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Sample records for comparative crystal-chemical analysis

  1. Crystal-Chemical Analysis Martian Minerals in Gale Crater

    NASA Technical Reports Server (NTRS)

    Morrison, S. M.; Downs, R. T.; Blake, D. F.; Bish, D. L.; Ming, D. W.; Morris, R. V.; Yen, A. S.; Chipera, S. J.; Treiman, A. H.; Vaniman, D. T.; hide

    2015-01-01

    The CheMin instrument on the Mars Science Laboratory rover Curiosity performed X-ray diffraction analyses on scooped soil at Rocknest and on drilled rock fines at Yellowknife Bay (John Klein and Cumberland samples), The Kimberley (Windjana sample), and Pahrump (Confidence Hills sample) in Gale crater, Mars. Samples were analyzed with the Rietveld method to determine the unit-cell parameters and abundance of each observed crystalline phase. Unit-cell parameters were used to estimate compositions of the major crystalline phases using crystal-chemical techniques. These phases include olivine, plagioclase and clinopyroxene minerals. Comparison of the CheMin sample unit-cell parameters with those in the literature provides an estimate of the chemical compositions of the major crystalline phases. Preliminary unit-cell parameters, abundances and compositions of crystalline phases found in Rocknest and Yellowknife Bay samples were reported in. Further instrument calibration, development of 2D-to- 1D pattern conversion corrections, and refinement of corrected data allows presentation of improved compositions for the above samples.

  2. Crystal-Chemical Analysis of Soil at Rocknest, Gale Crater

    NASA Technical Reports Server (NTRS)

    Morrison, S. M.; Downs, R. T.; Blake, D. F.; Bish, D. L.; Ming, D. W.; Morris, R. V.; Yen, A. S.; Chipera, S. J.; Treiman, A. H.; Vaniman, D. T.; hide

    2013-01-01

    The CheMin instrument on the Mars Science Laboratory rover Curiosity performed X-ray diffraction analysis on Martian soil [1] at Rocknest in Gale Crater. In particular, crystalline phases from scoop 5 were identified and analyzed with the Rietveld method [2]. Refined unit-cell parameters are reported in Table 1. Comparing these unit-cell parameters with those in the literature provides an estimate of the chemical composition of the crystalline phases. For instance, Fig. 1 shows the Mg-content of Fa-Fo olivine as a function of the b unit-cell parameter using literature data. Our refined b parameter is indicated by the black triangle.

  3. Comparative Analysis.

    DTIC Science & Technology

    1987-11-01

    Al" 56 COMPARATIVE ANALYSIS(U) MASSACJWSETTS INST OF TECH 1/1 CAMBRIDGE ARTIFICIAL INTELLIGENCE LAO 9 S MELD NOV B, RI-N-95i NMM4-85-K-0124...0 0 0 0 0 0 i. -~~ --- WU V1 2 fwx~, - - W-na alc F!LFI MASSACHUSETTS INSTITUTE OF TECHNOLOGY CO ARTIFICIAL INTELLIGENCE LABORATORY Lfl 0 Al/Memo...differential qualita- tive (DQ) analysis, which solves the task, providing explanations suitable for use by design systems, automated diagnosis, intelligent

  4. Aktashite Cu6Hg3As4S12 from the Aktash deposit, Altai, Russia: Refinement and crystal chemical analysis of the structure

    NASA Astrophysics Data System (ADS)

    Vasil'Ev, V. I.; Pervukhina, N. V.; Borisov, S. V.; Magarill, S. A.; Naumov, D. Yu.; Kurat'eva, N. V.

    2010-12-01

    The composition and structure of aktashite from the Aktash deposit, Gorny Altai, Russia, have been studied by electron microprobe and X-ray structural analysis. On the basis of close compositions and crystal structures, the identity of aktashite from the Gal-Khaya and Aktash deposits has been demonstrated. Crystals of aktashite are of trigonal symmetry; the unit-cell dimensions are: a = 13.7500(4), c = 9.3600(3) Å, V = 532.54(8) Å3, space group R3, Z = 3 for the composition of Cu6Hg3As4S12, R = 0.043. The structure of aktashite as a framework of vertex-shared HgS4- and CuS4- tetrahedrons of the same orientation is intimately related to the sphalerite-type structure. The earlier identified uncommon cluster group [As4] has been verified and its parameters have been refined. It is shown that the structure may be represented as construction blocks (As4S12)12- packed according to the law of the distorted cubic I-cell.

  5. Structure determination of KLaS2, KPrS2, KEuS2, KGdS2, KLuS2, KYS2, RbYS2, NaLaS2 and crystal-chemical analysis of the group 1 and thallium(I) rare-earth sulfide series.

    PubMed

    Fábry, Jan; Havlák, Lubomír; Dušek, Michal; Vaněk, Přemysl; Drahokoupil, Jan; Jurek, Karel

    2014-04-01

    One of the purposes of this work is to provide a crystallographic review of group 1 and thallium rare-earth ternary sulfides M(+)Ln(3+)S2. We have therefore determined crystal structures of KLaS2, KPrS2, KEuS2, KGdS2, KLuS2, KYS2, RbYS2, which belong to the α-NaFeO2 structural family (R3m), as well as NaLaS2, which is derived from the disordered NaCl structural type (Fm3m). The determined structures were compared with known members of the group 1 as well as thallium(I) rare-earth sulfides by the standard tools of crystal-chemical analysis such as comparison of bond-valences, analysis of interatomic distances and comparison of the unit-cell parameters. The results indicate why the cubic structural type is limited to Li(+) and Na(+) members of the series only. The analysis has also revealed frequent problems in the reported crystal structures, especially in the determination of the K(+) compounds, probably due to severe absorption and different accuracy and sensitivity of various instruments. Intense diffuse scattering has been discovered in NaLaS2, which will be the subject of further investigation. The newly determined as well as already known structures are summarized, together with critical comments about possible errors in the previous structure determinations.

  6. A crystal chemical study of stishovite

    SciTech Connect

    Hill, R.J.; Newton, M.D.; Gibbs, G.V.

    1983-04-01

    The crystal structure of stishovite, SiO/sub 2/, a=4.1773(1), c=2.6655(1) angstrom, space groups P4/sub 2//mnm, with Z=2, has been refined with 217 graphite-monochromatized MoK..cap alpha.. data (2THETA max=120/sup 0/) to R=0.012 (R/sub w/=0.014). Electron deformation density maps show a modest accumulation of charge density ascribed to partial covalent bonding in both the equatorial and axial bonds together with a delocalization of denstity in and around the shared octahedron edges with the shorter equatorial bonds showing higher peaks (0.47 e angstrom/sup -3/) than the longer axial bonds (0.29 e angstrom/sup -3/). Net atomic charges for Si and O determined by a population and KAPPA refinement by varying the occupancy and shape of their valence shells are +1.71 and -0.86(15)e, respectively. The observed structural distortions and charge distributions conform with the results of ab initio molecular orbital calculations undertaken on molecules designed to mimic the local geometry of the structure of stishovite. The Si-O bond length (1.73 angstrom) calculated for a neutral molecule with 6-coordinated Si is slightly shorter than that observed on the average (1.76 angstrom) for silicates and molecular crystals with 6-coodinated Si. In addition, the calculated geometrical parameters of two edge-sharing octahedra agree to within approx.5% of the observed geometry of stishovite. The calculated charge on Si is indicated to increase with coordination number and bond length in agreement with the larger net charge recorded for stishovite as compared with that recorded for ..cap alpha..-quartz, Q(Si)= +1.0e.Observed deformation maps are compared with theoretical ones calculated in the equatorial plan of the 6-coodinated molecule using molecular orbital theory with a split valence s, p basis supplemented with d-type polarization functions on Si.

  7. Fixed Target Comparative Analysis

    DTIC Science & Technology

    1991-12-01

    development was required to produce the 3D models to support evaluation of this 3D model -supported exploitation approach. The comparative analysis techniques...that were developed exploited the fact that the 3D site model data base was available during the automatic processing. This opened up a new range of...processing strategies during the automated image comparison function. In addition, the existence of the 3D site models allows for the development of an

  8. Hydrogrossular (Katoite): Vibrational, Crystal-Chemical and Thermodynamic Properties

    NASA Astrophysics Data System (ADS)

    Dachs, E.; Geiger, C. A.

    2011-12-01

    There is great current interest in understanding interactions between H2O and its components and various Earth materials. Here, questions such as the bulk water content of the mantle, and what phases can incorporate OH- and in what concentrations come immediately to mind. In this regard, the hydrogarnet substitution (i.e., O4H4↔SiO4) has received special attention, because it is a verified mechanism for allowing the incorporation of OH- in garnet and possibly in other silicates as well. At relatively low temperatures there is complete solid solution between Ca3Al2Si3O12 and Ca3Al2O12H12. The latter, pure OH-containing end-member is termed katoite/hydrogrossular. Its crystal structure has been investigated by various workers using X-ray and neutron diffraction, including at high pressures. Little is known about its vibrational properties and its thermodynamic behavior is not fully understood. Thus, we studied the low temperature IR spectra and measured the heat capacity of katoite in order to investigate its vibrational, crystal-chemical and thermophysical properties. Katoite was synthesized hydrothermally in Au capsules at 250 °C and 3 kb water pressure. X-ray powder measurements show that about 98-99% katoite was obtained. Powder IR spectra were recorded between 298 K and 10 K. The spectra are considerably different in the high wavenumber region, where O-H stretching modes occur. At room temperature the IR-active O-H band located around 3662 cm-1 is broad and it narrows and shifts to higher wavenumbers and also develops structure below about 80 K. Concomitantly, additional weak intensity O-H bands located around 3600 cm-1 begin to appear and they become sharper and increase in intensity with further decreases in temperature. The spectra indicate that the vibrational behavior of individual OH groups and their collective interactions measurably affect the lattice dynamic (i.e. thermodynamic) behavior. The low temperature heat capacity behavior was investigated

  9. Crystal-chemical characteristics of nontronites from bottom sediments of Pacific ocean

    NASA Astrophysics Data System (ADS)

    Palchik, N. A.; Moroz, T. N.; Grigorieva, T. N.; Nikandrova, N. K.; Miroshnichenko, L. V.

    2017-01-01

    A crystal-chemical analysis of the nontronite samples formed in deep-water sediments of the underwater Juan-de-Fuca ridge in the Pacific ocean has been performed using powder X-ray diffraction, IR spectroscopy, and Mössbauer spectroscopy. A comparison with the previously investigated nontronites from different regions of the Sea of Okhotsk showed that the structural features of these formations are due to the difference in the physicochemical parameters of their crystallization. The values of the basal interplanar spacing d 001 (within 11-13 Å) in the samples analyzed are determined by the degree of hydration and cation filling of the interlayer space, while the differences in the IR spectra are due to isomorphic substitutions in the structure. The character of cation distribution and the nature and concentration of stacking faults in nontronite structures are determined. The differences in the composition, structure, and properties of nontronites of different origin are confirmed by theoretical calculations of their structural parameters.

  10. Soft x-ray measurements using photoconductive type-IIa and single-crystal chemical vapor deposited diamond detectors

    SciTech Connect

    Moore, A. S.; Bentley, C. D.; Foster, J. M.; Goedhart, G.; Graham, P.; Taylor, M. J.; Hellewell, E.

    2008-10-15

    Photoconductive detectors (PCDs) are routinely used alongside vacuum x-ray diodes (XRDs) to provide an alternative x-ray flux measurement at laser facilities such as HELEN at AWE Aldermaston, UK, and Omega at the Laboratory for Laser Energetics. To evaluate diamond PCDs as an alternative to XRD arrays, calibration measurements made at the National Synchrotron Light Source (NSLS) at Brookhaven National Laboratory are used to accurately calculate the x-ray flux from a laser-heated target. This is compared to a flux measurement using the Dante XRD diagnostic. Estimates indicate that the photoinduced conductivity from measurements made at Omega are too large, and calculations using the radiometric calibrations made at the NSLS agree with this hypothesis. High-purity, single-crystal, chemical vapor deposited (CVD) diamond samples are compared to natural type-IIa PCDs and show promising high resistivity effects, the corollary of which preliminary results show is a slower response time.

  11. Soft x-ray measurements using photoconductive type-IIa and single-crystal chemical vapor deposited diamond detectors.

    PubMed

    Moore, A S; Bentley, C D; Foster, J M; Goedhart, G; Graham, P; Taylor, M J; Hellewell, E

    2008-10-01

    Photoconductive detectors (PCDs) are routinely used alongside vacuum x-ray diodes (XRDs) to provide an alternative x-ray flux measurement at laser facilities such as HELEN at AWE Aldermaston, UK, and Omega at the Laboratory for Laser Energetics. To evaluate diamond PCDs as an alternative to XRD arrays, calibration measurements made at the National Synchrotron Light Source (NSLS) at Brookhaven National Laboratory are used to accurately calculate the x-ray flux from a laser-heated target. This is compared to a flux measurement using the Dante XRD diagnostic. Estimates indicate that the photoinduced conductivity from measurements made at Omega are too large, and calculations using the radiometric calibrations made at the NSLS agree with this hypothesis. High-purity, single-crystal, chemical vapor deposited (CVD) diamond samples are compared to natural type-IIa PCDs and show promising high resistivity effects, the corollary of which preliminary results show is a slower response time.

  12. Comparative analysis of collaboration networks

    SciTech Connect

    Progulova, Tatiana; Gadjiev, Bahruz

    2011-03-14

    In this paper we carry out a comparative analysis of the word network as the collaboration network based on the novel by M. Bulgakov 'Master and Margarita', the synonym network of the Russian language as well as the Russian movie actor network. We have constructed one-mode projections of these networks, defined degree distributions for them and have calculated main characteristics. In the paper a generation algorithm of collaboration networks has been offered which allows one to generate networks statistically equivalent to the studied ones. It lets us reveal a structural correlation between word network, synonym network and movie actor network. We show that the degree distributions of all analyzable networks are described by the distribution of q-type.

  13. Comparative analysis of collaboration networks

    NASA Astrophysics Data System (ADS)

    Progulova, Tatiana; Gadjiev, Bahruz

    2011-03-01

    In this paper we carry out a comparative analysis of the word network as the collaboration network based on the novel by M. Bulgakov "Master and Margarita", the synonym network of the Russian language as well as the Russian movie actor network. We have constructed one-mode projections of these networks, defined degree distributions for them and have calculated main characteristics. In the paper a generation algorithm of collaboration networks has been offered which allows one to generate networks statistically equivalent to the studied ones. It lets us reveal a structural correlation between word network, synonym network and movie actor network. We show that the degree distributions of all analyzable networks are described by the distribution of q-type.

  14. Crystal chemical characterization of mullite-type aluminum borate compounds

    NASA Astrophysics Data System (ADS)

    Hoffmann, K.; Hooper, T. J. N.; Zhao, H.; Kolb, U.; Murshed, M. M.; Fischer, M.; Lührs, H.; Nénert, G.; Kudějová, P.; Senyshyn, A.; Schneider, H.; Hanna, J. V.; Gesing, Th. M.; Fischer, R. X.

    2017-03-01

    Al-rich aluminum borates were prepared by different synthesis routes using various Al/B ratios, characterized by diffraction methods, spectroscopy and prompt gamma activation analysis. The 11B NMR data show a small amount of BO4 species in all samples. The chemical analysis indicates a trend in the Al/B ratio instead of a fixed composition. Both methods indicate a solid solution Al5-xB1+xO9 where Al is substituted by B in the range of 1-3%. The structure of B-rich Al4B2O9 (C2/m, a=1488 pm, b=553 pm, c=1502 pm, ß=90.6°), was re-investigated by electron diffraction methods, showing that structural details vary within a crystallite. In most of the domains the atoms are orderly distributed, showing no signal for the postulated channel oxygen atom O5. The absence of O5 is supported by density functional theory calculations. Other domains show a probable disordered configuration of O5 and O10, indicated by diffuse scattering along the b direction.

  15. Synthesis and crystal chemical evolution of fresnoite powders

    SciTech Connect

    Wong, Chui L.; Madhavi, S.; Phonthammachai, N.; White, Timothy J.

    2012-03-15

    (Ba,Sr){sub 2}TiSi{sub 2}O{sub 8} fresnoite powders were prepared via a Pechini process in which citric acid and ethylene glycol were used as complexing agents. The resulting gel contained a homogeneous distribution of the metal ions that suppressed the formation of (Ba,Sr)TiO{sub 3} perovskite as a secondary phase during calcination. Phase development was examined as by isochronal and isothermal reaction analysis. A combination of thermo- and differential gravimetric analysis (TGA-DGA), quantitative X-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR) confirmed that calcination at 900 Degree-Sign C/12 h yielded finely crystalline ({approx}70 nm) Ba{sub 2}TiSi{sub 2}O{sub 8} (BTS) and Sr{sub 2}TiSi{sub 2}O{sub 8} (STS). The endmembers and compositional intermediates crystallized directly from the Pechini resin and indirectly through reaction of (Ba,Sr)CO{sub 3}, (Ba,Sr)TiO{sub 3} and a silica-rich glass intermediates. This new method for preparing fresnoite yields materials suitable for consolidation as dense monolithic dielectrics or for use as high surface area catalytic powders. - Graphical abstract: The Pechini synthesis of (Ba, Sr){sub 2}TiSi{sub 2}O{sub 8} titano-silicate fresnoites delivers finely divided precursors for applications as diverse as solid electrolytes and photocatalysis that exploit the unique Ti-O and Si-O bonding and structural morphology of these materials. Highlights: Black-Right-Pointing-Pointer A Pechini method for synthesizing (Ba,Sr){sub 2}TiSi{sub 2}O{sub 8} fresnoites is demonstrated. Black-Right-Pointing-Pointer The method minimizes a persistent glassy intermediate phase. Black-Right-Pointing-Pointer The Pechini process is generally applicable for tailoring fresnoites as functional materials.

  16. Crystal-chemical features of the solid solutions

    SciTech Connect

    Titov, V.V.; Kesler, Ya.A.; Gordeev, I.V.; Mozhaev, A.P.

    1988-04-01

    The unusual magnetic properties of the solid solutions of CuCr/sub 2/S/sub 4/ in Cu/sub 0.5/Mo/sub 0.5/Cr/sub 2/S/sub 4/ (M = Al, Ga, In) are closely related to the crystal chemistry of these compounds. Specimens for structural investigation were obtained by solid-phase synthesis in evacuated quartz capsules. X-ray phase analysis of all the compounds was made by the powder method in a DRON-1 diffractometer with Cu K..cap alpha.. filtered radiation. The experimental confirmation of the ordering of the cations in the tetrahedral sublattice of the investigated spinels was obtained by the authors from their IR absorption spectra taken in the range 400-33 cm/sup /minus/1/. The presence of seven intense absorption bands in the spectra of the specimens indicates that these materials belong to the space group F/anti/43m, i.e., that there is ordering in the A sublattice. Their investigation led them to the conclusion that in a number of cases the vibrational spectra of the crystals are more sensitive in the investigation of atomic ordering than the spectra of x-ray and neutron diffraction, in agreement with the theoretical predictions.

  17. Sociological analysis and comparative education

    NASA Astrophysics Data System (ADS)

    Woock, Roger R.

    1981-12-01

    It is argued that comparative education is essentially a derivative field of study, in that it borrows theories and methods from academic disciplines. After a brief humanistic phase, in which history and philosophy were central for comparative education, sociology became an important source. In the mid-50's and 60's, sociology in the United States was characterised by Structural Functionalism as a theory, and Social Survey as a dominant methodology. Both were incorporated into the development of comparative education. Increasingly in the 70's, and certainly today, the new developments in sociology are characterised by an attack on Positivism, which is seen as the philosophical position underlying both functionalism and survey methods. New or re-discovered theories with their attendant methodologies included Marxism, Phenomenological Sociology, Critical Theory, and Historical Social Science. The current relationship between comparative education and social science is one of uncertainty, but since social science is seen to be returning to its European roots, the hope is held out for the development of an integrated social theory and method which will provide a much stronger basis for developments in comparative education.

  18. Biomembrane phospholipid-oxide surface interactions: crystal chemical and thermodynamic basis.

    PubMed

    Sahai, Nita

    2002-08-15

    Quartz has the least favored surface among many oxides for bacterial attachment and for lipid bilayer or micelle interactions. Tetrahedrally coordinated crystalline silica polymorphs are membranolytic toward liposomes, lysosomes, erythrocytes, and macrophages. Amorphous silica, the octahedral silica polymorph, (stishovite), and oxides such as Al2O3, Fe2 O3, and TiO2 are less cytotoxic. Existing theories for membrane rupture that invoke interactions between oxide surfaces and cell membrane phospholipids (PLs) do not adequately explain these differences in membranolytic potential of the oxides. The author presents a crystal chemical, thermodynamic model for the initial interaction of oxide surfaces with the quaternary ammonium component of the PL's polar head group. The model includes solvation energy changes and electrostatic forces during adsorption, represented by the dielectric constant of the solid and the charge-to-radius ratio of the adsorbing solute. The nature of oxide-solute interactions compared with oxide-water, solute-water, and water-water interactions determines the membranolytic activity of the oxide, where the solute is TMA+, the quaternary ammonium moeity. Significant membrane rupture, as on quartz, requires unfavorable adsorption entropy (DeltaS(ads,TMA+)<0) to maximize disruption of normal membrane structure and requires favorable Gibbs free energy of exchange between TMA+ and the ambient Na+ ions (DeltaG(exc,TMA+/Na+) = DeltaG(ads,TMA+)-DeltaG(ads,Na+)<0) to maximize the extent of membrane affected. For amorphous silica, DeltaS(ads,TMA+) >0, so disruption of structure is limited, even though G(exc,TMA+/Na+) is <0. Stishovite and other oxides have DeltaS(ads,TMA+) <0, but now DeltaG(exc,TMA+/Na+) is>0 at the acidic to circumneutral pHs of cellular and subcellular organelle fluids. The model predicts the correct sequence of membranolytic ability: quartz > or = amorphous SiO2 >Al2O3 >Fe2O3 >TiO2. The model thus explains the relatively poor adhesion

  19. Crystal Chemical Substitutions of YBa2Cu3O7-d to Enhance Flux Pinning (Postprint)

    DTIC Science & Technology

    2012-02-01

    Cassinese, R. Di Capua, E. Di Gennaro, M . Iavarone, M.G. Maglione , R. Vaglio, Physica C 372-376 (2002) 703-705. X. Qi, M . Soorie, Z. Lockman, J.L...eserved. ISBN 1-59454-305-4 CRYSTAL CHEMICAL SUBSTITUTIO NS OF YBa2Cu30,-6 TO ENHANCE FLUX PINNING T. J. Haugan, J. C. Toli.Wer, J. M . Evans, J...RE substitutions for Y and/or Ba. B asic structural and physical properties of the RE and I I 194 T. J. Haugan, J. C. Tolliver, J. M . Evans and

  20. Comparing Techniques for Certified Static Analysis

    NASA Technical Reports Server (NTRS)

    Cachera, David; Pichardie, David

    2009-01-01

    A certified static analysis is an analysis whose semantic validity has been formally proved correct with a proof assistant. The recent increasing interest in using proof assistants for mechanizing programming language metatheory has given rise to several approaches for certification of static analysis. We propose a panorama of these techniques and compare their respective strengths and weaknesses.

  1. Development of Single Crystal Chemical Vapor Deposition Diamonds for Detector Applications

    SciTech Connect

    Harris Kagan; K.K. Gan; Richard Kass

    2009-03-31

    Diamond was studied as a possible radiation hard technology for use in future high radiation environments. With the commissioning of the LHC expected in 2009, and the LHC upgrades expected in 2013, all LHC experiments are planning for detector upgrades which require radiation hard technologies. Chemical Vapor Deposition (CVD) diamond has now been used extensively in beam conditions monitors as the innermost detectors in the highest radiation areas of BaBar, Belle and CDF and is installed in all LHC experiments. As a result, this material is now being discussed as an alternative sensor material for tracking very close to the interaction region of the super-LHC where the most extreme radiation conditions will exist. Our work addressed the further development of the new material, single-crystal Chemical Vapor Deposition diamond, towards reliable industrial production of large pieces and new geometries needed for detector applications.

  2. Development of Single Crystal Chemical Vapor Deposition Diamonds for Detector Applications

    SciTech Connect

    Rainer Wallny

    2012-10-15

    Diamond was studied as a possible radiation hard technology for use in future high radiation environments. With the commissioning of the LHC expected in 2010, and the LHC upgrades expected in 2015, all LHC experiments are planning for detector upgrades which require radiation hard technologies. Chemical Vapor Deposition (CVD) diamond has now been used extensively in beam conditions monitors as the innermost detectors in the highest radiation areas of BaBar, Belle and CDF and is installed and operational in all LHC experiments. As a result, this material is now being discussed as an alternative sensor material for tracking very close to the interaction region of the super-LHC where the most extreme radiation conditions will exist. Our work addressed the further development of the new material, single-crystal Chemical Vapor Deposition diamond, towards reliable industrial production of large pieces and new geometries needed for detector applications.

  3. Comparative Environmental Threat Analysis: Three Case Studies.

    ERIC Educational Resources Information Center

    Latour, J. B.; Reiling, R.

    1994-01-01

    Reviews how carrying capacity for different environmental problems is operationalized. Discusses whether it is possible to compare threats, using the exceeding of carrying capacity as a yardstick. Points out problems in comparative threat analysis using three case studies: threats to European groundwater resources, threats to ecosystems in Europe,…

  4. Comparative Environmental Threat Analysis: Three Case Studies.

    ERIC Educational Resources Information Center

    Latour, J. B.; Reiling, R.

    1994-01-01

    Reviews how carrying capacity for different environmental problems is operationalized. Discusses whether it is possible to compare threats, using the exceeding of carrying capacity as a yardstick. Points out problems in comparative threat analysis using three case studies: threats to European groundwater resources, threats to ecosystems in Europe,…

  5. Teacher Policy: A Framework for Comparative Analysis

    ERIC Educational Resources Information Center

    Tatto, Maria Teresa

    2008-01-01

    This article outlines a framework for analysis of teacher focused policy studies within an international and comparative perspective. Using the notion of the professional life cycle of teachers, the article examines examples of key empirical studies that illustrate the impact of policy on addressing such issues as teacher recruitment, education,…

  6. Howard University: A Comparative Fiscal Analysis.

    ERIC Educational Resources Information Center

    Inman, Deborah; And Others

    This report presents a fiscal analysis of Howard University (District of Columbia) including: (1) general education revenues; (2) education and general expenditures; and (3) faculty salaries. The study compared Howard University to four different groups of higher education institutions: similar private institutions with hospitals; public…

  7. Network Analysis in Comparative Social Sciences

    ERIC Educational Resources Information Center

    Vera, Eugenia Roldan; Schupp, Thomas

    2006-01-01

    This essay describes the pertinence of Social Network Analysis (SNA) for the social sciences in general, and discusses its methodological and conceptual implications for comparative research in particular. The authors first present a basic summary of the theoretical and methodological assumptions of SNA, followed by a succinct overview of its…

  8. Comparative genomic analysis of esophageal cancers.

    PubMed

    Caygill, Christine P J; Gatenby, Piers A C; Herceg, Zdenko; Lima, Sheila C S; Pinto, Luis F R; Watson, Anthony; Wu, Ming-Shiang

    2014-09-01

    The following, from the 12th OESO World Conference: Cancers of the Esophagus, includes commentaries on comparative genomic analysis of esophageal cancers: genomic polymorphisms, the genetic and epigenetic drivers in esophageal cancers, and the collection of data in the UK Barrett's Oesophagus Registry.

  9. National Launch System comparative economic analysis

    NASA Technical Reports Server (NTRS)

    Prince, A.

    1992-01-01

    Results are presented from an analysis of economic benefits (or losses), in the form of the life cycle cost savings, resulting from the development of the National Launch System (NLS) family of launch vehicles. The analysis was carried out by comparing various NLS-based architectures with the current Shuttle/Titan IV fleet. The basic methodology behind this NLS analysis was to develop a set of annual payload requirements for the Space Station Freedom and LEO, to design launch vehicle architectures around these requirements, and to perform life-cycle cost analyses on all of the architectures. A SEI requirement was included. Launch failure costs were estimated and combined with the relative reliability assumptions to measure the effects of losses. Based on the analysis, a Shuttle/NLS architecture evolving into a pressurized-logistics-carrier/NLS architecture appears to offer the best long-term cost benefit.

  10. National Launch System comparative economic analysis

    NASA Technical Reports Server (NTRS)

    Prince, A.

    1992-01-01

    Results are presented from an analysis of economic benefits (or losses), in the form of the life cycle cost savings, resulting from the development of the National Launch System (NLS) family of launch vehicles. The analysis was carried out by comparing various NLS-based architectures with the current Shuttle/Titan IV fleet. The basic methodology behind this NLS analysis was to develop a set of annual payload requirements for the Space Station Freedom and LEO, to design launch vehicle architectures around these requirements, and to perform life-cycle cost analyses on all of the architectures. A SEI requirement was included. Launch failure costs were estimated and combined with the relative reliability assumptions to measure the effects of losses. Based on the analysis, a Shuttle/NLS architecture evolving into a pressurized-logistics-carrier/NLS architecture appears to offer the best long-term cost benefit.

  11. Development of Single Crystal Chemical Vapor Deposition Diamonds for Detector Applications

    SciTech Connect

    Kagan, Harris; Kass, Richard; Gan, K. K.

    2014-01-23

    With the LHC upgrades in 2013, and further LHC upgrades scheduled in 2018, most LHC experiments are planning for detector upgrades which require more radiation hard technologies than presently available. At present all LHC experiments now have some form of diamond detector. As a result Chemical Vapor Deposition (CVD) diamond has now been used extensively in beam conditions monitors as the innermost detectors in the highest radiation areas of all LHC experiments. Moreover CVD diamond is now being discussed as an alternative sensor material for tracking very close to the interaction region of the HL-LHC where the most extreme radiation conditions will exist. Our work addressed the further development of the new material, single-crystal Chemical Vapor Deposition diamond, towards reliable industrial production of large pieces and new geometries needed for detector applications. Our accomplishments include: • Developed a two U.S.companies to produce electronic grade diamond, • Worked with companies and acquired large area diamond pieces, • Performed radiation hardness tests using various proton energies: 70 MeV (Cyric, Japan), 800 MeV (Los Alamos), and 24 GeV (CERN).

  12. Application of a single crystal chemical vapor deposition diamond detector for deuteron plasma neutron measurement

    NASA Astrophysics Data System (ADS)

    Xie, Xufei; Yuan, Xi; Zhang, Xing; Chen, Zhongjing; Peng, Xingyu; Du, Tengfei; Li, Tao; Hu, Zhimeng; Cui, Zhiqiang; Chen, Jinxiang; Li, Xiangqing; Zhang, Guohui; Fan, Tieshuan; Yuan, Guoliang; Yang, Jinwei; Yang, Qingwei

    2014-10-01

    A single crystal chemical vapor deposition (scCVD) diamond detector has been characterized and employed for the neutron measurement at the HL-2A tokamak device. The scCVD diamond detector has been deposited with 5 μm of lithium fluoride (LiF) layer to enhance the sensitivity to thermal neutrons. Time stability of the detector has been studied with α-source and good performance has been found for more than 12 h. Neutron irradiations have been performed in four quasi-monoenergetic neutron fields in the energy range from 2.50 MeV to 16.03 MeV. The measured response function of the scCVD diamond detector to 14.13 MeV neutrons shows a narrow 12C (n, α)9Be reaction peak which is well isolated from other structures by about 1 MeV in energy, indicating the great potential as a fast neutron spectrometer. Neutron measurement of deuterium plasma discharge was established at the HL-2A tokamak device, and good consistence has been revealed among this detector signal and other related signals.

  13. Image analysis in comparative genomic hybridization

    SciTech Connect

    Lundsteen, C.; Maahr, J.; Christensen, B.

    1995-01-01

    Comparative genomic hybridization (CGH) is a new technique by which genomic imbalances can be detected by combining in situ suppression hybridization of whole genomic DNA and image analysis. We have developed software for rapid, quantitative CGH image analysis by a modification and extension of the standard software used for routine karyotyping of G-banded metaphase spreads in the Magiscan chromosome analysis system. The DAPI-counterstained metaphase spread is karyotyped interactively. Corrections for image shifts between the DAPI, FITC, and TRITC images are done manually by moving the three images relative to each other. The fluorescence background is subtracted. A mean filter is applied to smooth the FITC and TRITC images before the fluorescence ratio between the individual FITC and TRITC-stained chromosomes is computed pixel by pixel inside the area of the chromosomes determined by the DAPI boundaries. Fluorescence intensity ratio profiles are generated, and peaks and valleys indicating possible gains and losses of test DNA are marked if they exceed ratios below 0.75 and above 1.25. By combining the analysis of several metaphase spreads, consistent findings of gains and losses in all or almost all spreads indicate chromosomal imbalance. Chromosomal imbalances are detected either by visual inspection of fluorescence ratio (FR) profiles or by a statistical approach that compares FR measurements of the individual case with measurements of normal chromosomes. The complete analysis of one metaphase can be carried out in approximately 10 minutes. 8 refs., 7 figs., 1 tab.

  14. Comparative performance analysis of mobile displays

    NASA Astrophysics Data System (ADS)

    Safaee-Rad, Reza; Aleksic, Milivoje

    2012-01-01

    Cell-phone display performance (in terms of color quality and optical efficiency) has become a critical factor in creating a positive user experience. As a result, there is a significant amount of effort by cell-phone OEMs to provide a more competitive display solution. This effort is focused on using different display technologies (with significantly different color characteristics) and more sophisticated display processors. In this paper, the results of a mobile-display comparative performance analysis are presented. Three cell-phones from major OEMs are selected and their display performances are measured and quantified. Comparative performance analysis is done using display characteristics such as display color gamut size, RGB-channels crosstalk, RGB tone responses, gray tracking performance, color accuracy, and optical efficiency.

  15. Comparative analysis of twelve Dothideomycete plant pathogens

    SciTech Connect

    Ohm, Robin; Aerts, Andrea; Salamov, Asaf; Goodwin, Stephen B.; Grigoriev, Igor

    2011-03-11

    The Dothideomycetes are one of the largest and most diverse groups of fungi. Many are plant pathogens and pose a serious threat to agricultural crops grown for biofuel, food or feed. Most Dothideomycetes have only a single host and related Dothideomycete species can have very diverse host plants. Twelve Dothideomycete genomes have currently been sequenced by the Joint Genome Institute and other sequencing centers. They can be accessed via Mycocosm which has tools for comparative analysis

  16. Embedded Hyperchaotic Generators: A Comparative Analysis

    NASA Astrophysics Data System (ADS)

    Sadoudi, Said; Tanougast, Camel; Azzaz, Mohamad Salah; Dandache, Abbas

    In this paper, we present a comparative analysis of FPGA implementation performances, in terms of throughput and resources cost, of five well known autonomous continuous hyperchaotic systems. The goal of this analysis is to identify the embedded hyperchaotic generator which leads to designs with small logic area cost, satisfactory throughput rates, low power consumption and low latency required for embedded applications such as secure digital communications between embedded systems. To implement the four-dimensional (4D) chaotic systems, we use a new structural hardware architecture based on direct VHDL description of the forth order Runge-Kutta method (RK-4). The comparative analysis shows that the hyperchaotic Lorenz generator provides attractive performances compared to that of others. In fact, its hardware implementation requires only 2067 CLB-slices, 36 multipliers and no block RAMs, and achieves a throughput rate of 101.6 Mbps, at the output of the FPGA circuit, at a clock frequency of 25.315 MHz with a low latency time of 316 ns. Consequently, these good implementation performances offer to the embedded hyperchaotic Lorenz generator the advantage of being the best candidate for embedded communications applications.

  17. Comparative Analysis of Ralstonia solanacearum Methylomes.

    PubMed

    Erill, Ivan; Puigvert, Marina; Legrand, Ludovic; Guarischi-Sousa, Rodrigo; Vandecasteele, Céline; Setubal, João C; Genin, Stephane; Guidot, Alice; Valls, Marc

    2017-01-01

    Ralstonia solanacearum is an important soil-borne plant pathogen with broad geographical distribution and the ability to cause wilt disease in many agriculturally important crops. Genome sequencing of multiple R. solanacearum strains has identified both unique and shared genetic traits influencing their evolution and ability to colonize plant hosts. Previous research has shown that DNA methylation can drive speciation and modulate virulence in bacteria, but the impact of epigenetic modifications on the diversification and pathogenesis of R. solanacearum is unknown. Sequencing of R. solanacearum strains GMI1000 and UY031 using Single Molecule Real-Time technology allowed us to perform a comparative analysis of R. solanacearum methylomes. Our analysis identified a novel methylation motif associated with a DNA methylase that is conserved in all complete Ralstonia spp. genomes and across the Burkholderiaceae, as well as a methylation motif associated to a phage-borne methylase unique to R. solanacearum UY031. Comparative analysis of the conserved methylation motif revealed that it is most prevalent in gene promoter regions, where it displays a high degree of conservation detectable through phylogenetic footprinting. Analysis of hyper- and hypo-methylated loci identified several genes involved in global and virulence regulatory functions whose expression may be modulated by DNA methylation. Analysis of genome-wide modification patterns identified a significant correlation between DNA modification and transposase genes in R. solanacearum UY031, driven by the presence of a high copy number of ISrso3 insertion sequences in this genome and pointing to a novel mechanism for regulation of transposition. These results set a firm foundation for experimental investigations into the role of DNA methylation in R. solanacearum evolution and its adaptation to different plants.

  18. Comparative Analysis of Ralstonia solanacearum Methylomes

    PubMed Central

    Erill, Ivan; Puigvert, Marina; Legrand, Ludovic; Guarischi-Sousa, Rodrigo; Vandecasteele, Céline; Setubal, João C.; Genin, Stephane; Guidot, Alice; Valls, Marc

    2017-01-01

    Ralstonia solanacearum is an important soil-borne plant pathogen with broad geographical distribution and the ability to cause wilt disease in many agriculturally important crops. Genome sequencing of multiple R. solanacearum strains has identified both unique and shared genetic traits influencing their evolution and ability to colonize plant hosts. Previous research has shown that DNA methylation can drive speciation and modulate virulence in bacteria, but the impact of epigenetic modifications on the diversification and pathogenesis of R. solanacearum is unknown. Sequencing of R. solanacearum strains GMI1000 and UY031 using Single Molecule Real-Time technology allowed us to perform a comparative analysis of R. solanacearum methylomes. Our analysis identified a novel methylation motif associated with a DNA methylase that is conserved in all complete Ralstonia spp. genomes and across the Burkholderiaceae, as well as a methylation motif associated to a phage-borne methylase unique to R. solanacearum UY031. Comparative analysis of the conserved methylation motif revealed that it is most prevalent in gene promoter regions, where it displays a high degree of conservation detectable through phylogenetic footprinting. Analysis of hyper- and hypo-methylated loci identified several genes involved in global and virulence regulatory functions whose expression may be modulated by DNA methylation. Analysis of genome-wide modification patterns identified a significant correlation between DNA modification and transposase genes in R. solanacearum UY031, driven by the presence of a high copy number of ISrso3 insertion sequences in this genome and pointing to a novel mechanism for regulation of transposition. These results set a firm foundation for experimental investigations into the role of DNA methylation in R. solanacearum evolution and its adaptation to different plants. PMID:28450872

  19. Computerized crystal-chemical classification of silicates and related materials with CRYSTANA and formula notation for classified structures

    NASA Astrophysics Data System (ADS)

    Klein, Hans-Joachim; Liebau, Friedrich

    2008-09-01

    The computer program CRYSTANA is described which implements a method for the crystal-chemical classification of silicates and related materials. This method is mainly based upon the topological structure of the connected units of a compound and can be applied when the units are built from tetrahedra as coordination polyhedra. The classification parameters and the rules which have to be applied for their determination are summarized and a formalization of the method is provided based upon a finite graph representation of the units. A description of how CRYSTANA can be used and which kind of output it produces is included. From this output crystal-chemical formulas can be derived, which differ slightly from an existing notation in order to meet recommendations of the International Union of Crystallography.

  20. A comparative analysis of frog early development

    PubMed Central

    del Pino, Eugenia M.; Venegas-Ferrín, Michael; Romero-Carvajal, Andrés; Montenegro-Larrea, Paola; Sáenz-Ponce, Natalia; Moya, Iván M.; Alarcón, Ingrid; Sudou, Norihiro; Yamamoto, Shinji; Taira, Masanori

    2007-01-01

    The current understanding of Xenopus laevis development provides a comparative background for the analysis of frog developmental modes. Our analysis of development in various frogs reveals that the mode of gastrulation is associated with developmental rate and is unrelated to egg size. In the gastrula of the rapidly developing embryos of the foam-nesting frogs Engystomops coloradorum and Engystomops randi, archenteron and notochord elongation overlapped with involution at the blastopore lip, as in X. laevis embryos. In embryos of dendrobatid frogs and in the frog without tadpoles Eleutherodactylus coqui, which develop somewhat more slowly than X. laevis, involution and archenteron elongation concomitantly occurred during gastrulation; whereas elongation of the notochord and, therefore, dorsal convergence and extension, occurred in the postgastrula. In contrast, in the slow developing embryos of the marsupial frog Gastrotheca riobambae, only involution occurred during gastrulation. The processes of archenteron and notochord elongation and convergence and extension were postgastrulation events. We produced an Ab against the homeodomain protein Lim1 from X. laevis as a tool for the comparative analysis of development. By the expression of Lim1, we were able to identify the dorsal side of the G. riobambae early gastrula, which otherwise was difficult to detect. Moreover, the Lim1 expression in the dorsal lip of the blastopore and notochord differed among the studied frogs, indicating variation in the timing of developmental events. The variation encountered gives evidence of the modular character of frog gastrulation. PMID:17606898

  1. Comparative Genome Analysis of Enterobacter cloacae

    PubMed Central

    Liu, Wing-Yee; Wong, Chi-Fat; Chung, Karl Ming-Kar; Jiang, Jing-Wei; Leung, Frederick Chi-Ching

    2013-01-01

    The Enterobacter cloacae species includes an extremely diverse group of bacteria that are associated with plants, soil and humans. Publication of the complete genome sequence of the plant growth-promoting endophytic E. cloacae subsp. cloacae ENHKU01 provided an opportunity to perform the first comparative genome analysis between strains of this dynamic species. Examination of the pan-genome of E. cloacae showed that the conserved core genome retains the general physiological and survival genes of the species, while genomic factors in plasmids and variable regions determine the virulence of the human pathogenic E. cloacae strain; additionally, the diversity of fimbriae contributes to variation in colonization and host determination of different E. cloacae strains. Comparative genome analysis further illustrated that E. cloacae strains possess multiple mechanisms for antagonistic action against other microorganisms, which involve the production of siderophores and various antimicrobial compounds, such as bacteriocins, chitinases and antibiotic resistance proteins. The presence of Type VI secretion systems is expected to provide further fitness advantages for E. cloacae in microbial competition, thus allowing it to survive in different environments. Competition assays were performed to support our observations in genomic analysis, where E. cloacae subsp. cloacae ENHKU01 demonstrated antagonistic activities against a wide range of plant pathogenic fungal and bacterial species. PMID:24069314

  2. Comparative analysis of black carbon in soils

    NASA Astrophysics Data System (ADS)

    Schmidt, Michael W. I.; Skjemstad, Jan O.; Czimczik, Claudia I.; Glaser, Bruno; Prentice, Ken M.; Gelinas, Yves; Kuhlbusch, Thomas A. J.

    2001-03-01

    Black carbon (BC), produced by incomplete combustion of fossil fuels and vegetation, occurs ubiquitously in soils and sediments. BC exists as a continuum from partly charred material to highly graphitized soot particles, with no general agreement on clear-cut boundaries of definition or analysis. In a comparative analysis, we measured BC forms in eight soil samples by six established methods. All methods involved removal of the non-BC components from the sample by thermal or chemical means or a combination of both. The remaining carbon, operationally defined as BC, was quantified via mass balance, elemental composition or by exploiting benzenecarboxylic acids as molecular markers or applying 13C MAS NMR (magic angle spinning nuclear magnetic resonance) spectroscopy. BC concentrations measured for individual samples vary over 2 orders of magnitude (up to a factor of 571). One possible explanation for this wide range of results is that the individual BC methods rely on operational definitions with clear-cut but different boundaries and developed for specific scientific questions, whereas BC represents a continuum of materials with widely contrasting physicochemical properties. Thus the methods are inherently designed to analytically determine different parts of the continuum, and it is crucial to know how measurements made by different techniques relate to each other. It is clear from this preliminary comparative analysis that a collection of BC reference materials should be established as soon as possible 1 ) to ensure long-term intralaboratory and interlaboratory data quality and 2) to facilitate comparative analyses between different analytical techniques and scientific approaches

  3. Inpatient care in Kazakhstan: A comparative analysis

    PubMed Central

    Kumar, Ainur B.; Izekenova, Aigulsum; Abikulova, Akmaral

    2013-01-01

    Background: Reforms in inpatient care are critical for the enhancement of the efficiency of health systems. It still remains the main costly sector of the health system, accounting for more than 60% of all expenditures. Inappropriate and ineffective use of the hospital infrastructure is also a big issue. We aimed to analyze statistical data on health indices and dynamics of the hospital stock in Kazakhstan in comparison with those of developed countries. Materials and Methods: Study design is comparative quantitative analysis of inpatient care indicators. We used information and analytical methods, content analysis, mathematical treatment, and comparative analysis of statistical data on health system and dynamics of hospital stock in Kazakhstan and some other countries of the world [Organization for Economic Cooperation and Development (OECD), USA, Canada, Russia, China, Japan, and Korea] over the period 2001-2011. Results: Despite substantial and continuous reductions over the past 10 years, hospitalization rates in Kazakhstan still remain high compared to some developed countries, including those of the OECD. In fact, the hospital stay length for all patients in Kazakhstan in 2011 is around 9.9 days, hospitalization ratio per 100 people is 16.3, and hospital beds capacity is 100 per 10,000 inhabitants. Conclusion: The decreased level of beds may adversely affect both medical organization and health system operations. Alternatives to the existing inpatient care are now being explored. The introduction of the unified national healthcare system allows shifting the primary focus on primary care organizations, which can decrease the demand on inpatient care as a result of improving the health status of people at the primary care level. PMID:24516484

  4. Fundus camera systems: a comparative analysis

    PubMed Central

    DeHoog, Edward; Schwiegerling, James

    2010-01-01

    Retinal photography requires the use of a complex optical system, called a fundus camera, capable of illuminating and imaging the retina simultaneously. The patent literature shows two design forms but does not provide the specifics necessary for a thorough analysis of the designs to be performed. We have constructed our own designs based on the patent literature in optical design software and compared them for illumination efficiency, image quality, ability to accommodate for patient refractive error, and manufacturing tolerances, a comparison lacking in the existing literature. PMID:19137032

  5. Stock index dynamics worldwide: a comparative analysis

    NASA Astrophysics Data System (ADS)

    Cortines, A. A. G.; Anteneodo, C.; Riera, R.

    2008-09-01

    We perform a comparative analysis of twenty-four daily stock indices across the world, encompassing developed and emerging markets. We compute, directly from the return empirical time series, the Kramers-Moyal (KM) expansion coefficients that govern the evolution of the probability density function of returns throughout timelags. Our study discloses universal patterns of the KM coefficients, which can be described in terms of a few microscopic parameters. These parameters allow to quantify features such as deviations from Gaussianity or from efficiency, providing a tool to discriminate market dynamics.

  6. Fundus camera systems: a comparative analysis.

    PubMed

    DeHoog, Edward; Schwiegerling, James

    2009-01-10

    Retinal photography requires the use of a complex optical system, called a fundus camera, capable of illuminating and imaging the retina simultaneously. The patent literature shows two design forms but does not provide the specifics necessary for a thorough analysis of the designs to be performed. We have constructed our own designs based on the patent literature in optical design software and compared them for illumination efficiency, image quality, ability to accommodate for patient refractive error, and manufacturing tolerances, a comparison lacking in the existing literature.

  7. Comparative assessment of differential network analysis methods.

    PubMed

    Lichtblau, Yvonne; Zimmermann, Karin; Haldemann, Berit; Lenze, Dido; Hummel, Michael; Leser, Ulf

    2017-09-01

    Differential network analysis (DiNA) denotes a recent class of network-based Bioinformatics algorithms which focus on the differences in network topologies between two states of a cell, such as healthy and disease, to identify key players in the discriminating biological processes. In contrast to conventional differential analysis, DiNA identifies changes in the interplay between molecules, rather than changes in single molecules. This ability is especially important in cases where effectors are changed, e.g. mutated, but their expression is not. A number of different DiNA approaches have been proposed, yet a comparative assessment of their performance in different settings is still lacking. In this paper, we evaluate 10 different DiNA algorithms regarding their ability to recover genetic key players from transcriptome data. We construct high-quality regulatory networks and enrich them with co-expression data from four different types of cancer. Next, we assess the results of applying DiNA algorithms on these data sets using a gold standard list (GSL). We find that local DiNA algorithms are generally superior to global algorithms, and that all DiNA algorithms outperform conventional differential expression analysis. We also assess the ability of DiNA methods to exploit additional knowledge in the underlying cellular networks. To this end, we enrich the cancer-type specific networks with known regulatory miRNAs and compare the algorithms performance in networks with and without miRNA. We find that including miRNAs consistently and considerably improves the performance of almost all tested algorithms. Our results underline the advantages of comprehensive cell models for the analysis of -omics data. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  8. Comparative analysis of solar photovoltaic monitoring systems

    NASA Astrophysics Data System (ADS)

    Madeti, Siva Ramakrishna; Singh, S. N.

    2017-07-01

    This paper is focused on comparative analysis of photovoltaic (PV) monitoring system for observing the performance and stability of the system. The cost and complexity of existing PV monitoring systems restricted their use to large scale PV plants. Over the past decade, different aspects of the PV monitoring systems were reported in the wide range of literature. In this paper, a comparative analysis of various PV monitoring systems is presented for the first time. It is based on analyzing six main characteristics of PV monitoring system, such as data transfer mechanism, controller, monitoring parameters, sampling interval, program development software and monitoring methods. The comparison of methodologies and the description of implementation process are discussed in this context. The key findings of this study will contribute to the development of a new PV monitoring system. The acquaintance of all these aspects is crucial for the development of effective, low cost, and viable PV monitoring systems for the small and medium scale PV plants without compromising on the desired performance.

  9. Comparative genome analysis of Basidiomycete fungi

    SciTech Connect

    Riley, Robert; Salamov, Asaf; Henrissat, Bernard; Nagy, Laszlo; Brown, Daren; Held, Benjamin; Baker, Scott; Blanchette, Robert; Boussau, Bastien; Doty, Sharon L.; Fagnan, Kirsten; Floudas, Dimitris; Levasseur, Anthony; Manning, Gerard; Martin, Francis; Morin, Emmanuelle; Otillar, Robert; Pisabarro, Antonio; Walton, Jonathan; Wolfe, Ken; Hibbett, David; Grigoriev, Igor

    2013-08-07

    Fungi of the phylum Basidiomycota (basidiomycetes), make up some 37percent of the described fungi, and are important in forestry, agriculture, medicine, and bioenergy. This diverse phylum includes symbionts, pathogens, and saprotrophs including the majority of wood decaying and ectomycorrhizal species. To better understand the genetic diversity of this phylum we compared the genomes of 35 basidiomycetes including 6 newly sequenced genomes. These genomes span extremes of genome size, gene number, and repeat content. Analysis of core genes reveals that some 48percent of basidiomycete proteins are unique to the phylum with nearly half of those (22percent) found in only one organism. Correlations between lifestyle and certain gene families are evident. Phylogenetic patterns of plant biomass-degrading genes in Agaricomycotina suggest a continuum rather than a dichotomy between the white rot and brown rot modes of wood decay. Based on phylogenetically-informed PCA analysis of wood decay genes, we predict that that Botryobasidium botryosum and Jaapia argillacea have properties similar to white rot species, although neither has typical ligninolytic class II fungal peroxidases (PODs). This prediction is supported by growth assays in which both fungi exhibit wood decay with white rot-like characteristics. Based on this, we suggest that the white/brown rot dichotomy may be inadequate to describe the full range of wood decaying fungi. Analysis of the rate of discovery of proteins with no or few homologs suggests the value of continued sequencing of basidiomycete fungi.

  10. Comparative Transcriptome Analysis of Four Prymnesiophyte Algae

    PubMed Central

    Koid, Amy E.; Liu, Zhenfeng; Terrado, Ramon; Jones, Adriane C.; Caron, David A.; Heidelberg, Karla B.

    2014-01-01

    Genomic studies of bacteria, archaea and viruses have provided insights into the microbial world by unveiling potential functional capabilities and molecular pathways. However, the rate of discovery has been slower among microbial eukaryotes, whose genomes are larger and more complex. Transcriptomic approaches provide a cost-effective alternative for examining genetic potential and physiological responses of microbial eukaryotes to environmental stimuli. In this study, we generated and compared the transcriptomes of four globally-distributed, bloom-forming prymnesiophyte algae: Prymnesium parvum, Chrysochromulina brevifilum, Chrysochromulina ericina and Phaeocystis antarctica. Our results revealed that the four transcriptomes possess a set of core genes that are similar in number and shared across all four organisms. The functional classifications of these core genes using the euKaryotic Orthologous Genes (KOG) database were also similar among the four study organisms. More broadly, when the frequencies of different cellular and physiological functions were compared with other protists, the species clustered by both phylogeny and nutritional modes. Thus, these clustering patterns provide insight into genomic factors relating to both evolutionary relationships as well as trophic ecology. This paper provides a novel comparative analysis of the transcriptomes of ecologically important and closely related prymnesiophyte protists and advances an emerging field of study that uses transcriptomics to reveal ecology and function in protists. PMID:24926657

  11. Comparative Genome Analysis of Basidiomycete Fungi

    SciTech Connect

    Riley, Robert; Salamov, Asaf; Morin, Emmanuelle; Nagy, Laszlo; Manning, Gerard; Baker, Scott; Brown, Daren; Henrissat, Bernard; Levasseur, Anthony; Hibbett, David; Martin, Francis; Grigoriev, Igor

    2012-03-19

    Fungi of the phylum Basidiomycota (basidiomycetes), make up some 37percent of the described fungi, and are important in forestry, agriculture, medicine, and bioenergy. This diverse phylum includes the mushrooms, wood rots, symbionts, and plant and animal pathogens. To better understand the diversity of phenotypes in basidiomycetes, we performed a comparative analysis of 35 basidiomycete fungi spanning the diversity of the phylum. Phylogenetic patterns of lignocellulose degrading genes suggest a continuum rather than a sharp dichotomy between the white rot and brown rot modes of wood decay. Patterns of secondary metabolic enzymes give additional insight into the broad array of phenotypes found in the basidiomycetes. We suggest that the profile of an organism in lignocellulose-targeting genes can be used to predict its nutritional mode, and predict Dacryopinax sp. as a brown rot; Botryobasidium botryosum and Jaapia argillacea as white rots.

  12. Hawaiian propolis: comparative analysis and botanical origin.

    PubMed

    Inui, Saori; Hosoya, Takahiro; Kumazaw, Shigenori

    2014-02-01

    Propolis is a resinous mixture of substances collected and processed from various botanical sources by honeybees (Apis mellifera). We recently obtained Hawaiian propolis, the study of which, to our knowledge, has not been reported. The purpose of this study was to analyze the composition of Hawaiian propolis and to identify its botanical origin. A comparative analysis of Hawaiian and Okinawan propolis and of the glandular trichomes on Macaranga tanarius fruit (the botanical origin of Okinawan propolis) was performed using reversed-phase high-performance liquid chromatography coupled with high resolution-electrospray mass spectrometry. Hawaiian propolis contained nine prenylflavonoids that were also isolated from Okinawan propolis. In conclusion, we suggest that the botanical origin of Hawaiian propolis is M. tanarius, the same as that of Okinawan propolis.

  13. Comparative metagenome analysis of an Alaskan glacier.

    PubMed

    Choudhari, Sulbha; Lohia, Ruchi; Grigoriev, Andrey

    2014-04-01

    The temperature in the Arctic region has been increasing in the recent past accompanied by melting of its glaciers. We took a snapshot of the current microbial inhabitation of an Alaskan glacier (which can be considered as one of the simplest possible ecosystems) by using metagenomic sequencing of 16S rRNA recovered from ice/snow samples. Somewhat contrary to our expectations and earlier estimates, a rich and diverse microbial population of more than 2,500 species was revealed including several species of Archaea that has been identified for the first time in the glaciers of the Northern hemisphere. The most prominent bacterial groups found were Proteobacteria, Bacteroidetes, and Firmicutes. Firmicutes were not reported in large numbers in a previously studied Alpine glacier but were dominant in an Antarctic subglacial lake. Representatives of Cyanobacteria, Actinobacteria and Planctomycetes were among the most numerous, likely reflecting the dependence of the ecosystem on the energy obtained through photosynthesis and close links with the microbial community of the soil. Principal component analysis (PCA) of nucleotide word frequency revealed distinct sequence clusters for different taxonomic groups in the Alaskan glacier community and separate clusters for the glacial communities from other regions of the world. Comparative analysis of the community composition and bacterial diversity present in the Byron glacier in Alaska with other environments showed larger overlap with an Arctic soil than with a high Arctic lake, indicating patterns of community exchange and suggesting that these bacteria may play an important role in soil development during glacial retreat.

  14. Comparative Analysis of Genome Sequences with VISTA

    DOE Data Explorer

    Dubchak, Inna

    VISTA is a comprehensive suite of programs and databases developed by and hosted at the Genomics Division of Lawrence Berkeley National Laboratory. They provide information and tools designed to facilitate comparative analysis of genomic sequences. Users have two ways to interact with the suite of applications at the VISTA portal. They can submit their own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignments of different species. A key menu option is the Enhancer Browser and Database at http://enhancer.lbl.gov/. The VISTA Enhancer Browser is a central resource for experimentally validated human noncoding fragments with gene enhancer activity as assessed in transgenic mice. Most of these noncoding elements were selected for testing based on their extreme conservation with other vertebrates. The results of this enhancer screen are provided through this publicly available website. The browser also features relevant results by external contributors and a large collection of additional genome-wide conserved noncoding elements which are candidate enhancer sequences. The LBL developers invite external groups to submit computational predictions of developmental enhancers. As of 10/19/2009 the database contains information on 1109 in vivo tested elements - 508 elements with enhancer activity.

  15. Comparative Sensitivity Analysis of Muscle Activation Dynamics

    PubMed Central

    Rockenfeller, Robert; Günther, Michael; Schmitt, Syn; Götz, Thomas

    2015-01-01

    We mathematically compared two models of mammalian striated muscle activation dynamics proposed by Hatze and Zajac. Both models are representative for a broad variety of biomechanical models formulated as ordinary differential equations (ODEs). These models incorporate parameters that directly represent known physiological properties. Other parameters have been introduced to reproduce empirical observations. We used sensitivity analysis to investigate the influence of model parameters on the ODE solutions. In addition, we expanded an existing approach to treating initial conditions as parameters and to calculating second-order sensitivities. Furthermore, we used a global sensitivity analysis approach to include finite ranges of parameter values. Hence, a theoretician striving for model reduction could use the method for identifying particularly low sensitivities to detect superfluous parameters. An experimenter could use it for identifying particularly high sensitivities to improve parameter estimation. Hatze's nonlinear model incorporates some parameters to which activation dynamics is clearly more sensitive than to any parameter in Zajac's linear model. Other than Zajac's model, Hatze's model can, however, reproduce measured shifts in optimal muscle length with varied muscle activity. Accordingly we extracted a specific parameter set for Hatze's model that combines best with a particular muscle force-length relation. PMID:26417379

  16. Drug design using comparative molecular surface analysis.

    PubMed

    Polanski, Jaroslaw

    2006-12-01

    Chemists have eagerly extended a concept of shape into the molecular scale in an attempt to explain molecular effects. Although the molecular surface that shapes a molecule is a fuzzy category, which makes important theoretical problems with its precise interpretation, shape analysis appears to be an efficient method providing an explanation for a variety of effects. Comparative molecular surface analysis (CoMSA) is a three-dimensional quantitative structure-activity relationship (3D QSAR) method used for the comparison of molecular surfaces and shapes. In this review, the authors demonstrate that 3D QSAR basically works as a visualisation tool that investigates molecular similarity and indicates pharmacophoric sites. In this context, CoMSA that is based on the Kohonen self-organising maps that allow the projection of three-dimensional molecular data into two-dimensional maps without topological distortion has an important advantage over the traditional 3D QSAR methods. However, It should be remembered that the majority of the 3D QSAR limitations are still important for this technique and consequently a strategy to use the molecular data to produce drugs in this way still maps a 'far and bumpy road'.

  17. Comparative analysis of the feline immunoglobulin repertoire.

    PubMed

    Steiniger, Sebastian C J; Glanville, Jacob; Harris, Douglas W; Wilson, Thomas L; Ippolito, Gregory C; Dunham, Steven A

    2017-01-25

    Next-Generation Sequencing combined with bioinformatics is a powerful tool for analyzing the large number of DNA sequences present in the expressed antibody repertoire and these data sets can be used to advance a number of research areas including antibody discovery and engineering. The accurate measurement of the immune repertoire sequence composition, diversity and abundance is important for understanding the repertoire response in infections, vaccinations and cancer immunology and could also be useful for elucidating novel molecular targets. In this study 4 individual domestic cats (Felis catus) were subjected to antibody repertoire sequencing with total number of sequences generated 1079863 for VH for IgG, 1050824 VH for IgM, 569518 for VK and 450195 for VL. Our analysis suggests that a similar VDJ expression patterns exists across all cats. Similar to the canine repertoire, the feline repertoire is dominated by a single subgroup, namely VH3. The antibody paratope of felines showed similar amino acid variation when compared to human, mouse and canine counterparts. All animals show a similarly skewed VH CDR-H3 profile and, when compared to canine, human and mouse, distinct differences are observed. Our study represents the first attempt to characterize sequence diversity in the expressed feline antibody repertoire and this demonstrates the utility of using NGS to elucidate entire antibody repertoires from individual animals. These data provide significant insight into understanding the feline immune system function.

  18. Comparative analysis of selected fuel cell vehicles

    SciTech Connect

    1993-05-07

    Vehicles powered by fuel cells operate more efficiently, more quietly, and more cleanly than internal combustion engines (ICEs). Furthermore, methanol-fueled fuel cell vehicles (FCVs) can utilize major elements of the existing fueling infrastructure of present-day liquid-fueled ICE vehicles (ICEVs). DOE has maintained an active program to stimulate the development and demonstration o fuel cell technologies in conjunction with rechargeable batteries in road vehicles. The purpose of this study is to identify and assess the availability of data on FCVs, and to develop a vehicle subsystem structure that can be used to compare both FCVs and ICEV, from a number of perspectives--environmental impacts, energy utilization, materials usage, and life cycle costs. This report focuses on methanol-fueled FCVs fueled by gasoline, methanol, and diesel fuel that are likely to be demonstratable by the year 2000. The comparative analysis presented covers four vehicles--two passenger vehicles and two urban transit buses. The passenger vehicles include an ICEV using either gasoline or methanol and an FCV using methanol. The FCV uses a Proton Exchange Membrane (PEM) fuel cell, an on-board methanol reformer, mid-term batteries, and an AC motor. The transit bus ICEV was evaluated for both diesel and methanol fuels. The transit bus FCV runs on methanol and uses a Phosphoric Acid Fuel Cell (PAFC) fuel cell, near-term batteries, a DC motor, and an on-board methanol reformer. 75 refs.

  19. A Comparative Analysis of Biomarker Selection Techniques

    PubMed Central

    Dessì, Nicoletta

    2013-01-01

    Feature selection has become the essential step in biomarker discovery from high-dimensional genomics data. It is recognized that different feature selection techniques may result in different set of biomarkers, that is, different groups of genes highly correlated to a given pathological condition, but few direct comparisons exist which quantify these differences in a systematic way. In this paper, we propose a general methodology for comparing the outcomes of different selection techniques in the context of biomarker discovery. The comparison is carried out along two dimensions: (i) measuring the similarity/dissimilarity of selected gene sets; (ii) evaluating the implications of these differences in terms of both predictive performance and stability of selected gene sets. As a case study, we considered three benchmarks deriving from DNA microarray experiments and conducted a comparative analysis among eight selection methods, representatives of different classes of feature selection techniques. Our results show that the proposed approach can provide useful insight about the pattern of agreement of biomarker discovery techniques. PMID:24324960

  20. Minimalist models for proteins: a comparative analysis.

    PubMed

    Tozzini, Valentina

    2010-08-01

    The last decade has witnessed a renewed interest in the coarse-grained (CG) models for biopolymers, also stimulated by the needs of modern molecular biology, dealing with nano- to micro-sized bio-molecular systems and larger than microsecond timescale. This combination of size and timescale is, in fact, hard to access by atomic-based simulations. Coarse graining the system is a route to be followed to overcome these limits, but the ways of practically implementing it are many and different, making the landscape of CG models very vast and complex. In this paper, the CG models are reviewed and their features, applications and performances compared. This analysis, restricted to proteins, focuses on the minimalist models, namely those reducing at minimum the number of degrees of freedom without losing the possibility of explicitly describing the secondary structures. This class includes models using a single or a few interacting centers (beads) for each amino acid. From this analysis several issues emerge. The difficulty in building these models resides in the need for combining transferability/predictive power with the capability of accurately reproducing the structures. It is shown that these aspects could be optimized by accurately choosing the force field (FF) terms and functional forms, and combining different parameterization procedures. In addition, in spite of the variety of the minimalist models, regularities can be found in the parameters values and in FF terms. These are outlined and schematically presented with the aid of a generic phase diagram of the polypeptide in the parameter space and, hopefully, could serve as guidelines for the development of minimalist models incorporating the maximum possible level of predictive power and structural accuracy.

  1. Predictive and comparative analysis of Ebolavirus proteins

    PubMed Central

    Cong, Qian; Pei, Jimin; Grishin, Nick V

    2015-01-01

    Ebolavirus is the pathogen for Ebola Hemorrhagic Fever (EHF). This disease exhibits a high fatality rate and has recently reached a historically epidemic proportion in West Africa. Out of the 5 known Ebolavirus species, only Reston ebolavirus has lost human pathogenicity, while retaining the ability to cause EHF in long-tailed macaque. Significant efforts have been spent to determine the three-dimensional (3D) structures of Ebolavirus proteins, to study their interaction with host proteins, and to identify the functional motifs in these viral proteins. Here, in light of these experimental results, we apply computational analysis to predict the 3D structures and functional sites for Ebolavirus protein domains with unknown structure, including a zinc-finger domain of VP30, the RNA-dependent RNA polymerase catalytic domain and a methyltransferase domain of protein L. In addition, we compare sequences of proteins that interact with Ebolavirus proteins from RESTV-resistant primates with those from RESTV-susceptible monkeys. The host proteins that interact with GP and VP35 show an elevated level of sequence divergence between the RESTV-resistant and RESTV-susceptible species, suggesting that they may be responsible for host specificity. Meanwhile, we detect variable positions in protein sequences that are likely associated with the loss of human pathogenicity in RESTV, map them onto the 3D structures and compare their positions to known functional sites. VP35 and VP30 are significantly enriched in these potential pathogenicity determinants and the clustering of such positions on the surfaces of VP35 and GP suggests possible uncharacterized interaction sites with host proteins that contribute to the virulence of Ebolavirus. PMID:26158395

  2. Comparative genomic analysis of the genus Enterococcus.

    PubMed

    Zhong, Zhi; Zhang, Wenyi; Song, Yuqin; Liu, Wenjun; Xu, Haiyan; Xi, Xiaoxia; Menghe, Bilige; Zhang, Heping; Sun, Zhihong

    2017-03-01

    As important lactic acid bacteria, Enterococcus species are widely used in the production of fermented food. However, as some strains of Enterococcus are opportunistic pathogens, their safety has not been generally accepted. In recent years, a large number of new species have been described and classified within the genus Enterococcus, so a better understanding of the genetic relationships and evolution of Enterococcus species is needed. In this study, the genomes of 29 type strains of Enterococcus species were sequenced. In combination with eight complete genome sequences from the Genbank database, the whole genomes of 37 strains of Enterococcus were comparatively analyzed. The average length of Enterococcus genomes was 3.20Mb and the average GC content was 37.99%. The core- and pan- genomes were defined based on the genomes of the 37 strains of Enterococcus. The core-genome contained 605 genes, a large proportion of which were associated with carbohydrate metabolism, protein metabolism, DNA and RNA metabolism. The phylogenetic tree showed that habitat is very important in the evolution of Enterococcus. The genetic relationships were closer in strains that come from similar habitats. According to the topology of the time tree, we found that humans and mammals may be the original hosts of Enterococcus, and then species from humans and mammals made a host-shift to plants, birds, food and other environments. However, it was just an evolutionary scenario, and more data and efforts were needed to prove this postulation. The comparative genomic analysis provided a snapshot of the evolution and genetic diversity of the genus Enterococcus, which paves the way for follow-up studies on its taxonomy and functional genomics. Copyright © 2017 Elsevier GmbH. All rights reserved.

  3. Comparative genomic analysis of prion genes

    PubMed Central

    Premzl, Marko; Gamulin, Vera

    2007-01-01

    Background The homologues of human disease genes are expected to contribute to better understanding of physiological and pathogenic processes. We made use of the present availability of vertebrate genomic sequences, and we have conducted the most comprehensive comparative genomic analysis of the prion protein gene PRNP and its homologues, shadow of prion protein gene SPRN and doppel gene PRND, and prion testis-specific gene PRNT so far. Results While the SPRN and PRNP homologues are present in all vertebrates, PRND is known in tetrapods, and PRNT is present in primates. PRNT could be viewed as a TE-associated gene. Using human as the base sequence for genomic sequence comparisons (VISTA), we annotated numerous potential cis-elements. The conserved regions in SPRNs harbour the potential Sp1 sites in promoters (mammals, birds), C-rich intron splicing enhancers and PTB intron splicing silencers in introns (mammals, birds), and hsa-miR-34a sites in 3'-UTRs (eutherians). We showed the conserved PRNP upstream regions, which may be potential enhancers or silencers (primates, dog). In the PRNP 3'-UTRs, there are conserved cytoplasmic polyadenylation element sites (mammals, birds). The PRND core promoters include highly conserved CCAAT, CArG and TATA boxes (mammals). We deduced 42 new protein primary structures, and performed the first phylogenetic analysis of all vertebrate prion genes. Using the protein alignment which included 122 sequences, we constructed the neighbour-joining tree which showed four major clusters, including shadoos, shadoo2s and prion protein-likes (cluster 1), fish prion proteins (cluster 2), tetrapode prion proteins (cluster 3) and doppels (cluster 4). We showed that the entire prion protein conformationally plastic region is well conserved between eutherian prion proteins and shadoos (18–25% identity and 28–34% similarity), and there could be a potential structural compatibility between shadoos and the left-handed parallel beta-helical fold

  4. A Comparative Analysis and Taxonomy of Comets

    NASA Astrophysics Data System (ADS)

    Osip, David James

    1995-01-01

    A comparative analysis of narrowband photometry observations of 85 comets yields a wealth of information about the nature of comets. The data set consists of 2020 observations obtained over 429 nights between 1976 and 1992 that are fully reduced in a consistent manner to molecular production rates of 5 emission species (OH, NH, CN, C _3, and C_2) as well as a comparative measure of the dust production rate. Ratios of these production rates serve as a means of exploring compositional variation between comets. Vaporization models are used to estimate the active surface area for each comet, which is indicative of intrinsic differences in activity level among comets. Orbital parameters distinguish comets by dynamical age and separate the database into several dynamical classes. The current investigation confirms a number of results from earlier studies. There are no significant or systematic variations of the various abundance ratios with heliocentric distance. Neither the cometary dust -to-gas ratio nor the activity level vary systematically with dynamical age or with heliocentric distance. There is no conclusive evidence suggesting changes in composition based on dynamical evolution of the comet. Also, this investigation finds for many comets the strong degree of homogeneity in abundance ratios suggested by other studies, particularly among the carbon bearing species. Results unique to the present database include a significant correlation between the cometary dust-to -gas ratio and perihelion distance of a comet, suggesting mantling effects on the nucleus. Additional evidence for mantling is provided by the large number of comets with very low levels of activity as measured by the surface active area and the low fractional active areas calculated for those comets with nucleus size estimates available. The most important result from this study, however, is a taxonomic classification of comets separating chemically distinct compositional groupings most likely due to

  5. An IR and Calorimetric Investigation of the Structural, Crystal-Chemical and Thermodynamic Properties of Hydrogrossular

    NASA Astrophysics Data System (ADS)

    Geiger, C. A.; Dachs, E.

