF/EGFR cell signaling and holoreceptor internalization. These data show that sEGFR is a potential circulating biomarker with a physiological protective role, providing a first approach to the functional role of the soluble isoform of EGFR. However, the impact of these data on daily clinical practice needs to be further investigated in larger prospective studies.

  9. Preliminary Evidence on the Diagnostic and Molecular Role of Circulating Soluble EGFR in Non-Small Cell Lung Cancer

    Science.gov (United States)

    Lococo, Filippo; Paci, Massimiliano; Rapicetta, Cristian; Rossi, Teresa; Sancisi, Valentina; Braglia, Luca; Cavuto, Silvio; Bisagni, Alessandra; Bongarzone, Italia; Noonan, Douglas M.; Albini, Adriana; Maramotti, Sally

    2015-01-01

    Assessment of biological diagnostic factors providing clinically-relevant information to guide physician decision-making are still needed for diseases with poor outcomes, such as non-small cell lung cancer (NSCLC). Epidermal growth factor receptor (EGFR) is a promising molecule in the clinical management of NSCLC. While the EGFR transmembrane form has been extensively investigated in large clinical trials, the soluble, circulating EGFR isoform (sEGFR), which may have a potential clinical use, has rarely been considered. This study investigates the use of sEGFR as a potential diagnostic biomarker for NSCLC and also characterizes the biological function of sEGFR to clarify the molecular mechanisms involved in the course of action of this protein. Plasma sEGFR levels from a heterogeneous cohort of 37 non-advanced NSCLC patients and 54 healthy subjects were analyzed by using an enzyme-linked immunosorbent assay. The biological function of sEGFR was analyzed in vitro using NSCLC cell lines, investigating effects on cell proliferation and migration. We found that plasma sEGFR was significantly decreased in the NSCLC patient group as compared to the control group (median value: 48.6 vs. 55.6 ng/mL respectively; p = 0.0002). Moreover, we demonstrated that sEGFR inhibits growth and migration of NSCLC cells in vitro through molecular mechanisms that included perturbation of EGF/EGFR cell signaling and holoreceptor internalization. These data show that sEGFR is a potential circulating biomarker with a physiological protective role, providing a first approach to the functional role of the soluble isoform of EGFR. However, the impact of these data on daily clinical practice needs to be further investigated in larger prospective studies. PMID:26295387

  10. Wavelet library for constrained devices

    Science.gov (United States)

    Ehlers, Johan Hendrik; Jassim, Sabah A.

    2007-04-01

    The wavelet transform is a powerful tool for image and video processing, useful in a range of applications. This paper is concerned with the efficiency of a certain fast-wavelet-transform (FWT) implementation and several wavelet filters, more suitable for constrained devices. Such constraints are typically found on mobile (cell) phones or personal digital assistants (PDA). These constraints can be a combination of; limited memory, slow floating point operations (compared to integer operations, most often as a result of no hardware support) and limited local storage. Yet these devices are burdened with demanding tasks such as processing a live video or audio signal through on-board capturing sensors. In this paper we present a new wavelet software library, HeatWave, that can be used efficiently for image/video processing/analysis tasks on mobile phones and PDA's. We will demonstrate that HeatWave is suitable for realtime applications with fine control and range to suit transform demands. We shall present experimental results to substantiate these claims. Finally this library is intended to be of real use and applied, hence we considered several well known and common embedded operating system platform differences; such as a lack of common routines or functions, stack limitations, etc. This makes HeatWave suitable for a range of applications and research projects.

  11. Molecular and Morphological Evidence Challenges the Records of the Extant Liverwort Ptilidium pulcherrimum in Eocene Baltic Amber.

    Science.gov (United States)

    Heinrichs, Jochen; Scheben, Armin; Lee, Gaik Ee; Váňa, Jiří; Schäfer-Verwimp, Alfons; Krings, Michael; Schmidt, Alexander R

    2015-01-01

    Preservation of liverworts in amber, a fossilized tree resin, is often exquisite. Twenty-three fossil species of liverworts have been described to date from Eocene (35-50 Ma) Baltic amber. In addition, two inclusions have been assigned to the extant species Ptilidium pulcherrimum (Ptilidiales or Porellales). However, the presence of the boreal P. pulcherrimum in the subtropical or warm-temperate Baltic amber forest challenges the phytogeographical interpretation of the Eocene flora. A re-investigation of one of the fossils believed to be P. pulcherrimum reveals that this specimen in fact represents the first fossil evidence of the genus Tetralophozia, and thus is re-described here as Tetralophozia groehnii sp. nov. A second fossil initially assigned to P. pulcherrimum is apparently lost, and can be reassessed only based on the original description and illustrations. This fossil is morphologically similar to the extant North Pacific endemic Ptilidium californicum, rather than P. pulcherrimum. Divergence time estimates based on chloroplast DNA sequences provide evidence of a Miocene origin of P. pulcherrimum, and thus also argue against the presence of this taxon in the Eocene. Ptilidium californicum originated 25-43 Ma ago. As a result, we cannot rule out that the Eocene fossil belongs to P. californicum. Alternatively, the fossil might represent a stem lineage element of Ptilidium or an early crown group species with morphological similarities to P. californicum.

  12. Energetics of the molecular gas in the H2 luminous radio galaxy 3C 326: Evidence for negative AGN feedback

    Science.gov (United States)

    Nesvadba, N. P. H.; Boulanger, F.; Salomé, P.; Guillard, P.; Lehnert, M. D.; Ogle, P.; Appleton, P.; Falgarone, E.; Pineau Des Forets, G.

    2010-10-01

    We present a detailed analysis of the gas conditions in the H2 luminous radio galaxy 3C 326 N at z ~ 0.1, which has a low star-formation rate (SFR ~ 0.07 M⊙ yr-1) in spite of a gas surface density similar to those in starburst galaxies. Its star-formation efficiency is likely a factor ~10-50 lower than those of ordinary star-forming galaxies. Combining new IRAM CO emission-line interferometry with existing Spitzer mid-infrared spectroscopy, we find that the luminosity ratio of CO and pure rotational H2 line emission is factors 10-100 lower than what is usually found. This suggests that most of the molecular gas is warm. The Na D absorption-line profile of 3C 326 N in the optical suggests an outflow with a terminal velocity of ~-1800 km s-1 and a mass outflow rate of 30-40 M⊙ yr-1, which cannot be explained by star formation. The mechanical power implied by the wind, of order 1043 erg s-1, is comparable to the bolometric luminosity of the emission lines of ionized and molecular gas. To explain these observations, we propose a scenario where a small fraction of the mechanical energy of the radio jet is deposited in the interstellar medium of 3C 326 N, which powers the outflow, and the line emission through a mass, momentum and energy exchange between the different gas phases of the ISM. Dissipation times are of order 107-8 yrs, similar or greater than the typical jet lifetime. Small ratios of CO and PAH surface brightnesses in another 7 H2 luminous radio galaxies suggest that a similar form of AGN feedback could be lowering star-formation efficiencies in these galaxies in a similar way. The local demographics of radio-loud AGN suggests that secular gas cooling in massive early-type galaxies of ≥1011 M⊙ could generally be regulated through a fundamentally similar form of “maintenance-phase” AGN feedback. Based on observations carried out with the IRAM Plateau de Bure Interferometer.

  13. Genomic, RNAseq, and Molecular Modeling Evidence Suggests That the Major Allergen Domain in Insects Evolved from a Homodimeric Origin

    Science.gov (United States)

    Randall, Thomas A.; Perera, Lalith; London, Robert E.; Mueller, Geoffrey A.

    2013-01-01

    The major allergen domain (MA) is widely distributed in insects. The crystal structure of a single Bla g 1 MA revealed a novel protein fold in which the fundamental structure was a duplex of two subsequences (monomers), which had diverged over time. This suggested that the evolutionary origin of the MA structure may have been a homodimer of this smaller subsequence. Using publicly available genomic data, the distribution of the basic unit of this class of proteins was determined to better understand its evolutionary history. The duplication and divergence is examined at three distinct levels of resolution: 1) within the orders Diptera and Hymenoptera, 2) within one genus Drosophila, and 3) within one species Aedes aegypti. Within the family Culicidae, we have found two separate occurrences of monomers as independent genes. The organization of the gene family in A. aegypti shows a common evolutionary origin for its monomer and several closely related MAs. Molecular modeling of the A. aegypti monomer with the unique Bla g 1 fold confirms the distant evolutionary relationship and supports the feasibility of homodimer formation from a single monomer. RNAseq data for A. aegypti confirms that the monomer is expressed in the mosquito similar to other A. aegypti MAs after a blood meal. Together, these data support the contention that the detected monomer shares similar functional characteristics to related MAs in other insects. An extensive search for this domain outside of Insecta confirms that the MAs are restricted to insects. PMID:24253356

  14. Direct spectroscopic evidence for competition between thermal molecular agitation and magnetic field in a tetrameric protein in aqueous solution

    Science.gov (United States)

    Calabrò, Emanuele; Magazù, Salvatore

    2018-05-01

    Samples of a typical tetrameric protein, the hemoglobin, at the concentration of 150 mg/ml in bidistilled water solution, were exposed to a uniform magnetic field at 200 mT at different temperatures of 15∘C, 40∘C and 65∘C. Fourier Transform Infrared Spectroscopy was used to analyze the response of the secondary structure of the protein to both stress agents, heating and static magnetic field. The most relevant result which was observed was the significant increasing in intensity of the Amide I band after exposure to the uniform magnetic field at the room temperature of 15∘C. This result can be explained assuming that protein's α-helices aligned along the direction of the applied magnetic field due to their large dipole moment, inducing the alignment of the entire protein. Increasing of temperature up to 40∘C and 65∘C induced a significant reduction of the increasing in intensity of the Amide I band. This effect may be easily explained assuming that Brownian motion of the protein in water solution caused by thermal molecular agitation increased with increasing of temperature, contrasting the effect of the torque of the magnetic field applied to the protein in water solution.

  15. Systematics of the grey mullets (Teleostei: Mugiliformes: Mugilidae): molecular phylogenetic evidence challenges two centuries of morphology-based taxonomy.

    Science.gov (United States)

    Durand, J-D; Shen, K-N; Chen, W-J; Jamandre, B W; Blel, H; Diop, K; Nirchio, M; Garcia de León, F J; Whitfield, A K; Chang, C-W; Borsa, P

    2012-07-01

    The family Mugilidae comprises mainly coastal marine species that are widely distributed in all tropical, subtropical and temperate seas. Mugilid species are generally considered to be ecologically important and they are a major food resource for human populations in certain parts of the world. The taxonomy and systematics of the Mugilidae are still much debated and based primarily on morphological characters. In this study, we provide the first comprehensive molecular systematic account of the Mugilidae using phylogenetic analyses of nucleotide sequence variation at three mitochondrial loci (16S rRNA, cytochrome oxidase I, and cytochrome b) for 257 individuals from 55 currently recognized species. The study covers all 20 mugilid genera currently recognized as being valid. The family comprises seven major lineages that radiated early on from the ancestor to all current forms. All genera that were represented by two species or more, except Cestraeus, turned out to be paraphyletic or polyphyletic. Thus, the present phylogenetic results generally disagree with the current taxonomy at the genus level and imply that the anatomical characters used for the systematics of the Mugilidae may be poorly informative phylogenetically. The present results should provide a sound basis for a taxonomic revision of the mugilid genera. A proportion of the species with large distribution ranges (including Moolgarda seheli, Mugil cephalus and M. curema) appear to consist of cryptic species, thus warranting further taxonomic and genetic work at the infra-generic level. Copyright © 2012 Elsevier Inc. All rights reserved.

  16. Molecular-level evidence provided by ultrahigh resolution mass spectrometry for oil-derived doc in groundwater at Bemidji, Minnesota

    Science.gov (United States)

    Islam, Ananna; Ahmed, Arif; Hur, Manhoi; Thorn, Kevin A.; Kim, Sunghwan

    2016-01-01

    Dissolved organic matter samples extracted from ground water at the USGS Bemidji oil spill site in Minnesota were investigated by ultrahigh resolution mass spectrometry. Principle component analysis (PCA) of the elemental composition assignments of the samples showed that the score plots for the contaminated sites were well separated from those for the uncontaminated sites. Additionally, spectra obtained from the same sampling site 7 and 19 years after the spill were grouped together in the score plot, strongly suggesting a steady state of contamination within the 12 year interval. The double bond equivalence (DBE) of Ox class compounds was broader for the samples from the contaminated sites, because of the complex nature of oil and the consequent formation of compounds with saturated and/or aromatic structures from the oxygenated products of oil. In addition, Ox class compounds with a relatively smaller number of x (x < 8; x = number of oxygen) and OxS1 class compounds were more abundant in the samples from the contaminated sites, because of the lower oxygen and higher sulfur contents of the oil compared to humic substances. The molecular-level signatures presented here can be a fundamental basis for in-depth analysis of oil contamination.

  17. Molecular evidence for the occurrence of tomato leaf curl New Delhi virus on chayote (Sechium edule) in southern India.

    Science.gov (United States)

    Nagendran, K; Mohankumar, S; Mohammed Faisal, P; Bagewadi, B; Karthikeyan, G

    2017-12-01

    During 2012-2014, mosaic disease on chayote in the farmers field of Kodaikanal region (high altitude zone) of Tamil Nadu was observed. The disease was characterized with severe mosaic, cupping and enation on leaves with reduced fruit size. Disease was found to causes an yield loss of more than 60% with the maximum disease incidence of 100% for the past 5 years consecutively. Preliminary serological and molecular screening indicated the association of begomovirus with the disease. Complete nucleotide sequence and phylogenetic analysis of DNA A revealed the identity of the virus as tomato leaf curl New Delhi virus (ToLCNDV). In recombination analysis study, the major parent was identified as ToLCNDV from Pakistan infecting tomato. Thus the present finding confirms expansion of new geographical region and host for ToLCNDV causing mosaic disease on chayote from Tamil Nadu. To our knowledge this is the first confirmed report for the occurrence of ToLCNDV on chayote in southern India.

  18. NMR and molecular modeling evidence for a G·A mismatch base pair in a purine-rich DNA duplex

    International Nuclear Information System (INIS)

    Li, Ying; Wilson, W.D.; Zon, G.

    1991-01-01

    1 H NMR experiments indicate that the oligomer 5'-d(ATGAGCGAATA) forms an unusual 10-base-pair duplex with 4 G·A base pairs and a 3' unpaired adenosine. NMR results indicate that guanoxine imino protons of the F·A mismatches are not hydrogen bonded but are stacked in the helix. A G→ I substitution in either G·A base pair causes a dramatic decrtease in duplex stability and indicates that hydrogen bonding of the guanosine amino group is critical. Nuclear Overhauser effect spectroscopy (NOESY) and two-dimensional correlated spectroscopy (COSY) results indicate that the overall duplex conformation is in the B-family. Cross-strand NOEs in two-dimensional NOESY spectra between a mismatched AH2 and an AH1' of the other mismatched base pair and between a mismatched GH8 and GNH1 of the other mismatch establish a purine-purine stacking pattern, adenosine over adenosine and guanosine over guanosine, which strongly stabilizes the duplex. A computer graphics molecular model of the ususual duplex was constructed with G·A base pairs containing A-NH 2 to GN3 and G-NH 2 to AN7 hydrogen bonds and B-form base pairs on both sides of the G·A pairs [5'-d(ATGAGC)]. The energy-minimized duplex satisfies all experimental constraints from NOESY and COSY results. A hydrogen bond from G-NH 2 of the mismatch to a phosphate oxygen is predicted

  19. Molecular-level evidence provided by ultrahigh resolution mass spectrometry for oil-derived doc in groundwater at Bemidji, Minnesota

    Science.gov (United States)

    Islam, Ananna; Ahmed, Arif; Hur, Manhoi; Thorn, Kevin A.; Kim, Sunghwan

    2016-01-01

    Dissolved organic matter samples extracted from ground water at the USGS Bemidji oil spill site in Minnesota were investigated by ultrahigh resolution mass spectrometry. Principle component analysis (PCA) of the elemental composition assignments of the samples showed that the score plots for the contaminated sites were well separated from those for the uncontaminated sites. Additionally, spectra obtained from the same sampling site 7 and 19 years after the spill were grouped together in the score plot, strongly suggesting a steady state of contamination within the 12 year interval. The double bond equivalence (DBE) of Ox class compounds was broader for the samples from the contaminated sites, because of the complex nature of oil and the consequent formation of compounds with saturated and/or aromatic structures from the oxygenated products of oil. In addition, Ox class compounds with a relatively smaller number of x (x molecular-level signatures presented here can be a fundamental basis for in-depth analysis of oil contamination.

  20. Molecular evidence of inefficient transduction of proliferating human B lymphocytes by VSV-pseudotyped HIV-1-derived lentivectors

    International Nuclear Information System (INIS)

    Serafini, M.; Naldini, L.; Introna, M.

    2004-01-01

    Lentiviral vectors are attractive tools to transduce dividing and nondividing cells. Human tonsillar B lymphocytes have been purified and induced to proliferate by the addition of anti-CD40 + IL-4 or anti-CD40 + anti-μ signals and transduced at high MOI with a VSV pseudotyped lentivector carrying the eGFP gene under the control of the PGK promoter. Parallel cultures of PHA-stimulated T lymphocytes containing a comparable amount of cycling cells during the infection reached over 70% eGFP transduction. By contrast, only less than 3% B lymphocytes became eGFP positive after 7 days from transduction. Molecular analysis of the viral life cycle shows that cytoplasmic retrotranscribed cDNA and nuclear 2LTR circles are detectable at lower levels and for a shorter period of time in proliferating B cells with respect to proliferating T lymphocytes. Moreover, FACS-sorted eGFP-positive and negative B cell populations were both positive for the presence of retrotranscribed cDNA and 2LTR circles nuclear forms. By contrast, nested Alu-LTR PCR allowed us to detect an integrated provirus in FACS-sorted eGFP-positive cells only. Together with the demonstration that infection in saturation conditions led to an increase in the percentage of transduced cells (reaching 9%), these findings suggest that in proliferating B lymphocytes, lentiviral transduction is an inefficient process blocked at the early steps of the viral life cycle possibly involving partially saturable restriction factors

  1. Babesia sp. BQ1 (Lintan): molecular evidence of experimental transmission to sheep by Haemaphysalis qinghaiensis and Haemaphysalis longicornis.

    Science.gov (United States)

    Guan, Guiquan; Moreau, Emmanuelle; Liu, Junlong; Hao, Xuefen; Ma, Miling; Luo, Jianxun; Chauvin, Alain; Yin, Hong

    2010-06-01

    Ovine babesiosis is an economically important disease induced by tick transmitted haemoparasites throughout the world. In China, several ovine Babesia strains have been isolated from field-collected ticks or sheep blood during the last two decades but little is known about the vector ticks and transmission pattern. Babesia sp. BQ1 (Lintan) is a Babesia strain infective for sheep and goats, isolated from blood of sheep experimentally infested with Haemaphysalis qinghaiensis collected in field. In the present study, we explored the experimental transmission of Babesia sp. BQ1 (Lintan) to sheep by H. qinghaiensis and Haemaphysalis longicornis. Based on the evidence from nested PCR, it suggested that H. qinghaiensis and H. longicornis are the potential vector ticks of Babesia sp. BQ1 (Lintan) and that larvae, nymphs and adults of both tick species were able to transmit Babesia sp. BQ1 (Lintan) to sheep. Parasites could be detected in the blood, by specific nested PCR, for one month post-infestation.

  2. Order-constrained linear optimization.

    Science.gov (United States)

    Tidwell, Joe W; Dougherty, Michael R; Chrabaszcz, Jeffrey S; Thomas, Rick P

    2017-11-01

    Despite the fact that data and theories in the social, behavioural, and health sciences are often represented on an ordinal scale, there has been relatively little emphasis on modelling ordinal properties. The most common analytic framework used in psychological science is the general linear model, whose variants include ANOVA, MANOVA, and ordinary linear regression. While these methods are designed to provide the best fit to the metric properties of the data, they are not designed to maximally model ordinal properties. In this paper, we develop an order-constrained linear least-squares (OCLO) optimization algorithm that maximizes the linear least-squares fit to the data conditional on maximizing the ordinal fit based on Kendall's τ. The algorithm builds on the maximum rank correlation estimator (Han, 1987, Journal of Econometrics, 35, 303) and the general monotone model (Dougherty & Thomas, 2012, Psychological Review, 119, 321). Analyses of simulated data indicate that when modelling data that adhere to the assumptions of ordinary least squares, OCLO shows minimal bias, little increase in variance, and almost no loss in out-of-sample predictive accuracy. In contrast, under conditions in which data include a small number of extreme scores (fat-tailed distributions), OCLO shows less bias and variance, and substantially better out-of-sample predictive accuracy, even when the outliers are removed. We show that the advantages of OCLO over ordinary least squares in predicting new observations hold across a variety of scenarios in which researchers must decide to retain or eliminate extreme scores when fitting data. © 2017 The British Psychological Society.

  3. Saw palmetto alters nuclear measurements reflecting DNA content in men with symptomatic BPH: evidence for a possible molecular mechanism.

    Science.gov (United States)

    Veltri, Robert W; Marks, Leonard S; Miller, M Craig; Bales, Wes D; Fan, John; Macairan, Maria Luz; Epstein, Jonathan I; Partin, Alan W

    2002-10-01

    To examine the nuclear chromatin characteristics of epithelial cells, looking for an SPHB-mediated effect on nuclear DNA structure and organization. Saw palmetto herbal blend (SPHB) causes contraction of prostate epithelial cells and suppression of tissue dihydrotestosterone levels in men with symptomatic benign prostatic hyperplasia, but a fundamental mechanism remains unknown. A 6-month randomized trial, comparing prostatic tissue of men treated with SPHB (n = 20) or placebo (n = 20), was performed. At baseline, the two groups were similar in age (65 versus 64 years), symptoms (International Prostate Symptom Score 18 versus 17), uroflow (maximal urinary flow rate 10 versus 11 mL/s), prostate volume (59 versus 58 cm(3)), prostate-specific antigen (4.2 versus 2.7 ng/mL), and percentage of epithelium (17% versus 16%). Prostatic tissue was obtained by sextant biopsy before and after treatment. Five-micron sections were Feulgen stained and quantitatively analyzed using the AutoCyte QUIC-DNA imaging system. Images were captured from 200 randomly selected epithelial cell nuclei, and 60 nuclear morphometric descriptors (NMDs) (eg, size, shape, DNA content, and textural features) were determined for each nucleus. Logistic regression analysis was used to assess the differences in the variances of the NMDs between the treated and untreated prostate epithelial cells. At baseline, the SPHB and placebo groups had similar NMD values. After 6 months of placebo, no significant change from baseline was found in the NMDs. However, after 6 months of SPHB, 25 of the 60 NMDs were significantly different compared with baseline, and a multivariate model for predicting treatment effect using 4 of the 25 was created (P <0.001). The multivariate model had an area under the receiver operating characteristic curve of 94% and an accuracy of 85%. Six months of SPHB treatment appears to alter the DNA chromatin structure and organization in prostate epithelial cells. Thus, a possible molecular

  4. Molecular isotopic evidence for anaerobic oxidation of methane in deep-sea hydrothermal vent environment in Okinawa Trough

    Science.gov (United States)

    Uchida, M.; Takai, K.; Inagaki, F.

    2003-04-01

    Large amount of methane in anoxic marine sediments as well as cold seeps and hydrothermal vents is recycled through for an anoxic oxidation of methane processes. Now that combined results of field and laboratory studies revealed that microbiological activity associated with syntrophic consortium of archaea performing reversed methanogenesis and sulfate-reducing bacteria is significant roles in methane recycling, anaerobic oxidation of methane (AOM). In this study, we examined the diversity of archaeal and bacterial assemblages of AOM using compound-specific stable carbon isotopic and phylogenetic analyses. "Iheya North" in Okinawa Trough is sediment-rich, back arc type hydrothermal system (27^o47'N, 126^o53'E). Sediment samples were collected from three sites where are "bubbling sites", yellow-colored microbial mats are formed with continuous bubbling from the seafloor bottom, vent mussel's colonies site together with slowly venting and simmering, and control site off 100 m distance from thermal vent. This subsea floor structure has important effect in the microbial ecosystem and interaction between their activity and geochemical processes in the subseafloor habitats. Culture-independent, molecular biological analysis clearly indicated the presence of thermophilic methanogens in deeper area having higher temperatures and potential activity of AMOs consortium in the shallower area. AMO is composed with sulfate-reducing bacterial components (Desulfosarcina spp.) and anoxic methane oxidizing archaea (ANME-2). These results were consistent with the results of compound-specific carbon analysis of archaeal biomarkers. They showed extremely depleted 13C contents (-80 ppm ˜ -100 ppm), which also appeared to be capable of directly oxidizing methane.

  5. Molecular evidence for the predation of Critically Endangered endemic Aphanius transgrediens from the stomach contents of world wide invasive Gambusia affinis.

    Science.gov (United States)

    Keskin, Emre

    2016-01-01

    Predation and competition among native and invasive species are difficult to study in aquatic environments. Identification of preys from semi-digested body parts sampled from stomach contents of the predator is very challenging. Recent studies were mainly based on use of DNA extracted from stomach content to identify the prey species. This study presents the molecular evidence that reveals the predation of critically endangered Aphanius transgrediens by world-wide invasive Gambusia affinis for a better understanding of the link between the invasion and the extinction of native species in freshwater ecosystems. DNA samples were extracted from semi-digested stomach contents of the invader and short fragments of mitochondrial NADH1 gene were amplified using species-specific primers designed in this study to make identification at species level. Existence of both the prey and the predator species were also confirmed using environmental DNA extracted from water samples.

  6. Dietary Plants for the Prevention and Management of Kidney Stones: Preclinical and Clinical Evidence and Molecular Mechanisms

    Science.gov (United States)

    Nirumand, Mina Cheraghi; Hajialyani, Marziyeh; Rahimi, Roja; Farzaei, Mohammad Hosein; Nabavi, Seyed Mohammad

    2018-01-01

    Kidney stones are one of the oldest known and common diseases in the urinary tract system. Various human studies have suggested that diets with a higher intake of vegetables and fruits play a role in the prevention of kidney stones. In this review, we have provided an overview of these dietary plants, their main chemical constituents, and their possible mechanisms of action. Camellia sinensis (green tea), Rubus idaeus (raspberry), Rubia cordifolia (common madder), Petroselinum crispum (parsley), Punica granatum (pomegranate), Pistacia lentiscus (mastic), Solanum xanthocarpum (yellow-fruit nightshade), Urtica dioica (stinging nettle), Dolichos biflorus (horse gram), Ammi visnaga (khella), Nigella sativa (black-cumin), Hibiscus sabdariffa (roselle), and Origanum vulgare (oregano) have received considerable interest based on scientific evidence. Beside these dietary plants, phytochemicals—such as catechin, epicatechin, epigallocatechin-3-gallate, diosmin, rutin, quercetin, hyperoside, and curcumin—as antioxidant dietary phyto-phenols were found to be effective for the prevention of urolithiasis (the process of stone formation in the urinary tract). The main underlying mechanisms of these dietary plants and their isolated phytonutrients in the management of urolithiasis include diuretic, antispasmodic, and antioxidant activity, as well as an inhibitory effect on crystallization, nucleation, and aggregation of crystals. The results as presented in this review demonstrate the promising role of dietary plants and phytophenols in the prevention and management of kidney stones. Further investigations are required to confirm the safety and efficacy of these compounds. PMID:29518971

  7. Dissecting molecular events in thyroid neoplasia provides evidence for distinct evolution of follicular thyroid adenoma and carcinoma.

    Science.gov (United States)

    Krause, Kerstin; Prawitt, Susanne; Eszlinger, Markus; Ihling, Christian; Sinz, Andrea; Schierle, Katrin; Gimm, Oliver; Dralle, Henning; Steinert, Frank; Sheu, Sien-Yi; Schmid, Kurt W; Fuhrer, Dagmar

    2011-12-01

    Benign hypofunctional cold thyroid nodules (CTNs) are a frequent scintiscan finding and need to be distinguished from thyroid carcinomas. The origin of CTNs with follicular morphologic features is unresolved. The DNA damage response might act as a physiologic barrier, inhibiting the progression of preneoplastic lesions to neoplasia. We investigated the following in hypofunctional follicular adenoma (FA) and follicular thyroid cancer (FTC): i) the mutation rate of frequently activated oncogenes, ii) the activation of DNA damage response checkpoints, and iii) the differential proteomic pattern between FA and FTC. Both FTC and FA, which did not harbor RAS, phosphoinositide-3-kinase, or PAX/peroxisome proliferator activated receptor-γ mutations, express various proteins in common and others that are more distinctly expressed in FTC rather than in FA or normal thyroid tissue. This finding is in line with the finding of constitutive DNA damage checkpoint activation (p-Chk2, γ-H2AX) and evidence for replicative stress causing genomic instability (increased cyclin E, retinoblastoma, or E2F1 mRNA expression) in FTC but not FA. We discuss the findings of the increased expression of translationally controlled tumor protein, phosphatase 2A inhibitor, and DJ-1 in FTC compared with FA identified by proteomics and their potential implication in follicular thyroid carcinogenesis. Our present findings argue for the definition of FA as a truly benign entity and against progressive development of FA to FTC. Copyright © 2011 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.

  8. Dietary Plants for the Prevention and Management of Kidney Stones: Preclinical and Clinical Evidence and Molecular Mechanisms.

    Science.gov (United States)

    Nirumand, Mina Cheraghi; Hajialyani, Marziyeh; Rahimi, Roja; Farzaei, Mohammad Hosein; Zingue, Stéphane; Nabavi, Seyed Mohammad; Bishayee, Anupam

    2018-03-07

    Kidney stones are one of the oldest known and common diseases in the urinary tract system. Various human studies have suggested that diets with a higher intake of vegetables and fruits play a role in the prevention of kidney stones. In this review, we have provided an overview of these dietary plants, their main chemical constituents, and their possible mechanisms of action. Camellia sinensis (green tea), Rubus idaeus (raspberry), Rubia cordifolia (common madder), Petroselinum crispum (parsley), Punica granatum (pomegranate), Pistacia lentiscus (mastic), Solanum xanthocarpum (yellow-fruit nightshade), Urtica dioica (stinging nettle), Dolichos biflorus ( horse gram ), Ammi visnaga (khella), Nigella sativa (black-cumin), Hibiscus sabdariffa (roselle), and Origanum vulgare (oregano) have received considerable interest based on scientific evidence. Beside these dietary plants, phytochemicals-such as catechin, epicatechin, epigallocatechin-3-gallate, diosmin, rutin, quercetin, hyperoside, and curcumin-as antioxidant dietary phyto-phenols were found to be effective for the prevention of urolithiasis (the process of stone formation in the urinary tract). The main underlying mechanisms of these dietary plants and their isolated phytonutrients in the management of urolithiasis include diuretic, antispasmodic, and antioxidant activity, as well as an inhibitory effect on crystallization, nucleation, and aggregation of crystals. The results as presented in this review demonstrate the promising role of dietary plants and phytophenols in the prevention and management of kidney stones. Further investigations are required to confirm the safety and efficacy of these compounds.

  9. Dietary Plants for the Prevention and Management of Kidney Stones: Preclinical and Clinical Evidence and Molecular Mechanisms

    Directory of Open Access Journals (Sweden)

    Mina Cheraghi Nirumand

    2018-03-01

    Full Text Available Kidney stones are one of the oldest known and common diseases in the urinary tract system. Various human studies have suggested that diets with a higher intake of vegetables and fruits play a role in the prevention of kidney stones. In this review, we have provided an overview of these dietary plants, their main chemical constituents, and their possible mechanisms of action. Camellia sinensis (green tea, Rubus idaeus (raspberry, Rubia cordifolia (common madder, Petroselinum crispum (parsley, Punica granatum (pomegranate, Pistacia lentiscus (mastic, Solanum xanthocarpum (yellow-fruit nightshade, Urtica dioica (stinging nettle, Dolichos biflorus (horse gram, Ammi visnaga (khella, Nigella sativa (black-cumin, Hibiscus sabdariffa (roselle, and Origanum vulgare (oregano have received considerable interest based on scientific evidence. Beside these dietary plants, phytochemicals—such as catechin, epicatechin, epigallocatechin-3-gallate, diosmin, rutin, quercetin, hyperoside, and curcumin—as antioxidant dietary phyto-phenols were found to be effective for the prevention of urolithiasis (the process of stone formation in the urinary tract. The main underlying mechanisms of these dietary plants and their isolated phytonutrients in the management of urolithiasis include diuretic, antispasmodic, and antioxidant activity, as well as an inhibitory effect on crystallization, nucleation, and aggregation of crystals. The results as presented in this review demonstrate the promising role of dietary plants and phytophenols in the prevention and management of kidney stones. Further investigations are required to confirm the safety and efficacy of these compounds.

  10. Molecular evidence of Rickettsia spp. in ixodid ticks and rodents in suburban, natural and rural habitats in Slovakia.

    Science.gov (United States)

    Minichová, Lenka; Hamšíková, Zuzana; Mahríková, Lenka; Slovák, Mirko; Kocianová, Elena; Kazimírová, Mária; Škultéty, Ľudovít; Štefanidesová, Katarína; Špitalská, Eva

    2017-03-24

    Natural foci of tick-borne spotted fever group (SFG) rickettsiae of public health concern have been found in Slovakia, but the role of rodents in their circulation is unclear. Ticks (Ixodes ricinus, Ixodes trianguliceps, Dermacentor marginatus, Dermacentor reticulatus, Haemaphysalis concinna and Haemaphysalis inermis) and tissues of rodents (Apodemus flavicollis, Apodemus sylvaticus, Myodes glareolus, Microtus arvalis, Microtus subterraneus and Micromys minutus) were examined for the presence of SFG rickettsiae and Coxiella burnetii by molecular methods. Suburban, natural and rural habitats were monitored to acquire information on the role of ticks and rodents in the agents' maintenance in various habitat types of Slovakia. The overall prevalence of rickettsial infection in questing I. ricinus and D. marginatus was 6.6% and 21.4%, respectively. Rickettsia helvetica, R. monacensis and non-identified rickettsial species were detected in I. ricinus, whereas R. slovaca and R. raoultii were identified in D. marginatus. Rickettsia spp.-infected I. ricinus occurred during the whole tick questing period. Rickettsia helvetica dominated (80.5%) followed by R. monacensis (6.5%). The species were present in all studied habitats. Rickettsia slovaca (66.7%) and R. raoultii (33.3%) were identified in D. marginatus from the rural habitat. Apodemus flavicollis was the most infested rodent species with I. ricinus, but My. glareolus carried the highest proportion of Rickettsia-positive I. ricinus larvae. Only 0.5% of rodents (A. flavicollis) and 5.2% of engorged I. ricinus removed from My. glareolus, A. flavicollis and M. arvalis were R. helvetica- and R. monacensis-positive. Coxiella burnetii was not detected in any of the tested samples. We hypothesize that rodents could play a role as carriers of infected ticks and contribute to the maintenance of rickettsial pathogens in natural foci. Long-term presence of SFG Rickettsia spp. was confirmed in questing ticks from different habitat

  11. Evidence of molecular evolution driven by recombination events influencing tropism in a novel human adenovirus that causes epidemic keratoconjunctivitis.

    Directory of Open Access Journals (Sweden)

    Michael P Walsh

    2009-06-01

    the first genomic, bioinformatic, and biological descriptions of the molecular evolution events engendering an emerging pathogenic adenovirus.

  12. Molecular Evidence for Radical Changes in Ocean Chemistry Across the Permian Triassic Boundary at Meishan in South China

    Science.gov (United States)

    Love, G. D.; Cao, C.; Jin, Y.; Summons, R. E.

    2004-12-01

    Samples from outcrop and from a new core drilled through the Permian Triassic Boundary at the type section at Meishan have been examined for biomarker and isotopic evidence of biotic and associated environmental change. Late Permian sediments from Meishan Beds 22-27 are characterized by indicators of anoxia including low Pr/Ph ratios and abundant aryl isoprenoids and isoreneieratane derived from the precursor carotenoid isorenieratene. The latter compounds are biomarkers for green sulfur bacteria (Chlorobiaceae) and are considered reliable indicators of euxinic water columns where sulfide extends to the photic zone. The peak of Chlorobiaceae biomarker abundance coincides with a rapid and synchronous drop in the ƒO13C and ƒO15N values of kerogen. On passing up into the Early Triassic, the biomarker signal for Chlorobiaceae wanes and is almost absent by Bed 30 where it is replaced by one for cyanobacteria including abundant hopanes and 2-methylhopanes and accompanying methyl and dimethyl alkanes. A very high value for the hopane/sterane ratio from Beds 30-38 indicates continuing dominant cyanobacterial productivity and only minor inputs from an algal plankton. The prevalence of aryl isoprenoids in P-Tr sediments at the Meishan section of South China is also recorded in a recently cored borehole, Hovea-3, of the Perth Basin, Western Australia. This suggests similar paleoenvironmental conditions prevailed across the Tethys Ocean during and immediately after the P-Tr Boundary. In particular, the presence of biomarkers for Chlorobiaceae at two separate locations indicates that water column euxinia was pervasive during the extinction event and suggests that sulfide may have been a key toxic agent.

  13. Novel molecular-level evidence of iodine binding to natural organic matter from Fourier transform ion cyclotron resonance mass spectrometry

    International Nuclear Information System (INIS)

    Xu, Chen; Chen, Hongmei; Sugiyama, Yuko; Zhang, Saijin; Li, Hsiu-Ping; Ho, Yi-Fang; Chuang, Chia-ying; Schwehr, Kathleen A.; Kaplan, Daniel I.; Yeager, Chris; Roberts, Kimberly A.; Hatcher, Patrick G.; Santschi, Peter H.

    2013-01-01

    Major fractions of radioiodine ( 129 I) are associated with natural organic matter (NOM) in the groundwater and surface soils of the Savannah River Site (SRS). Electrospray ionization coupled to Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS) was applied to elucidate the interactions between inorganic iodine species (iodide and iodate) and a fulvic acid (FA) extracted from a SRS surface soil. Iodate is likely reduced to reactive iodine species by the lignin- and tannin-like compounds or the carboxylic-rich alicyclic molecules (CRAM), during which condensed aromatics and lignin-like compounds were generated. Iodide is catalytically oxidized into reactive iodine species by peroxides, while FA is oxidized by peroxides into more aliphatic and less aromatic compounds. Only 9% of the total identified organo-iodine compounds derived from molecules originally present in the FA, whereas most were iodine binding to newly-produced compounds. The resulting iodinated molecules were distributed in three regions in the van Krevelen diagrams, denoting unsaturated hydrocarbons, lignin and protein. Moreover, characteristics of these organo-iodine compounds, such as their relatively low O/C ratios ( 2 or -HNCOR groups and a ring-activating functionality to favor the electrophilic substitution. The ESI-FTICR-MS technique provides novel evidence to better understand the reactivity and scavenging properties of NOM towards radioiodine and possible influence of NOM on 129 I migration. Highlights: ► IO 3 − reduced by lignin-, tannin-like compounds/carboxylic-rich alicyclic molecules ► Condensed aromatic and lignin-like compounds generated after iodate-iodination ► Aliphatic and less aromatic compounds formed after iodide-iodination ► Organo-iodine identified as unsaturated hydrocarbons, lignin and protein ► Organo-iodine with low O/C ratios imply less environmental mobility

  14. Molecular and biochemical evidences on the protective effects of triiodothyronine against phosphine-induced cardiac and mitochondrial toxicity.

    Science.gov (United States)

    Abdolghaffari, Amir Hossein; Baghaei, Amir; Solgi, Reza; Gooshe, Maziar; Baeeri, Maryam; Navaei-Nigjeh, Mona; Hassani, Shokoufeh; Jafari, Abbas; Rezayat, Seyed Mehdi; Dehpour, Ahmad Reza; Mehr, Shahram Ejtemaei; Abdollahi, Mohammad

    2015-10-15

    Aluminum phosphide (AlP) is a widely used fumigant and rodenticide. While AlP ingestion leads to high mortality, its exact mechanism of action is unclear. There are ample evidences suggesting cardioprotective effects of triiodothyronine (T3). In this study, we aimed to examine the potential of T3 in the protection of a rat model of AlP induced cardiotoxicity. In order to induce AlP intoxication animals were intoxicated with AlP (12 mg/kg; LD50) by gavage. In treatment groups, T3 (1, 2 and 3 μg/kg) was administered intra-peritoneally 30 min after AlP administration. Animals were connected to the electronic cardiovascular monitoring device simultaneously after T3 administration. Then, electrocardiogram (ECG), blood pressure (BP), and heart rate (HR) were monitored for 180 min. Additionally, 24h after AlP intoxication, rats were deceased and the hearts were dissected out for evaluation of oxidative stress, cardiac mitochondrial function (complexes I, II and IV), ATP/ADP ratio, caspases 3 & 9, and apoptosis by flow cytometry. The results demonstrated that AlP intoxication causes cardiac toxicity presenting with changes in ECG patterns such as decrement of HR, BP and abnormal QRS complexes, QTc and ST height. T3 at a dose of 3 μg/kg significantly improved ECG and also oxidative stress parameters. Furthermore, T3 administration could increase mitochondrial function and ATP levels within the cardiac cells. In addition, administration of T3 showed a reduction in apoptosis through diminishing the caspase activities and improving cell viability. Overall, the present data demonstrate the beneficial effects of T3 in cardiotoxicity of AlP. Copyright © 2015 Elsevier Inc. All rights reserved.

  15. Mutational analyses of molecularly cloned satellite tobacco mosaic virus during serial passage in plants: Evidence for hotspots of genetic change

    Science.gov (United States)

    Kurath, G.; Dodds, J.A.

    1995-01-01

    The high level of genetic diversity and rapid evolution of viral RNA genomes are well documented, but few studies have characterized the rate and nature of ongoing genetic change over time under controlled experimental conditions, especially in plant hosts. The RNA genome of satellite tobacco mosaic virus (STMV) was used as an effective model for such studies because of advantageous features of its genome structure and because the extant genetic heterogeneity of STMV has been characterized previously. In the present study, the process of genetic change over time was studied by monitoring multiple serial passage lines of STMV populations for changes in their consensus sequences. A total of 42 passage lines were initiated by inoculation of tobacco plants with a helper tobamovirus and one of four STMV RNA inocula that were transcribed from full-length infectious STMV clones or extracted from purified STMV type strain virions. Ten serial passages were carried out for each line and the consensus genotypes of progeny STMV populations were assessed for genetic change by RNase protection analyses of the entire 1,059-nt STMV genome. Three different types of genetic change were observed, including the fixation of novel mutations in 9 of 42 lines, mutation at the major heterogeneity site near nt 751 in 5 of the 19 lines inoculated with a single genotype, and selection of a single major genotype in 6 of the 23 lines inoculated with mixed genotypes. Sequence analyses showed that the majority of mutations were single base substitutions. The distribution of mutation sites included three clusters in which mutations occurred at or very near the same site, suggesting hot spots of genetic change in the STMV genome. The diversity of genetic changes in sibling lines is clear evidence for the important role of chance and random sampling events in the process of genetic diversification of STMV virus populations.

  16. Molecular evidence that rough endoplasmic reticulum is the site of calreticulin translation in Petunia pollen tubes growing in vitro.

