Science.gov

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.; Gellert, R.; Achilles, C. N..; Rampe, E. B.; Bristow, T. F.; Crisp, J. A.; Sarrazin, P. C.; Farmer, J. D.; DesMarais, D. J.; Grotzinger, J. P.; Stolper, E. M.; Morookian, J. M.; Wilson, M. A.; Spanovich, N.; Anderson, R. C.

    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.; Gellert, R.; Achilles, C. N.; Rampe, E. B.; Bristow, T. F.; Crisp, J. A.; Sarrazin, P. C.; DesMarais, D. J.; Morookian, J. M.; Anderson, R. C.

    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 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.

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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,…

  10. 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.

  11. Comparative analysis of rigidity across protein families.

    PubMed

    Wells, S A; Jimenez-Roldan, J E; Römer, R A

    2009-01-01

    We present a comparative study in which 'pebble game' rigidity analysis is applied to multiple protein crystal structures, for each of six different protein families. We find that the main-chain rigidity of a protein structure at a given hydrogen bond energy cutoff is quite sensitive to small structural variations, and conclude that the hydrogen bond constraints in rigidity analysis should be chosen so as to form and test specific hypotheses about the rigidity of a particular protein. Our comparative approach highlights two different characteristic patterns ('sudden' or 'gradual') for protein rigidity loss as constraints are removed, in line with recent results on the rigidity transitions of glassy networks. PMID:19773604

  12. MycoCAP - Mycobacterium Comparative Analysis Platform

    PubMed Central

    Choo, Siew Woh; Ang, Mia Yang; Dutta, Avirup; Tan, Shi Yang; Siow, Cheuk Chuen; Heydari, Hamed; Mutha, Naresh V. R.; Wee, Wei Yee; Wong, Guat Jah

    2015-01-01

    Mycobacterium spp. are renowned for being the causative agent of diseases like leprosy, Buruli ulcer and tuberculosis in human beings. With more and more mycobacterial genomes being sequenced, any knowledge generated from comparative genomic analysis would provide better insights into the biology, evolution, phylogeny and pathogenicity of this genus, thus helping in better management of diseases caused by Mycobacterium spp.With this motivation, we constructed MycoCAP, a new comparative analysis platform dedicated to the important genus Mycobacterium. This platform currently provides information of 2108 genome sequences of at least 55 Mycobacterium spp. A number of intuitive web-based tools have been integrated in MycoCAP particularly for comparative analysis including the PGC tool for comparison between two genomes, PathoProT for comparing the virulence genes among the Mycobacterium strains and the SuperClassification tool for the phylogenic classification of the Mycobacterium strains and a specialized classification system for strains of Mycobacterium abscessus. We hope the broad range of functions and easy-to-use tools provided in MycoCAP makes it an invaluable analysis platform to speed up the research discovery on mycobacteria for researchers. Database URL: http://mycobacterium.um.edu.my PMID:26666970

  13. MycoCAP - Mycobacterium Comparative Analysis Platform.

    PubMed

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

    2015-01-01

    Mycobacterium spp. are renowned for being the causative agent of diseases like leprosy, Buruli ulcer and tuberculosis in human beings. With more and more mycobacterial genomes being sequenced, any knowledge generated from comparative genomic analysis would provide better insights into the biology, evolution, phylogeny and pathogenicity of this genus, thus helping in better management of diseases caused by Mycobacterium spp.With this motivation, we constructed MycoCAP, a new comparative analysis platform dedicated to the important genus Mycobacterium. This platform currently provides information of 2108 genome sequences of at least 55 Mycobacterium spp. A number of intuitive web-based tools have been integrated in MycoCAP particularly for comparative analysis including the PGC tool for comparison between two genomes, PathoProT for comparing the virulence genes among the Mycobacterium strains and the SuperClassification tool for the phylogenic classification of the Mycobacterium strains and a specialized classification system for strains of Mycobacterium abscessus. We hope the broad range of functions and easy-to-use tools provided in MycoCAP makes it an invaluable analysis platform to speed up the research discovery on mycobacteria for researchers. Database URL: http://mycobacterium.um.edu.my. PMID:26666970

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. Single crystal chemical vapor deposit diamond detector for energetic plasma measurement in space

    NASA Astrophysics Data System (ADS)

    Ogasawara, K.; Broiles, T. W.; Coulter, K. E.; Dayeh, M. A.; Desai, M. I.; Livi, S. A.; McComas, D. J.; Walther, B. C.

    2015-03-01

    This study reports the performance of single crystal chemical vapor deposit diamond detectors for measuring space plasma and energetic particles: ~7 keV energy resolution for protons with a 14 keV threshold level, and good response linearity for ions and electrons as expected from Monte-Carlo calculations of primary particle energy loss. We investigated that these diamond detectors are able to operate at high temperature (> 70 ° C) and have fast response times (< 1 ns rise time). While silicon detectors have proven capability over this energy range for space plasma measurements, diamond detectors offer a faster response, higher temperature operation, greater radiation tolerance, and immunity to light.

  20. 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

  1. Comparative transcriptome analysis of four prymnesiophyte algae.

    PubMed

    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

  2. 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

  3. 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.

  4. Comparative proteomic analysis of compartmentalised Ras signalling

    PubMed Central

    Hernandez-Valladares, Maria; Prior, Ian A.

    2015-01-01

    Ras proteins are membrane bound signalling hubs that operate from both the cell surface and endomembrane compartments. However, the extent to which intracellular pools of Ras can contribute to cell signalling is debated. To address this, we have performed a global screen of compartmentalised Ras signalling. We find that whilst ER/Golgi- and endosomal-Ras only generate weak outputs, Ras localised to the mitochondria or Golgi significantly and distinctly influence both the abundance and phosphorylation of a wide range of proteins analysed. Our data reveal that ~80% of phosphosites exhibiting large (≥1.5-fold) changes compared to control can be modulated by organellar Ras signalling. The majority of compartmentalised Ras-specific responses are predicted to influence gene expression, RNA splicing and cell proliferation. Our analysis reinforces the concept that compartmentalisation influences Ras signalling and provides detailed insight into the widespread modulation of responses downstream of endomembranous Ras signalling. PMID:26620772

  5. 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.

  6. 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.

  7. 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

  8. Comparative Sensitivity Analysis of Muscle Activation Dynamics.

    PubMed

    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

  9. 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.

  10. Comparative statistical analysis of planetary surfaces

    NASA Astrophysics Data System (ADS)

    Schmidt, Frédéric; Landais, Francois; Lovejoy, Shaun

    2016-04-01

    In the present study, we aim to provide a statistical and comparative description of topographic fields by using the huge amount of topographic data available for different bodies in the solar system, including Earth, Mars, the Moon etc.. Our goal is to characterize and quantify the geophysical processes involved by a relevant statistical description. In each case, topographic fields exhibit an extremely high variability with details at each scale, from millimeter to thousands of kilometers. This complexity seems to prohibit global descriptions or global topography models. Nevertheless, this topographic complexity is well-known to exhibit scaling laws that establish a similarity between scales and permit simpler descriptions and models. Indeed, efficient simulations can be made using the statistical properties of scaling fields (fractals). But realistic simulations of global topographic fields must be multi (not mono) scaling behaviour, reflecting the extreme variability and intermittency observed in real fields that can not be generated by simple scaling models. A multiscaling theory has been developed in order to model high variability and intermittency. This theory is a good statistical candidate to model the topography field with a limited number of parameters (called the multifractal parameters). After a global analysis of Mars (Landais et. al, 2015) we have performed similar analysis on different body in the solar system including the Moon, Venus and mercury indicating that the mulifractal parameters might be relevant to explain the competition between several processes operating on multiple scales

  11. Interlayer Potassium And Its Neighboring Atoms in Micas: Crystal-Chemical Modeling And Xanes Spectroscopy

    SciTech Connect

    Brigatti, M.F.; Malferrari, D.; Poppi, M.; Mottana, A.; Cibin, G.; Marcelli, A.; Cinque, G.

    2009-05-12

    A detailed description of the interlayer site in trioctahedral true micas is presented based on a statistical appraisal of crystal-chemical, structural, and spectroscopic data determined on two sets of trioctahedral micas extensively studied by both X-ray diffraction refinement on single crystals (SC-XRD) and X-ray absorption fine spectroscopy (XAFS) at the potassium K-edge. Spectroscopy was carried out on both random powders and oriented cleavage flakes, the latter setting taking advantage of the polarized character of synchrotron radiation. Such an approach (AXANES) is shown to be complementary to crystal-chemical investigation based on SC-XRD refinement. However, the results are not definitive as they focus on few samples having extreme features only (e.g., end-members, unusual compositions, and samples with extreme and well-identified substitution mechanisms). The experimental absorption K-edge (XANES) for potassium was decomposed by calculation and extrapolated into a full in-plane absorption component ({sigma}{parallel}) and a full out-of-plane absorption component ({sigma}{perpendicular}). These two patterns reflect different structural features: {sigma}{parallel}represents the arrangement of the atoms located in the mica interlayer space and facing tetrahedral sheets; {sigma}{perpendicular} is associated with multiple-scattering interactions entering deep into the mica structure, thus also reflecting interactions with the heavy atoms (essentially Fe) located in the octahedral sheet. The out-of-plane patterns also provide insights into the electronic properties of the octahedral cations, such as their oxidation states (e.g., Fe{sup 2+} and Fe{sup 3+}) and their ordering (e.g., trans- vs. cis-setting). It is also possible to distinguish between F- and OH-rich micas due to peculiar absorption features originating from the F vs. OH occupancy of the O4 octahedral site. Thus, combining crystal-chemical, structural, and spectroscopic information is shown to be a

  12. Predictive and comparative analysis of Ebolavirus proteins.

    PubMed

    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

  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. PMID:24712530

  14. 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.

  15. 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.

  16. Comparative analysis of planetary laser ranging concepts

    NASA Astrophysics Data System (ADS)

    Dirkx, D.; Bauer, S.; Noomen, R.; Vermeersen, B. L. A.; Visser, P. N.

    2014-12-01

    missions for various combinations of clock and state arc length. Thereby, we quantify the relative capabilities of the one- and two-way laser range systems. In addition, we study the optimal data analysis strategies for these missions, which we apply for LRO orbit determination. Finally, we compare the performance of the laser ranging systems with typical DSN tracking.

  17. 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…

  18. Comparable Worth: An Analysis and Recommendations.

    ERIC Educational Resources Information Center

    Commission on Civil Rights, Washington, DC.

    This report discusses sex-based wage discrimination, the role of comparable worth doctrine in analyzing or combating such discrimination, and the appropriateness of the remedial prescriptions that comparable worth doctrine envisions. The report consists of a brief introduction and five chapters. Chapter 1 presents a brief overview of women in the…

  19. 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…

  20. 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.

  1. Comparative analysis of Orem's and King's theories.

    PubMed

    Hanucharurnkul, S

    1989-05-01

    Dorothea Orem and Imogene King are two nursing theorists who are contributing significantly to the development of nursing knowledge. This paper compares the similarities and differences in their strategies for theory development, their views of nursing metaparadigm concepts, and their theories of nursing system and goal attainment in terms of scope, usefulness, and their unique contribution to nursing science. PMID:2738232

  2. 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…

  3. General Education Requirements: A Comparative Analysis

    ERIC Educational Resources Information Center

    Warner, Darrell B.; Koeppel, Katie

    2009-01-01

    While "general education" is a phrase heavily used in higher education, Leskes and Wright note that it has multiple meanings: it can refer to those courses that a college or university requires all of its students must pass as a condition for graduation, a common curriculum, a distribution requirement, or even core texts. This analysis of general…

  4. Comparing Package Programs for Factor Analysis

    ERIC Educational Resources Information Center

    Wimberley, Ronald C.

    1978-01-01

    Earlier comparisons of packaged programs for factor analysis are updated because of recent revision in some programs. The top status of SPSS is no longer so apparent as formerly. BMD and SAS now have expanded options. SAS has flexibility and convenience. (Author)

  5. 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…

  6. Comparing Work Skills Analysis Tools. Project Report.

    ERIC Educational Resources Information Center

    Barker, Kathryn

    This document outlines the processes and outcomes of a research project conducted to review work skills analysis tools (products and/or services) that profile required job skills and/or assess individuals' acquired skills. The document begins with a brief literature review and discussion of pertinent terminology. Presented next is a list of…

  7. Light beam deflector performance: a comparative analysis.

    PubMed

    Zook, J D

    1974-04-01

    The performance of various types of analog light beam deflectors is summarized, and their relative positions in a deflector hierarchy are defined. The three types of deflectors considered are (1) mechanical (galvanometer) mirror deflectors, (2) acoustooptic deflectors, and (3) analog electrooptic deflectors. Material figures of merit are defined and compared, and the theoretical trade-off between speed and resolution is given for each type of deflector. PMID:20126095

  8. 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.

  9. 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).

  10. Comparative analysis of plant lycopene cyclases.

    PubMed

    Koc, Ibrahim; Filiz, Ertugrul; Tombuloglu, Huseyin

    2015-10-01

    Carotenoids are essential isoprenoid pigments produced by plants, algae, fungi and bacteria. Lycopene cyclase (LYC) commonly cyclize carotenoids, which is an important branching step in the carotenogenesis, at one or both end of the backbone. Plants have two types of LYC (β-LCY and ϵ-LCY). In this study, plant LYCs were analyzed. Based on domain analysis, all LYCs accommodate lycopene cyclase domain (Pf05834). Furthermore, motif analysis indicated that motifs were conserved among the plants. On the basis of phylogenetic analysis, β-LCYs and ϵ-LCYs were classified in β and ϵ groups. Monocot and dicot plants separated from each other in the phylogenetic tree. Subsequently, Oryza sativa Japonica Group and Zea mays of LYCs as monocot plants and Vitis vinifera and Solanum lycopersicum of LYCs as dicot plants were analyzed. According to nucleotide diversity analysis of β-LCY and ϵ-LCY genes, nucleotide diversities were found to be π: 0.30 and π: 0.25, respectively. The result highlighted β-LCY genes showed higher nucleotide diversity than ϵ-LCY genes. LYCs interacting genes and their co-expression partners were also predicted using String server. The obtained data suggested the importance of LYCs in carotenoid metabolism. 3D modeling revealed that depicted structures were similar in O. sativa, Z mays, S. lycopersicum, and V. vinifera β-LCYs and ϵ-LCYs. Likewise, the predicted binding sites were highly similar between O. sativa, Z mays, S. lycopersicum, and V. vinifera LCYs. Most importantly, analysis elucidated the V/IXGXGXXGXXXA motif for both type of LYC (β-LCY and ϵ-LCY). This motif related to Rossmann fold domain and probably provides a flat platform for binding of FAD in O. sativa, Z mays, S. lycopersicum, and V. vinifera β-LCYs and ϵ-LCYs with conserved structure. In addition to lycopene cyclase domain, the V/IXGXGXXGXXXA motif can be used for exploring LYCs proteins and to annotate the function of unknown proteins containing lycopene cyclase

  11. Comparative metabolic systems analysis of pathogenic Burkholderia.

    PubMed

    Bartell, Jennifer A; Yen, Phillip; Varga, John J; Goldberg, Joanna B; Papin, Jason A

    2014-01-01

    Burkholderia cenocepacia and Burkholderia multivorans are opportunistic drug-resistant pathogens that account for the majority of Burkholderia cepacia complex infections in cystic fibrosis patients and also infect other immunocompromised individuals. While they share similar genetic compositions, B. cenocepacia and B. multivorans exhibit important differences in pathogenesis. We have developed reconciled genome-scale metabolic network reconstructions of B. cenocepacia J2315 and B. multivorans ATCC 17616 in parallel (designated iPY1537 and iJB1411, respectively) to compare metabolic abilities and contextualize genetic differences between species. The reconstructions capture the metabolic functions of the two species and give insight into similarities and differences in their virulence and growth capabilities. The two reconstructions have 1,437 reactions in common, and iPY1537 and iJB1411 have 67 and 36 metabolic reactions unique to each, respectively. After curating the extensive reservoir of metabolic genes in Burkholderia, we identified 6 genes essential to growth that are unique to iPY1513 and 13 genes uniquely essential to iJB1411. The reconstructions were refined and validated by comparing in silico growth predictions to in vitro growth capabilities of B. cenocepacia J2315, B. cenocepacia K56-2, and B. multivorans ATCC 17616 on 104 carbon sources. Overall, we identified functional pathways that indicate B. cenocepacia can produce a wider array of virulence factors compared to B. multivorans, which supports the clinical observation that B. cenocepacia is more virulent than B. multivorans. The reconciled reconstructions provide a framework for generating and testing hypotheses on the metabolic and virulence capabilities of these two related emerging pathogens. PMID:24163337

  12. Comparative Metabolic Systems Analysis of Pathogenic Burkholderia

    PubMed Central

    Bartell, Jennifer A.; Yen, Phillip; Varga, John J.; Goldberg, Joanna B.

    2014-01-01

    Burkholderia cenocepacia and Burkholderia multivorans are opportunistic drug-resistant pathogens that account for the majority of Burkholderia cepacia complex infections in cystic fibrosis patients and also infect other immunocompromised individuals. While they share similar genetic compositions, B. cenocepacia and B. multivorans exhibit important differences in pathogenesis. We have developed reconciled genome-scale metabolic network reconstructions of B. cenocepacia J2315 and B. multivorans ATCC 17616 in parallel (designated iPY1537 and iJB1411, respectively) to compare metabolic abilities and contextualize genetic differences between species. The reconstructions capture the metabolic functions of the two species and give insight into similarities and differences in their virulence and growth capabilities. The two reconstructions have 1,437 reactions in common, and iPY1537 and iJB1411 have 67 and 36 metabolic reactions unique to each, respectively. After curating the extensive reservoir of metabolic genes in Burkholderia, we identified 6 genes essential to growth that are unique to iPY1513 and 13 genes uniquely essential to iJB1411. The reconstructions were refined and validated by comparing in silico growth predictions to in vitro growth capabilities of B. cenocepacia J2315, B. cenocepacia K56-2, and B. multivorans ATCC 17616 on 104 carbon sources. Overall, we identified functional pathways that indicate B. cenocepacia can produce a wider array of virulence factors compared to B. multivorans, which supports the clinical observation that B. cenocepacia is more virulent than B. multivorans. The reconciled reconstructions provide a framework for generating and testing hypotheses on the metabolic and virulence capabilities of these two related emerging pathogens. PMID:24163337

  13. 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

  14. Comparative analysis of GOCI ocean color products.

    PubMed

    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  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

  15. [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. PMID:25059059

  16. 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.

  17. Quantitative analysis of comparative genomic hybridization

    SciTech Connect

    Manoir, S. du; Bentz, M.; Joos, S. |

    1995-01-01

    Comparative genomic hybridization (CGH) is a new molecular cytogenetic method for the detection of chromosomal imbalances. Following cohybridization of DNA prepared from a sample to be studied and control DNA to normal metaphase spreads, probes are detected via different fluorochromes. The ratio of the test and control fluorescence intensities along a chromosome reflects the relative copy number of segments of a chromosome in the test genome. Quantitative evaluation of CGH experiments is required for the determination of low copy changes, e.g., monosomy or trisomy, and for the definition of the breakpoints involved in unbalanced rearrangements. In this study, a program for quantitation of CGH preparations is presented. This program is based on the extraction of the fluorescence ratio profile along each chromosome, followed by averaging of individual profiles from several metaphase spreads. Objective parameters critical for quantitative evaluations were tested, and the criteria for selection of suitable CGH preparations are described. The granularity of the chromosome painting and the regional inhomogeneity of fluorescence intensities in metaphase spreads proved to be crucial parameters. The coefficient of variation of the ratio value for chromosomes in balanced state (CVBS) provides a general quality criterion for CGH experiments. Different cutoff levels (thresholds) of average fluorescence ratio values were compared for their specificity and sensitivity with regard to the detection of chromosomal imbalances. 27 refs., 15 figs., 1 tab.

  18. Comparative analysis of selected hydromorphological assessment methods.

    PubMed

    Sípek, Václav; Matousková, Milada; Dvorák, Martin

    2010-10-01

    The European Water Framework Directive 2000/60/EC aims to achieve a good ecological status of all surface water bodies in Europe. The definition of the ecological status is based on the hydromorphological, hydrochemical, and hydrobiological features of water bodies. Numerous methods are applied for the purpose of hydromorphological status assessment. This study attempts to compare four different methods (EcoRivHab, LAWA Field and Overview Survey, and Rapid Bioassessment Protocol) that were applied at two study areas in the Czech part of the Elbe River Basin. The selected catchments represent areas with different sizes and physical geographic as well as socioeconomic characteristics. All the methods applied showed the capacity to identify the natural and even the completely changed reaches and provided good information on the river physical habitat state. However, they are varied from the viewpoint of the number of parameters, number of monitored zones, time and knowledge demands of the performed assessment. PMID:19760083

  19. 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.

  20. 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.

  1. 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

  2. A comparative analysis of trypanosomatid SNARE proteins.

    PubMed

    Murungi, Edwin; Barlow, Lael D; Venkatesh, Divya; Adung'a, Vincent O; Dacks, Joel B; Field, Mark C; Christoffels, Alan

    2014-04-01

    The Kinetoplastida are flagellated protozoa evolutionary distant and divergent from yeast and humans. Kinetoplastida include trypanosomatids, and a number of important pathogens. Trypanosoma brucei, Trypanosoma cruzi and Leishmania spp. inflict significant morbidity and mortality on humans and livestock as the etiological agents of human African trypanosomiasis, Chagas' disease and leishmaniasis respectively. For all of these organisms, intracellular trafficking is vital for maintenance of the host-pathogen interface, modulation/evasion of host immune system responses and nutrient uptake. Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) are critical components of the intracellular trafficking machinery in eukaryotes, mediating membrane fusion and contributing to organelle specificity. We asked how the SNARE complement evolved across the trypanosomatids. An in silico search of the predicted proteomes of T. b. brucei and T. cruzi was used to identify candidate SNARE sequences. Phylogenetic analysis, including comparisons with yeast and human SNAREs, allowed assignment of trypanosomatid SNAREs to the Q or R subclass, as well as identification of several SNAREs orthologous with those of opisthokonts. Only limited variation in number and identity of SNAREs was found, with Leishmania major having 27 and T. brucei 26, suggesting a stable SNARE complement post-speciation. Expression analysis of T. brucei SNAREs revealed significant differential expression between mammalian and insect infective forms, especially within R and Qb-SNARE subclasses, suggesting possible roles in adaptation to different environments. For trypanosome SNAREs with clear orthologs in opisthokonts, the subcellular localization of TbVAMP7C is endosomal while both TbSyn5 and TbSyn16B are at the Golgi complex, which suggests conservation of localization and possibly also function. Despite highly distinct life styles, the complement of trypanosomatid SNAREs is quite stable

  3. A comparative analysis of trypanosomatid SNARE proteins☆

    PubMed Central

    Murungi, Edwin; Barlow, Lael D.; Venkatesh, Divya; Adung'a, Vincent O.; Dacks, Joel B.; Field, Mark C.; Christoffels, Alan

    2014-01-01

    The Kinetoplastida are flagellated protozoa evolutionary distant and divergent from yeast and humans. Kinetoplastida include trypanosomatids, and a number of important pathogens. Trypanosoma brucei, Trypanosoma cruzi and Leishmania spp. inflict significant morbidity and mortality on humans and livestock as the etiological agents of human African trypanosomiasis, Chagas' disease and leishmaniasis respectively. For all of these organisms, intracellular trafficking is vital for maintenance of the host–pathogen interface, modulation/evasion of host immune system responses and nutrient uptake. Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) are critical components of the intracellular trafficking machinery in eukaryotes, mediating membrane fusion and contributing to organelle specificity. We asked how the SNARE complement evolved across the trypanosomatids. An in silico search of the predicted proteomes of T. b. brucei and T. cruzi was used to identify candidate SNARE sequences. Phylogenetic analysis, including comparisons with yeast and human SNAREs, allowed assignment of trypanosomatid SNAREs to the Q or R subclass, as well as identification of several SNAREs orthologous with those of opisthokonts. Only limited variation in number and identity of SNAREs was found, with Leishmania major having 27 and T. brucei 26, suggesting a stable SNARE complement post-speciation. Expression analysis of T. brucei SNAREs revealed significant differential expression between mammalian and insect infective forms, especially within R and Qb-SNARE subclasses, suggesting possible roles in adaptation to different environments. For trypanosome SNAREs with clear orthologs in opisthokonts, the subcellular localization of TbVAMP7C is endosomal while both TbSyn5 and TbSyn16B are at the Golgi complex, which suggests conservation of localization and possibly also function. Despite highly distinct life styles, the complement of trypanosomatid SNAREs is quite stable

  4. Comparative network analysis via differential graphlet communities

    PubMed Central

    Wong, Serene W H; Cercone, Nick; Jurisica, Igor

    2015-01-01

    While current protein interaction data provides a rich resource for molecular biology, it mostly lacks condition-specific details. Abundance of mRNA data for most diseases provides potential to model condition-specific transcriptional changes. Transcriptional data enables modeling disease mechanisms, and in turn provide potential treatments. While approaches to compare networks constructed from healthy and disease samples have been developed, they do not provide the complete comparison, evaluations are performed on very small networks, or no systematic network analyses are performed on differential network structures. We propose a novel method for efficiently exploiting network structure information in the comparison between any graphs, and validate results in non-small cell lung cancer. We introduce the notion of differential graphlet community to detect deregulated subgraphs between any graphs such that the network structure information is exploited. The differential graphlet community approach systematically captures network structure differences between any graphs. Instead of using connectivity of each protein or each edge, we used shortest path distributions on differential graphlet communities in order to exploit network structure information on identified deregulated subgraphs. We validated the method by analyzing three non-small cell lung cancer datasets and validated results on four independent datasets. We observed that the shortest path lengths are significantly longer for normal graphs than for tumor graphs between genes that are in differential graphlet communities, suggesting that tumor cells create "shortcuts" between biological processes that may not be present in normal conditions. PMID:25283527

  5. Comparative Analysis of Evapotranspiration Using Eddy Covariance

    NASA Astrophysics Data System (ADS)

    BAE, H.; Ji, H.; Lee, B.; Nam, K.; Jang, B.; Lee, C.; Jung, H.

    2013-12-01

    The eddy covariance method has been widely used to quantify evapotranspiration. However, independent measurements of energy components such as latent heat flux, sensible heat flux often lead to under-measurements, this is commonly known as a lack of closure of the surface energy balance. In response to this methodological problem, this study is addressed specifically to correction of the latent and heat sensible fluxes. The energy components observed in agricultural and grassland from January 2013 were measured using the eddy covariance method. As a result of the comparison of the available energy (Rn-G) with the sum of the latent and sensible heat fluxes, R-Squared values were 0.72 in the agricultural land, 0.78 in the grassland, indicating that the latent and sensible heat fluxes were under-measured. The obtained latent and sensible heat fluxes were then modified using the Bowen-ratio closure method. After this correction process, the values of the sum of the latent and sensible heat fluxes have increased by 39.7 percent in the agricultural land, 32.2 percent in the grassland respectively. Evapotranspiration will be calculated with both the unmodified and modified latent heat flux values, the results will be then thoroughly compared. The results will be finally verified by comparison with evapotranspiration obtained from energy balance based model.

  6. 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. PMID:23393031

  7. Community detection algorithms: A comparative analysis

    NASA Astrophysics Data System (ADS)

    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.

  8. 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

  9. 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.

  10. Pathway alignment: application to the comparative analysis of glycolytic enzymes.

    PubMed Central

    Dandekar, T; Schuster, S; Snel, B; Huynen, M; Bork, P

    1999-01-01

    Comparative analysis of metabolic pathways in different genomes yields important information on their evolution, on pharmacological targets and on biotechnological applications. In this study on glycolysis, three alternative ways of comparing biochemical pathways are combined: (1) analysis and comparison of biochemical data, (2) pathway analysis based on the concept of elementary modes, and (3) a comparative genome analysis of 17 completely sequenced genomes. The analysis reveals a surprising plasticity of the glycolytic pathway. Isoenzymes in different species are identified and compared; deviations from the textbook standard are detailed. Several potential pharmacological targets and by-passes (such as the Entner-Doudoroff pathway) to glycolysis are examined and compared in the different species. Archaean, bacterial and parasite specific adaptations are identified and described. PMID:10493919

  11. 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 ...

  12. 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

  13. 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.)

  14. 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…

  15. 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. PMID:22157075

  16. 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).

  17. 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.

  18. 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

  19. 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…

  20. 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…

  1. Comparative Analysis, Global Policy Studies and the Human Condition.

    ERIC Educational Resources Information Center

    Bertsch, Gary K.

    This paper examines the role that comparative analysis and global policy studies can play in explaining the human condition in the contemporary world. It investigates economic well-being, one dimension of the human condition, and examines some of the attributes that represent it and some of the forces that affect it in villages, social groupings,…

  2. 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…

  3. 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.

  4. 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. PMID:24959585

  5. 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.

  6. 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

  7. 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.

  8. [Comparative analysis of total cell protein electrophoregram of pathogenic Burkholderia].

    PubMed

    Budchenko, A A; Iliukhin, V I; Viktorov, D V

    2005-01-01

    Whole-cell proteins of 22 strain of Burkhoderia pseudomallei, including 13 B. mallei, 5 B. cepacia strains and 14 strains of opportunistically pathogenic Pseudomonas defined by 1D SDC-PAAG electrophoresis. Electrophoregrams contained 35 to 45 protein fractions sized 19 to 130 kDa, which were highly reproductive. On the basis of computer-aided comparative analysis of protein patterns the interspecies and intraspecies grouping of studied microorganisms was made. The cluster analysis of the similarity matrix of protein spectra made it possible to allocate two groups of strains at the level of similarity of 78%. Group I was formed by Burkholderia species that previously belonged to the II RNA-DNA homology group of Pseudomonas: B. pseudomallei, B. mallei, B. cepacia. All Pseudomonas species were added to the 2nd Group: P. aeruginosa, P. stutzeri, P. testosterone, P. fluorescens, P. putida, P. mendocina. Four phenons were isolated among the strains of B. pseudomallei and 2 phenons--among the strains of B. mallei at the threshold similarity level (89%). The authors conclude that the comparative analysis of electrophoregrams of whole-cell proteins can be useful in the identification and typing of pathogenic Burkholderia. PMID:15954473

  9. Comparative analysis of the river buffalo somatostatin gene.

    PubMed

    Stafuzza, N B; Borges, M M; Amaral, M E J

    2014-01-01

    The somatostatin protein plays a crucial role in the regulation of multiple biological functions, such as growth, fat deposition, and nutrient absorption in vertebrates. Polymorphisms in the somatostatin gene have been associated with growth traits in livestock species, including cattle and goat. In this study, we conducted complete molecular characterization of the somatostatin gene in Bubalus bubalis (Murrah breed) by sequencing a Murrah BAC clone spanning 72,489 base pairs (bp) in length. The buffalo somatostatin gene contains 1481 bp organized into a 5'-untranslated region (135 bp), exon 1 (139 bp), intron 1 (839 bp), exon 2 (212 bp), and 3'UTR (156 bp). Comparative analysis between the buffalo somatostatin DNA coding sequence and the amino acid sequence with other bovids (cattle, goat, and sheep), horse, pig, human, rodents (mouse and rat), and chicken. Identity varied from 83-99% on the DNA sequence level and 88-100% on the protein level. In addition, a comparison of gene sequences between Murrah and Mediterranean breeds revealed 6 potential single-nucleotide polymorphisms (1 in exon 1 and 5 in intron 1), which were validated in different buffalo populations. This comparative analysis provides basic information for future studies of different buffalo herds using the position candidate gene approach, quantitative trait loci analysis, and polymorphisms associated with growth traits. PMID:25501213

  10. 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.

  11. DNA sequence copy number analysis by Comparative Genomic Hybridization (CGH)

    SciTech Connect

    Pinkel, D.; Kallioniemi, A.; Kallioniemi, O.; Waldman, F.; Sudar, D.; Gray, I. ); Rutovitz, D.; Piper, I. )

    1993-01-01

    Comparative Genomic Hybridization (CGH) uses the kinetics of in situ hybridization to compare the copy numbers of different DNA sequences within the same genome and the copy numbers of the same sequences among different genomes. In a typical application genomic DNA from a tumor and from normal cells are differentially labeled and simultaneously hybridized to normal metaphase chromosomes, and detected with different fluorochromes. Properly registered images of each fluorochrome are obtained using a microscope equipped with multi-band filters and a CCD camera. Digital image analysis permits measurement of intensity ratio profiles along each of the target chromosomes. Studies of cells with known aberrations indicate that the intensity ratio at each position is proportional to the ratio of the copy numbers of the sequences that bind there in the tumor and normal genomes. Analytical challenges posed by the need to efficiently obtain copy number karyotypes are discussed.

  12. 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.

  13. 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. PMID:25688450

  14. 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.

  15. 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.

  16. Utility of array comparative genomic hybridization in cytogenetic analysis.

    PubMed

    Singh, Rashmi R; Cheung, K-John J; Horsman, Douglas E

    2011-01-01

    Conventional comparative genomic hybridization (CGH), high-resolution oligonucleotide, and BAC array CGH have modernized the field of cytogenetics to enable access to unbalanced genomic aberrations such as whole or partial chromosomal gains and losses. The basic principle of array CGH involves hybridizing differentially labeled proband/test (e.g., tumor) and normal reference DNA on an array of oligonucleotide or BAC clones instead of normal metaphases as in conventional CGH. The sub-megabase resolution tiling BAC arrays are extremely useful for the analysis of acquired aberrations in cancer genomes. Array CGH can be extremely useful to identify the chromosomal makeup of marker and ring chromosomes, to define/delineate the precise location/bands involved in structural aberrations and the accurate localization of translocation breakpoints in both simple and complex karyotypes either alone or in combination with standard karyotype analysis. PMID:21431645

  17. The DNA sequence and comparative analysis of human chromosome 10.

    PubMed

    Deloukas, P; Earthrowl, M E; Grafham, D V; Rubenfield, M; French, L; Steward, C A; Sims, S K; Jones, M C; Searle, S; Scott, C; Howe, K; Hunt, S E; Andrews, T D; Gilbert, J G R; Swarbreck, D; Ashurst, J L; Taylor, A; Battles, J; Bird, C P; Ainscough, R; Almeida, J P; Ashwell, R I S; Ambrose, K D; Babbage, A K; Bagguley, C L; Bailey, J; Banerjee, R; Bates, K; Beasley, H; Bray-Allen, S; Brown, A J; Brown, J Y; Burford, D C; Burrill, W; Burton, J; Cahill, P; Camire, D; Carter, N P; Chapman, J C; Clark, S Y; Clarke, G; Clee, C M; Clegg, S; Corby, N; Coulson, A; Dhami, P; Dutta, I; Dunn, M; Faulkner, L; Frankish, A; Frankland, J A; Garner, P; Garnett, J; Gribble, S; Griffiths, C; Grocock, R; Gustafson, E; Hammond, S; Harley, J L; Hart, E; Heath, P D; Ho, T P; Hopkins, B; Horne, J; Howden, P J; Huckle, E; Hynds, C; Johnson, C; Johnson, D; Kana, A; Kay, M; Kimberley, A M; Kershaw, J K; Kokkinaki, M; Laird, G K; Lawlor, S; Lee, H M; Leongamornlert, D A; Laird, G; Lloyd, C; Lloyd, D M; Loveland, J; Lovell, J; McLaren, S; McLay, K E; McMurray, A; Mashreghi-Mohammadi, M; Matthews, L; Milne, S; Nickerson, T; Nguyen, M; Overton-Larty, E; Palmer, S A; Pearce, A V; Peck, A I; Pelan, S; Phillimore, B; Porter, K; Rice, C M; Rogosin, A; Ross, M T; Sarafidou, T; Sehra, H K; Shownkeen, R; Skuce, C D; Smith, M; Standring, L; Sycamore, N; Tester, J; Thorpe, A; Torcasso, W; Tracey, A; Tromans, A; Tsolas, J; Wall, M; Walsh, J; Wang, H; Weinstock, K; West, A P; Willey, D L; Whitehead, S L; Wilming, L; Wray, P W; Young, L; Chen, Y; Lovering, R C; Moschonas, N K; Siebert, R; Fechtel, K; Bentley, D; Durbin, R; Hubbard, T; Doucette-Stamm, L; Beck, S; Smith, D R; Rogers, J

    2004-05-27

    The finished sequence of human chromosome 10 comprises a total of 131,666,441 base pairs. It represents 99.4% of the euchromatic DNA and includes one megabase of heterochromatic sequence within the pericentromeric region of the short and long arm of the chromosome. Sequence annotation revealed 1,357 genes, of which 816 are protein coding, and 430 are pseudogenes. We observed widespread occurrence of overlapping coding genes (either strand) and identified 67 antisense transcripts. Our analysis suggests that both inter- and intrachromosomal segmental duplications have impacted on the gene count on chromosome 10. Multispecies comparative analysis indicated that we can readily annotate the protein-coding genes with current resources. We estimate that over 95% of all coding exons were identified in this study. Assessment of single base changes between the human chromosome 10 and chimpanzee sequence revealed nonsense mutations in only 21 coding genes with respect to the human sequence. PMID:15164054

  18. 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.

  19. The DNA sequence and comparative analysis of human chromosome 20.

    PubMed

    Deloukas, P; Matthews, L H; Ashurst, J; Burton, J; Gilbert, J G; Jones, M; Stavrides, G; Almeida, J P; Babbage, A K; Bagguley, C L; Bailey, J; Barlow, K F; Bates, K N; Beard, L M; Beare, D M; Beasley, O P; Bird, C P; Blakey, S E; Bridgeman, A M; Brown, A J; Buck, D; Burrill, W; Butler, A P; Carder, C; Carter, N P; Chapman, J C; Clamp, M; Clark, G; Clark, L N; Clark, S Y; Clee, C M; Clegg, S; Cobley, V E; Collier, R E; Connor, R; Corby, N R; Coulson, A; Coville, G J; Deadman, R; Dhami, P; Dunn, M; Ellington, A G; Frankland, J A; Fraser, A; French, L; Garner, P; Grafham, D V; Griffiths, C; Griffiths, M N; Gwilliam, R; Hall, R E; Hammond, S; Harley, J L; Heath, P D; Ho, S; Holden, J L; Howden, P J; Huckle, E; Hunt, A R; Hunt, S E; Jekosch, K; Johnson, C M; Johnson, D; Kay, M P; Kimberley, A M; King, A; Knights, A; Laird, G K; Lawlor, S; Lehvaslaiho, M H; Leversha, M; Lloyd, C; Lloyd, D M; Lovell, J D; Marsh, V L; Martin, S L; McConnachie, L J; McLay, K; McMurray, A A; Milne, S; Mistry, D; Moore, M J; Mullikin, J C; Nickerson, T; Oliver, K; Parker, A; Patel, R; Pearce, T A; Peck, A I; Phillimore, B J; Prathalingam, S R; Plumb, R W; Ramsay, H; Rice, C M; Ross, M T; Scott, C E; Sehra, H K; Shownkeen, R; Sims, S; Skuce, C D; Smith, M L; Soderlund, C; Steward, C A; Sulston, J E; Swann, M; Sycamore, N; Taylor, R; Tee, L; Thomas, D W; Thorpe, A; Tracey, A; Tromans, A C; Vaudin, M; Wall, M; Wallis, J M; Whitehead, S L; Whittaker, P; Willey, D L; Williams, L; Williams, S A; Wilming, L; Wray, P W; Hubbard, T; Durbin, R M; Bentley, D R; Beck, S; Rogers, J

    The finished sequence of human chromosome 20 comprises 59,187,298 base pairs (bp) and represents 99.4% of the euchromatic DNA. A single contig of 26 megabases (Mb) spans the entire short arm, and five contigs separated by gaps totalling 320 kb span the long arm of this metacentric chromosome. An additional 234,339 bp of sequence has been determined within the pericentromeric region of the long arm. We annotated 727 genes and 168 pseudogenes in the sequence. About 64% of these genes have a 5' and a 3' untranslated region and a complete open reading frame. Comparative analysis of the sequence of chromosome 20 to whole-genome shotgun-sequence data of two other vertebrates, the mouse Mus musculus and the puffer fish Tetraodon nigroviridis, provides an independent measure of the efficiency of gene annotation, and indicates that this analysis may account for more than 95% of all coding exons and almost all genes. PMID:11780052

  20. 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. PMID:25721292

  1. Comparative analysis of the space power architecture studies

    NASA Technical Reports Server (NTRS)

    Sovie, Ronald J.

    1988-01-01

    The Strategic Defense Initiative Organization (SDIO) has recently completed the initial phase of Space Power Architecture Studies (SPAS). The initial effort consisted of three major contracted efforts and a comparative analysis performed by the SDIO Independent Evaluation Group (IEG) and the IEG Field Support Team. The purpose of the SPAS effort was to evaluate a wide range of power systems for SDIO applications using a wide range of attributes other than power-system mass and volume. Open cycle, closed cycle, and closed power system/weapon platform concepts were studied. The purpose of this paper is to summarize the salient results of these studies, identify important trends and future study needs.

  2. 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.

  3. Comparative context analysis of codon pairs on an ORFeome scale

    PubMed Central

    Moura, Gabriela; Pinheiro, Miguel; Silva, Raquel; Miranda, Isabel; Afreixo, Vera; Dias, Gaspar; Freitas, Adelaide; Oliveira, José L; Santos, Manuel AS

    2005-01-01

    Codon context is an important feature of gene primary structure that modulates mRNA decoding accuracy. We have developed an analytical software package and a graphical interface for comparative codon context analysis of all the open reading frames in a genome (the ORFeome). Using the complete ORFeome sequences of Saccharomyces cerevisiae, Schizosaccharomyces pombe, Candida albicans and Escherichia coli, we show that this methodology permits large-scale codon context comparisons and provides new insight on the rules that govern the evolution of codon-pair context. PMID:15774029

  4. 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.

  5. Genome-wide Comparative Analysis of Annexin Superfamily in Plants

    PubMed Central

    Jami, Sravan Kumar; Clark, Greg B.; Ayele, Belay T.; Ashe, Paula; Kirti, Pulugurtha Bharadwaja

    2012-01-01

    Most annexins are calcium-dependent, phospholipid-binding proteins with suggested functions in response to environmental stresses and signaling during plant growth and development. They have previously been identified and characterized in Arabidopsis and rice, and constitute a multigene family in plants. In this study, we performed a comparative analysis of annexin gene families in the sequenced genomes of Viridiplantae ranging from unicellular green algae to multicellular plants, and identified 149 genes. Phylogenetic studies of these deduced annexins classified them into nine different arbitrary groups. The occurrence and distribution of bona fide type II calcium binding sites within the four annexin domains were found to be different in each of these groups. Analysis of chromosomal distribution of annexin genes in rice, Arabidopsis and poplar revealed their localization on various chromosomes with some members also found on duplicated chromosomal segments leading to gene family expansion. Analysis of gene structure suggests sequential or differential loss of introns during the evolution of land plant annexin genes. Intron positions and phases are well conserved in annexin genes from representative genomes ranging from Physcomitrella to higher plants. The occurrence of alternative motifs such as K/R/HGD was found to be overlapping or at the mutated regions of the type II calcium binding sites indicating potential functional divergence in certain plant annexins. This study provides a basis for further functional analysis and characterization of annexin multigene families in the plant lineage. PMID:23133603

  6. 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.