    2012-04-01

    The garnet class of phases is extremely broad in terms of composition and structural properties. Garnet is found in nature and various synthetic garnet phases have a number of important technical applications. There exist the rock-forming silicate garnets that are so widespread geologically. An additional class is given by the so-called "hydrogarnets" in which the tetrahedral site (Wyckoff position 24d) is empty. At relatively low temperatures there is complete solid solution between Ca3Al2Si3O12 and Ca3Al2H12O12, for example. The substitution mechanism can be written as O4H4 \\lrarr SiO4. The latter, pure OH-containing end-member, which has not been found in nature, is termed katoite/hydrogrossular. Its structure has been investigated by various workers by X-ray and neutron diffraction and by proton NMR, IR and Raman spectroscopic methods. At ambient conditions the structure has the "standard" garnet cubic symmetry of Ia-3d. At high pressures, and possibly at low temperatures, a different structure may occur. We measured the low temperature IR spectra and heat capacity of katoite in order to understand its structural, crystal-chemical and thermophysical properties. A sample of Ca3Al2H12O12 was synthesized hydrothermally in Au capsules at 250 °C and 3 kb water pressure. X-ray powder measurements show that about 98-99% katoite was obtained. Powder IR spectra were recorded between 298 K and 10 K. The measured spectra are considerably different in the high wavenumber region, where O-H stretching modes occur, between 298 K and 10 K. At room temperature the IR-active O-H band located around 3662 cm-1 is broad and it narrows and shifts to higher wavenumbers and also develops structure below about 80 K. Concomitantly, additional weak intensity O-H bands located around 3600 cm-1 begin to appear and they become sharper and increase in intensity with further decreases in temperature down to 10 K. The spectra indicate that the vibrational behavior of individual OH groups and

  6. Crystal chemistry of natural and synthetic trioctahedral micas: Exploring the limits of geometric crystal chemical models

    NASA Astrophysics Data System (ADS)

    Mercier, Patrick H. J.

    of lattice parameter b versus average-octahedral-bond-length allowed the following distinction to be made: Unoxidized divalent synthetic solid solution series tend to evolve along constant flattening-angle lines whereas trivalent octahedral cation and vacancy bearing natural single-crystals and synthetic powders follow trends with varying flattening angles. We found that the bond length of a given interlayer cationic species monotonously increases as the tetrahedral rotation angle alpha decreases in trioctahedral-1 M single-crystals. An upper limit of tetrahedral rotation of alpha = 9.5° was demonstrated to occur in trioctahedral-1M K-rich micas having an sheet, for both synthetic powders and natural single-crystals. Other attempts at applying geometric crystal chemical models and at identifying structure-chemical relationships from structural refinement data will benefit from the perspective of our more complete and systematic approach based on pursuing simple geometrical models using 'regular' coordination polyhedrons and characteristic cation-specific bond lengths up to the limit beyond which such models are shown to necessarily breakdown because of unavoidable 'non-regular' polyhedral distortions. (Abstract shortened by UMI.)

  7. Comparing Results from Constant Comparative and Computer Software Methods: A Reflection about Qualitative Data Analysis

    ERIC Educational Resources Information Center

    Putten, Jim Vander; Nolen, Amanda L.

    2010-01-01

    This study compared qualitative research results obtained by manual constant comparative analysis with results obtained by computer software analysis of the same data. An investigated about issues of trustworthiness and accuracy ensued. Results indicated that the inductive constant comparative data analysis generated 51 codes and two coding levels…

  8. Comparing Results from Constant Comparative and Computer Software Methods: A Reflection about Qualitative Data Analysis

    ERIC Educational Resources Information Center

    Putten, Jim Vander; Nolen, Amanda L.

    2010-01-01

    This study compared qualitative research results obtained by manual constant comparative analysis with results obtained by computer software analysis of the same data. An investigated about issues of trustworthiness and accuracy ensued. Results indicated that the inductive constant comparative data analysis generated 51 codes and two coding levels…

  9. Human Capital Development: Comparative Analysis of BRICs

    ERIC Educational Resources Information Center

    Ardichvili, Alexandre; Zavyalova, Elena; Minina, Vera

    2012-01-01

    Purpose: The goal of this article is to conduct macro-level analysis of human capital (HC) development strategies, pursued by four countries commonly referred to as BRICs (Brazil, Russia, India, and China). Design/methodology/approach: This analysis is based on comparisons of macro indices of human capital and innovativeness of the economy and a…

  10. Human Capital Development: Comparative Analysis of BRICs

    ERIC Educational Resources Information Center

    Ardichvili, Alexandre; Zavyalova, Elena; Minina, Vera

    2012-01-01

    Purpose: The goal of this article is to conduct macro-level analysis of human capital (HC) development strategies, pursued by four countries commonly referred to as BRICs (Brazil, Russia, India, and China). Design/methodology/approach: This analysis is based on comparisons of macro indices of human capital and innovativeness of the economy and a…

  11. Question analysis for Indonesian comparative question

    NASA Astrophysics Data System (ADS)

    Saelan, A.; Purwarianti, A.; Widyantoro, D. H.

    2017-01-01

    Information seeking is one of human needs today. Comparing things using search engine surely take more times than search only one thing. In this paper, we analyzed comparative questions for comparative question answering system. Comparative question is a question that comparing two or more entities. We grouped comparative questions into 5 types: selection between mentioned entities, selection between unmentioned entities, selection between any entity, comparison, and yes or no question. Then we extracted 4 types of information from comparative questions: entity, aspect, comparison, and constraint. We built classifiers for classification task and information extraction task. Features used for classification task are bag of words, whether for information extraction, we used lexical, 2 previous and following words lexical, and previous label as features. We tried 2 scenarios: classification first and extraction first. For classification first, we used classification result as a feature for extraction. Otherwise, for extraction first, we used extraction result as features for classification. We found that the result would be better if we do extraction first before classification. For the extraction task, classification using SMO gave the best result (88.78%), while for classification, it is better to use naïve bayes (82.35%).

  12. MANAGEMENT AND COMPARATIVE ANALYSIS OF DATASET ENSEMBLES

    SciTech Connect

    Geveci, Berk

    2010-05-17

    The primary Phase I technical objective was to develop a prototype that demonstrates the functionality of all components required for an end-to-end meta-data management and comparative visualization system.

  13. Comparative Lifecycle Energy Analysis: Theory and Practice.

    ERIC Educational Resources Information Center

    Morris, Jeffrey; Canzoneri, Diana

    1992-01-01

    Explores the position that more energy is conserved through recycling secondary materials than is generated from municipal solid waste incineration. Discusses one component of a lifecycle analysis--a comparison of energy requirements for manufacturing competing products. Includes methodological issues, energy cost estimates, and difficulties…

  14. Comparative molecular analysis of endoevaporitic microbial communities.

    PubMed

    Sahl, Jason W; Pace, Norman R; Spear, John R

    2008-10-01

    A phylogenetic comparison of microbial communities in hypersaline evaporites was conducted on crusts from Guerrero Negro, Mexico, and Lindsey Lake, New Mexico, using culture-independent rRNA gene sequence analysis. Many sequences were shared between evaporites, which suggests that similar environments select for specific microbial lineages from a global metacommunity.

  15. Comparative Lifecycle Energy Analysis: Theory and Practice.

    ERIC Educational Resources Information Center

    Morris, Jeffrey; Canzoneri, Diana

    1992-01-01

    Explores the position that more energy is conserved through recycling secondary materials than is generated from municipal solid waste incineration. Discusses one component of a lifecycle analysis--a comparison of energy requirements for manufacturing competing products. Includes methodological issues, energy cost estimates, and difficulties…

  16. Comparative Analysis of Monographic Collections in Nursing.

    ERIC Educational Resources Information Center

    Bowden, Virginia M.; And Others

    The results of a project comparing the nursing monograph collections of academic health science center libraries in the Southwest are reported. Records for nursing monographs from the TALON (South Central Regional Medical Library Program) Union Catalog of Monographs from 1977-1983 were analyzed to reveal the distribution by year, publisher, and…

  17. A Comparative Analysis of Teacher Ethnotheories.

    ERIC Educational Resources Information Center

    Akkari, Abdeljalil; Serpell, Robert; Baker, Linda; Sonnenschein, Susan

    1998-01-01

    Compared the beliefs of African-American (AA) and European-American (EA) elementary teachers about teaching and literacy development. Teacher interviews found no differences in child development perceptions and approaches to literacy. AA teachers placed more emphasis on the themes of universal educability and teacher responsibility, while EA…

  18. Wellness Model of Supervision: A Comparative Analysis

    ERIC Educational Resources Information Center

    Lenz, A. Stephen; Sangganjanavanich, Varunee Faii; Balkin, Richard S.; Oliver, Marvarene; Smith, Robert L.

    2012-01-01

    This quasi-experimental study compared the effectiveness of the Wellness Model of Supervision (WELMS; Lenz & Smith, 2010) with alternative supervision models for developing wellness constructs, total personal wellness, and helping skills among counselors-in-training. Participants were 32 master's-level counseling students completing their…

  19. Comparative Naval Architecture Analysis of Diesel Submarines

    DTIC Science & Technology

    2005-06-01

    mission, cost, or other factors affect the architecture? This study examines and compares the naval architecture of selected diesel submarines from...79 A ppendix E : Subm arine Shape Factors ................................................................................... 90 5 List of...country. Do factors such as mission, cost, or tradition 10 affect submarine naval architecture? An in depth comparison is performed of six diesel

  20. Comparative analysis of the spatial analysis methods for hotspot identification.

    PubMed

    Yu, Hao; Liu, Pan; Chen, Jun; Wang, Hao

    2014-05-01

    Spatial analysis technique has been introduced as an innovative approach for hazardous road segments identification (HRSI). In this study, the performance of two spatial analysis methods and four conventional methods for HRSI was compared against three quantitative evaluation criteria. The spatial analysis methods considered in this study include the local spatial autocorrelation method and the kernel density estimation (KDE) method. It was found that the empirical Bayesian (EB) method and the KDE method outperformed other HRSI approaches. By transferring the kernel density function into a form that was analogous to the form of the EB function, we further proved that the KDE method can eventually be considered a simplified version of the EB method in which crashes reported at neighboring spatial units are used as the reference population for estimating the EB-adjusted crashes. Theoretically, the KDE method may outperform the EB method in HRSI when the neighboring spatial units provide more useful information on the expected crash frequency than a safety performance function does. Copyright © 2014 Elsevier Ltd. All rights reserved.

  1. Comparing methods for single paragraph similarity analysis.

    PubMed

    Stone, Benjamin; Dennis, Simon; Kwantes, Peter J

    2011-01-01

    The focus of this paper is two-fold. First, similarities generated from six semantic models were compared to human ratings of paragraph similarity on two datasets-23 World Entertainment News Network paragraphs and 50 ABC newswire paragraphs. Contrary to findings on smaller textual units such as word associations (Griffiths, Tenenbaum, & Steyvers, 2007), our results suggest that when single paragraphs are compared, simple nonreductive models (word overlap and vector space) can provide better similarity estimates than more complex models (LSA, Topic Model, SpNMF, and CSM). Second, various methods of corpus creation were explored to facilitate the semantic models' similarity estimates. Removing numeric and single characters, and also truncating document length improved performance. Automated construction of smaller Wikipedia-based corpora proved to be very effective, even improving upon the performance of corpora that had been chosen for the domain. Model performance was further improved by augmenting corpora with dataset paragraphs. Copyright © 2010 Cognitive Science Society, Inc.

  2. Comparative Analysis of Treatment Costs in EUROHOPE.

    PubMed

    Iversen, Tor; Aas, Eline; Rosenqvist, Gunnar; Häkkinen, Unto

    2015-12-01

    This study examines the challenges of estimating risk-adjusted treatment costs in international comparative research, specifically in the European Health Care Outcomes, Performance, and Efficiency (EuroHOPE) project. We describe the diverse format of resource data and challenges of converting these data into resource use indicators that allow meaningful cross-country comparisons. The three cost indicators developed in EuroHOPE are then described, discussed, and applied. We compare the risk-adjusted mean treatment costs of acute myocardial infarction for four of the seven countries in the EuroHOPE project, namely, Finland, Hungary, Norway, and Sweden. The outcome of the comparison depends on the time perspective as well as on the particular resource use indicator. We argue that these complementary indicators add to our understanding of the variation in resource use across countries.

  3. Comparative analysis of plant oil based fuels

    SciTech Connect

    Ziejewski, M.; Goettler, H.J.; Haines, H.; Huong, C.

    1995-12-31

    This paper presents the evaluation results from the analysis of different blends of fuels using the 13-mode standard SAE testing method. Six high oleic safflower oil blends, six ester blends, six high oleic sunflower oil blends, and six sunflower oil blends were used in this portion of the investigation. Additionally, the results from the repeated 13-mode tests for all the 25/75% mixtures with a complete diesel fuel test before and after each alternative fuel are presented.

  4. Multiattribute Decision Modeling Techniques: A Comparative Analysis

    DTIC Science & Technology

    1988-08-01

    Rating Technique (SMART) as a direct response to Raiffa’s (1969) article on multiattribute utility theory , which Edwards found extremcy stimulating but...approaches such as multiattribute utility /value assessment and hierarchical analysis and have applied these techniques to a number of non-military... multiattributed ) outcomes O(l)...O(k), and if the utility function is denoted by u and the probabilities of the k events are p(l)...p(k), then the

  5. A Comparative Analysis of Reinforcement Learning Methods

    DTIC Science & Technology

    1991-10-01

    reinforcement learning for both programming and adapting situated agents. In the first part of the paper we discuss two specific reinforcement learning algorithms: Q-learning and the Bucket Brigade. We introduce a special case of the Bucket Brigade, and analyze and compare its performance to Q-learning in a number of experiments. The second part of the paper discusses the key problems of reinforcement learning : time and space complexity, input generalization, sensitivity to parameter values, and selection of the reinforcement

  6. [Amaranth flour: characteristics, comparative analysis, application possibilities].

    PubMed

    Zharkov, I M; Miroshnichenko, L A; Zviagin, A A; Bavykina, I A

    2014-01-01

    Amaranth flour--a product of amaranth seeds processing--is a valuable industrial raw material that has an unique chemical composition and may be used for nutrition of people suffering from intolerance to traditional cereals protein, including celiac disease patients. The research aim was to study the composition of amaranth flour of two types compared with semolina which is traditionally used for nutrition by Russian population, as well as to compare the composition of milk amaranth flour porridge with milk semolina porridge. The composition of amaranth whole-ground flour and amaranth flour of premium grade processed from amaranth seeds grown in Voronezh region has been researched. It is to be noted that protein content in amaranth flour was 10.8-24.3% higher than in semolina, and its biological value and NPU-coefficient were higher by 22.65 and 46.51% respectively; lysine score in amaranth flour protein of premium grade came up to 107.54%, and in semolina protein only 40.95%. The level of digestible carbohydrates, including starch, was lower in amaranth flour than in semolina by 2.79-12.85 and 4.76-15.85% respectively, while fiber content was 15.5-30 fold higher. Fat content in amaranth flour of premium grade was 2,4 fold lower than in whole-ground amaranth flour but it was 45% higher than in semolina. The main advantage of amaranth flour protein compared to wheat protein is the predominance of albumins and globulins and a minimal content of prolamines and alpha-gliadin complete absence. The specifics of chemical composition allow the amaranth flour to be recommended for being included into nutrition of both healthy children and adults and also celiac disease patients.

  7. Comparative Analysis of GOCI Ocean Color Products

    PubMed Central

    Amin, Ruhul; Lewis, Mark David; Lawson, Adam; Gould, Richard W.; Martinolich, Paul; Li, Rong-Rong; Ladner, Sherwin; Gallegos, Sonia

    2015-01-01

    The Geostationary Ocean Color Imager (GOCI) is the first geostationary ocean color sensor in orbit that provides bio-optical properties from coastal and open waters around the Korean Peninsula at unprecedented temporal resolution. In this study, we compare the normalized water-leaving radiance (nLw) products generated by the Naval Research Laboratory Automated Processing System (APS) with those produced by the stand-alone software package, the GOCI Data Processing System (GDPS), developed by the Korean Ocean Research & Development Institute (KORDI). Both results are then compared to the nLw measured by the above water radiometer at the Ieodo site. This above-water radiometer is part of the Aerosol Robotic NETwork (AeroNET). The results indicate that the APS and GDPS processed nLw correlates well within the same image slot where the coefficient of determination (r2) is higher than 0.84 for all the bands from 412 nm to 745 nm. The agreement between APS and the AeroNET data is higher when compared to the GDPS results. The Root-Mean-Squared-Error (RMSE) between AeroNET and APS data ranges from 0.24 [mW/(cm2srμm)] at 555 nm to 0.52 [mW/(cm2srμm)] at 412 nm while RMSE between AeroNET and GDPS data ranges from 0.47 [mW/(cm2srμm)] at 443 nm to 0.69 [mW/(cm2srμm)] at 490 nm. PMID:26473861

  8. Comparative analysis of condensation models within DSMC

    SciTech Connect

    Bykov, Nikolay Y.; Gorbachev, Yuriy E.

    2014-12-09

    Two condensation process modeling approaches within DSMC methodology are compared. The first is based on the modified nucleation theory which correctly describes small clusters and the second on the kinetic theory and considers not only supercritical clusters, but clusters of all sizes including dimers. The relaxation of the size distribution function is calculated for the spatially homogeneous cases, where the monomer parameters are kept constant. As an example the vapour of Cu atoms is considered and importance of taking into account of the internal energies of clusters is shown. Peculiarities of the classical and kinetic approaches are discussed herein.

  9. Comparative Modal Analysis of Sieve Hardware Designs

    NASA Technical Reports Server (NTRS)

    Thompson, Nathaniel

    2012-01-01

    The CMTB Thwacker hardware operates as a testbed analogue for the Flight Thwacker and Sieve components of CHIMRA, a device on the Curiosity Rover. The sieve separates particles with a diameter smaller than 150 microns for delivery to onboard science instruments. The sieving behavior of the testbed hardware should be similar to the Flight hardware for the results to be meaningful. The elastodynamic behavior of both sieves was studied analytically using the Rayleigh Ritz method in conjunction with classical plate theory. Finite element models were used to determine the mode shapes of both designs, and comparisons between the natural frequencies and mode shapes were made. The analysis predicts that the performance of the CMTB Thwacker will closely resemble the performance of the Flight Thwacker within the expected steady state operating regime. Excitations of the testbed hardware that will mimic the flight hardware were recommended, as were those that will improve the efficiency of the sieving process.

  10. Comparative LIBS Analysis Of Calcified Tissues

    SciTech Connect

    Abdel-Salam, Z. A.; Harith, M. A.

    2008-09-23

    Signal enhancement, limits of detection, and relevance to environmental concentration for element in calcified tissues using LIBS with single and double laser pulses will be presented. These measurements were performed on three calcified tissues representing different matrices, namely enamel of human teeth, shells and eggshells. This method depends on the role of the laser induced shock wave on the ionization rate of the ablated target material atoms. The effect of the laser single and double pulse on the ionic to atomic ratio of calcium and magnesium spectral emission lines, CaII/CaI and MgII/MgI, will be presented and compared with the previous results and its relevance to the target material hardness. The results show that in case of single pulse the intensity ratios in calcium are higher than the double pulse while there is no appreciable difference between both in case of magnesium.

  11. Comparative LIBS Analysis Of Calcified Tissues

    NASA Astrophysics Data System (ADS)

    Abdel-Salam, Z. A.; Harith, M. A.

    2008-09-01

    Signal enhancement, limits of detection, and relevance to environmental concentration for element in calcified tissues using LIBS with single and double laser pulses will be presented. These measurements were performed on three calcified tissues representing different matrices, namely enamel of human teeth, shells and eggshells. This method depends on the role of the laser induced shock wave on the ionization rate of the ablated target material atoms. The effect of the laser single and double pulse on the ionic to atomic ratio of calcium and magnesium spectral emission lines, CaII/CaI and MgII/MgI, will be presented and compared with the previous results and its relevance to the target material hardness. The results show that in case of single pulse the intensity ratios in calcium are higher than the double pulse while there is no appreciable difference between both in case of magnesium.

  12. Comparative analysis of Goodwin's business cycle models

    NASA Astrophysics Data System (ADS)

    Antonova, A. O.; Reznik, S.; Todorov, M. D.

    2016-10-01

    We compare the behavior of solutions of Goodwin's business cycle equation in the form of neutral delay differential equation with fixed delay (NDDE model) and in the form of the differential equations of 3rd, 4th and 5th orders (ODE model's). Such ODE model's (Taylor series expansion of NDDE in powers of θ) are proposed in N. Dharmaraj and K. Vela Velupillai [6] for investigation of the short periodic sawthooth oscillations in NDDE. We show that the ODE's of 3rd, 4th and 5th order may approximate the asymptotic behavior of only main Goodwin's mode, but not the sawthooth modes. If the order of the Taylor series expansion exceeds 5, then the approximate ODE becomes unstable independently of time lag θ.

  13. Nutrient profiling schemes: overview and comparative analysis.

    PubMed

    Garsetti, Marcella; de Vries, Jan; Smith, Maurice; Amosse, Amélie; Rolf-Pedersen, Nathalie

    2007-12-01

    Nutrient profiling is a discipline aimed at classifying foods based on their nutritional composition. So far, several profiling schemes have been proposed for varied purposes world-wide. Primary aim to inventory the main profiling schemes that have been developed so far (both applied and not) and to summarise their main aspects. Secondary aim to critically review a selection of them, to test their "performance" and to evaluate their strengths and weaknesses. Scientific and popular search engines were used for identifying profiling schemes. Schemes were described concisely by providing details on four main "Building Blocks" or factors: (1) Food category declination: category-wise or "across the board"; (2) Reference amount: 100 g, 100 kcal; serving; (3) Cut-off use: thresholds or scores; (4) Nutrients Selection: balance between positive and negative nutrients and number of them. The "performance" analysis was done by testing how the selected schemes classify a sample of food. Profiling schemes display considerable variation based on the underlying approach, format and content. Moreover, the rationale of the schemes largely varies and seems to be inspired by either nutrient recommendations or regulations figures. When tested for "performance", the five selected schemes classify in the same way foods having either a very "positive" or a very "negative" nutrient profile, whereas they give inconsistent results for food products with intermediate characteristics. Strengths and weaknesses analysis shows the difficulty of finding schemes combining qualities such as simplicity, scientific relevance, ability to cope with changes in nutrient recommendations. Current proposed profiling schemes exhibit a wide range of differences both in terms of approaches and "performance". Nutrition scientists have now the challenge to develop the "ideal scheme" that, in our view, will have to be strict enough to ensure consumer protection but also flexible enough to encourage food industry

  14. Comparative Analysis of Cystatin Superfamily in Platyhelminths

    PubMed Central

    Guo, Aijiang

    2015-01-01

    The cystatin superfamily is comprised of cysteine proteinase inhibitors and encompasses at least 3 subfamilies: stefins, cystatins and kininogens. In this study, the platyhelminth cystatin superfamily was identified and grouped into stefin and cystatin subfamilies. The conserved domain of stefins (G, QxVxG) was observed in all members of platyhelminth stefins. The three characteristics of cystatins, the cystatin-like domain (G, QxVxG, PW), a signal peptide, and one or two conserved disulfide bonds, were observed in platyhelminths, with the exception of cestodes, which lacked the conserved disulfide bond. However, it is noteworthy that cestode cystatins had two tandem repeated domains, although the second tandem repeated domain did not contain a cystatin-like domain, which has not been previously reported. Tertiary structure analysis of Taenia solium cystatin, one of the cestode cystatins, demonstrated that the N-terminus of T. solium cystatin formed a five turn α-helix, a five stranded β-pleated sheet and a hydrophobic edge, similar to the structure of chicken cystatin. Although no conserved disulfide bond was found in T. solium cystatin, the models of T. solium cystatin and chicken cystatin corresponded at the site of the first disulfide bridge of the chicken cystatin. However, the two models were not similar regarding the location of the second disulfide bridge of chicken cystatin. These results showed that T. solium cystatin and chicken cystatin had similarities and differences, suggesting that the biochemistry of T. solium cystatin could be similar to chicken cystatin in its inhibitory function and that it may have further functional roles. The same results were obtained for other cestode cystatins. Phylogenetic analysis showed that cestode cystatins constituted an independent clade and implied that cestode cystatins should be considered to have formed a new clade during evolution. PMID:25853513

  15. Comparative analysis of cystatin superfamily in platyhelminths.

    PubMed

    Guo, Aijiang

    2015-01-01

    The cystatin superfamily is comprised of cysteine proteinase inhibitors and encompasses at least 3 subfamilies: stefins, cystatins and kininogens. In this study, the platyhelminth cystatin superfamily was identified and grouped into stefin and cystatin subfamilies. The conserved domain of stefins (G, QxVxG) was observed in all members of platyhelminth stefins. The three characteristics of cystatins, the cystatin-like domain (G, QxVxG, PW), a signal peptide, and one or two conserved disulfide bonds, were observed in platyhelminths, with the exception of cestodes, which lacked the conserved disulfide bond. However, it is noteworthy that cestode cystatins had two tandem repeated domains, although the second tandem repeated domain did not contain a cystatin-like domain, which has not been previously reported. Tertiary structure analysis of Taenia solium cystatin, one of the cestode cystatins, demonstrated that the N-terminus of T. solium cystatin formed a five turn α-helix, a five stranded β-pleated sheet and a hydrophobic edge, similar to the structure of chicken cystatin. Although no conserved disulfide bond was found in T. solium cystatin, the models of T. solium cystatin and chicken cystatin corresponded at the site of the first disulfide bridge of the chicken cystatin. However, the two models were not similar regarding the location of the second disulfide bridge of chicken cystatin. These results showed that T. solium cystatin and chicken cystatin had similarities and differences, suggesting that the biochemistry of T. solium cystatin could be similar to chicken cystatin in its inhibitory function and that it may have further functional roles. The same results were obtained for other cestode cystatins. Phylogenetic analysis showed that cestode cystatins constituted an independent clade and implied that cestode cystatins should be considered to have formed a new clade during evolution.

  16. Comparative analysis of Debrecen sunspot catalogues

    NASA Astrophysics Data System (ADS)

    Győri, L.; Ludmány, A.; Baranyi, T.

    2017-02-01

    Sunspot area data are important for studying solar activity and its long-term variations. At the Debrecen Heliophysical Observatory, we compiled three sunspot catalogues: the Debrecen Photoheliographic Data (DPD), the SDO/HMI Debrecen Data (HMIDD) and the SOHO/MDI Debrecen Data. For comparison, we also compiled an additional sunspot catalogue, the Greenwich Photoheliographic Data, from the digitized Royal Greenwich Observatory images for 1974-76. By comparing these catalogues when they overlap in time, we can investigate how various factors influence the measured area of sunspots, and, in addition, we can derive area cross-calibration factors for these catalogues. The main findings are as follows. Poorer seeing increases the individual corrected spot areas and decreases the number of small spots. Interestingly, the net result of these two effects for the total corrected spot area is zero. DPD daily total corrected sunspot areas are 5 per cent smaller than the HMIDD ones. Revised DPD daily total corrected umbra areas are 9 per cent smaller than those of HMIDD. The Greenwich photoheliographic areas are only a few per cent smaller than DPD areas. A 0.2° difference between the north directions of the DPD and MDI images is found. This value is nearly the same as was found (0.22°) by us in a previous paper comparing HMI and MDI images. The area measurement practice (spots smaller than 10 mh were not directly measured but an area of 2 mh was assigned to each) of the Solar Observing Optical Network cannot explain the large area deficit of the Solar Observing Optical Network.

  17. Crystal chemical characteristics and physical properties of ferrous minerals as the basis for the formation of functional materials

    NASA Astrophysics Data System (ADS)

    Shmakova, A.; Kanev, B.; Gömze, A. L.; Kotova, O.

    2017-02-01

    Crystal chemical characteristics and physical properties of ferrous minerals can be criteria for search and evaluation of mineral (natural) raw for the production of functional materials. Special attention will be given to new experimental methods of transformation of minerals at different methods of influence. As a probe to identify the relationship between the actual crystalline structure of the mineral and its technological properties we used the oxidation - reduction reactions of iron ore-forming minerals. We will show that the inexpensive and affordable methods of influence at ore and technological products result in the observed Fe2+— Fe3+ charge transfer, which result in the increase of the conversion degree of the structure and change of magnetic properties of the substance.

  18. Breastfeeding policy: a globally comparative analysis

    PubMed Central

    Raub, Amy; Earle, Alison

    2013-01-01

    Abstract Objective To explore the extent to which national policies guaranteeing breastfeeding breaks to working women may facilitate breastfeeding. Methods An analysis was conducted of the number of countries that guarantee breastfeeding breaks, the daily number of hours guaranteed, and the duration of guarantees. To obtain current, detailed information on national policies, original legislation as well as secondary sources on 182 of the 193 Member States of the United Nations were examined. Regression analyses were conducted to test the association between national policy and rates of exclusive breastfeeding while controlling for national income level, level of urbanization, female percentage of the labour force and female literacy rate. Findings Breastfeeding breaks with pay are guaranteed in 130 countries (71%) and unpaid breaks are guaranteed in seven (4%). No policy on breastfeeding breaks exists in 45 countries (25%). In multivariate models, the guarantee of paid breastfeeding breaks for at least 6 months was associated with an increase of 8.86 percentage points in the rate of exclusive breastfeeding (P < 0.05). Conclusion A greater percentage of women practise exclusive breastfeeding in countries where laws guarantee breastfeeding breaks at work. If these findings are confirmed in longitudinal studies, health outcomes could be improved by passing legislation on breastfeeding breaks in countries that do not yet ensure the right to breastfeed. PMID:24052676

  19. Community detection algorithms: a comparative analysis.

    PubMed

    Lancichinetti, Andrea; Fortunato, Santo

    2009-11-01

    Uncovering the community structure exhibited by real networks is a crucial step toward an understanding of complex systems that goes beyond the local organization of their constituents. Many algorithms have been proposed so far, but none of them has been subjected to strict tests to evaluate their performance. Most of the sporadic tests performed so far involved small networks with known community structure and/or artificial graphs with a simplified structure, which is very uncommon in real systems. Here we test several methods against a recently introduced class of benchmark graphs, with heterogeneous distributions of degree and community size. The methods are also tested against the benchmark by Girvan and Newman [Proc. Natl. Acad. Sci. U.S.A. 99, 7821 (2002)] and on random graphs. As a result of our analysis, three recent algorithms introduced by Rosvall and Bergstrom [Proc. Natl. Acad. Sci. U.S.A. 104, 7327 (2007); Proc. Natl. Acad. Sci. U.S.A. 105, 1118 (2008)], Blondel [J. Stat. Mech.: Theory Exp. (2008), P10008], and Ronhovde and Nussinov [Phys. Rev. E 80, 016109 (2009)] have an excellent performance, with the additional advantage of low computational complexity, which enables one to analyze large systems.

  20. Comparative analysis of de novo transcriptome assembly.

    PubMed

    Clarke, Kaitlin; Yang, Yi; Marsh, Ronald; Xie, Linglin; Zhang, Ke K

    2013-02-01

    The fast development of next-generation sequencing technology presents a major computational challenge for data processing and analysis. A fast algorithm, de Bruijn graph has been successfully used for genome DNA de novo assembly; nevertheless, its performance for transcriptome assembly is unclear. In this study, we used both simulated and real RNA-Seq data, from either artificial RNA templates or human transcripts, to evaluate five de novo assemblers, ABySS, Mira, Trinity, Velvet and Oases. Of these assemblers, ABySS, Trinity, Velvet and Oases are all based on de Bruijn graph, and Mira uses an overlap graph algorithm. Various numbers of RNA short reads were selected from the External RNA Control Consortium (ERCC) data and human chromosome 22. A number of statistics were then calculated for the resulting contigs from each assembler. Each experiment was repeated multiple times to obtain the mean statistics and standard error estimate. Trinity had relative good performance for both ERCC and human data, but it may not consistently generate full length transcripts. ABySS was the fastest method but its assembly quality was low. Mira gave a good rate for mapping its contigs onto human chromosome 22, but its computational speed is not satisfactory. Our results suggest that transcript assembly remains a challenge problem for bioinformatics society. Therefore, a novel assembler is in need for assembling transcriptome data generated by next generation sequencing technique.

  1. Vestibular migraine: comparative analysis between diagnostic criteria.

    PubMed

    Salmito, Márcio Cavalcante; Morganti, Lígia Oliveira Gonçalves; Nakao, Bruno Higa; Simões, Juliana Caminha; Duarte, Juliana Antoniolli; Ganança, Fernando Freitas

    2015-01-01

    There is a strong association between vertigo and migraine. Vestibular migraine (VM) was described in 1999, and diagnostic criteria were proposed in 2001 and revised in 2012. To compare the diagnostic criteria for VM proposed in 2001 with 2012 criteria with respect to their diagnostic power and therapeutic effect of VM prophylaxis. Clinical chart review of patients attended to in a VM clinic. The 2012 criteria made the diagnosis more specific, restricting the diagnosis of VM to a smaller number of patients, such that 87.7% of patients met 2001 criteria and 77.8% met 2012 criteria. Prophylaxis for VM was effective both for patients diagnosed by either set of criteria and for those who did not meet any of the criteria. The 2012 diagnostic criteria for VM limited the diagnosis of the disease to a smaller number of patients, mainly because of the type, intensity, and duration of dizziness. Patients diagnosed with migraine and associated dizziness demonstrated improvement after prophylactic treatment of VM, even when they did not meet diagnostic criteria. Copyright © 2015 Associação Brasileira de Otorrinolaringologia e Cirurgia Cérvico-Facial. Published by Elsevier Editora Ltda. All rights reserved.

  2. Recognizing chemicals in patents: a comparative analysis.

    PubMed

    Habibi, Maryam; Wiegandt, David Luis; Schmedding, Florian; Leser, Ulf

    2016-01-01

    Recently, methods for Chemical Named Entity Recognition (NER) have gained substantial interest, driven by the need for automatically analyzing todays ever growing collections of biomedical text. Chemical NER for patents is particularly essential due to the high economic importance of pharmaceutical findings. However, NER on patents has essentially been neglected by the research community for long, mostly because of the lack of enough annotated corpora. A recent international competition specifically targeted this task, but evaluated tools only on gold standard patent abstracts instead of full patents; furthermore, results from such competitions are often difficult to extrapolate to real-life settings due to the relatively high homogeneity of training and test data. Here, we evaluate the two state-of-the-art chemical NER tools, tmChem and ChemSpot, on four different annotated patent corpora, two of which consist of full texts. We study the overall performance of the tools, compare their results at the instance level, report on high-recall and high-precision ensembles, and perform cross-corpus and intra-corpus evaluations. Our findings indicate that full patents are considerably harder to analyze than patent abstracts and clearly confirm the common wisdom that using the same text genre (patent vs. scientific) and text type (abstract vs. full text) for training and testing is a pre-requisite for achieving high quality text mining results.

  3. Comparative and demographic analysis of orangutan genomes

    PubMed Central

    Locke, Devin P.; Hillier, LaDeana W.; Warren, Wesley C.; Worley, Kim C.; Nazareth, Lynne V.; Muzny, Donna M.; Yang, Shiaw-Pyng; Wang, Zhengyuan; Chinwalla, Asif T.; Minx, Pat; Mitreva, Makedonka; Cook, Lisa; Delehaunty, Kim D.; Fronick, Catrina; Schmidt, Heather; Fulton, Lucinda A.; Fulton, Robert S.; Nelson, Joanne O.; Magrini, Vincent; Pohl, Craig; Graves, Tina A.; Markovic, Chris; Cree, Andy; Dinh, Huyen H.; Hume, Jennifer; Kovar, Christie L.; Fowler, Gerald R.; Lunter, Gerton; Meader, Stephen; Heger, Andreas; Ponting, Chris P.; Marques-Bonet, Tomas; Alkan, Can; Chen, Lin; Cheng, Ze; Kidd, Jeffrey M.; Eichler, Evan E.; White, Simon; Searle, Stephen; Vilella, Albert J.; Chen, Yuan; Flicek, Paul; Ma, Jian; Raney, Brian; Suh, Bernard; Burhans, Richard; Herrero, Javier; Haussler, David; Faria, Rui; Fernando, Olga; Darré, Fleur; Farré, Domènec; Gazave, Elodie; Oliva, Meritxell; Navarro, Arcadi; Roberto, Roberta; Capozzi, Oronzo; Archidiacono, Nicoletta; Valle, Giuliano Della; Purgato, Stefania; Rocchi, Mariano; Konkel, Miriam K.; Walker, Jerilyn A.; Ullmer, Brygg; Batzer, Mark A.; Smit, Arian F. A.; Hubley, Robert; Casola, Claudio; Schrider, Daniel R.; Hahn, Matthew W.; Quesada, Victor; Puente, Xose S.; Ordoñez, Gonzalo R.; López-Otín, Carlos; Vinar, Tomas; Brejova, Brona; Ratan, Aakrosh; Harris, Robert S.; Miller, Webb; Kosiol, Carolin; Lawson, Heather A.; Taliwal, Vikas; Martins, André L.; Siepel, Adam; RoyChoudhury, Arindam; Ma, Xin; Degenhardt, Jeremiah; Bustamante, Carlos D.; Gutenkunst, Ryan N.; Mailund, Thomas; Dutheil, Julien Y.; Hobolth, Asger; Schierup, Mikkel H.; Chemnick, Leona; Ryder, Oliver A.; Yoshinaga, Yuko; de Jong, Pieter J.; Weinstock, George M.; Rogers, Jeffrey; Mardis, Elaine R.; Gibbs, Richard A.; Wilson, Richard K.

    2011-01-01

    “Orangutan” is derived from the Malay term “man of the forest” and aptly describes the Southeast Asian great apes native to Sumatra and Borneo. The orangutan species, Pongo abelii (Sumatran) and Pongo pygmaeus (Bornean), are the most phylogenetically distant great apes from humans, thereby providing an informative perspective on hominid evolution. Here we present a Sumatran orangutan draft genome assembly and short read sequence data from five Sumatran and five Bornean orangutan genomes. Our analyses reveal that, compared to other primates, the orangutan genome has many unique features. Structural evolution of the orangutan genome has proceeded much more slowly than other great apes, evidenced by fewer rearrangements, less segmental duplication, a lower rate of gene family turnover and surprisingly quiescent Alu repeats, which have played a major role in restructuring other primate genomes. We also describe the first primate polymorphic neocentromere, found in both Pongo species, emphasizing the gradual evolution of orangutan genome structure. Orangutans have extremely low energy usage for a eutherian mammal1, far lower than their hominid relatives. Adding their genome to the repertoire of sequenced primates illuminates new signals of positive selection in several pathways including glycolipid metabolism. From the population perspective, both Pongo species are deeply diverse; however, Sumatran individuals possess greater diversity than their Bornean counterparts, and more species-specific variation. Our estimate of Bornean/Sumatran speciation time, 400k years ago (ya), is more recent than most previous studies and underscores the complexity of the orangutan speciation process. Despite a smaller modern census population size, the Sumatran effective population size (Ne) expanded exponentially relative to the ancestral Ne after the split, while Bornean Ne declined over the same period. Overall, the resources and analyses presented here offer new opportunities

  4. Allograft materials in phalloplasty: a comparative analysis.

    PubMed

    Solomon, Mark P; Komlo, Caroline; Defrain, Molly

    2013-09-01

    Allograft use has increased recently with the rising use of allograft materials in breast surgery. There are few data that compare the performance of the various allograft materials in this application, despite marketing efforts by the manufacturers to present one allograft material as superior to another. Phalloplasty is a procedure that uses allografts for penis girth augmentation. Preparation of these grafts differs with each manufacturer. We report our experience with 3 different types of allografts for this procedure. This allows for the comparison of these materials in their performance with a single model. Forty-seven patients who underwent penis girth enhancement with allograft material were reviewed. All patients underwent circumferential grafting to the shaft of the penis at the level of Buck's fascia. Graft materials included AlloDerm (n = 9), Belladerm (n = 20), and Repriza (n = 21). Charts were reviewed for material type, presence and type of infection, wound exposure, and graft loss with attention to the type of allograft material that was used. Follow-up ranged from 1 to 120 months with an average of 11.25 months. Infection, defined as an open wound with graft exposure, occurred in 20 (42%) of 47 patients. Of these, graft exposure only occurred in 17 (36%) patients, whereas 3 (6%) patients sustained total graft loss. Graft exposure or loss occurred in 3 patients who had AlloDerm, 9 patients with Belladerm, and 8 patients with Repriza. No patients with AlloDerm sustained graft loss, whereas 2 patients with Belladerm and 1 patient with Repriza sustained graft loss. There were no statistical differences among these graft types with regard to infection or graft loss. Three different brands of allograft material were used in 1 surgical procedure and followed up for their performance with regard to exposure and infection. In this model, there is no difference in the rate of infection in these materials despite their different methods of preparation

  5. Crystal-Chemical Correlations in Chromites from Kimberlitic and Non-Kimberlitic Sources.

    NASA Astrophysics Data System (ADS)

    Freckelton, C. N.; Flemming, R. L.

    2009-05-01

    This study explores the utility of micro X-ray diffraction (μXRD) as a tool for diamond exploration, as a compliment to current industry-standard techniques such as electron probe microanalysis (EPMA). Here we examine chromite. As one of the first phases to crystallize in mantle rocks, it is a useful indicator of upper mantle magmatic conditions in rocks that have been sampled by kimberlites. In addition, chromite does not alter easily from chemical and physical weathering processes. As such, chromite is a useful kimberlite indicator mineral in diamond exploration. We present correlations between crystal structure (unit cell) and chemical composition of chromite, (Fe,Mg)[Cr, Al]2O4, using correlated μXRD and EPMA data for 133 chromites from a three source locations: Two kimberlite sources and one non-kimberlitic source from an Archean granite/greenstone terrain. Quantitative analysis was performed using Electron Probe Microanalysis (EPMA) at Mineral Services, South Africa, prior to the loan of the samples. Randomly-oriented chromite grains, approximately 500 μm in diameter, were analyzed as previously mounted for EPMA. Micro X-ray-diffraction was performed using a Bruker D8-Discover Diffractometer, with θ-θ geometry, with CuKα radiation, operating at 40 kV and 40 mA, with nominal beam diameter of 500 μm. The data were collected in omega scan mode. Two dimensional General Area Detector Diffraction System (GADDS) images were collected for 20 minutes per image, and integrated to produce one-dimensional plots of intensity versus 2θ, for subsequent unit cell refinement using CELREF. Although all samples in this study were considered to be 'chromite', a plot of Cr/(Cr+Al) versus Fe2+/(Fe2++Mg) shows extensive substitution among four dominant members: chromite (FeCr2O4), magnesio-chromite (MgCr2O4), spinel (MgAl2O4), and hercynite (FeAl2O4), where Mg and Fe2+ substitute for one another on the tetrahedral site, and Cr and Al substitute for one another on the

  6. Comparative Analysis of Bracket Slot Dimensions Evaluating Different Manufacturing Techniques

    DTIC Science & Technology

    2015-04-24

    Dimensions Evaluating Different Manufacturing Techniques JS. A. DeMeo APPROVED: fk_ 4 ’__/ . .S, M.S., Supervising Professor ,....-------__ ’ - ~l!i...manuscript entitled : "Comparative Analysis of Bracket Slot Dimensions Evaluating Different Manufactur ing Techniques" is appropriately acknowledged and...Harm s Way TITLE Comparative Analysis of Bracket Slot Dimensions Evaluating Different Manufacturing Techniques A THESIS Presented to the

  7. EMERGY ANALYSIS AND ECONOMIC ANALYSIS A COMPARATIVE STUDY

    EPA Science Inventory

    Our mission at USEPA is to protect human health and safeguard the natural environment. We aim to base our environmental regulations and policies on sound scientific and, where appropriate, economic analyses. Although EPA has conducted analysis of the impact of regulations on ...

  8. EMERGY ANALYSIS AND ECONOMIC ANALYSIS A COMPARATIVE STUDY

    EPA Science Inventory

    Our mission at USEPA is to protect human health and safeguard the natural environment. We aim to base our environmental regulations and policies on sound scientific and, where appropriate, economic analyses. Although EPA has conducted analysis of the impact of regulations on ...

  9. Crystal chemical and quantum chemical studies of Ba(Sr)-Nb oxide compounds

    NASA Technical Reports Server (NTRS)

    Zubkov, V. G.; Turzhevsky, S. A.; Pereliaev, V. A.; Liechtenstein, A. I.; Gubanov, V. A.

    1990-01-01

    The information available on the BaO(SrO)-NbO-NbO2 system with the niobium atom in the lower oxidation degree is very limited. Very few compounds have been found previously in this system. They are BaNbO3, SrxNbO3(0,7=x=1), Ba2Nb2O9, SrNb8O14; and some suggestions on the BaNb8O14 existence have been made also. At the same time Nb-based oxide compounds could be quite interesting in the search of new noncopper high T(sub c) superconductors Researchers studied Ba(Sr) NbxO2x-2 and Ba2(Sr2)-NbxO2x-1 compositions in the phase diagram of BaO(SrO)-NbO-NbO2 system. The synthesis of the materials was carried out in vacuum at the temperatures of 1000 to 1500 C. Barium carbonate and niobium pentoxide were used as initial components. X-ray analysis was carried out.

  10. Investigations of high mobility single crystal chemical vapor deposition diamond for radiotherapy photon beam monitoring

    SciTech Connect

    Tromson, D.; Descamps, C.; Tranchant, N.; Bergonzo, P.; Nesladek, M.; Isambert, A.

    2008-03-01

    The intrinsic properties of diamond make this material theoretically very suitable for applications in medical physics. Until now ionization chambers have been fabricated from natural stones and are commercialized by PTW, but their fairly high costs and long delivery times have often limited their use in hospital. The properties of commercialized intrinsic polycrystalline diamond were investigated in the past by many groups. The results were not completely satisfactory due to the nature of the polycrystalline material itself. In contrast, the recent progresses in the growth of high mobility single crystal synthetic diamonds prepared by chemical vapor deposition (CVD) technique offer new alternatives. In the framework of the MAESTRO project (Methods and Advanced Treatments and Simulations for Radio Oncology), the CEA-LIST is studying the potentialities of synthetic diamond for new techniques of irradiation such as intensity modulated radiation therapy. In this paper, we present the growth and characteristics of single crystal diamond prepared at CEA-LIST in the framework of the NoRHDia project (Novel Radiation Hard CVD Diamond Detector for Hadrons Physics), as well as the investigations of high mobility single crystal CVD diamond for radiotherapy photon beam monitoring: dosimetric analysis performed with the single crystal diamond detector in terms of stability and repeatability of the response signal, signal to noise ratio, response speed, linearity of the signal versus the absorbed dose, and dose rate. The measurements performed with photon beams using radiotherapy facilities demonstrate that single crystal CVD diamond is a good alternative for air ionization chambers for beam quality control.

  11. Structural and crystal chemical properties of rare-earth titanate pyrochlores

    SciTech Connect

    Farmer, James Matthew; Boatner, Lynn A; Chakoumakos, Bryan C; Du, Mao-Hua; Lance, Michael J; Rawn, Claudia J.; Bryan, Jeff C.

    2014-01-01

    Rare-earth titanates, RE2Ti2O7 (where RE = a rare-earth) with the pyrochlore structure continue to be investigated for use as potential stable host materials for nuclear and actinide-rich wastes. Accordingly, the present work is directed towards the elucidation of the fundamental structural, physical, and thermochemical properties of this class of compounds. Single-crystals of the rare earth pyrochlores were synthesized using a high-temperature flux technique and were subsequently characterized using single-crystal X-ray diffraction. The cubic lattice parameters display an approximately linear correlation with the RE-site cation radius. Theoretical calculations of the lattice constants and bond lengths of the subject materials were carried out using density functional theory, and the results are compared to the experimental values. The Sm and Eu titanates exhibit a covalency increase between the REO8 and TiO6 polyhedra resulting in a deviation from the increasing linear lattice parameter through the transition series. Gd2Ti2O7 with the 4f7 half-filled f-orbital Gd3+ sub-shell exhibits the lowest 48f oxygen positional parameter. The coefficient of thermal expansion for the rare-earth titanate series is approximately linear, and it has a range of 10.1 11.2 x 10-6 C-1. Raman spectroscopy indicated that the ~530 cm-1 peak associated with the Ti-O stretching mode follows a general trend of decreasing frequency with increasing RE reduced mass.

  12. The Constant Comparative Analysis Method Outside of Grounded Theory

    ERIC Educational Resources Information Center

    Fram, Sheila M.

    2013-01-01

    This commentary addresses the gap in the literature regarding discussion of the legitimate use of Constant Comparative Analysis Method (CCA) outside of Grounded Theory. The purpose is to show the strength of using CCA to maintain the emic perspective and how theoretical frameworks can maintain the etic perspective throughout the analysis. My…

  13. A Comparative Analysis of Charter Schools and Traditional Public Schools

    ERIC Educational Resources Information Center

    Smith, Jodi Renee Abbott

    2014-01-01

    The focus of this descriptive research study was to compare charter and traditional public schools on the academic knowledge of fifth grade students as measured by Arizona's Instrument to Measure Standards (AIMS) in a suburb of a large southwestern city. This analysis also compared charter and traditional public schools on AYP status. It was…

  14. Optical and crystal-chemical changes in aquamarines and yellow beryls from Thanh Hoa province, Vietnam induced by heat treatment

    NASA Astrophysics Data System (ADS)

    Fridrichová, Jana; Bačík, Peter; Rusinová, Petra; Antal, Peter; Škoda, Radek; Bizovská, Valéria; Miglierini, Marcel

    2015-04-01

    Optical and crystal-chemical changes in two beryl varieties after the heat treatment were determined using a wide spectrum of analytical methods. Studied aquamarines are generally more enriched in Fe (up to 0.25 apfu) and alkali (up to 0.08 apfu) than yellow beryls (up to 0.07 apfu Fe, up to 0.04 apfu alkali). The determined c/ a ratio of 0.997-0.998 classified all our studied beryls as "normal" beryls. While no crystal structure changes were observed in samples heated to 700 °C, those heated to 900 and 1,100 °C exhibited cracks and fissures. Reduced Fe occurred in samples heated between 300 and 700 °C, and subsequent oxidation from 900 to 1,100 °C induced changes in their colour and clarity. The Fe-bearing beryl colour is controlled by the position of the absorption edge and the presence of a broad band attributed to Fe2+ in the NIR region. Blue colour results from the absorption edge located deeper in the UV region and the presence of broad band in the NIR region. Shift of absorption edge to the visible region at the presence of the broad band gives a yellow colour. Although our studied beryls are enriched in H2O I molecule due to their low alkali content, the H2O II molecule is also present. The following two dehydration processes were observed: (1) release of one double-coordinating H2O II molecule at 300-500 °C and (2) total dehydration at 900-1,100 °C. The observed cracks and fissures likely resulted from channel water release in large beryl crystals.

  15. Alfresco—A Workbench for Comparative Genomic Sequence Analysis

    PubMed Central

    Jareborg, Niclas; Durbin, Richard

    2000-01-01

    Comparative analysis of genomic sequences provides a powerful tool for identifying regions of potential biologic function; by comparing corresponding regions of genomes from suitable species, protein coding or regulatory regions can be identified by their homology. This requires the use of several specific types of computational analysis tools. Many programs exist for these types of analysis; not many exist for overall view/control of the results, which is necessary for large-scale genomic sequence analysis. Using Java, we have developed a new visualization tool that allows effective comparative genome sequence analysis. The program handles a pair of sequences from putatively homologous regions in different species. Results from various different existing external analysis programs, such as database searching, gene prediction, repeat masking, and alignment programs, are visualized and used to find corresponding functional sequence domains in the two sequences. The user interacts with the program through a graphic display of the genome regions, in which an independently scrollable and zoomable symbolic representation of the sequences is shown. As an example, the analysis of two unannotated orthologous genomic sequences from human and mouse containing parts of the UTY locus is presented. PMID:10958633

  16. Comparative analysis of genomic signal processing for microarray data clustering.

    PubMed

    Istepanian, Robert S H; Sungoor, Ala; Nebel, Jean-Christophe

    2011-12-01

    Genomic signal processing is a new area of research that combines advanced digital signal processing methodologies for enhanced genetic data analysis. It has many promising applications in bioinformatics and next generation of healthcare systems, in particular, in the field of microarray data clustering. In this paper we present a comparative performance analysis of enhanced digital spectral analysis methods for robust clustering of gene expression across multiple microarray data samples. Three digital signal processing methods: linear predictive coding, wavelet decomposition, and fractal dimension are studied to provide a comparative evaluation of the clustering performance of these methods on several microarray datasets. The results of this study show that the fractal approach provides the best clustering accuracy compared to other digital signal processing and well known statistical methods.

  17. CRITICA: coding region identification tool invoking comparative analysis

    NASA Technical Reports Server (NTRS)

    Badger, J. H.; Olsen, G. J.; Woese, C. R. (Principal Investigator)

    1999-01-01

    Gene recognition is essential to understanding existing and future DNA sequence data. CRITICA (Coding Region Identification Tool Invoking Comparative Analysis) is a suite of programs for identifying likely protein-coding sequences in DNA by combining comparative analysis of DNA sequences with more common noncomparative methods. In the comparative component of the analysis, regions of DNA are aligned with related sequences from the DNA databases; if the translation of the aligned sequences has greater amino acid identity than expected for the observed percentage nucleotide identity, this is interpreted as evidence for coding. CRITICA also incorporates noncomparative information derived from the relative frequencies of hexanucleotides in coding frames versus other contexts (i.e., dicodon bias). The dicodon usage information is derived by iterative analysis of the data, such that CRITICA is not dependent on the existence or accuracy of coding sequence annotations in the databases. This independence makes the method particularly well suited for the analysis of novel genomes. CRITICA was tested by analyzing the available Salmonella typhimurium DNA sequences. Its predictions were compared with the DNA sequence annotations and with the predictions of GenMark. CRITICA proved to be more accurate than GenMark, and moreover, many of its predictions that would seem to be errors instead reflect problems in the sequence databases. The source code of CRITICA is freely available by anonymous FTP (rdp.life.uiuc.edu in/pub/critica) and on the World Wide Web (http:/(/)rdpwww.life.uiuc.edu).

  18. CRITICA: coding region identification tool invoking comparative analysis

    NASA Technical Reports Server (NTRS)

    Badger, J. H.; Olsen, G. J.; Woese, C. R. (Principal Investigator)

    1999-01-01

    Gene recognition is essential to understanding existing and future DNA sequence data. CRITICA (Coding Region Identification Tool Invoking Comparative Analysis) is a suite of programs for identifying likely protein-coding sequences in DNA by combining comparative analysis of DNA sequences with more common noncomparative methods. In the comparative component of the analysis, regions of DNA are aligned with related sequences from the DNA databases; if the translation of the aligned sequences has greater amino acid identity than expected for the observed percentage nucleotide identity, this is interpreted as evidence for coding. CRITICA also incorporates noncomparative information derived from the relative frequencies of hexanucleotides in coding frames versus other contexts (i.e., dicodon bias). The dicodon usage information is derived by iterative analysis of the data, such that CRITICA is not dependent on the existence or accuracy of coding sequence annotations in the databases. This independence makes the method particularly well suited for the analysis of novel genomes. CRITICA was tested by analyzing the available Salmonella typhimurium DNA sequences. Its predictions were compared with the DNA sequence annotations and with the predictions of GenMark. CRITICA proved to be more accurate than GenMark, and moreover, many of its predictions that would seem to be errors instead reflect problems in the sequence databases. The source code of CRITICA is freely available by anonymous FTP (rdp.life.uiuc.edu in/pub/critica) and on the World Wide Web (http:/(/)rdpwww.life.uiuc.edu).

  19. Computational Methods for the Analysis of Array Comparative Genomic Hybridization

    PubMed Central

    Chari, Raj; Lockwood, William W.; Lam, Wan L.

    2006-01-01

    Array comparative genomic hybridization (array CGH) is a technique for assaying the copy number status of cancer genomes. The widespread use of this technology has lead to a rapid accumulation of high throughput data, which in turn has prompted the development of computational strategies for the analysis of array CGH data. Here we explain the principles behind array image processing, data visualization and genomic profile analysis, review currently available software packages, and raise considerations for future software development. PMID:17992253

  20. Gap Analysis Comparing LLNL ISMS and ISO 14001

    SciTech Connect

    Doerr, T B

    2004-08-09

    A gap analysis was conducted comparing the Lawrence Livermore National Laboratory (LLNL) Integrated Safety Management System (ISMS) with the international standard ISO 14001 Environmental Management System and with Department of Energy (DOE) Order 450.1. This analysis was accomplished as part of LLNL's assessment of the impacts of adopting DOE Order 450.1 and comprises a portion of its continuous improvement efforts under ISMS.

  1. Quantifying garnet-melt trace element partitioning using lattice-strain theory: new crystal-chemical and thermodynamic constraints

    NASA Astrophysics Data System (ADS)

    van Westrenen, Wim; Draper, David S.

    2007-12-01

    Many geochemical models of major igneous differentiation events on the Earth, the Moon, and Mars invoke the presence of garnet or its high-pressure majoritic equivalent as a residual phase, based on its ability to fractionate critical trace element pairs (Lu/Hf, U/Th, heavy REE/light REE). As a result, quantitative descriptions of mid-ocean ridge and hot spot magmatism, and lunar, martian, and terrestrial magma oceans require knowledge of garnet-melt partition coefficients over a wide range of conditions. In this contribution, we present new crystal-chemical and thermodynamic constraints on the partitioning of rare earth elements (REE), Y and Sc between garnet and anhydrous silicate melt as a function of pressure ( P), temperature ( T), and composition ( X). Our approach is based on the interpretation of experimentally determined values of partition coefficients D using lattice-strain theory. In this and a companion paper (Draper and van Westrenen this issue) we derive new predictive equations for the ideal ionic radius of the dodecahedral garnet X-site, r 0(3+), its apparent Young’s modulus E X(3+), and the strain-free partition coefficient D 0(3+) for a fictive REE element J of ionic radius r 0(3+). The new calibrations remedy several shortcomings of earlier lattice-strain based attempts to model garnet-melt partitioning. A hitherto irresolvable temperature effect on r 0(3+) is identified, as is a pronounced decrease in E X(3+) as Al on the garnet Y site is progressively replaced by quadruvalent cations (Si, Ti) as pressure and garnet majorite content increase. D 0(3+) can be linked to the free energy of fusion of a hypothetical rare-earth garnet component JFe2Al3Si2O12 through simple activity-composition relations. By combining the three lattice-strain parameter models, garnet-anhydrous melt and majorite-anhydrous melt D values for the REE, Y and Sc can be predicted from P, T, garnet major element composition, and melt iron content at pressures from 2.5 25 GPa

  2. Tools for comparative protein structure modeling and analysis.

    PubMed

    Eswar, Narayanan; John, Bino; Mirkovic, Nebojsa; Fiser, Andras; Ilyin, Valentin A; Pieper, Ursula; Stuart, Ashley C; Marti-Renom, Marc A; Madhusudhan, M S; Yerkovich, Bozidar; Sali, Andrej

    2003-07-01

    The following resources for comparative protein structure modeling and analysis are described (http://salilab.org): MODELLER, a program for comparative modeling by satisfaction of spatial restraints; MODWEB, a web server for automated comparative modeling that relies on PSI-BLAST, IMPALA and MODELLER; MODLOOP, a web server for automated loop modeling that relies on MODELLER; MOULDER, a CPU intensive protocol of MODWEB for building comparative models based on distant known structures; MODBASE, a comprehensive database of annotated comparative models for all sequences detectably related to a known structure; MODVIEW, a Netscape plugin for Linux that integrates viewing of multiple sequences and structures; and SNPWEB, a web server for structure-based prediction of the functional impact of a single amino acid substitution.

  3. Comparative and Familial Analysis of Handedness in Great Apes

    ERIC Educational Resources Information Center

    Hopkins, William D.

    2006-01-01

    Historically, population-level handedness has been considered a hallmark of human evolution. Whether nonhuman primates exhibit population-level handedness remains a topic of considerable debate. This paper summarizes published data on handedness in great apes. Comparative analysis indicated that chimpanzees and bonobos show population-level right…

  4. Comparing Theories of Language Learning Strategies: A Confirmatory Factor Analysis.

    ERIC Educational Resources Information Center

    Hsiao, Tsung-Yuan; Oxford, Rebecca

    2002-01-01

    Compared classification theories of language learning strategies. Results from confirmatory factor analysis of data measured by the English-as-a-Second/Foreign-Language (ESL/EFL) version of the Strategy Inventory for Language Learning and collected from 517 college EFL learners are discussed. Suggests other possible approaches to strategy…

  5. A Comparative Analysis of Three Unique Theories of Organizational Learning

    ERIC Educational Resources Information Center

    Leavitt, Carol C.

    2011-01-01

    The purpose of this paper is to present three classical theories on organizational learning and conduct a comparative analysis that highlights their strengths, similarities, and differences. Two of the theories -- experiential learning theory and adaptive -- generative learning theory -- represent the thinking of the cognitive perspective, while…

  6. Comparative and Familial Analysis of Handedness in Great Apes

    ERIC Educational Resources Information Center

    Hopkins, William D.

    2006-01-01

    Historically, population-level handedness has been considered a hallmark of human evolution. Whether nonhuman primates exhibit population-level handedness remains a topic of considerable debate. This paper summarizes published data on handedness in great apes. Comparative analysis indicated that chimpanzees and bonobos show population-level right…

  7. A Framework for the Comparative Analysis of Farm Organizations.

    ERIC Educational Resources Information Center

    Molnar, Joseph J.

    Presenting a model for the comparative analysis of farm organizations, this paper analyzes the farm firm as a complex organization; identifies key structural dimensions of an agricultural production unit; and reviews various organizational perspectives for their utility in understanding and explaining the behavior of farm operations and farm…

  8. A Comparative Analysis of Method Books for Class Jazz Instruction

    ERIC Educational Resources Information Center

    Watson, Kevin E.

    2017-01-01

    The purpose of this study was to analyze and compare instructional topics and teaching approaches included in selected class method books for jazz pedagogy through content analysis methodology. Frequency counts for the number of pages devoted to each defined instructional content category were compiled and percentages of pages allotted to each…

  9. A comparative analysis of protected area planning and management frameworks

    Treesearch

    Per Nilsen; Grant Tayler

    1997-01-01

    A comparative analysis of the Recreation Opportunity Spectrum (ROS), Limits of Acceptable Change (LAC), a Process for Visitor Impact Management (VIM), Visitor Experience and Resource Protection (VERP), and the Management Process for Visitor Activities (known as VAMP) decision frameworks examines their origins; methodology; use of factors, indicators, and standards;...

  10. A Framework for the Comparative Analysis of Farm Organizations.

    ERIC Educational Resources Information Center

    Molnar, Joseph J.

    Presenting a model for the comparative analysis of farm organizations, this paper analyzes the farm firm as a complex organization; identifies key structural dimensions of an agricultural production unit; and reviews various organizational perspectives for their utility in understanding and explaining the behavior of farm operations and farm…

  11. Comparative analysis and visualization of multiple collinear genomes

    PubMed Central

    2012-01-01

    Background Genome browsers are a common tool used by biologists to visualize genomic features including genes, polymorphisms, and many others. However, existing genome browsers and visualization tools are not well-suited to perform meaningful comparative analysis among a large number of genomes. With the increasing quantity and availability of genomic data, there is an increased burden to provide useful visualization and analysis tools for comparison of multiple collinear genomes such as the large panels of model organisms which are the basis for much of the current genetic research. Results We have developed a novel web-based tool for visualizing and analyzing multiple collinear genomes. Our tool illustrates genome-sequence similarity through a mosaic of intervals representing local phylogeny, subspecific origin, and haplotype identity. Comparative analysis is facilitated through reordering and clustering of tracks, which can vary throughout the genome. In addition, we provide local phylogenetic trees as an alternate visualization to assess local variations. Conclusions Unlike previous genome browsers and viewers, ours allows for simultaneous and comparative analysis. Our browser provides intuitive selection and interactive navigation about features of interest. Dynamic visualizations adjust to scale and data content making analysis at variable resolutions and of multiple data sets more informative. We demonstrate our genome browser for an extensive set of genomic data sets composed of almost 200 distinct mouse laboratory strains. PMID:22536897

  12. Comparative Analysis of Cryptography Library in IoT

    NASA Astrophysics Data System (ADS)

    Kumar, Uday; Borgohain, Tuhin; Sanyal, Sugata

    2015-05-01

    The paper aims to do a survey along with a comparative analysis of the various cryptography libraries that are applicable in the field of Internet of Things (IoT). The first half of the paper briefly introduces the various cryptography libraries available in the field of cryptography along with a list of all the algorithms contained within the libraries. The second half of the paper deals with cryptography libraries specifically aimed for application in the field of Internet of Things. The various libraries and their performance analysis listed down in this paper are consolidated from various sources with the aim of providing a single comprehensive repository for reference to the various cryptography libraries and the comparative analysis of their features in IoT.

  13. MetaComp: comprehensive analysis software for comparative meta-omics including comparative metagenomics.

    PubMed

    Zhai, Peng; Yang, Longshu; Guo, Xiao; Wang, Zhe; Guo, Jiangtao; Wang, Xiaoqi; Zhu, Huaiqiu

    2017-10-02

    During the past decade, the development of high throughput nucleic sequencing and mass spectrometry analysis techniques have enabled the characterization of microbial communities through metagenomics, metatranscriptomics, metaproteomics and metabolomics data. To reveal the diversity of microbial communities and interactions between living conditions and microbes, it is necessary to introduce comparative analysis based upon integration of all four types of data mentioned above. Comparative meta-omics, especially comparative metageomics, has been established as a routine process to highlight the significant differences in taxon composition and functional gene abundance among microbiota samples. Meanwhile, biologists are increasingly concerning about the correlations between meta-omics features and environmental factors, which may further decipher the adaptation strategy of a microbial community. We developed a graphical comprehensive analysis software named MetaComp comprising a series of statistical analysis approaches with visualized results for metagenomics and other meta-omics data comparison. This software is capable to read files generated by a variety of upstream programs. After data loading, analyses such as multivariate statistics, hypothesis testing of two-sample, multi-sample as well as two-group sample and a novel function-regression analysis of environmental factors are offered. Here, regression analysis regards meta-omic features as independent variable and environmental factors as dependent variables. Moreover, MetaComp is capable to automatically choose an appropriate two-group sample test based upon the traits of input abundance profiles. We further evaluate the performance of its choice, and exhibit applications for metagenomics, metaproteomics and metabolomics samples. MetaComp, an integrative software capable for applying to all meta-omics data, originally distills the influence of living environment on microbial community by regression analysis

  14. BLAT-based comparative analysis for transposable elements: BLATCAT.

    PubMed

    Lee, Sangbum; Oh, Sumin; Kang, Keunsoo; Han, Kyudong

    2014-01-01

    The availability of several whole genome sequences makes comparative analyses possible. In primate genomes, the priority of transposable elements (TEs) is significantly increased because they account for ~45% of the primate genomes, they can regulate the gene expression level, and they are associated with genomic fluidity in their host genomes. Here, we developed the BLAST-like alignment tool (BLAT) based comparative analysis for transposable elements (BLATCAT) program. The BLATCAT program can compare specific regions of six representative primate genome sequences (human, chimpanzee, gorilla, orangutan, gibbon, and rhesus macaque) on the basis of BLAT and simultaneously carry out RepeatMasker and/or Censor functions, which are widely used Windows-based web-server functions to detect TEs. All results can be stored as a HTML file for manual inspection of a specific locus. BLATCAT will be very convenient and efficient for comparative analyses of TEs in various primate genomes.

  15. Dermoscopy analysis of RGB-images based on comparative features

    NASA Astrophysics Data System (ADS)

    Myakinin, Oleg O.; Zakharov, Valery P.; Bratchenko, Ivan A.; Artemyev, Dmitry N.; Neretin, Evgeny Y.; Kozlov, Sergey V.

    2015-09-01

    In this paper, we propose an algorithm for color and texture analysis for dermoscopic images of human skin based on Haar wavelets, Local Binary Patterns (LBP) and Histogram Analysis. This approach is a modification of «7-point checklist» clinical method. Thus, that is an "absolute" diagnostic method because one is using only features extracted from tumor's ROI (Region of Interest), which can be selected manually and/or using a special algorithm. We propose additional features extracted from the same image for comparative analysis of tumor and healthy skin. We used Euclidean distance, Cosine similarity, and Tanimoto coefficient as comparison metrics between color and texture features extracted from tumor's and healthy skin's ROI separately. A classifier for separating melanoma images from other tumors has been built by SVM (Support Vector Machine) algorithm. Classification's errors with and without comparative features between skin and tumor have been analyzed. Significant increase of recognition quality with comparative features has been demonstrated. Moreover, we analyzed two modes (manual and automatic) for ROI selecting on tumor and healthy skin areas. We have reached 91% of sensitivity using comparative features in contrast with 77% of sensitivity using the only "absolute" method. The specificity was the invariable (94%) in both cases.

  16. Evaluating the Risks of Clinical Research: Direct Comparative Analysis

    PubMed Central

    Abdoler, Emily; Roberson-Nay, Roxann; Pine, Daniel S.; Wendler, David

    2014-01-01

    Abstract Objectives: Many guidelines and regulations allow children and adolescents to be enrolled in research without the prospect of clinical benefit when it poses minimal risk. However, few systematic methods exist to determine when research risks are minimal. This situation has led to significant variation in minimal risk judgments, raising concern that some children are not being adequately protected. To address this concern, we describe a new method for implementing the widely endorsed “risks of daily life” standard for minimal risk. This standard defines research risks as minimal when they do not exceed the risks posed by daily life activities or routine examinations. Methods: This study employed a conceptual and normative analysis, and use of an illustrative example. Results: Different risks are composed of the same basic elements: Type, likelihood, and magnitude of harm. Hence, one can compare the risks of research and the risks of daily life by comparing the respective basic elements with each other. We use this insight to develop a systematic method, direct comparative analysis, for implementing the “risks of daily life” standard for minimal risk. The method offers a way of evaluating research procedures that pose the same types of risk as daily life activities, such as the risk of experiencing anxiety, stress, or other psychological harm. We thus illustrate how direct comparative analysis can be applied in practice by using it to evaluate whether the anxiety induced by a respiratory CO2 challenge poses minimal or greater than minimal risks in children and adolescents. Conclusions: Direct comparative analysis is a systematic method for applying the “risks of daily life” standard for minimal risk to research procedures that pose the same types of risk as daily life activities. It thereby offers a method to protect children and adolescents in research, while ensuring that important studies are not blocked because of unwarranted concerns about

  17. Comparative genomic analysis of eutherian interferon-γ-inducible GTPases.

    PubMed

    Premzl, Marko

    2012-11-01

    The interferon-γ-inducible GTPases, IFGGs, are intracellular proteins involved in immune response against pathogens. A comprehensive comparative genomic review and analysis of eutherian IFGGs was carried out using public genomic sequences. The 64 eutherian IFGG genes were examined in detail and annotated. The eutherian IFGG promoter types were first catalogued followed by a phylogenetic analysis of eutherian IFGGs, which described five major IFGG clusters. The patterns of differential gene expansions and protein regions that may regulate IFGG catalytic features suggested a new classification of eutherian IFGGs. This mini-review has also provided new tests of reliability of public genomic sequences as well as tests of protein molecular evolution.

  18. Comparative analysis of two DOPA dioxygenases from Phytolacca Americana.

    PubMed

    Takahashi, Kana; Yoshida, Kazuko; Sakuta, Masaaki

    2015-05-01

    The comparative analysis of two Phytolacca americana DOPA dioxygenases (PaDOD1 and PaDOD2) that may be involved in betalain biosynthesis was carried out. The recombinant protein of PaDOD catalyzed the conversion of DOPA to betalamic acid, whereas DOD activity was not detected in PaDOD2 in vitro. The role of DOD genes is discussed in the evolutionary context using phylogenetic analysis, suggesting that DOD might have been duplicated early in evolution and that accumulation of base substitutions could have led to the different characteristics of DODs within the betalain-producing Caryophyllales.

  19. The dog genome: survey sequencing and comparative analysis.

    PubMed

    Kirkness, Ewen F; Bafna, Vineet; Halpern, Aaron L; Levy, Samuel; Remington, Karin; Rusch, Douglas B; Delcher, Arthur L; Pop, Mihai; Wang, Wei; Fraser, Claire M; Venter, J Craig

    2003-09-26

    A survey of the dog genome sequence (6.22 million sequence reads; 1.5x coverage) demonstrates the power of sample sequencing for comparative analysis of mammalian genomes and the generation of species-specific resources. More than 650 million base pairs (>25%) of dog sequence align uniquely to the human genome, including fragments of putative orthologs for 18,473 of 24,567 annotated human genes. Mutation rates, conserved synteny, repeat content, and phylogeny can be compared among human, mouse, and dog. A variety of polymorphic elements are identified that will be valuable for mapping the genetic basis of diseases and traits in the dog.

  20. Comparative Genomics via Wavelet Analysis for Closely Related Bacteria

    NASA Astrophysics Data System (ADS)

    Song, Jiuzhou; Ware, Tony; Liu, Shu-Lin; Surette, M.

    2004-12-01

    Comparative genomics has been a valuable method for extracting and extrapolating genome information among closely related bacteria. The efficiency of the traditional methods is extremely influenced by the software method used. To overcome the problem here, we propose using wavelet analysis to perform comparative genomics. First, global comparison using wavelet analysis gives the difference at a quantitative level. Then local comparison using keto-excess or purine-excess plots shows precise positions of inversions, translocations, and horizontally transferred DNA fragments. We firstly found that the level of energy spectra difference is related to the similarity of bacteria strains; it could be a quantitative index to describe the similarities of genomes. The strategy is described in detail by comparisons of closely related strains: S.typhi CT18, S.typhi Ty2, S.typhimurium LT2, H.pylori 26695, and H.pylori J99.

