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Sample records for comparative crystal-chemical analysis

  1. Crystal-Chemical Analysis Martian Minerals in Gale Crater

    NASA Technical Reports Server (NTRS)

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

    DTIC Science & Technology

    1987-11-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2010-12-01

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

  5. Theories of Comparative Analysis

    DTIC Science & Technology

    1988-05-01

    model of a projectile fired from a cannon in a uniform gravitational field serves to demonstrate the problems due to qualitative arithmetic. Nei...recently demonstrated the qualitative Gauss rule, a type of algebraic manip- ulation that is solution preserving. While it cannot eliminate all...projectile fired from a cannon illustrates this point. Given an increase in muzzle velocity, Vft, as a perturbation, DQ " analysis predicts that apogee

  6. Time Dependent DD Neutrons Measurement Using a Single Crystal Chemical Vapor Deposition Diamond Detector on EAST

    NASA Astrophysics Data System (ADS)

    Du, Tengfei; Peng, Xingyu; Chen, Zhongjing; Hu, Zhimeng; Ge, Lijian; Hu, Liqun; Zhong, Guoqiang; Pu, Neng; Chen, Jinxiang; Fan, Tieshuan

    2016-09-01

    A single crystal chemical vapor deposition (scCVD) diamond detector has been successfully employed for neutron measurements in the EAST (Experimental Advanced Superconducting Tokamak) plasmas. The scCVD diamond detector coated with a 5 μm 6LiF (95% 6Li enriched) layer was placed inside a polyethylene moderator to enhance the detection efficiency. The time-dependent neutron emission from deuteron plasmas during neutral beam injection (NBI) heating was obtained. The measured results are compared with that of fission chamber detectors, which always act as standard neutron flux monitors. The scCVD diamond detector exhibits good reliability, stability and the capability to withstand harsh radiation environments despite its low detection efficiency due to the small active volume. supported by the National Magnetic Confinement Fusion Science Program of China (Nos. 2013GB106004 and 2012GB101003) and National Natural Science Foundation of China (No. 91226102)

  7. 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.

  8. Comparative analysis of collaboration networks

    NASA Astrophysics Data System (ADS)

    Progulova, Tatiana; Gadjiev, Bahruz

    2011-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2017-01-01

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

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

    PubMed

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

    2008-10-01

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

  11. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2017-03-01

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

  13. 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.

  14. 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.

  15. 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,…

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

    DTIC Science & Technology

    2012-02-01

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

  17. Network Analysis in Comparative Social Sciences

    ERIC Educational Resources Information Center

    Vera, Eugenia Roldan; Schupp, Thomas

    2006-01-01

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

  18. Teacher Policy: A Framework for Comparative Analysis

    ERIC Educational Resources Information Center

    Tatto, Maria Teresa

    2008-01-01

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

  19. Comparative genomic analysis of esophageal cancers.

    PubMed

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

    2014-09-01

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

  20. 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.

  1. 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.

  2. 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

  3. Embedded Hyperchaotic Generators: A Comparative Analysis

    NASA Astrophysics Data System (ADS)

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

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

  4. Comparative Genome Analysis of Enterobacter cloacae

    PubMed Central

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

    2013-01-01

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

  5. 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

  6. Stock index dynamics worldwide: a comparative analysis

    NASA Astrophysics Data System (ADS)

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

    2008-09-01

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

  7. Fundus camera systems: a comparative analysis.

    PubMed

    DeHoog, Edward; Schwiegerling, James

    2009-01-10

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

  8. Fundus camera systems: a comparative analysis

    PubMed Central

    DeHoog, Edward; Schwiegerling, James

    2010-01-01

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

  9. 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

  10. 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.

  11. Comparative Genome Analysis of Basidiomycete Fungi

    SciTech Connect

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

    2012-03-19

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

  12. Comparative analysis of the feline immunoglobulin repertoire.

    PubMed

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

    2017-01-25

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

  13. 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.

  14. 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.

  15. Comparative Sensitivity Analysis of Muscle Activation Dynamics

    PubMed Central

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

    2015-01-01

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

  16. 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.

  17. 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).

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

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

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

  19. Predictive and comparative analysis of Ebolavirus proteins

    PubMed Central

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

    2015-01-01

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

  20. Minimalist models for proteins: a comparative analysis.

    PubMed

    Tozzini, Valentina

    2010-08-01

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

  1. Comparative genomic analysis of prion genes

    PubMed Central

    Premzl, Marko; Gamulin, Vera

    2007-01-01

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

  2. 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.

  3. 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…

  4. 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…

  5. Question analysis for Indonesian comparative question

    NASA Astrophysics Data System (ADS)

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

    2017-01-01

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

  6. 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.

  7. 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…

  8. Comparative Analysis of Monographic Collections in Nursing.

    ERIC Educational Resources Information Center

    Bowden, Virginia M.; And Others

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

  9. Comparative Naval Architecture Analysis of Diesel Submarines

    DTIC Science & Technology

    2005-06-01

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

  10. 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…

  11. Comparative molecular analysis of endoevaporitic microbial communities.

    PubMed

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

    2008-10-01

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

  12. Comparative Analysis of Treatment Costs in EUROHOPE.

    PubMed

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

    2015-12-01

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

  13. A Comparative Analysis of Reinforcement Learning Methods

    DTIC Science & Technology

    1991-10-01

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

  14. Multiattribute Decision Modeling Techniques: A Comparative Analysis

    DTIC Science & Technology

    1988-08-01

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

  15. 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.

  16. 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

  17. [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.

  18. 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.

  19. Comparative analysis of Goodwin's business cycle models

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  20. 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.

  1. Comparative analysis of Debrecen sunspot catalogues

    NASA Astrophysics Data System (ADS)

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

    2017-02-01

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

  2. Comparative analysis of cystatin superfamily in platyhelminths.

    PubMed

    Guo, Aijiang

    2015-01-01

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

  3. 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.)

  4. Recognizing chemicals in patents: a comparative analysis.

    PubMed

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

    2016-01-01

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

  5. 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.

  6. Community detection algorithms: a comparative analysis.

    PubMed

    Lancichinetti, Andrea; Fortunato, Santo

    2009-11-01

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

  7. 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

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

    NASA Astrophysics Data System (ADS)

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

    2017-02-01

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

  9. 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 ...

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

    ERIC Educational Resources Information Center

    Smith, Jodi Renee Abbott

    2014-01-01

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

  11. 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…

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

    NASA Astrophysics Data System (ADS)

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

    2009-05-01

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

  13. 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.

  14. 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).

  15. 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

  16. 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.

  17. Tools for comparative protein structure modeling and analysis.

    PubMed

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

    2003-07-01

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

  18. 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.

  19. 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.

  20. 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…

  1. 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…

  2. 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…

  3. 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.

  4. 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.

  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 genomic analysis of eutherian interferon-γ-inducible GTPases.

    PubMed

    Premzl, Marko

    2012-11-01

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

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

    PubMed

    Takahashi, Kana; Yoshida, Kazuko; Sakuta, Masaaki

    2015-05-01

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

  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 Genomics via Wavelet Analysis for Closely Related Bacteria

    NASA Astrophysics Data System (ADS)

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

    2004-12-01

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

  11. 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.

  12. Comparative and Familial Analysis of Handedness in Great Apes

    PubMed Central

    Hopkins, William D.

    2007-01-01

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

  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.

  14. Sequence and comparative analysis of Leuconostoc dairy bacteriophages.

    PubMed

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

    2014-04-17

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

  15. Comparative analysis of NDE techniques with image processing

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

  16. 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.

  17. 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.

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

    PubMed

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

    1992-01-01

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

  19. 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.

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

    PubMed

    Hardin, S B

    1980-06-01

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

  1. 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.

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

    PubMed

    Carini, F; Varia, P; Valenza, V

    2001-01-01

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

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

    PubMed

    Ehret, G

    1977-09-01

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

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

    PubMed

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

    2000-12-15

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

  5. 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.

  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 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.

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

    PubMed Central

    Lin, Chan-Pin; Kuo, Chih-Horng

    2012-01-01

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

  9. 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

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

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

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

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

    PubMed

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

    2008-10-01

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

  12. Comparative Analysis of Vertebrate Diurnal/Circadian Transcriptomes

    PubMed Central

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

    2017-01-01

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

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

    PubMed

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

    2012-03-01

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

  14. 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.

  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. 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

  17. Comprehensive comparative analysis of kinesins in photosynthetic eukaryotes

    PubMed Central

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

    2006-01-01

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

  18. 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.

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

    PubMed

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

    2017-03-01

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

  20. Comparative Analysis on Nuclear Fuel Sustainability Aspect of FBR

    NASA Astrophysics Data System (ADS)

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

    2017-01-01

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

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

    PubMed

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

    2013-07-01

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

  2. 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.

  3. 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.

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

    PubMed Central

    Jahangir, Eiman; Comandé, Daniel; Rubinstein, Adolfo

    2011-01-01

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

  5. Comparative dynamic analysis of the full Grossman model.

    PubMed

    Ried, W

    1998-08-01

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

  6. 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

  7. 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

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

    NASA Astrophysics Data System (ADS)

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

    2013-11-01

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

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

    NASA Astrophysics Data System (ADS)

    Sanchez, Sergio; Plaza, Antonio

    2011-11-01

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

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

    PubMed

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

    2017-01-01

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

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

    PubMed

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

    2016-11-01

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

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

    PubMed

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

    2013-09-01

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

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

    PubMed

    Rashotte, Judy; Carnevale, F A

    2004-07-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed Central

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

    2003-01-01

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

  17. Comparative multiplex dosage analysis in spinocerebellar ataxia type 2 patients.

    PubMed

    Calì, F; Chiavetta, V; Ragalmuto, A; Vinci, M; Ruggeri, G; Schinocca, P; Romano, V

    2013-04-12

    We developed a new application of comparative multiplex dosage analysis (CMDA) for evaluation of the ataxin 2 gene. Expansions of the triplet CAG can cause spinocerebellar ataxia type 2 (SCA2), a neurodegenerative disease with an autosomal-dominant mode of inheritance. Molecular diagnosis of SCA2 is routinely based on the use of conventional PCR to detect the CAG expansion. However, PCR does not amplify an allele with an expansion of many triplets (>80), which is typically found in infantile and juvenile forms of SCA2, thus leading to false negatives. We propose the analysis of the ATXN2 gene by CMDA to complement existing methods currently used for the detection of large expansions of the CAG repeat. Using CMDA, the presence of any longer mutated allele in a heterozygous patient or fetus would be inferred due to dosage variation of the very frequent normal allele #22. CMDA can be completed in 1 day, at very low cost, and would be a useful tool for prenatal diagnosis and for diagnosis of presymptomatic forms of early-onset SCA2.

  18. 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.

  19. 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

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

    PubMed

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

    2016-01-01

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

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

    PubMed

    Ikegami, Keisuke; Yoshimura, Takashi

    2016-02-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

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

  4. 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

  5. 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.

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

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

    2012-01-01

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

  8. 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.

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

    PubMed

    Montgomery, Stuart; Hansen, Thomas; Kasper, Siegfried

    2011-03-01

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

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

    PubMed

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

    2015-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2007-05-01

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

  12. 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

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

    PubMed

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

    2009-04-01

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

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

    EPA Pesticide Factsheets

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

  15. Comparative analysis of the Monochamus alternatus immune system.

    PubMed

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

    2017-03-01

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

  16. 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.

  17. 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

  18. Comparative analysis of known miRNAs across platyhelminths.

    PubMed

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

    2013-08-01

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

  19. Noncoding RNA gene detection using comparative sequence analysis

    PubMed Central

    Rivas, Elena; Eddy, Sean R

    2001-01-01

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

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

    PubMed

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

    2004-09-15

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

  1. 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.

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

    PubMed

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

    2013-10-01

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

  3. 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.

  4. 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.

  5. 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.

  6. 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+.

  7. 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

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

    PubMed

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

    2013-01-01

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

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

    PubMed

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

    2016-12-18

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

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

    PubMed

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

    2005-10-01

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

  11. Comparative Analysis of Morphometric Characteristics of Scorpaenidae and Gobioninae

    PubMed Central

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

    2015-01-01

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

  12. 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

  13. 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…

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

    PubMed

    Sher, David J; Punglia, Rinaa S

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-02-01

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

  17. 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…

  18. 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…

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

    ERIC Educational Resources Information Center

    Correa, Hector

    1975-01-01

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

  20. 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:…

  1. 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…

  2. 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…

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

    EPA Science Inventory

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

  4. Comparative Effectiveness in Medicine: Analysis of Episiotomy Practice Patterns

    DTIC Science & Technology

    2011-12-01

    2009), Art . No.: CD000081. DOI: 10.1002/14651858.CD000081.pub2. http://www2.cochrane.org/ reviews /en/ab000081.html (accessed July 17, 2011). 38...episiotomy in the United States from 1979 to 2004, following recommendations made by the Cochrane Database of Systematic Reviews in 1999. The team...of Routine Episiotomy: A Systematic Review Meta analysis Screened 986 articles from 1950 to 2004 and included 26 for analysis. 2005 Graham et al

  5. 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.

  6. 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.

  7. 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.

  8. 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.

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

    ERIC Educational Resources Information Center

    King, Edmund

    1980-01-01

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

  10. 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…

  11. A Comparative Analysis of Day Care Licensing Standards.

    ERIC Educational Resources Information Center

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

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

  12. 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...

  13. 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…

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

    ERIC Educational Resources Information Center

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

    1990-01-01

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

  15. 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.…

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

    ERIC Educational Resources Information Center

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

    2008-01-01

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

  17. 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…

  18. 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…

  19. Comparative Analysis of the Concept of Shakespearean Tragedies

    ERIC Educational Resources Information Center

    Sipra, Muhammad Aslam; Nasir, Muhammad Haseeb

    2014-01-01

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

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

    PubMed

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

    2015-02-01

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

  1. 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…

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

    PubMed

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

    2006-01-01

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

  3. Comparative analysis of isotropic diffusion weighted imaging sequences

    NASA Astrophysics Data System (ADS)

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

    2017-02-01

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

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

    PubMed

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

    2014-02-01

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

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

    DTIC Science & Technology

    1982-02-01

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

  6. 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.

  7. 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

  8. 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.

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

    PubMed

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

    2015-09-01

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

  10. The Comparative Analysis of Inductor and Reluctance Wind Generators

    NASA Astrophysics Data System (ADS)

    Kamoliņš, Edmunds

    2009-01-01

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

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

    PubMed

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

    2007-12-01

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

  12. Comparative Analysis on Time Series with Included Structural Break

    NASA Astrophysics Data System (ADS)

    Andreeski, Cvetko J.; Vasant, Pandian

    2009-08-01

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

  13. Comparative Convergence Analysis of Nonlinear AMLI-Cycle Multigrid

    SciTech Connect

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

    2013-04-30

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

  14. In silico comparative analysis of SSR markers in plants

    PubMed Central

    2011-01-01

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

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

    PubMed

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

    2010-01-01

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

  16. 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

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

    PubMed

    Hazkani-Covo, Einat; Graur, Dan

    2007-01-01

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

  18. 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.

  19. 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.

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

    PubMed

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

    2016-01-01

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

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

    PubMed

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

    2016-09-01

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

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

    PubMed Central

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

    2017-01-01

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

  3. Comparing the results of five lifting analysis tools.

    PubMed

    Russell, Steven J; Winnemuller, Lori; Camp, Janice E; Johnson, Peter W

    2007-01-01

    The objective of this study was to compare the results of the NIOSH, ACGIH TLV, Snook, 3DSSPP and WA L&I lifting assessment instruments when applied to a uniform task (lifting and lowering milk cases with capacities of 15 and 23l). To enable comparisons between the various lifting assessment instruments, the outputs of each method were converted to an exposure index similar to the NIOSH Lifting Index. All instruments showed higher exposures associated with lifting the 23l cases versus the 15l cases. The NIOSH, ACGIH TLV and Snook methods were similar in their results with respect to the pattern of exposure over various height levels and the differences in exposures associated with lifting 15 and 23l cases. However, the WA L&I and 3DSSPP predicted substantially lower exposures. The reasons for instrument differences are presented so that practitioners can better select the methods they need and interpret the results appropriately.

  4. 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.

  5. 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.

  6. A Comparative Analysis of Acyl-Homoserine Lactone Synthase Assays.

    PubMed

    Shin, Daniel; Frane, Nicole D; Brecht, Ryan M; Keeler, Jesse; Nagarajan, Rajesh

    2015-12-01

    Quorum sensing is cell-to-cell communication that allows bacteria to coordinate attacks on their hosts by inducing virulent gene expression, biofilm production, and other cellular functions, including antibiotic resistance. AHL synthase enzymes synthesize N-acyl-l-homoserine lactones, commonly referred to as autoinducers, to facilitate quorum sensing in Gram-negative bacteria. Studying the synthases, however, has proven to be a difficult road. Two assays, including a radiolabeled assay and a colorimetric (DCPIP) assay are well-documented in literature to study AHL synthases. In this paper, we describe additional methods that include an HPLC-based, C-S bond cleavage and coupled assays to investigate this class of enzymes. In addition, we compare and contrast each assay for both acyl-CoA- and acyl-ACP-utilizing synthases. The expanded toolkit described in this study should facilitate mechanistic studies on quorum sensing signal synthases and expedite discovery of antivirulent compounds.

  7. Comparative analysis of large antenna spacecraft using the ideas system

    NASA Technical Reports Server (NTRS)

    Garrett, L. B.; Ferebee, M. J., Jr.

    1983-01-01

    A Land Mobile Satellite System (LMSS), capable of providing mobile communications for commercial and government applications in nonmetropolitan areas of the continental U.S. and Canada as an augmentation to existing and planned terrestrial systems, is being studied. The satellite system would provide 'narrow band' telecommunications services such as mobile radio, telephone, dispatch, safety, and special radio services, and thin-route fixed telephone and data services in the 806-890 MHz band and continuous emergency beacon monitoring in the 406-406.1 MHz band. A single Shuttle launch with an upper stage orbital transfer system would place the LMSS spacecraft in geosynchronous orbit over the continental U.S. in 1995 with a 10-year lifetime. The present investigation has the objective to evaluate, compare, and rank selected spacecraft concepts, to suggest design improvement to the individual concepts, and to identify technology needs.

  8. 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.

  9. 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.

  10. Comparative analysis of four disease prediction models of Parkinson's disease.

    PubMed

    Kumudini, Nadella; Naushad, Shaik Mohammad; Alex Stanley, Balraj; Niveditha, Manoharan; Sharmila, Gunasekaran; Kumaraswami, Konda; Borghain, Rupam; Mridula, Rukmini; Kutala, Vijay Kumar

    2016-01-01

    Parkinson's disease (PD) is a multi-factorial disorder with high-penetrant mutations accounting for small percentage of PD. Our previous studies demonstrated individual association of genetic variants in folate, xenobiotic, and dopamine metabolic pathways with PD risk. The rational of the study was to develop a risk prediction model for PD using these genetic polymorphisms along with synuclein (SNCA) polymorphism. We have generated additive, multifactor dimensionality reduction (MDR), recursive partitioning (RP), and artificial neural network (ANN) models using 21 SNPs as inputs and disease outcome as output. The clinical utility of all these models was assessed by plotting receiver operating characteristics curves where in area under the curve (AUC) was used as an index of diagnostic utility of the model. The additive model was the simplest and exhibited an AUC of 0.72. The MDR model showed significant gene-gene interactions between SNCA, DRD4VNTR, and DRD2A polymorphisms. The RP model showed SHMT C1420T as important determinant of PD risk. This variant allele was found to be protective and this protection was nullified by MTRR A66G. Inheritance of SHMT wild allele and SNCA intronic polymorphism was shown to increase the risk of PD. The ANN model showed higher diagnostic utility (AUC = 0.86) compared to all the models and was able to explain 56.6% cases of sporadic PD. To conclude, the ANN model developed using SNPs in folate, xenobiotic, and dopamine pathways along with SNCA has higher clinical utility in predicting PD risk compared to other models.

  11. 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

  12. 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

  13. Comparative study of mobile Raman instrumentation for art analysis.

    PubMed

    Vandenabeele, P; Castro, K; Hargreaves, M; Moens, L; Madariaga, J M; Edwards, H G M

    2007-04-04

    In archaeometry, one of the main concerns is to extract information from an art object, without damaging it. Raman spectroscopy is being applied in this research field with recent developments in mobile instrumentation facilitating more routine analysis. This research paper evaluates the performances of five mobile Raman instruments (Renishaw RA100, Renishaw Portable Raman Analyser RX210, Ocean Optics RSL-1, Delta Nu Inspector Raman, Mobile Art Analyser--MArtA) in three different laboratories. A set of samples were collected, in order to obtain information on the spectral performances of the instruments including: spectral resolution, calibration, laser cut-off, the ability to record spectra of organic and inorganic pigments through varnish layers and on the possibilities to identify biomaterials. Spectra were recorded from predefined regions on a canvas painting to simulate the investigation of artworks and the capabilities to record spectra from hardly accessible areas was evaluated.