    Science.gov (United States)

    Suwińska, Anna; Lenartowski, Robert; Smoliński, Dariusz Jan; Lenartowska, Marta

    2015-07-01

    In germinating pollen grains and growing pollen tubes, CRT is translated on ER membrane-bound ribosomes in the regions where its activity is required for stabilization of tip-focused Ca (2+) gradient. Pollen tube growth requires coordination of signaling, exocytosis, and actin cytoskeletal organization. Many of these processes are thought to be controlled by finely tuned regulation of cytoplasmic Ca(2+) in discrete regions of the tube cytoplasm. Most notably, a mechanism must function to maintain a steep gradient of Ca(2+) that exists at the tip of growing pollen tube. Several pieces of evidence point to calreticulin (CRT) as a key Ca(2+)-binding/-buffering protein involved in pollen germination and pollen tube growth. We previously hypothesized that in germinating pollen and growing tubes, CRT is translated on the ribosomes associated with endoplasmic reticulum (ER) in the regions where its activity might be required. In this report, we have addressed this idea by identifying the sites where CRT mRNA, CRT protein, 18S rRNA, and rough ER are localized in Petunia pollen tubes. We observed all four components in the germinal aperture of pollen grains and in subapical regions of elongating tubes. These results seem to support our idea that CRT is translated on ER membrane-bound ribosomes during pollen germination and pollen tube growth. In elongated pollen tubes, we found CRT mainly localized in the subapical zone, where ER and Golgi stacks are abundant. In eukaryotic cells, these organelles serve as mobile intracellular stores of easily releasable Ca(2+), which can be buffered by proteins such as CRT. Therefore, we postulate that subapical-localized CRT is involved in pollen tube growth by maintaining the stable tip-focused Ca(2+) gradient and thus modulating local Ca(2+) concentration within the tube cytoplasm.

  17. Novel molecular-level evidence of iodine binding to natural organic matter from Fourier transform ion cyclotron resonance mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Chen, E-mail: xuchen66@tamu.edu [Laboratory for Environmental and Oceanographic Research, Department of Marine Sciences, Texas A and M University, Building 3029, Galveston, TX 77551 (United States); Chen, Hongmei [Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529 (United States); Sugiyama, Yuko [Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529 (United States); University of Hyogo, 1-1-12, Shinzaike-honcho, Himeji, Hyogo 670-0092 (Japan); Zhang, Saijin; Li, Hsiu-Ping; Ho, Yi-Fang; Chuang, Chia-ying; Schwehr, Kathleen A. [Laboratory for Environmental and Oceanographic Research, Department of Marine Sciences, Texas A and M University, Building 3029, Galveston, TX 77551 (United States); Kaplan, Daniel I. [Savannah River National Laboratory, Aiken, SC 29808 (United States); Yeager, Chris [Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Roberts, Kimberly A. [Savannah River National Laboratory, Aiken, SC 29808 (United States); Hatcher, Patrick G. [Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529 (United States); Santschi, Peter H. [Laboratory for Environmental and Oceanographic Research, Department of Marine Sciences, Texas A and M University, Building 3029, Galveston, TX 77551 (United States)

    2013-04-01

    Major fractions of radioiodine ({sup 129}I) are associated with natural organic matter (NOM) in the groundwater and surface soils of the Savannah River Site (SRS). Electrospray ionization coupled to Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS) was applied to elucidate the interactions between inorganic iodine species (iodide and iodate) and a fulvic acid (FA) extracted from a SRS surface soil. Iodate is likely reduced to reactive iodine species by the lignin- and tannin-like compounds or the carboxylic-rich alicyclic molecules (CRAM), during which condensed aromatics and lignin-like compounds were generated. Iodide is catalytically oxidized into reactive iodine species by peroxides, while FA is oxidized by peroxides into more aliphatic and less aromatic compounds. Only 9% of the total identified organo-iodine compounds derived from molecules originally present in the FA, whereas most were iodine binding to newly-produced compounds. The resulting iodinated molecules were distributed in three regions in the van Krevelen diagrams, denoting unsaturated hydrocarbons, lignin and protein. Moreover, characteristics of these organo-iodine compounds, such as their relatively low O/C ratios (< 0.2 or < 0.4) and yet some degree of un-saturation close to that of lignin, have multiple important environmental implications concerning possibly less sterically-hindered aromatic ring system for iodine to get access to and a lower hydrophilicity of the molecules thus to retard their migration in the natural aquatic systems. Lastly, ∼ 69% of the identified organo-iodine species contains nitrogen, which is presumably present as -NH{sub 2} or -HNCOR groups and a ring-activating functionality to favor the electrophilic substitution. The ESI-FTICR-MS technique provides novel evidence to better understand the reactivity and scavenging properties of NOM towards radioiodine and possible influence of NOM on {sup 129}I migration. Highlights: ► IO{sub 3}{sup

  18. Preventive effect of the flavonoid, quercetin, on hepatic cancer in rats via oxidant/antioxidant activity: molecular and histological evidences

    Directory of Open Access Journals (Sweden)

    Seufi AlaaEddeen M

    2009-06-01

    preventive effect of quercetin on hepatocarcinoma in rats by RAPD-PCR, tracing the effect on p53 gene and by histopathological evidence. Hereby, it was proved that quercetin exerted its preventive effect via decreased oxidative stress and decreased antioxidant activity.

  19. Modeling the microstructural evolution during constrained sintering

    DEFF Research Database (Denmark)

    Bjørk, Rasmus; Frandsen, Henrik Lund; Tikare, V.

    A numerical model able to simulate solid state constrained sintering of a powder compact is presented. The model couples an existing kinetic Monte Carlo (kMC) model for free sintering with a finite element (FE) method for calculating stresses on a microstructural level. The microstructural response...... to the stress field as well as the FE calculation of the stress field from the microstructural evolution is discussed. The sintering behavior of two powder compacts constrained by a rigid substrate is simulated and compared to free sintering of the same samples. Constrained sintering result in a larger number...

  20. Enablers and constrainers to participation

    DEFF Research Database (Denmark)

    Desjardins, Richard; Milana, Marcella

    2007-01-01

    This paper briefly reviews some of evidence on participation patterns in Nordic countries and some of the defining parameters that may explain the observations. This is done in a comparative perspective by contrasting results from the 2003 Eurobarometer data between Nordic countries and a handful...... as to construct a tool for analyzing the targeting of adult learning policy, with regard to both its coverage and expected consequences. Our aim is to develop a means for a more in-depth analysis of the match-mismatch of public policy and persisting constraints to participation....

  1. Asymptotic Likelihood Distribution for Correlated & Constrained Systems

    CERN Document Server

    Agarwal, Ujjwal

    2016-01-01

    It describes my work as summer student at CERN. The report discusses the asymptotic distribution of the likelihood ratio for total no. of parameters being h and 2 out of these being are constrained and correlated.

  2. Constrained bidirectional propagation and stroke segmentation

    Energy Technology Data Exchange (ETDEWEB)

    Mori, S; Gillespie, W; Suen, C Y

    1983-03-01

    A new method for decomposing a complex figure into its constituent strokes is described. This method, based on constrained bidirectional propagation, is suitable for parallel processing. Examples of its application to the segmentation of Chinese characters are presented. 9 references.

  3. Mathematical Modeling of Constrained Hamiltonian Systems

    NARCIS (Netherlands)

    Schaft, A.J. van der; Maschke, B.M.

    1995-01-01

    Network modelling of unconstrained energy conserving physical systems leads to an intrinsic generalized Hamiltonian formulation of the dynamics. Constrained energy conserving physical systems are directly modelled as implicit Hamiltonian systems with regard to a generalized Dirac structure on the

  4. Client's Constraining Factors to Construction Project Management

    African Journals Online (AJOL)

    factors as a significant system that constrains project management success of public and ... finance for the project and prompt payment for work executed; clients .... consideration of the loading patterns of these variables, the major factor is ...

  5. On the origin of constrained superfields

    Energy Technology Data Exchange (ETDEWEB)

    Dall’Agata, G. [Dipartimento di Fisica “Galileo Galilei”, Università di Padova,Via Marzolo 8, 35131 Padova (Italy); INFN, Sezione di Padova,Via Marzolo 8, 35131 Padova (Italy); Dudas, E. [Centre de Physique Théorique, École Polytechnique, CNRS, Université Paris-Saclay,F-91128 Palaiseau (France); Farakos, F. [Dipartimento di Fisica “Galileo Galilei”, Università di Padova,Via Marzolo 8, 35131 Padova (Italy); INFN, Sezione di Padova,Via Marzolo 8, 35131 Padova (Italy)

    2016-05-06

    In this work we analyze constrained superfields in supersymmetry and supergravity. We propose a constraint that, in combination with the constrained goldstino multiplet, consistently removes any selected component from a generic superfield. We also describe its origin, providing the operators whose equations of motion lead to the decoupling of such components. We illustrate our proposal by means of various examples and show how known constraints can be reproduced by our method.

  6. Molecular environment of stable iodine and radioiodine (129I) in natural organic matter: Evidence inferred from NMR and binding experiments at environmentally relevant concentrations

    Science.gov (United States)

    Xu, Chen; Zhong, Junyan; Hatcher, Patrick G.; Zhang, Saijin; Li, Hsiu-Ping; Ho, Yi-Fang; Schwehr, Kathleen A.; Kaplan, Daniel I.; Roberts, Kimberly A.; Brinkmeyer, Robin; Yeager, Chris M.; Santschi, Peter H.

    2012-11-01

    129I is a major by-product of nuclear fission and had become one of the major radiation risk drivers at Department of Energy (DOE) sites. 129I is present at elevated levels in the surface soils of the Savannah River Site (SRS) F-Area and was found to be bound predominantly to soil organic matter (SOM). Naturally bound 127I and 129I to sequentially extracted humic acids (HAs), fulvic acids (FAs) and a water extractable colloid (WEC) were measured in a 129I-contaminated wetland surface soil located on the SRS. WEC is a predominantly colloidal organic fraction obtained from soil re-suspension experiments to mimic the fraction that may be released during groundwater exfiltration, storm water or surface runoff events. For the first time, NMR techniques were applied to infer the molecular environment of naturally occurring stable iodine and radioiodine binding to SOM. Iodine uptake partitioning coefficients (Kd) by these SOM samples at ambient iodine concentrations were also measured and related to quantitative structural analyses by 13C DPMAS NMR and solution state 1H NMR on the eight humic acid fractions. By assessing the molecular environment of iodine, it was found that it was closely associated with the aromatic regions containing esterified products of phenolic and formic acids or other aliphatic carboxylic acids, amide functionalities, quinone-like structures activated by electron-donating groups (e.g., NH2), or a hemicellulose-lignin-like complex with phenyl-glycosidic linkages. However, FAs and WEC contained much greater concentrations of 127I or 129I than HAs. The contrasting radioiodine contents among the three different types of SOM (HAs, FAs and WEC) suggest that the iodine binding environment cannot be explained solely by the difference in the amount of their reactive binding sites. Instead, indirect evidence indicates that the macro-molecular conformation, such as the hydrophobic aliphatic periphery hindering the active aromatic cores and the hydrophilic

  7. Molecular evolution of avian reovirus: evidence for genetic diversity and reassortment of the S-class genome segments and multiple cocirculating lineages

    International Nuclear Information System (INIS)

    Liu, Hung J.; Lee, Long H.; Hsu, Hsiao W.; Kuo, Liam C.; Liao, Ming H.

    2003-01-01

    Nucleotide sequences of the S-class genome segments of 17 field-isolates and vaccine strains of avian reovirus (ARV) isolated over a 23-year period from different hosts, pathotypes, and geographic locations were examined and analyzed to define phylogenetic profiles and evolutionary mechanism. The S1 genome segment showed noticeably higher divergence than the other S-class genes. The σC-encoding gene has evolved into six distinct lineages. In contrast, the other S-class genes showed less divergence than that of the σC-encoding gene and have evolved into two to three major distinct lineages, respectively. Comparative sequence analysis provided evidence indicating extensive sequence divergence between ARV and other orthoreoviruses. The evolutionary trees of each gene were distinct, suggesting that these genes evolve in an independent manner. Furthermore, variable topologies were the result of frequent genetic reassortment among multiple cocirculating lineages. Results showed genetic diversity correlated more closely with date of isolation and geographic sites than with host species and pathotypes. This is the first evidence demonstrating genetic variability among circulating ARVs through a combination of evolutionary mechanisms involving multiple cocirculating lineages and genetic reassortment. The evolutionary rates and patterns of base substitutions were examined. The evolutionary rate for the σC-encoding gene and σC protein was higher than for the other S-class genes and other family of viruses. With the exception of the σC-encoding gene, which nonsynonymous substitutions predominate over synonymous, the evolutionary process of the other S-class genes can be explained by the neutral theory of molecular evolution. Results revealed that synonymous substitutions predominate over nonsynonymous in the S-class genes, even though genetic diversity and substitution rates vary among the viruses

  8. Polyphyly of the spring-parsleys (Cymopterus): molecular and morphological evidence suggests complex relationships among the perennial endemic genera of western North American Apiaceae

    International Nuclear Information System (INIS)

    Downie, S.R.; Hartman, R.L.; Sun, F.-J.; Katz-Downie, D.S.

    2002-01-01

    Cladistic analyses of DNA sequences from the nuclear rDNA internal transcribed spacer region and cpDNA rps16 intron and, for a subset of taxa, the cpDNA trnF-trnL-trnT locus were carried out to evaluate the monophyly of Cymopterus and to ascertain its phylogenetic placement among the other perennial genera of Apiaceae (Umbelliferae) subfamily Apioideae endemic to western North America. To elucidate patterns in the evolution of specific fruit characters and to evaluate their utility in circumscribing genera unambiguously, additional evidence was procured from cross-sections of mature fruits and the results of cladistic analysis of 25 morphological characters. Analyses of the partitioned data sets resulted in weakly supported and largely unresolved phylogenetic hypotheses, possibly due to the rapid radiation of the group, whereas the combined analysis of all molecular evidence resulted in a well-resolved phylogeny with higher bootstrap support. The traditionally used fruit characters of wing shape and composition and orientation of mericarp compression are highly variable. The results of these analyses reveal that Cymopterus and Lomatium, the two largest genera of western North American Apiaceae, are polyphyletic, and that their species are inextricably linked with those of other endemic perennial genera of the region (such as, Aletes, Musineon, Oreoxis, Pseudocymopterus, Pteryxia, and Tauschia), many of which are also not monophyletic. Prior emphasis on characters of the fruit in all systems of classification of the group has led to highly artificial assemblages of species. A complete reassessment of generic limits of all western endemic Apiaceae is required, as is further systematic study of this intractable group. (author)

  9. Cichlid Fishes in the Angolan Headwaters Region: Molecular Evidence of the Ichthyofaunal Contact between the Cuanza and Okavango-Zambezi Systems

    Science.gov (United States)

    Musilová, Zuzana; Kalous, Lukáš; Petrtýl, Miloslav; Chaloupková, Petra

    2013-01-01

    The headwaters of five large African river basins flow through the Bié Plateau in Angola and still remain faunistically largely unexplored. We investigated fish fauna from the Cuanza and Okavango-Zambezi river systems from central Angola. We reconstructed molecular phylogenies of the most common cichlid species from the region, Tilapia sparrmanii and Serranochromis macrocephalus, using both mitochondrial and nuclear markers. We found evidence for ichthyofaunal contact and gene flow between the Cuanza and Okavango-Zambezi watersheds in the Bié Plateau in central Angola. Waterfalls and rapids also appeared to restrict genetic exchange among populations within the Cuanza basin. Further, we found that the Angolan Serranochromis cichlid fishes represent a monophyletic lineage with respect to other haplochromines, including the serranochromines from the Congo and Zambezi rivers. This study represents an important initial step in a biodiversity survey of this extremely poorly explored region, as well as giving further understanding to species distributions and gene flow both between and within river basins. PMID:23724120

  10. Molecular epidemiology of HIV type 1 infection in Iran: genomic evidence of CRF35_AD predominance and CRF01_AE infection among individuals associated with injection drug use.

    Science.gov (United States)

    Jahanbakhsh, Fatemeh; Ibe, Shiro; Hattori, Junko; Monavari, Seyed Hamid Reza; Matsuda, Masakazu; Maejima, Masami; Iwatani, Yasumasa; Memarnejadian, Arash; Keyvani, Hossein; Azadmanesh, Kayhan; Sugiura, Wataru

    2013-01-01

    To understand the molecular epidemiology of HIV-1 infection in Iran, we conducted the first study to analyze the genome sequence of Iranian HIV-1 isolates. For this cross-sectional study, we enrolled 10 HIV-1-infected individuals associated with injection drug use from Tehran, Shiraz, and Kermanshah. Near full-length genome sequences obtained from their plasma samples were used for phylogenetic tree and similarity plotting analyses. Among 10 isolates, nine were clearly identified as CRF35_AD and the remaining one as CRF01_AE. Interestingly, five of our Iranian CRF35_AD isolates made two clusters with 10 Afghan CRF35_AD isolates in a phylogenetic tree, indicating epidemiological connections among injection drug users in Iran and Afghanistan. In contrast, our CRF01_AE isolate had no genetic relationship with any other CRF01_AE isolates worldwide, even from Afghanistan. This study provides the first genomic evidence of HIV-1 CRF35_AD predominance and CRF01_AE infection among individuals associated with injection drug use in Iran.

  11. Towards weakly constrained double field theory

    Directory of Open Access Journals (Sweden)

    Kanghoon Lee

    2016-08-01

    Full Text Available We show that it is possible to construct a well-defined effective field theory incorporating string winding modes without using strong constraint in double field theory. We show that X-ray (Radon transform on a torus is well-suited for describing weakly constrained double fields, and any weakly constrained fields are represented as a sum of strongly constrained fields. Using inverse X-ray transform we define a novel binary operation which is compatible with the level matching constraint. Based on this formalism, we construct a consistent gauge transform and gauge invariant action without using strong constraint. We then discuss the relation of our result to the closed string field theory. Our construction suggests that there exists an effective field theory description for massless sector of closed string field theory on a torus in an associative truncation.

  12. Continuation of Sets of Constrained Orbit Segments

    DEFF Research Database (Denmark)

    Schilder, Frank; Brøns, Morten; Chamoun, George Chaouki

    Sets of constrained orbit segments of time continuous flows are collections of trajectories that represent a whole or parts of an invariant set. A non-trivial but simple example is a homoclinic orbit. A typical representation of this set consists of an equilibrium point of the flow and a trajectory...... that starts close and returns close to this fixed point within finite time. More complicated examples are hybrid periodic orbits of piecewise smooth systems or quasi-periodic invariant tori. Even though it is possible to define generalised two-point boundary value problems for computing sets of constrained...... orbit segments, this is very disadvantageous in practice. In this talk we will present an algorithm that allows the efficient continuation of sets of constrained orbit segments together with the solution of the full variational problem....

  13. Constrained principal component analysis and related techniques

    CERN Document Server

    Takane, Yoshio

    2013-01-01

    In multivariate data analysis, regression techniques predict one set of variables from another while principal component analysis (PCA) finds a subspace of minimal dimensionality that captures the largest variability in the data. How can regression analysis and PCA be combined in a beneficial way? Why and when is it a good idea to combine them? What kind of benefits are we getting from them? Addressing these questions, Constrained Principal Component Analysis and Related Techniques shows how constrained PCA (CPCA) offers a unified framework for these approaches.The book begins with four concre

  14. Molecular evolution of the Bovini tribe (Bovidae, Bovinae: Is there evidence of rapid evolution or reduced selective constraint in Domestic cattle?

    Directory of Open Access Journals (Sweden)

    McCulloch Alan

    2009-04-01

    Full Text Available Abstract Background If mutation within the coding region of the genome is largely not adaptive, the ratio of nonsynonymous (dN to synonymous substitutions (dS per site (dN/dS should be approximately equal among closely related species. Furthermore, dN/dS in divergence between species should be equivalent to dN/dS in polymorphisms. This hypothesis is of particular interest in closely related members of the Bovini tribe, because domestication has promoted rapid phenotypic divergence through strong artificial selection of some species while others remain undomesticated. We examined a number of genes that may be involved in milk production in Domestic cattle and a number of their wild relatives for evidence that domestication had affected molecular evolution. Elevated rates of dN/dS were further queried to determine if they were the result of positive selection, low effective population size (Ne or reduced selective constraint. Results We have found that the domestication process has contributed to higher dN/dS ratios in cattle, especially in the lineages leading to the Domestic cow (Bos taurus and Mithan (Bos frontalis and within some breeds of Domestic cow. However, the high rates of dN/dS polymorphism within B. taurus when compared to species divergence suggest that positive selection has not elevated evolutionary rates in these genes. Likewise, the low rate of dN/dS in Bison, which has undergone a recent population bottleneck, indicates a reduction in population size alone is not responsible for these observations. Conclusion The effect of selection depends on effective population size and the selection coefficient (Nes. Typically under domestication both selection pressure for traits important in fitness in the wild and Ne are reduced. Therefore, reduced selective constraint could be responsible for the observed elevated evolutionary ratios in domesticated species, especially in B. taurus and B. frontalis, which have the highest dN/dS in the

  15. Abundance of questing ticks and molecular evidence for pathogens in ticks in three parks of Emilia-Romagna region of Northern Italy

    Directory of Open Access Journals (Sweden)

    Sara Aureli

    2015-09-01

    Full Text Available Introduction and objective. Infectious and parasitic diseases transmitted by ticks, such as Lyme diseases, granulocytic anaplasmosis and piroplasmosis, have been frequently reported in Europe, with increasing attention to them as an emerging zoonotic problem. The presented study was performed to assess the distribution and the density of questing ticks in three regional parks of Emilia-Romagna region of Northern Italy, and to seek molecular evidence of potential human pathogens in tick populations. Materials and Methods. In the period April-October 2010, 8,139 questing ticks were collected: 6,734 larvae, 1,344 nymphs and only a few adults – 28 females and 33 males. The abundance of[i] Ixodes ricinus[/i] questing ticks was compared among different sampling sites and related to microclimate parameters. 1,544 out of 8,139 ticks were examined for the presence of pathogens: PCR was used to detect piroplasms DNA and Real time Taqman PCR for [i]Anaplasma phagocytophilum[/i] and [i]Borrelia burgdorferi[/i] s.l. Results. The predominant species was [i]I. ricinus[/i] (overall abundance 1,075.9/100 m[sup]2[/sup] ; more rarely, [i]Dermacentor marginatus[/i] (n = 37 – 0.45%, [i]Scaphixodes frontalis[/i] (n = 13 – 0.16%, [i]Hyalomma[/i] spp. (n = 6 – 0.07% and [i]Ixodes acuminatus[/i] (n = 3 – 0.04% were also found. 28 out of 324 (8.6% samples of ticks were PCR-positive for piroplasm DNA. 11 amplicons of 18S rRNA gene were identical to each other and had 100% identity with[i] Babesia[/i] EU1 ([i]Babesia venatorum[/i] using BLAST analysis. Real time Taqman PCR gave positive results for [i]A. phagocytophilum[/i] in 23 out of 292 samples (7.9%, and for [i]B. burgdorferi[/i] s.l. in 78 out of 292 samples (26.7%. [i]I. ricinu[/i]s was the only species found positive for pathogens by molecular analysis; 16 tick samples were co-infected with at least 2 pathogens. Discussion. The peak of nymph presence was in May, and the higher prevalence of pathogens

  16. The disjunct pattern of the Neotropical harvestman Discocyrtus dilatatus (Gonyleptidae explained by climate-driven range shifts in the Quaternary: Paleodistributional and molecular evidence.

    Directory of Open Access Journals (Sweden)

    Julia Vergara

    Full Text Available The disjunct distribution of the harvestman Discocyrtus dilatatus (Opiliones, Gonyleptidae is used as a case study to test the hypothesis of a trans-Chaco Pleistocene paleobridge during range expansion stages. This would have temporarily connected humid regions ('Mesopotamia' in northeastern Argentina, and the 'Yungas' in the northwest, NWA in the subtropical and temperate South American lowlands. The present study combines two independent approaches: paleodistributional reconstruction, using the Species Distribution Modeling method MaxEnt and projection onto Quaternary paleoclimates (6 kya, 21 kya, 130 kya, and phylogeographic analyses based on the cytochrome oxidase subunit I molecular marker. Models predict a maximal shrinkage during the warm Last Interglacial (130 kya, and the rise of the hypothesized paleobridge in the Last Glacial Maximum (21 kya, revealing that cold-dry stages (not warm-humid ones, as supposed enabled the range expansion of this species. The disjunction was formed in the mid-Holocene (6 kya and is intensified under current conditions. The median-joining network shows that NWA haplotypes are peripherally related to different Mesopotamian lineages; haplotypes from Santa Fe and Córdoba Provinces consistently occupy central positions in the network. According to the dated phylogeny, Mesopotamia-NWA expansion events would have occurred in the last glacial period, in many cases closely associated to the Last Glacial Maximum, with most divergence events occurring shortly thereafter. Only two (out of nine NWA haplotypes are shared with Mesopotamian localities. A single, presumably relictual NWA haplotype was found to have diverged much earlier, suggesting an ancient expansion event not recoverable by the paleodistributional models. Different measures of sequence statistics, genetic diversity, population structure and history of demographic changes are provided. This research offers the first available evidence for the historical

  17. Dynamic relationship between neurostimulation and N-acetylaspartate metabolism in the human visual cortex: evidence that NAA functions as a molecular water pump during visual stimulation.

    Science.gov (United States)

    Baslow, Morris H; Hrabe, Jan; Guilfoyle, David N

    2007-01-01

    N-acetyl-l-aspartic acid (NAA), an amino acid synthesized and stored primarily in neurons in the brain, has been proposed to be a molecular water pump (MWP) whose function is to rapidly remove water from neurons against a water gradient. In this communication, we describe the results of a functional (1)H proton magnetic resonance spectroscopy (fMRS) study, and provide evidence that in the human visual cortex, over a 10-min period of visual stimulation, there are stimulation-induced graded changes in the NAA MRS signal from that of a preceding 10-min baseline period with a decline in the NAA signal of 13.1% by the end of the 10-min stimulation period. Upon cessation of visual stimulation, the NAA signal gradually increases during a 10-min recovery period and once again approaches the baseline level. Because the NAA MRS signal reflects the NAA concentration, these changes indicate rapid focal changes in its concentration, and transient changes in its intercompartmental metabolism. These include its rates of synthesis and efflux from neurons and its hydrolysis by oligodendrocytes. During stimulation, the apparent rate of NAA efflux and hydrolysis increased 14.2 times, from 0.55 to 7.8 micromol g(-1) h(-1). During recovery, the apparent rate of synthesis increased 13.3 times, from 0.55 to 7.3 micromol g(-1) h(-1). The decline in the NAA signal during stimulation suggests that a rapid increase in the rate of NAA-obligated water release to extracellular fluid (ECF) is the initial and seminal event in response to neurostimulation. It is concluded that the NAA metabolic cycle in the visual cortex is intimately linked to rates of neuronal signaling, and that the functional cycle of NAA is associated with its release to ECF, thus supporting the hypothesis that an important function of the NAA metabolic cycle is that of an efflux MWP.

  18. Testing the excitation/inhibition imbalance hypothesis in a mouse model of the autism spectrum disorder: in vivo neurospectroscopy and molecular evidence for regional phenotypes.

    Science.gov (United States)

    Gonçalves, Joana; Violante, Inês R; Sereno, José; Leitão, Ricardo A; Cai, Ying; Abrunhosa, Antero; Silva, Ana Paula; Silva, Alcino J; Castelo-Branco, Miguel

    2017-01-01

    Excitation/inhibition (E/I) imbalance remains a widely discussed hypothesis in autism spectrum disorders (ASD). The presence of such an imbalance may potentially define a therapeutic target for the treatment of cognitive disabilities related to this pathology. Consequently, the study of monogenic disorders related to autism, such as neurofibromatosis type 1 (NF1), represents a promising approach to isolate mechanisms underlying ASD-related cognitive disabilities. However, the NF1 mouse model showed increased γ-aminobutyric acid (GABA) neurotransmission, whereas the human disease showed reduced cortical GABA levels. It is therefore important to clarify whether the E/I imbalance hypothesis holds true. We hypothesize that E/I may depend on distinct pre- and postsynaptic push-pull mechanisms that might be are region-dependent. In current study, we assessed two critical components of E/I regulation: the concentration of neurotransmitters and levels of GABA(A) receptors. Measurements were performed across the hippocampi, striatum, and prefrontal cortices by combined in vivo magnetic resonance spectroscopy (MRS) and molecular approaches in this ASD-related animal model, the Nf1 +/- mouse. Cortical and striatal GABA/glutamate ratios were increased. At the postsynaptic level, very high receptor GABA(A) receptor expression was found in hippocampus, disproportionately to the small reduction in GABA levels. Gabaergic tone (either by receptor levels change or GABA/glutamate ratios) seemed therefore to be enhanced in all regions, although by a different mechanism. Our data provides support for the hypothesis of E/I imbalance in NF1 while showing that pre- and postsynaptic changes are region-specific. All these findings are consistent with our previous physiological evidence of increased inhibitory tone. Such heterogeneity suggests that therapeutic approaches to address neurochemical imbalance in ASD may need to focus on targets where convergent physiological mechanisms can be

  19. Molecular Epidemiology of P. vivax in Iran: High Diversity and Complex Sub-Structure Using Neutral Markers, but No Evidence of Y976F Mutation at pvmdr1.

    Science.gov (United States)

    Hamedi, Yaghoob; Sharifi-Sarasiabi, Khojasteh; Dehghan, Farzaneh; Safari, Reza; To, Sheren; Handayuni, Irene; Trimarsanto, Hidayat; Price, Ric N; Auburn, Sarah

    2016-01-01

    Malaria remains endemic at low levels in the south-eastern provinces of Iran bordering Afghanistan and Pakistan, with the majority of cases attributable to P. vivax. The national guidelines recommend chloroquine (CQ) as blood-stage treatment for uncomplicated P. vivax, but the large influx of imported cases enhances the risk of introducing CQ resistance (CQR). The genetic diversity at pvmdr1, a putative modulator of CQR, and across nine putatively neutral short tandem repeat (STR) markers were assessed in P. vivax clinical isolates collected between April 2007 and January 2013 in Hormozgan Province, south-eastern Iran. One hundred blood samples were collected from patients with microscopy-confirmed P. vivax enrolled at one of five district clinics. In total 73 (73%) were autochthonous cases, 23 (23%) imported cases from Afghanistan or Pakistan, and 4 (4%) with unknown origin. 97% (97/100) isolates carried the F1076L mutation, but none carried the Y976F mutation. STR genotyping was successful in 71 (71%) isolates, including 57(57%) autochthonous and 11 (11%) imported cases. Analysis of population structure revealed 2 major sub-populations, K1 and K2, with further sub-structure within K2. The K1 sub-population had markedly lower diversity than K2 (HE = 0.06 vs HE = 0.82) suggesting that the sub-populations were sustained by distinct reservoirs with differing transmission dynamics, possibly reflecting local versus imported/introduced populations. No notable separation was observed between the local and imported cases although the sample size was limited. The contrasting low versus high diversity in the two sub-populations (K1 and K2) infers that a combination of local transmission and cross-border malaria from higher transmission regions shape the genetic make-up of the P. vivax population in south-eastern Iran. There was no molecular evidence of CQR amongst the local or imported cases, but ongoing clinical surveillance is warranted.

  20. Assessing bat droppings and predatory bird pellets for vector-borne bacteria: molecular evidence of bat-associated Neorickettsia sp. in Europe.

    Science.gov (United States)

    Hornok, Sándor; Szőke, Krisztina; Estók, Péter; Krawczyk, Aleksandra; Haarsma, Anne-Jifke; Kováts, Dávid; Boldogh, Sándor A; Morandini, Pál; Szekeres, Sándor; Takács, Nóra; Kontschán, Jenő; Meli, Marina L; Fernández de Mera, Isabel G; de la Fuente, José; Gyuranecz, Miklós; Sulyok, Kinga M; Weibel, Beatrice; Gönczi, Enikő; de Bruin, Arnout; Sprong, Hein; Hofmann-Lehmann, Regina

    2018-02-28

    In Europe, several species of bats, owls and kestrels exemplify highly urbanised, flying vertebrates, which may get close to humans or domestic animals. Bat droppings and bird pellets may have epidemiological, as well as diagnostic significance from the point of view of pathogens. In this work 221 bat faecal and 118 bird pellet samples were screened for a broad range of vector-borne bacteria using PCR-based methods. Rickettsia DNA was detected in 13 bat faecal DNA extracts, including the sequence of a rickettsial insect endosymbiont, a novel Rickettsia genotype and Rickettsia helvetica. Faecal samples of the pond bat (Myotis dasycneme) were positive for a Neorickettsia sp. and for haemoplasmas of the haemofelis group. In addition, two bird pellets (collected from a Long-eared Owl, Asio otus, and from a Common Kestrel, Falco tinnunculus) contained the DNA of a Rickettsia sp. and Anaplasma phagocytophilum, respectively. In both of these bird pellets the bones of Microtus arvalis were identified. All samples were negative for Borrelia burgdorferi s.l., Francisella tularensis, Coxiella burnetii and Chlamydiales. In conclusion, bats were shown to pass rickettsia and haemoplasma DNA in their faeces. Molecular evidence is provided for the presence of Neorickettsia sp. in bat faeces in Europe. In the evaluated regions bat faeces and owl/kestrel pellets do not appear to pose epidemiological risk from the point of view of F. tularensis, C. burnetii and Chlamydiales. Testing of bird pellets may provide an alternative approach to trapping for assessing the local occurrence of vector-borne bacteria in small mammals.

  1. Integrating molecular mechanisms and clinical evidence in the management of trastuzumab resistant or refractory HER-2⁺ metastatic breast cancer.

    Science.gov (United States)

    Wong, Hilda; Leung, Roland; Kwong, Ava; Chiu, Joanne; Liang, Raymond; Swanton, Charles; Yau, Thomas

    2011-01-01

    Human epidermal growth factor receptor (HER)-2(+) breast cancer is a distinct molecular and clinical entity, the prognosis of which is improved by trastuzumab. However, primary resistance to trastuzumab is observed in >50% of patients with HER-2(+) advanced breast cancer, and the majority of patients who initially respond to treatment eventually develop disease progression. To facilitate crosstrial comparisons and the understanding of resistance mechanisms, we propose a unifying definition of trastuzumab resistance as progression at first radiological reassessment at 8-12 weeks or within 3 months after first-line trastuzumab in the metastatic setting or new recurrences diagnosed during or within 12 months after adjuvant trastuzumab. In contrast, we define trastuzumab-refractory breast cancer as disease progression after two or more lines of trastuzumab-containing regimens that initially achieved disease response or stabilization at first radiological assessment. We review mechanisms of trastuzumab resistance mediated by p95HER-2 overexpression, phosphoinositide 3-kinase pathway activation, and signaling pathway activation driven by HER-3, epidermal growth factor receptor, and insulin-like growth factor 1 receptor. We distinguish in vitro from in vivo evidence, highlighting that most data describing trastuzumab resistance are derived from preclinical studies or small retrospective patient cohorts, and discuss targeted therapeutic approaches to overcome resistance. Prospective analysis through clinical trials with robust tissue collection procedures, prior to and following acquisition of resistance, integrated with next-generation tumor genome sequencing technologies, is identified as a priority area for development. The identification of predictive biomarkers is of paramount importance to optimize health economic costs and enhance stratification of anti-HER-2 targeted therapies.

  2. Low-lying excited states by constrained DFT

    Science.gov (United States)

    Ramos, Pablo; Pavanello, Michele

    2018-04-01

    Exploiting the machinery of Constrained Density Functional Theory (CDFT), we propose a variational method for calculating low-lying excited states of molecular systems. We dub this method eXcited CDFT (XCDFT). Excited states are obtained by self-consistently constraining a user-defined population of electrons, Nc, in the virtual space of a reference set of occupied orbitals. By imposing this population to be Nc = 1.0, we computed the first excited state of 15 molecules from a test set. Our results show that XCDFT achieves an accuracy in the predicted excitation energy only slightly worse than linear-response time-dependent DFT (TDDFT), but without incurring into problems of variational collapse typical of the more commonly adopted ΔSCF method. In addition, we selected a few challenging processes to test the limits of applicability of XCDFT. We find that in contrast to TDDFT, XCDFT is capable of reproducing energy surfaces featuring conical intersections (azobenzene and H3) with correct topology and correct overall energetics also away from the intersection. Venturing to condensed-phase systems, XCDFT reproduces the TDDFT solvatochromic shift of benzaldehyde when it is embedded by a cluster of water molecules. Thus, we find XCDFT to be a competitive method among single-reference methods for computations of excited states in terms of time to solution, rate of convergence, and accuracy of the result.

  3. On Tree-Constrained Matchings and Generalizations

    NARCIS (Netherlands)

    S. Canzar (Stefan); K. Elbassioni; G.W. Klau (Gunnar); J. Mestre

    2011-01-01

    htmlabstractWe consider the following \\textsc{Tree-Constrained Bipartite Matching} problem: Given two rooted trees $T_1=(V_1,E_1)$, $T_2=(V_2,E_2)$ and a weight function $w: V_1\\times V_2 \\mapsto \\mathbb{R}_+$, find a maximum weight matching $\\mathcal{M}$ between nodes of the two trees, such that

  4. Constrained systems described by Nambu mechanics

    International Nuclear Information System (INIS)

    Lassig, C.C.; Joshi, G.C.

    1996-01-01

    Using the framework of Nambu's generalised mechanics, we obtain a new description of constrained Hamiltonian dynamics, involving the introduction of another degree of freedom in phase space, and the necessity of defining the action integral on a world sheet. We also discuss the problem of quantizing Nambu mechanics. (authors). 5 refs

  5. Client's constraining factors to construction project management ...

    African Journals Online (AJOL)

    This study analyzed client's related factors that constrain project management success of public and private sector construction in Nigeria. Issues that concern clients in any project can not be undermined as they are the owners and the initiators of project proposals. It is assumed that success, failure or abandonment of ...

  6. Hyperbolicity and constrained evolution in linearized gravity

    International Nuclear Information System (INIS)

    Matzner, Richard A.

    2005-01-01

    Solving the 4-d Einstein equations as evolution in time requires solving equations of two types: the four elliptic initial data (constraint) equations, followed by the six second order evolution equations. Analytically the constraint equations remain solved under the action of the evolution, and one approach is to simply monitor them (unconstrained evolution). Since computational solution of differential equations introduces almost inevitable errors, it is clearly 'more correct' to introduce a scheme which actively maintains the constraints by solution (constrained evolution). This has shown promise in computational settings, but the analysis of the resulting mixed elliptic hyperbolic method has not been completely carried out. We present such an analysis for one method of constrained evolution, applied to a simple vacuum system, linearized gravitational waves. We begin with a study of the hyperbolicity of the unconstrained Einstein equations. (Because the study of hyperbolicity deals only with the highest derivative order in the equations, linearization loses no essential details.) We then give explicit analytical construction of the effect of initial data setting and constrained evolution for linearized gravitational waves. While this is clearly a toy model with regard to constrained evolution, certain interesting features are found which have relevance to the full nonlinear Einstein equations

  7. A Dynamic Programming Approach to Constrained Portfolios

    DEFF Research Database (Denmark)

    Kraft, Holger; Steffensen, Mogens

    2013-01-01

    This paper studies constrained portfolio problems that may involve constraints on the probability or the expected size of a shortfall of wealth or consumption. Our first contribution is that we solve the problems by dynamic programming, which is in contrast to the existing literature that applies...

  8. A model for optimal constrained adaptive testing

    NARCIS (Netherlands)

    van der Linden, Willem J.; Reese, Lynda M.

    2001-01-01

    A model for constrained computerized adaptive testing is proposed in which the information on the test at the ability estimate is maximized subject to a large variety of possible constraints on the contents of the test. At each item-selection step, a full test is first assembled to have maximum

  9. A model for optimal constrained adaptive testing

    NARCIS (Netherlands)

    van der Linden, Willem J.; Reese, Lynda M.

    1997-01-01

    A model for constrained computerized adaptive testing is proposed in which the information in the test at the ability estimate is maximized subject to a large variety of possible constraints on the contents of the test. At each item-selection step, a full test is first assembled to have maximum

  10. Neutron Powder Diffraction and Constrained Refinement

    DEFF Research Database (Denmark)

    Pawley, G. S.; Mackenzie, Gordon A.; Dietrich, O. W.

    1977-01-01

    The first use of a new program, EDINP, is reported. This program allows the constrained refinement of molecules in a crystal structure with neutron diffraction powder data. The structures of p-C6F4Br2 and p-C6F4I2 are determined by packing considerations and then refined with EDINP. Refinement is...

  11. Terrestrial Sagnac delay constraining modified gravity models

    Science.gov (United States)

    Karimov, R. Kh.; Izmailov, R. N.; Potapov, A. A.; Nandi, K. K.

    2018-04-01

    Modified gravity theories include f(R)-gravity models that are usually constrained by the cosmological evolutionary scenario. However, it has been recently shown that they can also be constrained by the signatures of accretion disk around constant Ricci curvature Kerr-f(R0) stellar sized black holes. Our aim here is to use another experimental fact, viz., the terrestrial Sagnac delay to constrain the parameters of specific f(R)-gravity prescriptions. We shall assume that a Kerr-f(R0) solution asymptotically describes Earth's weak gravity near its surface. In this spacetime, we shall study oppositely directed light beams from source/observer moving on non-geodesic and geodesic circular trajectories and calculate the time gap, when the beams re-unite. We obtain the exact time gap called Sagnac delay in both cases and expand it to show how the flat space value is corrected by the Ricci curvature, the mass and the spin of the gravitating source. Under the assumption that the magnitude of corrections are of the order of residual uncertainties in the delay measurement, we derive the allowed intervals for Ricci curvature. We conclude that the terrestrial Sagnac delay can be used to constrain the parameters of specific f(R) prescriptions. Despite using the weak field gravity near Earth's surface, it turns out that the model parameter ranges still remain the same as those obtained from the strong field accretion disk phenomenon.

  12. Chance constrained uncertain classification via robust optimization

    NARCIS (Netherlands)

    Ben-Tal, A.; Bhadra, S.; Bhattacharayya, C.; Saketha Nat, J.

    2011-01-01

    This paper studies the problem of constructing robust classifiers when the training is plagued with uncertainty. The problem is posed as a Chance-Constrained Program (CCP) which ensures that the uncertain data points are classified correctly with high probability. Unfortunately such a CCP turns out

  13. Integrating job scheduling and constrained network routing

    DEFF Research Database (Denmark)

    Gamst, Mette

    2010-01-01

    This paper examines the NP-hard problem of scheduling jobs on resources such that the overall profit of executed jobs is maximized. Job demand must be sent through a constrained network to the resource before execution can begin. The problem has application in grid computing, where a number...

  14. Neuroevolutionary Constrained Optimization for Content Creation

    DEFF Research Database (Denmark)

    Liapis, Antonios; Yannakakis, Georgios N.; Togelius, Julian

    2011-01-01

    and thruster types and topologies) independently of game physics and steering strategies. According to the proposed framework, the designer picks a set of requirements for the spaceship that a constrained optimizer attempts to satisfy. The constraint satisfaction approach followed is based on neuroevolution...... and survival tasks and are also visually appealing....