  7. Comparative proteomic analysis of ductal and lobular invasive breast carcinoma.

    PubMed

    Oliveira, N C S; Gomig, T H B; Milioli, H H; Cordeiro, F; Costa, G G; Urban, C A; Lima, R S; Cavalli, I J; Ribeiro, E M S F

    2016-01-01

    Breast cancer is the second most common cancer worldwide and the first among women. Invasive ductal carcinoma (IDC) and invasive lobular carcinoma (ILC) are the two major histological subtypes, and the clinical and molecular differences between them justify the search for new markers to distinguish them. As proteomic analysis allows for a powerful and analytical approach to identify potential biomarkers, we performed a comparative analysis of IDC and ILC samples by using two-dimensional electrophoresis and mass spectrometry. Twenty-three spots were identified corresponding to 10 proteins differentially expressed between the two subtypes. ACTB, ACTG, TPM3, TBA1A, TBA1B, VIME, TPIS, PDIA3, PDIA6, and VTDB were upregulated in ductal carcinoma compared to in lobular carcinoma samples. Overall, these 10 proteins have a key role in oncogenesis. Their specific functions and relevance in cancer initiation and progression are further discussed in this study. The identified peptides represent promising biomarkers for the differentiation of ductal and lobular breast cancer subtypes, and for future interventions based on tailored therapy. PMID:27173185

  8. 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

  9. 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

    2011-01-01

    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. PMID:21396338

  10. 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.

  11. Decentred comparative research: Context sensitive analysis of maternal health care.

    PubMed

    Wrede, Sirpa; Benoit, Cecilia; Bourgeault, Ivy Lynn; van Teijlingen, Edwin R; Sandall, Jane; De Vries, Raymond G

    2006-12-01

    Cross-national comparison is an important tool for health care research, but too often those who use this method fail to consider important inter-national differences in the social organisation of health care and in the relationship between health care practices and social experience. In this article we make the case for a context-sensitive and reflexive analysis of health care that allows researchers to understand the important ways that health care systems and practices are situated in time and place. Our approach--decentred comparative research--addresses the often unacknowledged ethnocentrism of traditional comparative research. Decentred cross-national research is a method that draws on the socially situated and distributed expertise of an international research team to develop key concepts and research questions. We used the decentred method to fashion a multilevel framework that used the meso level of organisation (i.e., health care organisations, professional groups and other concrete organisations) as an analytical starting point in our international study of maternity care in eight countries. Our method departs from traditional comparative health systems research that is most often conducted at the macro level. Our approach will help researchers develop new and socially robust knowledge about health care. PMID:16962695

  12. Rice fortification: a comparative analysis in mandated settings.

    PubMed

    Forsman, Carmen; Milani, Peiman; Schondebare, Jill A; Matthias, Dipika; Guyondet, Christophe

    2014-09-01

    Legal mandates can play an important role in the success of rice fortification programs that involve the private sector. However, merely enacting mandatory legislation does not guarantee success; it requires a coordinated, multidimensional cross-sector effort that addresses stewardship, develops an appropriate rice fortification technology, enables sustainable production and distribution channels through a range of private-sector players, ensures quality, generates consumer demand, and monitors progress. Furthermore, economic sustainability must be built into the supply chain and distribution network to enable the program to outlast government administrations and/or time-limited funding. Hence, mandates can serve as valuable long-term enablers of cross-sector mobilization and collaboration and as catalysts of civil society engagement in and ownership of fortification programs. This paper compares the rice fortification experiences of Costa Rica and the Philippines--two countries with mandates, yet distinctly different industry landscapes. Costa Rica has achieved national success through strong government stewardship and active market development--key elements of success regardless of industry structure. With a comparatively more diffuse rice industry structure, the Philippines has also had success in limited geographies where key stakeholders have played an active role in market development. A comparative analysis provides lessons that may be relevant to other rice fortification programs. PMID:24913356

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. Comparative Proteomics Analysis of Gastric Cancer Stem Cells

    PubMed Central

    Morisaki, Tamami; Yashiro, Masakazu; Kakehashi, Anna; Inagaki, Azusa; Kinoshita, Haruhito; Fukuoka, Tatsunari; Kasashima, Hiroaki; Masuda, Go; Sakurai, Katsunobu; Kubo, Naoshi; Muguruma, Kazuya; Ohira, Masaichi; Wanibuchi, Hideki; Hirakawa, Kosei

    2014-01-01

    Cancer stem cells (CSCs) are responsible for cancer progression, metastasis, and recurrence. To date, the specific markers of CSCs remain undiscovered. The aim of this study was to identify novel biomarkers of gastric CSCs for clinical diagnosis using proteomics technology. CSC-like SP cells, OCUM-12/SP cells, OCUM-2MD3/SP cells, and their parent OCUM-12 cells and OCUM-2MD3 cells were used in this study. Protein lysates from each cell line were analyzed using QSTAR Elite Liquid Chromatography with Tandem Mass Spectrometry, coupled with isobaric tags for relative and absolute quantitation technology. Candidate proteins detected by proteomics technology were validated by immunohistochemical analysis of 300 gastric cancers. Based on the results of LC-MS/MS, eight proteins, including RBBP6, GLG1, VPS13A, DCTPP1, HSPA9, HSPA4, ALDOA, and KRT18, were up-regulated in both OCUM-12/SP cells and OCUM-2MD3/SP cells when compared to their corresponding parent cells. RT-PCR analysis indicated that the expression level of RBBP6, HSPA4, DCTPP1, HSPA9, VPS13A, ALDOA, GLG1, and CK18 was high in OCUM-12/SP and OCUM-2MD3/SP, in compared with the control of parent OCUM-12 and OCUM-2MD3. These proteins were significantly associated with advanced invasion depth, lymph node metastasis, distant metastasis, or advanced clinical stage. RBBP6, DCTPP1, HSPA4, and ALDOA expression in particular were significantly associated with a poor prognosis in the 300 gastric cancer patients. RBBP6 was determined to be an independent prognostic factor. The motility-stimulating ability of OCUM-12/SP cells and OCUM-2MD3/SP cells was inhibited by RBBP6 siRNA. These findings might suggest that the eight proteins, RBBP6, GLG1, VPS13A, DCTPP1, HSPA9, HSPA4, ALDOA, and KRT18, utilizing comparative proteomics analysis, were perceived to be potential CSC markers of gastric cancer. Of the eight candidate proteins, RBBP6 was suggested to be a promising prognostic biomarker and a therapeutic target for gastric cancer

  19. 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

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

    PubMed

    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 (P thlA ) from C. acetobutylicum or native pta-ack promoter (P pta-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

  1. Comparative lipoplasty analysis of in vivo-treated adipose tissue.

    PubMed

    Rohrich, R J; Morales, D E; Krueger, J E; Ansari, M; Ochoa, O; Robinson, J; Beran, S J

    2000-05-01

    A comparative histologic and chemical analysis was undertaken of adipose tissue treated in vivo with traditional, ultrasound-assisted, and external ultrasound-assisted lipoplasty. A series of six healthy women undergoing elective liposuction according to the superwet technique using a 1:1 infiltration ratio with the estimated quantity of fat to be removed was included in the study. Four separate regions on each patient were treated independently in vivo with traditional liposuction, internal ultrasound-assisted liposuction, or external ultrasound-assisted liposuction for 7 minutes. External massage was used as a control. Four separate specimens of adipose tissue from each patient were assessed for cellular disruption using blinded histologic evaluation. The remainder of tissue was centrifuged to separate the aqueous phase from the cellular components and then spectrophotometrically analyzed for creatinine kinase and glycerol 3-phosphate dehydrogenase activity as markers of cellular disruption. Histologic analysis confirmed 70 to 90 percent cellular disruption with internal ultrasound-assisted liposuction. Suction-assisted and external ultrasound-assisted liposuction showed 5 to 25 percent disruption, whereas massage controls showed only 5 percent. Only internal ultrasound-assisted liposuction showed 5 to 20 percent thermal liquefaction. Absorbance analysis showed creatine kinase activity (sigma units) greatest in ultrasound-exposed tissue. Both external and internal ultrasound-assisted liposuction gave creatine kinase levels 28 to 33 percent greater than suction-assisted liposuction, which varied only 10 percent from controls. Glycerol 3-phosphate dehydrogenase activity was 44 percent greater for internal ultrasound-assisted liposuction than that detected with suction-assisted liposuction. Glycerol 3-phosphate dehydrogenase activity with external ultrasound-assisted liposuction and massage did not vary much from each other, at only 14 percent and 11 percent

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. Comparative and functional analysis of testis-specific genes.

    PubMed

    Liu, FuJun; Jin, ShaoHua; Li, Ning; Liu, Xin; Wang, HaiYan; Li, JianYuan

    2011-01-01

    The testis is the special male gonad responsible for spermatogenesis and steroidogenesis with complex gene expressions. Characterizing and comparing the testis-specific genes in different species can reveal key genes related to testis specific functions and provide supplementary information for study of human testis function. We screened testis-specific genes from Unigene libraries, total 317, 449 and 147 testis-specific genes were identified for human, mouse and rat, respectively. Ten from thirteen selected human testis-specific genes were validated exclusively expressed in the testis by reverse transcription polymerase chain reaction (RT-PCR). Systematic bioinformatics analysis showed that specific genes were mainly related to spermatogenesis and testis development process with significant Glycolysis and Pyruvate metabolism. Enrichment functions were discussed. PMID:21212513

  7. 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.

  8. Imaging hydrated microbial extracellular polymers: comparative analysis by electron microscopy.

    PubMed

    Dohnalkova, Alice C; Marshall, Matthew J; Arey, Bruce W; Williams, Kenneth H; Buck, Edgar C; Fredrickson, James 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 investigation of 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 by conventional electron microscopy approaches with 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 the nature of interactions between microbial extracellular polymers and their environment. PMID:21169451

  9. Comparing G: multivariate analysis of genetic variation in multiple populations.

    PubMed

    Aguirre, J D; Hine, E; McGuigan, K; Blows, M W

    2014-01-01

    The additive genetic variance-covariance matrix (G) summarizes the multivariate genetic relationships among a set of traits. The geometry of G describes the distribution of multivariate genetic variance, and generates genetic constraints that bias the direction of evolution. Determining if and how the multivariate genetic variance evolves has been limited by a number of analytical challenges in comparing G-matrices. Current methods for the comparison of G typically share several drawbacks: metrics that lack a direct relationship to evolutionary theory, the inability to be applied in conjunction with complex experimental designs, difficulties with determining statistical confidence in inferred differences and an inherently pair-wise focus. Here, we present a cohesive and general analytical framework for the comparative analysis of G that addresses these issues, and that incorporates and extends current methods with a strong geometrical basis. We describe the application of random skewers, common subspace analysis, the 4th-order genetic covariance tensor and the decomposition of the multivariate breeders equation, all within a Bayesian framework. We illustrate these methods using data from an artificial selection experiment on eight traits in Drosophila serrata, where a multi-generational pedigree was available to estimate G in each of six populations. One method, the tensor, elegantly captures all of the variation in genetic variance among populations, and allows the identification of the trait combinations that differ most in genetic variance. The tensor approach is likely to be the most generally applicable method to the comparison of G-matrices from any sampling or experimental design. PMID:23486079

  10. Comparative and evolutionary analysis of major peanut allergen gene families.

    PubMed

    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

    2014-09-01

    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

  11. 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

  12. Comparative analysis of 4x288 readouts and FPAs

    NASA Astrophysics Data System (ADS)

    Sizov, Fiodor F.; Reva, Vladimir P.; Derkach, Yurii P.; Vasiliev, Vladimir V.

    2005-10-01

    Comparative analysis of four 4x288 different designed readouts elaborated at the Institute of Microdevices and the Institute of Semiconductor Physics is presented. Also some features of design 576x6 readouts adduced. All the readouts have the direct injection input circuit with incorporated cells allowing testing without photodiodes. TDI registers have three delay elements between neighbor inputs. Some characteristics of 4x288 FPAs with mercury-cadmium-telluride TDI arrays are cited too. 2-phase and 4-phase CCD readouts (2.5 micron technology) have different channel types (surface, buried and semi-buried), which include 10 bit TDI registers in each channel, and 18 channel multiplexing to 16 outputs. Two polysili-con, one metal level and 400 A dielectric layers were used. The readouts characteristics: charge handling capacity, transfer characteristics, output nonlinearity characteristics, bias dispersion, etc. are presented. CCD technology used for data multiplication results in crosstalk increase, because of the presence of rather considerable transfer inefficiency at cryogenic temperatures. Using 2.5 micron CCD technology and 2.0 CMOS technology the readouts, which include the digital interface for dead pixels deselection, preliminary amplification circuits, 36 channel multiplication by CCD registers and 2 beat multiplication by analogue switches to 4 output amplifiers, were manufactured. One pocket CMOS technology with two polysilicon, two metal levels and 350 A dielectric layers were used. To increase the linearity of transfer characteristics and noise level decrease at the output of CCD the circuits of charge-voltage conversion on the base of operational amplifiers were used. This allows getting circuits with parameters close to those obtained by 0.8 - 1.0 micron CMOS technology. Also some characteristics of 4x288 readouts designed by 1.2 micron CMOS technology are discussed (two polysilicon and two metal levels). This one includes the circuits of auxiliary

  13. 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

  14. 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. PMID:25164757

  15. Comparative Metabolomic and Lipidomic Analysis of Phenotype Stratified Prostate Cells

    PubMed Central

    Booher, Christiana L.; Rhim, Johng S.; Rainville, Paul; Langridge, James; Baker, Andrew; Nyalwidhe, Julius O.

    2015-01-01

    Prostate cancer (PCa) is the most prevalent cancer amongst men and the second most common cause of cancer related-deaths in the USA. Prostate cancer is a heterogeneous disease ranging from indolent asymptomatic cases to very aggressive life threatening forms. The goal of this study was to identify differentially expressed metabolites and lipids in prostate cells with different tumorigenic phenotypes. We have used mass spectrometry metabolomic profiling, lipidomic profiling, bioinformatic and statistical methods to identify, quantify and characterize differentially regulated molecules in five prostate derived cell lines. We have identified potentially interesting species of different lipid subclasses including phosphatidylcholines (PCs), phosphatidylethanolamines (PEs), glycerophosphoinositols (PIs) and other metabolites that are significantly upregulated in prostate cancer cells derived from distant metastatic sites. Transcriptomic and biochemical analysis of key enzymes that are involved in lipid metabolism demonstrate the significant upregulation of choline kinase alpha in the metastatic cells compared to the non-malignant and non-metastatic cells. This suggests that different de novo lipogenesis and other specific signal transduction pathways are activated in aggressive metastatic cells as compared to normal and non-metastatic cells. PMID:26244785

  16. Comparative Analysis of Different LIDAR System Calibration Techniques

    NASA Astrophysics Data System (ADS)

    Miller, M.; Habib, A.

    2016-06-01

    With light detection and ranging (LiDAR) now being a crucial tool for engineering products and on the fly spatial analysis, it is necessary for the user community to have standardized calibration methods. The three methods in this study were developed and proven by the Digital Photogrammetry Research Group (DPRG) for airborne LiDAR systems and are as follows; Simplified, Quasi-Rigorous, and Rigorous. In lieu of using expensive control surfaces for calibration, these methods compare overlapping LiDAR strips to estimate the systematic errors. These systematic errors are quantified by these methods and include the lever arm biases, boresight biases, range bias and scan angle scale bias. These three methods comprehensively represent all of the possible flight configurations and data availability and this paper will test the limits of the method with the most assumptions, the simplified calibration, by using data that violates the assumptions it's math model is based on and compares the results to the quasi-rigorous and rigorous techniques. The overarching goal is to provide a LiDAR system calibration that does not require raw measurements which can be carried out with minimal control and flight lines to reduce costs. This testing is unique because the terrain used for calibration does not contain gable roofs, all other LiDAR system calibration testing and development has been done with terrain containing features with high geometric integrity such as gable roofs.

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

    PubMed Central

    Boyle, Alan P.; Araya, Carlos L.; Brdlik, Cathleen; Cayting, Philip; Cheng, Chao; Cheng, Yong; Gardner, Kathryn; Hillier, LaDeana; 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

    2014-01-01

    Summary Despite the large evolutionary distances, metazoan species show remarkable commonalities, which has helped establish fly and worm as model organisms for human biology1,2. 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. We mapped the genome-wide binding locations of 165 human, 93 worm, and 52 fly transcription-regulatory factors (RFs) 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 RF 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 in the regulatory underpinnings of model organism biology and how these relate to human biology, development, and disease. PMID:25164757

  18. 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.

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

    PubMed

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

    2015-09-01

    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. PMID:26192118

  20. 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. PMID:25296770

  1. FusoBase: an online Fusobacterium comparative genomic analysis platform

    PubMed Central

    Ang, Mia Yang; Heydari, Hamed; Jakubovics, Nick S.; Mahmud, Mahafizul Imran; Dutta, Avirup; Wee, Wei Yee; Wong, Guat Jah; Mutha, Naresh V.R.; Tan, Shi Yang; Choo, Siew Woh

    2014-01-01

    Fusobacterium are anaerobic gram-negative bacteria that have been associated with a wide spectrum of human infections and diseases. As the biology of Fusobacterium is still not well understood, comparative genomic analysis on members of this species will provide further insights on their taxonomy, phylogeny, pathogenicity and other information that may contribute to better management of infections and diseases. To facilitate the ongoing genomic research on Fusobacterium, a specialized database with easy-to-use analysis tools is necessary. Here we present FusoBase, an online database providing access to genome-wide annotated sequences of Fusobacterium strains as well as bioinformatics tools, to support the expanding scientific community. Using our custom-developed Pairwise Genome Comparison tool, we demonstrate how differences between two user-defined genomes and how insertion of putative prophages can be identified. In addition, Pathogenomics Profiling Tool is capable of clustering predicted genes across Fusobacterium strains and visualizing the results in the form of a heat map with dendrogram. Database URL: http://fusobacterium.um.edu.my. PMID:25149689

  2. Transcriptome profiling and comparative analysis of Panax ginseng adventitious roots

    PubMed Central

    Jayakodi, Murukarthick; Lee, Sang-Choon; Park, Hyun-Seung; Jang, Woojong; Lee, Yun Sun; Choi, Beom-Soon; Nah, Gyoung Ju; Kim, Do-Soon; Natesan, Senthil; Sun, Chao; Yang, Tae-Jin

    2014-01-01

    Background Panax ginseng Meyer is a traditional medicinal plant famous for its strong therapeutic effects and serves as an important herbal medicine. To understand and manipulate genes involved in secondary metabolic pathways including ginsenosides, transcriptome profiling of P. ginseng is essential. Methods RNA-seq analysis of adventitious roots of two P. ginseng cultivars, Chunpoong (CP) and Cheongsun (CS), was performed using the Illumina HiSeq platform. After transcripts were assembled, expression profiling was performed. Results Assemblies were generated from ∼85 million and ∼77 million high-quality reads from CP and CS cultivars, respectively. A total of 35,527 and 27,716 transcripts were obtained from the CP and CS assemblies, respectively. Annotation of the transcriptomes showed that approximately 90% of the transcripts had significant matches in public databases. We identified several candidate genes involved in ginsenoside biosynthesis. In addition, a large number of transcripts (17%) with different gene ontology designations were uniquely detected in adventitious roots compared to normal ginseng roots. Conclusion This study will provide a comprehensive insight into the transcriptome of ginseng adventitious roots, and a way for successful transcriptome analysis and profiling of resource plants with less genomic information. The transcriptome profiling data generated in this study are available in our newly created adventitious root transcriptome database (http://im-crop.snu.ac.kr/transdb/index.php) for public use. PMID:25379008

  3. 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

  4. Comparative genome analysis of Solanum lycopersicum and Solanum tuberosum

    PubMed Central

    Lall, Rohit; Thomas, George; Singh, Satendra; Singh, Archana; Wadhwa, Gulshan

    2013-01-01

    Solanum lycopersicum and Solanum tuberosum are agriculturally important crop species as they are rich sources of starch, protein, antioxidants, lycopene, beta-carotene, vitamin C, and fiber. The genomes of S. lycopersicum and S. tuberosum are currently available. However the linear strings of nucleotides that together comprise a genome sequence are of limited significance by themselves. Computational and bioinformatics approaches can be used to exploit the genomes for fundamental research for improving their varieties. The comparative genome analysis, Pfam analysis of predicted reviewed paralogous proteins was performed. It was found that S. lycopersicum proteins belong to more families, domains and clans in comparison with S. tuberosum. It was also found that mostly intergenic regions are conserved in two genomes followed by exons, intron and UTR. This can be exploited to predict regions between genomes that are similar to each other and to study the evolutionary relationship between two genomes, leading towards the development of disease resistance, stress tolerance and improved varieties of tomato. PMID:24307771

  5. Comparative sequence-structure analysis of Aves insulin

    PubMed Central

    Islam, Md Mirazul; Aktaruzzaman, M; Mohamed, Zahurin

    2015-01-01

    Normal blood glucose level depends on the availability of insulin and its ability to bind insulin receptor (IR) that regulates the downstream signaling pathway. Insulin sequence and blood glucose level usually vary among animals due to species specificity. The study of genetic variation of insulin, blood glucose level and diabetics symptoms development in Aves is interesting because of its optimal high blood glucose level than mammals. Therefore, it is of interest to study its evolutionary relationship with other mammals using sequence data. Hence, we compiled 32 Aves insulin from GenBank to compare its sequence-structure features with phylogeny for evolutionary inference. The analysis shows long conserved motifs (about 14 residues) for functional inference. These sequences show high leucine content (20%) with high instability index (>40). Amino acid position 11, 14, 16 and 20 are variable that may have contribution to binding to IR. We identified functionally critical variable residues in the dataset for possible genetic implication. Structural models of these sequences were developed for surface analysis towards functional representation. These data find application in the understanding of insulin function across species. PMID:25848166

  6. Sequence and comparative genomic analysis of actin-related proteins.

    PubMed

    Muller, Jean; Oma, Yukako; Vallar, Laurent; Friederich, Evelyne; Poch, Olivier; Winsor, Barbara

    2005-12-01

    Actin-related proteins (ARPs) are key players in cytoskeleton activities and nuclear functions. Two complexes, ARP2/3 and ARP1/11, also known as dynactin, are implicated in actin dynamics and in microtubule-based trafficking, respectively. ARP4 to ARP9 are components of many chromatin-modulating complexes. Conventional actins and ARPs codefine a large family of homologous proteins, the actin superfamily, with a tertiary structure known as the actin fold. Because ARPs and actin share high sequence conservation, clear family definition requires distinct features to easily and systematically identify each subfamily. In this study we performed an in depth sequence and comparative genomic analysis of ARP subfamilies. A high-quality multiple alignment of approximately 700 complete protein sequences homologous to actin, including 148 ARP sequences, allowed us to extend the ARP classification to new organisms. Sequence alignments revealed conserved residues, motifs, and inserted sequence signatures to define each ARP subfamily. These discriminative characteristics allowed us to develop ARPAnno (http://bips.u-strasbg.fr/ARPAnno), a new web server dedicated to the annotation of ARP sequences. Analyses of sequence conservation among actins and ARPs highlight part of the actin fold and suggest interactions between ARPs and actin-binding proteins. Finally, analysis of ARP distribution across eukaryotic phyla emphasizes the central importance of nuclear ARPs, particularly the multifunctional ARP4. PMID:16195354

  7. 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. PMID:23613770

  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. 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.

  10. Comparative kinetic analysis of two fungal β-glucosidases

    PubMed Central

    2010-01-01

    Background The enzymatic hydrolysis of cellulose is still considered as one of the main limiting steps of the biological production of biofuels from lignocellulosic biomass. It is a complex multistep process, and various kinetic models have been proposed. The cellulase enzymatic cocktail secreted by Trichoderma reesei has been intensively investigated. β-glucosidases are one of a number of cellulolytic enzymes, and catalyze the last step releasing glucose from the inhibitory cellobiose. β-glucosidase (BGL1) is very poorly secreted by Trichoderma reesei strains, and complete hydrolysis of cellulose often requires supplementation with a commercial β-glucosidase preparation such as that from Aspergillus niger (Novozymes SP188). Surprisingly, kinetic modeling of β-glucosidases lacks reliable data, and the possible differences between native T. reesei and supplemented β-glucosidases are not taken into consideration, possibly because of the difficulty of purifying BGL1. Results A comparative kinetic analysis of β-glucosidase from Aspergillus niger and BGL1 from Trichoderma reesei, purified using a new and efficient fast protein liquid chromatography protocol, was performed. This purification is characterized by two major steps, including the adsorption of the major cellulases onto crystalline cellulose, and a final purification factor of 53. Quantitative analysis of the resulting β-glucosidase fraction from T. reesei showed it to be 95% pure. Kinetic parameters were determined using cellobiose and a chromogenic artificial substrate. A new method allowing easy and rapid determination of the kinetic parameters was also developed. β-Glucosidase SP188 (Km = 0.57 mM; Kp = 2.70 mM) has a lower specific activity than BGL1 (Km = 0.38 mM; Kp = 3.25 mM) and is also more sensitive to glucose inhibition. A Michaelis-Menten model integrating competitive inhibition by the product (glucose) has been validated and is able to predict the β-glucosidase activity of both enzymes

  11. 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. PMID:22772837

  12. Comparative plasma proteome analysis of lymphoma-bearing SJL mice.

    PubMed

    Bhat, Vadiraja B; Choi, Man Ho; Wishnok, John S; Tannenbaum, Steven R

    2005-01-01

    In SJL mice, growth of RcsX lymphoma cells induces an inflammatory response by stimulating V(beta)16+ T cells. During inflammation, various serum protein levels can increase (e.g., acute phase reactants) or decrease (e.g., albumin), and most of these altered proteins are thus potential biomarkers. Although blood plasma is a valuable and promising sample for biomarker discovery for diseases or for novel drug targets, its proteome is complex. To address this, we have focused on a comprehensive comparison of the plasma proteomes from normal and RcsX-tumor-bearing SJL mice using the 1D-Gel-LC-MS/MS method after removing albumin and immunoglobulins. This analysis resulted in the identification of a total of 1079 nonredundant mouse plasma proteins; more than 480 in normal and 790 in RcsX-tumor-bearing SJL mouse plasma. Of these, only 191 proteins were found in common. The molecular weights ranged from 2 to 876 kDa, covering the pI values between 4.22 and 12.09, and included proteins with predicted transmembrane domains. By comparing the plasma proteomic profile of normal and RcsX-tumor-bearing SJL mice, we found significant changes in the levels of many proteins in RcsX-tumor-bearing mouse plasma. Most of the up-regulated proteins were identified as acute-phase proteins (APPs). Also, several unique proteins i.e., haptoglobin, proteosome subunits, fetuin-B, 14-3-3 zeta, MAGE-B4 antigen, etc, were found only in the tumor-bearing mouse plasma; either secreted, shed by membrane vesicles, or externalized due to cell death. These results affirm the effectiveness of this approach for protein identification from small samples, and for comparative proteomics in potential animal models of human disorders. PMID:16212437

  13. 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.

  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. PMID:24530623

  15. Comparative Analysis of Korean Human Gut Microbiota by Barcoded Pyrosequencing

    PubMed Central

    Nam, Young-Do; Jung, Mi-Ja; Roh, Seong Woon; Kim, Min-Soo; Bae, Jin-Woo

    2011-01-01

    Human gut microbiota plays important roles in harvesting energy from the diet, stimulating the proliferation of the intestinal epithelium, developing the immune system, and regulating fat storage in the host. Characterization of gut microbiota, however, has been limited to western people and is not sufficiently extensive to fully describe microbial communities. In this study, we investigated the overall composition of the gut microbiota and its host specificity and temporal stability in 20 Koreans using 454-pyrosequencing with barcoded primers targeting the V1 to V3 region of the bacterial 16S rRNA gene. A total of 303,402 high quality reads covered each sample and 8,427 reads were analyzed on average. The results were compared with those of individuals from the USA, China and Japan. In general, microbial communities were dominated by five previously identified phyla: Actinobacteria, Firmicutes, Bacteroidetes, Fusobacteria, and Proteobacteria. UPGMA cluster analysis showed that the species composition of gut microbiota was host-specific and stable over the duration of the test period, but the relative abundance of each member fluctuated. 43 core Korean gut microbiota were identified by comparison of sequences from each individual, of which 15 species level phylotypes were related to previously-reported butyrate-producing bacteria. UniFrac analysis revealed that human gut microbiota differed between countries: Korea, USA, Japan and China, but tended to vary less between individual Koreans, suggesting that gut microbial composition is related to internal and external characteristics of each country member such as host genetics and diet styles. PMID:21829445

  16. 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

  17. Comparative Analysis of State Fish Consumption Advisories Targeting Sensitive Populations

    PubMed Central

    Scherer, Alison C.; Tsuchiya, Ami; Younglove, Lisa R.; Burbacher, Thomas M.; Faustman, Elaine M.

    2008-01-01

    Objective Fish consumption advisories are issued to warn the public of possible toxicological threats from consuming certain fish species. Although developing fetuses and children are particularly susceptible to toxicants in fish, fish also contain valuable nutrients. Hence, formulating advice for sensitive populations poses challenges. We conducted a comparative analysis of advisory Web sites issued by states to assess health messages that sensitive populations might access. Data sources We evaluated state advisories accessed via the National Listing of Fish Advisories issued by the U.S. Environmental Protection Agency. Data extraction We created criteria to evaluate advisory attributes such as risk and benefit message clarity. Data synthesis All 48 state advisories issued at the time of this analysis targeted children, 90% (43) targeted pregnant women, and 58% (28) targeted women of childbearing age. Only six advisories addressed single contaminants, while the remainder based advice on 2–12 contaminants. Results revealed that advisories associated a dozen contaminants with specific adverse health effects. Beneficial health effects of any kind were specifically associated only with omega-3 fatty acids found in fish. Conclusions These findings highlight the complexity of assessing and communicating information about multiple contaminant exposure from fish consumption. Communication regarding potential health benefits conferred by specific fish nutrients was minimal and focused primarily on omega-3 fatty acids. This overview suggests some lessons learned and highlights a lack of both clarity and consistency in providing the breadth of information that sensitive populations such as pregnant women need to make public health decisions about fish consumption during pregnancy. PMID:19079708

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

    PubMed

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

    2015-01-01

    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. PMID:26505428

  19. Comparative analysis of two asymptotic approaches based on integral manifolds

    NASA Astrophysics Data System (ADS)

    Goldfarb, Igor; Gol'Dshtein, Vladimir; Maas, Ulrich

    2004-08-01

    A comparative analysis of the two powerful asymptotic methods, ILDM and MIM (intrinsic low-dimensional manifolds; method of invariant manifold), is presented in the paper. The two methods are based on the general theory of integral manifolds. The ILDM method is able to handle large systems of ODEs, whereas the MIM method treats systems with a limited number of unknown variables. The MIM method allows one to conduct analytical exploration of the original system and to obtain final expressions in compact form, whereas the ILDM method is a numerical approach that yields the numerical form of the desired surface. The ILDM method works well in a region where a rough splitting of the initial system exists. Regions of the phase space where splitting does not exist are problematic for the ILDM method. In these regions the MIM method provides additional information regarding the dynamical behaviour of the system. A number of simple examples are considered and analysed. It is shown that for the Semenov model (singularly perturbed system of ODEs) the ILDM method gives a surface which appears close to the first order (with respect to the corresponding small parameter) approximation of the stable (attracting) invariant manifolds. The complementary properties of the two asymptotic approaches suggests a feasible combination of the two methods, which is the subject of a future work.

  20. 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

  1. 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.

  2. Load-application devices: a comparative strain gauge analysis.

    PubMed

    Nishioka, Renato Sussumu; de Vasconcellos, Luis Gustavo Oliveira; Jóias, Renata Pilli; Rode, Sigmar de Mello

    2015-01-01

    In view of the low loading values commonly employed in dentistry, a load-application device (LAD) was developed as option to the universal testing machine (UTM), using strain gauge analysis. The aim of this study was to develop a load-application device (LAD) and compare the LAD with the UTM apparatus under axial and non-axial loads. An external hexagonal implant was inserted into a polyurethane block and one EsthetiCone abutment was connected to the implant. A plastic prosthetic cylinder was screwed onto the abutment and a conical pattern crown was fabricated using acrylic resin. An impression was made and ten identical standard acrylic resin patterns were obtained from the crown impression, which were cast in nickel-chromium alloy (n=10). Four strain gauges were bonded diametrically around the implant. The specimens were subjected to central (C) and lateral (L) axial loads of 30 kgf, on both devices: G1: LAD/C; G2: LAD/L; G3: UTM/C; G4: UTM/L. The data (με) were statistically analyzed by repeated measures ANOVA and Tukey's test (p<0.05). No statistically significant difference was found between the UTM and LAD devices, regardless of the type of load. It was concluded that the LAD is a reliable alternative, which induces microstrains to implants similar to those obtained with the UTM. PMID:26200149

  3. 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

  4. 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.

  5. 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.

  6. Comparative genomic analysis of ten Streptococcus pneumoniae temperate bacteriophages.

    PubMed

    Romero, Patricia; Croucher, Nicholas J; Hiller, N Luisa; Hu, Fen Z; Ehrlich, Garth D; Bentley, Stephen D; García, Ernesto; Mitchell, Tim J

    2009-08-01

    Streptococcus pneumoniae is an important human pathogen that often carries temperate bacteriophages. As part of a program to characterize the genetic makeup of prophages associated with clinical strains and to assess the potential roles that they play in the biology and pathogenesis in their host, we performed comparative genomic analysis of 10 temperate pneumococcal phages. All of the genomes are organized into five major gene clusters: lysogeny, replication, packaging, morphogenesis, and lysis clusters. All of the phage particles observed showed a Siphoviridae morphology. The only genes that are well conserved in all the genomes studied are those involved in the integration and the lysis of the host in addition to two genes, of unknown function, within the replication module. We observed that a high percentage of the open reading frames contained no similarities to any sequences catalogued in public databases; however, genes that were homologous to known phage virulence genes, including the pblB gene of Streptococcus mitis and the vapE gene of Dichelobacter nodosus, were also identified. Interestingly, bioinformatic tools showed the presence of a toxin-antitoxin system in the phage phiSpn_6, and this represents the first time that an addition system in a pneumophage has been identified. Collectively, the temperate pneumophages contain a diverse set of genes with various levels of similarity among them. PMID:19502408

  7. 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. PMID:23589541

  8. Comparative Analysis of Carbon Monoxide Tolerance among Thermoanaerobacter Species.

    PubMed

    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 × 10(5) 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

  9. A comparative analysis of network robustness against different link attacks

    NASA Astrophysics Data System (ADS)

    Duan, Boping; Liu, Jing; Zhou, Mingxing; Ma, Liangliang

    2016-04-01

    Recently, the study of optimizing network robustness has attracted increasing attentions, and the constraint that every node's degree cannot be changed is considered. Although this constraint maintains the node degree distribution consistently in order to reserve the structure of networks, it makes the network structure be lack of flexibility since many network structure always transform in the modern society. Given this consideration, in this paper, we analyze the robustness of networks through setting a new constraint; that is, only the number of edges should be unchanged. Then, we use the link-robustness index (Rl) as the measure of the network robustness against either random failures or intentional attacks, and make a comparative analysis of network robustness against different types of link attacks. Moreover, we use four types of networks as initial networks, namely scale-free networks, random networks, regular networks, and small-world networks. The experimental results show that the values of robustness measures for the optimized networks starting from different initial networks are similar under different link attacks, but the network topologies may be different. That is to say, networks with different topologies may have similar robustness in terms of the robustness measures. We also find that the optimized networks obtained by one link attack may not robust against other link attacks, sometimes, even weaker than the original networks. Therefore, before building networks, it is better to study which type of link attacks may happen.

  10. Comparative analysis of polymerization shrinkage of different resin composites.

    PubMed

    Barretto, Iana Coutinho; Pontes, Luana Farias; Carneiro, Karina Kato; Araujo, Jesuina Lamartine Nogueira; Ballester, Rafael Yague; Silva, Cecy Martins

    2015-01-01

    This study sought to compare the shrinkage of 3 resin composites after polymerization, using different curing modes and 2 methods of analysis, with 45 samples in each group. To evaluate free linear shrinkage, specimens were prepared in Teflon molds (8 mm diameter x 2 mm thick) with 1 of 2 methacrylate-based resins or a silorane-based resin. To evaluate wall-to-wall shrinkage, cavities (1.5 mm thick x 3 mm diameter) were prepared in 45 healthy bovine incisors and then restored. In both tests, the same curing lights were used: conventional quartz-tungsten-halogen, a conventional light-emitting diode (LED), and an exponential LED. Gaps were measured microscopically, and the gap percentage was calculated. The results were analyzed by 2-way ANOVA and Tukey's test (α = 0.05). Curing modes differed significantly in the free linear shrinkage test group, while resin composites did not. In the wall-to-wall shrinkage group, there were significant differences between the resin composites. PMID:25734285

  11. [Comparative analysis of seven marine biological source of mineral drugs].

    PubMed

    Si, Wei; A, Ru-na; Li, Shang-rong; Zhang, Jing-Xian; Wu, Wan-ying; Cui, Ya-jun

    2014-09-01

    The marine biological source of mineral drugs recorded in Chinese Pharmacopoeia (2010 version) mainly including pearl, nacre, clam shell, common oyster shell, ark shell, cuttle bone, and sea-ear shell are widely used in clinical. Calcium carbonate and a small amount of protein are the main components in this type of drugs. In this paper, a systematical and comparable study were carried out by determination of calcium carbonate by EDTA titration method, the crystal of calcium carbonate by X-Ray powder diffraction and the total amino acids (TAAs) of the hydrolyzed samples by ultraviolet spectrophotometry method. As a result, the crystal structure is calcite for common oyster shell, mixture of calcite and aragonite for nacre and sea-ear shell, aragonite for the other drugs. The content of calcium carbonate ranged from 86% to 96%. Cuttle bone has the highest amount of TAAs among the seven drugs which reached 1.7% while clam shell has the lowest content of 0.16% on average. In conclusion, an effective method was developed for the quality control of marine mineral drugs by comprehensive analysis of calcium carbonate and TAAs in the seven marine mineral drugs. PMID:25522620

  12. Comparative genomic analysis of seven Mycoplasma hyosynoviae strains

    PubMed Central

    Bumgardner, Eric A; Kittichotirat, Weerayuth; Bumgarner, Roger E; Lawrence, Paulraj K

    2015-01-01

    Infection with Mycoplasma hyosynoviae can result in debilitating arthritis in pigs, particularly those aged 10 weeks or older. Strategies for controlling this pathogen are becoming increasingly important due to the rise in the number of cases of arthritis that have been attributed to infection in recent years. In order to begin to develop interventions to prevent arthritis caused by M. hyosynoviae, more information regarding the specific proteins and potential virulence factors that its genome encodes was needed. However, the genome of this emerging swine pathogen had not been sequenced previously. In this report, we present a comparative analysis of the genomes of seven strains of M. hyosynoviae isolated from different locations in North America during the years 2010 to 2013. We identified several putative virulence factors that may contribute to the ability of this pathogen to adhere to host cells. Additionally, we discovered several prophage genes present within the genomes of three strains that show significant similarity to MAV1, a phage isolated from the related species, M. arthritidis. We also identified CRISPR-Cas and type III restriction and modification systems present in two strains that may contribute to their ability to defend against phage infection. PMID:25693846

  13. 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.

  14. 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+.

  15. Comparative Genomic Analysis of Mannheimia haemolytica from Bovine Sources.

    PubMed

    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

  16. 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

  17. A Comparative Analysis of Mitochondrial Genomes in Eustigmatophyte Algae.

    PubMed

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

    2016-03-01

    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

  18. Multisite surface electromyography and complementary healing intervention: a comparative analysis.

    PubMed

    Wirth, D P; Cram, J R

    1997-01-01

    A comparative analysis was conducted on a series of three experimental studies that examined the effect of various local and nonlocal (distant) complementary healing methods on multisite surface electromyographic (sEMG) and autonomic measures. The series concentrated sEMG electrode placement on specific neuromuscular paraspinal centers (cervical [C4], thoracic [T6], and lumbar [L3]), along with the frontalis region, due to the fact that these sites corresponded to the location of individual chakra centers as delineated in ancient Eastern medical and philosophical texts. It was hypothesized that the sEMG assessment procedure had the potential to provide objective, quantifiable correlates for complementary healing treatment effects, as well as assess the energy flow through the chakras during a healing treatment. The studies were the first of their kind to incorporate randomized, double-blind, placebo-controlled protocols in order to evaluate correlative neuromuscular multisite sEMG paraspinal measures with different complementary healing treatment interventions. Although the measurement protocols were similar between experiments, the results, demonstrated by the individual studies, varied. Whereas the overall findings of the series are encouraging because they indicate a potential objective scientific correlate to complementary healing treatment intervention, the results are considered preliminary in nature and appear to be linked to either the meditational experience of the subjects or dependent on the particular healer(s) used. Additional research is needed in order to establish the multisite sEMG assessment procedure as a reliable correlative measure for complementary healing treatment effects and to determine whether a consistent replicative treatment effect can be demonstrated independent of the specific subject population or practitioner(s) used. PMID:9449057

  19. 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

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

    PubMed

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

    2008-06-21

    In this study, we perform a scientific comparative analysis of using (60)Co beams in intensity-modulated radiation therapy (IMRT). In particular, we evaluate the treatment plan quality obtained with (i) 6 MV, 18 MV and (60)Co IMRT; (ii) different numbers of static multileaf collimator (MLC) delivered (60)Co beams and (iii) a helical tomotherapy (60)Co 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 (60)Co 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 (60)Co 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 (60)Co beam geometry achieved similar plan quality as static plans with 11 equidistant (60)Co beams. Furthermore, 18 MV plans were initially found not to provide the same target coverage as 6 MV and (60)Co plans; however, adjusting the trade-offs in the optimization model allowed equivalent target coverage for 18 MV. For plans with comparable

  1. 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

  2. [Crystal chemical and micromorphologic evaluation of ancient bone discoveries (Arabia Petraea, Jordan) from the 10th millennium B.C].

    PubMed

    Newesely, H

    1987-01-01

    As specialisations of osteoarchaeometry become increasingly developed, so the need of new analytical techniques and tests of a skillful applicability becomes more necessary. The crystal-chemical and micromorphological evaluations of preserved bone discoveries implicate reliable methods as X-ray diffraction, electron microscopy, and spectroscopy with the skeletal materials and the soil environment in which bones are found. The reactivity of soils varies widely as geological and sedimentological conditions offer typical but different environments: gravels, chalk soil, clay, salt soils, sands, cave earths are examples of this wide variety, including atmospheric and biogenetic implications. The last mentioned features are strongly effective also in aride regions, with the well known fluctations of high parching and dewiness. However, despite the diversity in deposition and burial modes only few parameters govern the gradual decomposition of bone material: 1. pH value of the surrounding medium; 2. humidity of the surrounding medium, may be governed directly by autolysis; 3. transport of matter, related to grain size, pore volume, solubility behaviour; 4. physical pressure; 5. destruction by microorganisms; as well as the surrounding medium will be altered by the uptake and the transformation of the products of bone decomposition. The materials of investigation were skeletal fragments buried of ea. 10,000 a within the soft dune sediment of the western border mountains of Wadi el Araba (Arabia Petraea, Jordan). The discovered bones are, as a common feature of this locality Basta, strongly sintered--indication on the afore mentioned reactivity of the aride soil as well. Bone fragments were partially burnt at Sabra locality and discolored, and sintered also at these circumstances. The reactivity of the bone fragments is shown in terms of exchange reactions within the crystal structure of the bone mineral, apatite Ca5(PO4)3OH at the calcium sites, hydroxyl sites, and

  3. 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…

  4. 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

  5. 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…

  6. 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:…

  7. 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…

  8. 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…

  9. 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 combinations of distinctive semantic features of…

  10. Science and Technology Policies and Priorities: A Comparative Analysis.

    ERIC Educational Resources Information Center

    Lederman, Leonard L.