  1. Comparative visual analysis of 3D urban wind simulations

    NASA Astrophysics Data System (ADS)

    Röber, Niklas; Salim, Mohamed; Grawe, David; Leitl, Bernd; Böttinger, Michael; Schlünzen, Heinke

    2016-04-01

    Climate simulations are conducted in large quantity for a variety of different applications. Many of these simulations focus on global developments and study the Earth's climate system using a coupled atmosphere ocean model. Other simulations are performed on much smaller regional scales, to study very small fine grained climatic effects. These microscale climate simulations pose similar, yet also different, challenges for the visualization and the analysis of the simulation data. Modern interactive visualization and data analysis techniques are very powerful tools to assist the researcher in answering and communicating complex research questions. This presentation discusses comparative visualization for several different wind simulations, which were created using the microscale climate model MITRAS. The simulations differ in wind direction and speed, but are all centered on the same simulation domain: An area of Hamburg-Wilhelmsburg that hosted the IGA/IBA exhibition in 2013. The experiments contain a scenario case to analyze the effects of single buildings, as well as examine the impact of the Coriolis force within the simulation. The scenario case is additionally compared with real measurements from a wind tunnel experiment to ascertain the accuracy of the simulation and the model itself. We also compare different approaches for tree modeling and evaluate the stability of the model. In this presentation, we describe not only our workflow to efficiently and effectively visualize microscale climate simulation data using common 3D visualization and data analysis techniques, but also discuss how to compare variations of a simulation and how to highlight the subtle differences in between them. For the visualizations we use a range of different 3D tools that feature techniques for statistical data analysis, data selection, as well as linking and brushing.

  2. Experimental and crystal chemical study of the basalt-eclogite transition in Mars and implications for martian magmatism

    NASA Astrophysics Data System (ADS)

    Papike, J. J.; Burger, P. V.; Shearer, C. K.; McCubbin, F. M.

    2013-03-01

    This paper represents the start of a campaign to identify possible source regions for pyroxene-phyric "enriched" and "depleted" martian basalts using high pressure studies on martian meteorite compositions that represent liquids or near liquids. Our first experiments focus upon mineralogical and crystal chemical aspects of the basalt-eclogite transformation on Mars. It is anticipated that like Earth, eclogites are not the dominant upper mantle assemblage. However, like Earth they may be important hosts for P, Cl, F, OH, Ti, REE, Sr, Y, high-field-strength elements, Hf, and Zr in the upper mantle. This initial experimental study evaluates the major and trace element crystal chemistry of potential martian eclogite assemblages using a martian melt composition (QUE 94201). This composition is appropriate for this study because it is evolved, so it is pyroxene-phyric, contains abundant phosphate, which is important for storage of REE, and is very well studied. In the high pressure experiments, garnet and omphacitic pyroxene are the dominant phases. The garnet has a compositional range from Al56.9Gr + An24.6Py18.5 to Al41.5Gr + An28.1Py30.4 to Al40.3Gr + An22.6Py37.1 (where Al = almandine, Gr+An = grossular + andradite, and Py = Pyrope) and the pyroxene has jadeite and acmite components of up to 26.0 and 9.9%, respectively. The garnet is enriched in REE over omphacite; this is especially true for the HREE which likely remain sequestered in residual garnet during melting. This observation suggests that garnet may play a key role in producing the relatively flat REE patterns of enriched martian basalts. The prime substitution couple that incorporates REE into garnet is: REE3+X Site + Mg2+Y Site ↔ R2+X Site + Al3+Y Site, where R2+ = Ca, Mn2+, Fe2+, and Mg. This is a very effective couple that accounts for both charge balance and ionic size restrictions in individual sites. The prime substitution couple that incorporates REE into omphacite is: REE3+M2 Site + Na1+M2 Site

  3. In situ crystal chemical study of solid diamond inclusions from Quaternary alluvial deposit in the Siberian craton

    NASA Astrophysics Data System (ADS)

    Dera, P. K.; Manghnani, M. H.; Hushur, A.; Sobolev, N. V.; Logvinova, A. M.; Newville, M.; Lanzirotti, A.

    2013-12-01

    Kimberlites belong to rare rock type available only within the Earth's cratonic areas and have been a subject of detailed studies because of the great depth of their origin in the mantle. Kimberlitic diamonds often contain pristine inclusions derived from significant depths with different histories of their origins. Many of kimberlitic diamonds were formed in ultramafic (peridotitic) and mafic (eclogitic) environments of the upper mantle. Thus far only a handful of comprehensive in situ studies including single-crystal X-ray diffraction characterization of pristine diamond solid inclusions have been reported (e.g. Kunz et al. 2001, Nestola et al. 2011). In this study five single-crystal solid inclusions from diamonds found in the Quaternary alluvial deposit in NW of the Siberian craton have been investigated using a combination of in situ single-crystal X-ray diffraction, Raman spectroscopy, synchrotron X-ray microfluorescence and X-ray Absorption Near Edge Spectroscopy (XANES). The grains were identified to be a suite of major upper mantle minerals including olivine, enstatite orthopyroxene (opx), C2/c omphacite clinopyroxene (cpx) and majoritic garnet (two grains), indicating eclogitic origin. All five inclusions are chemically homogeneous, do not show compositional zoning, and exhibit very similar major element chemistry, with significant amounts of Mn2+, Ni2+ and Cr3+ incorporated into the crystal structures, suggesting common geologic origin. All samples were studied in situ, while still embedded in the diamond crystals. High quality single-crystal X-ray diffraction data was collected at the Advanced Photon Source, Argonne National Laboratory to reveal details of the crystal structures and provide crystal chemical information. Some of the structural characteristics of the solid inclusions were found to be fairly uncommon, e.g. the orthoenstatite exhibits an unusually high Ca2+ content (Carlson et al. 1988), and omphacite occurs as the less common C2/c

  4. Comparing methods for analysis of biomedical hyperspectral image data

    NASA Astrophysics Data System (ADS)

    Leavesley, Silas J.; Sweat, Brenner; Abbott, Caitlyn; Favreau, Peter F.; Annamdevula, Naga S.; Rich, Thomas C.

    2017-02-01

    Over the past 2 decades, hyperspectral imaging technologies have been adapted to address the need for molecule-specific identification in the biomedical imaging field. Applications have ranged from single-cell microscopy to whole-animal in vivo imaging and from basic research to clinical systems. Enabling this growth has been the availability of faster, more effective hyperspectral filtering technologies and more sensitive detectors. Hence, the potential for growth of biomedical hyperspectral imaging is high, and many hyperspectral imaging options are already commercially available. However, despite the growth in hyperspectral technologies for biomedical imaging, little work has been done to aid users of hyperspectral imaging instruments in selecting appropriate analysis algorithms. Here, we present an approach for comparing the effectiveness of spectral analysis algorithms by combining experimental image data with a theoretical "what if" scenario. This approach allows us to quantify several key outcomes that characterize a hyperspectral imaging study: linearity of sensitivity, positive detection cut-off slope, dynamic range, and false positive events. We present results of using this approach for comparing the effectiveness of several common spectral analysis algorithms for detecting weak fluorescent protein emission in the midst of strong tissue autofluorescence. Results indicate that this approach should be applicable to a very wide range of applications, allowing a quantitative assessment of the effectiveness of the combined biology, hardware, and computational analysis for detecting a specific molecular signature.

  5. Comparative QSAR analysis of cyclo-oxygenase2 inhibiting drugs.

    PubMed

    Mohanapriya, Arumugam; Achuthan, Dayalan

    2012-01-01

    Cyclo-oxygenase 2 (COX2) inhibiting drugs were subjected to comparative quantitative structure activity relationship (QSAR) analysis with an attempt to derive and to understand the relationship between the biological activity and molecular descriptors by multiple regression analysis. The different drugs that inhibit cyclo-oxygenase 2 enzyme were compared instead of subjecting one drug and its derivatives to QSAR analysis. The study was conducted to look for the common structural features between the drugs which confer to a good biological activity. Based on the regression analysis the following descriptors were finalized as the components fitting best in the regression equations: Ss, SCBO, RBN, nN, SIC0, IC1, and H-055. These descriptors belong to constitution (Ss, SCBO, RBN, nN), information indices (SIC0, IC1) and atom centered fragments (H-055) category. Based on these descriptors QSAR models were generated and evaluated for best structure-activity correlation. The model generated from constitution and information indices descriptors corresponds to the essential structural features of the drugs and are found to have significant correlation with COX2 inhibiting activity. This study shall help in rational drug design and synthesis of new selective cyclo-oxygenase 2 inhibitors with predetermined affinity and activity.

  6. GATA: a graphic alignment tool for comparative sequence analysis.

    PubMed

    Nix, David A; Eisen, Michael B

    2005-01-17

    Several problems exist with current methods used to align DNA sequences for comparative sequence analysis. Most dynamic programming algorithms assume that conserved sequence elements are collinear. This assumption appears valid when comparing orthologous protein coding sequences. Functional constraints on proteins provide strong selective pressure against sequence inversions, and minimize sequence duplications and feature shuffling. For non-coding sequences this collinearity assumption is often invalid. For example, enhancers contain clusters of transcription factor binding sites that change in number, orientation, and spacing during evolution yet the enhancer retains its activity. Dot plot analysis is often used to estimate non-coding sequence relatedness. Yet dot plots do not actually align sequences and thus cannot account well for base insertions or deletions. Moreover, they lack an adequate statistical framework for comparing sequence relatedness and are limited to pairwise comparisons. Lastly, dot plots and dynamic programming text outputs fail to provide an intuitive means for visualizing DNA alignments. To address some of these issues, we created a stand alone, platform independent, graphic alignment tool for comparative sequence analysis (GATA http://gata.sourceforge.net/). GATA uses the NCBI-BLASTN program and extensive post-processing to identify all small sub-alignments above a low cut-off score. These are graphed as two shaded boxes, one for each sequence, connected by a line using the coordinate system of their parent sequence. Shading and colour are used to indicate score and orientation. A variety of options exist for querying, modifying and retrieving conserved sequence elements. Extensive gene annotation can be added to both sequences using a standardized General Feature Format (GFF) file. GATA uses the NCBI-BLASTN program in conjunction with post-processing to exhaustively align two DNA sequences. It provides researchers with a fine

  7. Comparative analysis of bio fouling microorganisms after treatment with glidarc

    NASA Astrophysics Data System (ADS)

    Hnatiuc, M.; Sabau, A.; Hnatiuc, B.; Ghita, S.

    2015-11-01

    The biofouling of the surfaces immersed in water is one of the most important problems which must be solved in the naval field. This phenomenon is amplified during the harbor operations, when the ships are stationary and there is a high density of microorganisms in the neritic area, developing the biofouling. For this reason, in order to prevent or delay the deposition of the first layers of biofouling, different methods have been used [1]. This paper presents the comparative analysis of microorganisms’ behavior obtained by using GlidArc technology for the treatment of the naval metallic surfaces [2, 3]. The main parameters identified for data processing were: the number of microorganisms shared from the point of view of sensibility to the used technology found on the metallic surfaces, the type of the naval paint and the treatment methods. For analysis it was used the epifluorescence microscopy method with. The comparative analysis follows the data processing which has the same input characteristics. Finally it was observed the microorganism's lifetime after the surface treatment.

  8. A comparative analysis of Media Lengua and Quichua vowel production.

    PubMed

    Stewart, Jesse

    2014-01-01

    This study presents a comparative analysis of F1 and F2 vowel frequencies from Pijal Media Lengua (PML) and Imbabura Quichua. Mixed-effects models are used to test Spanish-derived high and low vowels against their Quichua-derived counterparts for statistical significance. Spanish-derived and Quichua-derived high vowels are also tested against Spanish-derived mid vowels. This analysis suggests that PML may be manipulating as many as eight vowels where Spanishderived high and low vowels coexist as near-mergers with their Quichua-derived counterparts, while high and mid vowels coexist with partial overlap. Quichua, traditionally viewed as a three-vowel system, shows similar results and may be manipulating as many as six vowels. © 2015 S. Karger AG, Basel.

  9. Establishing a framework for comparative analysis of genome sequences

    SciTech Connect

    Bansal, A.K.

    1995-06-01

    This paper describes a framework and a high-level language toolkit for comparative analysis of genome sequence alignment The framework integrates the information derived from multiple sequence alignment and phylogenetic tree (hypothetical tree of evolution) to derive new properties about sequences. Multiple sequence alignments are treated as an abstract data type. Abstract operations have been described to manipulate a multiple sequence alignment and to derive mutation related information from a phylogenetic tree by superimposing parsimonious analysis. The framework has been applied on protein alignments to derive constrained columns (in a multiple sequence alignment) that exhibit evolutionary pressure to preserve a common property in a column despite mutation. A Prolog toolkit based on the framework has been implemented and demonstrated on alignments containing 3000 sequences and 3904 columns.

  10. Comparative analysis of nonverbal interpersonal communication of schizophrenics and normals.

    PubMed

    Hardin, S B

    1980-06-01

    The nonverbal communications of schizophrenics and normals in dyadic interactions were analyzed and compared. Twelve purposively selected women were videotaped in normal-normal, normal-schizophrenic, and schizophrenic-schizophrenic communication acts for 30 minutes. Using a PLATO IV computer program and a modified Kendon Kinesic Notation System, a priori sets of nonverbal behaviors were recorded at 1-second intervals. Frequency and duration scores for the sets of nonverbal behaviors with corresponding communication meanings were totaled. A nested analysis of variance showed that the three groups differed significantly (p less than .05) in engagement and defensiveness and that the normal interactors were the least imitative of the three groups. An analysis and description of the patterns of nonverbal communication also revealed differences, lending support to the theory of dysjunctive schizophrenic communication.

  11. Initial sequencing and comparative analysis of the mouse genome

    SciTech Connect

    Waterston, Robert H.; Lindblad-Toh, Kerstin; Birney, Ewan; Rogers, Jane; Abril, Josep F.; Agarwal, Pankaj; Agarwala, Richa; Ainscough, Rachel; Alexandersson, Marina; An, Peter; Antonarakis, Stylianos E.; Attwood, John; Baertsch, Robert; Bailey, Jonathon; Barlow, Karen; Beck, Stephan; Berry, Eric; Birren, Bruce; Bloom, Toby; Bork, Peer; Botcherby, Marc; Bray, Nicolas; Brent, Michael R.; Brown, Daniel G.; Brown, Stephen D.; Bult, Carol; Burton, John; Butler, Jonathan; Campbell, Robert D.; Carninci, Piero; Cawley, Simon; Chiaromonte, Francesca; Chinwalla, Asif T.; Church, Deanna M.; Clamp, Michele; Clee, Christopher; Collins, Francis S.; Cook, Lisa L.; Copley, Richard R.; Coulson, Alan; Couronne, Olivier; Cuff, James; Curwen, Val; Cutts, Tim; Daly, Mark; David, Robert; Davies, Joy; Delehaunty, Kimberly D.; Deri, Justin; Dermitzakis, Emmanouil T.; Dewey, Colin; Dickens, Nicholas J.; Diekhans, Mark; Dodge, Sheila; Dubchak, Inna; Dunn, Diane M.; Eddy, Sean R.; Elnitski, Laura; Emes, Richard D.; Eswara, Pallavi; Eyras, Eduardo; Felsenfeld, Adam; Fewell, Ginger A.; Flicek, Paul; Foley, Karen; Frankel, Wayne N.; Fulton, Lucinda A.; Fulton, Robert S.; Furey, Terrence S.; Gage, Diane; Gibbs, Richard A.; Glusman, Gustavo; Gnerre, Sante; Goldman, Nick; Goodstadt, Leo; Grafham, Darren; Graves, Tina A.; Green, Eric D.; Gregory, Simon; Guigo, Roderic; Guyer, Mark; Hardison, Ross C.; Haussler, David; Hayashizaki, Yoshihide; Hillier, LaDeana W.; Hinrichs, Angela; Hlavina, Wratko; Holzer, Timothy; Hsu, Fan; Hua, Axin; Hubbard, Tim; Hunt, Adrienne; Jackson, Ian; Jaffe, David B.; Johnson, L. Steven; Jones, Matthew; Jones, Thomas A.; Joy, Ann; Kamal, Michael; Karlsson, Elinor K.; Karolchik, Donna; Kasprzyk, Arkadiusz; Kawai, Jun; Keibler, Evan; Kells, Cristyn; Kent, W. James; Kirby, Andrew; Kolbe, Diana L.; Korf, Ian; Kucherlapati, Raju S.; Kulbokas III, Edward J.; Kulp, David; Landers, Tom; Leger, J.P.; Leonard, Steven; Letunic, Ivica; Levine, Rosie; et al.

    2002-12-15

    The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.

  12. [Comparative analysis of spatial organization of myoglobins. II. Secondary structure].

    PubMed

    Korobov, V N; Nazarenko, V I; Radomskiĭ, N F; Starodub, N F

    1992-01-01

    An analysis of probability of distribution curves of alpha-helical sites and bends of polypeptide chains of myoglobins in half-water mammals (beaver, nutria, muskrat, otter) carried out in comparison with those of myoglobins of the horse and Sperm whale (X-ray diffraction analysis has revealed their tertiary structure) has revealed a coincidence of the secondary structure sites end bends of the chain in the studied respiratory hemoproteins of muscles. Despite a considerable number of amino acid substitutions the profiles of alpha-helicity and B-bends of the compared proteins are practically identical. This indicates to the "resistance" of the probability curves to amino acid substitutions and to retention of the tertiary structure of myoglobins in evolutionary remote species of the animals.

  13. Comparative analysis of titanium oxide nanotubes ordered structure formation

    NASA Astrophysics Data System (ADS)

    Shchegoleva, S. A.; Titov, P. L.; Kondrikov, N. B.

    2017-09-01

    The comparative analysis of formation of highly-ordered nanotubes array of titanium oxide obtained by the method of anodizing in non-aqueous (No. 1) and semi-aqueous (No. 2) electrolytes is considered in this paper. Analysis of nanotubes formation current of both samples has shown that the fine structure of the current is observed: a series of small steps alternated by sharp swells. Attractor obtained from current implementation of sample No. 1 points at the existence of quasistochastic in terms of phase and strictly periodic mode of partial Levy flights. Attractor of sample No. 2 is more smoothed. Current realizations of both samples points at trigger mode of system behavior peculiar to auto-oscillating process.

  14. Initial sequencing and comparative analysis of the mouse genome.

    PubMed

    Waterston, Robert H; Lindblad-Toh, Kerstin; Birney, Ewan; Rogers, Jane; Abril, Josep F; Agarwal, Pankaj; Agarwala, Richa; Ainscough, Rachel; Alexandersson, Marina; An, Peter; Antonarakis, Stylianos E; Attwood, John; Baertsch, Robert; Bailey, Jonathon; Barlow, Karen; Beck, Stephan; Berry, Eric; Birren, Bruce; Bloom, Toby; Bork, Peer; Botcherby, Marc; Bray, Nicolas; Brent, Michael R; Brown, Daniel G; Brown, Stephen D; Bult, Carol; Burton, John; Butler, Jonathan; Campbell, Robert D; Carninci, Piero; Cawley, Simon; Chiaromonte, Francesca; Chinwalla, Asif T; Church, Deanna M; Clamp, Michele; Clee, Christopher; Collins, Francis S; Cook, Lisa L; Copley, Richard R; Coulson, Alan; Couronne, Olivier; Cuff, James; Curwen, Val; Cutts, Tim; Daly, Mark; David, Robert; Davies, Joy; Delehaunty, Kimberly D; Deri, Justin; Dermitzakis, Emmanouil T; Dewey, Colin; Dickens, Nicholas J; Diekhans, Mark; Dodge, Sheila; Dubchak, Inna; Dunn, Diane M; Eddy, Sean R; Elnitski, Laura; Emes, Richard D; Eswara, Pallavi; Eyras, Eduardo; Felsenfeld, Adam; Fewell, Ginger A; Flicek, Paul; Foley, Karen; Frankel, Wayne N; Fulton, Lucinda A; Fulton, Robert S; Furey, Terrence S; Gage, Diane; Gibbs, Richard A; Glusman, Gustavo; Gnerre, Sante; Goldman, Nick; Goodstadt, Leo; Grafham, Darren; Graves, Tina A; Green, Eric D; Gregory, Simon; Guigó, Roderic; Guyer, Mark; Hardison, Ross C; Haussler, David; Hayashizaki, Yoshihide; Hillier, LaDeana W; Hinrichs, Angela; Hlavina, Wratko; Holzer, Timothy; Hsu, Fan; Hua, Axin; Hubbard, Tim; Hunt, Adrienne; Jackson, Ian; Jaffe, David B; Johnson, L Steven; Jones, Matthew; Jones, Thomas A; Joy, Ann; Kamal, Michael; Karlsson, Elinor K; Karolchik, Donna; Kasprzyk, Arkadiusz; Kawai, Jun; Keibler, Evan; Kells, Cristyn; Kent, W James; Kirby, Andrew; Kolbe, Diana L; Korf, Ian; Kucherlapati, Raju S; Kulbokas, Edward J; Kulp, David; Landers, Tom; Leger, J P; Leonard, Steven; Letunic, Ivica; Levine, Rosie; Li, Jia; Li, Ming; Lloyd, Christine; Lucas, Susan; Ma, Bin; Maglott, Donna R; Mardis, Elaine R; Matthews, Lucy; Mauceli, Evan; Mayer, John H; McCarthy, Megan; McCombie, W Richard; McLaren, Stuart; McLay, Kirsten; McPherson, John D; Meldrim, Jim; Meredith, Beverley; Mesirov, Jill P; Miller, Webb; Miner, Tracie L; Mongin, Emmanuel; Montgomery, Kate T; Morgan, Michael; Mott, Richard; Mullikin, James C; Muzny, Donna M; Nash, William E; Nelson, Joanne O; Nhan, Michael N; Nicol, Robert; Ning, Zemin; Nusbaum, Chad; O'Connor, Michael J; Okazaki, Yasushi; Oliver, Karen; Overton-Larty, Emma; Pachter, Lior; Parra, Genís; Pepin, Kymberlie H; Peterson, Jane; Pevzner, Pavel; Plumb, Robert; Pohl, Craig S; Poliakov, Alex; Ponce, Tracy C; Ponting, Chris P; Potter, Simon; Quail, Michael; Reymond, Alexandre; Roe, Bruce A; Roskin, Krishna M; Rubin, Edward M; Rust, Alistair G; Santos, Ralph; Sapojnikov, Victor; Schultz, Brian; Schultz, Jörg; Schwartz, Matthias S; Schwartz, Scott; Scott, Carol; Seaman, Steven; Searle, Steve; Sharpe, Ted; Sheridan, Andrew; Shownkeen, Ratna; Sims, Sarah; Singer, Jonathan B; Slater, Guy; Smit, Arian; Smith, Douglas R; Spencer, Brian; Stabenau, Arne; Stange-Thomann, Nicole; Sugnet, Charles; Suyama, Mikita; Tesler, Glenn; Thompson, Johanna; Torrents, David; Trevaskis, Evanne; Tromp, John; Ucla, Catherine; Ureta-Vidal, Abel; Vinson, Jade P; Von Niederhausern, Andrew C; Wade, Claire M; Wall, Melanie; Weber, Ryan J; Weiss, Robert B; Wendl, Michael C; West, Anthony P; Wetterstrand, Kris; Wheeler, Raymond; Whelan, Simon; Wierzbowski, Jamey; Willey, David; Williams, Sophie; Wilson, Richard K; Winter, Eitan; Worley, Kim C; Wyman, Dudley; Yang, Shan; Yang, Shiaw-Pyng; Zdobnov, Evgeny M; Zody, Michael C; Lander, Eric S

    2002-12-05

    The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.

  15. Comparative and Familial Analysis of Handedness in Great Apes

    PubMed Central

    Hopkins, William D.

    2007-01-01

    Historically, population-level handedness has been considered a hallmark of human evolution. Whether nonhuman primates exhibit population-level handedness remains a topic of considerable debate. This paper summarizes published data on handedness in great apes. Comparative analysis indicated that chimpanzees and bonobos show population-level right handedness, whereas gorillas and orangutans do not. All ape species showed evidence of population-level handedness when considering specific tasks. Familial analyses in chimpanzees indicated that offspring and maternal (but not paternal) handedness was significantly positively correlated, but this finding was contingent upon the classification criteria used to evaluate hand preference. Overall, the proportion of right handedness is lower in great apes compared with humans, and various methodological and theoretical explanations for this discrepancy are discussed. PMID:16822166

  16. Comparative analysis of NDE techniques with image processing

    NASA Astrophysics Data System (ADS)

    Rathod, Vijay R.; Anand, R. S.; Ashok, Alaknanda

    2012-12-01

    The paper reports comparative results of nondestructive testing (NDT) based experimentation done on created flaws in the casting at the Central Foundry Forge Plant (CFFP) of Bharat Heavy Electrical Ltd. India (BHEL). The present experimental study is aimed at comparing the evaluation of image processing methods applied on the radiographic images of welding defects such as slag inclusion, porosity, lack-of-root penetration and cracks with other NDT methods. Different image segmentation techniques have been proposed here for identifying the above created welding defects. Currently, there is a large amount of research work going on in the field of automated system for inspection, analysis and detection of flaws in the weldments. Comparison of other NDT methods and application of image processing on the radiographic images of weld defects are aimed to detect defects reliably and to make accept/reject decisions as per the international standard.

  17. Stigma, sex work, and substance use: a comparative analysis.

    PubMed

    Benoit, Cecilia; McCarthy, Bill; Jansson, Mikael

    2015-03-01

    Stigma is a widely used concept in social science research and an extensive literature claims that stigmatisation contributes to numerous negative health outcomes. However, few studies compare groups that vary in the extent to which they are stigmatised and even fewer studies examine stigma's independent and mediating effects. This article addresses these gaps in a comparative study of perceived stigma and drug use among three low-income feminised service occupations: sex work, food and alcoholic beverage serving, and barbering and hairstyling. An analysis of longitudinal data shows positive associations between sex work, perceived stigma, and socially less acceptable drug use (for example, heroin and cocaine), and that stigma mediates part of the link between sex work and the use of these drugs. Our overall findings suggest that perceived stigma is pronounced among those who work in the sex industry and negatively affects health independently of sex work involvement.

  18. Comparative and functional analysis of cardiovascular-related genes

    SciTech Connect

    Cheng, Jan-Fang; Pennacchio, Len A.

    2003-09-01

    The ability to detect putative cis-regulatory elements in cardiovascular-related genes has been accelerated by the availability of genomic sequence data from numerous vertebrate species and the recent development of comparative genomic tools. This improvement is anticipated to lead to a better understanding of the complex regulatory architecture of cardiovascular (CV) genes and how genetic variants in these non-coding regions can potentially play a role in cardiovascular disease. This manuscript reviews a recently established database dedicated to the comparative sequence analysis of 250 human CV genes of known importance, 37 of which currently contain sequence comparison data for organisms beyond those of human, mouse and rat. These data have provided a glimpse into the variety of possible insights from deep vertebrate sequence comparisons and the identification of putative gene regulatory elements.

  19. Comparative analysis of evaluation techniques for transport policies

    SciTech Connect

    Browne, David; Ryan, Lisa

    2011-04-15

    The objective of this paper is to examine and compare the use of a number of policy evaluation tools, which can be used to measure the impact of transport policies and programmes as part of a strategic environmental assessment (SEA) or sustainability appraisal. The evaluation tools that were examined include cost-benefit analysis (CBA), cost-effectiveness analysis (CEA) and multi-criteria decision analysis (MCDA). It was concluded that both CEA and CBA are useful for estimating the costs and/or benefits associated with transport policies but are constrained by the difficulty in quantifying non-market impacts and monetising total costs and benefits. Furthermore, CEA is limited to identifying the most 'cost-effective policy' for achieving a single, narrowly defined objective, usually greenhouse gas (GHG) reduction and is, therefore, not suitable for evaluating policy options with ancillary costs or a variety of potential benefits. Thus, CBA or CEA evaluation should be complemented by a complete environmental and socio-economic impact assessment approach such as MCDA. This method allows for participatory analysis and qualitative assessment but is subject to caveats such as subjectivity and value-laden judgments.

  20. Comparative study of analysis methods in biospeckle phenomenon

    NASA Astrophysics Data System (ADS)

    da Silva, Emerson Rodrigo; Muramatsu, Mikiya

    2008-04-01

    In this work we present a review of main statistical properties of speckle patterns and accomplish a comparative study of the more used methods for analysis and extraction of information from optical grainy. The first and second order space-time statistics are dicussed in an overview perspective. The biospeckle phenomenon has detailed attention, specially in its application on monitoring of activity in tissues. The main techniques used to obtain information from speckle patterns are presented, with special prominence to autocorrelation function, co-occurrence matrices, Fujii's method, Briers' contrast and spatial and temporal contrast analisys (LASCA and LASTCA). An incipient method for analysis, based on the study of sucessive correlations contrast, is introduced. Numerical simulations, using diferent probability density functions for velocities of scatterers, were made with two objectives: to test the analysis methods and to give subsidies for interpretation of in vivo results. Vegetable and animal tissues are investigated, achieving the monitoring of senescence process and vascularization maps on leaves, the accompaniment of fungi contamined fruits, the mapping of activity in flowers and the analisys of healing in rats subjected to abdominal surgery. Experiments using the biospeckle phenomenon in microscopy are carried out. At last, it is evaluated the potentiality of biospeckle as diagnosis tool in chronic vein ulcer cared with low intensity laser therapy and the better analysis methods for each kind of tissue are pointed.

  1. Comparative psychoacoustics: perspectives of peripheral sound analysis in mammals.

    PubMed

    Ehret, G

    1977-09-01

    Psychophysical data on hearing in mammals are summarized. The data are then correlated to the anatomy and physiology of the ear. Common mechanisms of sound transfer and analysis in the acoustic system, with stress on the auditory periphery, are discussed. In this paper an attempt is made to bring basic psychoacoustic data from man and mammals in a logical line with the anatomy, physiology, and biophysics of the ear. This comparative approach is based on man and those five mammals, including bat and dolphin, for which sufficient data are available.

  2. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.

    PubMed

    Riechmann, J L; Heard, J; Martin, G; Reuber, L; Jiang, C; Keddie, J; Adam, L; Pineda, O; Ratcliffe, O J; Samaha, R R; Creelman, R; Pilgrim, M; Broun, P; Zhang, J Z; Ghandehari, D; Sherman, B K; Yu, G

    2000-12-15

    The completion of the Arabidopsis thaliana genome sequence allows a comparative analysis of transcriptional regulators across the three eukaryotic kingdoms. Arabidopsis dedicates over 5% of its genome to code for more than 1500 transcription factors, about 45% of which are from families specific to plants. Arabidopsis transcription factors that belong to families common to all eukaryotes do not share significant similarity with those of the other kingdoms beyond the conserved DNA binding domains, many of which have been arranged in combinations specific to each lineage. The genome-wide comparison reveals the evolutionary generation of diversity in the regulation of transcription.

  3. Comparative biomorphologic analysis about three dentinal adhesives of last generations.

    PubMed

    Carini, F; Varia, P; Valenza, V

    2001-01-01

    The aim of this work consists in a comparative biomorphological analysis of the properties of infiltration and of adhesion to dental tissues of three among the more used enamel dentinal adhesives of the last generation known with the commercial name of Syntac, Excite and Prompt. The results have given evidence that Syntac has got short adhesion, Excite has got good capacity of infiltration and moderate adhesion, Prompt seems to possess a capacity of infiltration equal to Excite's one, but a better adhesion besides an easier modality of use.

  4. The digital storytelling process: A comparative analysis from various experts

    NASA Astrophysics Data System (ADS)

    Hussain, Hashiroh; Shiratuddin, Norshuhada

    2016-08-01

    Digital Storytelling (DST) is a method of delivering information to the audience. It combines narrative and digital media content infused with the multimedia elements. In order for the educators (i.e the designers) to create a compelling digital story, there are sets of processes introduced by experts. Nevertheless, the experts suggest varieties of processes to guide them; of which some are redundant. The main aim of this study is to propose a single guide process for the creation of DST. A comparative analysis is employed where ten DST models from various experts are analysed. The process can also be implemented in other multimedia materials that used the concept of DST.

  5. STABILIZING SELECTION AND THE COMPARATIVE ANALYSIS OF ADAPTATION.

    PubMed

    Hansen, Thomas F

    1997-10-01

    Comparative studies tend to differ from optimality and functionality studies in how they treat adaptation. While the comparative approach focuses on the origin and change of traits, optimality studies assume that adaptations are maintained at an optimum by stabilizing selection. This paper presents a model of adaptive evolution on a macroevolutionary time scale that includes the maintenance of traits at adaptive optima by stabilizing selection as the dominant evolutionary force. Interspecific variation is treated as variation in the position of adaptive optima. The model illustrates how phylogenetic constraints not only lead to correlations between phylogenetically related species, but also to imperfect adaptations. From this model, a statistical comparative method is derived that can be used to estimate the effect of a selective factor on adaptive optima in a way that would be consistent with an optimality study of adaptation to this factor. The method is illustrated with an analysis of dental evolution in fossil horses. The use of comparative methods to study evolutionary trends is also discussed. © 1997 The Society for the Study of Evolution.

  6. Feature-level sentiment analysis by using comparative domain corpora

    NASA Astrophysics Data System (ADS)

    Quan, Changqin; Ren, Fuji

    2016-06-01

    Feature-level sentiment analysis (SA) is able to provide more fine-grained SA on certain opinion targets and has a wider range of applications on E-business. This study proposes an approach based on comparative domain corpora for feature-level SA. The proposed approach makes use of word associations for domain-specific feature extraction. First, we assign a similarity score for each candidate feature to denote its similarity extent to a domain. Then we identify domain features based on their similarity scores on different comparative domain corpora. After that, dependency grammar and a general sentiment lexicon are applied to extract and expand feature-oriented opinion words. Lastly, the semantic orientation of a domain-specific feature is determined based on the feature-oriented opinion lexicons. In evaluation, we compare the proposed method with several state-of-the-art methods (including unsupervised and semi-supervised) using a standard product review test collection. The experimental results demonstrate the effectiveness of using comparative domain corpora.

  7. Comparative transcriptome analysis of the metal hyperaccumulator Noccaea caerulescens

    PubMed Central

    Halimaa, Pauliina; Blande, Daniel; Aarts, Mark G. M.; Tuomainen, Marjo; Tervahauta, Arja; Kärenlampi, Sirpa

    2014-01-01

    The metal hyperaccumulator Noccaea caerulescens is an established model to study the adaptation of plants to metalliferous soils. Various comparators have been used in these studies. The choice of suitable comparators is important and depends on the hypothesis to be tested and methods to be used. In high-throughput analyses such as microarray, N. caerulescens has been compared to non-tolerant, non-accumulator plants like Arabidopsis thaliana or Thlaspi arvense rather than to the related hypertolerant or hyperaccumulator plants. An underutilized source is N. caerulescens populations with considerable variation in their capacity to accumulate and tolerate metals. Whole transcriptome sequencing (RNA-Seq) is revealing interesting variation in their gene expression profiles. Combining physiological characteristics of N. caerulescens accessions with their RNA-Seq has a great potential to provide detailed insight into the underlying molecular mechanisms, including entirely new gene products. In this review we will critically consider comparative transcriptome analyses carried out to explore metal hyperaccumulation and hypertolerance of N. caerulescens, and demonstrate the potential of RNA-Seq analysis as a tool in evolutionary genomics. PMID:24904610

  8. Comparative analysis of five protein-protein interaction corpora.

    PubMed

    Pyysalo, Sampo; Airola, Antti; Heimonen, Juho; Björne, Jari; Ginter, Filip; Salakoski, Tapio

    2008-04-11

    Growing interest in the application of natural language processing methods to biomedical text has led to an increasing number of corpora and methods targeting protein-protein interaction (PPI) extraction. However, there is no general consensus regarding PPI annotation and consequently resources are largely incompatible and methods are difficult to evaluate. We present the first comparative evaluation of the diverse PPI corpora, performing quantitative evaluation using two separate information extraction methods as well as detailed statistical and qualitative analyses of their properties. For the evaluation, we unify the corpus PPI annotations to a shared level of information, consisting of undirected, untyped binary interactions of non-static types with no identification of the words specifying the interaction, no negations, and no interaction certainty. We find that the F-score performance of a state-of-the-art PPI extraction method varies on average 19 percentage units and in some cases over 30 percentage units between the different evaluated corpora. The differences stemming from the choice of corpus can thus be substantially larger than differences between the performance of PPI extraction methods, which suggests definite limits on the ability to compare methods evaluated on different resources. We analyse a number of potential sources for these differences and identify factors explaining approximately half of the variance. We further suggest ways in which the difficulty of the PPI extraction tasks codified by different corpora can be determined to advance comparability. Our analysis also identifies points of agreement and disagreement in PPI corpus annotation that are rarely explicitly stated by the authors of the corpora. Our comparative analysis uncovers key similarities and differences between the diverse PPI corpora, thus taking an important step towards standardization. In the course of this study we have created a major practical contribution in

  9. Comparative Analysis of Gene Content Evolution in Phytoplasmas and Mycoplasmas

    PubMed Central

    Lin, Chan-Pin; Kuo, Chih-Horng

    2012-01-01

    Phytoplasmas and mycoplasmas are two groups of important pathogens in the bacterial class Mollicutes. Because of their economical and clinical importance, these obligate pathogens have attracted much research attention. However, difficulties involved in the empirical study of these bacteria, particularly the fact that phytoplasmas have not yet been successfully cultivated outside of their hosts despite decades of attempts, have greatly hampered research progress. With the rapid advancements in genome sequencing, comparative genome analysis provides a new approach to facilitate our understanding of these bacteria. In this study, our main focus is to investigate the evolution of gene content in phytoplasmas, mycoplasmas, and their common ancestor. By using a phylogenetic framework for comparative analysis of 12 complete genome sequences, we characterized the putative gains and losses of genes in these obligate parasites. Our results demonstrated that the degradation of metabolic capacities in these bacteria has occurred predominantly in the common ancestor of Mollicutes, prior to the evolutionary split of phytoplasmas and mycoplasmas. Furthermore, we identified a list of genes that are acquired by the common ancestor of phytoplasmas and are conserved across all strains with complete genome sequences available. These genes include several putative effectors for the interactions with hosts and may be good candidates for future functional characterization. PMID:22479625

  10. The Comparative Analysis of Aversive and Ordinary Noise.

    NASA Astrophysics Data System (ADS)

    Mobley, C. Marion, Jr.

    There is a vast amount of literature concerning the psychological and physiological effects of ordinary noise on the individual. However, few publications have addressed the analysis of aversive noise. This research analyzes three noises which produce the familiar goose flesh or chilling effect responsivity. These aversive sounds which are made by chalk squeaking on the chalkboard, fingernails on the chalkboard and rubbing styrofoam against a smooth surface are digitally compared to ordinary noise to show how these aversive sounds differ from sounds which are only annoying. This work, which uses Fast Fourier Transform (FFT) analysis is a combination with cross correlation analysis and other innovative methods to produce comparative data on noises, illustrates subtle differences between ordinary and aversive noise which may be useful for future work in acoustics or experimental psychology. The literature review shows disagreement among the numerous works on the effects of ordinary noise on human subjects. One explanation for this difference is the failure to adequately measure and define the dynamic nature of the noise used. The existing literature also establishes that a mixture of tones plus random noise is more annoying (but not aversive) than either the random noise or the tones alone. This investigation shows that one property of aversive noises is the combination of randomness plus tones which vary rapidly with time. This paper utilizes a new digital technique which improves the FFT analyzer resolution by a factor of 25. The resulting +/-2 Hz accuracy facilitated the presentation of frequency variation as a function of time data. Other computer generated graphical data includes the percent harmonic deviation as a function of time, the rate of change of fundamental frequency, and the rate of change in harmonic deviation. From these dynamic data, average values are calculated which show the aversive noise to be consistently greater in mean frequency deviation

  11. Comparability of mixed IC₅₀ data - a statistical analysis.

    PubMed

    Kalliokoski, Tuomo; Kramer, Christian; Vulpetti, Anna; Gedeck, Peter

    2013-01-01

    The biochemical half maximal inhibitory concentration (IC50) is the most commonly used metric for on-target activity in lead optimization. It is used to guide lead optimization, build large-scale chemogenomics analysis, off-target activity and toxicity models based on public data. However, the use of public biochemical IC50 data is problematic, because they are assay specific and comparable only under certain conditions. For large scale analysis it is not feasible to check each data entry manually and it is very tempting to mix all available IC50 values from public database even if assay information is not reported. As previously reported for Ki database analysis, we first analyzed the types of errors, the redundancy and the variability that can be found in ChEMBL IC50 database. For assessing the variability of IC50 data independently measured in two different labs at least ten IC50 data for identical protein-ligand systems against the same target were searched in ChEMBL. As a not sufficient number of cases of this type are available, the variability of IC50 data was assessed by comparing all pairs of independent IC50 measurements on identical protein-ligand systems. The standard deviation of IC50 data is only 25% larger than the standard deviation of Ki data, suggesting that mixing IC50 data from different assays, even not knowing assay conditions details, only adds a moderate amount of noise to the overall data. The standard deviation of public ChEMBL IC50 data, as expected, resulted greater than the standard deviation of in-house intra-laboratory/inter-day IC50 data. Augmenting mixed public IC50 data by public Ki data does not deteriorate the quality of the mixed IC50 data, if the Ki is corrected by an offset. For a broad dataset such as ChEMBL database a Ki- IC50 conversion factor of 2 was found to be the most reasonable.

  12. Comparative Analysis of Vertebrate Diurnal/Circadian Transcriptomes

    PubMed Central

    Boyle, Greg; Richter, Kerstin; Priest, Henry D.; Traver, David; Mockler, Todd C.; Chang, Jeffrey T.; Kay, Steve A.

    2017-01-01

    From photosynthetic bacteria to mammals, the circadian clock evolved to track diurnal rhythms and enable organisms to anticipate daily recurring changes such as temperature and light. It orchestrates a broad spectrum of physiology such as the sleep/wake and eating/fasting cycles. While we have made tremendous advances in our understanding of the molecular details of the circadian clock mechanism and how it is synchronized with the environment, we still have rudimentary knowledge regarding its connection to help regulate diurnal physiology. One potential reason is the sheer size of the output network. Diurnal/circadian transcriptomic studies are reporting that around 10% of the expressed genome is rhythmically controlled. Zebrafish is an important model system for the study of the core circadian mechanism in vertebrate. As Zebrafish share more than 70% of its genes with human, it could also be an additional model in addition to rodent for exploring the diurnal/circadian output with potential for translational relevance. Here we performed comparative diurnal/circadian transcriptome analysis with established mouse liver and other tissue datasets. First, by combining liver tissue sampling in a 48h time series, transcription profiling using oligonucleotide arrays and bioinformatics analysis, we profiled rhythmic transcripts and identified 2609 rhythmic genes. The comparative analysis revealed interesting features of the output network regarding number of rhythmic genes, proportion of tissue specific genes and the extent of transcription factor family expression. Undoubtedly, the Zebrafish model system will help identify new vertebrate outputs and their regulators and provides leads for further characterization of the diurnal cis-regulatory network. PMID:28076377

  13. Texture analysis of multiple sclerosis: a comparative study.

    PubMed

    Zhang, Jing; Tong, Longzheng; Wang, Lei; Li, Ning

    2008-10-01

    The difficulty of using magnetic resonance imaging (MRI) to support early diagnosis of multiple sclerosis (MS) stems from the subtle pathological changes in the central nervous system (CNS). In this study, texture analysis was performed on MR images of MS patients and normal controls and a combined set of texture features were explored in order to better discriminate tissues between MS lesions, normal appearing white matter (NAWM) and normal white matter (NWM). Features were extracted from gradient matrix, run-length (RL) matrix, gray level co-occurrence matrix (GLCM), autoregressive (AR) model and wavelet analysis, and were selected based on greatest difference between different tissue types. The results of the combined set of texture features were compared with our previous results of GLCM-based features alone. The results of this study demonstrated that (1) with the combined set of texture features, classification was perfect (100%) between MS lesions and NAWM (or NWM), less successful (88.89%) among the three tissue types and worst (58.33%) between NAWM and NWM; (2) compared with GLCM-based features, the combined set of texture features were better at discriminating MS lesions and NWM, equally good at discriminating MS lesions and NAWM and at all three tissue types, but less effective in classification between NAWM and NWM. This study suggested that texture analysis with the combined set of texture features may be equally good or more advantageous than the commonly used GLCM-based features alone in discriminating MS lesions and NWM/NAWM and in supporting early diagnosis of MS.

  14. Extreme storm surges: a comparative study of frequency analysis approaches

    NASA Astrophysics Data System (ADS)

    Hamdi, Y.; Bardet, L.; Duluc, C.-M.; Rebour, V.

    2014-08-01

    In France, nuclear facilities were designed around very low probabilities of failure. Nevertheless, some extreme climatic events have given rise to exceptional observed surges (outliers) much larger than other observations, and have clearly illustrated the potential to underestimate the extreme water levels calculated with the current statistical methods. The objective of the present work is to conduct a comparative study of three approaches to extreme value analysis, including the annual maxima (AM), the peaks-over-threshold (POT) and the r-largest order statistics (r-LOS). These methods are illustrated in a real analysis case study. All data sets were screened for outliers. Non-parametric tests for randomness, homogeneity and stationarity of time series were used. The shape and scale parameter stability plots, the mean excess residual life plot and the stability of the standard errors of return levels were used to select optimal thresholds and r values for the POT and r-LOS method, respectively. The comparison of methods was based on (i) the uncertainty degrees, (ii) the adequacy criteria and tests, and (iii) the visual inspection. It was found that the r-LOS and POT methods have reduced the uncertainty on the distribution parameters and return level estimates and have systematically shown values of the 100 and 500-year return levels smaller than those estimated with the AM method. Results have also shown that none of the compared methods has allowed a good fit at the right tail of the distribution in the presence of outliers. As a perspective, the use of historical information was proposed in order to increase the representativeness of outliers in data sets. Findings are of practical relevance, not only to nuclear energy operators in France, for applications in storm surge hazard analysis and flood management, but also for the optimal planning and design of facilities to withstand extreme environmental conditions, with an appropriate level of risk.

  15. Mycobacterial species as case-study of comparative genome analysis.

    PubMed

    Zakham, F; Belayachi, L; Ussery, D; Akrim, M; Benjouad, A; El Aouad, R; Ennaji, M M

    2011-02-08

    The genus Mycobacterium represents more than 120 species including important pathogens of human and cause major public health problems and illnesses. Further, with more than 100 genome sequences from this genus, comparative genome analysis can provide new insights for better understanding the evolutionary events of these species and improving drugs, vaccines, and diagnostics tools for controlling Mycobacterial diseases. In this present study we aim to outline a comparative genome analysis of fourteen Mycobacterial genomes: M. avium subsp. paratuberculosis K—10, M. bovis AF2122/97, M. bovis BCG str. Pasteur 1173P2, M. leprae Br4923, M. marinum M, M. sp. KMS, M. sp. MCS, M. tuberculosis CDC1551, M. tuberculosis F11, M. tuberculosis H37Ra, M. tuberculosis H37Rv, M. tuberculosis KZN 1435 , M. ulcerans Agy99,and M. vanbaalenii PYR—1, For this purpose a comparison has been done based on their length of genomes, GC content, number of genes in different data bases (Genbank, Refseq, and Prodigal). The BLAST matrix of these genomes has been figured to give a lot of information about the similarity between species in a simple scheme. As a result of multiple genome analysis, the pan and core genome have been defined for twelve Mycobacterial species. We have also introduced the genome atlas of the reference strain M. tuberculosis H37Rv which can give a good overview of this genome. And for examining the phylogenetic relationships among these bacteria, a phylogenic tree has been constructed from 16S rRNA gene for tuberculosis and non tuberculosis Mycobacteria to understand the evolutionary events of these species.

  16. Comparative analysis of EPA cost-benefit methodologies

    SciTech Connect

    Poch, L.; Gillette, J.; Veil, J.

    1998-05-01

    In recent years, reforming the regulatory process has received much attention from diverse groups such as environmentalists, the government, and industry. A cost-benefit analysis can be a useful way to organize and compare the favorable and unfavorable impacts a proposed action night have on society. Since 1981, two Executive Orders have required the U.S. Environmental Protection Agency (EPA) and other regulatory agencies to perform cost-benefit analyses in support of regulatory decision making. At the EPA, a cost-benefit analysis is published as a document called a regulatory impact analysis (RIA). This report reviews cost-benefit methodologies used by three EPA program offices: Office of Air and Radiation, Office of Solid Waste, and Office of Water. These offices were chosen because they promulgate regulations that affect the policies of this study`s sponsor (U.S. Department of Energy, Office of Fossil Energy) and the technologies it uses. The study was conducted by reviewing 11 RIAs recently published by the three offices and by interviewing staff members in the offices. To draw conclusions about the EPA cost-benefit methodologies, their components were compared with those of a standard methodology (i.e., those that should be included in a comprehensive cost-benefit methodology). This study focused on the consistency of the approaches as well as their strengths and weaknesses, since differences in the cost-benefit methodologies themselves or in their application can cause confusion and preclude consistent comparison of regulations both within and among program offices.

  17. In silico comparative genomic analysis of GABAA receptor transcriptional regulation.

    PubMed

    Joyce, Christopher J

    2007-06-30

    Subtypes of the GABAA receptor subunit exhibit diverse temporal and spatial expression patterns. In silico comparative analysis was used to predict transcriptional regulatory features in individual mammalian GABAA receptor subunit genes, and to identify potential transcriptional regulatory components involved in the coordinate regulation of the GABAA receptor gene clusters. Previously unreported putative promoters were identified for the beta2, gamma1, gamma3, epsilon, theta and pi subunit genes. Putative core elements and proximal transcriptional factors were identified within these predicted promoters, and within the experimentally determined promoters of other subunit genes. Conserved intergenic regions of sequence in the mammalian GABAA receptor gene cluster comprising the alpha1, beta2, gamma2 and alpha6 subunits were identified as potential long range transcriptional regulatory components involved in the coordinate regulation of these genes. A region of predicted DNase I hypersensitive sites within the cluster may contain transcriptional regulatory features coordinating gene expression. A novel model is proposed for the coordinate control of the gene cluster and parallel expression of the alpha1 and beta2 subunits, based upon the selective action of putative Scaffold/Matrix Attachment Regions (S/MARs). The putative regulatory features identified by genomic analysis of GABAA receptor genes were substantiated by cross-species comparative analysis and now require experimental verification. The proposed model for the coordinate regulation of genes in the cluster accounts for the head-to-head orientation and parallel expression of the alpha1 and beta2 subunit genes, and for the disruption of transcription caused by insertion of a neomycin gene in the close vicinity of the alpha6 gene, which is proximal to a putative critical S/MAR.

  18. White matter degeneration in schizophrenia: a comparative diffusion tensor analysis

    NASA Astrophysics Data System (ADS)

    Ingalhalikar, Madhura A.; Andreasen, Nancy C.; Kim, Jinsuh; Alexander, Andrew L.; Magnotta, Vincent A.

    2010-03-01

    Schizophrenia is a serious and disabling mental disorder. Diffusion tensor imaging (DTI) studies performed on schizophrenia have demonstrated white matter degeneration either due to loss of myelination or deterioration of fiber tracts although the areas where the changes occur are variable across studies. Most of the population based studies analyze the changes in schizophrenia using scalar indices computed from the diffusion tensor such as fractional anisotropy (FA) and relative anisotropy (RA). The scalar measures may not capture the complete information from the diffusion tensor. In this paper we have applied the RADTI method on a group of 9 controls and 9 patients with schizophrenia. The RADTI method converts the tensors to log-Euclidean space where a linear regression model is applied and hypothesis testing is performed between the control and patient groups. Results show that there is a significant difference in the anisotropy between patients and controls especially in the parts of forceps minor, superior corona radiata, anterior limb of internal capsule and genu of corpus callosum. To check if the tensor analysis gives a better idea of the changes in anisotropy, we compared the results with voxelwise FA analysis as well as voxelwise geodesic anisotropy (GA) analysis.

  19. Multivariate Comparative Analysis of Stock Exchanges: The European Perspective

    NASA Astrophysics Data System (ADS)

    Koralun-Bereźnicka, Julia

    The aim of the research is to perform a multivariate comparative analysis of 20 European stock exchanges in order to identify the main similarities between the objects. Due to the convergence process of capital markets in Europe the similarities between stock exchanges could be expected to increase over time. The research is meant to show whether and how these similarities change. Consequently, the distances between clusters of similar stock exchanges should become less significant, which the analysis also aims at verifying. The basis of comparison is a set of 48 monthly variables from the period January, 2003 to December, 2006. The variables are classified into three categories: size of the market, equity trading and bonds. The paper aims at identifying the clusters of alike stock exchanges and at finding the characteristic features of each of the distinguished groups. The obtained categorization to some extent corresponds with the division of the European Union into “new” and “old” member countries. Clustering method, performed for each quarter separately, also reveals that the classification is fairly stable in time. The factor analysis, which was carried out to reduce the number of variables, reveals three major factors behind the data, which are related with the earlier mentioned categories of variables.

  20. Comparative genomic analysis between Corynebacterium pseudotuberculosis strains isolated from buffalo

    PubMed Central

    Figueiredo, Henrique; Ramos, Rommel; Guimarães, Luis Carlos; Pereira, Felipe Luiz; Dorella, Fernanda Alves; Selim, Salah Abdel Karim; Salaheldean, Mohammad; Silva, Artur

    2017-01-01

    Corynebacterium pseudotuberculosis is a Gram-positive, pleomorphic, facultative intracellular pathogen that causes Oedematous Skin Disease (OSD) in buffalo. To better understand the pathogenic mechanisms of OSD, we performed a comparative genomic analysis of 11 strains of C. pseudotuberculosis isolated from different buffalo found to be infected in Egypt during an outbreak that occurred in 2008. Sixteen previously described pathogenicity islands (PiCp) were present in all of the new buffalo strains, but one of them, PiCp12, had an insertion that contained both a corynephage and a diphtheria toxin gene, both of which may play a role in the adaptation of C. pseudotuberculosis to this new host. Synteny analysis showed variations in the site of insertion of the corynephage during the same outbreak. A gene functional comparison showed the presence of a nitrate reductase operon that included genes involved in molybdenum cofactor biosynthesis, which is necessary for a positive nitrate reductase phenotype and is a possible adaptation for intracellular survival. Genomes from the buffalo strains also had fusions in minor pilin genes in the spaA and spaD gene cluster (spaCX and spaYEF), which could suggest either an adaptation to this particular host, or mutation events in the immediate ancestor before this particular epidemic. A phylogenomic analysis confirmed a clear separation between the Ovis and Equi biovars, but also showed what appears to be a clustering by host species within the Equi strains. PMID:28445543

  1. [A comparative analysis of Stachybotrys chartarum strains isolated in Russia].

    PubMed

    Elanskiĭ, S N; Petrunina, Ia V; Lavrova, O I; Likhachev, A N

    2004-01-01

    This work deals with a comparative analysis of Stachybotrys chartarum strains isolated from various artificial cellulose-containing materials and natural substrates in the geographically distant regions of Russia. The analysis included the determination of the spore size, the strain toxicity to Paramecium caudatum, the strain resistance to the fungicides Benomil, Olilen, and Tilt, and the PCR study of the genome structure with the aid of a primer that was complementary to the core sequence of the SINE retrotransposon. It was found that some of the strains that were isolated from different areas and from different substrates differ in their toxicity, fungicide resistance, and genome structure. The PCR analysis showed the absence of any correlation between the genome structure, the strain properties, the geographic area, and the substrates from which the strains were isolated. The pheno- and genotypic diversity of the strains and their different vegetative compatibility suggest the existence of an intraspecies diversity of the S. chartarum strains that were isolated in different geographic areas. The absence of any correlation between the pheno- and genotypic properties of the strains and the substrates from which they were isolated implies that the colonization of artificial substrates by S. chartarum occurred occasionally from natural habitats. The S. chartarum populations that live on artificial substrates are unlikely to have their own evolutionary history.

  2. Comparative analysis of solid waste management in 20 cities.

    PubMed

    Wilson, David C; Rodic, Ljiljana; Scheinberg, Anne; Velis, Costas A; Alabaster, Graham

    2012-03-01

    This paper uses the 'lens' of integrated and sustainable waste management (ISWM) to analyse the new data set compiled on 20 cities in six continents for the UN-Habitat flagship publication Solid Waste Management in the World's Cities. The comparative analysis looks first at waste generation rates and waste composition data. A process flow diagram is prepared for each city, as a powerful tool for representing the solid waste system as a whole in a comprehensive but concise way. Benchmark indicators are presented and compared for the three key physical components/drivers: public health and collection; environment and disposal; and resource recovery--and for three governance strategies required to deliver a well-functioning ISWM system: inclusivity; financial sustainability; and sound institutions and pro-active policies. Key insights include the variety and diversity of successful models - there is no 'one size fits all'; the necessity of good, reliable data; the importance of focusing on governance as well as technology; and the need to build on the existing strengths of the city. An example of the latter is the critical role of the informal sector in the cities in many developing countries: it not only delivers recycling rates that are comparable with modern Western systems, but also saves the city authorities millions of dollars in avoided waste collection and disposal costs. This provides the opportunity for win-win solutions, so long as the related wider challenges can be addressed.

  3. An example of qualitative comparative analysis in nursing research.

    PubMed

    Donnelly, Frank; Wiechula, Richard

    2013-07-01

    To describe an example of qualitative comparative analysis (QCA) in a study about the role of clinical placement, nursing education and patient outcomes. Clinical placement is often considered an essential aspect of nursing education and an invaluable way to prepare students for the reality of nursing. However, many questions about the role of clinical placement remain unanswered, such as duration, style and learning outcomes. QCA is a novel approach to data analysis, which has been used for some time in social science research, and may be useful in tackling such questions. Participants (n= 16) involved in a case study using questionnaire, in-depth interview and document analysis. Few examples of QCA exist in nursing-related research. Examination of approaches to social sciences and educational research, and the conditions that influence nursing education and clinical placement were conducted via a number of online database searches. The paper presents an example of how QCA was used to consider whether there is any causal relationship between certain features of clinical placement, such as duration, level of preparation, level of benefit, and the capacity of recently graduated registered nurses to provide a range of nursing interventions for pneumonia, falls and pressure-area care. Effective and contemporary curriculum design requires examination of the components of clinical placement that influence graduates and their learning, particularly important at a time when access to the clinical placement setting is becoming increasingly difficult. This paper should stimulate nurse researchers to consider the potential for QCA and case study in addressing many of the complex questions that lend themselves to research designs with small numbers of participants. This paper will be of interest to nurse researchers looking for innovative approaches to data analysis and educators responsible for curriculum design and the delivery of clinical placement experience. A greater

  4. Comprehensive comparative analysis of kinesins in photosynthetic eukaryotes

    PubMed Central

    Richardson, Dale N; Simmons, Mark P; Reddy, Anireddy SN

    2006-01-01

    Background Kinesins, a superfamily of molecular motors, use microtubules as tracks and transport diverse cellular cargoes. All kinesins contain a highly conserved ~350 amino acid motor domain. Previous analysis of the completed genome sequence of one flowering plant (Arabidopsis) has resulted in identification of 61 kinesins. The recent completion of genome sequencing of several photosynthetic and non-photosynthetic eukaryotes that belong to divergent lineages offers a unique opportunity to conduct a comprehensive comparative analysis of kinesins in plant and non-plant systems and infer their evolutionary relationships. Results We used the kinesin motor domain to identify kinesins in the completed genome sequences of 19 species, including 13 newly sequenced genomes. Among the newly analyzed genomes, six represent photosynthetic eukaryotes. A total of 529 kinesins was used to perform comprehensive analysis of kinesins and to construct gene trees using the Bayesian and parsimony approaches. The previously recognized 14 families of kinesins are resolved as distinct lineages in our inferred gene tree. At least three of the 14 kinesin families are not represented in flowering plants. Chlamydomonas, a green alga that is part of the lineage that includes land plants, has at least nine of the 14 known kinesin families. Seven of ten families present in flowering plants are represented in Chlamydomonas, indicating that these families were retained in both the flowering-plant and green algae lineages. Conclusion The increase in the number of kinesins in flowering plants is due to vast expansion of the Kinesin-14 and Kinesin-7 families. The Kinesin-14 family, which typically contains a C-terminal motor, has many plant kinesins that have the motor domain at the N terminus, in the middle, or the C terminus. Several domains in kinesins are present exclusively either in plant or animal lineages. Addition of novel domains to kinesins in lineage-specific groups contributed to the

  5. Industrial Acetogenic Biocatalysts: A Comparative Metabolic and Genomic Analysis

    PubMed Central

    Bengelsdorf, Frank R.; Poehlein, Anja; Linder, Sonja; Erz, Catarina; Hummel, Tim; Hoffmeister, Sabrina; Daniel, Rolf; Dürre, Peter

    2016-01-01

    Synthesis gas (syngas) fermentation by anaerobic acetogenic bacteria employing the Wood–Ljungdahl pathway is a bioprocess for production of biofuels and biocommodities. The major fermentation products of the most relevant biocatalytic strains (Clostridium ljungdahlii, C. autoethanogenum, C. ragsdalei, and C. coskatii) are acetic acid and ethanol. A comparative metabolic and genomic analysis using the mentioned biocatalysts might offer targets for metabolic engineering and thus improve the production of compounds apart from ethanol. Autotrophic growth and product formation of the four wild type (WT) strains were compared in uncontrolled batch experiments. The genomes of C. ragsdalei and C. coskatii were sequenced and the genome sequences of all four biocatalytic strains analyzed in comparative manner. Growth and product spectra (acetate, ethanol, 2,3-butanediol) of C. autoethanogenum, C. ljungdahlii, and C. ragsdalei were rather similar. In contrast, C. coskatii produced significantly less ethanol and its genome sequence lacks two genes encoding aldehyde:ferredoxin oxidoreductases (AOR). Comparative genome sequence analysis of the four WT strains revealed high average nucleotide identity (ANI) of C. ljungdahlii and C. autoethanogenum (99.3%) and C. coskatii (98.3%). In contrast, C. ljungdahlii WT and C. ragsdalei WT showed an ANI-based similarity of only 95.8%. Additionally, recombinant C. ljungdahlii strains were constructed that harbor an artificial acetone synthesis operon (ASO) consisting of the following genes: adc, ctfA, ctfB, and thlA (encoding acetoacetate decarboxylase, acetoacetyl-CoA:acetate/butyrate:CoA-transferase subunits A and B, and thiolase) under the control of thlA promoter (PthlA) from C. acetobutylicum or native pta-ack promoter (Ppta-ack) from C. ljungdahlii. Respective recombinant strains produced 2-propanol rather than acetone, due to the presence of a NADPH-dependent primary-secondary alcohol dehydrogenase that converts acetone to 2

  6. Imaging hydrated microbial extracellular polymers: Comparative analysis by electron microscopy

    SciTech Connect

    Dohnalkova, A.C.; Marshall, M. J.; Arey, B. W.; Williams, K. H.; Buck, E. C.; Fredrickson, J. K.

    2011-01-01

    Microbe-mineral and -metal interactions represent a major intersection between the biosphere and geosphere but require high-resolution imaging and analytical tools for investigating microscale associations. Electron microscopy has been used extensively for geomicrobial investigations and although used bona fide, the traditional methods of sample preparation do not preserve the native morphology of microbiological components, especially extracellular polymers. Herein, we present a direct comparative analysis of microbial interactions using conventional electron microscopy approaches of imaging at room temperature and a suite of cryogenic electron microscopy methods providing imaging in the close-to-natural hydrated state. In situ, we observed an irreversible transformation of the hydrated bacterial extracellular polymers during the traditional dehydration-based sample preparation that resulted in their collapse into filamentous structures. Dehydration-induced polymer collapse can lead to inaccurate spatial relationships and hence could subsequently affect conclusions regarding nature of interactions between microbial extracellular polymers and their environment.

  7. Comparative dynamic analysis of the full Grossman model.

    PubMed

    Ried, W

    1998-08-01

    The paper applies the method of comparative dynamic analysis to the full Grossman model. For a particular class of solutions, it derives the equations implicitly defining the complete trajectories of the endogenous variables. Relying on the concept of Frisch decision functions, the impact of any parametric change on an endogenous variable can be decomposed into a direct and an indirect effect. The focus of the paper is on marginal changes in the rate of health capital depreciation. It also analyses the impact of either initial financial wealth or the initial stock of health capital. While the direction of most effects remains ambiguous in the full model, the assumption of a zero consumption benefit of health is sufficient to obtain a definite for any direct or indirect effect.

  8. Comparative analysis of solar minima with EUV tomography

    NASA Astrophysics Data System (ADS)

    Lloveras, D. G.; Nuevo, F. A.; Vásquez, A. M.; Frazin, R. A.

    2016-08-01

    Due to the dynamo mechanism of the Sun, the magnetic activity of its atmosphere presents a periodic cycle about 11 years long. The last three solar cycles have shown a systematic decrease of activity, with the last minimum (2008/2009) being considerably more quiet than the previous one (1996), as well as magnetically weaker. We present a comparative analysis of three--dimensional thermodynamical structure of the lower corona for last two minimima, based on differential emission measure tomography. The study is combined with potential extrapolations of the coronal magnetic field. To study the minima of 1996 and 2009 we use data taken by the instruments EIT/SOHO y EUVI/STEREO, respectively. The aim of the work is to establish if there were systematic thermodynamical differences in the lower corona during the two minima.

  9. Comparative analysis of DG and solar PV water pumping system

    NASA Astrophysics Data System (ADS)

    Tharani, Kusum; Dahiya, Ratna

    2016-03-01

    Looking at present day electricity scenario, there is a major electricity crisis in rural areas. The farmers are still dependant on the monsoon rains for their irrigation needs and livestock maintenance. Some of the agrarian population has opted to use Diesel Generators for pumping water in their fields. But taking into consideration the economics and environmental conditions, the above choice is not suitable for longer run. An effort to shift from non-renewable sources such as diesel to renewable energy source such as solar has been highlighted. An approximate comparative analysis showing the life cycle costs of a PV pumping system with Diesel Generator powered water pumping is done using MATLAB/STMULTNK.

  10. Cardiovascular disease research in Latin America: A comparative bibliometric analysis

    PubMed Central

    Jahangir, Eiman; Comandé, Daniel; Rubinstein, Adolfo

    2011-01-01

    AIM: To investigate the number of publications in cardiovascular disease (CVD) in Latin America and the Caribbean over the last decade. METHODS: We performed a bibliometric analysis in PubMed from 2001 to 2010 for Latin America and the Caribbean, the United States, Canada, Europe, China, and India. RESULTS: Latin America published 4% of articles compared with 26% from the United States/Canada and 42% from Europe. In CVD, Latin America published 4% of articles vs 23% from the United States/Canada and 40% from Europe. The number of publications in CVD in Latin America increased from 41 in 2001 to 726 in 2010. CONCLUSION: Latin America, while publishing more articles than previously, lags behind developed countries. Further advances in research infrastructure are necessary to develop prevention strategies for this region. PMID:22216374

  11. Phylogeny and comparative genome analysis of a Basidiomycete fungi

    SciTech Connect

    Riley, Robert W.; Salamov, Asaf; Grigoriev, Igor; Hibbett, David

    2011-03-14

    Fungi of the phylum Basidiomycota, make up some 37percent of the described fungi, and are important from the perspectives of forestry, agriculture, medicine, and bioenergy. This diverse phylum includes the mushrooms, wood rots, plant pathogenic rusts and smuts, and some human pathogens. To better understand these important fungi, we have undertaken a comparative genomic analysis of the Basidiomycetes with available sequenced genomes. We report a phylogeny that sheds light on previously unclear evolutionary relationships among the Basidiomycetes. We also define a `core proteome? based on protein families conserved in all Basidiomycetes. We identify key expansions and contractions in protein families that may be responsible for the degradation of plant biomass such as cellulose, hemicellulose, and lignin. Finally, we speculate as to the genomic changes that drove such expansions and contractions.

  12. A comparative analysis of soft computing techniques for gene prediction.

    PubMed

    Goel, Neelam; Singh, Shailendra; Aseri, Trilok Chand

    2013-07-01

    The rapid growth of genomic sequence data for both human and nonhuman species has made analyzing these sequences, especially predicting genes in them, very important and is currently the focus of many research efforts. Beside its scientific interest in the molecular biology and genomics community, gene prediction is of considerable importance in human health and medicine. A variety of gene prediction techniques have been developed for eukaryotes over the past few years. This article reviews and analyzes the application of certain soft computing techniques in gene prediction. First, the problem of gene prediction and its challenges are described. These are followed by different soft computing techniques along with their application to gene prediction. In addition, a comparative analysis of different soft computing techniques for gene prediction is given. Finally some limitations of the current research activities and future research directions are provided.

  13. Comparative analysis of human gut microbiota by barcoded pyrosequencing.

    PubMed

    Andersson, Anders F; Lindberg, Mathilda; Jakobsson, Hedvig; Bäckhed, Fredrik; Nyrén, Pål; Engstrand, Lars

    2008-07-30

    Humans host complex microbial communities believed to contribute to health maintenance and, when in imbalance, to the development of diseases. Determining the microbial composition in patients and healthy controls may thus provide novel therapeutic targets. For this purpose, high-throughput, cost-effective methods for microbiota characterization are needed. We have employed 454-pyrosequencing of a hyper-variable region of the 16S rRNA gene in combination with sample-specific barcode sequences which enables parallel in-depth analysis of hundreds of samples with limited sample processing. In silico modeling demonstrated that the method correctly describes microbial communities down to phylotypes below the genus level. Here we applied the technique to analyze microbial communities in throat, stomach and fecal samples. Our results demonstrate the applicability of barcoded pyrosequencing as a high-throughput method for comparative microbial ecology.

  14. A comparative analysis of the accuracy of implant transfer techniques.

    PubMed

    Hsu, C C; Millstein, P L; Stein, R S

    1993-06-01

    Four different implant transfer techniques using two master cast systems (solid cast and Zeiser system) were evaluated and compared with respect to the accuracy with which abutment positions were reproduced. A stainless steel experimental analogue with two anterior and two posterior fixtures and abutments was fabricated. Polyether impressions (14 each) were made by use of four techniques, (I) nonsplinted, (II) splinted with dental floss and acrylic resin, (III) splinted with orthodontic wire and acrylic resin, and (IV) splinted with acrylic resin alone. The fourteen impressions of each technique were divided into two equal groups: group 1, solid cast system, and group 2, Zeiser system. The abutments of each master cast were measured vertically and horizontally with a profile projector. Statistical analysis indicated no significant difference between the splinted and nonsplinted techniques. The Zeiser system provided more accurate interabutment relationships for the posterior region than the solid cast system.

  15. Imaging Hydrated Microbial Extracellular Polymers: Comparative Analysis by Electron Microscopy

    SciTech Connect

    Dohnalkova, Alice; Marshall, Matthew J.; Arey, Bruce W.; Williams, Kenneth H.; Buck, Edgar C.; Fredrickson, Jim K.

    2011-02-01

    Microbe-mineral and -metal interactions represent a major intersection between the biosphere and geosphere but require high-resolution imaging and analytical tools for investigating microscale associations. Electron microscopy has been used extensively for geomicrobial investigations and although used bona fide, the traditional methods of sample preparation do not preserve the native morphology of microbiological components, especially extracellular polymers. Herein, we present a direct comparative analysis of microbial interactions using conventional electron microscopy approaches of imaging at room temperature and a suite of cryo-electron microscopy methods providing imaging in the close-to-natural hydrated state. In situ, we observed an irreversible transformation of bacterial extracellular polymers during the traditional dehydration-based sample preparation that resulted in the collapse of hydrated gel-like EPS into filamentous structures. Dehydration-induced polymer collapse can lead to inaccurate spatial relationships and hence could subsequently affect conclusions regarding nature of interactions between microbial extracellular polymers and their environment.

  16. Comparative Analysis on Nuclear Fuel Sustainability Aspect of FBR

    NASA Astrophysics Data System (ADS)

    Permana, Sidik; Irwanto, Dwi; Suzuki, Mitsutoshi; Saito, Masaki

    2017-01-01

    Recycle program of spent nuclear fuel (SNF) will have some challanges in term of fuel cycle capability and its facilities as well as nuclear non-proliferation concern of special nuclear materials. A different analysis approach as a comparative study have been analyzed based on breeding ratio and heavy metal inventory ratio concepts in fast breeder reactor (FBR) type. Breeding ratio and heavy metal inventory obtain higher than unity which shows breeding gain or surplus inventory of heavy metals are obtained. Breeding ratio indicates the fuel conversion capability from conversion process of fertile materials into fissile material such as fertile materials of U-238, Pu-238, Pu-240 and fissile materials of Pu-239 and Pu-241. Inventory ratio approaches are appropriate to estimate some selected actinide as a mass inventory production such as plutonium inventory ratio which estimate the surplus mass inventory from the ratio of produced plutonium at the net of operation to the initial inventory ratio.

  17. Comparative proteomics analysis of spermary and ovary in Hyriopsis schlegelii.

    PubMed

    Shi, Jianwu; Wang, Dexia; Zhou, Yan; Gu, Yiran; Wu, Di; Wang, Junhua; Hong, Yijiang

    2017-03-01

    We provide the first large-scale quantitative proteomics analysis in Hyriopsis schlegelii. To investigate the proteins expressed in the gonads, a quantitative proteomics approach has been utilized to analyze differentially expressed proteins between the spermary and ovary. In this study, we identified and quantified 2416 proteins in the gonads of Hyriopsis schlegelii. Of these, 559 proteins showed significantly different expression between the spermary and ovary. Some specific proteins expressed in either the spermary or ovary were identified in Hyriopsis schlegelii. In addition, a series of proteins related to gametogenesis were also identified. Compared with previous reports, many proteins in Hyriopsis schlegelii identified here have different expression patterns between the spermary and ovary. The special hermaphroditism in Hyriopsis schlegelii may contribute to these inconsistent results. The provided proteomics data could be considered as a starting point for subsequent studies focusing on the proteins involved in sexual gland development and maturity.