  15. Models of Flux Tubes from Constrained Relaxation

    Indian Academy of Sciences (India)

    tribpo

    J. Astrophys. Astr. (2000) 21, 299 302. Models of Flux Tubes from Constrained Relaxation. Α. Mangalam* & V. Krishan†, Indian Institute of Astrophysics, Koramangala,. Bangalore 560 034, India. *e mail: mangalam @ iiap. ernet. in. † e mail: vinod@iiap.ernet.in. Abstract. We study the relaxation of a compressible plasma to ...

  16. A Molecular Genetic Lab to Generate Inclusive and Exclusive Forensic Evidence: Two Suspects, a Victim, and a Bloodstained T-Shirt

    Science.gov (United States)

    Smit, Julie; Heath, Daniel D.; Walter, Ryan P.

    2014-01-01

    Molecular genetic laboratory exercises can be ineffective due the student's lack of connection to the complex and sequential protocols. In this inquiry-based molecular genetic laboratory exercise, we harness students' fascination with human forensics and provide a real-life scenario using biomolecular techniques to identify "whose…

  17. Molecular Epidemiology of P. vivax in Iran: High Diversity and Complex Sub-Structure Using Neutral Markers, but No Evidence of Y976F Mutation at pvmdr1.

    Directory of Open Access Journals (Sweden)

    Yaghoob Hamedi

    Full Text Available Malaria remains endemic at low levels in the south-eastern provinces of Iran bordering Afghanistan and Pakistan, with the majority of cases attributable to P. vivax. The national guidelines recommend chloroquine (CQ as blood-stage treatment for uncomplicated P. vivax, but the large influx of imported cases enhances the risk of introducing CQ resistance (CQR.The genetic diversity at pvmdr1, a putative modulator of CQR, and across nine putatively neutral short tandem repeat (STR markers were assessed in P. vivax clinical isolates collected between April 2007 and January 2013 in Hormozgan Province, south-eastern Iran. One hundred blood samples were collected from patients with microscopy-confirmed P. vivax enrolled at one of five district clinics. In total 73 (73% were autochthonous cases, 23 (23% imported cases from Afghanistan or Pakistan, and 4 (4% with unknown origin. 97% (97/100 isolates carried the F1076L mutation, but none carried the Y976F mutation. STR genotyping was successful in 71 (71% isolates, including 57(57% autochthonous and 11 (11% imported cases. Analysis of population structure revealed 2 major sub-populations, K1 and K2, with further sub-structure within K2. The K1 sub-population had markedly lower diversity than K2 (HE = 0.06 vs HE = 0.82 suggesting that the sub-populations were sustained by distinct reservoirs with differing transmission dynamics, possibly reflecting local versus imported/introduced populations. No notable separation was observed between the local and imported cases although the sample size was limited.The contrasting low versus high diversity in the two sub-populations (K1 and K2 infers that a combination of local transmission and cross-border malaria from higher transmission regions shape the genetic make-up of the P. vivax population in south-eastern Iran. There was no molecular evidence of CQR amongst the local or imported cases, but ongoing clinical surveillance is warranted.

  18. Multifidus Muscle Changes After Back Injury Are Characterized by Structural Remodeling of Muscle, Adipose and Connective Tissue, but Not Muscle Atrophy: Molecular and Morphological Evidence.

    Science.gov (United States)

    Hodges, Paul W; James, Gregory; Blomster, Linda; Hall, Leanne; Schmid, Annina; Shu, Cindy; Little, Chris; Melrose, James

    2015-07-15

    Longitudinal case-controlled animal study. To investigate putative cellular mechanisms to explain structural changes in muscle and adipose and connective tissues of the back muscles after intervertebral disc (IVD) injury. Structural back muscle changes are ubiquitous with back pain/injury and considered relevant for outcome, but their exact nature, time course, and cellular mechanisms remain elusive. We used an animal model that produces phenotypic back muscle changes after IVD injury to study these issues at the cellular/molecular level. Multifidus muscle was harvested from both sides of the spine at L1-L2 and L3-L4 IVDs in 27 castrated male sheep at 3 (n = 10) or 6 (n = 17) months after a surgical anterolateral IVD injury at both levels. Ten control sheep underwent no surgery (3 mo, n = 4; 6 mo, n = 6). Tissue was harvested at L4 for histological analysis of cross-sectional area of muscle and adipose and connective tissue (whole muscle), plus immunohistochemistry to identify proportion and cross-sectional area of individual muscle fiber types in the deepest fascicle. Quantitative polymerase chain reaction measured gene expression of typical cytokines/signaling molecules at L2. Contrary to predictions, there was no multifidus muscle atrophy (whole muscle or individual fiber). There was increased adipose and connective tissue (fibrotic proliferation) cross-sectional area and slow-to-fast muscle fiber transition at 6 but not 3 months. Within the multifidus muscle, increases in the expression of several cytokines (tumor necrosis factor α and interleukin-1β) and molecules that signal trophic/atrophic processes for the 3 tissue types (e.g., growth factor pathway [IGF-1, PI3k, Akt1, mTOR], potent tissue modifiers [calcineurin, PCG-1α, and myostatin]) were present. This study provides cellular evidence that refutes the presence of multifidus muscle atrophy accompanying IVD degeneration at this intermediate time point. Instead, adipose/connective tissue increased in

  19. Self-constrained inversion of potential fields

    Science.gov (United States)

    Paoletti, V.; Ialongo, S.; Florio, G.; Fedi, M.; Cella, F.

    2013-11-01

    We present a potential-field-constrained inversion procedure based on a priori information derived exclusively from the analysis of the gravity and magnetic data (self-constrained inversion). The procedure is designed to be applied to underdetermined problems and involves scenarios where the source distribution can be assumed to be of simple character. To set up effective constraints, we first estimate through the analysis of the gravity or magnetic field some or all of the following source parameters: the source depth-to-the-top, the structural index, the horizontal position of the source body edges and their dip. The second step is incorporating the information related to these constraints in the objective function as depth and spatial weighting functions. We show, through 2-D and 3-D synthetic and real data examples, that potential field-based constraints, for example, structural index, source boundaries and others, are usually enough to obtain substantial improvement in the density and magnetization models.

  20. Cosmogenic photons strongly constrain UHECR source models

    Directory of Open Access Journals (Sweden)

    van Vliet Arjen

    2017-01-01

    Full Text Available With the newest version of our Monte Carlo code for ultra-high-energy cosmic ray (UHECR propagation, CRPropa 3, the flux of neutrinos and photons due to interactions of UHECRs with extragalactic background light can be predicted. Together with the recently updated data for the isotropic diffuse gamma-ray background (IGRB by Fermi LAT, it is now possible to severely constrain UHECR source models. The evolution of the UHECR sources especially plays an important role in the determination of the expected secondary photon spectrum. Pure proton UHECR models are already strongly constrained, primarily by the highest energy bins of Fermi LAT’s IGRB, as long as their number density is not strongly peaked at recent times.

  1. A constrained supersymmetric left-right model

    Energy Technology Data Exchange (ETDEWEB)

    Hirsch, Martin [AHEP Group, Instituto de Física Corpuscular - C.S.I.C./Universitat de València, Edificio de Institutos de Paterna, Apartado 22085, E-46071 València (Spain); Krauss, Manuel E. [Bethe Center for Theoretical Physics & Physikalisches Institut der Universität Bonn, Nussallee 12, 53115 Bonn (Germany); Institut für Theoretische Physik und Astronomie, Universität Würzburg,Emil-Hilb-Weg 22, 97074 Wuerzburg (Germany); Opferkuch, Toby [Bethe Center for Theoretical Physics & Physikalisches Institut der Universität Bonn, Nussallee 12, 53115 Bonn (Germany); Porod, Werner [Institut für Theoretische Physik und Astronomie, Universität Würzburg,Emil-Hilb-Weg 22, 97074 Wuerzburg (Germany); Staub, Florian [Theory Division, CERN,1211 Geneva 23 (Switzerland)

    2016-03-02

    We present a supersymmetric left-right model which predicts gauge coupling unification close to the string scale and extra vector bosons at the TeV scale. The subtleties in constructing a model which is in agreement with the measured quark masses and mixing for such a low left-right breaking scale are discussed. It is shown that in the constrained version of this model radiative breaking of the gauge symmetries is possible and a SM-like Higgs is obtained. Additional CP-even scalars of a similar mass or even much lighter are possible. The expected mass hierarchies for the supersymmetric states differ clearly from those of the constrained MSSM. In particular, the lightest down-type squark, which is a mixture of the sbottom and extra vector-like states, is always lighter than the stop. We also comment on the model’s capability to explain current anomalies observed at the LHC.

  2. Coding for Two Dimensional Constrained Fields

    DEFF Research Database (Denmark)

    Laursen, Torben Vaarbye

    2006-01-01

    a first order model to model higher order constraints by the use of an alphabet extension. We present an iterative method that based on a set of conditional probabilities can help in choosing the large numbers of parameters of the model in order to obtain a stationary model. Explicit results are given...... for the No Isolated Bits constraint. Finally we present a variation of the encoding scheme of bit-stuffing that is applicable to the class of checkerboard constrained fields. It is possible to calculate the entropy of the coding scheme thus obtaining lower bounds on the entropy of the fields considered. These lower...... bounds are very tight for the Run-Length limited fields. Explicit bounds are given for the diamond constrained field as well....

  3. Communication Schemes with Constrained Reordering of Resources

    DEFF Research Database (Denmark)

    Popovski, Petar; Utkovski, Zoran; Trillingsgaard, Kasper Fløe

    2013-01-01

    This paper introduces a communication model inspired by two practical scenarios. The first scenario is related to the concept of protocol coding, where information is encoded in the actions taken by an existing communication protocol. We investigate strategies for protocol coding via combinatorial...... reordering of the labelled user resources (packets, channels) in an existing, primary system. However, the degrees of freedom of the reordering are constrained by the operation of the primary system. The second scenario is related to communication systems with energy harvesting, where the transmitted signals...... are constrained by the energy that is available through the harvesting process. We have introduced a communication model that covers both scenarios and elicits their key feature, namely the constraints of the primary system or the harvesting process. We have shown how to compute the capacity of the channels...

  4. Q-deformed systems and constrained dynamics

    International Nuclear Information System (INIS)

    Shabanov, S.V.

    1993-01-01

    It is shown that quantum theories of the q-deformed harmonic oscillator and one-dimensional free q-particle (a free particle on the 'quantum' line) can be obtained by the canonical quantization of classical Hamiltonian systems with commutative phase-space variables and a non-trivial symplectic structure. In the framework of this approach, classical dynamics of a particle on the q-line coincides with the one of a free particle with friction. It is argued that q-deformed systems can be treated as ordinary mechanical systems with the second-class constraints. In particular, second-class constrained systems corresponding to the q-oscillator and q-particle are given. A possibility of formulating q-deformed systems via gauge theories (first-class constrained systems) is briefly discussed. (orig.)

  5. Online constrained model-based reinforcement learning

    CSIR Research Space (South Africa)

    Van Niekerk, B

    2017-08-01

    Full Text Available Constrained Model-based Reinforcement Learning Benjamin van Niekerk School of Computer Science University of the Witwatersrand South Africa Andreas Damianou∗ Amazon.com Cambridge, UK Benjamin Rosman Council for Scientific and Industrial Research, and School... MULTIPLE SHOOTING Using direct multiple shooting (Bock and Plitt, 1984), problem (1) can be transformed into a structured non- linear program (NLP). First, the time horizon [t0, t0 + T ] is partitioned into N equal subintervals [tk, tk+1] for k = 0...

  6. Constraining supergravity models from gluino production

    International Nuclear Information System (INIS)

    Barbieri, R.; Gamberini, G.; Giudice, G.F.; Ridolfi, G.

    1988-01-01

    The branching ratios for gluino decays g tilde → qanti qΧ, g tilde → gΧ into a stable undetected neutralino are computed as functions of the relevant parameters of the underlying supergravity theory. A simple way of constraining supergravity models from gluino production emerges. The effectiveness of hadronic versus e + e - colliders in the search for supersymmetry can be directly compared. (orig.)

  7. Cosmicflows Constrained Local UniversE Simulations

    Science.gov (United States)

    Sorce, Jenny G.; Gottlöber, Stefan; Yepes, Gustavo; Hoffman, Yehuda; Courtois, Helene M.; Steinmetz, Matthias; Tully, R. Brent; Pomarède, Daniel; Carlesi, Edoardo

    2016-01-01

    This paper combines observational data sets and cosmological simulations to generate realistic numerical replicas of the nearby Universe. The latter are excellent laboratories for studies of the non-linear process of structure formation in our neighbourhood. With measurements of radial peculiar velocities in the local Universe (cosmicflows-2) and a newly developed technique, we produce Constrained Local UniversE Simulations (CLUES). To assess the quality of these constrained simulations, we compare them with random simulations as well as with local observations. The cosmic variance, defined as the mean one-sigma scatter of cell-to-cell comparison between two fields, is significantly smaller for the constrained simulations than for the random simulations. Within the inner part of the box where most of the constraints are, the scatter is smaller by a factor of 2 to 3 on a 5 h-1 Mpc scale with respect to that found for random simulations. This one-sigma scatter obtained when comparing the simulated and the observation-reconstructed velocity fields is only 104 ± 4 km s-1, I.e. the linear theory threshold. These two results demonstrate that these simulations are in agreement with each other and with the observations of our neighbourhood. For the first time, simulations constrained with observational radial peculiar velocities resemble the local Universe up to a distance of 150 h-1 Mpc on a scale of a few tens of megaparsecs. When focusing on the inner part of the box, the resemblance with our cosmic neighbourhood extends to a few megaparsecs (<5 h-1 Mpc). The simulations provide a proper large-scale environment for studies of the formation of nearby objects.

  8. Dynamic Convex Duality in Constrained Utility Maximization

    OpenAIRE

    Li, Yusong; Zheng, Harry

    2016-01-01

    In this paper, we study a constrained utility maximization problem following the convex duality approach. After formulating the primal and dual problems, we construct the necessary and sufficient conditions for both the primal and dual problems in terms of FBSDEs plus additional conditions. Such formulation then allows us to explicitly characterize the primal optimal control as a function of the adjoint process coming from the dual FBSDEs in a dynamic fashion and vice versa. Moreover, we also...

  9. Statistical mechanics of budget-constrained auctions

    OpenAIRE

    Altarelli, F.; Braunstein, A.; Realpe-Gomez, J.; Zecchina, R.

    2009-01-01

    Finding the optimal assignment in budget-constrained auctions is a combinatorial optimization problem with many important applications, a notable example being the sale of advertisement space by search engines (in this context the problem is often referred to as the off-line AdWords problem). Based on the cavity method of statistical mechanics, we introduce a message passing algorithm that is capable of solving efficiently random instances of the problem extracted from a natural distribution,...

  10. Constraining neutron star matter with Quantum Chromodynamics

    CERN Document Server

    Kurkela, Aleksi; Schaffner-Bielich, Jurgen; Vuorinen, Aleksi

    2014-01-01

    In recent years, there have been several successful attempts to constrain the equation of state of neutron star matter using input from low-energy nuclear physics and observational data. We demonstrate that significant further restrictions can be placed by additionally requiring the pressure to approach that of deconfined quark matter at high densities. Remarkably, the new constraints turn out to be highly insensitive to the amount --- or even presence --- of quark matter inside the stars.

  11. The taruca (Hippocamelus antisensis) and the red brocket deer (Mazama americana) as intermediate hosts of Taenia hydatigena in Peru, morphological and molecular evidence.

    Science.gov (United States)

    Gomez-Puerta, Luis A; Pacheco, Joel; Gonzales-Viera, Omar; Lopez-Urbina, Maria T; Gonzalez, Armando E

    2015-09-15

    In the present report metacestodes were collected from the mesentery of a taruca (Hippocamelus antisensis) and from the omentum of a red brocket deer (Mazama americana) in Peru. Various metacestodes parameters, including rostellar hook characteristics, were measured. Molecular analysis was performed to amplify the mitochondrial cytochrome c oxidase subunit 1 gene from metacestode isolates. Metacestodes were identified as T. hydatigena by morphology and molecular methods. This constitutes the first molecular detection of T. hydatigena metacestodes in the taruca and the red brocket deer and demonstrates that these animal species are natural intermediate hosts for this parasite. Copyright © 2015 Elsevier B.V. All rights reserved.

  12. Constraining the mass of the Local Group

    Science.gov (United States)

    Carlesi, Edoardo; Hoffman, Yehuda; Sorce, Jenny G.; Gottlöber, Stefan

    2017-03-01

    The mass of the Local Group (LG) is a crucial parameter for galaxy formation theories. However, its observational determination is challenging - its mass budget is dominated by dark matter that cannot be directly observed. To meet this end, the posterior distributions of the LG and its massive constituents have been constructed by means of constrained and random cosmological simulations. Two priors are assumed - the Λ cold dark matter model that is used to set up the simulations, and an LG model that encodes the observational knowledge of the LG and is used to select LG-like objects from the simulations. The constrained simulations are designed to reproduce the local cosmography as it is imprinted on to the Cosmicflows-2 data base of velocities. Several prescriptions are used to define the LG model, focusing in particular on different recent estimates of the tangential velocity of M31. It is found that (a) different vtan choices affect the peak mass values up to a factor of 2, and change mass ratios of MM31 to MMW by up to 20 per cent; (b) constrained simulations yield more sharply peaked posterior distributions compared with the random ones; (c) LG mass estimates are found to be smaller than those found using the timing argument; (d) preferred Milky Way masses lie in the range of (0.6-0.8) × 1012 M⊙; whereas (e) MM31 is found to vary between (1.0-2.0) × 1012 M⊙, with a strong dependence on the vtan values used.

  13. Molecular evidence for association of chlamydiales bacteria with epitheliocystis in leafy seadragon (Phycodurus eques), silver perch (Bidyanus bidyanus), and barramundi (Lates calcarifer).

    NARCIS (Netherlands)

    Meijer, Adam; Roholl, Paul J M; Ossewaarde, Jacobus M; Jones, Brian; Nowak, Barbara F

    2006-01-01

    Epitheliocystis in leafy seadragon (Phycodurus eques), silver perch (Bidyanus bidyanus), and barramundi (Lates calcarifer), previously associated with chlamydial bacterial infection using ultrastructural analysis, was further investigated by using molecular and immunocytochemical methods.

  14. E-cadherin expression phenotypes associated with molecular subtypes in invasive non-lobular breast cancer: evidence from a retrospective study and meta-analysis.

    Science.gov (United States)

    Liu, Jiang-Bo; Feng, Chen-Yi; Deng, Miao; Ge, Dong-Feng; Liu, De-Chun; Mi, Jian-Qiang; Feng, Xiao-Shan

    2017-08-01

    This retrospective study and meta-analysis was designed to explore the relationship between E-cadherin (E-cad) expression and the molecular subtypes of invasive non-lobular breast cancer, especially in early-stage invasive ductal carcinoma (IDC). A total of 156 post-operative cases of early-stage IDCs were retrospectively collected for the immunohistochemistry (IHC) detection of E-cad expression. The association of E-cad expression with molecular subtypes of early-stage IDCs was analyzed. A literature search was conducted in March 2016 to retrieve publications on E-cad expression in association with molecular subtypes of invasive non-lobular breast cancer, and a meta-analysis was performed to estimate the relational statistics. E-cad was expressed in 82.7% (129/156) of early-stage IDCs. E-cad expression was closely associated with the molecular types of early-stage IDCs (P cancer (TNBC) than in other molecular subtypes (TNBC vs. luminal A: RR = 3.45, 95% CI = 2.79-4.26; TNBC vs. luminal B: RR = 2.41, 95% CI = 1.49-3.90; TNBC vs. HER2-enriched: RR = 1.95, 95% CI = 1.24-3.07). Early-stage IDCs or invasive non-lobular breast cancers with the TNBC molecular phenotype have a higher risk for the loss of E-cad expression than do tumors with non-TNBC molecular phenotypes, suggesting that E-cad expression phenotypes were closely related to molecular subtypes and further studies are needed to clarify the underlying mechanism.

  15. Constrained Unfolding of a Helical Peptide: Implicit versus Explicit Solvents.

    Directory of Open Access Journals (Sweden)

    Hailey R Bureau

    Full Text Available Steered Molecular Dynamics (SMD has been seen to provide the potential of mean force (PMF along a peptide unfolding pathway effectively but at significant computational cost, particularly in all-atom solvents. Adaptive steered molecular dynamics (ASMD has been seen to provide a significant computational advantage by limiting the spread of the trajectories in a staged approach. The contraction of the trajectories at the end of each stage can be performed by taking a structure whose nonequilibrium work is closest to the Jarzynski average (in naive ASMD or by relaxing the trajectories under a no-work condition (in full-relaxation ASMD--namely, FR-ASMD. Both approaches have been used to determine the energetics and hydrogen-bonding structure along the pathway for unfolding of a benchmark peptide initially constrained as an α-helix in a water environment. The energetics are quite different to those in vacuum, but are found to be similar between implicit and explicit solvents. Surprisingly, the hydrogen-bonding pathways are also similar in the implicit and explicit solvents despite the fact that the solvent contact plays an important role in opening the helix.

  16. Molecular sources of residual cardiovascular risk, clinical signals, and innovative solutions: relationship with subclinical disease, undertreatment, and poor adherence: implications of new evidence upon optimizing cardiovascular patient outcomes

    Directory of Open Access Journals (Sweden)

    Kones R

    2013-10-01

    Full Text Available Richard KonesCardiometabolic Research Institute, Houston, TX, USAAbstract: Residual risk, the ongoing appreciable risk of major cardiovascular events (MCVE in statin-treated patients who have achieved evidence-based lipid goals, remains a concern among cardiologists. Factors that contribute to this continuing risk are atherogenic non-low-density lipoprotein (LDL particles and atherogenic processes unrelated to LDL cholesterol, including other risk factors, the inherent properties of statin drugs, and patient characteristics, ie, genetics and behaviors. In addition, providers, health care systems, the community, public policies, and the environment play a role. Major statin studies suggest an average 28% reduction in LDL cholesterol and a 31% reduction in relative risk, leaving a residual risk of about 69%. Incomplete reductions in risk, and failure to improve conditions that create risk, may result in ongoing progression of atherosclerosis, with new and recurring lesions in original and distant culprit sites, remodeling, arrhythmias, rehospitalizations, invasive procedures, and terminal disability. As a result, identification of additional agents to reduce residual risk, particularly administered together with statin drugs, has been an ongoing quest. The current model of atherosclerosis involves many steps during which disease may progress independently of guideline-defined elevations in LDL cholesterol. Differences in genetic responsiveness to statin therapy, differences in ability of the endothelium to regenerate and repair, and differences in susceptibility to nonlipid risk factors, such as tobacco smoking, hypertension, and molecular changes associated with obesity and diabetes, may all create residual risk. A large number of inflammatory and metabolic processes may also provide eventual therapeutic targets to lower residual risk. Classically, epidemiologic and other evidence suggested that raising high-density lipoprotein (HDL cholesterol

  17. Microscopic Mechanism of Doping-Induced Kinetically Constrained Crystallization in Phase-Change Materials.

    Science.gov (United States)

    Lee, Tae Hoon; Loke, Desmond; Elliott, Stephen R

    2015-10-07

    A comprehensive microscopic mechanism of doping-induced kinetically constrained crystallization in phase-change materials is provided by investigating structural and dynamical dopant characteristics via ab initio molecular dynamics simulations. The information gained from this study may provide a basis for a fast screening of dopant species for electronic memory devices, or for understanding the general physics involved in the crystallization of doped glasses. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Predicting sintering deformation of ceramic film constrained by rigid substrate using anisotropic constitutive law

    International Nuclear Information System (INIS)

    Li Fan; Pan Jingzhe; Guillon, Olivier; Cocks, Alan

    2010-01-01

    Sintering of ceramic films on a solid substrate is an important technology for fabricating a range of products, including solid oxide fuel cells, micro-electronic PZT films and protective coatings. There is clear evidence that the constrained sintering process is anisotropic in nature. This paper presents a study of the constrained sintering deformation using an anisotropic constitutive law. The state of the material is described using the sintering strains rather than the relative density. In the limiting case of free sintering, the constitutive law reduces to a conventional isotropic constitutive law. The anisotropic constitutive law is used to calculate sintering deformation of a constrained film bonded to a rigid substrate and the compressive stress required in a sinter-forging experiment to achieve zero lateral shrinkage. The results are compared with experimental data in the literature. It is shown that the anisotropic constitutive law can capture the behaviour of the materials observed in the sintering experiments.

  19. Cascading Constrained 2-D Arrays using Periodic Merging Arrays

    DEFF Research Database (Denmark)

    Forchhammer, Søren; Laursen, Torben Vaarby

    2003-01-01

    We consider a method for designing 2-D constrained codes by cascading finite width arrays using predefined finite width periodic merging arrays. This provides a constructive lower bound on the capacity of the 2-D constrained code. Examples include symmetric RLL and density constrained codes...

  20. Operator approach to solutions of the constrained BKP hierarchy

    International Nuclear Information System (INIS)

    Shen, Hsin-Fu; Lee, Niann-Chern; Tu, Ming-Hsien

    2011-01-01

    The operator formalism to the vector k-constrained BKP hierarchy is presented. We solve the Hirota bilinear equations of the vector k-constrained BKP hierarchy via the method of neutral free fermion. In particular, by choosing suitable group element of O(∞), we construct rational and soliton solutions of the vector k-constrained BKP hierarchy.

  1. Evidence-Based Diagnostic Algorithm for Glioma: Analysis of the Results of Pathology Panel Review and Molecular Parameters of EORTC 26951 and 26882 Trials.

    Science.gov (United States)

    Kros, Johan M; Huizer, Karin; Hernández-Laín, Aurelio; Marucci, Gianluca; Michotte, Alex; Pollo, Bianca; Rushing, Elisabeth J; Ribalta, Teresa; French, Pim; Jaminé, David; Bekka, Nawal; Lacombe, Denis; van den Bent, Martin J; Gorlia, Thierry

    2015-06-10

    With the rapid discovery of prognostic and predictive molecular parameters for glioma, the status of histopathology in the diagnostic process should be scrutinized. Our project aimed to construct a diagnostic algorithm for gliomas based on molecular and histologic parameters with independent prognostic values. The pathology slides of 636 patients with gliomas who had been included in EORTC 26951 and 26882 trials were reviewed using virtual microscopy by a panel of six neuropathologists who independently scored 18 histologic features and provided an overall diagnosis. The molecular data for IDH1, 1p/19q loss, EGFR amplification, loss of chromosome 10 and chromosome arm 10q, gain of chromosome 7, and hypermethylation of the promoter of MGMT were available for some of the cases. The slides were divided in discovery (n = 426) and validation sets (n = 210). The diagnostic algorithm resulting from analysis of the discovery set was validated in the latter. In 66% of cases, consensus of overall diagnosis was present. A diagnostic algorithm consisting of two molecular markers and one consensus histologic feature was created by conditional inference tree analysis. The order of prognostic significance was: 1p/19q loss, EGFR amplification, and astrocytic morphology, which resulted in the identification of four diagnostic nodes. Validation of the nodes in the validation set confirmed the prognostic value (P diagnostic algorithm for anaplastic glioma based on multivariable analysis of consensus histopathology and molecular parameters. © 2015 by American Society of Clinical Oncology.

  2. Molecular biology of lung cancer: Diagnosis and management of lung cancer, 3rd ed: American College of Chest Physicians evidence-based clinical practice guidelines.

    Science.gov (United States)

    Nana-Sinkam, Serge Patrick; Powell, Charles A

    2013-05-01

    Based on recent bench and clinical research, the treatment of lung cancer has been refined, with treatments allocated according to histology and specific molecular features. For example, targeting mutations such as epidermal growth factor receptor (EGFR) with tyrosine kinase inhibitors has been particularly successful as a treatment modality, demonstrating response rates in selected patients with adenocarcinoma tumors harboring EGFR mutations that are significantly higher than those for conventional chemotherapy. However, the development of new targeted therapies is, in part, highly dependent on an improved understanding of the molecular underpinnings of tumor initiation and progression, knowledge of the role of molecular aberrations in disease progression, and the development of highly reproducible platforms for high-throughput biomarker discovery and testing. In this article, we review clinically relevant research directed toward understanding the biology of lung cancer. The clinical purposes of this research are (1) to identify susceptibility variants and field molecular alterations that will promote the early detection of tumors and (2) to identify tumor molecular alterations that serve as therapeutic targets, prognostic biomarkers, or predictors of tumor response. We focus on research developments in the understanding of lung cancer somatic DNA mutations, chromosomal aberrations, epigenetics, and the tumor microenvironment, and how they can advance diagnostics and therapeutics.

  3. Feature and Pose Constrained Visual Aided Inertial Navigation for Computationally Constrained Aerial Vehicles

    Science.gov (United States)

    Williams, Brian; Hudson, Nicolas; Tweddle, Brent; Brockers, Roland; Matthies, Larry

    2011-01-01

    A Feature and Pose Constrained Extended Kalman Filter (FPC-EKF) is developed for highly dynamic computationally constrained micro aerial vehicles. Vehicle localization is achieved using only a low performance inertial measurement unit and a single camera. The FPC-EKF framework augments the vehicle's state with both previous vehicle poses and critical environmental features, including vertical edges. This filter framework efficiently incorporates measurements from hundreds of opportunistic visual features to constrain the motion estimate, while allowing navigating and sustained tracking with respect to a few persistent features. In addition, vertical features in the environment are opportunistically used to provide global attitude references. Accurate pose estimation is demonstrated on a sequence including fast traversing, where visual features enter and exit the field-of-view quickly, as well as hover and ingress maneuvers where drift free navigation is achieved with respect to the environment.

  4. Constraining the sources and cycling of dissolved organic carbon in a large oligotrophic lake using radiocarbon analyses

    Science.gov (United States)

    Zigah, Prosper K.; Minor, Elizabeth C.; McNichol, Ann P.; Xu, Li; Werne, Josef P.

    2017-07-01

    We measured the concentrations and isotopic compositions of solid phase extracted (SPE) dissolved organic carbon (DOC) and high molecular weight (HMW) DOC and their constituent organic components in order to better constrain the sources and cycling of DOC in a large oligotrophic lacustrine system (Lake Superior, North America). SPE DOC constituted a significant proportion (41-71%) of the lake DOC relative to HMW DOC (10-13%). Substantial contribution of 14C-depleted components to both SPE DOC (Δ14C = 25-43‰) and HMW DOC (Δ14C = 22-32‰) was evident during spring mixing, and depressed their radiocarbon values relative to the lake dissolved inorganic carbon (DIC; Δ14C ∼ 59‰). There was preferential removal of 14C-depleted (older) and thermally recalcitrant components from HMW DOC and SPE DOC in the summer. Contemporary photoautotrophic addition to HMW DOC was observed during summer stratification in contrast to SPE DOC, which decreased in concentration during stratification. Serial thermal oxidation radiocarbon analysis revealed a diversity of sources (both contemporary and older) within the SPE DOC, and also showed distinct components within the HMW DOC. The thermally labile components of HMW DOC were 14C-enriched and are attributed to heteropolysaccharides (HPS), peptides/amide and amino sugars (AMS) relative to the thermally recalcitrant components reflecting the presence of older material, perhaps carboxylic-rich alicyclic molecules (CRAM). The solvent extractable lipid-like fraction of HMW DOC was very 14C-depleted (as old as 1270-2320 14C years) relative to the carbohydrate-like and protein-like substances isolated by acid hydrolysis of HMW DOC. Our data constrain relative influences of contemporary DOC and old DOC, and DOC cycling in a modern freshwater ecosystem.

  5. Incomplete Dirac reduction of constrained Hamiltonian systems

    Energy Technology Data Exchange (ETDEWEB)

    Chandre, C., E-mail: chandre@cpt.univ-mrs.fr

    2015-10-15

    First-class constraints constitute a potential obstacle to the computation of a Poisson bracket in Dirac’s theory of constrained Hamiltonian systems. Using the pseudoinverse instead of the inverse of the matrix defined by the Poisson brackets between the constraints, we show that a Dirac–Poisson bracket can be constructed, even if it corresponds to an incomplete reduction of the original Hamiltonian system. The uniqueness of Dirac brackets is discussed. The relevance of this procedure for infinite dimensional Hamiltonian systems is exemplified.

  6. Capturing Hotspots For Constrained Indoor Movement

    DEFF Research Database (Denmark)

    Ahmed, Tanvir; Pedersen, Torben Bach; Lu, Hua

    2013-01-01

    Finding the hotspots in large indoor spaces is very important for getting overloaded locations, security, crowd management, indoor navigation and guidance. The tracking data coming from indoor tracking are huge in volume and not readily available for finding hotspots. This paper presents a graph......-based model for constrained indoor movement that can map the tracking records into mapping records which represent the entry and exit times of an object in a particular location. Then it discusses the hotspots extraction technique from the mapping records....

  7. Quantization of soluble classical constrained systems

    International Nuclear Information System (INIS)

    Belhadi, Z.; Menas, F.; Bérard, A.; Mohrbach, H.

    2014-01-01

    The derivation of the brackets among coordinates and momenta for classical constrained systems is a necessary step toward their quantization. Here we present a new approach for the determination of the classical brackets which does neither require Dirac’s formalism nor the symplectic method of Faddeev and Jackiw. This approach is based on the computation of the brackets between the constants of integration of the exact solutions of the equations of motion. From them all brackets of the dynamical variables of the system can be deduced in a straightforward way

  8. Quantization of soluble classical constrained systems

    Energy Technology Data Exchange (ETDEWEB)

    Belhadi, Z. [Laboratoire de physique et chimie quantique, Faculté des sciences, Université Mouloud Mammeri, BP 17, 15000 Tizi Ouzou (Algeria); Laboratoire de physique théorique, Faculté des sciences exactes, Université de Bejaia, 06000 Bejaia (Algeria); Menas, F. [Laboratoire de physique et chimie quantique, Faculté des sciences, Université Mouloud Mammeri, BP 17, 15000 Tizi Ouzou (Algeria); Ecole Nationale Préparatoire aux Etudes d’ingéniorat, Laboratoire de physique, RN 5 Rouiba, Alger (Algeria); Bérard, A. [Equipe BioPhysStat, Laboratoire LCP-A2MC, ICPMB, IF CNRS No 2843, Université de Lorraine, 1 Bd Arago, 57078 Metz Cedex (France); Mohrbach, H., E-mail: herve.mohrbach@univ-lorraine.fr [Equipe BioPhysStat, Laboratoire LCP-A2MC, ICPMB, IF CNRS No 2843, Université de Lorraine, 1 Bd Arago, 57078 Metz Cedex (France)

    2014-12-15

    The derivation of the brackets among coordinates and momenta for classical constrained systems is a necessary step toward their quantization. Here we present a new approach for the determination of the classical brackets which does neither require Dirac’s formalism nor the symplectic method of Faddeev and Jackiw. This approach is based on the computation of the brackets between the constants of integration of the exact solutions of the equations of motion. From them all brackets of the dynamical variables of the system can be deduced in a straightforward way.

  9. Molecular evidence of cryptic diversity in Paracaryophyllaeus (Cestoda: Caryophyllidea), parasites of loaches (Cobitidae) in Eurasia, including description of P. vladkae n. sp

    Czech Academy of Sciences Publication Activity Database

    Scholz, Tomáš; Oros, M.; Bazsalovicsová, E.; Brabec, Jan; Waeschenbach, A.; Xi, B. W.; Aydoğdu, A.; Besprozvannykh, V. V.; Shimazu, T.; Kraľová-Hromadová, I.; Littlewood, D. T. J.

    2014-01-01

    Roč. 63, č. 6 (2014), s. 841-850 ISSN 1383-5769 R&D Projects: GA ČR GBP505/12/G112 Institutional support: RVO:60077344 Keywords : Taxonomy * Molecular phylogeny * Caryophyllidea * Species complex * Freshwater fishes * Eurasia Subject RIV: EG - Zoology Impact factor: 1.859, year: 2014

  10. A centennial record of anthropogenic impacts and extreme weather events in southwestern Taiwan: Evidence from sedimentary molecular markers in coastal margin

    Energy Technology Data Exchange (ETDEWEB)

    Kuo, Li-Jung; Lee, Chon-Lin; Louchouarn, Patrick; Huh, Chih-An; Liu, James T.; Chen, Jian-Cheng; Lee, Kun-Je

    2014-09-15

    A 100-year history of human and natural disturbances in southwestern Taiwan was reconstructed using a suite of molecular markers in four dated sediment cores from the upper slope region off the Gaoping River mouth. Trends in polycyclic aromatic hydrocarbons (PAHs) tracked Taiwan's industrialization/urbanization starting in the 1970s, and the enactment of environmental regulatory policies thereafter.

  11. Molecular evidence for the polyphyletic origin of low pH adaptation in the genus .i.Klebsormidium./i. (Klebsormidiophyceae, Streptophyta)

    Czech Academy of Sciences Publication Activity Database

    Škaloud, P.; Lukešová, Alena; Malavasi, V.; Ryšánek, D.; Hrčková, Kristýna; Rindi, F.

    2014-01-01

    Roč. 147, č. 3 (2014), s. 333-345 ISSN 2032-3913 Institutional support: RVO:60077344 Keywords : acid mine drainage * acid ophilic algae * acid otolerant algae * extremophiles * molecular systematics * taxonomy Subject RIV: EF - Botanics Impact factor: 0.986, year: 2014

  12. Controls on the molecular and carbon isotopic composition of organic matter deposited in a Kimmeridgian euxinic shelf sea: Evidence for preservation of carbohydrates through sulfurisation

    NARCIS (Netherlands)

    Sinninghe Damsté, J.S.; Kaam-Peters, H.M.E. van; Schouten, S.; Koster, J.

    1998-01-01

    Thirteen samples from the Kimmeridge Clay Formation (KCF) in Dorset, covering all different lithologies, were studied using bulk and molecular geochemical and microscopical techniques. Our data show that the positive correlation between TOC and 13CTOC reported for shales (Huc et al., 1992) also

  13. Morphological, molecular and biological evidence reveal two cryptic species in Mecinus janthinus Germar (Coleoptera, Curculionidae), a successful biological control agent of Dalmatian toadflax, Linaria dalmatica (Lamiales, Plantaginaceae)

    Science.gov (United States)

    Ivo Tosevski; Roberto Caldara; Jelena Jovic; Gerardo Hernandez-Vera; Cosimo Baviera; Andre Gassmann; Brent C. Emerson

    2011-01-01

    A combined morphological, molecular and biological study shows that the weevil species presently named Mecinus janthinus is actually composed of two different cryptic species: M. janthinus Germar, 1821 and M. janthiniformis Tosevski & Caldara sp.n. These species are morphologically distinguishable from each other by a few very subtle morphological characters. On...

  14. Molecular tools for bathing water assessment in Europe: Balancing social science research with a rapidly developing environmental science evidence-base.

    Science.gov (United States)

    Oliver, David M; Hanley, Nick D; van Niekerk, Melanie; Kay, David; Heathwaite, A Louise; Rabinovici, Sharyl J M; Kinzelman, Julie L; Fleming, Lora E; Porter, Jonathan; Shaikh, Sabina; Fish, Rob; Chilton, Sue; Hewitt, Julie; Connolly, Elaine; Cummins, Andy; Glenk, Klaus; McPhail, Calum; McRory, Eric; McVittie, Alistair; Giles, Amanna; Roberts, Suzanne; Simpson, Katherine; Tinch, Dugald; Thairs, Ted; Avery, Lisa M; Vinten, Andy J A; Watts, Bill D; Quilliam, Richard S

    2016-02-01

    The use of molecular tools, principally qPCR, versus traditional culture-based methods for quantifying microbial parameters (e.g., Fecal Indicator Organisms) in bathing waters generates considerable ongoing debate at the science-policy interface. Advances in science have allowed the development and application of molecular biological methods for rapid (~2 h) quantification of microbial pollution in bathing and recreational waters. In contrast, culture-based methods can take between 18 and 96 h for sample processing. Thus, molecular tools offer an opportunity to provide a more meaningful statement of microbial risk to water-users by providing near-real-time information enabling potentially more informed decision-making with regard to water-based activities. However, complementary studies concerning the potential costs and benefits of adopting rapid methods as a regulatory tool are in short supply. We report on findings from an international Working Group that examined the breadth of social impacts, challenges, and research opportunities associated with the application of molecular tools to bathing water regulations.

  15. Pole shifting with constrained output feedback

    International Nuclear Information System (INIS)

    Hamel, D.; Mensah, S.; Boisvert, J.

    1984-03-01

    The concept of pole placement plays an important role in linear, multi-variable, control theory. It has received much attention since its introduction, and several pole shifting algorithms are now available. This work presents a new method which allows practical and engineering constraints such as gain limitation and controller structure to be introduced right into the pole shifting design strategy. This is achieved by formulating the pole placement problem as a constrained optimization problem. Explicit constraints (controller structure and gain limits) are defined to identify an admissible region for the feedback gain matrix. The desired pole configuration is translated into an appropriate cost function which must be closed-loop minimized. The resulting constrained optimization problem can thus be solved with optimization algorithms. The method has been implemented as an algorithmic interactive module in a computer-aided control system design package, MVPACK. The application of the method is illustrated to design controllers for an aircraft and an evaporator. The results illustrate the importance of controller structure on overall performance of a control system

  16. Changes in epistemic frameworks: Random or constrained?

    Directory of Open Access Journals (Sweden)

    Ananka Loubser

    2012-11-01

    Full Text Available Since the emergence of a solid anti-positivist approach in the philosophy of science, an important question has been to understand how and why epistemic frameworks change in time, are modified or even substituted. In contemporary philosophy of science three main approaches to framework-change were detected in the humanist tradition:1. In both the pre-theoretical and theoretical domains changes occur according to a rather constrained, predictable or even pre-determined pattern (e.g. Holton.2. Changes occur in a way that is more random or unpredictable and free from constraints (e.g. Kuhn, Feyerabend, Rorty, Lyotard.3. Between these approaches, a middle position can be found, attempting some kind of synthesis (e.g. Popper, Lakatos.Because this situation calls for clarification and systematisation, this article in fact tried to achieve more clarity on how changes in pre-scientific frameworks occur, as well as provided transcendental criticism of the above positions. This article suggested that the above-mentioned positions are not fully satisfactory, as change and constancy are not sufficiently integrated. An alternative model was suggested in which changes in epistemic frameworks occur according to a pattern, neither completely random nor rigidly constrained, which results in change being dynamic but not arbitrary. This alternative model is integral, rather than dialectical and therefore does not correspond to position three. 

  17. Fringe instability in constrained soft elastic layers.

    Science.gov (United States)

    Lin, Shaoting; Cohen, Tal; Zhang, Teng; Yuk, Hyunwoo; Abeyaratne, Rohan; Zhao, Xuanhe

    2016-11-04

    Soft elastic layers with top and bottom surfaces adhered to rigid bodies are abundant in biological organisms and engineering applications. As the rigid bodies are pulled apart, the stressed layer can exhibit various modes of mechanical instabilities. In cases where the layer's thickness is much smaller than its length and width, the dominant modes that have been studied are the cavitation, interfacial and fingering instabilities. Here we report a new mode of instability which emerges if the thickness of the constrained elastic layer is comparable to or smaller than its width. In this case, the middle portion along the layer's thickness elongates nearly uniformly while the constrained fringe portions of the layer deform nonuniformly. When the applied stretch reaches a critical value, the exposed free surfaces of the fringe portions begin to undulate periodically without debonding from the rigid bodies, giving the fringe instability. We use experiments, theory and numerical simulations to quantitatively explain the fringe instability and derive scaling laws for its critical stress, critical strain and wavelength. We show that in a force controlled setting the elastic fingering instability is associated with a snap-through buckling that does not exist for the fringe instability. The discovery of the fringe instability will not only advance the understanding of mechanical instabilities in soft materials but also have implications for biological and engineered adhesives and joints.