    1987-01-01

    Compares the science and technology strategies and priorities of France, Germany, Japan, Sweden, the United Kingdom, and the United States. Analyzes the similarities and differences, historical settings, research and development allocations, coordinating mechanisms, outputs, dissatisfactions, and recent changes. (TW)

  11. 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...

  12. Traditional analysis of aquifer tests: Comparing apples to oranges?

    NASA Astrophysics Data System (ADS)

    Wu, Cheng-Mau; Yeh, Tian-Chyi J.; Zhu, Junfeng; Lee, Tim Hau; Hsu, Nien-Sheng; Chen, Chu-Hui; Sancho, Albert Folch

    2005-09-01

    Traditional analysis of aquifer tests uses the observed drawdown at one well, induced by pumping at another well, for estimating the transmissivity (T) and storage coefficient (S) of an aquifer. The analysis relies on Theis' solution or Jacob's approximate solution, which assumes aquifer homogeneity. Aquifers are inherently heterogeneous at different scales. If the observation well is screened in a low-permeability zone while the pumping well is located in a high-permeability zone, the resulting situation contradicts the homogeneity assumption in the traditional analysis. As a result, what does the traditional interpretation of the aquifer test tell us? Using numerical experiments and a first-order correlation analysis, we investigate this question. Results of the investigation suggest that the effective T and S for an equivalent homogeneous aquifer of Gaussian random T and S fields vary with time as well as the principal directions of the effective T. The effective T and S converge to the geometric and arithmetic means, respectively, at large times. Analysis of the estimated T and S, using drawdown from a single observation well, shows that at early time both estimates vary with time. The estimated S stabilizes rapidly to the value dominated by the storage coefficient heterogeneity in between the pumping and the observation wells. At late time the estimated T approaches but does not equal the effective T. It represents an average value over the cone of depression but influenced by the location, size, and degree of heterogeneity as the cone of depression evolves.

  13. 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. PMID:26948618

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. A Comparative Analysis of Teenagers Who Smoke Different Cigarette Brands.

    ERIC Educational Resources Information Center

    Enomoto, Carl E.

    2000-01-01

    Analyzes and compares the survey responses of teenagers who smoke different cigarette brands, specifically Marlboro, Camel, and Newport. Differences were seen across brands but teen smokers had similar opinions about quitting. Given the differences across brands, more flexible approaches may be needed to address teenage smoking. (Author/MKA)

  19. Comparative Analysis of Online vs. Face-to-Face Instruction.

    ERIC Educational Resources Information Center

    Johnson, Scott D.; Aragon, Steven R.; Shaik, Najmuddin; Palma-Rivas, Nilda

    This empirical study compared a graduate online course with an equivalent course taught in a traditional face-to-face format. Comparisons included student ratings of instructor and course quality; assessment of course interaction, structure, and support; and learning outcomes such as course grades and student self-assessment of ability to perform…

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  1. Comparative Analysis of Local Planning and Development of Magnet Schools.

    ERIC Educational Resources Information Center

    Blank, Rolf K.

    This paper, based on a recent comparative study of magnet schools conducted by the Department of Education, describes the features of successfully designed magnet schools. First, the paper highlights some of the major findings from the study on which it is based. Although there is a wide degree of variation in the design, development, and…

  2. Comparative genomic analysis of the Tribolium immune system

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The red flour beetle Tribolium castaneum has contributed a wealth of knowledge on insect development but limited information about innate immunity. With its complete nucleotide sequence determined, we have taken the opportunity to annotate immunity-related genes and compare them with homologous mole...

  3. 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…

  4. 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…

  5. 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…

  6. 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…

  7. Comparative proteomic analysis of virulent and rifampicin attenuated Flavobacterium psychrophilum

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Flavobacterium psychrophilum is the etiologic agent of bacterial coldwater disease and rainbow trout fry syndrome. In this study we compared a wild-type strain (CSF 259.93) with a rifampicin resistant and virulence attenuated strain of F. psychrophilum (CSF 259.93B.17). The attenuated strain harbour...

  8. 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. The…

  9. Analysis of Early Childhood Programs: A Search for Comparative Dimensions.

    ERIC Educational Resources Information Center

    Lay, Margaret; Dopyera, John

    To help educators obtain more specific comparative data on preschool programs, this paper develops some common constructs for the objective assessment of any program. The constructs proposed are: (1) density, the total amount of sensory stimulation encountered within a given time span; (2) variety, the extent to which the program provides…

  10. A Comparative Analysis of Higher Education Ranking Systems in Europe

    ERIC Educational Resources Information Center

    Hendel, Darwin D.; Stolz, Ingo

    2008-01-01

    According to Altbach in 2004, "everyone wants a world-class university". Corresponding developmental efforts undertaken by higher education institutions are very often referenced to improvements in ranking results. Surprisingly, there is relatively little analysis of variations in higher education ranking systems across countries regarding how…

  11. Comparative Molecular Analysis of Endoevaporitic Microbial Communities▿ †

    PubMed Central

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

    2008-01-01

    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. PMID:18757573

  12. COMPARATIVE STRATEGIES FOR USING CLUSTER ANALYSIS TO ASSESS DIETARY PATTERNS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this study was to characterize dietary patterns using two different cluster analysis strategies. In this cross-sectional study, diet information was assessed by five 24-hour recalls collected over 10 months. All foods were classified into 24 food subgroups. Demographic, health, and ...

  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. 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…

  15. A Comparative Investigation of Rotation Criteria within Exploratory Factor Analysis

    ERIC Educational Resources Information Center

    Sass, Daniel A.; Schmitt, Thomas A.

    2010-01-01

    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…

  16. [Comparative analysis of adolescent fertility in Senegal and Mali].

    PubMed

    Traore, B

    1990-08-01

    A demographer has analyzed data on women aged 15-19 from the Demographic and Health Surveys of Mali and of Senegal to compare their adolescent fertility rates and the determinants of adolescent fertility. 50% of married women in Mali were first married at 15.7 years compared to 16.6 years in Senegal. 30% of teens were married before age 14 in Mali compared to 14% in Senegal. In fact, single women were two times more common in Senegal than in Mali (56.5% vs. 24.6%). 71.5% of teens in Mali were married compared to 41.9% in Senegal. 28% of female teens lived in urban areas in Mali compared to 44.8% in Senegal. In Mali, the marriage law states that men must be at least 18 and women must be at least 15. Reasons women marry before age 15 include marriage based on degree of physical development rather than age, unofficial weddings, and misrepresentation of age. Thus, it is not unusual to meet married women aged 13, 14, and 15 in rural areas. In Senegal, however, the minimum marriage age was 20 for men and 16 for women. Despite the differences, among married women, pregnant adolescents comprised the same proportion (16.5% in Mali and 16.9% in Senegal). Yet, 44.5% of female teens in Mali have a child compared to 26.1% in Senegal. Fecund teens comprised 59.4% in Mali and 54.5% in Senegal. Even though teens in Mali were less likely to know about contraception (41.3% vs. 74.6%), they were more likely to use it (16.1% vs. 11.5%). They may have been using it to space their second birth. Between 1957-1961 and 1967-1971, adolescent fertility remained constant, while it increased during the 1970s. It fell during 1982-1986. In Senegal, between 1956-1960 and 1961-1965, adolescent fertility increased, while it remained constant between 1961-1965 and 1976-1980. During 1981-1985, it decreased markedly. The decrease in adolescent fertility in the 1980s paralleled an increase in female education. PMID:12346455

  17. Arbor: Comparative Analysis Workflows for the Tree of Life

    PubMed Central

    Harmon, Luke J.; Baumes, Jeffrey; Hughes, Charles; Soberon, Jorge; Specht, Chelsea D; Turner, Wesley; Lisle, Curtis; Thacker, Robert W.

    2013-01-01

    We describe our efforts to develop a software package, Arbor, that will enable scientific research in all aspects of comparative biology. This software will enable developmental biologists, geneticists, ecologists, geographers, paleobiologists, educators, and students to analyze diverse types of comparative data at multiple phylogenetic and spatiotemporal scales using an intuitive visual interface. Arbor’s user-defined workflows will be exported and shared so that entire analyses can be quickly replicated with new or updated data. Arbor will also be designed to easily and seamlessly expand to include novel analytical tools as they are developed. Here we describe the core components of Arbor, as well as provide details of one proposed test case to illustrate the software’s key functionality. PMID:23811960

  18. 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

  19. 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. PMID:21655146

  20. 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.

  1. A comparative study of a new cardiotocography analysis program.

    PubMed

    Chen, Chen-Yu; Chen, Ju-Cheng; Yu, Chun; Lin, Chii-Wann

    2009-01-01

    Cardiotocography (CTG) is a frequently used technique of fetal monitoring to evaluate the well being of the fetus during pregnancy and in labor. The surveillance technique depends on the analysis of characteristic fetal heart rate patterns and uterine contractions. Computerized analyses can mitigate the intra-observer and inter-observer variability of visual CTG recording explanation, decrease the examination time, and the need of additional tests for fetal health. Several studies also showed that the signal processing techniques could help to determine the fetal heart rate (FHR) patterns, but all of them were only suitable for physicians. Following the criteria and consensuses of National Institute of Child Health and Human Development in April 2008, we developed a LabVIEW based FHR and uterine contraction (UC) pattern analysis software. This software has great potential for home-care use. The signal processing methods utilized in this study are median filter and peak/valley detection method. The analysis performance was verified by nineteen pregnant women's data. The accuracy of FHR baseline, baseline variability, early deceleration, UC frequency and NST all reach 100%. The accuracy of acceleration frequency reaches 90%. The accuracy of late and variable decelerations reaches 95%. PMID:19965213

  2. 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. PMID:26560923

  3. 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

  4. 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. PMID:26824579

  5. The comparative analysis of various aerospace system concepts

    NASA Astrophysics Data System (ADS)

    Shkadov, L. M.; Denisov, V. Ye.; Lazarev, V. V.; Plokhikh, V. P.; Buzuluk, V. I.; Volodin, S. V.; Chervonenko, K. A.; Skipenko, V. V.

    1995-01-01

    Consideration is given to fully reusable winged two- and single-stage systems powered by hydrogen/oxygen rocket engines, which differ in types of takeoff [horizontal takeoff (HTO) using an undercarriage; ground sled-assisted takeoff; air launch from a subsonic carrier; and launching-pad vertical takeoff (VTO)]. The systems have been optimized and compared using two criteria: payload mass and "dry mass to payload mass" ratio. The influence of the gross weight of a system and the technological level on the criteria involved is being investigated.

  6. Comparative analysis of high performance solvers for solving Stokes equation

    NASA Astrophysics Data System (ADS)

    Ganzha, M.; Lirkov, I.; Paprzycki, M.

    2013-10-01

    We consider the time dependent Stokes equation on a finite time interval and on a uniform rectangular mesh, written in terms of velocity and pressure. A parallel algorithm, based on a direction splitting approach is implemented. We are targeting the massively parallel computer as well as clusters consisting of many-core nodes. The implementation was tested on the IBM Blue Gene/P supercomputer and two Linux clusters. We compared the results from the direction splitting algorithm with the results from a state-of-the-art Finite Element software package for solving of Stokes equation.

  7. Dynamic plantar pressure analysis. Comparing common insole materials.

    PubMed

    Sanfilippo, P B; Stess, R M; Moss, K M

    1992-10-01

    A comparison of five commonly used insole materials (Spenco, PPT, Plastazote, Nickelplast, and Pelite) was made to evaluate their effectiveness in reducing plantar vertical pressures on human subjects during walking. With the use of the EMED-SF pedograph force plate system, dynamic measures of vertical force, force-time integral, peak plantar pressure, pressure-time integral, and area of foot-to-ground contact were compared with the force plate covered with each of the insole materials and without any interface material. PMID:1474483

  8. 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.

  9. 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. PMID:19958344

  10. 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

  11. 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

  12. CACG: a database for comparative analysis of conjoined genes.

    PubMed

    Kim, Dae-Soo; Kim, Dong-Wook; Kim, Min-Young; Nam, Seong-Hyeuk; Choi, Sang-Haeng; Kim, Ryong Nam; Kang, Aram; Kim, Aeri; Park, Hong-Seog

    2012-07-01

    A conjoined gene is defined as one formed at the time of transcription by combining at least part of one exon from each of two or more distinct genes that lie on the same chromosome, in the same or opposite orientation, which translate independently into different proteins. We comparatively studied the extent of conjoined genes in thirteen genomes by analyzing the public databases of expressed sequence tags and mRNA sequences using a set of computational tools designed to identify conjoined genes on the same DNA strand or opposite DNA strands of the same genomic locus. The CACG database, available at http://cgc.kribb.re.kr/map/, includes a number of conjoined genes (7131-human, 2-chimpanzee, 5-orangutan, 57-chicken, 4-rhesus monkey, 651-cow, 27-dog, 2512-mouse, 263-rat, 1482-zebrafish, 5-horse, 29-sheep, and 8-medaka) and is very effective and easy to use to analyze the evolutionary process of conjoined genes when comparing different species. PMID:22584068

  13. 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. PMID:24261408

  14. Short communication: A comparative analysis of recombinant chymosins.

    PubMed

    Vallejo, J A; Ageitos, J M; Poza, M; Villa, T G

    2012-02-01

    The first step in cheesemaking is the milk clotting process, in which κ-caseinolytic enzymes contribute to micelle precipitation. The best enzyme for this purpose is chymosin because of its high degree of specificity toward κ-casein. Although recombinant bovine chymosin is the most frequently used chymosin in the industry, new sources of recombinant chymosin, such as goat, camel, or buffalo, are now available. The present work represents a comparative study of 4 different recombinant chymosins (goat and buffalo chymosins expressed in Pichia pastoris, and bovine and camel chymosin expressed in Aspergillus niger). Recombinant goat chymosin exhibited the best catalytic efficiency compared with the buffalo, bovine, or camel recombinant enzymes. Moreover, recombinant goat chymosin exhibited the best specific proteolytic activity, a wider pH range of action, and a lower glycosylation degree than the other 3 enzymes. In conclusion, we propose that recombinant goat chymosin represents a serious alternative to recombinant bovine chymosin for use in the cheesemaking industry. PMID:22281325

  15. A comparative collision-based analysis of human gait.

    PubMed

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

    2013-11-22

    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

  16. Comparative analysis of redirection methods for asteroid resource exploitation

    NASA Astrophysics Data System (ADS)

    Bazzocchi, Michael C. F.; Emami, M. Reza

    2016-03-01

    An in-depth analysis and systematic comparison of asteroid redirection methods are performed within a resource exploitation framework using different assessment mechanisms. Through this framework, mission objectives and constraints are specified for the redirection of an asteroid from a near-Earth orbit to a stable orbit in the Earth-Moon system. The paper provides a detailed investigation of five redirection methods, i.e., ion beam, tugboat, gravity tractor, laser sublimation, and mass ejector, with respect to their capabilities for a redirection mission. A set of mission level criteria are utilized to assess the performance of each redirection method, and the means of assigning attributes to each criterion is discussed in detail. In addition, the uncertainty in physical characteristics of the asteroid population is quantified through the use of Monte Carlo analysis. The Monte Carlo simulation provides insight into the performance robustness of the redirection methods with respect to the targeted asteroid range. Lastly, the attributes for each redirection method are aggregated using three different multicriteria assessment approaches, i.e., the Analytical Hierarchy Process, a utility-based approach, and a fuzzy aggregation mechanism. The results of each assessment approach as well as recommendations for further studies are discussed in detail.

  17. Comparative Proteomic Analysis of Yak Follicular Fluid during Estrus

    PubMed Central

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

    2016-01-01

    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. PMID:26954118

  18. 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.

  19. Comparative analysis of ACTH and corticosterone sampling methods in rats.

    PubMed

    Vahl, Torsten P; Ulrich-Lai, Yvonne M; Ostrander, Michelle M; Dolgas, C Mark; Elfers, Eileen E; Seeley, Randy J; D'Alessio, David A; Herman, James P

    2005-11-01

    A frequently debated question for studies involving the measurement of stress hormones in rodents is the optimal method for collecting blood with minimal stress to the animal. Some investigators prefer the implantation of indwelling catheters to allow for frequent sampling. Others argue that the implantation of a catheter creates a chronic stress to the animal that confounds stress hormone measures and therefore rely on tail vein sampling. Moreover, some investigators measure hormones in trunk blood samples obtained after anesthesia, a practice that may itself raise hormone levels. To address these controversies, we 1) compared plasma ACTH and corticosterone (Cort) concentrations in pre- and poststress rat blood samples obtained via previously implanted vena cava catheters, tail vein nicks, or clipping the tip off the tail and 2) compared plasma ACTH and Cort in rat blood samples obtained by decapitation with and without anesthesia. Rats sampled via indwelling catheters displayed lower prestress ACTH levels than those sampled by tail vein nick if the time to acquire samples was not limited; however, elevated basal ACTH was not observed in samples obtained by tail clip or tail nick when the samples were obtained within 3 min. Baseline Cort levels were similar in all groups. After restraint stress, the profile of the plasma ACTH and Cort responses was not affected by sampling method. Decapitation with prior administration of CO2 or pentobarbital sodium increased plasma ACTH levels approximately 13- and 2-fold, respectively, when compared with decapitation without anesthesia. These data indicate that tail vein nicking, tail clipping, or indwelling venous catheters can be used for obtaining plasma for ACTH and Cort during acute stress studies without confounding the measurements. However, the elevation in basal ACTH seen in the tail vein nick group at baseline suggests that sampling needs to be completed rapidly (<3 min) to avoid the initiation of the pituitary stress

  20. 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

  1. Comparative analysis of SN1987A antineutrino fluence

    NASA Astrophysics Data System (ADS)

    Vissani, Francesco

    2015-01-01

    We discuss the electron antineutrino fluence derived from the events detected by Kamiokande-II, IMB and Baksan on 23 February 1987. The data are analysed adopting a new simple and accurate formula for the signal, improving on the previous modeling of the detectors response, considering the possibility of background events. We perform several alternative analyses to quantify the relevance of various descriptions, approximations and biases. In particular, we study the effect of: omitting Baksan data or neglecting the background, using simplified formulae for the signal, modifying the fluence to account for oscillations and pinching, including the measured times and angles of the events, using other descriptions of detector response, etc. We show that most of these effects are small or negligible and argue, by comparing the allowed regions for astrophysical parameters, that the results are stable. We comment on the accordance with theoretical results and on open questions.

  2. 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.

  3. Satellite microwave observations of a storm complex: A comparative analysis

    NASA Technical Reports Server (NTRS)

    Martin, D. W.

    1985-01-01

    The hypothesis that cold events correspond to a particular stage in a class of thunderstorms was tested. That class is a storms class which updrafts are: (1) strong, broad and moist, and (2) extend well above the freezing level. Condition (1) implies strong mesoscale forcing. Condition (2) implies a tall updraft or a relatively low freezing level. Such storms should have big, intense radar echoes and cold, fast-growing anvils. The thunderstorm events were analyzed by radar, rain gauge and GOES infrared observations. Radar was the starting point for detection and definition of the hypothesized thunderstorms. The radar signature is compared to the signature of the storm in rain gauge observations, satellite infrared images and satellite microwave images.

  4. 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.

  5. 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.

  6. Comparative analysis and fusion of spatiotemporal information for footstep recognition.

    PubMed

    Vera-Rodriguez, Ruben; Mason, John S D; Fierrez, Julian; Ortega-Garcia, Javier

    2013-04-01

    Footstep recognition is a relatively new biometric which aims to discriminate people using walking characteristics extracted from floor-based sensors. This paper reports for the first time a comparative assessment of the spatiotemporal information contained in the footstep signals for person recognition. Experiments are carried out on the largest footstep database collected to date, with almost 20,000 valid footstep signals and more than 120 people. Results show very similar performance for both spatial and temporal approaches (5 to 15 percent EER depending on the experimental setup), and a significant improvement is achieved for their fusion (2.5 to 10 percent EER). The assessment protocol is focused on the influence of the quantity of data used in the reference models, which serves to simulate conditions of different potential applications such as smart homes or security access scenarios. PMID:22868647

  7. Comparative analysis of nonlinear optofluidic processes in microdroplets

    NASA Astrophysics Data System (ADS)

    Zhang, Peng; Jung, Sunghwan; Lee, Aram; Xu, Yong

    2016-06-01

    Our prior work has shown that high quality (Q ) factor whispering gallery modes (WGMs) in liquid microdroplets can potentially induce single-photon-level nonlinear effects through radiation pressure on the interface. However, little is known about the nonlinear effects of other processes involving scattering force and thermocapillarity. In this study, we establish a numerical framework that can calculate the fluid motion and the resultant nonlinearity induced by the optical scattering force and thermocapillarity. Then, we compare the magnitude of various nonlinear optofluidic processes induced by the radiation pressure, the thermocapillary effect, the scattering-induced optical force, and the Kerr effect. Using realistic fluid parameters, we show that the radiation pressure due to the WGM produces the strongest nonlinear optofluidic effect.

  8. 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.

  9. Federated queries for comparative effectiveness research: performance analysis.

    PubMed

    Price, Ronald C; Huth, Derick; Smith, Jody; Harper, Steve; Pace, Wilson; Pulver, Gerald; Kahn, Michael G; Schilling, Lisa M; Facelli, Julio C

    2012-01-01

    This paper presents a study of the performance of federated queries implemented in a system that simulates the architecture proposed for the Scalable Architecture for Federated Translational Inquiries Network (SAFTINet). Performance tests were conducted using both physical hardware and virtual machines within the test laboratory of the Center for High Performance Computing at the University of Utah. Tests were performed on SAFTINet networks ranging from 4 to 32 nodes with databases containing synthetic data for several million patients. The results show that the caGrid FQE (Federated Query Engine) is capable and suitable for comparative effectiveness research (CER) federated queries given its nearly linear scalability as partner nodes increase in number. The results presented here are also important for the specification of the hardware required to run a CER grid. PMID:22941983

  10. Comparative analysis of nonlinear optofluidic processes in microdroplets.

    PubMed

    Zhang, Peng; Jung, Sunghwan; Lee, Aram; Xu, Yong

    2016-06-01

    Our prior work has shown that high quality (Q) factor whispering gallery modes (WGMs) in liquid microdroplets can potentially induce single-photon-level nonlinear effects through radiation pressure on the interface. However, little is known about the nonlinear effects of other processes involving scattering force and thermocapillarity. In this study, we establish a numerical framework that can calculate the fluid motion and the resultant nonlinearity induced by the optical scattering force and thermocapillarity. Then, we compare the magnitude of various nonlinear optofluidic processes induced by the radiation pressure, the thermocapillary effect, the scattering-induced optical force, and the Kerr effect. Using realistic fluid parameters, we show that the radiation pressure due to the WGM produces the strongest nonlinear optofluidic effect. PMID:27415370

  11. 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.

  12. Police Suicide in Small Departments: A Comparative Analysis

    PubMed Central

    Violanti, John M.; Mnatsakanova, Anna; Hartley, Tara A.; Andrew, Michael E.; Burchfiel, Cecil M.

    2015-01-01

    The majority of police suicide research has focused on larger police departments. Very little research has been done within small departments. The present study compared suicide rates between small and larger police departments. Two Hundred ninty-eight departments were drawn from the U.S. Public Safety Officer Benefits database totaling 119,624 officers. Annual suicide rates were calculated per 100,000 for each of four category (by size of department) and p-values from Chi-square tests were employed to assess differences in rates across categories. The annual suicide rate varied significantly across departments. Smaller police departments had a significantly higher suicide rate than large departments. Possible reasons include lack of availability for mental health assistance, increased workload and danger, and community visibility. PMID:23894796

  13. Comparative Analysis of Mutant Tyrosine Kinase Chemical Rescue†

    PubMed Central

    Muratore, Kathryn E.; Seeliger, Markus A.; Wang, Zhihong; Fomina, Dina; Neiswinger, Johnathan; Havranek, James J.; Baker, David; Kuriyan, John; Cole, Philip A.

    2009-01-01

    Protein tyrosine kinases are critical cell signaling enzymes. These enzymes have a highly conserved Arg residue in their catalytic loop which is present two residues or four residues downstream from an absolutely conserved Asp catalytic base. Prior studies on protein tyrosine kinases Csk and Src revealed the potential for chemical rescue of catalytically-deficient mutant kinases (Arg to Ala mutations) by small diamino compounds, particularly imidazole, however the potency and efficiency of rescue was greater for Src. This current study further examines the structural and kinetic basis of rescue for mutant Src as compared to mutant Abl tyrosine kinase. An X-ray crystal structure of R388A Src revealed the surprising finding that a histidine residue of the N-terminus of a symmetry-related kinase inserts into the active site of the adjacent Src and mimics the hydrogen bonding pattern seen in wild-type protein tyrosine kinases. Abl R367A shows potent and efficient rescue more comparable to Src, even though its catalytic loop is more like that of Csk. Various enzyme redesigns of the active sites indicate that the degree and specificity of rescue is somewhat flexible, but the overall properties of the enzymes and rescue agents play an overarching role. The newly discovered rescue agent 2-aminoimidazole is about as efficient as imidazole in rescuing R/A Src and Abl. Rate vs. pH studies with these imidazole analogs suggest that the protonated imidazolium is the preferred form for chemical rescue, consistent with structural models. The efficient rescue seen with mutant Abl points to the potential of this approach to be used effectively to analyze Abl phosphorylation pathways in cells. PMID:19260709

  14. 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

  15. 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

  16. Comparative analysis of Staphylococcus aureus and Escherichia coli microcalorimetric growth

    PubMed Central

    2013-01-01

    Background Microcalorimetric bacterial growth studies have illustrated that thermograms differ significantly with both culture media and strain. The present contribution examines the possibility of discriminating between certain bacterial strains by microcalorimetry and the qualitative and quantitative contribution of the sample volume to the observed thermograms. Growth patterns of samples of Staphylococcus aureus (ATCC 25923) and Escherichia coli (ATCC 25922) were analyzed. Certain features of the thermograms that may serve to distinguish between these bacterial strains were identified. Results The thermograms of the two bacterial strains with sample volumes ranging from 0.3 to 0.7 ml and same initial bacterial concentration were analyzed. Both strains exhibit a roughly 2-peak shape that differs by peak amplitude and position along the time scale. Seven parameters corresponding to the thermogram key points related to time and heat flow values were proposed and statistically analyzed. The most relevant parameters appear to be the time to reach a heat flow of 0.05 mW (1.67 ± 0.46 h in E. coli vs. 2.99 ± 0.53 h in S. aureus, p < 0.0001), the time to reach the first peak (3.84 ± 0.5 h vs. 5.17 ± 0.49 h, p < 0.0001) and the first peak value (0.19 ± 0.02 mW vs. 0.086 ± 0.012 mW, p < 0.0001). The statistical analysis on 4 parameters of volume-normalized heat flow thermograms showed that the time to reach a volume-normalized heat flow of 0.1 mW/ml (1.75 ± 0.37 h in E. coli vs. 2.87 ± 0.65 h in S. aureus, p < 0.005), the time to reach the first volume-normalized peak (3.78 ± 0.47 h vs. 5.12 ± 0.52 h, p < 0.0001) and the first volume-normalized peak value (0.35 ± 0.05 mW/ml vs. 0.181 ± 0.040 mW/ml, p < 0.0001) seem to be the most relevant. Peakfit® decomposition and analysis of the observed thermograms complements the statistical analysis via quantitative arguments

  17. Comparative analysis of spectral coherence in microresonator frequency combs.

    PubMed

    Torres-Company, Victor; Castelló-Lurbe, David; Silvestre, Enrique

    2014-02-24

    Microresonator combs exploit parametric oscillation and nonlinear mixing in an ultrahigh-Q cavity. This new comb generator offers unique potential for chip integration and access to high repetition rates. However, time-domain studies reveal an intricate spectral coherence behavior in this type of platform. In particular, coherent, partially coherent or incoherent combs have been observed using the same microresonator under different pumping conditions. In this work, we provide a numerical analysis of the coherence dynamics that supports the above experimental findings and verify particular design rules to achieve spectrally coherent microresonator combs. A particular emphasis is placed in understanding the differences between so-called Type I and Type II combs. PMID:24663786

  18. 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.

  19. Apples, oranges, and angles: Comparative kinematic analysis of disparate limbs.

    PubMed

    Gatesy, Stephen M; Pollard, Nancy S

    2011-08-01

    Tetrapod limbs exhibit diverse postures and movements during terrestrial locomotion. As with morphological traits, the history of kinematic evolution should be accessible to reconstruction through analysis of limb motion patterns in a phylogenetic framework. However, the angular data comprising most kinematic descriptions appear to suffer from limitations that preclude meaningful comparison among disparate species. Using simple planar models, we discuss how geometric constraints render joint and elevation angles independent of neither morphology, degree of crouch, nor one another during the stance phase of locomotion. The implicit null hypothesis of potential similarity is invalidated because angular data are not viably transferable among limbs of dissimilar proportion and/or degree of crouch. Overlooking or dismissing the effect of constraints on angular parameterization hampers efforts to quantitatively elucidate the evolution of locomotion. We advocate a search for alternative methods of measuring limb movement that can decouple intersegmental coordination from morphology and posture. PMID:21600220

  20. 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. PMID:16765586

  1. Comparative Spectroscopic Analysis of B[e] Supergiants and LBV

    NASA Astrophysics Data System (ADS)

    Borges Fernandes, M.

    2000-02-01

    The upper HRD is populated by massive stars. These objects have, as a characteristic, a substantial mass loss, due mostly to radiation pressure, throughout their whole lives. However about the evolution of these stars, the only secure informations are that they are B or O type stars in the zero age main sequence and they finish their lifes in a supernova explosion. The difficulties, to ascertain the others evolutive stages of these objects, are that they do not exhibit (in most cases) photosferic absorption lines, due to their complex circumstellar medium, preventing the estimate of the physical parameters. Moreover, these phases are relatively "shorts", and so we have a little sample of objects. Among the "short" phases, we detach the B[e] Supergiant (B[e]sg) and the Luminous Blue Variable (LBV) phases. The stars in these two evolutive stages show similar characteristics in the optical spectrum. They are, the presence in B type stars, of forbidden emission lines of [FeII], [OI] (in the B[e]sg) and [NII] (in the LBV). The presence of strong Balmer emission lines, low excitation permitted emission lines of predominantly low ionization metals, e.g. FeII in the optical spectrum and a strong near or mid-infrared excess due to hot circumstellar dust. In general, the Balmer lines (and sometimes HeI and FeII lines too) show P-Cygni profiles, due to mass loss. In despite of the similarities, the LBV are separated of the B[e]sg, due to strong spectral-photometric variability. Then it is necessary a detailed spectroscopical analysis of some objects, to obtain not only a better classification, like a B[e]sg or LBV, but useful informations to perform in the future a physical model. We have done such analysis for five stars in the Galaxy: HD 87643, HD 89249, HR Car, GG Car and CPD-529243. With our new data, others presented by literature, and a long time monitoring of these stars, we believe that in the near future, it will be possible to determine a correct classification to

  2. 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

  3. Comparative analysis of whole blood lysis methods for flow cytometry.

    PubMed

    Bossuyt, X; Marti, G E; Fleisher, T A

    1997-06-15

    We performed a parallel evaluation of six whole blood lysis methods comparing light scatter and quantitative fluorescence intensity based on quantitative flow cytometry, of selected lymphocyte subsets and CD34+ cells. Leukocytes prepared with FACS Lysing Solution (BDIS), Immunolyse (Coulter) and Optilyse B (Immunotech) consistently gave lower forward scatter values than those prepared with ACK (BioWhitaker), Ortho-mune (Ortho) and ImmunoPrep (Coulter). Debris, defined as CD45 negative events with the threshold off, accounted approximately 80% of all events with ACK and Ortho-mune. The other lysing methods consistently yielded less debris (approximately 50%) with Immunolyse generating only approximately 16% debris. Optilyse and FACS lyse consistently displayed the lowest percentage of lymphoid cells (CD45+/CD14-) in the three part differential. The percentage of CD3+, CD20+, CD5+, and CD16/CD56+ cells was consistent with all methods but CD4 and CD8 determinants showed inconsistent variation with ACK and Ortho-mune. In addition, the fluorescence intensity of CD14 PE and CD8 PE staining was markedly decreased on cells prepared with ImmunoPrep. Finally, the clearest separation of CD34+ cells was observed with ACK and Ortho-mune. Our data demonstrate that the method used for red cell lysis can have definite impact on immunophenotyping and selected methods appear to be more suitable for specific applications. PMID:9222098

  4. 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. PMID:17371500

  5. Comparative analysis of two bacteriophages of Xanthomonas arboricola pv. juglandis.

    PubMed

    Dömötör, Dóra; Frank, Tamara; Rákhely, Gábor; Doffkay, Zsolt; Schneider, György; Kovács, Tamás

    2016-09-01

    Walnut blight caused by Xanthomonas arboricola pv. juglandis (Xaj) is one of the most frequent infective diseases of walnut, resulting in serious economic losses. One potential solution to control this disease could be the application of bacteriophages. In this study, 24 phages were isolated from soil and walnut aerial tissues infected with Xaj. Two polyvalent bacteriophages, Xaj2 and Xaj24 were chosen for further characterization including their morphological, physiological and genomic analyses. Xaj2 was classified as Siphoviridae whereas Xaj24 belonged to the Podoviridae family. Both phages demonstrated lytic effect on Xaj in laboratory trials. Complete genomes of Xaj2 and Xaj24 were determined. Genomes of Xaj2 and Xaj24 consisted of 49.241 and 44.861 nucleotides encoding 80 and 53 genes, respectively. Comparative genome analyses have revealed that Xaj2 had a unique genome sequence, while Xaj24 was a phiKMV-like phage and it was most similar to the Prado phage which is virulent for Xylella fastidiosa and Xanthomonas spp. In this study, we present the first two complete Xaj phage sequences enabling an insight into the genomics of Xaj phages. PMID:27275846

  6. Computational methods for comparative analysis of plant small RNAs.

    PubMed

    Mahalingam, Gayathri; Meyers, Blake C

    2010-01-01

    Small RNAs play an important role in plant development, stress responses, and epigenetic regulation, primarily through their role in transcriptional and post-transcriptional silencing of specific target genes and loci. Most if not all plants utilize these small RNA signaling networks. We have developed a deep-sequencing based dataset of plant small RNAs, based on the hypothesis that comparisons among the complex pool of small RNAs from diverse plants will identify novel types of conserved, regulated, or species-specific molecules. A database containing upward of hundreds of millions of plant small RNA sequences is being created for comparative analyses. This small RNA database will allow the experimental characterization of the majority of the biologically important small RNAs for a range of plant species. This database can be accessed from our website (http://smallrna.udel.edu/). A variety of web-based tools have been developed for analyses of these data. Here, we focus on these tools, and we describe how the users can implement these tools to analyze and interpret the small RNA data and how the users could use similar approaches for other sets of plant small RNAs from diverse species. PMID:19802596

  7. Comparative, transcriptome analysis of self-organizing optic tissues

    PubMed Central

    Andrabi, Munazah; Kuraku, Shigehiro; Takata, Nozomu; Sasai, Yoshiki; Love, Nick R.

    2015-01-01

    Embryonic stem (ES) cells have a remarkable capacity to self-organize complex, multi-layered optic cups in vitro via a culture technique called SFEBq. During both SFEBq and in vivo optic cup development, Rax (Rx) expressing neural retina epithelial (NRE) tissues utilize Fgf and Wnt/β-catenin signalling pathways to differentiate into neural retina (NR) and retinal-pigmented epithelial (RPE) tissues, respectively. How these signaling pathways affect gene expression during optic tissue formation has remained largely unknown, especially at the transcriptome scale. Here, we address this question using RNA-Seq. We generated Rx+ optic tissue using SFEBq, exposed these tissues to either Fgf or Wnt/β-catenin stimulation, and assayed their gene expression across multiple time points using RNA-Seq. This comparative dataset will help elucidate how Fgf and Wnt/β-catenin signaling affect gene expression during optic tissue differentiation and will help inform future efforts to optimize in vitro optic tissue culture technology. PMID:26110066

  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. PMID:25420536

  9. Comparative transcriptomic analysis of human and Drosophila extracellular vesicles.

    PubMed

    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

  10. 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

  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. PMID:25534625

  12. Comparative Proteomic Analysis of Cysteine Oxidation in Colorectal Cancer Patients

    PubMed Central

    Yang, Hee-Young; Chay, Kee-Oh; Kwon, Joseph; Kwon, Sang-Oh; Park, Young-Kyu; Lee, Tae-Hoon

    2013-01-01

    Oxidative stress promotes damage to cellular proteins, lipids, membranes and DNA, and plays a key role in the development of cancer. Reactive oxygen species disrupt redox homeostasis and promote tumor formation by initiating aberrant activation of signaling pathways that lead to tumorigenesis. We used shotgun proteomics to identify proteins containing oxidation-sensitive cysteines in tissue specimens from colorectal cancer patients. We then compared the patterns of cysteine oxidation in the membrane fractions between the tumor and non-tumor tissues. Using nano-UPLC-MSE proteomics, we identified 31 proteins containing 37 oxidation-sensitive cysteines. These proteins were observed with IAM-binding cysteines in non-tumoral region more than tumoral region of CRC patients. Then using the Ingenuity pathway program, we evaluated the cellular canonical networks connecting those proteins. Within the networks, proteins with multiple connections were related with organ morphology, cellular metabolism, and various disorders. We have thus identified networks of proteins whose redox status is altered by oxidative stress, perhaps leading to changes in cellular functionality that promotes tumorigenesis. PMID:23677378

  13. A comparative analysis of acoustic energy models for churches.

    PubMed

    Berardi, Umberto; Cirillo, Ettore; Martellotta, Francesco

    2009-10-01

    Different models to improve prediction of energy-based acoustic parameters in churches have been proposed by different researchers [E. Cirillo and F. Martellotta, J. Acoust. Soc. Am. 118, 232-248 (2005); T. Zamarreño et al., J. Acoust. Soc. Am. 121, 234-250 (2006)]. They all suggested variations to the "revised" theory proposed by Barron and Lee [J. Acoust. Soc. Am. 84, 618-628 (1988)], starting from experimental observations. The present paper compares these models and attempts to generalize their use taking advantage of the measurements carried out in 24 Italian churches differing in style, typology, and location. The whole sample of churches was divided into two groups. The first was used to fine-tune existing models, with particular reference to the "mu model," which was originally tested only on Mudejar-Gothic churches. Correlations between model parameters and major typological and architectural factors were found, leading to a classification that greatly simplifies parameter choice. Finally, the reliability of each model was verified on the rest of the sample, showing that acoustic parameters can be predicted with reasonable accuracy provided that one of the specifically modified theories is used. The results show that the model requiring more input parameters performs slightly better than the other which, conversely, is simpler to apply. PMID:19813798

  14. 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. PMID:26053332

  15. 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

  16. 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 scheduler's assumptions.

  17. Comparative analysis of protocols for DNA extraction from soybean caterpillars.

    PubMed

    Palma, J; Valmorbida, I; da Costa, I F D; Guedes, J V C

    2016-01-01

    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. PMID:27173218

  18. 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

  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. 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

  1. 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

  2. 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

  3. 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.

  4. 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. PMID:18829288

  5. [Comparative proteomic analysis of cancerous and adjacent normal lung tissues].

    PubMed

    Lee, Ki Beom; Pi, Kyung Bae

    2010-01-01

    Lung cancer is the leading cause of cancer-related mortality in industrialized countries. Unfortunately, most lung cancers are found too late for a cure, therefore early detection and treatment is very important. We have applied proteomic analysis by using two-dimensional gel electrophoresis and peptide mass fingerprinting techniques for examination of cancerous and adjacent non-cancerous lung tissues from the same patient. The aim of the study was to find proteins, which could be used as biomarkers for diagnosis and monitoring of this disease. Indeed, we found differences in expression of several proteins, related to various cellular activities, such as, chaperoning (e.g., GRP96, GRP78, HSP27), metabolism and oxidation stress (e.g., L-fucose, GST), cytoskeleton (e.g., tubulin beta 2/3, beta actin), cell adhesion (e.g., annexin A5/3), binding proteins (e.g., 14-3-3 theta) and signal transduction. These changes may be important for progression of carcinogenesis; they may be used as the molecular-support for future diagnostic markers. PMID:21395069

  6. Comparative analysis of Paenibacillus larvae genotypes isolated in Connecticut.

    PubMed

    Dingman, Douglas W

    2015-08-01

    Ninety-six strains of Paenibacillus larvae, causative agent of American foulbrood in honey bee (Apis mellifera) larvae, collected from Connecticut, USA (CT), honey bees, and 12 P. larvae strains not from CT, were genotyped via ERIC-PCR and XbaI-RFLP analysis. All CT-isolates, five strains isolated in South America, three strains from North America (not CT), and one strain isolated in Australia grouped into the ERIC I genotype. Three P. larvae formerly subsp. pulvifaciens strains grouped into ERIC III and IV genotypes. XbaI-RFLP genotyping showed three genotypes within the CT-isolates, and two were identified as XbaI-RFLP Type I and III. The third XbaI-RFLP genotype (Type Ib) represented one of four new XbaI-RFLP genotypes identified. Comparison of genotype results for the P. larvae strains tested was used to develop a correlation between ERIC-PCR genotyping and XbaI-RFLP genotyping. Sixteen CT-isolates were tetracycline-resistant and demonstrated PCR amplification using oligonucleotide primers for tetL. All 16 isolates grouped within XbaI-RFLP Type Ib, suggesting limited introduction of a tetracycline-resistant strain into CT. PMID:25929327

  7. 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

    2015-01-01

    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

  8. [Comparative clinical analysis of histological systems of adrenocortical tumors diagnosis].