  18. Primate phylogeny studied by comparative determinant analysis. A preliminary report.

    PubMed

    Bauer, K

    1993-01-01

    In this preliminary report the divergence times for the major primate groups are given, calculated from a study by comparative determinant analysis of 69 proteins (equaling 0.1% of the whole genetic information). With an origin of the primate order set at 80 million years before present, the ages of the last common ancestors (LCAs) of man and the major primate groups obtained this way are as follows: Pan troglodytes 5.2; Gorilla gorilla 7.4; Pongo pygmaeus 19.2; Hylobates lar 20.3; Old World monkeys 31.4; Lagothrix lagotricha 46.0; Cebus albifrons 59.5; three lemur species 67.0, and Galago crassicaudatus 73.3 million years. The LCA results and the approach are shortly discussed. A full account of this extended investigation including results on nonprimate mammals and on the determinant structures and the immunologically derived evolutionary rates of the proteins analyzed will be published elsewhere.

  19. Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis

    PubMed Central

    Irie, Naoki; Kuratani, Shigeru

    2011-01-01

    One of the central issues in evolutionary developmental biology is how we can formulate the relationships between evolutionary and developmental processes. Two major models have been proposed: the 'funnel-like' model, in which the earliest embryo shows the most conserved morphological pattern, followed by diversifying later stages, and the 'hourglass' model, in which constraints are imposed to conserve organogenesis stages, which is called the phylotypic period. Here we perform a quantitative comparative transcriptome analysis of several model vertebrate embryos and show that the pharyngula stage is most conserved, whereas earlier and later stages are rather divergent. These results allow us to predict approximate developmental timetables between different species, and indicate that pharyngula embryos have the most conserved gene expression profiles, which may be the source of the basic body plan of vertebrates. PMID:21427719

  20. Extreme storm surges: a comparative study of frequency analysis approaches

    NASA Astrophysics Data System (ADS)

    Hamdi, Y.; Bardet, L.; Duluc, C.-M.; Rebour, V.

    2013-11-01

    In France, nuclear facilities were designed to very low probabilities of failure. Nevertheless, exceptional climatic events have given rise to surges much larger than observations (outliers) and had clearly illustrated the potential to underestimate the extreme water levels calculated with the current statistical methods. The objective of the present work is to conduct a comparative study of three approaches including the Annual Maxima (AM), the Peaks-Over Threshold (POT) and the r-Largest Order Statistics (r-LOS). These methods are illustrated in a real analysis case study. All the data sets were screened for outliers. Non-parametric tests for randomness, homogeneity and stationarity of time series were used. The shape and scale parameters stability plots, the mean excess residual life plot and the stability of the standard errors of return levels were used to select optimal thresholds and r values for the POT and r-LOS method, respectively. The comparison of methods was based on: (i) the uncertainty degrees, (ii) the adequacy criteria and tests and (iii) the visual inspection. It was found that the r-LOS and POT methods have reduced the uncertainty on the distributions parameters and return level estimates and have systematically shown values of the 100 and 500 yr return levels smaller than those estimated with the AM method. Results have also shown that none of the compared methods has allowed a good fitting at the right tail of the distribution in the presence of outliers. As a perspective, the use of historical information was proposed in order to increase the representativity of outliers in data sets. Findings are of practical relevance not only to nuclear energy operators in France, for applications in storm surge hazard analysis and flood management, but also for the optimal planning and design of facilities to withstand extreme environmental conditions, with an appropriate level of risk.

  1. Comparative analysis of hepatocellular carcinoma and cirrhosis gene expression profiles

    PubMed Central

    Jiang, Mingming; Zeng, Qingfang; Dai, Suiping; Liang, Huixia; Dai, Fengying; Xie, Xueling; Lu, Kunlin; Gao, Chunfang

    2017-01-01

    Gene expression data of hepatocellular carcinoma (HCC) was compared with that of cirrhosis (C) to identify critical genes in HCC. A total of five gene expression data sets were downloaded from Gene Expression Omnibus. HCC and healthy samples were combined as dataset HCC, whereas cirrhosis samples were included in dataset C. A network was constructed for dataset HCC with the package R for performing Weighted Gene Co-expression Network Analysis. Modules were identified by cluster analysis with the packages flashClust and dynamicTreeCut. Hub genes were screened out by calculating connectivity. Functional annotations were assigned to the hub genes using the Database for Annotation, Visualization and Integration Discovery, and functional annotation networks were visualized with Cytoscape. Following the exclusion of outlier samples, 394 HCC samples and 47 healthy samples were included in dataset HCC and 233 cirrhosis samples were included in dataset C. A total of 6 modules were identified in the weighted gene co-expression network of dataset HCC (blue, brown, turquoise, green, red and yellow). Modules blue, brown and turquoise had high preservation whereas module yellow exhibited the lowest preservation. These modules were associated with transcription, mitosis, cation transportation, cation homeostasis, secretion and regulation of cyclase activity. Various hub genes of module yellow were cytokines, including chemokine (C-C motif) ligand 22 and interleukin-19, which may be important in the development of HCC. Gene expression profiles of HCC were compared with those of cirrhosis and numerous critical genes were identified, which may contribute to the progression of HCC. Further studies on these genes may improve the understanding of HCC pathogenesis. PMID:27959423

  2. Comparative expression pathway analysis of human and canine mammary tumors

    PubMed Central

    Uva, Paolo; Aurisicchio, Luigi; Watters, James; Loboda, Andrey; Kulkarni, Amit; Castle, John; Palombo, Fabio; Viti, Valentina; Mesiti, Giuseppe; Zappulli, Valentina; Marconato, Laura; Abramo, Francesca; Ciliberto, Gennaro; Lahm, Armin; La Monica, Nicola; de Rinaldis, Emanuele

    2009-01-01

    Background Spontaneous tumors in dog have been demonstrated to share many features with their human counterparts, including relevant molecular targets, histological appearance, genetics, biological behavior and response to conventional treatments. Mammary tumors in dog therefore provide an attractive alternative to more classical mouse models, such as transgenics or xenografts, where the tumour is artificially induced. To assess the extent to which dog tumors represent clinically significant human phenotypes, we performed the first genome-wide comparative analysis of transcriptional changes occurring in mammary tumors of the two species, with particular focus on the molecular pathways involved. Results We analyzed human and dog gene expression data derived from both tumor and normal mammary samples. By analyzing the expression levels of about ten thousand dog/human orthologous genes we observed a significant overlap of genes deregulated in the mammary tumor samples, as compared to their normal counterparts. Pathway analysis of gene expression data revealed a great degree of similarity in the perturbation of many cancer-related pathways, including the 'PI3K/AKT', 'KRAS', 'PTEN', 'WNT-beta catenin' and 'MAPK cascade'. Moreover, we show that the transcriptional relationships between different gene signatures observed in human breast cancer are largely maintained in the canine model, suggesting a close interspecies similarity in the network of cancer signalling circuitries. Conclusion Our data confirm and further strengthen the value of the canine mammary cancer model and open up new perspectives for the evaluation of novel cancer therapeutics and the development of prognostic and diagnostic biomarkers to be used in clinical studies. PMID:19327144

  3. A comparative analysis of GPU implementations of spectral unmixing algorithms

    NASA Astrophysics Data System (ADS)

    Sanchez, Sergio; Plaza, Antonio

    2011-11-01

    Spectral unmixing is a very important task for remotely sensed hyperspectral data exploitation. It involves the separation of a mixed pixel spectrum into its pure component spectra (called endmembers) and the estimation of the proportion (abundance) of each endmember in the pixel. Over the last years, several algorithms have been proposed for: i) automatic extraction of endmembers, and ii) estimation of the abundance of endmembers in each pixel of the hyperspectral image. The latter step usually imposes two constraints in abundance estimation: the non-negativity constraint (meaning that the estimated abundances cannot be negative) and the sum-toone constraint (meaning that the sum of endmember fractional abundances for a given pixel must be unity). These two steps comprise a hyperspectral unmixing chain, which can be very time-consuming (particularly for high-dimensional hyperspectral images). Parallel computing architectures have offered an attractive solution for fast unmixing of hyperspectral data sets, but these systems are expensive and difficult to adapt to on-board data processing scenarios, in which low-weight and low-power integrated components are essential to reduce mission payload and obtain analysis results in (near) real-time. In this paper, we perform an inter-comparison of parallel algorithms for automatic extraction of pure spectral signatures or endmembers and for estimation of the abundance of endmembers in each pixel of the scene. The compared techniques are implemented in graphics processing units (GPUs). These hardware accelerators can bridge the gap towards on-board processing of this kind of data. The considered algorithms comprise the orthogonal subspace projection (OSP), iterative error analysis (IEA) and N-FINDR algorithms for endmember extraction, as well as unconstrained, partially constrained and fully constrained abundance estimation. The considered implementations are inter-compared using different GPU architectures and hyperspectral

  4. Comparative and Evolutionary Analysis of Major Peanut Allergen Gene Families

    PubMed Central

    Ratnaparkhe, Milind B.; Lee, Tae-Ho; Tan, Xu; Wang, Xiyin; Li, Jingping; Kim, Changsoo; Rainville, Lisa K.; Lemke, Cornelia; Compton, Rosana O.; Robertson, Jon; Gallo, Maria; Bertioli, David J.; Paterson, Andrew H.

    2014-01-01

    Peanut (Arachis hypogaea L.) causes one of the most serious food allergies. Peanut seed proteins, Arah1, Arah2, and Arah3, are considered to be among the most important peanut allergens. To gain insights into genome organization and evolution of allergen-encoding genes, approximately 617 kb from the genome of cultivated peanut and 215 kb from a wild relative were sequenced including three Arah1, one Arah2, eight Arah3, and two Arah6 gene family members. To assign polarity to differences between homoeologous regions in peanut, we used as outgroups the single orthologous regions in Medicago, Lotus, common bean, chickpea, and pigeonpea, which diverged from peanut about 50 Ma and have not undergone subsequent polyploidy. These regions were also compared with orthologs in many additional dicot plant species to help clarify the timing of evolutionary events. The lack of conservation of allergenic epitopes between species, and the fact that many different proteins can be allergenic, makes the identification of allergens across species by comparative studies difficult. The peanut allergen genes are interspersed with low-copy genes and transposable elements. Phylogenetic analyses revealed lineage-specific expansion and loss of low-copy genes between species and homoeologs. Arah1 syntenic regions are conserved in soybean, pigeonpea, tomato, grape, Lotus, and Arabidopsis, whereas Arah3 syntenic regions show genome rearrangements. We infer that tandem and segmental duplications led to the establishment of the Arah3 gene family. Our analysis indicates differences in conserved motifs in allergen proteins and in the promoter regions of the allergen-encoding genes. Phylogenetic analysis and genomic organization studies provide new insights into the evolution of the major peanut allergen-encoding genes. PMID:25193311

  5. Nucleic acid structure analysis: Local, mathematically rigorous, comparable

    SciTech Connect

    Babcock, M.S.

    1993-01-01

    A more sophisticated mathematical treatments for analyzing nucleic acid coordinate data is presented. The methodology is both rigorous and comparable for parameterizing nucleic acids in terms of the local structural morphology of complementary and neighboring base pairs. Chapter 1 clearly defines the problems of nucleic acid structure parameterization by examining the consequences of the EMBO workshop guidelines published in 1989. Chapter 2 defines mathematics to rigorously and comparably calculate all of the parameters for nucleic acid structure from a local viewpoint. The mathematics satisfies all EMBO guidelines for local structural parameters. One of the main features making this program flexible is that any base pair relationship can be rigorously analyzed. This is because the meaning of zero for the complementary base parameters is clearly definable for any base pairing relationship. Chapter 3 analyses and explains why certain pairwise parameter correlations were observed between rotational and translational parameters. It was observed that the method of calculating the rotational parameters greatly affected the calculated translational parameters. As a result of our analysis, we determined the optimum location about which rotations should be performed in order to reduce and/or eliminate the correlations which are artifacts of the mathematics employed and do not reflect true structural properties of nucleic acids. Chapter 4 presents an analysis of the available nucleic acid X-ray crystallographic structural data, showing that the experimental base pairs do not generally have the ideal Watson-Crick structure. By utilizing a hybrid between helical and Cartesian parameterization methods, the relative distribution of the complementary base parameters was examined as a function of the nearest neighboring base pairs. The final chapter includes a review article explaining each of the available methods in plain English as well as giving the mathematics.

  6. Comparative analysis of hepatocellular carcinoma and cirrhosis gene expression profiles.

    PubMed

    Jiang, Mingming; Zeng, Qingfang; Dai, Suiping; Liang, Huixia; Dai, Fengying; Xie, Xueling; Lu, Kunlin; Gao, Chunfang

    2017-01-01

    Gene expression data of hepatocellular carcinoma (HCC) was compared with that of cirrhosis (C) to identify critical genes in HCC. A total of five gene expression data sets were downloaded from Gene Expression Omnibus. HCC and healthy samples were combined as dataset HCC, whereas cirrhosis samples were included in dataset C. A network was constructed for dataset HCC with the package R for performing Weighted Gene Co‑expression Network Analysis. Modules were identified by cluster analysis with the packages flashClust and dynamicTreeCut. Hub genes were screened out by calculating connectivity. Functional annotations were assigned to the hub genes using the Database for Annotation, Visualization and Integration Discovery, and functional annotation networks were visualized with Cytoscape. Following the exclusion of outlier samples, 394 HCC samples and 47 healthy samples were included in dataset HCC and 233 cirrhosis samples were included in dataset C. A total of 6 modules were identified in the weighted gene co‑expression network of dataset HCC (blue, brown, turquoise, green, red and yellow). Modules blue, brown and turquoise had high preservation whereas module yellow exhibited the lowest preservation. These modules were associated with transcription, mitosis, cation transportation, cation homeostasis, secretion and regulation of cyclase activity. Various hub genes of module yellow were cytokines, including chemokine (C‑C motif) ligand 22 and interleukin‑19, which may be important in the development of HCC. Gene expression profiles of HCC were compared with those of cirrhosis and numerous critical genes were identified, which may contribute to the progression of HCC. Further studies on these genes may improve the understanding of HCC pathogenesis.

  7. Bisphenol A alters gut microbiome: Comparative metagenomics analysis.

    PubMed

    Lai, Keng-Po; Chung, Yan-Tung; Li, Rong; Wan, Hin-Ting; Wong, Chris Kong-Chu

    2016-11-01

    Mounting evidence has shown that an alteration of the gut microbiota is associated with diet, and plays an important role in animal health and metabolic diseases. However, little is known about the influence of environmental contaminants on the gut microbial community. Bisphenol A (BPA), which is widely used for manufacturing plastic products, has recently been classified as an environmental obesogen. Although many studies have demonstrated the metabolic-disrupting effects of BPA on liver and pancreatic functions, the possible effects of this synthetic compound on the metabolic diversity of the intestinal microbiota is unknown. Using 16S rRNA gene sequencing analysis on caecum samples of CD-1 mice, the present study aimed to test the hypothesis that dietary BPA intake may influence the gut microbiota composition and functions, an important attributing factor to development of the metabolic syndrome. A high-fat diet (HFD) and high-sucrose diet (HSD) were included as the positive controls for comparing the changes in the intestinal microbial profiles. Our results demonstrated a significant reduction of species diversity in the gut microbiota of BPA-fed mice. Alpha and beta diversity analyses showed that dietary BPA intake led to a similar gut microbial community structure as that induced by HFD and HSD in mice. In addition, comparative analysis of the microbial communities revealed that both BPA and a HFD favored the growth of Proteobacteria, a microbial marker of dysbiosis. Consistently, growth induction of the family Helicobacteraceae and reduction of the Firmicutes and Clostridia populations were observed in the mice fed BPA or a HFD. Collectively, our study highlighted that the effects of dietary BPA intake on the shift of microbial community structure were similar to those of a HFD and HSD, and revealed microbial markers for the development of diseases associated with an unstable microbiota.

  8. Nephelines from the Somma-Vesuvius volcanic complex (Southern Italy): crystal-chemical, structural and genetic investigations

    NASA Astrophysics Data System (ADS)

    Balassone, Giuseppina; Kahlenberg, Volker; Altomare, Angela; Mormone, Angela; Rizzi, Rosanna; Saviano, Michele; Mondillo, Nicola

    2013-05-01

    Sixteen nephelines from different geological occurrences were sampled at the type-locality, the Somma-Vesuvius volcanic complex (southern Italy), and investigated for their chemistry and crystal structure obtained by both single-crystal and powder X-ray diffraction. Nepheline-bearing samples are metamorphic or from magmatic ejecta and pumice deposits. The lower K contents characterize the pumice- and some metamorphic-derived nephelines, whereas the higher ones are found in some samples from magmatic nodules. The amount of the anorthite molecule, quite low on average, can be more variable in the metamorphic nephelines. The crystal-structure investigations on Somma-Vesuvius samples compare well with previous studies of natural nephelines. All 16 nepheline samples adopt space group P63. The observed lattice parameters vary between 9.9768-9.9946 Å (for a) and 8.3614-8.3777 Å (for c), respectively. Furthermore, chemical analysis revealed that all specimens exhibit an excess of Si relative the ideal Si:Al ratio of 1:1. The analysis of the T-O distances in our samples clearly indicates a distinct ordering process of aluminium and silicon on the tetrahedral sites which is an agreement with Loewenstein's rule. A linear correlation between the distance of symmetry equivalent split atoms O(1)-O(1)' and the T(1)-O(1)-T(2) tilt angle was observed. The average (B = Na) distances of all crystals are very similar which is consistent with the outcome of the site population refinement indicating full occupancy with sodium. Oriented precession-type sections of reciprocal space indicated the presence of at least the most intense family of satellite peaks, demonstrating that this group of satellite reflections can occur not only in nephelines from pegmatites and ijolites but also in rocks from completely different petrological settings.

  9. Nephelines from the Somma-Vesuvius volcanic complex (Southern Italy): crystal-chemical, structural and genetic investigations

    NASA Astrophysics Data System (ADS)

    Balassone, Giuseppina; Kahlenberg, Volker; Altomare, Angela; Mormone, Angela; Rizzi, Rosanna; Saviano, Michele; Mondillo, Nicola

    2014-02-01

    Sixteen nephelines from different geological occurrences were sampled at the type-locality, the Somma-Vesuvius volcanic complex (southern Italy), and investigated for their chemistry and crystal structure obtained by both single-crystal and powder X-ray diffraction. Nepheline-bearing samples are metamorphic or from magmatic ejecta and pumice deposits. The lower K contents characterize the pumice- and some metamorphic-derived nephelines, whereas the higher ones are found in some samples from magmatic nodules. The amount of the anorthite molecule, quite low on average, can be more variable in the metamorphic nephelines. The crystal-structure investigations on Somma-Vesuvius samples compare well with previous studies of natural nephelines. All 16 nepheline samples adopt space group P63. The observed lattice parameters vary between 9.9768-9.9946 Å (for a) and 8.3614-8.3777 Å (for c), respectively. Furthermore, chemical analysis revealed that all specimens exhibit an excess of Si relative the ideal Si:Al ratio of 1:1. The analysis of the T-O distances in our samples clearly indicates a distinct ordering process of aluminium and silicon on the tetrahedral sites which is an agreement with Loewenstein's rule. A linear correlation between the distance of symmetry equivalent split atoms O(1)-O(1)' and the T(1)-O(1)- T(2) tilt angle was observed. The average < B-O> ( B = Na) distances of all crystals are very similar which is consistent with the outcome of the site population refinement indicating full occupancy with sodium. Oriented precession-type sections of reciprocal space indicated the presence of at least the most intense family of satellite peaks, demonstrating that this group of satellite reflections can occur not only in nephelines from pegmatites and ijolites but also in rocks from completely different petrological settings.

  10. Comparative analysis of methods for genome-wide nucleosome cartography.

    PubMed

    Quintales, Luis; Vázquez, Enrique; Antequera, Francisco

    2015-07-01

    Nucleosomes contribute to compacting the genome into the nucleus and regulate the physical access of regulatory proteins to DNA either directly or through the epigenetic modifications of the histone tails. Precise mapping of nucleosome positioning across the genome is, therefore, essential to understanding the genome regulation. In recent years, several experimental protocols have been developed for this purpose that include the enzymatic digestion, chemical cleavage or immunoprecipitation of chromatin followed by next-generation sequencing of the resulting DNA fragments. Here, we compare the performance and resolution of these methods from the initial biochemical steps through the alignment of the millions of short-sequence reads to a reference genome to the final computational analysis to generate genome-wide maps of nucleosome occupancy. Because of the lack of a unified protocol to process data sets obtained through the different approaches, we have developed a new computational tool (NUCwave), which facilitates their analysis, comparison and assessment and will enable researchers to choose the most suitable method for any particular purpose. NUCwave is freely available at http://nucleosome.usal.es/nucwave along with a step-by-step protocol for its use. © The Author 2014. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

  11. Comparative analysis reveals the underlying mechanism of vertebrate seasonal reproduction.

    PubMed

    Ikegami, Keisuke; Yoshimura, Takashi

    2016-02-01

    Animals utilize photoperiodic changes as a calendar to regulate seasonal reproduction. Birds have highly sophisticated photoperiodic mechanisms and functional genomics analysis in quail uncovered the signal transduction pathway regulating avian seasonal reproduction. Birds detect light with deep brain photoreceptors. Long day (LD) stimulus induces secretion of thyroid-stimulating hormone (TSH) from the pars tuberalis (PT) of the pituitary gland. PT-derived TSH locally activates thyroid hormone (TH) in the hypothalamus, which induces gonadotropin-releasing hormone (GnRH) and hence gonadotropin secretion. However, during winter, low temperatures increase serum TH for adaptive thermogenesis, which accelerates germ cell apoptosis by activating the genes involved in metamorphosis. Therefore, TH has a dual role in the regulation of seasonal reproduction. Studies using TSH receptor knockout mice confirmed the involvement of PT-derived TSH in mammalian seasonal reproduction. In addition, studies in mice revealed that the tissue-specific glycosylation of TSH diversifies its function in the circulation to avoid crosstalk. In contrast to birds and mammals, one of the molecular machineries necessary for the seasonal reproduction of fish are localized in the saccus vasculosus from the photoreceptor to the neuroendocrine output. Thus, comparative analysis is a powerful tool to uncover the universality and diversity of fundamental properties in various organisms.

  12. Comparative analysis of quantitative efficiency evaluation methods for transportation networks

    PubMed Central

    He, Yuxin; Hong, Jian

    2017-01-01

    An effective evaluation of transportation network efficiency could offer guidance for the optimal control of urban traffic. Based on the introduction and related mathematical analysis of three quantitative evaluation methods for transportation network efficiency, this paper compares the information measured by them, including network structure, traffic demand, travel choice behavior and other factors which affect network efficiency. Accordingly, the applicability of various evaluation methods is discussed. Through analyzing different transportation network examples it is obtained that Q-H method could reflect the influence of network structure, traffic demand and user route choice behavior on transportation network efficiency well. In addition, the transportation network efficiency measured by this method and Braess’s Paradox can be explained with each other, which indicates a better evaluation of the real operation condition of transportation network. Through the analysis of the network efficiency calculated by Q-H method, it can also be drawn that a specific appropriate demand is existed to a given transportation network. Meanwhile, under the fixed demand, both the critical network structure that guarantees the stability and the basic operation of the network and a specific network structure contributing to the largest value of the transportation network efficiency can be identified. PMID:28399165

  13. Comparative analysis of actigraphy performance in healthy young subjects.

    PubMed

    Bellone, Giannina J; Plano, Santiago A; Cardinali, Daniel P; Chada, Daniel Pérez; Vigo, Daniel E; Golombek, Diego A

    2016-01-01

    Sleep-related health disorders are increasing worldwide; diagnosis and treatment of such sleep diseases are commonly invasive and sometimes unpractical or expensive. Actigraphy has been recently introduced as a tool for the study of sleep and circadian disorders; however, there are several devices that claim to be useful for research and have not been thoroughly tested. This comparative study provides activity, sleep and temperature information regarding several of the most commonly used actigraphers: Micro-Mini Motion Logger; Act Trust; Misfit Flash; Fitbit Flex & Thermochron. Twenty-two healthy young subjects were assessed with five different commercial actigraphs (Micro-Mini Motionlogger Watch, Condor Act Trust, MisFit Flash and Fitbit Flex) and a temperature recorder (Thermochron), and also completed a sleep diary for a week. There were not significant differences in the analysis of rest-activity pattern between devices. Temperature rhythm comparison between the Act Trust and the Thermochron showed significant differences in rhythm percentage (p<0.05) and mesor (p<0.0563) but not in amplitude or acrophase. Although data accessibility and ease of use was very different for the diverse devices, there were no significant differences for sleep onset, total sleep time and sleep efficiency recordings, where applicable. In conclusion, depending on the type of study and analysis desired (as well as cost and compliance of use), we propose some relative advantages for the different actigraphy/temperature recording devices.

  14. Protein intrinsic disorder toolbox for comparative analysis of viral proteins

    PubMed Central

    Goh, Gerard Kian-Meng; Dunker, A Keith; Uversky, Vladimir N

    2008-01-01

    To examine the usefulness of protein disorder predictions as a tool for the comparative analysis of viral proteins, a relational database has been constructed. The database includes proteins from influenza A and HIV-related viruses. Annotations include viral protein sequence, disorder prediction, structure, and function. Location of each protein within a virion, if known, is also denoted. Our analysis reveals a clear relationship between proximity to the RNA core and the percentage of predicted disordered residues for a set of influenza A virus proteins. Neuraminidases (NA) and hemagglutinin (HA) of major influenza A pandemics tend to pair in such a way that both proteins tend to be either ordered-ordered or disordered-disordered by prediction. This may be the result of these proteins evolving from being lipid-associated. High abundance of intrinsic disorder in envelope and matrix proteins from HIV-related viruses likely represents a mechanism where HIV virions can escape immune response despite the availability of antibodies for the HIV-related proteins. This exercise provides an example showing how the combined use of intrinsic disorder predictions and relational databases provides an improved understanding of the functional and structural behaviour of viral proteins. PMID:18831795

  15. Comparative analysis of essential genes in prokaryotic genomic islands

    PubMed Central

    Zhang, Xi; Peng, Chong; Zhang, Ge; Gao, Feng

    2015-01-01

    Essential genes are thought to encode proteins that carry out the basic functions to sustain a cellular life, and genomic islands (GIs) usually contain clusters of horizontally transferred genes. It has been assumed that essential genes are not likely to be located in GIs, but systematical analysis of essential genes in GIs has not been explored before. Here, we have analyzed the essential genes in 28 prokaryotes by statistical method and reached a conclusion that essential genes in GIs are significantly fewer than those outside GIs. The function of 362 essential genes found in GIs has been explored further by BLAST against the Virulence Factor Database (VFDB) and the phage/prophage sequence database of PHAge Search Tool (PHAST). Consequently, 64 and 60 eligible essential genes are found to share the sequence similarity with the virulence factors and phage/prophages-related genes, respectively. Meanwhile, we find several toxin-related proteins and repressors encoded by these essential genes in GIs. The comparative analysis of essential genes in genomic islands will not only shed new light on the development of the prediction algorithm of essential genes, but also give a clue to detect the functionality of essential genes in genomic islands. PMID:26223387

  16. Comparative performance analysis: Commercial cut-flower rose production

    SciTech Connect

    Whittier, J.; Fischer, C.L.

    1990-04-01

    A comparative performance analysis has been conducted to examine the various factors associated with establishing and operating a commercial rose cut-flower greenhouse in ten different locations across the United States. Plant productivity, defined as net blooms produced per plant per year, is largely dependent upon local climatic conditions and technological improvements. Regional variations in productivity have been explicitly analyzed. The greenhouse operation is assumed to be four acres in size and the facilities utilize current technologies. The operation is designed as a professionally-organized company with an owner/manager, grower, and salesperson. The primary product is a red hybrid tea rose for sales. Selling markets vary by location, but in general they are large metropolitan areas. The analysis strongly indicates that new installations for cut-flower rose production are profitable in several areas in the U.S. Southwest, particularly in New Mexico, Arizona, and Texas. No ones stands out as a favored location. Las Cruces, New Mexico, has the highest net present volume and return on investment results. 68 refs., 1 fig., 8 tabs.

  17. Sequence and comparative analysis of Leuconostoc dairy bacteriophages.

    PubMed

    Kot, Witold; Hansen, Lars H; Neve, Horst; Hammer, Karin; Jacobsen, Susanne; Pedersen, Per D; Sørensen, Søren J; Heller, Knut J; Vogensen, Finn K

    2014-04-17

    Bacteriophages attacking Leuconostoc species may significantly influence the quality of the final product. There is however limited knowledge of this group of phages in the literature. We have determined the complete genome sequences of nine Leuconostoc bacteriophages virulent to either Leuconostoc mesenteroides or Leuconostoc pseudomesenteroides strains. The phages have dsDNA genomes with sizes ranging from 25.7 to 28.4 kb. Comparative genomics analysis helped classify the 9 phages into two classes, which correlates with the host species. High percentage of similarity within the classes on both nucleotide and protein levels was observed. Genome comparison also revealed very high conservation of the overall genomic organization between the classes. The genes were organized in functional modules responsible for replication, packaging, head and tail morphogenesis, cell lysis and regulation and modification, respectively. No lysogeny modules were detected. To our knowledge this report provides the first comparative genomic work done on Leuconostoc dairy phages. Copyright © 2014 Elsevier B.V. All rights reserved.

  18. Medical and nursing clinical decision making: a comparative epistemological analysis.

    PubMed

    Rashotte, Judy; Carnevale, F A

    2004-07-01

    The aim of this article is to explore the complex forms of knowledge involved in diagnostic and interventional decision making by comparing the processes in medicine and nursing, including nurse practitioners. Many authors assert that the practice of clinical decision making involves the application of theoretical knowledge (acquired in the classroom and textbooks) as well as research evidence, upon concrete particular cases. This approach draws on various universal principles and algorithms to facilitate the task. On the other hand, others argue that this involves an intuitive form of judgement that is difficult to teach, one that is acquired principally through experience. In an exploration of these issues, this article consists of three sections. A clarification of terms commonly used when discussing decision making is provided in the first section. In the second section, an epistemological analysis of decision making is presented by examining several perspectives and comparing them for their use in the nursing and medical literature. Bunge's epistemological framework for decision making (based on scientific realism) is explored for its fit with the aims of medicine and nursing. The final section presents a discussion of knowledge utilization and decision making as it relates to the implications for the education and ongoing development of nurse practitioners. It is concluded that Donald Schön's conception of reflective practice best characterizes the skillful conduct of clinical decision making.

  19. OGRe: a relational database for comparative analysis of mitochondrial genomes

    PubMed Central

    Jameson, Daniel; Gibson, Andrew P.; Hudelot, Cendrine; Higgs, Paul G.

    2003-01-01

    Organellar Genome Retrieval (OGRe) is a relational database of complete mitochondrial genome sequences for over 250 Metazoan species. OGRe provides a resource for the comparative analysis of mitochondrial genomes at several levels. At the sequence level, OGRe allows the retrieval of any selected set of mitochondrial genes from any selected set of species. Species are classified using a taxonomic system that allows easy selection of related groups of species. Sequence alignments are also available for some species. At the level of individual nucleotides, the system contains information on base frequencies and codon usage frequencies that can be compared between organisms. At the level of whole genomes, OGRe provides several ways of visualizing information on gene order. Diagrams illustrating the genome arrangement can be generated for any selected set of species automatically from the information in the database. Searches can be done based on gene arrangement to find sets of species that have the same order as one another. Diagrams for pairwise comparison of species can be produced that show the positions of break-points in the gene order and use colour to highlight the sections of the genome that have moved. OGRe is available from http://www.bioinf.man.ac.uk/ogre. PMID:12519982

  20. N-terminal protein processing: A comparative proteogenomic analysis

    SciTech Connect

    Bonissone, Stefano; Gupta, Nitin; Romine, Margaret F.; Bradshaw, Ralph A.; Pevzner, Pavel A.

    2013-01-01

    N-Terminal Methionine Excision (NME) is a universally conserved mechanism with the same specificity across all life forms that removes the first Methionine in proteins when the second residue is Gly, Ala, Ser, Cys, Thr, Pro, or Val. In spite of its necessity for proper cell functioning, the functional role of NME remains unclear. In 1988, Arfin and Bradshaw connected NME with the N-end protein degradation rule and postulated that the role of NME is to expose the stabilizing residues with the goal to resist protein degradation. While this explanation (that treats 7 stabilizing residues in the same manner) has become the de facto dogma of NME, comparative proteogenomics analysis of NME tells a different story. We suggest that the primary role of NME is to expose only two (rather than seven) amino acids Ala and Ser for post-translational modifications (e.g., acetylation) rather than to regulate protein degradation. We argue that, contrary to the existing view, NME is not crucially important for proteins with 5 other stabilizing residue at the 2nd positions that are merely bystanders (their function is not affected by NME) that become exposed to NME because their sizes are comparable or smaller than the size of Ala and Ser.

  1. Comparative Genomics Analysis in Prunoideae to Identify Biologically Relevant Polymorphisms

    PubMed Central

    Koepke, Tyson; Schaeffer, Scott; Harper, Artemus; Dicenta, Federico; Edwards, Mark; Henry, Robert J.; Møller, Birger Lindberg; Meisel, Lee; Oraguzie, Nnadozie; Silva, Herman; Sánchez-Pérez, Raquel; Dhingra, Amit

    2013-01-01

    Prunus is an economically important genus with a wide range of physiological and biological variability. Using the peach genome as a reference, sequencing reads from four almond accessions and one sweet cherry cultivar were used for comparative analysis of these three Prunus species. Reference mapping enabled the identification of many biological relevant polymorphisms within the individuals. Examining the depth of the polymorphisms and the overall scaffold coverage, we identified many potentially interesting regions including hundreds of small scaffolds with no coverage from any individual. Nonsense mutations account for about 70,000 of the 13 million identified single nucleotide polymorphisms (SNPs). Blast2GO analyses on these nonsense SNPs revealed several interesting results. First, nonsense SNPs were not evenly distributed across all gene ontology terms. Specifically, in comparison to peach, sweet cherry is found to have nonsense SNPs in two 1-aminocyclopropane-1-carboxylate synthase (ACS) genes and two 1-aminocyclopropane-1-carboxylate oxidase (ACO) genes. These polymorphisms may be at the root of the non-climacteric ripening of sweet cherry. A set of candidate genes associated with bitterness in almond were identified by comparing sweet and bitter almond sequences. To the best of our knowledge, this is the first report in plants of nonsense SNP abundance in a genus being linked to specific GO terms. PMID:23763653

  2. Comparative analysis of regulatory information and circuits across distant species.

    PubMed

    Boyle, Alan P; Araya, Carlos L; Brdlik, Cathleen; Cayting, Philip; Cheng, Chao; Cheng, Yong; Gardner, Kathryn; Hillier, LaDeana W; Janette, Judith; Jiang, Lixia; Kasper, Dionna; Kawli, Trupti; Kheradpour, Pouya; Kundaje, Anshul; Li, Jingyi Jessica; Ma, Lijia; Niu, Wei; Rehm, E Jay; Rozowsky, Joel; Slattery, Matthew; Spokony, Rebecca; Terrell, Robert; Vafeados, Dionne; Wang, Daifeng; Weisdepp, Peter; Wu, Yi-Chieh; Xie, Dan; Yan, Koon-Kiu; Feingold, Elise A; Good, Peter J; Pazin, Michael J; Huang, Haiyan; Bickel, Peter J; Brenner, Steven E; Reinke, Valerie; Waterston, Robert H; Gerstein, Mark; White, Kevin P; Kellis, Manolis; Snyder, Michael

    2014-08-28

    Despite the large evolutionary distances between metazoan species, they can show remarkable commonalities in their biology, and this has helped to establish fly and worm as model organisms for human biology. Although studies of individual elements and factors have explored similarities in gene regulation, a large-scale comparative analysis of basic principles of transcriptional regulatory features is lacking. Here we map the genome-wide binding locations of 165 human, 93 worm and 52 fly transcription regulatory factors, generating a total of 1,019 data sets from diverse cell types, developmental stages, or conditions in the three species, of which 498 (48.9%) are presented here for the first time. We find that structural properties of regulatory networks are remarkably conserved and that orthologous regulatory factor families recognize similar binding motifs in vivo and show some similar co-associations. Our results suggest that gene-regulatory properties previously observed for individual factors are general principles of metazoan regulation that are remarkably well-preserved despite extensive functional divergence of individual network connections. The comparative maps of regulatory circuitry provided here will drive an improved understanding of the regulatory underpinnings of model organism biology and how these relate to human biology, development and disease.

  3. Bursaphelenchus xylophilus and B. mucronatus secretomes: a comparative proteomic analysis

    PubMed Central

    Cardoso, Joana M. S.; Anjo, Sandra I.; Fonseca, Luís; Egas, Conceição; Manadas, Bruno; Abrantes, Isabel

    2016-01-01

    The pinewood nematode, Bursaphelenchus xylophilus, recognized as a worldwide major forest pest, is a migratory endoparasitic nematode with capacity to feed on pine tissues and also on fungi colonizing the trees. Bursaphelenchus mucronatus, the closest related species, differs from B. xylophilus on its pathogenicity, making this nematode a good candidate for comparative analyses. Secretome profiles of B. xylophilus and B. mucronatus were obtained and proteomic differences were evaluated by quantitative SWATH-MS. From the 681 proteins initially identified, 422 were quantified and compared between B. xylophilus and B. mucronatus secretomes and from these, 243 proteins were found differentially regulated: 158 and 85 proteins were increased in B. xylophilus and B. mucronatus secretomes, respectively. While increased proteins in B. xylophilus secretome revealed a strong enrichment in proteins with peptidase activity, the increased proteins in B. mucronatus secretome were mainly related to oxidative stress responses. The changes in peptidases were evaluated at the transcription level by RT-qPCR, revealing a correlation between the mRNA levels of four cysteine peptidases with secretion levels. The analysis presented expands our knowledge about molecular basis of B. xylophilus and B. mucronatus hosts interaction and supports the hypothesis of a key role of secreted peptidases in B. xylophilus pathogenicity. PMID:27941947

  4. Comparative proteomic analysis of floral color variegation in peach.

    PubMed

    Zhou, Yong; Wu, Xinxin; Zhang, Zhen; Gao, Zhihong

    2015-09-04

    Variegation in flower is a special trait in ornamental peach (Prunus persica L.). To investigate the mechanism of color variegation, we used a combination of two dimensional gel electrophoresis and mass spectrometry to explore the proteomic profiles between variegated flower (VF) and red flower (RF) buds of the peach cultivar 'Sahong Tao'. More than 500 highly reproducible protein spots (P < 0.05) were detected and 72 protein spots showed a greater than two-fold difference in their values. We identified 70 proteins that may play roles in petal coloration. The mRNA levels of the corresponding genes were detected using quantitative RT-PCR. The results show that most of the proteins are involved in energy and metabolism, which provide energy and substrates. We found that LDOX, WD40, ACC, and PPO II are related to the pigment biosynthetic pathway. The activity of PPO enzyme was further validated and showed the higher with significant differences in RF compared with the VF ones. Moreover, the four UCH proteins are involved in protein fate and may be important in post-translational modifications in peach flowers. Our study is the first comparative proteomic analysis of floral variegation and will contribute to further investigations into the molecular mechanism of flower petal coloration in ornamental peach. Copyright © 2015 Elsevier Inc. All rights reserved.

  5. Comparative genomics analysis in Prunoideae to identify biologically relevant polymorphisms.

    PubMed

    Koepke, Tyson; Schaeffer, Scott; Harper, Artemus; Dicenta, Federico; Edwards, Mark; Henry, Robert J; Møller, Birger L; Meisel, Lee; Oraguzie, Nnadozie; Silva, Herman; Sánchez-Pérez, Raquel; Dhingra, Amit

    2013-09-01

    Prunus is an economically important genus with a wide range of physiological and biological variability. Using the peach genome as a reference, sequencing reads from four almond accessions and one sweet cherry cultivar were used for comparative analysis of these three Prunus species. Reference mapping enabled the identification of many biological relevant polymorphisms within the individuals. Examining the depth of the polymorphisms and the overall scaffold coverage, we identified many potentially interesting regions including hundreds of small scaffolds with no coverage from any individual. Non-sense mutations account for about 70 000 of the 13 million identified single nucleotide polymorphisms (SNPs). Blast2GO analyses on these non-sense SNPs revealed several interesting results. First, non-sense SNPs were not evenly distributed across all gene ontology terms. Specifically, in comparison with peach, sweet cherry is found to have non-sense SNPs in two 1-aminocyclopropane-1-carboxylate synthase (ACS) genes and two 1-aminocyclopropane-1-carboxylate oxidase (ACO) genes. These polymorphisms may be at the root of the nonclimacteric ripening of sweet cherry. A set of candidate genes associated with bitterness in almond were identified by comparing sweet and bitter almond sequences. To the best of our knowledge, this is the first report in plants of non-sense SNP abundance in a genus being linked to specific GO terms.

  6. A meta-analysis comparing ALIF, PLIF, TLIF and LLIF.

    PubMed

    Teng, Ian; Han, Julian; Phan, Kevin; Mobbs, Ralph

    2017-10-01

    Lumbar interbody fusions have been widely used to treat degenerative lumbar disease that fails to respond to conservative treatment. This procedure is divided according to its approach: anterior lumbar interbody fusion (ALIF), posterior lumbar interbody fusion (PLIF), transforaminal lumbar interbody fusion (TLIF) and lateral lumbar interbody fusion (LLIF). Each approach has its own theoretical advantages and disadvantages; however, there have been no studies that compared these. Various full-text databases were systematically searched through December 2015. Data regarding the radiological, operative and clinical outcomes of each lumbar interbody fusion were extracted. All outcomes were pooled using random effects meta-analysis, with the relative risk (RR) and/or weighted mean difference (WMD) as the summary statistic. Thirty studies met the inclusion criteria. The ALIF procedure has been studied most intensively, followed by PLIF, TLIF and LLIF respectively. All four approaches had similar fusion rates (p=0.320 & 0.703). ALIF has superior radiological outcome, achieving better postoperative disc height (p=0.002 & 0.005) and postoperative segmental lordosis (p=0.013 & 0.000). TLIF had better Oswestry Disability Index scores (p=0.025 & 0.000) while PLIF had the greatest blood loss (p=0.032 & 0.006). Complication rates were similar between approaches. Other comparisons were either inconclusive or lacked data. There was marked less studies comparing against LLIF. Each approach has their own risks and benefits but similar fusion rates. Despite the large number of studies, there is little data overall when comparing specific aspects of lumbar interbody fusions. More studies, especially RCTs are needed to further explore this topic. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. Comparative secretome analysis of rat stomach under different nutritional status.

    PubMed

    Senin, Lucia L; Roca-Rivada, Arturo; Castelao, Cecilia; Alonso, Jana; Folgueira, Cintia; Casanueva, Felipe F; Pardo, Maria; Seoane, Luisa M

    2015-02-26

    Obesity is a major public health threat for many industrialised countries. Bariatric surgery is the most effective treatment against obesity, suggesting that gut derived signals are crucial for energy balance regulation. Several descriptive studies have proven the presence of gastric endogenous systems that modulate energy homeostasis; however, these systems and the interactions between them are still not well known. In the present study, we show for the first time the comparative 2-DE gastric secretome analysis under different nutritional status. We have identified 38 differently secreted proteins by comparing stomach secretomes from tissue explant cultures of rats under feeding, fasting and re-feeding conditions. Among the proteins identified, glyceraldehyde-3-phosphate dehydrogenase was found to be more abundant in gastric secretome and plasma after re-feeding, and downregulated in obesity. Additionally, two calponin-1 species were decreased in feeding state, and other were modulated by nutritional and metabolic conditions. These and other secreted proteins identified in this work may be considered as potential gastrokines implicated in food intake regulation. The present work has an important impact in the field of obesity, especially in the regulation of body weight maintenance by the stomach. Nowadays, the most effective treatment in the fight against obesity is bariatric surgery, which suggests that stomach derived signals might be crucial for the regulation of the energy homeostasis. However, until now, the knowledge about the gastrokines and its mechanism of action has been poorly elucidated. In the present work, we had updated a previously validated explant secretion model for proteomic studies; this analysis allowed us, for the first time, to study the gastric secretome without interferences from other organs. We had identified 38 differently secreted proteins comparing ex vivo cultured stomachs from rats under feeding, fasting and re-feeding regimes

  8. SILAC-based comparative analysis of pathogenic Escherichia coli secretomes.

    PubMed

    Boysen, Anders; Borch, Jonas; Krogh, Thøger Jensen; Hjernø, Karin; Møller-Jensen, Jakob

    2015-09-01

    Comparative studies of pathogenic bacteria and their non-pathogenic counterparts has led to the discovery of important virulence factors thereby generating insight into mechanisms of pathogenesis. Protein-based antigens for vaccine development are primarily selected among unique virulence-related factors produced by the pathogen of interest. However, recent work indicates that proteins that are not unique to the pathogen but instead selectively expressed compared to its non-pathogenic counterpart could also be vaccine candidates or targets for drug development. Modern methods in quantitative proteome analysis have the potential to discover both classes of proteins and hence form an important tool for discovering therapeutic targets. Adherent-invasive Escherichia coli (AIEC) and Enterotoxigenic E. coli (ETEC) are pathogenic variants of E. coli which cause intestinal disease in humans. AIEC is associated with Crohn's disease (CD), a chronic inflammatory condition of the gastrointestinal tract whereas ETEC is the major cause of human diarrhea which affects hundreds of millions annually. In spite of the disease burden associated with these pathogens, effective vaccines conferring long-term protection are still needed. In order to identify proteins with therapeutic potential, we have used mass spectrometry-based Stable Isotope Labeling with Amino acids in Cell culture (SILAC) quantitative proteomics method which allows us to compare the proteomes of pathogenic strains to commensal E. coli. In this study, we grew the pathogenic strains ETEC H10407, AIEC LF82 and the non-pathogenic reference strain E. coli K-12 MG1655 in parallel and used SILAC to compare protein levels in OMVs and culture supernatant. We have identified well-known virulence factors from both AIEC and ETEC, thus validating our experimental approach. In addition we find proteins that are not unique to the pathogenic strains but expressed at levels different from the commensal strain, including the

  9. Whole genome comparative analysis of four Georgian grape cultivars.

    PubMed

    Tabidze, V; Pipia, I; Gogniashvili, M; Kunelauri, N; Ujmajuridze, L; Pirtskhalava, M; Vishnepolsky, B; Hernandez, A G; Fields, C J; Beridze, Tengiz

    2017-08-07

    Grapevine is the one of the most important fruit species in the world. Comparative genome sequencing of grape cultivars is very important for the interpretation of the grape genome and understanding its evolution. The genomes of four Georgian grape cultivars-Chkhaveri, Saperavi, Meskhetian green, and Rkatsiteli, belonging to different haplogroups, were resequenced. The shotgun genomic libraries of grape cultivars were sequenced on an Illumina HiSeq. Pinot Noir nuclear, mitochondrial, and chloroplast DNA were used as reference. Mitochondrial DNA of Chkhaveri closely matches that of the reference Pinot noir mitochondrial DNA, with the exception of 16 SNPs found in the Chkhaveri mitochondrial DNA. The number of SNPs in mitochondrial DNA from Saperavi, Meskhetian green, and Rkatsiteli was 764, 702, and 822, respectively. Nuclear DNA differs from the reference by 1,800,675 nt in Chkhaveri, 1,063,063 nt in Meskhetian green, 2,174,995 in Saperavi, and 5,011,513 in Rkatsiteli. Unlike mtDNA Pinot noir, chromosomal DNA is closer to the Meskhetian green than to other cultivars. Substantial differences in the number of SNPs in mitochondrial and nuclear DNA of Chkhaveri and Pinot noir cultivars are explained by backcrossing or introgression of their wild predecessors before or during the process of domestication. Annotation of chromosomal DNA of Georgian grape cultivars by MEGANTE, a web-based annotation system, shows 66,745 predicted genes (Chkhaveri-17,409; Saperavi-17,021; Meskhetian green-18,355; and Rkatsiteli-13,960). Among them, 106 predicted genes and 43 pseudogenes of terpene synthase genes were found in chromosomes 12, 18 random (18R), and 19. Four novel TPS genes not present in reference Pinot noir DNA were detected. Two of them-germacrene A synthase (Chromosome 18R) and (-) germacrene D synthase (Chromosome 19) can be identified as putatively full-length proteins. This work performs the first attempt of the comparative whole genome analysis of different haplogroups

  10. Efficacy of escitalopram compared to citalopram: a meta-analysis.

    PubMed

    Montgomery, Stuart; Hansen, Thomas; Kasper, Siegfried

    2011-03-01

    The aim of this review was to assess the clinical relevance of the relative antidepressant efficacy of escitalopram and citalopram by meta-analysis. Studies in major depressive disorder (MDD) with both escitalopram and citalopram treatment arms were identified. Adult patients had to meet DSM-IV criteria for MDD. The primary outcome measure was the treatment difference in Montgomery-Asberg Depression Rating Scale (MADRS) total score at week 8 (or last assessment if <8 wk). Secondary outcome measures were response (≥ 50% improvement from baseline) and remission (MADRS ≤ 12). A search of the literature and websites found eight randomized controlled trials (RCTs) and onr naturalistic trial, with a total of 2009 patients (escitalopram, n=995; citalopram, n=1014). Escitalopram was significantly more effective than citalopram in overall treatment effect, with an estimated mean treatment difference of 1.7 points at week 8 (or last assessment if <8 wk) on the MADRS (95% CI 0.8-2.6, p=0.0002) (six RCTs used the MADRS), and in responder rate (8.3 percentage points, 95% CI 4.4-12.3) (eight RCTs) and remitter rate (17.6 percentage points, 95% CI 12.1-23.1) analyses (reported for four RCTs), corresponding to number-needed-to-treat (NNT) values of 11.9 (p<0.0001) for response and 5.7 (p<0.0001) for remission. The overall odds ratios were 1.44 (p<0.0003) for response and 1.86 (p<0.0001) for remission, in favour of escitalopram. In this meta-analysis, the statistically significant superior efficacy of escitalopram compared to citalopram was shown to be clinically relevant.

  11. Domain graph of Arabidopsis proteome by comparative analysis.

    PubMed

    Liu, Song; Zhang, Chi; Zhou, Yaoqi

    2005-01-01

    The domain graph of domains and domain combinations of Arabidopsis thaliana is established based on pfam 14.0 database and analyzed via comparison with 10 eukaryotic, 30 bacterial, and 16 archaeal proteomes. The comparative analysis of the domain graphs provides a useful platform for revealing global insights on the evolution of plant kingdom. More importantly, it is a powerful tool for searching not only the possible new function of both plant-specific and nonspecific domains via specific domain combinations in Arabidopsis thaliana but also the functional role of unknown domains. As an example, we present the functional link between ubiquitin and Myb_DNA-binding domains via Bromodomain as the plant specific evidence for the association between transcription and ubiquitin. We further show that PentatricoPeptide Repeats (PPR) proteins have plant-specific links with a wide variety of domains responsible for RNA binding/metabolism, modulation of protein-protein interactions, ubiquitin-conjugation, cell growth/maintenance, catalysis, and others. This further supports the recently proposed association of PPR proteins with specific RNA transcripts and defined effector proteins. Moreover, the domain graph built from tissue-specific genes is frequently associated with DNA binding domains, suggesting that the differentiation of tissue cell types is contributed mostly by tissue-specific transcriptional process. DOGMA (DOmain Graph via coMparitive analysis for Arabidopsis thaliana) is available on-line with a variety of search tools at http://theory.med.buffalo.edu/DOGMA. The database, which allows user-specified search for plant specific domains and their combinations, will be useful as an additional tool for annotation of the proteins that play specific roles in plants and other organisms.

  12. A comparative analysis of metacommunity types in the freshwater realm.

    PubMed

    Heino, Jani; Soininen, Janne; Alahuhta, Janne; Lappalainen, Jyrki; Virtanen, Risto

    2015-04-01

    Most metacommunity studies have taken a direct mechanistic approach, aiming to model the effects of local and regional processes on local communities within a metacommunity. An alternative approach is to focus on emergent patterns at the metacommunity level through applying the elements of metacommunity structure (EMS; Oikos, 97, 2002, 237) analysis. The EMS approach has very rarely been applied in the context of a comparative analysis of metacommunity types of main microbial, plant, and animal groups. Furthermore, to our knowledge, no study has associated metacommunity types with their potential ecological correlates in the freshwater realm. We assembled data for 45 freshwater metacommunities, incorporating biologically highly disparate organismal groups (i.e., bacteria, algae, macrophytes, invertebrates, and fish). We first examined ecological correlates (e.g., matrix properties, beta diversity, and average characteristics of a metacommunity, including body size, trophic group, ecosystem type, life form, and dispersal mode) of the three elements of metacommunity structure (i.e., coherence, turnover, and boundary clumping). Second, based on those three elements, we determined which metacommunity types prevailed in freshwater systems and which ecological correlates best discriminated among the observed metacommunity types. We found that the three elements of metacommunity structure were not strongly related to the ecological correlates, except that turnover was positively related to beta diversity. We observed six metacommunity types. The most common were Clementsian and quasi-nested metacommunity types, whereas Random, quasi-Clementsian, Gleasonian, and quasi-Gleasonian types were less common. These six metacommunity types were best discriminated by beta diversity and the first axis of metacommunity ecological traits, ranging from metacommunities of producer organisms occurring in streams to those of large predatory organisms occurring in lakes. Our results showed

  13. A comparative analysis of metacommunity types in the freshwater realm

    PubMed Central

    Heino, Jani; Soininen, Janne; Alahuhta, Janne; Lappalainen, Jyrki; Virtanen, Risto

    2015-01-01

    Most metacommunity studies have taken a direct mechanistic approach, aiming to model the effects of local and regional processes on local communities within a metacommunity. An alternative approach is to focus on emergent patterns at the metacommunity level through applying the elements of metacommunity structure (EMS; Oikos, 97, 2002, 237) analysis. The EMS approach has very rarely been applied in the context of a comparative analysis of metacommunity types of main microbial, plant, and animal groups. Furthermore, to our knowledge, no study has associated metacommunity types with their potential ecological correlates in the freshwater realm. We assembled data for 45 freshwater metacommunities, incorporating biologically highly disparate organismal groups (i.e., bacteria, algae, macrophytes, invertebrates, and fish). We first examined ecological correlates (e.g., matrix properties, beta diversity, and average characteristics of a metacommunity, including body size, trophic group, ecosystem type, life form, and dispersal mode) of the three elements of metacommunity structure (i.e., coherence, turnover, and boundary clumping). Second, based on those three elements, we determined which metacommunity types prevailed in freshwater systems and which ecological correlates best discriminated among the observed metacommunity types. We found that the three elements of metacommunity structure were not strongly related to the ecological correlates, except that turnover was positively related to beta diversity. We observed six metacommunity types. The most common were Clementsian and quasi-nested metacommunity types, whereas Random, quasi-Clementsian, Gleasonian, and quasi-Gleasonian types were less common. These six metacommunity types were best discriminated by beta diversity and the first axis of metacommunity ecological traits, ranging from metacommunities of producer organisms occurring in streams to those of large predatory organisms occurring in lakes. Our results showed

  14. Comparative proteomic analysis of Saccharomyces cerevisiae under different nitrogen sources.

    PubMed

    Zhao, Shaohui; Zhao, Xinrui; Zou, Huijun; Fu, Jianwei; Du, Guocheng; Zhou, Jingwen; Chen, Jian

    2014-04-14

    In cultures containing multiple sources of nitrogen, Saccharomyces cerevisiae exhibits a sequential use of nitrogen sources through a mechanism known as nitrogen catabolite repression (NCR). To identify proteins differentially expressed due to NCR, proteomic analysis of S. cerevisiae S288C under different nitrogen source conditions was performed using two-dimensional gel electrophoresis (2-DE), revealing 169 candidate protein spots. Among these 169 protein spots, 121 were identified by matrix assisted laser desorption ionization-time of flight/time of flight mass spectrometry (MALDI-TOF/TOF). The identified proteins were closely associated with four main biological processes through Gene Ontology (GO) categorical analysis. The identification of the potential proteins and cellular processes related to NCR offer a global overview of changes elicited by different nitrogen sources, providing clues into how yeast adapt to different nutritional conditions. Moreover, by comparing our proteomic data with corresponding mRNA data, proteins regulated at the transcriptional and post-transcriptional level could be distinguished. Biological significance In S. cerevisiae, different nitrogen sources provide different growth characteristics and generate different metabolites. The nitrogen catabolite repression (NCR) process plays an important role for S. cerevisiae in the ordinal utilization of different nitrogen sources. NCR process can result in significant shift of global metabolic networks. Previous works on NCR primarily focused on transcriptomic level. The results obtained in this study provided a global atlas of the proteome changes triggered by different nitrogen sources and would facilitate the understanding of mechanisms for how yeast could adapt to different nutritional conditions. Copyright © 2014 Elsevier B.V. All rights reserved.

  15. Comparative analysis of polygalacturonase in the fruit of strawberry cultivars.

    PubMed

    Zhou, H C; Li, G; Zhao, X; Li, L J

    2015-10-19

    The role of polygalacturonase (PG) in the development, ripening, and softening of fruit from two strawberry cultivars with different flesh firmness and softening characteristics was compared. Changes in PG activity and gene expression during development, ripening and softening were measured. The PG genes from each cultivar were cloned and analyzed, and were classified with other PG genes using phylogenetic analysis. In Toyonoka fruit, PG activity increased gradually, reaching a peak during the pink stage, and remained at this level during post-harvest softening. Changes in PG gene expression were consistent with PG activity in these softer fruits. In the firmer Sweet Charlie fruits, PG activity was detected during the initial development stage, reaching a peak at the white stage, thereafter decreasing gradually with ripening and remaining at this lower level throughout softening. Changes in PG gene expression and PG activity were not consistent in these fruit. For both Toyonoka and Sweet Charlie PG genes (FaTPG and FaSCPG, respectively), the open reading frame was 1218 bp, encoding 405 amino acids. Five different nucleotide sites were observed between the two sequences, leading to two amino acid sequence mutations. FaTPG, FaSCPG, and PG genes from the Fragaria vesca genome were classified into three clades using phylogenetic analysis. The clade containing PG genes involved in fruit softening had functional similarity but there were no functional differences between FaTPG and FaSCPG. Differences in PG activity, gene sequence, and gene expression may have led to different roles of PG during ripening and softening in strawberries with different textures.

  16. Specialty and Full-Service Hospitals: A Comparative Cost Analysis

    PubMed Central

    Carey, Kathleen; Burgess, James F; Young, Gary J

    2008-01-01

    Objective To compare the costs of physician-owned cardiac, orthopedic, and surgical single specialty hospitals with those of full-service hospital competitors. Data Sources The primary data sources are the Medicare Cost Reports for 1998–2004 and hospital inpatient discharge data for three of the states where single specialty hospitals are most prevalent, Texas, California, and Arizona. The latter were obtained from the Texas Department of State Health Services, the California Office of Statewide Health Planning and Development, and the Agency for Healthcare Research and Quality Healthcare Cost and Utilization Project. Additional data comes from the American Hospital Association Annual Survey Database. Study Design We identified all physician-owned cardiac, orthopedic, and surgical specialty hospitals in these three states as well as all full-service acute care hospitals serving the same market areas, defined using Dartmouth Hospital Referral Regions. We estimated a hospital cost function using stochastic frontier regression analysis, and generated hospital specific inefficiency measures. Application of t-tests of significance compared the inefficiency measures of specialty hospitals with those of full-service hospitals to make general comparisons between these classes of hospitals. Principal Findings Results do not provide evidence that specialty hospitals are more efficient than the full-service hospitals with whom they compete. In particular, orthopedic and surgical specialty hospitals appear to have significantly higher levels of cost inefficiency. Cardiac hospitals, however, do not appear to be different from competitors in this respect. Conclusions Policymakers should not embrace the assumption that physician-owned specialty hospitals produce patient care more efficiently than their full-service hospital competitors. PMID:18662170

  17. Model for Comparative Analysis of Antigen Receptor Repertoires

    PubMed Central

    Rempala, Grzegorz A.; Seweryn, Michał; Ignatowicz, Leszek

    2010-01-01

    In modern molecular biology one of the standard ways of analyzing a vertebrate immune system is to sequence and compare the counts of specific antigen receptor clones (either immunoglobulins or T-cell receptors) derived from various tissues under different experimental or clinical conditions. The resulting statistical challenges are difficult and do not fit readily into the standard statistical framework of contingency tables primarily due to the serious under-sampling of the receptor populations. This under-sampling is caused, on one hand, by the extreme diversity of antigen receptor repertoires maintained by the immune system and, on the other, by the high cost and labor intensity of the receptor data collection process. In most of the recent immunological literature the differences across antigen receptor populations are examined via non-parametric statistical measures of the species overlap and diversity borrowed from ecological studies. While this approach is robust in a wide range of situations, it seems to provide little insight into the underlying clonal size distribution and the overall mechanism differentiating the receptor populations. As a possible alternative, the current paper presents a parametric method that adjusts for the data under-sampling as well as provides a unifying approach to a simultaneous comparison of multiple receptor groups by means of the modern statistical tools of unsupervised learning. The parametric model is based on a flexible multivariate Poisson-lognormal distribution and is seen to be a natural generalization of the univariate Poisson-lognormal models used in the ecological studies of biodiversity patterns. The procedure for evaluating a model’s fit is described along with the public domain software developed to perform the necessary diagnostics. The model-driven analysis is seen to compare favorably vis a vis traditional methods when applied to the data from T-cell receptors in transgenic mice populations. PMID:20955715

  18. Comparative Analysis of the Mitochondrial Physiology of Pancreatic β Cells

    PubMed Central

    Kim, Chul; Patel, Pinal; Gouvin, Lindsey M.; Brown, Melissa L.; Khalil, Ahmed; Henchey, Elizabeth M; Heuck, Alejandro P.; Yadava, Nagendra

    2014-01-01

    The mitochondrial metabolism of β cells is thought to be highly specialized. Its direct comparison with other cells using isolated mitochondria is limited by the availability of islets/β cells in sufficient quantity. In this study, we have compared mitochondrial metabolism of INS1E/β cells with other cells in intact and permeabilized states. To selectively permeabilize the plasma membrane, we have evaluated the use of perfringolysin-O (PFO) in conjunction with microplate-based respirometry. PFO is a protein that binds membranes based on a threshold level of active cholesterol. Therefore, unless active cholesterol reaches a threshold level in mitochondria, they are expected to remain untouched by PFO. Cytochrome c sensitivity tests showed that in PFO-permeabilized cells, the mitochondrial integrity was completely preserved. Our data show that a time-dependent decline of the oligomycin-insensitive respiration observed in INS1E cells was due to a limitation in substrate supply to the respiratory chain. We predict that it is linked with the β cell-specific metabolism involving metabolites shuttling between the cytoplasm and mitochondria. In permeabilized β cells, the Complex l-dependent respiration was either transient or absent because of the inefficient TCA cycle. The TCA cycle insufficiency was confirmed by analysis of the CO2 evolution. This may be linked with lower levels of NAD+, which is required as a co-factor for CO2 producing reactions of the TCA cycle. β cells showed comparable OxPhos and respiratory capacities that were not affected by the inorganic phosphate (Pi) levels in the respiration medium. They showed lower ADP-stimulation of the respiration on different substrates. We believe that this study will significantly enhance our understanding of the β cell mitochondrial metabolism. PMID:25309834

  19. Comparative analysis of existing models for power-grid synchronization

    NASA Astrophysics Data System (ADS)

    Nishikawa, Takashi; Motter, Adilson E.

    2015-01-01

    The dynamics of power-grid networks is becoming an increasingly active area of research within the physics and network science communities. The results from such studies are typically insightful and illustrative, but are often based on simplifying assumptions that can be either difficult to assess or not fully justified for realistic applications. Here we perform a comprehensive comparative analysis of three leading models recently used to study synchronization dynamics in power-grid networks—a fundamental problem of practical significance given that frequency synchronization of all power generators in the same interconnection is a necessary condition for a power grid to operate. We show that each of these models can be derived from first principles within a common framework based on the classical model of a generator, thereby clarifying all assumptions involved. This framework allows us to view power grids as complex networks of coupled second-order phase oscillators with both forcing and damping terms. Using simple illustrative examples, test systems, and real power-grid datasets, we study the inherent frequencies of the oscillators as well as their coupling structure, comparing across the different models. We demonstrate, in particular, that if the network structure is not homogeneous, generators with identical parameters need to be modeled as non-identical oscillators in general. We also discuss an approach to estimate the required (dynamical) system parameters that are unavailable in typical power-grid datasets, their use for computing the constants of each of the three models, and an open-source MATLAB toolbox that we provide for these computations.

  20. Comparative Analysis of Acinetobacters: Three Genomes for Three Lifestyles

    PubMed Central

    Vallenet, David; Nordmann, Patrice; Barbe, Valérie; Poirel, Laurent; Mangenot, Sophie; Bataille, Elodie; Dossat, Carole; Gas, Shahinaz; Kreimeyer, Annett; Lenoble, Patricia; Oztas, Sophie; Poulain, Julie; Segurens, Béatrice; Robert, Catherine; Abergel, Chantal; Claverie, Jean-Michel; Raoult, Didier; Médigue, Claudine; Weissenbach, Jean; Cruveiller, Stéphane

    2008-01-01

    Acinetobacter baumannii is the source of numerous nosocomial infections in humans and therefore deserves close attention as multidrug or even pandrug resistant strains are increasingly being identified worldwide. Here we report the comparison of two newly sequenced genomes of A. baumannii. The human isolate A. baumannii AYE is multidrug resistant whereas strain SDF, which was isolated from body lice, is antibiotic susceptible. As reference for comparison in this analysis, the genome of the soil-living bacterium A. baylyi strain ADP1 was used. The most interesting dissimilarities we observed were that i) whereas strain AYE and A. baylyi genomes harbored very few Insertion Sequence elements which could promote expression of downstream genes, strain SDF sequence contains several hundred of them that have played a crucial role in its genome reduction (gene disruptions and simple DNA loss); ii) strain SDF has low catabolic capacities compared to strain AYE. Interestingly, the latter has even higher catabolic capacities than A. baylyi which has already been reported as a very nutritionally versatile organism. This metabolic performance could explain the persistence of A. baumannii nosocomial strains in environments where nutrients are scarce; iii) several processes known to play a key role during host infection (biofilm formation, iron uptake, quorum sensing, virulence factors) were either different or absent, the best example of which is iron uptake. Indeed, strain AYE and A. baylyi use siderophore-based systems to scavenge iron from the environment whereas strain SDF uses an alternate system similar to the Haem Acquisition System (HAS). Taken together, all these observations suggest that the genome contents of the 3 Acinetobacters compared are partly shaped by life in distinct ecological niches: human (and more largely hospital environment), louse, soil. PMID:18350144

  1. A comparative analysis of biclustering algorithms for gene expression data.

    PubMed

    Eren, Kemal; Deveci, Mehmet; Küçüktunç, Onur; Çatalyürek, Ümit V

    2013-05-01

    The need to analyze high-dimension biological data is driving the development of new data mining methods. Biclustering algorithms have been successfully applied to gene expression data to discover local patterns, in which a subset of genes exhibit similar expression levels over a subset of conditions. However, it is not clear which algorithms are best suited for this task. Many algorithms have been published in the past decade, most of which have been compared only to a small number of algorithms. Surveys and comparisons exist in the literature, but because of the large number and variety of biclustering algorithms, they are quickly outdated. In this article we partially address this problem of evaluating the strengths and weaknesses of existing biclustering methods. We used the BiBench package to compare 12 algorithms, many of which were recently published or have not been extensively studied. The algorithms were tested on a suite of synthetic data sets to measure their performance on data with varying conditions, such as different bicluster models, varying noise, varying numbers of biclusters and overlapping biclusters. The algorithms were also tested on eight large gene expression data sets obtained from the Gene Expression Omnibus. Gene Ontology enrichment analysis was performed on the resulting biclusters, and the best enrichment terms are reported. Our analyses show that the biclustering method and its parameters should be selected based on the desired model, whether that model allows overlapping biclusters, and its robustness to noise. In addition, we observe that the biclustering algorithms capable of finding more than one model are more successful at capturing biologically relevant clusters.

  2. Feedback interventions and driving speed: A parametric and comparative analysis

    PubMed Central

    Houten, Ron Van; Nau, Paul A.

    1983-01-01

    Five experiments were conducted to assess the effects of several variables on the efficacy of feedback in reducing driving speed. Experiment 1 systematically varied the criterion used to define speeding, and results showed that the use of a lenient criterion (20 km/hr over the speed limit), which allowed for the posting of high percentages of drivers not speeding, was more effective in reducing speeding than the use of a stringent criterion (10 km/hr over the speed limit). In Experiment 2 an analysis revealed that posting feedback reduced speeding on a limited access highway and the effects persisted to some degree up to 6 km. Experiments 3 and 4 compared the effectiveness of an unmanned parked police vehicle (Experiment 3) and a police air patrol speeding program (Experiment 4) with the feedback sign and determined whether the presence of either of these enforcement variables could potentiate the efficacy of the sign. The results of both experiments demonstrated that although the two enforcement programs initially produced larger effects than the feedback sign, the magnitude of their effect attenuated over time. Experiment 5 compared the effectiveness of a traditional enforcement program with a warning program which included handing out a flier providing feedback on the number and types of accidents occuring on the road during the past year. This experiment demonstrated that the warning program produced a marked reduction in speeding and the traditional enforcement program did not. Furthermore, the warning program and a feedback sign together produced an even greater reduction in speeding than either alone. PMID:16795666

  3. Comparative Proteomic Analysis of Two Uveitis Models in Lewis Rats

    PubMed Central

    Pepple, Kathryn L.; Rotkis, Lauren; Wilson, Leslie; Sandt, Angela; Van Gelder, Russell N.

    2015-01-01

    Purpose Inflammation generates changes in the protein constituents of the aqueous humor. Proteins that change in multiple models of uveitis may be good biomarkers of disease or targets for therapeutic intervention. The present study was conducted to identify differentially-expressed proteins in the inflamed aqueous humor. Methods Two models of uveitis were induced in Lewis rats: experimental autoimmune uveitis (EAU) and primed mycobacterial uveitis (PMU). Differential gel electrophoresis was used to compare naïve and inflamed aqueous humor. Differentially-expressed proteins were separated by using 2-D gel electrophoresis and excised for identification with matrix-assisted laser desorption/ionization–time of flight (MALDI-TOF). Expression of select proteins was verified by Western blot analysis in both the aqueous and vitreous. Results The inflamed aqueous from both models demonstrated an increase in total protein concentration when compared to naïve aqueous. Calprotectin, a heterodimer of S100A8 and S100A9, was increased in the aqueous in both PMU and EAU. In the vitreous, S100A8 and S100A9 were preferentially elevated in PMU. Apolipoprotein E was elevated in the aqueous of both uveitis models but was preferentially elevated in EAU. Beta-B2–crystallin levels decreased in the aqueous and vitreous of EAU but not PMU. Conclusions The proinflammatory molecules S100A8 and S100A9 were elevated in both models of uveitis but may play a more significant role in PMU than EAU. The neuroprotective protein β-B2–crystallin was found to decline in EAU. Therapies to modulate these proteins in vivo may be good targets in the treatment of ocular inflammation. PMID:26747776

  4. Comparative Analysis of Genome Sequences Covering the Seven Cronobacter Species

    PubMed Central

    Cummings, Craig A.; Shih, Rita; Degoricija, Lovorka; Rico, Alain; Brzoska, Pius; Hamby, Stephen E.; Masood, Naqash; Hariri, Sumyya; Sonbol, Hana; Chuzhanova, Nadia; McClelland, Michael; Furtado, Manohar R.; Forsythe, Stephen J.