  18. Natural selection constrains neutral diversity across a wide range of species.

    Science.gov (United States)

    Corbett-Detig, Russell B; Hartl, Daniel L; Sackton, Timothy B

    2015-04-01

    The neutral theory of molecular evolution predicts that the amount of neutral polymorphisms within a species will increase proportionally with the census population size (Nc). However, this prediction has not been borne out in practice: while the range of Nc spans many orders of magnitude, levels of genetic diversity within species fall in a comparatively narrow range. Although theoretical arguments have invoked the increased efficacy of natural selection in larger populations to explain this discrepancy, few direct empirical tests of this hypothesis have been conducted. In this work, we provide a direct test of this hypothesis using population genomic data from a wide range of taxonomically diverse species. To do this, we relied on the fact that the impact of natural selection on linked neutral diversity depends on the local recombinational environment. In regions of relatively low recombination, selected variants affect more neutral sites through linkage, and the resulting correlation between recombination and polymorphism allows a quantitative assessment of the magnitude of the impact of selection on linked neutral diversity. By comparing whole genome polymorphism data and genetic maps using a coalescent modeling framework, we estimate the degree to which natural selection reduces linked neutral diversity for 40 species of obligately sexual eukaryotes. We then show that the magnitude of the impact of natural selection is positively correlated with Nc, based on body size and species range as proxies for census population size. These results demonstrate that natural selection removes more variation at linked neutral sites in species with large Nc than those with small Nc and provides direct empirical evidence that natural selection constrains levels of neutral genetic diversity across many species. This implies that natural selection may provide an explanation for this longstanding paradox of population genetics.

  19. Constraining the break of spatial diffeomorphism invariance with Planck data

    Science.gov (United States)

    Graef, L. L.; Benetti, M.; Alcaniz, J. S.

    2017-07-01

    The current most accepted paradigm for the early universe cosmology, the inflationary scenario, shows a good agreement with the recent Cosmic Microwave Background (CMB) and polarization data. However, when the inflation consistency relation is relaxed, these observational data exclude a larger range of red tensor tilt values, prevailing the blue ones which are not predicted by the minimal inflationary models. Recently, it has been shown that the assumption of spatial diffeomorphism invariance breaking (SDB) in the context of an effective field theory of inflation leads to interesting observational consequences. Among them, the possibility of generating a blue tensor spectrum, which can recover the specific consistency relation of the String Gas Cosmology, for a certain choice of parameters. We use the most recent CMB data to constrain the SDB model and test its observational viability through a Bayesian analysis assuming as reference an extended ΛCDM+tensor perturbation model, which considers a power-law tensor spectrum parametrized in terms of the tensor-to-scalar ratio, r, and the tensor spectral index, nt. If the inflation consistency relation is imposed, r=-8 nt, we obtain a strong evidence in favor of the reference model whereas if such relation is relaxed, a weak evidence in favor of the model with diffeomorphism breaking is found. We also use the same CMB data set to make an observational comparison between the SDB model, standard inflation and String Gas Cosmology.

  20. Constraining the break of spatial diffeomorphism invariance with Planck data

    Energy Technology Data Exchange (ETDEWEB)

    Graef, L.L.; Benetti, M.; Alcaniz, J.S., E-mail: leilagraef@on.br, E-mail: micolbenetti@on.br, E-mail: alcaniz@on.br [Departamento de Astronomia, Observatório Nacional, R. Gen. José Cristino, 77—São Cristóvão, 20921-400, Rio de Janeiro, RJ (Brazil)

    2017-07-01

    The current most accepted paradigm for the early universe cosmology, the inflationary scenario, shows a good agreement with the recent Cosmic Microwave Background (CMB) and polarization data. However, when the inflation consistency relation is relaxed, these observational data exclude a larger range of red tensor tilt values, prevailing the blue ones which are not predicted by the minimal inflationary models. Recently, it has been shown that the assumption of spatial diffeomorphism invariance breaking (SDB) in the context of an effective field theory of inflation leads to interesting observational consequences. Among them, the possibility of generating a blue tensor spectrum, which can recover the specific consistency relation of the String Gas Cosmology, for a certain choice of parameters. We use the most recent CMB data to constrain the SDB model and test its observational viability through a Bayesian analysis assuming as reference an extended ΛCDM+tensor perturbation model, which considers a power-law tensor spectrum parametrized in terms of the tensor-to-scalar ratio, r , and the tensor spectral index, n {sub t} . If the inflation consistency relation is imposed, r =−8 n {sub t} , we obtain a strong evidence in favor of the reference model whereas if such relation is relaxed, a weak evidence in favor of the model with diffeomorphism breaking is found. We also use the same CMB data set to make an observational comparison between the SDB model, standard inflation and String Gas Cosmology.

  1. New morphological and molecular evidence confirm the presence of the Norwegian skate Dipturus nidarosiensis (Storm, 1881) in the Mediterranean Sea and extend its distribution to the western basin

    OpenAIRE

    RAMÍREZ-AMARO, S.; ORDINES, F.; ÁNGEL PUERTO, M.; GARCÍA, C.; RAMON, C.; TERRASA, B.; MASSUTÍ, E.

    2017-01-01

    The present study confirms the presence of the Norwegian skate Dipturus nidarosiensis (Storm, 1881) in the Mediterranean Sea, by means of morphological traits and molecular markers providing the first record of this species in the Alboran Sea. Cannas et al. (2010) reported D. nidarosiensis for the first time in the Mediterranean from specimens captured in the central western basin, but Ebert & Stehmann (2013) and Stehmann et al. (2015) considered these records "likely refer to the smaller mor...

  2. MOLECULAR CLOUDS IN THE TRIFID NEBULA M20: POSSIBLE EVIDENCE FOR A CLOUD-CLOUD COLLISION IN TRIGGERING THE FORMATION OF THE FIRST GENERATION STARS

    International Nuclear Information System (INIS)

    Torii, K.; Enokiya, R.; Sano, H.; Yoshiike, S.; Hanaoka, N.; Ohama, A.; Furukawa, N.; Dawson, J. R.; Moribe, N.; Oishi, K.; Nakashima, Y.; Okuda, T.; Yamamoto, H.; Kawamura, A.; Mizuno, N.; Onishi, T.; Fukui, Y.; Maezawa, H.; Mizuno, A.

    2011-01-01

    A large-scale study of the molecular clouds toward the Trifid Nebula, M20, has been made in the J = 2-1 and J = 1-0 transitions of 12 CO and 13 CO. M20 is ionized predominantly by an O7.5 star HD164492. The study has revealed that there are two molecular components at separate velocities peaked toward the center of M20 and that their temperatures-30-50 K as derived by a large velocity gradient analysis-are significantly higher than the 10 K of their surroundings. We identify the two clouds as the parent clouds of the first generation stars in M20. The mass of each cloud is estimated to be ∼10 3 M sun and their separation velocity is ∼8 km s -1 over ∼1-2 pc. We find that the total mass of stars and molecular gas in M20 is less than ∼3.2 x 10 3 M sun , which is too small by an order of magnitude to gravitationally bind the system. We argue that the formation of the first generation stars, including the main ionizing O7.5 star, was triggered by the collision between the two clouds in a short timescale of ∼1 Myr, a second example alongside Westerlund 2, where a super-star cluster may have been formed due to cloud-cloud collision triggering.

  3. Molecular nanomagnets

    CERN Document Server

    Gatteschi, Dante; Villain, Jacques

    2006-01-01

    Nanomagnetism is a rapidly expanding area of research which appears to be able to provide novel applications. Magnetic molecules are at the very bottom of the possible size of nanomagnets and they provide a unique opportunity to observe the coexistence of classical and quantum properties. The discovery in the early 90's that a cluster comprising twelve manganese ions shows hysteresis of molecular origin, and later proved evidence of quantum effects, opened a new research area whichis still flourishing through the collaboration of chemists and physicists. This book is the first attempt to cover

  4. Scheduling of resource-constrained projects

    CERN Document Server

    Klein, Robert

    2000-01-01

    Project management has become a widespread instrument enabling organizations to efficiently master the challenges of steadily shortening product life cycles, global markets and decreasing profit margins. With projects increasing in size and complexity, their planning and control represents one of the most crucial management tasks. This is especially true for scheduling, which is concerned with establishing execution dates for the sub-activities to be performed in order to complete the project. The ability to manage projects where resources must be allocated between concurrent projects or even sub-activities of a single project requires the use of commercial project management software packages. However, the results yielded by the solution procedures included are often rather unsatisfactory. Scheduling of Resource-Constrained Projects develops more efficient procedures, which can easily be integrated into software packages by incorporated programming languages, and thus should be of great interest for practiti...

  5. Constrained mathematics evaluation in probabilistic logic analysis

    Energy Technology Data Exchange (ETDEWEB)

    Arlin Cooper, J

    1998-06-01

    A challenging problem in mathematically processing uncertain operands is that constraints inherent in the problem definition can require computations that are difficult to implement. Examples of possible constraints are that the sum of the probabilities of partitioned possible outcomes must be one, and repeated appearances of the same variable must all have the identical value. The latter, called the 'repeated variable problem', will be addressed in this paper in order to show how interval-based probabilistic evaluation of Boolean logic expressions, such as those describing the outcomes of fault trees and event trees, can be facilitated in a way that can be readily implemented in software. We will illustrate techniques that can be used to transform complex constrained problems into trivial problems in most tree logic expressions, and into tractable problems in most other cases.

  6. Constraining dark sectors with monojets and dijets

    International Nuclear Information System (INIS)

    Chala, Mikael; Kahlhoefer, Felix; Nardini, Germano; Schmidt-Hoberg, Kai; McCullough, Matthew

    2015-03-01

    We consider dark sector particles (DSPs) that obtain sizeable interactions with Standard Model fermions from a new mediator. While these particles can avoid observation in direct detection experiments, they are strongly constrained by LHC measurements. We demonstrate that there is an important complementarity between searches for DSP production and searches for the mediator itself, in particular bounds on (broad) dijet resonances. This observation is crucial not only in the case where the DSP is all of the dark matter but whenever - precisely due to its sizeable interactions with the visible sector - the DSP annihilates away so efficiently that it only forms a dark matter subcomponent. To highlight the different roles of DSP direct detection and LHC monojet and dijet searches, as well as perturbativity constraints, we first analyse the exemplary case of an axial-vector mediator and then generalise our results. We find important implications for the interpretation of LHC dark matter searches in terms of simplified models.

  7. Constrained KP models as integrable matrix hierarchies

    International Nuclear Information System (INIS)

    Aratyn, H.; Ferreira, L.A.; Gomes, J.F.; Zimerman, A.H.

    1997-01-01

    We formulate the constrained KP hierarchy (denoted by cKP K+1,M ) as an affine [cflx sl](M+K+1) matrix integrable hierarchy generalizing the Drinfeld endash Sokolov hierarchy. Using an algebraic approach, including the graded structure of the generalized Drinfeld endash Sokolov hierarchy, we are able to find several new universal results valid for the cKP hierarchy. In particular, our method yields a closed expression for the second bracket obtained through Dirac reduction of any untwisted affine Kac endash Moody current algebra. An explicit example is given for the case [cflx sl](M+K+1), for which a closed expression for the general recursion operator is also obtained. We show how isospectral flows are characterized and grouped according to the semisimple non-regular element E of sl(M+K+1) and the content of the center of the kernel of E. copyright 1997 American Institute of Physics

  8. Quantum cosmology of classically constrained gravity

    International Nuclear Information System (INIS)

    Gabadadze, Gregory; Shang Yanwen

    2006-01-01

    In [G. Gabadadze, Y. Shang, hep-th/0506040] we discussed a classically constrained model of gravity. This theory contains known solutions of General Relativity (GR), and admits solutions that are absent in GR. Here we study cosmological implications of some of these new solutions. We show that a spatially-flat de Sitter universe can be created from 'nothing'. This universe has boundaries, and its total energy equals to zero. Although the probability to create such a universe is exponentially suppressed, it favors initial conditions suitable for inflation. Then we discuss a finite-energy solution with a nonzero cosmological constant and zero space-time curvature. There is no tunneling suppression to fluctuate into this state. We show that for a positive cosmological constant this state is unstable-it can rapidly transition to a de Sitter universe providing a new unsuppressed channel for inflation. For a negative cosmological constant the space-time flat solutions is stable.

  9. Multiple Clustering Views via Constrained Projections

    DEFF Research Database (Denmark)

    Dang, Xuan-Hong; Assent, Ira; Bailey, James

    2012-01-01

    Clustering, the grouping of data based on mutual similarity, is often used as one of principal tools to analyze and understand data. Unfortunately, most conventional techniques aim at finding only a single clustering over the data. For many practical applications, especially those being described...... in high dimensional data, it is common to see that the data can be grouped into different yet meaningful ways. This gives rise to the recently emerging research area of discovering alternative clusterings. In this preliminary work, we propose a novel framework to generate multiple clustering views....... The framework relies on a constrained data projection approach by which we ensure that a novel alternative clustering being found is not only qualitatively strong but also distinctively different from a reference clustering solution. We demonstrate the potential of the proposed framework using both synthetic...

  10. Shape space exploration of constrained meshes

    KAUST Repository

    Yang, Yongliang

    2011-12-12

    We present a general computational framework to locally characterize any shape space of meshes implicitly prescribed by a collection of non-linear constraints. We computationally access such manifolds, typically of high dimension and co-dimension, through first and second order approximants, namely tangent spaces and quadratically parameterized osculant surfaces. Exploration and navigation of desirable subspaces of the shape space with regard to application specific quality measures are enabled using approximants that are intrinsic to the underlying manifold and directly computable in the parameter space of the osculant surface. We demonstrate our framework on shape spaces of planar quad (PQ) meshes, where each mesh face is constrained to be (nearly) planar, and circular meshes, where each face has a circumcircle. We evaluate our framework for navigation and design exploration on a variety of inputs, while keeping context specific properties such as fairness, proximity to a reference surface, etc. © 2011 ACM.

  11. Shape space exploration of constrained meshes

    KAUST Repository

    Yang, Yongliang; Yang, Yijun; Pottmann, Helmut; Mitra, Niloy J.

    2011-01-01

    We present a general computational framework to locally characterize any shape space of meshes implicitly prescribed by a collection of non-linear constraints. We computationally access such manifolds, typically of high dimension and co-dimension, through first and second order approximants, namely tangent spaces and quadratically parameterized osculant surfaces. Exploration and navigation of desirable subspaces of the shape space with regard to application specific quality measures are enabled using approximants that are intrinsic to the underlying manifold and directly computable in the parameter space of the osculant surface. We demonstrate our framework on shape spaces of planar quad (PQ) meshes, where each mesh face is constrained to be (nearly) planar, and circular meshes, where each face has a circumcircle. We evaluate our framework for navigation and design exploration on a variety of inputs, while keeping context specific properties such as fairness, proximity to a reference surface, etc. © 2011 ACM.

  12. Constrained vertebrate evolution by pleiotropic genes.

    Science.gov (United States)

    Hu, Haiyang; Uesaka, Masahiro; Guo, Song; Shimai, Kotaro; Lu, Tsai-Ming; Li, Fang; Fujimoto, Satoko; Ishikawa, Masato; Liu, Shiping; Sasagawa, Yohei; Zhang, Guojie; Kuratani, Shigeru; Yu, Jr-Kai; Kusakabe, Takehiro G; Khaitovich, Philipp; Irie, Naoki

    2017-11-01

    Despite morphological diversification of chordates over 550 million years of evolution, their shared basic anatomical pattern (or 'bodyplan') remains conserved by unknown mechanisms. The developmental hourglass model attributes this to phylum-wide conserved, constrained organogenesis stages that pattern the bodyplan (the phylotype hypothesis); however, there has been no quantitative testing of this idea with a phylum-wide comparison of species. Here, based on data from early-to-late embryonic transcriptomes collected from eight chordates, we suggest that the phylotype hypothesis would be better applied to vertebrates than chordates. Furthermore, we found that vertebrates' conserved mid-embryonic developmental programmes are intensively recruited to other developmental processes, and the degree of the recruitment positively correlates with their evolutionary conservation and essentiality for normal development. Thus, we propose that the intensively recruited genetic system during vertebrates' organogenesis period imposed constraints on its diversification through pleiotropic constraints, which ultimately led to the common anatomical pattern observed in vertebrates.

  13. Constraining Lyman continuum escape using Machine Learning

    Science.gov (United States)

    Giri, Sambit K.; Zackrisson, Erik; Binggeli, Christian; Pelckmans, Kristiaan; Cubo, Rubén; Mellema, Garrelt

    2018-05-01

    The James Webb Space Telescope (JWST) will observe the rest-frame ultraviolet/optical spectra of galaxies from the epoch of reionization (EoR) in unprecedented detail. While escaping into the intergalactic medium, hydrogen-ionizing (Lyman continuum; LyC) photons from the galaxies will contribute to the bluer end of the UV slope and make nebular emission lines less prominent. We present a method to constrain leakage of the LyC photons using the spectra of high redshift (z >~ 6) galaxies. We simulate JWST/NIRSpec observations of galaxies at z =6-9 by matching the fluxes of galaxies observed in the Frontier Fields observations of galaxy cluster MACS-J0416. Our method predicts the escape fraction fesc with a mean absolute error Δfesc ~ 0.14. The method also predicts the redshifts of the galaxies with an error .

  14. Statistical mechanics of budget-constrained auctions

    International Nuclear Information System (INIS)

    Altarelli, F; Braunstein, A; Realpe-Gomez, J; Zecchina, R

    2009-01-01

    Finding the optimal assignment in budget-constrained auctions is a combinatorial optimization problem with many important applications, a notable example being in the sale of advertisement space by search engines (in this context the problem is often referred to as the off-line AdWords problem). On the basis of the cavity method of statistical mechanics, we introduce a message-passing algorithm that is capable of solving efficiently random instances of the problem extracted from a natural distribution, and we derive from its properties the phase diagram of the problem. As the control parameter (average value of the budgets) is varied, we find two phase transitions delimiting a region in which long-range correlations arise

  15. Constraining Dark Sectors with Monojets and Dijets

    CERN Document Server

    Chala, Mikael; McCullough, Matthew; Nardini, Germano; Schmidt-Hoberg, Kai

    2015-01-01

    We consider dark sector particles (DSPs) that obtain sizeable interactions with Standard Model fermions from a new mediator. While these particles can avoid observation in direct detection experiments, they are strongly constrained by LHC measurements. We demonstrate that there is an important complementarity between searches for DSP production and searches for the mediator itself, in particular bounds on (broad) dijet resonances. This observation is crucial not only in the case where the DSP is all of the dark matter but whenever - precisely due to its sizeable interactions with the visible sector - the DSP annihilates away so efficiently that it only forms a dark matter subcomponent. To highlight the different roles of DSP direct detection and LHC monojet and dijet searches, as well as perturbativity constraints, we first analyse the exemplary case of an axial-vector mediator and then generalise our results. We find important implications for the interpretation of LHC dark matter searches in terms of simpli...

  16. Statistical mechanics of budget-constrained auctions

    Science.gov (United States)

    Altarelli, F.; Braunstein, A.; Realpe-Gomez, J.; Zecchina, R.

    2009-07-01

    Finding the optimal assignment in budget-constrained auctions is a combinatorial optimization problem with many important applications, a notable example being in the sale of advertisement space by search engines (in this context the problem is often referred to as the off-line AdWords problem). On the basis of the cavity method of statistical mechanics, we introduce a message-passing algorithm that is capable of solving efficiently random instances of the problem extracted from a natural distribution, and we derive from its properties the phase diagram of the problem. As the control parameter (average value of the budgets) is varied, we find two phase transitions delimiting a region in which long-range correlations arise.

  17. Constrained least squares regularization in PET

    International Nuclear Information System (INIS)

    Choudhury, K.R.; O'Sullivan, F.O.

    1996-01-01

    Standard reconstruction methods used in tomography produce images with undesirable negative artifacts in background and in areas of high local contrast. While sophisticated statistical reconstruction methods can be devised to correct for these artifacts, their computational implementation is excessive for routine operational use. This work describes a technique for rapid computation of approximate constrained least squares regularization estimates. The unique feature of the approach is that it involves no iterative projection or backprojection steps. This contrasts with the familiar computationally intensive algorithms based on algebraic reconstruction (ART) or expectation-maximization (EM) methods. Experimentation with the new approach for deconvolution and mixture analysis shows that the root mean square error quality of estimators based on the proposed algorithm matches and usually dominates that of more elaborate maximum likelihood, at a fraction of the computational effort

  18. Constraining dark sectors with monojets and dijets

    Energy Technology Data Exchange (ETDEWEB)

    Chala, Mikael; Kahlhoefer, Felix; Nardini, Germano; Schmidt-Hoberg, Kai [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); McCullough, Matthew [European Organization for Nuclear Research (CERN), Geneva (Switzerland). Theory Div.

    2015-03-15

    We consider dark sector particles (DSPs) that obtain sizeable interactions with Standard Model fermions from a new mediator. While these particles can avoid observation in direct detection experiments, they are strongly constrained by LHC measurements. We demonstrate that there is an important complementarity between searches for DSP production and searches for the mediator itself, in particular bounds on (broad) dijet resonances. This observation is crucial not only in the case where the DSP is all of the dark matter but whenever - precisely due to its sizeable interactions with the visible sector - the DSP annihilates away so efficiently that it only forms a dark matter subcomponent. To highlight the different roles of DSP direct detection and LHC monojet and dijet searches, as well as perturbativity constraints, we first analyse the exemplary case of an axial-vector mediator and then generalise our results. We find important implications for the interpretation of LHC dark matter searches in terms of simplified models.

  19. Hard exclusive meson production to constrain GPDs

    Energy Technology Data Exchange (ETDEWEB)

    Wolbeek, Johannes ter; Fischer, Horst; Gorzellik, Matthias; Gross, Arne; Joerg, Philipp; Koenigsmann, Kay; Malm, Pasquale; Regali, Christopher; Schmidt, Katharina; Sirtl, Stefan; Szameitat, Tobias [Physikalisches Institut, Albert-Ludwigs-Universitaet Freiburg, Freiburg im Breisgau (Germany); Collaboration: COMPASS Collaboration

    2014-07-01

    The concept of Generalized Parton Distributions (GPDs) combines the two-dimensional spatial information, given by form factors, with the longitudinal momentum information from the PDFs. Thus, GPDs provide a three-dimensional 'tomography' of the nucleon. Furthermore, according to Ji's sum rule, the GPDs H and E enable access to the total angular momenta of quarks, antiquarks and gluons. While H can be approached using electroproduction cross section, hard exclusive meson production off a transversely polarized target can help to constrain the GPD E. At the COMPASS experiment at CERN, two periods of data taking were performed in 2007 and 2010, using a longitudinally polarized 160 GeV/c muon beam and a transversely polarized NH{sub 3} target. This talk introduces the data analysis of the process μ + p → μ' + p' + V, and recent results are presented.

  20. Molecular Gas in a Submillimeter Galaxy at z = 4.5: Evidence for a Major Merger at 1 Billion Years after the Big Bang

    Science.gov (United States)

    Schinnerer, E.; Carilli, C. L.; Capak, P.; Martinez-Sansigre, A.; Scoville, N. Z.; Smolčić, V.; Taniguchi, Y.; Yun, M. S.; Bertoldi, F.; Le Fevre, O.; de Ravel, L.

    2008-12-01

    We report the detection of CO molecular line emission in the z = 4.5 millimeter-detected galaxy COSMOS J100054+023436 (hereafter J1000+0234) using the IRAM Plateau de Bure interferometer (PdBI) and NRAO's Very Large Array (VLA). The 12CO(4-3) line as observed with PdBI has a full line width of ~1000 km s-1, an integrated line flux of 0.66 Jy km s-1, and a CO luminosity of 3.2 × 1010 L⊙. Comparison to the 3.3 σ detection of the CO(2-1) line emission with the VLA suggests that the molecular gas is likely thermalized to the J = 4-3 transition level. The corresponding molecular gas mass is 2.6 × 1010 M⊙ assuming an ULIRG-like conversion factor. From the spatial offset of the red- and blueshifted line peaks and the line width a dynamical mass of 1.1 × 1011 M⊙ is estimated assuming a merging scenario. The molecular gas distribution coincides with the rest-frame optical and radio position of the object while being offset by 0.5'' from the previously detected Lyα emission. J1000+0234 exhibits very typical properties for lower redshift (z ~ 2) submillimeter galaxies (SMGs) and thus is very likely one of the long sought after high-redshift (z > 4) objects of this population. The large CO(4-3) line width taken together with its highly disturbed rest-frame UV geometry suggest an ongoing major merger about a billion years after the big bang. Given its large star formation rate (SFR) of >1000 M⊙ yr-1 and molecular gas content this object could be the precursor of a "red and dead" elliptical observed at a redshift of z = 2. Based on observations carried out with the IRAM Plateau de Bure Interferometer. IRAM is supported by INSU/CNRS (France), MPG (Germany), and IGN (Spain).

  1. Fast optimization of statistical potentials for structurally constrained phylogenetic models

    Directory of Open Access Journals (Sweden)

    Rodrigue Nicolas

    2009-09-01

    Full Text Available Abstract Background Statistical approaches for protein design are relevant in the field of molecular evolutionary studies. In recent years, new, so-called structurally constrained (SC models of protein-coding sequence evolution have been proposed, which use statistical potentials to assess sequence-structure compatibility. In a previous work, we defined a statistical framework for optimizing knowledge-based potentials especially suited to SC models. Our method used the maximum likelihood principle and provided what we call the joint potentials. However, the method required numerical estimations by the use of computationally heavy Markov Chain Monte Carlo sampling algorithms. Results Here, we develop an alternative optimization procedure, based on a leave-one-out argument coupled to fast gradient descent algorithms. We assess that the leave-one-out potential yields very similar results to the joint approach developed previously, both in terms of the resulting potential parameters, and by Bayes factor evaluation in a phylogenetic context. On the other hand, the leave-one-out approach results in a considerable computational benefit (up to a 1,000 fold decrease in computational time for the optimization procedure. Conclusion Due to its computational speed, the optimization method we propose offers an attractive alternative for the design and empirical evaluation of alternative forms of potentials, using large data sets and high-dimensional parameterizations.

  2. Constrained optimization via simulation models for new product innovation

    Science.gov (United States)

    Pujowidianto, Nugroho A.

    2017-11-01

    We consider the problem of constrained optimization where the decision makers aim to optimize the primary performance measure while constraining the secondary performance measures. This paper provides a brief overview of stochastically constrained optimization via discrete event simulation. Most review papers tend to be methodology-based. This review attempts to be problem-based as decision makers may have already decided on the problem formulation. We consider constrained optimization models as there are usually constraints on secondary performance measures as trade-off in new product development. It starts by laying out different possible methods and the reasons using constrained optimization via simulation models. It is then followed by the review of different simulation optimization approach to address constrained optimization depending on the number of decision variables, the type of constraints, and the risk preferences of the decision makers in handling uncertainties.

  3. Molecular gas in the H II-region complex RCW 166: Possible evidence for an early phase of cloud-cloud collision prior to the bubble formation

    Science.gov (United States)

    Ohama, Akio; Kohno, Mikito; Fujita, Shinji; Tsutsumi, Daichi; Hattori, Yusuke; Torii, Kazufumi; Nishimura, Atsushi; Sano, Hidetoshi; Yamamoto, Hiroaki; Tachihara, Kengo; Fukui, Yasuo

    2018-05-01

    Young H II regions are an important site for the study of O star formation based on distributions of ionized and molecular gas. We reveal that two molecular clouds at ˜48 km s-1 and ˜53 km s-1 are associated with the H II regions G018.149-00.283 in RCW 166 by using the JCMT CO High-Resolution Survey (COHRS) of the 12CO(J = 3-2) emission. G018.149-00.283 comprises a bright ring at 8 μm and an extended H II region inside the ring. The ˜48 km s-1 cloud delineates the ring, and the ˜53 km s-1 cloud is located within the ring, indicating a complementary distribution between the two molecular components. We propose a hypothesis that high-mass stars within G018.149-00.283 were formed by triggering during cloud-cloud collision at a projected velocity separation of ˜5 km s-1. We argue that G018.149-00.283 is in an early evolutionary stage, ˜0.1 Myr after the collision according to the scheme detailed by Habe and Ohta (1992, PASJ, 44, 203), which will be followed by a bubble formation stage like RCW 120. We also suggest that nearby H II regions N21 and N22 are candidates for bubbles possibly formed by cloud-cloud collision. Inoue and Fukui (2013, ApJ, 774, L31) showed that the interface gas becomes highly turbulent and realizes a high-mass accretion rate of 10-3-10-4 M⊙ yr-1 by magnetohydrodynamical numerical simulations, which offers an explanation of the O-star formation. The fairly high frequency of cloud-cloud collision in RCW 166 is probably due to the high cloud density in this part of the Scutum arm.

  4. Molecular clouds in the NGC 6334 and NGC 6357 region: Evidence for a 100 pc-scale cloud-cloud collision triggering the Galactic mini-starbursts

    Science.gov (United States)

    Fukui, Yasuo; Kohno, Mikito; Yokoyama, Keiko; Torii, Kazufumi; Hattori, Yusuke; Sano, Hidetoshi; Nishimura, Atsushi; Ohama, Akio; Yamamoto, Hiroaki; Tachihara, Kengo

    2018-05-01

    We carried out new CO (J = 1-0, 2-1, and 3-2) observations with NANTEN2 and ASTE in the region of the twin Galactic mini-starbursts NGC 6334 and NGC 6357. We detected two velocity molecular components of 12 km s-1 velocity separation, which is continuous over 3° along the plane. In NGC 6334 the two components show similar two-peaked intensity distributions toward the young H II regions and are linked by a bridge feature. In NGC 6357 we found spatially complementary distribution between the two velocity components as well as a bridge feature in velocity. Based on these results we hypothesize that the two clouds in the two regions collided with each other in the past few Myr and triggered the formation of the starbursts over ˜ 100 pc. We suggest that the formation of the starbursts happened toward the collisional region of extent ˜ 10 pc with initial high molecular column densities. For NGC 6334 we present a scenario which includes spatial variation of the colliding epoch due to non-uniform cloud separation. The scenario possibly explains the apparent age differences among the young O stars in NGC 6334, which range from 104 yr to 106 yr; the latest collision happened within 105 yr toward the youngest stars in NGC 6334 I(N) and I which exhibit molecular outflows without H II regions. For NGC 6357 the O stars were formed a few Myr ago, and the cloud dispersal by the O stars is significant. We conclude that cloud-cloud collision offers a possible explanation of the mini-starburst over a 100 pc scale.

  5. Molecular insights into human monoamine oxidase (MAO) inhibition by 1,4-naphthoquinone: evidences for menadione (vitamin K3) acting as a competitive and reversible inhibitor of MAO.

    Science.gov (United States)

    Coelho Cerqueira, Eduardo; Netz, Paulo Augusto; Diniz, Cristiane; Petry do Canto, Vanessa; Follmer, Cristian

    2011-12-15

    Monoamine oxidase (MAO) catalyzes the oxidative deamination of biogenic and exogenous amines and its inhibitors have therapeutic value for several conditions including affective disorders, stroke, neurodegenerative diseases and aging. The discovery of 2,3,6-trimethyl-1,4-naphthoquinone (TMN) as a nonselective and reversible inhibitor of MAO, has suggested 1,4-naphthoquinone (1,4-NQ) as a potential scaffold for designing new MAO inhibitors. Combining molecular modeling tools and biochemical assays we evaluate the kinetic and molecular details of the inhibition of human MAO by 1,4-NQ, comparing it with TMN and menadione. Menadione (2-methyl-1,4-naphthoquinone) is a multitarget drug that acts as a precursor of vitamin K and an inducer of mitochondrial permeability transition. Herein we show that MAO-B was inhibited competitively by 1,4-NQ (K(i)=1.4 μM) whereas MAO-A was inhibited by non-competitive mechanism (K(i)=7.7 μM). Contrasting with TMN and 1,4-NQ, menadione exhibited a 60-fold selectivity for MAO-B (K(i)=0.4 μM) in comparison with MAO-A (K(i)=26 μM), which makes it as selective as rasagiline. Fluorescence and molecular modeling data indicated that these inhibitors interact with the flavin moiety at the active site of the enzyme. Additionally, docking studies suggest the phenyl side groups of Tyr407 and Tyr444 (for MAO-A) or Tyr398 and Tyr435 (for MAO-B) play an important role in the interaction of the enzyme with 1,4-NQ scaffold through forces of dispersion as verified for menadione, TMN and 1,4-NQ. Taken together, our findings reveal the molecular details of MAO inhibition by 1,4-NQ scaffold and show for the first time that menadione acts as a competitive and reversible inhibitor of human MAO. Copyright © 2011 Elsevier Ltd. All rights reserved.

  6. Molecular evidence of malaria and zoonotic diseases among rapid diagnostic test-negative febrile patients in low-transmission season, Mali

    DEFF Research Database (Denmark)

    Touré, Mahamoudou; Petersen, Pelle T; Bathily, Sidy N'd

    2017-01-01

    From November to December 2012 in Sélingué-Mali, blood samples from 88 febrile patients who tested negative by malaria Paracheck (®) rapid diagnostic tests (RDTs) were used to assess the presence of sub-RDT Plasmodium falciparum as well as Borrelia, Coxiella burnetii, and Babesia applying molecular...... tools. Plasmodium sp. was present among 57 (60.2%) of the 88 malaria RDT-negative patients, whereas the prevalence of Borrelia, C. burnetii, and Babesia were 3.4% (N = 3), 1.1% (N = 1), and 0.0%, respectively. The additional diagnostic use of polymerase chain reaction (PCR) identified a high proportion...

  7. Magnetohydrodynamic Models of Molecular Tornadoes

    Science.gov (United States)

    Au, Kelvin; Fiege, Jason D.

    2017-07-01

    Recent observations near the Galactic Center (GC) have found several molecular filaments displaying striking helically wound morphology that are collectively known as molecular tornadoes. We investigate the equilibrium structure of these molecular tornadoes by formulating a magnetohydrodynamic model of a rotating, helically magnetized filament. A special analytical solution is derived where centrifugal forces balance exactly with toroidal magnetic stress. From the physics of torsional Alfvén waves we derive a constraint that links the toroidal flux-to-mass ratio and the pitch angle of the helical field to the rotation laws, which we find to be an important component in describing the molecular tornado structure. The models are compared to the Ostriker solution for isothermal, nonmagnetic, nonrotating filaments. We find that neither the analytic model nor the Alfvén wave model suffer from the unphysical density inversions noted by other authors. A Monte Carlo exploration of our parameter space is constrained by observational measurements of the Pigtail Molecular Cloud, the Double Helix Nebula, and the GC Molecular Tornado. Observable properties such as the velocity dispersion, filament radius, linear mass, and surface pressure can be used to derive three dimensionless constraints for our dimensionless models of these three objects. A virial analysis of these constrained models is studied for these three molecular tornadoes. We find that self-gravity is relatively unimportant, whereas magnetic fields and external pressure play a dominant role in the confinement and equilibrium radial structure of these objects.

  8. Magnetohydrodynamic Models of Molecular Tornadoes

    Energy Technology Data Exchange (ETDEWEB)

    Au, Kelvin; Fiege, Jason D., E-mail: fiege@physics.umanitoba.ca [Department of Physics and Astronomy, University of Manitoba Winnipeg, MB R3T 2N2 (Canada)

    2017-07-10

    Recent observations near the Galactic Center (GC) have found several molecular filaments displaying striking helically wound morphology that are collectively known as molecular tornadoes. We investigate the equilibrium structure of these molecular tornadoes by formulating a magnetohydrodynamic model of a rotating, helically magnetized filament. A special analytical solution is derived where centrifugal forces balance exactly with toroidal magnetic stress. From the physics of torsional Alfvén waves we derive a constraint that links the toroidal flux-to-mass ratio and the pitch angle of the helical field to the rotation laws, which we find to be an important component in describing the molecular tornado structure. The models are compared to the Ostriker solution for isothermal, nonmagnetic, nonrotating filaments. We find that neither the analytic model nor the Alfvén wave model suffer from the unphysical density inversions noted by other authors. A Monte Carlo exploration of our parameter space is constrained by observational measurements of the Pigtail Molecular Cloud, the Double Helix Nebula, and the GC Molecular Tornado. Observable properties such as the velocity dispersion, filament radius, linear mass, and surface pressure can be used to derive three dimensionless constraints for our dimensionless models of these three objects. A virial analysis of these constrained models is studied for these three molecular tornadoes. We find that self-gravity is relatively unimportant, whereas magnetic fields and external pressure play a dominant role in the confinement and equilibrium radial structure of these objects.

  9. Molecular clouds toward the super star cluster NGC 3603; possible evidence for a cloud-cloud collision in triggering the cluster formation

    Energy Technology Data Exchange (ETDEWEB)

    Fukui, Y.; Ohama, A.; Hanaoka, N.; Furukawa, N.; Torii, K.; Hasegawa, K.; Fukuda, T.; Soga, S.; Moribe, N.; Kuroda, Y.; Hayakawa, T.; Kuwahara, T.; Yamamoto, H.; Okuda, T. [Department of Astrophysics, Nagoya University, Chikusa-ku, Nagoya 464-8602 (Japan); Dawson, J. R. [School of Mathematics and Physics, University of Tasmania, Sandy Bay Campus, Churchill Avenue, Sandy Bay, TAS 7005 (Australia); Mizuno, N.; Kawamura, A. [National Astronomical Observatory of Japan, Mitaka, Tokyo 181-8588 (Japan); Onishi, T.; Maezawa, H. [Department of Astrophysics, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Sakai, Osaka 599-8531 (Japan); Mizuno, A., E-mail: fukui@a.phys.nagoya-u.ac.jp [Solar-terrestrial Environment Laboratory, Nagoya University, Chikusa-ku, Nagoya 464-8601 (Japan)

    2014-01-01

    We present new large field observations of molecular clouds with NANTEN2 toward the super star cluster NGC 3603 in the transitions {sup 12}CO(J = 2-1, J = 1-0) and {sup 13}CO(J = 2-1, J = 1-0). We suggest that two molecular clouds at 13 km s{sup –1} and 28 km s{sup –1} are associated with NGC 3603 as evidenced by higher temperatures toward the H II region, as well as morphological correspondence. The mass of the clouds is too small to gravitationally bind them, given their relative motion of ∼20 km s{sup –1}. We suggest that the two clouds collided with each other 1 Myr ago to trigger the formation of the super star cluster. This scenario is able to explain the origin of the highest mass stellar population in the cluster, which is as young as 1 Myr and is segregated within the central sub-pc of the cluster. This is the second super star cluster along with Westerlund 2 where formation may have been triggered by a cloud-cloud collision.

  10. Evidence for the molecular-scale origin of the suppression of physical ageing in confined polymer: fluorescence and dielectric spectroscopy studies of polymer-silica nanocomposites

    International Nuclear Information System (INIS)

    Priestley, Rodney D; Rittigstein, Perla; Broadbelt, Linda J; Fukao, Koji; Torkelson, John M

    2007-01-01

    Fluorescence spectroscopy was used to characterize the rate of physical ageing at room temperature in nanocomposites of silica (10-15 nm diameter) nanoparticles in poly(methyl methacrylate) (PMMA). The physical ageing rate was reduced by more than a factor of 20 in 0.4 vol% silica-PMMA nanocomposites relative to neat PMMA. The molecular-scale origin of this nearly complete arresting of physical ageing was investigated with dielectric spectroscopy. The strength of the β relaxation process was reduced by nearly 50% in the nanocomposite relative to neat PMMA. This reduced strength of the β process results from dipoles (ester groups) having hindered motions or being virtually immobile on the timescale being probed at a frequency of 100 Hz. This hindered mobility results from hydrogen bonding between PMMA ester side groups and hydroxyl units on the surface of the silica nanoparticles. In contrast, no reduction in physical ageing rate was observed upon addition of silica to polystyrene, which cannot form hydrogen bonds with the silica surfaces. Thus, the molecular origin of the suppressed physical ageing in silica-PMMA nanocomposites is the interfacial hydrogen bonding, which leads to a major reduction in the strength of the β process, i.e., the β process is largely responsible for the observed physical ageing

  11. Molecular systematics of the freshwater stingrays (myliobatiformes: potamotrygonidae) of the Amazon, Orinoco, Magdalena, Esequibo, Caribbean, and Maracaibo basins (Colombia - Venezuela): evidence from three mitochondrial genes.

    Science.gov (United States)

    Garcia, David Alejandro; Lasso, Carlos Andres; Morales, Monica; Caballero, Susana Josefina

    2016-11-01

    Lack of adequate information about the taxonomic and evolutionary relationships, ecology, biology, and distribution of several species belonging to the family Potamotrygonidae makes these species vulnerable to anthropic activities, including commercial overexploitation for the ornamental fish market. The aim of this study was to investigate the systematic relationships among genera and species belonging to this family by analyses of three mitochondrial gene regions. Samples were collected from the main river basins in Colombia and Venezuela for four genera and seven species of the family, as well as for what appear to be unidentified species. Three mitochondrial molecular markers COI, Cytb, and ATP6 were amplified and sequenced. Maximum likelihood and Bayesian inference analysis were performed to obtain topologies for each marker and for a concatenated dataset including the three genes. Small dataset may compromise some methods estimations of sequence divergence in the ATP6 marker. Monophyly of the four genera in Potamotrygonidae was confirmed and phylogenetic relationships among members of the Potamotrygon genus were not clearly resolved. However, results obtained with the molecular marker Cytb appear to offer a good starting point to differentiate among genera and species as a tool that could be used for barcoding. The application of this gene as a barcode could be applied for management and regulation of extraction practices for these genera. Sequencing complete mitochondrial genomes would be the next step for testing evolutionary hypothesis among these genera. Population structure analyses should be undertaken for Paratrygon, Potamotrygon magdalenae and motoro.

  12. GAKG-RGEKG an Epitope That Provokes Immune Cross-Reactivity between Prevotella sp. and Human Collagen: Evidence of Molecular Mimicry in Chronic Periodontitis

    Directory of Open Access Journals (Sweden)

    Gustavo Alberto Obando-Pereda

    2016-01-01

    Full Text Available Periodontal disease afflicts 20% of world population. This process usually occurs in the form of being lethargic and chronic, and consequently this disease is known as chronic process. All chronic diseases constantly cause activation of the immune system, and therefore the presentation of microbial peptides which are presented to lymphocytes by professional antigen presenting cells can present microbial peptides very similar to important structures of human economy causing autoimmune diseases, process known as molecular mimicry. Thus, the aim of this study was to verify the presence of molecular mimicry phenomenon between periodontopathogens and human proteins. Blasting microbes of Socransky periodontal complexes against human collagen were performed and then the proteins with similarities were modelled and were screened in the MHI binding virtual methods. The epitopes selected were produced and plasma of chronic periodontal volunteers was obtained and a dot immunobinding assay was performed. Hypothetical protein of Prevotella sp. and human collagen epitopes with high similarities were positive for dot immunobinding assay. With this result it can be suggested that the mimicry phenomena can occur on periodontal disease.