  14. Marine invertebrate lipases: Comparative and functional genomic analysis.

    PubMed

    Rivera-Perez, Crisalejandra

    2015-09-01

    Lipases are key enzymes involved in lipid digestion, storage and mobilization of reserves during fasting or heightened metabolic demand. This is a highly conserved process, essential for survival. The genomes of five marine invertebrate species with distinctive digestive system were screened for the six major lipase families. The two most common families in marine invertebrates, the neutral an acid lipases, are also the main families in mammals and insects. The number of lipases varies two-fold across analyzed genomes. A high degree of orthology with mammalian lipases was observed. Interestingly, 19% of the marine invertebrate lipases have lost motifs required for catalysis. Analysis of the lid and loop regions of the neutral lipases suggests that many marine invertebrates have a functional triacylglycerol hydrolytic activity as well as some acid lipases. A revision of the expression profiles and functional activity on sequences in databases and scientific literature provided information regarding the function of these families of enzymes in marine invertebrates.

  15. Comparative Exergetic Analysis of Joule-Thomson Liquefiers

    NASA Astrophysics Data System (ADS)

    Chorowski, Maciej

    2004-06-01

    The Joule-Thomson microliquefiers are very reliable and noiseless cryocoolers, specially well fitted for cryostating small electronic devices, IR detectors or cryosurgical probes. Their essential drawback is low thermodynamic efficiency imposing high supply gas pressure, usually above 10 MPa. An exergetic analysis of the microliquefier has been performed and exergy-loss sources identified. Some of the losses can be avoided if a pure gas is replaced with a proper gas mixture and in result the supply gas pressure can be lowered significantly. The efficiencies and working parameters of Joule-Thomson microliquefier fed with pure N2 and the mixtures N2 - CH4 and N2 - R13 have been estimated and measured. The mixture properties have been calculated using the Peng-Robinson equation of state. The possibility to use a liquid-solid phase transition in a cooling-power "on-off" control loop has been observed.

  16. Decision Analysis Tool to Compare Energy Pathways for Transportation

    SciTech Connect

    Bloyd, Cary N.

    2010-06-30

    With the goals of reducing greenhouse gas emissions, oil imports, and energy costs, a wide variety of automotive technologies are proposed to replace the traditional gasoline-powered internal combustion engine (g-ICE). Biomass is seen as an important domestic energy feedstock, and there are multiple pathways in which it can be linked to the transport sector. Contenders include the use of cellulosic ethanol from biomass to replace gasoline or the use of a biomass-fueled combined cycle electrical power generation facility in conjunction plug-in hybrid electric vehicles (PHEVs). This paper reviews a project that is developing a scenario decision analysis tool to assist policy makers, program managers, and others to obtain a better understanding of these uncertain possibilities and how they may interact over time.

  17. 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.

  18. 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.

  19. Qualitative analysis in gay men's health research: comparing thematic, critical discourse, and conversation analysis.

    PubMed

    Aguinaldo, Jeffrey P

    2012-01-01

    Gay men's health typically relies on traditional forms of qualitative analysis, such as thematic analysis, and would benefit from a diversity of analytic approaches. Such diversity offers public health researchers a breadth of tools to address different kinds of research questions and, thus, substantiate different types of social phenomenon relevant to the health and wellbeing of gay men. In this article, I compare and contrast three qualitative analytic approaches: thematic, critical discourse, and conversation analysis. I demonstrate and distinguish their key analytic assumptions by applying each approach to a single data excerpt taken from a public health interview conducted for a broader study on gay men's health. I engage in a discussion of each approach in relation to three themes: its utility for gay men's health, its approach to dilemmas of voice, and its capacity for reflexivity. I advocate that qualitative researchers should capitalise on the full range of qualitative analytic approaches to achieve the goals of gay men's health. However, I specifically encourage qualitative researchers to engage with conversation analysis, not only because of its capacity to resolve dilemmas of voice and to achieve reflexivity, but also for its ability to capture forms of social life hitherto undocumented through thematic and critical discourse analysis.

  20. Os odontoideum in identical twins: Comparative gene expression analysis

    PubMed Central

    Straus, David; Xu, Shunbin; Traynelis, Vincent C.

    2014-01-01

    Background: Os odontoideum is a well identified anomaly of the craniovertebral junction. Since its initial description, there has been a continuous debate regarding the nature of its etiology: Whether congenital or traumatic. We sought to compare the gene expression profiles in patients with congenital os odontoideum, those with traumatic os odontoideum and controls. Methods: We have evaluated a pair of identical twins both with os odontoideum. We identified two additional patients with and four subjects without os odontoideum. We analyzed the gene expression profiles in these patients using a custom TaqMan microarray and quantitative reverse transcriptase polymerase chain reaction (qRT-PCR). The relative gene expression profiles in the two identical twins, the two nontwin patients with os odontoideum and the controls were assessed. Results: A total of 213 genes with significantly different expression between the twin os odontoideum patients and the subjects without os odontoideum were detected. CACNG6, PHEX, CACNAD3, IL2, FAS, TUFT1, KIT, TGFBR2, and IGF2 were expressed at levels greater than 100-fold more in the twins. There were six genes with significantly different expression profiles in the twins as compared with the nontwin os odontoideum patients: CMK4, ATF1, PLCG1, TAB1, E2F3, and ATF4. There were no statistically significant differences in gene expression in the four patients with os odontoideum and the subjects without. Trends, however, were noted in MMP8, KIT, HIF1A, CREB3, PWHAZ, TGFBR1, NFKB2, FGFR1, IPO8, STAT1, COL1A1, and BMP3. Conclusions: Os odontoideum has multiple etiologies, both traumatic and congenital and perhaps some represent a combination of the two. This work has identified a number of genes that show increased expression in a pair of twins with congenital os odontoideum and also demonstrates trends in gene expression profiles between a larger group of os odontoideum patients and non-os patients. A number of these genes are related to

  1. 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

  2. Comparative analysis of proteome and transcriptome variation in mouse.

    PubMed

    Ghazalpour, Anatole; Bennett, Brian; Petyuk, Vladislav A; Orozco, Luz; Hagopian, Raffi; Mungrue, Imran N; Farber, Charles R; Sinsheimer, Janet; Kang, Hyun M; Furlotte, Nicholas; Park, Christopher C; Wen, Ping-Zi; Brewer, Heather; Weitz, Karl; Camp, David G; Pan, Calvin; Yordanova, Roumyana; Neuhaus, Isaac; Tilford, Charles; Siemers, Nathan; Gargalovic, Peter; Eskin, Eleazar; Kirchgessner, Todd; Smith, Desmond J; Smith, Richard D; Lusis, Aldons J

    2011-06-01

    The relationships between the levels of transcripts and the levels of the proteins they encode have not been examined comprehensively in mammals, although previous work in plants and yeast suggest a surprisingly modest correlation. We have examined this issue using a genetic approach in which natural variations were used to perturb both transcript levels and protein levels among inbred strains of mice. We quantified over 5,000 peptides and over 22,000 transcripts in livers of 97 inbred and recombinant inbred strains and focused on the 7,185 most heritable transcripts and 486 most reliable proteins. The transcript levels were quantified by microarray analysis in three replicates and the proteins were quantified by Liquid Chromatography-Mass Spectrometry using O(18)-reference-based isotope labeling approach. We show that the levels of transcripts and proteins correlate significantly for only about half of the genes tested, with an average correlation of 0.27, and the correlations of transcripts and proteins varied depending on the cellular location and biological function of the gene. We examined technical and biological factors that could contribute to the modest correlation. For example, differential splicing clearly affects the analyses for certain genes; but, based on deep sequencing, this does not substantially contribute to the overall estimate of the correlation. We also employed genome-wide association analyses to map loci controlling both transcript and protein levels. Surprisingly, little overlap was observed between the protein- and transcript-mapped loci. We have typed numerous clinically relevant traits among the strains, including adiposity, lipoprotein levels, and tissue parameters. Using correlation analysis, we found that a low number of clinical trait relationships are preserved between the protein and mRNA gene products and that the majority of such relationships are specific to either the protein levels or transcript levels. Surprisingly

  3. 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

  4. 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

  5. Work satisfaction among California registered nurses: a longitudinal comparative analysis.

    PubMed

    Tellez, Michelle

    2012-01-01

    California's minimum nurse-to-patient staffing ratio law, the nation's first, was implemented in 2004. This study had two aims: (a) to evaluate the effect of the nurse-to-patient ratios law on nurse job satisfaction in order to advance the debate over the merits of nurse staffing law, and (b) to compare California nurses who were satisfied against those who were not, in order to facilitate the development targeted retention interventions based on empirical evidence. The sample's overall job satisfaction increased significantly as the years passed, suggesting the nurse-to-patient ratios law was associated with improvements in nurse satisfaction. Satisfied RNs were more likely to have a balanced and financially secure life that included a partner, children living at home, higher hourly wages, and higher income from sources other than a nursing job. Nurses working in direct patient care positions remained dissatisfied in larger proportions than those working in other types of positions, even after the nurse-to-patient ratios were implemented. More nurses are satisfied today than before the ratios; nevertheless, far too many nurses (18.5%) have job satisfaction scores that are neutral or worse.

  6. 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

  7. [COMPARATIVE ANALYSIS OF ANTIBACTERIAL EFFECT OF PHYTOANTIBIOTICS AND ANTIBIOTICS].

    PubMed

    Akhvlediani, L; Koiava, T; Lomtadze, L; Joxadze, M; Msxiladze, L; Berashvili, D; Bakuridze, A

    2016-11-01

    The objective of this study was to determine the antibacterial activity of individual medicines and containing sum of the phyto-extracts against the bacteria causing nosocomial infections in compare to antibiotics. In the investigation were involved four strains of gram-negative bacteria Escherichia coli, Klebsiella pneumoniae, Staphylococcus aureus and Acinetobacter spp. Each object was investigated on antibiotic resistance using Kirby-Bauer diffusion method on 22 types of antibiotics. The objects of the study were: Sanguinarine, Chelerythrine and Berberine hydrochloride (of lab quality); essential oils and aromatic waters of Eucalyptus, Salvia and Lavanda. For determination their antibacterial activity was used Raits serological dilution method with adaptation. The results show that the antibiotic resistant bacteria did not rise in non-diluted and 1:1 diluted test-tubes. In 1:5 diluted test-tubes was observed a little turbidity and growth, as for in other test-tubes - intensive growth. The investigated phyto-medicines show the higher antibacterial activity than the antibiotics.

  8. A comparative analysis of the evolution of imperfect mimicry.

    PubMed

    Penney, Heather D; Hassall, Christopher; Skevington, Jeffrey H; Abbott, Kevin R; Sherratt, Thomas N

    2012-03-21

    Although exceptional examples of adaptation are frequently celebrated, some outcomes of natural selection seem far from perfect. For example, many hoverflies (Diptera: Syrphidae) are harmless (Batesian) mimics of stinging Hymenoptera. However, although some hoverfly species are considered excellent mimics, other species bear only a superficial resemblance to their models and it is unclear why this is so. To evaluate hypotheses that have been put forward to explain interspecific variation in the mimetic fidelity of Palearctic Syrphidae we use a comparative approach. We show that the most plausible explanation is that predators impose less selection for mimetic fidelity on smaller hoverfly species because they are less profitable prey items. In particular, our findings, in combination with previous results, allow us to reject several key hypotheses for imperfect mimicry: first, human ratings of mimetic fidelity are positively correlated with both morphometric measures and avian rankings, indicating that variation in mimetic fidelity is not simply an illusion based on human perception; second, no species of syrphid maps out in multidimensional space as being intermediate in appearance between several different hymenopteran model species, as the multimodel hypothesis requires; and third, we find no evidence for a negative relationship between mimetic fidelity and abundance, which calls into question the kin-selection hypothesis. By contrast, a strong positive relationship between mimetic fidelity and body size supports the relaxed-selection hypothesis, suggesting that reduced predation pressure on less profitable prey species limits the selection for mimetic perfection.

  9. Competencies and frameworks in interprofessional education: a comparative analysis.

    PubMed

    Thistlethwaite, Jill E; Forman, Dawn; Matthews, Lynda R; Rogers, Gary D; Steketee, Carole; Yassine, Tagrid

    2014-06-01

    Health professionals need preparation and support to work in collaborative practice teams, a requirement brought about by an aging population and increases in chronic and complex diseases. Therefore, health professions education has seen the introduction of interprofessional education (IPE) competency frameworks to provide a common lens through which disciplines can understand, describe, and implement team-based practices. Whilst an admirable aim, often this has resulted in more confusion with the introduction of varying definitions about similar constructs, particularly in relation to what IPE actually means.The authors explore the nature of the terms competency and framework, while critically appraising the concept of competency frameworks and competency-based education. They distinguish between competencies for health professions that are profession specific, those that are generic, and those that may be achieved only through IPE. Four IPE frameworks are compared to consider their similarities and differences, which ultimately influence how IPE is implemented. They are the Interprofessional Capability Framework (United Kingdom), the National Interprofessional Competency Framework (Canada), the Core Competencies for Interprofessional Collaborative Practice (United States), and the Curtin University Interprofessional Capability Framework (Australia).The authors highlight the need for further discussion about establishing a common language, strengthening ways in which academic environments work with practice environments, and improving the assessment of interprofessional competencies and teamwork, including the development of assessment tools for collaborative practice. They also argue that for IPE frameworks to be genuinely useful, they need to augment existing curricula by emphasizing outcomes that might be attained only through interprofessional activity.

  10. 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.

  11. Subpicosecond and picosecond laser ablation of dental enamel: comparative analysis

    NASA Astrophysics Data System (ADS)

    Rode, Andrei V.; Madsen, Nathan R.; Kolev, Vesselin Z.; Gamaly, Eugene G.; Luther-Davies, Barry; Dawes, Judith M.; Chan, A.

    2004-06-01

    We report the use of sub-picosecond near-IR and ps UV pulsed lasers for precision ablation of freshly extracted human teeth. The sub-picosecond laser wavelength was ~800nm, with pulsewidth 150 fs and pulse repetition rate of 1kHz; the UV laser produced 10 ps pulses at 266 nm with pulse rate of ~1.2x105 pulses/s; both lasers produced ~1 W of output energy, and the laser fluence was kept at the same level of 10-25 J/cm2. Laser radiation from both laser were effectively absorbed in the teeth enamel, but the mechanisms of absorption were radically different: the near-IR laser energy was absorbed in a plasma layer formed through the optical breakdown mechanism initiated by multiphoton absorption, while the UV-radiation was absorbed due to molecular photodissociation of the enamel and conventional thermal deposition. The rise in the intrapulpal temperature was monitored by embedded thermocouples, and was shown to remain low with subpicosecond laser pulses, but risen up to 30°C, well above the 5°C pain level with the UV-laser. This study demonstrates the potential for ultra-short-pulsed lasers to precision and painless ablation of dental enamel, and indicated the optimal combination of laser parameters in terms of pulse energy, duration, intensity, and repetition rate, required for the laser ablation rates comparable to that of mechanical drill.

  12. Comparative Analysis of Cherenkov Light Detectors in an Oil Drum

    NASA Astrophysics Data System (ADS)

    Niduaza, Rexavalmar; Wedel, Zachary; Castro, Juan; Zavala, Favian; Fan, Sewan; Fatuzzo, Laura

    2014-03-01

    The multi-pixel photon counters (MPPC) has been used in a number of research development in astro-particle physics and particle physics. In an effort to further implement the MPPC detector, we constructed a modular experimental setup using a 16-inch tall acrylic cylinder filled with distilled water as the light producing medium to determine its feasibility as a possible detector for weak Cherenkov light. We have since progressed towards utilizing an oil drum (approximately 30 gallons) as our light-tight container replacing our prototype. In this talk, we would discuss the results regarding our investigation utilizing 1-inch and 3-inch photo-multiplier tubes (PMTs) in an oil drum as we did for our prototype. We would also present our experimental findings comparing our prototype and our oil drum setup using PMTs in coincidence with the MPPC coupled with wavelength-shifting fibers that are submerged in distilled water inside the oil drum vessel. Department of Education grant nymber P031S90007.

  13. 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.

  14. A Comparative Biocompatibility Analysis of Ternary Nitinol Alloys

    PubMed Central

    Haider, Waseem; Munroe, Norman; Pulletikurthi, Chandan; Singh Gill, Puneet K.; Amruthaluri, Sushma

    2009-01-01

    Nitinol alloys are rapidly being utilized as the material of choice in a variety of applications in the medical industry. It has been used for self-expanding stents, graft support systems, and various other devices for minimally invasive interventional and endoscopic procedures. However, the biocompatibility of this alloy remains a concern to many practitioners in the industry due to nickel sensitivity experienced by many patients. In recent times, several new Nitinol alloys have been introduced with the addition of a ternary element. Nevertheless, there is still a dearth of information concerning the biocompatibility and corrosion resistance of these alloys. This study compared the biocompatibility of two ternary Nitinol alloys prepared by powder metallurgy (PM) and arc melting (AM) and critically assessed the influence of the ternary element. ASTM F 2129-08 cyclic polarization in vitro corrosion tests were conducted to evaluate the corrosion resistance in phosphate buffered saline (PBS). The growth of endothelial cells on NiTi was examined using optical microscopy. PMID:19956791

  15. 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

  16. 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

  17. Interspecific variation of warning calls in piranhas: a comparative analysis

    PubMed Central

    Mélotte, Geoffrey; Vigouroux, Régis; Michel, Christian; Parmentier, Eric

    2016-01-01

    Fish sounds are known to be species-specific, possessing unique temporal and spectral features. We have recorded and compared sounds in eight piranha species to evaluate the potential role of acoustic communication as a driving force in clade diversification. All piranha species showed the same kind of sound-producing mechanism: sonic muscles originate on vertebrae and attach to a tendon surrounding the bladder ventrally. Contractions of the sound-producing muscles force swimbladder vibration and dictate the fundamental frequency. It results the calling features of the eight piranha species logically share many common characteristics. In all the species, the calls are harmonic sounds composed of multiple continuous cycles. However, the sounds of Serrasalmus elongatus (higher number of cycles and high fundamental frequency) and S. manueli (long cycle periods and low fundamental frequency) are clearly distinguishable from the other species. The sonic mechanism being largely conserved throughout piranha evolution, acoustic communication can hardly be considered as the main driving force in the diversification process. However, sounds of some species are clearly distinguishable despite the short space for variations supporting the need for specific communication. Behavioural studies are needed to clearly understand the eventual role of the calls during spawning events. PMID:27782184

  18. 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

  19. 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

  20. Interspecific variation of warning calls in piranhas: a comparative analysis.

    PubMed

    Mélotte, Geoffrey; Vigouroux, Régis; Michel, Christian; Parmentier, Eric

    2016-10-26

    Fish sounds are known to be species-specific, possessing unique temporal and spectral features. We have recorded and compared sounds in eight piranha species to evaluate the potential role of acoustic communication as a driving force in clade diversification. All piranha species showed the same kind of sound-producing mechanism: sonic muscles originate on vertebrae and attach to a tendon surrounding the bladder ventrally. Contractions of the sound-producing muscles force swimbladder vibration and dictate the fundamental frequency. It results the calling features of the eight piranha species logically share many common characteristics. In all the species, the calls are harmonic sounds composed of multiple continuous cycles. However, the sounds of Serrasalmus elongatus (higher number of cycles and high fundamental frequency) and S. manueli (long cycle periods and low fundamental frequency) are clearly distinguishable from the other species. The sonic mechanism being largely conserved throughout piranha evolution, acoustic communication can hardly be considered as the main driving force in the diversification process. However, sounds of some species are clearly distinguishable despite the short space for variations supporting the need for specific communication. Behavioural studies are needed to clearly understand the eventual role of the calls during spawning events.

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

    PubMed

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

    2016-04-07

    Genomic DNA extraction is crucial for molecular research, including diagnostic and genome characterization of different organisms. The aim of this study was to comparatively analyze protocols of DNA extraction based on cell lysis by sarcosyl, cetyltrimethylammonium bromide, and sodium dodecyl sulfate, and to determine the most efficient method applicable to soybean caterpillars. DNA was extracted from specimens of Chrysodeixis includens and Spodoptera eridania using the aforementioned three methods. DNA quantification was performed using spectrophotometry and high molecular weight DNA ladders. The purity of the extracted DNA was determined by calculating the A260/A280 ratio. Cost and time for each DNA extraction method were estimated and analyzed statistically. The amount of DNA extracted by these three methods was sufficient for PCR amplification. The sarcosyl method yielded DNA of higher purity, because it generated a clearer pellet without viscosity, and yielded high quality amplification products of the COI gene I. The sarcosyl method showed lower cost per extraction and did not differ from the other methods with respect to preparation times. Cell lysis by sarcosyl represents the best method for DNA extraction in terms of yield, quality, and cost effectiveness.

  2. 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.

  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. A comparative critical analysis of modern task-parallel runtimes.

    SciTech Connect

    Wheeler, Kyle Bruce; Stark, Dylan; Murphy, Richard C.