    PubMed

    Bokhyan, V Yu; Stilidi, I S; Pavlovskaya, A I

    2015-01-01

    Differential diagnosis of adrenocortical cancer (ACC) and cortical adenoma presents certain difficulties since there is no specific histological criterion allowing to distinguish tumors of the adrenal cortex with malignant clinical course. Currently there are offered several systems, and the most widely spread have the index Weiss (IW) and the modified index Weiss (MIW). The accuracy of one or another of the proposed systems remains a matter of debate. There was analyzed own experience on the use of IW and MIW in the diagnosis of 91 cases of the ACC and 13 cases of cortex adenomas of the size at least 5 cm. For the diagnosis of large adenomas sensitivity IW was 77%, MIW--100%. For the diagnosis of metastatic and non-metastatic ACC--100% and 97%, 100% and 86%, respectively (p > 0.05). In multivariate analysis of life expectancy of patients the definition of IW and MIW had a prognostic significance. MIW was less subjective, more simple and convenient to be used and it showed a great informative value at the reclassification of certain "adenomas" into ACC. However to use it on their own, without IW, was impractical as MIW had wider gray area and did not reach the threshold value in some cases of ACC. For the diagnosis of tumors of the adrenal cortex IW remains a standard; when a value was equal of 2 or in cases of doubt it was necessary to calculate MIW as well. PMID:26995980

  9. Systematic Characterization and Comparative Analysis of the Rabbit Immunoglobulin Repertoire

    PubMed Central

    Lavinder, Jason J.; Hoi, Kam Hon; Reddy, Sai T.; Wine, Yariv; Georgiou, George

    2014-01-01

    Rabbits have been used extensively as a model system for the elucidation of the mechanism of immunoglobulin diversification and for the production of antibodies. We employed Next Generation Sequencing to analyze Ig germline V and J gene usage, CDR3 length and amino acid composition, and gene conversion frequencies within the functional (transcribed) IgG repertoire of the New Zealand white rabbit (Oryctolagus cuniculus). Several previously unannotated rabbit heavy chain variable (VH) and light chain variable (VL) germline elements were deduced bioinformatically using multidimensional scaling and k-means clustering methods. We estimated the gene conversion frequency in the rabbit at 23% of IgG sequences with a mean gene conversion tract length of 59±36 bp. Sequencing and gene conversion analysis of the chicken, human, and mouse repertoires revealed that gene conversion occurs much more extensively in the chicken (frequency 70%, tract length 79±57 bp), was observed to a small, yet statistically significant extent in humans, but was virtually absent in mice. PMID:24978027

  10. 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.

  11. Comparative proteome analysis of butachlor-degrading bacteria

    NASA Astrophysics Data System (ADS)

    Wang, Jinhua; Lu, Yitong; Chen, Yingying

    2008-01-01

    A Pseudomonas putida strain, named ER1, was isolated from an agricultural soil and found to actively degrade the herbicide butachlor. The enzyme extracted from ER1 could degrade butachlor. Furthermore, incubation of ER1 in a medium containing 50 mg/kg of butachlor after 3 days resulted in the high butachlor-degrading enzyme activity of ER1. Response of ER1 to butachlor might be related to changes in protein composition at both quantitative and qualitative levels. Total proteins were extracted from control strain (incubated in the medium without butachlor) and the treated strain (incubated in the medium with butachlor). The proteins were separated by two-dimensional gel electrophoresis. Of the total number of ER1 protein, 11 spots were significantly changed under butachlor stress. Analysis by matrix-assisted laser desorption/ionization mass spectrometry and tandem mass spectrometry coupled with database searching allowed the function of some proteins which were similar to the hydrolases activity or oxidoreductase activity.

  12. 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

  13. 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

  14. Functional Annotation and Comparative Analysis of a Zygopteran Transcriptome.

    PubMed

    Shanku, Alexander G; McPeek, Mark A; Kern, Andrew D

    2013-03-11

    In this paper we present a de novo assembly of the transcriptome of the damselfly, Enallagma hageni, through the use of 454 pyrosequencing. E. hageni is a member of the suborder Zygoptera within the order Odonata, and the Odonata are the basal lineage of the winged insects (Pterygota). To date, sequence data used in phylogenetic analysis of Enallagma species have been derived from either mtDNA or ribosomal nuclear DNA. This transcriptome contained 31,661 contigs that were assembled and translated into 14,813 individual open reading frames. Using these data, we constructed an extensive dataset of 634 orthologous nuclear protein-coding genes across 11 species of Arthropoda, and used Bayesian techniques to elucidate Enallagma's place in the Arthropod phylogenetic tree. Additionally, we demonstrate that the Enallagma transcriptome contains 169 genes that are evolving at rates that differ relative to the rest of the transcriptome (29 accelerated and 140 decreased), and through multiple Gene Ontology searches and clustering methods, we present the first functional-annotation of any palaeopteran's transcriptome in the literature. PMID:23550132

  15. rCAD: A Novel Database Schema for the Comparative Analysis of RNA.

    PubMed

    Ozer, Stuart; Doshi, Kishore J; Xu, Weijia; Gutell, Robin R

    2011-12-31

    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

  16. Comparative Analysis of Codon Usage Bias Patterns in Microsporidian Genomes

    PubMed Central

    Xiang, Heng; Zhang, Ruizhi; Butler, Robert R.; Liu, Tie; Zhang, Li; Pombert, Jean-François; Zhou, Zeyang

    2015-01-01

    The sub-3 Mbp genomes from microsporidian species of the Encephalitozoon genus are the smallest known among eukaryotes and paragons of genomic reduction and compaction in parasites. However, their diminutive stature is not characteristic of all Microsporidia, whose genome sizes vary by an order of magnitude. This large variability suggests that different evolutionary forces are applied on the group as a whole. In this study, we have compared the codon usage bias (CUB) between eight taxonomically distinct microsporidian genomes: Encephalitozoon intestinalis, Encephalitozoon cuniculi, Spraguea lophii, Trachipleistophora hominis, Enterocytozoon bieneusi, Nematocida parisii, Nosema bombycis and Nosema ceranae. While the CUB was found to be weak in all eight Microsporidia, nearly all (98%) of the optimal codons in S. lophii, T. hominis, E. bieneusi, N. parisii, N. bombycis and N. ceranae are fond of A/U in third position whereas most (64.6%) optimal codons in the Encephalitozoon species E. intestinalis and E. cuniculi are biased towards G/C. Although nucleotide composition biases are likely the main factor driving the CUB in Microsporidia according to correlation analyses, directed mutational pressure also likely affects the CUB as suggested by ENc-plots, correspondence and neutrality analyses. Overall, the Encephalitozoon genomes were found to be markedly different from the other microsporidians and, despite being the first sequenced representatives of this lineage, are uncharacteristic of the group as a whole. The disparities observed cannot be attributed solely to differences in host specificity and we hypothesize that other forces are at play in the lineage leading to Encephalitozoon species. PMID:26057384

  17. Comparative Analysis of Codon Usage Bias Patterns in Microsporidian Genomes.

    PubMed

    Xiang, Heng; Zhang, Ruizhi; Butler, Robert R; Liu, Tie; Zhang, Li; Pombert, Jean-François; Zhou, Zeyang

    2015-01-01

    The sub-3 Mbp genomes from microsporidian species of the Encephalitozoon genus are the smallest known among eukaryotes and paragons of genomic reduction and compaction in parasites. However, their diminutive stature is not characteristic of all Microsporidia, whose genome sizes vary by an order of magnitude. This large variability suggests that different evolutionary forces are applied on the group as a whole. In this study, we have compared the codon usage bias (CUB) between eight taxonomically distinct microsporidian genomes: Encephalitozoon intestinalis, Encephalitozoon cuniculi, Spraguea lophii, Trachipleistophora hominis, Enterocytozoon bieneusi, Nematocida parisii, Nosema bombycis and Nosema ceranae. While the CUB was found to be weak in all eight Microsporidia, nearly all (98%) of the optimal codons in S. lophii, T. hominis, E. bieneusi, N. parisii, N. bombycis and N. ceranae are fond of A/U in third position whereas most (64.6%) optimal codons in the Encephalitozoon species E. intestinalis and E. cuniculi are biased towards G/C. Although nucleotide composition biases are likely the main factor driving the CUB in Microsporidia according to correlation analyses, directed mutational pressure also likely affects the CUB as suggested by ENc-plots, correspondence and neutrality analyses. Overall, the Encephalitozoon genomes were found to be markedly different from the other microsporidians and, despite being the first sequenced representatives of this lineage, are uncharacteristic of the group as a whole. The disparities observed cannot be attributed solely to differences in host specificity and we hypothesize that other forces are at play in the lineage leading to Encephalitozoon species. PMID:26057384

  18. 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

  19. Comparative analysis of current diagnostic criteria for gestational diabetes mellitus

    PubMed Central

    Boyadzhieva, Mariya V; Atanasova, Iliana; Zacharieva, Sabina; Tankova, Tsvetalina; Dimitrova, Violeta

    2012-01-01

    Background To compare current guidelines for diagnosis of gestational diabetes mellitus (GDM) and to identify the ones that are the most relevant for application among pregnant Bulgarian population. Methods A total of 800 pregnant women at high risk for GDM underwent 75 g oral glucose tolerance test between 24 and 28 weeks of gestation as antenatal screening. The results were interpreted and classified according to the guidelines of the International Association of Diabetes and Pregnancy Study Groups (IADPSG), American Diabetes Association (ADA), Australasian Diabetes in Pregnancy Society, Canadian Diabetes Association, European Association for the Study of Diabetes, New Zealand Society for the study of Diabetes and World Health Organization. Results The application of different diagnostic criteria resulted in prevalences of GDM between 10.8% and 31.6%. Using any two sets of criteria, women who were classified differently varied between 0.1% and 21.1% (P < 0.001).The IADPSG criteria were the most inclusive criteria and resulted in the highest prevalence of GDM. There was a significant difference in the major metabolic parameters between GDM and control groups, regardless of which of the diagnostic criteria applied. GDM diagnosed according to all criteria resulted in increased proportion of delivery by caesarean section (CS). However, only ADA and IADPSG criteria identified both increased macrosomia (odds ratio, 2.36; 2.29) and CS rate. Conclusion The need for GDM screening is indisputable. In our view, the new IADPSG guidelines offer a unique opportunity for a unified national and global approach to GDM.

  20. GNE Myopathy and Cell Apoptosis: A Comparative Mutation Analysis.

    PubMed

    Singh, Reema; Arya, Ranjana

    2016-07-01

    In a number of genetic disorders such as GNE myopathy, it is not clear how mutations in target genes result in disease phenotype. GNE myopathy is a progressive neuro-degenerative disorder associated with homozygous or compound heterozygous missense mutations in either epimerase or kinase domain of UDP-GlcNAc 2-epimerase/ManNAc kinase (GNE). This bifunctional enzyme catalyses the rate limiting step in sialic acid biosynthesis. Many mechanisms have been suggested as possible cause of muscle degeneration. These include hyposialylation of critical proteins, defects in cytoskeletal network, sarcomere organization and apoptosis. In order to elucidate the role of GNE in cell apoptosis, we have used HEK cell-based model system overexpressing pathologically relevant GNE mutations. These cells display a reduction in the levels of sialic acid-bound glycoconjugates. These mutants GNE overexpressing cells have defect in cell proliferation as compared to vector or wild-type GNE (wtGNE) controls. Moreover, effect of different GNE mutations on cell apoptosis was also observed using staining with annexin V-FITC and TUNEL assay. The downstream apoptosis signalling pathway involving activation of caspases and increased PARP cleavage were observed in all GNE mutant cell lines. In addition, morpho-structural changes in mitochondria in cells overexpressing different GNE mutants were noticed by transmission electron microscopy, and mitochondrial transmembrane potential was found to be altered in absence of functional GNE. Our results clearly indicate role of GNE in mitochondria-dependent cell apoptosis and provide insights into the pathomechanism of GNE myopathy. PMID:25976366

  1. 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.

  2. 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.

  3. A comparative analysis of spindle morphometrics across metazoans

    PubMed Central

    Crowder, Marina E.; Strzelecka, Magdalena; Wilbur, Jeremy D.; Good, Matthew C.; von Dassow, George; Heald, Rebecca

    2015-01-01

    Summary Cell division in all eukaryotes depends on function of the spindle, a microtubule-based structure that segregates chromosomes to generate daughter cells in mitosis or haploid gametes in meiosis. Spindle size adapts to changes in cell size and shape, which vary dramatically across species and within a multicellular organism, but the nature of scaling events and their underlying mechanisms are poorly understood. Cell size variations are most pronounced in early animal development, as egg diameters range from tens of microns up to millimeters across animal phyla, and decrease several orders of magnitude during rapid reductive divisions. During early embryogenesis in the model organisms X. laevis and C. elegans, the spindle scales with cell size [1,2], a phenomenon regulated by molecules that modulate microtubule dynamics [3–6], as well as by limiting cytoplasmic volume [7,8]. However, it is not known to what extent spindle scaling is conserved across organisms and among different cell types. Here we show that in a range of metazoan phyla, mitotic spindle length decreased with cell size across a ~30 fold difference in zygote size. Maximum spindle length varied, but linear spindle scaling occurred similarly in all species once embryonic cell diameter reduced to 140 μm. In contrast, we find that the female meiotic spindle does not scale as closely to egg size, adopting a more uniform size across species that likely reflects its specialized function. Our analysis reveals that spindle morphometrics change abruptly, within one cell cycle, at the transition from meiosis to mitosis in most animals. PMID:26004761

  4. Phylogenetic comparative methods complement discriminant function analysis in ecomorphology.

    PubMed

    Barr, W Andrew; Scott, Robert S

    2014-04-01

    In ecomorphology, Discriminant Function Analysis (DFA) has been used as evidence for the presence of functional links between morphometric variables and ecological categories. Here we conduct simulations of characters containing phylogenetic signal to explore the performance of DFA under a variety of conditions. Characters were simulated using a phylogeny of extant antelope species from known habitats. Characters were modeled with no biomechanical relationship to the habitat category; the only sources of variation were body mass, phylogenetic signal, or random "noise." DFA on the discriminability of habitat categories was performed using subsets of the simulated characters, and Phylogenetic Generalized Least Squares (PGLS) was performed for each character. Analyses were repeated with randomized habitat assignments. When simulated characters lacked phylogenetic signal and/or habitat assignments were random, <5.6% of DFAs and <8.26% of PGLS analyses were significant. When characters contained phylogenetic signal and actual habitats were used, 33.27 to 45.07% of DFAs and <13.09% of PGLS analyses were significant. False Discovery Rate (FDR) corrections for multiple PGLS analyses reduced the rate of significance to <4.64%. In all cases using actual habitats and characters with phylogenetic signal, correct classification rates of DFAs exceeded random chance. In simulations involving phylogenetic signal in both predictor variables and predicted categories, PGLS with FDR was rarely significant, while DFA often was. In short, DFA offered no indication that differences between categories might be explained by phylogenetic signal, while PGLS did. As such, PGLS provides a valuable tool for testing the functional hypotheses at the heart of ecomorphology. PMID:24382658

  5. 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.

  6. 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.

  7. 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

  8. Comparative Analysis of Techniques to Purify Plasma Membrane Proteins

    PubMed Central

    Weekes, Michael P.; Antrobus, Robin; Lill, Jennie R.; Duncan, Lidia M.; Hör, Simon; Lehner, Paul J.

    2010-01-01

    The aim of this project was to identify the best method for the enrichment of plasma membrane (PM) proteins for proteomics experiments. Following tryptic digestion and extended liquid chromatography-tandem mass spectrometry acquisitions, data were processed using MaxQuant and Gene Ontology (GO) terms used to determine protein subcellular localization. The following techniques were examined for the total number and percentage purity of PM proteins identified: (a) whole cell lysate (total number, 84–112; percentage purity, 9–13%); (b) crude membrane preparation (104–111; 17–20%); (c) biotinylation of surface proteins with N-hydroxysulfosuccinimydyl-S,S-biotin and streptavidin pulldown (78–115; 27–31%); (d) biotinylation of surface glycoproteins with biocytin hydrazide and streptavidin pulldown (41–54; 59–85%); or (e) biotinylation of surface glycoproteins with amino-oxy-biotin (which labels the sialylated fraction of PM glycoproteins) and streptavidin pulldown (120; 65%). A two- to threefold increase in the overall number of proteins identified was achieved by using stop and go extraction tip (StageTip)-based anion exchange (SAX) fractionation. Combining technique (e) with SAX fractionation increased the number of proteins identified to 281 (54%). Analysis of GO terms describing these proteins identified a large subset of proteins integral to the membrane with no subcellular assignment. These are likely to be of PM location and bring the total PM protein identifications to 364 (68%). This study suggests that selective biotinylation of the cell surface using amino-oxy-biotin in combination with SAX fractionation is a useful method for identification of sialylated PM proteins. PMID:20808639

  9. 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

  10. 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

  11. 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

  12. 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…

  13. 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

  14. Investigations on the Crystal-Chemical Behavior of Transition-Metal-Bearing Aluminosilicate Garnet Solid Solutions Using 27Al and 29Si NMR Spectroscopy

    NASA Astrophysics Data System (ADS)

    Palke, A. C.; Geiger, C. A.; Stebbins, J. F.

    2015-12-01

    The petrological importance of silicate garnet is derived from the presence of three distinct cation sites of varying size and coordination number. This allows for a wide range of trace, minor, and major element substitutions. However, a full and precise crystal-chemical understanding of the nature of transition metals in garnet is not at hand. Possible mechanisms of various charge-balanced substitutions (e.g. octahedral Ti4+ or tetrahedral Al3+) and the structural state of solid solutions (i.e. short- to long-range ordering) need study. We report on ongoing efforts in these directions using 27Al and 29Si Magic-Angle Spinning Nuclear Magnetic Resonance (MAS-NMR) spectroscopy. Early work on synthetic and natural Fe- and Mn-bearing pyrope- and grossular-rich garnets focused on the effect these paramagnetic transition metals have in measuring and interpreting NMR spectra. These results have been expanded with NMR measurements on synthetic pyrope-rich garnets containing other paramagnetic transition metals including Cr3+, V3+, Co2+, and Ni2+ as well as diamagnetic Ti4+. NMR peaks are severely broadened in the presence of even small concentrations of Cr3+, Mn2+, and Fe3+ leading to a loss of spectral resolution. On the other hand, the spectra of garnet containing V3+, Fe2+, Co2+, and Ni2+ have better resolution and show separate paramagnetically shifted NMR peaks. In some cases, crystal-chemical information can be obtained because of the large frequency separations between the NMR peaks that can be assigned to various local atomic configurations around Al and Si. Furthermore, the 27Al NMR spectrum of a synthetic pyrope garnet with about 2% diamagnetic Ti4+ on the octahedral site showed the absence of any tetrahedral Al3+, which rules out the substitution mechanism VITi + IVAl = VIAl + IVSi in the solid solution. Our NMR investigations on garnet are now being made at the exploratory level. We think that NMR spectra of diamagnetic garnet can provide information on a

  15. Comparative analysis of the speed performance of texture analysis algorithms on a graphic processing unit (GPU)

    NASA Astrophysics Data System (ADS)

    Triana-Martinez, J.; Orjuela-Vargas, S. A.; Philips, W.

    2013-03-01

    This paper compares the speed performance of a set of classic image algorithms for evaluating texture in images by using CUDA programming. We include a summary of the general program mode of CUDA. We select a set of texture algorithms, based on statistical analysis, that allow the use of repetitive functions, such as the Coocurrence Matrix, Haralick features and local binary patterns techniques. The memory allocation time between the host and device memory is not taken into account. The results of this approach show a comparison of the texture algorithms in terms of speed when executed on CPU and GPU processors. The comparison shows that the algorithms can be accelerated more than 40 times when implemented using CUDA environment.

  16. 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.

  17. Comparative molecular field analysis and comparative molecular similarity index analysis studies on 1H NMR chemical shift of NH group of diaryl triazene derivatives.

    PubMed

    Rofouie, M K; Salahinejad, M; Ghasemi, J B; Aghaei, A

    2013-05-01

    Comparative molecular field analysis (CoMFA), comparative molecular field analysis region focusing (CoMFA-RF) for optimizing the region for the final partial least square analysis, and comparative molecular similarity indices analysis (CoMSIA) methods were employed to develop three-dimensional quantitative structure-activity relationship (3D-QSAR) models of (1)H NMR chemical shift of NH proton of diaryl triazene derivatives. The best orientation was searched by all-orientation search (AOS) strategy to minimize the effect of the initial orientation of the structures. The predictive abilities of CoMFA-RF and CoMSIA models were determined using a test set of ten compounds affording predictive correlation coefficients of 0.721 and 0.754, respectively, indicating good predictive power. For further model validation, cross validation (leave one out), progressive scrambling, and bootstrapping were also applied. The accuracy and speed of obtained 3D-QSAR models for the prediction of (1)H NMR chemical shifts of NH group of diaryl triazene derivatives were greater compared to some computational well-known procedures. PMID:23456682

  18. [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. PMID:27071261

  19. 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.

  20. A comparative analysis of gamma and hadron families at the superhigh energies recorded in experiment Pamir

    NASA Technical Reports Server (NTRS)

    Azimov, S. A.; Mulladjanov, E. J.; Nosov, A. N.; Nuritdinov, H.; Talipov, D. A.; Halilov, D. A.; Yuldashbaev, T. S.

    1985-01-01

    A comparative analysis of hadron and gamma families which have undergone the decascading procedure is made. Results are compared with different models of interactions. In hadron families with energies Summary E sub H sup gamma 20 TeV as well as in gamma families with energies Summary E sub gamma 70 TeV, increasing azimuthal anisotropy is observed.

  1. 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…

  2. The Governance of Higher Education Regionalisation: Comparative Analysis of the Bologna Process and MERCOSUR-Educativo

    ERIC Educational Resources Information Center

    Verger, Antoni; Hermo, Javier Pablo

    2010-01-01

    The article analyses two processes of higher education regionalisation, MERCOSUR-Educativo in Latin America and the Bologna Process in Europe, from a comparative perspective. The comparative analysis is centered on the content and the governance of both processes and, specifically, on the reasons of their uneven evolution and implementation. We…

  3. 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…

  4. The Calculation and Presentation of Management Information from Comparative Budget Analysis.

    ERIC Educational Resources Information Center

    Taylor, Bryan J. R.

    1986-01-01

    A comparative budget analysis approach employed by British universities is discussed. The British funding system analyzes in detail unit costs and marginal costs and undertakes comparative assessments of expenditure patterns and priorities for a group of 95 institutions with similar objectives, in which each has autonomy in resource allocation.…

  5. 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…

  6. 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…

  7. 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…

  8. 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…

  9. 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…

  10. A Comparative Analysis of the Porcine, Murine, and Human Immune Systems

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A literature and laboratory-based analysis compared selected features of genotype, phenotype, and functional expression of the porcine, murine, and human immune systems. A total of 147 parameters were examined. Post-genomic analysis found about 300 unique mRNA coding sequences between mice and hum...

  11. Oil and gas development and coastal income inequality: A comparative analysis. Final report

    SciTech Connect

    Tolbert, C.M.

    1994-11-30

    This research employed parish-and county-level data from the 1970, 1980, and 1990 censuses in a comparative analysis of family income inequality. We examined inequality trends in coastal Louisiana parishes and in Florida panhandle counties where there has been no significant onshore or offshore development. The analysis framework spanned key decades that correspond to expansion and subsequent contraction in oil and gas industry activity. A comparative inequality analysis revealed very different patterns of income inequality for Florida and Louisiana. While Florida inequality primarily trended downward across time, inequality in Louisiana exhibited a great deal of volatility and, by 1990, was higher than in 1970 in several cases.

  12. Comparative analysis of methods for determination of arsenic in coal and coal ash

    SciTech Connect

    Vukasinovic-Pesic, V.L.; Blagojevic, N.Z.; Rajakovic, L.V.

    2009-07-01

    In this paper the comparative analysis of different methods for the preparation and analysis of arsenic content in coal and coal ash have been presented. The suggested method is coal digestion method, i.e., coal ash digestion using the mixture of acids: nitric and sulphuric in presence of vanadium-pentoxide as catalyzer. The comparative analysis of different recording techniques (AAS-GH, AAS-GF and ICP-AES) has also been presented. For arsenic recording the suggested technique is AAS-GF technique. The obtained results show that the method of high precision, high sensitivity and high reproductivity has been obtained.

  13. Comparative risk analysis for the Rocky Flats Plant integrated project planning

    SciTech Connect

    Jones, M.E.; Shain, D.I.

    1994-05-01

    The Rocky Flats Plant is developing, with active stakeholder a comprehensive planning strategy that will support transition of the Rocky Flats Plant from a nuclear weapons production facility to site cleanup and final disposition. Final disposition of the Rocky Flats Plant materials and contaminants requires consideration of the interrelated nature of sitewide problems, such as material movement and disposition, facility and land use endstates, costs relative risks to workers and the public, and waste disposition. Comparative Risk Analysis employs both incremental risk and cumulative risk evaluations to compare risks from postulated options or endstates. These postulated options or endstates can be various remedial alternatives, or future endstate uses of federal agency land. Currently, there does not exist any approved methodology that aggregates various incremental risk estimates. Comparative Risk Analysis has been developed to aggregate various incremental risk estimates to develop a site cumulative risk estimate. This paper discusses development of the Comparative Risk Analysis methodology, stakeholder participation and lessons learned from these challenges.

  14. Factors responsible for crystal-chemical variations in the solid solutions from illite to aluminoceladonite and from glauconite to celadonite

    SciTech Connect

    Drits, Victor A.; Zviagina, Bella B.; McCarty, Douglas K.; Salyn, Alfred L.

    2010-03-29

    Several finely dispersed low-temperature dioctahedral micas and micaceous minerals that form solid solutions from (Mg, Fe)-free illite to aluminoceladonite via Mg-rich illite, and from Fe{sup 3+}-rich glauconite to celadonite have been studied by X-ray diffraction and chemical analysis. The samples have 1M and 1Md structures. The transitions from illite to aluminoceladonite and from glauconite to celadonite are accompanied by a consistent decrease in the mica structural-unit thickness (2:1 layer + interlayer) or csin{beta}. In the first sample series csin{beta} decreases from 10.024 to 9.898 {angstrom}, and in the second from 10.002 to 9.961 {angstrom}. To reveal the basic factors responsible for these regularities, structural modeling was carried out to deduce atomic coordinates for 1M dioctahedral mica based on the unit-cell parameters and cation composition. For each sample series, the relationships among csin{beta}, maximum and mean thicknesses of octahedral and tetrahedral sheets and of the 2:1 layer, interlayer distance, and variations of the tetrahedral rotation angle, {alpha}, and the degree of basal surface corrugation, {Delta}Z, have been analyzed in detail. The transitions from illite to aluminoceladonite and from glauconite to celadonite are accompanied by a slight increase in the mean thickness of the 2:1 layers and a steady decrease in the {alpha} angles, whereas the interlayer distance becomes smaller. These results are consistent with the generally accepted model where tetrahedral rotation is the main factor for the interlayer contraction in muscovite-phengite structures: the smaller the rotation angle ({alpha}) the larger the ditrigonal ring of the tetrahedral sheet and the interlayer pseudo-hexagonal cavity, allowing the interlayer cation to sink and thus shorten the c parameter. A new insight into the interpretation of the contraction of the mica layer thickness in dioctahedral micas has been achieved with the discovery that micas with the same

  15. Crystal-chemical controls on the partitioning of Sr and Ba between plagioclase feldspar, silicate melts, and hydrothermal solutions

    NASA Astrophysics Data System (ADS)

    Blundy, Jonathan D.; Wood, Bernard J.

    1991-01-01

    The isothermal (750°C) experiments of LAGACHE and DUJON (1987) reveal that the partitioning of Sr between plagioclase feldspar and hydrothermal solutions is a funtion of the anorthite (An) content of the plagioclase, indicating that crystal chemistry may exert a powerful influence on trace element partitioning. In order to compare these results with those on trace element partitioning between plagioclase and silicate melts we have compiled from the literature a large dataset of experimental and volcanic distribution coefficients ( D's) for Sr (and Ba). These data, which span a compositional range from lunar basalt to high silica rhyolite and a temperature range of over 650°C, show a relationship between DSr (and DBa) and mole fraction An ( XAn) which is similar to that exhibited by the hydrothermal results obtained at constant temperature. Plots of In DSr and In DBa versus XAn are linear with negative slope, indicating that both elements are more compatible in albite than anorthite. In terms of molar distribution coefficients ( D Sr∗) the hydrothermal and silicate melt data display an identical linear relationship between RT In D Sr∗ (where T is the absolute temperature in K and R is the gas constant, 8.314 JK -1 mol -1) and XAn. We conclude therefore that crystal chemistry provides the dominant control on partitioning of Sr and Ba into plagioclase and that the effects of temperature, pressure, and fluid composition are minor. Apparent relationships between DSr (and DBa) and the reciprocal temperature (1/ T) are artefacts of the linear relationships between XAn and 1/ T in the experimental studies. By defining a Henry's law standard state for the silicate melts and hydrothermal solutions, and considering plagioclases to be ternary regular solutions, we are able to relate the observed relationships between RT In D i∗ (where i is Ba or Sr) and XAn to the excess free energies of the trace element partitioning reactions between plagioclase and melt or

  16. Combined implementation of holographic and speckle interferometry for comparative local stress analysis at different vibration modes

    NASA Astrophysics Data System (ADS)

    Novikov, Sergey A.; Pisarev, Vladimir S.; Dzuba, Alexander S.; Grigoriev, Vladimir D.

    1998-09-01

    New capability of combined application of time-averaged holographic interferometry and defocused speckle photography, allowing us a comparative analysis of local stresses corresponding to different vibration modes, is considered. The main aspects of the technique developed are illustrated by using as an example bending oscillations of thin square plate with a large central circular hole. Experimental results are compared with corresponding numerical data obtained by means of the MSC/NASTRAN software.

  17. Accuracy of bite mark analysis from food substances: A comparative study

    PubMed Central

    Daniel, M. Jonathan; Pazhani, Ambiga

    2015-01-01

    Aims and Objectives: The aims and objectives of the study were to compare the accuracy of bite mark analysis from three different food substances-apple, cheese and chocolate using two techniques-the manual docking procedure and computer assisted overlay generation technique and to compare the accuracy of the two techniques for bite mark analysis on food substances. Materials and Methods: The individuals who participated in the study were made to bite on three food substances-apple, cheese, and chocolate. Dentate individuals were included in the study. Edentulous individuals and individuals having a missing anterior tooth were excluded from the study. The dental casts of the individual were applied to the positive cast of the bitten food substance to determine docking or matching. Then, computer generated overlays were compared with bite mark pattern on the foodstuff. Results: The results were tabulated and the comparison of bite mark analysis on the three different food substances was analyzed by Kruskall-Wallis ANOVA test and the comparison of the two techniques was analyzed by Spearman's Rho correlation coefficient. Conclusion: On comparing the bite marks analysis from the three food substances-apple, cheese and chocolate, the accuracy was found to be greater for chocolate and cheese than apple. PMID:26816463

  18. Multilevel Structural Equation Models for the Analysis of Comparative Data on Educational Performance

    ERIC Educational Resources Information Center

    Goldstein, Harvey; Bonnet, Gerard; Rocher, Thierry

    2007-01-01

    The Programme for International Student Assessment comparative study of reading performance among 15-year-olds is reanalyzed using statistical procedures that allow the full complexity of the data structures to be explored. The article extends existing multilevel factor analysis and structural equation models and shows how this can extract richer…

  19. Peer Assessment in the Digital Age: A Meta-Analysis Comparing Peer and Teacher Ratings

    ERIC Educational Resources Information Center

    Li, Hongli; Xiong, Yao; Zang, Xiaojiao; Kornhaber, Mindy L.; Lyu, Youngsun; Chung, Kyung Sun; Suen, Hoi K.

    2016-01-01

    Given the wide use of peer assessment, especially in higher education, the relative accuracy of peer ratings compared to teacher ratings is a major concern for both educators and researchers. This concern has grown with the increase of peer assessment in digital platforms. In this meta-analysis, using a variance-known hierarchical linear modelling…

  20. Summary of an Extended Comparative Analysis on European Private Higher Education

    ERIC Educational Resources Information Center

    Fried, Jochen; Glass, Anna; Baumgartl, Bernd

    2006-01-01

    In November 2005, UNESCO-CEPES organized a conference on Private Higher Education in Europe and Quality Assurance and Accreditation from the Perspective of the Bologna Process Objectives. Thirteen country reports and a comparative analysis study were commissioned for this specific initiative. The countries included in the project were: Albania,…

  1. A Comparative Meta-Analysis of 5E and Traditional Approaches in Turkey

    ERIC Educational Resources Information Center

    Anil, Özgür; Batdi, Veli

    2015-01-01

    The aim of this study is to compare the 5E learning model with traditional learning methods in terms of their effect on students' academic achievement, retention and attitude scores. In this context, the meta-analytic method known as the "analysis of analyses" was used and a review undertaken of the studies and theses (N = 14) executed…

  2. A Comparative Analysis of User Preferences for for Major Internet Based Education Media in China

    ERIC Educational Resources Information Center

    Wan, Chunyang; Jiang, Yanqing

    2014-01-01

    Internet based education media are developing at an amazing rate and being seen as an upstart that will likely take the place of traditional education means worldwide in the future. This paper presents the results of a comparative analysis on user preferences for four major categories of internet-based media used in China. In this paper, we first…

  3. International Organisations and the Evaluation of Education Systems: A Critical Comparative Analysis

    ERIC Educational Resources Information Center

    Neves, Claudia

    2008-01-01

    This article seeks to develop research involving a macro-level critical comparative analysis of reference documents produced by international organisations (UNDP, OECD, UNESCO, the World Bank and the European Union) which guide world education policy decisions. The primary objective was to consider the key guidelines currently defined for…

  4. Comparing Response Rates in E-Mail and Paper Surveys: A Meta-Analysis

    ERIC Educational Resources Information Center

    Shih, Tse-Hua; Fan, Xitao

    2009-01-01

    This meta-analysis examined 35 study results within last 10 years that directly compared the response rates of e-mail versus mail surveys. Individual studies reported inconsistent findings concerning the response rate difference between e-mail and mail surveys, but e-mail surveys generally have lower response rate (about 20% lower on the average)…

  5. Dealing with Complex Causality in Realist Synthesis: The Promise of Qualitative Comparative Analysis

    ERIC Educational Resources Information Center

    Sager, Fritz; Andereggen, Celine

    2012-01-01

    In this article, the authors state two arguments: first, that the four categories of context, politics, polity, and policy make an adequate framework for systematic review being both exhaustive and parsimonious; second, that the method of qualitative comparative analysis (QCA) is an appropriate methodical approach for gaining realistic results…

  6. Asian Students' Conceptions of Future Civic Engagement: Comparing Clusters Using Person-Centered Analysis

    ERIC Educational Resources Information Center

    Chow, Joseph Kui Foon; Kennedy, Kerry J.

    2015-01-01

    Researchers in comparative education have suggested different ways in which their field of study can be enhanced by considering units of analysis at different levels rather than focusing on a single level such as the nation-state (Bray and Thomas, 1995; Torney-Purta and Barber, 2011). The study reported here seeks to contribute to this area of…

  7. Rethinking Critical Mathematics: A Comparative Analysis of Critical, Reform, and Traditional Geometry Instructional Texts

    ERIC Educational Resources Information Center

    Brantlinger, Andrew

    2011-01-01

    This paper presents findings from a comparative analysis of three similar secondary geometry texts, one critical unit, one standards-based reform unit, and one specialist chapter. I developed the critical unit as I took the tenets of critical mathematics (CM) and substantiated them in printed curricular materials in which to teach as part of a…

  8. A SWOT Analysis of Male and Female Students' Performance in Chemistry: A Comparative Study

    ERIC Educational Resources Information Center

    Ezeudu, Florence O.; Chiaha, Gertrude-Theresa Uzoamaka; Anazor, Lynda Chioma; Eze, Justina Uzoamaka; Omeke, Faith Chinwe

    2015-01-01

    The purpose of this study was to do a SWOT analysis and compare performances of male and female students in chemistry. Four research questions and four null hypotheses guided the study. Two boys', two girls' and two coeducational schools involving 1319 males and 1831 females, were selected by a stratified, deliberate sampling technique. A…

  9. Trend Analysis on Mathematics Achievements: A Comparative Study Using TIMSS Data

    ERIC Educational Resources Information Center

    Ker, H. W.

    2013-01-01

    Research addressed the importance of mathematics education for the students' preparation to enter scientific and technological workforce. This paper utilized Trends in International Mathematics and Science Study (TIMSS) 2011 data to conduct a global comparative analysis on mathematics performance at varied International Benchmark levels. The…

  10. Comparative Critical Discourse Analysis of Student and Teacher Editions of Secondary Christian American Literature Textbooks

    ERIC Educational Resources Information Center

    Agiro, Christa Preston

    2012-01-01

    This article discusses the comparative application of critical discourse analysis to student and teacher editions of the two most widely used high school American literature textbooks by Christian publishers, examining them through the lens of critical theory. The study examined all parts of the student and teacher editions, excepting literary…

  11. Causal Comparative Analysis: Comprehensive Literacy Approach or the Traditional Reading Approach

    ERIC Educational Resources Information Center

    Fuda, Jessica Ann

    2009-01-01

    A comparative analysis study, examining the significance in reading achievement between students in the Comprehensive Literacy Program to students in the Traditional Basal Reading Approach was conducted. Implementation of the Comprehensive Literacy Program was an effort to lessen the achievement gap between proficient and low progressing students.…

  12. Replication Research in Comparative Genre Analysis in English for Academic Purposes

    ERIC Educational Resources Information Center

    Basturkmen, Helen

    2014-01-01

    In recent years a number of comparative studies based on an established approach to genre analysis have been published in the English for Academic Purposes (EAP) literature. Studies in this emerging strand of research typically aim to identify how the rhetorical structure of a particular genre (a text type) or part of a genre may vary across…

  13. Distance Education and the Six Regional Accrediting Commissions: A Comparative Analysis

    ERIC Educational Resources Information Center

    Howell, Scott L.; Baker, Katherine; Zuehl, Jennett; Johansen, Justin

    2007-01-01

    Background: The last comparative analysis of how the six regional accrediting commissions review distance education programs was conducted in 2000. A few months later in March 2001 all six accrediting bodies did something that they hadn't done before, they adopted common standards for reviewing distance education programs. Purpose: The purpose was…

  14. A Comparative Analysis of Black and Mexican American Residential Segregation in Southwestern Cities.

    ERIC Educational Resources Information Center

    Meier, Michael; Feagin, Joe

    Discrimination, poverty, and ethnic attachment or choice have been identified as 3 factors that might explain residential segregation. This paper purported: (1) to comparatively document the nature and extent of metropolitan segregation of Mexican Americans and Blacks in the Southwest; (2) to perform an exploratory analysis of the significance of…

  15. How Does Distance Education Compare with Classroom Instruction? A Meta-Analysis of the Empirical Literature

    ERIC Educational Resources Information Center

    Bernard, Robert M.; Abrami, Philip C.; Lou, Yiping; Borokhovsk, Evgueni; Wade, Anne; Wozney, Lori; Wallet, Peter Andrew; Fiset, Manon; Huang, Binru

    2004-01-01

    A meta-analysis of the comparative distance education (DE) literature between 1985 and 2002 was conducted. In total, 232 studies containing 688 independent achievement, attitude, and retention outcomes were analyzed. Overall results indicated effect sizes of essentially zero on all three measures and wide variability. This suggests that many…

  16. Analysis of the allohexaploid bread wheat genome (Triticum aestivum) using comparative whole genome shotgun sequencing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The large 17 Gb allopolyploid genome of bread wheat is a major challenge for genome analysis because it is composed of three closely- related and independently maintained genomes, with genes dispersed as small “islands” separated by vast tracts of repetitive DNA. We used a novel comparative genomi...

  17. A Comparative Analysis of Numbers and Biology Content Domains between Turkey and the USA

    ERIC Educational Resources Information Center

    Incikabi, Lutfi; Ozgelen, Sinan; Tjoe, Hartono

    2012-01-01

    This study aimed to compare Mathematics and Science programs focusing on TIMSS content domains of Numbers and Biology that produced the largest achievement gap among students from Turkey and the USA. Specifically, it utilized the content analysis method within Turkish and New York State (NYS) frameworks. The procedures of study included matching…

  18. How to Construct More Accurate Student Models: Comparing and Optimizing Knowledge Tracing and Performance Factor Analysis

    ERIC Educational Resources Information Center

    Gong, Yue; Beck, Joseph E.; Heffernan, Neil T.

    2011-01-01

    Student modeling is a fundamental concept applicable to a variety of intelligent tutoring systems (ITS). However, there is not a lot of practical guidance on how to construct and train such models. This paper compares two approaches for student modeling, Knowledge Tracing (KT) and Performance Factors Analysis (PFA), by evaluating their predictive…

  19. Factor Analysis with Ordinal Indicators: A Monte Carlo Study Comparing DWLS and ULS Estimation

    ERIC Educational Resources Information Center

    Forero, Carlos G.; Maydeu-Olivares, Alberto; Gallardo-Pujol, David

    2009-01-01

    Factor analysis models with ordinal indicators are often estimated using a 3-stage procedure where the last stage involves obtaining parameter estimates by least squares from the sample polychoric correlations. A simulation study involving 324 conditions (1,000 replications per condition) was performed to compare the performance of diagonally…

  20. Case Problems for Problem-Based Pedagogical Approaches: A Comparative Analysis

    ERIC Educational Resources Information Center

    Dabbagh, Nada; Dass, Susan

    2013-01-01

    A comparative analysis of 51 case problems used in five problem-based pedagogical models was conducted to examine whether there are differences in their characteristics and the implications of such differences on the selection and generation of ill-structured case problems. The five pedagogical models were: situated learning, goal-based scenario,…

  1. Underrepresentation of Women in the Academic Profession: A Comparative Analysis of the North American Region

    ERIC Educational Resources Information Center

    Metcalfe, Amy Scott; Gonzalez, Laura Padilla

    2013-01-01

    The present study addresses women's underrepresentation in the academic profession, as well as the need for policies and practices aimed at this issue. It compares underrepresentation of academic women in North American countries, and explores, throughout a bivariate analysis, personal, professional, as well as institutional variables related to…

  2. Postsecondary Plans of U.S. and Japanese High School Seniors: An Introductory Comparative Analysis.

    ERIC Educational Resources Information Center

    Stocking, Carol B.; Curry, Glen David

    Using data gathered from the High School and Beyond study, a comparative analysis of the social processes related to the postsecondary plans of high school seniors in the United States and Japan was conducted. Differentiations are seen between students choosing to enter the labor market directly from school and those choosing to attend a trade or…

  3. Comparative proteomic analysis of genetically modified maize grown under different agroecosystems conditions in Brazil

    PubMed Central

    2013-01-01

    Background Profiling technologies allow the simultaneous measurement and comparison of thousands of cell components without prior knowledge of their identity. In the present study, we used two-dimensional gel electrophoresis combined with mass spectrometry to evaluate protein expression of Brazilian genetically modified maize hybrid grown under different agroecosystems conditions. To this effect, leaf samples were subjected to comparative analysis using the near-isogenic non-GM hybrid as the comparator. Results In the first stage of the analysis, the main sources of variation in the dataset were identified by using Principal Components Analysis which correlated most of the variation to the different agroecosystems conditions. Comparative analysis within each field revealed a total of thirty two differentially expressed proteins between GM and non-GM samples that were identified and their molecular functions were mainly assigned to carbohydrate and energy metabolism, genetic information processing and stress response. Conclusions To the best of our knowledge this study represents the first evidence of protein identities with differentially expressed isoforms in Brazilian MON810 genetic background hybrid grown under field conditions. As global databases on outputs from “omics” analysis become available, these could provide a highly desirable benchmark for safety assessments. PMID:24304660

  4. Comparative analysis of seismic response characteristics of pile-soil-structure interaction system

    NASA Astrophysics Data System (ADS)

    Kong, Desen; Luan, Maotian; Wang, Weiming

    2006-01-01

    The study on the earthquake-resistant performance of a pile-soil-structure interaction system is a relatively complicated and primarily important issue in civil engineering practice. In this paper, a computational model and computation procedures for pile-supported structures, which can duly consider the pile-soil interaction effect, are established by the finite element method. Numerical implementation is made in the time domain. A simplified approximation for the seismic response analysis of pile-soil-structure systems is briefly presented. Then a comparative study is performed for an engineering example with numerical results computed respectively by the finite element method and the simplified method. Through comparative analysis, it is shown that the results obtained by the simplified method well agree with those achieved by the finite element method. The numerical results and findings will offer instructive guidelines for earthquake-resistant analysis and design of pile-supported structures.