  13. Proteomic and transcriptomic analysis of Arabidopsis seeds: molecular evidence for successive processing of seed proteins and its implication in the stress response to sulfur nutrition.

    Science.gov (United States)

    Higashi, Yasuhiro; Hirai, Masami Yokota; Fujiwara, Toru; Naito, Satoshi; Noji, Masaaki; Saito, Kazuki

    2006-11-01

    Seed storage proteins are synthesized as sources of carbon, nitrogen and sulfur for the next generation of plants. Their composition changes according to nutritional conditions. Here, we report the precise molecular identification of seed proteins by proteomic analysis of wild-type Arabidopsis thaliana and methionine-over-accumulating mutant mto1-1 plants. The identities of 50 protein spots were determined in the protein extract of mature Arabidopsis seeds by two-dimensional (2D) gel electrophoresis and subsequent mass spectrometric analysis. Of these protein spots, 42 were identified as derived from 12S globulins or 2S albumins. These results indicate that approximately 84% of protein species in Arabidopsis seeds are derived from a few genes coding for 12S globulins and 2S albumins. Extensive mass spectrometric analysis of the 42 spots revealed that successive C-terminal degradation occurred on the 12S globulins. The feasibility of this C-terminal processing was rationalized by molecular modeling of the three-dimensional structure of 12S globulins. The C-terminal degradation at glutamic acid residues of the 12S globulin subunits was repressed under sulfur-deficient conditions. Transcriptome analysis was combined with proteomic analysis to elucidate the mechanism of changes in seed protein composition in response to sulfur deficiency. The results suggest that seed storage proteins in Arabidopsis undergo multi-layer regulation, with emphasis on post-translational modifications that enable the plant to respond to sulfur deficiency.

  14. Reflected stochastic differential equation models for constrained animal movement

    Science.gov (United States)

    Hanks, Ephraim M.; Johnson, Devin S.; Hooten, Mevin B.

    2017-01-01

    Movement for many animal species is constrained in space by barriers such as rivers, shorelines, or impassable cliffs. We develop an approach for modeling animal movement constrained in space by considering a class of constrained stochastic processes, reflected stochastic differential equations. Our approach generalizes existing methods for modeling unconstrained animal movement. We present methods for simulation and inference based on augmenting the constrained movement path with a latent unconstrained path and illustrate this augmentation with a simulation example and an analysis of telemetry data from a Steller sea lion (Eumatopias jubatus) in southeast Alaska.

  15. Anomalous ortho-para conversion of solid hydrogen in constrained geometries

    International Nuclear Information System (INIS)

    Rall, M.; Brison, J.P.; Sullivan, N.S.

    1991-01-01

    Using cw NMR techniques, we have measured the ortho-para conversion of solid hydrogen constrained to the interior of the molecular cages of zeolite. The conversion observed in the constrained geometry is very different from that of bulk solid hydrogen. Two distinct conversion rates were observed for short and long times. An apparently bimolecular conversion rate of 0.43% h -1 (one-fourth of the bulk value) dominates during the first 500 h, and the rate then increases to 2.2% h -1 . The initial slow rate is explained in terms of a reduced number of nearest neighbors and possible wall effects, and the fast rate is attributed to the formation of small ortho-H 2 Rclusters at later times. Surface effects due to magnetic impurities do not appear to determine the conversion rate in the samples studied

  16. A constrained approach to multiscale stochastic simulation of chemically reacting systems

    KAUST Repository

    Cotter, Simon L.

    2011-01-01

    Stochastic simulation of coupled chemical reactions is often computationally intensive, especially if a chemical system contains reactions occurring on different time scales. In this paper, we introduce a multiscale methodology suitable to address this problem, assuming that the evolution of the slow species in the system is well approximated by a Langevin process. It is based on the conditional stochastic simulation algorithm (CSSA) which samples from the conditional distribution of the suitably defined fast variables, given values for the slow variables. In the constrained multiscale algorithm (CMA) a single realization of the CSSA is then used for each value of the slow variable to approximate the effective drift and diffusion terms, in a similar manner to the constrained mean-force computations in other applications such as molecular dynamics. We then show how using the ensuing Fokker-Planck equation approximation, we can in turn approximate average switching times in stochastic chemical systems. © 2011 American Institute of Physics.

  17. Resource Management in Constrained Dynamic Situations

    Science.gov (United States)

    Seok, Jinwoo

    Resource management is considered in this dissertation for systems with limited resources, possibly combined with other system constraints, in unpredictably dynamic environments. Resources may represent fuel, power, capabilities, energy, and so on. Resource management is important for many practical systems; usually, resources are limited, and their use must be optimized. Furthermore, systems are often constrained, and constraints must be satisfied for safe operation. Simplistic resource management can result in poor use of resources and failure of the system. Furthermore, many real-world situations involve dynamic environments. Many traditional problems are formulated based on the assumptions of given probabilities or perfect knowledge of future events. However, in many cases, the future is completely unknown, and information on or probabilities about future events are not available. In other words, we operate in unpredictably dynamic situations. Thus, a method is needed to handle dynamic situations without knowledge of the future, but few formal methods have been developed to address them. Thus, the goal is to design resource management methods for constrained systems, with limited resources, in unpredictably dynamic environments. To this end, resource management is organized hierarchically into two levels: 1) planning, and 2) control. In the planning level, the set of tasks to be performed is scheduled based on limited resources to maximize resource usage in unpredictably dynamic environments. In the control level, the system controller is designed to follow the schedule by considering all the system constraints for safe and efficient operation. Consequently, this dissertation is mainly divided into two parts: 1) planning level design, based on finite state machines, and 2) control level methods, based on model predictive control. We define a recomposable restricted finite state machine to handle limited resource situations and unpredictably dynamic environments

  18. Molecular clouds toward three Spitzer bubbles S116, S117, and S118: Evidence for a cloud-cloud collision which formed the three H II regions and a 10 pc scale molecular cavity

    Science.gov (United States)

    Fukui, Yasuo; Ohama, Akio; Kohno, Mikito; Torii, Kazufumi; Fujita, Shinji; Hattori, Yusuke; Nishimura, Atsushi; Yamamoto, Hiroaki; Tachihara, Kengo

    2018-05-01

    We carried out a molecular-line study toward the three Spitzer bubbles S116, S117, and S118, which show active formation of high-mass stars. We found molecular gas consisting of two components with a velocity difference of ˜5 km s-1. One of them, the small cloud, has a typical velocity of -63 km s-1 and the other, the large cloud, has one of -58 km s-1. The large cloud has a nearly circular intensity depression, the size of which is similar to that of the small cloud. We present an interpretation that its cavity was created by a collision between the two clouds and that this collision compressed the gas into a dense layer elongating along the western rim of the small cloud. In this scenario, the O stars including those in the three Spitzer bubbles were formed in the interface layer compressed by the collision. Assuming that the relative motion of the clouds has a tilt of 45° to the line of sight, we estimate that the collision continued for the last 1 Myr at a relative velocity of ˜10 km s-1. In the S116-S117-S118 system the H II regions are located outside of the cavity. This morphology is ascribed to the density-bound distribution of the large cloud which caused the H II regions to expand more easily toward the outer part of the large cloud than towards the inside of the cavity. The present case proves that a cloud-cloud collision creates a cavity without the action of O-star feedback, and suggests that the collision-compressed layer is highly filamentary.

  19. Molecular genetic studies of natives on Easter Island: evidence of an early European and Amerindian contribution to the Polynesian gene pool.

    Science.gov (United States)

    Lie, B A; Dupuy, B M; Spurkland, A; Fernández-Viña, M A; Hagelberg, E; Thorsby, E

    2007-01-01

    Most archaeological and linguistic evidence suggest a Polynesian origin of the population of Easter Island (Rapanui), and this view has been supported by the identification of Polynesian mitochondrial DNA (mtDNA) polymorphisms in prehistoric skeletal remains. However, some evidence of an early South American contact also exists (the sweet potato, bottle gourd etc.), but genetic studies have so far failed to show an early Amerindian contribution to the gene pool on Easter Island. To address this issue, we analyzed mtDNA and Y chromosome markers and performed high-resolution human leukocyte antigen (HLA) genotyping of DNA harvested from previously collected sera of 48 reputedly nonadmixed native Easter Islanders. All individuals carried mtDNA types and HLA alleles previously found in Polynesia, and most men carried Y chromosome markers of Polynesian origin, providing further evidence of a Polynesian origin of the population of Easter Island. A few individuals carried HLA alleles and/or Y chromosome markers of European origin. More interestingly, some individuals carried the HLA alleles A*0212 and B*3905, which are of typical Amerindian origin. The genealogy of some of the individuals carrying these non-Polynesian HLA alleles and their haplotypic backgrounds suggest an introduction into Easter Island in the early 1800s, or earlier. Thus, there may have been an early European and Amerindian contribution to the Polynesian gene pool of Easter Island.

  20. Sequential unconstrained minimization algorithms for constrained optimization

    International Nuclear Information System (INIS)

    Byrne, Charles

    2008-01-01

    The problem of minimizing a function f(x):R J → R, subject to constraints on the vector variable x, occurs frequently in inverse problems. Even without constraints, finding a minimizer of f(x) may require iterative methods. We consider here a general class of iterative algorithms that find a solution to the constrained minimization problem as the limit of a sequence of vectors, each solving an unconstrained minimization problem. Our sequential unconstrained minimization algorithm (SUMMA) is an iterative procedure for constrained minimization. At the kth step we minimize the function G k (x)=f(x)+g k (x), to obtain x k . The auxiliary functions g k (x):D subset of R J → R + are nonnegative on the set D, each x k is assumed to lie within D, and the objective is to minimize the continuous function f:R J → R over x in the set C = D-bar, the closure of D. We assume that such minimizers exist, and denote one such by x-circumflex. We assume that the functions g k (x) satisfy the inequalities 0≤g k (x)≤G k-1 (x)-G k-1 (x k-1 ), for k = 2, 3, .... Using this assumption, we show that the sequence {(x k )} is decreasing and converges to f(x-circumflex). If the restriction of f(x) to D has bounded level sets, which happens if x-circumflex is unique and f(x) is closed, proper and convex, then the sequence {x k } is bounded, and f(x*)=f(x-circumflex), for any cluster point x*. Therefore, if x-circumflex is unique, x* = x-circumflex and {x k } → x-circumflex. When x-circumflex is not unique, convergence can still be obtained, in particular cases. The SUMMA includes, as particular cases, the well-known barrier- and penalty-function methods, the simultaneous multiplicative algebraic reconstruction technique (SMART), the proximal minimization algorithm of Censor and Zenios, the entropic proximal methods of Teboulle, as well as certain cases of gradient descent and the Newton–Raphson method. The proof techniques used for SUMMA can be extended to obtain related results

  1. Explaining evolution via constrained persistent perfect phylogeny

    Science.gov (United States)

    2014-01-01

    Background The perfect phylogeny is an often used model in phylogenetics since it provides an efficient basic procedure for representing the evolution of genomic binary characters in several frameworks, such as for example in haplotype inference. The model, which is conceptually the simplest, is based on the infinite sites assumption, that is no character can mutate more than once in the whole tree. A main open problem regarding the model is finding generalizations that retain the computational tractability of the original model but are more flexible in modeling biological data when the infinite site assumption is violated because of e.g. back mutations. A special case of back mutations that has been considered in the study of the evolution of protein domains (where a domain is acquired and then lost) is persistency, that is the fact that a character is allowed to return back to the ancestral state. In this model characters can be gained and lost at most once. In this paper we consider the computational problem of explaining binary data by the Persistent Perfect Phylogeny model (referred as PPP) and for this purpose we investigate the problem of reconstructing an evolution where some constraints are imposed on the paths of the tree. Results We define a natural generalization of the PPP problem obtained by requiring that for some pairs (character, species), neither the species nor any of its ancestors can have the character. In other words, some characters cannot be persistent for some species. This new problem is called Constrained PPP (CPPP). Based on a graph formulation of the CPPP problem, we are able to provide a polynomial time solution for the CPPP problem for matrices whose conflict graph has no edges. Using this result, we develop a parameterized algorithm for solving the CPPP problem where the parameter is the number of characters. Conclusions A preliminary experimental analysis shows that the constrained persistent perfect phylogeny model allows to

  2. RCW 36 in the Vela Molecular Ridge: Evidence for high-mass star-cluster formation triggered by cloud-cloud collision

    Science.gov (United States)

    Sano, Hidetoshi; Enokiya, Rei; Hayashi, Katsuhiro; Yamagishi, Mitsuyoshi; Saeki, Shun; Okawa, Kazuki; Tsuge, Kisetsu; Tsutsumi, Daichi; Kohno, Mikito; Hattori, Yusuke; Yoshiike, Satoshi; Fujita, Shinji; Nishimura, Atsushi; Ohama, Akio; Tachihara, Kengo; Torii, Kazufumi; Hasegawa, Yutaka; Kimura, Kimihiro; Ogawa, Hideo; Wong, Graeme F.; Braiding, Catherine; Rowell, Gavin; Burton, Michael G.; Fukui, Yasuo

    2018-05-01

    A collision between two molecular clouds is one possible candidate for high-mass star formation. The H II region RCW 36, located in the Vela molecular ridge, contains a young star cluster (˜ 1 Myr old) and two O-type stars. We present new CO observations of RCW 36 made with NANTEN2, Mopra, and ASTE using 12CO(J = 1-0, 2-1, 3-2) and 13CO(J = 2-1) emission lines. We have discovered two molecular clouds lying at the velocities VLSR ˜ 5.5 and 9 km s-1. Both clouds are likely to be physically associated with the star cluster, as verified by the good spatial correspondence among the two clouds, infrared filaments, and the star cluster. We also found a high intensity ratio of ˜ 0.6-1.2 for CO J = 3-2/1-0 toward both clouds, indicating that the gas temperature has been increased due to heating by the O-type stars. We propose that the O-type stars in RCW 36 were formed by a collision between the two clouds, with a relative velocity separation of 5 km s-1. The complementary spatial distributions and the velocity separation of the two clouds are in good agreement with observational signatures expected for O-type star formation triggered by a cloud-cloud collision. We also found a displacement between the complementary spatial distributions of the two clouds, which we estimate to be 0.3 pc assuming the collision angle to be 45° relative to the line-of-sight. We estimate the collision timescale to be ˜ 105 yr. It is probable that the cluster age found by Ellerbroek et al. (2013b, A&A, 558, A102) is dominated by the low-mass members which were not formed under the triggering by cloud-cloud collision, and that the O-type stars in the center of the cluster are explained by the collisional triggering independently from the low-mass star formation.

  3. Evidence for radical anion formation during liquid secondary ion mass spectrometry analysis of oligonucleotides and synthetic oligomeric analogues: a deconvolution algorithm for molecular ion region clusters.

    Science.gov (United States)

    Laramée, J A; Arbogast, B; Deinzer, M L

    1989-10-01

    It is shown that one-electron reduction is a common process that occurs in negative ion liquid secondary ion mass spectrometry (LSIMS) of oligonucleotides and synthetic oligonucleosides and that this process is in competition with proton loss. Deconvolution of the molecular anion cluster reveals contributions from (M-2H).-, (M-H)-, M.-, and (M + H)-. A model based on these ionic species gives excellent agreement with the experimental data. A correlation between the concentration of species arising via one-electron reduction [M.- and (M + H)-] and the electron affinity of the matrix has been demonstrated. The relative intensity of M.- is mass-dependent; this is rationalized on the basis of base-stacking. Base sequence ion formation is theorized to arise from M.- radical anion among other possible pathways.

  4. Evidence for natural molecular hydrogen seepage associated with Carolina bays (surficial, ovoid depressions on the Atlantic Coastal Plain, Province of the USA)

    Science.gov (United States)

    Zgonnik, Viacheslav; Beaumont, Valérie; Deville, Eric; Larin, Nikolay; Pillot, Daniel; Farrell, Kathleen M.

    2015-12-01

    A study of soil gases was made in North Carolina (USA) in and around morphological depressions called "Carolina bays." This type of depression is observed over the Atlantic coastal plains of the USA, but their origin remains debated. Significant concentrations of molecular hydrogen (H2) were detected, notably around the bays. These measurements suggest that Carolina bays are the surficial expression of fluid flow pathways for hydrogen gas moving from depth to the surface. The potential mechanisms of H2 production and transport and the geological controls on the fluid migration pathways are discussed, with reference to the hypothesis that Carolina bays are the result of local collapses caused by the alteration of rock along the deep pathways of H2 migrating towards the surface. The present H2 seepages are comparable to those in similar structures previously observed in the East European craton.

  5. Preliminary evidence for associations between molecular markers and quantitative traits in a set of bread wheat (Triticum aestivum L.) cultivars and breeding lines.

    Science.gov (United States)

    Abdollahi Mandoulakani, Babak; Nasri, Shilan; Dashchi, Sahar; Arzhang, Sorour; Bernousi, Iraj; Abbasi Holasou, Hossein

    The identification of polymorphic markers associated with various quantitative traits allows us to test their performance for the exploitation of the extensive quantitative variation maintained in gene banks. In the current study, a set of 97 wheat germplasm accessions including 48 cultivars and 49 breeding lines were evaluated for 18 agronomic traits. The accessions were also genotyped with 23 ISSR, nine IRAP and 20 REMAP markers, generating a total of 658 clear and scorable bands, 86% of which were polymorphic. Both neighbor-joining dendrogram and Bayesian analysis of clustering of individuals revealed that the accessions could be divided into four genetically distinct groups, indicating the presence of a population structure in current wheat germplasm. Associations between molecular markers and 18 agronomic traits were analyzed using the mixed linear model (MLM) approach. A total of 94 loci were found to be significantly associated with agronomic traits (P≤0.01). The highest number of bands significantly associated with the 18 traits varied from 11 for number of spikelets spike -1 (NSS) to two for grain yield in row (GRY). Loci ISSR16-9 and REMAP13-10 were associated with three different traits. The results of the current study provide useful information about the performance of retrotransposon-based and ISSR molecular markers that could be helpful in selecting potentially elite gene bank samples for wheat-breeding programs. Copyright © 2017 Académie des sciences. Published by Elsevier Masson SAS. All rights reserved.

  6. Molecular evidence of cryptic diversity in Paracaryophyllaeus (Cestoda: Caryophyllidea), parasites of loaches (Cobitidae) in Eurasia, including description of P. vladkae n. sp.

    Science.gov (United States)

    Scholz, Tomáš; Oros, Mikuláš; Bazsalovicsová, Eva; Brabec, Jan; Waeschenbach, Andrea; Xi, Bing-Wen; Aydoğdu, Ali; Besprozvannykh, Vladimir; Shimazu, Takeshi; Králová-Hromadová, Ivica; Littlewood, D Timothy J

    2014-12-01

    Molecular phylogenetic analysis of an extensive collection of monozoic tapeworms of the genus Paracaryophyllaeus Kulakovskaya, 1961 (Cestoda: Caryophyllidea), parasites of loaches (Cypriniformes: Cobitidae) in Eurasia, has revealed cryptic species diversity within this long-time monotypic genus, especially in the Paracaryophyllaeus gotoi (Motomura, 1927) species complex [syn. Paracaryophyllaeus dubininorum (Kulakovskaya, 1961); type species]. Three independent, well-supported clades were discovered on the basis of molecular data: (i) specimens from Misgurnus anguillicaudatus and Cobitis lutheri from China, Russian Far East and Japan - called herein P. cf. gotoi 1, which may be conspecific with P. gotoi (Motomura, 1927), although in the absence of sequence data for P. gotoi from its type locality (basin of the River Kumkan in Korea), no certain inferences about their identity can currently be made; (ii) specimens from M. anguillicaudatus from China and Japan - P. cf. gotoi 2, which are morphologically indistinguishable from those of P. cf. gotoi 1; and (iii) morphologically distinct tapeworms from the endemic loach Cobitis bilseli from southwestern Turkey (Beyşehir Lake), which are described herein as a new species. Paracaryophyllaeus vladkae Scholz, Oros and Aydoğdu n. sp. differs from the remaining species of the genus in the following characteristics: the testes begin anterior to the first vitelline follicles (versus posterior), the body is short and robust (versus more elongate and slender), and the scolex is wide, rounded or apically tapered (versus claviform to truncate). Species composition of the genus, host specificity of species and geographical distribution are briefly discussed. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  7. Prospective comparison of molecular signatures in urothelial cancer of the bladder and the upper urinary tract--is there evidence for discordant biology?

    Science.gov (United States)

    Krabbe, Laura-Maria; Lotan, Yair; Bagrodia, Aditya; Gayed, Bishoy A; Darwish, Oussama M; Youssef, Ramy F; Bolenz, Christian; Sagalowsky, Arthur I; Raj, Ganesh V; Shariat, Shahrokh F; Kapur, Payal; Margulis, Vitaly

    2014-04-01

    Upper tract urothelial carcinoma is rare and less well studied than bladder cancer. It remains questionable if findings in bladder cancer can safely be extrapolated to upper tract urothelial carcinoma. We prospectively evaluate molecular profiles of upper tract urothelial carcinoma and bladder cancer using a cell cycle biomarker panel. Immunohistochemical staining for p21, p27, p53, cyclin E and Ki-67 was prospectively performed for 96 patients with upper tract urothelial carcinoma and 159 patients with bladder cancer with nonmetastatic high grade urothelial carcinoma treated with extirpative surgery. Data were compared between the groups according to pathological stage. Primary outcome was assessment of differences in marker expression. Secondary outcome was difference in survival according to marker status. During a median followup of 22.0 months 31.2% of patients with upper tract urothelial carcinoma and 28.3% of patients with bladder cancer had disease recurrence, and 20.8% and 27.7% died of upper tract urothelial carcinoma and bladder cancer, respectively. The number of altered markers was not significantly different between the study groups. Overall 34 patients (35.4%) with upper tract urothelial carcinoma and 62 (39.0%) with bladder cancer had an unfavorable marker score (more than 2 markers altered). There were no significant differences between upper tract urothelial carcinoma and bladder cancer in the alteration status of markers, the number of altered markers and biomarker score when substratified by pathological stage. There were no significant differences in survival outcomes between patients with upper tract urothelial carcinoma and those with bladder cancer according to the number of altered markers and biomarker score. Our results demonstrate the molecular similarity of upper tract urothelial carcinoma and bladder cancer in terms of cell cycle and proliferative tissue markers. These findings have important implications and support the further

  8. Constrained Sypersymmetric Flipped SU (5) GUT Phenomenology

    Energy Technology Data Exchange (ETDEWEB)

    Ellis, John; /CERN /King' s Coll. London; Mustafayev, Azar; /Minnesota U., Theor. Phys. Inst.; Olive, Keith A.; /Minnesota U., Theor. Phys. Inst. /Minnesota U. /Stanford U., Phys. Dept. /SLAC

    2011-08-12

    We explore the phenomenology of the minimal supersymmetric flipped SU(5) GUT model (CFSU(5)), whose soft supersymmetry-breaking (SSB) mass parameters are constrained to be universal at some input scale, Min, above the GUT scale, M{sub GUT}. We analyze the parameter space of CFSU(5) assuming that the lightest supersymmetric particle (LSP) provides the cosmological cold dark matter, paying careful attention to the matching of parameters at the GUT scale. We first display some specific examples of the evolutions of the SSB parameters that exhibit some generic features. Specifically, we note that the relationship between the masses of the lightest neutralino {chi} and the lighter stau {tilde {tau}}{sub 1} is sensitive to M{sub in}, as is the relationship between m{sub {chi}} and the masses of the heavier Higgs bosons A,H. For these reasons, prominent features in generic (m{sub 1/2}, m{sub 0}) planes such as coannihilation strips and rapid-annihilation funnels are also sensitive to Min, as we illustrate for several cases with tan {beta} = 10 and 55. However, these features do not necessarily disappear at large Min, unlike the case in the minimal conventional SU(5) GUT. Our results are relatively insensitive to neutrino masses.

  9. Constrained supersymmetric flipped SU(5) GUT phenomenology

    Energy Technology Data Exchange (ETDEWEB)

    Ellis, John [CERN, TH Division, PH Department, Geneva 23 (Switzerland); King' s College London, Theoretical Physics and Cosmology Group, Department of Physics, London (United Kingdom); Mustafayev, Azar [University of Minnesota, William I. Fine Theoretical Physics Institute, Minneapolis, MN (United States); Olive, Keith A. [University of Minnesota, William I. Fine Theoretical Physics Institute, Minneapolis, MN (United States); Stanford University, Department of Physics and SLAC, Palo Alto, CA (United States)

    2011-07-15

    We explore the phenomenology of the minimal supersymmetric flipped SU(5) GUT model (CFSU(5)), whose soft supersymmetry-breaking (SSB) mass parameters are constrained to be universal at some input scale, M{sub in}, above the GUT scale, M{sub GUT}. We analyze the parameter space of CFSU(5) assuming that the lightest supersymmetric particle (LSP) provides the cosmological cold dark matter, paying careful attention to the matching of parameters at the GUT scale. We first display some specific examples of the evolutions of the SSB parameters that exhibit some generic features. Specifically, we note that the relationship between the masses of the lightest neutralino {chi} and the lighter stau {tau}{sub 1} is sensitive to M{sub in}, as is the relationship between m{sub {chi}} and the masses of the heavier Higgs bosons A,H. For these reasons, prominent features in generic (m{sub 1/2},m{sub 0}) planes such as coannihilation strips and rapid-annihilation funnels are also sensitive to M{sub in}, as we illustrate for several cases with tan {beta}=10 and 55. However, these features do not necessarily disappear at large M{sub in}, unlike the case in the minimal conventional SU(5) GUT. Our results are relatively insensitive to neutrino masses. (orig.)

  10. Joint Chance-Constrained Dynamic Programming

    Science.gov (United States)

    Ono, Masahiro; Kuwata, Yoshiaki; Balaram, J. Bob

    2012-01-01

    This paper presents a novel dynamic programming algorithm with a joint chance constraint, which explicitly bounds the risk of failure in order to maintain the state within a specified feasible region. A joint chance constraint cannot be handled by existing constrained dynamic programming approaches since their application is limited to constraints in the same form as the cost function, that is, an expectation over a sum of one-stage costs. We overcome this challenge by reformulating the joint chance constraint into a constraint on an expectation over a sum of indicator functions, which can be incorporated into the cost function by dualizing the optimization problem. As a result, the primal variables can be optimized by a standard dynamic programming, while the dual variable is optimized by a root-finding algorithm that converges exponentially. Error bounds on the primal and dual objective values are rigorously derived. We demonstrate the algorithm on a path planning problem, as well as an optimal control problem for Mars entry, descent and landing. The simulations are conducted using a real terrain data of Mars, with four million discrete states at each time step.

  11. Constraining the roughness degree of slip heterogeneity

    KAUST Repository

    Causse, Mathieu

    2010-05-07

    This article investigates different approaches for assessing the degree of roughness of the slip distribution of future earthquakes. First, we analyze a database of slip images extracted from a suite of 152 finite-source rupture models from 80 events (Mw = 4.1–8.9). This results in an empirical model defining the distribution of the slip spectrum corner wave numbers (kc) as a function of moment magnitude. To reduce the “epistemic” uncertainty, we select a single slip model per event and screen out poorly resolved models. The number of remaining models (30) is thus rather small. In addition, the robustness of the empirical model rests on a reliable estimation of kc by kinematic inversion methods. We address this issue by performing tests on synthetic data with a frequency domain inversion method. These tests reveal that due to smoothing constraints used to stabilize the inversion process, kc tends to be underestimated. We then develop an alternative approach: (1) we establish a proportionality relationship between kc and the peak ground acceleration (PGA), using a k−2 kinematic source model, and (2) we analyze the PGA distribution, which is believed to be better constrained than slip images. These two methods reveal that kc follows a lognormal distribution, with similar standard deviations for both methods.

  12. Technologies for a greenhouse-constrained society

    International Nuclear Information System (INIS)

    Kuliasha, M.A.; Zucker, A.; Ballew, K.J.

    1992-01-01

    This conference explored how three technologies might help society adjust to life in a greenhouse-constrained environment. Technology experts and policy makers from around the world met June 11--13, 1991, in Oak Ridge, Tennessee, to address questions about how energy efficiency, biomass, and nuclear technologies can mitigate the greenhouse effect and to explore energy production and use in countries in various stages of development. The conference was organized by Oak Ridge National Laboratory and sponsored by the US Department of Energy. Energy efficiency biomass, and nuclear energy are potential substitutes for fossil fuels that might help slow or even reverse the global warming changes that may result from mankind's thirst for energy. Many other conferences have questioned whether the greenhouse effect is real and what reductions in greenhouse gas emissions might be necessary to avoid serious ecological consequences; this conference studied how these reductions might actually be achieved. For these conference proceedings, individuals papers are processed separately for the Energy Data Base

  13. Constrained Supersymmetric Flipped SU(5) GUT Phenomenology

    CERN Document Server

    Ellis, John; Olive, Keith A

    2011-01-01

    We explore the phenomenology of the minimal supersymmetric flipped SU(5) GUT model (CFSU(5)), whose soft supersymmetry-breaking (SSB) mass parameters are constrained to be universal at some input scale, $M_{in}$, above the GUT scale, $M_{GUT}$. We analyze the parameter space of CFSU(5) assuming that the lightest supersymmetric particle (LSP) provides the cosmological cold dark matter, paying careful attention to the matching of parameters at the GUT scale. We first display some specific examples of the evolutions of the SSB parameters that exhibit some generic features. Specifically, we note that the relationship between the masses of the lightest neutralino and the lighter stau is sensitive to $M_{in}$, as is the relationship between the neutralino mass and the masses of the heavier Higgs bosons. For these reasons, prominent features in generic $(m_{1/2}, m_0)$ planes such as coannihilation strips and rapid-annihilation funnels are also sensitive to $M_{in}$, as we illustrate for several cases with tan(beta)...

  14. Constrained supersymmetric flipped SU(5) GUT phenomenology

    International Nuclear Information System (INIS)

    Ellis, John; Mustafayev, Azar; Olive, Keith A.

    2011-01-01

    We explore the phenomenology of the minimal supersymmetric flipped SU(5) GUT model (CFSU(5)), whose soft supersymmetry-breaking (SSB) mass parameters are constrained to be universal at some input scale, M in , above the GUT scale, M GUT . We analyze the parameter space of CFSU(5) assuming that the lightest supersymmetric particle (LSP) provides the cosmological cold dark matter, paying careful attention to the matching of parameters at the GUT scale. We first display some specific examples of the evolutions of the SSB parameters that exhibit some generic features. Specifically, we note that the relationship between the masses of the lightest neutralino χ and the lighter stau τ 1 is sensitive to M in , as is the relationship between m χ and the masses of the heavier Higgs bosons A,H. For these reasons, prominent features in generic (m 1/2 ,m 0 ) planes such as coannihilation strips and rapid-annihilation funnels are also sensitive to M in , as we illustrate for several cases with tan β=10 and 55. However, these features do not necessarily disappear at large M in , unlike the case in the minimal conventional SU(5) GUT. Our results are relatively insensitive to neutrino masses. (orig.)

  15. Scheduling Aircraft Landings under Constrained Position Shifting

    Science.gov (United States)

    Balakrishnan, Hamsa; Chandran, Bala

    2006-01-01

    Optimal scheduling of airport runway operations can play an important role in improving the safety and efficiency of the National Airspace System (NAS). Methods that compute the optimal landing sequence and landing times of aircraft must accommodate practical issues that affect the implementation of the schedule. One such practical consideration, known as Constrained Position Shifting (CPS), is the restriction that each aircraft must land within a pre-specified number of positions of its place in the First-Come-First-Served (FCFS) sequence. We consider the problem of scheduling landings of aircraft in a CPS environment in order to maximize runway throughput (minimize the completion time of the landing sequence), subject to operational constraints such as FAA-specified minimum inter-arrival spacing restrictions, precedence relationships among aircraft that arise either from airline preferences or air traffic control procedures that prevent overtaking, and time windows (representing possible control actions) during which each aircraft landing can occur. We present a Dynamic Programming-based approach that scales linearly in the number of aircraft, and describe our computational experience with a prototype implementation on realistic data for Denver International Airport.

  16. Should we still believe in constrained supersymmetry?

    International Nuclear Information System (INIS)

    Balazs, Csaba; Buckley, Andy; Carter, Daniel; Farmer, Benjamin; White, Martin

    2013-01-01

    We calculate partial Bayes factors to quantify how the feasibility of the constrained minimal supersymmetric standard model (CMSSM) has changed in the light of a series of observations. This is done in the Bayesian spirit where probability reflects a degree of belief in a proposition and Bayes' theorem tells us how to update it after acquiring new information. Our experimental baseline is the approximate knowledge that was available before LEP, and our comparison model is the Standard Model with a simple dark matter candidate. To quantify the amount by which experiments have altered our relative belief in the CMSSM since the baseline data we compute the partial Bayes factors that arise from learning in sequence the LEP Higgs constraints, the XENON100 dark matter constraints, the 2011 LHC supersymmetry search results, and the early 2012 LHC Higgs search results. We find that LEP and the LHC strongly shatter our trust in the CMSSM (with M 0 and M 1/2 below 2 TeV), reducing its posterior odds by approximately two orders of magnitude. This reduction is largely due to substantial Occam factors induced by the LEP and LHC Higgs searches. (orig.)

  17. Electricity in a Climate-Constrained World

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2012-07-01

    After experiencing a historic drop in 2009, electricity generation reached a record high in 2010, confirming the close linkage between economic growth and electricity usage. Unfortunately, CO2 emissions from electricity have also resumed their growth: Electricity remains the single-largest source of CO2 emissions from energy, with 11.7 billion tonnes of CO2 released in 2010. The imperative to 'decarbonise' electricity and improve end-use efficiency remains essential to the global fight against climate change. The IEA’s Electricity in a Climate-Constrained World provides an authoritative resource on progress to date in this area, including statistics related to CO2 and the electricity sector across ten regions of the world (supply, end-use and capacity additions). It also presents topical analyses on the challenge of rapidly curbing CO2 emissions from electricity. Looking at policy instruments, it focuses on emissions trading in China, using energy efficiency to manage electricity supply crises and combining policy instruments for effective CO2 reductions. On regulatory issues, it asks whether deregulation can deliver decarbonisation and assesses the role of state-owned enterprises in emerging economies. And from technology perspectives, it explores the rise of new end-uses, the role of electricity storage, biomass use in Brazil, and the potential of carbon capture and storage for ‘negative emissions’ electricity supply.

  18. Source-constrained retrieval influences the encoding of new information.

    Science.gov (United States)

    Danckert, Stacey L; MacLeod, Colin M; Fernandes, Myra A

    2011-11-01

    Jacoby, Shimizu, Daniels, and Rhodes (Psychonomic Bulletin & Review, 12, 852-857, 2005) showed that new words presented as foils among a list of old words that had been deeply encoded were themselves subsequently better recognized than new words presented as foils among a list of old words that had been shallowly encoded. In Experiment 1, by substituting a deep-versus-shallow imagery manipulation for the levels-of-processing manipulation, we demonstrated that the effect is robust and that it generalizes, also occurring with a different type of encoding. In Experiment 2, we provided more direct evidence for context-related encoding during tests of deeply encoded words, showing enhanced priming for foils presented among deeply encoded targets when participants made the same deep-encoding judgments on those items as had been made on the targets during study. In Experiment 3, we established that the findings from Experiment 2 are restricted to this specific deep judgment task and are not a general consequence of these foils being associated with deeply encoded items. These findings provide support for the source-constrained retrieval hypothesis of Jacoby, Shimizu, Daniels, and Rhodes: New information can be influenced by how surrounding items are encoded and retrieved, as long as the surrounding items recruit a coherent mode of processing.

  19. Constrained variability of modeled T:ET ratio across biomes

    Science.gov (United States)

    Fatichi, Simone; Pappas, Christoforos

    2017-07-01

    A large variability (35-90%) in the ratio of transpiration to total evapotranspiration (referred here as T:ET) across biomes or even at the global scale has been documented by a number of studies carried out with different methodologies. Previous empirical results also suggest that T:ET does not covary with mean precipitation and has a positive dependence on leaf area index (LAI). Here we use a mechanistic ecohydrological model, with a refined process-based description of evaporation from the soil surface, to investigate the variability of T:ET across biomes. Numerical results reveal a more constrained range and higher mean of T:ET (70 ± 9%, mean ± standard deviation) when compared to observation-based estimates. T:ET is confirmed to be independent from mean precipitation, while it is found to be correlated with LAI seasonally but uncorrelated across multiple sites. Larger LAI increases evaporation from interception but diminishes ground evaporation with the two effects largely compensating each other. These results offer mechanistic model-based evidence to the ongoing research about the patterns of T:ET and the factors influencing its magnitude across biomes.

  20. Phylogenetic constrains on mycorrhizal specificity in eight Dendrobium (Orchidaceae) species.

    Science.gov (United States)

    Xing, Xiaoke; Ma, Xueting; Men, Jinxin; Chen, Yanhong; Guo, Shunxing

    2017-05-01

    Plant phylogeny constrains orchid mycorrhizal (OrM) fungal community composition in some orchids. Here, we investigated the structures of the OrM fungal communities of eight Dendrobium species in one niche to determine whether similarities in the OrM fungal communities correlated with the phylogeny of the host plants and whether the Dendrobium-OrM fungal interactions are phylogenetically conserved. A phylogeny based on DNA data was constructed for the eight coexisting Dendrobium species, and the OrM fungal communities were characterized by their roots. There were 31 different fungal lineages associated with the eight Dendrobium species. In total, 82.98% of the identified associations belonging to Tulasnellaceae, and a smaller proportion involved members of the unknown Basidiomycota (9.67%). Community analyses revealed that phylogenetically related Dendrobium tended to interact with a similar set of Tulasnellaceae fungi. The interactions between Dendrobium and Tulasnellaceae fungi were significantly influenced by the phylogenetic relationships among the Dendrobium species. Our results provide evidence that the mycorrhizal specificity in the eight coexisting Dendrobium species was phylogenetically conserved.

  1. A discretized algorithm for the solution of a constrained, continuous ...

    African Journals Online (AJOL)

    A discretized algorithm for the solution of a constrained, continuous quadratic control problem. ... The results obtained show that the Discretized constrained algorithm (DCA) is much more accurate and more efficient than some of these techniques, particularly the FSA. Journal of the Nigerian Association of Mathematical ...

  2. I/O-Efficient Construction of Constrained Delaunay Triangulations

    DEFF Research Database (Denmark)

    Agarwal, Pankaj Kumar; Arge, Lars; Yi, Ke

    2005-01-01

    In this paper, we designed and implemented an I/O-efficient algorithm for constructing constrained Delaunay triangulations. If the number of constraining segments is smaller than the memory size, our algorithm runs in expected O( N B logM/B NB ) I/Os for triangulating N points in the plane, where...

  3. Regional Responses to Constrained Water Availability

    Science.gov (United States)

    Cui, Y.; Calvin, K. V.; Hejazi, M. I.; Clarke, L.; Kim, S. H.; Patel, P.

    2017-12-01

    There have been many concerns about water as a constraint to agricultural production, electricity generation, and many other human activities in the coming decades. Nevertheless, how different countries/economies would respond to such constraints has not been explored. Here, we examine the responding mechanism of binding water availability constraints at the water basin level and across a wide range of socioeconomic, climate and energy technology scenarios. Specifically, we look at the change in water withdrawals between energy, land-use and other sectors within an integrated framework, by using the Global Change Assessment Model (GCAM) that also endogenizes water use and allocation decisions based on costs. We find that, when water is taken into account as part of the production decision-making, countries/basins in general fall into three different categories, depending on the change of water withdrawals and water re-allocation between sectors. First, water is not a constraining factor for most of the basins. Second, advancements in water-saving technologies of the electricity generation cooling systems are sufficient of reducing water withdrawals to meet binding water availability constraints, such as in China and the EU-15. Third, water-saving in the electricity sector alone is not sufficient and thus cannot make up the lowered water availability from the binding case; for example, many basins in Pakistan, Middle East and India have to largely reduce irrigated water withdrawals by either switching to rain-fed agriculture or reducing production. The dominant responding strategy for individual countries/basins is quite robust across the range of alternate scenarios that we test. The relative size of water withdrawals between energy and agriculture sectors is one of the most important factors that affect the dominant mechanism.

  4. Constraining Cosmic Evolution of Type Ia Supernovae

    Energy Technology Data Exchange (ETDEWEB)

    Foley, Ryan J.; Filippenko, Alexei V.; Aguilera, C.; Becker, A.C.; Blondin, S.; Challis, P.; Clocchiatti, A.; Covarrubias, R.; Davis, T.M.; Garnavich, P.M.; Jha, S.; Kirshner, R.P.; Krisciunas, K.; Leibundgut, B.; Li, W.; Matheson, T.; Miceli, A.; Miknaitis, G.; Pignata, G.; Rest, A.; Riess, A.G.; /UC, Berkeley, Astron. Dept. /Cerro-Tololo InterAmerican Obs. /Washington U., Seattle, Astron. Dept. /Harvard-Smithsonian Ctr. Astrophys. /Chile U., Catolica /Bohr Inst. /Notre Dame U. /KIPAC, Menlo Park /Texas A-M /European Southern Observ. /NOAO, Tucson /Fermilab /Chile U., Santiago /Harvard U., Phys. Dept. /Baltimore, Space Telescope Sci. /Johns Hopkins U. /Res. Sch. Astron. Astrophys., Weston Creek /Stockholm U. /Hawaii U. /Illinois U., Urbana, Astron. Dept.

    2008-02-13

    We present the first large-scale effort of creating composite spectra of high-redshift type Ia supernovae (SNe Ia) and comparing them to low-redshift counterparts. Through the ESSENCE project, we have obtained 107 spectra of 88 high-redshift SNe Ia with excellent light-curve information. In addition, we have obtained 397 spectra of low-redshift SNe through a multiple-decade effort at Lick and Keck Observatories, and we have used 45 ultraviolet spectra obtained by HST/IUE. The low-redshift spectra act as a control sample when comparing to the ESSENCE spectra. In all instances, the ESSENCE and Lick composite spectra appear very similar. The addition of galaxy light to the Lick composite spectra allows a nearly perfect match of the overall spectral-energy distribution with the ESSENCE composite spectra, indicating that the high-redshift SNe are more contaminated with host-galaxy light than their low-redshift counterparts. This is caused by observing objects at all redshifts with similar slit widths, which corresponds to different projected distances. After correcting for the galaxy-light contamination, subtle differences in the spectra remain. We have estimated the systematic errors when using current spectral templates for K-corrections to be {approx}0.02 mag. The variance in the composite spectra give an estimate of the intrinsic variance in low-redshift maximum-light SN spectra of {approx}3% in the optical and growing toward the ultraviolet. The difference between the maximum-light low and high-redshift spectra constrain SN evolution between our samples to be < 10% in the rest-frame optical.