    2012-12-01

    The rise in node-level parallelism has increased interest in task-based parallel runtimes for a wide array of application areas. Applications have a wide variety of task spawning patterns which frequently change during the course of application execution, based on the algorithm or solver kernel in use. Task scheduling and load balance regimes, however, are often highly optimized for specific patterns. This paper uses four basic task spawning patterns to quantify the impact of specific scheduling policy decisions on execution time. We compare the behavior of six publicly available tasking runtimes: Intel Cilk, Intel Threading Building Blocks (TBB), Intel OpenMP, GCC OpenMP, Qthreads, and High Performance ParalleX (HPX). With the exception of Qthreads, the runtimes prove to have schedulers that are highly sensitive to application structure. No runtime is able to provide the best performance in all cases, and those that do provide the best performance in some cases, unfortunately, provide extremely poor performance when application structure does not match the schedulers assumptions.

  5. Comparative analysis of Beggiatoa from hypersaline and marine environments.

    PubMed

    de Albuquerque, Julia Peixoto; Keim, Carolina Neumann; Lins, Ulysses

    2010-07-01

    The main criterion to classify a microorganism as belonging to the genus Beggiatoa is its morphology. All multicellular, colorless, gliding bacterial filaments containing sulfur globules described so far belong to this genus. At the ultrastructural level, they show also a very complex cell envelope structure. Here we describe uncultured vacuolated and non-vacuolated bacteria from two different environments showing all characteristics necessary to assign a bacterium to the genus Beggiatoa. We also intended to investigate whether narrow and vacuolate Beggiatoa do differ morphologically as much as they do phylogenetically. Both large, vacuolated trichomes and narrow filaments devoid of vacuoles were observed. We confirmed the identity of the narrow filaments by 16S rRNA phylogenetic analysis. The diameters of the trichomes ranged from 2.4 to 34 microm, and their lengths ranged from 10 microm to over 30 mm. Narrow trichomes moved by gliding at 3.0 microm/s; large filaments moved at 1.5 microm/s. Periplasmic sulfur inclusions were observed in both types of filaments, whereas phosphorus-rich bodies were found only in narrow trichomes. On the other hand, nitrate vacuoles were observed only in large trichomes. Ultra-thin section transmission electron microscopy showed differences between the cell ultrastructure of narrow (non-vacuolated) and large (vacuolated) Beggiatoa. We observed that cell envelopes from narrow Beggiatoa consist of five layers, whereas cell envelopes from large trichomes contain four layers.

  6. 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

  7. Family policies in OECD countries: a comparative analysis.

    PubMed

    Thévenon, Olivier

    2011-01-01

    This article discusses the diversity of family policy models in 28 OECD countries in terms of the balance between their different objectives and the mix of instruments adopted to implement the policies. Cross-country policy differences are investigated by applying a principal component analysis to comprehensive country-level data from the OECD Family database covering variables such as parental leave conditions, childcare service provision, and financial support to families. The results find persistent differences in the family policy patterns embedded in different contexts of work-family "outcomes." Country classifications of family policy packages only partially corroborate categorizations in earlier studies, owing to considerable within-group heterogeneity and the presence of group outliers. The Nordic countries outdistance the others with comprehensive support to working parents with very young children. Anglo-Saxon countries provide much less support for working parents with very young children, and financial support is targeted on low-income and large families and focuses on preschool and early elementary education. Continental and Eastern European countries form a more heterogeneous group, while the support received by families in Southern Europe and in Asian countries is much lower in all its dimensions.

  8. 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.

  9. 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

  10. Comparative genomic analysis of teleost fish bmal genes.

    PubMed

    Wang, Han

    2009-05-01

    Bmal1 (Brain and muscle ARNT like 1) gene is a key circadian clock gene. Tetrapods also have the second Bmal gene, Bmal2. Fruit fly has only one bmal1/cycle gene. Interrogation of the five teleost fish genome sequences coupled with phylogenetic and splice site analyses found that zebrafish have two bmal1 genes, bmal1a and bmal1b, and bmal2a; Japanese pufferfish (fugu), green spotted pufferfish (tetraodon) and Japanese medaka fish each have two bmal2 genes, bmal2a and bmal2b, and bmal1a; and three-spine stickleback have bmal1a and bmal2b. Syntenic analysis further indicated that zebrafish bmal1a/bmal1b, and fugu, tetraodon and medaka bmal2a/bmal2b are ancient duplicates. Although the dN/dS ratios of these four fish bmal duplicates are all <1, implicating they have been under purifying selection, the Tajima relative rate test showed that fugu, tetraodon and medaka bmal2a/bmal2b have asymmetric evolutionary rates, suggesting that one of these duplicates have been subject to positive selection or relaxed functional constraint. These results support the notion that teleost fish bmal genes were derived from the fish-specific genome duplication (FSGD), divergent resolution following the duplication led to retaining different ancient bmal duplicates in different fishes, which could have shaped the evolution of the complex teleost fish timekeeping mechanisms.

  11. Comparative analysis of the methods for SADT determination.

    PubMed

    Kossoy, A A; Sheinman, I Ya

    2007-04-11

    The self-accelerating decomposition temperature (SADT) is an important parameter that characterizes thermal safety at transport of self-reactive substances. A great many articles were published focusing on various methodological aspects of SADT determination. Nevertheless there remain several serious problems that require further analysis and solution. Some of them are considered in the paper. Firstly four methods suggested by the United Nations "Recommendations on the Transport of Dangerous Goods" (TDG) are surveyed in order to reveal their features and limitations. The inconsistency between two definitions of SADT is discussed afterwards. One definition is the basis for the US SADT test and the heat accumulation storage test (Dewar test), another one is used when the Adiabatic storage test or the Isothermal storage test are applied. It is shown that this inconsistency may result in getting different and, in some cases, unsafe estimates of SADT. Then the applicability of the Dewar test for determination of SADT for solids is considered. It is shown that this test can be restrictedly applied for solids provided that the appropriate scale-up procedure is available. The advanced method based on the theory of regular cooling mode is proposed, which ensures more reliable results of the Dewar test application. The last part of the paper demonstrates how the kinetics-based simulation method helps in evaluation of SADT in those complex but practical cases (in particular, stack of packagings) when neither of the methods recommended by TDG can be used.

  12. A comparative protein function analysis databaseof different Leishmania strains

    PubMed Central

    Dikhit, Manas Ranjan; Nathasharma, Yangya Prasad; Patel, Lelin; Rana, Sindhu Prava; Sahoo, Ganesh Chandra; Das, Pradeep

    2011-01-01

    A complete understanding of different protein functional families and template information opens new avenues for novel drug development. Protein identification and analysis software performs a central role in the investigation of proteins and leads to the development of refined database for description of proteins of different Leishmania strains. There are certain databases for different strains that lack template information and functional family annotation. Rajendra Memorial Research Institute of Medical Sciences (RMRIMS) has developed a web-based unique database to provide information about functional families of different proteins and its template information in different Leishmania species. Based on the template information users can model the tertiary structure of protein. The database facilitates significant relationship between template information and possible protein functional families assigned to different proteins by SVMProt. This database is designed to provide comprehensive descriptions of certain important proteins found in four different species of Leishmania i.e. L. donovani, L. infantum, L. major and L. braziliensis. A specific characterization information table provides information related to species and specific functional families. This database aims to be a resource for scientists working on proteomics. The database is freely available at http://biomedinformri.org/calp/. PMID:21464840

  13. West European public opinion on security: a comparative analysis

    SciTech Connect

    Brown, R.M.

    1985-01-01

    This dissertation empirically explored the security opinion formation process within the British, French, and West Germany populations. Basic theory assumed two sources of security opinion. First, the actions and official statements of political elites furnish strong but transient influence in forming public attitudes, which, in turn, are a basis for opinions. Second, attributes predispose individuals to adopt attitudes, and thus opinions. The influence of attributes is less forceful than are elite cues, but attributes give some stability to opinion - attributes being immutable or slow to change. The analysis of the influence of attributes and attitudes on opinion was based on results of 1976-1982 public opinion surveys. The findings both supported the assumptions on the opinion forming roles of attributes and elite cues and addressed related issues of current interest. The probable security predisposition of the contemporary West European successor generation, an altered role for Europeans holding post material values, and the functional - as opposed to geographic - nature of the supranationalist attitude were among major topics addressed. The dissertation ends with a prediction on mid-term stability and change in the role and functioning of the Atlantic alliance.

  14. Comparative analysis of HOG pathway proteins to generate hypotheses for functional analysis.

    PubMed

    Krantz, Marcus; Becit, Evren; Hohmann, Stefan

    2006-03-01

    Comparative genomics allows comparison of different proteins that execute presumably identical functions in different organisms. In contrast to paralogues, orthologues per definition perform the same function and interact with the same partners and, consequently, should display conservation in all these properties. We have employed 20 fungal genomes to analyse key components of the high osmolarity glycerol signalling pathway of Saccharomyces cerevisiae. Among the proteins scrutinised are a complete phosphotransfer module, a MAP kinase, two scaffold proteins, one of which is also a MAPKK, and two transcription factors. Sequence alignments, domain structure and size analysis, combined with the rich information available in the literature, allowed us to probe previous structural and functional studies and to generate hypotheses for future experimental studies. Although certain domains are too highly conserved across fungal species for meaningful comparative studies, others, like interaction domains, can be studied in closely related species. Moreover, putative functionally relevant sites for protein modifications can be identified in such comparative studies. We provide several relevant examples and present a number of previously un(der)characterised domains of potential functional significance in osmosensing and signal transduction. We propose that any functional protein analysis in fungi should make use of the unique resource that fungal genome sequences offer.

  15. Comparative Analysis of Six Lagerstroemia Complete Chloroplast Genomes

    PubMed Central

    Xu, Chao; Dong, Wenpan; Li, Wenqing; Lu, Yizeng; Xie, Xiaoman; Jin, Xiaobai; Shi, Jipu; He, Kaihong; Suo, Zhili

    2017-01-01

    Crape myrtles are economically important ornamental trees of the genus Lagerstroemia L. (Lythraceae), with a distribution from tropical to northern temperate zones. They are positioned phylogenetically to a large subclade of rosids (in the eudicots) which contain more than 25% of all the angiosperms. They commonly bloom from summer till fall and are of significant value in city landscape and environmental protection. Morphological traits are shared inter-specifically among plants of Lagerstroemia to certain extent and are also influenced by environmental conditions and different developmental stages. Thus, classification of plants in Lagerstroemia at species and cultivar levels is still a challenging task. Chloroplast (cp) genome sequences have been proven to be an informative and valuable source of cp DNA markers for genetic diversity evaluation. In this study, the complete cp genomes of three Lagerstroemia species were newly sequenced, and three other published cp genome sequences of Lagerstroemia were retrieved for comparative analyses in order to obtain an upgraded understanding of the application value of genetic information from the cp genomes. The six cp genomes ranged from 152,049 bp (L. subcostata) to 152,526 bp (L. speciosa) in length. We analyzed nucleotide substitutions, insertions/deletions, and simple sequence repeats in the cp genomes, and discovered 12 relatively highly variable regions that will potentially provide plastid markers for further taxonomic, phylogenetic, and population genetics studies in Lagerstroemia. The phylogenetic relationships of the Lagerstroemia taxa inferred from the datasets from the cp genomes obtained high support, indicating that cp genome data may be useful in resolving relationships in this genus. PMID:28154574

  16. Comparative in vitro analysis of topical hemostatic agents.

    PubMed

    Wagner, W R; Pachence, J M; Ristich, J; Johnson, P C

    1996-12-01

    Hemostatic agents are broadly utilized across the surgical specialties. While specific characteristics desirable for individual applications may vary, these agents generally are expected to aid the patient's coagulation system in the rapid development of an occlusive clot. Six commonly utilized hemostatic agents were quantitatively compared in terms of their ability to mediate platelet aggregation, deposition and activation, and initiate gross clot formation in a series of in vitro tests. Three types of collagen sponges (Actifoam, Helistat, Instat), microfibrillar collagen (Avitene), a gelatin sponge (Gelfoam), and oxidized regenerated cellulose (Surgicel) were studied. Platelet aggregation: Citrated platelet rich plasma (PRP) was contacted with hemostatic agents both with and without thrombin in a stirred cuvette and the platelet count was measured over 5 min. Platelet deposition: To approximate arterial wounds, PRP was perfused in a controlled manner through hemostatic agents, and the effluent platelet count was measured over time. Platelet activation: ATP secretion from PRP contacted with hemostatic agents in a stirred cuvette was measured at 1 and 5 min. Clot formation: The clotting time of nonanticoagulated whole blood contacted with the hemostatic agents was measured. Materials which depleted platelets most rapidly and effectively in the perfusion system (Avitene, Helistat, and Actifoam) were also the most effective inducers of platelet aggregation and secretion. Clot formation (likely to be platelet dependent) was also more rapid in this group. An overall activity ranking combined the relative performance of each hemostatic agent on the various tests: Actifoam approximately Avitene > Helistat > Gelfoam > Instat > Surgicel. The activity ranking generally reflects the materials used in these agents (collagen > gelatin > oxidized regenerated cellulose), as well as their processing (chemical crosslinking in collagen sponges may lower activity). Such in vitro

  17. Array comparative genomic hybridization analysis of olfactory neuroblastoma.

    PubMed

    Guled, Mohamed; Myllykangas, Samuel; Frierson, Henry F; Mills, Stacey E; Knuutila, Sakari; Stelow, Edward B

    2008-06-01

    Olfactory neuroblastoma is an unusual neuroectodermal malignancy, which is thought to arise at the olfactory membrane of the sinonasal tract. Due to its rarity, little is understood regarding its molecular and cytogenetic abnormalities. The aim of the current study is to identify specific DNA copy number changes in olfactory neuroblastoma. Thirteen dissected tissue samples were analyzed using array comparative genomic hybridization. Our results show that gene copy number profiles of olfactory neuroblastoma samples are complex. The most frequent changes included gains at 7q11.22-q21.11, 9p13.3, 13q, 20p/q, and Xp/q, and losses at 2q31.1, 2q33.3, 2q37.1, 6q16.3, 6q21.33, 6q22.1, 22q11.23, 22q12.1, and Xp/q. Gains were more frequent than losses, and high-stage tumors showed more alterations than low-stage olfactory neuroblastoma. Frequent changes in high-stage tumors were gains at 13q14.2-q14.3, 13q31.1, and 20q11.21-q11.23, and loss of Xp21.1 (in 66% of cases). Gains at 5q35, 13q, and 20q, and losses at 2q31.1, 2q33.3, and 6q16-q22, were present in 50% of cases. The identified regions of gene copy number change have been implicated in a variety of tumors, especially carcinomas. In addition, our results indicate that gains in 20q and 13q may be important in the progression of this cancer, and that these regions possibly harbor genes with functional relevance in olfactory neuroblastoma.

  18. Adrenocortical adenoma and carcinoma: histopathological and molecular comparative analysis.

    PubMed

    Stojadinovic, Alexander; Brennan, Murray F; Hoos, Axel; Omeroglu, Atilla; Leung, Denis H Y; Dudas, Maria E; Nissan, Aviram; Cordon-Cardo, Carlos; Ghossein, Ronald A

    2003-08-01

    We compared histomorphological features and molecular expression profiles of adrenocortical adenomas (ACAd) and carcinomas (ACCa). A critical histopathological review (mean, 11 slides per patient) was conducted of 37 ACAd and 67 ACCa. Paraffin-embedded tissue cores of ACAd (n = 33) and ACCa (n = 38) were arrayed in triplicate on tissue microarrays. Expression profiles of p53, mdm-2, p21, Bcl-2, cyclin D1, p27, and Ki-67 were investigated by immunohistochemistry and correlated with histopathology and patient outcome using standard statistical methodology. Median follow-up period was 5 years. Tumor necrosis, atypical mitoses, and >1 mitosis per 50 high-power fields were factors that were highly specific for ACCa (P <.001). Number (0 to 4) of unfavorable markers [Ki-67 (+), p21 (+), p27 (+), mdm-2(-)] expressed was significantly associated with mitotic activity and morphologic index (i.e., number of adverse morphologic features) and highly predictive of malignancy (P <.001). Ki-67 overexpression occurred in 0 ACAd and 36% ACCa (P <.001) and was significantly associated with mitotic rate and unfavorable morphologic index (P <.001). Tumor necrosis, atypical mitoses, >5 mitoses per 50 high-power fields, sinusoidal invasion, histologic index of >5, and presence of more than two unfavorable molecular markers were associated significantly with metastasis in ACCa. Well-established histopathologic criteria and Ki-67 can specifically distinguish ACCAd from ACCa. Tumor cell proliferation (Ki-67) correlates with mitotic activity and morphologic index. Tumor morphology is a better predictor of metastatic risk in ACCa than current immunohistochemistry-detected cell cycle regulatory and proliferation-associated proteins.

  19. Comparative analysis of human and bovine teeth: radiographic density.

    PubMed

    Tanaka, Jefferson Luis Oshiro; Medici Filho, Edmundo; Salgado, José Antônio Pereira; Salgado, Miguel Angel Castillo; Moraes, Luiz Cesar de; Moraes, Mari Eli Leonelli de; Castilho, Julio Cezar de Melo

    2008-01-01

    Since bovine teeth have been used as substitutes for human teeth in in vitro dental studies, the aim of this study was to compare the radiographic density of bovine teeth with that of human teeth to evaluate their usability for radiographic studies. Thirty bovine and twenty human teeth were cut transversally in 1 millimeter-thick slices. The slices were X-rayed using a digital radiographic system and an intraoral X-ray machine at 65 kVp and 7 mA. The exposure time (0.08 s) and the target-sensor distance (40 cm) were standardized for all the radiographs. The radiographic densities of the enamel, coronal dentin and radicular dentin of each slice were obtained separately using the 'histogram' tool of Adobe Photoshop 7.0 software. The mean radiographic densities of the enamel, coronal dentin and radicular dentin were calculated by the arithmetic mean of the slices of each tooth. One-way ANOVA demonstrated statistically significant differences for the densities of bovine and human enamel (p < 0.05) and for bovine and human coronal dentin (p < 0.05). No statistically significant differences were found for the bovine and human radicular dentin (p > 0.05). Based on the results, the authors concluded that: a) the radiographic density of bovine enamel is significantly higher than that of human enamel; b) the radiodensity of bovine coronal dentin is statistically lower than the radiodensity of human coronal dentin; bovine radicular dentin is also less radiodense than human radicular dentin, although this difference was not statistically significant; c) bovine teeth should be used with care in radiographic in vitro studies.

  20. Comparative and demographic analysis of orang-utan genomes.

    PubMed

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

    2011-01-27

    'Orang-utan' is derived from a Malay term meaning 'man of the forest' and aptly describes the southeast Asian great apes native to Sumatra and Borneo. The orang-utan species, Pongo abelii (Sumatran) and Pongo pygmaeus (Bornean), are the most phylogenetically distant great apes from humans, thereby providing an informative perspective on hominid evolution. Here we present a Sumatran orang-utan draft genome assembly and short read sequence data from five Sumatran and five Bornean orang-utan genomes. Our analyses reveal that, compared to other primates, the orang-utan genome has many unique features. Structural evolution of the orang-utan genome has proceeded much more slowly than other great apes, evidenced by fewer rearrangements, less segmental duplication, a lower rate of gene family turnover and surprisingly quiescent Alu repeats, which have played a major role in restructuring other primate genomes. We also describe a primate polymorphic neocentromere, found in both Pongo species, emphasizing the gradual evolution of orang-utan genome structure. Orang-utans have extremely low energy usage for a eutherian mammal, far lower than their hominid relatives. Adding their genome to the repertoire of sequenced primates illuminates new signals of positive selection in several pathways including glycolipid metabolism. From the population perspective, both Pongo species are deeply diverse; however, Sumatran individuals possess greater diversity than their Bornean counterparts, and more species-specific variation. Our estimate of Bornean/Sumatran speciation time, 400,000 years ago, is more recent than most previous studies and underscores the complexity of the orang-utan speciation process. Despite a smaller modern census population size, the Sumatran effective population size (N(e)) expanded exponentially relative to the ancestral N(e) after the split, while Bornean N(e) declined over the same period. Overall, the resources and analyses presented here offer new

  1. 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

  2. Comparative Analysis of Amaryllidaceae Alkaloids from Three Lycoris Species.

    PubMed

    Tian, Yongqiang; Zhang, Chunyun; Guo, Mingquan

    2015-12-07

    The major active constituents from Amaryllidaceae family were reported to be Amaryllidaceae alkaloids (AAs), which exhibited a wide spectrum of biological activities, such as anti-tumor, anti-viral, and acetyl-cholinesterase-inhibitory activities. In order to better understand their potential as a source of bioactive AAs and the phytochemical variations among three different species of Lycoris herbs, the HPLC fingerprint profiles of Lycoris aurea (L. aurea), L. radiata, and L. guangxiensis were firstly determined and compared using LC-UV and LC-MS/MS. As a result, 39 peaks were resolved and identified as AAs, of which nine peaks were found in common for all these three species, while the other 30 peaks could be revealed as characteristic AAs for L. aurea, L. radiata and L. guangxiensis, respectively. Thus, these AAs can be used as chemical markers for the identification and quality control of these plant species. To further reveal correlations between chemical components and their pharmaceutical activities of these species at the molecular level, the bioactivities of the total AAs from the three plant species were also tested against HepG2 cells with the inhibitory rate at 78.02%, 84.91% and 66.81% for L. aurea, L. radiata and L. guangxiensis, respectively. This study firstly revealed that the three species under investigation were different not only in the types of AAs, but also in their contents, and both contributed to their pharmacological distinctions. To the best of our knowledge, the current research provides the most detailed phytochemical profiles of AAs in these species, and offers valuable information for future valuation and exploitation of these medicinal plants.