  5. Comparative analysis of gene expression by microarray analysis of male and female flowers of Asparagus officinalis.

    PubMed

    Gao, Wu-Jun; Li, Shu-Fen; Zhang, Guo-Jun; Wang, Ning-Na; Deng, Chuan-Liang; Lu, Long-Dou

    2013-01-01

    To identify rapidly a number of genes probably involved in sex determination and differentiation of the dioecious plant Asparagus officinalis, gene expression profiles in early flower development for male and female plants were investigated by microarray assay with 8,665 probes. In total, 638 male-biased and 543 female-biased genes were identified. These genes with biased-expression for male and female were involved in a variety of processes associated with molecular functions, cellular components, and biological processes, suggesting that a complex mechanism underlies the sex development of asparagus. Among the differentially expressed genes involved in the reproductive process, a number of genes associated with floral development were identified. Reverse transcription-PCR was performed for validation, and the results were largely consistent with those obtained by microarray analysis. The findings of this study might contribute to understanding of the molecular mechanisms of sex determination and differentiation in dioecious asparagus and provide a foundation for further studies of this plant. PMID:23748756

  6. Comparative risk analysis for the Rocky Flats Plant Integrated Project Planning

    SciTech Connect

    Jones, M.E.; Shain, D.I.

    1994-12-31

    The Rocky Flats Plant is developing a comprehensive planning strategy that will support transition of the Rocky Flats Plant from a nuclear weapons production facility to site cleanup and final disposition. Final disposition of the Rocky Flats Plant materials and contaminants requires consideration of the interrelated nature of sitewide problems, such as material movement and disposition, facility and land use endstates, costs, relative risks to workers and the public, and waste disposition. Comparative Risk Analysis employs both incremental risk and cumulative risk evaluations to compare risk from postulated options or endstates. Comparative Risk Analysis is an analytical tool for the Rocky Flats Plant Integrated Project Planning which can assist a decision-maker in evaluating relative risks among proposed remedial options or future endstates. It addresses the cumulative risks imposed by the Rocky Flats Plant and provides risk information, both human health and ecological, to aid in reducing unnecessary resource and monetary expenditures. Currently, there is no approved methodology that aggregates various risk estimates. Along with academic and field expert review, the Comparative Risk Analysis methodology is being reviewed and refined. A Rocky Flats Plant Risk Assessment Focus Group was established. Stakeholder involvement in the development provides an opportunity to influence the information delivered to a decision-maker. This paper discusses development of the methodology.

  7. MultiMetEval: Comparative and Multi-Objective Analysis of Genome-Scale Metabolic Models

    PubMed Central

    Gevorgyan, Albert; Kierzek, Andrzej M.; Breitling, Rainer; Takano, Eriko

    2012-01-01

    Comparative metabolic modelling is emerging as a novel field, supported by the development of reliable and standardized approaches for constructing genome-scale metabolic models in high throughput. New software solutions are needed to allow efficient comparative analysis of multiple models in the context of multiple cellular objectives. Here, we present the user-friendly software framework Multi-Metabolic Evaluator (MultiMetEval), built upon SurreyFBA, which allows the user to compose collections of metabolic models that together can be subjected to flux balance analysis. Additionally, MultiMetEval implements functionalities for multi-objective analysis by calculating the Pareto front between two cellular objectives. Using a previously generated dataset of 38 actinobacterial genome-scale metabolic models, we show how these approaches can lead to exciting novel insights. Firstly, after incorporating several pathways for the biosynthesis of natural products into each of these models, comparative flux balance analysis predicted that species like Streptomyces that harbour the highest diversity of secondary metabolite biosynthetic gene clusters in their genomes do not necessarily have the metabolic network topology most suitable for compound overproduction. Secondly, multi-objective analysis of biomass production and natural product biosynthesis in these actinobacteria shows that the well-studied occurrence of discrete metabolic switches during the change of cellular objectives is inherent to their metabolic network architecture. Comparative and multi-objective modelling can lead to insights that could not be obtained by normal flux balance analyses. MultiMetEval provides a powerful platform that makes these analyses straightforward for biologists. Sources and binaries of MultiMetEval are freely available from https://github.com/PiotrZakrzewski/MetEval/downloads. PMID:23272111

  8. Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors.

    PubMed

    Feber, Andrew; Wilson, Gareth A; Zhang, Lu; Presneau, Nadege; Idowu, Bernadine; Down, Thomas A; Rakyan, Vardhman K; Noon, Luke A; Lloyd, Alison C; Stupka, Elia; Schiza, Vassia; Teschendorff, Andrew E; Schroth, Gary P; Flanagan, Adrienne; Beck, Stephan

    2011-04-01

    Aberrant DNA methylation (DNAm) was first linked to cancer over 25 yr ago. Since then, many studies have associated hypermethylation of tumor suppressor genes and hypomethylation of oncogenes to the tumorigenic process. However, most of these studies have been limited to the analysis of promoters and CpG islands (CGIs). Recently, new technologies for whole-genome DNAm (methylome) analysis have been developed, enabling unbiased analysis of cancer methylomes. By using MeDIP-seq, we report a sequencing-based comparative methylome analysis of malignant peripheral nerve sheath tumors (MPNSTs), benign neurofibromas, and normal Schwann cells. Analysis of these methylomes revealed a complex landscape of DNAm alterations. In contrast to what has been reported for other tumor types, no significant global hypomethylation was observed in MPNSTs using methylome analysis by MeDIP-seq. However, a highly significant (P < 10(-100)) directional difference in DNAm was found in satellite repeats, suggesting these repeats to be the main target for hypomethylation in MPNSTs. Comparative analysis of the MPNST and Schwann cell methylomes identified 101,466 cancer-associated differentially methylated regions (cDMRs). Analysis showed these cDMRs to be significantly enriched for two satellite repeat types (SATR1 and ARLα) and suggests an association between aberrant DNAm of these sequences and transition from healthy cells to malignant disease. Significant enrichment of hypermethylated cDMRs in CGI shores (P < 10(-60)), non-CGI-associated promoters (P < 10(-4)) and hypomethylated cDMRs in SINE repeats (P < 10(-100)) was also identified. Integration of DNAm and gene expression data showed that the expression pattern of genes associated with CGI shore cDMRs was able to discriminate between disease phenotypes. This study establishes MeDIP-seq as an effective method to analyze cancer methylomes. PMID:21324880

  9. Comparative genome analysis and genome-guided physiological analysis of Roseobacter litoralis

    PubMed Central

    2011-01-01

    Background Roseobacter litoralis OCh149, the type species of the genus, and Roseobacter denitrificans OCh114 were the first described organisms of the Roseobacter clade, an ecologically important group of marine bacteria. Both species were isolated from seaweed and are able to perform aerobic anoxygenic photosynthesis. Results The genome of R. litoralis OCh149 contains one circular chromosome of 4,505,211 bp and three plasmids of 93,578 bp (pRLO149_94), 83,129 bp (pRLO149_83) and 63,532 bp (pRLO149_63). Of the 4537 genes predicted for R. litoralis, 1122 (24.7%) are not present in the genome of R. denitrificans. Many of the unique genes of R. litoralis are located in genomic islands and on plasmids. On pRLO149_83 several potential heavy metal resistance genes are encoded which are not present in the genome of R. denitrificans. The comparison of the heavy metal tolerance of the two organisms showed an increased zinc tolerance of R. litoralis. In contrast to R. denitrificans, the photosynthesis genes of R. litoralis are plasmid encoded. The activity of the photosynthetic apparatus was confirmed by respiration rate measurements, indicating a growth-phase dependent response to light. Comparative genomics with other members of the Roseobacter clade revealed several genomic regions that were only conserved in the two Roseobacter species. One of those regions encodes a variety of genes that might play a role in host association of the organisms. The catabolism of different carbon and nitrogen sources was predicted from the genome and combined with experimental data. In several cases, e.g. the degradation of some algal osmolytes and sugars, the genome-derived predictions of the metabolic pathways in R. litoralis differed from the phenotype. Conclusions The genomic differences between the two Roseobacter species are mainly due to lateral gene transfer and genomic rearrangements. Plasmid pRLO149_83 contains predominantly recently acquired genetic material whereas pRLO149

  10. Unique gene expression profile in osteoarthritis synovium compared with cartilage: analysis of publicly accessible microarray datasets.

    PubMed

    Park, Robin; Ji, Jong Dae

    2016-06-01

    The purpose of this study was to identify a gene expression signature in osteoarthritis (OA) synovium and genomic pathways likely to be involved in the pathogenesis of OA. Four publicly accessible microarray studies from synovium of OA patients were integrated, and a transcriptomic and network-based meta-analysis was performed. Based on pathways according to the Kyoto Encyclopedia of Genes and Genomes, functional enrichment analysis was performed. Meta-analysis results of OA synovium were compared to two previously published studies of OA cartilage to determine the relative number of common and specific DEGs of the cartilage and synovium. According to our meta-analysis, a total of 1350 genes were found to be differentially expressed in the synovium of OA patients as compared to that of healthy controls. Pathway analysis found 41 significant pathways in the total DEGs, and 22 and 16 pathways in the upregulated and downregulated DEGs, respectively. Cell adhesion molecules and cytokine-cytokine receptor interaction were the most significant pathway in the upregulated and downregulated DEGs, respectively. Comparison of meta-analysis results of OA synovium with results of two previous studies of OA cartilage identified 85 common genes and 1632 cartilage-specific DEGs and 1265 synovium-specific DEGs in the first study; and 142 common genes, and 856 cartilage-specific DEGs and 1208 synovium-specific DEGs in the second study. Our results show a small overlap between the DEGs of the synovium compared to DEGs of the cartilage, suggesting different pathogenic mechanisms that are specific to the synovium. PMID:26942917

  11. A comparative analysis of electronic and molecular quantum dot cellular automata

    SciTech Connect

    Umamahesvari, H. E-mail: ajithavijay1@gmail.com; Ajitha, D. E-mail: ajithavijay1@gmail.com

    2015-06-24

    This paper presents a comparative analysis of electronic quantum-dot cellular automata (EQCA) and Magnetic quantum dot Cellular Automata (MQCA). QCA is a computing paradigm that encodes and processes information by the position of individual electrons. To enhance the high dense and ultra-low power devices, various researches have been actively carried out to find an alternative way to continue and follow Moore’s law, so called “beyond CMOS technology”. There have been several proposals for physically implementing QCA, EQCA and MQCA are the two important QCAs reported so far. This paper provides a comparative study on these two QCAs.

  12. A comparative analysis of electronic and molecular quantum dot cellular automata

    NASA Astrophysics Data System (ADS)

    Umamahesvari, H.; Ajitha, D.

    2015-06-01

    This paper presents a comparative analysis of electronic quantum-dot cellular automata (EQCA) and Magnetic quantum dot Cellular Automata (MQCA). QCA is a computing paradigm that encodes and processes information by the position of individual electrons. To enhance the high dense and ultra-low power devices, various researches have been actively carried out to find an alternative way to continue and follow Moore's law, so called "beyond CMOS technology". There have been several proposals for physically implementing QCA, EQCA and MQCA are the two important QCAs reported so far. This paper provides a comparative study on these two QCAs

  13. Comparative quality analysis of models of total electron content in the ionosphere

    NASA Astrophysics Data System (ADS)

    Ivanov, V. B.; Gorbachev, O. A.; Kholmogorov, A. A.

    2016-05-01

    We present a brief description and comparative analysis of the Klobuchar, GEMTEC, and NTCM-GL models of total electron content in the ionosphere. The quality of model performance against experimental data on the total electron content is compared. Statistical estimates for the residual positioning error are obtained for each of these models on the basis of the international Global Navigation Satellite Systems (GNSS) Service data. The GEMTEC and NTCM-GL models are shown to have a higher positioning accuracy than the Klobuchar model. The best results of the ionospheric error correction are provided by the GEMTEC model.

  14. Improving skill development: an exploratory study comparing a philosophical and an applied ethical analysis technique

    NASA Astrophysics Data System (ADS)

    Al-Saggaf, Yeslam; Burmeister, Oliver K.

    2012-09-01

    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 ICT students and professionals. In particular the skill development focused on includes: being able to recognise ethical challenges and formulate coherent responses; distancing oneself from subjective judgements; developing ethical literacy; identifying stakeholders; and communicating ethical decisions made, to name a few.

  15. Seventy-meter antenna performance predictions: GTD analysis compared with traditional ray-tracing methods

    NASA Technical Reports Server (NTRS)

    Schredder, J. M.

    1988-01-01

    A comparative analysis was performed, using both the Geometrical Theory of Diffraction (GTD) and traditional pathlength error analysis techniques, for predicting RF antenna gain performance and pointing corrections. The NASA/JPL 70 meter antenna with its shaped surface was analyzed for gravity loading over the range of elevation angles. Also analyzed were the effects of lateral and axial displacements of the subreflector. Significant differences were noted between the predictions of the two methods, in the effect of subreflector displacements, and in the optimal subreflector positions to focus a gravity-deformed main reflector. The results are of relevance to future design procedure.

  16. 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

  17. Comparative Analysis of Salmonella Genomes Identifies a Metabolic Network for Escalating Growth in the Inflamed Gut

    PubMed Central

    Nuccio, Sean-Paul; Bäumler, Andreas J.

    2014-01-01

    ABSTRACT The Salmonella genus comprises a group of pathogens associated with illnesses ranging from gastroenteritis to typhoid fever. We performed an in silico analysis of comparatively reannotated Salmonella genomes to identify genomic signatures indicative of disease potential. By removing numerous annotation inconsistencies and inaccuracies, the process of reannotation identified a network of 469 genes involved in central anaerobic metabolism, which was intact in genomes of gastrointestinal pathogens but degrading in genomes of extraintestinal pathogens. This large network contained pathways that enable gastrointestinal pathogens to utilize inflammation-derived nutrients as well as many of the biochemical reactions used for the enrichment and biochemical discrimination of Salmonella serovars. Thus, comparative genome analysis identifies a metabolic network that provides clues about the strategies for nutrient acquisition and utilization that are characteristic of gastrointestinal pathogens. PMID:24643865

  18. Comparative analysis of marine paleogene sections and biota from West Siberia and the Arctic Region

    NASA Astrophysics Data System (ADS)

    Akhmet'ev, M. A.; Zaporozhets, N. I.; Iakovleva, A. I.; Aleksandrova, G. N.; Beniamovsky, V. N.; Oreshkina, T. V.; Gnibidenko, Z. N.; Dolya, Zh. A.

    2010-12-01

    The analysis of the main biospheric events that took place in West Siberia and the Arctic region during the Early Paleogene revealed the paleogeographic and paleobiogeographic unity of marine sedimentation basins and close biogeographic relations between their separate parts. Most biotic and abiotic events of the first half of the Paleogene in the Arctic region and West Siberia were synchronous, unidirectional, and interrelated. Shelf settings, sedimentation breaks, and microfaunal assemblages characteristic of these basins during the Paleogene are compared. The comparative analysis primarily concerned events of the Paleocene-Eocene thermal maximum (PETM) and beds with Azolla (aquatic fern). The formation of the Eocene Azolla Beds in the Arctic region and West Siberia was asynchronous, although it proceeded in line with a common scenario related to the development of a system of estuarine-type currents in a sea basin partly isolated from the World Ocean.

  19. A COMPARATIVE ANALYSIS BETWEEN FRANCE AND JAPAN ON LOCAL GOVERNMENTS' INVOLVEMENT IN NUCLEAR SAFETY GOVERNANCE

    NASA Astrophysics Data System (ADS)

    Sugawara, Shin-Etsu; Shiroyama, Hideaki

    This paper shows a comparative analysis between France and Japan on the way of the local governments' involvement in nuclear safety governance through some interviews. In France, a law came into force that requires related local governments to establish "Commision Locale d'Information" (CLI), which means the local governments officially involve in nuclear regulatory activity. Meanwhile, in Japan, related local governments substantially involve in the operation of nuclear facilities through the "safety agreements" in spite of the lack of legal authority. As a result of comparative analysis, we can point out some institutional input from French cases as follows: to clarify the local governments' roles in the nuclear regulation system, to establish the official channels of communication among nuclear utilities, national regulatory authorities and local governments, and to stipulate explicitly the transparency as a purpose of safety regulation.

  20. Comparative Investigation of Body Composition in Male Dogs Using CT and Body Fat Analysis Software

    PubMed Central

    KOBAYASHI, Toyokazu; KOIE, Hiroshi; KUSUMI, Akiko; KITAGAWA, Masato; KANAYAMA, Kiichi; OTSUJI, Kazuya

    2013-01-01

    ABSTRACT In small animal veterinary practices, body condition score (BCS) is generally used to diagnose obesity. However, BCS does not constitute objective data. In this study, we investigated the value of using human body fat analysis software for male dogs. We also compared changes in body fat after neutering. Changes in body fat at the time of neutering (age 1 year) and 1 year later were compared by performing CT scanning and using human body fat analysis software. We found that body fat increased in all the individuals tested. In terms of the site of fat accumulation, subcutaneous fat was more pronounced than visceral fat with a marked increase on the dorsal side of the abdomen rather than the thorax. PMID:24212506

  1. Comparative analysis of methods for real-time analytical control of chemotherapies preparations.

    PubMed

    Bazin, Christophe; Cassard, Bruno; Caudron, Eric; Prognon, Patrice; Havard, Laurent

    2015-10-15

    Control of chemotherapies preparations are now an obligation in France, though analytical control is compulsory. Several methods are available and none of them is presumed as ideal. We wanted to compare them so as to determine which one could be the best choice. We compared non analytical (visual and video-assisted, gravimetric) and analytical (HPLC/FIA, UV/FT-IR, UV/Raman, Raman) methods thanks to our experience and a SWOT analysis. The results of the analysis show great differences between the techniques, but as expected none us them is without defects. However they can probably be used in synergy. Overall for the pharmacist willing to get involved, the implementation of the control for chemotherapies preparations must be widely anticipated, with the listing of every parameter, and remains according to us an analyst's job. PMID:26299761

  2. Culture and health reporting: a comparative content analysis of newspapers in the United States and China.

    PubMed

    Tang, Lu; Peng, Wei

    2015-01-01

    Health reporting has the potential to educate the public and promote health behaviors. Culture influences the style of such communication. Following the theorization of national cultures by Hofstede and Hofstede (2005) and Wilber (2000), this study compares health reporting in the United States and China through a content analysis of leading newspapers. The authors discover significant differences in health reporting in terms of controllability attribution, temporal orientation, citation of authority sources, and use of statistics. As one of the first comparative content analysis studies of health reporting in Eastern and Western cultures, this study provides a unique cultural lens for health communication scholars to better understand health information in the news media. PMID:25411911

  3. Comparative loss analysis and efficiency performance of resonance-based PDP sustain drivers

    NASA Astrophysics Data System (ADS)

    Kwak, S.-S.; Kim, I.-G.; Lee, J.

    2016-01-01

    Sustain drivers based on the LC resonant operation have a significant influence on the entire circuit efficiency and cost of plasma display panels (PDPs). Although circuit efficiency of PDP drivers is extremely important, theoretical loss analysis and comparative studies of the sustain drivers have been missed in the literature, despite a variety of developed PDP sustain drivers. This paper presents in detail theoretical analyses and systematic comparisons of semiconductor losses in the PDP sustain drivers, including the inevitable conduction losses by the displacement currents, the undesirable extra conduction losses, the switching losses by the forced current commutations and the switching losses by the step voltage changes. Based on derived theoretical analysis and comparative features, sustain drivers are evaluated in terms of PDP operating speed as well as circuits' efficiency.

  4. A comparative analysis on different nanofluid models for the oscillatory stagnation point flow

    NASA Astrophysics Data System (ADS)

    Nadeem, S.; Khan, A. U.; Saleem, S.

    2016-08-01

    In this study we have presented the comparative analysis of the oscillatory stagnation point flow of nanofluids. Both the phase flow model and Buongiorno model are discussed for oscillatory stagnation point flows and a comparison between experimental model and theoretical model is presented. The resulting partial differential equations for oscillatory two-dimensional flows are simplified in a fixed frame and a moving frame of reference subject to the assumed form of solutions. The homotopy analysis method is used to solve the reduced system of coupled nonlinear ordinary differential equations. The consequences are examined through graphs and tables. It is also found that comparatively both the Boungiorno nanofluid model and phase flow model are of compatible order for a special set of parameters but generally such results do not hold.

  5. Lookup Tables Versus Stacked Rasch Analysis in Comparing Pre- and Postintervention Adult Strabismus-20 Data

    PubMed Central

    Leske, David A.; Hatt, Sarah R.; Liebermann, Laura; Holmes, Jonathan M.

    2016-01-01

    Purpose We compare two methods of analysis for Rasch scoring pre- to postintervention data: Rasch lookup table versus de novo stacked Rasch analysis using the Adult Strabismus-20 (AS-20). Methods One hundred forty-seven subjects completed the AS-20 questionnaire prior to surgery and 6 weeks postoperatively. Subjects were classified 6 weeks postoperatively as “success,” “partial success,” or “failure” based on angle and diplopia status. Postoperative change in AS-20 scores was compared for all four AS-20 domains (self-perception, interactions, reading function, and general function) overall and by success status using two methods: (1) applying historical Rasch threshold measures from lookup tables and (2) performing a stacked de novo Rasch analysis. Change was assessed by analyzing effect size, improvement exceeding 95% limits of agreement (LOA), and score distributions. Results Effect sizes were similar for all AS-20 domains whether obtained from lookup tables or stacked analysis. Similar proportions exceeded 95% LOAs using lookup tables versus stacked analysis. Improvement in median score was observed for all AS-20 domains using lookup tables and stacked analysis (P < 0.0001 for all comparisons). Conclusions The Rasch-scored AS-20 is a responsive and valid instrument designed to measure strabismus-specific health-related quality of life. When analyzing pre- to postoperative change in AS-20 scores, Rasch lookup tables and de novo stacked Rasch analysis yield essentially the same results. Translational Relevance We describe a practical application of lookup tables, allowing the clinician or researcher to score the Rasch-calibrated AS-20 questionnaire without specialized software. PMID:26933524

  6. Comparative analysis of multisensor satellite monitoring of Arctic sea-ice

    USGS Publications Warehouse

    Belchansky, G.I.; Mordvintsev, I.N.; Douglas, D.C.

    1999-01-01

    This report represents comparative analysis of nearly coincident Russian OKEAN-01 polar orbiting satellite data, Special Sensor Microwave Imager (SSM/I) and Advanced Very High Resolution Radiometer (AVHRR) imagery. OKEAN-01 ice concentration algorithms utilize active and passive microwave measurements and a linear mixture model for measured values of the brightness temperature and the radar backscatter. SSM/I and AVHRR ice concentrations were computed with NASA Team algorithm and visible and thermal-infrared wavelength AVHRR data, accordingly

  7. [Comparative analysis of mortality among population of industrial mono-cities in Sverdlovsky region].

    PubMed

    2011-01-01

    The article covers comparative analysis of mortality causes and levels, with special consideration of mortality with malignancies, among dwellers of Asbest (enterprise forming company town - Pulbic Corporation "Uralasbest" - world leader in extraction and concentration of chrysotile asbestos) and Kamensk-Uralsky (enterprises forming company town - non-ferrous metallurgy plants), agricultural agea and population of Sverdlovsk region over 10 years (1997-2006). Major attention was paid to influence of dust containing chrysotile asbestos fibers. PMID:21786637

  8. COMPARATIVE ANALYSIS OF SELECTED EDDY CURRENT TRANSDUCERS FOR TITANIUM ALLOY EVALUATION

    SciTech Connect

    Chady, T.; Sikora, R.; Baniukiewicz, P.; Lopato, P.; Kowalczyk, J.; Psuj, G.; Caryk, M.

    2010-02-22

    Titanium alloy based details due to their mechanical properties continue to be in extensive use in various structures (mainly aerospace, automotive and petro-chemical industrial applications). In this paper comparative study of various types of eddy current NDT transducers for testing titanium elements was done. Probes of absolute, differential and array configurations were constructed and analyzed. Two and three dimensional numerical analysis (FEM) were done in order to find the best type and configuration of the proposed transducers.

  9. Comparative Analysis of Selected Eddy Current Transducers for Titanium Alloy Evaluation

    NASA Astrophysics Data System (ADS)

    Chady, T.; Sikora, R.; Baniukiewicz, P.; Lopato, P.; Kowalczyk, J.; Psuj, G.; Caryk, M.

    2010-02-01

    Titanium alloy based details due to their mechanical properties continue to be in extensive use in various structures (mainly aerospace, automotive and petro-chemical industrial applications). In this paper comparative study of various types of eddy current NDT transducers for testing titanium elements was done. Probes of absolute, differential and array configurations were constructed and analyzed. Two and three dimensional numerical analysis (FEM) were done in order to find the best type and configuration of the proposed transducers.

  10. Comparative analysis of medicinal plants used in traditional medicine in Italy and Tunisia

    PubMed Central

    Leporatti, Maria Lucia; Ghedira, Kamel

    2009-01-01

    Background Italy and Tunisia (Africa for the Romans), facing each other on the opposite sides of the Mediterranean Sea, have been historically linked since the ancient times. Over the centuries both countries were mutually dominated so the vestiges and traces of a mutual influence are still present. The aim of the present study is to conduct a comparative analysis of the medicinal species present in the respective Floras in order to explore potential analogies and differences in popular phytotherapy that have come out from those reciprocal exchanges having taken place over the centuries Methods The comparative analysis based on the respective floras of both countries takes into consideration the bulk of medicinal species mutually present in Italy and Tunisia, but it focuses on the species growing in areas which are similar in climate. The medicinal uses of these species are considered in accordance with the ethnobotanical literature. Results A list of 153 medicinal species belonging to 60 families, present in both floras and used in traditional medicine, was drawn. A considerable convergence in therapeutic uses of many species emerged from these data. Conclusion This comparative analysis strengthens the firm belief that ethno-botanical findings represent not only an important shared heritage, developed over the centuries, but also a considerable mass of data that should be exploited in order to provide new and useful knowledge. PMID:19857257

  11. Comparative proteomics analysis of oral cancer cell lines: identification of cancer associated proteins

    PubMed Central

    2014-01-01

    Background A limiting factor in performing proteomics analysis on cancerous cells is the difficulty in obtaining sufficient amounts of starting material. Cell lines can be used as a simplified model system for studying changes that accompany tumorigenesis. This study used two-dimensional gel electrophoresis (2DE) to compare the whole cell proteome of oral cancer cell lines vs normal cells in an attempt to identify cancer associated proteins. Results Three primary cell cultures of normal cells with a limited lifespan without hTERT immortalization have been successfully established. 2DE was used to compare the whole cell proteome of these cells with that of three oral cancer cell lines. Twenty four protein spots were found to have changed in abundance. MALDI TOF/TOF was then used to determine the identity of these proteins. Identified proteins were classified into seven functional categories – structural proteins, enzymes, regulatory proteins, chaperones and others. IPA core analysis predicted that 18 proteins were related to cancer with involvements in hyperplasia, metastasis, invasion, growth and tumorigenesis. The mRNA expressions of two proteins – 14-3-3 protein sigma and Stress-induced-phosphoprotein 1 – were found to correlate with the corresponding proteins’ abundance. Conclusions The outcome of this analysis demonstrated that a comparative study of whole cell proteome of cancer versus normal cell lines can be used to identify cancer associated proteins. PMID:24422745

  12. An analysis comparing "Sim Huddles" to traditional simulation for obstetric emergency preparedness.

    PubMed

    Sweeney, Jennifer; Maietta, Renee; Olson, Karla

    2015-01-01

    Health care professionals in obstetrics must be prepared to respond when emergencies arise. Simulation provides the opportunity to train in a team setting but can be resource-intensive. A postprogram implementation analysis compared high-fidelity in-situ simulation to a novel approach called "Sim Huddles." Sim Huddles are conducted in a quick, informal, low-fidelity staff huddle format incorporating concepts of TeamSTEPPS®. Postsimulation participant surveys from nine Sim Huddles were compared to nine traditional in-situ simulations. Results show similar achievement of learning goals and statistically significant improvement in self-reported confidence (p = .002) from the traditional in-situ format (mean = 4.32, sd = .771) compared to the Sim Huddle format (mean = 4.74, sd = .480). Sim Huddles can provide effective training with less time and fewer resources than what is required of traditional, high-fidelity simulation. PMID:25690812

  13. Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation

    PubMed Central

    Rasko, David A.; Worsham, Patricia L.; Abshire, Terry G.; Stanley, Scott T.; Bannan, Jason D.; Wilson, Mark R.; Langham, Richard J.; Decker, R. Scott; Jiang, Lingxia; Read, Timothy D.; Phillippy, Adam M.; Salzberg, Steven L.; Pop, Mihai; Van Ert, Matthew N.; Kenefic, Leo J.; Keim, Paul S.; Fraser-Liggett, Claire M.; Ravel, Jacques

    2011-01-01

    Before the anthrax letter attacks of 2001, the developing field of microbial forensics relied on microbial genotyping schemes based on a small portion of a genome sequence. Amerithrax, the investigation into the anthrax letter attacks, applied high-resolution whole-genome sequencing and comparative genomics to identify key genetic features of the letters’ Bacillus anthracis Ames strain. During systematic microbiological analysis of the spore material from the letters, we identified a number of morphological variants based on phenotypic characteristics and the ability to sporulate. The genomes of these morphological variants were sequenced and compared with that of the B. anthracis Ames ancestor, the progenitor of all B. anthracis Ames strains. Through comparative genomics, we identified four distinct loci with verifiable genetic mutations. Three of the four mutations could be directly linked to sporulation pathways in B. anthracis and more specifically to the regulation of the phosphorylation state of Spo0F, a key regulatory protein in the initiation of the sporulation cascade, thus linking phenotype to genotype. None of these variant genotypes were identified in single-colony environmental B. anthracis Ames isolates associated with the investigation. These genotypes were identified only in B. anthracis morphotypes isolated from the letters, indicating that the variants were not prevalent in the environment, not even the environments associated with the investigation. This study demonstrates the forensic value of systematic microbiological analysis combined with whole-genome sequencing and comparative genomics. PMID:21383169

  14. Comparative diversity analysis in sandy littoral ecosystems of the western Mediterranean

    NASA Astrophysics Data System (ADS)

    Colombini, I.; Fallaci, M.; Milanesi, F.; Scapini, F.; Chelazzi, L.

    2003-10-01

    A comparative faunal analysis was carried out in sandy littoral localities differing both morphologically and in human impact. The study sites were located in the western Mediterranean basin along the coasts of Morocco, Tunisia, the Maltese Islands and Italy. These were typical beach-dune ecosystems more (Smir, Morocco; Zouara, Tunisia; Burano, Italy) or less (Ir-Ramla tat-Torri, Malta and Ir-Ramla l-Hamra, Gozo) structurally developed accordingly. Species richness was evaluated using standard trapping techniques with pitfall traps along the transects perpendicular to the shoreline. Only isopods and coleopterans were used in the analysis. In each locality, an analysis was conducted on both the beach and the dune separately, and on the entire ecosystem in the two seasons (spring and autumn). Species were studied both quantitatively and qualitatively using ecological coefficients (relative abundance) and Fisher's diversity index. To evaluate the evenness of the community, Shannon-Weaver index was calculated and compared with Brillouin index. For both indices, the maximum values were computed and were used to obtain the evenness of the community through Pielou index. In addition, Simpson's dominance index was considered. Percentages of similarities between localities were analysed in the two seasons and in total using the Renkonen index. The overall analysis showed that general trends could be found for both orders that were studied and gave indications on habitat quality. The study showed that when monitoring was carried out systematically both in space and time, arthropods could be used as important tool to assess beach health.

  15. IMG/M 4 version of the integrated metagenome comparative analysis system.

    PubMed

    Markowitz, Victor M; Chen, I-Min A; Chu, Ken; Szeto, Ernest; Palaniappan, Krishna; Pillay, Manoj; Ratner, Anna; Huang, Jinghua; Pagani, Ioanna; Tringe, Susannah; Huntemann, Marcel; Billis, Konstantinos; Varghese, Neha; Tennessen, Kristin; Mavromatis, Konstantinos; Pati, Amrita; Ivanova, Natalia N; Kyrpides, Nikos C

    2014-01-01

    IMG/M (http://img.jgi.doe.gov/m) provides support for comparative analysis of microbial community aggregate genomes (metagenomes) in the context of a comprehensive set of reference genomes from all three domains of life, as well as plasmids, viruses and genome fragments. IMG/M's data content and analytical tools have expanded continuously since its first version was released in 2007. Since the last report published in the 2012 NAR Database Issue, IMG/M's database architecture, annotation and data integration pipelines and analysis tools have been extended to copewith the rapid growth in the number and size of metagenome data sets handled by the system. IMG/M data marts provide support for the analysis of publicly available genomes, expert review of metagenome annotations (IMG/M ER: http://img.jgi.doe.gov/mer) and Human Microbiome Project (HMP)-specific metagenome samples (IMG/M HMP: http://img.jgi.doe.gov/imgm_hmp). PMID:24136997

  16. Sequence and comparative analysis of the MIP gene in Chinese straw mushroom, Volvariella volvacea.

    PubMed

    Chen, Bing-Zhi; Gui, Fu; Xie, Bao-Gui; Zou, Feng; Jiang, Yu-Ji; Deng, You-Jin

    2012-09-01

    The mitochondrial intermediate peptidase (MIP) gene is conserved in fungi. It is linked closely with the mating-type A (mtA) gene. In this study, a fragment of the MIP gene in Volvariella volvacea (Bull. ex Fr.) Singer was first cloned by homologue-based cloning technology. Subsequently, the entire MIP DNA sequence (PYd21-MIP) was obtained after the fragment was compared with the genomic data through BLAST analysis. The PYd21-MIP sequence appeared to be homologous with the MIP gene in other fungi. Phylogenetic analysis of PYd21-MIP and other MIP sequences from diverse fungi agreed with the current organism phylogeny. Analysis of protein domains by InterProScan software and motif searching demonstrated that PYd21-MIP encodes a homologous MIP protein. These data support the hypothesis that the PYd21-MIP protein is a Hog-MIP protein homologue from V. volvacea. PMID:22937907

  17. Analysis of RNAseq datasets from a comparative infectious disease zebrafish model using GeneTiles bioinformatics.

    PubMed

    Veneman, Wouter J; de Sonneville, Jan; van der Kolk, Kees-Jan; Ordas, Anita; Al-Ars, Zaid; Meijer, Annemarie H; Spaink, Herman P

    2015-03-01

    We present a RNA deep sequencing (RNAseq) analysis of a comparison of the transcriptome responses to infection of zebrafish larvae with Staphylococcus epidermidis and Mycobacterium marinum bacteria. We show how our developed GeneTiles software can improve RNAseq analysis approaches by more confidently identifying a large set of markers upon infection with these bacteria. For analysis of RNAseq data currently, software programs such as Bowtie2 and Samtools are indispensable. However, these programs that are designed for a LINUX environment require some dedicated programming skills and have no options for visualisation of the resulting mapped sequence reads. Especially with large data sets, this makes the analysis time consuming and difficult for non-expert users. We have applied the GeneTiles software to the analysis of previously published and newly obtained RNAseq datasets of our zebrafish infection model, and we have shown the applicability of this approach also to published RNAseq datasets of other organisms by comparing our data with a published mammalian infection study. In addition, we have implemented the DEXSeq module in the GeneTiles software to identify genes, such as glucagon A, that are differentially spliced under infection conditions. In the analysis of our RNAseq data, this has led to the possibility to improve the size of data sets that could be efficiently compared without using problem-dedicated programs, leading to a quick identification of marker sets. Therefore, this approach will also be highly useful for transcriptome analyses of other organisms for which well-characterised genomes are available. PMID:25503064

  18. Comparative Pathway Analyzer--a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms.

    PubMed

    Oehm, Sebastian; Gilbert, David; Tauch, Andreas; Stoye, Jens; Goesmann, Alexander

    2008-07-01

    In order to understand the phenotype of any living system, it is essential to not only investigate its genes, but also the specific metabolic pathway variant of the organism of interest, ideally in comparison with other organisms. The Comparative Pathway Analyzer, CPA, calculates and displays the differences in metabolic reaction content between two sets of organisms. Because results are highly dependent on the distribution of organisms into these two sets and the appropriate definition of these sets often is not easy, we provide hierarchical clustering methods for the identification of significant groupings. CPA also visualizes the reaction content of several organisms simultaneously allowing easy comparison. Reaction annotation data and maps for visualizing the results are taken from the KEGG database. Additionally, users can upload their own annotation data. This website is free and open to all users and there is no login requirement. It is available at https://www.cebitec.uni-bielefeld.de/groups/brf/software/cpa/index.html. PMID:18539612

  19. Comparative Mitogenomic Analysis of Damsel Bugs Representing Three Tribes in the Family Nabidae (Insecta: Hemiptera)

    PubMed Central

    Song, Fan; Shi, Aimin; Zhou, Xuguo; Cai, Wanzhi

    2012-01-01

    Background Nabidae, a family of predatory heteropterans, includes two subfamilies and five tribes. We previously reported the complete mitogenome of Alloeorhynchus bakeri, a representative of the tribe Prostemmatini in the subfamily Prostemmatinae. To gain a better understanding of architecture and evolution of mitogenome in Nabidae, mitogenomes of five species representing two tribes (Gorpini and Nabini) in the subfamily Nabinae were sequenced, and a comparative mitogenomic analysis of three nabid tribes in two subfamilies was carried out. Methodology/Principal Findings Nabid mitogenomes share a similar nucleotide composition and base bias, except for the control region, where differences are observed at the subfamily level. In addition, the pattern of codon usage is influenced by the GC content and consistent with the standard invertebrate mitochondrial genetic code and the preference for A+T-rich codons. The comparison among orthologous protein-coding genes shows that different genes have been subject to different rates of molecular evolution correlated with the GC content. The stems and anticodon loops of tRNAs are extremely conserved, and the nucleotide substitutions are largely restricted to TψC and DHU loops and extra arms, with insertion-deletion polymorphisms. Comparative analysis shows similar rates of substitution between the two rRNAs. Long non-coding regions are observed in most Gorpini and Nabini mtDNAs in-between trnI-trnQ and/or trnS2-nad1. The lone exception, Nabis apicalis, however, has lost three tRNAs. Overall, phylogenetic analysis using mitogenomic data is consistent with phylogenies constructed mainly form morphological traits. Conclusions/Significance This comparative mitogenomic analysis sheds light on the architecture and evolution of mitogenomes in the family Nabidae. Nucleotide diversity and mitogenomic traits are phylogenetically informative at subfamily level. Furthermore, inclusion of a broader range of samples representing various

  20. Wastewater-Based Epidemiology of Stimulant Drugs: Functional Data Analysis Compared to Traditional Statistical Methods

    PubMed Central

    Salvatore, Stefania; Bramness, Jørgen Gustav; Reid, Malcolm J.; Thomas, Kevin Victor; Harman, Christopher; Røislien, Jo

    2015-01-01

    Background Wastewater-based epidemiology (WBE) is a new methodology for estimating the drug load in a population. Simple summary statistics and specification tests have typically been used to analyze WBE data, comparing differences between weekday and weekend loads. Such standard statistical methods may, however, overlook important nuanced information in the data. In this study, we apply functional data analysis (FDA) to WBE data and compare the results to those obtained from more traditional summary measures. Methods We analysed temporal WBE data from 42 European cities, using sewage samples collected daily for one week in March 2013. For each city, the main temporal features of two selected drugs were extracted using functional principal component (FPC) analysis, along with simpler measures such as the area under the curve (AUC). The individual cities’ scores on each of the temporal FPCs were then used as outcome variables in multiple linear regression analysis with various city and country characteristics as predictors. The results were compared to those of functional analysis of variance (FANOVA). Results The three first FPCs explained more than 99% of the temporal variation. The first component (FPC1) represented the level of the drug load, while the second and third temporal components represented the level and the timing of a weekend peak. AUC was highly correlated with FPC1, but other temporal characteristic were not captured by the simple summary measures. FANOVA was less flexible than the FPCA-based regression, and even showed concordance results. Geographical location was the main predictor for the general level of the drug load. Conclusion FDA of WBE data extracts more detailed information about drug load patterns during the week which are not identified by more traditional statistical methods. Results also suggest that regression based on FPC results is a valuable addition to FANOVA for estimating associations between temporal patterns and covariate

  1. Comparative Transcriptome Analysis Reveals Substantial Tissue Specificity in Human Aortic Valve

    PubMed Central

    Wang, Jun; Wang, Ying; Gu, Weidong; Ni, Buqing; Sun, Haoliang; Yu, Tong; Gu, Wanjun; Chen, Liang; Shao, Yongfeng

    2016-01-01

    RNA sequencing (RNA-seq) has revolutionary roles in transcriptome identification and quantification of different types of tissues and cells in many organisms. Although numerous RNA-seq data derived from many types of human tissues and cell lines, little is known on the transcriptome repertoire of human aortic valve. In this study, we sequenced the total RNA prepared from two calcified human aortic valves and reported the whole transcriptome of human aortic valve. Integrating RNA-seq data of 13 human tissues from Human Body Map 2 Project, we constructed a transcriptome repertoire of human tissues, including 19,505 protein-coding genes and 4,948 long intergenic noncoding RNAs (lincRNAs). Among them, 263 lincRNAs were identified as novel noncoding transcripts in our data. By comparing transcriptome data among different human tissues, we observed substantial tissue specificity of RNA transcripts, both protein-coding genes and lincRNAs, in human aortic valve. Further analysis revealed that aortic valve-specific lincRNAs were more likely to be recently derived from repetitive elements in the primate lineage, but were less likely to be conserved at the nucleotide level. Expression profiling analysis showed significant lower expression levels of aortic valve-specific protein-coding genes and lincRNA genes, when compared with genes that were universally expressed in various tissues. Isoform-level expression analysis also showed that a majority of mRNA genes had a major isoform expressed in the human aortic valve. To our knowledge, this is the first comparative transcriptome analysis between human aortic valve and other human tissues. Our results are helpful to understand the transcriptome diversity of human tissues and the underlying mechanisms that drive tissue specificity of protein-coding genes and lincRNAs in human aortic valve. PMID:27493474

  2. Comparative Transcriptome Analysis Reveals Substantial Tissue Specificity in Human Aortic Valve.

    PubMed

    Wang, Jun; Wang, Ying; Gu, Weidong; Ni, Buqing; Sun, Haoliang; Yu, Tong; Gu, Wanjun; Chen, Liang; Shao, Yongfeng