  5. Laterally constrained inversion for CSAMT data interpretation

    Science.gov (United States)

    Wang, Ruo; Yin, Changchun; Wang, Miaoyue; Di, Qingyun

    2015-10-01

    Laterally constrained inversion (LCI) has been successfully applied to the inversion of dc resistivity, TEM and airborne EM data. However, it hasn't been yet applied to the interpretation of controlled-source audio-frequency magnetotelluric (CSAMT) data. In this paper, we apply the LCI method for CSAMT data inversion by preconditioning the Jacobian matrix. We apply a weighting matrix to Jacobian to balance the sensitivity of model parameters, so that the resolution with respect to different model parameters becomes more uniform. Numerical experiments confirm that this can improve the convergence of the inversion. We first invert a synthetic dataset with and without noise to investigate the effect of LCI applications to CSAMT data, for the noise free data, the results show that the LCI method can recover the true model better compared to the traditional single-station inversion; and for the noisy data, the true model is recovered even with a noise level of 8%, indicating that LCI inversions are to some extent noise insensitive. Then, we re-invert two CSAMT datasets collected respectively in a watershed and a coal mine area in Northern China and compare our results with those from previous inversions. The comparison with the previous inversion in a coal mine shows that LCI method delivers smoother layer interfaces that well correlate to seismic data, while comparison with a global searching algorithm of simulated annealing (SA) in a watershed shows that though both methods deliver very similar good results, however, LCI algorithm presented in this paper runs much faster. The inversion results for the coal mine CSAMT survey show that a conductive water-bearing zone that was not revealed by the previous inversions has been identified by the LCI. This further demonstrates that the method presented in this paper works for CSAMT data inversion.

  6. The cost-constrained traveling salesman problem

    Energy Technology Data Exchange (ETDEWEB)

    Sokkappa, P.R.

    1990-10-01

    The Cost-Constrained Traveling Salesman Problem (CCTSP) is a variant of the well-known Traveling Salesman Problem (TSP). In the TSP, the goal is to find a tour of a given set of cities such that the total cost of the tour is minimized. In the CCTSP, each city is given a value, and a fixed cost-constraint is specified. The objective is to find a subtour of the cities that achieves maximum value without exceeding the cost-constraint. Thus, unlike the TSP, the CCTSP requires both selection and sequencing. As a consequence, most results for the TSP cannot be extended to the CCTSP. We show that the CCTSP is NP-hard and that no K-approximation algorithm or fully polynomial approximation scheme exists, unless P = NP. We also show that several special cases are polynomially solvable. Algorithms for the CCTSP, which outperform previous methods, are developed in three areas: upper bounding methods, exact algorithms, and heuristics. We found that a bounding strategy based on the knapsack problem performs better, both in speed and in the quality of the bounds, than methods based on the assignment problem. Likewise, we found that a branch-and-bound approach using the knapsack bound was superior to a method based on a common branch-and-bound method for the TSP. In our study of heuristic algorithms, we found that, when selecting modes for inclusion in the subtour, it is important to consider the neighborhood'' of the nodes. A node with low value that brings the subtour near many other nodes may be more desirable than an isolated node of high value. We found two types of repetition to be desirable: repetitions based on randomization in the subtour buildings process, and repetitions encouraging the inclusion of different subsets of the nodes. By varying the number and type of repetitions, we can adjust the computation time required by our method to obtain algorithms that outperform previous methods.

  7. Sistemática, taxonomía y domesticación de alpacas y llamas: nueva evidencia cromosómica y molecular Systematics, taxonomy and domestication of alpaca and llama: new chromosomal and molecular evidence

    Directory of Open Access Journals (Sweden)

    JUAN C MARÍN

    2007-06-01

    Full Text Available Existen cuatro especies de camélidos sudamericanos, dos de ellos silvestres, guanaco (Lama guanicoe y vicuña (Vicugna vicugna, y dos formas domésticas, alpaca (Lama pacos y llama (Lama glama, cuyo origen ha sido objeto de debate. En el presente estudio la variación en el patrón de bandas G de los cromosomas de llamas y alpacas y la secuencia de dos genes mitocondriales han sido usados para estudiar el origen y la clasificación de llamas y alpacas. Patrones de bandas cromosómicas similares fueron observados en las cuatro especies de Lamini, incluso similares a los descritos para camello, Camelus bactrianus. Sin embargo, se encontraron finas y consistentes diferencias en los brazos cortos del cromosoma 1, permitiendo separar a camellos, guanacos y llamas, de las de vicuñas y alpacas. Este patrón fue consistente incluso en un híbrido guanaco x alpaca. Relaciones equivalentes fueron encontradas en las secuencias completas del gen para citocromo b, así como en el árbol de expansión mínima de las secuencias parciales de la región control, agrupando a guanacos con llamas y a vicuñas con alpacas. Los análisis filogenéticos mostraron a V. vicugna y a L. guanicoe como grupos recíprocamente monofHéticos. El análisis de las secuencias de ambos genes mostró dos ciados entre las vicuñas, concordantes con las subespecies reconocidas para esta especie, pero los resultados obtenidos para guanacos no reflejaron la existencia de las cuatro subespecies previamente propuestas. El análisis combinado de variaciones cromosómicas y moleculares demostraron una alta similitud genética entre alpacas y vicuñas, así como entre llamas y guanacos. Aunque se revela hibridización direccional, nuestros resultados apoyan fuertemente la hipótesis de que la llama se deriva de L. guanicoe, y la alpaca de V. vicugna, apoyando la reclasificación de la alpaca como V. pacosFour camelid species exist in South America: two wild, the guanaco (Lama guanicoe and

  8. Molecular and Histopathologic Evidence for Systemic Infection by Mycobacterium Bovis in A Patient with Tuberculous Enteritis, Peritonitis, and Meningitis: A Case Report

    Directory of Open Access Journals (Sweden)

    Cheng-Yu Wei

    2004-06-01

    Full Text Available Mycobacterium bovis infection has been reported in several patients with AIDS in other countries. The prevalence of tuberculosis in Taiwan is higher than the World Health Organization standard. However, reports of M. bovis infection are rare. A 47-year-old male had the habit of drinking uncooked fresh deer's blood and unpasteurized deer's milk. He suffered from acute abdominal pain and underwent emergency laparotomy. Pathology demonstrated tuberculosis enteritis with colon perforation. The molecular diagnosis by nested polymerase chain reaction assay and single-strand conformation polymorphism assay showed M. bovis infection in the small intestine, mesenteric lymph nodes, and cerebrospinal fluid (CSF. Our results suggest that the most likely portal of entry of M. bovis is the gastrointestinal rather than the respiratory tract. Ingested M. bovis from unpasteurized deer's milk probably entered the mucosal macrophages of the intestine and then the draining mesenteric lymph nodes. As immunity declined, bacilli from the mesenteric lymph nodes disseminated to other organs and into the CSF.

  9. A centennial record of anthropogenic impacts and extreme weather events in southwestern Taiwan: Evidence from sedimentary molecular markers in coastal margin

    International Nuclear Information System (INIS)

    Kuo, Li-Jung; Lee, Chon-Lin; Louchouarn, Patrick; Huh, Chih-An; Liu, James T.; Chen, Jian-Cheng; Lee, Kun-Je

    2014-01-01

    Highlights: • Historical reconstruction of human and natural disturbances in SW Taiwan. • Comparative analysis of PAHs and lignin to evaluate sources/processes. • Distinct timing of PAH maxima between western Pacific, Europe and North America. • Consistently low (Ad/Al) v suggests quick transport of TOM by mountainous rivers. • Both PAHs and lignin point to turbidite flows driven by typhoon floods. - Abstract: A 100-year history of human and natural disturbances in southwestern Taiwan was reconstructed using a suite of molecular markers in four dated sediment cores from the upper slope region off the Gaoping River mouth. Trends in polycyclic aromatic hydrocarbons (PAHs) tracked Taiwan’s industrialization/urbanization starting in the 1970s, and the enactment of environmental regulatory policies thereafter. The predominant pyrogenic sources include vehicular, smelter, and coal combustion but spatial differences are observed among sub-regions of the shelf. Profiles of lignin oxidation products (LOPs) point to a significant increase in terrestrial organic matter inputs driven by land development after the 1970s. Low lignin diagenetic signature ratios [(Ad/Al) v ] in all sediments suggest quick transport of fresh plant material from land to sea via mountainous rivers. Shifts in PAHs, LOPs, and radionuclides in recent sediments reveal the deposition of turbidites resulting from typhoon-induced floods. Multiproxy analysis illustrates the interplay between anthropogenic activities and natural processes

  10. First molecular evidence of the simultaneous human infection with two species of Echinococcus granulosus sensu lato: Echinococcus granulosus sensu stricto and Echinococcus canadensis.

    Science.gov (United States)

    Oudni-M'rad, Myriam; M'rad, Selim; Ksia, Amine; Lamiri, Rachida; Mekki, Mongi; Nouri, Abdellatif; Mezhoud, Habib; Babba, Hamouda

    2016-03-01

    Cystic echinococcosis is a widespread zoonotic parasitic disease especially in Tunisia which is one of the most endemic countries in the Mediterranean area. The etiological agent, Echinococcus granulosus sensu lato, implies dogs and other canids as definitive hosts and different herbivore species as intermediate hosts. Human contamination occurs during the consumption of parasite eggs passed in the environment through canid feces. Hydatid cysts coming from a child operated for multiple echinococcosis were collected and analyzed in order to genotype and to obtain some epidemiological molecular information. Three targets, ribosomal DNA ITS1 fragment, NADH dehydrogenase subunit 1 (nad1), and mitochondrial cytochrome c oxydase subunit 1 (CO1) genes, were amplified and analyzed by RFLP and sequencing approach. This study presents the first worldwide report in human of a simultaneous infection with Echinococcus granulosus sensu stricto (genotype G1) and Echinococcus canadensis (genotype G6) species. This is also the first report of the presence of E. canadensis in the Tunisian population which argues in favor of a greater importance of this species in human infestation in Tunisia than previously believed.

  11. A centennial record of anthropogenic impacts and extreme weather events in southwestern Taiwan: evidence from sedimentary molecular markers in coastal margin.

    Science.gov (United States)

    Kuo, Li-Jung; Lee, Chon-Lin; Louchouarn, Patrick; Huh, Chih-An; Liu, James T; Chen, Jian-Cheng; Lee, Kun-Je

    2014-09-15

    A 100-year history of human and natural disturbances in southwestern Taiwan was reconstructed using a suite of molecular markers in four dated sediment cores from the upper slope region off the Gaoping River mouth. Trends in polycyclic aromatic hydrocarbons (PAHs) tracked Taiwan's industrialization/urbanization starting in the 1970s, and the enactment of environmental regulatory policies thereafter. The predominant pyrogenic sources include vehicular, smelter, and coal combustion but spatial differences are observed among sub-regions of the shelf. Profiles of lignin oxidation products (LOPs) point to a significant increase in terrestrial organic matter inputs driven by land development after the 1970s. Low lignin diagenetic signature ratios [(Ad/Al)v] in all sediments suggest quick transport of fresh plant material from land to sea via mountainous rivers. Shifts in PAHs, LOPs, and radionuclides in recent sediments reveal the deposition of turbidites resulting from typhoon-induced floods. Multiproxy analysis illustrates the interplay between anthropogenic activities and natural processes. Copyright © 2014 Elsevier Ltd. All rights reserved.

  12. In1-ghrelin, a splice variant of ghrelin gene, is associated with the evolution and aggressiveness of human neuroendocrine tumors: Evidence from clinical, cellular and molecular parameters

    Science.gov (United States)

    Gahete, Manuel D.; Ramos-Levi, Ana; Ibáñez-Costa, Alejandro; Rivero-Cortés, Esther; Serrano-Somavilla, Ana; Adrados, Magdalena; Culler, Michael D.; Castaño, Justo P.; Marazuela, Mónica

    2015-01-01

    Ghrelin system comprises a complex family of peptides, receptors (GHSRs), and modifying enzymes [e.g. ghrelin-O-acyl-transferase (GOAT)] that control multiple pathophysiological processes. Aberrant alternative splicing is an emerging cancer hallmark that generates altered proteins with tumorigenic capacity. Indeed, In1-ghrelin and truncated-GHSR1b splicing variants can promote development/progression of certain endocrine-related cancers. Here, we determined the expression levels of key ghrelin system components in neuroendocrine tumor (NETs) and explored their potential functional role. Twenty-six patients with NETs were prospectively/retrospectively studied [72 samples from primary and metastatic tissues (30 normal/42 tumors)] and clinical data were obtained. The role of In1-ghrelin in aggressiveness was studied in vitro using NET cell lines (BON-1/QGP-1). In1-ghrelin, GOAT and GHSR1a/1b expression levels were elevated in tumoral compared to normal/adjacent tissues. Moreover, In1-ghrelin, GOAT, and GHSR1b expression levels were positively correlated within tumoral, but not within normal/adjacent samples, and were higher in patients with progressive vs. with stable/cured disease. Finally, In1-ghrelin increased aggressiveness (e.g. proliferation/migration) of NET cells. Altogether, our data strongly suggests a potential implication of ghrelin system in the pathogenesis and/or clinical outcome of NETs, and warrant further studies on their possible value for the future development of molecular biomarkers with diagnostic/prognostic/therapeutic value. PMID:26124083

  13. Pinworm diversity in free-ranging howler monkeys (Alouatta spp.) in Mexico: Morphological and molecular evidence for two new Trypanoxyuris species (Nematoda: Oxyuridae).

    Science.gov (United States)

    Solórzano-García, Brenda; Nadler, Steven A; Pérez-Ponce de León, Gerardo

    2016-10-01

    Two new species of Trypanoxyuris are described from the intestine of free-ranging howler monkeys in Mexico, Trypanoxyuris multilabiatus n. sp. from the mantled howler Alouatta palliata, and Trypanoxyuris pigrae n. sp. from the black howler Alouatta pigra. An integrative taxonomic approach is followed, where conspicuous morphological traits and phylogenetic trees based on DNA sequences are used to test the validity of the two new species. The mitochondrial cytochrome oxidase subunit 1 gene, and the nuclear ribosomal 18S and 28S rRNA genes were used for evolutionary analyses, with the concatenated dataset of all three genes used for maximum likelihood and Bayesian phylogenetic analyses. The two new species of pinworms from howler monkeys were morphologically distinct and formed reciprocally monophyletic lineages in molecular phylogenetic trees. The three species from howler monkeys, T. multilabiatus n. sp., T. pigrae n. sp., and Trypanoxyuris minutus, formed a monophyletic group with high bootstrap and posterior probability support values. Phylogenetic patterns inferred from sequence data support the hypothesis of a close evolutionary association between these primate hosts and their pinworm parasites. The results suggest that the diversity of pinworm parasites from Neotropical primates might be underestimated. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  14. THE TWO MOLECULAR CLOUDS IN RCW 38: EVIDENCE FOR THE FORMATION OF THE YOUNGEST SUPER STAR CLUSTER IN THE MILKY WAY TRIGGERED BY CLOUD–CLOUD COLLISION

    Energy Technology Data Exchange (ETDEWEB)

    Fukui, Y.; Torii, K.; Ohama, A.; Hasegawa, K.; Hattori, Y.; Sano, H.; Yamamoto, H.; Tachihara, K. [Department of Physics, Nagoya University, Chikusa-ku, Nagoya, Aichi 464-8601 (Japan); Ohashi, S.; Fujii, K.; Kuwahara, S. [Department of Astronomy, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 133-0033 (Japan); Mizuno, N.; Okuda, T. [National Astronomical Observatory of Japan, Mitaka, Tokyo 181-8588 (Japan); Dawson, J. R. [Department of Physics and Astronomy and MQ Research Centre in Astronomy, Astrophysics and Astrophotonics, Macquarie University, NSW 2109 (Australia); Onishi, T. [Department of Astrophysics, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Nakaku, Sakai, Osaka 599-8531 (Japan); Mizuno, A., E-mail: torii@a.phys.nagoya-u.ac.jp [Solar-Terrestrial Environment Laboratory, Nagoya University, Chikusa-ku, Nagoya 464-8601 (Japan)

    2016-03-20

    We present distributions of two molecular clouds having velocities of 2 and 14 km s{sup −1} toward RCW 38, the youngest super star cluster in the Milky Way, in the {sup 12}CO J = 1–0 and 3–2 and {sup 13}CO J = 1–0 transitions. The two clouds are likely physically associated with the cluster as verified by the high intensity ratio of the J = 3–2 emission to the J = 1–0 emission, the bridging feature connecting the two clouds in velocity, and their morphological correspondence with the infrared dust emission. The velocity difference is too large for the clouds to be gravitationally bound. We frame a hypothesis that the two clouds are colliding with each other by chance to trigger formation of the ∼20 O stars that are localized within ∼0.5 pc of the cluster center in the 2 km s{sup −1} cloud. We suggest that the collision is currently continuing toward part of the 2 km s{sup −1} cloud where the bridging feature is localized. This is the third super star cluster alongside Westerlund 2 and NGC 3603 where cloud–cloud collision has triggered the cluster formation. RCW 38 is the youngest super star cluster in the Milky Way, holding a possible sign of on-going O star formation, and is a promising site where we may be able to witness the moment of O star formation.

  15. Morphologic and molecular study of hemoparasites in wild corvids and evidence of sequence identity with Plasmodium DNA detected in captive black-footed penguins (Spheniscus demersus).

    Science.gov (United States)

    Leclerc, Antoine; Chavatte, Jean-Marc; Landau, Irène; Snounou, Georges; Petit, Thierry

    2014-09-01

    A morphologic and molecular epidemiologic investigation was conducted on a captive African black-footed penguin (Spheniscus demersus) colony with a history of Plasmodium infections at La Palmyre Zoo (France). Each penguin received 12.5 mg of pyrimethamine twice a week as a prophylaxis every year from April to November. Although Plasmodium parasites were not detected in blood smears and tissues collected from the penguins, various blood parasites were recorded in blood smears from wild Eurasian magpies (Pica pica) and carrion crows (Corvus corone) sampled at the same time in the study area. These parasites consisted of several Plasmodium spp. (P. lenoblei, P. dorsti, P bioccai, P. relictum, P. dherteae, P. beaucournui, P. maior, P. tranieri, and P. snounoui), Parahaemoproteus spp., Trypanosoma spp., and Leucocytozoon spp. On the other hand, nested polymerase chain reaction enabled detection of Plasmodium DNA in 28/44 (64%) penguins, 15/25 (60%) magpies, and 4/9 (44%) crows. Sequencing and phylogenetic analyses indicated that the parasite DNA amplified from the penguins, magpies, and crows were similar. Magpies and crows could therefore act as a reservoir for penguin Plasmodium infections, which may be more prevalent than previously thought. Morphologic characterization of the Plasmodium spp. detected in the penguins, as well as further biological and epidemiologic studies, are needed to fully understand the transmission of Plasmodium parasites to captive penguins.

  16. No molecular epidemiological evidence supporting household transmission of zoonotic Giardia duodenalis and Cryptosporidium spp. from pet dogs and cats in the province of Álava, Northern Spain.

    Science.gov (United States)

    de Lucio, Aida; Bailo, Begoña; Aguilera, María; Cardona, Guillermo A; Fernández-Crespo, Juan C; Carmena, David

    2017-06-01

    The role of pet dogs and cats as suitable source of human infections by the diarrheagenic protozoan parasites Giardia duodenalis and Cryptosporidium spp. has been a topic of intense debate for long time and still remains a largely unsolved problem. In this cross-sectional molecular epidemiological survey we attempted to investigate whether zoonotic (or zooanthroponotic) disease transmission was occurring among humans and domestic dogs and cats sharing the same spatial and temporal setting in both rural and urban areas of the province of Álava, Northern Spain. A total of 268 (including 179 human, 55 canine, and 34 feline) individual faecal specimens were obtained from 63 family households during February-March and November-December 2014. Detection of G. duodenalis cysts and Cryptosporidium spp. oocysts was achieved by direct fluorescence microscopy (DFAT) and PCR-based methods targeting the small subunit (SSU) ribosomal RNA gene of the parasites. Giardia-positive isolates were subsequently sub-genotyped at the glutamate dehydrogenase (GDH) and β-giardin (BG) genes. Overall, G. duodenalis infections were identified in 3.4% (6/179) of humans, 29% (16/55) of dogs, and 5.9% (2/34) of cats, respectively. Cryptosporidium spp. infections were detected in 1.1% (2/179) of humans, 5.5% (3/55) of dogs, and 8.8% (3/34) of cats, respectively. Simultaneous infections in human and canine/feline hosts by G. duodenalis or Cryptosporidium spp. were only demonstrated in a single household in which a cat and its owner tested positive for Cryptosporidium by DFAT, but this result could not be confirmed by SSU-PCR. Infections were homogeneously distributed among the studied human or animal populations irrespectively of their sex, age group, or geographical region of origin. Inadequate washing of raw vegetables and fruits was the only risk factor significantly associated to a higher likelihood of having human giardiosis/cryptosporidiosis. Molecular characterization of G. duodenalis

  17. Distinctly Different Glass Transition Behaviors of Trehalose Mixed with Na2HPO 4 or NaH 2PO 4: Evidence for its Molecular Origin.

    Science.gov (United States)

    Weng, Lindong; Elliott, Gloria D

    2015-07-01

    The present study is aimed at understanding how the interactions between sugar molecules and phosphate ions affect the glass transition temperature of their mixtures, and the implications for pharmaceutical formulations. The glass transition temperature (Tg) and the α-relaxation temperature (Tα) of dehydrated trehalose/sodium phosphate mixtures (monobasic or dibasic) were determined by differential scanning calorimetry and dynamic mechanical analysis, respectively. Molecular dynamics simulations were also conducted to investigate the microscopic interactions between sugar molecules and phosphate ions. The hydrogen-bonding characteristics and the self-aggregation features of these mixtures were quantified and compared. Thermal analysis measurements demonstrated that the addition of NaH2PO4 decreased both the glass transition temperature and the α-relaxation temperature of the dehydrated trehalose/NaH2PO4 mixture compared to trehalose alone while both Tg and Tα were increased by adding Na2HPO4 to pure trehalose. The hydrogen-bonding interactions between trehalose and HPO4(2-) were found to be stronger than both the trehalose-trehalose hydrogen bonds and those formed between trehalose and H2PO4(-). The HPO4(2-) ions also aggregated into smaller clusters than H2PO4(-) ions. The trehalose/Na2HPO4 mixture yielded a higher T g than pure trehalose because marginally self-aggregated HPO4(2-) ions established a strengthened hydrogen-bonding network with trehalose molecules. In contrast H2PO4(-) ions served only as plasticizers, resulting in a lower Tg of the mixtures than trehalose alone, creating large-sized ionic pockets, weakening interactions, and disrupting the original hydrogen-bonding network amongst trehalose molecules.

  18. Degradation of contaminants by Cu{sup +}-activated molecular oxygen in aqueous solutions: Evidence for cupryl species (Cu{sup 3+})

    Energy Technology Data Exchange (ETDEWEB)

    Feng, Yong, E-mail: fengy@hku.hk [Department of Civil Engineering, The University of Hong Kong, Pokfulam Road (Hong Kong); Lee, Po-Heng, E-mail: phlee@polyu.edu.hk [Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon (Hong Kong); Wu, Deli, E-mail: wudeli@tongji.edu.cn [State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science & Engineering, Tongji University, Shanghai 200092 (China); Zhou, Zhengyuan, E-mail: zzy247@hku.hk [Department of Civil Engineering, The University of Hong Kong, Pokfulam Road (Hong Kong); Li, Hangkong, E-mail: hangkong@hku.hk [Department of Civil Engineering, The University of Hong Kong, Pokfulam Road (Hong Kong); Shih, Kaimin, E-mail: kshih@hku.hk [Department of Civil Engineering, The University of Hong Kong, Pokfulam Road (Hong Kong)

    2017-06-05

    Highlights: • Sulfadiazine and methylene blue were nearly completely degraded by Cu{sup +}-O{sub 2} oxidation. • Reaction of Cu{sup +} and hydrogen peroxide produced Cu{sup 3+} as the major active species. • 5,5-dimethyl-2-hydroxypyrrolidine-N-oxyl (DMPO-OH) was found in the reaction process. • Benzoic acid and electron paramagnetic resonance are not capable to differentiate Cu{sup 3+} and ·OH. - Abstract: Copper ions (Cu{sup 2+} and Cu{sup +}) have shown potential as Fenton-like activators for the circumneutral removal of organic contaminants from aqueous solutions. However, the major active species (cupryl species (Cu{sup 3+}) versus hydroxyl radical (·OH)) produced during the activation of hydrogen peroxide by Cu{sup +} remain unclear. In this study, Cu{sup +}-O{sub 2} oxidation, in which hydrogen peroxide is produced via the activated decomposition of dissolved molecular oxygen, was used to degrade sulfadiazine, methylene blue, and benzoic acid. The results showed that both sulfadiazine and methylene blue could be efficiently degraded by Cu{sup +}-O{sub 2} oxidation in a wide effective pH range from 2.0 to 10.0. Quenching experiments with different alcohols and the effect of Br{sup −} suggested that Cu{sup 3+} rather than ·OH was the major active species. Electron paramagnetic resonance detected 5,5-dimethyl-2-hydroxypyrrolidine-N-oxyl (DMPO-OH), which was probably produced by the oxidation of DMPO by Cu{sup 3+} or ·OH formed as a product of Cu{sup 3+} decomposition. 4-hydroxybenzoic acid was produced during the degradation of benzoic acid by Cu{sup 3+}. The findings of this study may help to explain the inconsistency regarding the dominant active species produced by the interaction of Cu{sup +} and hydrogen peroxide.

  19. Constraining the SIF - GPP relationship via estimation of NPQ

    Science.gov (United States)

    Silva, C. E.; Yang, X.; Tang, J.; Lee, J. E.; Cushman, K.; Toh Yuan Kun, L.; Kellner, J. R.

    2016-12-01

    Airborne and satellite measurements of solar-induced fluorescence (SIF) have the potential to improve estimates of gross primary production (GPP). Plants dissipate absorbed photosynthetically active radiation (APAR) among three de-excitation pathways: SIF, photochemical quenching (PQ), which results in electron transport and the production of ATP and NADPH consumed during carbon fixation (i.e., GPP), and heat dissipation via conversion of xanthophyll pigments (non-photochemical quenching: NPQ). As a result, the relationship between SIF and GPP is a function of NPQ and may vary temporally and spatially with environmental conditions (e.g., light and water availability) and plant traits (e.g., leaf N content). Accurate estimates of any one of the de-excitation pathways require measurement of the other two. Here we combine half-hourly measurements of canopy APAR and SIF with eddy covariance estimates of GPP at Harvard Forest to close the canopy radiation budget and infer canopy NPQ throughout the 2013 growing season. We use molecular-level photosynthesis equations to compute PQ (umol photons m-2s-1) from GPP (umol CO2 m-2s-1) and invert an integrated canopy radiative transfer and leaf-level photosynthesis/fluorescence model (SCOPE) to quantify hemispherically and spectrally-integrated SIF emission (umol photons m-2s-1) from single band (760 nm) top-of-canopy SIF measurements. We estimate half-hourly NPQ as the residual required to close the radiation budget (NPQ = APAR - SIF - PQ). Our future work will test estimated NPQ against simultaneously acquired measurements of the photochemical reflectance index (PRI), a spectral index sensitive to xanthopyll pigments. By constraining two of the three de-excitation pathways, simultaneous SIF and PRI measurements are likely to improve GPP estimates, which are crucial to the study of climate - carbon cycle interactions.

  20. Molecular evidence for a diverse green algal community growing in the hair of sloths and a specific association with Trichophilus welckeri (Chlorophyta, Ulvophyceae

    Directory of Open Access Journals (Sweden)

    Chiarello Adriano G

    2010-03-01

    Full Text Available Abstract Background Sloths are slow-moving arboreal mammals inhabiting tropical rainforests in Central and South America. The six living species of sloths are occasionally reported to display a greenish discoloration of their pelage. Trichophilus welckeri, a green algal species first described more than a century ago, is widely believed to discolor the animals fur and provide the sloth with effective camouflage. However, this phenomenon has not been explored in any detail and there is little evidence to substantiate this widely held opinion. Results Here we investigate the genetic diversity of the eukaryotic community present in fur of all six extant species of sloth. Analysis of 71 sloth hair samples yielding 426 partial 18S rRNA gene sequences demonstrates a diverse eukaryotic microbial assemblage. Phylogenetic analysis reveals that sloth fur hosts a number of green algal species and suggests that acquisition of these organisms from the surrounding rainforest plays an important role in the discoloration of sloth fur. However, an alga corresponding to the morphological description of Trichophilus welckeri was found to be frequent and abundant on sloth fur. Phylogenetic analysis demonstrated the retention of this alga on the fur of sloths independent of geographic location. Conclusions These results demonstrate a unique diverse microbial eukaryotic community in the fur of sloths from Central and South America. Our analysis streghtens the case for symbiosis between sloths and Trichophilus welckeri.

  1. New molecular evidence for fragmentation between two distant populations of the threatened stingless bee Melipona subnitida Ducke (Hymenoptera, Apidae, Meliponini

    Directory of Open Access Journals (Sweden)

    Geice R. Silva

    2014-06-01

    Full Text Available For a snapshot assessment of the genetic diversity present within Melipona subnitida, an endemic stingless bee distributed in the semi-arid region of northeastern Brazil, populations separated by over 1,000 km distance were analyzed by ISSR genotyping. This is a prerequisite for the establishment of efficient management and conservation practices. From 21 ISSR primers tested, only nine revealed consistent and polymorphic bands (loci. PCR reactions resulted in 165 loci, of which 92 were polymorphic (57.5%. Both ΦST (ARLEQUIN and θB (HICKORY presented high values of similar magnitude (0.34, p<0.0001 and 0.33, p<0.0001, respectively, showing that these two groups were highly structured. The dendrogram obtained by the cluster analysis and the scatter-plot of the PCoA corroborate with the data presented by the AMOVA and θB tests. Clear evidence of subdivision among sampling sites was also observed by the Bayesian grouping model analysis (STRUCTURE of the ISSR data. It is clear from this study that conservation strategies should take into account the heterogeneity of these two separate populations, and address actions towards their sustainability by integrating our findings with ecological tools.

  2. Functional and molecular evidence for heteromeric association of P2Y1 receptor with P2Y2 and P2Y4 receptors in mouse granulocytes.

    Science.gov (United States)

    Ribeiro-Filho, Antonio Carlos; Buri, Marcus Vinicius; Barros, Carlos Castilho; Dreyfuss, Juliana Luporini; Nader, Helena Bonciani; Justo, Giselle Zenker; Craveiro, Rogério Bastos; Pesquero, João Bosco; Miranda, Antonio; Ferreira, Alice Teixeira; Paredes-Gamero, Edgar Julian

    2016-07-07

    All hematopoietic cells express P2 receptors, however pharmacological characteristics such as expression and affinity in granulocytes are unknown. Pharmacological characteristics of P2 receptors were evaluated by Ca(2+) measurements using Fura-2 fluorophore. P2 receptors expression were analyzed by flow cytometry and RT-PCR. P2 interaction were shown by coimmunoprecipitation, western blotting and FRET. Granulocytes were responsive to P2Y agonists, whereas P2X agonists were ineffective. Ca(2+) increase, elicited by ADP and UTP was dependent on intracellular stocks and sensitive to G-coupled receptor inhibition. Moreover, MRS2179, a specific antagonist of the P2Y1 receptor, abolished ADP response. Interestingly, ADP and UTP exhibited full heterologous desensitization, suggesting that these agonists interact with the same receptor. The heteromeric association between P2Y1 receptor and the P2Y2 and P2Y4 receptors was shown by immunoprecipitation and FRET analysis. Clear evidence of heteromeric association of P2Y receptors was found during the evaluation of P2 receptors present in mice granulocytes, which could impact in the classical pharmacology of P2Y receptors in granulocytes.

  3. KINETIC CONSEQUENCES OF CONSTRAINING RUNNING BEHAVIOR

    Directory of Open Access Journals (Sweden)

    John A. Mercer

    2005-06-01

    Full Text Available It is known that impact forces increase with running velocity as well as when stride length increases. Since stride length naturally changes with changes in submaximal running velocity, it was not clear which factor, running velocity or stride length, played a critical role in determining impact characteristics. The aim of the study was to investigate whether or not stride length influences the relationship between running velocity and impact characteristics. Eight volunteers (mass=72.4 ± 8.9 kg; height = 1.7 ± 0.1 m; age = 25 ± 3.4 years completed two running conditions: preferred stride length (PSL and stride length constrained at 2.5 m (SL2.5. During each condition, participants ran at a variety of speeds with the intent that the range of speeds would be similar between conditions. During PSL, participants were given no instructions regarding stride length. During SL2.5, participants were required to strike targets placed on the floor that resulted in a stride length of 2.5 m. Ground reaction forces were recorded (1080 Hz as well as leg and head accelerations (uni-axial accelerometers. Impact force and impact attenuation (calculated as the ratio of head and leg impact accelerations were recorded for each running trial. Scatter plots were generated plotting each parameter against running velocity. Lines of best fit were calculated with the slopes recorded for analysis. The slopes were compared between conditions using paired t-tests. Data from two subjects were dropped from analysis since the velocity ranges were not similar between conditions resulting in the analysis of six subjects. The slope of impact force vs. velocity relationship was different between conditions (PSL: 0.178 ± 0.16 BW/m·s-1; SL2.5: -0.003 ± 0.14 BW/m·s-1; p < 0.05. The slope of the impact attenuation vs. velocity relationship was different between conditions (PSL: 5.12 ± 2.88 %/m·s-1; SL2.5: 1.39 ± 1.51 %/m·s-1; p < 0.05. Stride length was an important factor

  4. Molecular Expression and Pharmacological Evidence for a Functional Role of Kv7 Channel Subtypes in Guinea Pig Urinary Bladder Smooth Muscle

    Science.gov (United States)

    Afeli, Serge A. Y.; Malysz, John; Petkov, Georgi V.

    2013-01-01

    Voltage-gated Kv7 (KCNQ) channels are emerging as essential regulators of smooth muscle excitability and contractility. However, their physiological role in detrusor smooth muscle (DSM) remains to be elucidated. Here, we explored the molecular expression and function of Kv7 channel subtypes in guinea pig DSM by RT-PCR, qRT-PCR, immunohistochemistry, electrophysiology, and isometric tension recordings. In whole DSM tissue, mRNAs for all Kv7 channel subtypes were detected in a rank order: Kv7.1~Kv7.2Kv7.3~Kv7.5Kv7.4. In contrast, freshly-isolated DSM cells showed mRNA expression of: Kv7.1~Kv7.2Kv7.5Kv7.3~Kv7.4. Immunohistochemical confocal microscopy analyses of DSM, conducted by using co-labeling of Kv7 channel subtype-specific antibodies and α-smooth muscle actin, detected protein expression for all Kv7 channel subtypes, except for the Kv7.4, in DSM cells. L-364373 (R-L3), a Kv7.1 channel activator, and retigabine, a Kv7.2-7.5 channel activator, inhibited spontaneous phasic contractions and the 10-Hz electrical field stimulation (EFS)-induced contractions of DSM isolated strips. Linopiridine and XE991, two pan-Kv7 (effective at Kv7.1-Kv7.5 subtypes) channel inhibitors, had opposite effects increasing DSM spontaneous phasic and 10 Hz EFS-induced contractions. EFS-induced DSM contractions generated by a wide range of stimulation frequencies were decreased by L-364373 (10 µM) or retigabine (10 µM), and increased by XE991 (10 µM). Retigabine (10 µM) induced hyperpolarization and inhibited spontaneous action potentials in freshly-isolated DSM cells. In summary, Kv7 channel subtypes are expressed at mRNA and protein levels in guinea pig DSM cells. Their pharmacological modulation can control DSM contractility and excitability; therefore, Kv7 channel subtypes provide potential novel therapeutic targets for urinary bladder dysfunction. PMID:24073284

  5. Molecular and Microbial Mechanisms Increasing Soil C Storage Under Future Rates of Anthropogenic N Deposition

    Energy Technology Data Exchange (ETDEWEB)

    Zak, Donald R. [Univ. of Michigan, Ann Arbor, MI (United States)

    2017-11-17

    A growing body of evidence reveals that anthropogenic N deposition can reduce the microbial decay of plant detritus and increase soil C storage across a wide range of terrestrial ecosystems. This aspect of global change has the potential to constrain the accumulation of anthropogenic CO2 in the Earth’s atmosphere, and hence slow the pace of climate warming. The molecular and microbial mechanisms underlying this biogeochemical response are not understood, and they are not a component of any coupled climate-biogeochemical model estimating ecosystem C storage, and hence, the future climate of an N-enriched Earth. Here, we report the use of genomic-enabled approaches to identify the molecular underpinnings of the microbial mechanisms leading to greater soil C storage in response to anthropogenic N deposition, thereby enabling us to better anticipate changes in soil C storage.

  6. Placental invasion, preeclampsia risk and adaptive molecular evolution at the origin of the great apes: evidence from genome-wide analyses.

    Science.gov (United States)

    Crosley, E J; Elliot, M G; Christians, J K; Crespi, B J

    2013-02-01

    Recent evidence from chimpanzees and gorillas has raised doubts that preeclampsia is a uniquely human disease. The deep extravillous trophoblast (EVT) invasion and spiral artery remodeling that characterizes our placenta (and is abnormal in preeclampsia) is shared within great apes, setting Homininae apart from Hylobatidae and Old World Monkeys, which show much shallower trophoblast invasion and limited spiral artery remodeling. We hypothesize that the evolution of a more invasive placenta in the lineage ancestral to the great apes involved positive selection on genes crucial to EVT invasion and spiral artery remodeling. Furthermore, identification of placentally-expressed genes under selection in this lineage may identify novel genes involved in placental development. We tested for positive selection in approximately 18,000 genes using the ratio of non-synonymous to synonymous amino acid substitution for protein-coding DNA. DAVID Bioinformatics Resources identified biological processes enriched in positively selected genes, including processes related to EVT invasion and spiral artery remodeling. Analyses revealed 295 and 264 genes under significant positive selection on the branches ancestral to Hominidae (Human, Chimp, Gorilla, Orangutan) and Homininae (Human, Chimp, Gorilla), respectively. Gene ontology analysis of these gene sets demonstrated significant enrichments for several functional gene clusters relevant to preeclampsia risk, and sets of placentally-expressed genes that have been linked with preeclampsia and/or trophoblast invasion in other studies. Our study represents a novel approach to the identification of candidate genes and amino acid residues involved in placental pathologies by implicating them in the evolution of highly-invasive placenta. Copyright © 2012 Elsevier Ltd. All rights reserved.

  7. Molecular evidence confirms the taxonomic separation of Lutzomyia tihuiliensis from Lutzomyia pia (Diptera: Psychodidae) and the usefulness of pleural pigmentation patterns in species identification.

    Science.gov (United States)

    Pérez-Doria, Alveiro; Bejarano, Eduar Elías; Sierra, Diana; Vélez, Iván Darío

    2008-07-01

    The phlebotomine sand flies Lutzomyia pia (Fairchild & Hertig 1961) and Lutzomyia tihuiliensis Le Pont, Torrez-Espejo & Dujardin 1997 (Diptera: Psychodidae) belong to the pia series of the Lu. verrucarum species group, which includes several species that bite humans in Andean foci of leishmaniasis. The females of these two species exhibit isometry and isomorphism in anatomical structures of the head and terminalia commonly used in taxonomic identification of sand flies. They can only be differentiated based on subtle differences in the pigmentation of the pleura. In Lu. tihuiliensis, this is restricted to the basal portions of the katepimeron and katepisternum, whereas in Lu. pia both structures are totally pigmented. Taking into account the subtle morphological differences between these species, the objective of the current study was to evaluate the specific taxonomic status of Lu. tihuiliensis with respect to Lu. pia. A 475-bp portion of the mitochondrial genome was sequenced, composed of the 3' end of the cytochrome b gene, intergenic spacer 1, the transfer RNA gene for serine, intergenic spacer 2, and the 3' end of the gene NAD dehydrogenase 1. Genetic analysis confirms that Lu. tihuiliensis and Lu. pia constitute two distinct species and this is supported by four strong lines of evidence, i.e., the paired genetic distances, size differences and amino acid composition of the cytochrome b protein, presence and absence of intergenic spacer one and divergence observed in the sequence of the transfer RNA gene for serine. It also confirms the validity of the pleural pigmentation pattern as a species diagnostic character and the importance of performing a detailed examination of this character during morphological determination of phlebotomine sand flies in the series pia.

  8. Molecular cloning and functional analysis of the phosphomannomutase (PMM) gene from Dendrobium officinale and evidence for the involvement of an abiotic stress response during germination.

    Science.gov (United States)

    He, Chunmei; Zeng, Songjun; Teixeira da Silva, Jaime A; Yu, Zhenming; Tan, Jianwen; Duan, Jun

    2017-07-01

    Phosphomannomutase (PMM, EC 5.4.2.8) catalyzes the interconversion of mannose-6-phosphate to mannose-1-phosphate, the precursor for the synthesis of GDP-mannose. In this study, the complementary DNA (cDNA) of the Phosphomannomutase (PMM) gene was initially cloned from Dendrobium officinale by RACE method. Transient transform result showed that the DoPMM protein was localized in the cytoplasm. The DoPMM gene was highly expressed in the stems of D. officinale both in vegetative and reproductive developmental stages. The putative promoter was cloned by TAIL-PCR and used for searched cis-elements. Stress-related cis-elements like ABRE, TCA-element, and MBS were found in the promoter regions. The DoPMM gene was up-regulated after treatment with abscisic acid, salicylic acid, cold, polyethylene glycol, and NaCl. The total ascorbic acid (AsA) and polysaccharide content in all of the 35S::DoPMM Arabidopsis thaliana transgenic lines #1, #2, and #5 showed a 40, 39, and 31% increase in AsA and a 77, 22, and 39% increase in polysaccharides, respectively more than wild-type (WT) levels. All three 35S::DoPMM transgenic lines exhibited a higher germination percentage than WT plants when seeded on half-strength MS medium supplemented with 150 mM NaCl or 300 mM mannitol. These results provide genetic evidence for the involvement of PMM genes in the biosynthesis of AsA and polysaccharides and the mediation of PMM genes in abiotic stress tolerance during seed germination in A. thaliana.

  9. Evidence for anthropophily in five species of phlebotomine sand flies (Diptera: Psychodidae) from northern Colombia, revealed by molecular identification of bloodmeals.