    2012-01-01

    Background Species of Cronobacter are widespread in the environment and are occasional food-borne pathogens associated with serious neonatal diseases, including bacteraemia, meningitis, and necrotising enterocolitis. The genus is composed of seven species: C. sakazakii, C. malonaticus, C. turicensis, C. dublinensis, C. muytjensii, C. universalis, and C. condimenti. Clinical cases are associated with three species, C. malonaticus, C. turicensis and, in particular, with C. sakazakii multilocus sequence type 4. Thus, it is plausible that virulence determinants have evolved in certain lineages. Methodology/Principal Findings We generated high quality sequence drafts for eleven Cronobacter genomes representing the seven Cronobacter species, including an ST4 strain of C. sakazakii. Comparative analysis of these genomes together with the two publicly available genomes revealed Cronobacter has over 6,000 genes in one or more strains and over 2,000 genes shared by all Cronobacter. Considerable variation in the presence of traits such as type six secretion systems, metal resistance (tellurite, copper and silver), and adhesins were found. C. sakazakii is unique in the Cronobacter genus in encoding genes enabling the utilization of exogenous sialic acid which may have clinical significance. The C. sakazakii ST4 strain 701 contained additional genes as compared to other C. sakazakii but none of them were known specific virulence-related genes. Conclusions/Significance Genome comparison revealed that pair-wise DNA sequence identity varies between 89 and 97% in the seven Cronobacter species, and also suggested various degrees of divergence. Sets of universal core genes and accessory genes unique to each strain were identified. These gene sequences can be used for designing genus/species specific detection assays. Genes encoding adhesins, T6SS, and metal resistance genes as well as prophages are found in only subsets of genomes and have contributed considerably to the variation of

  5. Mental health network governance: comparative analysis across Canadian regions

    PubMed Central

    Wiktorowicz, Mary E; Fleury, Marie-Josée; Adair, Carol E; Lesage, Alain; Goldner, Elliot; Peters, Suzanne

    2010-01-01

    Objective Modes of governance were compared in ten local mental health networks in diverse contexts (rural/urban and regionalized/non-regionalized) to clarify the governance processes that foster inter-organizational collaboration and the conditions that support them. Methods Case studies of ten local mental health networks were developed using qualitative methods of document review, semi-structured interviews and focus groups that incorporated provincial policy, network and organizational levels of analysis. Results Mental health networks adopted either a corporate structure, mutual adjustment or an alliance governance model. A corporate structure supported by regionalization offered the most direct means for local governance to attain inter-organizational collaboration. The likelihood that networks with an alliance model developed coordination processes depended on the presence of the following conditions: a moderate number of organizations, goal consensus and trust among the organizations, and network-level competencies. In the small and mid-sized urban networks where these conditions were met their alliance realized the inter-organizational collaboration sought. In the large urban and rural networks where these conditions were not met, externally brokered forms of network governance were required to support alliance based models. Discussion In metropolitan and rural networks with such shared forms of network governance as an alliance or voluntary mutual adjustment, external mediation by a regional or provincial authority was an important lever to foster inter-organizational collaboration. PMID:21289999

  6. Mental health network governance: comparative analysis across Canadian regions.

    PubMed

    Wiktorowicz, Mary E; Fleury, Marie-Josée; Adair, Carol E; Lesage, Alain; Goldner, Elliot; Peters, Suzanne

    2010-10-26

    Modes of governance were compared in ten local mental health networks in diverse contexts (rural/urban and regionalized/non-regionalized) to clarify the governance processes that foster inter-organizational collaboration and the conditions that support them. Case studies of ten local mental health networks were developed using qualitative methods of document review, semi-structured interviews and focus groups that incorporated provincial policy, network and organizational levels of analysis. Mental health networks adopted either a corporate structure, mutual adjustment or an alliance governance model. A corporate structure supported by regionalization offered the most direct means for local governance to attain inter-organizational collaboration. The likelihood that networks with an alliance model developed coordination processes depended on the presence of the following conditions: a moderate number of organizations, goal consensus and trust among the organizations, and network-level competencies. In the small and mid-sized urban networks where these conditions were met their alliance realized the inter-organizational collaboration sought. In the large urban and rural networks where these conditions were not met, externally brokered forms of network governance were required to support alliance based models. In metropolitan and rural networks with such shared forms of network governance as an alliance or voluntary mutual adjustment, external mediation by a regional or provincial authority was an important lever to foster inter-organizational collaboration.

  7. Comparative Analysis of Expressed Sequences in Phytophthora sojae1

    PubMed Central

    Qutob, Dinah; Hraber, Peter T.; Sobral, Bruno W.S.; Gijzen, Mark

    2000-01-01

    Phytophthora sojae (Kaufmann and Gerdemann) is an oomycete that causes stem and root rot on soybean (Glycine max L. Merr) plants. We have constructed three cDNA libraries using mRNA isolated from axenically grown mycelium and zoospores and from tissue isolated from plant hypocotyls 48 h after inoculation with zoospores. A total of 3,035 expressed sequence tags (ESTs) were generated from the three cDNA libraries, representing an estimated 2,189 cDNA transcripts. The ESTs were classified according to putative function based on similarity to known proteins, and were analyzed for redundancy within and among the three source libraries. Distinct expression patterns were observed for each library. By analysis of the percentage G+C content of the ESTs, we estimate that two-thirds of the ESTs from the infected plant library are derived from P. sojae cDNA transcripts. The ESTs originating from this study were also compared with a collection of Phytophthora infestans ESTs and with all other non-human ESTs to assess the similarity of the P. sojae sequences to existing EST data. This collection of cDNA libraries, ESTs, and accompanying annotation will provide a new resource for studies on oomycetes and on soybean responses to pathogen challenge. PMID:10806241

  8. A Comparative Investigation of Rotation Criteria Within Exploratory Factor Analysis.

    PubMed

    Sass, Daniel A; Schmitt, Thomas A

    2010-01-29

    Exploratory factor analysis (EFA) is a commonly used statistical technique for examining the relationships between variables (e.g., items) and the factors (e.g., latent traits) they depict. There are several decisions that must be made when using EFA, with one of the more important being choice of the rotation criterion. This selection can be arduous given the numerous rotation criteria available and the lack of research/literature that compares their function and utility. Historically, researchers have chosen rotation criteria based on whether or not factors are correlated and have failed to consider other important aspects of their data. This study reviews several rotation criteria, demonstrates how they may perform with different factor pattern structures, and highlights for researchers subtle but important differences between each rotation criterion. The choice of rotation criterion is critical to ensure researchers make informed decisions as to when different rotation criteria may or may not be appropriate. The results suggest that depending on the rotation criterion selected and the complexity of the factor pattern matrix, the interpretation of the interfactor correlations and factor pattern loadings can vary substantially. Implications and future directions are discussed.

  9. Comparative proteomic analysis of rice shoots exposed to high arsenate.

    PubMed

    Liu, Yanli; Li, Ming; Han, Chao; Wu, Fengxia; Tu, Bingkun; Yang, Pingfang

    2013-10-01

    Consumption of arsenic contaminated water and cereals is a serious threat to humans all over the world. Rice (Oryza sativa "Nipponbare"), as a main cereal crop, can accumulate arsenic more than 10-fold that of in other cereals. To gain a comprehensive understanding of the response of rice subjected to 100 µM arsenate stress, a comparative proteomic analysis of rice shoots in combination with morphological and biochemical investigations have been performed in this study. The results demonstrated that arsenate suppressed the growth of rice seedlings, destroyed the cellular ultra-structure and changed the homeostasis of reactive oxygen species. Moreover, a total of 38 differentially displayed proteins, which were mainly involved in metabolism, redox and protein-metabolism, were identified. The data suggest the arsenic can inhibit rice growth through negatively affecting chloroplast structure and photosynthesis. In addition, upregulation of the proteins involved in redox and protein metabolism might help the rice to be resistant or tolerant to arsenic toxicity. In general, this study improves our understanding about the rice arsenic responsive mechanism.

  10. A Comparative Analysis of Community Wind Power DevelopmentModels

    SciTech Connect

    Bolinger, Mark; Wiser, Ryan; Wind, Tom; Juhl, Dan; Grace, Robert; West, Peter

    2005-05-20

    For years, farmers in the United States have looked with envy on their European counterparts ability to profitably farm the wind through ownership of distributed, utility-scale wind projects. Only within the past few years, however, has farmer- or community-owned windpower development become a reality in the United States. The primary hurdle to this type of development in the United States has been devising and implementing suitable business and legal structures that enable such projects to take advantage of tax-based federal incentives for windpower. This article discusses the limitations of such incentives in supporting farmer- or community-owned wind projects, describes four ownership structures that potentially overcome such limitations, and finally conducts comparative financial analysis on those four structures, using as an example a hypothetical 1.5 MW farmer-owned project located in the state of Oregon. We find that material differences in the competitiveness of each structure do exist, but that choosing the best structure for a given project will largely depend on the conditions at hand; e.g., the ability of the farmer(s) to utilize tax credits, preference for individual versus cooperative ownership, and the state and utility service territory in which the project will be located.

  11. Sequencing and comparative analysis of the gorilla MHC genomic sequence.

    PubMed

    Wilming, Laurens G; Hart, Elizabeth A; Coggill, Penny C; Horton, Roger; Gilbert, James G R; Clee, Chris; Jones, Matt; Lloyd, Christine; Palmer, Sophie; Sims, Sarah; Whitehead, Siobhan; Wiley, David; Beck, Stephan; Harrow, Jennifer L

    2013-01-01

    Major histocompatibility complex (MHC) genes play a critical role in vertebrate immune response and because the MHC is linked to a significant number of auto-immune and other diseases it is of great medical interest. Here we describe the clone-based sequencing and subsequent annotation of the MHC region of the gorilla genome. Because the MHC is subject to extensive variation, both structural and sequence-wise, it is not readily amenable to study in whole genome shotgun sequence such as the recently published gorilla genome. The variation of the MHC also makes it of evolutionary interest and therefore we analyse the sequence in the context of human and chimpanzee. In our comparisons with human and re-annotated chimpanzee MHC sequence we find that gorilla has a trimodular RCCX cluster, versus the reference human bimodular cluster, and additional copies of Class I (pseudo)genes between Gogo-K and Gogo-A (the orthologues of HLA-K and -A). We also find that Gogo-H (and Patr-H) is coding versus the HLA-H pseudogene and, conversely, there is a Gogo-DQB2 pseudogene versus the HLA-DQB2 coding gene. Our analysis, which is freely available through the VEGA genome browser, provides the research community with a comprehensive dataset for comparative and evolutionary research of the MHC.

  12. Comparative genomic analysis of two brucellaphages of distant origins.

    PubMed

    Flores, Victor; López-Merino, Ahidé; Mendoza-Hernandez, Guillermo; Guarneros, Gabriel

    2012-04-01

    Here, we present the first complete genome sequence of brucellaphage Tbilisi (Tb) and compared it with that of Pr, a broad host-range brucellaphage recently isolated in Mexico. The genomes consist of 41,148 bp (Tb) and 38,253 bp (Pr), they differ mainly in the region encoding structural proteins, in which the genome of Tb shows two major insertions. Both genomes share 99.87% nucleotide identity, a high percentage of identity among phages isolated at so globally distant locations and temporally different occasions. Sequence analysis revealed 57 conserved ORFs, three transcriptional terminators and four putative transcriptional promoters. The co-occurrence of an ORF encoding a putative DnaA-like protein and a putative oriC-like origin of replication was found in both brucellaphages genomes, a feature not described in any other phage genome. These elements suggest that DNA replication in brucellaphages differs from other phages, and might resemble that of bacterial chromosomes. Copyright © 2012 Elsevier Inc. All rights reserved.

  13. Sequencing and comparative analysis of the gorilla MHC genomic sequence

    PubMed Central

    Wilming, Laurens G.; Hart, Elizabeth A.; Coggill, Penny C.; Horton, Roger; Gilbert, James G. R.; Clee, Chris; Jones, Matt; Lloyd, Christine; Palmer, Sophie; Sims, Sarah; Whitehead, Siobhan; Wiley, David; Beck, Stephan; Harrow, Jennifer L.

    2013-01-01

    Major histocompatibility complex (MHC) genes play a critical role in vertebrate immune response and because the MHC is linked to a significant number of auto-immune and other diseases it is of great medical interest. Here we describe the clone-based sequencing and subsequent annotation of the MHC region of the gorilla genome. Because the MHC is subject to extensive variation, both structural and sequence-wise, it is not readily amenable to study in whole genome shotgun sequence such as the recently published gorilla genome. The variation of the MHC also makes it of evolutionary interest and therefore we analyse the sequence in the context of human and chimpanzee. In our comparisons with human and re-annotated chimpanzee MHC sequence we find that gorilla has a trimodular RCCX cluster, versus the reference human bimodular cluster, and additional copies of Class I (pseudo)genes between Gogo-K and Gogo-A (the orthologues of HLA-K and -A). We also find that Gogo-H (and Patr-H) is coding versus the HLA-H pseudogene and, conversely, there is a Gogo-DQB2 pseudogene versus the HLA-DQB2 coding gene. Our analysis, which is freely available through the VEGA genome browser, provides the research community with a comprehensive dataset for comparative and evolutionary research of the MHC. PMID:23589541

  14. A Comparative Analysis of Life-Cycle Assessment Tools for ...

    EPA Pesticide Factsheets

    We identified and evaluated five life-cycle assessment tools that community decision makers can use to assess the environmental and economic impacts of end-of-life (EOL) materials management options. The tools evaluated in this report are waste reduction mode (WARM), municipal solid waste-decision support tool (MSW-DST), solid waste optimization life-cycle framework (SWOLF), environmental assessment system for environmental technologies (EASETECH), and waste and resources assessment for the environment (WRATE). WARM, MSW-DST, and SWOLF were developed for US-specific materials management strategies, while WRATE and EASETECH were developed for European-specific conditions. All of the tools (with the exception of WARM) allow specification of a wide variety of parameters (e.g., materials composition and energy mix) to a varying degree, thus allowing users to model specific EOL materials management methods even outside the geographical domain they are originally intended for. The flexibility to accept user-specified input for a large number of parameters increases the level of complexity and the skill set needed for using these tools. The tools were evaluated and compared based on a series of criteria, including general tool features, the scope of the analysis (e.g., materials and processes included), and the impact categories analyzed (e.g., climate change, acidification). A series of scenarios representing materials management problems currently relevant to c

  15. Noncoding RNA gene detection using comparative sequence analysis

    PubMed Central

    Rivas, Elena; Eddy, Sean R

    2001-01-01

    Background Noncoding RNA genes produce transcripts that exert their function without ever producing proteins. Noncoding RNA gene sequences do not have strong statistical signals, unlike protein coding genes. A reliable general purpose computational genefinder for noncoding RNA genes has been elusive. Results We describe a comparative sequence analysis algorithm for detecting novel structural RNA genes. The key idea is to test the pattern of substitutions observed in a pairwise alignment of two homologous sequences. A conserved coding region tends to show a pattern of synonymous substitutions, whereas a conserved structural RNA tends to show a pattern of compensatory mutations consistent with some base-paired secondary structure. We formalize this intuition using three probabilistic "pair-grammars": a pair stochastic context free grammar modeling alignments constrained by structural RNA evolution, a pair hidden Markov model modeling alignments constrained by coding sequence evolution, and a pair hidden Markov model modeling a null hypothesis of position-independent evolution. Given an input pairwise sequence alignment (e.g. from a BLASTN comparison of two related genomes) we classify the alignment into the coding, RNA, or null class according to the posterior probability of each class. Conclusions We have implemented this approach as a program, QRNA, which we consider to be a prototype structural noncoding RNA genefinder. Tests suggest that this approach detects noncoding RNA genes with a fair degree of reliability. PMID:11801179

  16. A Comparative Analysis of Life-Cycle Assessment Tools for ...

    EPA Pesticide Factsheets

    We identified and evaluated five life-cycle assessment tools that community decision makers can use to assess the environmental and economic impacts of end-of-life (EOL) materials management options. The tools evaluated in this report are waste reduction mode (WARM), municipal solid waste-decision support tool (MSW-DST), solid waste optimization life-cycle framework (SWOLF), environmental assessment system for environmental technologies (EASETECH), and waste and resources assessment for the environment (WRATE). WARM, MSW-DST, and SWOLF were developed for US-specific materials management strategies, while WRATE and EASETECH were developed for European-specific conditions. All of the tools (with the exception of WARM) allow specification of a wide variety of parameters (e.g., materials composition and energy mix) to a varying degree, thus allowing users to model specific EOL materials management methods even outside the geographical domain they are originally intended for. The flexibility to accept user-specified input for a large number of parameters increases the level of complexity and the skill set needed for using these tools. The tools were evaluated and compared based on a series of criteria, including general tool features, the scope of the analysis (e.g., materials and processes included), and the impact categories analyzed (e.g., climate change, acidification). A series of scenarios representing materials management problems currently relevant to c

  17. A comparative quadrant analysis of turbulence in a plant canopy

    NASA Astrophysics Data System (ADS)

    Yue, Wusi; Meneveau, Charles; Parlange, Marc B.; Zhu, Weihong; van Hout, René; Katz, Joseph

    2007-05-01

    Large-eddy simulation (LES) of turbulence in plant canopies has traditionally been validated using bulk statistical quantities such as mean velocity and variance profiles. However, turbulent exchanges between a plant canopy and the atmosphere are dominated by large-scale coherent structures, and therefore LES must also be validated using statistical tools that are sensitive to details of coherent structures. In this study, LES and measurements using particle image velocimetry (PIV) are compared near the top of the canopy by means of a quadrant-hole analysis of turbulent kinetic energy, vorticity, and dissipation rate. The LES resolves coarse features of individual corn plants and uses the Lagrangian scale-dependent dynamic subgrid model. At the measurement location, there is good agreement between the LES predictions and the field data in terms of most conditionally sampled quantities, confirming the applicability of LES for fundamental studies of vegetation-air interactions and coherent structures. The simulation results confirm that sweeps (the fourth-quadrant events) contribute the largest fraction of turbulent kinetic energy, vorticity, and dissipation rate inside the plant canopy. The magnitudes of the vorticity and dissipation rate at the top of the canopy are highest in the first quadrant (rare events of outward interactions).

  18. Comparative analysis of used car price evaluation models

    NASA Astrophysics Data System (ADS)

    Chen, Chuancan; Hao, Lulu; Xu, Cong

    2017-05-01

    An accurate used car price evaluation is a catalyst for the healthy development of used car market. Data mining has been applied to predict used car price in several articles. However, little is studied on the comparison of using different algorithms in used car price estimation. This paper collects more than 100,000 used car dealing records throughout China to do empirical analysis on a thorough comparison of two algorithms: linear regression and random forest. These two algorithms are used to predict used car price in three different models: model for a certain car make, model for a certain car series and universal model. Results show that random forest has a stable but not ideal effect in price evaluation model for a certain car make, but it shows great advantage in the universal model compared with linear regression. This indicates that random forest is an optimal algorithm when handling complex models with a large number of variables and samples, yet it shows no obvious advantage when coping with simple models with less variables.

  19. A combined approach for comparative exoproteome analysis of Corynebacterium pseudotuberculosis

    PubMed Central

    2011-01-01

    Background Bacterial exported proteins represent key components of the host-pathogen interplay. Hence, we sought to implement a combined approach for characterizing the entire exoproteome of the pathogenic bacterium Corynebacterium pseudotuberculosis, the etiological agent of caseous lymphadenitis (CLA) in sheep and goats. Results An optimized protocol of three-phase partitioning (TPP) was used to obtain the C. pseudotuberculosis exoproteins, and a newly introduced method of data-independent MS acquisition (LC-MSE) was employed for protein identification and label-free quantification. Additionally, the recently developed tool SurfG+ was used for in silico prediction of sub-cellular localization of the identified proteins. In total, 93 different extracellular proteins of C. pseudotuberculosis were identified with high confidence by this strategy; 44 proteins were commonly identified in two different strains, isolated from distinct hosts, then composing a core C. pseudotuberculosis exoproteome. Analysis with the SurfG+ tool showed that more than 75% (70/93) of the identified proteins could be predicted as containing signals for active exportation. Moreover, evidence could be found for probable non-classical export of most of the remaining proteins. Conclusions Comparative analyses of the exoproteomes of two C. pseudotuberculosis strains, in addition to comparison with other experimentally determined corynebacterial exoproteomes, were helpful to gain novel insights into the contribution of the exported proteins in the virulence of this bacterium. The results presented here compose the most comprehensive coverage of the exoproteome of a corynebacterial species so far. PMID:21241507

  20. Comparative analysis of hazardous household waste in two Mexican regions.

    PubMed

    Delgado, Otoniel Buenrostro; Ojeda-Benítez, Sara; Márquez-Benavides, Liliana

    2007-01-01

    Household hazardous waste (HHW) generation in two Mexican regions was examined, a northern region (bordering with the USA) and a central region. The aim of this work was to determine the dynamics of solid waste generation and to be able to compare the results of both regions, regarding consumption patterns and solid waste generation rates. In the northern region, household solid waste was analysed quantitatively. In order to perform this analysis, the population was categorized into three socioeconomic strata (lower, middle, upper). Waste characterization revealed the presence of products that give origin to household hazardous waste. In the northern region (Mexicali city), household hazardous waste comprised 3.7% of municipal solid waste, the largest categories in this fraction were home care products (29.2%), cleaning products (19.5%) and batteries and electronic equipment (15.7%). In the central region, HHW comprised 1.03% of municipal solid waste; the main categories in this fraction were represented by cleaning products (39%), self care products (27.3%), and insecticides (14.4%). In Mexicali, the socioeconomic study demonstrated that the production of HHW is independent of the income level. Furthermore, the composition of the solid waste stream in both regions suggested the influence of another set of variables such as local climate, migration patterns and marketing coverage. Further research is needed in order to establish the effect of low quantities of HHW upon the environment and public health.

  1. Comparative Analysis of Carbon Monoxide Tolerance among Thermoanaerobacter Species

    PubMed Central

    Alves, Joana I.; Alves, M. Madalena; Plugge, Caroline M.; Stams, Alfons J. M.; Sousa, Diana Z.

    2016-01-01

    An anaerobic thermophilic strain (strain PCO) was isolated from a syngas-converting enrichment culture. Syngas components cannot be used by strain PCO, but the new strain is very tolerant to carbon monoxide (pCO = 1.7 × 105 Pa, 100% CO). 16S rRNA gene analysis and DNA-DNA hybridization revealed that strain PCO is a strain of Thermoanaerobacter thermohydrosulfuricus. The physiology of strain PCO and other Thermoanaerobacter species was compared, focusing on their tolerance to carbon monoxide. T. thermohydrosulfuricus, T. brockii subsp. finnii, T. pseudethanolicus, and T. wiegelii were exposed to increased CO concentrations in the headspace, while growth, glucose consumption and product formation were monitored. Remarkably, glucose conversion rates by Thermoanaerobacter species were not affected by CO. All the tested strains fermented glucose to mainly lactate, ethanol, acetate, and hydrogen, but final product concentrations differed. In the presence of CO, ethanol production was generally less affected, but H2 production decreased with increasing CO partial pressure. This study highlights the CO resistance of Thermoanaerobacter species. PMID:27621723

  2. Geomorphometric comparative analysis of Latin-American volcanoes

    NASA Astrophysics Data System (ADS)

    Camiz, Sergio; Poscolieri, Maurizio; Roverato, Matteo

    2017-07-01

    The geomorphometric classifications of three groups of volcanoes situated in the Andes Cordillera, Central America, and Mexico are performed and compared. Input data are eight local topographic gradients (i.e. elevation differences) obtained by processing each volcano raster ASTER-GDEM data. The pixels of each volcano DEM have been classified into 17 classes through a K-means clustering procedure following principal component analysis of the gradients. The spatial distribution of the classes, representing homogeneous terrain units, is shown on thematic colour maps, where colours are assigned according to mean slope and aspect class values. The interpretation of the geomorphometric classification of the volcanoes is based on the statistics of both gradients and morphometric parameters (slope, aspect and elevation). The latter were used for a comparison of the volcanoes, performed through classes' slope/aspect scatterplots and multidimensional methods. In this paper, we apply the mentioned methodology on 21 volcanoes, randomly chosen from Mexico to Patagonia, to show how it may contribute to detect geomorphological similarities and differences among them. As such, both its descriptive and graphical abilities may be a useful complement to future volcanological studies.

  3. Comparative analysis of ATRX, a chromatin remodeling protein.

    PubMed

    Park, Daniel J; Pask, Andrew J; Huynh, Kim; Renfree, Marilyn B; Harley, Vincent R; Graves, Jennifer A Marshall

    2004-09-15

    The ATRX protein, associated with X-linked alpha-thalassaemia, mental retardation and developmental abnormalities including genital dysgenesis, has been proposed to function as a global transcriptional regulator within a multi-protein complex. However, an understanding of the composition and mechanics of this machinery has remained elusive. We applied inter-specific comparative analysis to identify conserved elements which may be involved in regulating the conformation of chromatin. As part of this study, we cloned and sequenced the entire translatable coding region (7.4 kb) of the ATRX gene from a model marsupial (tammar wallaby, Macropus eugenii). We identify an ATRX ancestral core, conserved between plants, fish and mammals, comprising the cysteine-rich and SWI2/SNF2 helicase-like regions and protein interaction domains. Our data are consistent with the model of the cysteine-rich region as a DNA-binding zinc finger adjacent to a protein-binding (plant homeodomain-like) domain. Alignment of vertebrate ATRX sequences highlights other conserved elements, including a negatively charged mammalian sequence which we propose to be involved in binding of positively charged histone tails.

  4. Comparative analysis of marine ecosystems: international production modelling workshop.

    PubMed

    Link, Jason S; Megrey, Bernard A; Miller, Thomas J; Essington, Tim; Boldt, Jennifer; Bundy, Alida; Moksness, Erlend; Drinkwater, Ken F; Perry, R Ian

    2010-12-23

    Understanding the drivers that dictate the productivity of marine ecosystems continues to be a globally important issue. A vast literature identifies three main processes that regulate the production dynamics of such ecosystems: biophysical, exploitative and trophodynamic. Exploring the prominence among this 'triad' of drivers, through a synthetic analysis, is critical for understanding how marine ecosystems function and subsequently produce fisheries resources of interest to humans. To explore this topic further, an international workshop was held on 10-14 May 2010, at the National Academy of Science's Jonsson Center in Woods Hole, MA, USA. The workshop compiled the data required to develop production models at different hierarchical levels (e.g. species, guild, ecosystem) for many of the major Northern Hemisphere marine ecosystems that have supported notable fisheries. Analyses focused on comparable total system biomass production, functionally equivalent species production, or simulation studies for 11 different marine fishery ecosystems. Workshop activities also led to new analytical tools. Preliminary results suggested common patterns driving overall fisheries production in these ecosystems, but also highlighted variation in the relative importance of each among ecosystems.

  5. Transcription factor motif quality assessment requires systematic comparative analysis

    PubMed Central

    Kibet, Caleb Kipkurui; Machanick, Philip

    2016-01-01

    Transcription factor (TF) binding site prediction remains a challenge in gene regulatory research due to degeneracy and potential variability in binding sites in the genome. Dozens of algorithms designed to learn binding models (motifs) have generated many motifs available in research papers with a subset making it to databases like JASPAR, UniPROBE and Transfac. The presence of many versions of motifs from the various databases for a single TF and the lack of a standardized assessment technique makes it difficult for biologists to make an appropriate choice of binding model and for algorithm developers to benchmark, test and improve on their models. In this study, we review and evaluate the approaches in use, highlight differences and demonstrate the difficulty of defining a standardized motif assessment approach. We review scoring functions, motif length, test data and the type of performance metrics used in prior studies as some of the factors that influence the outcome of a motif assessment. We show that the scoring functions and statistics used in motif assessment influence ranking of motifs in a TF-specific manner. We also show that TF binding specificity can vary by source of genomic binding data. We also demonstrate that information content of a motif is not in isolation a measure of motif quality but is influenced by TF binding behaviour. We conclude that there is a need for an easy-to-use tool that presents all available evidence for a comparative analysis. PMID:27092243

  6. Comparative analysis of the Monochamus alternatus immune system.

    PubMed

    Zhou, Jiao; Zhao, Li-Lin; Yu, Hai-Ying; Zhang, Wei; Ahmad, Faheem; Hu, Song-Nian; Zou, Zhen; Sun, Jiang-Hua

    2017-03-01

    The pine sawyer beetle, Monochamus alternatus, is regarded as a notorious forest pest in Asia, vectoring an invasive pathogenic nematode, Bursaphelenchus xylophilus, which is known to cause pine wilt disease. However, little sequence information is available for this vector beetle. This hampered the research on its immune system. Based on transcriptome of M. alternatus, we have identified and characterized 194 immunity-related genes in M. alternatus, and compared them with homologues molecules from other species known to exhibit immune responses against invading microbes. The lower number of putative immunity-related genes in M. alternatus were attributed to fewer C-type lectin, serine protease (SP) and anti-microbial peptide (AMP) genes. Phylogenetic analysis revealed that M. alternatus had a unique recognition gene, galectin3, orthologues of which was not identified in Tribolium castaneum, Drosophila melanogastor, Anopheles gambiae, and Apis mellifera. This suggested a lineage-specific gene evolution for coleopteran insects. Our study provides the comprehensive sequence resources of the immunity-related genes of M. alternatus, presenting valuable information for better understanding of the molecular mechanism of innate immunity processes in M. alternatus against B. xylophilus. This article is protected by copyright. All rights reserved.

  7. Ion channel gates: comparative analysis of energy barriers.

    PubMed

    Tai, Kaihsu; Haider, Shozeb; Grottesi, Alessandro; Sansom, Mark S P

    2009-04-01

    The energetic profile of an ion translated along the axis of an ion channel should reveal whether the structure corresponds to a functionally open or closed state of the channel. In this study, we explore the combined use of Poisson-Boltzmann electrostatic calculations and evaluation of van der Waals interactions between ion and pore to provide an initial appraisal of the gating state of a channel. This approach is exemplified by its application to the bacterial inward rectifier potassium channel KirBac3.1, where it reveals the closed gate to be formed by a ring of leucine (L124) side chains. We have extended this analysis to a comparative survey of gating profiles, including model hydrophobic nanopores, the nicotinic acetylcholine receptor, and a number of potassium channel structures and models. This enables us to identify three gating regimes, and to show the limitation of this computationally inexpensive method. For a (closed) gate radius of 0.4 nm < R < 0.8 nm, a hydrophobic gate may be present. For a gate radius of 0.2 nm < R < 0.4 nm, both electrostatic and van der Waals interactions will contribute to the barrier height. Below R = 0.2 nm, repulsive van der Waals interactions are likely to dominate, resulting in a sterically occluded gate. In general, the method is more useful when the channel is wider; for narrower channels, the flexibility of the protein may allow otherwise-unsurmountable energetic barriers to be overcome.

  8. Comparative analysis of ADS gene promoter in seven Artemisia species.

    PubMed

    Ranjbar, Mojtaba; Naghavi, Mohammad Reza; Alizadeh, Hoshang

    2014-12-01

    Artemisinin is the most effective antimalarial drug that is derived from Artemisia annua. Amorpha-4,11-diene synthase (ADS) controls the first committed step in artemisinin biosynthesis. The ADS gene expression is regulated by transcription factors which bind to the cis-acting elements on the ADS promoter and are probably responsible for the ADS gene expression difference in the Artemisia species. To identify the elements that are significantly involved in ADS gene expression, the ADS gene promoter of the seven Artemisia species was isolated and comparative analysis was performed on the ADS promoter sequences of these species. Results revealed that some of the cis-elements were unique or in terms of number were more in the high artemisinin producer species, A. annua, than the other species. We have reported that the light-responsive elements, W-box, CAAT-box, 5'-UTR py-rich stretch, TATA-box sequence and tandem repeat sequences have been identified as important factors in the increased expression of ADS gene.

  9. Comparative analysis of PSO algorithms for PID controller tuning

    NASA Astrophysics Data System (ADS)

    Štimac, Goranka; Braut, Sanjin; Žigulić, Roberto

    2014-09-01

    The active magnetic bearing(AMB) suspends the rotating shaft and maintains it in levitated position by applying controlled electromagnetic forces on the rotor in radial and axial directions. Although the development of various control methods is rapid, PID control strategy is still the most widely used control strategy in many applications, including AMBs. In order to tune PID controller, a particle swarm optimization(PSO) method is applied. Therefore, a comparative analysis of particle swarm optimization(PSO) algorithms is carried out, where two PSO algorithms, namely (1) PSO with linearly decreasing inertia weight(LDW-PSO), and (2) PSO algorithm with constriction factor approach(CFA-PSO), are independently tested for different PID structures. The computer simulations are carried out with the aim of minimizing the objective function defined as the integral of time multiplied by the absolute value of error(ITAE). In order to validate the performance of the analyzed PSO algorithms, one-axis and two-axis radial rotor/active magnetic bearing systems are examined. The results show that PSO algorithms are effective and easily implemented methods, providing stable convergence and good computational efficiency of different PID structures for the rotor/AMB systems. Moreover, the PSO algorithms prove to be easily used for controller tuning in case of both SISO and MIMO system, which consider the system delay and the interference among the horizontal and vertical rotor axes.

  10. Comparative analysis of known miRNAs across platyhelminths.

    PubMed

    Jin, Xiaoliang; Lu, Lixia; Su, Hailong; Lou, Zhongzi; Wang, Fang; Zheng, Yadong; Xu, Guo-Tong

    2013-08-01

    MicroRNAs (miRNAs) are a subtype of small regulatory RNAs that are involved in numerous biological processes through small RNA-induced silencing networks. In an attempt to explore the phylogeny of miRNAs across five platyhelminths, we integrated annotated miRNAs and their full genomes. We identified conserved miRNA clusters and, in particular, miR-71/2 was conserved from planarian to parasitic flatworms and was expanded in free-living Schmidtea mediterranea. Analysis of 22 miRNA loci provided compelling evidence that most known miRNAs are conserved across platyhelminths. Meanwhile, we also observed alterations of known protein-coding genes flanking miRNA(s), such as transcriptional direction conversion and locus relocation, in around ~ 41% of 22 known miRNA loci. Compared with Echinococcus multilocularis, the majority of these events occurred in evolution-distant Hymenolepis microstoma, Schistosoma japonicum or/and S. mediterranea. These results imply rearrangement events occurred near the known miRNA loci. © 2013 FEBS.

  11. Engine System Loads Analysis Compared to Hot-Fire Data

    NASA Technical Reports Server (NTRS)

    Frady, Gregory P.; Jennings, John M.; Mims, Katherine; Brunty, Joseph; Christensen, Eric R.; McConnaughey, Paul R. (Technical Monitor)

    2002-01-01

    Early implementation of structural dynamics finite element analyses for calculation of design loads is considered common design practice for high volume manufacturing industries such as automotive and aeronautical industries. However with the rarity of rocket engine development programs starts, these tools are relatively new to the design of rocket engines. In the NASA MC-1 engine program, the focus was to reduce the cost-to-weight ratio. The techniques for structural dynamics analysis practices, were tailored in this program to meet both production and structural design goals. Perturbation of rocket engine design parameters resulted in a number of MC-1 load cycles necessary to characterize the impact due to mass and stiffness changes. Evolution of loads and load extraction methodologies, parametric considerations and a discussion of load path sensitivities are important during the design and integration of a new engine system. During the final stages of development, it is important to verify the results of an engine system model to determine the validity of the results. During the final stages of the MC-1 program, hot-fire test results were obtained and compared to the structural design loads calculated by the engine system model. These comparisons are presented in this paper.

  12. Statistical correlation analysis for comparing vibration data from test and analysis

    NASA Technical Reports Server (NTRS)

    Butler, T. G.; Strang, R. F.; Purves, L. R.; Hershfeld, D. J.

    1986-01-01

    A theory was developed to compare vibration modes obtained by NASTRAN analysis with those obtained experimentally. Because many more analytical modes can be obtained than experimental modes, the analytical set was treated as expansion functions for putting both sources in comparative form. The dimensional symmetry was developed for three general cases: nonsymmetric whole model compared with a nonsymmetric whole structural test, symmetric analytical portion compared with a symmetric experimental portion, and analytical symmetric portion with a whole experimental test. The theory was coded and a statistical correlation program was installed as a utility. The theory is established with small classical structures.

  13. Comparative chemical analysis of dew and rain water

    NASA Astrophysics Data System (ADS)

    Lekouch, Imad; Mileta, Marina; Muselli, Marc; Milimouk-Melnytchouk, Irène; Šojat, Višnja; Kabbachi, Belkacem; Beysens, Daniel

    2010-02-01

    Dew and rain water were collected and analyzed during 3 years (2004-2006) in Zadar, Croatia. The goal was to characterize the chemical properties of dew water versus rain water (and the atmosphere in which they form) and to determine the extent to which they can be used as potable water. The corresponding parameters were measured: pH, electrical conductivity (EC), major anions (HCO 3-, Cl -, SO 42-, NO 3-), and major cations (NH 4+, Na +, K +, Ca 2+, Mg 2+). The mean pH and EC values were comparable for both dew and rain water, pH = 6.7 (dew) and pH = 6.35 (rain), EC = 195 µS cm - 1 (dew) and EC = 178 µS cm - 1 (rain). The ratio (SO 42- + NO 3-)/(Ca 2+ + Mg 2+) was lower than 1, indicating the alkaline nature of both dew and rain water. Both dew and rain water exhibited low mineralization. The analysis of the major ions showed that the concentration of cations is high compared to that of anions (presumably because the NO 2-, HCOO - and CH 3COO - ions were not measured), with Ca² +, Na + and Mg 2+ as the main ions. In order to discriminate between the marine and non-marine origin of ions, the sea-salt fraction (SSF) was calculated by taking Na + as a reference. The small SSF value in dew suggests a considerable contribution of non-marine origin for components Ca ²+, K +, SO 42- and NO 3-, except Cl -. In contrast, in rain water, the values of the non sea-salt fraction (NSSF) indicate that only Ca² + and NO 3- are not influenced by sea proximity. The study of the neutralization factor, NF, reveals the descending order of the cations in dew and rain water, NF Ca²+ > NF Mg²+ > NF K+ > NF NH4+. The dew and rain water are in conformity with the World Health Organization directives for potability, except for Mg 2+.

  14. A Comparative Analysis of Mitochondrial Genomes in Eustigmatophyte Algae

    PubMed Central

    Ševčíková, Tereza; Klimeš, Vladimír; Zbránková, Veronika; Strnad, Hynek; Hroudová, Miluše; Vlček, Čestmír; Eliáš, Marek

    2016-01-01

    Eustigmatophyceae (Ochrophyta, Stramenopiles) is a small algal group with species of the genus Nannochloropsis being its best studied representatives. Nuclear and organellar genomes have been recently sequenced for several Nannochloropsis spp., but phylogenetically wider genomic studies are missing for eustigmatophytes. We sequenced mitochondrial genomes (mitogenomes) of three species representing most major eustigmatophyte lineages, Monodopsis sp. MarTras21, Vischeria sp. CAUP Q 202 and Trachydiscus minutus, and carried out their comparative analysis in the context of available data from Nannochloropsis and other stramenopiles, revealing a number of noticeable findings. First, mitogenomes of most eustigmatophytes are highly collinear and similar in the gene content, but extensive rearrangements and loss of three otherwise ubiquitous genes happened in the Vischeria lineage; this correlates with an accelerated evolution of mitochondrial gene sequences in this lineage. Second, eustigmatophytes appear to be the only ochrophyte group with the Atp1 protein encoded by the mitogenome. Third, eustigmatophyte mitogenomes uniquely share a truncated nad11 gene encoding only the C-terminal part of the Nad11 protein, while the N-terminal part is encoded by a separate gene in the nuclear genome. Fourth, UGA as a termination codon and the cognate release factor mRF2 were lost from mitochondria independently by the Nannochloropsis and T. minutus lineages. Finally, the rps3 gene in the mitogenome of Vischeria sp. is interrupted by the UAG codon, but the genome includes a gene for an unusual tRNA with an extended anticodon loop that we speculate may serve as a suppressor tRNA to properly decode the rps3 gene. PMID:26872774

  15. Comparative Analysis of Principal Components Can be Misleading.

    PubMed

    Uyeda, Josef C; Caetano, Daniel S; Pennell, Matthew W

    2015-07-01

    Most existing methods for modeling trait evolution are univariate, although researchers are often interested in investigating evolutionary patterns and processes across multiple traits. Principal components analysis (PCA) is commonly used to reduce the dimensionality of multivariate data so that univariate trait models can be fit to individual principal components. The problem with using standard PCA on phylogenetically structured data has been previously pointed out yet it continues to be widely used in the literature. Here we demonstrate precisely how using standard PCA can mislead inferences: The first few principal components of traits evolved under constant-rate multivariate Brownian motion will appear to have evolved via an "early burst" process. A phylogenetic PCA (pPCA) has been proprosed to alleviate these issues. However, when the true model of trait evolution deviates from the model assumed in the calculation of the pPCA axes, we find that the use of pPCA suffers from similar artifacts as standard PCA. We show that data sets with high effective dimensionality are particularly likely to lead to erroneous inferences. Ultimately, all of the problems we report stem from the same underlying issue--by considering only the first few principal components as univariate traits, we are effectively examining a biased sample of a multivariate pattern. These results highlight the need for truly multivariate phylogenetic comparative methods. As these methods are still being developed, we discuss potential alternative strategies for using and interpreting models fit to univariate axes of multivariate data. © The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  16. Comparative Analysis of Morphometric Characteristics of Scorpaenidae and Gobioninae

    PubMed Central

    Park, In-Seok; Gil, Hyun Woo; Oh, Ji Su; Choi, Hui Jung; Kim, Chi Hong

    2015-01-01

    Measurements of closely related sets of classical and truss dimensions were analyzed to discriminate species of scorpaenidae including the dark banded rockfish, Sebastes inermis, the black rockfish, S. schlegeli, and gobioninae including the striped shiner, Pungtungia herzi, and the slender shiner, Pseudopungtungia tenuicorpa. The measurements of the dimensions were arc sin square root transformed, and compared as a function of the standard length of each species for statistical analysis. For values of the classical dimensions of the rockfish, 6 were greater for the dark banded rockfish than for the black rockfish, 1 value was smaller for the former, and for 2 values there was no statistically significant difference (P > 0.05). For values of the classical dimensions of the shiners, 9 values were greater for the striped shiner than for the slender shiner, 2 values were smaller for the former, and for 1 value there was no statistically significant difference (P > 0.01). For values of the truss dimensions of the rockfish, 6 were greater for the dark banded rockfish than for the black rockfish, 1 was smaller for the former, and for 4 values there was no statistically significant difference (P > 0.05). For values of the truss dimensions of the shiners, 13 values were greater for the striped shiner than for the slender shiner, 3 values were smaller for the former, and for 6 values there was no statistically significant difference (P > 0.01). The dimension sets used in this study may be useful as taxonomic indicators for discriminating among fish species in Korea. PMID:27004265

  17. Comparative genomic analysis of Chlamydia trachomatis oculotropic and genitotropic strains.

    PubMed

    Carlson, John H; Porcella, Stephen F; McClarty, Grant; Caldwell, Harlan D

    2005-10-01

    Chlamydia trachomatis infection is an important cause of preventable blindness and sexually transmitted disease (STD) in humans. C. trachomatis exists as multiple serovariants that exhibit distinct organotropism for the eye or urogenital tract. We previously reported tissue-tropic correlations with the presence or absence of a functional tryptophan synthase and a putative GTPase-inactivating domain of the chlamydial toxin gene. This suggested that these genes may be the primary factors responsible for chlamydial disease organotropism. To test this hypothesis, the genome of an oculotropic trachoma isolate (A/HAR-13) was sequenced and compared to the genome of a genitotropic (D/UW-3) isolate. Remarkably, the genomes share 99.6% identity, supporting the conclusion that a functional tryptophan synthase enzyme and toxin might be the principal virulence factors underlying disease organotropism. Tarp (translocated actin-recruiting phosphoprotein) was identified to have variable numbers of repeat units within the N and C portions of the protein. A correlation exists between lymphogranuloma venereum serovars and the number of N-terminal repeats. Single-nucleotide polymorphism (SNP) analysis between the two genomes highlighted the minimal genetic variation. A disproportionate number of SNPs were observed within some members of the polymorphic membrane protein (pmp) autotransporter gene family that corresponded to predicted T-cell epitopes that bind HLA class I and II alleles. These results implicate Pmps as novel immune targets, which could advance future chlamydial vaccine strategies. Lastly, a novel target for PCR diagnostics was discovered that can discriminate between ocular and genital strains. This discovery will enhance epidemiological investigations in nations where both trachoma and chlamydial STD are endemic.

  18. Neuropeptidomics in Triatoma infestans. Comparative transcriptomic analysis among triatomines.

    PubMed

    Traverso, Lucila; Sierra, Ivana; Sterkel, Marcos; Francini, Flavio; Ons, Sheila

    2016-12-18

    Chagas' disease, affecting up to 6-7 million people worldwide, is transmitted to humans through the feces of triatomine kissing bugs. From these, Rhodnius prolixus, Triatoma dimidiata, Triatoma infestans and Triatoma pallidipennis are important vectors distributed throughout the Latin American subcontinent. Resistance to pyrethroids has been developed by some triatomine populations, especially T. infestans, obstructing their control. Given their role in the regulation of physiological processes, neuroendocrine-derived factors have been proposed as a source of molecular targets for new-generation insecticides. However, the involvement of neuropeptides in insecticide metabolism and resistance in insects has been poorly studied. In the present work, the sequences of 20 neuropeptide precursor genes in T. infestans, 16 in T. dimidiata, and 13 in T. pallidipennis detected in transcriptomic databases are reported, and a comparative analysis in triatomines is presented. A total of 59 neuropeptides were validated by liquid chromatography-tandem mass spectrometry in brain and nervous ganglia from T. infestans, revealing the existence of differential post-translational modifications, extended and truncated forms. The results suggest a high sequence conservation in some neuropeptide systems in triatomines, whereas remarkable differences occur in several others within the core domains. Comparisons of the basal expression levels for several neuropeptide precursor genes between pyrethroid sensitive and resistant population of T. infestans are also presented here, in order to introduce a proof of concept to test the involvement of neuropeptides in insecticide resistance. From the precursors tested, NVP and ITG peptides are significantly higher expressed in the resistant population. To our knowledge, this is the first report to associate differential neuropeptide expression with insecticide resistance. The information provided here contributes to creating conditions to widely

  19. Comparative analysis of metagenomes of Italian top soil improvers.

    PubMed

    Gigliucci, Federica; Brambilla, Gianfranco; Tozzoli, Rosangela; Michelacci, Valeria; Morabito, Stefano

    2017-05-01

    Biosolids originating from Municipal Waste Water Treatment Plants are proposed as top soil improvers (TSI) for their beneficial input of organic carbon on agriculture lands. Their use to amend soil is controversial, as it may lead to the presence of emerging hazards of anthropogenic or animal origin in the environment devoted to food production. In this study, we used a shotgun metagenomics sequencing as a tool to perform a characterization of the hazards related with the TSIs. The samples showed the presence of many virulence genes associated to different diarrheagenic E. coli pathotypes as well as of different antimicrobial resistance-associated genes. The genes conferring resistance to Fluoroquinolones was the most relevant class of antimicrobial resistance genes observed in all the samples tested. To a lesser extent traits associated with the resistance to Methicillin in Staphylococci and genes conferring resistance to Streptothricin, Fosfomycin and Vancomycin were also identified. The most represented metal resistance genes were cobalt-zinc-cadmium related, accounting for 15-50% of the sequence reads in the different metagenomes out of the total number of those mapping on the class of resistance to compounds determinants. Moreover the taxonomic analysis performed by comparing compost-based samples and biosolids derived from municipal sewage-sludges treatments divided the samples into separate populations, based on the microbiota composition. The results confirm that the metagenomics is efficient to detect genomic traits associated with pathogens and antimicrobial resistance in complex matrices and this approach can be efficiently used for the traceability of TSI samples using the microorganisms' profiles as indicators of their origin. Copyright © 2017 Elsevier Inc. All rights reserved.

  20. Hidden Markov models for evolution and comparative genomics analysis.

    PubMed

    Bykova, Nadezda A; Favorov, Alexander V; Mironov, Andrey A

    2013-01-01

    The problem of reconstruction of ancestral states given a phylogeny and data from extant species arises in a wide range of biological studies. The continuous-time Markov model for the discrete states evolution is generally used for the reconstruction of ancestral states. We modify this model to account for a case when the states of the extant species are uncertain. This situation appears, for example, if the states for extant species are predicted by some program and thus are known only with some level of reliability; it is common for bioinformatics field. The main idea is formulation of the problem as a hidden Markov model on a tree (tree HMM, tHMM), where the basic continuous-time Markov model is expanded with the introduction of emission probabilities of observed data (e.g. prediction scores) for each underlying discrete state. Our tHMM decoding algorithm allows us to predict states at the ancestral nodes as well as to refine states at the leaves on the basis of quantitative comparative genomics. The test on the simulated data shows that the tHMM approach applied to the continuous variable reflecting the probabilities of the states (i.e. prediction score) appears to be more accurate then the reconstruction from the discrete states assignment defined by the best score threshold. We provide examples of applying our model to the evolutionary analysis of N-terminal signal peptides and transcription factor binding sites in bacteria. The program is freely available at http://bioinf.fbb.msu.ru/~nadya/tHMM and via web-service at http://bioinf.fbb.msu.ru/treehmmweb.

  1. A comparative study of RNA-seq analysis strategies.

    PubMed

    Jänes, Jürgen; Hu, Fengyuan; Lewin, Alexandra; Turro, Ernest

    2015-11-01

    Three principal approaches have been proposed for inferring the set of transcripts expressed in RNA samples using RNA-seq. The simplest approach uses curated annotations, which assumes the transcripts in a sample are a subset of the transcripts listed in a curated database. A more ambitious method involves aligning reads to a reference genome and using the alignments to infer the transcript structures, possibly with the aid of a curated transcript database. The most challenging approach is to assemble reads into putative transcripts de novo without the aid of reference data. We have systematically assessed the properties of these three approaches through a simulation study. We have found that the sensitivity of computational transcript set estimation is severely limited. Computational approaches (both genome-guided and de novo assembly) produce a large number of artefacts, which are assigned large expression estimates and absorb a substantial proportion of the signal when performing expression analysis. The approach using curated annotations shows good expression correlation even when the annotations are incomplete. Furthermore, any incorrect transcripts present in a curated set do not absorb much signal, so it is preferable to have a curation set with high sensitivity than high precision. Software to simulate transcript sets, expression values and sequence reads under a wider range of parameter values and to compare sensitivity, precision and signal-to-noise ratios of different methods is freely available online (https://github.com/boboppie/RSSS) and can be expanded by interested parties to include methods other than the exemplars presented in this article. © The Author 2015. Published by Oxford University Press.

  2. Online Patient Resources for Liposuction: A Comparative Analysis of Readability.

    PubMed

    Vargas, Christina R; Ricci, Joseph A; Chuang, Danielle J; Lee, Bernard T

    2016-03-01

    As patients strive to become informed about health care, inadequate functional health literacy is a significant barrier. Nearly half of American adults have poor or marginal health literacy skills and the National Institutes of Health and American Medical Association have recommended that patient information should be written at a sixth grade level. The aim of this study is to identify the most commonly used online patient information about liposuction and to evaluate its readability relative to average American literacy. An internet search of "liposuction" was performed and the 10 most popular websites identified. User and location data were disabled and sponsored results excluded. All relevant, patient-directed articles were downloaded and formatted into plain text. Articles were then analyzed using 10 established readability tests. A comparison group was constructed to identify the most popular online consumer information about tattooing. Mean readability scores and specific article characteristics were compared. A total of 80 articles were collected from websites about liposuction. Readability analysis revealed an overall 13.6 grade reading level (range, 10-16 grade); all articles exceeded the target sixth grade level. Consumer websites about tattooing were significantly easier to read, with a mean 7.8 grade level. These sites contained significantly fewer characters per word and words per sentence, as well as a smaller proportion of complex, long, and unfamiliar words. Online patient resources about liposuction are potentially too difficult for a large number of Americans to understand. Liposuction websites are significantly harder to read than consumer websites about tattooing. Aesthetic surgeons are advised to discuss with patients resources they use and guide patients to appropriate information for their skill level.

  3. Comparative Genomic Analysis of Mannheimia haemolytica from Bovine Sources

    PubMed Central

    Klima, Cassidy L.; Cook, Shaun R.; Zaheer, Rahat; Laing, Chad; Gannon, Vick P.; Xu, Yong; Rasmussen, Jay; Potter, Andrew; Hendrick, Steve; Alexander, Trevor W.; McAllister, Tim A.

    2016-01-01

    Bovine respiratory disease is a common health problem in beef production. The primary bacterial agent involved, Mannheimia haemolytica, is a target for antimicrobial therapy and at risk for associated antimicrobial resistance development. The role of M. haemolytica in pathogenesis is linked to serotype with serotypes 1 (S1) and 6 (S6) isolated from pneumonic lesions and serotype 2 (S2) found in the upper respiratory tract of healthy animals. Here, we sequenced the genomes of 11 strains of M. haemolytica, representing all three serotypes and performed comparative genomics analysis to identify genetic features that may contribute to pathogenesis. Possible virulence associated genes were identified within 14 distinct prophage, including a periplasmic chaperone, a lipoprotein, peptidoglycan glycosyltransferase and a stress response protein. Prophage content ranged from 2–8 per genome, but was higher in S1 and S6 strains. A type I-C CRISPR-Cas system was identified in each strain with spacer diversity and organization conserved among serotypes. The majority of spacers occur in S1 and S6 strains and originate from phage suggesting that serotypes 1 and 6 may be more resistant to phage predation. However, two spacers complementary to the host chromosome targeting a UDP-N-acetylglucosamine 2-epimerase and a glycosyl transferases group 1 gene are present in S1 and S6 strains only indicating these serotypes may employ CRISPR-Cas to regulate gene expression to avoid host immune responses or enhance adhesion during infection. Integrative conjugative elements are present in nine of the eleven genomes. Three of these harbor extensive multi-drug resistance cassettes encoding resistance against the majority of drugs used to combat infection in beef cattle, including macrolides and tetracyclines used in human medicine. The findings here identify key features that are likely contributing to serotype related pathogenesis and specific targets for vaccine design intended to reduce the

  4. Comparative analysis of 60Co intensity-modulated radiation therapy

    NASA Astrophysics Data System (ADS)

    Fox, Christopher; Romeijn, H. Edwin; Lynch, Bart; Men, Chunhua; Aleman, Dionne M.; Dempsey, James F.

    2008-06-01

    In this study, we perform a scientific comparative analysis of using 60Co beams in intensity-modulated radiation therapy (IMRT). In particular, we evaluate the treatment plan quality obtained with (i) 6 MV, 18 MV and 60Co IMRT; (ii) different numbers of static multileaf collimator (MLC) delivered 60Co beams and (iii) a helical tomotherapy 60Co beam geometry. We employ a convex fluence map optimization (FMO) model, which allows for the comparison of plan quality between different beam energies and configurations for a given case. A total of 25 clinical patient cases that each contain volumetric CT studies, primary and secondary delineated targets, and contoured structures were studied: 5 head-and-neck (H&N), 5 prostate, 5 central nervous system (CNS), 5 breast and 5 lung cases. The DICOM plan data were anonymized and exported to the University of Florida optimized radiation therapy (UFORT) treatment planning system. The FMO problem was solved for each case for 5-71 equidistant beams as well as a helical geometry for H&N, prostate, CNS and lung cases, and for 3-7 equidistant beams in the upper hemisphere for breast cases, all with 6 MV, 18 MV and 60Co dose models. In all cases, 95% of the target volumes received at least the prescribed dose with clinical sparing criteria for critical organs being met for all structures that were not wholly or partially contained within the target volume. Improvements in critical organ sparing were found with an increasing number of equidistant 60Co beams, yet were marginal above 9 beams for H&N, prostate, CNS and lung. Breast cases produced similar plans for 3-7 beams. A helical 60Co beam geometry achieved similar plan quality as static plans with 11 equidistant 60Co beams. Furthermore, 18 MV plans were initially found not to provide the same target coverage as 6 MV and 60Co plans; however, adjusting the trade-offs in the optimization model allowed equivalent target coverage for 18 MV. For plans with comparable target coverage

  5. Decision analysis and cost-effectiveness analysis for comparative effectiveness research--a primer.

    PubMed

    Sher, David J; Punglia, Rinaa S

    2014-01-01

    Although the analysis of real-world data is the foundation of comparative effectiveness analysis, not all clinical questions are easily approached with patient-derived information. Decision analysis is a set of modeling and analytic tools that simulate treatment and disease processes, including the incorporation of patient preferences, thus generating optimal treatment strategies for varying patient, disease, and treatment conditions. Although decision analysis is informed by evidence-derived outcomes, its ability to test treatment strategies under different conditions that are realistic but not necessarily reported in the literature makes it a useful and complementary technique to more standard data analysis. Similarly, cost-effectiveness analysis is a discipline in which the relative costs and benefits of treatment alternatives are rigorously compared. With the well-recognized increase in highly technical, costly radiation therapy technologies, the cost-effectiveness of these different treatments would come under progressively more scrutiny. In this review, we discuss the theoretical and practical aspects of decision analysis and cost-effectiveness analysis, providing examples that highlight their methodology and utility.

  6. Addressing Informatics Barriers to Conducting Observational Comparative Effectiveness Research: A Comparative Case Analysis

    ERIC Educational Resources Information Center

    Boone, Christopher P. D.

    2013-01-01

    Background: The U.S. health care system has been under immense scrutiny for ever-increasing costs and poor health outcomes for its patients. Comparative Effectiveness Research (CER) has emerged as a generally accepted practice by providers, policy makers, and scientists as an approach to identify the most clinical- and cost-effective interventions…

  7. Addressing Informatics Barriers to Conducting Observational Comparative Effectiveness Research: A Comparative Case Analysis

    ERIC Educational Resources Information Center

    Boone, Christopher P. D.

    2013-01-01

    Background: The U.S. health care system has been under immense scrutiny for ever-increasing costs and poor health outcomes for its patients. Comparative Effectiveness Research (CER) has emerged as a generally accepted practice by providers, policy makers, and scientists as an approach to identify the most clinical- and cost-effective interventions…

  8. Comparative analysis of aerosols elemental distribution in some Romanian regions

    NASA Astrophysics Data System (ADS)

    Amemiya, Susumu; Masuda, Toshio; Popa-Simil, Liviu; Mateescu, Liviu

    1996-04-01

    The study's main aim is obtaining aerosols particulate elemental distribution and mapping it for some Romanian regions, in order to obtain preliminary information regarding the concentrations of aerosol particles and networking strategy versus local conditions. For this we used the mobile sampling strategy, but taking care on all local specific conditions and weather. In the summer of 1993, in July we took about 8 samples on a rather large territory of SE Romania which were analysed and mapped. The regions which showed an interesting behaviour or doubts such as Bucharest and Dobrogea were zoomed in near the same period of 1994, for comparing the new details with the global aspect previously obtained. An attempt was made to infer the minimum necessary number of stations in a future monitoring network. A mobile sampler was used, having tow polycarbonate filter posts of 8 and 0.4 μm. PIXE elemental analysis was performed on a 2.5 MV Van de Graaff accelerator, by using a proton beam. More than 15 elements were measured. Suggestive 2D and 3D representations were drawn, as well as histogram charts for the concentrations' distribution in the specific regions at the specified times. In spite of the poor samples from the qualitative point of view the experiment surprised us by the good coincidence (good agreement) with realities in terrain known by other means long time ago, and highlighted the power of PIXE methods in terms of money and time. Conclusions over the link between industry, traffic, vegetation, wether, surface waters, soil composition, power plant exhaust and so on, on the one hand, and surface concentration distribution, on the other, were drawn. But the method's weak points were also highlighted; these are weather dependencies (especially air masses movement and precipitation), local relief, microclimate and vegetation, and of course localisation of the sampling point versus the pollution sources and their regime. The paper contains a synthesis of the whole

  9. Comparative proteomic analysis of human lung telocytes with fibroblasts

    PubMed Central

    Zheng, Yonghua; Cretoiu, Dragos; Yan, Guoquan; Cretoiu, Sanda Maria; Popescu, Laurentiu M; Wang, Xiangdong

    2014-01-01

    Telocytes (TCs) were recently described as interstitial cells with very long prolongations named telopodes (Tps; http://www.telocytes.com). Establishing the TC proteome is a priority to show that TCs are a distinct type of cells. Therefore, we examined the molecular aspects of lung TCs by comparison with fibroblasts (FBs). Proteins extracted from primary cultures of these cells were analysed by automated 2-dimensional nano-electrospray ionization liquid chromatography tandem mass spectrometry (2D Nano-ESI LC-MS/MS). Differentially expressed proteins were screened by two-sample t-test (P < 0.05) and fold change (>2), based on the bioinformatics analysis. We identified hundreds of proteins up- or down-regulated, respectively, in TCs as compared with FBs. TC proteins with known identities are localized in the cytoskeleton (87%) and plasma membrane (13%), while FB up-regulated proteins are in the cytoskeleton (75%) and destined to extracellular matrix (25%). These identified proteins were classified into different categories based on their molecular functions and biological processes. While the proteins identified in TCs are mainly involved in catalytic activity (43%) and as structural molecular activity (25%), the proteins in FBs are involved in catalytic activity (24%) and in structural molecular activity, particularly synthesis of collagen and other extracellular matrix components (25%). Anyway, our data show that TCs are completely different from FBs. In conclusion, we report here the first extensive identification of proteins from TCs using a quantitative proteomics approach. Protein expression profile shows many up-regulated proteins e.g. myosin-14, periplakin, suggesting that TCs might play specific roles in mechanical sensing and mechanochemical conversion task, tissue homoeostasis and remodelling/renewal. Furthermore, up-regulated proteins matching those found in extracellular vesicles emphasize TCs roles in intercellular signalling and stem cell niche

  10. Comparative risk analysis, priority setting, and public participation

    SciTech Connect

    Kramer, K.A.; Snyder, M.

    1994-12-31

    Over thirty governments (Tribal, State, and Local) are engaging in a comparative environmental risk process to help set priorities in their environmental management programs. The comparative risk approach in these governments includes human health risk, ecological risk, quality of life risk, public values assessment, environmental justice and other tools. All of these components, not just the more quantifiable risk assessments, play a vital role in setting priorities for the governments. The comparative risk projects of Colorado, California, Washington, and Seattle among others will be described to demonstrate the key elements of current environmental comparative risk projects.

  11. Comparing Active Pediatric Obesity Treatments Using Meta-Analysis

    ERIC Educational Resources Information Center

    Gilles, Allyson; Cassano, Michael; Shepherd, Elizabeth J.; Higgins, Diana; Hecker, Jeffrey E.; Nangle, Douglas W.

    2008-01-01

    The current meta-analysis reviews research on the treatment of pediatric obesity focusing on studies that have been published since 1994. Eleven studies (22 comparisons, 115 effect sizes, N = 447) were included in the present meta-analysis. Results indicated that comprehensive behavioral interventions may be improved in at least two ways:…

  12. A Comparative Assessment of Greek Universities' Efficiency Using Quantitative Analysis

    ERIC Educational Resources Information Center

    Katharaki, Maria; Katharakis, George

    2010-01-01

    In part due to the increased demand for higher education, typical evaluation frameworks for universities often address the key issue of available resource utilisation. This study seeks to estimate the efficiency of 20 public universities in Greece through quantitative analysis (including performance indicators, data envelopment analysis (DEA) and…

  13. The Risky Shift in Policy Decision Making: A Comparative Analysis

    ERIC Educational Resources Information Center

    Wilpert, B.; And Others

    1976-01-01

    Based on analysis of data on 432 decision-makers from around the world, this study examines the decision-making phenomenon that individuals tend to move toward riskier decisions after group discussion. Findings of the analysis contradicted earlier studies, showing a consistent shift toward greater risk avoidance. Available from Elsevier Scientific…

  14. Comparing Active Pediatric Obesity Treatments Using Meta-Analysis

    ERIC Educational Resources Information Center

    Gilles, Allyson; Cassano, Michael; Shepherd, Elizabeth J.; Higgins, Diana; Hecker, Jeffrey E.; Nangle, Douglas W.

    2008-01-01

    The current meta-analysis reviews research on the treatment of pediatric obesity focusing on studies that have been published since 1994. Eleven studies (22 comparisons, 115 effect sizes, N = 447) were included in the present meta-analysis. Results indicated that comprehensive behavioral interventions may be improved in at least two ways:…

  15. The Risky Shift in Policy Decision Making: A Comparative Analysis

    ERIC Educational Resources Information Center

    Wilpert, B.; And Others

    1976-01-01

    Based on analysis of data on 432 decision-makers from around the world, this study examines the decision-making phenomenon that individuals tend to move toward riskier decisions after group discussion. Findings of the analysis contradicted earlier studies, showing a consistent shift toward greater risk avoidance. Available from Elsevier Scientific…

  16. Comparative Analysis of Languages for Machine Processing. Interim Report.

    ERIC Educational Resources Information Center

    Zierer, Ernesto; And Others

    This report gives the results obtained in the semantic and syntactic analysis of the Japanese particles "de,""ni,""e," and "wo" in comparison to their equivalents in English, German, and Spanish. The study is based on the so-called "Correlational Analysis" as proposed by Ernst von Glaserfeld. The…

  17. Comparative Analysis of Languages for Machine Processing. Interim Report.

    ERIC Educational Resources Information Center

    Zierer, Ernesto; And Others

    This report gives the results obtained in the semantic and syntactic analysis of the Japanese particles "de,""ni,""e," and "wo" in comparison to their equivalents in English, German, and Spanish. The study is based on the so-called "Correlational Analysis" as proposed by Ernst von Glaserfeld. The…

  18. A Comparative Study of Science, Systems Analysis and Futurism

    ERIC Educational Resources Information Center

    Correa, Hector

    1975-01-01

    The proper framework for studying different methods of problem-solving is to recognize that there are different approaches to the analysis of reality. Three approaches--science, systems analysis, and futurism--are considered within the framework of the "theory of knowledge." (Author/IRT)

  19. A Comparative Study of Science, Systems Analysis and Futurism

    ERIC Educational Resources Information Center

    Correa, Hector

    1975-01-01

    The proper framework for studying different methods of problem-solving is to recognize that there are different approaches to the analysis of reality. Three approaches--science, systems analysis, and futurism--are considered within the framework of the "theory of knowledge." (Author/IRT)

  20. A Comparative Assessment of Greek Universities' Efficiency Using Quantitative Analysis

    ERIC Educational Resources Information Center

    Katharaki, Maria; Katharakis, George

    2010-01-01

    In part due to the increased demand for higher education, typical evaluation frameworks for universities often address the key issue of available resource utilisation. This study seeks to estimate the efficiency of 20 public universities in Greece through quantitative analysis (including performance indicators, data envelopment analysis (DEA) and…

  1. Community College Student Mental Health: A Comparative Analysis

    ERIC Educational Resources Information Center

    Katz, Daniel Seth; Davison, Karen

    2014-01-01

    This study explores community college student mental health by comparing the responses of California community college and traditional university students on the American College Health Association-National College Health Assessment II (ACHA-NCHA II). Using MANOVA, we compared community college and traditional university students, examining…

  2. TOOLS FOR COMPARATIVE ANALYSIS OF ALTERNATIVES: COMPETING OR COMPLEMENTARY PERSPECTIVES?

    EPA Science Inventory

    A third generation of environmental policymaking and risk management will increasingly impose environmental measures, which may give rise to analyzing countervailing risks. Therefore, a comprehensive analysis of these risks associated with the decision alternatives at hand will e...

  3. TOOLS FOR COMPARATIVE ANALYSIS OF ALTERNATIVES: COMPETING OR COMPLEMENTARY PERSPECTIVES?

    EPA Science Inventory

    A third generation of environmental policymaking and risk management will increasingly impose environmental measures, which may give rise to analyzing countervailing risks. Therefore, a comprehensive analysis of these risks associated with the decision alternatives at hand will e...

  4. Comparative experimental analysis of composite pulses in 14N NQR.

    PubMed

    Mikhaltsevitch, V T; Rudakov, T N; Flexman, J H; Hayes, P A; Chisholm, W P

    2004-01-01

    Experimental results of comparing composite pulses in nitrogen-14 NQR, that are analogous to common 90 degrees RF pulses in powder, are presented. All tested pulses have been taken from publications in journals. Comparative diagrams of the measurement results for induction signals and echo signals are presented. The results of the measurements demonstrate that the best outcomes are achieved when the composite pulse (45)0(95)180(164)0 is used.

  5. Comparative analysis of pressure vessel integrity for various LOCA conditions

    NASA Astrophysics Data System (ADS)

    Çolak, Üner; Özdere, Oya

    2001-09-01

    In this study, integrity analysis is performed for a classical four loop PWR pressure vessel fabricated from SA533B type ferritic steel. Pressure vessel behavior is analyzed by deterministic and probabilistic methods under transient conditions, which may cause pressurized thermal shock (PTS). In deterministic analysis, the change of material properties and the mechanical state of the vessel are analyzed against changes in coolant pressure and temperature. Probabilistic analysis is performed to obtain pressure vessel beltline region weld failure probabilities in transient conditions. Overall vessel failure probabilities are evaluated based on the results of deterministic analyses. Computer code VISA-II is utilized for the calculation of vessel failure probabilities. Among three cases considered in this study, a medium break loss of coolant accident induced by a 50 cm2 break in the hot leg yields the highest vessel rupture probability. The maximum nil ductility temperature in all cases is still below the NRC PTS limit.

  6. Ten lessons with Carl Woese about RNA and comparative analysis.

    PubMed

    Gutell, Robin R

    2014-01-01

    A few years before I started my graduate studies, Carl Woese was establishing a collaboration with his friend, colleague, and my PhD advisor, Harry Noller. Carl was introducing comparative methods to Harry's lab to determine the secondary structure for the 16S and 23S rRNAs. In addition to an experimental project that had minimal to no success, I was attempting to predict an RNA secondary structure from a single sequence. I determined after a few months that the complexity of RNA folding was much greater than ever anticipated. Ten lessons were learned about the dynamics of RNA folding, the comparative methods used to accurately predict the RNAs secondary structure and the beginnings of its tertiary structure, the use of comparative methods to reveal much more than ever anticipated about RNA structure, other applications beyond RNA structure, and the lessons about the process of scientific discovery.

  7. Comparative Analysis of Three Proposed Federal Renewable Electricity Standards

    SciTech Connect

    Sullivan, P.; Logan, J.; Bird, L.; Short, W.

    2009-05-01

    This paper analyzes potential impacts of proposed national renewable electricity standard (RES) legislation. An RES is a mandate requiring certain electricity retailers to provide a minimum share of their electricity sales from qualifying renewable power generation. The analysis focuses on draft bills introduced individually by Senator Jeff Bingaman and Representative Edward Markey, and jointly by Representative Henry Waxman and Markey. The analysis uses NREL's Regional Energy Deployment System (ReEDS) model to evaluate the impacts of the proposed RES requirements on the U.S. energy sector in four scenarios.

  8. A Comparative Analysis of Three Proposed Federal Renewable Electricity Standards

    SciTech Connect

    Sullivan, Patrick; Logan, Jeffrey; Bird, Lori; Short, Walter

    2009-05-01

    This paper analyzes potential impacts of proposed national renewable electricity standard (RES) legislation. An RES is a mandate requiring certain electricity retailers to provide a minimum share of their electricity sales from qualifying renewable power generation. The analysis focuses on draft bills introduced individually by Senator Jeff Bingaman and Representative Edward Markey, and jointly by Representative Henry Waxman and Markey. The analysis uses NREL's Regional Energy Deployment System (ReEDS) model to evaluate the impacts of the proposed RES requirements on the U.S. energy sector in four scenarios.

  9. Comparing active pediatric obesity treatments using meta-analysis.

    PubMed

    Gilles, Allyson; Cassano, Michael; Shepherd, Elizabeth J; Higgins, Diana; Hecker, Jeffrey E; Nangle, Douglas W

    2008-10-01

    The current meta-analysis reviews research on the treatment of pediatric obesity focusing on studies that have been published since 1994. Eleven studies (22 comparisons, 115 effect sizes, N = 447) were included in the present meta-analysis. Results indicated that comprehensive behavioral interventions may be improved in at least two ways: increasing the "dose" of behavioral components and increasing parental involvement. Although limited to just one investigation, support for the use of medication was also found. The addition of cognitive therapy techniques did not appear to increase, and possibly detracted from, the efficacy of established treatments.

  10. Comparative nutritional compositions and proteomics analysis of transgenic Xa21 rice seeds compared to conventional rice.

    PubMed

    Gayen, Dipak; Paul, Soumitra; Sarkar, Sailendra Nath; Datta, Swapan K; Datta, Karabi

    2016-07-15

    Transgenic rice expressing the Xa21 gene have enhanced resistant to most devastating bacterial blight diseases caused by Xanthomonas oryzae pv. oryzae (Xoo). However, identification of unintended modifications, owing to the genetic modification, is an important aspect of transgenic crop safety assessment. In this study, the nutritional compositions of seeds from transgenic rice plants expressing the Xa21 gene were compared against non-transgenic rice seeds. In addition, to detect any changes in protein translation levels as a result of Xa21 gene expression, rice seed proteome analyses were also performed by two-dimensional gel electrophoresis. No significant differences were found in the nutritional compositions (proximate components, amino acids, minerals, vitamins and anti-nutrients) of the transgenic and non-transgenic rice seeds. Although gel electrophoresis identified 11 proteins that were differentially expressed between the transgenic and non-transgenic seed, only one of these (with a 20-fold up-regulation in the transgenic seed) shows nutrient reservoir activity. No new toxins or allergens were detected in the transgenic seeds.

  11. Comparative genomic analysis as a tool for biologicaldiscovery

    SciTech Connect

    Nobrega, Marcelo A.; Pennacchio, Len A.

    2003-03-30

    Biology is a discipline rooted in comparisons. Comparative physiology has assembled a detailed catalogue of the biological similarities and differences between species, revealing insights into how life has adapted to fill a wide-range of environmental niches. For example, the oxygen and carbon dioxide carrying capacity of vertebrate has evolved to provide strong advantages for species respiring at sea level, at high elevation or within water. Comparative- anatomy, -biochemistry, -pharmacology, -immunology and -cell biology have provided the fundamental paradigms from which each discipline has grown.