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. 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

  9. Analysis of T-RFLP data using analysis of variance and ordination methods: a comparative study.

    PubMed

    Culman, S W; Gauch, H G; Blackwood, C B; Thies, J E

    2008-09-01

    The analysis of T-RFLP data has developed considerably over the last decade, but there remains a lack of consensus about which statistical analyses offer the best means for finding trends in these data. In this study, we empirically tested and theoretically compared ten diverse T-RFLP datasets derived from soil microbial communities using the more common ordination methods in the literature: principal component analysis (PCA), nonmetric multidimensional scaling (NMS) with Sørensen, Jaccard and Euclidean distance measures, correspondence analysis (CA), detrended correspondence analysis (DCA) and a technique new to T-RFLP data analysis, the Additive Main Effects and Multiplicative Interaction (AMMI) model. Our objectives were i) to determine the distribution of variation in T-RFLP datasets using analysis of variance (ANOVA), ii) to determine the more robust and informative multivariate ordination methods for analyzing T-RFLP data, and iii) to compare the methods based on theoretical considerations. For the 10 datasets examined in this study, ANOVA revealed that the variation from Environment main effects was always small, variation from T-RFs main effects was large, and variation from T-RFxEnvironment (TxE) interactions was intermediate. Larger variation due to TxE indicated larger differences in microbial communities between environments/treatments and thus demonstrated the utility of ANOVA to provide an objective assessment of community dissimilarity. The comparison of statistical methods typically yielded similar empirical results. AMMI, T-RF-centered PCA, and DCA were the most robust methods in terms of producing ordinations that consistently reached a consensus with other methods. In datasets with high sample heterogeneity, NMS analyses with Sørensen and Jaccard distance were the most sensitive for recovery of complex gradients. The theoretical comparison showed that some methods hold distinct advantages for T-RFLP analysis, such as estimations of variation

  10. 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

  11. 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.

  12. Comparative analysis of tissue reactions to anesthetic solutions: histological analysis in subcutaneous tissue of rats.

    PubMed Central

    Ribeiro, Paulo Domingos; Sanches, Marcio Giampietro; Okamoto, Tetuo

    2003-01-01

    Postanesthetic pain is a relatively common complication after local anesthesia. This complication may be caused by the anesthetic technique or by the anesthetic solution used. Tissue reactions induced by the anesthetic solutions may be one of the factors resulting in pain after anesthesia. The objective of this study was to comparatively analyze tissue reactions induced by different anesthetic solutions in the subcutaneous tissue of rats. The following solutions were utilized: 2% lidocaine without vasoconstrictor; a 0.5% bupivacaine solution with 1:200,000 adrenaline; a 4% articaine solution and 2% mepivacaine, both with 1:100,000 adrenaline; and a 0.9% sodium chloride solution as a control. Sterilized absorbent paper cones packed inside polyethylene tubes were soaked in the solutions and implanted in the subcutaneous region. The sacrifice periods were 1, 2, 5, and 10 days after surgery. The specimens were prepared and stained with hematoxylin and eosin for histological analysis. The results showed that there is a difference in tissue irritability produced by the local anesthetic solutions. The results also showed that there is no relation between the concentration of the drug and the inflammatory intensity, that the mepivacaine and articaine solutions promoted less inflammatory reaction than the bupivacaine, and that the lidocaine solution produced the least intense inflammation. Images Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 Figure 9 Figure 10 Figure 11 PMID:14959905

  13. 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.

  14. 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…

  15. The Effects of Attrition on Baseline Comparability in Randomized Experiments in Education: A Meta-Analysis

    ERIC Educational Resources Information Center

    Valentine, Jeffrey C.; McHugh, Cathleen M.

    2007-01-01

    Using meta-analysis, randomized experiments in education that either clearly did or clearly did not experience student attrition were examined for the baseline comparability of groups. Results from 35 studies suggested that after attrition, the observed measures of baseline comparability of groups did not differ more than would be expected given…

  16. 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…

  17. 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…

  18. Postmodernism Debates and Comparative Education: A Critical Discourse Analysis. Essay Review.

    ERIC Educational Resources Information Center

    Mehta, Sonia; Ninnes, Peter

    2003-01-01

    Detailed discourse analysis is presented for two articles that suggest that postmodernism has little to offer comparative education and should be resisted. The two texts, focusing on postmodernism as the antithesis of comparative education and on the "lost promise" of postmodernism, demonstrate the use of language to convey messages that limit or…

  19. 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…

  20. 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…

  1. Comparing the Classification Accuracy among Nonparametric, Parametric Discriminant Analysis and Logistic Regression Methods.

    ERIC Educational Resources Information Center

    Ferrer, Alvaro J. Arce; Wang, Lin

    This study compared the classification performance among parametric discriminant analysis, nonparametric discriminant analysis, and logistic regression in a two-group classification application. Field data from an organizational survey were analyzed and bootstrapped for additional exploration. The data were observed to depart from multivariate…

  2. 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…

  3. 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…

  4. 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.

  5. 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.

  6. 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.

  7. e-Fungi: a data resource for comparative analysis of fungal genomes

    PubMed Central

    Hedeler, Cornelia; Wong, Han Min; Cornell, Michael J; Alam, Intikhab; Soanes, Darren M; Rattray, Magnus; Hubbard, Simon J; Talbot, Nicholas J; Oliver, Stephen G; Paton, Norman W

    2007-01-01

    Background The number of sequenced fungal genomes is ever increasing, with about 200 genomes already fully sequenced or in progress. Only a small percentage of those genomes have been comprehensively studied, for example using techniques from functional genomics. Comparative analysis has proven to be a useful strategy for enhancing our understanding of evolutionary biology and of the less well understood genomes. However, the data required for these analyses tends to be distributed in various heterogeneous data sources, making systematic comparative studies a cumbersome task. Furthermore, comparative analyses benefit from close integration of derived data sets that cluster genes or organisms in a way that eases the expression of requests that clarify points of similarity or difference between species. Description To support systematic comparative analyses of fungal genomes we have developed the e-Fungi database, which integrates a variety of data for more than 30 fungal genomes. Publicly available genome data, functional annotations, and pathway information has been integrated into a single data repository and complemented with results of comparative analyses, such as MCL and OrthoMCL cluster analysis, and predictions of signaling proteins and the sub-cellular localisation of proteins. To access the data, a library of analysis tasks is available through a web interface. The analysis tasks are motivated by recent comparative genomics studies, and aim to support the study of evolutionary biology as well as community efforts for improving the annotation of genomes. Web services for each query are also available, enabling the tasks to be incorporated into workflows. Conclusion The e-Fungi database provides fungal biologists with a resource for comparative studies of a large range of fungal genomes. Its analysis library supports the comparative study of genome data, functional annotation, and results of large scale analyses over all the genomes stored in the database

  8. Highly comparative time-series analysis: the empirical structure of time series and their methods.

    PubMed

    Fulcher, Ben D; Little, Max A; Jones, Nick S

    2013-06-06

    The process of collecting and organizing sets of observations represents a common theme throughout the history of science. However, despite the ubiquity of scientists measuring, recording and analysing the dynamics of different processes, an extensive organization of scientific time-series data and analysis methods has never been performed. Addressing this, annotated collections of over 35 000 real-world and model-generated time series, and over 9000 time-series analysis algorithms are analysed in this work. We introduce reduced representations of both time series, in terms of their properties measured by diverse scientific methods, and of time-series analysis methods, in terms of their behaviour on empirical time series, and use them to organize these interdisciplinary resources. This new approach to comparing across diverse scientific data and methods allows us to organize time-series datasets automatically according to their properties, retrieve alternatives to particular analysis methods developed in other scientific disciplines and automate the selection of useful methods for time-series classification and regression tasks. The broad scientific utility of these tools is demonstrated on datasets of electroencephalograms, self-affine time series, heartbeat intervals, speech signals and others, in each case contributing novel analysis techniques to the existing literature. Highly comparative techniques that compare across an interdisciplinary literature can thus be used to guide more focused research in time-series analysis for applications across the scientific disciplines.

  9. Highly comparative time-series analysis: the empirical structure of time series and their methods

    PubMed Central

    Fulcher, Ben D.; Little, Max A.; Jones, Nick S.

    2013-01-01

    The process of collecting and organizing sets of observations represents a common theme throughout the history of science. However, despite the ubiquity of scientists measuring, recording and analysing the dynamics of different processes, an extensive organization of scientific time-series data and analysis methods has never been performed. Addressing this, annotated collections of over 35 000 real-world and model-generated time series, and over 9000 time-series analysis algorithms are analysed in this work. We introduce reduced representations of both time series, in terms of their properties measured by diverse scientific methods, and of time-series analysis methods, in terms of their behaviour on empirical time series, and use them to organize these interdisciplinary resources. This new approach to comparing across diverse scientific data and methods allows us to organize time-series datasets automatically according to their properties, retrieve alternatives to particular analysis methods developed in other scientific disciplines and automate the selection of useful methods for time-series classification and regression tasks. The broad scientific utility of these tools is demonstrated on datasets of electroencephalograms, self-affine time series, heartbeat intervals, speech signals and others, in each case contributing novel analysis techniques to the existing literature. Highly comparative techniques that compare across an interdisciplinary literature can thus be used to guide more focused research in time-series analysis for applications across the scientific disciplines. PMID:23554344

  10. HARDMAN Comparability Analysis Methodology Guide. Volume 2. Problem Definition. Step 1 - Systems Analysis

    DTIC Science & Technology

    1985-04-01

    performance measure and a performance standard. Functions and sub-function provided earlier are at a high level of abstraction, while performance... Measures and Standards 1C-1 Distinctions Between the Predecessor, Baseline Comparison, and Proposed Systems 1.4-1 EIC Assignment Example 1.4-2 TB 750...analysis flow diagrams depict, at a high level, the general flow of data and the interrelationship of the individual HAROMAN substeps (see Volume I

  11. 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…

  12. A Comparative Analysis of the Educational Priorities and Capacity of Rural School Districts

    ERIC Educational Resources Information Center

    Wallin, Dawn

    2008-01-01

    This article outlines a comparative analysis of three studies (one provincial, and two school division) that examined the congruence between the priorities of the Manitoba government's "Kindergarten to Senior 4 (K-S4) Education Agenda for Student Success" and priorities identified by stakeholders in a rural Manitoba (Canada) school…

  13. Comparative Evaluation of Two Superior Stopping Rules for Hierarchical Cluster Analysis.

    ERIC Educational Resources Information Center

    Atlas, Robert S.; Overall, John E.

    1994-01-01

    A split-sample replication stopping rule for hierarchical cluster analysis is compared with the internal criterion previously found superior by Milligan and Cooper (1985) in their comparison of 30 different procedures. Situations under which the methods are equivalent or not equally useful are discussed. (SLD)

  14. 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)…

  15. 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…

  16. 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…

  17. 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,…

  18. The Family Support System: Comparative Analysis of Research Projects Funded by the Administration on Aging.

    ERIC Educational Resources Information Center

    Hofer, Andrew

    This paper presents a comparative analysis of eight research projects funded by the Administration on Aging during the 1970s which focused on the family as caregivers and support systems for elderly relatives. A brief description is provided for each project analyzed in this report as well as highlights of major findings, including that the family…

  19. 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…

  20. The Regulation of Broadcasting in the United States: A Comparative Analysis. Publication No. 75-6.

    ERIC Educational Resources Information Center

    Mosco, Vincent

    An analysis of the American system of broadcasting and its regulation by the Federal Communications Commission sought to compare decision-making processes and outcomes in four cases involving innovations in the broadcasting market. The innovations, which were chosen to exemplify common elements in the commission's decision-making, included…

  1. Comparative Analysis of Pedagogical Technologies in the Context of Future Agrarians' Multicultural Education in the USA

    ERIC Educational Resources Information Center

    Kravets, Ruslan

    2015-01-01

    In the article the comparative analysis of pedagogical technologies in the USA has been carried out in the context of future agrarians' multicultural education. The essence of traditional and innovative pedagogical technologies and the peculiarities of their realization at higher educational establishments have been viewed. The expediency of…

  2. 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…

  3. 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…

  4. 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…

  5. 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…

  6. Information Operations Versus Civilian Marketing and Advertising: A Comparative Analysis to Improve IO Planning and Strategy

    DTIC Science & Technology

    2008-03-01

    concepts, relevant to IO, which are known successful marketing practices. Successful marketing strategy includes the basic “ 4Ps of marketing ...OPERATIONS VERSUS CIVILIAN MARKETING AND ADVERTISING: A COMPARATIVE ANALYSIS TO IMPROVE IO PLANNING AND STRATEGY by Dan Chilton March 2008... strategy . The objective of this work is to analyze and develop the concept of utilizing civilian advertising and marketing fundamentals for

  7. Survey Sequencing and Comparative Analysis of the Elephant Shark (Callorhinchus milii) Genome

    PubMed Central

    Venkatesh, Byrappa; Kirkness, Ewen F; Loh, Yong-Hwee; Halpern, Aaron L; Lee, Alison P; Johnson, Justin; Dandona, Nidhi; Viswanathan, Lakshmi D; Tay, Alice; Venter, J. Craig; Strausberg, Robert L; Brenner, Sydney

    2007-01-01

    Owing to their phylogenetic position, cartilaginous fishes (sharks, rays, skates, and chimaeras) provide a critical reference for our understanding of vertebrate genome evolution. The relatively small genome of the elephant shark, Callorhinchus milii, a chimaera, makes it an attractive model cartilaginous fish genome for whole-genome sequencing and comparative analysis. Here, the authors describe survey sequencing (1.4× coverage) and comparative analysis of the elephant shark genome, one of the first cartilaginous fish genomes to be sequenced to this depth. Repetitive sequences, represented mainly by a novel family of short interspersed element–like and long interspersed element–like sequences, account for about 28% of the elephant shark genome. Fragments of approximately 15,000 elephant shark genes reveal specific examples of genes that have been lost differentially during the evolution of tetrapod and teleost fish lineages. Interestingly, the degree of conserved synteny and conserved sequences between the human and elephant shark genomes are higher than that between human and teleost fish genomes. Elephant shark contains putative four Hox clusters indicating that, unlike teleost fish genomes, the elephant shark genome has not experienced an additional whole-genome duplication. These findings underscore the importance of the elephant shark as a critical reference vertebrate genome for comparative analysis of the human and other vertebrate genomes. This study also demonstrates that a survey-sequencing approach can be applied productively for comparative analysis of distantly related vertebrate genomes. PMID:17407382

  8. 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…

  9. 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…

  10. 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…

  11. 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…

  12. Comparing multiple competing interventions in the absence of randomized trials using clinical risk-benefit analysis

    PubMed Central

    2012-01-01

    Background To demonstrate the use of risk-benefit analysis for comparing multiple competing interventions in the absence of randomized trials, we applied this approach to the evaluation of five anticoagulants to prevent thrombosis in patients undergoing orthopedic surgery. Methods Using a cost-effectiveness approach from a clinical perspective (i.e. risk benefit analysis) we compared thromboprophylaxis with warfarin, low molecular weight heparin, unfractionated heparin, fondaparinux or ximelagatran in patients undergoing major orthopedic surgery, with sub-analyses according to surgery type. Proportions and variances of events defining risk (major bleeding) and benefit (thrombosis averted) were obtained through a meta-analysis and used to define beta distributions. Monte Carlo simulations were conducted and used to calculate incremental risks, benefits, and risk-benefit ratios. Finally, net clinical benefit was calculated for all replications across a range of risk-benefit acceptability thresholds, with a reference range obtained by estimating the case fatality rate - ratio of thrombosis to bleeding. Results The analysis showed that compared to placebo ximelagatran was superior to other options but final results were influenced by type of surgery, since ximelagatran was superior in total knee replacement but not in total hip replacement. Conclusions Using simulation and economic techniques we demonstrate a method that allows comparing multiple competing interventions in the absence of randomized trials with multiple arms by determining the option with the best risk-benefit profile. It can be helpful in clinical decision making since it incorporates risk, benefit, and personal risk acceptance. PMID:22233221

  13. 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…

  14. 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

  15. 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…

  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. Comparative Analysis of Leasing versus Buying General Purpose Vehicles (Sedan) in the Korean Air Force

    DTIC Science & Technology

    2002-03-01

    COMPARATIVE ANALYSIS OF LEASING VERSUS BUYING GENERAL PURPOSE VEHICLES (SEDAN) IN THE KOREAN AIR FORCE...leasing versus buying vehicle study started from the recognition of this situation in which ROKAF needs an efficient and effective vehicle procurement...versus buying vehicles , which has been used in buying versus leasing decision. This research analyzed two variables, logistics benefits and costs, and

  18. 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…

  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. 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

  1. Genome Sequence, Comparative Analysis, and Evolutionary Insights into Chitinases of Entomopathogenic Fungus Hirsutella thompsonii

    PubMed Central

    Agrawal, Yamini; Khatri, Indu; Subramanian, Srikrishna; Shenoy, Belle Damodara

    2015-01-01

    Hirsutella thompsonii (Ht) is a fungal pathogen of acarines and the primary cause of epizootics among mites. The draft genomes of two isolates of Ht (MTCC 3556: Ht3, 34.6 Mb and MTCC 6686: Ht6, 34.7 Mb) are presented and compared with the genomes of Beauveria bassiana (Bb) ARSEF 2860 and Ophiocordyceps sinensis (Os) CO18. Comparative analysis of carbohydrate active enzymes, pathogen–host interaction genes, metabolism-associated genes, and genes involved in biosynthesis of secondary metabolites in the four genomes was carried out. Reduction in gene family sizes in Ht3 and Os as compared with Ht6 and Bb is observed. Analysis of the mating type genes in Ht reveals the presence of MAT idiomorphs which is suggestive of cryptic sexual traits in Ht. We further identify and classify putative chitinases that may function as virulence factors in fungal entomopathogens due to their role in degradation of arthropod cuticle. PMID:25716828

  2. Protein Dynamics from NMR: The Slowly Relaxing Local Structure Analysis Compared with Model-Free Analysis

    PubMed Central

    Meirovitch, Eva; Shapiro, Yury E.; Polimeno, Antonino; Freed, Jack H.

    2009-01-01

    15N-1H spin relaxation is a powerful method for deriving information on protein dynamics. The traditional method of data analysis is model-free (MF), where the global and local N-H motions are independent and the local geometry is simplified. The common MF analysis consists of fitting single-field data. The results are typically field-dependent, and multi-field data cannot be fit with standard fitting schemes. Cases where known functional dynamics has not been detected by MF were identified by us and others. Recently we applied to spin relaxation in proteins the Slowly Relaxing Local Structure (SRLS) approach which accounts rigorously for mode-mixing and general features of local geometry. SRLS was shown to yield MF in appropriate asymptotic limits. We found that the experimental spectral density corresponds quite well to the SRLS spectral density. The MF formulae are often used outside of their validity ranges, allowing small data sets to be force-fitted with good statistics but inaccurate best-fit parameters. This paper focuses on the mechanism of force-fitting and its implications. It is shown that MF force-fits the experimental data because mode-mixing, the rhombic symmetry of the local ordering and general features of local geometry are not accounted for. Combined multi-field multi-temperature data analyzed by MF may lead to the detection of incorrect phenomena, while conformational entropy derived from MF order parameters may be highly inaccurate. On the other hand, fitting to more appropriate models can yield consistent physically insightful information. This requires that the complexity of the theoretical spectral densities matches the integrity of the experimental data. As shown herein, the SRLS densities comply with this requirement. PMID:16821820

  3. A comparative 2D QSAR study on a series of hydroxamic acid-based histone deacetylase inhibitors vis-à-vis comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA).

    PubMed

    Bajpai, Anubha; Agarwal, Neeraj; Gupta, Satya P

    2014-06-01

    A quantitative structure-activity relationship (QSAR) study was performed on a series of indole amide analogues reported by Dai et al. [Bioorg Med Chem Lett (2003), 13, 1897-1901] to act as histone deacetylase (HDAC) inhibitors. The multiple regression analysis (MRA) revealed a model showing the significant dependence of the activity on molar refractivity (MR) and global topological charge index (GTCI) of the compounds, suggesting that inhibition of the HDAC by this series of compounds might involve the dispersion interaction with the receptor, where charge transfer between pairs of atoms might greatly help to polarize the molecule. The MRA results were then compared with those obtained by Guo et al. [Bioorg Med Chem (2005), 13, 5424-5434] by comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). It was found that MRA gave as good results and had as good predictive ability as CoMFA and CoMSIA. Besides, MRA was also able to throw the light on the physicochemical properties of the molecules that were involved in drug-receptor interactions, while CoMFA and CoMSIA could not. The dispersion interaction between the molecule and the active site of the receptor is suggested to be the main interaction.

  4. 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.