    2016-01-01

    RNA sequencing (RNA-seq) has revolutionary roles in transcriptome identification and quantification of different types of tissues and cells in many organisms. Although numerous RNA-seq data derived from many types of human tissues and cell lines, little is known on the transcriptome repertoire of human aortic valve. In this study, we sequenced the total RNA prepared from two calcified human aortic valves and reported the whole transcriptome of human aortic valve. Integrating RNA-seq data of 13 human tissues from Human Body Map 2 Project, we constructed a transcriptome repertoire of human tissues, including 19,505 protein-coding genes and 4,948 long intergenic noncoding RNAs (lincRNAs). Among them, 263 lincRNAs were identified as novel noncoding transcripts in our data. By comparing transcriptome data among different human tissues, we observed substantial tissue specificity of RNA transcripts, both protein-coding genes and lincRNAs, in human aortic valve. Further analysis revealed that aortic valve-specific lincRNAs were more likely to be recently derived from repetitive elements in the primate lineage, but were less likely to be conserved at the nucleotide level. Expression profiling analysis showed significant lower expression levels of aortic valve-specific protein-coding genes and lincRNA genes, when compared with genes that were universally expressed in various tissues. Isoform-level expression analysis also showed that a majority of mRNA genes had a major isoform expressed in the human aortic valve. To our knowledge, this is the first comparative transcriptome analysis between human aortic valve and other human tissues. Our results are helpful to understand the transcriptome diversity of human tissues and the underlying mechanisms that drive tissue specificity of protein-coding genes and lincRNAs in human aortic valve. PMID:27493474

  3. Comparative Analysis of Genomics and Proteomics in Bacillus thuringiensis 4.0718

    PubMed Central

    Rang, Jie; He, Hao; Wang, Ting; Ding, Xuezhi; Zuo, Mingxing; Quan, Meifang; Sun, Yunjun; Yu, Ziquan; Hu, Shengbiao; Xia, Liqiu

    2015-01-01

    Bacillus thuringiensis is a widely used biopesticide that produced various insecticidal active substances during its life cycle. Separation and purification of numerous insecticide active substances have been difficult because of the relatively short half-life of such substances. On the other hand, substances can be synthetized at different times during development, so samples at different stages have to be studied, further complicating the analysis. A dual genomic and proteomic approach would enhance our ability to identify such substances, and particularily using mass spectrometry-based proteomic methods. The comparative analysis for genomic and proteomic data have showed that not all of the products deduced from the annotated genome could be identified among the proteomic data. For instance, genome annotation results showed that 39 coding sequences in the whole genome were related to insect pathogenicity, including five cry genes. However, Cry2Ab, Cry1Ia, Cytotoxin K, Bacteriocin, Exoenzyme C3 and Alveolysin could not be detected in the proteomic data obtained. The sporulation-related proteins were also compared analysis, results showed that the great majority sporulation-related proteins can be detected by mass spectrometry. This analysis revealed Spo0A~P, SigF, SigE(+), SigK(+) and SigG(+), all known to play an important role in the process of spore formation regulatory network, also were displayed in the proteomic data. Through the comparison of the two data sets, it was possible to infer that some genes were silenced or were expressed at very low levels. For instance, found that cry2Ab seems to lack a functional promoter while cry1Ia may not be expressed due to the presence of transposons. With this comparative study a relatively complete database can be constructed and used to transform hereditary material, thereby prompting the high expression of toxic proteins. A theoretical basis is provided for constructing highly virulent engineered bacteria and for

  4. Comparative Genomic Analysis of Brucella melitensis Vaccine Strain M5 Provides Insights into Virulence Attenuation

    PubMed Central

    Zhang, Wen; Wang, Heng; Zhao, Hongyan; Piao, Dongri; Tian, Guozhong; Chen, Chen; Cui, Buyun

    2013-01-01

    The Brucella melitensis vaccine strain M5 is widely used to prevent and control brucellosis in animals. In this study, we determined the whole-genome sequence of M5, and conducted a comprehensive comparative analysis against the whole-genome sequence of the virulent strain 16 M and other reference strains. This analysis revealed 11 regions of deletion (RDs) and 2 regions of insertion (RIs) within the M5 genome. Among these regions, the sequences encompassed in 5 RDs and 1 RI showed consistent variation, with a large deletion between the M5 and the 16 M genomes. RD4 and RD5 showed the large diversity among all Brucella genomes, both in RD length and RD copy number. Thus, RD4 and RD5 are potential sites for typing different Brucella strains. Other RD and RI regions exhibited multiple single nucleotide polymorphisms (SNPs). In addition, a genome fragment with a 56 kb rearrangement was determined to be consistent with previous studies. Comparative genomic analysis indicated that genomic island inversion in Brucella was widely present. With the genetic pattern common among all strains analyzed, these 2 RDs, 1 RI, and one inversion region are potential sites for detection of genomic differences. Several SNPs of important virulence-related genes (motB, dhbC, sfuB, dsbAB, aidA, aroC, and lysR) were also detected, and may be used to determine the mechanism of virulence attenuation. Collectively, this study reveals that comparative analysis between wild-type and vaccine strains can provide resources for the study of virulence and microevolution of Brucella. PMID:23967122

  5. Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi

    PubMed Central

    2013-01-01

    Background Fungi produce a variety of carbohydrate activity enzymes (CAZymes) for the degradation of plant polysaccharide materials to facilitate infection and/or gain nutrition. Identifying and comparing CAZymes from fungi with different nutritional modes or infection mechanisms may provide information for better understanding of their life styles and infection models. To date, over hundreds of fungal genomes are publicly available. However, a systematic comparative analysis of fungal CAZymes across the entire fungal kingdom has not been reported. Results In this study, we systemically identified glycoside hydrolases (GHs), polysaccharide lyases (PLs), carbohydrate esterases (CEs), and glycosyltransferases (GTs) as well as carbohydrate-binding modules (CBMs) in the predicted proteomes of 103 representative fungi from Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. Comparative analysis of these CAZymes that play major roles in plant polysaccharide degradation revealed that fungi exhibit tremendous diversity in the number and variety of CAZymes. Among them, some families of GHs and CEs are the most prevalent CAZymes that are distributed in all of the fungi analyzed. Importantly, cellulases of some GH families are present in fungi that are not known to have cellulose-degrading ability. In addition, our results also showed that in general, plant pathogenic fungi have the highest number of CAZymes. Biotrophic fungi tend to have fewer CAZymes than necrotrophic and hemibiotrophic fungi. Pathogens of dicots often contain more pectinases than fungi infecting monocots. Interestingly, besides yeasts, many saprophytic fungi that are highly active in degrading plant biomass contain fewer CAZymes than plant pathogenic fungi. Furthermore, analysis of the gene expression profile of the wheat scab fungus Fusarium graminearum revealed that most of the CAZyme genes related to cell wall degradation were up-regulated during plant infection. Phylogenetic analysis also

  6. Success Factors of European Syndromic Surveillance Systems: A Worked Example of Applying Qualitative Comparative Analysis

    PubMed Central

    Ziemann, Alexandra; Fouillet, Anne; Brand, Helmut; Krafft, Thomas

    2016-01-01

    Introduction Syndromic surveillance aims at augmenting traditional public health surveillance with timely information. To gain a head start, it mainly analyses existing data such as from web searches or patient records. Despite the setup of many syndromic surveillance systems, there is still much doubt about the benefit of the approach. There are diverse interactions between performance indicators such as timeliness and various system characteristics. This makes the performance assessment of syndromic surveillance systems a complex endeavour. We assessed if the comparison of several syndromic surveillance systems through Qualitative Comparative Analysis helps to evaluate performance and identify key success factors. Materials and Methods We compiled case-based, mixed data on performance and characteristics of 19 syndromic surveillance systems in Europe from scientific and grey literature and from site visits. We identified success factors by applying crisp-set Qualitative Comparative Analysis. We focused on two main areas of syndromic surveillance application: seasonal influenza surveillance and situational awareness during different types of potentially health threatening events. Results We found that syndromic surveillance systems might detect the onset or peak of seasonal influenza earlier if they analyse non-clinical data sources. Timely situational awareness during different types of events is supported by an automated syndromic surveillance system capable of analysing multiple syndromes. To our surprise, the analysis of multiple data sources was no key success factor for situational awareness. Conclusions We suggest to consider these key success factors when designing or further developing syndromic surveillance systems. Qualitative Comparative Analysis helped interpreting complex, mixed data on small-N cases and resulted in concrete and practically relevant findings. PMID:27182731

  7. Comparative genomic hybridization analysis of newly established retinoblastoma cell lines of adherent growth compared with Y79 of nonadherent growth.

    PubMed

    Kim, Jeong Hun; Kim, Jin Hyoung; Yu, Young Suk; Kim, Dong Hun; Kim, Yong Kyu; Kim, Kyu-Won

    2008-08-01

    Retinoblastoma (RB) shows cytogenetic aberrations involving genes other than RB gene located on 13q14. We analyzed genomic aberration in newly established RB cell lines SNUOT-RB1 and SNUOT-RB4 of adherent growth and Y79 cell line of nonadherent growth by microarray comparative genomic hybridization. SNUOT-RB1 showed 44 significant copy number changes (gain in 11 and loss in 33, P<0.0005). SNUOT-RB4 showed 42 significant copy number changes (gain in 8 and loss in 34, P<0.0005). Y79 cell line had the greatest gain of 19.65-fold in the locus of MYCN gene 2p24.1, whereas SNUOT-RB1 and SNUOT-RB4 showed no significant gain. SNUOT-RB1 and SNUOT-RB4 gained chromosomal copy numbers commonly in chromosome 11, especially in locus 11q13, which is responsible for cancer-related genes such as CCND1, MEN1, and FGF3. Losses of copy numbers occurred in chromosomes 3, 9, 10, 11, 16, and 17. In summary, SNUOT-RB1 and SNUOT-RB4 represented similar pattern in gain and loss of chromosomal copy number changes, while different from Y79. The loss of CYLD gene of tumor suppressor gene, 16q12-q13, was only on locus of common involvement in 3 cell lines. PMID:18799932

  8. Probabilistic Analysis for Comparing Fatigue Data Based on Johnson-Weibull Parameters

    NASA Technical Reports Server (NTRS)

    Hendricks, Robert C.; Zaretsky, Erwin V.; Vicek, Brian L.

    2007-01-01

    Probabilistic failure analysis is essential when analysis of stress-life (S-N) curves is inconclusive in determining the relative ranking of two or more materials. In 1964, L. Johnson published a methodology for establishing the confidence that two populations of data are different. Simplified algebraic equations for confidence numbers were derived based on the original work of L. Johnson. Using the ratios of mean life, the resultant values of confidence numbers deviated less than one percent from those of Johnson. It is possible to rank the fatigue lives of different materials with a reasonable degree of statistical certainty based on combined confidence numbers. These equations were applied to rotating beam fatigue tests that were conducted on three aluminum alloys at three stress levels each. These alloys were AL 2024, AL 6061, and AL 7075. The results were analyzed and compared using ASTM Standard E739-91 and the Johnson-Weibull analysis. The ASTM method did not statistically distinguish between AL 6010 and AL 7075. Based on the Johnson-Weibull analysis confidence numbers greater than 99 percent, AL 2024 was found to have the longest fatigue life, followed by AL 7075, and then AL 6061. The ASTM Standard and the Johnson-Weibull analysis result in the same stress-life exponent p for each of the three aluminum alloys at the median or L(sub 50) lives.

  9. Genome-scale metabolic modeling of Mucor circinelloides and comparative analysis with other oleaginous species.

    PubMed

    Vongsangnak, Wanwipa; Klanchui, Amornpan; Tawornsamretkit, Iyarest; Tatiyaborwornchai, Witthawin; Laoteng, Kobkul; Meechai, Asawin

    2016-06-01

    We present a novel genome-scale metabolic model iWV1213 of Mucor circinelloides, which is an oleaginous fungus for industrial applications. The model contains 1213 genes, 1413 metabolites and 1326 metabolic reactions across different compartments. We demonstrate that iWV1213 is able to accurately predict the growth rates of M. circinelloides on various nutrient sources and culture conditions using Flux Balance Analysis and Phenotypic Phase Plane analysis. Comparative analysis of three oleaginous genome-scale models, including M. circinelloides (iWV1213), Mortierella alpina (iCY1106) and Yarrowia lipolytica (iYL619_PCP) revealed that iWV1213 possesses a higher number of genes involved in carbohydrate, amino acid, and lipid metabolisms that might contribute to its versatility in nutrient utilization. Moreover, the identification of unique and common active reactions among the Zygomycetes oleaginous models using Flux Variability Analysis unveiled a set of gene/enzyme candidates as metabolic engineering targets for cellular improvement. Thus, iWV1213 offers a powerful metabolic engineering tool for multi-level omics analysis, enabling strain optimization as a cell factory platform of lipid-based production. PMID:26911256

  10. Comparative analysis of bacterial profiles in unstimulated and stimulated saliva samples

    PubMed Central

    Belstrøm, Daniel; Holmstrup, Palle; Bardow, Allan; Kokaras, Alexis; Fiehn, Nils-Erik; Paster, Bruce J.

    2016-01-01

    Background and objective The microbial profiles of stimulated saliva samples have been shown to differentiate between patients with periodontitis, patients with dental caries, and orally healthy individuals. Saliva was stimulated to allow for easy and rapid collection; however, microbial composition may not reflect the more natural, unstimulated state. The purpose of this study was to validate whether stimulated saliva is an adequate surrogate for unstimulated saliva in determining salivary microbiomes. Design Unstimulated (n=20) and stimulated (n=20) saliva samples were collected from 20 orally and systemically healthy, non-smoking participants. Salivary bacterial profiles were analyzed by means of the Human Oral Microbe Identification using Next Generation Sequencing (HOMINGS), and statistical analysis was performed using Mann–Whitney test with Benjamini–Hochberg's correction for multiple comparison, cluster analysis, principal component analysis, and correspondence analysis. Results From a total of 40 saliva samples, 496 probe targets were identified with a mean number of targets per sample of 203 (range: 146–303), and a mean number of probe targets of 206 and 200 in unstimulated and stimulated saliva samples, respectively (p=0.62). Based on all statistical methods used for this study, the microbial profiles of unstimulated and stimulated saliva samples collected from the same person were not statistically significantly different. Conclusions Analysis of bacterial salivary profiles in unstimulated and stimulated saliva samples collected from the same individual showed comparable results. Thus, the results verify that stimulated saliva is an adequate surrogate of unstimulated saliva for microbiome-related studies. PMID:26987356

  11. Comparative Genomic Analysis of Drosophila melanogaster and Vector Mosquito Developmental Genes

    PubMed Central

    Behura, Susanta K.; Haugen, Morgan; Flannery, Ellen; Sarro, Joseph; Tessier, Charles R.; Severson, David W.; Duman-Scheel, Molly

    2011-01-01

    Genome sequencing projects have presented the opportunity for analysis of developmental genes in three vector mosquito species: Aedes aegypti, Culex quinquefasciatus, and Anopheles gambiae. A comparative genomic analysis of developmental genes in Drosophila melanogaster and these three important vectors of human disease was performed in this investigation. While the study was comprehensive, special emphasis centered on genes that 1) are components of developmental signaling pathways, 2) regulate fundamental developmental processes, 3) are critical for the development of tissues of vector importance, 4) function in developmental processes known to have diverged within insects, and 5) encode microRNAs (miRNAs) that regulate developmental transcripts in Drosophila. While most fruit fly developmental genes are conserved in the three vector mosquito species, several genes known to be critical for Drosophila development were not identified in one or more mosquito genomes. In other cases, mosquito lineage-specific gene gains with respect to D. melanogaster were noted. Sequence analyses also revealed that numerous repetitive sequences are a common structural feature of Drosophila and mosquito developmental genes. Finally, analysis of predicted miRNA binding sites in fruit fly and mosquito developmental genes suggests that the repertoire of developmental genes targeted by miRNAs is species-specific. The results of this study provide insight into the evolution of developmental genes and processes in dipterans and other arthropods, serve as a resource for those pursuing analysis of mosquito development, and will promote the design and refinement of functional analysis experiments. PMID:21754989

  12. EDGAR: A software framework for the comparative analysis of prokaryotic genomes

    PubMed Central

    Blom, Jochen; Albaum, Stefan P; Doppmeier, Daniel; Pühler, Alfred; Vorhölter, Frank-Jörg; Zakrzewski, Martha; Goesmann, Alexander

    2009-01-01

    Background The introduction of next generation sequencing approaches has caused a rapid increase in the number of completely sequenced genomes. As one result of this development, it is now feasible to analyze large groups of related genomes in a comparative approach. A main task in comparative genomics is the identification of orthologous genes in different genomes and the classification of genes as core genes or singletons. Results To support these studies EDGAR – "Efficient Database framework for comparative Genome Analyses using BLAST score Ratios" – was developed. EDGAR is designed to automatically perform genome comparisons in a high throughput approach. Comparative analyses for 582 genomes across 75 genus groups taken from the NCBI genomes database were conducted with the software and the results were integrated into an underlying database. To demonstrate a specific application case, we analyzed ten genomes of the bacterial genus Xanthomonas, for which phylogenetic studies were awkward due to divergent taxonomic systems. The resultant phylogeny EDGAR provided was consistent with outcomes from traditional approaches performed recently and moreover, it was possible to root each strain with unprecedented accuracy. Conclusion EDGAR provides novel analysis features and significantly simplifies the comparative analysis of related genomes. The software supports a quick survey of evolutionary relationships and simplifies the process of obtaining new biological insights into the differential gene content of kindred genomes. Visualization features, like synteny plots or Venn diagrams, are offered to the scientific community through a web-based and therefore platform independent user interface , where the precomputed data sets can be browsed. PMID:19457249

  13. Diclofenac topical solution compared with oral diclofenac: a pooled safety analysis

    PubMed Central

    Roth, Sanford H; Fuller, Philip

    2011-01-01

    Background Topical nonsteroidal anti-inflammatory drug (NSAID) formulations, which produce less systemic exposure compared with oral formulations, are an option for the management of osteoarthritis (OA). However, the overall safety and efficacy of these agents compared with oral or systemic therapy remains controversial. Methods Two 12-week, double-blind, double-dummy, randomized, controlled, multicenter studies compared the safety and efficacy profiles of diclofenac topical solution (TDiclo) with oral diclofenac (ODiclo). Each study independently showed that TDiclo had similar efficacy to ODiclo. To compare the safety profiles of TDiclo and ODiclo, a pooled safety analysis was performed for 927 total patients who had radiologically confirmed symptomatic OA of the knee. This pooled analysis included patients treated with TDiclo, containing 45.5% dimethyl sulfoxide (DMSO), and those treated with ODiclo. Safety assessments included monitoring of adverse events (AEs), recording of vital signs, dermatologic evaluation of the study knee, and clinical laboratory evaluation. Results AEs occurred in 312 (67.1%) patients using TDiclo versus 298 (64.5%) of those taking ODiclo. The most common AE with TDiclo was dry skin at the application site (24.1% vs 1.9% with ODiclo; P < 0.0001). Fewer gastrointestinal (25.4% vs 39.0%; P < 0.0001) and cardiovascular (1.5% vs 3.5%; P = 0.055) AEs occurred with TDiclo compared with ODiclo. ODiclo was associated with significantly greater increases in liver enzymes and creatinine, and greater decreases in creatinine clearance and hemoglobin (P < 0.001 for all). Conclusions These findings suggest that TDiclo represents a useful alternative to oral NSAID therapy in the management of OA, with a more favorable safety profile. PMID:21811391

  14. Comparative Metagenomic Analysis of Coral Microbial Communities Using a Reference-Independent Approach

    PubMed Central

    Carlos, Camila; Castro, Daniel Bedo Assumpção; Ottoboni, Laura M. M.

    2014-01-01

    By comparing the SEED and Pfam functional profiles of metagenomes of two Brazilian coral species with 29 datasets that are publicly available, we were able to identify some functions, such as protein secretion systems, that are overrepresented in the metagenomes of corals and may play a role in the establishment and maintenance of bacteria-coral associations. However, only a small percentage of the reads of these metagenomes could be annotated by these reference databases, which may lead to a strong bias in the comparative studies. For this reason, we have searched for identical sequences (99% of nucleotide identity) among these metagenomes in order to perform a reference-independent comparative analysis, and we were able to identify groups of microbial communities that may be under similar selective pressures. The identification of sequences shared among the metagenomes was found to be even better for the identification of groups of communities with similar niche requirements than the traditional analysis of functional profiles. This approach is not only helpful for the investigation of similarities between microbial communities with high proportion of unknown reads, but also enables an indirect overview of gene exchange between communities. PMID:25379670

  15. Imageless Navigation Versus Conventional Open Wedge High Tibial Osteotomy: A Meta-Analysis of Comparative Studies

    PubMed Central

    Kim, Hyun Jung; Yoon, Jung-Ro; Choi, Gi Won

    2016-01-01

    Purpose To summarize and compare radiological and clinical outcomes of open wedge high tibial osteotomy (HTO) using imageless computer-assisted navigation with conventional HTO. Methods A literature search of online register databases was conducted. The risk ratio (RR) of radiological outliers and mean differences in clinical outcomes were compared between navigated and conventional HTOs. Radiological results were evaluated by subgroup analyses according to the study period (concurrent/consecutive) and the use of locking fixation device. Results Seven comparative studies with a total sample size of 406 knees were included in this review. Radiographically, the mechanical axis [MA] was within the acceptable range (0°–6°) in 83.7% of the navigation HTO group, showing significant difference from 62.1% of the conventional HTO group. Clinically, despite the forest plot demonstrating a general trend of favoring the navigation system, there were not sufficient studies to determine statistical significance in the meta-analysis. None of the subgroup analyses demonstrated significant differences in the RR of MA outliers. Conclusions The present meta-analysis indicates that the use of navigation in open wedge HTO improves the precision of mechanical alignment by decreasing the incidence of outliers; however, the clinical benefit is not conclusive. Additionally, none of the subgroup analyses demonstrated significant difference in the RR of MA outliers. PMID:26955609

  16. The stoma appliances market in five European countries: a comparative analysis.

    PubMed

    Cornago, Dante; Garattini, Livio

    2002-01-01

    This comparative exercise analysed the domestic market for stoma appliances in five European countries--Denmark, France, Germany, Italy and the United Kingdom. National legislation, prescription procedures, delivery modalities and the market were investigated in each country. The analysis involved reviewing national and international literature on stoma appliances and interviewing a selected expert panel of market operators in each country comprising at least one health authority representative, one distributor of medical devices and one manufacturer. No specific relationship was found between the health care system framework and the stoma market, except for a greater inclination towards home care in national health services. All five countries reimburse stoma bags, but the distribution of these appliances varies widely, ranging from Denmark, where home delivery is mandatory, to Italy, where any channel can be used. The comparative analysis underlined two important features of the stoma bag market: the discretion of enterostomists in directing patients towards a specific brand of bags, and the patients' high brand loyalty. Despite that, the analysis did not identify any single country that could be considered a benchmark for stoma bag regulation. Each country deals with stoma appliances in different ways, making this a very fragmented market. PMID:14618747

  17. Pricing and reimbursement of in-patent drugs in seven European countries: a comparative analysis.

    PubMed

    Garattini, Livio; Cornago, Dante; De Compadri, Paola

    2007-08-01

    The main objective of this comparative analysis was to assess regulations applied by EU governments to reward potentially innovative drugs. We focused on the pharmaceutical policy for in-patent drugs in seven EU countries: Belgium, France, Germany, Italy, the Netherlands, Spain, and the UK. A common scheme was applied to all seven countries: first, pricing and reimbursement procedures for new and innovative drugs were investigated; secondly, we focused on the use in the regulatory process of economic evaluations. The analysis involved reviewing the literature and interviewing a selected panel of local experts in each country. According to our comparative analysis, a first sensible step might be to classify active ingredients as those addressing neglected pathologies and those for diseases that are already successfully treated, thus offering more limited therapeutic gains by definition. A reasonable solution to reward real innovation could be to admit a premium price for very innovative drugs according to their estimated cost-effectiveness. New drugs with modest improvement could be grouped in therapeutic clusters and submitted to a common reference price, despite patent expiration. Such a "dual approach" could be a sensible compromise to restrict pharmaceutical expenditure while at the same time rewarding companies that invest in high-risk basic research. PMID:17125881

  18. A comparative molecular analysis of water-filled limestone sinkholes in north-eastern Mexico.

    PubMed

    Sahl, Jason W; Gary, Marcus O; Harris, J Kirk; Spear, John R

    2011-01-01

    Sistema Zacatón in north-eastern Mexico is host to several deep, water-filled, anoxic, karstic sinkholes (cenotes). These cenotes were explored, mapped, and geochemically and microbiologically sampled by the autonomous underwater vehicle deep phreatic thermal explorer (DEPTHX). The community structure of the filterable fraction of the water column and extensive microbial mats that coat the cenote walls was investigated by comparative analysis of small-subunit (SSU) 16S rRNA gene sequences. Full-length Sanger gene sequence analysis revealed novel microbial diversity that included three putative bacterial candidate phyla and three additional groups that showed high intra-clade distance with poorly characterized bacterial candidate phyla. Limited functional gene sequence analysis in these anoxic environments identified genes associated with methanogenesis, sulfate reduction and anaerobic ammonium oxidation. A directed, barcoded amplicon, multiplex pyrosequencing approach was employed to compare ∼100,000 bacterial SSU gene sequences from water column and wall microbial mat samples from five cenotes in Sistema Zacatón. A new, high-resolution sequence distribution profile (SDP) method identified changes in specific phylogenetic types (phylotypes) in microbial mats at varied depths; Mantel tests showed a correlation of the genetic distances between mat communities in two cenotes and the geographic location of each cenote. Community structure profiles from the water column of three neighbouring cenotes showed distinct variation; statistically significant differences in the concentration of geochemical constituents suggest that the variation observed in microbial communities between neighbouring cenotes are due to geochemical variation. PMID:20738374

  19. Protein extraction from Ca-alginate encapsulated plant material for comparative proteomic analysis.

    PubMed

    Domżalska, Lucyna; Mikuła, Anna; Rybczyński, Jan J

    2016-10-01

    The extensive use of encapsulation material in biotechnology drove the need to develop analytical techniques for this type of material. This study focuses on the specific problems of protein extraction from Ca-alginate encapsulated plant material. Proteomics is one of the fast-developing analysis categories, specifically for stress resistance and developmental changes in plant material. Sample preparation is a critical step in a two-dimensional gel electrophoresis proteome approach and is essential for good results. The aim was to avoid preliminary manipulations and get good quality material for comparative proteome analysis technique 2DE. The phenol extraction method and the complex method with preliminary TCA precipitation, SDS buffer and phenol phase were compared with respect to the efficiency and quality of the resulting 2DE gel. The most appropriate method turned out to be the TCA/phenol method with the phenol fractioning technique adapted to the gentian cell suspension. It resulted in a high protein concentration and good quality sample that could be analyzed using the standard separation procedures of 2DE and spectrometric identification with high efficiency. The work presented here confirms the possibility of obtaining a sufficient protein sample for effective proteomic analysis from a small number of capsules. PMID:27235574

  20. Comparative analysis of coal use options for reducing the dependence of utilities on imported oil

    SciTech Connect

    Eggers, Jr, A J

    1980-01-03

    The President and the Congress are finalizing National Goals to reduce the Nation's dependence on imported oil. A key element of these goals is the conversion of utilities from oil-fired to coal-fired to yield an import reduction of 0.75 MBD by 1990. Since these utilities already exist at fixed locations, this element of the National Goals has the focus of Appolo, Polaris, Minuteman and other major successful programs. It is indicated, therefore, that the program development and management techniques employed in these programs may have useful application to the utility conversion program. These techniques include comparative systems and mission mode analysis, and the application of these techniques to the utility conversion program is discussed. It is observed that the conversions of coal-capable utilities will most likely be achieved in the first half of the next decade, while those for non coal-capable utilities will likely occur in the latter half of the next decade. It is suggested that DOE/RA initiate an in-house task force effort to make a comparative analysis of conversion alternatives to meet this goal. This analysis is discussed in some detail and it should consider the coal delivery as well as the conversion elements of the overall coal use system with a view to focusing on problems which must be addressed, and discarding those which are of no consequence to meeting the National Goal.

  1. [RANK INDICES METHOD AND ITS USE FOR THE COMPARATIVE ANALYSIS OF POPULATION HEALTH].

    PubMed

    Bolshakov, A M; Krutko, V N; Smirnova, T M; Chankov, S V

    2016-01-01

    There is presented a calculation method aimed to elevate the informative value of the integral indices of the social and hygienic monitoringfor purposes of comparative analysis. The method of rank indices is based on the ranking of monitoring objects on the values of primary indices on the base of which there are calculated the integral such indices as, for example, life expectancy. There are presented results of the use of this method for the comparative analysis of mortality rate in WHO Member States for the period of 1990-2011. There were revealed specialfeatures of mortality trends which cannot be detected when using only mortality rates or the life expectancy. In particular, for Russia there was shown that, in spite of the downward trend in child and adolescent mortality rate observed in the last decade, the country's world rankings for these indices fail to achieve the level of 1990. This means that the competitiveness of the country, sharply declined in the 90's, was not restored until now. There are described some features of the use of the method of rank indices for the analysis of indices of the environment state, public health and its socio-economic determinants. PMID:27266035

  2. Comparative analysis of mycobacterium and related actinomycetes yields insight into the evolution of mycobacterium tuberculosis pathogenesis

    PubMed Central

    2012-01-01

    Background The sequence of the pathogen Mycobacterium tuberculosis (Mtb) strain H37Rv has been available for over a decade, but the biology of the pathogen remains poorly understood. Genome sequences from other Mtb strains and closely related bacteria present an opportunity to apply the power of comparative genomics to understand the evolution of Mtb pathogenesis. We conducted a comparative analysis using 31 genomes from the Tuberculosis Database (TBDB.org), including 8 strains of Mtb and M. bovis, 11 additional Mycobacteria, 4 Corynebacteria, 2 Streptomyces, Rhodococcus jostii RHA1, Nocardia farcinia, Acidothermus cellulolyticus, Rhodobacter sphaeroides, Propionibacterium acnes, and Bifidobacterium longum. Results Our results highlight the functional importance of lipid metabolism and its regulation, and reveal variation between the evolutionary profiles of genes implicated in saturated and unsaturated fatty acid metabolism. It also suggests that DNA repair and molybdopterin cofactors are important in pathogenic Mycobacteria. By analyzing sequence conservation and gene expression data, we identify nearly 400 conserved noncoding regions. These include 37 predicted promoter regulatory motifs, of which 14 correspond to previously validated motifs, as well as 50 potential noncoding RNAs, of which we experimentally confirm the expression of four. Conclusions Our analysis of protein evolution highlights gene families that are associated with the adaptation of environmental Mycobacteria to obligate pathogenesis. These families include fatty acid metabolism, DNA repair, and molybdopterin biosynthesis. Our analysis reinforces recent findings suggesting that small noncoding RNAs are more common in Mycobacteria than previously expected. Our data provide a foundation for understanding the genome and biology of Mtb in a comparative context, and are available online and through TBDB.org. PMID:22452820

  3. Comparative Transcriptome Analysis of Cultivated and Wild Watermelon during Fruit Development.

    PubMed

    Guo, Shaogui; Sun, Honghe; Zhang, Haiying; Liu, Jingan; Ren, Yi; Gong, Guoyi; Jiao, Chen; Zheng, Yi; Yang, Wencai; Fei, Zhangjun; Xu, Yong

    2015-01-01

    Watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] is an important vegetable crop world-wide. Watermelon fruit quality is a complex trait determined by various factors such as sugar content, flesh color and flesh texture. Fruit quality and developmental process of cultivated and wild watermelon are highly different. To systematically understand the molecular basis of these differences, we compared transcriptome profiles of fruit tissues of cultivated watermelon 97103 and wild watermelon PI296341-FR. We identified 2,452, 826 and 322 differentially expressed genes in cultivated flesh, cultivated mesocarp and wild flesh, respectively, during fruit development. Gene ontology enrichment analysis of these genes indicated that biological processes and metabolic pathways related to fruit quality such as sweetness and flavor were significantly changed only in the flesh of 97103 during fruit development, while those related to abiotic stress response were changed mainly in the flesh of PI296341-FR. Our comparative transcriptome profiling analysis identified critical genes potentially involved in controlling fruit quality traits including α-galactosidase, invertase, UDP-galactose/glucose pyrophosphorylase and sugar transporter genes involved in the determination of fruit sugar content, phytoene synthase, β-carotene hydroxylase, 9-cis-epoxycarotenoid dioxygenase and carotenoid cleavage dioxygenase genes involved in carotenoid metabolism, and 4-coumarate:coenzyme A ligase, cellulose synthase, pectinesterase, pectinesterase inhibitor, polygalacturonase inhibitor and α-mannosidase genes involved in the regulation of flesh texture. In addition, we found that genes in the ethylene biosynthesis and signaling pathway including ACC oxidase, ethylene receptor and ethylene responsive factor showed highly ripening-associated expression patterns, indicating a possible role of ethylene in fruit development and ripening of watermelon, a non-climacteric fruit. Our analysis provides

  4. Comparative Transcriptome Analysis of Cultivated and Wild Watermelon during Fruit Development

    PubMed Central

    Guo, Shaogui; Sun, Honghe; Zhang, Haiying; Liu, Jingan; Ren, Yi; Gong, Guoyi; Jiao, Chen; Zheng, Yi; Yang, Wencai; Fei, Zhangjun; Xu, Yong

    2015-01-01

    Watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] is an important vegetable crop world-wide. Watermelon fruit quality is a complex trait determined by various factors such as sugar content, flesh color and flesh texture. Fruit quality and developmental process of cultivated and wild watermelon are highly different. To systematically understand the molecular basis of these differences, we compared transcriptome profiles of fruit tissues of cultivated watermelon 97103 and wild watermelon PI296341-FR. We identified 2,452, 826 and 322 differentially expressed genes in cultivated flesh, cultivated mesocarp and wild flesh, respectively, during fruit development. Gene ontology enrichment analysis of these genes indicated that biological processes and metabolic pathways related to fruit quality such as sweetness and flavor were significantly changed only in the flesh of 97103 during fruit development, while those related to abiotic stress response were changed mainly in the flesh of PI296341-FR. Our comparative transcriptome profiling analysis identified critical genes potentially involved in controlling fruit quality traits including α-galactosidase, invertase, UDP-galactose/glucose pyrophosphorylase and sugar transporter genes involved in the determination of fruit sugar content, phytoene synthase, β-carotene hydroxylase, 9-cis-epoxycarotenoid dioxygenase and carotenoid cleavage dioxygenase genes involved in carotenoid metabolism, and 4-coumarate:coenzyme A ligase, cellulose synthase, pectinesterase, pectinesterase inhibitor, polygalacturonase inhibitor and α-mannosidase genes involved in the regulation of flesh texture. In addition, we found that genes in the ethylene biosynthesis and signaling pathway including ACC oxidase, ethylene receptor and ethylene responsive factor showed highly ripening-associated expression patterns, indicating a possible role of ethylene in fruit development and ripening of watermelon, a non-climacteric fruit. Our analysis provides

  5. History counts: a comparative analysis of racial/color categorization in US and Brazilian censuses.

    PubMed Central

    Nobles, M

    2000-01-01

    Categories of race (ethnicity, color, or both) have appeared and continue to appear in the demographic censuses of numerous countries, including the United States and Brazil. Until recently, such categorization had largely escaped critical scrutiny, being viewed and treated as a technical procedure requiring little conceptual clarity or historical explanation. Recent political developments and methodological changes, in US censuses especially, have engendered a critical reexamination of both the comparative and the historical dimensions of categorization. The author presents a comparative analysis of the histories of racial/color categorization in American and Brazilian censuses and shows that racial (and color) categories have appeared in these censuses because of shifting ideas about race and the enduring power of these ideas as organizers of political, economic, and social life in both countries. These categories have not appeared simply as demographic markers. The author demonstrates that censuses are instruments at a state's disposal and are not simply detached registers of population and performance. PMID:11076243

  6. History counts: a comparative analysis of racial/color categorization in US and Brazilian censuses.

    PubMed

    Nobles, M

    2000-11-01

    Categories of race (ethnicity, color, or both) have appeared and continue to appear in the demographic censuses of numerous countries, including the United States and Brazil. Until recently, such categorization had largely escaped critical scrutiny, being viewed and treated as a technical procedure requiring little conceptual clarity or historical explanation. Recent political developments and methodological changes, in US censuses especially, have engendered a critical reexamination of both the comparative and the historical dimensions of categorization. The author presents a comparative analysis of the histories of racial/color categorization in American and Brazilian censuses and shows that racial (and color) categories have appeared in these censuses because of shifting ideas about race and the enduring power of these ideas as organizers of political, economic, and social life in both countries. These categories have not appeared simply as demographic markers. The author demonstrates that censuses are instruments at a state's disposal and are not simply detached registers of population and performance. PMID:11076243

  7. Ultrastructural analysis of adult mouse neocortex comparing aldehyde perfusion with cryo fixation

    PubMed Central

    Korogod, Natalya; Petersen, Carl CH; Knott, Graham W

    2015-01-01

    Analysis of brain ultrastructure using electron microscopy typically relies on chemical fixation. However, this is known to cause significant tissue distortion including a reduction in the extracellular space. Cryo fixation is thought to give a truer representation of biological structures, and here we use rapid, high-pressure freezing on adult mouse neocortex to quantify the extent to which these two fixation methods differ in terms of their preservation of the different cellular compartments, and the arrangement of membranes at the synapse and around blood vessels. As well as preserving a physiological extracellular space, cryo fixation reveals larger numbers of docked synaptic vesicles, a smaller glial volume, and a less intimate glial coverage of synapses and blood vessels compared to chemical fixation. The ultrastructure of mouse neocortex therefore differs significantly comparing cryo and chemical fixation conditions. DOI: http://dx.doi.org/10.7554/eLife.05793.001 PMID:26259873

  8. Complete genome sequencing and comparative genomic analysis of functionally diverse Lysinibacillus sphaericus III(3)7.

    PubMed

    Rey, Andrés; Silva-Quintero, Laura; Dussán, Jenny

    2016-09-01

    Lysinibacillus sphaericus III(3)7 is a native Colombian strain, the first one isolated from soil samples. This strain has shown high levels of pathogenic activity against Culex quinquefaciatus larvae in laboratory assays compared to other members of the same species. Using Pacific Biosciences sequencing technology we sequenced, annotated (de novo) and described the genome of strain III(3)7, achieving a complete genome sequence status. We then performed a comparative analysis between the newly sequenced genome and the ones previously reported for Colombian isolates L. sphaericus OT4b.31, CBAM5 and OT4b.25, with the inclusion of L. sphaericus C3-41 that has been used as a reference genome for most of previous genome sequencing projects. We concluded that L. sphaericus III(3)7 is highly similar with strain OT4b.25 and shares high levels of synteny with isolates CBAM5 and C3-41. PMID:27419068

  9. The Integrated Microbial Genomes (IMG) System: An Expanding Comparative Analysis Resource

    SciTech Connect

    Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna; Chu, Ken; Szeto, Ernest; Grechkin, Yuri; Ratner, Anna; Anderson, Iain; Lykidis, Athanasios; Mavromatis, Konstantinos; Ivanova, Natalia N.; Kyrpides, Nikos C.

    2009-09-13

    The integrated microbial genomes (IMG) system serves as a community resource for comparative analysis of publicly available genomes in a comprehensive integrated context. IMG contains both draft and complete microbial genomes integrated with other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. IMG provides tools and viewers for analyzing and reviewing the annotations of genes and genomes in a comparative context. Since its first release in 2005, IMG's data content and analytical capabilities have been constantly expanded through regular releases. Several companion IMG systems have been set up in order to serve domain specific needs, such as expert review of genome annotations. IMG is available at .

  10. A comparative analysis of alternative fuels for the INEL vehicle fleet

    SciTech Connect

    Priebe, S.; Boyer, W.; Church, K.

    1992-11-01

    This report summarizes the results of a comparative systems analysis of various alternative fuels for use in the buses, mid-size vehicles, and automobiles that make up the vehicle fleet at the Idaho National Engineering Laboratory (INEL). The study was performed as part of the Laboratory Directed Research and Development (LDRD) Program for EG&G Idaho, Inc. Regulations will require the INEL to reduce total gasoline and diesel fuel use 10% by 1995 compared with 1991 levels, and will require that 50% of all new vehicles be fueled by some type of alternative fuel by 1998. A model was developed to analyze how these goals could be achieved, and what the cost would be to implement the goals.

  11. A comparative analysis of alternative fuels for the INEL vehicle fleet

    SciTech Connect

    Priebe, S.; Boyer, W.; Church, K.

    1992-11-01

    This report summarizes the results of a comparative systems analysis of various alternative fuels for use in the buses, mid-size vehicles, and automobiles that make up the vehicle fleet at the Idaho National Engineering Laboratory (INEL). The study was performed as part of the Laboratory Directed Research and Development (LDRD) Program for EG G Idaho, Inc. Regulations will require the INEL to reduce total gasoline and diesel fuel use 10% by 1995 compared with 1991 levels, and will require that 50% of all new vehicles be fueled by some type of alternative fuel by 1998. A model was developed to analyze how these goals could be achieved, and what the cost would be to implement the goals.

  12. Ultrastructural analysis of adult mouse neocortex comparing aldehyde perfusion with cryo fixation.

    PubMed

    Korogod, Natalya; Petersen, Carl C H; Knott, Graham W

    2015-01-01

    Analysis of brain ultrastructure using electron microscopy typically relies on chemical fixation. However, this is known to cause significant tissue distortion including a reduction in the extracellular space. Cryo fixation is thought to give a truer representation of biological structures, and here we use rapid, high-pressure freezing on adult mouse neocortex to quantify the extent to which these two fixation methods differ in terms of their preservation of the different cellular compartments, and the arrangement of membranes at the synapse and around blood vessels. As well as preserving a physiological extracellular space, cryo fixation reveals larger numbers of docked synaptic vesicles, a smaller glial volume, and a less intimate glial coverage of synapses and blood vessels compared to chemical fixation. The ultrastructure of mouse neocortex therefore differs significantly comparing cryo and chemical fixation conditions. PMID:26259873

  13. Comparative analysis of computational methods for periodic transonic flows at low and high frequencies

    NASA Astrophysics Data System (ADS)

    Mohaghegh, M. R.; Malek-Jafarian, M.

    2015-12-01

    This paper presents a comparative analysis via simulation of time-periodic unsteady inviscid flow at low and high frequencies using Time Spectral Method (TSM) and comparing it with the traditional methods such as BDF and Explicit Structured Adaptive Grid Method. The TSM uses a Fourier representation in time. Mathematical tools used here are discrete Fourier transformations. The TSM has been proposed for the fast and efficient computation of periodic unsteady flows. This method has been evaluated and has been validated with NACA pitching airfoils that are widely used and prevalent 2D external aerodynamics test cases. To validate the results presented by the TSM are compared with experimental data and two the other methods. It shows a significant reduction in the computational expense compared to the conventional time-accurate methods, due to taking advantage of the periodic nature of flow by Fourier representation for temporal discretization that has a high accuracy. Also it has shown that TSM can be applied accurately for ample rang of variations of frequency (NACA 64A010 (CT6)) and variations in angle of attacks (NACA 0012 (CT1)).

  14. Geriatric Small Bowel Obstruction: An Analysis of Treatment and Outcomes Compared to a Younger Cohort

    PubMed Central

    Krause, William R.; Webb, Travis P.