  12. Environmental Education in Macedonian Schools: A Comparative Analysis of Textbooks

    ERIC Educational Resources Information Center

    Srbinovski, Mile

    2013-01-01

    The purpose of this article is to describe and discuss an analysis of the extent to which environmental issues are addressed in the textbooks in the schools of the Republic of Macedonia. Research has analyzed a range of textbooks (279) published in the past 15 years. Our fundamental conclusion is that the inclusion of environmental issues in the…

  13. Environmental Education in Macedonian Schools: A Comparative Analysis of Textbooks

    ERIC Educational Resources Information Center

    Srbinovski, Mile

    2013-01-01

    The purpose of this article is to describe and discuss an analysis of the extent to which environmental issues are addressed in the textbooks in the schools of the Republic of Macedonia. Research has analyzed a range of textbooks (279) published in the past 15 years. Our fundamental conclusion is that the inclusion of environmental issues in the…

  14. Comparative Analysis of the Concept of Shakespearean Tragedies

    ERIC Educational Resources Information Center

    Sipra, Muhammad Aslam; Nasir, Muhammad Haseeb

    2014-01-01

    In this article, the analysis of Shakespearean tragedies is presented. It reveals that Shakespeare's plays are full of conflicting thoughts, and expression is so convincing that it is not possible to plan a system of philosophy out of them. Each character, from the king to the clown, from the most highly intellectual to the simpleton, judges life…

  15. Comparative analysis of African swine fever virus genotypes and serogroups.

    PubMed

    Malogolovkin, Alexander; Burmakina, Galina; Titov, Ilya; Sereda, Alexey; Gogin, Andrey; Baryshnikova, Elena; Kolbasov, Denis

    2015-02-01

    African swine fever virus (ASFV) causes highly lethal hemorrhagic disease among pigs, and ASFV's extreme antigenic diversity hinders vaccine development. We show that p72 ASFV phylogenetic analysis does not accurately define ASFV hemadsorption inhibition assay serogroups. Thus, conventional ASFV genotyping cannot discriminate between viruses of different virulence or predict efficacy of a specific ASFV vaccine.

  16. Reading in Two Languages: A Comparative Miscue Analysis

    ERIC Educational Resources Information Center

    Mikulec, Erin

    2015-01-01

    The purpose of the present study is to investigate what miscue analysis, a method described as a "window" into the reading process, can reveal about first and second language reading. Two participants, native English speakers proficient in Spanish, read and retold two folktales: one in English and one in Spanish. The researcher performed…

  17. Reading in Two Languages: A Comparative Miscue Analysis

    ERIC Educational Resources Information Center

    Mikulec, Erin

    2015-01-01

    The purpose of the present study is to investigate what miscue analysis, a method described as a "window" into the reading process, can reveal about first and second language reading. Two participants, native English speakers proficient in Spanish, read and retold two folktales: one in English and one in Spanish. The researcher performed…

  18. Comparative Analysis of African Swine Fever Virus Genotypes and Serogroups

    PubMed Central

    Burmakina, Galina; Titov, Ilya; Sereda, Alexey; Gogin, Andrey; Baryshnikova, Elena; Kolbasov, Denis

    2015-01-01

    African swine fever virus (ASFV) causes highly lethal hemorrhagic disease among pigs, and ASFV’s extreme antigenic diversity hinders vaccine development. We show that p72 ASFV phylogenetic analysis does not accurately define ASFV hemadsorption inhibition assay serogroups. Thus, conventional ASFV genotyping cannot discriminate between viruses of different virulence or predict efficacy of a specific ASFV vaccine. PMID:25625574

  19. Comparative analysis of Medicare spending for medical imaging: sustained dramatic slowdown compared with other services.

    PubMed

    Lee, David W; Duszak, Richard; Hughes, Danny R

    2013-12-01

    The purpose of this study was to assess trends in Medicare spending growth for medical imaging relative to other services and the Deficit Reduction Act (DRA). We calculated per-beneficiary Part B Medicare medical imaging expenditures for three-digit Berenson-Eggers Type of Service (BETOS) categories using Physician Supplier Procedure Summary Master Files for 32 million beneficiaries from 2000 to 2011. We adjusted BETOS categories to address changes in coding and payment policy and excluded categories with 2011 aggregate spending less than $500 million. We computed and ranked compound annual growth rates over three periods: pre-DRA (2000-2005), DRA transition period (2005-2007), and post-DRA (2007-2011). Forty-four modified BETOS categories fulfilled the inclusion criteria. Between 2000 and 2006, Medicare outlays for nonimaging services grew by 6.8% versus 12.0% for imaging services. In the ensuing 5 years, annual growth in spending for nonimaging continued at 3.6% versus a decline of 3.5% for imaging. Spending growth for all services during the pre-DRA, DRA, and post-DRA periods were 7.8%, 3.8%, and 2.9 compared with 15.0%, -3.4%, and -2.2% for advanced imaging services. Advanced imaging was among the fastest growing categories of Medicare services in the early 2000s but was in the bottom 2% of spending categories in 2011. Between 2007 and 2011, the fastest growing service categories were evaluation and management services with other specialists (29.1%), nursing home visits (11.2%), anesthesia (9.1%), and other ambulatory procedures (9.0%). Slowing volume growth and massive Medicare payment cuts have left medical imaging near the bottom of all service categories contributing to growth in Medicare spending.

  20. Child Sexual Abuse and Adolescent Prostitution: A Comparative Analysis.

    ERIC Educational Resources Information Center

    Seng, Magnus J.

    1989-01-01

    Explored relationship between sexual abuse and adolescent prostitution by comparing 70 sexually abused children with 35 prostitution-involved children on 22 variables. Findings suggest that relationship is not direct, but involves runaway behavior as intervening variable. Concludes that it is not so much sexual abuse that leads to prostitution, as…

  1. Reference Management Software: A Comparative Analysis of Four Products

    ERIC Educational Resources Information Center

    Gilmour, Ron; Cobus-Kuo, Laura

    2011-01-01

    Reference management (RM) software is widely used by researchers in the health and natural sciences. Librarians are often called upon to provide support for these products. The present study compares four prominent RMs: CiteULike, RefWorks, Mendeley, and Zotero, in terms of features offered and the accuracy of the bibliographies that they…

  2. A Comparative Analysis of Personality Organization in Juvenile Anorexia Nervosa.

    ERIC Educational Resources Information Center

    Strober, Michael

    1981-01-01

    To identify distinguishing features of personality associated with anorexia nervosa in adolescence, the Cattell High School Personality Questionnaire responses of 50 anorectics were compared with matched groups of depressed and antisocial adolescent females. Results indicated that anorectics displayed greater conformity, neurotic anxieties,…

  3. A Comparative Analysis of Day Care Licensing Standards.

    ERIC Educational Resources Information Center

    Hawaii Univ., Honolulu. Head Start Research and Evaluation Center.

    This report focuses on the major similarities and differences of three sets of day care licensing standards (model, state, and federal) in order to provide an information base for isolating the problems, concerns, and issues involved in day care licensing. Sets of standards compared are: (1) "OCD Guides for Day Care Licensing," 1973…

  4. Critical Citizenship Education in England and France: A Comparative Analysis

    ERIC Educational Resources Information Center

    Johnson, Laura; Morris, Paul

    2012-01-01

    The promotion of "critical citizenship" has become a key objective of official school curricula around the world. Using an analytic framework developed by the authors, this paper identifies the diverse conceptions of critical citizenship that are promoted, by comparing the official school curricula for citizenship in England and France.…

  5. USMC Fire and Emergency Services: A Comparative Business Case Analysis

    DTIC Science & Technology

    2005-12-01

    based on Site Visits conducted by the author to six DoD Fire Departments within California and Arizona (4 Marine Corps, 1 Air Force and 1 Navy...The Site Visits were completed to compare and contrast emergency service organizational structures, core capabilities and resource inputs. Moreover

  6. Comparative analysis of Asian citrus psyllid and Potato psyllid antennae

    USDA-ARS?s Scientific Manuscript database

    The comparative investigation of the morphological basis for olfactory reception in two psyllid species, Diaphorina citri (the Asian citrus psyllid), and Bacterocera cockerelli (the potato/tomato psyllid) (both species Hemiptera:Psyllidae) was performed using scanning electron microscopy to elucidat...

  7. Sustainability of Social Programs: A Comparative Case Study Analysis

    ERIC Educational Resources Information Center

    Savaya, Riki; Spiro, Shimon; Elran-Barak, Roni

    2008-01-01

    The article reports on the findings of a comparative case study of six projects that operated in Israel between 1980 and 2000. The study findings identify characteristics of the programs, the host organizations, and the social and political environment, which differentiated programs that are sustained from those that are not. The findings reaffirm…

  8. Environment Reporters and U.S. Journalists: A Comparative Analysis

    ERIC Educational Resources Information Center

    Sachsman, David B.; Simon, James; Valenti, JoAnn Myer

    2008-01-01

    This study provides baseline data regarding environment reporters in the twenty-first century, and then compares this baseline information about a specialized journalism beat to existing studies of U.S. journalists in general. This comparison between 652 environmental journalists working at daily newspapers and television stations and more than…

  9. An International Comparative Analysis of Sustainability Transformation across Seven Universities

    ERIC Educational Resources Information Center

    Ferrer-Balas, D.; Adachi, J.; Banas, S.; Davidson, C. I.; Hoshikoshi, A.; Mishra, A.; Motodoa, Y.; Onga, M.; Ostwald, M.

    2008-01-01

    Purpose: The purpose of this paper is to identify the key aspects of transformation of universities towards sustainability, such as the ideal characteristics of the "sustainable university", and the drivers and barriers in the transformation, by comparing the strategies of seven universities world-wide. Design/methodology/approach: A…

  10. A Comparative Analysis of Entrepreneur and College Business Student Values.

    ERIC Educational Resources Information Center

    Solomon, George T.; Fernald, Jr., Lloyd W.

    1990-01-01

    The study compared values of 123 senior-level college business students and 400 Florida entrepreneurs. Findings indicated value differences between entrepreneurs and students, as well as between female entrepreneurs and female students, but few differences between male entrepreneurs and male students. (DB)

  11. Sociological analysis and comparative education: A brief bibliographical background

    NASA Astrophysics Data System (ADS)

    Bash, Leslie

    1981-12-01

    The bibliography cites English language material at the intersection of two fields of study: sociology of education and comparative education. The collection of material is biased (a) toward the general reader rather than the specialist already working in the area, and (b) toward the identification of overlap between the two fields of study.

  12. Education and the 1980s: A Comparative Analysis.

    ERIC Educational Resources Information Center

    King, Edmund

    1980-01-01

    The author introduces and synthesizes the papers in this theme issue on world education in the 1980s, highlighting the contrast between today's pessimism and the optimism of earlier decades. He cites the need for more comparative study of such worldwide educational problems as accountability, access, and the education/work relationship. (SJL)

  13. Child Sexual Abuse and Adolescent Prostitution: A Comparative Analysis.

    ERIC Educational Resources Information Center

    Seng, Magnus J.

    1989-01-01

    Explored relationship between sexual abuse and adolescent prostitution by comparing 70 sexually abused children with 35 prostitution-involved children on 22 variables. Findings suggest that relationship is not direct, but involves runaway behavior as intervening variable. Concludes that it is not so much sexual abuse that leads to prostitution, as…

  14. A comparative analysis of mail and internet surveys

    Treesearch

    Benjamin D. Poole; David K. Loomis

    2010-01-01

    Th e field of survey research is constantly evolving with the introduction of new technologies. Each new mini-revolution brings criticism about the accuracy of the new survey method. The latest development in the survey research field has been increased reliance on Internet surveys. This paper compares data collected through a mixed-mode (mail and Internet) survey of...

  15. Academic Freedom in Europe: A Preliminary Comparative Analysis

    ERIC Educational Resources Information Center

    Karran, Terence

    2007-01-01

    Using comparative data from 23 states within the European Union (EU), this paper is a preliminary assessment of the protection for, and (by extension) the health of, academic freedom in the universities of the nations of the EU. The paper examines constitutional and legislative protection for academic freedom, along with legal regulations…

  16. YersiniaBase: a genomic resource and analysis platform for comparative analysis of Yersinia.

    PubMed

    Tan, Shi Yang; Dutta, Avirup; Jakubovics, Nicholas S; Ang, Mia Yang; Siow, Cheuk Chuen; Mutha, Naresh Vr; Heydari, Hamed; Wee, Wei Yee; Wong, Guat Jah; Choo, Siew Woh

    2015-01-16

    Yersinia is a Gram-negative bacteria that includes serious pathogens such as the Yersinia pestis, which causes plague, Yersinia pseudotuberculosis, Yersinia enterocolitica. The remaining species are generally considered non-pathogenic to humans, although there is evidence that at least some of these species can cause occasional infections using distinct mechanisms from the more pathogenic species. With the advances in sequencing technologies, many genomes of Yersinia have been sequenced. However, there is currently no specialized platform to hold the rapidly-growing Yersinia genomic data and to provide analysis tools particularly for comparative analyses, which are required to provide improved insights into their biology, evolution and pathogenicity. To facilitate the ongoing and future research of Yersinia, especially those generally considered non-pathogenic species, a well-defined repository and analysis platform is needed to hold the Yersinia genomic data and analysis tools for the Yersinia research community. Hence, we have developed the YersiniaBase, a robust and user-friendly Yersinia resource and analysis platform for the analysis of Yersinia genomic data. YersiniaBase has a total of twelve species and 232 genome sequences, of which the majority are Yersinia pestis. In order to smooth the process of searching genomic data in a large database, we implemented an Asynchronous JavaScript and XML (AJAX)-based real-time searching system in YersiniaBase. Besides incorporating existing tools, which include JavaScript-based genome browser (JBrowse) and Basic Local Alignment Search Tool (BLAST), YersiniaBase also has in-house developed tools: (1) Pairwise Genome Comparison tool (PGC) for comparing two user-selected genomes; (2) Pathogenomics Profiling Tool (PathoProT) for comparative pathogenomics analysis of Yersinia genomes; (3) YersiniaTree for constructing phylogenetic tree of Yersinia. We ran analyses based on the tools and genomic data in YersiniaBase and the

  17. Comparing distributions of environmental outcomes for regulatory environmental justice analysis.

    PubMed

    Maguire, Kelly; Sheriff, Glenn

    2011-05-01

    Economists have long been interested in measuring distributional impacts of policy interventions. As environmental justice (EJ) emerged as an ethical issue in the 1970s, the academic literature has provided statistical analyses of the incidence and causes of various environmental outcomes as they relate to race, income, and other demographic variables. In the context of regulatory impacts, however, there is a lack of consensus regarding what information is relevant for EJ analysis, and how best to present it. This paper helps frame the discussion by suggesting a set of questions fundamental to regulatory EJ analysis, reviewing past approaches to quantifying distributional equity, and discussing the potential for adapting existing tools to the regulatory context.

  18. [Comparative analysis of efficacy of certain neuroprotectors in ischemic stroke].

    PubMed

    Skorokhodov, A P; Dudina, A A; Kolesnikova, E A; Koron, A E; Kobantsev, Iu A; Sedova, A A

    2006-01-01

    Cortexin, nootropil and cerebrolysin have been used as neuroprotective medications in the acute period of ischemic stroke (IS). Clinical efficacy of cortexin and nootropil has been compared in 2 therapeutic series in 35 patients and that of cortexin and cerebrolysin--in 45 patients. The efficacy was assessed using several clinical and psychometric scales with statistical processing of the results. The data obtained suggest that in patients with moderate IS the drugs exert a similar and rather marked effect which was stronger comparing to the treatment without these drugs. At the same time, a domestic neuroprotector cortexin has some advantages, especially with regard to the absence of side-effects and "price-dose-therapeutic effect" criterion.

  19. Comparative analysis of isotropic diffusion weighted imaging sequences

    NASA Astrophysics Data System (ADS)

    Vellmer, Sebastian; Stirnberg, Rüdiger; Edelhoff, Daniel; Suter, Dieter; Stöcker, Tony; Maximov, Ivan I.

    2017-02-01

    Visualisation of living tissue structure and function is a challenging problem of modern imaging techniques. Diffusion MRI allows one to probe in vivo structures on a micrometer scale. However, conventional diffusion measurements are time-consuming procedures, because they require several measurements with different gradient directions. Considerable time savings are therefore possible by measurement schemes that generate an isotropic diffusion weighting in a single shot. Multiple approaches for generating isotropic diffusion weighting are known and have become very popular as useful tools in clinical research. Thus, there is a strong need for a comprehensive comparison of different isotropic weighting approaches. In the present work we introduce two new sequences based on simple (co)sine modulations and compare their performance to established q-space magic-angle spinning sequences and conventional DTI, using a diffusion phantom assembled from microcapillaries and in vivo experiments at 7 T. The advantages and disadvantages of all compared schemes are demonstrated and discussed.

  20. Burnout syndrome in psychotherapists: a comparative analysis of five nations.

    PubMed

    Puig, Ana; Yoon, Eunhui; Callueng, Carmelo; An, Sunghee; Lee, Sang Min

    2014-02-01

    Burnout is a common phenomenon among psychotherapists. The purpose of this study was to test the Counselor Burnout Inventory (CBI; Lee et al., 2007) measurement invariance, as well as compare means of five latent variables (i.e., CBI subscales of Exhaustion, Incompetence, Negative Work Environment, Devaluing Client, and Deterioration in Personal Life) across five nations (United States, Korea, Japan, Philippines, and Hong Kong) using structural equation modeling. The results indicated that the assumptions of configural, factor loading, and intercept invariance were satisfied across the five nations. When comparing means of five latent variables, the results indicated differential burnout tendencies across the five nations. Implications for psychotherapists' burnout prevention and future research are discussed.

  1. Decision Analysis Tool to Compare Energy Pathways for Transportation

    SciTech Connect

    Bloyd, Cary N.; Stork, Kevin

    2011-02-01

    With the goals of reducing greenhouse gas emissions, oil imports, and energy costs, a wide variety of automotive technologies are proposed to replace the traditional gasoline-powered internal combustion engine (g-ICE). A prototype model, Analytica Transportation Energy Analysis Model (ATEAM), has been developed using the Analytica decision modeling environment, visualizing the structure as a hierarchy of influence diagrams. The report summarized the FY2010 ATEAM accomplishments.

  2. A comparative image analysis of radial Fourier-Chebyshev moments

    NASA Astrophysics Data System (ADS)

    Li, Bo

    2017-08-01

    On the basis of the discrete Fourier functions and the discrete Chebyshev polynomials, a new set of radial orthogonal moment functions were presented. The new moments construct a new discrete orthogonal plane, and take a new sampling method that overcomes the default of classical method, which can be effectively used in the image analysis. The experimental results show that the new radial moments are superior to the conventional moments in image reconstruction and computing efficiency.

  3. Endoscopic versus external approach dacryocystorhinostomy: A comparative analysis

    PubMed Central

    Saha, Rinki; Sinha, Anuradha; Phukan, Jyoti Prakash

    2013-01-01

    Background: Dacryocystorhinostomy (DCR) consists of creating a lacrimal drainage pathway to the nasal cavity to restore permanent drainage of previously obstructed excreting system. Aim: To compare the result and advantages of both endonasal endoscopic and external DCR regarding the patency rate, patient compliance and complications. Study Design: Prospective non-randomized comparative study. Materials and Methods: Study was conducted for 16 months duration in a teaching hospital with 50 cases of endoscopic and 30 cases of external DCR with a follow-up of minimum 6 months. Data regarding surgical outcome and complications were analysed and compared using χ2 test. Results: Total 72 patients were included in the study with six having bilateral involvement, out of which 20 were male and 52 were female. The mean age for endoscopic and external DCR was 33.6 years and 46.0 years, respectively. Right eye (63.8%) was involved more commonly than left eye (36.2%). Epiphora was the commonest presenting symptom (63.7%). Mean duration of surgery was much lengthier in external (mean 119.6 minutes) than endoscopic (mean 49.0 minutes) DCR. Bleeding was the most common immediate postoperative complication seen in 33.3% and 10.0% of external and endoscopic DCR cases, respectively. Primary surgical success rate was 90% and 96.7% for endoscopic and external DCR, respectively (P = 0.046). Among the endoscopic DCR group, four patients underwent revision surgery giving a total successful surgical outcome of 98% at third month of follow-up. However, at 6 month of follow-up, success rate was 92% for endoscopic DCR and 93.3% for external DCR. The difference was not statistically significant (P = 0.609). Conclusion: Intranasal endoscopic DCR is a simple, minimally invasive, day care procedure and had comparable result with conventional external DCR. PMID:23901178

  4. A Comparative Analysis of Equatorial Spread F and VHF Scintillation

    DTIC Science & Technology

    1982-02-01

    longitude because the scintillation activity at Accra, Ghana (Northern Hemisphere) is similar to that at Huancayo , Peru (Southern Hemisphere). 23...Fejer compared the reversal time (from upward by day to downward by night) as a function of time of year at Huancayo and Kodaikanal. This comparison is...of interest because Huancayo is located near Jicamarca and Kodaikanal (India) is reasonably close to Kwajalein.i" 23 Fejer found that the reversal time

  5. Comparative Analysis of Genome Diversity in Bullmastiff Dogs

    PubMed Central

    Mortlock, Sally-Anne; Khatkar, Mehar S.; Williamson, Peter

    2016-01-01

    Management and preservation of genomic diversity in dog breeds is a major objective for maintaining health. The present study was undertaken to characterise genomic diversity in Bullmastiff dogs using both genealogical and molecular analysis. Genealogical analysis of diversity was conducted using a database consisting of 16,378 Bullmastiff pedigrees from year 1980 to 2013. Additionally, a total of 188 Bullmastiff dogs were genotyped using the 170,000 SNP Illumina CanineHD Beadchip. Genealogical parameters revealed a mean inbreeding coefficient of 0.047; 142 total founders (f); an effective number of founders (fe) of 79; an effective number of ancestors (fa) of 62; and an effective population size of the reference population of 41. Genetic diversity and the degree of genome-wide homogeneity within the breed were also investigated using molecular data. Multiple-locus heterozygosity (MLH) was equal to 0.206; runs of homozygosity (ROH) as proportion of the genome, averaged 16.44%; effective population size was 29.1, with an average inbreeding coefficient of 0.035, all estimated using SNP Data. Fine-scale population structure was analysed using NETVIEW, a population analysis pipeline. Visualisation of the high definition network captured relationships among individuals within and between subpopulations. Effects of unequal founder use, and ancestral inbreeding and selection, were evident. While current levels of Bullmastiff heterozygosity, inbreeding and homozygosity are not unusual, a relatively small effective population size indicates that a breeding strategy to reduce the inbreeding rate may be beneficial. PMID:26824579

  6. Comparative analysis of imaging configurations and objectives for Fourier microscopy.

    PubMed

    Kurvits, Jonathan A; Jiang, Mingming; Zia, Rashid

    2015-11-01

    Fourier microscopy is becoming an increasingly important tool for the analysis of optical nanostructures and quantum emitters. However, achieving quantitative Fourier space measurements requires a thorough understanding of the impact of aberrations introduced by optical microscopes that have been optimized for conventional real-space imaging. Here we present a detailed framework for analyzing the performance of microscope objectives for several common Fourier imaging configurations. To this end, we model objectives from Nikon, Olympus, and Zeiss using parameters that were inferred from patent literature and confirmed, where possible, by physical disassembly. We then examine the aberrations most relevant to Fourier microscopy, including the alignment tolerances of apodization factors for different objective classes, the effect of magnification on the modulation transfer function, and vignetting-induced reductions of the effective numerical aperture for wide-field measurements. Based on this analysis, we identify an optimal objective class and imaging configuration for Fourier microscopy. In addition, the Zemax files for the objectives and setups used in this analysis have been made publicly available as a resource for future studies.

  7. Comparative Analysis of Genome Diversity in Bullmastiff Dogs.

    PubMed

    Mortlock, Sally-Anne; Khatkar, Mehar S; Williamson, Peter

    2016-01-01

    Management and preservation of genomic diversity in dog breeds is a major objective for maintaining health. The present study was undertaken to characterise genomic diversity in Bullmastiff dogs using both genealogical and molecular analysis. Genealogical analysis of diversity was conducted using a database consisting of 16,378 Bullmastiff pedigrees from year 1980 to 2013. Additionally, a total of 188 Bullmastiff dogs were genotyped using the 170,000 SNP Illumina CanineHD Beadchip. Genealogical parameters revealed a mean inbreeding coefficient of 0.047; 142 total founders (f); an effective number of founders (fe) of 79; an effective number of ancestors (fa) of 62; and an effective population size of the reference population of 41. Genetic diversity and the degree of genome-wide homogeneity within the breed were also investigated using molecular data. Multiple-locus heterozygosity (MLH) was equal to 0.206; runs of homozygosity (ROH) as proportion of the genome, averaged 16.44%; effective population size was 29.1, with an average inbreeding coefficient of 0.035, all estimated using SNP Data. Fine-scale population structure was analysed using NETVIEW, a population analysis pipeline. Visualisation of the high definition network captured relationships among individuals within and between subpopulations. Effects of unequal founder use, and ancestral inbreeding and selection, were evident. While current levels of Bullmastiff heterozygosity, inbreeding and homozygosity are not unusual, a relatively small effective population size indicates that a breeding strategy to reduce the inbreeding rate may be beneficial.

  8. [Comparative analysis of efficiency indicators in ambulatory surgery].

    PubMed

    Rodríguez Ortega, María; Porrero Carro, José Luis; Aranaz Andrés, Jesús María; Castillo Fe, María José; Alonso García, María Teresa; Sánchez-Cabezudo Díaz-Guerra, Carlos

    2017-05-25

    To find comparative elements for quality control in major ambulatory surgery (MAS) units. Descriptive and comparative study of the Ambulatory Care Index (AI) and Substitution Index (SI) in the Santa Cristina Hospital Surgery Service (Madrid, Spain) compared to Key Indicators (KI) of the National Health Service (NHS). 7,817 MAS procedures (between 2006 and 2014) were analysed. The average annual AI was 54%, higher (p <0.0001) than «ambulatory surgery» KI. The hernia outpatient procedures (average 72%) were also superior to the national KI (p <0.0001), but ambulatory haemorrhoidectomy (average 33.6%) was clearly lower (p <0.0001). KI of the NHS are useful and allow to establish a proper development in the global AI and hernia outpatient surgery with opportunities for improvement in haemorrhoidectomy. Their collection should be careful, not including minor surgeries. Also, their usefulness could be increased if data was broken down by speciality and by complexity. Copyright © 2017 SESPAS. Publicado por Elsevier España, S.L.U. All rights reserved.

  9. Initial sequence and comparative analysis of the cat genome

    PubMed Central

    Pontius, Joan U.; Mullikin, James C.; Smith, Douglas R.; Lindblad-Toh, Kerstin; Gnerre, Sante; Clamp, Michele; Chang, Jean; Stephens, Robert; Neelam, Beena; Volfovsky, Natalia; Schäffer, Alejandro A.; Agarwala, Richa; Narfström, Kristina; Murphy, William J.; Giger, Urs; Roca, Alfred L.; Antunes, Agostinho; Menotti-Raymond, Marilyn; Yuhki, Naoya; Pecon-Slattery, Jill; Johnson, Warren E.; Bourque, Guillaume; Tesler, Glenn; O’Brien, Stephen J.

    2007-01-01

    The genome sequence (1.9-fold coverage) of an inbred Abyssinian domestic cat was assembled, mapped, and annotated with a comparative approach that involved cross-reference to annotated genome assemblies of six mammals (human, chimpanzee, mouse, rat, dog, and cow). The results resolved chromosomal positions for 663,480 contigs, 20,285 putative feline gene orthologs, and 133,499 conserved sequence blocks (CSBs). Additional annotated features include repetitive elements, endogenous retroviral sequences, nuclear mitochondrial (numt) sequences, micro-RNAs, and evolutionary breakpoints that suggest historic balancing of translocation and inversion incidences in distinct mammalian lineages. Large numbers of single nucleotide polymorphisms (SNPs), deletion insertion polymorphisms (DIPs), and short tandem repeats (STRs), suitable for linkage or association studies were characterized in the context of long stretches of chromosome homozygosity. In spite of the light coverage capturing ∼65% of euchromatin sequence from the cat genome, these comparative insights shed new light on the tempo and mode of gene/genome evolution in mammals, promise several research applications for the cat, and also illustrate that a comparative approach using more deeply covered mammals provides an informative, preliminary annotation of a light (1.9-fold) coverage mammal genome sequence. PMID:17975172

  10. Comparative Analysis of Volcanic Inflation—Deflation Cycles

    NASA Astrophysics Data System (ADS)

    Walwer, D.; Ghil, M.; Calais, E.

    2016-12-01

    GPS geodetic data together with INSAR images are often used to formulate kinematic models of the sources of volcanic deformations. The increasing amount of data now available allows one to produce time series that are several years long and thus capture continuously the history of volcanic deformations, in particular their nonlinear behavior. This information is highly valuable in helping understand the dynamics of volcanic systems.Nonlinear deformation signals are, however, difficult to extract from the background noise inherent in the GPS time series. It is also arduous to unravel the signal of interest from other nonlinear signals, such as the seasonal oscillations associated with mass variations in the atmosphere, the ocean, and the hydrological reservoirs. Here we use Multichannel Singular Spectrum Analysis (M-SSA) — an advanced, data-adaptive method for time series analysis that exploits simultaneously the temporal and spatial correlations of geophysical fields — to extract such deformation signals.We apply M-SSA to GPS data sets from four volcanoes: Akutan, Alaska; Okmok, Alaska; Westdahl, Alaska; and Piton de la Fournaise, La Reunion. Our analyses show that all four volcanoes share similar features in their deformation history, suggesting similarities in the dynamics that generate the inflation-deflation cycles. In particular, all four volcanic systems exhibit sawtooth-shaped oscillations with slow inflations followed by slower deflations, with time scales that vary from 6 months to 4 years. This relation of dynamical similarity is further highlighted by the phase portrait reconstruction of the four systems in the plane of deformation vs. rate-of-deformation, as obtained from the deformation signals extracted from the GPS time series using M-SSA.The inflating phase of these oscillations is followed by eruptions at Okmok volcano and at Piton de la Fournaise. These analysis results suggest that these volcanic inflation—deflation cycles are associated

  11. Comparative Analysis of Alcohol Control Policies in 30 Countries

    PubMed Central

    Brand, Donald A; Saisana, Michaela; Rynn, Lisa A; Pennoni, Fulvia; Lowenfels, Albert B

    2007-01-01

    Background Alcohol consumption causes an estimated 4% of the global disease burden, prompting goverments to impose regulations to mitigate the adverse effects of alcohol. To assist public health leaders and policymakers, the authors developed a composite indicator—the Alcohol Policy Index—to gauge the strength of a country's alcohol control policies. Methods and Findings The Index generates a score based on policies from five regulatory domains—physical availability of alcohol, drinking context, alcohol prices, alcohol advertising, and operation of motor vehicles. The Index was applied to the 30 countries that compose the Organization for Economic Cooperation and Development and regression analysis was used to examine the relationship between policy score and per capita alcohol consumption. Countries attained a median score of 42.4 of a possible 100 points, ranging from 14.5 (Luxembourg) to 67.3 (Norway). The analysis revealed a strong negative correlation between score and consumption (r = −0.57; p = 0.001): a 10-point increase in the score was associated with a one-liter decrease in absolute alcohol consumption per person per year (95% confidence interval, 0.4–1.5 l). A sensitivity analysis demonstrated the robustness of the Index by showing that countries' scores and ranks remained relatively stable in response to variations in methodological assumptions. Conclusions The strength of alcohol control policies, as estimated by the Alcohol Policy Index, varied widely among 30 countries located in Europe, Asia, North America, and Australia. The study revealed a clear inverse relationship between policy strength and alcohol consumption. The Index provides a straightforward tool for facilitating international comparisons. In addition, it can help policymakers review and strengthen existing regulations aimed at minimizing alcohol-related harm and estimate the likely impact of policy changes. PMID:17455992

  12. Comparative Analysis on Time Series with Included Structural Break

    NASA Astrophysics Data System (ADS)

    Andreeski, Cvetko J.; Vasant, Pandian

    2009-08-01

    The time series analysis (ARIMA models) is a good approach for identification of time series. But, if we have structural break in the time series, we cannot create only one model of time series. Further more, if we don't have enough data between two structural breaks, it's impossible to create valid time series models for identification of the time series. This paper explores the possibility of identification of the inflation process dynamics via of the system-theoretic, by means of both Box-Jenkins ARIMA methodologies and artificial neural networks.

  13. Comparative Convergence Analysis of Nonlinear AMLI-Cycle Multigrid

    SciTech Connect

    Hu, Xiaozhe; Vassilevski, Panayot S.; Xu, Jinchao

    2013-04-30

    The purpose of our paper is to provide a comprehensive convergence analysis of the nonlinear algebraic multilevel iteration (AMLI)-cycle multigrid (MG) method for symmetric positive definite problems. We show that the nonlinear AMLI-cycle MG method is uniformly convergent, based on classical assumptions for approximation and smoothing properties. Furthermore, under only the assumption that the smoother is convergent, we show that the nonlinear AMLI-cycle method is always better (or not worse) than the respective V-cycle MG method. Finally, numerical experiments are presented to illustrate the theoretical results.

  14. Framework for Comparative Risk Analysis of Dredged Material Disposal Options.

    DTIC Science & Technology

    1986-10-01

    biomagnification of some organochlorine compounds (e.g., DDT , PCB). The objectives of the following analysis are to: 9 Describe the limitations of the...common carcinogens may lead to average lifetime cancer risks as high as 7x10- 4 (Table A-i. Cigarette smokers experience higher risks; e.%., on the order...0.060000000 92-94 4,4’- DDT , DD, DDE 3.000000000 1.000000000 0.100000000 35 2,4-dinitrotoluene 3.000000000 1.000000000 0.100000000 3 acrylonitrile 4.000000000

  15. Comparative analysis on some filters for wrapped phase maps

    SciTech Connect

    Kemao, Qian; Le Tran Hoai Nam; Feng Lin; Soon, Seah Hock

    2007-10-20

    Some effective filtering methods for wrapped phase maps, a regularized phase-tracking method (RPT) without the regularization term, a multiple-parameter least-square method (MPLS), a windowed Fourier ridges method (WFR), an autocorrelation function method (ACF), and a sine/cosine average filter (SCAF), are analyzed in order to establish their transversal relationship. The analysis shows that principles of the RPT,MPLS, WFR, and ACF are equivalent and the SCAF also leads to the WFR by some extension, which elegantly unifies all these methods for filtering unwrapped phase maps.

  16. Comparative analysis on some filters for wrapped phase maps.

    PubMed

    Kemao, Qian; Nam, Le Tran Hoai; Feng, Lin; Soon, Seah Hock

    2007-10-20

    Some effective filtering methods for wrapped phase maps, a regularized phase-tracking method (RPT) without the regularization term, a multiple-parameter least-square method (MPLS), a windowed Fourier ridges method (WFR), an autocorrelation function method (ACF), and a sine/cosine average filter (SCAF), are analyzed in order to establish their transversal relationship. The analysis shows that principles of the RPT, MPLS, WFR, and ACF are equivalent and the SCAF also leads to the WFR by some extension, which elegantly unifies all these methods for filtering unwrapped phase maps.

  17. Quantitative analysis of cadmium selenide nanocrystal concentration by comparative techniques.

    PubMed

    Kuçur, Erol; Boldt, Frank M; Cavaliere-Jaricot, Sara; Ziegler, Jan; Nann, Thomas

    2007-12-01

    In this paper, we compared atomic absorption spectroscopy (AAS), anodic stripping voltammetry (ASV), and UV-vis spectroscopy for the determination of the concentration of CdSe nanocrystal (NC) solutions. The experimental results were combined with crystallographic calculations of the NC size, which led to a very accurate determination of the nanocrystal concentration--a crucial parameter for bioanalytical applications. Furthermore, such a combined approach can be extended to the determination of shell thickness of core/shell materials (e.g., CdSe/ZnS).

  18. The Comparative Analysis of Inductor and Reluctance Wind Generators

    NASA Astrophysics Data System (ADS)

    Kamoliņš, Edmunds

    2009-01-01

    In the presented work two designs of brushless generators are compared: inductor and reluctance. Both designs are multipolar and also can be applied as directly driven wind generators. Both one and the second designs are basically similar, but in the inductor generator are windings of excitation or permanent magnets which complicate a design, increase consumption of the copper and energy losses. In work shown that reluctance generator has no winding of excitation, it is simple and more reliable, it has less weight. It's more competitive for use in low power wind plants.

  19. Comparative analysis of eukaryotic cell-free expression systems.

    PubMed

    Hartsough, Emily M; Shah, Pankti; Larsen, Andrew C; Chaput, John C

    2015-09-01

    Cell-free protein synthesis (CFPS) allows researchers to rapidly generate functional proteins independent of cell culture. Although advances in eukaryotic lysates have increased the amount of protein that can be produced, the nuances of different translation systems lead to variability in protein production. To help overcome this problem, we have compared the relative yield and template requirements for three commonly used commercial cell-free translation systems: wheat germ extract (WGE), rabbit reticulocyte lysate (RRL), and HeLa cell lysate (HCL). Our results provide a general guide for researchers interested in using cell-free translation to generate recombinant protein for biomedical applications.

  20. Comparative analysis of affinity-based 5-hydroxymethylation enrichment techniques

    PubMed Central

    Thomson, John P.; Hunter, Jennifer M.; Nestor, Colm E.; Dunican, Donncha S.; Terranova, Rémi; Moggs, Jonathan G.; Meehan, Richard R.

    2013-01-01

    The epigenetic modification of 5-hydroxymethylcytosine (5hmC) is receiving great attention due to its potential role in DNA methylation reprogramming and as a cell state identifier. Given this interest, it is important to identify reliable and cost-effective methods for the enrichment of 5hmC marked DNA for downstream analysis. We tested three commonly used affinity-based enrichment techniques; (i) antibody, (ii) chemical capture and (iii) protein affinity enrichment and assessed their ability to accurately and reproducibly report 5hmC profiles in mouse tissues containing high (brain) and lower (liver) levels of 5hmC. The protein-affinity technique is a poor reporter of 5hmC profiles, delivering 5hmC patterns that are incompatible with other methods. Both antibody and chemical capture-based techniques generate highly similar genome-wide patterns for 5hmC, which are independently validated by standard quantitative PCR (qPCR) and glucosyl-sensitive restriction enzyme digestion (gRES-qPCR). Both antibody and chemical capture generated profiles reproducibly link to unique chromatin modification profiles associated with 5hmC. However, there appears to be a slight bias of the antibody to bind to regions of DNA rich in simple repeats. Ultimately, the increased specificity observed with chemical capture-based approaches makes this an attractive method for the analysis of locus-specific or genome-wide patterns of 5hmC. PMID:24214958

  1. Plant Reactome: a resource for plant pathways and comparative analysis

    PubMed Central

    Naithani, Sushma; Preece, Justin; D'Eustachio, Peter; Gupta, Parul; Amarasinghe, Vindhya; Dharmawardhana, Palitha D.; Wu, Guanming; Fabregat, Antonio; Elser, Justin L.; Weiser, Joel; Keays, Maria; Fuentes, Alfonso Munoz-Pomer; Petryszak, Robert; Stein, Lincoln D.; Ware, Doreen; Jaiswal, Pankaj

    2017-01-01

    Plant Reactome (http://plantreactome.gramene.org/) is a free, open-source, curated plant pathway database portal, provided as part of the Gramene project. The database provides intuitive bioinformatics tools for the visualization, analysis and interpretation of pathway knowledge to support genome annotation, genome analysis, modeling, systems biology, basic research and education. Plant Reactome employs the structural framework of a plant cell to show metabolic, transport, genetic, developmental and signaling pathways. We manually curate molecular details of pathways in these domains for reference species Oryza sativa (rice) supported by published literature and annotation of well-characterized genes. Two hundred twenty-two rice pathways, 1025 reactions associated with 1173 proteins, 907 small molecules and 256 literature references have been curated to date. These reference annotations were used to project pathways for 62 model, crop and evolutionarily significant plant species based on gene homology. Database users can search and browse various components of the database, visualize curated baseline expression of pathway-associated genes provided by the Expression Atlas and upload and analyze their Omics datasets. The database also offers data access via Application Programming Interfaces (APIs) and in various standardized pathway formats, such as SBML and BioPAX. PMID:27799469

  2. Comparative Proteomic Analysis of Yak Follicular Fluid during Estrus.

    PubMed

    Guo, Xian; Pei, Jie; Ding, Xuezhi; Chu, Min; Bao, Pengjia; Wu, Xiaoyun; Liang, Chunnian; Yan, Ping

    2016-09-01

    The breeding of yaks is highly seasonal, there are many crucial proteins involved in the reproduction control program, especially in follicular development. In order to isolate differential proteins between mature and immature follicular fluid (FF) of yak, the FF from yak follicles with different sizes were sampled respectively, and two-dimensional gel electrophoresis (2-DE) of the proteins was carried out. After silver staining, the Image Master 2D platinum software was used for protein analysis and matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS) was performed for differential protein identification. The expression level of transferrin and enolase superfamily member 1 (ENOSF1) was determined by Western blotting for verification analysis. The results showed that 2-DE obtained an electrophoresis map of proteins from mature and immature yak FF with high resolution and repeatability. A comparison of protein profiles identified 12 differently expressed proteins, out of which 10 of them were upregulated while 2 were downregulated. Western blotting showed that the expression of transferrin and ENOSF1 was enhanced with follicular development. Both the obtained protein profiles and the differently expressed proteins identified in this study provided experimental data related to follicular development during yak breeding seasons. This study also laid the foundation for understanding the microenvironment during oocyte development.

  3. Comparative analysis of cation/proton antiporter superfamily in plants

    SciTech Connect

    Ye, Chuyu; Yang, Xiaohan; Xia, Xinli; Yin, Weilun

    2013-01-01

    The cation/proton antiporter superfamily is associated with the transport of monovalent cations across membranes. This superfamily was annotated in the Arabidopsis genome and some members were functionally characterized. In the present study, a systematic analysis of the cation/proton antiporter genes in diverse plant specieswas reported.We identified 240 cation/proton antiporters in alga, moss, and angiosperm. A phylogenetic tree was constructed showing these 240members are separated into three families, i.e., Na+/H+ exchangers, K+ efflux antiporters, and cation/H+ exchangers. Our analysis revealed that tandem and/or segmental duplications contribute to the expansion of cation/H+ exchangers in the examined angiospermspecies. Sliding windowanalysis of the nonsynonymous/synonymous substitution ratios showed some differences in the evolutionary fate of cation/proton antiporter paralogs. Furthermore, we identified over-represented motifs among these 240 proteins and foundmostmotifs are family specific, demonstrating diverse evolution of the cation/proton antiporters among three families. In addition, we investigated the co-expressed genes of the cation/proton antiporters in Arabidopsis thaliana. The results showed some biological processes are enriched in the co-expressed genes, suggesting the cation/proton antiporters may be involved in these biological processes. Taken together, this study furthers our knowledge on cation/proton antiporters in plants.

  4. Comparative analysis of infrared images degraded by lossy compression techniques

    NASA Astrophysics Data System (ADS)

    Toussaint, W. A.; Weber, Reed A.

    2015-09-01

    This work addresses image degradation introduced by lossy compression techniques and the effects of such degradation on signal detection statistics for applications in fast-framing (<100 Hz) IR image analysis. As future space systems make use of increasingly higher pixel count IR focal plane arrays, data generation rates are anticipated to become too copious for continuous download. The prevailing solution to this issue has been to compress image data prior to downlink. While this solution is application independent for lossless compression, the expected benefits of lossy compression, including higher compression ratio, necessitate several application specific trades in order to characterize preservation of critical information within the data. Current analyses via standard statistical image processing techniques following tunably lossy compression algorithms (JPEG2000, JPEG-LS) allow for detection statistics nearly identical to analyses following standard lossless compression techniques, such as Rice and PNG, even at degradation levels offering a greater than twofold increase in compression ratio. Ongoing efforts focus on repeating the analysis for other tunably lossy compression techniques while also assessing the relative computational burden of each algorithm. Current results suggest that lossy compression techniques can preserve critical information in fast-framing IR data while either significantly reducing downlink bandwidth requirements or significantly increasing the usable focal plane array window size.

  5. Comparative analysis of 4 impression techniques for implants.

    PubMed

    Cabral, Leonardo Moreira; Guedes, Carlos Gramani

    2007-06-01

    This in vitro study investigated 4 impression techniques to determine their dimensional accuracy in comparison with a standard technique. A master metal framework with 2 inner hex implants (SIN; Sistema de Implante Nacional Ltda., Sao Paulo, Brazil) was used as a standard for the comparisons. Sixty master casts were prepared to evaluate 4 impression techniques: (1) indirect impression technique with tapered transfer copings, (2) direct impression technique with unsplinted squared transfer copings, (3) direct impression technique with squared transfer copings splinted with acrylic resin, and (4) direct impression technique with squared transfer copings with acrylic resin splints sectioned 17 minutes after setting and welded with the same resin. A profile projector was used to measure the distance between the copings attached to the analogs. Mean distances (mm) were calculated from 3 measurements for each sample in the master casts and in the master metal framework. Analysis of variance and the Tukey HSD test were used for statistical analysis of data (alpha = 0.05). The results for the direct technique with squared transfer copings with acrylic resin splints sectioned and welded after setting were not significantly different from results for the master metal framework. Considering the methodology used and the results obtained, the direct impression technique with squared transfer copings with acrylic resin splints sectioned and welded after setting had better results than the other techniques studied.

  6. Comparative molecular analysis of bacterial species associated with periodontal disease.

    PubMed

    De Iuliis, V; Ursi, S; Di Tommaso, L M; Caruso, M; Marino, A; D Ercole, S; Caputi, S; Sinjari, B; Festa, F; Macri, M; Martinotti, S; Vitullo, G; Toniato, E

    2016-01-01

    Periodontal disease is an inflammatory disorder affecting the supporting teeth structures, including gingiva, periodontal ligament and alveolar bone, causing loss of connective tissue, reabsorption of alveolar bone and formation of periodontal pockets. The aim of this study is to find a correlation between bacterial growth and periodontal disease. Fifty-seven patients aged between 21 and 65 years, median age 46 years, were enrolled. According to gingival pocket depth, ranging from 3 to 7 mm, patients were divided into two groups: the first (30 patients, 53%) with deep pockets ³ 5 mm and the second (27 patients, 47%) less than 5 mm. The samples taken were processed for microbiological analysis by absolute quantitative real-time Taq-Man technique. Patients affected by periodontal disease were 32 (56%) and patients with gingival bleeding were 35 (61%). This data showed that the presence, the type and the bacterial load in gingival pockets were strongly correlated with gingival depth, periodontal disease and gingival bleeding. Quantitative microbiological analysis is a key point to improve patient compliance, allowing to choose the specific antibiotic treatment. avoiding antibiotic resistance and ensuring the successful outcome of therapy for periodontal disease.

  7. Comparative analysis of two emerging rice seed bacterial pathogens.

    PubMed

    Fory, P A; Triplett, L; Ballen, C; Abello, J F; Duitama, J; Aricapa, M G; Prado, G A; Correa, F; Hamilton, J; Leach, J E; Tohme, J; Mosquera, G M

    2014-05-01

    Seed sterility and grain discoloration limit rice production in Colombia and several Central American countries. In samples of discolored rice seed grown in Colombian fields, the species Burkholderia glumae and B. gladioli were isolated, and field isolates were compared phenotypically. An artificial inoculation assay was used to determine that, although both bacterial species cause symptoms on rice grains, B. glumae is a more aggressive pathogen, causing yield reduction and higher levels of grain sterility. To identify putative virulence genes differing between B. glumae and B. gladioli, four previously sequenced genomes of Asian and U.S. strains of the two pathogens were compared with each other and with two draft genomes of Colombian B. glumae and B. gladioli isolates generated for this study. Whereas previously characterized Burkholderia virulence factors are highly conserved between the two species, B. glumae and B. gladioli strains are predicted to encode distinct groups of genes encoding type VI secretion systems, transcriptional regulators, and membrane-sensing proteins. This study shows that both B. glumae and B. gladioli can threaten grain quality, although only one species affects yield. Furthermore, genotypic differences between the two strains are identified that could contribute to disease phenotypic differences.

  8. A comparative collision-based analysis of human gait

    PubMed Central

    Lee, David V.; Comanescu, Tudor N.; Butcher, Michael T.; Bertram, John E. A.

    2013-01-01

    This study compares human walking and running, and places them within the context of other mammalian gaits. We use a collision-based approach to analyse the fundamental dynamics of the centre of mass (CoM) according to three angles derived from the instantaneous force and velocity vectors. These dimensionless angles permit comparisons across gait, species and size. The collision angle Φ, which is equivalent to the dimensionless mechanical cost of transport CoTmech, is found to be three times greater during running than walking of humans. This threefold difference is consistent with previous studies of walking versus trotting of quadrupeds, albeit tends to be greater in the gaits of humans and hopping bipeds than in quadrupeds. Plotting the collision angle Φ together with the angles of the CoM force vector Θ and velocity vector Λ results in the functional grouping of bipedal and quadrupedal gaits according to their CoM dynamics—walking, galloping and ambling are distinguished as separate gaits that employ collision reduction, whereas trotting, running and hopping employ little collision reduction and represent more of a continuum that is influenced by dimensionless speed. Comparable with quadrupedal mammals, collision fraction (the ratio of actual to potential collision) is 0.51 during walking and 0.89 during running, indicating substantial collision reduction during walking, but not running, of humans. PMID:24089334

  9. Comparative molecular biological analysis of membrane transport genes in organisms

    PubMed Central

    Nagata, Toshifumi; Iizumi, Shigemi; Satoh, Kouji

    2008-01-01

    Comparative analyses of membrane transport genes revealed many differences in the features of transport homeostasis in eight diverse organisms, ranging from bacteria to animals and plants. In bacteria, membrane-transport systems depend mainly on single genes encoding proteins involved in an ATP-dependent pump and secondary transport proteins that use H+ as a co-transport molecule. Animals are especially divergent in their channel genes, and plants have larger numbers of P-type ATPase and secondary active transporters than do other organisms. The secondary transporter genes have diverged evolutionarily in both animals and plants for different co-transporter molecules. Animals use Na+ ions for the formation of concentration gradients across plasma membranes, dependent on secondary active transporters and on membrane voltages that in turn are dependent on ion transport regulation systems. Plants use H+ ions pooled in vacuoles and the apoplast to transport various substances; these proton gradients are also dependent on secondary active transporters. We also compared the numbers of membrane transporter genes in Arabidopsis and rice. Although many transporter genes are similar in these plants, Arabidopsis has a more diverse array of genes for multi-efflux transport and for response to stress signals, and rice has more secondary transporter genes for carbohydrate and nutrient transport. Electronic supplementary material The online version of this article (doi:10.1007/s11103-007-9287-z) contains supplementary material, which is available to authorized users. PMID:18293089

  10. In silico comparative analysis of SSR markers in plants

    PubMed Central

    2011-01-01

    Background The adverse environmental conditions impose extreme limitation to growth and plant development, restricting the genetic potential and reflecting on plant yield losses. The progress obtained by classic plant breeding methods aiming at increasing abiotic stress tolerances have not been enough to cope with increasing food demands. New target genes need to be identified to reach this goal, which requires extensive studies of the related biological mechanisms. Comparative analyses in ancestral plant groups can help to elucidate yet unclear biological processes. Results In this study, we surveyed the occurrence patterns of expressed sequence tag-derived microsatellite markers for model plants. A total of 13,133 SSR markers were discovered using the SSRLocator software in non-redundant EST databases made for all eleven species chosen for this study. The dimer motifs are more frequent in lower plant species, such as green algae and mosses, and the trimer motifs are more frequent for the majority of higher plant groups, such as monocots and dicots. With this in silico study we confirm several microsatellite plant survey results made with available bioinformatics tools. Conclusions The comparative studies of EST-SSR markers among all plant lineages is well suited for plant evolution studies as well as for future studies of transferability of molecular markers. PMID:21247422

  11. Comparative hypsometric analysis of both Earth and Venus topographic distributions

    NASA Technical Reports Server (NTRS)

    Rosenblatt, P.; Pinet, P. C.; Thouvenot, E.

    1993-01-01

    Previous studies have compared the global topographic distribution of both planets by means of differential hypsometric curves. For the purpose of comparison, the terrestrial oceanic load was removed, and a reference base level was acquired. It was chosen on the basis of geometric considerations and reflected the geometric shape of the mean dynamical equilibrium figure of the planetary surface in both cases. This reference level corresponds to the well-known sea level for the Earth; for Venus, given its slow rate of rotation, a sphere of radius close to the mean, median and modal values of the planetary radii distribution were considered and the radius value of 6051 km arbitrarily taken. These studies were based on the low resolution (100 x 100 sq km) coverage of Venus obtained by the Pioneer Venus altimeter and on the 1 deg x 1 deg terrestrial topography. But, apart from revealing the distinct contrast existing between the Earth's bimodal and Venus' strong unimodal topographic distribution, the choice of such a reference level is inadequate and even misleading for the comparative geophysical understanding of the planetary relief distribution. The present work reinvestigates the comparison between Earth and Venus hypsometric distribution on the basis of the high-resolution data provided, on one hand, by the recent Magellan global topographic coverage of Venus' surface, and on the other hand, by the detailed NCAR 5 x 5 ft. grid topographic database currently available for the Earth's surface.

  12. A comparative analysis of DNA barcode microarray feature size

    PubMed Central

    Ammar, Ron; Smith, Andrew M; Heisler, Lawrence E; Giaever, Guri; Nislow, Corey

    2009-01-01

    Background Microarrays are an invaluable tool in many modern genomic studies. It is generally perceived that decreasing the size of microarray features leads to arrays with higher resolution (due to greater feature density), but this increase in resolution can compromise sensitivity. Results We demonstrate that barcode microarrays with smaller features are equally capable of detecting variation in DNA barcode intensity when compared to larger feature sizes within a specific microarray platform. The barcodes used in this study are the well-characterized set derived from the Yeast KnockOut (YKO) collection used for screens of pooled yeast (Saccharomyces cerevisiae) deletion mutants. We treated these pools with the glycosylation inhibitor tunicamycin as a test compound. Three generations of barcode microarrays at 30, 8 and 5 μm features sizes independently identified the primary target of tunicamycin to be ALG7. Conclusion We show that the data obtained with 5 μm feature size is of comparable quality to the 30 μm size and propose that further shrinking of features could yield barcode microarrays with equal or greater resolving power and, more importantly, higher density. PMID:19825181

  13. A comparative analysis of numt evolution in human and chimpanzee.

    PubMed

    Hazkani-Covo, Einat; Graur, Dan

    2007-01-01

    Mitochondrial DNA sequences are frequently transferred into the nuclear genome, giving rise to numts (nuclear DNA sequences of mitochondrial origin). So far, the evolutionary history of numts has largely been studied by using single genomes. Here, we present the first attempt to study numt evolution in a comparative manner by using a pairwise genomic alignment. The total number of numts was estimated to be 452 in human and 469 in chimpanzee. numts that were found in both genomes at identical loci were deemed to be orthologous; 391 numts (>80%) were classified as such. The preponderance of orthologous numts is due to the very short divergence time between the 2 hominoids. The rest of numts were deemed to be nonorthologous. Nonorthologous numts were subdivided into 1) ancestral numts that have lost an ortholog in one species through deletion (12 in human and 11 in chimpanzee), 2) new numts acquired by the insertion of a mitochondrial sequence after the divergence of the 2 species (34 in human and 46 in chimpanzee), and 3) paralogous numts created by the tandem duplication of a preexisting numt (2 in human). This approach also enabled us to reconstruct the numt repertoire in the common ancestor of humans and chimpanzees (409 numts). Our comparative approach is also useful in identifying the exact boundaries of numts.

  14. Comparative flow cytometric analysis of immunofunctionalized nanowire and nanoparticle signatures.

    PubMed

    Prina-Mello, Adriele; Whelan, Aine M; Atzberger, Ann; McCarthy, Joseph E; Byrne, Fiona; Davies, Gemma-Louise; Coey, J M D; Volkov, Yuri; Gun'ko, Yurii K

    2010-01-01

    Flow cytometry is one of the gold-standard techniques used in clinical medicine for quantitative immunoassaying. The continuous development of its probes, commonly fluorescent nanoparticles, is important. Lately, the introduction of quantitative multiplexed immunoassay has challenged the use of nanoparticles as probes. Functionalized fluorescent silica-based magnetic nanowires are investigated under flow cytometry as a novel probe category. The preparation and full characterization of these multimodal nanowires is reported and compared to those of silica-based magnetic nanoparticles by flow cytometry. Full characterization includes transmission electron microscopy and fluorescence microscopy imaging, flow cytometric assaying, superconducting quantum interference device (SQUID) magnetization, and Mössbauer spectroscopy measurements. This work shows that loaded silica nanowires have intrinsic geometrical advantages when compared to similar spherical particles due to their unique "flow cytometry fingerprint" when utilized as magnetic carriers for immunodetection applications. These advantages account for a 17% yield in detecting the functional binding between THP-1 and ICAM-1, by utilizing a much lower concentration than that required for the nanoparticles.

  15. Comparative analysis of muscle architecture in primate arm and forearm.

    PubMed

    Kikuchi, Yasuhiro

    2010-04-01

    A comparative study of myological morphology, i.e. muscle mass (MM), muscle fascicle length and muscle physiological cross-sectional area (an indicator of the force capacity of muscles), was conducted in nine primate species: human (Homo sapiens), chimpanzee (Pan troglodytes), gibbon (Hylobates spp.), papio (Papio hamadryas), lutong (Trachypithecus francoisi), green monkey (Chlorocebus aethiops), macaque monkey (Macaca spp.), capuchin monkey (Cebus albifrons) and squirrel monkey (Saimiri sciureus). The MM distributions and the percentages in terms of functional categories were calculated as the ratios of the muscle masses. Moreover, individual normalized data were compared directly amongst species, independent of size differences. The results show that the different ratios of forearm-rotation muscles between chimpanzee and gibbons may be related to the differences in their main positional behaviour, i.e. knuckle-walking in chimpanzees and brachiation in gibbons, and the different frequencies of arm-raising locomotion between these two species. Moreover, monkeys have larger normalized MM values for the elbow extensor muscles than apes, which may be attributed to the fact that almost all monkeys engage in quadrupedal locomotion. The characteristics of the muscle internal parameters of ape and human are discussed in comparison with those of monkey.

  16. A Comparative Analysis of Mandated Benefit Laws, 1949–2002

    PubMed Central

    Laugesen, Miriam J; Paul, Rebecca R; Luft, Harold S; Aubry, Wade; Ganiats, Theodore G

    2006-01-01

    Objective To understand and compare the trends in mandated benefits laws in the United States. Data Sources/Study Setting Mandated benefit laws enacted in 50 states and the District of Columbia for the period 1949–2002 were compiled from multiple published compendia. Study Design Laws that require private insurers and health plans to cover particular services, types of diseases, or care by specific providers in 50 states and the District of Columbia are compared for the period 1949–2002. Legislation is compared by year, by average and total frequency, by state, by type (provider, health care service, or preventive), and according to whether it requires coverage or an offer of coverage. Data Collection/Extraction Method Data from published tables were entered into a spreadsheet and analyzed using statistical software. Principal Findings A total of 1,471 laws mandated coverage for 76 types of providers and services. The most common type of mandated coverage is for specific health care services (670 laws for 34 different services), followed by laws for services offered by specific professionals and other providers (507 mandated benefits laws for 25 types of providers), and coverage for specific preventive services (295 laws for 17 benefits). On average, a mandated benefit law has been adopted or significantly revised by 19 states, and each state has approximately 29 mandates. Only two benefits (minimum maternity stay and breast reconstruction) are mandated in all 51 jurisdictions and these were also federally mandated benefits. The mean number of total mandated benefit laws adopted or significantly revised per year was 17 per year in the 1970s, 36 per year in the 1980s, 59 per year in the 1990s, and 76 per year between 2000 and 2002. Since 1990, mandate adoption increased substantially, with around 55 percent of all mandated benefit laws enacted between 1990 and 2002. Conclusions There was a large increase in the number of mandated benefits laws during the managed

  17. Comparative study of mobile Raman instrumentation for art analysis.

    PubMed

    Vandenabeele, P; Castro, K; Hargreaves, M; Moens, L; Madariaga, J M; Edwards, H G M

    2007-04-04

    In archaeometry, one of the main concerns is to extract information from an art object, without damaging it. Raman spectroscopy is being applied in this research field with recent developments in mobile instrumentation facilitating more routine analysis. This research paper evaluates the performances of five mobile Raman instruments (Renishaw RA100, Renishaw Portable Raman Analyser RX210, Ocean Optics RSL-1, Delta Nu Inspector Raman, Mobile Art Analyser--MArtA) in three different laboratories. A set of samples were collected, in order to obtain information on the spectral performances of the instruments including: spectral resolution, calibration, laser cut-off, the ability to record spectra of organic and inorganic pigments through varnish layers and on the possibilities to identify biomaterials. Spectra were recorded from predefined regions on a canvas painting to simulate the investigation of artworks and the capabilities to record spectra from hardly accessible areas was evaluated.

  18. Decision Analysis Tool to Compare Energy Pathways for Transportation

    SciTech Connect

    Bloyd, Cary N.

    2010-06-30

    With the goals of reducing greenhouse gas emissions, oil imports, and energy costs, a wide variety of automotive technologies are proposed to replace the traditional gasoline-powered internal combustion engine (g-ICE). Biomass is seen as an important domestic energy feedstock, and there are multiple pathways in which it can be linked to the transport sector. Contenders include the use of cellulosic ethanol from biomass to replace gasoline or the use of a biomass-fueled combined cycle electrical power generation facility in conjunction plug-in hybrid electric vehicles (PHEVs). This paper reviews a project that is developing a scenario decision analysis tool to assist policy makers, program managers, and others to obtain a better understanding of these uncertain possibilities and how they may interact over time.

  19. Comparative Exergetic Analysis of Joule-Thomson Liquefiers

    NASA Astrophysics Data System (ADS)

    Chorowski, Maciej

    2004-06-01

    The Joule-Thomson microliquefiers are very reliable and noiseless cryocoolers, specially well fitted for cryostating small electronic devices, IR detectors or cryosurgical probes. Their essential drawback is low thermodynamic efficiency imposing high supply gas pressure, usually above 10 MPa. An exergetic analysis of the microliquefier has been performed and exergy-loss sources identified. Some of the losses can be avoided if a pure gas is replaced with a proper gas mixture and in result the supply gas pressure can be lowered significantly. The efficiencies and working parameters of Joule-Thomson microliquefier fed with pure N2 and the mixtures N2 - CH4 and N2 - R13 have been estimated and measured. The mixture properties have been calculated using the Peng-Robinson equation of state. The possibility to use a liquid-solid phase transition in a cooling-power "on-off" control loop has been observed.

  20. Comparative analysis of student self-reflections on course projects

    NASA Astrophysics Data System (ADS)

    Pomales-García, Cristina; Cortés Barreto, Kenneth

    2014-11-01

    This study presents the skills, experiences, and values identified in project self-reflections of 161 undergraduate engineering students. Self-reflections from two different engineering design courses, which provide experiences in project-based learning (PBL), are analysed through the content analysis methodology. Results show that 'application', 'true life', 'satisfaction', and 'communication' are the common keywords shared in the reflections. Multiple hypothesis tests to identify differences between courses, project types, years, and gender suggest that there are no significant differences between experiences, skills, and values self-reported by students who completed either a case study or an industry project. Based on research findings, recommendations will be provided to enhance the engineering curriculum based on PBL experiences to support the development of relevant professional skills and experiences.

  1. Assigning protein functions by comparative genome analysis protein phylogenetic profiles

    DOEpatents

    Pellegrini, Matteo; Marcotte, Edward M.; Thompson, Michael J.; Eisenberg, David; Grothe, Robert; Yeates, Todd O.

    2003-05-13

    A computational method system, and computer program are provided for inferring functional links from genome sequences. One method is based on the observation that some pairs of proteins A' and B' have homologs in another organism fused into a single protein chain AB. A trans-genome comparison of sequences can reveal these AB sequences, which are Rosetta Stone sequences because they decipher an interaction between A' and B. Another method compares the genomic sequence of two or more organisms to create a phylogenetic profile for each protein indicating its presence or absence across all the genomes. The profile provides information regarding functional links between different families of proteins. In yet another method a combination of the above two methods is used to predict functional links.

  2. Child sexual abuse and adolescent prostitution: a comparative analysis.

    PubMed

    Seng, M J

    1989-01-01

    In several studies, child sexual abuse has been identified as a characteristic of adolescent prostitution. The implication of these findings, especially for girls, is that the two phenomena are related in that childhood sexual abuse perhaps leads to prostitution. The present study explored the relationship between sexual abuse and adolescent prostitution by comparing 70 sexually abused children with 35 prostitution-involved children on 22 variables. Findings suggest that the relationship is not directed, but involves runaway behavior as an intervening variable. It is not so much that sexual abuse leads to prostitution as it is that running away leads to prostitution. Implications for treatment of both sexually abused and prostitution-involved children also are discussed.

  3. Reaching a representative sample of college students: A comparative analysis.

    PubMed

    Giovenco, Daniel P; Gundersen, Daniel A; Delnevo, Cristine D

    2016-01-01

    To explore the feasibility of a random-digit dial (RDD) cellular phone survey in order to reach a national and representative sample of college students. Demographic distributions from the 2011 National Young Adult Health Survey (NYAHS) were benchmarked against enrollment numbers from the Integrated Postsecondary Education System (IPEDS). The sample quality was compared with the Harvard School of Public Health College Alcohol Study (1993), National College Health Risk Behavior Survey (1995), and National College Health Assessment (2011). Overall, the NYAHS performed as well, if not better, than previous college health surveys at reaching important demographic subgroups. Cellular phone RDD is one feasible approach for studies of the general population of college students that can potentially generate national estimates of health behavior.

  4. Indications for quantum computation requirements from comparative brain analysis

    NASA Astrophysics Data System (ADS)

    Bernroider, Gustav; Baer, Wolfgang

    2010-04-01

    Whether or not neuronal signal properties can engage 'non-trivial', i.e. functionally significant, quantum properties, is the subject of an ongoing debate. Here we provide evidence that quantum coherence dynamics can play a functional role in ion conduction mechanism with consequences on the shape and associative character of classical membrane signals. In particular, these new perspectives predict that a specific neuronal topology (e.g. the connectivity pattern of cortical columns in the primate brain) is less important and not really required to explain abilities in perception and sensory-motor integration. Instead, this evidence is suggestive for a decisive role of the number and functional segregation of ion channel proteins that can be engaged in a particular neuronal constellation. We provide evidence from comparative brain studies and estimates of computational capacity behind visual flight functions suggestive for a possible role of quantum computation in biological systems.

  5. A comparative analysis of static and dynamic load balancing strategies

    NASA Technical Reports Server (NTRS)

    Iqbal, M. Ashraf; Bokhari, Shahid H.; Saltz, Joel H.

    1986-01-01

    The problem of uniformly distributing the load of a parallel program over a multiprocessor system was considered. A program was analyzed whose structure permits the computation of the optimal static solution. Then four strategies for load balancing were described and their performance compared. The strategies are: (1) the optimal static assignment algorithm which is guaranteed to yield the best static solution, (2) the static binary dissection method which is very fast but suboptimal, (3) the greedy algorithm, a static fully polynomial time approximation scheme, which estimates the optimal solution to arbitrary accuracy, and (4) the predictive dynamic load balancing heuristic which uses information on the precedence relationships within the program and outperforms any of the static methods. It is also shown that the overhead incurred by the dynamic heuristic is reduced considerably if it is started off with a static assignment provided by either of the three strategies.

  6. Comparative analysis of large antenna spacecraft using the ideas system

    NASA Technical Reports Server (NTRS)

    Garrett, L. B.; Ferebee, M. J., Jr.

    1983-01-01

    A Land Mobile Satellite System (LMSS), capable of providing mobile communications for commercial and government applications in nonmetropolitan areas of the continental U.S. and Canada as an augmentation to existing and planned terrestrial systems, is being studied. The satellite system would provide 'narrow band' telecommunications services such as mobile radio, telephone, dispatch, safety, and special radio services, and thin-route fixed telephone and data services in the 806-890 MHz band and continuous emergency beacon monitoring in the 406-406.1 MHz band. A single Shuttle launch with an upper stage orbital transfer system would place the LMSS spacecraft in geosynchronous orbit over the continental U.S. in 1995 with a 10-year lifetime. The present investigation has the objective to evaluate, compare, and rank selected spacecraft concepts, to suggest design improvement to the individual concepts, and to identify technology needs.

  7. Comparative Bacterial Proteomics: Analysis of the Core Genome Concept

    PubMed Central

    Callister, Stephen J.; McCue, Lee Ann; Turse, Joshua E.; Monroe, Matthew E.; Auberry, Kenneth J.; Smith, Richard D.; Adkins, Joshua N.; Lipton, Mary S.

    2008-01-01

    While comparative bacterial genomic studies commonly predict a set of genes indicative of common ancestry, experimental validation of the existence of this core genome requires extensive measurement and is typically not undertaken. Enabled by an extensive proteome database developed over six years, we have experimentally verified the expression of proteins predicted from genomic ortholog comparisons among 17 environmental and pathogenic bacteria. More exclusive relationships were observed among the expressed protein content of phenotypically related bacteria, which is indicative of the specific lifestyles associated with these organisms. Although genomic studies can establish relative orthologous relationships among a set of bacteria and propose a set of ancestral genes, our proteomics study establishes expressed lifestyle differences among conserved genes and proposes a set of expressed ancestral traits. PMID:18253490

  8. Comparative analysis of toxin detection in biological and enviromental samples

    NASA Astrophysics Data System (ADS)

    Ogert, Robert A.; Burans, James; O'Brien, Tom; Ligler, Frances S.

    1994-03-01

    The basic recognition schemes underlying the principles of standard enzyme-linked immunosorbent assay (ELISA) and radioimmunoassay (RIA) protocols are increasingly being adapted for use with new detection devices. A direct comparison was made using a fiber optic biosensor that employs evanescent wave detection and an ELISA using avidin-biotin. The assays were developed for the detection of Ricinus communis agglutinin II, also known as ricin or RCA60. Detection limits between the two methods were comparable for ricin in phosphate buffered saline (PBS), however results in complex samples differed slightly. In PBS, sensitivity for ricin was 1 ng/ml using the fiber optic device and 500 pg/ml using the ELISA. The fiber optic sensor could not detect ricin directly in urine or serum spiked with 5 ng/ml ricin, however, the ELISA showed detection but at reduced levels to the PBS control.

  9. A Comparative Analysis of Acyl-Homoserine Lactone Synthase Assays.

    PubMed

    Shin, Daniel; Frane, Nicole D; Brecht, Ryan M; Keeler, Jesse; Nagarajan, Rajesh

    2015-12-01

    Quorum sensing is cell-to-cell communication that allows bacteria to coordinate attacks on their hosts by inducing virulent gene expression, biofilm production, and other cellular functions, including antibiotic resistance. AHL synthase enzymes synthesize N-acyl-l-homoserine lactones, commonly referred to as autoinducers, to facilitate quorum sensing in Gram-negative bacteria. Studying the synthases, however, has proven to be a difficult road. Two assays, including a radiolabeled assay and a colorimetric (DCPIP) assay are well-documented in literature to study AHL synthases. In this paper, we describe additional methods that include an HPLC-based, C-S bond cleavage and coupled assays to investigate this class of enzymes. In addition, we compare and contrast each assay for both acyl-CoA- and acyl-ACP-utilizing synthases. The expanded toolkit described in this study should facilitate mechanistic studies on quorum sensing signal synthases and expedite discovery of antivirulent compounds.

  10. Comparing the results of five lifting analysis tools.

    PubMed

    Russell, Steven J; Winnemuller, Lori; Camp, Janice E; Johnson, Peter W

    2007-01-01

    The objective of this study was to compare the results of the NIOSH, ACGIH TLV, Snook, 3DSSPP and WA L&I lifting assessment instruments when applied to a uniform task (lifting and lowering milk cases with capacities of 15 and 23l). To enable comparisons between the various lifting assessment instruments, the outputs of each method were converted to an exposure index similar to the NIOSH Lifting Index. All instruments showed higher exposures associated with lifting the 23l cases versus the 15l cases. The NIOSH, ACGIH TLV and Snook methods were similar in their results with respect to the pattern of exposure over various height levels and the differences in exposures associated with lifting 15 and 23l cases. However, the WA L&I and 3DSSPP predicted substantially lower exposures. The reasons for instrument differences are presented so that practitioners can better select the methods they need and interpret the results appropriately.

  11. A comparative analysis of static and dynamic load balancing strategies

    NASA Technical Reports Server (NTRS)

    Iqbal, M. Ashraf; Bokhari, Shahid H.; Saltz, Joel H.

    1986-01-01

    The problem of uniformly distributing the load of a parallel program over a multiprocessor system was considered. A program was analyzed whose structure permits the computation of the optimal static solution. Then four strategies for load balancing were described and their performance compared. The strategies are: (1) the optimal static assignment algorithm which is guaranteed to yield the best static solution, (2) the static binary dissection method which is very fast but suboptimal, (3) the greedy algorithm, a static fully polynomial time approximation scheme, which estimates the optimal solution to arbitrary accuracy, and (4) the predictive dynamic load balancing heuristic which uses information on the precedence relationships within the program and outperforms any of the static methods. It is also shown that the overhead incurred by the dynamic heuristic is reduced considerably if it is started off with a static assignment provided by either of the three strategies.