  5. Provision of family planning services in Tanzania: a comparative analysis of public and private facilities.

    PubMed

    Kakoko, Deodatus C; Ketting, Evert; Kamazima, Switbert R; Ruben, Ruerd

    2012-12-01

    Adherence to the policy guidelines and standards is necessary for family planning services. We compared public and private facilities in terms of provision of family planning services. We analyzed data from health facility questionnaire of the 2006 Tanzania Service Provision Assessment survey, based on 529 health facilities. Majority of public facilities (95.4%) offered family planning services, whereas more than half of private facilities (52.1%) did not offer those. Public facilities were more likely to offer modern contraceptives as compared to private facilities. However, private facilities were more likely to offer counseling on natural methods of family planning [AOR = 2.12 (1.15-3.92), P < or = 0.001]. Public facilities were more likely to report having guidelines or protocols for family planning services and various kinds of visual aids for family planning and STIs when compared to private facilities. This comparative analysis entails the need to enforce the standards of family planning services in Tanzania.

  6. 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.

  7. 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.

  8. A comparative study of multivariable robustness analysis methods as applied to integrated flight and propulsion control

    NASA Technical Reports Server (NTRS)

    Schierman, John D.; Lovell, T. A.; Schmidt, David K.

    1993-01-01

    Three multivariable robustness analysis methods are compared and contrasted. The focus of the analysis is on system stability and performance robustness to uncertainty in the coupling dynamics between two interacting subsystems. Of particular interest is interacting airframe and engine subsystems, and an example airframe/engine vehicle configuration is utilized in the demonstration of these approaches. The singular value (SV) and structured singular value (SSV) analysis methods are compared to a method especially well suited for analysis of robustness to uncertainties in subsystem interactions. This approach is referred to here as the interacting subsystem (IS) analysis method. This method has been used previously to analyze airframe/engine systems, emphasizing the study of stability robustness. However, performance robustness is also investigated here, and a new measure of allowable uncertainty for acceptable performance robustness is introduced. The IS methodology does not require plant uncertainty models to measure the robustness of the system, and is shown to yield valuable information regarding the effects of subsystem interactions. In contrast, the SV and SSV methods allow for the evaluation of the robustness of the system to particular models of uncertainty, and do not directly indicate how the airframe (engine) subsystem interacts with the engine (airframe) subsystem.

  9. Comparative process analysis of fullerene production by the arc and the radio-frequency discharge methods.

    PubMed

    Marković, Z; Todorović-Marković, B; Mohai, I; Farkas, Z; Kovats, E; Szepvolgyi, J; Otasević, D; Scheier, P; Feil, S; Romcević, N

    2007-01-01

    In this work, comparative analysis of processes in carbon arc and radio frequency (RF) plasma during fullerene synthesis has been presented. The kinetic model of fullerene formation developed earlier has been verified in both types of plasma reactors. The fullerene yield depended on carbon concentration, velocity of plasma flame and rotational temperature of C2 radicals predominantly. When mean rotational temperature of C2 radicals was 3000 K, the fullerene yield was the highest regardless of the type of used reactor. The zone of fullerene formation is larger significantly in RF plasma reactor compared to arc reactor.

  10. 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.

  11. Comparative estimation of vibrational entropy changes in proteins through normal modes analysis.

    PubMed

    Carrington, Benjamin J; Mancera, Ricardo L

    2004-10-01

    We compare the vibrational entropy changes of proteins calculated using a full and a number of approximate normal modes analysis methods. The vibrational entropy differences for three conformational changes and three protein binding interactions were computed. In general, the approximate methods yield good estimates of the vibrational entropy change in a fraction of the time required by full normal modes analysis. The absolute entropies are either overestimated or greatly underestimated, but the difference is sufficiently accurate for some methods. This indicates that some of the approximate methods can give reasonable estimates of the associated vibrational entropy changes, making them suitable for inclusion in free energy calculations.

  12. 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.

  13. Comparative Analysis of HIV-1 and Murine Leukemia Virus Three-Dimensional Nuclear Distributions

    PubMed Central

    Quercioli, Valentina; Di Primio, Cristina; Casini, Antonio; Mulder, Lubbertus C. F.; Vranckx, Lenard S.; Borrenberghs, Doortje; Gijsbers, Rik; Debyser, Zeger

    2016-01-01

    Recent advances in fluorescence microscopy allow three-dimensional analysis of HIV-1 preintegration complexes in the nuclei of infected cells. To extend this investigation to gammaretroviruses, we engineered a fluorescent Moloney murine leukemia virus (MLV) system consisting of MLV-integrase fused to enhanced green fluorescent protein (MLV-IN-EGFP). A comparative analysis of lentiviral (HIV-1) and gammaretroviral (MLV) fluorescent complexes in the nuclei of infected cells revealed their different spatial distributions. This research tool has the potential to achieve new insight into the nuclear biology of these retroviruses. PMID:26962222

  14. 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.

  15. [Comparative proteome analysis of blood plasma of patients with early-stage chronic cerebral ischemia].

    PubMed

    Kisrieva, Y S; Petushkova, N A; Samenkova, N F; Kuznetsova, G P; Larina, O V; Zavialova, M G; Teryaeva, N B; Belyaev, A Y; Karuzina, I I

    2016-07-01

    In the present study, we explored the technology of liquid chromatography-mass spectrometry (HPLC-MS/MS) for the proteome analysis of blood plasma of patients with early chronic cerebral ischemia. Analysis of mass-spectrometer data carried out in automatic mode using the software Progenesis LS-MS. As a result of this study identified 43 proteins. The differences identified in the study group compared with the control in 7 proteins. It was found that in the early stages of chronic cerebral ischemia proteome changes in blood plasma affect proteins related to the immune system, the system for the maintenance of hemostasis and lipid metabolism.

  16. Comparative Analysis and Approximations of Space -Charge Formation in Langmuir Electrodes Including Temperature Effects.

    NASA Astrophysics Data System (ADS)

    Valdeblànquez, Eder

    2001-10-01

    Eder Valdeblànquez,Universidad del Zulia,Apartado 4011-A 526,Maracaibo,Venezuela. ABSTRACT: In this paper by space charge effect in Langmuir probes are compared for different kind of symmetries; plane, cylindrical and spherical. A detailed analysis is performed here including temperature effects, and therefore kinetic theory is used instead of fluid equations as other authors. The strongly non-linear equations obtained here have been solved first by numerical analysis and later by approximations using Bessel functions. The accuracy of each approximaton is also discussed. Space Charge effects are important in plane geometries than in the case of cylindrical or spherical symmetries.

  17. 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

  18. CAMBer: an approach to support comparative analysis of multiple bacterial strains

    PubMed Central

    2011-01-01

    Background There is a large amount of inconsistency in gene structure annotations of bacterial strains. This inconsistency is a frustrating impedance to effective comparative genomic analysis of bacterial strains in promising applications such as gaining insights into bacterial drug resistance. Results Here, we propose CAMBer as an approach to support comparative analysis of multiple bacterial strains. CAMBer produces what we called multigene families. Each multigene family reveals genes that are in one-to-one correspondence in the bacterial strains, thereby permitting their annotations to be integrated. We present results of our method applied to three human pathogens: Escherichia coli, Mycobacterium tuberculosis and Staphylococcus aureus. Conclusions As a result, more accurate and more comprehensive annotations of the bacterial strains can be produced. PMID:21989220

  19. 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.

  20. Comparative analysis for performance of brown coal combustion in a vortex furnace with improved design

    NASA Astrophysics Data System (ADS)

    Krasinsky, D. V.

    2016-09-01

    Comparative study of 3D numerical simulation of fluid flow and coal-firing processes was applied for flame combustion of Kansk-Achinsk brown coal in a vortex furnace of improved design with bottom injection of secondary air. The analysis of engineering performance of this furnace was carried out for several operational modes as a function of coal grinding fineness and coal input rate. The preferable operational regime for furnace was found.

  1. 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.

  2. [Comparative analysis of phospholipid composition in erythrocytes of mouse-like rodents of different species].

    PubMed

    Shevchenko, O G; Shishkina, L N

    2011-01-01

    Comparative analysis of phospholipid quantitative composition of blood erythrocytes has been performed in white (laboratory mice and rats) and wild (tundra voles) mouse-like rodents. A non-characteristic of mammals low relative content of sphingomyelin is revealed in erythrocyte phospholipids in tundra voles. A hypothesis is put forward that the unique composition of erythrocyte lipids is a peculiar evolutionary developed strategy of adaptation aimed at survival under condition of constant circulation of agents of leptospirosis in populations of this species.

  3. [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.

  4. Evaluating collaborations in comparative effectiveness research: opportunities and challenges for social network analysis.

    PubMed

    Zickafoose, Joseph S; Kimmey, Laura D; Tomas, Amber; Esposito, Dominick; Rich, Eugene

    2014-11-01

    Multidisciplinary, multi-institutional collaboration has become a key feature of comparative effectiveness research (CER), and CER funders have made promotion of these types of collaboration an implicit, and sometimes explicit, goal of funding. An important challenge in evaluating CER programs is understanding if and how different forms of collaboration are associated with successful CER projects. This article explores the potential use of social network analysis to address research questions about the associations between collaboration and the success of CER projects.

  5. 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

  6. A comparative neutron activation analysis study of common generic manipulated and reference medicines commercialized in Brazil.

    PubMed

    Leal, A S; Menezes, M A B C; Rodrigues, R R; Andonie, O; Vermaercke, P; Sneyers, L

    2008-10-01

    In this work, a comparative study of neutron activation analysis (NAA) was performed by the nuclear institutes: CDTN/CNEN-Brazil, CCHEN-Chile and the SCK.CEN-Belgium aiming to investigate some generic, manipulated and reference medicines largely commercialized in Brazil. Some impurities such as: As, Ba, Br, Ce, Co, Cr, Eu, Fe, Hf, Sb, Sc, Sm, Ti and Zn were found, and the heterogeneity of the samples pointed out the lack of an efficient public system of quality control.

  7. Comparative Genome Analysis of Filamentous Fungi Reveals Gene Family Expansions Associated with Fungal Pathogenesis

    PubMed Central

    Soanes, Darren M.; Alam, Intikhab; Cornell, Mike; Wong, Han Min; Hedeler, Cornelia; Paton, Norman W.; Rattray, Magnus; Hubbard, Simon J.; Oliver, Stephen G.; Talbot, Nicholas J.

    2008-01-01

    Fungi and oomycetes are the causal agents of many of the most serious diseases of plants. Here we report a detailed comparative analysis of the genome sequences of thirty-six species of fungi and oomycetes, including seven plant pathogenic species, that aims to explore the common genetic features associated with plant disease-causing species. The predicted translational products of each genome have been clustered into groups of potential orthologues using Markov Chain Clustering and the data integrated into the e-Fungi object-oriented data warehouse (http://www.e-fungi.org.uk/). Analysis of the species distribution of members of these clusters has identified proteins that are specific to filamentous fungal species and a group of proteins found only in plant pathogens. By comparing the gene inventories of filamentous, ascomycetous phytopathogenic and free-living species of fungi, we have identified a set of gene families that appear to have expanded during the evolution of phytopathogens and may therefore serve important roles in plant disease. We have also characterised the predicted set of secreted proteins encoded by each genome and identified a set of protein families which are significantly over-represented in the secretomes of plant pathogenic fungi, including putative effector proteins that might perturb host cell biology during plant infection. The results demonstrate the potential of comparative genome analysis for exploring the evolution of eukaryotic microbial pathogenesis. PMID:18523684

  8. COMPARATIVE ANALYSIS OF MICROARRAY DATA IDENTIFIES COMMON RESPONSES TO CALORIC RESTRICTION AMONG MOUSE TISSUES

    PubMed Central

    Swindell, William R.

    2009-01-01

    Caloric restriction has been extensively investigated as an intervention that both extends lifespan and delays age-related disease in mammals. In mice, much interest has centered on evaluating gene expression changes induced by caloric restriction (CR) in particular tissue types, but the overall systemic effect of CR among multiple tissues has been examined less extensively. This study presents a comparative analysis of microarray datasets that have collectively examined the effects of CR in ten different tissue types (liver, heart, muscle, hypothalamus, hippocampus, white adipose tissue, colon, kidney, lung, cochlea). Using novel methods for comparative analysis of microarray data, detailed comparisons of the effects of CR among tissues are provided, and 28 genes for which expression response to CR is most shared among tissues are identified. These genes characterize common responses to CR, which consist of both activation and inhibition of stress-response pathways. With respect to liver tissue, transcriptional effects of CR exhibited surprisingly little overlap with those of aging, and a variable degree of overlap with the potential CR-mimetic drug resveratrol. These analyses shed light on the systemic transcriptional activity associated with CR diets, and also illustrate new approaches for comparative analysis of microarray datasets in the context of aging biology. PMID:18155270

  9. In silico comparative genome analysis of malaria parasite Plasmodium falciparum and Plasmodium vivax chromosome 4.

    PubMed

    Taherian Fard, Atefeh; Salman, Amna; Kazemi, Bahram; Bokhari, Habib

    2009-06-01

    Malarial parasite has long been a subject of research for a large community of scientists and has yet to be conquered. One of the main obstacles to effectively control this disease is rapidly evolving genetic structure of Plasmodium parasite itself. In this study, we focused on chromosome 4 of the Plasmodium falciparum and Plasmodium vivax species and carried out comparative studies of genes that are responsible for antigenic variation in respective species. Comparative analysis of genes responsible for antigenic variation (var and vir genes in P. falciparum and P. vivax, respectively) showed significant difference in their respective nucleotide sequence lengths as well as amino acid composition. The possible association of exon's length on pathogenecity of respective Plasmodium species was also investigated, and analysis of gene structure showed that on the whole, exon lengths in P. falciparum are larger compared to P. vivax. Analysis of tandem repeats across the genome has shown that the size of repetitive sequences has a direct effect on chromosomes length, which can also be a potential reason for P. falciparum's greater variability and hence pathogenecity than P. vivax.

  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 analysis of Salmonella genomes identifies a metabolic network for escalating growth in the inflamed gut.

    PubMed

    Nuccio, Sean-Paul; Bäumler, Andreas J

    2014-03-18

    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. IMPORTANCE While some Salmonella serovars cause infections that remain localized to the gut, others disseminate throughout the body. Here, we compared Salmonella genomes to identify characteristics that distinguish gastrointestinal from extraintestinal pathogens. We identified a large metabolic network that is functional in gastrointestinal pathogens but decaying in extraintestinal pathogens. While taxonomists have used traits from this network empirically for many decades for the enrichment and biochemical discrimination of Salmonella serovars, our findings suggest that it is part of a "business plan" for growth in the inflamed gastrointestinal tract. By identifying a large metabolic network characteristic of Salmonella serovars associated with gastroenteritis, our in silico analysis provides a blueprint for potential strategies to utilize inflammation-derived nutrients and edge out competing gut microbes.

  12. A comparative analysis of lipid-complexed and liposomal amphotericin B preparations in haematological oncology.

    PubMed

    Clark, A D; McKendrick, S; Tansey, P J; Franklin, I M; Chopra, R

    1998-10-01

    No comparative clinical information on the properties of lipid-associated amphotericin preparations is presently available. In this single-centre retrospective analysis over a 5-year period the indications, efficacy and toxicity of true liposomal amphotericin (AmBisome) were compared with a lipid complexed preparation (Abelcet). In a novel approach APACHE III scores were used in addition to neutrophil counts, disease status and additional immunosuppression to accurately assess the severity of illness in both groups and enable valid comparison. Overall, AmBisome at a median dose of 1.9 mg/kg/d was found to have similar clinical outcome to Abelcet at a median dose of 4.8 mg/kg/d. Nephrotoxicity and electrolyte abnormalities were similar in both groups. Rigors and febrile episodes were more common with Abelcet. Prospective randomized comparative trials are required to clarify the optimum dosages and therapeutic and economic issues associated with these agents.

  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).

  16. MGcV: the microbial genomic context viewer for comparative genome analysis

    PubMed Central

    2013-01-01

    Background Conserved gene context is used in many types of comparative genome analyses. It is used to provide leads on gene function, to guide the discovery of regulatory sequences, but also to aid in the reconstruction of metabolic networks. We present the Microbial Genomic context Viewer (MGcV), an interactive, web-based application tailored to strengthen the practice of manual comparative genome context analysis for bacteria. Results MGcV is a versatile, easy-to-use tool that renders a visualization of the genomic context of any set of selected genes, genes within a phylogenetic tree, genomic segments, or regulatory elements. It is tailored to facilitate laborious tasks such as the interactive annotation of gene function, the discovery of regulatory elements, or the sequence-based reconstruction of gene regulatory networks. We illustrate that MGcV can be used in gene function annotation by visually integrating information on prokaryotic genes, like their annotation as available from NCBI with other annotation data such as Pfam domains, sub-cellular location predictions and gene-sequence characteristics such as GC content. We also illustrate the usefulness of the interactive features that allow the graphical selection of genes to facilitate data gathering (e.g. upstream regions, ID’s or annotation), in the analysis and reconstruction of transcription regulation. Moreover, putative regulatory elements and their corresponding scores or data from RNA-seq and microarray experiments can be uploaded, visualized and interpreted in (ranked-) comparative context maps. The ranked maps allow the interpretation of predicted regulatory elements and experimental data in light of each other. Conclusion MGcV advances the manual comparative analysis of genes and regulatory elements by providing fast and flexible integration of gene related data combined with straightforward data retrieval. MGcV is available at http://mgcv.cmbi.ru.nl. PMID:23547764

  17. Whole genome comparative analysis of channel catfish (Ictalurus punctatus) with four model fish species

    PubMed Central

    2013-01-01

    Background Comparative mapping is a powerful tool to study evolution of genomes. It allows transfer of genome information from the well-studied model species to non-model species. Catfish is an economically important aquaculture species in United States. A large amount of genome resources have been developed from catfish including genetic linkage maps, physical maps, BAC end sequences (BES), integrated linkage and physical maps using BES-derived markers, physical map contig-specific sequences, and draft genome sequences. Application of such genome resources should allow comparative analysis at the genome scale with several other model fish species. Results In this study, we conducted whole genome comparative analysis between channel catfish and four model fish species with fully sequenced genomes, zebrafish, medaka, stickleback and Tetraodon. A total of 517 Mb draft genome sequences of catfish were anchored to its genetic linkage map, which accounted for 62% of the total draft genome sequences. Based on the location of homologous genes, homologous chromosomes were determined among catfish and the four model fish species. A large number of conserved syntenic blocks were identified. Analysis of the syntenic relationships between catfish and the four model fishes supported that the catfish genome is most similar to the genome of zebrafish. Conclusion The organization of the catfish genome is similar to that of the four teleost species, zebrafish, medaka, stickleback, and Tetraodon such that homologous chromosomes can be identified. Within each chromosome, extended syntenic blocks were evident, but the conserved syntenies at the chromosome level involve extensive inter-chromosomal and intra-chromosomal rearrangements. This whole genome comparative map should facilitate the whole genome assembly and annotation in catfish, and will be useful for genomic studies of various other fish species. PMID:24215161

  18. 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

  19. 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

  20. 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

  1. Comparative genomic analysis of Brucella melitensis vaccine strain M5 provides insights into virulence attenuation.

    PubMed

    Jiang, Hai; Du, Pengcheng; 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.

  2. 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

  3. Health and health-related indicators in slum, rural, and urban communities: a comparative analysis

    PubMed Central

    Mberu, Blessing U.; Haregu, Tilahun Nigatu; Kyobutungi, Catherine; Ezeh, Alex C.

    2016-01-01

    Background It is generally assumed that urban slum residents have worse health status when compared with other urban populations, but better health status than their rural counterparts. This belief/assumption is often because of their physical proximity and assumed better access to health care services in urban areas. However, a few recent studies have cast doubt on this belief. Whether slum dwellers are better off, similar to, or worse off as compared with rural and other urban populations remain poorly understood as indicators for slum dwellers are generally hidden in urban averages. Objective The aim of this study was to compare health and health-related indicators among slum, rural, and other urban populations in four countries where specific efforts have been made to generate health indicators specific to slum populations. Design We conducted a comparative analysis of health indicators among slums, non-slums, and all urban and rural populations as well as national averages in Bangladesh, Kenya, Egypt, and India. We triangulated data from demographic and health surveys, urban health surveys, and special cross-sectional slum surveys in these countries to assess differences in health indicators across the residential domains. We focused the comparisons on child health, maternal health, reproductive health, access to health services, and HIV/AIDS indicators. Within each country, we compared indicators for slums with non-slum, city/urban averages, rural, and national indicators. Between-country differences were also highlighted. Results In all the countries, except India, slum children had much poorer health outcomes than children in all other residential domains, including those in rural areas. Childhood illnesses and malnutrition were higher among children living in slum communities compared to those living elsewhere. Although treatment seeking was better among slum children as compared with those in rural areas, this did not translate to better mortality

  4. Comparative analysis of microsatellites in chloroplast genomes of lower and higher plants.

    PubMed

    George, Biju; Bhatt, Bhavin S; Awasthi, Mayur; George, Binu; Singh, Achuit K

    2015-11-01

    Microsatellites, or simple sequence repeats (SSRs), contain repetitive DNA sequence where tandem repeats of one to six base pairs are present number of times. Chloroplast genome sequences have been  shown to possess extensive variations in the length, number and distribution of SSRs. However, a comparative analysis of chloroplast microsatellites is not available. Considering their potential importance in generating genomic diversity, we have systematically analysed the abundance and distribution of simple and compound microsatellites in 164 sequenced chloroplast genomes from wide range of plants. The key findings of these studies are (1) a large number of mononucleotide repeats as compared to SSR(2-6)(di-, tri-, tetra-, penta-, hexanucleotide repeats) are present in all chloroplast genomes investigated, (2) lower plants such as algae show wide variation in relative abundance, density and distribution of microsatellite repeats as compared to flowering plants, (3) longer SSRs are excluded from coding regions of most chloroplast genomes, (4) GC content has a weak influence on number, relative abundance and relative density of mononucleotide as well as SSR(2-6). However, GC content strongly showed negative correlation with relative density (R (2) = 0.5, P < 0.05) and relative abundance (R (2) = 0.6, P < 0.05) of cSSRs. In summary, our comparative studies of chloroplast genomes illustrate the variable distribution of microsatellites and revealed that chloroplast genome of smaller plants possesses relatively more genomic diversity compared to higher plants.