    2016-01-01

    Background Small bowel obstruction (SBO) is a common condition, but little is known about its presentation, management, and outcomes in geriatric patients. Methods A retrospective review was performed comparing geriatric (≥65 years of age) and non-geriatric patients admitted with SBO. Admission characteristics, treatment, and outcomes were compared. Data analysis included Student’s t test and chi-square test or Fisher exact test. Results Among 80 geriatric and 136 non-geriatric patients no difference was observed between admission characteristics, treatment, time to or type of surgery, length of post-op stay, or overall complications. Cardiac complications (15% vs 0%, p=0.0082) and sub-acute care facility discharge (29% vs 5%, p<0.001) were more common for geriatric patients. Conclusions Compared to younger adults, elderly patients with SBO have similar presentations and overall outcomes with the exception of cardiac morbidity and discharge disposition. Pre-operative attention to cardiac risk profile and discharge disposition discussion should be encouraged. Summary This study analyzes geriatric patients presenting with small bowel obstruction when cared for by an Acute Care Surgery service. Compared to younger adults, the presentation, treatment response, and outcomes are similar with the exception of cardiac complications and discharge destination. PMID:25048569

  15. IMG 4 version of the integrated microbial genomes comparative analysis system.

    PubMed

    Markowitz, Victor M; Chen, I-Min A; Palaniappan, Krishna; Chu, Ken; Szeto, Ernest; Pillay, Manoj; Ratner, Anna; Huang, Jinghua; Woyke, Tanja; Huntemann, Marcel; Anderson, Iain; Billis, Konstantinos; Varghese, Neha; Mavromatis, Konstantinos; Pati, Amrita; Ivanova, Natalia N; Kyrpides, Nikos C

    2014-01-01

    The Integrated Microbial Genomes (IMG) data warehouse integrates genomes from all three domains of life, as well as plasmids, viruses and genome fragments. IMG provides tools for analyzing and reviewing the structural and functional annotations of genomes in a comparative context. IMG's data content and analytical capabilities have increased continuously since its first version released in 2005. Since the last report published in the 2012 NAR Database Issue, IMG's annotation and data integration pipelines have evolved while new tools have been added for recording and analyzing single cell genomes, RNA Seq and biosynthetic cluster data. Different IMG datamarts provide support for the analysis of publicly available genomes (IMG/W: http://img.jgi.doe.gov/w), expert review of genome annotations (IMG/ER: http://img.jgi.doe.gov/er) and teaching and training in the area of microbial genome analysis (IMG/EDU: http://img.jgi.doe.gov/edu). PMID:24165883

  16. Comparative analysis of high-resolution chromosome techniques for leukemic bone marrows

    SciTech Connect

    Yunis, J.J.

    1982-09-01

    High-resolution direct and synchronization culture techniques for chromosome analysis of leukemic bone marrow cells can now be utilized. In this article, three different techniques are quantitatively compared for their consistency in successful cytogenetic analysis, reliability in the detection of clones with chromosomal abnormalities, and usefulness for the precise delineation of break points involved in structural chromosomal rearrangements. Bone marrow samples from 15 consecutive patients with acute nonlymphocytic leukemia (ANLL) were studied using an improved direct technique, amethopterin cell synchronization with thymidine release, and amethopterin cell synchronization with bromodeoxyuridine (BrdU) release. The results obtained with the amethopterin cell synchronization technique and thymidine release suggest that it should be the method of choice in the detection of chromosome defects in bone marrow of patients with ANLL.

  17. Comparing sugar components of cereal and pseudocereal flour by GC-MS analysis.

    PubMed

    Ačanski, Marijana M; Vujić, Djura N

    2014-02-15

    Gas chromatography with mass spectrometry was used for carrying out a qualitative analysis of the ethanol soluble flour extract of different types of cereals bread wheat and spelt and pseudocereals (amaranth and buckwheat). TMSI (trimethylsilylimidazole) was used as a reagent for the derivatisation of carbohydrates into trimethylsilyl ethers. All samples were first defatted with hexane. (In our earlier investigations, hexane extracts were used for the analysis of fatty acid of lipid components.) Many components of pentoses, hexoses and disaccharides were identified using 73 and 217 Da mass and the Wiley Online Library search. The aim of this paper is not to identify and find new components, but to compare sugar components of tested samples of flour of cereals bread wheat and spelt and pseudocereals (amarnath and buckwheat). Results were analysed using descriptive statistics (dendrograms and PCA). The results show that this method can be used for making a distinction among different types of flour. PMID:24128539

  18. Comparative analysis of air pollution emissions by electric utilities: Public policy implications

    NASA Astrophysics Data System (ADS)

    Freedman, Martin; Jaggi, Bikki

    1991-09-01

    One of the objectives of US environmental regulations was to reduce industrial air pollution emissions, especially from the electric utility industry, the major industrial air polluter. In this study, a comparative analysis of air pollution emissions from fossil-fuel-burning electric utility plants is conducted. The analysis focuses on a 12-yr period from 1975 to 1987 for three air pollutants: particulates, surfur dioxide, and nitrogen oxides. The results indicate that particulate emissions have been significantly reduced but that sulfur dioxide and nitrogen oxides are still major problems for a number of plants. Furthermore, the disparity in the performance by plants indicates that by using current technology, the industry as a whole could greatly reduce these emissions. These results have policy implication for future environmental legislation.

  19. Comparative genomic analysis of Brazilian Leptospira kirschneri serogroup Pomona serovar Mozdok.

    PubMed

    Moreno, Luisa Z; Kremer, Frederico S; Miraglia, Fabiana; Loureiro, Ana P; Eslabao, Marcus R; Dellagostin, Odir A; Lilenbaum, Walter; Moreno, Andrea M

    2016-08-01

    Leptospira kirschneri is one of the pathogenic species of the Leptospira genus. Human and animal infection from L. kirschneri gained further attention over the last few decades. Here we present the isolation and characterisation of Brazilian L. kirschneri serogroup Pomona serovar Mozdok strain M36/05 and the comparative genomic analysis with Brazilian human strain 61H. The M36/05 strain caused pulmonary hemorrhagic lesions in the hamster model, showing high virulence. The studied genomes presented high symmetrical identity and the in silico multilocus sequence typing analysis resulted in a new allelic profile (ST101) that so far has only been associated with the Brazilian L. kirschneri serogroup Pomona serovar Mozdok strains. Considering the environmental conditions and high genomic similarity observed between strains, we suggest the existence of a Brazilian L. kirschneri serogroup Pomona serovar Mozdok lineage that could represent a high public health risk; further studies are necessary to confirm the lineage significance and distribution. PMID:27581124

  20. Comparative analysis on some spatial-domain filters for fringe pattern denoising.

    PubMed

    Wang, Haixia; Kemao, Qian

    2011-04-20

    Fringe patterns produced by various optical interferometric techniques encode information such as shape, deformation, and refractive index. Noise affects further processing of the fringe patterns. Denoising is often needed before fringe pattern demodulation. Filtering along the fringe orientation is an effective option. Such filters include coherence enhancing diffusion, spin filtering with curve windows, second-order oriented partial-differential equations, and the regularized quadratic cost function for oriented fringe pattern filtering. These filters are analyzed to establish the relationships among them. Theoretical analysis shows that the four filters are largely equivalent to each other. Quantitative results are given on simulated fringe patterns to validate the theoretical analysis and to compare the performance of these filters. PMID:21509060

  1. Genetic Characterization and Comparative Genome Analysis of Brucella melitensis Isolates from India

    PubMed Central

    Azam, Sarwar; Rao, Sashi Bhushan; Jakka, Padmaja; NarasimhaRao, Veera; Bhargavi, Bindu; Gupta, Vivek Kumar

    2016-01-01

    Brucellosis is the most frequent zoonotic disease worldwide, with over 500,000 new human infections every year. Brucella melitensis, the most virulent species in humans, primarily affects goats and the zoonotic transmission occurs by ingestion of unpasteurized milk products or through direct contact with fetal tissues. Brucellosis is endemic in India but no information is available on population structure and genetic diversity of Brucella spp. in India. We performed multilocus sequence typing of four B. melitensis strains isolated from naturally infected goats from India. For more detailed genetic characterization, we carried out whole genome sequencing and comparative genome analysis of one of the B. melitensis isolates, Bm IND1. Genome analysis identified 141 unique SNPs, 78 VNTRs, 51 Indels, and 2 putative prophage integrations in the Bm IND1 genome. Our data may help to develop improved epidemiological typing tools and efficient preventive strategies to control brucellosis. PMID:27525259

  2. Neo-Deterministic and Probabilistic Seismic Hazard Assessments: a Comparative Analysis

    NASA Astrophysics Data System (ADS)

    Peresan, Antonella; Magrin, Andrea; Nekrasova, Anastasia; Kossobokov, Vladimir; Panza, Giuliano F.

    2016-04-01

    Objective testing is the key issue towards any reliable seismic hazard assessment (SHA). Different earthquake hazard maps must demonstrate their capability in anticipating ground shaking from future strong earthquakes before an appropriate use for different purposes - such as engineering design, insurance, and emergency management. Quantitative assessment of maps performances is an essential step also in scientific process of their revision and possible improvement. Cross-checking of probabilistic models with available observations and independent physics based models is recognized as major validation procedure. The existing maps from the classical probabilistic seismic hazard analysis (PSHA), as well as those from the neo-deterministic analysis (NDSHA), which have been already developed for several regions worldwide (including Italy, India and North Africa), are considered to exemplify the possibilities of the cross-comparative analysis in spotting out limits and advantages of different methods. Where the data permit, a comparative analysis versus the documented seismic activity observed in reality is carried out, showing how available observations about past earthquakes can contribute to assess performances of the different methods. Neo-deterministic refers to a scenario-based approach, which allows for consideration of a wide range of possible earthquake sources as the starting point for scenarios constructed via full waveforms modeling. The method does not make use of empirical attenuation models (i.e. Ground Motion Prediction Equations, GMPE) and naturally supplies realistic time series of ground shaking (i.e. complete synthetic seismograms), readily applicable to complete engineering analysis and other mitigation actions. The standard NDSHA maps provide reliable envelope estimates of maximum seismic ground motion from a wide set of possible scenario earthquakes, including the largest deterministically or historically defined credible earthquake. In addition

  3. Comparative genomic analysis of Brazilian Leptospira kirschneri serogroup Pomona serovar Mozdok.

    PubMed

    Moreno, Luisa Z; Kremer, Frederico S; Miraglia, Fabiana; Loureiro, Ana P; Eslabao, Marcus R; Dellagostin, Odir A; Lilenbaum, Walter; Moreno, Andrea M

    2016-07-11

    Leptospira kirschneri is one of the pathogenic species of the Leptospira genus. Human and animal infection from L. kirschneri gained further attention over the last few decades. Here we present the isolation and characterisation of Brazilian L. kirschneri serogroup Pomona serovar Mozdok strain M36/05 and the comparative genomic analysis with Brazilian human strain 61H. The M36/05 strain caused pulmonary hemorrhagic lesions in the hamster model, showing high virulence. The studied genomes presented high symmetrical identity and the in silico multilocus sequence typing analysis resulted in a new allelic profile (ST101) that so far has only been associated with the Brazilian L. kirschneri serogroup Pomona serovar Mozdok strains. Considering the environmental conditions and high genomic similarity observed between strains, we suggest the existence of a Brazilian L. kirschneri serogroup Pomona serovar Mozdok lineage that could represent a high public health risk; further studies are necessary to confirm the lineage significance and distribution. PMID:27409843

  4. Comparative Analysis of the Macroscale Structural Connectivity in the Macaque and Human Brain

    PubMed Central

    Bezgin, Gleb; Uylings, Harry B. M.; Roebroeck, Alard; Stiers, Peter

    2014-01-01

    The macaque brain serves as a model for the human brain, but its suitability is challenged by unique human features, including connectivity reconfigurations, which emerged during primate evolution. We perform a quantitative comparative analysis of the whole brain macroscale structural connectivity of the two species. Our findings suggest that the human and macaque brain as a whole are similarly wired. A region-wise analysis reveals many interspecies similarities of connectivity patterns, but also lack thereof, primarily involving cingulate regions. We unravel a common structural backbone in both species involving a highly overlapping set of regions. This structural backbone, important for mediating information across the brain, seems to constitute a feature of the primate brain persevering evolution. Our findings illustrate novel evolutionary aspects at the macroscale connectivity level and offer a quantitative translational bridge between macaque and human research. PMID:24676052

  5. Comparative genomic analysis of Brazilian Leptospira kirschneri serogroup Pomona serovar Mozdok

    PubMed Central

    Moreno, Luisa Z; Kremer, Frederico S; Miraglia, Fabiana; Loureiro, Ana P; Eslabao, Marcus R; Dellagostin, Odir A; Lilenbaum, Walter; Moreno, Andrea M

    2016-01-01

    Leptospira kirschneri is one of the pathogenic species of the Leptospira genus. Human and animal infection from L. kirschneri gained further attention over the last few decades. Here we present the isolation and characterisation of Brazilian L. kirschneri serogroup Pomona serovar Mozdok strain M36/05 and the comparative genomic analysis with Brazilian human strain 61H. The M36/05 strain caused pulmonary hemorrhagic lesions in the hamster model, showing high virulence. The studied genomes presented high symmetrical identity and the in silico multilocus sequence typing analysis resulted in a new allelic profile (ST101) that so far has only been associated with the Brazilian L. kirschneri serogroup Pomona serovar Mozdok strains. Considering the environmental conditions and high genomic similarity observed between strains, we suggest the existence of a Brazilian L. kirschneri serogroup Pomona serovar Mozdok lineage that could represent a high public health risk; further studies are necessary to confirm the lineage significance and distribution. PMID:27581124

  6. Genetic Characterization and Comparative Genome Analysis of Brucella melitensis Isolates from India.

    PubMed

    Azam, Sarwar; Rao, Sashi Bhushan; Jakka, Padmaja; NarasimhaRao, Veera; Bhargavi, Bindu; Gupta, Vivek Kumar; Radhakrishnan, Girish

    2016-01-01

    Brucellosis is the most frequent zoonotic disease worldwide, with over 500,000 new human infections every year. Brucella melitensis, the most virulent species in humans, primarily affects goats and the zoonotic transmission occurs by ingestion of unpasteurized milk products or through direct contact with fetal tissues. Brucellosis is endemic in India but no information is available on population structure and genetic diversity of Brucella spp. in India. We performed multilocus sequence typing of four B. melitensis strains isolated from naturally infected goats from India. For more detailed genetic characterization, we carried out whole genome sequencing and comparative genome analysis of one of the B. melitensis isolates, Bm IND1. Genome analysis identified 141 unique SNPs, 78 VNTRs, 51 Indels, and 2 putative prophage integrations in the Bm IND1 genome. Our data may help to develop improved epidemiological typing tools and efficient preventive strategies to control brucellosis. PMID:27525259

  7. A comparative analysis of stakeholder power in the Mexican and U.S. health care systems.

    PubMed

    Kirby, Eric G

    2006-01-01

    The primary focus of this paper is to analyze the Mexican health care system and the forces driving its change. To facilitate this, the paper conducts an analysis of the key stakeholders in both the U.S. and Mexican health care systems. The Mexican system is dominated by an autocratic federal government that is gradually relinquishing its role as provider of health care in exchange for control of the reform efforts. The U.S. system is characterized by a relatively equal distribution of power among the key stakeholders, in which changes occur primarily through incrementalism. The results of the analysis indicate that the key differences lie in terms of relative stakeholder power and rate of change in the systems. Compared with the U.S.,Mexico is making rapid changes to its health care system and both countries are struggling with the same key issues: Cost, access, and quality. PMID:17255070

  8. IMG 4 version of the integrated microbial genomes comparative analysis system

    SciTech Connect

    Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna; Chu, Ken; Szeto, Ernest; Pillay, Manoj; Ratner, Anna; Huang, Jinghua; Woyke, Tanja; Huntemann, Marcel; Anderson, Iain; Billis, Konstantinos; Varghese, Neha; Mavromatis, Konstantinos; Pati, Amrita; Ivanova, Natalia N.; Kyrpides, Nikos C.

    2013-10-27

    The Integrated Microbial Genomes (IMG) data warehouse integrates genomes from all three domains of life, as well as plasmids, viruses and genome fragments. IMG provides tools for analyzing and reviewing the structural and functional annotations of genomes in a comparative context. IMG’s data content and analytical capabilities have increased continuously since its first version released in 2005. Since the last report published in the 2012 NAR Database Issue, IMG’s annotation and data integration pipelines have evolved while new tools have been added for recording and analyzing single cell genomes, RNA Seq and biosynthetic cluster data. Finally, different IMG datamarts provide support for the analysis of publicly available genomes (IMG/W: http://img.jgi.doe.gov/w), expert review of genome annotations (IMG/ER: http://img.jgi.doe.gov/er) and teaching and training in the area of microbial genome analysis (IMG/EDU: http://img.jgi.doe.gov/edu).

  9. Comparative structure analysis of non-polar organic ferrofluids stabilized by saturated mono-carboxylic acids.

    PubMed

    Avdeev, M V; Bica, D; Vékás, L; Aksenov, V L; Feoktystov, A V; Marinica, O; Rosta, L; Garamus, V M; Willumeit, R

    2009-06-01

    The structure of ferrofluids (magnetite in decahydronaphtalene) stabilized with saturated mono-carboxylic acids of different chain lengths (lauric, myristic, palmitic and stearic acids) is studied by means of magnetization analysis and small-angle neutron scattering. It is shown that in case of saturated acid surfactants, magnetite nanoparticles are dispersed in the carrier approximately with the same size distribution whose mean value and width are significantly less as compared to the classical stabilization with non-saturated oleic acid. The found thickness of the surfactant shell around magnetite is analyzed with respect to stabilizing properties of mono-carboxylic acids. PMID:19376524

  10. Comparative Analysis of Different Measurement Techniques for MLC Characterization: Preliminary Results

    SciTech Connect

    Larraga-Gutierrez, J. M.; Ballesteros-Zebadua, P.; Garcia-Garduno, O. A.; Martinez-Davalos, A.; Rodriguez-Villafuerte, M.; Moreno-Jimenez, S.; Celis, M. A.

    2008-08-11

    Radiation transmission, leakage and beam penumbra are essential dosimetric parameters related to the commissioning of a multileaf collimation system. This work shows a comparative analysis of commonly used film detectors: X-OMAT V2 and EDR2 radiographic films, and GafChromic EBT registered radiochromic film. The results show that X-OMAT over-estimates radiation leakage and 80-20% beam penumbra. However, according to the reference values reported by the manufacturer for these dosimetric parameters, all three films are adequate for MLC dosimetric characterization, but special care must be taken when X-OMAT V2 film is used due to its low energy photon dependence.

  11. Comparative analysis of pulse shape discrimination methods in a 6Li loaded plastic scintillator

    NASA Astrophysics Data System (ADS)

    Balmer, Matthew J. I.; Gamage, Kelum A. A.; Taylor, Graeme C.

    2015-07-01

    Three algorithms for discriminating between fast neutrons, thermal neutrons and gamma rays in a 6Li loaded plastic scintillator have been compared. Following a literature review of existing pulse shape discrimination techniques, the performance of the charge comparison method, triangular filtering and frequency gradient analysis were investigated in this work. The scintillator was exposed to three different mixed gamma/neutron radiation fields. The figure of merit of neutron/gamma separation was investigated over a broad energy range, as well as for the neutron capture energy region. After optimisation, all three methods were found to perform similarly in terms of neutron/gamma separation.

  12. Mind and consciousness in yoga - Vedanta: A comparative analysis with western psychological concepts.

    PubMed

    Prabhu, H R Aravinda; Bhat, P S

    2013-01-01

    Study of mind and consciousness through established scientific methods is often difficult due to the observed-observer dichotomy. Cartesian approach of dualism considering the mind and matter as two diverse and unconnected entities has been questioned by oriental schools of Yoga and Vedanta as well as the recent quantum theories of modern physics. Freudian and Neo-freudian schools based on the Cartesian model have been criticized by the humanistic schools which come much closer to the vedantic approach of unitariness. A comparative analysis of the two approaches is discussed. PMID:23858252

  13. Comparative analysis of surface soil moisture retrieval using VSWI and TVDI in karst areas

    NASA Astrophysics Data System (ADS)

    Yan, Hongbo; Zhou, Guoqing; Lu, Xianjian

    2015-12-01

    Vegetation Supply Water Index (VSWI) and Temperature Vegetation dryness Index (TVDI) are two most commonly used methods for surface soil moisture (SSM) retrieval using electromagnetic spectrum of visible, near infrared and thermal infrared band. Both of them take into account the effect of vegetation index (VI) and surface temperature (Ts) on SSM. A comparative analysis of the ability and effect of the two methods for SSM retrieval in karst areas was carried out, using the remote sensing data of Landsat 8 OLI_TIRS. The study area is located in Guilin, which is a typical karst area. The experimental results show that TVDI is more suitable for SSM retrieval in karst areas.

  14. [Shape conservatism and shaping variability. The comparative analysis of Hydrozoa and Scyphozoa early development].

    PubMed

    Kraus, Iu A

    2002-01-01

    The morphogenetic pathways based on the self-organization take an important part in the early development of White Sea Cnidarians--Dynamena pumila (Hydrozoa) and Aurelia aurita (Scyphozoa). Comparative analysis of their early development revealed two patterns of embryonic spatial structure reproduced in the morphogenesis of both species in spite of the differences of morphogenetic paths. These are toroidal and bilaterally symmetrical shapes. It is possible that these shapes correspond to the equilibrium states of developing system and their stable reproduction is a result of epigenetic rather than genetic program. PMID:12298180

  15. Theoretical Analysis of the Sensitivity and Speed Improvement of ISIS over a Comparable Traditional Hyperspectral Imager

    SciTech Connect

    Brian R. Stallard; Stephen M. Gentry

    1998-09-01

    The analysis presented herein predicts that, under signal-independent noise limited conditions, an Information-efficient Spectral Imaging Sensor (ISIS) style hyperspectral imaging system design can obtain significant signal-to-noise ratio (SNR) and speed increase relative to a comparable traditional hyperspectral imaging (HSI) instrument. Factors of forty are reasonable for a single vector, and factors of eight are reasonable for a five-vector measurement. These advantages can be traded with other system parameters in an overall sensor system design to allow a variety of applications to be done that otherwise would be impossible within the constraints of the traditional HSI style design.

  16. Comparative analysis of early ontogeny in Bursatella leachii and Aplysia californica

    PubMed Central

    Vue, Zer; Capo, Thomas R.; Bardales, Ana T.

    2014-01-01

    Opisthobranch molluscs exhibit fascinating body plans associated with the evolution of shell loss in multiple lineages. Sea hares in particular are interesting because Aplysia californica is a well-studied model organism that offers a large suite of genetic tools. Bursatella leachii is a related tropical sea hare that lacks a shell as an adult and therefore lends itself to comparative analysis with A. californica. We have established an enhanced culturing procedure for B. leachii in husbandry that enabled the study of shell formation and loss in this lineage with respect to A. californica life staging. PMID:25538871

  17. Comparing Functional Analysis and Paired-choice Assessment Results in Classroom Settings

    PubMed Central

    Berg, Wendy K; Wacker, David P; Cigrand, Karla; Merkle, Steve; Wade, Jeanie; Henry, Kim; Wang, Yu-Chia

    2007-01-01

    The results of a functional analysis of problem behavior and a paired-choice assessment were compared to determine whether the same social reinforcers were identified for problem behavior and an appropriate response (time allocation). The two assessments were conducted in classroom settings with 4 adolescents with mental retardation who engaged in severe problem behavior. Each student's classroom teacher served as the therapist for all phases of assessment. The two assessment procedures identified the same social reinforcers for problem and appropriate behavior for 3 of 4 participants. PMID:17970268

  18. Mind and consciousness in yoga – Vedanta: A comparative analysis with western psychological concepts

    PubMed Central

    Prabhu, H. R. Aravinda; Bhat, P. S.

    2013-01-01

    Study of mind and consciousness through established scientific methods is often difficult due to the observed-observer dichotomy. Cartesian approach of dualism considering the mind and matter as two diverse and unconnected entities has been questioned by oriental schools of Yoga and Vedanta as well as the recent quantum theories of modern physics. Freudian and Neo-freudian schools based on the Cartesian model have been criticized by the humanistic schools which come much closer to the vedantic approach of unitariness. A comparative analysis of the two approaches is discussed. PMID:23858252

  19. Comparative analysis of steam delivery cost for surface and downhole steam drive technologies

    SciTech Connect

    Hart, C.M.

    1981-10-01

    A basis is established for evaluating the economic performances of the technologies for enhanced recovery of heavy crude being investigated through the Department of Energy's Project DEEP STEAM. Conventional surface steam drive is compared with: (1) thermally efficient delivery (through insulated strings) of surface generated steam; (2) low pressure combustion downhole steam generation; (3) high pressure combustion downhole steam generation; (4) high pressure combustion downhole steam generation using air as the oxygen source; and (5) high pressure combustion downhole steam generation substituting pure oxygen for air. A parametric analysis is performed for varying depths, injection rates, and steam qualities.

  20. Genome sequence and comparative genome analysis of Pseudomonas syringae pv. syringae type strain ATCC 19310.

    PubMed

    Park, Yong-Soon; Jeong, Haeyoung; Sim, Young Mi; Yi, Hwe-Su; Ryu, Choong-Min

    2014-04-01

    Pseudomonas syringae pv. syringae (Psy) is a major bacterial pathogen of many economically important plant species. Despite the severity of its impact, the genome sequence of the type strain has not been reported. Here, we present the draft genome sequence of Psy ATCC 19310. Comparative genomic analysis revealed that Psy ATCC 19310 is closely related to Psy B728a. However, only a few type III effectors, which are key virulence factors, are shared by the two strains, indicating the possibility of host-pathogen specificity and genome dynamics, even under the pathovar level. PMID:24444998

  1. Comparative Analysis of Protein Glycosylation Pathways in Humans and the Fungal Pathogen Candida albicans

    PubMed Central

    Martínez-Duncker, Iván; Díaz-Jímenez, Diana F.; Mora-Montes, Héctor M.

    2014-01-01

    Protein glycosylation pathways are present in all kingdoms of life and are metabolic pathways found in all the life kingdoms. Despite sharing commonalities in their synthesis, glycans attached to glycoproteins have species-specific structures generated by the presence of different sets of enzymes and acceptor substrates in each organism. In this review, we present a comparative analysis of the main glycosylation pathways shared by humans and the fungal pathogen Candida albicans: N-linked glycosylation, O-linked mannosylation and glycosylphosphatidylinositol-anchorage. The knowledge of similarities and divergences between these metabolic pathways could help find new pharmacological targets for C. albicans infection. PMID:25104959

  2. Comparative analysis of prophage-like elements in Helicobacter sp. genomes

    PubMed Central

    Fan, Xiangyu; Li, Yumei; He, Rong

    2016-01-01

    Prophages are regarded as one of the factors underlying bacterial virulence, genomic diversification, and fitness, and are ubiquitous in bacterial genomes. Information on Helicobacter sp. prophages remains scarce. In this study, sixteen prophages were identified and analyzed in detail. Eight of them are described for the first time. Based on a comparative genomic analysis, these sixteen prophages can be classified into four different clusters. Phylogenetic relationships of Cluster A Helicobacter prophages were investigated. Furthermore, genomes of Helicobacter prophages from Clusters B, C, and D were analyzed. Interestingly, some putative antibiotic resistance proteins and virulence factors were associated with Helicobacter prophages. PMID:27169002

  3. Comparative genomic analysis of four representative plant growth-promoting rhizobacteria in Pseudomonas

    PubMed Central

    2013-01-01

    Background Some Pseudomonas strains function as predominant plant growth-promoting rhizobacteria (PGPR). Within this group, Pseudomonas chlororaphis and Pseudomonas fluorescens are non-pathogenic biocontrol agents, and some Pseudomonas aeruginosa and Pseudomonas stutzeri strains are PGPR. P. chlororaphis GP72 is a plant growth-promoting rhizobacterium with a fully sequenced genome. We conducted a genomic analysis comparing GP72 with three other pseudomonad PGPR: P. fluorescens Pf-5, P. aeruginosa M18, and the nitrogen-fixing strain P. stutzeri A1501. Our aim was to identify the similarities and differences among these strains using a comparative genomic approach to clarify the mechanisms of plant growth-promoting activity. Results The genome sizes of GP72, Pf-5, M18, and A1501 ranged from 4.6 to 7.1 M, and the number of protein-coding genes varied among the four species. Clusters of Orthologous Groups (COGs) analysis assigned functions to predicted proteins. The COGs distributions were similar among the four species. However, the percentage of genes encoding transposases and their inactivated derivatives (COG L) was 1.33% of the total genes with COGs classifications in A1501, 0.21% in GP72, 0.02% in Pf-5, and 0.11% in M18. A phylogenetic analysis indicated that GP72 and Pf-5 were the most closely related strains, consistent with the genome alignment results. Comparisons of predicted coding sequences (CDSs) between GP72 and Pf-5 revealed 3544 conserved genes. There were fewer conserved genes when GP72 CDSs were compared with those of A1501 and M18. Comparisons among the four Pseudomonas species revealed 603 conserved genes in GP72, illustrating common plant growth-promoting traits shared among these PGPR. Conserved genes were related to catabolism, transport of plant-derived compounds, stress resistance, and rhizosphere colonization. Some strain-specific CDSs were related to different kinds of biocontrol activities or plant growth promotion. The GP72 genome

  4. Comparative effectiveness of long term drug treatment strategies to prevent asthma exacerbations: network meta-analysis

    PubMed Central

    Gemperli, Armin; Cohen, Judith; Rubinstein, Sidney M; Sterk, Peter J; Reddel, Helen K; Jüni, Peter; ter Riet, Gerben

    2014-01-01

    Objective To determine the comparative effectiveness and safety of current maintenance strategies in preventing exacerbations of asthma. Design Systematic review and network meta-analysis using Bayesian statistics. Data sources Cochrane systematic reviews on chronic asthma, complemented by an updated search when appropriate. Eligibility criteria Trials of adults with asthma randomised to maintenance treatments of at least 24 weeks duration and that reported on asthma exacerbations in full text. Low dose inhaled corticosteroid treatment was the comparator strategy. The primary effectiveness outcome was the rate of severe exacerbations. The secondary outcome was the composite of moderate or severe exacerbations. The rate of withdrawal was analysed as a safety outcome. Results 64 trials with 59 622 patient years of follow-up comparing 15 strategies and placebo were included. For prevention of severe exacerbations, combined inhaled corticosteroids and long acting β agonists as maintenance and reliever treatment and combined inhaled corticosteroids and long acting β agonists in a fixed daily dose performed equally well and were ranked first for effectiveness. The rate ratios compared with low dose inhaled corticosteroids were 0.44 (95% credible interval 0.29 to 0.66) and 0.51 (0.35 to 0.77), respectively. Other combined strategies were not superior to inhaled corticosteroids and all single drug treatments were inferior to single low dose inhaled corticosteroids. Safety was best for conventional best (guideline based) practice and combined maintenance and reliever therapy. Conclusions Strategies with combined inhaled corticosteroids and long acting β agonists are most effective and safe in preventing severe exacerbations of asthma, although some heterogeneity was observed in this network meta-analysis of full text reports. PMID:24919052

  5. Comparative proteomic analysis of bronchoalveolar lavage of familial and sporadic cases of idiopathic pulmonary fibrosis.

    PubMed

    Carleo, A; Bargagli, E; Landi, C; Bennett, D; Bianchi, L; Gagliardi, A; Carnemolla, C; Perari, M G; Cillis, G; Armini, A; Bini, L; Rottoli, P

    2016-01-01

    Idiopathic pulmonary fibrosis (IPF) is a chronic lung disease characterized by progressive deterioration of the alveolar integrity. Among IPF identified phenotypes, that of familial (f-)IPF is usually associated with several gene mutations which are seldom observed in sporadic (s-)IPF. This study aimed at investigating the molecular patterns and variability in f-IPF and s-IPF patients through a differential proteomic analysis. Protein patterns of bronchoalveolar lavage fluid (BALF) samples from 10 familial and 17 sporadic IPF patients were compared using 2D electrophoresis and mass spectrometry. Principal component analysis (PCA) was applied to proteomic data and an enrichment analysis was also performed to characterize specific pathogenic mechanisms and to identify potential biomarkers. BALF samples from f-IPF showed 87 protein spots differentially expressed than those from s-IPF samples; once identified, these spots revealed 22 unique proteins. The functional analysis showed that the endothelial reticulum stress probably plays a central pathogenetic role in f-IPF with an up-regulation of proteins involved in wounding and immune responses, coagulation system, and ion homeostasis. Up-regulated proteins in the s-IPF group were those involved in the oxidative stress response. PCA analysis of differentially expressed proteins clearly distinguished f-IPF from s-IPF patients, and in agreement with radiological and histological patterns, pointed out a higher heterogeneity in f-IPF than s-IPF samples. The 'Slit/Robo signaling', 'clathrin-coated vesicle' and 'cytoskeleton remodelling', were extrapolated by 'pathways analysis' and the results of 'diseases (by biomarkers)' highlighted a 'connective tissue and autoimmune disease', two aspects of increasing interest in IPF. PMID:27082636

  6. Meta-Analysis Comparing Zero-Profile Spacer and Anterior Plate in Anterior Cervical Fusion

    PubMed Central

    Lu, Teng; Liang, Baobao; Xu, Junkui; Zhou, Jun; Lv, Hongjun; Qin, Jie; Cai, Xuan; Huang, Sihua; Li, Haopeng; Wang, Dong; He, Xijing

    2015-01-01

    Background Anterior plate fusion is an effective procedure for the treatment of cervical spinal diseases but is accompanied by a high incidence of postoperative dysphagia. A zero profile (Zero-P) spacer is increasingly being used to reduce postoperative dysphagia and other potential complications associated with surgical intervention. Studies comparing the Zero-P spacer and anterior plate have reported conflicting results. Methodology A meta-analysis was conducted to compare the safety, efficacy, radiological outcomes and complications associated with the use of a Zero-P spacer versus an anterior plate in anterior cervical spine fusion for the treatment of cervical spinal disease. We comprehensively searched PubMed, Embase, the Cochrane Library and other databases and performed a meta-analysis of all randomized controlled trials (RCTs) and prospective or retrospective comparative studies assessing the two techniques. Results Ten studies enrolling 719 cervical spondylosis patients were included. The pooled data showed significant differences in the operation time [SMD = –0.58 (95% CI = −0.77 to 0.40, p < 0.01)] and blood loss [SMD = −0.40, 95% CI (−0.59 to –0.21), p < 0.01] between the two groups. Compared to the anterior plate group, the Zero-P group exhibited a significantly improved JOA score and reduced NDI and VAS. However, anterior plate fusion had greater postoperative segmental and cervical Cobb’s angles than the Zero-P group at the last follow-up. The fusion rate in the two groups was similar. More importantly, the Zero-P group had a lower incidence of earlier and later postoperative dysphagia. Conclusions Compared to anterior plate fusion, Zero-P is a safer and effective procedure, with a similar fusion rate and lower incidence of earlier and later postoperative dysphagia. However, the results of this meta-analysis should be accepted with caution due to the limitations of the study. Further evaluation and large-sample RCTs are required to

  7. Isolation and Comparative Genomic Analysis of T1-Like Shigella Bacteriophage pSf-2.

    PubMed

    Jun, Jin Woo; Kim, Hyoun Joong; Yun, Sae Kil; Chai, Ji Young; Lee, Byeong Chun; Park, Se Chang

    2016-03-01

    The increasing prevalence of antibiotic-resistant Shigella sp. emphasizes that alternatives to conventional antibiotics are needed. Siphoviridae bacteriophage (phage), pSf-2, infecting S. flexneri ATCC(®) 12022 was isolated from Geolpocheon stream in Korea. Morphological analysis by transmission electron microscopy revealed that pSf-2 has a head of about 57 ± 4 nm in diameter with a long tail of 136 ± 3 nm in length and 15 ± 2 nm in width. One-step growth analysis revealed that pSf-2 has latent period of 30 min and burst size of 16 PFU/infected cell. The DNA genome of pSf-2 is composed of 50,109 bp with a G+C content of 45.44 %. The genome encodes 83 putative ORFs, 19 putative promoters, and 23 transcriptional terminator regions. Genome sequence analysis of pSf-2 and comparative analysis with the homologous T1-like Shigella phages, Shfl1 and pSf-1, revealed that pSf-2 is a novel T1-like Shigella phage. These results showed that pSf-2 might have a high potential as a biocontrol agent to control shigellosis. Also, the genomic information may lead to further understanding of phage biodiversity, especially T1-like phages. PMID:26612033

  8. Comparative metagenomic analysis of human gut microbiome composition using two different bioinformatic pipelines.

    PubMed

    D'Argenio, Valeria; Casaburi, Giorgio; Precone, Vincenza; Salvatore, Francesco

    2014-01-01

    Technological advances in next-generation sequencing-based approaches have greatly impacted the analysis of microbial community composition. In particular, 16S rRNA-based methods have been widely used to analyze the whole set of bacteria present in a target environment. As a consequence, several specific bioinformatic pipelines have been developed to manage these data. MetaGenome Rapid Annotation using Subsystem Technology (MG-RAST) and Quantitative Insights Into Microbial Ecology (QIIME) are two freely available tools for metagenomic analyses that have been used in a wide range of studies. Here, we report the comparative analysis of the same dataset with both QIIME and MG-RAST in order to evaluate their accuracy in taxonomic assignment and in diversity analysis. We found that taxonomic assignment was more accurate with QIIME which, at family level, assigned a significantly higher number of reads. Thus, QIIME generated a more accurate BIOM file, which in turn improved the diversity analysis output. Finally, although informatics skills are needed to install QIIME, it offers a wide range of metrics that are useful for downstream applications and, not less important, it is not dependent on server times. PMID:24719854

  9. Comparing Visual and Statistical Analysis in Single-Case Studies Using Published Studies

    PubMed Central

    Harrington, Magadalena; Velicer, Wayne F.

    2015-01-01

    Little is known about the extent to which interrupted time-series analysis (ITSA) can be applied to short, single-case study designs and whether those applications produce results consistent with visual analysis (VA). This paper examines the extent to which ITSA can be applied to single-case study designs and compares the results based on two methods: ITSA and VA, using papers published in the Journal of Applied Behavior Analysis in 2010. The study was made possible by the development of software called UnGraph® which facilitates the recovery of raw data from the graphs. ITSA was successfully applied to 94% of the examined graphs with the number of observations ranging from 8 to 136. Moderate to high lag 1 autocorrelations (> .50) were found for 46% of the data series. Effect sizes similar to group-level Cohen’s d were identified based on the tertile distribution. Effects ranging from 0.00 to 0.99 were classified as small, those ranging from 1.00 to 2.49 as medium, and large effect sizes were defined as 2.50 or greater. Comparison of the conclusions from VA and ITSA had a low level of agreement (Kappa = .14, accounting for the agreement expected by chance). The results demonstrate that ITSA can be broadly implemented in applied behavior analysis research. These two methods should be viewed as complimentary and used concurrently. PMID:26609876

  10. Human, vector and parasite Hsp90 proteins: A comparative bioinformatics analysis

    PubMed Central

    Faya, Ngonidzashe; Penkler, David L.; Tastan Bishop, Özlem

    2015-01-01

    The treatment of protozoan parasitic diseases is challenging, and thus identification and analysis of new drug targets is important. Parasites survive within host organisms, and some need intermediate hosts to complete their life cycle. Changing host environment puts stress on parasites, and often adaptation is accompanied by the expression of large amounts of heat shock proteins (Hsps). Among Hsps, Hsp90 proteins play an important role in stress environments. Yet, there has been little computational research on Hsp90 proteins to analyze them comparatively as potential parasitic drug targets. Here, an attempt was made to gain detailed insights into the differences between host, vector and parasitic Hsp90 proteins by large-scale bioinformatics analysis. A total of 104 Hsp90 sequences were divided into three groups based on their cellular localizations; namely cytosolic, mitochondrial and endoplasmic reticulum (ER). Further, the parasitic proteins were divided according to the type of parasite (protozoa, helminth and ectoparasite). Primary sequence analysis, phylogenetic tree calculations, motif analysis and physicochemical properties of Hsp90 proteins suggested that despite the overall structural conservation of these proteins, parasitic Hsp90 proteins have unique features which differentiate them from human ones, thus encouraging the idea that protozoan Hsp90 proteins should be further analyzed as potential drug targets. PMID:26793431

  11. Comparative analysis of sequentiality using SDIS-GSEQ and THEME: a concrete example in soccer.

    PubMed

    Lapresa, Daniel; Arana, Javier; Anguera, M Teresa; Garzón, Belén

    2013-01-01

    Within an observational design aimed at studying what type of soccer is better adapted to the possibilities of the 11-12 year-old child, a comparison was made of the results obtained using two fully consolidated analysis techniques in observational methods, and which form the basis in the development of two respective software programs: SDIS-GSEQ and THEME, which allow one to detect the existence of sequential patterns hidden in a data set. This work is intended to shed light on the comparison of results obtained using these two analysis techniques. In particular, the data used for the analysis are multicode event data (using the lexicon of the sequential analysis), and do not incorporate the duration parameter. Accordingly, for the detection of regular structures using the THEME program (T-patterns), a constant duration has conventionally been assigned to each occurrence. Using THEME, among the greatest number of sequential structures detected, diachronic and synchronic correspondence was observed (T-patterns reflecting identical multi-events) with each and every one of the sequential patterns obtained using the lag technique, by the SDIS-GSEQ software. This coincidence strengthens the link between the algorithms that support SDIS-GSEQ and THEME. The results indicate that 7-a-side soccer and 9-a-side soccer types facilitate the spatial mastery of the game by the child, compared with the adult form, 11-a-side soccer. PMID:23688033

  12. Comparative transcriptome analysis of papilla and skin in the sea cucumber, Apostichopus japonicus

    PubMed Central

    Kong, Derong; Sun, He; Gu, Chenlei; Wang, Hongdi; Qiu, Xuemei; Chang, Yaqing; Liu, Zhanjiang

    2016-01-01

    Papilla and skin are two important organs of the sea cucumber. Both tissues have ectodermic origin, but they are morphologically and functionally very different. In the present study, we performed comparative transcriptome analysis of the papilla and skin from the sea cucumber (Apostichopus japonicus) in order to identify and characterize gene expression profiles by using RNA-Seq technology. We generated 30.6 and 36.4 million clean reads from the papilla and skin and de novo assembled in 156,501 transcripts. The Gene Ontology (GO) analysis indicated that cell part, metabolic process and catalytic activity were the most abundant GO category in cell component, biological process and molecular funcation, respectively. Comparative transcriptome analysis between the papilla and skin allowed the identification of 1,059 differentially expressed genes, of which 739 genes were expressed at higher levels in papilla, while 320 were expressed at higher levels in skin. In addition, 236 differentially expressed unigenes were not annotated with any database, 160 of which were apparently expressed at higher levels in papilla, 76 were expressed at higher levels in skin. We identified a total of 288 papilla-specific genes, 171 skin-specific genes and 600 co-expressed genes. Also, 40 genes in papilla-specific were not annotated with any database, 2 in skin-specific. Development-related genes were also enriched, such as fibroblast growth factor, transforming growth factor-β, collagen-α2 and Integrin-α2, which may be related to the formation of the papilla and skin in sea cucumber. Further pathway analysis identified ten KEGG pathways that were differently enriched between the papilla and skin. The findings on expression profiles between two key organs of the sea cucumber should be valuable to reveal molecular mechanisms involved in the development of organs that are related but with morphological differences in the sea cucumber. PMID:26989617

  13. Comparative transcriptome analysis of papilla and skin in the sea cucumber, Apostichopus japonicus.

    PubMed

    Zhou, Xiaoxu; Cui, Jun; Liu, Shikai; Kong, Derong; Sun, He; Gu, Chenlei; Wang, Hongdi; Qiu, Xuemei; Chang, Yaqing; Liu, Zhanjiang; Wang, Xiuli

    2016-01-01

    Papilla and skin are two important organs of the sea cucumber. Both tissues have ectodermic origin, but they are morphologically and functionally very different. In the present study, we performed comparative transcriptome analysis of the papilla and skin from the sea cucumber (Apostichopus japonicus) in order to identify and characterize gene expression profiles by using RNA-Seq technology. We generated 30.6 and 36.4 million clean reads from the papilla and skin and de novo assembled in 156,501 transcripts. The Gene Ontology (GO) analysis indicated that cell part, metabolic process and catalytic activity were the most abundant GO category in cell component, biological process and molecular funcation, respectively. Comparative transcriptome analysis between the papilla and skin allowed the identification of 1,059 differentially expressed genes, of which 739 genes were expressed at higher levels in papilla, while 320 were expressed at higher levels in skin. In addition, 236 differentially expressed unigenes were not annotated with any database, 160 of which were apparently expressed at higher levels in papilla, 76 were expressed at higher levels in skin. We identified a total of 288 papilla-specific genes, 171 skin-specific genes and 600 co-expressed genes. Also, 40 genes in papilla-specific were not annotated with any database, 2 in skin-specific. Development-related genes were also enriched, such as fibroblast growth factor, transforming growth factor-β, collagen-α2 and Integrin-α2, which may be related to the formation of the papilla and skin in sea cucumber. Further pathway analysis identified ten KEGG pathways that were differently enriched between the papilla and skin. The findings on expression profiles between two key organs of the sea cucumber should be valuable to reveal molecular mechanisms involved in the development of organs that are related but with morphological differences in the sea cucumber. PMID:26989617

  14. Comparative Transcriptomic Analysis Reveals Similarities and Dissimilarities in Saccharomyces cerevisiae Wine Strains Response to Nitrogen Availability

    PubMed Central

    Barbosa, Catarina; García-Martínez, José; Pérez-Ortín, José E.; Mendes-Ferreira, Ana

    2015-01-01

    Nitrogen levels in grape-juices are of major importance in winemaking ensuring adequate yeast growth and fermentation performance. Here we used a comparative transcriptome analysis to uncover wine yeasts responses to nitrogen availability during fermentation. Gene expression was assessed in three genetically and phenotypically divergent commercial wine strains (CEG, VL1 and QA23), under low (67 mg/L) and high nitrogen (670 mg/L) regimes, at three time points during fermentation (12h, 24h and 96h). Two-way ANOVA analysis of each fermentation condition led to the identification of genes whose expression was dependent on strain, fermentation stage and on the interaction of both factors. The high fermenter yeast strain QA23 was more clearly distinct from the other two strains, by differential expression of genes involved in flocculation, mitochondrial functions, energy generation and protein folding and stabilization. For all strains, higher transcriptional variability due to fermentation stage was seen in the high nitrogen fermentations. A positive correlation between maximum fermentation rate and the expression of genes involved in stress response was observed. The finding of common genes correlated with both fermentation activity and nitrogen up-take underlies the role of nitrogen on yeast fermentative fitness. The comparative analysis of genes differentially expressed between both fermentation conditions at 12h, where the main difference was the level of nitrogen available, showed the highest variability amongst strains revealing strain-specific responses. Nevertheless, we were able to identify a small set of genes whose expression profiles can quantitatively assess the common response of the yeast strains to varying nitrogen conditions. The use of three contrasting yeast strains in gene expression analysis prompts the identification of more reliable, accurate and reproducible biomarkers that will facilitate the diagnosis of deficiency of this nutrient in the grape

  15. Comparative gene expression analysis of ovarian carcinoma and normal ovarian epithelium by serial analysis of gene expression.