    Science.gov (United States)

    Paternina, Luís E; Verbel-Vergara, Daniel; Romero-Ricardo, Luís; Pérez-Doria, Alveiro; Paternina-Gómez, Margaret; Martínez, Lily; Bejarano, Eduar E

    2016-01-01

    Identification of the bloodmeal sources of phlebotomine sand flies is fundamental to determining which species are anthropophilic and understanding the transmission of Leishmania parasites in natural epidemiological settings. The objective of this study was to identify sand fly bloodmeals in the mixed leishmaniasis focus of the department of Sucre, northern Colombia. In all 141 engorged female sand flies were analyzed, after being captured in intradomiciliary, peridomiciliary and extradomiciliary habitats with Shannon and CDC traps and by active searching in diurnal resting sites. Bloodmeals were identified by sequencing and analysis of a 358bp fragment of the mitochondrial gene Cytochrome b (CYB) and a 330bp fragment of the nuclear gene prepronociceptin (PNOC). Using both genes 105 vertebrate bloodmeals were identified, with an efficiency of 72% for CYB but only 7% for PNOC. Ten species of vertebrates were identified as providing bloodmeal sources for 8 sand fly species: Homo sapiens (Lutzomyia evansi, Lutzomyia panamensis, Lutzomyia micropyga, Lutzomyia shannoni and Lutzomyia atroclavata), Equus caballus (L. evansi, L. panamensis and Lutzomyia cayennensis cayennensis), Equus asinus (L. evansi and L. panamensis), Bos taurus (L. evansi, L. panamensis and L. c. cayennensis), Tamandua mexicana (L. shannoni and Lutzomyia trinidadensis), Proechimys guyanensis (L. evansi, L. panamensis and L. c. cayennensis), Mabuya sp. (Lutzomyia micropyga), Anolissp. (L. micropyga), Sus scrofa (L. evansi and Lutzomyia gomezi) and Gallus gallus (L. evansi). Cattle, donkeys, humans and pigs were significantly more important than other animals (P=0.0001) as hosts of L. evansi, this being the most abundant sand fly species. The five Lutzomyia species in which blood samples of human origin were detected included L. micropyga and L. atroclavata, constituting the first evidence of anthropophily in both species. Copyright © 2015 Elsevier B.V. All rights reserved.

  10. Onomatopoeia characters extraction from comic images using constrained Delaunay triangulation

    Science.gov (United States)

    Liu, Xiangping; Shoji, Kenji; Mori, Hiroshi; Toyama, Fubito

    2014-02-01

    A method for extracting onomatopoeia characters from comic images was developed based on stroke width feature of characters, since they nearly have a constant stroke width in a number of cases. An image was segmented with a constrained Delaunay triangulation. Connected component grouping was performed based on the triangles generated by the constrained Delaunay triangulation. Stroke width calculation of the connected components was conducted based on the altitude of the triangles generated with the constrained Delaunay triangulation. The experimental results proved the effectiveness of the proposed method.

  11. Evidence of a local negative role for cocaine and amphetamine regulated transcript (CART, inhibins and low molecular weight insulin like growth factor binding proteins in regulation of granulosa cell estradiol production during follicular waves in cattle

    Directory of Open Access Journals (Sweden)

    Ireland James J

    2006-04-01

    Full Text Available Abstract The ability of ovarian follicles to produce large amounts of estradiol is a hallmark of follicle health status. Estradiol producing capacity is lost in ovarian follicles before morphological signs of atresia. A prominent wave like pattern of growth of antral follicles is characteristic of monotocous species such as cattle, horses and humans. While our knowledge of the role of pituitary gonadotropins in support of antral follicle growth and development is well established, the intrinsic factors that suppress estradiol production and may help promote atresia during follicular waves are not well understood. Numerous growth factors and cytokines have been reported to suppress granulosa cell estradiol production in vitro, but the association of expression of many such factors in vivo with follicle health status and their physiological significance are not clear. The purpose of this review is to discuss the in vivo and in vitro evidence supporting a local physiological role for cocaine and amphetamine regulated transcript, inhibins and low molecular weight insulin like growth factor binding proteins in negative regulation of granulosa cell estradiol production, with emphasis on evidence from the bovine model system.

  12. Transmission of Leishmania infantum in the Canine Leishmaniasis Focus of Mont-Rolland, Senegal: Ecological, Parasitological and Molecular Evidence for a Possible Role of Sergentomyia Sand Flies.

    Directory of Open Access Journals (Sweden)

    Massila Wagué Senghor

    2016-11-01

    Full Text Available Leishmania (L. infantum is the causative agent in an endemic focus of canine leishmaniasis in the Mont-Rolland district (Thiès, Senegal. In this area, the transmission cycle is well established and more than 30% of dogs and 20% of humans are seropositive for L. infantum. However, the sand fly species involved in L. infantum transmission cycle are still unknown. Between 2007 and 2010, 3654 sand flies were collected from different environments (indoor, peridomestic, farming and sylvatic areas to identify the main L. infantum vector(s. Nine sand fly species were identified. The Phlebotomus genus (n = 54 specimens; Phlebotomus (Ph duboscqi and Phlebotomus (Ph. rodhaini was markedly under-represented in comparison to the Sergentomyia genus (n = 3600 specimens; Sergentomyia (Se adleri, Se. clydei, Se. antennata, Se. buxtoni, Se. dubia, Se. schwetzi and Se. magna. Se. dubia and Se. schwetzi were the dominant species indoor and in peridomestic environments, near humans and dogs. Blood-meal analysis indicated their anthropophilic behavior. Some Se. schwetzi specimens fed also on dogs. The dissection of females in the field allowed isolating L. infantum from sand flies of the Sergentomyia genus (0.4% of Se. dubia and 0.79% of Se. schwetzi females. It is worth noting that one Se. dubia female not engorged and not gravid revealed highly motile metacyclic of L. infantum in the anterior part of the midgut. PCR-based diagnosis and sequencing targeting Leishmania kinetoplast DNA (kDNA highlighted a high rate of L. infantum-positive females (5.38% of Se. dubia, 4.19% of Se. schwetzi and 3.64% of Se. magna. More than 2% of these positive females were unfed, suggesting the parasite survival after blood-meal digestion or egg laying. L. infantum prevalence in Se. schwetzi was associated with its seroprevalence in dogs and humans and L. infantum prevalence in Se. dubia was associated with its seroprevalence in humans. These evidences altogether strongly suggest that

  13. Molecular evidence for the existence of lipopolysaccharide-induced TNF-alpha factor (LITAF) and Rel/NF-kB pathways in disk abalone (Haliotis discus discus).

    Science.gov (United States)

    De Zoysa, Mahanama; Nikapitiya, Chamilani; Oh, Chulhong; Whang, Ilson; Lee, Jae-Seong; Jung, Sung-Ju; Choi, Cheol Young; Lee, Jehee

    2010-01-01

    The lipopolysaccharide-induced TNF-alpha factor (LITAF) and Rel family nuclear factor kappaB (Rel/NF-kB) are two important transcription factors which play major roles in the regulating inflammatory cytokine, apoptosis and immune related genes. Here, we report the discovery of disk abalone LITAF (AbLITAF) and Rel/NF-kB (AbRel/NF-kB) homologues and their immune responses. Full-length cDNA of AbLITAF consists of 441 bp open reading frame (ORF) that translates into putative peptide of 147 aa. Analysis of AbLITAF sequence showed it has characteristic LITAF (Zn(+2)) binding domain with two CXXC motifs. Phylogenetic analysis results further revealed that AbLITAF is a member of LITAF family. AbRel/NF-kB is 584 aa protein that contains several characteristic motifs including Rel homology domain (RHD), Rel protein signature, DNA binding motif, nuclear localization signal (NLS) and transcription factor immunoglobulin - like fold (TIG) similar to their invertebrate and vertebrate counterparts. Tissue specific analysis results showed that both AbLITAF and AbRel/NF-kB mRNA was expressed ubiquitously in all selected tissues in constitutive manner. However, constitutive expression of AbLITAF was higher than AbRel/NF-kB in all tissues except mantle. Upon immune challenge by bacteria (Vibrio alginolyticus, Vibrio parahemolyticus and Lysteria monocytogenes) and viral hemoragic septicemia virus (VHSV), AbLITAF showed the significant up-regulation in gills while AbRel/NF-kB transcription was not change significantly. Based on transcriptional response against immune challenge, we could suggest that regulation of TNF-alpha expression may have occurred mainly by LITAF activation rather than NF-kB in disk abalone. The cumulative data from other molluscs and our data with reference to TNF-alpha, LITAF and Rel/NF-kB from disk abalone provide strong evidence that LITAF and NF-kB are independent pathways likely to occur throughout the Phylum mollusca. 2010 Elsevier Ltd. All rights reserved.

  14. Carbon-constrained scenarios. Final report

    International Nuclear Information System (INIS)

    2009-05-01

    This report provides the results of the study entitled 'Carbon-Constrained Scenarios' that was funded by FONDDRI from 2004 to 2008. The study was achieved in four steps: (i) Investigating the stakes of a strong carbon constraint for the industries participating in the study, not only looking at the internal decarbonization potential of each industry but also exploring the potential shifts of the demand for industrial products. (ii) Developing an hybrid modelling platform based on a tight dialog between the sectoral energy model POLES and the macro-economic model IMACLIM-R, in order to achieve a consistent assessment of the consequences of an economy-wide carbon constraint on energy-intensive industrial sectors, while taking into account technical constraints, barriers to the deployment of new technologies and general economic equilibrium effects. (iii) Producing several scenarios up to 2050 with different sets of hypotheses concerning the driving factors for emissions - in particular the development styles. (iv) Establishing an iterative dialog between researchers and industry representatives on the results of the scenarios so as to improve them, but also to facilitate the understanding and the appropriate use of these results by the industrial partners. This report provides the results of the different scenarios computed in the course of the project. It is a partial synthesis of the work that has been accomplished and of the numerous exchanges that this study has induced between modellers and stakeholders. The first part was written in April 2007 and describes the first reference scenario and the first mitigation scenario designed to achieve stabilization at 450 ppm CO 2 at the end of the 21. century. This scenario has been called 'mimetic' because it has been build on the assumption that the ambitious climate policy would coexist with a progressive convergence of development paths toward the current paradigm of industrialized countries: urban sprawl, general

  15. FXR agonist activity of conformationally constrained analogs of GW 4064.

    Science.gov (United States)

    Akwabi-Ameyaw, Adwoa; Bass, Jonathan Y; Caldwell, Richard D; Caravella, Justin A; Chen, Lihong; Creech, Katrina L; Deaton, David N; Madauss, Kevin P; Marr, Harry B; McFadyen, Robert B; Miller, Aaron B; Navas, Frank; Parks, Derek J; Spearing, Paul K; Todd, Dan; Williams, Shawn P; Bruce Wisely, G

    2009-08-15

    Two series of conformationally constrained analogs of the FXR agonist GW 4064 1 were prepared. Replacement of the metabolically labile stilbene with either benzothiophene or naphthalene rings led to the identification of potent full agonists 2a and 2g.

  16. Automated Precision Maneuvering and Landing in Extreme and Constrained Environments

    Data.gov (United States)

    National Aeronautics and Space Administration — Autonomous, precise maneuvering and landing in extreme and constrained environments is a key enabler for future NASA missions. Missions to map the interior of a...

  17. Security constrained optimal power flow by modern optimization tools

    African Journals Online (AJOL)

    Security constrained optimal power flow by modern optimization tools. ... International Journal of Engineering, Science and Technology ... If you would like more information about how to print, save, and work with PDFs, Highwire Press ...

  18. Affine Lie algebraic origin of constrained KP hierarchies

    International Nuclear Information System (INIS)

    Aratyn, H.; Gomes, J.F.; Zimerman, A.H.

    1994-07-01

    It is presented an affine sl(n+1) algebraic construction of the basic constrained KP hierarchy. This hierarchy is analyzed using two approaches, namely linear matrix eigenvalue problem on hermitian symmetric space and constrained KP Lax formulation and we show that these approaches are equivalent. The model is recognized to be generalized non-linear Schroedinger (GNLS) hierarchy and it is used as a building block for a new class of constrained KP hierarchies. These constrained KP hierarchies are connected via similarity-Backlund transformations and interpolate between GNLS and multi-boson KP-Toda hierarchies. The construction uncovers origin of the Toda lattice structure behind the latter hierarchy. (author). 23 refs

  19. Slow logarithmic relaxation in models with hierarchically constrained dynamics

    OpenAIRE

    Brey, J. J.; Prados, A.

    2000-01-01

    A general kind of models with hierarchically constrained dynamics is shown to exhibit logarithmic anomalous relaxation, similarly to a variety of complex strongly interacting materials. The logarithmic behavior describes most of the decay of the response function.

  20. Synthesis of conformationally constrained peptidomimetics using multicomponent reactions

    NARCIS (Netherlands)

    Scheffelaar, R.; Klein Nijenhuis, R.A.; Paravidino, M.; Lutz, M.; Spek, A.L.; Ehlers, A.W.; de Kanter, F.J.J.; Groen, M.B.; Orru, R.V.A.; Ruijter, E.

    2009-01-01

    A novel modular synthetic approach toward constrained peptidomimetics is reported. The approach involves a highly efficient three-step sequence including two multicomponent reactions, thus allowing unprecedented diversification of both the peptide moieties and the turn-inducing scaffold. The

  1. Filter Pattern Search Algorithms for Mixed Variable Constrained Optimization Problems

    National Research Council Canada - National Science Library

    Abramson, Mark A; Audet, Charles; Dennis, Jr, J. E

    2004-01-01

    .... This class combines and extends the Audet-Dennis Generalized Pattern Search (GPS) algorithms for bound constrained mixed variable optimization, and their GPS-filter algorithms for general nonlinear constraints...

  2. Capacity Constrained Routing Algorithms for Evacuation Route Planning

    National Research Council Canada - National Science Library

    Lu, Qingsong; George, Betsy; Shekhar, Shashi

    2006-01-01

    .... In this paper, we propose a new approach, namely a capacity constrained routing planner which models capacity as a time series and generalizes shortest path algorithms to incorporate capacity constraints...

  3. Wave speed in excitable random networks with spatially constrained connections.

    Directory of Open Access Journals (Sweden)

    Nikita Vladimirov

    Full Text Available Very fast oscillations (VFO in neocortex are widely observed before epileptic seizures, and there is growing evidence that they are caused by networks of pyramidal neurons connected by gap junctions between their axons. We are motivated by the spatio-temporal waves of activity recorded using electrocorticography (ECoG, and study the speed of activity propagation through a network of neurons axonally coupled by gap junctions. We simulate wave propagation by excitable cellular automata (CA on random (Erdös-Rényi networks of special type, with spatially constrained connections. From the cellular automaton model, we derive a mean field theory to predict wave propagation. The governing equation resolved by the Fisher-Kolmogorov PDE fails to describe wave speed. A new (hyperbolic PDE is suggested, which provides adequate wave speed v( that saturates with network degree , in agreement with intuitive expectations and CA simulations. We further show that the maximum length of connection is a much better predictor of the wave speed than the mean length. When tested in networks with various degree distributions, wave speeds are found to strongly depend on the ratio of network moments / rather than on mean degree , which is explained by general network theory. The wave speeds are strikingly similar in a diverse set of networks, including regular, Poisson, exponential and power law distributions, supporting our theory for various network topologies. Our results suggest practical predictions for networks of electrically coupled neurons, and our mean field method can be readily applied for a wide class of similar problems, such as spread of epidemics through spatial networks.

  4. Identification of Constrained Cancer Driver Genes Based on Mutation Timing

    Science.gov (United States)

    Sakoparnig, Thomas; Fried, Patrick; Beerenwinkel, Niko

    2015-01-01

    Cancer drivers are genomic alterations that provide cells containing them with a selective advantage over their local competitors, whereas neutral passengers do not change the somatic fitness of cells. Cancer-driving mutations are usually discriminated from passenger mutations by their higher degree of recurrence in tumor samples. However, there is increasing evidence that many additional driver mutations may exist that occur at very low frequencies among tumors. This observation has prompted alternative methods for driver detection, including finding groups of mutually exclusive mutations and incorporating prior biological knowledge about gene function or network structure. Dependencies among drivers due to epistatic interactions can also result in low mutation frequencies, but this effect has been ignored in driver detection so far. Here, we present a new computational approach for identifying genomic alterations that occur at low frequencies because they depend on other events. Unlike passengers, these constrained mutations display punctuated patterns of occurrence in time. We test this driver–passenger discrimination approach based on mutation timing in extensive simulation studies, and we apply it to cross-sectional copy number alteration (CNA) data from ovarian cancer, CNA and single-nucleotide variant (SNV) data from breast tumors and SNV data from colorectal cancer. Among the top ranked predicted drivers, we find low-frequency genes that have already been shown to be involved in carcinogenesis, as well as many new candidate drivers. The mutation timing approach is orthogonal and complementary to existing driver prediction methods. It will help identifying from cancer genome data the alterations that drive tumor progression. PMID:25569148

  5. Constrained multi-degree reduction with respect to Jacobi norms

    KAUST Repository

    Ait-Haddou, Rachid; Barton, Michael

    2015-01-01

    We show that a weighted least squares approximation of Bézier coefficients with factored Hahn weights provides the best constrained polynomial degree reduction with respect to the Jacobi L2L2-norm. This result affords generalizations to many previous findings in the field of polynomial degree reduction. A solution method to the constrained multi-degree reduction with respect to the Jacobi L2L2-norm is presented.

  6. Clustering Using Boosted Constrained k-Means Algorithm

    Directory of Open Access Journals (Sweden)

    Masayuki Okabe

    2018-03-01

    Full Text Available This article proposes a constrained clustering algorithm with competitive performance and less computation time to the state-of-the-art methods, which consists of a constrained k-means algorithm enhanced by the boosting principle. Constrained k-means clustering using constraints as background knowledge, although easy to implement and quick, has insufficient performance compared with metric learning-based methods. Since it simply adds a function into the data assignment process of the k-means algorithm to check for constraint violations, it often exploits only a small number of constraints. Metric learning-based methods, which exploit constraints to create a new metric for data similarity, have shown promising results although the methods proposed so far are often slow depending on the amount of data or number of feature dimensions. We present a method that exploits the advantages of the constrained k-means and metric learning approaches. It incorporates a mechanism for accepting constraint priorities and a metric learning framework based on the boosting principle into a constrained k-means algorithm. In the framework, a metric is learned in the form of a kernel matrix that integrates weak cluster hypotheses produced by the constrained k-means algorithm, which works as a weak learner under the boosting principle. Experimental results for 12 data sets from 3 data sources demonstrated that our method has performance competitive to those of state-of-the-art constrained clustering methods for most data sets and that it takes much less computation time. Experimental evaluation demonstrated the effectiveness of controlling the constraint priorities by using the boosting principle and that our constrained k-means algorithm functions correctly as a weak learner of boosting.

  7. New Exact Penalty Functions for Nonlinear Constrained Optimization Problems

    Directory of Open Access Journals (Sweden)

    Bingzhuang Liu

    2014-01-01

    Full Text Available For two kinds of nonlinear constrained optimization problems, we propose two simple penalty functions, respectively, by augmenting the dimension of the primal problem with a variable that controls the weight of the penalty terms. Both of the penalty functions enjoy improved smoothness. Under mild conditions, it can be proved that our penalty functions are both exact in the sense that local minimizers of the associated penalty problem are precisely the local minimizers of the original constrained problem.

  8. Constrained multi-degree reduction with respect to Jacobi norms

    KAUST Repository

    Ait-Haddou, Rachid

    2015-12-31

    We show that a weighted least squares approximation of Bézier coefficients with factored Hahn weights provides the best constrained polynomial degree reduction with respect to the Jacobi L2L2-norm. This result affords generalizations to many previous findings in the field of polynomial degree reduction. A solution method to the constrained multi-degree reduction with respect to the Jacobi L2L2-norm is presented.

  9. Constraints on extra dimensions from precision molecular spectroscopy

    NARCIS (Netherlands)

    Salumbides, E.J.; Schellekens, A.N.; Gato-Rivera, B.; Ubachs, W.M.G.

    2015-01-01

    Accurate investigations of quantum-level energies in molecular systems are shown to provide a testing ground to constrain the size of compactified extra dimensions. This is made possible by recent progress in precision metrology with ultrastable lasers on energy levels in neutral molecular hydrogen

  10. Free and constrained symplectic integrators for numerical general relativity

    International Nuclear Information System (INIS)

    Richter, Ronny; Lubich, Christian

    2008-01-01

    We consider symplectic time integrators in numerical general relativity and discuss both free and constrained evolution schemes. For free evolution of ADM-like equations we propose the use of the Stoermer-Verlet method, a standard symplectic integrator which here is explicit in the computationally expensive curvature terms. For the constrained evolution we give a formulation of the evolution equations that enforces the momentum constraints in a holonomically constrained Hamiltonian system and turns the Hamilton constraint function from a weak to a strong invariant of the system. This formulation permits the use of the constraint-preserving symplectic RATTLE integrator, a constrained version of the Stoermer-Verlet method. The behavior of the methods is illustrated on two effectively (1+1)-dimensional versions of Einstein's equations, which allow us to investigate a perturbed Minkowski problem and the Schwarzschild spacetime. We compare symplectic and non-symplectic integrators for free evolution, showing very different numerical behavior for nearly-conserved quantities in the perturbed Minkowski problem. Further we compare free and constrained evolution, demonstrating in our examples that enforcing the momentum constraints can turn an unstable free evolution into a stable constrained evolution. This is demonstrated in the stabilization of a perturbed Minkowski problem with Dirac gauge, and in the suppression of the propagation of boundary instabilities into the interior of the domain in Schwarzschild spacetime

  11. Cement-in-cement acetabular revision with a constrained tripolar component.

    Science.gov (United States)

    Leonidou, Andreas; Pagkalos, Joseph; Luscombe, Jonathan

    2012-02-17

    Dislocation of a total hip replacement (THR) is common following total hip arthroplasty (THA). When nonoperative management fails to maintain reduction, revision surgery is considered. The use of constrained acetabular liners has been extensively described. Complete removal of the old cement mantle during revision THA can be challenging and is associated with significant complications. Cement-in-cement revision is an established technique. However, the available clinical and experimental studies focus on femoral stem revision. The purpose of this study was to present a case of cement-in-cement acetabular revision with a constrained component for recurrent dislocations and to investigate the current best evidence for this technique. This article describes the case of a 74-year-old woman who underwent revision of a Charnley THR for recurrent low-energy dislocations. A tripolar constrained acetabular component was cemented over the primary cement mantle following removal of the original liner by reaming, roughening the surface, and thoroughly irrigating and drying the primary cement. Clinical and radiological results were good, with the Oxford Hip Score improving from 11 preoperatively to 24 at 6 months postoperatively. The good short-term results of this case and the current clinical and biomechanical data encourage the use of the cement-in-cement technique for acetabular revision. Careful irrigation, drying, and roughening of the primary surface are necessary. Copyright 2012, SLACK Incorporated.

  12. Constraining holographic cosmology using Planck data

    Science.gov (United States)

    Afshordi, Niayesh; Gould, Elizabeth; Skenderis, Kostas

    2017-06-01

    Holographic cosmology offers a novel framework for describing the very early Universe in which cosmological predictions are expressed in terms of the observables of a three-dimensional quantum field theory (QFT). This framework includes conventional slow-roll inflation, which is described in terms of a strongly coupled QFT, but it also allows for qualitatively new models for the very early Universe, where the dual QFT may be weakly coupled. The new models describe a universe which is nongeometric at early times. While standard slow-roll inflation leads to a (near-) power-law primordial power spectrum, perturbative super-renormalizable QFTs yield a new holographic spectral shape. Here, we compare the two predictions against cosmological observations. We use CosmoMC to determine the best fit parameters, and MultiNest for Bayesian evidence, comparing the likelihoods. We find that the dual QFT should be nonperturbative at the very low multipoles (l ≲30 ), while for higher multipoles (l ≳30 ) the new holographic model, based on perturbative QFT, fits the data just as well as the standard power-law spectrum assumed in Λ CDM cosmology. This finding opens the door to applications of nonperturbative QFT techniques, such as lattice simulations, to observational cosmology on gigaparsec scales and beyond.

  13. Constructing a New Theory from Old Ideas and New Evidence

    Science.gov (United States)

    Rhodes, Marjorie; Wellman, Henry

    2013-01-01

    A central tenet of constructivist models of conceptual development is that children's initial conceptual level constrains how they make sense of new evidence and thus whether exposure to evidence will prompt conceptual change. Yet little experimental evidence directly examines this claim for the case of sustained, fundamental conceptual…

  14. Magnetismo Molecular (Molecular Magentism)

    Energy Technology Data Exchange (ETDEWEB)

    Reis, Mario S [Universidade Federal Fluminense, Brasil; Moreira Dos Santos, Antonio F [ORNL

    2010-07-01

    The new synthesis processes in chemistry open a new world of research, new and surprising materials never before found in nature can now be synthesized and, as a wonderful result, observed a series of physical phenomena never before imagined. Among these are many new materials the molecular magnets, the subject of this book and magnetic properties that are often reflections of the quantum behavior of these materials. Aside from the wonderful experience of exploring something new, the theoretical models that describe the behavior these magnetic materials are, in most cases, soluble analytically, which allows us to know in detail the physical mechanisms governing these materials. Still, the academic interest in parallel this subject, these materials have a number of properties that are promising to be used in technological devices, such as in computers quantum magnetic recording, magnetocaloric effect, spintronics and many other devices. This volume will journey through the world of molecular magnets, from the structural description of these materials to state of the art research.

  15. Constrained Local UniversE Simulations: a Local Group factory

    Science.gov (United States)

    Carlesi, Edoardo; Sorce, Jenny G.; Hoffman, Yehuda; Gottlöber, Stefan; Yepes, Gustavo; Libeskind, Noam I.; Pilipenko, Sergey V.; Knebe, Alexander; Courtois, Hélène; Tully, R. Brent; Steinmetz, Matthias

    2016-05-01

    Near-field cosmology is practised by studying the Local Group (LG) and its neighbourhood. This paper describes a framework for simulating the `near field' on the computer. Assuming the Λ cold dark matter (ΛCDM) model as a prior and applying the Bayesian tools of the Wiener filter and constrained realizations of Gaussian fields to the Cosmicflows-2 (CF2) survey of peculiar velocities, constrained simulations of our cosmic environment are performed. The aim of these simulations is to reproduce the LG and its local environment. Our main result is that the LG is likely a robust outcome of the ΛCDMscenario when subjected to the constraint derived from CF2 data, emerging in an environment akin to the observed one. Three levels of criteria are used to define the simulated LGs. At the base level, pairs of haloes must obey specific isolation, mass and separation criteria. At the second level, the orbital angular momentum and energy are constrained, and on the third one the phase of the orbit is constrained. Out of the 300 constrained simulations, 146 LGs obey the first set of criteria, 51 the second and 6 the third. The robustness of our LG `factory' enables the construction of a large ensemble of simulated LGs. Suitable candidates for high-resolution hydrodynamical simulations of the LG can be drawn from this ensemble, which can be used to perform comprehensive studies of the formation of the LG.

  16. Molecular, Serological And Microbiological Profiling Evidence Of ...

    African Journals Online (AJOL)

    All items that the boy had contact with including a laboratory coat, bunch of keys and shoes were swabbed. Finally samples of all the boy's food and drinks were taken. Microbiological, Serological and Polymerase Chain Reaction (PCR) Profiling Assays. l the samples were cultured on Sorbitol - MacConkey (SMAC) agar, ...

  17. Molecular hematology

    National Research Council Canada - National Science Library

    Provan, Drew; Gribben, John

    2010-01-01

    ... The molecular basis of hemophilia, 219 Paul LF Giangrande 4 The genetics of acute myeloid leukemias, 42 Carolyn J Owen & Jude Fitzgibbon 19 The molecular basis of von Willebrand disease, 233 Luciano Baronc...

  18. In vitro transcription of a torsionally constrained template

    DEFF Research Database (Denmark)

    Bentin, Thomas; Nielsen, Peter E

    2002-01-01

    RNA polymerase (RNAP) and the DNA template must rotate relative to each other during transcription elongation. In the cell, however, the components of the transcription apparatus may be subject to rotary constraints. For instance, the DNA is divided into topological domains that are delineated...... of torsionally constrained DNA by free RNAP. We asked whether or not a newly synthesized RNA chain would limit transcription elongation. For this purpose we developed a method to immobilize covalently closed circular DNA to streptavidin-coated beads via a peptide nucleic acid (PNA)-biotin conjugate in principle...... constrained. We conclude that transcription of a natural bacterial gene may proceed with high efficiency despite the fact that newly synthesized RNA is entangled around the template in the narrow confines of torsionally constrained supercoiled DNA....

  19. Fabrication of (PPC/NCC)/PVA composites with inner-outer double constrained structure and improved glass transition temperature.

    Science.gov (United States)

    Cui, Shaoying; Li, Li; Wang, Qi

    2018-07-01

    Improving glass transition temperature (T g ) and mechanical property of the environment-friendly poly(propylene carbonate) via intermacromolecular complexation through hydrogen bonding is attractive and of great importance. A novel and effective strategy to prepare (polypropylene carbonate/nanocrystalline cellulose)/polyvinyl alcohol ((PPC/NCC)/PVA) composites with inner-outer double constrained structure was reported in this work. Outside the PPC phase, PVA, as a strong skeleton at microscale, could constrain the movement of PPC molecular chains by forming hydrogen bonding with PPC at the interface of PPC and PVA phases; inside the PPC phase, the rod-like NCC could restrain the flexible molecular chains of PPC at nanoscale by forming multi-hydrogen bonding with PPC. Under the synergistic effect of this novel inner-outer double constrained structure, T g , mechanical properties and thermal stability of (PPC/NCC)/PVA composite were significantly increased, e.g. T g of the composite researched the maximum value of 49.6 °C, respectively 15.6 °C, 5.7 °C and 4.2 °C higher than that of PPC, PPC/NCC and PPC/PVA composite. Copyright © 2018 Elsevier Ltd. All rights reserved.

  20. Constraining the Antarctic contribution to interglacial sea-level rise

    Science.gov (United States)

    Naish, T.; Mckay, R. M.; Barrett, P. J.; Levy, R. H.; Golledge, N. R.; Deconto, R. M.; Horgan, H. J.; Dunbar, G. B.

    2015-12-01

    Observations, models and paleoclimate reconstructions suggest that Antarctica's marine-based ice sheets behave in an unstable manner with episodes of rapid retreat in response to warming climate. Understanding the processes involved in this "marine ice sheet instability" is key for improving estimates of Antarctic ice sheet contribution to future sea-level rise. Another motivating factor is that far-field sea-level reconstructions and ice sheet models imply global mean sea level (GMSL) was up to 20m and 10m higher, respectively, compared with present day, during the interglacials of the warm Pliocene (~4-3Ma) and Late Pleistocene (at ~400ka and 125ka). This was when atmospheric CO2 was between 280 and 400ppm and global average surface temperatures were 1- 3°C warmer, suggesting polar ice sheets are highly sensitive to relatively modest increases in climate forcing. Such magnitudes of GMSL rise not only require near complete melt of the Greenland Ice Sheet and the West Antarctic Ice Sheet, but a substantial retreat of marine-based sectors of East Antarctic Ice Sheet. Recent geological drilling initiatives on the continental margin of Antarctica from both ship- (e.g. IODP; International Ocean Discovery Program) and ice-based (e.g. ANDRILL/Antarctic Geological Drilling) platforms have provided evidence supporting retreat of marine-based ice. However, without direct access through the ice sheet to archives preserved within sub-glacial sedimentary basins, the volume and extent of ice sheet retreat during past interglacials cannot be directly constrained. Sediment cores have been successfully recovered from beneath ice shelves by the ANDRILL Program and ice streams by the WISSARD (Whillans Ice Stream Sub-glacial Access Research Drilling) Project. Together with the potential of the new RAID (Rapid Access Ice Drill) initiative, these demonstrate the technological feasibility of accessing the subglacial bed and deeper sedimentary archives. In this talk I will outline the

  1. Effects of deformability and thermal motion of lipid membrane on electroporation: By molecular dynamics simulations

    KAUST Repository

    Sun, Sheng; Yin, Guangyao; Lee, Yi-Kuen; Wong, Joseph T.Y.; Zhang, Tong-Yi

    2011-01-01

    Effects of mechanical properties and thermal motion of POPE lipid membrane on electroporation were studied by molecular dynamics simulations. Among simulations in which specific atoms of lipids were artificially constrained at their equilibrium

  2. Node Discovery and Interpretation in Unstructured Resource-Constrained Environments

    DEFF Research Database (Denmark)

    Gechev, Miroslav; Kasabova, Slavyana; Mihovska, Albena D.

    2014-01-01

    for the discovery, linking and interpretation of nodes in unstructured and resource-constrained network environments and their interrelated and collective use for the delivery of smart services. The model is based on a basic mathematical approach, which describes and predicts the success of human interactions...... in the context of long-term relationships and identifies several key variables in the context of communications in resource-constrained environments. The general theoretical model is described and several algorithms are proposed as part of the node discovery, identification, and linking processes in relation...

  3. Value, Cost, and Sharing: Open Issues in Constrained Clustering

    Science.gov (United States)

    Wagstaff, Kiri L.

    2006-01-01

    Clustering is an important tool for data mining, since it can identify major patterns or trends without any supervision (labeled data). Over the past five years, semi-supervised (constrained) clustering methods have become very popular. These methods began with incorporating pairwise constraints and have developed into more general methods that can learn appropriate distance metrics. However, several important open questions have arisen about which constraints are most useful, how they can be actively acquired, and when and how they should be propagated to neighboring points. This position paper describes these open questions and suggests future directions for constrained clustering research.

  4. Constraining the physical state by symmetries

    Science.gov (United States)

    Fatibene, L.; Ferraris, M.; Magnano, G.

    2017-03-01

    After reviewing the hole argument and its relations with initial value problem and general covariance, we shall discuss how much freedom one has to define the physical state in a generally covariant field theory (with or without internal gauge symmetries). Our analysis relies on Cauchy problems, thus it is restricted to globally hyperbolic spacetimes. We shall show that in generally covariant theories on a compact space (as well as for internal gauge symmetries on any spacetime) one has no freedom and one is forced to declare as physically equivalent two configurations which differ by a global spacetime diffeomorphism (or by an internal gauge transformation) as it is usually prescribed. On the contrary, when space is not compact, the result does not hold true and one may have different options to define physically equivalent configurations, still preserving determinism. For this scenario to be effective, the group G of formal transformations needs to be a subgroup of dynamical symmetries (otherwise field equations, which are written in terms of configurations would not induce equations for the physical state classes) and it must contain the group D generated by Cauchy transformations (otherwise the equations induced on physical state classes would not be well posed, either). We argue that it is exactly because of this double inclusion that the hole argument in its initial problem formulation is more powerful than in its boundary formulation. In the boundary formulation of the hole argument one still has that the group G of formal transformations is a subgroup of dynamical symmetries, but there is no evidence for it to contain a particular non-trivial subgroup.In this paper we shall show that this scenario is exactly implemented in generally covariant theories. In the last section we shall show it to be implemented in gauge theories as well.Norton also argued (see [1]) that the definition of physical state is something to be discussed in physics and it is not

  5. Molecular imaging in oncology

    Energy Technology Data Exchange (ETDEWEB)

    Schober, Otmar; Riemann, Burkhard (eds.) [Universitaetsklinikum Muenster (Germany). Klinik fuer Nuklearmedizin

    2013-02-01

    Considers in detail all aspects of molecular imaging in oncology, ranging from basic research to clinical applications in the era of evidence-based medicine. Examines technological issues and probe design. Discusses preclinical studies in detail, with particular attention to multimodality imaging. Presents current clinical use of PET/CT, SPECT/CT, and optical imagingWritten by acknowledged experts. The impact of molecular imaging on diagnostics, therapy, and follow-up in oncology is increasing significantly. The process of molecular imaging includes key biotarget identification, design of specific molecular imaging probes, and their preclinical evaluation, e.g., in vivo using small animal studies. A multitude of such innovative molecular imaging probes have already entered clinical diagnostics in oncology. There is no doubt that in future the emphasis will be on multimodality imaging in which morphological, functional, and molecular imaging techniques are combined in a single clinical investigation that will optimize diagnostic processes. This handbook addresses all aspects of molecular imaging in oncology, ranging from basic research to clinical applications in the era of evidence-based medicine. The first section is devoted to technology and probe design, and examines a variety of PET and SPECT tracers as well as multimodality probes. Preclinical studies are then discussed in detail, with particular attention to multimodality imaging. In the third section, diverse clinical applications are presented, and the book closes by looking at future challenges. This handbook will be of value to all who are interested in the revolution in diagnostic oncology that is being brought about by molecular imaging.

  6. Molecular imaging in oncology

    International Nuclear Information System (INIS)

    Schober, Otmar; Riemann, Burkhard

    2013-01-01

    Considers in detail all aspects of molecular imaging in oncology, ranging from basic research to clinical applications in the era of evidence-based medicine. Examines technological issues and probe design. Discusses preclinical studies in detail, with particular attention to multimodality imaging. Presents current clinical use of PET/CT, SPECT/CT, and optical imagingWritten by acknowledged experts. The impact of molecular imaging on diagnostics, therapy, and follow-up in oncology is increasing significantly. The process of molecular imaging includes key biotarget identification, design of specific molecular imaging probes, and their preclinical evaluation, e.g., in vivo using small animal studies. A multitude of such innovative molecular imaging probes have already entered clinical diagnostics in oncology. There is no doubt that in future the emphasis will be on multimodality imaging in which morphological, functional, and molecular imaging techniques are combined in a single clinical investigation that will optimize diagnostic processes. This handbook addresses all aspects of molecular imaging in oncology, ranging from basic research to clinical applications in the era of evidence-based medicine. The first section is devoted to technology and probe design, and examines a variety of PET and SPECT tracers as well as multimodality probes. Preclinical studies are then discussed in detail, with particular attention to multimodality imaging. In the third section, diverse clinical applications are presented, and the book closes by looking at future challenges. This handbook will be of value to all who are interested in the revolution in diagnostic oncology that is being brought about by molecular imaging.

  7. Magnetic exchange couplings from constrained density functional theory: an efficient approach utilizing analytic derivatives.

    Science.gov (United States)

    Phillips, Jordan J; Peralta, Juan E

    2011-11-14

    We introduce a method for evaluating magnetic exchange couplings based on the constrained density functional theory (C-DFT) approach of Rudra, Wu, and Van Voorhis [J. Chem. Phys. 124, 024103 (2006)]. Our method shares the same physical principles as C-DFT but makes use of the fact that the electronic energy changes quadratically and bilinearly with respect to the constraints in the range of interest. This allows us to use coupled perturbed Kohn-Sham spin density functional theory to determine approximately the corrections to the energy of the different spin configurations and construct a priori the relevant energy-landscapes obtained by constrained spin density functional theory. We assess this methodology in a set of binuclear transition-metal complexes and show that it reproduces very closely the results of C-DFT. This demonstrates a proof-of-concept for this method as a potential tool for studying a number of other molecular phenomena. Additionally, routes to improving upon the limitations of this method are discussed. © 2011 American Institute of Physics

  8. Beyond Evidence-Based Belief Formation: How Normative Ideas Have Constrained Conceptual Change Research

    Science.gov (United States)

    Ohlsson, Stellan

    2013-01-01

    The cognitive sciences, including psychology and education, have their roots in antiquity. In the historically early disciplines like logic and philosophy, the purpose of inquiry was normative. Logic sought to formalize valid inferences, and the various branches of philosophy sought to identify true and certain knowledge. Normative principles are…

  9. Maturation Constrains the Effect of Exposure in Linking Language and Thought: Evidence from Healthy Preterm Infants

    Science.gov (United States)

    Perszyk, Danielle R.; Ferguson, Brock; Waxman, Sandra R.

    2018-01-01

    The power of human language rests upon its intricate links to human cognition. By 3 months of age, listening to language supports infants' ability to form object categories, a building block of cognition. Moreover, infants display a systematic shift between 3 and 4 months--a shift from familiarity to novelty preferences--in their expression of…

  10. Increasing genomic diversity and evidence of constrained lifestyle evolution due to insertion sequences in Aeromonas salmonicida.

    Science.gov (United States)

    Vincent, Antony T; Trudel, Mélanie V; Freschi, Luca; Nagar, Vandan; Gagné-Thivierge, Cynthia; Levesque, Roger C; Charette, Steve J

    2016-01-12

    Aeromonads make up a group of Gram-negative bacteria that includes human and fish pathogens. The Aeromonas salmonicida species has the peculiarity of including five known subspecies. However, few studies of the genomes of A. salmonicida subspecies have been reported to date. We sequenced the genomes of additional A. salmonicida isolates, including three from India, using next-generation sequencing in order to gain a better understanding of the genomic and phylogenetic links between A. salmonicida subspecies. Their relative phylogenetic positions were confirmed by a core genome phylogeny based on 1645 gene sequences. The Indian isolates, which formed a sub-group together with A. salmonicida subsp. pectinolytica, were able to grow at either at 18 °C and 37 °C, unlike the A. salmonicida psychrophilic isolates that did not grow at 37 °C. Amino acid frequencies, GC content, tRNA composition, loss and gain of genes during evolution, pseudogenes as well as genes under positive selection and the mobilome were studied to explain this intraspecies dichotomy. Insertion sequences appeared to be an important driving force that locked the psychrophilic strains into their particular lifestyle in order to conserve their genomic integrity. This observation, based on comparative genomics, is in agreement with previous results showing that insertion sequence mobility induced by heat in A. salmonicida subspecies causes genomic plasticity, resulting in a deleterious effect on the virulence of the bacterium. We provide a proof-of-concept that selfish DNAs play a major role in the evolution of bacterial species by modeling genomes.

  11. Coherent Structures and Entropy in Constrained, Modulationally Unstable, Nonintegrable Systems

    International Nuclear Information System (INIS)

    Rumpf, Benno; Newell, Alan C.

    2001-01-01

    Many studies have shown that nonintegrable systems with modulational instabilities constrained by more than one conservation law exhibit universal long time behavior involving large coherent structures in a sea of small fluctuations. We show how this behavior can be explained in detail by simple thermodynamic arguments

  12. Invariant set computation for constrained uncertain discrete-time systems

    NARCIS (Netherlands)

    Athanasopoulos, N.; Bitsoris, G.

    2010-01-01

    In this article a novel approach to the determination of polytopic invariant sets for constrained discrete-time linear uncertain systems is presented. First, the problem of stabilizing a prespecified initial condition set in the presence of input and state constraints is addressed. Second, the

  13. Applications of a Constrained Mechanics Methodology in Economics

    Science.gov (United States)

    Janova, Jitka

    2011-01-01

    This paper presents instructive interdisciplinary applications of constrained mechanics calculus in economics on a level appropriate for undergraduate physics education. The aim of the paper is (i) to meet the demand for illustrative examples suitable for presenting the background of the highly expanding research field of econophysics even at the…

  14. Excision technique in constrained formulations of Einstein equations: collapse scenario

    International Nuclear Information System (INIS)

    Cordero-Carrión, I; Vasset, N; Novak, J; Jaramillo, J L

    2015-01-01

    We present a new excision technique used in constrained formulations of Einstein equations to deal with black hole in numerical simulations. We show the applicability of this scheme in several scenarios. In particular, we present the dynamical evolution of the collapse of a neutron star to a black hole, using the CoCoNuT code and this excision technique. (paper)

  15. Constraining the evolution of the Hubble Parameter using cosmic chronometers

    Science.gov (United States)

    Dickinson, Hugh

    2017-08-01

    Substantial investment is being made in space- and ground-based missions with the goal of revealing the nature of the observed cosmic acceleration. This is one of the most important unsolved problems in cosmology today.We propose here to constrain the evolution of the Hubble parameter [H(z)] between 1.3 fundamental nature of dark energy.