  5. Comparative genomic analysis of Drosophila melanogaster and vector mosquito developmental genes.

    PubMed

    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.

  6. [THE COMPARATIVE ANALYSIS OF TECHNIQUES OF IDENTIFICATION OF CORYNEBACTERIUM NON DIPHTHERIAE].

    PubMed

    Kharseeva, G G; Voronina, N A; Mironov, A Yu; Alutina, E L

    2015-12-01

    The comparative analysis was carried out concerning effectiveness of three techniques of identification of Corynebacterium non diphtheriae: bacteriological, molecular genetic (sequenation on 16SpRNA) andmass-spectrometric (MALDI-ToFMS). The analysis covered 49 strains of Corynebacterium non diphtheriae (C.pseudodiphheriticum, C.amycolatum, C.propinquum, C.falsenii) and 2 strains of Corynebacterium diphtheriae isolated under various pathology form urogenital tract and upper respiratory ways. The corinbacteria were identified using bacteriologic technique, sequenation on 16SpRNA and mass-spectrometric technique (MALDIToF MS). The full concordance of results of species' identification was marked in 26 (51%) of strains of Corynebacterium non diphtheriae at using three analysis techniques; in 43 (84.3%) strains--at comparison of bacteriologic technique with sequenation on 16S pRNA and in 29 (57%)--at mass-spectrometric analysis and sequenation on 16S pRNA. The bacteriologic technique is effective for identification of Corynebacterium diphtheriae. The precise establishment of species belonging of corynebacteria with variable biochemical characteristics the molecular genetic technique of analysis is to be applied. The mass-spectrometric technique (MALDI-ToF MS) requires further renewal of data bases for identifying larger spectrum of representatives of genus Corynebacterium.

  7. Comparative Genome-Wide Analysis of the Malate Dehydrogenase Gene Families in Cotton

    PubMed Central

    Imran, Muhammad; Tang, Kai; Liu, Jin-Yuan

    2016-01-01

    Malate dehydrogenases (MDHs) play crucial roles in the physiological processes of plant growth and development. In this study, 13 and 25 MDH genes were identified from Gossypium raimondii and Gossypium hirsutum, respectively. Using these and 13 previously reported Gossypium arboretum MDH genes, a comparative molecular analysis between identified MDH genes from G. raimondii, G. hirsutum, and G. arboretum was performed. Based on multiple sequence alignments, cotton MDHs were divided into five subgroups: mitochondrial MDH, peroxisomal MDH, plastidial MDH, chloroplastic MDH and cytoplasmic MDH. Almost all of the MDHs within the same subgroup shared similar gene structure, amino acid sequence, and conserved motifs in their functional domains. An analysis of chromosomal localization suggested that segmental duplication played a major role in the expansion of cotton MDH gene families. Additionally, a selective pressure analysis indicated that purifying selection acted as a vital force in the evolution of MDH gene families in cotton. Meanwhile, an expression analysis showed the distinct expression profiles of GhMDHs in different vegetative tissues and at different fiber developmental stages, suggesting the functional diversification of these genes in cotton growth and fiber development. Finally, a promoter analysis indicated redundant but typical cis-regulatory elements for the potential functions and stress activity of many MDH genes. This study provides fundamental information for a better understanding of cotton MDH gene families and aids in functional analyses of the MDH genes in cotton fiber development. PMID:27829020

  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. 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

  10. A comparative analysis of three non-invasive human-machine interfaces for the disabled.

    PubMed

    Ravindra, Vikram; Castellini, Claudio

    2014-01-01

    In the framework of rehabilitation robotics, a major role is played by the human-machine interface (HMI) used to gather the patient's intent from biological signals, and convert them into control signals for the robotic artifact. Surprisingly, decades of research have not yet declared what the optimal HMI is in this context; in particular, the traditional approach based upon surface electromyography (sEMG) still yields unreliable results due to the inherent variability of the signal. To overcome this problem, the scientific community has recently been advocating the discovery, analysis, and usage of novel HMIs to supersede or augment sEMG; a comparative analysis of such HMIs is therefore a very desirable investigation. In this paper, we compare three such HMIs employed in the detection of finger forces, namely sEMG, ultrasound imaging, and pressure sensing. The comparison is performed along four main lines: the accuracy in the prediction, the stability over time, the wearability, and the cost. A psychophysical experiment involving ten intact subjects engaged in a simple finger-flexion task was set up. Our results show that, at least in this experiment, pressure sensing and sEMG yield comparably good prediction accuracies as opposed to ultrasound imaging; and that pressure sensing enjoys a much better stability than sEMG. Given that pressure sensors are as wearable as sEMG electrodes but way cheaper, we claim that this HMI could represent a valid alternative/augmentation to sEMG to control a multi-fingered hand prosthesis.

  11. Comparative genome analysis across a kingdom of eukaryotic organisms: Specialization and diversification in the Fungi

    PubMed Central

    Cornell, Michael J.; Alam, Intikhab; Soanes, Darren M.; Wong, Han Min; Hedeler, Cornelia; Paton, Norman W.; Rattray, Magnus; Hubbard, Simon J.; Talbot, Nicholas J.; Oliver, Stephen G.

    2007-01-01

    The recent proliferation of genome sequencing in diverse fungal species has provided the first opportunity for comparative genome analysis across a eukaryotic kingdom. Here, we report a comparative study of 34 complete fungal genome sequences, representing a broad diversity of Ascomycete, Basidiomycete, and Zygomycete species. We have clustered all predicted protein-encoding gene sequences from these species to provide a means of investigating gene innovations, gene family expansions, protein family diversification, and the conservation of essential gene functions—empirically determined in Saccharomyces cerevisiae—among the fungi. The results are presented with reference to a phylogeny of the 34 fungal species, based on 29 universally conserved protein-encoding gene sequences. We contrast this phylogeny with one based on gene presence and absence and show that, while the two phylogenies are largely in agreement, there are differences in the positioning of some species. We have investigated levels of gene duplication and demonstrate that this varies greatly between fungal species, although there are instances of coduplication in distantly related fungi. We have also investigated the extent of orthology for protein families and demonstrate unexpectedly high levels of diversity among genes involved in lipid metabolism. These analyses have been collated in the e-Fungi data warehouse, providing an online resource for comparative genomic analysis of the fungi. PMID:17984228

  12. Comparative analysis of animal growth: a primate continuum revealed by a new dimensionless growth rate coefficient.

    PubMed

    Vinicius, Lucio; Mumby, Hannah S

    2013-05-01

    The comparative analysis of animal growth still awaits full integration into life-history studies, partially due to the difficulty of defining a comparable measure of growth rate across species. Using growth data from 50 primate species, we introduce a modified "general growth model" and a dimensionless growth rate coefficient β that controls for size scaling and phylogenetic effects in the distribution of growth rates. Our results contradict the prevailing idea that slow growth characterizes primates as a group: the observed range of β values shows that not all primates grow slowly, with galago species exhibiting growth rates similar or above the mammalian average, while other strepsirrhines and most New World monkeys show limited reduction in growth rates. Low growth rate characterizes apes and some papionines. Phylogenetic regressions reveal associations between β and life-history variables, providing tests for theories of primate growth evolution. We also show that primate slow growth is an exclusively postnatal phenomenon. Our study exemplifies how the dimensionless approach promotes the integration of growth rate data into comparative life-history analysis, and demonstrates its potential applicability to other cases of adaptive diversification of animal growth patterns.

  13. 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.

  14. Mapping the field of medical sociology: a comparative analysis of journals.

    PubMed

    Seale, Clive

    2008-07-01

    A comparative keyword analysis of the content of nine leading journals is used to suggest potential new directions for medical sociology. The major British and American journals in sociology and medical sociology tend to publish authors based in their own countries, contrasting with the internationalism of other social science disciplines relevant to health, although Sociology of Health and Illness is an exception to this. Medical sociology journals on both sides of the Atlantic focus on individual experience more than general sociology journals, which focus more on social systems levels of analysis. While journal contents reveal British medical sociology to be relatively atheoretical when compared with British general sociology journals, American medical sociology appears relatively apolitical on the same comparison with American general journals. American journals of sociology publish more quantitative studies than their British equivalents, more studies concerning race and other social divisions in American society, and less work drawing on social constructionist perspectives or that is engaged with social theory. Analysis of health and health care at societal and global levels and a deeper engagement with the political and public issues that concern non-sociologists represents a possible future for a medical sociology that is internationally relevant and outward looking.

  15. 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.

  16. Comparative proteomic analysis of urine and laser microdissected glomeruli in IgA nephropathy.

    PubMed

    Ning, Xiaoyuan; Yin, Zhong; Li, Zuoxiang; Xu, Jiayun; Wang, Linna; Shen, Wanjun; Lu, Yang; Cai, Guangyan; Zhang, Xueguang; Chen, Xiangmei

    2017-01-21

    The purpose of the present study was to identify the differential proteins that synchronously change in urine and glomeruli and could be used to monitor glomerular lesions of IgA nephropathy (IgAN). The proteomes of urine and glomeruli from 4 IgAN patients who were graded III/IV according to the grading system of Lee et al were compared to the urine proteomes of 4 healthy volunteers and the glomeruli proteomes of adjacent normal tissue from 4 patients with renal tumors, respectively. Western blot, enzyme-linked immunosorbent assay and immunofluorescence assay were applied to verify the results of the proteomic analysis. In the proteomic analysis of urine from IgAN patients and healthy volunteers, 714 proteins were identified, with 246 proteins identified as differential proteins. In the proteomic analysis of glomeruli from renal biopsy tissue of IgAN patients and from adjacent normal tissue of patients with renal tumors, 161 proteins were identified altogether, and 20 proteins of these were recognized as differential proteins. After comparatively analyzing the differential proteins identified in the urine and glomeruli, five synchronously changed differential proteins were found: complement C9, Ig kappa chain C region and three cytoskeleton proteins. In summary, our findings indicate that certain immunological indices in urine appear to be associated with glomerular lesions of IgAN. This article is protected by copyright. All rights reserved.

  17. Comparative Analysis of Methanogenic Communities in Different Laboratory-Scale Anaerobic Digesters

    PubMed Central

    Ziganshin, Ayrat M.; Ziganshina, Elvira E.

    2016-01-01

    Comparative analysis of methanogenic archaea compositions and dynamics in 11 laboratory-scale continuous stirred tank reactors fed with different agricultural materials (chicken manure, cattle manure, maize straw, maize silage, distillers grains, and Jatropha press cake) was carried out by analysis of the methyl coenzyme-M reductase α-subunit (mcrA) gene. Various taxa within Methanomicrobiales, Methanobacteriaceae, Methanosarcinaceae, Methanosaetaceae, and Methanomassiliicoccales were detected in the biogas reactors but in different proportions depending on the substrate type utilized as well as various process parameters. Improved coverage and higher taxonomic resolution of methanogens were obtained compared to a previous 16S rRNA gene based study of the same reactors. Some members of the genus Methanoculleus positively correlated with the relative methane content, whereas opposite correlations were found for Methanobacterium. Specific biogas production was found to be significantly correlating with Methanosarcinaceae. Statistical analysis also disclosed that some members of the genus Methanoculleus positively correlated with the ammonia level, whereas the prevalence of Methanocorpusculum, Methanobacterium, and Methanosaeta was negatively correlated with this parameter. These results suggest that the application of methanogenic archaea adapted to specific feedstock might enhance the anaerobic digestion of such waste materials in full-scale biogas reactors. PMID:28074084

  18. Blue copper proteins: a comparative analysis of their molecular interaction properties.

    PubMed Central

    De Rienzo, F.; Gabdoulline, R. R.; Menziani, M. C.; Wade, R. C.

    2000-01-01

    Blue copper proteins are type-I copper-containing redox proteins whose role is to shuttle electrons from an electron donor to an electron acceptor in bacteria and plants. A large amount of experimental data is available on blue copper proteins; however, their functional characterization is hindered by the complexity of redox processes in biological systems. We describe here the application of a semiquantitative method based on a comparative analysis of molecular interaction fields to gain insights into the recognition properties of blue copper proteins. Molecular electrostatic and hydrophobic potentials were computed and compared for a set of 33 experimentally-determined structures of proteins from seven blue copper subfamilies, and the results were quantified by means of similarity indices. The analysis provides a classification of the blue copper proteins and shows that (I) comparison of the molecular electrostatic potentials provides useful information complementary to that highlighted by sequence analysis; (2) similarities in recognition properties can be detected for proteins belonging to different subfamilies, such as amicyanins and pseudoazurins, that may be isofunctional proteins; (3) dissimilarities in interaction properties, consistent with experimentally different binding specificities, may be observed between proteins belonging to the same subfamily, such as cyanobacterial and eukaryotic plastocyanins; (4) proteins with low sequence identity, such as azurins and pseudoazurins, can have sufficient similarity to bind to similar electron donors and acceptors while having different binding specificity profiles. PMID:10975566

  19. Prognosis of Hepatocellular Carcinoma after Liver Transplantation: Comparative Analysis with Partial Hepatectomy

    PubMed Central

    Lee, Kyuho; Lee, Kyoung-Bun; Yi, Nam-Joon; Suh, Kyung-Suk; Jang, Ja-June

    2017-01-01

    Background Liver transplantation (LT) is the treatment of choice for hepatocellular carcinoma (HCC). The aim of this study was to investigate the recurrence rate of HCC after LT and prognostic factors for recurrence by comparing LT with non-transplanted resection. Methods The participants were 338 patients who underwent LT between 1996 and 2012 at Seoul National University Hospital (LT group) and 520 HCC patients who underwent partial hepatectomy between 1995 and 2006 (control group, non-LT group). Results In the LT group, 68 of 338 patients (19.8%) showed relapse, and the recurrence rate was lower than that in the non-LT group (64.9%, 357/520, p < .001). Stratification analysis by American Joint Committee on Cancer (AJCC) stage showed that the stage I-II LT group had a lower recurrence rate than the non-LT group. Univariate comparative analysis demonstrated that multiplicity of tumor, tumor size, gross type, Edmondson- Steiner (ES) nuclear grade, extent of tumor, angioinvasion, AJCC stage, Milan criteria, University of California at San Francisco criteria on explant pathology (all p < .001), positive expression of cytokeratin 19 (p = .002), and preoperative α-fetoprotein (AFP) (p < .001) were predictors of tumor recurrence. In multivariate analysis, LT, preoperative AFP, multiplicity of tumor, extent of tumor, size of tumor, and ES nuclear grade were independent prognostic factors. Conclusions LT might have a protective effect against the late recurrence of stage I-II HCC compared to non-LT, and the prognostic factors for recurrence were similar to previously well-known prognostic factors for HCC. PMID:28013531

  20. A comparative analysis of simulated and observed photosynthetic CO2 uptake in two coniferous forest canopies.

    PubMed

    Ibrom, Andreas; Jarvis, Paul G; Clement, Robert; Morgenstern, Kai; Oltchev, Alexander; Medlyn, Belinda E; Wang, Ying Ping; Wingate, Lisa; Moncrieff, John B; Gravenhorst, Gode

    2006-07-01

    Gross canopy photosynthesis (P(g)) can be simulated with canopy models or retrieved from turbulent carbon dioxide (CO2) flux measurements above the forest canopy. We compare the two estimates and illustrate our findings with two case studies. We used the three-dimensional canopy model MAESTRA to simulate P(g) of two spruce forests differing in age and structure. Model parameter acquisition and model sensitivity to selected model parameters are described, and modeled results are compared with independent flux estimates. Despite higher photon fluxes at the site, an older German Norway spruce (Picea abies L. (Karst.)) canopy took up 25% less CO2 from the atmosphere than a young Scottish Sitka spruce (Picea sitchensis (Bong.) Carr.) plantation. The average magnitudes of P(g) and the differences between the two canopies were satisfactorily represented by the model. The main reasons for the different uptake rates were a slightly smaller quantum yield and lower absorptance of the Norway spruce stand because of a more clumped canopy structure. The model did not represent the scatter in the turbulent CO2 flux densities, which was of the same order of magnitude as the non-photosynthetically-active-radiation-induced biophysical variability in the simulated P(g). Analysis of residuals identified only small systematic differences between the modeled flux estimates and turbulent flux measurements at high vapor pressure saturation deficits. The merits and limitations of comparative analysis for quality evaluation of both methods are discussed. From this analysis, we recommend use of both parameter sets and model structure as a basis for future applications and model development.

  1. Comparative structural and energetic analysis of WW domain-peptide interactions.

    PubMed

    Schleinkofer, Karin; Wiedemann, Urs; Otte, Livia; Wang, Ting; Krause, Gerd; Oschkinat, Hartmut; Wade, Rebecca C

    2004-11-26

    WW domains are small globular protein interaction modules found in a wide spectrum of proteins. They recognize their target proteins by binding specifically to short linear peptide motifs that are often proline-rich. To infer the determinants of the ligand binding propensities of WW domains, we analyzed 42 WW domains. We built models of the 3D structures of the WW domains and their peptide complexes by comparative modeling supplemented with experimental data from peptide library screens. The models provide new insights into the orientation and position of the peptide in structures of WW domain-peptide complexes that have not yet been determined experimentally. From a protein interaction property similarity analysis (PIPSA) of the WW domain structures, we show that electrostatic potential is a distinguishing feature of WW domains and we propose a structure-based classification of WW domains that expands the existent ligand-based classification scheme. Application of the comparative molecular field analysis (CoMFA), GRID/GOLPE and comparative binding energy (COMBINE) analysis methods permitted the derivation of quantitative structure-activity relationships (QSARs) that aid in identifying the specificity-determining residues within WW domains and their ligand-recognition motifs. Using these QSARs, a new group-specific sequence feature of WW domains that target arginine-containing peptides was identified. Finally, the QSAR models were applied to the design of a peptide to bind with greater affinity than the known binding peptide sequences of the yRSP5-1 WW domain. The prediction was verified experimentally, providing validation of the QSAR models and demonstrating the possibility of rationally improving peptide affinity for WW domains. The QSAR models may also be applied to the prediction of the specificity of WW domains with uncharacterized ligand-binding properties.

  2. The Comparative Effectiveness of Outpatient Treatment for Adolescent Substance Abuse: A Meta-Analysis

    PubMed Central

    Tanner-Smith, Emily E.; Wilson, Sandra Jo; Lipsey, Mark W.

    2012-01-01

    Meta-analysis was used to synthesize research on the effects of outpatient treatment on substance use outcomes for adolescents with substance use disorders. An extensive literature search located 45 eligible experimental or quasi-experimental studies reporting 73 treatment-comparison group pairs, with many of the comparison groups also receiving some treatment. The first analysis examined 250 effect sizes for the substance use outcomes of adolescents receiving different types of treatment relative to the respective comparison groups. As a category, family therapy programs were found to be more effective than their comparison conditions, whereas no treatment programs were less effective. However, not all treatment types were compared with each other in the available research, making it difficult to assess the comparative effectiveness of the different treatments. To provide a more differentiated picture of the relative improvement in substance use outcomes for different treatments, a second analysis examined 311 pre-post effect sizes measuring changes in substance use for adolescents in the separate treatment and comparison arms of the studies. The adolescents in almost all types of treatment showed reductions in substance use. The greatest improvements were found for family therapy and mixed and group counseling. Longer treatment duration was associated with smaller improvements, but other treatment characteristics and participant characteristics had little relationship to the pre-post changes in substance use. Based on these findings family therapy is the treatment with the strongest evidence of comparative effectiveness, although most types of treatment appear to be beneficial in helping adolescents reduce their substance use. PMID:22763198

  3. 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 .

  4. A Reference Methylome Database and Analysis Pipeline to Facilitate Integrative and Comparative Epigenomics

    PubMed Central

    Song, Qiang; Decato, Benjamin; Hong, Elizabeth E.; Zhou, Meng; Fang, Fang; Qu, Jianghan; Garvin, Tyler; Kessler, Michael; Zhou, Jun; Smith, Andrew D.

    2013-01-01

    DNA methylation is implicated in a surprising diversity of regulatory, evolutionary processes and diseases in eukaryotes. The introduction of whole-genome bisulfite sequencing has enabled the study of DNA methylation at a single-base resolution, revealing many new aspects of DNA methylation and highlighting the usefulness of methylome data in understanding a variety of genomic phenomena. As the number of publicly available whole-genome bisulfite sequencing studies reaches into the hundreds, reliable and convenient tools for comparing and analyzing methylomes become increasingly important. We present MethPipe, a pipeline for both low and high-level methylome analysis, and MethBase, an accompanying database of annotated methylomes from the public domain. Together these resources enable researchers to extract interesting features from methylomes and compare them with those identified in public methylomes in our database. PMID:24324667

  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. Comparative analysis of analytical solutions for F2P(x ,t ) in the DGLAP approach

    NASA Astrophysics Data System (ADS)

    Choudhury, D. K.; Borah, Neelakshi N. K.