    PubMed

    Peters, David G; Kudla, Donna M; Deloia, Julie A; Chu, Tian Jiao; Fairfull, Liane; Edwards, Robert P; Ferrell, Robert E

    2005-07-01

    Despite the poor prognosis of ovarian cancer and the importance of early diagnosis, there are no reliable noninvasive biomarkers for detection in the early stages of disease. Therefore, to identify novel ovarian cancer markers with potential utility in early-stage screening protocols, we have undertaken an unbiased and comprehensive analysis of gene expression in primary ovarian tumors and normal human ovarian surface epithelium (HOSE) using Serial Analysis of Gene Expression (SAGE). Specifically, we have generated SAGE libraries from three serous adenocarcinomas of the ovary and, using novel statistical tools, have compared these to SAGE data derived from two pools of normal HOSE. Significantly, in contrast to previous SAGE-based studies, our normal SAGE libraries are not derived from cultured cell lines. We have also compared our data with publicly available SAGE data obtained from primary tumors and "normal" HOSE-derived cell lines. We have thus identified several known and novel genes whose expressions are elevated in ovarian cancer. These include but are not limited to CLDN3, WFDC2, FOLR1, COL18A1, CCND1, and FLJ12988. Furthermore, we found marked differences in gene expression patterns in primary HOSE tissue compared with cultured HOSE. The use of HOSE tissue as a control for these experiments, along with hierarchical clustering analysis, identified several potentially novel biomarkers of ovarian cancer, including TACC3, CD9, GNAI2, AHCY, CCT3, and HMGA1. In summary, these data identify several genes whose elevated expressions have not been observed previously in ovarian cancer, confirm the validity of several existing markers, and provide a foundation for future studies in the understanding and management of this disease. PMID:16030107

  16. A comparative study of principal component analysis and independent component analysis in eddy current pulsed thermography data processing.

    PubMed

    Bai, Libing; Gao, Bin; Tian, Shulin; Cheng, Yuhua; Chen, Yifan; Tian, Gui Yun; Woo, W L

    2013-10-01

    Eddy Current Pulsed Thermography (ECPT), an emerging Non-Destructive Testing and Evaluation technique, has been applied for a wide range of materials. The lateral heat diffusion leads to decreasing of temperature contrast between defect and defect-free area. To enhance the flaw contrast, different statistical methods, such as Principal Component Analysis and Independent Component Analysis, have been proposed for thermography image sequences processing in recent years. However, there is lack of direct and detailed independent comparisons in both algorithm implementations. The aim of this article is to compare the two methods and to determine the optimized technique for flaw contrast enhancement in ECPT data. Verification experiments are conducted on artificial and thermal fatigue nature crack detection. PMID:24182145

  17. Discovery and Analysis of Intersecting Datasets: JMARS as a Comparative Science Platform

    NASA Astrophysics Data System (ADS)

    Carter, S.; Christensen, P. R.; Dickenshied, S.; Anwar, S.; Noss, D.

    2014-12-01

    A great deal can be discovered from comparing and studying a chosen region or area on a planetary body. In this age, science has an enormous amount of instruments and data to study from; often the first obstacle can be finding the right information. Developed at Arizona State University, Java Mission-planning and Analysis for Remote Sensing (JMARS), enables users to easily find and study related datasets. JMARS supports a long list of planetary bodies in our solar system, including Earth, the Moon, Mars, and other planets, satellites, and asteroids. Within JMARS a user can start with a particular area and search for all datasets that have images/information intersecting that region of interest. Once a user has found data they are interested in comparing, they can view the image at once and see the numeric information at that location. This information can be analyzed in a few powerful ways. If the dataset of interest varies with time but the location stays constant, then the user may want to compare specific locations through time. This can be done the Investigate Tool in JMARS. Users can create a Data Spike and the information at that point will be plotted through time. If the region does not have a temporal dataset, then a different method would be suitable and involves a profile line. Also using the Investigate Tool, a user can create a Data Profile (a line which can contain as many vertices as necessary) and all numeric data underneath the line will be plotted on one graph for easy comparison. This can be used to compare differences between similar datasets - perhaps the same measurement but from different instruments - or to find correlations from one dataset to another. A third form of analysis is planned for future development. This method involves entire areas (polygons). Sampling of the different data sources beneath an area can reveal statistics like maximum, minimum, and average values, and standard deviation. These values can be compared to other data

  18. Comparative genome analysis of lignin biosynthesis gene families across the plant kingdom

    PubMed Central

    2009-01-01

    Background As a major component of plant cell wall, lignin plays important roles in mechanical support, water transport, and stress responses. As the main cause for the recalcitrance of plant cell wall, lignin modification has been a major task for bioenergy feedstock improvement. The study of the evolution and function of lignin biosynthesis genes thus has two-fold implications. First, the lignin biosynthesis pathway provides an excellent model to study the coordinative evolution of a biochemical pathway in plants. Second, understanding the function and evolution of lignin biosynthesis genes will guide us to develop better strategies for bioenergy feedstock improvement. Results We analyzed lignin biosynthesis genes from fourteen plant species and one symbiotic fungal species. Comprehensive comparative genome analysis was carried out to study the distribution, relatedness, and family expansion of the lignin biosynthesis genes across the plant kingdom. In addition, we also analyzed the comparative synteny map between rice and sorghum to study the evolution of lignin biosynthesis genes within the Poaceae family and the chromosome evolution between the two species. Comprehensive lignin biosynthesis gene expression analysis was performed in rice, poplar and Arabidopsis. The representative data from rice indicates that different fates of gene duplications exist for lignin biosynthesis genes. In addition, we also carried out the biomass composition analysis of nine Arabidopsis mutants with both MBMS analysis and traditional wet chemistry methods. The results were analyzed together with the genomics analysis. Conclusion The research revealed that, among the species analyzed, the complete lignin biosynthesis pathway first appeared in moss; the pathway is absent in green algae. The expansion of lignin biosynthesis gene families correlates with substrate diversity. In addition, we found that the expansion of the gene families mostly occurred after the divergence of monocots

  19. Evaluation of Ion Mobility-Mass Spectrometry for Comparative Analysis of Monoclonal Antibodies.

    PubMed

    Ferguson, Carly N; Gucinski-Ruth, Ashley C

    2016-05-01

    Analytical techniques capable of detecting changes in structure are necessary to monitor the quality of monoclonal antibody drug products. Ion mobility mass spectrometry offers an advanced mode of characterization of protein higher order structure. In this work, we evaluated the reproducibility of ion mobility mass spectrometry measurements and mobiligrams, as well as the suitability of this approach to differentiate between and/or characterize different monoclonal antibody drug products. Four mobiligram-derived metrics were identified to be reproducible across a multi-day window of analysis. These metrics were further applied to comparative studies of monoclonal antibody drug products representing different IgG subclasses, manufacturers, and lots. These comparisons resulted in some differences, based on the four metrics derived from ion mobility mass spectrometry mobiligrams. The use of collision-induced unfolding resulted in more observed differences. Use of summed charge state datasets and the analysis of metrics beyond drift time allowed for a more comprehensive comparative study between different monoclonal antibody drug products. Ion mobility mass spectrometry enabled detection of differences between monoclonal antibodies with the same target protein but different production techniques, as well as products with different targets. These differences were not always detectable by traditional collision cross section studies. Ion mobility mass spectrometry, and the added separation capability of collision-induced unfolding, was highly reproducible and remains a promising technique for advanced analytical characterization of protein therapeutics. Graphical Abstract ᅟ. PMID:26988372

  20. Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae.

    PubMed

    Galagan, James E; Calvo, Sarah E; Cuomo, Christina; Ma, Li-Jun; Wortman, Jennifer R; Batzoglou, Serafim; Lee, Su-In; Baştürkmen, Meray; Spevak, Christina C; Clutterbuck, John; Kapitonov, Vladimir; Jurka, Jerzy; Scazzocchio, Claudio; Farman, Mark; Butler, Jonathan; Purcell, Seth; Harris, Steve; Braus, Gerhard H; Draht, Oliver; Busch, Silke; D'Enfert, Christophe; Bouchier, Christiane; Goldman, Gustavo H; Bell-Pedersen, Deborah; Griffiths-Jones, Sam; Doonan, John H; Yu, Jaehyuk; Vienken, Kay; Pain, Arnab; Freitag, Michael; Selker, Eric U; Archer, David B; Peñalva, Miguel A; Oakley, Berl R; Momany, Michelle; Tanaka, Toshihiro; Kumagai, Toshitaka; Asai, Kiyoshi; Machida, Masayuki; Nierman, William C; Denning, David W; Caddick, Mark; Hynes, Michael; Paoletti, Mathieu; Fischer, Reinhard; Miller, Bruce; Dyer, Paul; Sachs, Matthew S; Osmani, Stephen A; Birren, Bruce W

    2005-12-22

    The aspergilli comprise a diverse group of filamentous fungi spanning over 200 million years of evolution. Here we report the genome sequence of the model organism Aspergillus nidulans, and a comparative study with Aspergillus fumigatus, a serious human pathogen, and Aspergillus oryzae, used in the production of sake, miso and soy sauce. Our analysis of genome structure provided a quantitative evaluation of forces driving long-term eukaryotic genome evolution. It also led to an experimentally validated model of mating-type locus evolution, suggesting the potential for sexual reproduction in A. fumigatus and A. oryzae. Our analysis of sequence conservation revealed over 5,000 non-coding regions actively conserved across all three species. Within these regions, we identified potential functional elements including a previously uncharacterized TPP riboswitch and motifs suggesting regulation in filamentous fungi by Puf family genes. We further obtained comparative and experimental evidence indicating widespread translational regulation by upstream open reading frames. These results enhance our understanding of these widely studied fungi as well as provide new insight into eukaryotic genome evolution and gene regulation. PMID:16372000

  1. Comparative study of state-of-the-art algorithms for hyperspectral image analysis

    NASA Astrophysics Data System (ADS)

    Rivera-Borrero, Carlos; Hunt, Shawn D.

    2007-04-01

    This work studies the end-to-end performance of hyperspectral classification and unmixing systems. Specifically, it compares widely used current state of the art algorithms with those developed at the University of Puerto Rico. These include algorithms for image enhancement, band subset selection, feature extraction, supervised and unsupervised classification, and constrained and unconstrained abundance estimation. The end to end performance for different combinations of algorithms is evaluated. The classification algorithms are compared in terms of percent correct classification. This method, however, cannot be applied to abundance estimation, as the binary evaluation used for supervised and unsupervised classification is not directly applicable to unmixing performance analysis. A procedure to evaluate unmixing performance is described in this paper and tested using coregistered data acquired by various sensors at different spatial resolutions. Performance results are generally specific to the image used. In an effort to try and generalize the results, a formal description of the complexity of the images used for the evaluations is required. Techniques for image complexity analysis currently available for automatic target recognizers are included and adapted to quantify the performance of the classifiers for different image classes.

  2. Comparative Analysis of Transcriptomes from Secondary Reproductives of Three Reticulitermes Termite Species

    PubMed Central

    Dedeine, Franck; Weinert, Lucy A.; Bigot, Diane; Josse, Thibaut; Ballenghien, Marion; Cahais, Vincent; Galtier, Nicolas; Gayral, Philippe

    2015-01-01

    Termites are eusocial insects related to cockroaches that feed on lignocellulose. These insects are key species in ecosystems since they recycle a large amount of nutrients but also are pests, exerting major economic impacts. Knowledge on the molecular pathways underlying reproduction, caste differentiation or lignocellulose digestion would largely benefit from additional transcriptomic data. This study focused on transcriptomes of secondary reproductive females (nymphoid neotenics). Thirteen transcriptomes were used: 10 of Reticulitermes flavipes and R. grassei sequenced from a previous study, and two transcriptomes of R. lucifugus sequenced for the present study. After transcriptome assembly and read mapping, we examined interspecific variations of genes expressed by termites or gut microorganisms. A total of 18,323 orthologous gene clusters were detected. Functional annotation and taxonomic assignment were performed on a total of 41,287 predicted contigs in the three termite species. Between the termite species studied, functional categories of genes were comparable. Gene ontology (GO) terms analysis allowed the discovery of 9 cellulases and a total of 79 contigs potentially involved in 11 enzymatic activities used in wood metabolism. Altogether, results of this study illustrate the strong potential for the use of comparative interspecific transcriptomes, representing a complete resource for future studies including differentially expressed genes between castes or SNP analysis for population genetics. PMID:26698123

  3. The complete chloroplast genome sequence of Morus mongolica and a comparative analysis within the Fabidae clade.

    PubMed

    Kong, Weiqing; Yang, Jinhong

    2016-02-01

    The complete nucleotide sequence of the Morus mongolica chloroplast (cp) genome was reported and characterized in this study. The cp genome is a circular molecule of 158,459 bp containing a pair of 25,678 bp IR regions, separated by small and large single-copy regions of 19,736 and 87,363 bp, respectively. The number and relative positions of the 114 unique genes (80 PCGs, 30 tRNAs, and 4 rRNA genes) are almost identical to Morus indica cp genome. Further detailed comparative analyses revealed one hypervariable region, which is responsible for 88% of the total variation, and 64 indel events between two individuals. There are 78 simple sequence repeats (SSRs) in M. mongolica cp genome, in which 58 of them are mononucleotide repeats. Comparative analysis with M. indica cp genome indicated 22 SSRs with length polymorphisms and 1 SSR with nucleotide content polymorphism. The phylogenetic analysis of 60 PCGs from 62 cp genomes provided strong support for the monophyletic, single origin of Fabidae (N2-fixing) clade. PMID:26205390

  4. Comparative proteomic analysis provides insight into cadmium stress responses in brown algae Sargassum fusiforme.

    PubMed

    Zhang, Aiqin; Xu, Tao; Zou, Huixi; Pang, Qiuying

    2015-06-01

    Sargassum fusiforme is one of the most widely consumed seaweeds in China, Korea and Japan. In this work, we performed growth analysis and comparative proteomics to investigate the molecular mechanisms of the response to 1 day and 5 days Cd stress in S. fusiforme. Our results showed a significant decrease in growth rate and an increase in Cd ion content in S. fusiforme in response to Cd treatment. Comparative proteomic analysis revealed 25 and 51 differentially expressed protein spots in S. fusiforme under 1 day and 5 days Cd stress, respectively. A great number of these proteins was metabolic enzymes involved in carbohydrate metabolism and energy metabolism. Many proteins involved in the processing of genetic information showed a decrease in abundance under 1 day Cd stress. In contrast, 9 of the identified protein spots primarily involved in genetic information processing and carbohydrate metabolism were greatly enriched under 5 days Cd stress. Overall, our investigation indicated that Cd stress negatively affects the metabolic activity of S. fusiforme through the down-regulation of key metabolic enzymes. In addition, S. fusiforme may adapt to 5 days Cd stress by promoting consumption of photoassimilates through the up-regulation of glycolysis and the citrate cycle to supply energy for survival. PMID:25827747

  5. Institutional Knots: A Comparative Analysis of Cord Blood Policy in Canada and the United States.

    PubMed

    Denburg, Avram

    2016-02-01

    Umbilical cord blood is a rich source of blood stem cells, which are of critical clinical importance in the treatment of a variety of malignant and genetic conditions requiring stem cell transplantation. Many countries have established national public cord blood banks; such banks often coexist with a panoply of private options for cord blood banking. Until recently, Canada was the only G8 country without a national cord blood bank. This differs markedly from the United States, which years ago established a national cord blood bank policy and inventory. This article investigates potential reasons for this discrepancy through a comparative analysis of the evolution of programs and policies on national cord blood banking in Canada and the United States. My analysis suggests that cross-national discrepancies in policy on public cord blood banking were determined primarily by institutional factors, principal among them formal governmental structure and the legacy of past policies. Institutional entrepreneurialism in the health sector played a constitutive role in the earlier evolution of national cord blood policy in the United States as compared to Canada. PMID:26567379

  6. Comparative analysis of protein unfoldedness in human housekeeping and non-housekeeping proteins.

    PubMed

    Pandey, Neeraj; Ganapathi, Mythily; Kumar, Kaushal; Dasgupta, Dipayan; Das Sutar, Sushanta Kumar; Dash, Debasis

    2004-11-22

    Absence of any regular structure is increasingly being observed in structural studies of proteins. These disordered regions or random coils, which have been observed under physiological conditions, are indicators of protein plasticity. The wide variety of interactions possible due to the flexibility of these 'natively disordered' regions confers functional advantage to the protein and the organism in general. This concept is underscored by the increasing proportion of intrinsically unstructured proteins seen with the ascension in the complexity of the organisms. The 'natively unfolded/disordered' state of the protein can be predicted utilizing Uversky's or Dunker's algorithm. We utilized Uversky's prediction scheme and based on the unique position of a protein in the charge-hydrophobicity plot, a derived net score was used to predict the overall disorder of the human housekeeping and non-housekeeping proteins. Substantial numbers of proteins in both the classes were predicted to be unfolded. However, comparative genomic analysis of predicted unfolded Homo sapiens proteins with homologues in Caenorhabditis elegans, Drosophila melanogaster and Mus musculus revealed significant increase in unfoldedness in non-housekeeping proteins in comparison with housekeeping proteins. Our analysis in the evolutionary context suggests addition or substitution of amino acid residues which favour unfoldedness in non-housekeeping proteins compared to housekeeping proteins. PMID:15238363

  7. Methods for detecting saddle-type objects from spatio-temporal data: A comparative analysis

    NASA Astrophysics Data System (ADS)

    Donner, S.; Padberg, K.; Donner, R.; Kurths, J.

    2009-04-01

    The positions of saddle points and their associated invariant manifolds are known to play a crucial role in understanding transport processes in two-dimensional steady flows. Since the relevant data are often only coarsely gridded, a reliable detection of fixed points in spatio-temporal discretised vector fields is a problem of contemporary interest. Unsteady flows may additionally exhibit distinguished hyperbolic trajectories and associated manifolds - often only defined on a finite-time span - that continue to organise particle transport. As these objects are known to be Lagrangian their exact position can typically not be deduced from analysing single velocity fields. In the literature, several methods are described for approximating hyperbolic objects in steady and unsteady flows, but it is usually not clear how well they perform for a specific data set. This contribution presents a comparative analysis of the performance of three common methods (finite-time Lyapunov exponents, hyperbolicity time, leaking). In addition, a simple statistic approach based on a gradient approximation of the velocity fields is used to approximate instantaneous stagnation points. The results are evaluated with respect to the errors in the total number and location of analytically known saddle points for two different two-dimensional steady velocity fields. The reliability is statistically tested by applying multiplicative Gaussian white noise to the original data and repeating all procedures. In a second step of analysis, the different methods are applied to time-dependent versions of these velocity fields, where candidates for hyperbolic trajectories are detected and compared.

  8. Evaluation of Ion Mobility-Mass Spectrometry for Comparative Analysis of Monoclonal Antibodies

    NASA Astrophysics Data System (ADS)

    Ferguson, Carly N.; Gucinski-Ruth, Ashley C.

    2016-05-01

    Analytical techniques capable of detecting changes in structure are necessary to monitor the quality of monoclonal antibody drug products. Ion mobility mass spectrometry offers an advanced mode of characterization of protein higher order structure. In this work, we evaluated the reproducibility of ion mobility mass spectrometry measurements and mobiligrams, as well as the suitability of this approach to differentiate between and/or characterize different monoclonal antibody drug products. Four mobiligram-derived metrics were identified to be reproducible across a multi-day window of analysis. These metrics were further applied to comparative studies of monoclonal antibody drug products representing different IgG subclasses, manufacturers, and lots. These comparisons resulted in some differences, based on the four metrics derived from ion mobility mass spectrometry mobiligrams. The use of collision-induced unfolding resulted in more observed differences. Use of summed charge state datasets and the analysis of metrics beyond drift time allowed for a more comprehensive comparative study between different monoclonal antibody drug products. Ion mobility mass spectrometry enabled detection of differences between monoclonal antibodies with the same target protein but different production techniques, as well as products with different targets. These differences were not always detectable by traditional collision cross section studies. Ion mobility mass spectrometry, and the added separation capability of collision-induced unfolding, was highly reproducible and remains a promising technique for advanced analytical characterization of protein therapeutics.

  9. Comparative proteomic analysis of engineered Saccharomyces cerevisiae with enhanced free fatty acid accumulation.

    PubMed

    Chen, Liwei; Lee, Jaslyn Jie Lin; Zhang, Jianhua; Chen, Wei Ning

    2016-02-01

    The engineered Saccharomyces cerevisiae strain △faa1△faa4 [Acot5s] was demonstrated to accumulate more free fatty acids (FFA) previously. Here, comparative proteomic analysis was performed to get a global overview of metabolic regulation in the strain. Over 500 proteins were identified, and 82 of those proteins were found to change significantly in the engineered strains. Proteins involved in glycolysis, acetate metabolism, fatty acid synthesis, TCA cycle, glyoxylate cycle, the pentose phosphate pathway, respiration, transportation, and stress response were found to be upregulated in △faa1△faa4 [Acot5s] as compared to the wild type. On the other hand, proteins involved in glycerol, ethanol, ergosterol, and cell wall synthesis were downregulated. Taken together with our metabolite analysis, our results showed that the disruption of Faa1 and Faa4 and expression of Acot5s in the engineered strain △faa1△faa4 [Acot5s] not only relieved the feedback inhibition of fatty acyl-CoAs on fatty acid synthesis, but also caused a major metabolic rearrangement. The rearrangement redirected carbon flux toward the pathways which generate the essential substrates and cofactors for fatty acid synthesis, such as acetyl-CoA, ATP, and NADPH. Therefore, our results help shed light on the mechanism for the increased production of fatty acids in the engineered strains, which is useful in providing information for future studies in biofuel production. PMID:26450510

  10. Clinical gait analysis: comparing explicit state duration HMMs using a reference-based index.

    PubMed

    Karg, Michelle; Seiberl, Wolfgang; Kreuzpointner, Florian; Haas, Johannes-Peter; Kulic, Dana

    2015-03-01

    In clinical gait analysis, the gait of a patient is recorded with optical motion capture and compared with a healthy reference group. High-dimensional gait datasets are difficult to interpret; machine learning can provide guidance regarding the most relevant gait phases and joint angles for visual analysis and quantify the difference between healthy and pathological gait. We propose an explicit state duration hidden Markov model (HMM) modeling the timeseries data of a subject or a group and the use of a reference-based measure that compares the most likely observations in each state. Based on this stochastic framework, the similarity between healthy and pathological gait can be quantified for each state, each joint angle, and each subject. This concept also includes an overall gait index useful for group comparison or the assessment of an individual's gait. For visualization, joint angle timeseries can be generated from the explicit state duration HMM. The accuracy of the explicit state duration HMM and the performance of the reference-based measures are evaluated on a dataset including strides of healthy subjects and patients suffering from arthritis. PMID:25343762

  11. New tools for comparing microscopy images: quantitative analysis of cell types in Bacillus subtilis.

    PubMed

    van Gestel, Jordi; Vlamakis, Hera; Kolter, Roberto

    2015-02-15

    Fluorescence microscopy is a method commonly used to examine individual differences between bacterial cells, yet many studies still lack a quantitative analysis of fluorescence microscopy data. Here we introduce some simple tools that microbiologists can use to analyze and compare their microscopy images. We show how image data can be converted to distribution data. These data can be subjected to a cluster analysis that makes it possible to objectively compare microscopy images. The distribution data can further be analyzed using distribution fitting. We illustrate our methods by scrutinizing two independently acquired data sets, each containing microscopy images of a doubly labeled Bacillus subtilis strain. For the first data set, we examined the expression of srfA and tapA, two genes which are expressed in surfactin-producing and matrix-producing cells, respectively. For the second data set, we examined the expression of eps and tapA; these genes are expressed in matrix-producing cells. We show that srfA is expressed by all cells in the population, a finding which contrasts with a previously reported bimodal distribution of srfA expression. In addition, we show that eps and tapA do not always have the same expression profiles, despite being expressed in the same cell type: both operons are expressed in cell chains, while single cells mainly express eps. These findings exemplify that the quantification and comparison of microscopy data can yield insights that otherwise would go unnoticed. PMID:25448819

  12. Comparative analysis of the essential oil composition of Murraya paniculata and M. exotica.

    PubMed

    Lv, Hai-Ning; Guo, Xiao-Yu; Tu, Peng-Fei; Jiang, Yong

    2013-10-01

    Murrayae Folium et Cacumen (MFC) is a traditional Chinese medicine (TCM) derived from the leaves and twigs of two aromatic species of Rutaceae: Murraya paniculata (L.) Jack and M. exotica L. It has long been used as a folk medicine in South China for the treatment of a variety of disorders, particularly for inflammatory lesions and pains. In the present study, a detailed chemical examination as well as a comparative analysis of the essential oil composition of M. paniculata and M. exotica was conducted by gas chromatography-mass spectrometry (GC-MS). A total of 141 volatile components were identified from the essential oil of these two plants. Sesquiterpenes were found to be the predominant constituents, accounting for 92.8% of the oil from M. paniculata and 87.9% of that from M. exotica. A comparative analysis of the essential oil composition of these two plants revealed a high level of similarity in their main constituents, such as the co-occurrence of E-caryophyllene, spathulenol and delta-elemene, which gave the chemical evidence for their equal medicinal application as MFC in TCMs. Moreover, in combination with literature reports, E-caryophyllene was theoretically deduced as one of the pharmacologically effective components of MFC that is responsible for treating inflammatory lesions and for local anaesthesia. PMID:24354205

  13. Comparative proteomic analysis of tobacco expressing cyanobacterial flavodoxin and its wild type under drought stress.

    PubMed

    Gharechahi, Javad; Hajirezaei, Mohammad-Reza; Salekdeh, Ghasem Hosseini

    2015-03-01

    Tobacco plants expressing cyanobacterial flavodoxin (Fld) show enhanced tolerance to a wide range of abiotic stresses including drought, temperature and UV. The mechanisms of adaptation to stress conditions under Fld expression are largely unknown. Here, we applied comparative proteomic analysis to uncover the changes in the proteome profile of Fld-expressing plants in response to drought stress. Using high-resolution two-dimensional gel electrophoresis, we were able to detect 930 protein spots and compare their abundance. We found changes up to 1.5 fold for 52 spots under drought in transgenic and/or wild type plants. Using combined MALDI-TOF/TOF and ESI-Q/TOF analysis 39 (24 in wild type, 11 in transgenic, and 4 in both) drought-responsive proteins (DRPs) could be identified. The majority of DRPs are known to be involved in photosynthesis, carbohydrate and energy metabolism, amino acid and protein synthesis and processing, and oxidative stress responses. Among candidate DRPs, the abundance of remurin, ferredoxin-NADP reductase, chloroplast manganese stabilizing protein-II, phosphoglycerate mutase, and glutathione S-transferase decreased in drought stressed Fld-tobacco while S-formylglutathione hydrolase and pyridoxine biosynthesis protein abundance increased. In wild type plants, drought caused a reduction of proteins related to carbohydrate metabolism. These results suggest that the stress tolerance conferred by Fld expression is strongly related to control mechanisms regarding carbohydrate and energy metabolism as well as oxidative stress responses. PMID:25506766

  14. Comparative Analysis of Transcriptomes from Secondary Reproductives of Three Reticulitermes Termite Species.

    PubMed

    Dedeine, Franck; Weinert, Lucy A; Bigot, Diane; Josse, Thibaut; Ballenghien, Marion; Cahais, Vincent; Galtier, Nicolas; Gayral, Philippe

    2015-01-01

    Termites are eusocial insects related to cockroaches that feed on lignocellulose. These insects are key species in ecosystems since they recycle a large amount of nutrients but also are pests, exerting major economic impacts. Knowledge on the molecular pathways underlying reproduction, caste differentiation or lignocellulose digestion would largely benefit from additional transcriptomic data. This study focused on transcriptomes of secondary reproductive females (nymphoid neotenics). Thirteen transcriptomes were used: 10 of Reticulitermes flavipes and R. grassei sequenced from a previous study, and two transcriptomes of R. lucifugus sequenced for the present study. After transcriptome assembly and read mapping, we examined interspecific variations of genes expressed by termites or gut microorganisms. A total of 18,323 orthologous gene clusters were detected. Functional annotation and taxonomic assignment were performed on a total of 41,287 predicted contigs in the three termite species. Between the termite species studied, functional categories of genes were comparable. Gene ontology (GO) terms analysis allowed the discovery of 9 cellulases and a total of 79 contigs potentially involved in 11 enzymatic activities used in wood metabolism. Altogether, results of this study illustrate the strong potential for the use of comparative interspecific transcriptomes, representing a complete resource for future studies including differentially expressed genes between castes or SNP analysis for population genetics. PMID:26698123

  15. A comparative analysis of the DNA recombination repair pathway in mycobacterial genomes.

    PubMed

    Singh, Amandeep; Bhagavat, Raghu; Vijayan, M; Chandra, Nagasuma

    2016-07-01

    In prokaryotes, repair by homologous recombination provides a major means to reinstate the genetic information lost in DNA damage. Recombination repair pathway in mycobacteria has multiple differences as compared to that in Escherichia coli. Of about 20 proteins known to be involved in the pathway, a set of 9 proteins, namely, RecF, RecO, RecR, RecA, SSBa, RuvA, RuvB and RuvC was found to be indispensable among the 43 mycobacterial strains. A domain level analysis indicated that most domains involved in recombination repair are unique to these proteins and are present as single copies in the genomes. Synteny analysis reveals that the gene order of proteins involved in the pathway is not conserved, suggesting that they may be regulated differently in different species. Sequence conservation among the same protein from different strains suggests the importance of RecO-RecA and RecFOR-RecA presynaptic pathways in the repair of double strand-breaks and single strand-breaks respectively. New annotations obtained from the analysis, include identification of a protein with a probable Holliday junction binding role present in 41 mycobacterial genomes and that of a RecB-like nuclease, containing a cas4 domain, present in 42 genomes. New insights into the binding of small molecules to the relevant proteins are provided by binding pocket analysis using three dimensional structural models. Analysis of the various features of the recombination repair pathway, presented here, is likely to provide a framework for further exploring stress response and emergence of drug resistance in mycobacteria. PMID:27450012

  16. Correction: Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi

    PubMed Central

    2014-01-01

    Abstract The version of this article published in BMC Genomics 2013, 14: 274, contains 9 unpublished genomes (Botryobasidium botryosum, Gymnopus luxurians, Hypholoma sublateritium, Jaapia argillacea, Hebeloma cylindrosporum, Conidiobolus coronatus, Laccaria amethystina, Paxillus involutus, and P. rubicundulus) downloaded from JGI website. In this correction, we removed these genomes after discussion with editors and data producers whom we should have contacted before downloading these genomes. Removing these data did not alter the principle results and conclusions of our original work. The relevant Figures 1, 2, 3, 4 and 6; and Table 1 have been revised. Additional files 1, 3, 4, and 5 were also revised. We would like to apologize for any confusion or inconvenience this may have caused. Background Fungi produce a variety of carbohydrate activity enzymes (CAZymes) for the degradation of plant polysaccharide materials to facilitate infection and/or gain nutrition. Identifying and comparing CAZymes from fungi with different nutritional modes or infection mechanisms may provide information for better understanding of their life styles and infection models. To date, over hundreds of fungal genomes are publicly available. However, a systematic comparative analysis of fungal CAZymes across the entire fungal kingdom has not been reported. Results In this study, we systemically identified glycoside hydrolases (GHs), polysaccharide lyases (PLs), carbohydrate esterases (CEs), and glycosyltransferases (GTs) as well as carbohydrate-binding modules (CBMs) in the predicted proteomes of 94 representative fungi from Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. Comparative analysis of these CAZymes that play major roles in plant polysaccharide degradation revealed that fungi exhibit tremendous diversity in the number and variety of CAZymes. Among them, some families of GHs and CEs are the most prevalent CAZymes that are distributed in all of the fungi analyzed

  17. Comparative genome analysis of Pseudomonas genomes including Populus-associated isolates

    SciTech Connect

    Jun, Se Ran; Wassenaar, Trudy; Nookaew, Intawat; Hauser, Loren John; Wanchai, Visanu; Land, Miriam L.; Timm, Collin M.; Lu, Tse-Yuan S.; Schadt, Christopher Warren; Doktycz, Mitchel John; Pelletier, Dale A; Ussery, David W

    2016-01-01

    The Pseudomonas genus contains a metabolically versatile group of organisms that are known to occupy numerous ecological niches including the rhizosphere and endosphere of many plants influencing phylogenetic diversity and heterogeneity. In this study, comparative genome analysis was performed on over one thousand Pseudomonas genomes, including 21 Pseudomonas strains isolated from the roots of native Populus deltoides. Based on average amino acid identity, genomic clusters were identified within the Pseudomonas genus, which showed agreements with clades by NCBI and cliques by IMG. The P. fluorescens group was organized into 20 distinct genomic clusters, representing enormous diversity and heterogeneity. The species P. aeruginosa showed clear distinction in their genomic relatedness compared to other Pseudomonas species groups based on the pan and core genome analysis. The 19 isolates of our 21 Populus-associated isolates formed three distinct subgroups within the P. fluorescens major group, supported by pathway profiles analysis, while two isolates were more closely related to P. chlororaphis and P. putida. The specific genes to Populus-associated subgroups were identified where genes specific to subgroup 1 include several sensory systems such as proteins which act in two-component signal transduction, a TonB-dependent receptor, and a phosphorelay sensor; specific genes to subgroup 2 contain unique hypothetical genes; and genes specific to subgroup 3 organisms have a different hydrolase activity. IMPORTANCE The comparative genome analyses of the genus Pseudomonas that included Populus-associated isolates resulted in novel insights into high diversity of Pseudomonas. Consistent and robust genomic clusters with phylogenetic homogeneity were identified, which resolved species-clades that are not clearly defined by 16S rRNA gene sequence analysis alone. The genomic clusters may be reflective of distinct ecological niches to which the organisms have adapted, but this

  18. Comparative genome analysis of Pseudomonas genomes including Populus-associated isolates

    DOE PAGESBeta

    Jun, Se Ran; Wassenaar, Trudy; Nookaew, Intawat; Hauser, Loren John; Wanchai, Visanu; Land, Miriam L.; Timm, Collin M.; Lu, Tse-Yuan S.; Schadt, Christopher Warren; Doktycz, Mitchel John; et al

    2016-01-01

    The Pseudomonas genus contains a metabolically versatile group of organisms that are known to occupy numerous ecological niches including the rhizosphere and endosphere of many plants influencing phylogenetic diversity and heterogeneity. In this study, comparative genome analysis was performed on over one thousand Pseudomonas genomes, including 21 Pseudomonas strains isolated from the roots of native Populus deltoides. Based on average amino acid identity, genomic clusters were identified within the Pseudomonas genus, which showed agreements with clades by NCBI and cliques by IMG. The P. fluorescens group was organized into 20 distinct genomic clusters, representing enormous diversity and heterogeneity. The speciesmore » P. aeruginosa showed clear distinction in their genomic relatedness compared to other Pseudomonas species groups based on the pan and core genome analysis. The 19 isolates of our 21 Populus-associated isolates formed three distinct subgroups within the P. fluorescens major group, supported by pathway profiles analysis, while two isolates were more closely related to P. chlororaphis and P. putida. The specific genes to Populus-associated subgroups were identified where genes specific to subgroup 1 include several sensory systems such as proteins which act in two-component signal transduction, a TonB-dependent receptor, and a phosphorelay sensor; specific genes to subgroup 2 contain unique hypothetical genes; and genes specific to subgroup 3 organisms have a different hydrolase activity. IMPORTANCE The comparative genome analyses of the genus Pseudomonas that included Populus-associated isolates resulted in novel insights into high diversity of Pseudomonas. Consistent and robust genomic clusters with phylogenetic homogeneity were identified, which resolved species-clades that are not clearly defined by 16S rRNA gene sequence analysis alone. The genomic clusters may be reflective of distinct ecological niches to which the organisms have adapted, but

  19. Comparative coronary risks of apixaban, rivaroxaban and dabigatran: a meta-analysis and adjusted indirect comparison

    PubMed Central

    Loke, Yoon K; Pradhan, Shiva; Yeong, Jessica Ka-yan; Kwok, Chun Shing

    2014-01-01

    Aims There are concerns regarding increased risk of acute coronary syndrome with dabigatran. We aimed to assess whether alternative treatment options such as rivaroxaban or apixaban carry a similar risk as compared with dabigatran. Methods We searched MEDLINE and EMBASE for randomized controlled trials of apixaban, dabigatran or rivaroxaban against control (placebo, heparin or vitamin K antagonist). We pooled odds ratios (OR) for adverse coronary events (acute coronary syndrome or myocardial infarction) using fixed effect meta-analysis and assessed heterogeneity with I2. We conducted adjusted indirect comparisons to compare risk of adverse coronary events with apixaban or rivaroxaban vs. dabigatran. Results Twenty-seven randomized controlled trials met the inclusion criteria. Dabigatran was associated with a significantly increased risk of adverse coronary events in pooled analysis of nine trials (OR 1.45, 95% CI 1.14, 1.86). There was no signal for coronary risk with apixaban from nine trials (pooled OR 0.89, 95% CI 0.78, 1.03) or rivaroxaban from nine trials (pooled OR 0.81, 95% CI 0.72, 0.93). Overall, adjusted indirect comparison suggested that both apixaban (OR 0.61, 95% CI 0.44, 0.85) and rivaroxaban (OR 0.54; 95% CI 0.39, 0.76) were associated with lower coronary risk than dabigatran. Restricting the indirect comparison to a vitamin K antagonist as a common control, yielded similar findings, OR 0.57 (95% CI 0.39, 0.85) for apixaban vs. dabigatran and 0.53 (95% CI 0.37, 0.77) for rivaroxaban vs. dabigatran. Conclusions There are significant differences in the comparative safety of apixaban, rivaroxaban and dabigatran with regards to acute coronary adverse events. PMID:24617578

  20. The Sambungmacan 3 Homo erectus calvaria: a comparative morphometric and morphological analysis.

    PubMed

    Delson, E; Harvati, K; Reddy, D; Marcus, L F; Mowbray, K; Sawyer, G J; Jacob, T; Márquez, S

    2001-04-01

    The Sambungmacan (Sm) 3 calvaria, discovered on Java in 1977, was illegally removed from Indonesia in 1998 and appeared in New York City in early 1999 at the Maxilla & Mandible, Ltd. natural history shop. Here we undertake an analysis of its phylogenetic and systematic position using geometric morphometrics and comparative morphology. The coordinates of points in the sagittal plane from glabella to opisthion were resampled to yield "lines" of 50 semi-landmarks. Coordinates of glabella, bregma, lambda, inion, and opisthion were also collected and analyzed separately. Casts of Homo erectus fossils from Indonesia, China, and Kenya and of "archaic H. sapiens" from Kabwe and Petralona, as well as 10 modern human crania, were used as the primary comparative sample. The modern humans were well separated from the fossils in a graphical superimposition of Procrustes-aligned semi-landmarks as well as in principal component and canonical discriminant analyses. In all of these, Sm 3 falls intermediate between the fossil and modern groups. Morphological comparisons of Sm 3 with a selection of Homo erectus fossils revealed its greatest similarity to specimens from Ngandong and the Sm 1 calvaria. Compared to all other H. erectus, Sm 3 was distinctive in its more vertical supratoral plane, less anteriorly projecting glabella and less sharply angled occiput. In these features it was somewhat similar to modern humans. It is not yet possible to determine if this similarity implies an evolutionary relationship or (more likely) individual or local populational variation. Several features of Sm 3 (small size, gracile supraorbital torus and lack of angular torus, and position in principal component analysis) suggest that it was a female. The use of geometric morphometrics provides a means to statistically test the shapes of such fossils in a manner not easily duplicated by other methods. The intermediate position of Sm 3 between fossil and modern samples in several different subanalyses