  12. Comparative analysis of large antenna spacecraft using the ideas system

    NASA Technical Reports Server (NTRS)

    Garrett, L. B.; Ferebee, M. J., Jr.

    1983-01-01

    A Land Mobile Satellite System (LMSS), capable of providing mobile communications for commercial and government applications in nonmetropolitan areas of the continental U.S. and Canada as an augmentation to existing and planned terrestrial systems, is being studied. The satellite system would provide 'narrow band' telecommunications services such as mobile radio, telephone, dispatch, safety, and special radio services, and thin-route fixed telephone and data services in the 806-890 MHz band and continuous emergency beacon monitoring in the 406-406.1 MHz band. A single Shuttle launch with an upper stage orbital transfer system would place the LMSS spacecraft in geosynchronous orbit over the continental U.S. in 1995 with a 10-year lifetime. The present investigation has the objective to evaluate, compare, and rank selected spacecraft concepts, to suggest design improvement to the individual concepts, and to identify technology needs.

  13. Comparative Bacterial Proteomics: Analysis of the Core Genome Concept

    SciTech Connect

    Callister, Stephen J.; McCue, Lee Ann; Turse, Josh E.; Monroe, Matthew E.; Auberry, Kenneth J.; Smith, Richard D.; Adkins, Joshua N.; Lipton, Mary S.

    2008-02-06

    Comparative bacterial genomic studies commonly predict a set of genes indicative of common ancestry. Experimental validation of the existence of this core genome requires extensive measurement and is not typically undertaken. Enabled by an extensive proteome database development over a six year period, we experimentally verified the expression of proteins predicted from genomic ortholog comparisons among 17 environmental and pathogenic bacteria. More exclusive relationships were observed among the expressed protein content of phenotypically related bacteria, which is indicative of the specific lifestyles associated with these organisms. While genomic studies establish relative orthologous relationships among a set of bacteria and propose a set of ancestral genes, our proteomics study establishes expressed lifestyle differences among conserved genes and proposes a set of expressed ancestral traits.

  14. Quantifying Drosophila food intake: comparative analysis of current methodology

    PubMed Central

    Deshpande, Sonali A.; Carvalho, Gil B.; Amador, Ariadna; Phillips, Angela M.; Hoxha, Sany; Lizotte, Keith J.; Ja, William W.

    2014-01-01

    Food intake is a fundamental parameter in animal studies. Despite the prevalent use of Drosophila in laboratory research, precise measurements of food intake remain challenging in this model organism. Here, we compare several common Drosophila feeding assays: the Capillary Feeder (CAFE), food-labeling with a radioactive tracer or a colorimetric dye, and observations of proboscis extension (PE). We show that the CAFE and radioisotope-labeling provide the most consistent results, have the highest sensitivity, and can resolve differences in feeding that dye-labeling and PE fail to distinguish. We conclude that performing the radiolabeling and CAFE assays in parallel is currently the best approach for quantifying Drosophila food intake. Understanding the strengths and limitations of food intake methodology will greatly advance Drosophila studies of nutrition, behavior, and disease. PMID:24681694

  15. An environmental analysis for comparing waste management options and strategies.

    PubMed

    Marchettini, N; Ridolfi, R; Rustici, M

    2007-01-01

    The debate on different waste management practices has become an issue of utmost importance as human activities have overloaded the assimilative capacity of the biosphere. Recent Italian law on solid waste management recommends an increase in material recycling and energy recovery, and only foresees landfill disposal for inert materials and residues from recovery and recycling. A correct waste management policy should be based on the principles of sustainable development, according to which our refuse is not simply regarded as something to eliminate but rather as a potential resource. This requires the creation of an integrated waste management plan that makes full use of all available technologies. In this context, eMergy analysis is applied to evaluate three different forms of waste treatment and construct an approach capable of assessing the whole strategy of waste management. The evaluation included how much investment is needed for each type of waste management and how much "utility" is extracted from wastes, through the use of two indicators: Environmental yield ratio (EYR) and Net eMergy. Our results show that landfill is the worst system in terms of eMergy costs and eMergy benefits. Composting is the most efficient system in recovering eMergy (highest EYR) from municipal solid waste (MSW) while incineration is capable of saving the greatest quantity of eMergy per gram of MSW (highest net eMergy). This analysis has made it possible to assess the sustainability and the efficiency of individual options but could also be used to assess a greater environmental strategy for waste management, considering a system that might include landfills, incineration, composting, etc.

  16. Endoscopic forceps for ureteroscopy: a comparative in vitro analysis.

    PubMed

    Sarkissian, Carl; Marchini, Giovanni Scala; Monga, Manoj

    2013-03-01

    To evaluate the functional characteristics of different ureteroscopic graspers. The Captura (2.8F, Cook Medical, Bloomington, IN), Platinum (3.0F, Bard Urological, Covington, GA), TriClaw (2.4F, UroGyn Medical, Inc., Valapraiso, IN), Graspit (2.6F, Boston Scientific, Natick, MA), and Boston Scientific Tricep (2.4F, 3.0F, and 3.0F non-retracting) graspers were tested. Opening dynamics were evaluated using high-resolution images. Grip strength was determined by measuring the maximum tensional force applied while grasping stone models attached to an inline load cell. Safety profile was evaluated by the maximum force required to perforate aluminum foil. Impact on ureteroscope deflection was assessed by measurement of maximum deflection (baseline = 247°) and bending radius after advancing each grasper through a flexible ureteroscope working channel. The Tukey test for inequality assuming unequal variance with Bonferroni adjustment was used to compare grip strength and perforation forces. The Tricep (2.4F, 3.0F NR, and 3.0F) and Captura graspers required the least distance (7.9-8.1 mm) to attain a grasping width of 5 mm. When compared across all stone models, the TriClaw and Graspit had greater grip strengths than all other devices. The Captura (1.92 ± 0.43 N) and Tricep 2.4F (1.72 ± 0.88 N) required the greatest forces to perforate aluminum foil. Ureteroscope deflection was least impacted by the Tricep 2.4F (213°, 1.35 cm radius), Graspit (207°, 1.35 cm radius), TriClaw (206°, 1.3 cm radius), and all graspers could be deployed and operated at maximum deflection. There are significant differences in opening dynamics, grip strength, perforation forces, and ureteroscope deflection among ureteroscopic graspers that may predict clinical performance capabilities. Copyright © 2013 Elsevier Inc. All rights reserved.

  17. A comparative analysis of outpatient costs in HIV treatment programs.

    PubMed

    Sarti, Flavia Mori; Nishijima, Marislei; Campino, Antonio Carlos Coelho; Cyrillo, Denise Cavallini

    2012-01-01

    To analyze the costs of human immunodeficiency virus (HIV) outpatient treatment for individuals with different CD4 cell counts in the Brazilian public health system, and to compare to costs in other national health systems. A retrospective survey was conducted in five public outpatient clinics of the Brazilian national HIV program in the city of São Paulo. Data on healthcare services provided for a period of one year of HIV outpatient treatment were gathered from randomly selected medical records. Prices of inputs used were obtained through market research and public sector databases. Information on costs of HIV outpatient treatment in other national health systems were gathered from the literature. Annual costs of HIV outpatient treatment from each country were converted into 2010 U.S. dollars. Annual cost of HIV outpatient treatment for the Brazilian national public program was US$ 2,572.92 in 2006 in São Paulo, ranging from US$ 1,726.19 for patients with CD4 cell count > 500 to US$ 3,693.28 for patients with 51 < CD4 cell count < 200. Antiretrovirals (ARVs) represented approximately 62.0% of annual HIV outpatient costs. Comparing among different health systems during the same period, HIV outpatient treatment presented higher costs in countries where HIV treatment is provided by the private sector. The main cost drivers of HIV outpatient treatment in different health systems were: ARVs, other medications, health professional services, and diagnostic exams. Nevertheless, the magnitude of cost drivers varied among HIV outpatient treatment programs due to health system efficiency. The data presented may be a valuable tool for public policy evaluation of HIV treatment programs worldwide.

  18. Informed consent in colonoscopy: A comparative analysis of 2 methods.

    PubMed

    Sanguinetti, J M; Lotero Polesel, J C; Iriarte, S M; Ledesma, C; Canseco Fuentes, S E; Caro, L E

    2015-01-01

    The manner in which informed consent is obtained varies. The aim of this study is to evaluate the level of knowledge about colonoscopy and comparing 2 methods of obtaining informed consent. A comparative, cross-sectional, observational study was conducted on patients that underwent colonoscopy in a public hospital (Group A) and in a private hospital (Group B). Group A received information verbally from a physician, as well as in the form of printed material, and Group B only received printed material. A telephone survey was carried out one or 2 weeks later. The study included a total of 176 subjects (group A [n=55] and group B [n=121]). As regards education level, 69.88% (n=123) of the patients had completed university education, 23.29% (n= 41) secondary level, 5.68% (n=10) primary level, and the remaining subjects (n=2) had not completed any level of education. All (100%) of the subjects knew the characteristics of the procedure, and 99.43% were aware of its benefits. A total of 97.7% received information about complications, 93.7% named some of them, and 25% (n=44) remembered major complications. All the subjects received, read, and signed the informed consent statement before the study. There were no differences between the groups with respect to knowledge of the characteristics and benefits of the procedure, or the receipt and reading of the consent form. Group B responded better in relation to complications (P=.0027) and group A had a better recollection of the major complications (P<.0001). Group A had a higher number of affirmative answers (P<.0001). The combination of verbal and written information provides the patient with a more comprehensive level of knowledge about the procedure. Copyright © 2014 Asociación Mexicana de Gastroenterología. Published by Masson Doyma México S.A. All rights reserved.

  19. Comparative Analysis of the Flexural Stiffness of Pinniped Vibrissae.

    PubMed

    Ginter Summarell, Carly C; Ingole, Sudeep; Fish, Frank E; Marshall, Christopher D

    2015-01-01

    Vibrissae are important components of the mammalian tactile sensory system and are used to detect vibrotactile stimuli in the environment. Pinnipeds have the largest and most highly innervated vibrissae among mammals, and the hair shafts function as a biomechanical filter spanning the environmental stimuli and the neural mechanoreceptors deep in the follicle-sinus complex. Therefore, the material properties of these structures are critical in transferring vibrotactile information to the peripheral nervous system. Vibrissae were tested as cantilever beams and their flexural stiffness (EI) was measured to test the hypotheses that the shape of beaded vibrissae reduces EI and that vibrissae are anisotropic. EI was measured at two locations on each vibrissa, 25% and 50% of the overall length, and at two orientations to the point force. EI differed in orientations that were normal to each other, indicating a functional anisotropy. Since vibrissae taper from base to tip, the second moment of area (I) was lower at 50% than 25% of total length. The anterior orientation exhibited greater EI values at both locations compared to the dorsal orientation for all species. Smooth vibrissae were generally stiffer than beaded vibrissae. The profiles of beaded vibrissae are known to decrease the amplitude of vibrations when protruded into a flow field. The lower EI values of beaded vibrissae, along with the reduced vibrations, may function to enhance the sensitivity of mechanoreceptors to detection of small changes in flow from swimming prey by increasing the signal to noise ratio. This study builds upon previous morphological and hydrodynamic analyses of vibrissae and is the first comparative study of the mechanical properties of pinniped vibrissae.

  20. Comparative Analysis of the Flexural Stiffness of Pinniped Vibrissae

    PubMed Central

    Ginter Summarell, Carly C.; Ingole, Sudeep; Fish, Frank E.; Marshall, Christopher D.

    2015-01-01

    Vibrissae are important components of the mammalian tactile sensory system and are used to detect vibrotactile stimuli in the environment. Pinnipeds have the largest and most highly innervated vibrissae among mammals, and the hair shafts function as a biomechanical filter spanning the environmental stimuli and the neural mechanoreceptors deep in the follicle-sinus complex. Therefore, the material properties of these structures are critical in transferring vibrotactile information to the peripheral nervous system. Vibrissae were tested as cantilever beams and their flexural stiffness (EI) was measured to test the hypotheses that the shape of beaded vibrissae reduces EI and that vibrissae are anisotropic. EI was measured at two locations on each vibrissa, 25% and 50% of the overall length, and at two orientations to the point force. EI differed in orientations that were normal to each other, indicating a functional anisotropy. Since vibrissae taper from base to tip, the second moment of area (I) was lower at 50% than 25% of total length. The anterior orientation exhibited greater EI values at both locations compared to the dorsal orientation for all species. Smooth vibrissae were generally stiffer than beaded vibrissae. The profiles of beaded vibrissae are known to decrease the amplitude of vibrations when protruded into a flow field. The lower EI values of beaded vibrissae, along with the reduced vibrations, may function to enhance the sensitivity of mechanoreceptors to detection of small changes in flow from swimming prey by increasing the signal to noise ratio. This study builds upon previous morphological and hydrodynamic analyses of vibrissae and is the first comparative study of the mechanical properties of pinniped vibrissae. PMID:26132102

  1. Comparative risk analysis of technological hazards (a review).

    PubMed Central

    Kates, R W; Kasperson, J X

    1983-01-01

    Hazards are threats to people and what they value and risks are measures of hazards. Comparative analyses of the risks and hazards of technology can be dated to Starr's 1969 paper [Starr, C. (1969) Science 165, 1232-1238] but are rooted in recent trends in the evolution of technology, the identification of hazard, the perception of risk, and the activities of society. These trends have spawned an interdisciplinary quasi profession with new terminology, methodology, and literature. A review of 54 English-language monographs and book-length collections, published between 1970 and 1983, identified seven recurring themes: (i) overviews of the field of risk assessment, (ii) efforts to estimate and quantify risk, (iii) discussions of risk acceptability, (iv) perception, (v) analyses of regulation, (vi) case studies of specific technological hazards, and (vii) agenda for research. Within this field, science occupies a unique niche, for many technological hazards transcend the realm of ordinary experience and require expert study. Scientists can make unique contributions to each area of hazard management but their primary contribution is the practice of basic science. Beyond that, science needs to further risk assessment by understanding the more subtle processes of hazard creation and by establishing conventions for estimating risk and for presenting and handling uncertainty. Scientists can enlighten the discussion of tolerable risk by setting risks into comparative contexts, by studying the process of evaluation, and by participating as knowledgeable individuals, but they cannot decide the issue. Science can inform the hazard management process by broadening the range of alternative control actions and modes of implementation and by devising methods to evaluate their effectiveness. PMID:6580625

  2. A comparative assessment of statistical methods for extreme weather analysis

    NASA Astrophysics Data System (ADS)

    Schlögl, Matthias; Laaha, Gregor

    2017-04-01

    Extreme weather exposure assessment is of major importance for scientists and practitioners alike. We compare different extreme value approaches and fitting methods with respect to their value for assessing extreme precipitation and temperature impacts. Based on an Austrian data set from 25 meteorological stations representing diverse meteorological conditions, we assess the added value of partial duration series over the standardly used annual maxima series in order to give recommendations for performing extreme value statistics of meteorological hazards. Results show the merits of the robust L-moment estimation, which yielded better results than maximum likelihood estimation in 62 % of all cases. At the same time, results question the general assumption of the threshold excess approach (employing partial duration series, PDS) being superior to the block maxima approach (employing annual maxima series, AMS) due to information gain. For low return periods (non-extreme events) the PDS approach tends to overestimate return levels as compared to the AMS approach, whereas an opposite behavior was found for high return levels (extreme events). In extreme cases, an inappropriate threshold was shown to lead to considerable biases that may outperform the possible gain of information from including additional extreme events by far. This effect was neither visible from the square-root criterion, nor from standardly used graphical diagnosis (mean residual life plot), but from a direct comparison of AMS and PDS in synoptic quantile plots. We therefore recommend performing AMS and PDS approaches simultaneously in order to select the best suited approach. This will make the analyses more robust, in cases where threshold selection and dependency introduces biases to the PDS approach, but also in cases where the AMS contains non-extreme events that may introduce similar biases. For assessing the performance of extreme events we recommend conditional performance measures that focus

  3. Comparative analysis of four disease prediction models of Parkinson's disease.

    PubMed

    Kumudini, Nadella; Naushad, Shaik Mohammad; Alex Stanley, Balraj; Niveditha, Manoharan; Sharmila, Gunasekaran; Kumaraswami, Konda; Borghain, Rupam; Mridula, Rukmini; Kutala, Vijay Kumar

    2016-01-01

    Parkinson's disease (PD) is a multi-factorial disorder with high-penetrant mutations accounting for small percentage of PD. Our previous studies demonstrated individual association of genetic variants in folate, xenobiotic, and dopamine metabolic pathways with PD risk. The rational of the study was to develop a risk prediction model for PD using these genetic polymorphisms along with synuclein (SNCA) polymorphism. We have generated additive, multifactor dimensionality reduction (MDR), recursive partitioning (RP), and artificial neural network (ANN) models using 21 SNPs as inputs and disease outcome as output. The clinical utility of all these models was assessed by plotting receiver operating characteristics curves where in area under the curve (AUC) was used as an index of diagnostic utility of the model. The additive model was the simplest and exhibited an AUC of 0.72. The MDR model showed significant gene-gene interactions between SNCA, DRD4VNTR, and DRD2A polymorphisms. The RP model showed SHMT C1420T as important determinant of PD risk. This variant allele was found to be protective and this protection was nullified by MTRR A66G. Inheritance of SHMT wild allele and SNCA intronic polymorphism was shown to increase the risk of PD. The ANN model showed higher diagnostic utility (AUC = 0.86) compared to all the models and was able to explain 56.6% cases of sporadic PD. To conclude, the ANN model developed using SNPs in folate, xenobiotic, and dopamine pathways along with SNCA has higher clinical utility in predicting PD risk compared to other models.

  4. Endothelial Mesenchymal Transition: Comparative Analysis of Different Induction Methods.

    PubMed

    Pinto, Mariana T; Covas, Dimas T; Kashima, Simone; Rodrigues, Claudia O

    2016-01-01

    Endothelial-Mesenchymal-Transition (EndMT) plays an essential role in cardiovascular development, and recently became an attractive therapeutic target based on evidence supporting its involvement in fibrosis and cancer. Important questions that remain to be answered are related to the molecular mechanisms that control EndMT in different organs and distinct pathological conditions. The lack of a detailed protocol for induction of EndMT and the assumption that TGF-β isoforms play similar roles on different types of endothelial cells, limit progress in the field. The aim of this study was to compare the induction of EndMT by TGF-β isoforms in endothelial cells of different sources, and define a detailed protocol for EndMT assessment in vitro. We compared the dose-dependent effect of TGF-β isoforms, under normoxia and hypoxia, on the induction of EndMT in human coronary and pulmonary artery endothelial cells. Our results suggest that endothelial cells undergo spontaneous EndMT with time in culture under the conditions tested. The extent of EndMT induction by TGF-β was dependent on the dose and endothelial cell type. Furthermore, the potential of TGF-β to induce EndMT was reduced under hypoxia relative to normoxia. Our work suggests that the response of endothelial cells to TGF-β is intrinsic to the dose, cell type and environment. Optimization of induction conditions may be essential, as pathways triggering EndMT may vary during development and pathological conditions. Therefore, caution is needed regarding indiscriminate use of TGF-β to induce EndMT for mechanistic studies.

  5. Qualitative analysis in gay men's health research: comparing thematic, critical discourse, and conversation analysis.

    PubMed

    Aguinaldo, Jeffrey P

    2012-01-01

    Gay men's health typically relies on traditional forms of qualitative analysis, such as thematic analysis, and would benefit from a diversity of analytic approaches. Such diversity offers public health researchers a breadth of tools to address different kinds of research questions and, thus, substantiate different types of social phenomenon relevant to the health and wellbeing of gay men. In this article, I compare and contrast three qualitative analytic approaches: thematic, critical discourse, and conversation analysis. I demonstrate and distinguish their key analytic assumptions by applying each approach to a single data excerpt taken from a public health interview conducted for a broader study on gay men's health. I engage in a discussion of each approach in relation to three themes: its utility for gay men's health, its approach to dilemmas of voice, and its capacity for reflexivity. I advocate that qualitative researchers should capitalise on the full range of qualitative analytic approaches to achieve the goals of gay men's health. However, I specifically encourage qualitative researchers to engage with conversation analysis, not only because of its capacity to resolve dilemmas of voice and to achieve reflexivity, but also for its ability to capture forms of social life hitherto undocumented through thematic and critical discourse analysis.

  6. Comparative Analysis of Proteome and Transcriptome Variation in Mouse

    PubMed Central

    Hagopian, Raffi; Mungrue, Imran N.; Farber, Charles R.; Sinsheimer, Janet; Kang, Hyun M.; Furlotte, Nicholas; Park, Christopher C.; Wen, Ping-Zi; Brewer, Heather; Weitz, Karl; Camp, David G.; Pan, Calvin; Yordanova, Roumyana; Neuhaus, Isaac; Tilford, Charles; Siemers, Nathan; Gargalovic, Peter; Eskin, Eleazar; Kirchgessner, Todd; Smith, Desmond J.; Smith, Richard D.; Lusis, Aldons J.

    2011-01-01

    The relationships between the levels of transcripts and the levels of the proteins they encode have not been examined comprehensively in mammals, although previous work in plants and yeast suggest a surprisingly modest correlation. We have examined this issue using a genetic approach in which natural variations were used to perturb both transcript levels and protein levels among inbred strains of mice. We quantified over 5,000 peptides and over 22,000 transcripts in livers of 97 inbred and recombinant inbred strains and focused on the 7,185 most heritable transcripts and 486 most reliable proteins. The transcript levels were quantified by microarray analysis in three replicates and the proteins were quantified by Liquid Chromatography–Mass Spectrometry using O(18)-reference-based isotope labeling approach. We show that the levels of transcripts and proteins correlate significantly for only about half of the genes tested, with an average correlation of 0.27, and the correlations of transcripts and proteins varied depending on the cellular location and biological function of the gene. We examined technical and biological factors that could contribute to the modest correlation. For example, differential splicing clearly affects the analyses for certain genes; but, based on deep sequencing, this does not substantially contribute to the overall estimate of the correlation. We also employed genome-wide association analyses to map loci controlling both transcript and protein levels. Surprisingly, little overlap was observed between the protein- and transcript-mapped loci. We have typed numerous clinically relevant traits among the strains, including adiposity, lipoprotein levels, and tissue parameters. Using correlation analysis, we found that a low number of clinical trait relationships are preserved between the protein and mRNA gene products and that the majority of such relationships are specific to either the protein levels or transcript levels. Surprisingly

  7. Comparative analysis of proteome and transcriptome variation in mouse.

    PubMed

    Ghazalpour, Anatole; Bennett, Brian; Petyuk, Vladislav A; Orozco, Luz; Hagopian, Raffi; Mungrue, Imran N; Farber, Charles R; Sinsheimer, Janet; Kang, Hyun M; Furlotte, Nicholas; Park, Christopher C; Wen, Ping-Zi; Brewer, Heather; Weitz, Karl; Camp, David G; Pan, Calvin; Yordanova, Roumyana; Neuhaus, Isaac; Tilford, Charles; Siemers, Nathan; Gargalovic, Peter; Eskin, Eleazar; Kirchgessner, Todd; Smith, Desmond J; Smith, Richard D; Lusis, Aldons J

    2011-06-01

    The relationships between the levels of transcripts and the levels of the proteins they encode have not been examined comprehensively in mammals, although previous work in plants and yeast suggest a surprisingly modest correlation. We have examined this issue using a genetic approach in which natural variations were used to perturb both transcript levels and protein levels among inbred strains of mice. We quantified over 5,000 peptides and over 22,000 transcripts in livers of 97 inbred and recombinant inbred strains and focused on the 7,185 most heritable transcripts and 486 most reliable proteins. The transcript levels were quantified by microarray analysis in three replicates and the proteins were quantified by Liquid Chromatography-Mass Spectrometry using O(18)-reference-based isotope labeling approach. We show that the levels of transcripts and proteins correlate significantly for only about half of the genes tested, with an average correlation of 0.27, and the correlations of transcripts and proteins varied depending on the cellular location and biological function of the gene. We examined technical and biological factors that could contribute to the modest correlation. For example, differential splicing clearly affects the analyses for certain genes; but, based on deep sequencing, this does not substantially contribute to the overall estimate of the correlation. We also employed genome-wide association analyses to map loci controlling both transcript and protein levels. Surprisingly, little overlap was observed between the protein- and transcript-mapped loci. We have typed numerous clinically relevant traits among the strains, including adiposity, lipoprotein levels, and tissue parameters. Using correlation analysis, we found that a low number of clinical trait relationships are preserved between the protein and mRNA gene products and that the majority of such relationships are specific to either the protein levels or transcript levels. Surprisingly

  8. Comparative Analysis of Old-Age Mortality Estimations in Africa

    PubMed Central

    Bendavid, Eran; Seligman, Benjamin; Kubo, Jessica

    2011-01-01

    Background Survival to old ages is increasing in many African countries. While demographic tools for estimating mortality up to age 60 have improved greatly, mortality patterns above age 60 rely on models based on little or no demographic data. These estimates are important for social planning and demographic projections. We provide direct estimations of older-age mortality using survey data. Methods Since 2005, nationally representative household surveys in ten sub-Saharan countries record counts of living and recently deceased household members: Burkina Faso, Côte d'Ivoire, Ethiopia, Namibia, Nigeria, Swaziland, Tanzania, Uganda, Zambia, and Zimbabwe. After accounting for age heaping using multiple imputation, we use this information to estimate probability of death in 5-year intervals (5qx). We then compare our 5qx estimates to those provided by the World Health Organization (WHO) and the United Nations Population Division (UNPD) to estimate the differences in mortality estimates, especially among individuals older than 60 years old. Findings We obtained information on 505,827 individuals (18.4% over age 60, 1.64% deceased). WHO and UNPD mortality models match our estimates closely up to age 60 (mean difference in probability of death -1.1%). However, mortality probabilities above age 60 are lower using our estimations than either WHO or UNPD. The mean difference between our sample and the WHO is 5.9% (95% CI 3.8–7.9%) and between our sample is UNPD is 13.5% (95% CI 11.6–15.5%). Regardless of the comparator, the difference in mortality estimations rises monotonically above age 60. Interpretation Mortality estimations above age 60 in ten African countries exhibit large variations depending on the method of estimation. The observed patterns suggest the possibility that survival in some African countries among adults older than age 60 is better than previously thought. Improving the quality and coverage of vital information in developing countries will become

  9. Comparative analysis of hospital energy use: pacific northwest and scandinavia.

    PubMed

    Burpee, Heather; McDade, Erin

    2014-01-01

    This study aimed to establish the potential for significant energy reduction in hospitals in the United States by providing evidence of Scandinavian operational precedents with high Interior Environmental Quality (IEQ) and substantially lower energy profiles than comparable U.S. facilities. These facilities set important precedents for design teams seeking operational examples for achieving aggressive energy and interior environmental quality goals. This examination of operational hospitals is intended to offer hospital owners, designers, and building managers a strong case and concrete framework for strategies to achieve exceptionally high performing buildings. Energy efficient hospitals have the potential to significantly impact the U.S.'s overall energy profile, and key stakeholders in the hospital industry need specific, operationally grounded precedents in order to successfully implement informed energy reduction strategies. This study is an outgrowth of previous research evaluating high quality, low energy hospitals that serve as examples for new high performance hospital design, construction, and operation. Through extensive interviews, numerous site visits, the development of case studies, and data collection, this team has established thorough qualitative and quantitative analyses of several contemporary hospitals in Scandinavia and the Pacific Northwest. Many Scandinavian hospitals demonstrate a low energy profile, and when analyzed in comparison with U.S. hospitals, such Scandinavian precedents help define the framework required to make significant changes in the U.S. hospital building industry. Eight hospitals, four Scandinavian and four Pacific Northwest, were quantitatively compared using the Environmental Protection Agency's Portfolio Manager, allowing researchers to answer specific questions about the impact of energy source and architectural and mechanical strategies on energy efficiency in operational hospitals. Specific architectural, mechanical

  10. [Comparative analysis of lymphoscintigraphy between lipedema and lower limb lymphedema].

    PubMed

    Boursier, V; Pecking, A; Vignes, S

    2004-12-01

    Lipedema is characterized by bilateral enlargement of the legs due to abnormal deposition of fat tissue from pelvis to ankles. It is seen most frequently in obese women. Lipedema appears to be a distinct clinical entity but may be confounded with lymphedema. To analyze and to compare between lipedema and lymphedema the qualitative and quantitative aspects of lymphoscintigraphy. Fifteen women with lipedema were recruited. Mean age of onset of lipedema was 31.5 +/- 15 years. Body mass index was 35.1 +/- 7.9 kg/m2, 13 women were obese. Lipedema was compared to 15 cases of primary lymphedema (women: 13, men: 2) of the lower limbs (unilateral: 13, bilateral: 2), with a mean age at onset of 28.7 +/- 12.6 years. Lymphoscintigraphy of the lower limbs with morphologic (visualization of inguinal lymph nodes) and kinetic (half-life, lymphatic speed of the colloid) studies was performed in all cases. Absence of visualization of inguinal lymph nodes was observed in 14/15 cases of lymphedema and in 1/15 cases of lipedema (p<0.001). In the 13 cases of unilateral lymphedema, colloid half-life was higher in the pathologic limb than in the controlateral limb (230 +/- 92 vs 121 +/- 36 minutes, p<0.01) and lymphatic speed of the colloid was slower (6.91 +/- 0.86 vs 8.16 +/- 1.02 cm/min, p<0.001). The two patients with bilateral lymphedema had an increased half-life and decreased lymphatic speed of the colloid. Colloid half-life was significantly higher in lipedema than in controlateral limbs of lymphedema (154 +/- 23 vs 121 +/- 36 minutes, p<0.01) with no difference in lymphatic speed of the colloid. Colloid half-life was significantly higher in lymphedema than in lipedema (230 +/- 92 vs 154 +/- 23 minutes, p<0.01) and the lymphatic speed of the colloid was slower (6.91 +/- 0.86 vs 8.10 +/- 0.45 cm/min, p<0.001). Lower limb lymphoscintigraphy showed lymphatic insufficiency in lipedema without morphologic abnormality as seen in lymphedema. Lymphoscintigraphy is not indispensable but is

  11. Os odontoideum in identical twins: Comparative gene expression analysis

    PubMed Central

    Straus, David; Xu, Shunbin; Traynelis, Vincent C.

    2014-01-01

    Background: Os odontoideum is a well identified anomaly of the craniovertebral junction. Since its initial description, there has been a continuous debate regarding the nature of its etiology: Whether congenital or traumatic. We sought to compare the gene expression profiles in patients with congenital os odontoideum, those with traumatic os odontoideum and controls. Methods: We have evaluated a pair of identical twins both with os odontoideum. We identified two additional patients with and four subjects without os odontoideum. We analyzed the gene expression profiles in these patients using a custom TaqMan microarray and quantitative reverse transcriptase polymerase chain reaction (qRT-PCR). The relative gene expression profiles in the two identical twins, the two nontwin patients with os odontoideum and the controls were assessed. Results: A total of 213 genes with significantly different expression between the twin os odontoideum patients and the subjects without os odontoideum were detected. CACNG6, PHEX, CACNAD3, IL2, FAS, TUFT1, KIT, TGFBR2, and IGF2 were expressed at levels greater than 100-fold more in the twins. There were six genes with significantly different expression profiles in the twins as compared with the nontwin os odontoideum patients: CMK4, ATF1, PLCG1, TAB1, E2F3, and ATF4. There were no statistically significant differences in gene expression in the four patients with os odontoideum and the subjects without. Trends, however, were noted in MMP8, KIT, HIF1A, CREB3, PWHAZ, TGFBR1, NFKB2, FGFR1, IPO8, STAT1, COL1A1, and BMP3. Conclusions: Os odontoideum has multiple etiologies, both traumatic and congenital and perhaps some represent a combination of the two. This work has identified a number of genes that show increased expression in a pair of twins with congenital os odontoideum and also demonstrates trends in gene expression profiles between a larger group of os odontoideum patients and non-os patients. A number of these genes are related to

  12. A comparative protein function analysis databaseof different Leishmania strains

    PubMed Central

    Dikhit, Manas Ranjan; Nathasharma, Yangya Prasad; Patel, Lelin; Rana, Sindhu Prava; Sahoo, Ganesh Chandra; Das, Pradeep

    2011-01-01

    A complete understanding of different protein functional families and template information opens new avenues for novel drug development. Protein identification and analysis software performs a central role in the investigation of proteins and leads to the development of refined database for description of proteins of different Leishmania strains. There are certain databases for different strains that lack template information and functional family annotation. Rajendra Memorial Research Institute of Medical Sciences (RMRIMS) has developed a web-based unique database to provide information about functional families of different proteins and its template information in different Leishmania species. Based on the template information users can model the tertiary structure of protein. The database facilitates significant relationship between template information and possible protein functional families assigned to different proteins by SVMProt. This database is designed to provide comprehensive descriptions of certain important proteins found in four different species of Leishmania i.e. L. donovani, L. infantum, L. major and L. braziliensis. A specific characterization information table provides information related to species and specific functional families. This database aims to be a resource for scientists working on proteomics. The database is freely available at http://biomedinformri.org/calp/. PMID:21464840

  13. Comparative environmental analysis of waste brominated plastic thermal treatments.

    PubMed

    Bientinesi, M; Petarca, L

    2009-03-01

    The aim of this research activity is to investigate the environmental impact of different thermal treatments of waste electric and electronic equipment (WEEE), applying a life cycle assessment methodology. Two scenarios were assessed, which both allow the recovery of bromine: (A) the co-combustion of WEEE and green waste in a municipal solid waste combustion plant, and (B) the staged-gasification of WEEE and combustion of produced syngas in gas turbines. Mass and energy balances on the two scenarios were set and the analysis of the life cycle inventory and the life cycle impact assessment were conducted. Two impact assessment methods (Ecoindicator 99 and Impact 2002+) were slightly modified and then used with both scenarios. The results showed that scenario B (staged-gasification) had a potentially smaller environmental impact than scenario A (co-combustion). In particular, the thermal treatment of staged-gasification was more energy efficient than co-combustion, and therefore scenario B performed better than scenario A, mainly in the impact categories of "fossil fuels" and "climate change". Moreover, the results showed that scenario B allows a higher recovery of bromine than scenario A; however, Br recovery leads to environmental benefits for both the scenarios. Finally the study demonstrates that WEEE thermal treatment for energy and matter recovery is an eco-efficient way to dispose of this kind of waste.

  14. Comparative transcriptome analysis of grapevine in response to copper stress

    PubMed Central

    Leng, Xiangpeng; Jia, Haifeng; Sun, Xin; Shangguan, Lingfei; Mu, Qian; Wang, Baoju; Fang, Jinggui

    2015-01-01

    Grapevine is one of the most economically important and widely cultivated fruit crop worldwide. With the industrialization and the popular application of cupric fungicides in grape industry, copper stress and copper pollution are also the factors affecting grape production and berry and wine quality. Here, 3,843 transcripts were significantly differently expressed genes in response to Cu stress by RNA-seq, which included 1,892 up-regulated and 1,951 down-regulated transcripts. During this study we found many known and novel Cu-induced and -repressed genes. Biological analysis of grape samples were indicated that exogenous Cu can influence chlorophylls metabolism and photosynthetic activities of grapevine. Most ROS detoxification systems, including antioxidant enzyme, stress-related proteins and secondary metabolites were strongly induced. Concomitantly, abscisic acid functioned as a negative regulator in Cu stress, in opposite action to ethylene, auxin, jasmonic acid, and brassinolide. This study also identified a set of Cu stress specifically activated genes coding copper transporter, P1B-type ATPase, multidrug transporters. Overall, this work was carried out to gain insights into the copper-regulated and stress-responsive mechanisms in grapevine at transcriptome level. This research can also provide some genetic information that can help us in better vinery management and breeding Cu-resistant grape cultivars. PMID:26673527

  15. Comparative genomic analysis of teleost fish bmal genes.

    PubMed

    Wang, Han

    2009-05-01

    Bmal1 (Brain and muscle ARNT like 1) gene is a key circadian clock gene. Tetrapods also have the second Bmal gene, Bmal2. Fruit fly has only one bmal1/cycle gene. Interrogation of the five teleost fish genome sequences coupled with phylogenetic and splice site analyses found that zebrafish have two bmal1 genes, bmal1a and bmal1b, and bmal2a; Japanese pufferfish (fugu), green spotted pufferfish (tetraodon) and Japanese medaka fish each have two bmal2 genes, bmal2a and bmal2b, and bmal1a; and three-spine stickleback have bmal1a and bmal2b. Syntenic analysis further indicated that zebrafish bmal1a/bmal1b, and fugu, tetraodon and medaka bmal2a/bmal2b are ancient duplicates. Although the dN/dS ratios of these four fish bmal duplicates are all <1, implicating they have been under purifying selection, the Tajima relative rate test showed that fugu, tetraodon and medaka bmal2a/bmal2b have asymmetric evolutionary rates, suggesting that one of these duplicates have been subject to positive selection or relaxed functional constraint. These results support the notion that teleost fish bmal genes were derived from the fish-specific genome duplication (FSGD), divergent resolution following the duplication led to retaining different ancient bmal duplicates in different fishes, which could have shaped the evolution of the complex teleost fish timekeeping mechanisms.

  16. Family policies in OECD countries: a comparative analysis.

    PubMed

    Thévenon, Olivier

    2011-01-01

    This article discusses the diversity of family policy models in 28 OECD countries in terms of the balance between their different objectives and the mix of instruments adopted to implement the policies. Cross-country policy differences are investigated by applying a principal component analysis to comprehensive country-level data from the OECD Family database covering variables such as parental leave conditions, childcare service provision, and financial support to families. The results find persistent differences in the family policy patterns embedded in different contexts of work-family "outcomes." Country classifications of family policy packages only partially corroborate categorizations in earlier studies, owing to considerable within-group heterogeneity and the presence of group outliers. The Nordic countries outdistance the others with comprehensive support to working parents with very young children. Anglo-Saxon countries provide much less support for working parents with very young children, and financial support is targeted on low-income and large families and focuses on preschool and early elementary education. Continental and Eastern European countries form a more heterogeneous group, while the support received by families in Southern Europe and in Asian countries is much lower in all its dimensions.

  17. Comparative environmental analysis of waste brominated plastic thermal treatments

    SciTech Connect

    Bientinesi, M. Petarca, L.

    2009-03-15

    The aim of this research activity is to investigate the environmental impact of different thermal treatments of waste electric and electronic equipment (WEEE), applying a life cycle assessment methodology. Two scenarios were assessed, which both allow the recovery of bromine: (A) the co-combustion of WEEE and green waste in a municipal solid waste combustion plant, and (B) the staged-gasification of WEEE and combustion of produced syngas in gas turbines. Mass and energy balances on the two scenarios were set and the analysis of the life cycle inventory and the life cycle impact assessment were conducted. Two impact assessment methods (Ecoindicator 99 and Impact 2002+) were slightly modified and then used with both scenarios. The results showed that scenario B (staged-gasification) had a potentially smaller environmental impact than scenario A (co-combustion). In particular, the thermal treatment of staged-gasification was more energy efficient than co-combustion, and therefore scenario B performed better than scenario A, mainly in the impact categories of 'fossil fuels' and 'climate change'. Moreover, the results showed that scenario B allows a higher recovery of bromine than scenario A; however, Br recovery leads to environmental benefits for both the scenarios. Finally the study demonstrates that WEEE thermal treatment for energy and matter recovery is an eco-efficient way to dispose of this kind of waste.

  18. Comparative transcriptome analysis of grapevine in response to copper stress.

    PubMed

    Leng, Xiangpeng; Jia, Haifeng; Sun, Xin; Shangguan, Lingfei; Mu, Qian; Wang, Baoju; Fang, Jinggui

    2015-12-17

    Grapevine is one of the most economically important and widely cultivated fruit crop worldwide. With the industrialization and the popular application of cupric fungicides in grape industry, copper stress and copper pollution are also the factors affecting grape production and berry and wine quality. Here, 3,843 transcripts were significantly differently expressed genes in response to Cu stress by RNA-seq, which included 1,892 up-regulated and 1,951 down-regulated transcripts. During this study we found many known and novel Cu-induced and -repressed genes. Biological analysis of grape samples were indicated that exogenous Cu can influence chlorophylls metabolism and photosynthetic activities of grapevine. Most ROS detoxification systems, including antioxidant enzyme, stress-related proteins and secondary metabolites were strongly induced. Concomitantly, abscisic acid functioned as a negative regulator in Cu stress, in opposite action to ethylene, auxin, jasmonic acid, and brassinolide. This study also identified a set of Cu stress specifically activated genes coding copper transporter, P1B-type ATPase, multidrug transporters. Overall, this work was carried out to gain insights into the copper-regulated and stress-responsive mechanisms in grapevine at transcriptome level. This research can also provide some genetic information that can help us in better vinery management and breeding Cu-resistant grape cultivars.

  19. Comparative analysis of Beggiatoa from hypersaline and marine environments.

    PubMed

    de Albuquerque, Julia Peixoto; Keim, Carolina Neumann; Lins, Ulysses

    2010-07-01

    The main criterion to classify a microorganism as belonging to the genus Beggiatoa is its morphology. All multicellular, colorless, gliding bacterial filaments containing sulfur globules described so far belong to this genus. At the ultrastructural level, they show also a very complex cell envelope structure. Here we describe uncultured vacuolated and non-vacuolated bacteria from two different environments showing all characteristics necessary to assign a bacterium to the genus Beggiatoa. We also intended to investigate whether narrow and vacuolate Beggiatoa do differ morphologically as much as they do phylogenetically. Both large, vacuolated trichomes and narrow filaments devoid of vacuoles were observed. We confirmed the identity of the narrow filaments by 16S rRNA phylogenetic analysis. The diameters of the trichomes ranged from 2.4 to 34 microm, and their lengths ranged from 10 microm to over 30 mm. Narrow trichomes moved by gliding at 3.0 microm/s; large filaments moved at 1.5 microm/s. Periplasmic sulfur inclusions were observed in both types of filaments, whereas phosphorus-rich bodies were found only in narrow trichomes. On the other hand, nitrate vacuoles were observed only in large trichomes. Ultra-thin section transmission electron microscopy showed differences between the cell ultrastructure of narrow (non-vacuolated) and large (vacuolated) Beggiatoa. We observed that cell envelopes from narrow Beggiatoa consist of five layers, whereas cell envelopes from large trichomes contain four layers.

  20. Marine invertebrate lipases: Comparative and functional genomic analysis.

    PubMed

    Rivera-Perez, Crisalejandra

    2015-09-01

    Lipases are key enzymes involved in lipid digestion, storage and mobilization of reserves during fasting or heightened metabolic demand. This is a highly conserved process, essential for survival. The genomes of five marine invertebrate species with distinctive digestive system were screened for the six major lipase families. The two most common families in marine invertebrates, the neutral an acid lipases, are also the main families in mammals and insects. The number of lipases varies two-fold across analyzed genomes. A high degree of orthology with mammalian lipases was observed. Interestingly, 19% of the marine invertebrate lipases have lost motifs required for catalysis. Analysis of the lid and loop regions of the neutral lipases suggests that many marine invertebrates have a functional triacylglycerol hydrolytic activity as well as some acid lipases. A revision of the expression profiles and functional activity on sequences in databases and scientific literature provided information regarding the function of these families of enzymes in marine invertebrates. Copyright © 2015 Elsevier Inc. All rights reserved.

  1. West European public opinion on security: a comparative analysis

    SciTech Connect

    Brown, R.M.

    1985-01-01

    This dissertation empirically explored the security opinion formation process within the British, French, and West Germany populations. Basic theory assumed two sources of security opinion. First, the actions and official statements of political elites furnish strong but transient influence in forming public attitudes, which, in turn, are a basis for opinions. Second, attributes predispose individuals to adopt attitudes, and thus opinions. The influence of attributes is less forceful than are elite cues, but attributes give some stability to opinion - attributes being immutable or slow to change. The analysis of the influence of attributes and attitudes on opinion was based on results of 1976-1982 public opinion surveys. The findings both supported the assumptions on the opinion forming roles of attributes and elite cues and addressed related issues of current interest. The probable security predisposition of the contemporary West European successor generation, an altered role for Europeans holding post material values, and the functional - as opposed to geographic - nature of the supranationalist attitude were among major topics addressed. The dissertation ends with a prediction on mid-term stability and change in the role and functioning of the Atlantic alliance.

  2. Delineation of Steroid-Degrading Microorganisms through Comparative Genomic Analysis

    PubMed Central

    Bergstrand, Lee H.; Cardenas, Erick; Holert, Johannes; Van Hamme, Jonathan D.

    2016-01-01

    ABSTRACT Steroids are ubiquitous in natural environments and are a significant growth substrate for microorganisms. Microbial steroid metabolism is also important for some pathogens and for biotechnical applications. This study delineated the distribution of aerobic steroid catabolism pathways among over 8,000 microorganisms whose genomes are available in the NCBI RefSeq database. Combined analysis of bacterial, archaeal, and fungal genomes with both hidden Markov models and reciprocal BLAST identified 265 putative steroid degraders within only Actinobacteria and Proteobacteria, which mainly originated from soil, eukaryotic host, and aquatic environments. These bacteria include members of 17 genera not previously known to contain steroid degraders. A pathway for cholesterol degradation was conserved in many actinobacterial genera, particularly in members of the Corynebacterineae, and a pathway for cholate degradation was conserved in members of the genus Rhodococcus. A pathway for testosterone and, sometimes, cholate degradation had a patchy distribution among Proteobacteria. The steroid degradation genes tended to occur within large gene clusters. Growth experiments confirmed bioinformatic predictions of steroid metabolism capacity in nine bacterial strains. The results indicate there was a single ancestral 9,10-seco-steroid degradation pathway. Gene duplication, likely in a progenitor of Rhodococcus, later gave rise to a cholate degradation pathway. Proteobacteria and additional Actinobacteria subsequently obtained a cholate degradation pathway via horizontal gene transfer, in some cases facilitated by plasmids. Catabolism of steroids appears to be an important component of the ecological niches of broad groups of Actinobacteria and individual species of Proteobacteria. PMID:26956583

  3. Comparative analysis of the methods for SADT determination.

    PubMed

    Kossoy, A A; Sheinman, I Ya

    2007-04-11

    The self-accelerating decomposition temperature (SADT) is an important parameter that characterizes thermal safety at transport of self-reactive substances. A great many articles were published focusing on various methodological aspects of SADT determination. Nevertheless there remain several serious problems that require further analysis and solution. Some of them are considered in the paper. Firstly four methods suggested by the United Nations "Recommendations on the Transport of Dangerous Goods" (TDG) are surveyed in order to reveal their features and limitations. The inconsistency between two definitions of SADT is discussed afterwards. One definition is the basis for the US SADT test and the heat accumulation storage test (Dewar test), another one is used when the Adiabatic storage test or the Isothermal storage test are applied. It is shown that this inconsistency may result in getting different and, in some cases, unsafe estimates of SADT. Then the applicability of the Dewar test for determination of SADT for solids is considered. It is shown that this test can be restrictedly applied for solids provided that the appropriate scale-up procedure is available. The advanced method based on the theory of regular cooling mode is proposed, which ensures more reliable results of the Dewar test application. The last part of the paper demonstrates how the kinetics-based simulation method helps in evaluation of SADT in those complex but practical cases (in particular, stack of packagings) when neither of the methods recommended by TDG can be used.

  4. Comparative analysis of HOG pathway proteins to generate hypotheses for functional analysis.

    PubMed

    Krantz, Marcus; Becit, Evren; Hohmann, Stefan

    2006-03-01

    Comparative genomics allows comparison of different proteins that execute presumably identical functions in different organisms. In contrast to paralogues, orthologues per definition perform the same function and interact with the same partners and, consequently, should display conservation in all these properties. We have employed 20 fungal genomes to analyse key components of the high osmolarity glycerol signalling pathway of Saccharomyces cerevisiae. Among the proteins scrutinised are a complete phosphotransfer module, a MAP kinase, two scaffold proteins, one of which is also a MAPKK, and two transcription factors. Sequence alignments, domain structure and size analysis, combined with the rich information available in the literature, allowed us to probe previous structural and functional studies and to generate hypotheses for future experimental studies. Although certain domains are too highly conserved across fungal species for meaningful comparative studies, others, like interaction domains, can be studied in closely related species. Moreover, putative functionally relevant sites for protein modifications can be identified in such comparative studies. We provide several relevant examples and present a number of previously un(der)characterised domains of potential functional significance in osmosensing and signal transduction. We propose that any functional protein analysis in fungi should make use of the unique resource that fungal genome sequences offer.

  5. Ageism in Belgium and Burundi: a comparative analysis

    PubMed Central

    Marquet, Manon; Missotten, Pierre; Schroyen, Sarah; Nindaba, Desiderate; Adam, Stéphane

    2016-01-01

    Background Recent cross-cultural comparisons between Asian and Western cultures have shown that ageism arises more from the lack of availability of social and economic resources for older adults than from the culture itself. We tested this assumption by conducting a survey among people living in a least developed country compared with those living in a developed country. Participants and methods Twenty-seven Belgians living in Belgium, 29 Burundians living in Belgium, and 32 Burundians living in Burundi were included in this study. Their attitudes toward older adults were assessed using several self-reported measures. Results Statistical analyses confirmed that older people are more negatively perceived by Burundians living in Burundi than by Burundians and Belgians living in Belgium, whose attitudes did not differ from each other. Conclusion Consistent with our hypothesis, our results suggest that the level of development of a country and more particularly the lack of government spending on older people (pension and health care systems) may contribute to their younger counterparts perceiving them more negatively. PMID:27601889

  6. Interspecific variation of warning calls in piranhas: a comparative analysis.

    PubMed

    Mélotte, Geoffrey; Vigouroux, Régis; Michel, Christian; Parmentier, Eric

    2016-10-26

    Fish sounds are known to be species-specific, possessing unique temporal and spectral features. We have recorded and compared sounds in eight piranha species to evaluate the potential role of acoustic communication as a driving force in clade diversification. All piranha species showed the same kind of sound-producing mechanism: sonic muscles originate on vertebrae and attach to a tendon surrounding the bladder ventrally. Contractions of the sound-producing muscles force swimbladder vibration and dictate the fundamental frequency. It results the calling features of the eight piranha species logically share many common characteristics. In all the species, the calls are harmonic sounds composed of multiple continuous cycles. However, the sounds of Serrasalmus elongatus (higher number of cycles and high fundamental frequency) and S. manueli (long cycle periods and low fundamental frequency) are clearly distinguishable from the other species. The sonic mechanism being largely conserved throughout piranha evolution, acoustic communication can hardly be considered as the main driving force in the diversification process. However, sounds of some species are clearly distinguishable despite the short space for variations supporting the need for specific communication. Behavioural studies are needed to clearly understand the eventual role of the calls during spawning events.

  7. Interspecific variation of warning calls in piranhas: a comparative analysis

    PubMed Central

    Mélotte, Geoffrey; Vigouroux, Régis; Michel, Christian; Parmentier, Eric

    2016-01-01

    Fish sounds are known to be species-specific, possessing unique temporal and spectral features. We have recorded and compared sounds in eight piranha species to evaluate the potential role of acoustic communication as a driving force in clade diversification. All piranha species showed the same kind of sound-producing mechanism: sonic muscles originate on vertebrae and attach to a tendon surrounding the bladder ventrally. Contractions of the sound-producing muscles force swimbladder vibration and dictate the fundamental frequency. It results the calling features of the eight piranha species logically share many common characteristics. In all the species, the calls are harmonic sounds composed of multiple continuous cycles. However, the sounds of Serrasalmus elongatus (higher number of cycles and high fundamental frequency) and S. manueli (long cycle periods and low fundamental frequency) are clearly distinguishable from the other species. The sonic mechanism being largely conserved throughout piranha evolution, acoustic communication can hardly be considered as the main driving force in the diversification process. However, sounds of some species are clearly distinguishable despite the short space for variations supporting the need for specific communication. Behavioural studies are needed to clearly understand the eventual role of the calls during spawning events. PMID:27782184

  8. Intergenerational living arrangements in Myanmar and Thailand: a comparative analysis.

    PubMed

    Knodel, John; Pothisiri, Wiraporn

    2015-03-01

    The present study compares living arrangements and related intergenerational support in Myanmar and Thailand based on recent national surveys of older persons in both countries and prior surveys in Thailand. The countries share relatively similar cultural contexts but differ radically in economic development. Substantially higher percentages of older persons in Myanmar currently coreside with their children and are considerably more likely to have non-coresident children living in the same locality. They are also less likely to live with a spouse and to have children living at a substantial distance. Older persons in Myanmar are much less likely to have phone contact with children living away and less likely to receive visits. Thai elders are considerably more likely to provide custodial care to grandchildren with absent parents and to live in skip generation households. Older Thais are also considerably more likely to receive substantial remittances from non-coresident children. The living arrangements of older age Thais in the past, however, more closely resembles the current situation in Myanmar. It appears that current differences are largely attributable to the more advanced Thai economic development through its associated impacts on migration, fertility and mortality. Contrasting political situations and government priorities also likely play a role. The results provide insights into the implications of development for older persons and suggest that if the recent course of political transformation and opening to the global economy continues in Myanmar, living arrangements there may well follow the trends in Thailand over past decades.

  9. Comparative teratogenicity analysis of valnoctamide, risperidone, and olanzapine in mice.

    PubMed

    Wlodarczyk, Bogdan J; Ogle, Krystal; Lin, Linda Ying; Bialer, Meir; Finnell, Richard H

    2015-09-01

    Based on the recent findings from animal studies, it has been proposed that the therapeutic use of valnoctamide, an anxiolytic drug developed in the early 1960s, be extended to treat other neurological disorders such as epilepsy and bipolar disease. Given the scarcity of adequate data on its prenatal toxicity, a comparative teratogenicity study of valnoctamide and two of the most commonly used drugs to treat bipolar disorder, risperidone and olanzapine, was carried out in a mouse model system. Pregnant dams were treated with the aforementioned three drugs at the dose levels calculated as an equal proportion of the respective LD50 values of these drugs. The main reproductive indices examined included the numbers of implantations and resorptions, viable and dead fetuses, and fetal gross, visceral and skeletal abnormalities. The outcomes of the present study indicated that olanzapine was the most teratogenic of the three drugs, inducing maternal-, embryo-, and fetotoxicity. Risperidone also exerted a significant prenatal toxicity, but its adverse effect was less pronounced than that induced by olanzapine. Valnoctamide did not show any teratogenic effect, even when used in relatively higher dosages than olanzapine and risperidone. The observed increased skeletal abnormalities in one of the valnoctamide treatment groups were nonspecific and, as such, signaled a modest developmental delay rather than an indication that the compound could induce structural malformations. Under our experimental conditions, valnoctamide demonstrated the lowest prenatal toxicity of the three tested drugs. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  10. Comparative Analysis of Cherenkov Light Detectors in an Oil Drum

    NASA Astrophysics Data System (ADS)

    Niduaza, Rexavalmar; Wedel, Zachary; Castro, Juan; Zavala, Favian; Fan, Sewan; Fatuzzo, Laura

    2014-03-01

    The multi-pixel photon counters (MPPC) has been used in a number of research development in astro-particle physics and particle physics. In an effort to further implement the MPPC detector, we constructed a modular experimental setup using a 16-inch tall acrylic cylinder filled with distilled water as the light producing medium to determine its feasibility as a possible detector for weak Cherenkov light. We have since progressed towards utilizing an oil drum (approximately 30 gallons) as our light-tight container replacing our prototype. In this talk, we would discuss the results regarding our investigation utilizing 1-inch and 3-inch photo-multiplier tubes (PMTs) in an oil drum as we did for our prototype. We would also present our experimental findings comparing our prototype and our oil drum setup using PMTs in coincidence with the MPPC coupled with wavelength-shifting fibers that are submerged in distilled water inside the oil drum vessel. Department of Education grant nymber P031S90007.

  11. Comparative analysis of modeled nitrogen removal by shellfish farms.

    PubMed

    Rose, Julie M; Bricker, Suzanne B; Ferreira, Joao G

    2015-02-15

    The use of shellfish aquaculture for nutrient removal and reduction of coastal eutrophication has been proposed. Published literature has indicated that nitrogen contained in harvested shellfish can be accurately estimated from shell length:nitrogen content ratios. The range of nitrogen that could be removed by a typical farm in a specific estuarine or coastal setting is also of interest to regulators and planners. Farm Aquaculture Resource Management (FARM) model outputs of nitrogen removal at the shellfish farm scale have been summarized here, from 14 locations in 9 countries across 4 continents. Modeled nitrogen removal ranged from 105 lbs acre(-1) year(-1) (12 g m(-2) year(-1)) to 1356 lbs acre(-1) year(-1) (152 g m(-2) year(-1)). Mean nitrogen removal was 520 lbs acre(-1) year(-1) (58 g m(-2) year(-1)). These model results are site-specific in nature, but compare favorably to reported nitrogen removal effectiveness of agricultural best management practices and stormwater control measures. Published by Elsevier Ltd.

  12. A Comparative Biocompatibility Analysis of Ternary Nitinol Alloys

    PubMed Central

    Haider, Waseem; Munroe, Norman; Pulletikurthi, Chandan; Singh Gill, Puneet K.; Amruthaluri, Sushma

    2009-01-01

    Nitinol alloys are rapidly being utilized as the material of choice in a variety of applications in the medical industry. It has been used for self-expanding stents, graft support systems, and various other devices for minimally invasive interventional and endoscopic procedures. However, the biocompatibility of this alloy remains a concern to many practitioners in the industry due to nickel sensitivity experienced by many patients. In recent times, several new Nitinol alloys have been introduced with the addition of a ternary element. Nevertheless, there is still a dearth of information concerning the biocompatibility and corrosion resistance of these alloys. This study compared the biocompatibility of two ternary Nitinol alloys prepared by powder metallurgy (PM) and arc melting (AM) and critically assessed the influence of the ternary element. ASTM F 2129-08 cyclic polarization in vitro corrosion tests were conducted to evaluate the corrosion resistance in phosphate buffered saline (PBS). The growth of endothelial cells on NiTi was examined using optical microscopy. PMID:19956791

  13. Islamic Medicine and Evolutionary Medicine: A Comparative Analysis

    PubMed Central

    Saniotis, Arthur

    2012-01-01

    The advent of evolutionary medicine in the last two decades has provided new insights into the causes of human disease and possible preventative strategies. One of the strengths of evolutionary medicine is that it follows a multi-disciplinary approach. Such an approach is vital to future biomedicine as it enables for the infiltration of new ideas. Although evolutionary medicine uses Darwinian evolution as a heuristic for understanding human beings’ susceptibility to disease, this is not necessarily in conflict with Islamic medicine. It should be noted that current evolutionary theory was first expounded by various Muslim scientists such as al-Jāḥiẓ, al-Ṭūsī, Ibn Khaldūn and Ibn Maskawayh centuries before Darwin and Wallace. In this way, evolution should not be viewed as being totally antithetical to Islam. This article provides a comparative overview of Islamic medicine and Evolutionary medicine as well as drawing points of comparison between the two approaches which enables their possible future integration. PMID:23864992

  14. International Migration and Gender in Latin America: A Comparative Analysis

    PubMed Central

    Massey, Douglas S.; Fischer, Mary J.; Capoferro, Chiara

    2010-01-01

    We review census data to assess the standing of five Latin American nations on a gender continuum ranging from patriarchal to matrifocal. We show that Mexico and Costa Rica lie close to one another with a highly patriarchal system of gender relations whereas Nicaragua and the Dominican Republic are similar in having a matrifocal system. Puerto Rico occupies a middle position, blending characteristics of both systems. These differences yield different patterns of female relative to male migration. Female householders in the two patriarchal settings displayed low rates of out-migration compared with males, whereas in the two matrifocal countries the ratio of female to male migration was much higher, in some case exceeding their male counterparts. Multivariate analyses showed that in patriarchal societies, a formal or informal union with a male dramatically lowers the odds of female out-migration, whereas in matrifocal societies marriage and cohabitation have no real effect. The most important determinants of female migration from patriarchal settings are the migrant status of the husband or partner, having relatives in the United States, and the possession of legal documents. In matrifocal settings, however, female migration is less related to the possession of documents, partner’s migrant status, or having relatives in the United States and more strongly related to the woman’s own migratory experience. Whereas the process of cumulative causation appears to be driven largely by men in patriarchal societies, it is women who dominate the process in matrifocal settings. PMID:21399742

  15. Comparative analysis of vocabulary in children with cochlear implants.

    PubMed

    Teixeira, Marina Santos; Oliveira, Carlos Augusto Costa Pires de; Caldas, Fernanda Ferreira; Serra, Lucieny Silva Martin; Cardoso, Carolina Costa; Deperon, Tatiana Medeiros; Bahmad, Fayez

    2014-01-01

    The use of tests assessing the speech of patients who underwent cochlear implant (CI) surgery is warranted to increase knowledge on the development of these patients' language skills. The ABFW Child Language Test evaluates vocabulary, phonology, fluency, and pragmatics and can be administered to these children. To evaluate the vocabulary of children using CI. This study included 16 children who underwent CI surgery between 1-4 years and 11 months old. Patients were divided into five groups according to age upon CI activation. In comparison with the age of brain's auditory development vs. chronological age of hearing children, all children using CI performed better. The comparison between children using unilateral CI and bilateral CI showed that those using bilateral CI had better results. When we compared children's performance considering the chronological age of deaf and hearing children, hearing children performed better. However, there were similar results when patients effectively used their CI and attended auditory rehabilitation sessions. In our study, the vocabulary of children using CI is similar to the vocabulary of hearing children.

  16. Hospital profitability and capital structure: a comparative analysis.

    PubMed Central

    Valvona, J; Sloan, F A

    1988-01-01

    This article compares the financial performance of hospitals by ownership type and of five publicly traded hospital companies with other industries, using such indicators as profit margins, return on equity (ROE) and total capitalization, and debt-to-equity ratios. We also examine stock returns to investors for the five hospital companies versus other industries, as well as the relative roles of debt and equity in new financing. Investor-owned hospitals had substantially greater margins and ROE than did other hospital types. In 1982, investor-owned chain hospitals had a ROE of 26 percent, 18 points above the average for all hospitals. Stock returns on the five selected hospital companies were more than twice as large as returns on other industries between 1972 and 1983. However, after 1983, returns for these companies fell dramatically in absolute terms and relative to other industries. We also found investor-owned hospitals to be much more highly levered than their government and voluntary counterparts, and more highly levered than other industries as well. PMID:3403274

  17. [COMPARATIVE ANALYSIS OF ANTIBACTERIAL EFFECT OF PHYTOANTIBIOTICS AND ANTIBIOTICS].

    PubMed

    Akhvlediani, L; Koiava, T; Lomtadze, L; Joxadze, M; Msxiladze, L; Berashvili, D; Bakuridze, A

    2016-11-01

    The objective of this study was to determine the antibacterial activity of individual medicines and containing sum of the phyto-extracts against the bacteria causing nosocomial infections in compare to antibiotics. In the investigation were involved four strains of gram-negative bacteria Escherichia coli, Klebsiella pneumoniae, Staphylococcus aureus and Acinetobacter spp. Each object was investigated on antibiotic resistance using Kirby-Bauer diffusion method on 22 types of antibiotics. The objects of the study were: Sanguinarine, Chelerythrine and Berberine hydrochloride (of lab quality); essential oils and aromatic waters of Eucalyptus, Salvia and Lavanda. For determination their antibacterial activity was used Raits serological dilution method with adaptation. The results show that the antibiotic resistant bacteria did not rise in non-diluted and 1:1 diluted test-tubes. In 1:5 diluted test-tubes was observed a little turbidity and growth, as for in other test-tubes - intensive growth. The investigated phyto-medicines show the higher antibacterial activity than the antibiotics.

  18. Work satisfaction among California registered nurses: a longitudinal comparative analysis.

    PubMed

    Tellez, Michelle

    2012-01-01

    California's minimum nurse-to-patient staffing ratio law, the nation's first, was implemented in 2004. This study had two aims: (a) to evaluate the effect of the nurse-to-patient ratios law on nurse job satisfaction in order to advance the debate over the merits of nurse staffing law, and (b) to compare California nurses who were satisfied against those who were not, in order to facilitate the development targeted retention interventions based on empirical evidence. The sample's overall job satisfaction increased significantly as the years passed, suggesting the nurse-to-patient ratios law was associated with improvements in nurse satisfaction. Satisfied RNs were more likely to have a balanced and financially secure life that included a partner, children living at home, higher hourly wages, and higher income from sources other than a nursing job. Nurses working in direct patient care positions remained dissatisfied in larger proportions than those working in other types of positions, even after the nurse-to-patient ratios were implemented. More nurses are satisfied today than before the ratios; nevertheless, far too many nurses (18.5%) have job satisfaction scores that are neutral or worse.

  19. Human echinococcosis in Bulgaria: a comparative epidemiological analysis.

    PubMed Central

    Todorov, T.; Boeva, V.

    1999-01-01

    The present article describes the importance of human echinococcosis as a public health problem in Bulgaria, outlines the control measures carried out and evaluates comparatively the situation over three periods spanning 46 years (1950-1995). During the first period (1950-62), a total of 6469 new surgically confirmed cases of hydatid disease were recorded in Bulgaria, with an annual incidence of 6.5 per 100,000 population, and the infestation rate in domestic animals and dogs was high. Echinococcosis was endemic throughout the country. The organization of a control campaign, initiated in 1960, led to a considerable improvement in the situation during the second period (1971-82). Morbidity among humans gradually decreased, with an average incidence of 2.0 per 100,000, and the proportion of infected animals also fell. The distribution of echinococcosis was characterized as sporadic or of low endemicity. During the third period (1983-95), owing to administrative irregularities and economic changes, funds for supporting the campaign were reduced and control structures were dismantled. As a result, the incidence rose to 3.3 per 100,000. Echinococcosis again became endemic, in some regions hyperendemic. The findings provide convincing evidence that cessation of control measures or reduction of campaign activity can lead to intensification in the transmission of Echinococcus granulosus and to a resurgence in echinococcosis to previous levels. PMID:10083708

  20. Comparative analysis of Meissner's corpuscles in the fingertips of primates.

    PubMed

    Verendeev, Andrey; Thomas, Christian; McFarlin, Shannon C; Hopkins, William D; Phillips, Kimberley A; Sherwood, Chet C

    2015-07-01

    Meissner's corpuscles (MCs) are tactile mechanoreceptors found in the glabrous skin of primates, including fingertips. These receptors are characterized by sensitivity to light touch, and therefore might be associated with the evolution of manipulative abilities of the hands in primates. We examined MCs in different primate species, including common marmoset (Callithrix jacchus, n = 5), baboon (Papio anubis, n = 2), rhesus macaque (Macaca mulatta, n = 3), chimpanzee (Pan troglodytes, n = 3), bonobo (Pan paniscus, n = 1) and human (Homo sapiens, n = 8). Fingertips of the first, second and fourth digits were collected from both hands of specimens, dissected and histologically stained using hematoxylin and eosin. The density (MCs per 1 mm(2) ) and the size (cross-sectional diameter of MCs) were quantified. Overall, there were no differences in the densities of MCs or their size among the digits or between the hands for any species examined. However, MCs varied across species. We found a trend for higher densities of MCs in macaques and humans compared with chimpanzees and bonobos; moreover, apes had larger MCs than monkeys. We further examined whether the density or size of MCs varied as a function of body mass, measures of dexterity and dietary frugivory. Among these variables, only body size accounted for a significant amount of variation in the size of MCs.

  1. Competencies and frameworks in interprofessional education: a comparative analysis.

    PubMed

    Thistlethwaite, Jill E; Forman, Dawn; Matthews, Lynda R; Rogers, Gary D; Steketee, Carole; Yassine, Tagrid

    2014-06-01

    Health professionals need preparation and support to work in collaborative practice teams, a requirement brought about by an aging population and increases in chronic and complex diseases. Therefore, health professions education has seen the introduction of interprofessional education (IPE) competency frameworks to provide a common lens through which disciplines can understand, describe, and implement team-based practices. Whilst an admirable aim, often this has resulted in more confusion with the introduction of varying definitions about similar constructs, particularly in relation to what IPE actually means.The authors explore the nature of the terms competency and framework, while critically appraising the concept of competency frameworks and competency-based education. They distinguish between competencies for health professions that are profession specific, those that are generic, and those that may be achieved only through IPE. Four IPE frameworks are compared to consider their similarities and differences, which ultimately influence how IPE is implemented. They are the Interprofessional Capability Framework (United Kingdom), the National Interprofessional Competency Framework (Canada), the Core Competencies for Interprofessional Collaborative Practice (United States), and the Curtin University Interprofessional Capability Framework (Australia).The authors highlight the need for further discussion about establishing a common language, strengthening ways in which academic environments work with practice environments, and improving the assessment of interprofessional competencies and teamwork, including the development of assessment tools for collaborative practice. They also argue that for IPE frameworks to be genuinely useful, they need to augment existing curricula by emphasizing outcomes that might be attained only through interprofessional activity.

  2. Comparative transcriptomic analysis of human and Drosophila extracellular vesicles

    PubMed Central

    Lefebvre, Fabio Alexis; Benoit Bouvrette, Louis Philip; Perras, Lilyanne; Blanchet-Cohen, Alexis; Garnier, Delphine; Rak, Janusz; Lécuyer, Éric

    2016-01-01

    Extracellular vesicles (EVs) are membrane-enclosed nanoparticles containing specific repertoires of genetic material. In mammals, EVs can mediate the horizontal transfer of various cargos and signaling molecules, notably miRNA and mRNA species. Whether this form of intercellular communication prevails in other metazoans remains unclear. Here, we report the first parallel comparative morphologic and transcriptomic characterization of EVs from Drosophila and human cellular models. Electronic microscopy revealed that human and Drosophila cells release similar EVs with diameters ranging from 30 to 200 nm, which contain complex populations of transcripts. RNA-seq identified abundant ribosomal RNAs, related pseudogenes and retrotransposons in human and Drosophila EVs. Vault RNAs and Y RNAs abounded in human samples, whereas small nucleolar RNAs involved in pseudouridylation were most prevalent in Drosophila EVs. Numerous mRNAs were identified, largely consisting of exonic sequences displaying full-length read coverage and enriched for translation and electronic transport chain functions. By analogy with human systems, these sizeable similarities suggest that EVs could potentially enable RNA-mediated intercellular communication in Drosophila. PMID:27282340

  3. Ageism in Belgium and Burundi: a comparative analysis.

    PubMed

    Marquet, Manon; Missotten, Pierre; Schroyen, Sarah; Nindaba, Desiderate; Adam, Stéphane

    2016-01-01

    Recent cross-cultural comparisons between Asian and Western cultures have shown that ageism arises more from the lack of availability of social and economic resources for older adults than from the culture itself. We tested this assumption by conducting a survey among people living in a least developed country compared with those living in a developed country. Twenty-seven Belgians living in Belgium, 29 Burundians living in Belgium, and 32 Burundians living in Burundi were included in this study. Their attitudes toward older adults were assessed using several self-reported measures. Statistical analyses confirmed that older people are more negatively perceived by Burundians living in Burundi than by Burundians and Belgians living in Belgium, whose attitudes did not differ from each other. Consistent with our hypothesis, our results suggest that the level of development of a country and more particularly the lack of government spending on older people (pension and health care systems) may contribute to their younger counterparts perceiving them more negatively.

  4. Comparative Analysis of Testis Protein Evolution in Rodents

    PubMed Central

    Turner, Leslie M.; Chuong, Edward B.; Hoekstra, Hopi E.

    2008-01-01

    Genes expressed in testes are critical to male reproductive success, affecting spermatogenesis, sperm competition, and sperm–egg interaction. Comparing the evolution of testis proteins at different taxonomic levels can reveal which genes and functional classes are targets of natural and sexual selection and whether the same genes are targets among taxa. Here we examine the evolution of testis-expressed proteins at different levels of divergence among three rodents, mouse (Mus musculus), rat (Rattus norvegicus), and deer mouse (Peromyscus maniculatus), to identify rapidly evolving genes. Comparison of expressed sequence tags (ESTs) from testes suggests that proteins with testis-specific expression evolve more rapidly on average than proteins with maximal expression in other tissues. Genes with the highest rates of evolution have a variety of functional roles including signal transduction, DNA binding, and egg–sperm interaction. Most of these rapidly evolving genes have not been identified previously as targets of selection in comparisons among more divergent mammals. To determine if these genes are evolving rapidly among closely related species, we sequenced 11 of these genes in six Peromyscus species and found evidence for positive selection in five of them. Together, these results demonstrate rapid evolution of functionally diverse testis-expressed proteins in rodents, including the identification of amino acids under lineage-specific selection in Peromyscus. Evidence for positive selection among closely related species suggests that changes in these proteins may have consequences for reproductive isolation. PMID:18689890

  5. Subpicosecond and picosecond laser ablation of dental enamel: comparative analysis

    NASA Astrophysics Data System (ADS)

    Rode, Andrei V.; Madsen, Nathan R.; Kolev, Vesselin Z.; Gamaly, Eugene G.; Luther-Davies, Barry; Dawes, Judith M.; Chan, A.