    2017-01-01

    Coupled Dokshitzer-Gribov-Lipatov-Altarelli-Parisi equations involving singlet quark and gluon distributions are explored by a Taylor expansion at small x as two first-order partial differential equations in two variables: Bjorken x and t (t =l n Q/2Λ2). The system of equations are then solved by Lagrange's method and the method of characteristics. We obtain the proton structure function F2P(x ,t ) by combining the corresponding nonsinglet and singlet structure functions with both methods. Analytical solutions for F2P(x ,t ) thus obtained are compared with the recent data published by the H1 and ZEUS Collaborations as well as with NNPDF3.0 parametrization, and their compatibility is checked. Comparative analysis favors the analytical solution by Lagrange's method; the plausible reasons behind that are also discussed.

  7. 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.

  8. 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.

  9. Burning water: a comparative analysis of the energy return on water invested.

    PubMed

    Mulder, Kenneth; Hagens, Nathan; Fisher, Brendan

    2010-02-01

    While various energy-producing technologies have been analyzed to assess the amount of energy returned per unit of energy invested, this type of comprehensive and comparative approach has rarely been applied to other potentially limiting inputs such as water, land, and time. We assess the connection between water and energy production and conduct a comparative analysis for estimating the energy return on water invested (EROWI) for several renewable and non-renewable energy technologies using various Life Cycle Analyses. Our results suggest that the most water-efficient, fossil-based technologies have an EROWI one to two orders of magnitude greater than the most water-efficient biomass technologies, implying that the development of biomass energy technologies in scale sufficient to be a significant source of energy may produce or exacerbate water shortages around the globe and be limited by the availability of fresh water.

  10. 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

  11. Comparative analysis of the DNA staining efficiencies of different fluorescent dyes in preparative agarose gel electrophoresis.

    PubMed

    Huang, Qing; Fu, Wei-Ling

    2005-01-01

    Ethidium bromide (EB) is a mutagen and toxin that is widely used in the laboratory for visualization of nucleic acids. Safer nucleic acid stains, such as SYBR Gold, SYBR Green, GoldView, GeneFinder, and GoldStar, have been developed. However, there has been no systematic comparative analysis of the staining efficiencies of these dyes. In the present study, SYBR Gold, SYBR Green I, GoldView and EB were compared. Although both SYBR Gold and SYBR Green alter electrophoretic mobility and thus DNA size estimates, they are cost-effective alternatives to EB. SYBR Gold was more sensitive than SYBR Green I at detecting short fragments, but 50-bp bands were clearly visible using either dye when visualized with a long integration time. SYBR Gold or SYBR Green I are sensitive and relatively safe alternatives to EB. In our laboratory, the SYBR Gold method is now used routinely by all members of our group with great consistency and success.

  12. 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

  13. 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.

  14. 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

  15. [Social representations at work: comparative analysis of working and non-working teens].

    PubMed

    Oliveira, Denize Cristina de; Fischer, Frida Marina; Teixeira, Maria Cristina Triguero Veloz; Sá, Celso Pereira de; Gomes, Antonio Marcos Tosoli

    2010-05-01

    The fact that adolescents are compelled to work can usually be explained as caused by financial needs of their families. The objectives of this study are to characterize the content and the structure of the social representation of adolescence work, by working and non working adolescents, 14 to 18 years old; compare the representations in both groups, and to evaluate if the hypotheses of the central core of representation are confirmed by other technique of social representations analysis. The sample included 724 high school students of a public school of São Paulo city. Data collection was carried out through word free evocation technique, using "work" as inductor term, and employing 21 focal groups. The results show the representations of work in both groups are significantly associated to positive moral and psychosocial meanings. The greatest part of the elements classified as central core hypotheses was confirmed in the several thematic axis of the content analysis of focal groups.

  16. 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).

  17. Comparative computational analysis of the Cahn-Hilliard equation with emphasis on C1-continuous methods

    NASA Astrophysics Data System (ADS)

    Kaessmair, S.; Steinmann, P.

    2016-10-01

    The numerical treatment of the fourth-order Cahn-Hilliard equation is nonstandard. Using a Galerkin-method necessitates, for instance, piecewise smooth and globally C1-continuous basis functions or a mixed formulation. The latter is obtained introducing an auxiliary field which allows to rephrase the Cahn-Hilliard equation as a set of two coupled second-order equations. In view of this, the formulation in terms of the primal unknown appears to be a more intuitive and natural choice but requires a C1-continuous interpolation. Therefore, isogeometric analysis, using a spline basis, and natural element analysis are addressed in the present contribution. Mixed second-order finite element methods introducing the chemical potential or alternatively a nonlocal concentration as auxiliary field serve as references to which both higher-order methods are compared in terms of accuracy and efficiency.

  18. 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

  19. The genome sequence of Blochmannia floridanus: Comparative analysis of reduced genomes

    PubMed Central

    Gil, Rosario; Silva, Francisco J.; Zientz, Evelyn; Delmotte, François; González-Candelas, Fernando; Latorre, Amparo; Rausell, Carolina; Kamerbeek, Judith; Gadau, Jürgen; Hölldobler, Bert; van Ham, Roeland C. H. J.; Gross, Roy; Moya, Andrés

    2003-01-01

    Bacterial symbioses are widespread among insects, probably being one of the key factors of their evolutionary success. We present the complete genome sequence of Blochmannia floridanus, the primary endosymbiont of carpenter ants. Although these ants feed on a complex diet, this symbiosis very likely has a nutritional basis: Blochmannia is able to supply nitrogen and sulfur compounds to the host while it takes advantage of the host metabolic machinery. Remarkably, these bacteria lack all known genes involved in replication initiation (dnaA, priA, and recA). The phylogenetic analysis of a set of conserved protein-coding genes shows that Bl. floridanus is phylogenetically related to Buchnera aphidicola and Wigglesworthia glossinidia, the other endosymbiotic bacteria whose complete genomes have been sequenced so far. Comparative analysis of the five known genomes from insect endosymbiotic bacteria reveals they share only 313 genes, a number that may be close to the minimum gene set necessary to sustain endosymbiotic life. PMID:12886019

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

    PubMed Central

    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

  1. Comparative analysis of INTOR-like designs: Status and preliminary results

    SciTech Connect

    Flanagan, C.A.; Galambos, J.D.; Peng, P.K.M.; Reid, R.L.; Strickler, D.J.

    1987-07-01

    This document provides an interim status report on the INTOR tasks related to the critical analysis of INTOR-like designs. At the INTOR Workshop in December 1986, and updated at the INTOR related Specialists' Meeting in March 1987, a series of comparative analysis studies was established. Initial results were targeted for completion for the July INTOR meeting and final results completed for the November INTOR meeting. The goal of the analytic comparisons is to evaluate and determine the specific impact of how different choices affect the design. The results of such an analytic determination should allow the international community to identify and agree upon which aspects of choice have what influence on the International Thermonuclear Experimental Reactor (ITER) design.

  2. 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).

  3. Sensitivity Analysis of Remote Sensing Data: Comparing the Response of Vegetation Indices in Tropical Areas.

    NASA Astrophysics Data System (ADS)

    Bonifaz, R.

    2005-12-01

    During the past two decades, satellite remote sensing systems possessing high temporal resolution, but typically moderate or coarse spatial resolution, have increasingly been used to characterize and map vegetation dynamics. Assessing the seasonality of tropical vegetation has, however, been especially challenging. Tropical regimes of temperature and precipitation are generally less variable and pronounced than those in other biomes, and variations in plant growth are often more subtle. Using samples from selected tropical land cover types (tropical rain forest, tropical grasses, tropical deciduous forest, mixed forest and agricultural areas), sensitivity analysis will be carried out comparing different 'greenness' indices such as the Normalized Difference Vegetation Index (NDVI), the Enhanced Vegetation Index (EVI) and the Wide Dynamic Range Vegetation Index (WDRVI) derived from the MODIS/TERRA sensor. This analysis will potentially allow the selection of the best index to describe the particular behavior of tropical vegetation for further characterization of seasonal changes of such areas.

  4. 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.

  5. 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

  6. Comparative genome analysis of Prevotella ruminicola and Prevotella bryantii: insights into their environmental niche.

    PubMed

    Purushe, Janaki; Fouts, Derrick E; Morrison, Mark; White, Bryan A; Mackie, Roderick I; Coutinho, Pedro M; Henrissat, Bernard; Nelson, Karen E

    2010-11-01

    The Prevotellas comprise a diverse group of bacteria that has received surprisingly limited attention at the whole genome-sequencing level. In this communication, we present the comparative analysis of the genomes of Prevotella ruminicola 23 (GenBank: CP002006) and Prevotella bryantii B(1)4 (GenBank: ADWO00000000), two gastrointestinal isolates. Both P. ruminicola and P. bryantii have acquired an extensive repertoire of glycoside hydrolases that are targeted towards non-cellulosic polysaccharides, especially GH43 bifunctional enzymes. Our analysis demonstrates the diversity of this genus. The results from these analyses highlight their role in the gastrointestinal tract, and provide a template for additional work on genetic characterization of these species.

  7. 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.

  8. 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.

  9. Comparative analysis of gene expression for convergent evolution of camera eye between octopus and human.

    PubMed

    Ogura, Atsushi; Ikeo, Kazuho; Gojobori, Takashi

    2004-08-01

    Although the camera eye of the octopus is very similar to that of humans, phylogenetic and embryological analyses have suggested that their camera eyes have been acquired independently. It has been known as a typical example of convergent evolution. To study the molecular basis of convergent evolution of camera eyes, we conducted a comparative analysis of gene expression in octopus and human camera eyes. We sequenced 16,432 ESTs of the octopus eye, leading to 1052 nonredundant genes that have matches in the protein database. Comparing these 1052 genes with 13,303 already-known ESTs of the human eye, 729 (69.3%) genes were commonly expressed between the human and octopus eyes. On the contrary, when we compared octopus eye ESTs with human connective tissue ESTs, the expression similarity was quite low. To trace the evolutionary changes that are potentially responsible for camera eye formation, we also compared octopus-eye ESTs with the completed genome sequences of other organisms. We found that 1019 out of the 1052 genes had already existed at the common ancestor of bilateria, and 875 genes were conserved between humans and octopuses. It suggests that a larger number of conserved genes and their similar gene expression may be responsible for the convergent evolution of the camera eye.

  10. 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)).

  11. Comparative first- and second-law analysis of an absorption cycle

    NASA Astrophysics Data System (ADS)

    Perez-Blanco, H.; Pan, L.

    1985-07-01

    Generally, the basis of efficiency calculations and optimization studies of absorption cycles is the first law of thermodynamics. It is often argued that a first-law analysis does not produce all the information needed to optimize the absorption system. According to this line of thought, only an analysis based on the second law of thermodynamics gives the needed information. Assessment of the usefulness of second-law analysis as applied to absorption cycles seems adequate to determine the potential benefits of gathering the additional data for the absorbent-refrigerant combinations currently under consideration. To this end, a comparative first- and second-law analysis of a single-effect, lithium bromide-water absorption cycle is carried out here. An existing computer program and entropy values from the literature are used to analyze the cycle. The effects of temperature approaches in each heat exchanger and external heating/cooling fluid flow rates on the cycle performance are determined. A comparison of the results obtained via first- and second-law analyses reveals that the usefulness of the information depends on the boundaries of the system under consideration. Optimization of the absorption cycle itself, without considering the effect of external heating/cooling fluid flow rates at all, can be accomplished by first-law analysis. However, optimization of not only the cycle but also the external flow rates (i.e., the overall thermal system) is better accomplished by second-law analysis. Another interesting result of this study is that a critical temperature approach for cycle optimization can be found for the generator. In practical terms, this means that improving the heat exchanger in the generator will not always enhance the thermal performance of the cycle.

  12. [Comparative analysis of changes in rats organisms exposed to microgravity and head-down suspension].

    PubMed

    Il'in, E A; Kaplanskiĭ, A S

    1998-01-01

    Comparative analysis of metabolic and structural shifts in rats following 14 days of microgravity aboard biosatellite Cosmos-2044 and their tail-suspended synchronous controls gave evidence that suspension-induced deprivation of hind limbs of support loading yields inherent to microgravity shifts the endocrine control of energy, plastic, and mineral metabolism. The conclusion has been drawn that tail-suspension can be used as a model of the microgravity effects on the musculoskeletal apparatus and the endocrine systems controlling metabolism in muscles and bones.

  13. 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

  14. 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.

  15. 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

  16. 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

  17. [Comparative analysis of the genetic structure of Red Polish cattle in Poland and the Ukraine].

    PubMed

    Oblap, R V; Zvezhkhovski, L; Ivanchenko, E V; Glazko, V I

    2002-01-01

    Comparative analysis of genetic structure of two groups of Red Polish cattle, which reproduce in Poland and Ukraine, was made. Six molecular-genetic markers (kappa-casein, beta-lactoglobulin, leptin, myostatin, growth hormone, and pituitary-specific transcription factor Pit-I) were tested by PCR-RFLP. No significant differences between the considered intrabreed groups were found. High frequency of some alleles (Csn kappa B, Blg B, and Gh L) related to the important productivity traits were observed. The rare alleles in some genes were revealed. The obtained results are evidence of the unique characteristics of the investigated breed.

  18. 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.

  19. Comparative conformational analysis of [{text{[D - P}}{text{n}}^{text{5}}

    NASA Astrophysics Data System (ADS)

    Wilkes, Brian C.; Schiller, Peter W.

    1991-08-01

    A theoretical conformational analysis (molecular mechanics study) of the δ opioid receptor-selective enkephalin analog [{{H - Tyr - D - P}}{{n - OH}}] (DPDPE) was performed, based on the use of the SYBYL software. The study led to the identification of several conformers that were significantly lower in energy than previously reported candidate conformers of DPDPE which, for comparative purposes, were also minimized by using the standard SYBYL force field. The results revealed a considerable degree of conformational flexibility of the DPDPE molecule, and suggested that incorporation of further conformational constraints into this enkephalin analog will be necessary in order to elucidate its receptor-bound conformation.

  20. Comparative analysis of post-focal filamentation of focused UV and IR laser pulses in air

    SciTech Connect

    Geints, Yu E; Zemlyanov, A A; Ionin, A A; Mokrousova, D V; Seleznev, L V; Sinitsyn, D V; Sunchugasheva, E S

    2015-04-30

    We report the results of laboratory experiments and numerical calculations of the spatial position and structure of a plasma channel produced in air by high-power focused femtosecond laser radiation with wavelengths of 740 and 248 nm as a result of its self-focusing and filamentation. A comparative analysis of the physical patterns of filamentation of IR and UV laser beams with variations in the beam focal length, transverse size and power is performed. It is found that a plasma channel beyond the linear focal waist of the laser beam is formed differently for two different spectral ranges. (nonlinear optical phenomena)

  1. A meta-analysis comparing the sensitivity of bees to pesticides.

    PubMed

    Arena, Maria; Sgolastra, Fabio

    2014-04-01

    The honey bee Apis mellifera, the test species used in the current environmental risk assessment procedure, is generally considered as extremely sensitive to pesticides when compared to other bee species, although a quantitative approach for comparing the difference in sensitivity among bees has not yet been reported. A systematic review of the relevant literature on the topic followed by a meta-analysis has been performed. Both the contact and oral acute LD50 and the chronic LC50 reported in laboratory studies for as many substances as possible have been extracted from the papers in order to compare the sensitivity to pesticides of honey bees and other bee species (Apiformes). The sensitivity ratio R between the endpoint for the species a (A. mellifera) and the species s (bees other than A. mellifera) was calculated for a total of 150 case studies including 19 bee species. A ratio higher than 1 indicated that the species s was more sensitive to pesticides than honey bees. The meta-analysis showed a high variability of sensitivity among bee species (R from 0.001 to 2085.7), however, in approximately 95 % of the cases the sensitivity ratio was below 10. The effect of pesticides in domestic and wild bees is dependent on the intrinsic sensitivity of single bee species as well as their specific life cycle, nesting activity and foraging behaviour. Current data indicates a need for more comparative information between honey bees and non-Apis bees as well as separate pesticide risk assessment procedures for non-Apis bees.

  2. The top skin-associated genes: a comparative analysis of human and mouse skin transcriptomes.

    PubMed

    Gerber, Peter Arne; Buhren, Bettina Alexandra; Schrumpf, Holger; Homey, Bernhard; Zlotnik, Albert; Hevezi, Peter

    2014-06-01

    The mouse represents a key model system for the study of the physiology and biochemistry of skin. Comparison of skin between mouse and human is critical for interpretation and application of data from mouse experiments to human disease. Here, we review the current knowledge on structure and immunology of mouse and human skin. Moreover, we present a systematic comparison of human and mouse skin transcriptomes. To this end, we have recently used a genome-wide database of human gene expression to identify genes highly expressed in skin, with no, or limited expression elsewhere - human skin-associated genes (hSAGs). Analysis of our set of hSAGs allowed us to generate a comprehensive molecular characterization of healthy human skin. Here, we used a similar database to generate a list of mouse skin-associated genes (mSAGs). A comparative analysis between the top human (n=666) and mouse (n=873) skin-associated genes (SAGs) revealed a total of only 30.2% identity between the two lists. The majority of shared genes encode proteins that participate in structural and barrier functions. Analysis of the top functional annotation terms revealed an overlap for morphogenesis, cell adhesion, structure, and signal transduction. The results of this analysis, discussed in the context of published data, illustrate the diversity between the molecular make up of skin of both species and grants a probable explanation, why results generated in murine in vivo models often fail to translate into the human.

  3. Consensus comparative analysis of human embryonic stem cell-derived cardiomyocytes.

    PubMed

    Zhang, Shaohong; Poon, Ellen; Xie, Dongqing; Boheler, Kenneth R; Li, Ronald A; Wong, Hau-San

    2015-01-01

    Global transcriptional analyses have been performed with human embryonic stem cells (hESC) derived cardiomyocytes (CMs) to identify molecules and pathways important for human CM differentiation, but variations in culture and profiling conditions have led to greatly divergent results among different studies. Consensus investigation to identify genes and gene sets enriched in multiple studies is important for revealing differential gene expression intrinsic to human CM differentiation independent of the above variables, but reliable methods of conducting such comparison are lacking. We examined differential gene expression between hESC and hESC-CMs from multiple microarray studies. For single gene analysis, we identified genes that were expressed at increased levels in hESC-CMs in seven datasets and which have not been previously highlighted. For gene set analysis, we developed a new algorithm, consensus comparative analysis (CSSCMP), capable of evaluating enrichment of gene sets from heterogeneous data sources. Based on both theoretical analysis and experimental validation, CSSCMP is more efficient and less susceptible to experimental variations than traditional methods. We applied CSSCMP to hESC-CM microarray data and revealed novel gene set enrichment (e.g., glucocorticoid stimulus), and also identified genes that might mediate this response. Our results provide important molecular information intrinsic to hESC-CM differentiation. Data and Matlab codes can be downloaded from S1 Data.

  4. 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

  5. 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.

  6. 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.

  7. Comparative transcriptomic analysis reveals similarities and dissimilarities in Saccharomyces cerevisiae wine strains response to nitrogen availability.