  16. Nonmonotonic Skeptical Consequence Relation in Constrained Default Logic

    Directory of Open Access Journals (Sweden)

    Mihaiela Lupea

    2010-12-01

    Full Text Available This paper presents a study of the nonmonotonic consequence relation which models the skeptical reasoning formalised by constrained default logic. The nonmonotonic skeptical consequence relation is defined using the sequent calculus axiomatic system. We study the formal properties desirable for a good nonmonotonic relation: supraclassicality, cut, cautious monotony, cumulativity, absorption, distribution. 

  17. Extended shadow test approach for constrained adaptive testing

    NARCIS (Netherlands)

    Veldkamp, Bernard P.; Ariel, A.

    2002-01-01

    Several methods have been developed for use on constrained adaptive testing. Item pool partitioning, multistage testing, and testlet-based adaptive testing are methods that perform well for specific cases of adaptive testing. The weighted deviation model and the Shadow Test approach can be more

  18. Time-constrained project scheduling with adjacent resources

    NARCIS (Netherlands)

    Hurink, Johann L.; Kok, A.L.; Paulus, J.J.; Schutten, Johannes M.J.

    We develop a decomposition method for the Time-Constrained Project Scheduling Problem (TCPSP) with adjacent resources. For adjacent resources the resource units are ordered and the units assigned to a job have to be adjacent. On top of that, adjacent resources are not required by single jobs, but by

  19. Evaluation of constrained mobility for programmability in network management

    NARCIS (Netherlands)

    Bohoris, C.; Liotta, A.; Pavlou, G.; Ambler, A.P.; Calo, S.B.; Kar, G.

    2000-01-01

    In recent years, a significant amount of research work has addressed the use of code mobility in network management. In this paper, we introduce first three aspects of code mobility and argue that constrained mobility offers a natural and easy approach to network management programmability. While

  20. Testing a Constrained MPC Controller in a Process Control Laboratory

    Science.gov (United States)

    Ricardez-Sandoval, Luis A.; Blankespoor, Wesley; Budman, Hector M.

    2010-01-01

    This paper describes an experiment performed by the fourth year chemical engineering students in the process control laboratory at the University of Waterloo. The objective of this experiment is to test the capabilities of a constrained Model Predictive Controller (MPC) to control the operation of a Double Pipe Heat Exchanger (DPHE) in real time.…

  1. In vitro transcription of a torsionally constrained template

    DEFF Research Database (Denmark)

    Bentin, Thomas; Nielsen, Peter E

    2002-01-01

    of torsionally constrained DNA by free RNAP. We asked whether or not a newly synthesized RNA chain would limit transcription elongation. For this purpose we developed a method to immobilize covalently closed circular DNA to streptavidin-coated beads via a peptide nucleic acid (PNA)-biotin conjugate in principle...

  2. GPS-based ionospheric tomography with a constrained adaptive ...

    Indian Academy of Sciences (India)

    Gauss weighted function is introduced to constrain the tomography system in the new method. It can resolve the ... the research focus in the fields of space geodesy and ... ment of GNSS such as GPS, Glonass, Galileo and. Compass, as these ...

  3. Constrained variational calculus for higher order classical field theories

    Energy Technology Data Exchange (ETDEWEB)

    Campos, Cedric M; De Leon, Manuel; De Diego, David MartIn, E-mail: cedricmc@icmat.e, E-mail: mdeleon@icmat.e, E-mail: david.martin@icmat.e [Instituto de Ciencias Matematicas, CSIC-UAM-UC3M-UCM, Serrano 123, 28006 Madrid (Spain)

    2010-11-12

    We develop an intrinsic geometrical setting for higher order constrained field theories. As a main tool we use an appropriate generalization of the classical Skinner-Rusk formalism. Some examples of applications are studied, in particular to the geometrical description of optimal control theory for partial differential equations.

  4. Identification of different geologic units using fuzzy constrained resistivity tomography

    Science.gov (United States)

    Singh, Anand; Sharma, S. P.

    2018-01-01

    Different geophysical inversion strategies are utilized as a component of an interpretation process that tries to separate geologic units based on the resistivity distribution. In the present study, we present the results of separating different geologic units using fuzzy constrained resistivity tomography. This was accomplished using fuzzy c means, a clustering procedure to improve the 2D resistivity image and geologic separation within the iterative minimization through inversion. First, we developed a Matlab-based inversion technique to obtain a reliable resistivity image using different geophysical data sets (electrical resistivity and electromagnetic data). Following this, the recovered resistivity model was converted into a fuzzy constrained resistivity model by assigning the highest probability value of each model cell to the cluster utilizing fuzzy c means clustering procedure during the iterative process. The efficacy of the algorithm is demonstrated using three synthetic plane wave electromagnetic data sets and one electrical resistivity field dataset. The presented approach shows improvement on the conventional inversion approach to differentiate between different geologic units if the correct number of geologic units will be identified. Further, fuzzy constrained resistivity tomography was performed to examine the augmentation of uranium mineralization in the Beldih open cast mine as a case study. We also compared geologic units identified by fuzzy constrained resistivity tomography with geologic units interpreted from the borehole information.

  5. Constrained variational calculus for higher order classical field theories

    International Nuclear Information System (INIS)

    Campos, Cedric M; De Leon, Manuel; De Diego, David MartIn

    2010-01-01

    We develop an intrinsic geometrical setting for higher order constrained field theories. As a main tool we use an appropriate generalization of the classical Skinner-Rusk formalism. Some examples of applications are studied, in particular to the geometrical description of optimal control theory for partial differential equations.

  6. Bounds on the capacity of constrained two-dimensional codes

    DEFF Research Database (Denmark)

    Forchhammer, Søren; Justesen, Jørn

    2000-01-01

    Bounds on the capacity of constrained two-dimensional (2-D) codes are presented. The bounds of Calkin and Wilf apply to first-order symmetric constraints. The bounds are generalized in a weaker form to higher order and nonsymmetric constraints. Results are given for constraints specified by run-l...

  7. The balance of payment-constrained economic growth in Ethiopia ...

    African Journals Online (AJOL)

    The objective of this paper is to empirically test the validity of the simplified version of the balance of payment-constrained economic growth model for Ethiopia during the period 1971-20082. According to the model, economies only grow at a pace allowed by the constraints imposed by the requirement of balance of payment ...

  8. Toward cognitively constrained models of language processing : A review

    NARCIS (Netherlands)

    Vogelzang, Margreet; Mills, Anne C.; Reitter, David; van Rij, Jacolien; Hendriks, Petra; van Rijn, Hedderik

    2017-01-01

    Language processing is not an isolated capacity, but is embedded in other aspects of our cognition. However, it is still largely unexplored to what extent and how language processing interacts with general cognitive resources. This question can be investigated with cognitively constrained

  9. The Balance of Payment-Constrained Economic Growth in Ethiopia ...

    African Journals Online (AJOL)

    Administrator

    Page 100 financial liberalization and export promotion strategy necessarily lead to better growth performance. Rather, one should consider not only exports of goods and services, but also the income elasticity of imports. The balance of payments-constrained growth model postulates that the rate of growth in any country is ...

  10. Evaluating potentialities and constrains of Problem Based Learning curriculum

    DEFF Research Database (Denmark)

    Guerra, Aida

    2013-01-01

    This paper presents a research design to evaluate Problem Based Learning (PBL) curriculum potentialities and constrains for future changes. PBL literature lacks examples of how to evaluate and analyse established PBL learning environments to address new challenges posed. The research design......) in the curriculum and a mean to choose cases for further case study (third phase)....

  11. Binary classification posed as a quadratically constrained quadratic ...

    Indian Academy of Sciences (India)

    Binary classification is posed as a quadratically constrained quadratic problem and solved using the proposed method. Each class in the binary classification problem is modeled as a multidimensional ellipsoid to forma quadratic constraint in the problem. Particle swarms help in determining the optimal hyperplane or ...

  12. GPS-based ionospheric tomography with a constrained adaptive ...

    Indian Academy of Sciences (India)

    According to the continuous smoothness of the variations of ionospheric electron density (IED) among neighbouring voxels, Gauss weighted function is introduced to constrain the tomography system in the new method. It can resolve the dependence on the initial values for those voxels without any GPS rays traversing them ...

  13. Time-constrained project scheduling with adjacent resources

    NARCIS (Netherlands)

    Hurink, Johann L.; Kok, A.L.; Paulus, J.J.; Schutten, Johannes M.J.

    2008-01-01

    We develop a decomposition method for the Time-Constrained Project Scheduling Problem (TCPSP) with Adjacent Resources. For adjacent resources the resource units are ordered and the units assigned to a job have to be adjacent. On top of that, adjacent resources are not required by single jobs, but by

  14. Constrained relationship agency as the risk factor for intimate ...

    African Journals Online (AJOL)

    We used structural equation modelling to identify and measure constrained relationship agency (CRA) as a latent variable, and then tested the hypothesis that CRA plays a significant role in the pathway between IPV and transactional sex. After controlling for CRA, receiving more material goods from a sexual partner was ...

  15. Chance-constrained optimization of demand response to price signals

    DEFF Research Database (Denmark)

    Dorini, Gianluca Fabio; Pinson, Pierre; Madsen, Henrik

    2013-01-01

    within a recursive least squares (RLS) framework using data measurable at the grid level, in an adaptive fashion. Optimal price signals are generated by embedding the FIR models within a chance-constrained optimization framework. The objective is to keep the price signal as unchanged as possible from...

  16. Solution of a Complex Least Squares Problem with Constrained Phase.

    Science.gov (United States)

    Bydder, Mark

    2010-12-30

    The least squares solution of a complex linear equation is in general a complex vector with independent real and imaginary parts. In certain applications in magnetic resonance imaging, a solution is desired such that each element has the same phase. A direct method for obtaining the least squares solution to the phase constrained problem is described.

  17. Dark matter, constrained minimal supersymmetric standard model, and lattice QCD.

    Science.gov (United States)

    Giedt, Joel; Thomas, Anthony W; Young, Ross D

    2009-11-13

    Recent lattice measurements have given accurate estimates of the quark condensates in the proton. We use these results to significantly improve the dark matter predictions in benchmark models within the constrained minimal supersymmetric standard model. The predicted spin-independent cross sections are at least an order of magnitude smaller than previously suggested and our results have significant consequences for dark matter searches.

  18. Constrained Quantum Mechanics: Chaos in Non-Planar Billiards

    Science.gov (United States)

    Salazar, R.; Tellez, G.

    2012-01-01

    We illustrate some of the techniques to identify chaos signatures at the quantum level using as guiding examples some systems where a particle is constrained to move on a radial symmetric, but non-planar, surface. In particular, two systems are studied: the case of a cone with an arbitrary contour or "dunce hat billiard" and the rectangular…

  19. Constrained control of a once-through boiler with recirculation

    DEFF Research Database (Denmark)

    Trangbæk, K

    2008-01-01

    There is an increasing need to operate power plants at low load for longer periods of time. When a once-through boiler operates at a sufficiently low load, recirculation is introduced, significantly altering the control structure. This paper illustrates the possibilities for using constrained con...

  20. On the Integrated Job Scheduling and Constrained Network Routing Problem

    DEFF Research Database (Denmark)

    Gamst, Mette

    This paper examines the NP-hard problem of scheduling a number of jobs on a finite set of machines such that the overall profit of executed jobs is maximized. Each job demands a number of resources, which must be sent to the executing machine via constrained paths. Furthermore, two resource demand...

  1. Effective Teaching of Economics: A Constrained Optimization Problem?

    Science.gov (United States)

    Hultberg, Patrik T.; Calonge, David Santandreu

    2017-01-01

    One of the fundamental tenets of economics is that decisions are often the result of optimization problems subject to resource constraints. Consumers optimize utility, subject to constraints imposed by prices and income. As economics faculty, instructors attempt to maximize student learning while being constrained by their own and students'…

  2. Vacuum expectation values in a scalar constrained theory

    International Nuclear Information System (INIS)

    Alonso, F.; Julve, J.; Tiemblo, A.

    1985-01-01

    A class of finite Green functions in the context of a scalar constrained theory is studied. In a particular model the one-point GFs show that the vacuum expectation values for some fields vanish while one of them remains finite, a feature exhibited by the Goldstone and Higgs fields respectively. (orig.)

  3. Lagrangian formalism for constrained systems. 2. Gauge symmetries

    International Nuclear Information System (INIS)

    Pyatov, P.N.

    1990-01-01

    Using the Lagrangian formalism for constrained systems all gauge symmetries peculiar for a given Lagrangian system and in establishing the relation between them and the constraints are constructed. Besides, the question about the possible dependence of gauge transformations on accelerations and other higher order time derivatives of coordinates is clarified. 14 refs

  4. Factors constraining accessibility and usage of information among ...

    African Journals Online (AJOL)

    Various factors may negatively impact on information acquisition and utilisation. To improve understanding of the determinants of information acquisition and utilisation, this study investigated the factors constraining accessibility and usage of poultry management information in three rural districts of Tanzania. The findings ...

  5. Constrained Geocast to Support Cooperative Adaptive Cruise Control (CACC) Merging

    NARCIS (Netherlands)

    Klein Wolterink, W.; Heijenk, Geert; Karagiannis, Georgios

    2010-01-01

    In this paper we introduce a new geocasting concept to target vehicles based on where they will be in the direct future, in stead of their current position. We refer to this concept as constrained geocast. This may be useful in situations where vehicles have interdependencies based on (future)

  6. Combining fossil and molecular data to date the diversification of New World Primates.

    Science.gov (United States)

    Schrago, C G; Mello, B; Soares, A E R

    2013-11-01

    Recent methodological advances in molecular dating associated with the growing availability of sequence data have prompted the study of the evolution of New World Anthropoidea in recent years. Motivated by questions regarding historical biogeography or the mode of evolution, these works aimed to obtain a clearer scenario of Platyrrhini origins and diversification. Although some consensus was found, disputed issues, especially those relating to the evolutionary affinities of fossil taxa, remain. The use of fossil taxa for divergence time analysis is traditionally restricted to the provision of calibration priors. However, new analytical approaches have been developed that incorporate fossils as terminals and, thus, directly assign ages to the fossil tips. In this study, we conducted a combined analysis of molecular and morphological data, including fossils, to derive the timescale of New World anthropoids. Differently from previous studies that conducted total-evidence analysis of molecules and morphology, our approach investigated the morphological clock alone. Our results corroborate the hypothesis that living platyrrhines diversified in the last 20 Ma and that Miocene Patagonian fossils compose an independent evolutionary radiation that diversified in the late Oligocene. When compared to the node ages inferred from the molecular timescale, the inclusion of fossils augmented the precision of the estimates for nodes constrained by the fossil tips. We show that morphological data can be analysed using the same methodological framework applied in relaxed molecular clock studies. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

  7. Microbial decomposers not constrained by climate history along a Mediterranean climate gradient in southern California.

    Science.gov (United States)

    Baker, Nameer R; Khalili, Banafshe; Martiny, Jennifer B H; Allison, Steven D

    2018-06-01

    Microbial decomposers mediate the return of CO 2 to the atmosphere by producing extracellular enzymes to degrade complex plant polymers, making plant carbon available for metabolism. Determining if and how these decomposer communities are constrained in their ability to degrade plant litter is necessary for predicting how carbon cycling will be affected by future climate change. We analyzed mass loss, litter chemistry, microbial biomass, extracellular enzyme activities, and enzyme temperature sensitivities in grassland litter transplanted along a Mediterranean climate gradient in southern California. Microbial community composition was manipulated by caging litter within bags made of nylon membrane that prevent microbial immigration. To test whether grassland microbes were constrained by climate history, half of the bags were inoculated with local microbial communities native to each gradient site. We determined that temperature and precipitation likely interact to limit microbial decomposition in the extreme sites along our gradient. Despite their unique climate history, grassland microbial communities were not restricted in their ability to decompose litter under different climate conditions across the gradient, although microbial communities across our gradient may be restricted in their ability to degrade different types of litter. We did find some evidence that local microbial communities were optimized based on climate, but local microbial taxa that proliferated after inoculation into litterbags did not enhance litter decomposition. Our results suggest that microbial community composition does not constrain C-cycling rates under climate change in our system, but optimization to particular resource environments may act as more general constraints on microbial communities. © 2018 by the Ecological Society of America.

  8. Molecular Diagnostics

    OpenAIRE

    Choe, Hyonmin; Deirmengian, Carl A.; Hickok, Noreen J.; Morrison, Tiffany N.; Tuan, Rocky S.

    2015-01-01

    Orthopaedic infections are complex conditions that require immediate diagnosis and accurate identification of the causative organisms to facilitate appropriate management. Conventional methodologies for diagnosis of these infections sometimes lack accuracy or sufficient rapidity. Current molecular diagnostics are an emerging area of bench-to-bedside research in orthopaedic infections. Examples of promising molecular diagnostics include measurement of a specific biomarker in the synovial fluid...

  9. Molecular genetics

    International Nuclear Information System (INIS)

    Parkinson, D.R.; Krontiris, T.G.

    1986-01-01

    In this chapter the authors review new findings concerning the molecular genetics of malignant melanoma in the context of other information obtained from clinical, epidemiologic, and cytogenetic studies in this malignancy. These new molecular approaches promise to provide a more complete understanding of the mechanisms involved in the development of melanoma, thereby suggesting new methods for its treatment and prevention

  10. Molecular Modeling

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 9; Issue 5. Molecular Modeling: A Powerful Tool for Drug Design and Molecular Docking. Rama Rao Nadendla. General Article Volume 9 Issue 5 May 2004 pp 51-60. Fulltext. Click here to view fulltext PDF. Permanent link:

  11. Crustal evolution at mantle depths constrained from Pamir xenoliths

    Science.gov (United States)

    Kooijman, E.; Hacker, B. R.; Smit, M. A.; Kylander-Clark, A. R.; Ratschbacher, L.

    2012-12-01

    Lower crustal xenoliths erupted in the Pamir at ~11 Ma provide an exclusive opportunity to study the evolution of crust at mantle depths during a continent-continent collision. To investigate, and constrain the timing of, the petrologic processes that occurred during burial to the peak conditions (2.5-2.8 GPa, 1000-1100 °C; [1]), we performed chemical- and isotope analyses of accessory minerals in 10 xenoliths, ranging from eclogites to grt-ky-qtz granulites. In situ laser ablation split-stream ICPMS yielded 1) U-Pb ages, Ti concentrations and REE in zircon, 2) U/Th-Pb ages and REE in monazite, and 3) U-Pb ages and trace elements in rutile. In addition, garnet, and biotite and K-feldspar were dated using Lu-Hf and 40Ar/39Ar geochronology, respectively. Zircon and monazite U-(Th-)Pb ages are 101.9±1.8, 53.7±1.0, 39.1±0.8, 21.7±0.4, 18.2±0.5, 16.9±0.8, 15.1±0.3 (2σ) and 12.5-11.1 Ma; most samples showed several or all of these populations. The 53.7 Ma and older ages are xenocrystic or detrital. For younger ages, zircon and monazite in individual samples recorded different ages-although zircon in one rock and monazite in another can be the same age. The 39.1 Ma zircon and monazite mostly occur as inclusions in minerals of the garnet-bearing assemblage that represents the early, low-P stages of burial. Garnet Lu-Hf ages of 37.8±0.3 Ma support garnet growth at this time. Spinifex-like textures containing 21.7-11.1 Ma zircon and monazite record short-lived partial melting events during burial. Aligned kyanite near these patches indicates associated deformation. Zircons yielding ≤12.5 Ma exhibit increased Eu/Eu* and markedly decreased HREE concentrations, interpreted to record feldspar breakdown and omphacite growth during increasing pressure. Rutile U-Pb cooling ages are 10.8±0.3 Ma in all samples. This agrees with the weighted mean 40Ar/39Ar age of eight biotite, K-feldspar and whole rock separates of 11.00+0.16/-0.09 Ma. Rutile in eclogites provides Zr

  12. Constraining movement alters the recruitment of motor processes in mental rotation.

    Science.gov (United States)

    Moreau, David

    2013-02-01

    Does mental rotation depend on the readiness to act? Recent evidence indicates that the involvement of motor processes in mental rotation is experience-dependent, suggesting that different levels of expertise in sensorimotor interactions lead to different strategies to solve mental rotation problems. Specifically, experts in motor activities perceive spatial material as objects that can be acted upon, triggering covert simulation of rotations. Because action simulation depends on the readiness to act, movement restriction should therefore disrupt mental rotation performance in individuals favoring motor processes. In this experiment, wrestlers and non-athletes judged whether pairs of three-dimensional stimuli were identical or different, with their hands either constrained or unconstrained. Wrestlers showed higher performance than controls in the rotation of geometric stimuli, but this difference disappeared when their hands were constrained. However, movement restriction had similar consequences for both groups in the rotation of hands. These findings suggest that expert's advantage in mental rotation of abstract objects is based on the readiness to act, even when physical manipulation is impossible.

  13. Aiding the search: Examining individual differences in multiply-constrained problem solving.

    Science.gov (United States)

    Ellis, Derek M; Brewer, Gene A

    2018-07-01

    Understanding and resolving complex problems is of vital importance in daily life. Problems can be defined by the limitations they place on the problem solver. Multiply-constrained problems are traditionally examined with the compound remote associates task (CRAT). Performance on the CRAT is partially dependent on an individual's working memory capacity (WMC). These findings suggest that executive processes are critical for problem solving and that there are reliable individual differences in multiply-constrained problem solving abilities. The goals of the current study are to replicate and further elucidate the relation between WMC and CRAT performance. To achieve these goals, we manipulated preexposure to CRAT solutions and measured WMC with complex-span tasks. In Experiment 1, we report evidence that preexposure to CRAT solutions improved problem solving accuracy, WMC was correlated with problem solving accuracy, and that WMC did not moderate the effect of preexposure on problem solving accuracy. In Experiment 2, we preexposed participants to correct and incorrect solutions. We replicated Experiment 1 and found that WMC moderates the effect of exposure to CRAT solutions such that high WMC participants benefit more from preexposure to correct solutions than low WMC (although low WMC participants have preexposure benefits as well). Broadly, these results are consistent with theories of working memory and problem solving that suggest a mediating role of attention control processes. Published by Elsevier Inc.

  14. Constraining the brachial plexus does not compromise regional control in oropharyngeal carcinoma

    International Nuclear Information System (INIS)

    Robert, Mutter W; Wolden, Suzanne L; Lee, Nancy Y; Lok, Benjamin H; Dutta, Pinaki R; Riaz, Nadeem; Setton, Jeremy; Berry, Sean L; Goenka, Anuj; Zhang, Zhigang; Rao, Shyam S

    2013-01-01

    Accumulating evidence suggests that brachial plexopathy following head and neck cancer radiotherapy may be underreported and that this toxicity is associated with a dose–response. Our purpose was to determine whether the dose to the brachial plexus (BP) can be constrained, without compromising regional control. The radiation plans of 324 patients with oropharyngeal carcinoma (OPC) treated with intensity-modulated radiation therapy (IMRT) were reviewed. We identified 42 patients (13%) with gross nodal disease <1 cm from the BP. Normal tissue constraints included a maximum dose of 66 Gy and a D 05 of 60 Gy for the BP. These criteria took precedence over planning target volume (PTV) coverage of nodal disease near the BP. There was only one regional failure in the vicinity of the BP, salvaged with neck dissection (ND) and regional re-irradiation. There have been no reported episodes of brachial plexopathy to date. In combined-modality therapy, including ND as salvage, regional control did not appear to be compromised by constraining the dose to the BP. This approach may improve the therapeutic ratio by reducing the long-term risk of brachial plexopathy

  15. Attentive Reading With Constrained Summarization Adapted to Address Written Discourse in People With Mild Aphasia.

    Science.gov (United States)

    Obermeyer, Jessica A; Edmonds, Lisa A

    2018-03-01

    The purpose of this study was to examine the preliminary efficacy of Attentive Reading and Constrained Summarization-Written (ARCS-W) in people with mild aphasia. ARCS-W adapts an existing treatment, ARCS (Rogalski & Edmonds, 2008), to address discourse level writing in mild aphasia. ARCS-W focuses on the cognitive and linguistic skills required for discourse production. This study was a within-subject pre-postdesign. Three people with mild aphasia participated. ARCS-W integrates attentive reading or listening with constrained summarization of discourse level material in spoken and written modalities. Outcomes included macro- (main concepts) and microlinguistic (correct information units, complete utterances) discourse measures, confrontation naming, aphasia severity, and functional communication. All 3 participants demonstrated some generalization to untrained spoken and written discourse at the word, sentence, and text levels. Reduced aphasia severity and/or increased functional communication and confrontation naming were also observed in some participants. The findings of this study provide preliminary evidence of the efficacy of ARCS-W to improve spoken and written discourse in mild aphasia. Different generalization patterns suggest different mechanisms of improvement. Further research and replication are required to better understand how ARCS-W can impact discourse abilities.

  16. Constraining new physics models with isotope shift spectroscopy

    Science.gov (United States)

    Frugiuele, Claudia; Fuchs, Elina; Perez, Gilad; Schlaffer, Matthias

    2017-07-01

    Isotope shifts of transition frequencies in atoms constrain generic long- and intermediate-range interactions. We focus on new physics scenarios that can be most strongly constrained by King linearity violation such as models with B -L vector bosons, the Higgs portal, and chameleon models. With the anticipated precision, King linearity violation has the potential to set the strongest laboratory bounds on these models in some regions of parameter space. Furthermore, we show that this method can probe the couplings relevant for the protophobic interpretation of the recently reported Be anomaly. We extend the formalism to include an arbitrary number of transitions and isotope pairs and fit the new physics coupling to the currently available isotope shift measurements.

  17. Balancing computation and communication power in power constrained clusters

    Science.gov (United States)

    Piga, Leonardo; Paul, Indrani; Huang, Wei

    2018-05-29

    Systems, apparatuses, and methods for balancing computation and communication power in power constrained environments. A data processing cluster with a plurality of compute nodes may perform parallel processing of a workload in a power constrained environment. Nodes that finish tasks early may be power-gated based on one or more conditions. In some scenarios, a node may predict a wait duration and go into a reduced power consumption state if the wait duration is predicted to be greater than a threshold. The power saved by power-gating one or more nodes may be reassigned for use by other nodes. A cluster agent may be configured to reassign the unused power to the active nodes to expedite workload processing.

  18. A Few Expanding Integrable Models, Hamiltonian Structures and Constrained Flows

    International Nuclear Information System (INIS)

    Zhang Yufeng

    2011-01-01

    Two kinds of higher-dimensional Lie algebras and their loop algebras are introduced, for which a few expanding integrable models including the coupling integrable couplings of the Broer-Kaup (BK) hierarchy and the dispersive long wave (DLW) hierarchy as well as the TB hierarchy are obtained. From the reductions of the coupling integrable couplings, the corresponding coupled integrable couplings of the BK equation, the DLW equation, and the TB equation are obtained, respectively. Especially, the coupling integrable coupling of the TB equation reduces to a few integrable couplings of the well-known mKdV equation. The Hamiltonian structures of the coupling integrable couplings of the three kinds of soliton hierarchies are worked out, respectively, by employing the variational identity. Finally, we decompose the BK hierarchy of evolution equations into x-constrained flows and t n -constrained flows whose adjoint representations and the Lax pairs are given. (general)

  19. Optimal Power Constrained Distributed Detection over a Noisy Multiaccess Channel

    Directory of Open Access Journals (Sweden)

    Zhiwen Hu

    2015-01-01

    Full Text Available The problem of optimal power constrained distributed detection over a noisy multiaccess channel (MAC is addressed. Under local power constraints, we define the transformation function for sensor to realize the mapping from local decision to transmitted waveform. The deflection coefficient maximization (DCM is used to optimize the performance of power constrained fusion system. Using optimality conditions, we derive the closed-form solution to the considered problem. Monte Carlo simulations are carried out to evaluate the performance of the proposed new method. Simulation results show that the proposed method could significantly improve the detection performance of the fusion system with low signal-to-noise ratio (SNR. We also show that the proposed new method has a robust detection performance for broad SNR region.

  20. Transient thermal stresses in a circular cylinder with constrained ends

    International Nuclear Information System (INIS)

    Goshima, Takahito; Miyao, Kaju

    1986-01-01

    This paker deals with the transient thermal stresses in a finite circular cylinder constrained at both end surfaces and subjected to axisymmetric temperature distribution on the lateral surface. The thermoelastic problem is formulated in terms of a thermoelastic displacement potential and three harmonic stress functions. Numerical calculations are carried out for the case of the uniform temperature distribution on the lateral surface. The stress distributions on the constrained end and the free suface are shown graphically, and the singularity in stresses appearing at the circumferencial edge is considered. Moreover, the approximate solution based upon the plane strain theory is introduced in order to compare the rigorous one, and it is considered how the length of the cylinder and the time proceeds affect on the accuracy of the approximation. (author)

  1. Dark matter scenarios in a constrained model with Dirac gauginos

    CERN Document Server

    Goodsell, Mark D.; Müller, Tobias; Porod, Werner; Staub, Florian

    2015-01-01

    We perform the first analysis of Dark Matter scenarios in a constrained model with Dirac Gauginos. The model under investigation is the Constrained Minimal Dirac Gaugino Supersymmetric Standard model (CMDGSSM) where the Majorana mass terms of gauginos vanish. However, $R$-symmetry is broken in the Higgs sector by an explicit and/or effective $B_\\mu$-term. This causes a mass splitting between Dirac states in the fermion sector and the neutralinos, which provide the dark matter candidate, become pseudo-Dirac states. We discuss two scenarios: the universal case with all scalar masses unified at the GUT scale, and the case with non-universal Higgs soft-terms. We identify different regions in the parameter space which fullfil all constraints from the dark matter abundance, the limits from SUSY and direct dark matter searches and the Higgs mass. Most of these points can be tested with the next generation of direct dark matter detection experiments.

  2. Constraining the noncommutative spectral action via astrophysical observations.

    Science.gov (United States)

    Nelson, William; Ochoa, Joseph; Sakellariadou, Mairi

    2010-09-03

    The noncommutative spectral action extends our familiar notion of commutative spaces, using the data encoded in a spectral triple on an almost commutative space. Varying a rather simple action, one can derive all of the standard model of particle physics in this setting, in addition to a modified version of Einstein-Hilbert gravity. In this Letter we use observations of pulsar timings, assuming that no deviation from general relativity has been observed, to constrain the gravitational sector of this theory. While the bounds on the coupling constants remain rather weak, they are comparable to existing bounds on deviations from general relativity in other settings and are likely to be further constrained by future observations.

  3. The bounds of feasible space on constrained nonconvex quadratic programming

    Science.gov (United States)

    Zhu, Jinghao

    2008-03-01

    This paper presents a method to estimate the bounds of the radius of the feasible space for a class of constrained nonconvex quadratic programmingsE Results show that one may compute a bound of the radius of the feasible space by a linear programming which is known to be a P-problem [N. Karmarkar, A new polynomial-time algorithm for linear programming, Combinatorica 4 (1984) 373-395]. It is proposed that one applies this method for using the canonical dual transformation [D.Y. Gao, Canonical duality theory and solutions to constrained nonconvex quadratic programming, J. Global Optimization 29 (2004) 377-399] for solving a standard quadratic programming problem.

  4. THE DUBINS TRAVELING SALESMAN PROBLEM WITH CONSTRAINED COLLECTING MANEUVERS

    Directory of Open Access Journals (Sweden)

    Petr Váňa

    2016-11-01

    Full Text Available In this paper, we introduce a variant of the Dubins traveling salesman problem (DTSP that is called the Dubins traveling salesman problem with constrained collecting maneuvers (DTSP-CM. In contrast to the ordinary formulation of the DTSP, in the proposed DTSP-CM, the vehicle is requested to visit each target by specified collecting maneuver to accomplish the mission. The proposed problem formulation is motivated by scenarios with unmanned aerial vehicles where particular maneuvers are necessary for accomplishing the mission, such as object dropping or data collection with sensor sensitive to changes in vehicle heading. We consider existing methods for the DTSP and propose its modifications to use these methods to address a variant of the introduced DTSP-CM, where the collecting maneuvers are constrained to straight line segments.

  5. Constraint-Based Local Search for Constrained Optimum Paths Problems

    Science.gov (United States)

    Pham, Quang Dung; Deville, Yves; van Hentenryck, Pascal

    Constrained Optimum Path (COP) problems arise in many real-life applications and are ubiquitous in communication networks. They have been traditionally approached by dedicated algorithms, which are often hard to extend with side constraints and to apply widely. This paper proposes a constraint-based local search (CBLS) framework for COP applications, bringing the compositionality, reuse, and extensibility at the core of CBLS and CP systems. The modeling contribution is the ability to express compositional models for various COP applications at a high level of abstraction, while cleanly separating the model and the search procedure. The main technical contribution is a connected neighborhood based on rooted spanning trees to find high-quality solutions to COP problems. The framework, implemented in COMET, is applied to Resource Constrained Shortest Path (RCSP) problems (with and without side constraints) and to the edge-disjoint paths problem (EDP). Computational results show the potential significance of the approach.

  6. Exact methods for time constrained routing and related scheduling problems

    DEFF Research Database (Denmark)

    Kohl, Niklas

    1995-01-01

    of customers. In the VRPTW customers must be serviced within a given time period - a so called time window. The objective can be to minimize operating costs (e.g. distance travelled), fixed costs (e.g. the number of vehicles needed) or a combination of these component costs. During the last decade optimization......This dissertation presents a number of optimization methods for the Vehicle Routing Problem with Time Windows (VRPTW). The VRPTW is a generalization of the well known capacity constrained Vehicle Routing Problem (VRP), where a fleet of vehicles based at a central depot must service a set...... of J?rnsten, Madsen and S?rensen (1986), which has been tested computationally by Halse (1992). Both methods decompose the problem into a series of time and capacity constrained shotest path problems. This yields a tight lower bound on the optimal objective, and the dual gap can often be closed...

  7. A constrained approximation for nuclear barrier penetration and fission

    International Nuclear Information System (INIS)

    Tang, H.H.K.; Negele, J.W.; Massachusetts Inst. of Tech., Cambridge; Massachusetts Inst. of Tech., Cambridge

    1983-01-01

    An approximation to the time-dependent mean-field theory for barrier penetration by a nucleus is obtained in terms of constrained Hartree-Fock wave functions and a coherent velocity field. A discrete approximation to the continuum theory suitable for practical numerical calculations is presented and applied to three illustrative models. Potential application of the theory to the study of nuclear fission is discussed. (orig.)

  8. A Globally Convergent Parallel SSLE Algorithm for Inequality Constrained Optimization

    Directory of Open Access Journals (Sweden)

    Zhijun Luo

    2014-01-01

    Full Text Available A new parallel variable distribution algorithm based on interior point SSLE algorithm is proposed for solving inequality constrained optimization problems under the condition that the constraints are block-separable by the technology of sequential system of linear equation. Each iteration of this algorithm only needs to solve three systems of linear equations with the same coefficient matrix to obtain the descent direction. Furthermore, under certain conditions, the global convergence is achieved.

  9. Multivariable controller for discrete stochastic amplitude-constrained systems

    Directory of Open Access Journals (Sweden)

    Hannu T. Toivonen

    1983-04-01

    Full Text Available A sub-optimal multivariable controller for discrete stochastic amplitude-constrained systems is presented. In the approach the regulator structure is restricted to the class of linear saturated feedback laws. The stationary covariances of the controlled system are evaluated by approximating the stationary probability distribution of the state by a gaussian distribution. An algorithm for minimizing a quadratic loss function is given, and examples are presented to illustrate the performance of the sub-optimal controller.

  10. Modeling constrained sintering of bi-layered tubular structures

    DEFF Research Database (Denmark)

    Tadesse Molla, Tesfaye; Kothanda Ramachandran, Dhavanesan; Ni, De Wei

    2015-01-01

    Constrained sintering of tubular bi-layered structures is being used in the development of various technologies. Densification mismatch between the layers making the tubular bi-layer can generate stresses, which may create processing defects. An analytical model is presented to describe the densi...... and thermo-mechanical analysis. Results from the analytical model are found to agree well with finite element simulations as well as measurements from sintering experiment....

  11. Tree dimension in verification of constrained Horn clauses

    DEFF Research Database (Denmark)

    Kafle, Bishoksan; Gallagher, John Patrick; Ganty, Pierre

    2018-01-01

    In this paper, we show how the notion of tree dimension can be used in the verification of constrained Horn clauses (CHCs). The dimension of a tree is a numerical measure of its branching complexity and the concept here applies to Horn clause derivation trees. Derivation trees of dimension zero c...... algorithms using these constructions to decompose a CHC verification problem. One variation of this decomposition considers derivations of successively increasing dimension. The paper includes descriptions of implementations and experimental results....

  12. Distributionally Robust Joint Chance Constrained Problem under Moment Uncertainty

    Directory of Open Access Journals (Sweden)

    Ke-wei Ding

    2014-01-01

    Full Text Available We discuss and develop the convex approximation for robust joint chance constraints under uncertainty of first- and second-order moments. Robust chance constraints are approximated by Worst-Case CVaR constraints which can be reformulated by a semidefinite programming. Then the chance constrained problem can be presented as semidefinite programming. We also find that the approximation for robust joint chance constraints has an equivalent individual quadratic approximation form.

  13. Superalloy design - A Monte Carlo constrained optimization method

    CSIR Research Space (South Africa)

    Stander, CM

    1996-01-01

    Full Text Available optimization method C. M. Stander Division of Materials Science and Technology, CSIR, PO Box 395, Pretoria, Republic of South Africa Received 74 March 1996; accepted 24 June 1996 A method, based on Monte Carlo constrained... successful hit, i.e. when Liow < LMP,,, < Lhiph, and for all the properties, Pj?, < P, < Pi@?. If successful this hit falls within the ROA. Repeat steps 4 and 5 to find at least ten (or more) successful hits with values...

  14. Hydrologic and hydraulic flood forecasting constrained by remote sensing data

    Science.gov (United States)

    Li, Y.; Grimaldi, S.; Pauwels, V. R. N.; Walker, J. P.; Wright, A. J.

    2017-12-01

    Flooding is one of the most destructive natural disasters, resulting in many deaths and billions of dollars of damages each year. An indispensable tool to mitigate the effect of floods is to provide accurate and timely forecasts. An operational flood forecasting system typically consists of a hydrologic model, converting rainfall data into flood volumes entering the river system, and a hydraulic model, converting these flood volumes into water levels and flood extents. Such a system is prone to various sources of uncertainties from the initial conditions, meteorological forcing, topographic data, model parameters and model structure. To reduce those uncertainties, current forecasting systems are typically calibrated and/or updated using ground-based streamflow measurements, and such applications are limited to well-gauged areas. The recent increasing availability of spatially distributed remote sensing (RS) data offers new opportunities to improve flood forecasting skill. Based on an Australian case study, this presentation will discuss the use of 1) RS soil moisture to constrain a hydrologic model, and 2) RS flood extent and level to constrain a hydraulic model.The GRKAL hydrological model is calibrated through a joint calibration scheme using both ground-based streamflow and RS soil moisture observations. A lag-aware data assimilation approach is tested through a set of synthetic experiments to integrate RS soil moisture to constrain the streamflow forecasting in real-time.The hydraulic model is LISFLOOD-FP which solves the 2-dimensional inertial approximation of the Shallow Water Equations. Gauged water level time series and RS-derived flood extent and levels are used to apply a multi-objective calibration protocol. The effectiveness with which each data source or combination of data sources constrained the parameter space will be discussed.

  15. Constrained convex minimization via model-based excessive gap

    OpenAIRE

    Tran Dinh, Quoc; Cevher, Volkan

    2014-01-01

    We introduce a model-based excessive gap technique to analyze first-order primal- dual methods for constrained convex minimization. As a result, we construct new primal-dual methods with optimal convergence rates on the objective residual and the primal feasibility gap of their iterates separately. Through a dual smoothing and prox-function selection strategy, our framework subsumes the augmented Lagrangian, and alternating methods as special cases, where our rates apply.

  16. A constrained variational calculation for beta-stable matter

    International Nuclear Information System (INIS)

    Howes, C.; Bishop, R.F.; Irvine, J.M

    1978-01-01

    A method of lowest-order constrained variation previously applied by the authors to asymmetric nuclear matter is extended to include electrons and muons making the nucleon fluid electrically neutral and stable against beta decay. The equilibrium composition of a nucleon fluid is calculated as a function of baryon number density and an equation of state for beta-stable matter is deduced for the Reid soft-core interaction. (author)

  17. Nonlinear Chance Constrained Problems: Optimality Conditions, Regularization and Solvers

    Czech Academy of Sciences Publication Activity Database

    Adam, Lukáš; Branda, Martin

    2016-01-01

    Roč. 170, č. 2 (2016), s. 419-436 ISSN 0022-3239 R&D Projects: GA ČR GA15-00735S Institutional support: RVO:67985556 Keywords : Chance constrained programming * Optimality conditions * Regularization * Algorithms * Free MATLAB codes Subject RIV: BB - Applied Statistics, Operational Research Impact factor: 1.289, year: 2016 http://library.utia.cas.cz/separaty/2016/MTR/adam-0460909.pdf

  18. How market environment may constrain global franchising in emerging markets

    OpenAIRE

    Baena Graciá, Verónica

    2011-01-01

    Although emerging markets are some of the fastest growing economies in the world and represent countries that are experiencing a substantial economic transformation, little is known about the factors influencing country selection for expansion in those markets. In an attempt to enhance the knowledge that managers and scholars have on franchising expansion, the present study examines how market conditions may constrain international diffusion of franchising in emerging markets. They are: i) ge...

  19. Anti-B-B Mixing Constrains Topcolor-Assisted Technicolor

    International Nuclear Information System (INIS)

    Burdman, Gustavo; Lane, Kenneth; Rador, Tonguc

    2000-01-01

    We argue that extended technicolor augmented with topcolor requires that all mixing between the third and the first two quark generations resides in the mixing matrix of left-handed down quarks. Then, the anti-B d -B d mixing that occurs in topcolor models constrains the coloron and Z(prime) boson masses to be greater than about 5 TeV. This implies fine tuning of the topcolor couplings to better than 1 percent

  20. Applications of a constrained mechanics methodology in economics

    Science.gov (United States)

    Janová, Jitka

    2011-11-01

    This paper presents instructive interdisciplinary applications of constrained mechanics calculus in economics on a level appropriate for undergraduate physics education. The aim of the paper is (i) to meet the demand for illustrative examples suitable for presenting the background of the highly expanding research field of econophysics even at the undergraduate level and (ii) to enable the students to gain a deeper understanding of the principles and methods routinely used in mechanics by looking at the well-known methodology from the different perspective of economics. Two constrained dynamic economic problems are presented using the economic terminology in an intuitive way. First, the Phillips model of the business cycle is presented as a system of forced oscillations and the general problem of two interacting economies is solved by the nonholonomic dynamics approach. Second, the Cass-Koopmans-Ramsey model of economical growth is solved as a variational problem with a velocity-dependent constraint using the vakonomic approach. The specifics of the solution interpretation in economics compared to mechanics is discussed in detail, a discussion of the nonholonomic and vakonomic approaches to constrained problems in mechanics and economics is provided and an economic interpretation of the Lagrange multipliers (possibly surprising for the students of physics) is carefully explained. This paper can be used by the undergraduate students of physics interested in interdisciplinary physics applications to gain an understanding of the current scientific approach to economics based on a physical background, or by university teachers as an attractive supplement to classical mechanics lessons.