    2004-06-01

    We report the use of sub-picosecond near-IR and ps UV pulsed lasers for precision ablation of freshly extracted human teeth. The sub-picosecond laser wavelength was ~800nm, with pulsewidth 150 fs and pulse repetition rate of 1kHz; the UV laser produced 10 ps pulses at 266 nm with pulse rate of ~1.2x105 pulses/s; both lasers produced ~1 W of output energy, and the laser fluence was kept at the same level of 10-25 J/cm2. Laser radiation from both laser were effectively absorbed in the teeth enamel, but the mechanisms of absorption were radically different: the near-IR laser energy was absorbed in a plasma layer formed through the optical breakdown mechanism initiated by multiphoton absorption, while the UV-radiation was absorbed due to molecular photodissociation of the enamel and conventional thermal deposition. The rise in the intrapulpal temperature was monitored by embedded thermocouples, and was shown to remain low with subpicosecond laser pulses, but risen up to 30°C, well above the 5°C pain level with the UV-laser. This study demonstrates the potential for ultra-short-pulsed lasers to precision and painless ablation of dental enamel, and indicated the optimal combination of laser parameters in terms of pulse energy, duration, intensity, and repetition rate, required for the laser ablation rates comparable to that of mechanical drill.

  6. A comparative analysis of the evolution of imperfect mimicry.

    PubMed

    Penney, Heather D; Hassall, Christopher; Skevington, Jeffrey H; Abbott, Kevin R; Sherratt, Thomas N

    2012-03-21

    Although exceptional examples of adaptation are frequently celebrated, some outcomes of natural selection seem far from perfect. For example, many hoverflies (Diptera: Syrphidae) are harmless (Batesian) mimics of stinging Hymenoptera. However, although some hoverfly species are considered excellent mimics, other species bear only a superficial resemblance to their models and it is unclear why this is so. To evaluate hypotheses that have been put forward to explain interspecific variation in the mimetic fidelity of Palearctic Syrphidae we use a comparative approach. We show that the most plausible explanation is that predators impose less selection for mimetic fidelity on smaller hoverfly species because they are less profitable prey items. In particular, our findings, in combination with previous results, allow us to reject several key hypotheses for imperfect mimicry: first, human ratings of mimetic fidelity are positively correlated with both morphometric measures and avian rankings, indicating that variation in mimetic fidelity is not simply an illusion based on human perception; second, no species of syrphid maps out in multidimensional space as being intermediate in appearance between several different hymenopteran model species, as the multimodel hypothesis requires; and third, we find no evidence for a negative relationship between mimetic fidelity and abundance, which calls into question the kin-selection hypothesis. By contrast, a strong positive relationship between mimetic fidelity and body size supports the relaxed-selection hypothesis, suggesting that reduced predation pressure on less profitable prey species limits the selection for mimetic perfection.

  7. Comparative functional analysis of the lac operons in Streptococcus pyogenes.

    PubMed

    Loughman, Jennifer A; Caparon, Michael G

    2007-04-01

    Having no known environmental reservoir, Streptococcus pyogenes, a bacterium responsible for a wider variety of human diseases than any other bacterial species, must rely on its host for metabolic substrates. Although a streptococcal aldolase, LacD.1, has been adapted to virulence gene regulation, both LacD.1 and a paralogous protein, LacD.2, are predicted to function in the tagatose 6-phosphate pathway for lactose and galactose utilization. In order to gain insight into the mechanism of the LacD.1 regulatory pathway and the role of genome context in the emergence of LacD.1's novel regulatory functions, we compared the function and regulation of the Lac.1 and Lac.2 loci. The Lac.1 operon is not inducible, and regulation by LacD.1 is independent of a functional tagatose 6-phosphate pathway and enhanced by the conserved truncation of upstream Lac.1 genes. In contrast, Lac.2 expression is sensitive to environmental carbohydrates, and LacD.2, not LacD.1, contributes to growth on galactose. Thus, we conclude that the Lac.1 locus has been specialized to participate in regulation, leaving efficient utilization of carbohydrate sources to the Lac.2 locus. The adaptation of LacD for transcription regulation may be an underappreciated strategy among prokaryotes, as homologues of this multifaceted enzyme are present in a broad range of species.

  8. Comparative analysis of protocols for DNA extraction from soybean caterpillars.

    PubMed

    Palma, J; Valmorbida, I; da Costa, I F D; Guedes, J V C

    2016-04-07

    Genomic DNA extraction is crucial for molecular research, including diagnostic and genome characterization of different organisms. The aim of this study was to comparatively analyze protocols of DNA extraction based on cell lysis by sarcosyl, cetyltrimethylammonium bromide, and sodium dodecyl sulfate, and to determine the most efficient method applicable to soybean caterpillars. DNA was extracted from specimens of Chrysodeixis includens and Spodoptera eridania using the aforementioned three methods. DNA quantification was performed using spectrophotometry and high molecular weight DNA ladders. The purity of the extracted DNA was determined by calculating the A260/A280 ratio. Cost and time for each DNA extraction method were estimated and analyzed statistically. The amount of DNA extracted by these three methods was sufficient for PCR amplification. The sarcosyl method yielded DNA of higher purity, because it generated a clearer pellet without viscosity, and yielded high quality amplification products of the COI gene I. The sarcosyl method showed lower cost per extraction and did not differ from the other methods with respect to preparation times. Cell lysis by sarcosyl represents the best method for DNA extraction in terms of yield, quality, and cost effectiveness.

  9. A comparative critical analysis of modern task-parallel runtimes.

    SciTech Connect

    Wheeler, Kyle Bruce; Stark, Dylan; Murphy, Richard C.

    2012-12-01

    The rise in node-level parallelism has increased interest in task-based parallel runtimes for a wide array of application areas. Applications have a wide variety of task spawning patterns which frequently change during the course of application execution, based on the algorithm or solver kernel in use. Task scheduling and load balance regimes, however, are often highly optimized for specific patterns. This paper uses four basic task spawning patterns to quantify the impact of specific scheduling policy decisions on execution time. We compare the behavior of six publicly available tasking runtimes: Intel Cilk, Intel Threading Building Blocks (TBB), Intel OpenMP, GCC OpenMP, Qthreads, and High Performance ParalleX (HPX). With the exception of Qthreads, the runtimes prove to have schedulers that are highly sensitive to application structure. No runtime is able to provide the best performance in all cases, and those that do provide the best performance in some cases, unfortunately, provide extremely poor performance when application structure does not match the schedulers assumptions.

  10. Comparative Analysis of Radiometer Systems Using Non-Stationary Processes

    NASA Technical Reports Server (NTRS)

    Racette, Paul; Lang, Roger; Krebs, Carolyn A. (Technical Monitor)

    2002-01-01

    Radiometers require periodic calibration to correct for instabilities in the receiver response. Various calibration techniques exist that minimize the effect of instabilities in the receivers. The optimal technique depends upon many parameters. Some parameters are constrained by the particular application and others can be chosen in the system design. For example, the measurement uncertainty may be reduced to the limits of the resolution of the measurement (sensitivity) if periodic absolute calibration can be performed with sufficient frequency. However if the period between calibrations is long, a reference-differencing technique, i.e. Dicke-type design, can yield better performance. The measurement uncertainty not only depends upon the detection scheme but also on the number of pixels between calibrations, the integration time per pixel, integration time per calibration reference measurement, calibration reference temperature, and the brightness temperature of what is being measured. The best scheme for reducing the measurement uncertainty also depends, in large part, on the stability of the receiver electronics. In this presentation a framework for evaluating calibration schemes for a wide range of system architectures is presented. Two methods for treating receiver non-stationarity are compared with radiometer measurements.

  11. Comparative Analysis Study of Open Source GIS in Malaysia

    NASA Astrophysics Data System (ADS)

    Rasid, Muhammad Zamir Abdul; Kamis, Naddia; Khuizham Abd Halim, Mohd

    2014-06-01

    Open source origin might appear like a major prospective change which is qualified to deliver in various industries and also competing means in developing countries. The leading purpose of this research study is to basically discover the degree of adopting Open Source Software (OSS) that is connected with Geographic Information System (GIS) application within Malaysia. It was derived based on inadequate awareness with regards to the origin ideas or even on account of techie deficiencies in the open origin instruments. This particular research has been carried out based on two significant stages; the first stage involved a survey questionnaire: to evaluate the awareness and acceptance level based on the comparison feedback regarding OSS and commercial GIS. This particular survey was conducted among three groups of candidates: government servant, university students and lecturers, as well as individual. The approaches of measuring awareness in this research were based on a comprehending signal plus a notion signal for each survey questions. These kinds of signs had been designed throughout the analysis in order to supply a measurable and also a descriptive signal to produce the final result. The second stage involved an interview session with a major organization that carries out available origin internet GIS; the Federal Department of Town and Country Planning Peninsular Malaysia (JPBD). The impact of this preliminary study was to understand the particular viewpoint of different groups of people on the available origin, and also their insufficient awareness with regards to origin ideas as well as likelihood may be significant root of adopting level connected with available origin options.

  12. Comparative analysis of physicochemical properties of root perforation sealer materials

    PubMed Central

    Dorileo, Maura Cristiane Gonçales Orçati; Pedro, Fábio Luis Miranda; Bandeca, Matheus Coelho; Guedes, Orlando Aguirre; Villa, Ricardo Dalla

    2014-01-01

    Objectives This study evaluated the solubility, dimensional alteration, pH, electrical conductivity, and radiopacity of root perforation sealer materials. Materials and Methods For the pH test, the samples were immersed in distilled water for different periods of time. Then, the samples were retained in plastic recipients, and the electrical conductivity of the solution was measured. The solubility, dimensional alteration, and radiopacity properties were evaluated according to Specification No. 57 of the American National Standards Institute/American Dental Association (ANSI/ADA). Statistical analyses were carried out using analysis of variance (ANOVA) and Tukey's test at a significance level of 5%. When the sample distribution was not normal, a nonparametric ANOVA was performed with a Kruskal-Wallis test (α = 0.05). Results The results showed that white structural Portland cement (PC) had the highest solubility, while mineral trioxide aggregate (MTA)-based cements, ProRoot MTA (Dentsply-Tulsa Dental) and MTA BIO (Ângelus Ind. Prod.), had the lowest values. MTA BIO showed the lowest dimensional alteration values and white PC presented the highest values. No differences among the tested materials were observed in the the pH and electrical conductivity analyses. Only the MTA-based cements met the ANSI/ADA recommendations regarding radiopacity, overcoming the three steps of the aluminum step wedge. Conclusions On the basis of these results, we concluded that the values of solubility and dimensional alteration of the materials were in accordance with the ANSI/ADA specifications. PCs did not fulfill the ANSI/ADA requirements regarding radiopacity. No differences were observed among the materials with respect to the pH and electrical conductivity analyses. PMID:25110644

  13. A Comparative Analysis of Global Cropping Systems Models and Maps

    NASA Astrophysics Data System (ADS)

    Anderson, W. B.; You, L.; Wood, S.; Wood-Sichra, U.; Wu, W.

    2013-12-01

    Agricultural practices have dramatically altered the land cover of the Earth, but the spatial extent and intensity of these practices is often difficult to catalogue. Cropland accounts for nearly 15 million km2 of the Earth's land cover - amounting to 12% of the Earth's ice-free land surface - yet information on the distribution and performance of specific crops is often available only through national or sub-national statistics. While remote sensing products offer spatially disaggregated information, those currently available on a global scale are ill-suited for many applications due to the limited separation of crop types within the area classified as cropland. Recently, however, there have been multiple independent efforts to incorporate the detailed information available from statistical surveys with supplemental spatial information to produce a spatially explicit global dataset specific to individual cropss for the year 2000. While these datasets provide analysts and decision makers with improved information on global cropping systems, the final global cropping maps differ from one another substantially. This study aims to explore and quantify systematic similarities and differences between four major global cropping systems products: the monthly irrigated and rainfed crop areas around the year 2000 (MIRAC2000) dataset, the spatial production allocation model (SPAM), the global agro-ecological zone (GAEZ) dataset, and the dataset developed by Monfreda et al., 2008. The analysis explores not only the final cropping systems maps but also the interdependencies of each product, methodological differences and modeling assumptions, which will provide users with information vital for discerning between datasets in selecting a product appropriate for each intended application.

  14. Urban Detection, Delimitation and Morphology: Comparative Analysis of Selective "MEGACITIES"

    NASA Astrophysics Data System (ADS)

    Alhaddad, B.; Arellano, B. E.; Roca, J.

    2012-08-01

    Over the last 50 years, the world has faced an impressive growth of urban population. The walled city, close to the outside, an "island"for economic activities and population density within the rural land, has led to the spread of urban life and urban networks in almost all the territory. There was, as said Margalef (1999), "a topological inversion of the landscape". The "urban" has gone from being an island in the ocean of rural land vastness, to represent the totally of the space in which are inserted natural and rural "systems". New phenomena such as the fall of the fordist model of production, the spread of urbanization known as urban sprawl, and the change of scale of the metropolis, covering increasingly large regions, called "megalopolis" (Gottmann, 1961), have characterized the century. However there are no rigorous databases capable of measuring and evaluating the phenomenon of megacities and in general the process of urbanization in the contemporary world. The aim of this paper is to detect, identify and analyze the morphology of the megacities through remote sensing instruments as well as various indicators of landscape. To understand the structure of these heterogeneous landscapes called megacities, land consumption and spatial complexity needs to be quantified accurately. Remote sensing might be helpful in evaluating how the different land covers shape urban megaregions. The morphological landscape analysis allows establishing the analogies and the differences between patterns of cities and studying the symmetry, growth direction, linearity, complexity and compactness of the urban form. The main objective of this paper is to develop a new methodology to detect urbanized land of some megacities around the world (Tokyo, Mexico, Chicago, New York, London, Moscow, Sao Paulo and Shanghai) using Landsat 7 images.

  15. Comparative Analysis of Carbon Plasma in Arc and RF Reactors

    SciTech Connect

    Todorovic-Markovic, B.; Markovic, Z.; Mohai, I.; Szepvolgyi, J.

    2004-12-01

    Results on studies of molecular spectra emitted in the initial stages of fullerene formation during the processing of graphite powder in induction RF reactor and evaporation of graphite electrodes in arc reactor are presented in this paper. It was found that C2 radicals were dominant molecular species in both plasmas. C2 radicals have an important role in the process of fullerene synthesis. The rotational-vibrational temperatures of C2 and CN species were calculated by fitting the experimental spectra to the simulated ones. The results of optical emission study of C2 radicals generated in carbon arc plasma have shown that rotational temperature of C2 species depends on carbon concentration and current intensity significantly. The optical emission study of induction RF plasma and SEM analysis of graphite powder before and after plasma treatment have shown that evaporation of the processed graphite powder depends on feed rate and composition of gas phase significantly. Based on the obtained results, it was concluded that in the plasma region CN radicals could be formed by the reaction of C2 species with atomic nitrogen at smaller loads. At larger feed rate of graphite powder, CN species were produced by surface reaction of the hot carbon particles with nitrogen atoms. The presence of nitrogen in induction RF plasma reduces the fullerene yield significantly. The fullerene yield obtained in two different reactors was: 13% in arc reactor and 4.1% in induction RF reactor. However, the fullerene production rate was higher in induction RF reactor-6.4 g/h versus 1.7 g/h in arc reactor.

  16. Comparative analysis of positive and negative attitudes toward statistics

    NASA Astrophysics Data System (ADS)

    Ghulami, Hassan Rahnaward; Ab Hamid, Mohd Rashid; Zakaria, Roslinazairimah

    2015-02-01

    Many statistics lecturers and statistics education researchers are interested to know the perception of their students' attitudes toward statistics during the statistics course. In statistics course, positive attitude toward statistics is a vital because it will be encourage students to get interested in the statistics course and in order to master the core content of the subject matters under study. Although, students who have negative attitudes toward statistics they will feel depressed especially in the given group assignment, at risk for failure, are often highly emotional, and could not move forward. Therefore, this study investigates the students' attitude towards learning statistics. Six latent constructs have been the measurement of students' attitudes toward learning statistic such as affect, cognitive competence, value, difficulty, interest, and effort. The questionnaire was adopted and adapted from the reliable and validate instrument of Survey of Attitudes towards Statistics (SATS). This study is conducted among engineering undergraduate engineering students in the university Malaysia Pahang (UMP). The respondents consist of students who were taking the applied statistics course from different faculties. From the analysis, it is found that the questionnaire is acceptable and the relationships among the constructs has been proposed and investigated. In this case, students show full effort to master the statistics course, feel statistics course enjoyable, have confidence that they have intellectual capacity, and they have more positive attitudes then negative attitudes towards statistics learning. In conclusion in terms of affect, cognitive competence, value, interest and effort construct the positive attitude towards statistics was mostly exhibited. While negative attitudes mostly exhibited by difficulty construct.

  17. [Comparative analysis of quality labels of health websites].

    PubMed

    Padilla-Garrido, N; Aguado-Correa, F; Huelva-López, L; Ortega-Moreno, M

    2016-01-01

    The search for health related information on the Internet is a growing phenomenon, buts its main drawback is the lack of reliability of information consulted. The aim of this study was to analyse and compare existing quality labels of health websites. A cross-sectional study was performed by searching Medline, IBECS, Google, and Yahoo, in both English and Spanish, between 8 and 9 March, 2015. Different keywords were used depending on whether the search was conducted in medical databases or generic search engines. The quality labels were classified according to their origin, analysing their character, year of implementation, the existence of the accreditation process, number of categories, criteria and standards, possibility of self-assessment, number of levels of certification, certification scope, validity, analytical quality of content, fee, results of the accreditation process, application and number of websites granted the seal, and quality labels obtained by the accrediting organisation. Seven quality labels, five of Spanish origin (WMA, PAWS, WIS, SEAFORMEC and M21) and two international ones (HONcode and Health Web Site Accreditation), were analysed. There was disparity in carrying out the accreditation process, with some not detailing key aspects of the process, or providing incomplete, outdated, or even inaccurate information. The most rigorous guaranteed the level of confidence that the websites had in relation to the content of information, but none checked the quality of them. Although rigorous quality labels may become useful, the deficiencies in some of them cast doubt on their current usefulness. Copyright © 2015 SECA. Publicado por Elsevier España, S.L.U. All rights reserved.

  18. Comparative Analysis of Amaryllidaceae Alkaloids from Three Lycoris Species.

    PubMed

    Tian, Yongqiang; Zhang, Chunyun; Guo, Mingquan

    2015-12-07

    The major active constituents from Amaryllidaceae family were reported to be Amaryllidaceae alkaloids (AAs), which exhibited a wide spectrum of biological activities, such as anti-tumor, anti-viral, and acetyl-cholinesterase-inhibitory activities. In order to better understand their potential as a source of bioactive AAs and the phytochemical variations among three different species of Lycoris herbs, the HPLC fingerprint profiles of Lycoris aurea (L. aurea), L. radiata, and L. guangxiensis were firstly determined and compared using LC-UV and LC-MS/MS. As a result, 39 peaks were resolved and identified as AAs, of which nine peaks were found in common for all these three species, while the other 30 peaks could be revealed as characteristic AAs for L. aurea, L. radiata and L. guangxiensis, respectively. Thus, these AAs can be used as chemical markers for the identification and quality control of these plant species. To further reveal correlations between chemical components and their pharmaceutical activities of these species at the molecular level, the bioactivities of the total AAs from the three plant species were also tested against HepG2 cells with the inhibitory rate at 78.02%, 84.91% and 66.81% for L. aurea, L. radiata and L. guangxiensis, respectively. This study firstly revealed that the three species under investigation were different not only in the types of AAs, but also in their contents, and both contributed to their pharmacological distinctions. To the best of our knowledge, the current research provides the most detailed phytochemical profiles of AAs in these species, and offers valuable information for future valuation and exploitation of these medicinal plants.

  19. Comparative analysis in cereals of a key proline catabolism gene.

    PubMed

    Ayliffe, Michael A; Mitchell, Heidi J; Deuschle, Karen; Pryor, Anthony J

    2005-12-01

    Proline accumulation and catabolism play significant roles in adaptation to a variety of plant stresses including osmotic stress, drought, temperature, freezing, UV irradiation, heavy metals and pathogen infection. In this study, the gene Delta1 -pyrroline-5-carboxylate dehydrogenase (P5CDH), which catalyzes the second step in the conversion of proline to glutamate, is characterized in a number of cereal species. P5CDH genes from hexaploid wheat, Triticum turgidum (durum wheat), Aegilops tauschii, Triticum monococcum, barley, maize and rice were shown to be conserved in terms of gene structure and sequence, present as a single copy per haploid, non-polyploid genome and located in evolutionarily conserved linkage groups. A wheat cDNA sequence was shown by yeast complementation to encode a functional P5CDH activity. A divergently-transcribed rab7 gene was identified immediately 5' of P5CDH in all grasses examined, except rice. The rab7/P5CDH intergenic region in these species, which presumably encompasses 5' regulatory elements of both genes, showed a distinct pattern of sequence evolution with sequences in juxtaposition to each ORF conserved between barley, wheat, A. tauschii and T. monococcum. More distal 5' sequence in this intergenic region showed a higher rate of divergence, with no homology observed between these regions in the wheat and barley genomes. Maize and rice showed no similarity in regions 5' of P5CDH when compared with wheat, barley, and each other, apart from a 22 bp region of conserved non-coding sequence (CNS) that is similar to a proline response element identified in the promoter of the Arabidopsis proline dehydrogenase gene. A palindromic motif similar to this cereal CNS was also identified 5' of the Arabidopsis AtP5CDH gene showing conservation of this sequence in monocot and dicot lineages.

  20. COMPARATIVE ANALYSIS OF THE SHRINKAGE STRESS OF COMPOSITE RESINS

    PubMed Central

    Pereira, Rosana Aparecida; de Araujo, Paulo Amarante; Castañeda-Espinosa, Juan Carlos; Mondelli, Rafael Francisco Lia

    2008-01-01

    The aim of this study was to compare the shrinkage stress of composite resins by three methods. In the first method, composites were inserted between two stainless steel plates. One of the plates was connected to a 20 kgf load cell of a universal testing machine (EMIC-DL-500). In the second method, disk-shaped cavities were prepared in 2-mm-thick Teflon molds and filled with the different composites. Gaps between the composites and molds formed after polymerization were evaluated microscopically. In the third method, the wall-to-wall shrinkage stress of the resins that were placed in bovine dentin cavities was evaluated. The gaps were measured microscopically. Data were analyzed by one-way ANOVA and Tukey's test (α=0.05). The obtained contraction forces were: Grandio = 12.18 ± 0.428N; Filtek Z 250 = 11.80 ± 0.760N; Filtek Supreme = 11.80 ± 0.707 N; and Admira = 11.89 ± 0.647 N. The gaps obtained between composites and Teflon molds were: Filtek Z 250 = 0.51 ± 0.0357%; Filtek Supreme = 0.36 ± 0.0438%; Admira = 0.25 ± 0.0346% and Grandio = 0.16 ± 0.008%. The gaps obtained in wall-to-wall contraction were: Filtek Z 250 = 11.33 ± 2.160 μm; Filtek Supreme = 10.66 ± 1.211μm; Admira = 11.16 ± 2.041 μm and Grandio = 10.50 ± 1.224 μm. There were no significant differences among the composite resins obtained with the first (shrinkage stress generated during polymerization) and third method (wall-to-wall shrinkage). The composite resins obtained with the second method (Teflon method) differed significantly regarding gap formation. PMID:19089286

  1. Comparative and demographic analysis of orang-utan genomes.

    PubMed

    Locke, Devin P; Hillier, LaDeana W; Warren, Wesley C; Worley, Kim C; Nazareth, Lynne V; Muzny, Donna M; Yang, Shiaw-Pyng; Wang, Zhengyuan; Chinwalla, Asif T; Minx, Pat; Mitreva, Makedonka; Cook, Lisa; Delehaunty, Kim D; Fronick, Catrina; Schmidt, Heather; Fulton, Lucinda A; Fulton, Robert S; Nelson, Joanne O; Magrini, Vincent; Pohl, Craig; Graves, Tina A; Markovic, Chris; Cree, Andy; Dinh, Huyen H; Hume, Jennifer; Kovar, Christie L; Fowler, Gerald R; Lunter, Gerton; Meader, Stephen; Heger, Andreas; Ponting, Chris P; Marques-Bonet, Tomas; Alkan, Can; Chen, Lin; Cheng, Ze; Kidd, Jeffrey M; Eichler, Evan E; White, Simon; Searle, Stephen; Vilella, Albert J; Chen, Yuan; Flicek, Paul; Ma, Jian; Raney, Brian; Suh, Bernard; Burhans, Richard; Herrero, Javier; Haussler, David; Faria, Rui; Fernando, Olga; Darré, Fleur; Farré, Domènec; Gazave, Elodie; Oliva, Meritxell; Navarro, Arcadi; Roberto, Roberta; Capozzi, Oronzo; Archidiacono, Nicoletta; Della Valle, Giuliano; Purgato, Stefania; Rocchi, Mariano; Konkel, Miriam K; Walker, Jerilyn A; Ullmer, Brygg; Batzer, Mark A; Smit, Arian F A; Hubley, Robert; Casola, Claudio; Schrider, Daniel R; Hahn, Matthew W; Quesada, Victor; Puente, Xose S; Ordoñez, Gonzalo R; López-Otín, Carlos; Vinar, Tomas; Brejova, Brona; Ratan, Aakrosh; Harris, Robert S; Miller, Webb; Kosiol, Carolin; Lawson, Heather A; Taliwal, Vikas; Martins, André L; Siepel, Adam; Roychoudhury, Arindam; Ma, Xin; Degenhardt, Jeremiah; Bustamante, Carlos D; Gutenkunst, Ryan N; Mailund, Thomas; Dutheil, Julien Y; Hobolth, Asger; Schierup, Mikkel H; Ryder, Oliver A; Yoshinaga, Yuko; de Jong, Pieter J; Weinstock, George M; Rogers, Jeffrey; Mardis, Elaine R; Gibbs, Richard A; Wilson, Richard K

    2011-01-27

    'Orang-utan' is derived from a Malay term meaning 'man of the forest' and aptly describes the southeast Asian great apes native to Sumatra and Borneo. The orang-utan species, Pongo abelii (Sumatran) and Pongo pygmaeus (Bornean), are the most phylogenetically distant great apes from humans, thereby providing an informative perspective on hominid evolution. Here we present a Sumatran orang-utan draft genome assembly and short read sequence data from five Sumatran and five Bornean orang-utan genomes. Our analyses reveal that, compared to other primates, the orang-utan genome has many unique features. Structural evolution of the orang-utan genome has proceeded much more slowly than other great apes, evidenced by fewer rearrangements, less segmental duplication, a lower rate of gene family turnover and surprisingly quiescent Alu repeats, which have played a major role in restructuring other primate genomes. We also describe a primate polymorphic neocentromere, found in both Pongo species, emphasizing the gradual evolution of orang-utan genome structure. Orang-utans have extremely low energy usage for a eutherian mammal, far lower than their hominid relatives. Adding their genome to the repertoire of sequenced primates illuminates new signals of positive selection in several pathways including glycolipid metabolism. From the population perspective, both Pongo species are deeply diverse; however, Sumatran individuals possess greater diversity than their Bornean counterparts, and more species-specific variation. Our estimate of Bornean/Sumatran speciation time, 400,000 years ago, is more recent than most previous studies and underscores the complexity of the orang-utan speciation process. Despite a smaller modern census population size, the Sumatran effective population size (N(e)) expanded exponentially relative to the ancestral N(e) after the split, while Bornean N(e) declined over the same period. Overall, the resources and analyses presented here offer new

  2. Comparative proteome analysis of egg yolk plasma proteins during storage.

    PubMed

    Gao, Dan; Qiu, Ning; Liu, Yaping; Ma, Meihu

    2017-06-01

    Physical changes such as chicken egg white thinning and egg yolk flattening occur during storage, implying a decline in egg quality. To reveal the deteriorative process related to chicken egg internal quality, a comparative proteomic method was used in this study to analyze the alterations in egg yolk plasma proteins at different storage times (0, 20 and 40 days) under an ambient temperature of 22 ± 2 °C. Using two-dimensional electrophoresis followed by matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry, 33 protein spots representing 12 proteins were identified with significant (P < 0.05) alterations in abundance at different storage times. The proteins that showed significant changes in abundance included serum albumin, vitellogenin fragments, IgY chains, ovalbumin, ovoinhibitor, α2 -macroglobulin-like protein 1-like, hemopexin, transthyretin, apolipoprotein A-I and β2 -glycoprotein I precursor. Accelerating degradation for most egg yolk plasma proteins was observed after prolonged storage (from day 20 to day 40). It is likely that the increased degradation of protease inhibitors such as ovoinhibitor and α2 -macroglobulin-like protein 1-like during prolonged storage lead to an imbalance of protease and antiprotease in egg yolk, which may play a key role in the degradation of egg yolk proteins. These findings will provide an insight into the effects of storage on egg yolk protein changes and give a deeper understanding of the deteriorative process of chicken egg yolk. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  3. Comparative analysis of human and bovine teeth: radiographic density.

    PubMed

    Tanaka, Jefferson Luis Oshiro; Medici Filho, Edmundo; Salgado, José Antônio Pereira; Salgado, Miguel Angel Castillo; Moraes, Luiz Cesar de; Moraes, Mari Eli Leonelli de; Castilho, Julio Cezar de Melo

    2008-01-01

    Since bovine teeth have been used as substitutes for human teeth in in vitro dental studies, the aim of this study was to compare the radiographic density of bovine teeth with that of human teeth to evaluate their usability for radiographic studies. Thirty bovine and twenty human teeth were cut transversally in 1 millimeter-thick slices. The slices were X-rayed using a digital radiographic system and an intraoral X-ray machine at 65 kVp and 7 mA. The exposure time (0.08 s) and the target-sensor distance (40 cm) were standardized for all the radiographs. The radiographic densities of the enamel, coronal dentin and radicular dentin of each slice were obtained separately using the 'histogram' tool of Adobe Photoshop 7.0 software. The mean radiographic densities of the enamel, coronal dentin and radicular dentin were calculated by the arithmetic mean of the slices of each tooth. One-way ANOVA demonstrated statistically significant differences for the densities of bovine and human enamel (p < 0.05) and for bovine and human coronal dentin (p < 0.05). No statistically significant differences were found for the bovine and human radicular dentin (p > 0.05). Based on the results, the authors concluded that: a) the radiographic density of bovine enamel is significantly higher than that of human enamel; b) the radiodensity of bovine coronal dentin is statistically lower than the radiodensity of human coronal dentin; bovine radicular dentin is also less radiodense than human radicular dentin, although this difference was not statistically significant; c) bovine teeth should be used with care in radiographic in vitro studies.

  4. Array comparative genomic hybridization analysis of olfactory neuroblastoma.

    PubMed

    Guled, Mohamed; Myllykangas, Samuel; Frierson, Henry F; Mills, Stacey E; Knuutila, Sakari; Stelow, Edward B

    2008-06-01

    Olfactory neuroblastoma is an unusual neuroectodermal malignancy, which is thought to arise at the olfactory membrane of the sinonasal tract. Due to its rarity, little is understood regarding its molecular and cytogenetic abnormalities. The aim of the current study is to identify specific DNA copy number changes in olfactory neuroblastoma. Thirteen dissected tissue samples were analyzed using array comparative genomic hybridization. Our results show that gene copy number profiles of olfactory neuroblastoma samples are complex. The most frequent changes included gains at 7q11.22-q21.11, 9p13.3, 13q, 20p/q, and Xp/q, and losses at 2q31.1, 2q33.3, 2q37.1, 6q16.3, 6q21.33, 6q22.1, 22q11.23, 22q12.1, and Xp/q. Gains were more frequent than losses, and high-stage tumors showed more alterations than low-stage olfactory neuroblastoma. Frequent changes in high-stage tumors were gains at 13q14.2-q14.3, 13q31.1, and 20q11.21-q11.23, and loss of Xp21.1 (in 66% of cases). Gains at 5q35, 13q, and 20q, and losses at 2q31.1, 2q33.3, and 6q16-q22, were present in 50% of cases. The identified regions of gene copy number change have been implicated in a variety of tumors, especially carcinomas. In addition, our results indicate that gains in 20q and 13q may be important in the progression of this cancer, and that these regions possibly harbor genes with functional relevance in olfactory neuroblastoma.

  5. Comparative in vitro analysis of topical hemostatic agents.

    PubMed

    Wagner, W R; Pachence, J M; Ristich, J; Johnson, P C

    1996-12-01

    Hemostatic agents are broadly utilized across the surgical specialties. While specific characteristics desirable for individual applications may vary, these agents generally are expected to aid the patient's coagulation system in the rapid development of an occlusive clot. Six commonly utilized hemostatic agents were quantitatively compared in terms of their ability to mediate platelet aggregation, deposition and activation, and initiate gross clot formation in a series of in vitro tests. Three types of collagen sponges (Actifoam, Helistat, Instat), microfibrillar collagen (Avitene), a gelatin sponge (Gelfoam), and oxidized regenerated cellulose (Surgicel) were studied. Platelet aggregation: Citrated platelet rich plasma (PRP) was contacted with hemostatic agents both with and without thrombin in a stirred cuvette and the platelet count was measured over 5 min. Platelet deposition: To approximate arterial wounds, PRP was perfused in a controlled manner through hemostatic agents, and the effluent platelet count was measured over time. Platelet activation: ATP secretion from PRP contacted with hemostatic agents in a stirred cuvette was measured at 1 and 5 min. Clot formation: The clotting time of nonanticoagulated whole blood contacted with the hemostatic agents was measured. Materials which depleted platelets most rapidly and effectively in the perfusion system (Avitene, Helistat, and Actifoam) were also the most effective inducers of platelet aggregation and secretion. Clot formation (likely to be platelet dependent) was also more rapid in this group. An overall activity ranking combined the relative performance of each hemostatic agent on the various tests: Actifoam approximately Avitene > Helistat > Gelfoam > Instat > Surgicel. The activity ranking generally reflects the materials used in these agents (collagen > gelatin > oxidized regenerated cellulose), as well as their processing (chemical crosslinking in collagen sponges may lower activity). Such in vitro

  6. Comparative Analysis of Six Lagerstroemia Complete Chloroplast Genomes

    PubMed Central

    Xu, Chao; Dong, Wenpan; Li, Wenqing; Lu, Yizeng; Xie, Xiaoman; Jin, Xiaobai; Shi, Jipu; He, Kaihong; Suo, Zhili

    2017-01-01

    Crape myrtles are economically important ornamental trees of the genus Lagerstroemia L. (Lythraceae), with a distribution from tropical to northern temperate zones. They are positioned phylogenetically to a large subclade of rosids (in the eudicots) which contain more than 25% of all the angiosperms. They commonly bloom from summer till fall and are of significant value in city landscape and environmental protection. Morphological traits are shared inter-specifically among plants of Lagerstroemia to certain extent and are also influenced by environmental conditions and different developmental stages. Thus, classification of plants in Lagerstroemia at species and cultivar levels is still a challenging task. Chloroplast (cp) genome sequences have been proven to be an informative and valuable source of cp DNA markers for genetic diversity evaluation. In this study, the complete cp genomes of three Lagerstroemia species were newly sequenced, and three other published cp genome sequences of Lagerstroemia were retrieved for comparative analyses in order to obtain an upgraded understanding of the application value of genetic information from the cp genomes. The six cp genomes ranged from 152,049 bp (L. subcostata) to 152,526 bp (L. speciosa) in length. We analyzed nucleotide substitutions, insertions/deletions, and simple sequence repeats in the cp genomes, and discovered 12 relatively highly variable regions that will potentially provide plastid markers for further taxonomic, phylogenetic, and population genetics studies in Lagerstroemia. The phylogenetic relationships of the Lagerstroemia taxa inferred from the datasets from the cp genomes obtained high support, indicating that cp genome data may be useful in resolving relationships in this genus. PMID:28154574

  7. Comparative genomic analysis of the Tribolium immune system

    PubMed Central

    Zou, Zhen; Evans, Jay D; Lu, Zhiqiang; Zhao, Picheng; Williams, Michael; Sumathipala, Niranji; Hetru, Charles; Hultmark, Dan; Jiang, Haobo

    2007-01-01

    Background Tribolium castaneum is a species of Coleoptera, the largest and most diverse order of all eukaryotes. Components of the innate immune system are hardly known in this insect, which is in a key phylogenetic position to inform us about genetic innovations accompanying the evolution of holometabolous insects. We have annotated immunity-related genes and compared them with homologous molecules from other species. Results Around 300 candidate defense proteins are identified based on sequence similarity to homologs known to participate in immune responses. In most cases, paralog counts are lower than those of Drosophila melanogaster or Anopheles gambiae but are substantially higher than those of Apis mellifera. The genome contains probable orthologs for nearly all members of the Toll, IMD, and JAK/STAT pathways. While total numbers of the clip-domain serine proteinases are approximately equal in the fly (29), mosquito (32) and beetle (30), lineage-specific expansion of the family is discovered in all three species. Sixteen of the thirty-one serpin genes form a large cluster in a 50 kb region that resulted from extensive gene duplications. Among the nine Toll-like proteins, four are orthologous to Drosophila Toll. The presence of scavenger receptors and other related proteins indicates a role of cellular responses in the entire system. The structures of some antimicrobial peptides drastically differ from those in other orders of insects. Conclusion A framework of information on Tribolium immunity is established, which may serve as a stepping stone for future genetic analyses of defense responses in a nondrosophiline genetic model insect. PMID:17727709

  8. A comparative effectiveness analysis of three continuous glucose monitors.

    PubMed

    Damiano, Edward R; El-Khatib, Firas H; Zheng, Hui; Nathan, David M; Russell, Steven J

    2013-02-01

    To compare three continuous glucose monitoring (CGM) devices in subjects with type 1 diabetes under closed-loop blood glucose (BG) control. Six subjects with type 1 diabetes (age 52 ± 14 years, diabetes duration 32 ± 14 years) each participated in two 51-h closed-loop BG control experiments in the hospital. Venous plasma glucose (PG) measurements (GlucoScout, International Biomedical) obtained every 15 min (2,360 values) were paired in time with corresponding CGM glucose (CGMG) measurements obtained from three CGM devices, the Navigator (Abbott Diabetes Care), the Seven Plus (DexCom), and the Guardian (Medtronic), worn simultaneously by each subject. Errors in paired PG-CGMG measurements and data reporting percentages were obtained for each CGM device. The Navigator had the best overall accuracy, with an aggregate mean absolute relative difference (MARD) of all paired points of 11.8 ± 11.1% and an average MARD across all 12 experiments of 11.8 ± 3.8%. The Seven Plus and Guardian produced aggregate MARDs of all paired points of 16.5 ± 17.8% and 20.3 ± 18.0%, respectively, and average MARDs across all 12 experiments of 16.5 ± 6.7% and 20.2 ± 6.8%, respectively. Data reporting percentages, a measure of reliability, were 76% for the Seven Plus and nearly 100% for the Navigator and Guardian. A comprehensive head-to-head-to-head comparison of three CGM devices for BG values from 36 to 563 mg/dL revealed marked differences in performance characteristics that include accuracy, precision, and reliability. The Navigator outperformed the other two in these areas.

  9. Adrenocortical adenoma and carcinoma: histopathological and molecular comparative analysis.

    PubMed

    Stojadinovic, Alexander; Brennan, Murray F; Hoos, Axel; Omeroglu, Atilla; Leung, Denis H Y; Dudas, Maria E; Nissan, Aviram; Cordon-Cardo, Carlos; Ghossein, Ronald A

    2003-08-01

    We compared histomorphological features and molecular expression profiles of adrenocortical adenomas (ACAd) and carcinomas (ACCa). A critical histopathological review (mean, 11 slides per patient) was conducted of 37 ACAd and 67 ACCa. Paraffin-embedded tissue cores of ACAd (n = 33) and ACCa (n = 38) were arrayed in triplicate on tissue microarrays. Expression profiles of p53, mdm-2, p21, Bcl-2, cyclin D1, p27, and Ki-67 were investigated by immunohistochemistry and correlated with histopathology and patient outcome using standard statistical methodology. Median follow-up period was 5 years. Tumor necrosis, atypical mitoses, and >1 mitosis per 50 high-power fields were factors that were highly specific for ACCa (P <.001). Number (0 to 4) of unfavorable markers [Ki-67 (+), p21 (+), p27 (+), mdm-2(-)] expressed was significantly associated with mitotic activity and morphologic index (i.e., number of adverse morphologic features) and highly predictive of malignancy (P <.001). Ki-67 overexpression occurred in 0 ACAd and 36% ACCa (P <.001) and was significantly associated with mitotic rate and unfavorable morphologic index (P <.001). Tumor necrosis, atypical mitoses, >5 mitoses per 50 high-power fields, sinusoidal invasion, histologic index of >5, and presence of more than two unfavorable molecular markers were associated significantly with metastasis in ACCa. Well-established histopathologic criteria and Ki-67 can specifically distinguish ACCAd from ACCa. Tumor cell proliferation (Ki-67) correlates with mitotic activity and morphologic index. Tumor morphology is a better predictor of metastatic risk in ACCa than current immunohistochemistry-detected cell cycle regulatory and proliferation-associated proteins.

  10. Analysis of T-RFLP data using analysis of variance and ordination methods: a comparative study.

    PubMed

    Culman, S W; Gauch, H G; Blackwood, C B; Thies, J E

    2008-09-01

    The analysis of T-RFLP data has developed considerably over the last decade, but there remains a lack of consensus about which statistical analyses offer the best means for finding trends in these data. In this study, we empirically tested and theoretically compared ten diverse T-RFLP datasets derived from soil microbial communities using the more common ordination methods in the literature: principal component analysis (PCA), nonmetric multidimensional scaling (NMS) with Sørensen, Jaccard and Euclidean distance measures, correspondence analysis (CA), detrended correspondence analysis (DCA) and a technique new to T-RFLP data analysis, the Additive Main Effects and Multiplicative Interaction (AMMI) model. Our objectives were i) to determine the distribution of variation in T-RFLP datasets using analysis of variance (ANOVA), ii) to determine the more robust and informative multivariate ordination methods for analyzing T-RFLP data, and iii) to compare the methods based on theoretical considerations. For the 10 datasets examined in this study, ANOVA revealed that the variation from Environment main effects was always small, variation from T-RFs main effects was large, and variation from T-RFxEnvironment (TxE) interactions was intermediate. Larger variation due to TxE indicated larger differences in microbial communities between environments/treatments and thus demonstrated the utility of ANOVA to provide an objective assessment of community dissimilarity. The comparison of statistical methods typically yielded similar empirical results. AMMI, T-RF-centered PCA, and DCA were the most robust methods in terms of producing ordinations that consistently reached a consensus with other methods. In datasets with high sample heterogeneity, NMS analyses with Sørensen and Jaccard distance were the most sensitive for recovery of complex gradients. The theoretical comparison showed that some methods hold distinct advantages for T-RFLP analysis, such as estimations of variation

  11. Comparative genomic analysis of the compound Brassica napus Rf locus.

    PubMed

    Gaborieau, Lydiane; Brown, Gregory G

    2016-10-26

    The plant trait of cytoplasmically-inherited male sterility (CMS) and its suppression by nuclear restorer-of-fertility (Rf) genes can be viewed as a genetic arms race between the mitochondrial and nuclear genomes. Most nuclear Rf genes have been shown to encode P-type pentatricopeptide repeat proteins (PPRs). Phylogenetic analysis of P-class PPRs from sequenced plants genomes has shown that Rf-proteins cluster in a distinct clade of P-class PPRs, RFL-PPRs, that display hallmarks of positive evolutionary selection. Genes encoding RFL-PPRs (RFLs) within a given plant genome tend to be closely related both in sequence and position, but a detailed understanding of how such species-specific expansion occurs is lacking. In the canola, (oilseed rape) species Brassica napus, previous work has indicated the nuclear restorer genes for the two native forms of CMS, Rfn (for nap CMS) and Rfp (pol CMS), represent alternate haplotypes, or alleles, of a single nuclear locus. Fine genetic mapping indicates that Rfn does indeed localize to the same genomic region as Rfp. We find this region is enriched in RFL genes, three of which, based on their position and expression, represent potential candidates for Rfn; one of these genes, designated PPR4, is a preferred candidate in that it is not expressed in the nap CMS line. Comparison of the corresponding regions of the genomes of B. rapa, B. oleracea, Arabidopsis thaliana and A. lyrata provides insight into the expansion of this group of RFL genes in different lines of evolutionary descent. Unlike other nuclear restorer loci containing multiple RFL genes, the RFL genes in the Rf region of B. napus are not present in tandem arrays but rather are dispersed in genomic location. The genes do not share similar flanking non-coding regions and do not contain introns, indicating that they have duplicated primarily through a retrotransposition-mediated process. In contrast, segmental duplication has been responsible for the distribution of the

  12. Comparative Analysis of Uninhibited and Constrained Avian Wing Aerodynamics

    NASA Astrophysics Data System (ADS)

    Cox, Jordan A.

    The flight of birds has intrigued and motivated man for many years. Bird flight served as the primary inspiration of flying machines developed by Leonardo Da Vinci, Otto Lilienthal, and even the Wright brothers. Avian flight has once again drawn the attention of the scientific community as unmanned aerial vehicles (UAV) are not only becoming more popular, but smaller. Birds are once again influencing the designs of aircraft. Small UAVs operating within flight conditions and low Reynolds numbers common to birds are not yet capable of the high levels of control and agility that birds display with ease. Many researchers believe the potential to improve small UAV performance can be obtained by applying features common to birds such as feathers and flapping flight to small UAVs. Although the effects of feathers on a wing have received some attention, the effects of localized transient feather motion and surface geometry on the flight performance of a wing have been largely overlooked. In this research, the effects of freely moving feathers on a preserved red tailed hawk wing were studied. A series of experiments were conducted to measure the aerodynamic forces on a hawk wing with varying levels of feather movement permitted. Angle of attack and air speed were varied within the natural flight envelope of the hawk. Subsequent identical tests were performed with the feather motion constrained through the use of externally-applied surface treatments. Additional tests involved the study of an absolutely fixed geometry mold-and-cast wing model of the original bird wing. Final tests were also performed after applying surface coatings to the cast wing. High speed videos taken during tests revealed the extent of the feather movement between wing models. Images of the microscopic surface structure of each wing model were analyzed to establish variations in surface geometry between models. Recorded aerodynamic forces were then compared to the known feather motion and surface

  13. A comparative analysis of perspectives of Mileva Maric Einstein

    NASA Astrophysics Data System (ADS)

    Barnett, Carol C.

    This dissertation examines the controversy surrounding Mileva Maric Einstein and the allegations subsequent to the publication of love letters during the time that Mileva Maric and Albert Einstein were students and during the early years of their marriage. It also examines the role of women in science from a historical perspective. Chapter One surveys the history of women in science from antiquity to the late nineteenth century and the patterns of gender related and restricting practices such as education, publication, the problem of mentoring and the issue of the lack of historical recognition. Chapter Two provides a comparative analyses between the lives of Mileva Maric Einstein and Marie Sklodowska Curie. Both had very similar social and educational backgrounds yet Marie Curie was able to work and publish jointly with her husband and received (although belatedly) international recognition for her work. On the other hand, Mileva Maric Einstein was never able to complete her degree and lived a life of obscurity and unfulfilled professional dreams. Both highly educated and intelligent women, but with drastically different outcomes in their professional and personal lives. Chapter Three examines the one book devoted to the life of Mileva Maric Einstein, Im Schatten Albert Einsteins: Das Tragische Leben der Mileva Einstein-Maric (In The Shadow of Albert Einstein: The Tragic Life of Mileva Maric), by Desanka Trbuhovic-Gjuric, Paul Haupt Publishers, 1985. It addresses the subjective as well as constructive and destructive criticisms of the various critical camps and provides examples of the statements made by the author which prompted a controversy within the academic and scientific communities. Appropriate responses are provided from various members of the scientific community to reflect the diversity of opinion and the intensity of the debate. Chapter Four addresses the problem of historicity and various interpretations of evidence which might suggest that the role

  14. Comparative analysis between Payen and Daedalia Planum lava fields

    NASA Astrophysics Data System (ADS)

    Giacomini, Lorenza; Massironi, Matteo; Pasquarè, Giorgio; Carli, Cristian; Martellato, Elena; Frigeri, Alessandro; Cremonese, Gabriele; Bistacchi, Andrea; Federico, Costanzo

    The Payen volcanic complex is a large Quaternary fissural structure belonging to the back-arc extensional area of the Andes in the Mendoza Province (Argentina). From the eastern portion of this volcanic structure huge pahoehoe lava flows were emitted, extending more than 180 km from the feeding vents. These huge flows propagated over the nearly flat surface of the Pampean foreland (ca 0.3° slope). The very low viscosity of the olivine basalt lavas, coupled with the inflation process are the most probable explanation for their considerable length. In an inflation process a thin viscoelastic crust, produced at an early stage, is later inflated by the underlying fluid core, which remains hot and fluid thanks to the thermal-shield effect of the crust. The inflation shows some typical morphological fingerprints like tumuli, lava lobes, lava rises and lava ridges. In order to compare the morphology of the Argentinean Payen flows with lava flows on Mars, MOLA, THEMIS, MOC, MRO/HIRISE, and MEX/OMEGA data have been analysed, providing a multi-scale characterisation of Martian flows. Mars Global Surveyor/MOLA data were used to investigate the topographic environment over which flows propagated on Mars in order to detect very low angle slopes where possibly inflation processes could have developed. Then Mars Odyssey/THEMIS and Mars Global Surveyor's MOC data were used to detect Martian lava flows with inflation "fingerprints", whereas OMEGA data were used to obtain some inferences about their composition. Finally the MRO/HIRISE images recently acquired, can provide further details and constraints on surface morphologies and lava fronts. All these data were used to analyze Daedalia Planum lava field, at about 300 km southwest of Arsia Mons, and clear morphological similarities with the longest flows of the Payen lava fields were found. These striking morphological analogies suggest that inflation process is quite common also for the Daedalia field. This is also supported by

  15. Pharmacological interventions for melanoma: Comparative analysis using bayesian meta-analysis

    PubMed Central

    Gao, Guozhen; Yang, Zheng; Guo, Shuzhong; Yue, Bo; Qiu, Jianhua

    2016-01-01

    We conducted a network meta-analysis in order to compare different strategies for managing melanoma patients. Electronic databases were searched for eligible randomized trials that compared different strategies in efficacy and tolerability. Five interventions were associated with a significant improvement in PFS over chemotherapy (all HR < 1): Ipilimumab, Tremelimumab, Nivolumab, Pembrolizumab 2 mg/kg and Ipilimumab + Nivolumab. Three interventions exhibited significantly improved OS results over chemotherapy (all HR < 1): Ipilimumab, Nivolumab and Ipilimumab + Chemotherapy. Four interventions were superior to chemotherapy in CR and PR (all OR > 1): Nivolumab, Pembrolizumab 10 mg/kg, Pembrolizumab 2 mg/kg and Ipilimumab + Nivolumab. However, the other seven interventions were associated with an increased risk of pruritus compared to chemotherapy (all OR > 1). Ipilimumab, Tremelimumab, Ipilimumab + Nivolumab and Ipilimumab + Chemotherapy might result in a higher risk of diarrhea compared to chemotherapy (all OR > 1). Immune checkpoint therapy or combined interventions might be more effective than chemotherapy for managing melanoma patients. However, chemotherapy appears to be more tolerable than these combined strategies with respect to adverse events. PMID:27764796

  16. International Commercial Remote Sensing Practices and Policies: A Comparative Analysis

    NASA Astrophysics Data System (ADS)

    Stryker, Timothy

    sensing satellite industry. In commissioning this study, NOAA's goal was to better understand the role that U.S. Government policies and regulations have in shaping the prospects for emerging commercial remote sensing satellite firms. The study assessed the risks against broader trends in the larger U.S. remote sensing industry and geospatial technology and effective policy implementation. The Department of Commerce is working with NOAA licensees to identify foreign actions which could restrict market access by U.S. firms, and seeking to provide a "level playing field" for U.S. service providers. The Department of Commerce has dedicated new resources to its licensing activities. In Fiscal Year 2002, the Department obtained 1.2 million in funding to support the NOAA program, through staff, equipment, technical support, constituent outreach, and market and policy studies. To better understand the market and make more well-informed licensing decisions, NOAA is participating in a broad-based market study effort under the direction of the American Society for Photogrammetry and Remote Sensing (ASPRS) and NASA's Commercial Remote Sensing Program. This study is providing long-term analysis of the commercial remote sensing industry. It is being supported by interviews with industry and government experts, a web-based survey, and a thorough review and analysis of related literature. The project should more clearly determine future remote sensing needs and requirements, and maximize the industry's baselines, standards, and socio-economic potential. NOAA, through its participation in this study, has gained important new insights into the status and future trends of this industry. The study's initial findings estimate 2001 industry revenue at 2 billion, growing at 13% per year, to an approximate level of 6 billion in 2010 (in constant, calendar year 2000 dollars). Currently, across all sectors, the most active market segments are in nati onal /glo bal security, mapping

  17. rCAD: A Novel Database Schema for the Comparative Analysis of RNA

    PubMed Central

    Ozer, Stuart; Doshi, Kishore J.; Xu, Weijia; Gutell, Robin R.

    2013-01-01

    Beyond its direct involvement in protein synthesis with mRNA, tRNA, and rRNA, RNA is now being appreciated for its significance in the overall metabolism and regulation of the cell. Comparative analysis has been very effective in the identification and characterization of RNA molecules, including the accurate prediction of their secondary structure. We are developing an integrative scalable data management and analysis system, the RNA Comparative Analysis Database (rCAD), implemented with SQL Server to support RNA comparative analysis. The platformagnostic database schema of rCAD captures the essential relationships between the different dimensions of information for RNA comparative analysis datasets. The rCAD implementation enables a variety of comparative analysis manipulations with multiple integrated data dimensions for advanced RNA comparative analysis workflows. In this paper, we describe details of the rCAD schema design and illustrate its usefulness with two usage scenarios. PMID:24772454

  18. Comparative Analysis of Enrollment and Financial Strength of Private Institutions. AIR 1989 Annual Forum Paper.

    ERIC Educational Resources Information Center

    Glover, Robert H.; Mills, Michael R.

    A research design, decision support system, and results of a comparative analysis of enrollment and financial strength (of private institutions granting masters and doctoral degrees) are presented. Cluster analysis, discriminant analysis, multiple regression, and an interactive decision support system are used to compare the enrollment and…

  19. a Study of New Optical Materials. I. Crystal-Chemical Development of New Optical Frequency Converters. I. New Hosts for Chromium

    NASA Astrophysics Data System (ADS)

    Schaffers, Kathleen Irene

    The emphasis of this work has been in two areas of optical materials--the crystal-chemical development of new optical frequency converters and the synthesis and study of the new hosts for Cr^{3+} luminescence and lasing. A simple method has been developed to identify promising frequency-doubling materials containing triangular oxoanions by estimation of nonlinear susceptibilities. Implementation of this method and its results have generated predictive capabilities in determining the relationships among crystal structure, nonlinear properties, and threshold powers. The new noncentrosymmetric borate SrLiB_9O _{15} is discussed; its structure is built from a 3-dimensional condensation of B_3O_7 units with channels alternately filled with Sr and Li atoms. From these studies, a prescription for new pyroborate frequency converters has been developed. The material CdCl _2C_3H_7 NO_2, has been synthesized and structurally characterized by single-crystal X-ray diffraction. Three new alkaline-earth beryllium borates, built from unique 2- and 3-dimensional networks and frameworks, have been identified. The structure of SrBe_2 (BO_3)_2 consists of layers of composition (Be_2(BO _3)_2]^{2- } interleaved by Sr atoms. CaBeB_2 O_5 is constructed from a CaO_9 polyhedral network and a beryllium borate network. In BaBe_2(BO _3)_2 the structure is composed of a beryllium borate framework intermingled with a Ba-centered dodecahedral framework. Several materials with potential as hosts for Cr^{3+} lasing have been analyzed. The structural study of the laser host LiSrAlF _6 revealed the distortions at the Al site that contribute to the unique optical properties of the Cr^{3+}-doped crystals. The family of solid state oxide A_6MM ^'(BO_3) _6 is one of the largest families of oxide reported to date. Metal site preferences, disorder, solid solubility, and the interrelationship between this structure and the layered structure type of Ba_3Sc(BO _3)_3 are detailed. An optimal synthetic

  20. A Comparative Evaluation of Mixed Dentition Analysis on Reliability of Cone Beam Computed Tomography Image Compared to Plaster Model

    PubMed Central

    Gowd, Snigdha; Shankar, T; Dash, Samarendra; Sahoo, Nivedita; Chatterjee, Suravi; Mohanty, Pritam

    2017-01-01

    Aims and Objective: The aim of the study was to evaluate the reliability of cone beam computed tomography (CBCT) obtained image over plaster model for the assessment of mixed dentition analysis. Materials and Methods: Thirty CBCT-derived images and thirty plaster models were derived from the dental archives, and Moyer's and Tanaka-Johnston analyses were performed. The data obtained were interpreted and analyzed statistically using SPSS 10.0/PC (SPSS Inc., Chicago, IL, USA). Descriptive and analytical analysis along with Student's t-test was performed to qualitatively evaluate the data and P < 0.05 was considered statistically significant. Results: Statistically, significant results were obtained on data comparison between CBCT-derived images and plaster model; the mean for Moyer's analysis in the left and right lower arch for CBCT and plaster model was 21.2 mm, 21.1 mm and 22.5 mm, 22.5 mm, respectively. Conclusion: CBCT-derived images were less reliable as compared to data obtained directly from plaster model for mixed dentition analysis. PMID:28852639

  1. A Comparative Evaluation of Mixed Dentition Analysis on Reliability of Cone Beam Computed Tomography Image Compared to Plaster Model.

    PubMed

    Gowd, Snigdha; Shankar, T; Dash, Samarendra; Sahoo, Nivedita; Chatterjee, Suravi; Mohanty, Pritam

    2017-01-01

    The aim of the study was to evaluate the reliability of cone beam computed tomography (CBCT) obtained image over plaster model for the assessment of mixed dentition analysis. Thirty CBCT-derived images and thirty plaster models were derived from the dental archives, and Moyer's and Tanaka-Johnston analyses were performed. The data obtained were interpreted and analyzed statistically using SPSS 10.0/PC (SPSS Inc., Chicago, IL, USA). Descriptive and analytical analysis along with Student's t-test was performed to qualitatively evaluate the data and P < 0.05 was considered statistically significant. Statistically, significant results were obtained on data comparison between CBCT-derived images and plaster model; the mean for Moyer's analysis in the left and right lower arch for CBCT and plaster model was 21.2 mm, 21.1 mm and 22.5 mm, 22.5 mm, respectively. CBCT-derived images were less reliable as compared to data obtained directly from plaster model for mixed dentition analysis.

  2. Comparative Genome Analysis in the Integrated Microbial Genomes(IMG) System

    SciTech Connect

    Kyrpides, Nikos C.; Markowitz, Victor M.

    2006-03-01

    Comparative genome analysis is critical for the effectiveexploration of a rapidly growing number of complete and draft sequencesfor microbial genomes. The Integrated Microbial Genomes (IMG) system(img.jgi.doe.gov) has been developed as a community resource thatprovides support for comparative analysis of microbial genomes in anintegrated context. IMG allows users to navigate the multidimensionalmicrobial genome data space and focus their analysis on a subset ofgenes, genomes, and functions of interest. IMG provides graphicalviewers, summaries and occurrence profile tools for comparing genes,pathways and functions (terms) across specific genomes. Genes can befurther examined using gene neighborhoods and compared with sequencealignment tools.

  3. Qualitative Comparative Analysis, Necessary Conditions, and Limited Diversity: Some Problematic Consequences of Schneider and Wagemann's Enhanced Standard Analysis

    ERIC Educational Resources Information Center

    Cooper, Barry; Glaesser, Judith

    2016-01-01

    We discuss a recent development in the set theoretic analysis of data sets characterized by limited diversity. Ragin, in developing his Qualitative Comparative Analysis (QCA), developed a standard analysis that produces parsimonious, intermediate, and complex Boolean solutions of truth tables. Schneider and Wagemann argue this standard analysis…

  4. [Comparative analysis of trace elements in five marine-derived shell TCM using multivariate statistical analysis].

    PubMed

    Zhang, Shuai; Chen, Zhen; Fu, Yu-qiang; Gong, Hui-li; Guan, Hua-shi; Liu, Hong-bing

    2015-11-01

    A comparable study were carried out by determination of trace elements on five marine-derived shell traditional Chinese medicine (TCM) (Ostreae Concha, Haliotidis Concha, Margaritifera Concha, Meretricis Concha, and Arcae Concha), which were recorded in the Chinese Pharmacopoeia (2010 version). Seven trace elements in 51 batches of this type of shell TCM were analyzed by Inductively Coupled Plasma Mass Spectrometry (ICP-MS), combined with principal component analysis (PCA) methods. The content of element Se, which exhibited significant differences among different drugs, could be used as a key element to distinguish this type of drugs. Meanwhile, the contents of elements Co, Cu, Mo, and Ba in Haliotidis Concha, Co and As in Margaritifera Concha, Mo and As in Meretricis Concha, Mo, As, and Ba in Arcae Concha, and Zn in Meretricis Concha were relatively stable. In the PCA plot, Arcae Concha and Meretricis Concha could be efficiently distinguished from Ostreae Concha together with Haliotidis Concha, and Margaritifera Concha. The results also showed a correlation with their medicinal function. In conclusion, trace elements in marine-derived shell TCM could not be neglected for their quality control.

  5. Comparative analysis of tissue reactions to anesthetic solutions: histological analysis in subcutaneous tissue of rats.

    PubMed Central

    Ribeiro, Paulo Domingos; Sanches, Marcio Giampietro; Okamoto, Tetuo

    2003-01-01

    Postanesthetic pain is a relatively common complication after local anesthesia. This complication may be caused by the anesthetic technique or by the anesthetic solution used. Tissue reactions induced by the anesthetic solutions may be one of the factors resulting in pain after anesthesia. The objective of this study was to comparatively analyze tissue reactions induced by different anesthetic solutions in the subcutaneous tissue of rats. The following solutions were utilized: 2% lidocaine without vasoconstrictor; a 0.5% bupivacaine solution with 1:200,000 adrenaline; a 4% articaine solution and 2% mepivacaine, both with 1:100,000 adrenaline; and a 0.9% sodium chloride solution as a control. Sterilized absorbent paper cones packed inside polyethylene tubes were soaked in the solutions and implanted in the subcutaneous region. The sacrifice periods were 1, 2, 5, and 10 days after surgery. The specimens were prepared and stained with hematoxylin and eosin for histological analysis. The results showed that there is a difference in tissue irritability produced by the local anesthetic solutions. The results also showed that there is no relation between the concentration of the drug and the inflammatory intensity, that the mepivacaine and articaine solutions promoted less inflammatory reaction than the bupivacaine, and that the lidocaine solution produced the least intense inflammation. Images Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 Figure 9 Figure 10 Figure 11 PMID:14959905

  6. Comparative Cost Analysis of Housing and Case Management Program for Chronically Ill Homeless Adults Compared to Usual Care

    PubMed Central

    Basu, Anirban; Kee, Romina; Buchanan, David; Sadowski, Laura S

    2012-01-01

    Objective To assess the costs of a housing and case management program in a novel sample—homeless adults with chronic medical illnesses. Data Source The study used data from multiple sources: (1) electronic medical records for hospital, emergency room, and ambulatory medical and mental health visits; (2) institutional and regional databases for days in respite centers, jails, or prisons; and (3) interviews for days in nursing homes, shelters, substance abuse treatment centers, and case manager visits. Total costs were estimated using unit costs for each service. Study Design Randomized controlled trial of 407 homeless adults with chronic medical illnesses enrolled at two hospitals in Chicago, Illinois, and followed for 18 months. Principal Findings Compared to usual care, the intervention group generated an average annual cost savings of (−)$6,307 per person (95 percent CI: −16,616, 4,002; p = .23). Subgroup analyses of chronically homeless and those with HIV showed higher per person, annual cost savings of (−)$9,809 and (−)$6,622, respectively. Results were robust to sensitivity analysis using unit costs. Conclusion The findings of this comprehensive, comparative cost analyses demonstrated an important average annual savings, though in this underpowered study these savings did not achieve statistical significance. PMID:22098257

  7. An Analysis Technique/Automated Tool for Comparing and Tracking Analysis Modes of Different Finite Element Models

    NASA Technical Reports Server (NTRS)

    Towner, Robert L.; Band, Jonathan L.

    2012-01-01

    An analysis technique was developed to compare and track mode shapes for different Finite Element Models. The technique may be applied to a variety of structural dynamics analyses, including model reduction validation (comparing unreduced and reduced models), mode tracking for various parametric analyses (e.g., launch vehicle model dispersion analysis to identify sensitivities to modal gain for Guidance, Navigation, and Control), comparing models of different mesh fidelity (e.g., a coarse model for a preliminary analysis compared to a higher-fidelity model for a detailed analysis) and mode tracking for a structure with properties that change over time (e.g., a launch vehicle from liftoff through end-of-burn, with propellant being expended during the flight). Mode shapes for different models are compared and tracked using several numerical indicators, including traditional Cross-Orthogonality and Modal Assurance Criteria approaches, as well as numerical indicators obtained by comparing modal strain energy and kinetic energy distributions. This analysis technique has been used to reliably identify correlated mode shapes for complex Finite Element Models that would otherwise be difficult to compare using traditional techniques. This improved approach also utilizes an adaptive mode tracking algorithm that allows for automated tracking when working with complex models and/or comparing a large group of models.

  8. Comparative proteomics analysis of degenerative eye lenses of nocturnal rice eel and catfish as compared to diurnal zebrafish

    PubMed Central

    Lin, Yi-Reng; Mok, Hin-Kiu; Wu, Yuan-Heng; Liang, Shih-Shin; Hsiao, Chang-Chun; Huang, Chun-Hao

    2013-01-01

    mammalian lenses. In contrast, β- and γ-crystallins were more abundant in lenses of these three piscine species, similar to mammalian lenses. By proteomics analysis, the most abundant β-crystallins were found to comprise a diverse group of βA1a, βA1–2, βA2a, βA2–2, βA4, βB1, βB2, and βB3 subunit crystallins; the monomeric γ-crystallin class contains γB, γD, γM2, γM3, γM5, γM7, γN–A, γN–B, γS1, and γS2 crystallins. Conclusions In cave or nocturnal animals, the eye is sometimes reduced or eliminated because of adaptation to life in visual darkness. The comparative proteomics analysis of degenerative and normal lenses forms a firm molecular basis to investigate further the evolution of piscine lenses in the future. The total numbers of α-, β-, and γ-crystallins in the three fish species as revealed by the current proteomics methodology clearly indicate the complexity and diversity of crystallin species present in the piscine class of vertebrates. The unexpected finding that α-crystallin is absent in the degenerative eye lenses of rice eel may have some bearing on the chaperone function of α-crystallin in regard to its protective role of preventing protein aggregation in diurnal vertebrate lenses to maintain functional transparency. PMID:23559856

  9. Comparative proteomics analysis of degenerative eye lenses of nocturnal rice eel and catfish as compared to diurnal zebrafish.

    PubMed

    Lin, Yi-Reng; Mok, Hin-Kiu; Wu, Yuan-Heng; Liang, Shih-Shin; Hsiao, Chang-Chun; Huang, Chun-Hao; Chiou, Shyh-Horng

    2013-01-01

    - and γ-crystallins were more abundant in lenses of these three piscine species, similar to mammalian lenses. By proteomics analysis, the most abundant β-crystallins were found to comprise a diverse group of βA1a, βA1-2, βA2a, βA2-2, βA4, βB1, βB2, and βB3 subunit crystallins; the monomeric γ-crystallin class contains γB, γD, γM2, γM3, γM5, γM7, γN-A, γN-B, γS1, and γS2 crystallins. In cave or nocturnal animals, the eye is sometimes reduced or eliminated because of adaptation to life in visual darkness. The comparative proteomics analysis of degenerative and normal lenses forms a firm molecular basis to investigate further the evolution of piscine lenses in the future. The total numbers of α-, β-, and γ-crystallins in the three fish species as revealed by the current proteomics methodology clearly indicate the complexity and diversity of crystallin species present in the piscine class of vertebrates. The unexpected finding that α-crystallin is absent in the degenerative eye lenses of rice eel may have some bearing on the chaperone function of α-crystallin in regard to its protective role of preventing protein aggregation in diurnal vertebrate lenses to maintain functional transparency.

  10. Statistics Education Research in Malaysia and the Philippines: A Comparative Analysis

    ERIC Educational Resources Information Center

    Reston, Enriqueta; Krishnan, Saras; Idris, Noraini

    2014-01-01

    This paper presents a comparative analysis of statistics education research in Malaysia and the Philippines by modes of dissemination, research areas, and trends. An electronic search for published research papers in the area of statistics education from 2000-2012 yielded 20 for Malaysia and 19 for the Philippines. Analysis of these papers showed…

  11. Wallerstein's World-Systems Analysis in Comparative Education: A Case Study

    ERIC Educational Resources Information Center

    Griffiths, Tom G.; Knezevic, Lisa

    2010-01-01

    Since the 1970s, using his world-systems analysis, Immanuel Wallerstein has developed a wide-ranging framework for the social sciences, with potential applications for comparative educational research. In this paper we outline key aspects of Wallerstein's theorising, and then analyse the uptake, understandings, and applications of his analysis in…

  12. A Comparative Analysis of PISA Scientific Literacy Framework in Finnish and Thai Science Curricula

    ERIC Educational Resources Information Center

    Sothayapetch, Pavinee; Lavonen, Jari; Juuti, Kalle

    2013-01-01

    A curriculum is a master plan that regulates teaching and learning. This paper compares Finnish and Thai primary school level science curricula to the PISA 2006 Scientific Literacy Framework. Curriculum comparison was made following the procedure of deductive content analysis. In the analysis, there were four main categories adopted from PISA…

  13. Statistics Education Research in Malaysia and the Philippines: A Comparative Analysis

    ERIC Educational Resources Information Center

    Reston, Enriqueta; Krishnan, Saras; Idris, Noraini

    2014-01-01

    This paper presents a comparative analysis of statistics education research in Malaysia and the Philippines by modes of dissemination, research areas, and trends. An electronic search for published research papers in the area of statistics education from 2000-2012 yielded 20 for Malaysia and 19 for the Philippines. Analysis of these papers showed…

  14. Comparing the Classification Accuracy among Nonparametric, Parametric Discriminant Analysis and Logistic Regression Methods.

    ERIC Educational Resources Information Center

    Ferrer, Alvaro J. Arce; Wang, Lin

    This study compared the classification performance among parametric discriminant analysis, nonparametric discriminant analysis, and logistic regression in a two-group classification application. Field data from an organizational survey were analyzed and bootstrapped for additional exploration. The data were observed to depart from multivariate…

  15. Wallerstein's World-Systems Analysis in Comparative Education: A Case Study

    ERIC Educational Resources Information Center

    Griffiths, Tom G.; Knezevic, Lisa

    2010-01-01

    Since the 1970s, using his world-systems analysis, Immanuel Wallerstein has developed a wide-ranging framework for the social sciences, with potential applications for comparative educational research. In this paper we outline key aspects of Wallerstein's theorising, and then analyse the uptake, understandings, and applications of his analysis in…

  16. Improving Skill Development: An Exploratory Study Comparing a Philosophical and an Applied Ethical Analysis Technique

    ERIC Educational Resources Information Center

    Al-Saggaf, Yeslam; Burmeister, Oliver K.

    2012-01-01

    This exploratory study compares and contrasts two types of critical thinking techniques; one is a philosophical and the other an applied ethical analysis technique. The two techniques analyse an ethically challenging situation involving ICT that a recent media article raised to demonstrate their ability to develop the ethical analysis skills of…

  17. Communicating Comparative Findings from Meta-Analysis in Educational Research: Some Examples and Suggestions

    ERIC Educational Resources Information Center

    Higgins, Steve; Katsipataki, Maria

    2016-01-01

    This article reviews some of the strengths and limitations of the comparative use of meta-analysis findings, using examples from the Sutton Trust-Education Endowment Foundation Teaching and Learning "Toolkit" which summarizes a range of educational approaches to improve pupil attainment in schools. This comparative use of quantitative…

  18. Postmodernism Debates and Comparative Education: A Critical Discourse Analysis. Essay Review.

    ERIC Educational Resources Information Center

    Mehta, Sonia; Ninnes, Peter

    2003-01-01

    Detailed discourse analysis is presented for two articles that suggest that postmodernism has little to offer comparative education and should be resisted. The two texts, focusing on postmodernism as the antithesis of comparative education and on the "lost promise" of postmodernism, demonstrate the use of language to convey messages that limit or…

  19. The Effects of Attrition on Baseline Comparability in Randomized Experiments in Education: A Meta-Analysis

    ERIC Educational Resources Information Center

    Valentine, Jeffrey C.; McHugh, Cathleen M.

    2007-01-01

    Using meta-analysis, randomized experiments in education that either clearly did or clearly did not experience student attrition were examined for the baseline comparability of groups. Results from 35 studies suggested that after attrition, the observed measures of baseline comparability of groups did not differ more than would be expected given…

  20. A Comparative Analysis of the Moral Judgments of Younger Students: (1930 and 2000)

    ERIC Educational Resources Information Center

    Kravtsova, M. M.

    2006-01-01

    In this comparative analysis, the author aimed to reproduce V.S. Merlin's and M.F. Khriakova's 1930 study of children's social concepts in order to find out how today's students account for the actions of characters in stories and to compare their answers to the responses given in the earlier study. In this study, the author defines "moral…