    PubMed

    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 (12 h, 24 h and 96 h). 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 12 h, 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

  8. 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

  9. 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

  10. 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

  11. Comparative analysis of methods for estimating arm segment parameters and joint torques from inverse dynamics.

    PubMed

    Piovesan, Davide; Pierobon, Alberto; Dizio, Paul; Lackner, James R

    2011-03-01

    A common problem in the analyses of upper limb unfettered reaching movements is the estimation of joint torques using inverse dynamics. The inaccuracy in the estimation of joint torques can be caused by the inaccuracy in the acquisition of kinematic variables, body segment parameters (BSPs), and approximation in the biomechanical models. The effect of uncertainty in the estimation of body segment parameters can be especially important in the analysis of movements with high acceleration. A sensitivity analysis was performed to assess the relevance of different sources of inaccuracy in inverse dynamics analysis of a planar arm movement. Eight regression models and one water immersion method for the estimation of BSPs were used to quantify the influence of inertial models on the calculation of joint torques during numerical analysis of unfettered forward arm reaching movements. Thirteen subjects performed 72 forward planar reaches between two targets located on the horizontal plane and aligned with the median plane. Using a planar, double link model for the arm with a floating shoulder, we calculated the normalized joint torque peak and a normalized root mean square (rms) of torque at the shoulder and elbow joints. Statistical analyses quantified the influence of different BSP models on the kinetic variable variance for given uncertainty on the estimation of joint kinematics and biomechanical modeling errors. Our analysis revealed that the choice of BSP estimation method had a particular influence on the normalized rms of joint torques. Moreover, the normalization of kinetic variables to BSPs for a comparison among subjects showed that the interaction between the BSP estimation method and the subject specific somatotype and movement kinematics was a significant source of variance in the kinetic variables. The normalized joint torque peak and the normalized root mean square of joint torque represented valuable parameters to compare the effect of BSP estimation methods

  12. 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

  13. Comparative analysis on reproducibility among 5 intraoral scanners: sectional analysis according to restoration type and preparation outline form

    PubMed Central

    2016-01-01

    PURPOSE The trueness and precision of acquired images of intraoral digital scanners could be influenced by restoration type, preparation outline form, scanning technology and the application of power. The aim of this study is to perform the comparative evaluation of the 3-dimensional reproducibility of intraoral scanners (IOSs). MATERIALS AND METHODS The phantom containing five prepared teeth was scanned by the reference scanner (Dental Wings) and 5 test IOSs (E4D dentist, Fastscan, iTero, Trios and Zfx Intrascan). The acquired images of the scanner groups were compared with the image from the reference scanner (trueness) and within each scanner groups (precision). Statistical analysis was performed using independent two-samples t-test and analysis of variance (α=.05). RESULTS The average deviations of trueness and precision of Fastscan, iTero and Trios were significantly lower than the other scanners. According to the restoration type, significantly higher trueness was observed in crown and inlay than in bridge. However, no significant difference was observed among four sites of preparation outline form. If compared by the characteristics of IOS, high trueness was observed in the group adopting the active triangulation and using powder. However, there was no significant difference between the still image acquisition and video acquisition groups. CONCLUSION Except for two intraoral scanners, Fastscan, iTero and Trios displayed comparable levels of trueness and precision values in tested phantom model. Difference in trueness was observed depending on the restoration type, the preparation outline form and characteristics of IOS, which should be taken into consideration when the intraoral scanning data are utilized. PMID:27826385

  14. A comparative analysis of coverage decisions for outpatient pharmaceuticals: evidence from Denmark, Norway and Sweden.

    PubMed

    Grepstad, Mari; Kanavos, Panos

    2015-02-01

    This study analyses the reasons for differences and similarities in coverage recommendations for outpatient pharmaceuticals in Denmark, Norway and Sweden, following HTA appraisals. A comparative analysis of all outpatient drug appraisals carried out between January 2009 and December 2012, including an analysis of divergent coverage recommendations made by all three countries was performed. Agreement levels between HTA agencies were measured using kappa scores. Consultations with stakeholders in the three countries were carried out to complement the discussion on HTA processes and reimbursement outcomes. Nineteen outpatient drug-indication pairs appraised in each of the three countries were identified, of which 6 pairs (32%) had divergent coverage recommendations. An uneven distribution of coverage recommendations was observed, with the highest overlap in appraisals between Norway and Sweden (free-marginal kappa 0.89). Similarities were found in priority setting principles, mode of appraisal and reasoning for coverage recommendations. The study shows that health economic evaluation is less prominent or explicit in outpatient drug appraisals in Denmark than in Norway and Sweden, that all three countries could benefit from improved communication between appraisers and manufacturers, and that final coverage recommendations rely on factors other than safety, comparative efficacy or cost-effectiveness.

  15. Meta-analysis of ceftriaxone compared with penicillin for the treatment of syphilis.

    PubMed

    Liang, Zhen; Chen, Ya-Ping; Yang, Chun-Sheng; Guo, Wen; Jiang, Xiao-Xiao; Xu, Xi-Feng; Feng, Shou-Xin; Liu, Yan-Qun; Jiang, Guan

    2016-01-01

    Penicillin is the gold standard for treating syphilis. However, allergic reactions, poor drug tolerance and limited efficacy in patients remain a challenging problem. The objective of this meta-analysis was to compare the efficacy of ceftriaxone and penicillin based on data obtained from published randomised controlled trials (RCTs). The Cochrane Library, Medline, EBSCO, EMBASE and Ovid databases were searched for RCTs of ceftriaxone vs. penicillin for the treatment of syphilis. Estimated risk ratios (RRs) and 95% confidence intervals (CIs) were used to investigate the following outcome measures: 3-month response rate; 6-month response rate; 12-month response rate; relapse rate; serofast rate; and failure rate. Seven RCTs involving 281 participants (159 patients who received ceftriaxone and 122 patients who received penicillin) were included in the meta-analysis. There were no significant differences in 3-month response rate (RR=1.12, 95% CI 0.89-1.42), 6-month response rate (RR=1.02, 95% CI 0.75-1.38), 12-month response rate (RR=1.04, 95% CI 0.82-1.32), relapse rate (RR=0.91, 95% CI 0.45-1.84), serofast rate (RR=0.69, 95% CI 0.22-2.12) or failure rate (RR=0.66, 95% CI 0.03-15.76) in patients treated with ceftriaxone compared with those treated with penicillin. In conclusion, there is no evidence in the literature that ceftriaxone is less efficient than penicillin.

  16. Comparing measurement error correction methods for rate-of-change exposure variables in survival analysis.

    PubMed

    Veronesi, Giovanni; Ferrario, Marco M; Chambless, Lloyd E

    2013-12-01

    In this article we focus on comparing measurement error correction methods for rate-of-change exposure variables in survival analysis, when longitudinal data are observed prior to the follow-up time. Motivational examples include the analysis of the association between changes in cardiovascular risk factors and subsequent onset of coronary events. We derive a measurement error model for the rate of change, estimated through subject-specific linear regression, assuming an additive measurement error model for the time-specific measurements. The rate of change is then included as a time-invariant variable in a Cox proportional hazards model, adjusting for the first time-specific measurement (baseline) and an error-free covariate. In a simulation study, we compared bias, standard deviation and mean squared error (MSE) for the regression calibration (RC) and the simulation-extrapolation (SIMEX) estimators. Our findings indicate that when the amount of measurement error is substantial, RC should be the preferred method, since it has smaller MSE for estimating the coefficients of the rate of change and of the variable measured without error. However, when the amount of measurement error is small, the choice of the method should take into account the event rate in the population and the effect size to be estimated. An application to an observational study, as well as examples of published studies where our model could have been applied, are also provided.

  17. Comparative analysis of RNA sequencing methods for degraded or low-input samples.

    PubMed

    Adiconis, Xian; Borges-Rivera, Diego; Satija, Rahul; DeLuca, David S; Busby, Michele A; Berlin, Aaron M; Sivachenko, Andrey; Thompson, Dawn Anne; Wysoker, Alec; Fennell, Timothy; Gnirke, Andreas; Pochet, Nathalie; Regev, Aviv; Levin, Joshua Z

    2013-07-01

    RNA-seq is an effective method for studying the transcriptome, but it can be difficult to apply to scarce or degraded RNA from fixed clinical samples, rare cell populations or cadavers. Recent studies have proposed several methods for RNA-seq of low-quality and/or low-quantity samples, but the relative merits of these methods have not been systematically analyzed. Here we compare five such methods using metrics relevant to transcriptome annotation, transcript discovery and gene expression. Using a single human RNA sample, we constructed and sequenced ten libraries with these methods and compared them against two control libraries. We found that the RNase H method performed best for chemically fragmented, low-quality RNA, and we confirmed this through analysis of actual degraded samples. RNase H can even effectively replace oligo(dT)-based methods for standard RNA-seq. SMART and NuGEN had distinct strengths for measuring low-quantity RNA. Our analysis allows biologists to select the most suitable methods and provides a benchmark for future method development.

  18. Comparative analysis of superintegrons: engineering extensive genetic diversity in the Vibrionaceae.

    PubMed

    Rowe-Magnus, Dean A; Guerout, Anne-Marie; Biskri, Latefa; Bouige, Philippe; Mazel, Didier

    2003-03-01

    Integrons are natural tools for bacterial evolution and innovation. Their involvement in the capture and dissemination of antibiotic-resistance genes among Gram-negative bacteria is well documented. Recently, massive ancestral versions, the superintegrons (SIs), were discovered in the genomes of diverse proteobacterial species. SI gene cassettes with an identifiable activity encode proteins related to simple adaptive functions, including resistance, virulence, and metabolic activities, and their recruitment was interpreted as providing the host with an adaptive advantage. Here, we present extensive comparative analysis of SIs identified among the Vibrionaceae. Each was at least 100 kb in size, reaffirming the participation of SIs in the genome plasticity and heterogeneity of these species. Phylogenetic and localization data supported the sedentary nature of the functional integron platform and its coevolution with the host genome. Conversely, comparative analysis of the SI cassettes was indicative of both a wide range of origin for the entrapped genes and of an active cassette assembly process in these bacterial species. The signature attC sites of each species displayed conserved structural characteristics indicating that symmetry rather than sequence was important in the recognition of such a varied collection of target recombination sequences by a single site-specific recombinase. Our discovery of various addiction module cassettes within each of the different SIs indicates a possible role for them in the overall stability of large integron cassette arrays.

  19. 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.

  20. Comparative Proteomic Analysis of Cotton Fiber Development and Protein Extraction Method Comparison in Late Stage Fibers

    PubMed Central

    Mujahid, Hana; Pendarvis, Ken; Reddy, Joseph S.; Nallamilli, Babi Ramesh Reddy; Reddy, K. R.; Nanduri, Bindu; Peng, Zhaohua

    2016-01-01

    The distinct stages of cotton fiber development and maturation serve as a single-celled model for studying the molecular mechanisms of plant cell elongation, cell wall development and cellulose biosynthesis. However, this model system of plant cell development is compromised for proteomic studies due to a lack of an efficient protein extraction method during the later stages of fiber development, because of a recalcitrant cell wall and the presence of abundant phenolic compounds. Here, we compared the quality and quantities of proteins extracted from 25 dpa (days post anthesis) fiber with multiple protein extraction methods and present a comprehensive quantitative proteomic study of fiber development from 10 dpa to 25 dpa. Comparative analysis using a label-free quantification method revealed 287 differentially-expressed proteins in the 10 dpa to 25 dpa fiber developmental period. Proteins involved in cell wall metabolism and regulation, cytoskeleton development and carbohydrate metabolism among other functional categories in four fiber developmental stages were identified. Our studies provide protocols for protein extraction from maturing fiber tissues for mass spectrometry analysis and expand knowledge of the proteomic profile of cotton fiber development. PMID:28248216

  1. 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.

  2. Plastome Sequence Determination and Comparative Analysis for Members of the Lolium-Festuca Grass Species Complex

    PubMed Central

    Hand, Melanie L.; Spangenberg, German C.; Forster, John W.; Cogan, Noel O. I.

    2013-01-01

    Chloroplast genome sequences are of broad significance in plant biology, due to frequent use in molecular phylogenetics, comparative genomics, population genetics, and genetic modification studies. The present study used a second-generation sequencing approach to determine and assemble the plastid genomes (plastomes) of four representatives from the agriculturally important Lolium-Festuca species complex of pasture grasses (Lolium multiflorum, Festuca pratensis, Festuca altissima, and Festuca ovina). Total cellular DNA was extracted from either roots or leaves, was sequenced, and the output was filtered for plastome-related reads. A comparison between sources revealed fewer plastome-related reads from root-derived template but an increase in incidental bacterium-derived sequences. Plastome assembly and annotation indicated high levels of sequence identity and a conserved organization and gene content between species. However, frequent deletions within the F. ovina plastome appeared to contribute to a smaller plastid genome size. Comparative analysis with complete plastome sequences from other members of the Poaceae confirmed conservation of most grass-specific features. Detailed analysis of the rbcL–psaI intergenic region, however, revealed a “hot-spot” of variation characterized by independent deletion events. The evolutionary implications of this observation are discussed. The complete plastome sequences are anticipated to provide the basis for potential organelle-specific genetic modification of pasture grasses. PMID:23550121

  3. Comparative Genomics Analysis of Two Different Virulent Bovine Pasteurella multocida Isolates

    PubMed Central

    Pan, Tingting; Li, Tian; Wu, Rui

    2016-01-01

    The Pasteurella multocida capsular type A isolates can cause pneumonia and bovine respiratory disease (BRD). In this study, comparative genomics analysis was carried out to identify the virulence genes in two different virulent P. multocida capsular type A isolates (high virulent PmCQ2 and low virulent PmCQ6). The draft genome sequence of PmCQ2 is 2.32 Mbp and contains 2,002 protein-coding genes, 9 insertion sequence (IS) elements, and 1 prophage region. The draft genome sequence of PmCQ6 is 2.29 Mbp and contains 1,970 protein-coding genes, 2 IS elements, and 3 prophage regions. The genome alignment analysis revealed that the genome similarity between PmCQ2 and PmCQ6 is 99% with high colinearity. To identify the candidate genes responsible for virulence, the PmCQ2 and PmCQ6 were compared together with that of the published genomes of high virulent Pm36950 and PmHN06 and avirulent Pm3480 and Pm70 (capsular type F). Five genes and two insertion sequences are identified in high virulent strains but not in low virulent or avirulent strains. These results indicated that these genes or insertion sequences might be responsible for the virulence of P. multocida, providing prospective candidates for further studies on the pathogenesis and the host-pathogen interactions of P. multocida. PMID:28070502

  4. 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.

  5. 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.

  6. Comparative clinical effects of hydromorphone and morphine: a meta-analysis.

    PubMed

    Felden, L; Walter, C; Harder, S; Treede, R-D; Kayser, H; Drover, D; Geisslinger, G; Lötsch, J

    2011-09-01

    We have conducted a meta-analysis of the clinical effects of morphine and hydromorphone to compare their benefit in analgesia. Embase and Medline were searched with an end-date of June 2009 for randomized, controlled trials or observational studies that addressed comparative analgesic and side-effects or particular side-effects. Two researchers independently identified included studies and extracted the data. Estimates of opioid effects were combined by using a random-effects model. Meta-analysis of eight studies suggested that hydromorphone (494 patients) provides slightly better (P=0.012) clinical analgesia than morphine (510 patients). The effect-size was small (Cohen's d=0.266) and disappeared when one study was removed, although the advantage of hydromorphone was more evident in studies of better quality (Jadad's rating). Side-effects were similar, for example, nausea (P=0.383, nine studies, 456 patients receiving hydromorphone and 460 morphine); vomiting (P=0.306, six studies, 246 patients receiving hydromorphone and 239 morphine); or itching (P=0.249, eight studies, 405 patients receiving hydromorphone, 410 morphine). This suggests some advantage of hydromorphone over morphine for analgesia. Additional potential clinical pharmacological advantages with regard to side-effects, such as safety in renal failure or during acute analgesia titration, are based on limited evidence and require substantiation by further studies.

  7. 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.

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

    DOE PAGES

    Jun, Se Ran; Wassenaar, Trudy; Nookaew, Intawat; ...

    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

  9. 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

  10. 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

  11. Comparative Proteomics Analysis of Two Strains of Neisseria meningitidis Serogroup B and Neisseria lactamica

    PubMed Central

    Sheikhi, Raheleh; Amin, Mansour; Hamidinia, Maryam; Assarehzadegan, Mohammad Ali; Rostami, Soodabeh; Mojtahedi, Zahra

    2015-01-01

    Background: Antigenic similarities between Neisseria lactamica as a commensal species and N. meningitidis serogroup B (NmB) as an important cause of meningitis infection have been considered for the development of an effective vaccine based on their common proteins to prevent life-threatening bacterial meningitis. Objectives: The main aims of this study were to determine whole proteome profiles of N. lactamica strains and to compare them with whole proteome profile of a reference strain of NmB for identification of some of common proteins between the two species. Materials and Methods: We compared the whole proteomic profiles of N. lactamica strains and a reference strain of NmB. Lysates from bacterial strains were resolved by two-dimensional gel electrophoresis (2-DE), followed by Coomassie Brilliant blue staining. Some of the protein spots were excised from the gel and subjected to matrix-assisted laser desorption/ionization-tandem time-of-flight mass spectrometry (MALDI-TOF/TOF MS) analysis. Results: The analysis of Coomassie-stained gels using ImageMaster 2D Platinum software identified approximately 800 reproducible protein spots in the range of pI 4.5 - 9.5 and Mr of 8 - 100 kDa for each 2-DE gel of the studied bacterial strains. By comparing proteome maps of 2-DE gels, more than 200 common protein spots were recognized between the two species. Forty-eight common protein spots between the studied bacterial strains were identified by MALDI-TOF/TOF-MS. The results indicated that among the protein spots identified by MOLDI-TOF/TOF mass spectrometry, the groups of proteins included cell surface, energy metabolism, amino acid transport and metabolism, coenzyme metabolism, defense, multifunctional cellular processes, DNA, RNA and protein synthesis, ribosomal structure, regulatory functions, replication, transcription, translation, unknown and hypothetical proteins with unknown function. We found that N. lactamica strains have a proteome profile somewhat similar to

  12. Comparing illicit drug use in 19 European cities through sewage analysis.

    PubMed

    Thomas, Kevin V; Bijlsma, Lubertus; Castiglioni, Sara; Covaci, Adrian; Emke, Erik; Grabic, Roman; Hernández, Félix; Karolak, Sara; Kasprzyk-Hordern, Barbara; Lindberg, Richard H; Lopez de Alda, Miren; Meierjohann, Axel; Ort, Christoph; Pico, Yolanda; Quintana, José B; Reid, Malcolm; Rieckermann, Jörg; Terzic, Senka; van Nuijs, Alexander L N; de Voogt, Pim

    2012-08-15

    The analysis of sewage for urinary biomarkers of illicit drugs is a promising and complementary approach for estimating the use of these substances in the general population. For the first time, this approach was simultaneously applied in 19 European cities, making it possible to directly compare illicit drug loads in Europe over a 1-week period. An inter-laboratory comparison study was performed to evaluate the analytical performance of the participating laboratories. Raw 24-hour composite sewage samples were collected from 19 European cities during a single week in March 2011 and analyzed for the urinary biomarkers of cocaine, amphetamine, ecstasy, methamphetamine and cannabis using in-house optimized and validated analytical methods. The load of each substance used in each city was back-calculated from the measured concentrations. The data show distinct temporal and spatial patterns in drug use across Europe. Cocaine use was higher in Western and Central Europe and lower in Northern and Eastern Europe. The extrapolated total daily use of cocaine in Europe during the study period was equivalent to 356 kg/day. High per capita ecstasy loads were observed in Dutch cities, as well as in Antwerp and London. In general, cocaine and ecstasy loads were significantly elevated during the weekend compared to weekdays. Per-capita loads of methamphetamine were highest in Helsinki and Turku, Oslo and Budweis, while the per capita loads of cannabis were similar throughout Europe. This study shows that a standardized analysis for illicit drug urinary biomarkers in sewage can be applied to estimate and compare the use of these substances at local and international scales. This approach has the potential to deliver important information on drug markets (supply indicator).

  13. Comparative Genomic Analysis of the Endosymbionts of Herbivorous Insects Reveals Eco-Environmental Adaptations: Biotechnology Applications

    PubMed Central

    Shi, Weibing; Xie, Shangxian; Chen, Xueyan; Sun, Su; Zhou, Xin; Liu, Lantao; Gao, Peng; Kyrpides, Nikos C.; No, En-Gyu; Yuan, Joshua S.

    2013-01-01

    Metagenome analysis of the gut symbionts of three different insects was conducted as a means of comparing taxonomic and metabolic diversity of gut microbiomes to diet and life history of the insect hosts. A second goal was the discovery of novel biocatalysts for biorefinery applications. Grasshopper and cutworm gut symbionts were sequenced and compared with the previously identified metagenome of termite gut microbiota. These insect hosts represent three different insect orders and specialize on different food types. The comparative analysis revealed dramatic differences among the three insect species in the abundance and taxonomic composition of the symbiont populations present in the gut. The composition and abundance of symbionts was correlated with their previously identified capacity to degrade and utilize the different types of food consumed by their hosts. The metabolic reconstruction revealed that the gut metabolome of cutworms and grasshoppers was more enriched for genes involved in carbohydrate metabolism and transport than wood-feeding termite, whereas the termite gut metabolome was enriched for glycosyl hydrolase (GH) enzymes relevant to lignocellulosic biomass degradation. Moreover, termite gut metabolome was more enriched with nitrogen fixation genes than those of grasshopper and cutworm gut, presumably due to the termite's adaptation to the high fiber and less nutritious food types. In order to evaluate and exploit the insect symbionts for biotechnology applications, we cloned and further characterized four biomass-degrading enzymes including one endoglucanase and one xylanase from both the grasshopper and cutworm gut symbionts. The results indicated that the grasshopper symbiont enzymes were generally more efficient in biomass degradation than the homologous enzymes from cutworm symbionts. Together, these results demonstrated a correlation between the composition and putative metabolic functionality of the gut microbiome and host diet, and suggested

  14. A Comparative Analysis of Three Non-Invasive Human-Machine Interfaces for the Disabled

    PubMed Central

    Ravindra, Vikram; Castellini, Claudio

    2014-01-01

    In the framework of rehabilitation robotics, a major role is played by the human–machine interface (HMI) used to gather the patient’s intent from biological signals, and convert them into control signals for the robotic artifact. Surprisingly, decades of research have not yet declared what the optimal HMI is in this context; in particular, the traditional approach based upon surface electromyography (sEMG) still yields unreliable results due to the inherent variability of the signal. To overcome this problem, the scientific community has recently been advocating the discovery, analysis, and usage of novel HMIs to supersede or augment sEMG; a comparative analysis of such HMIs is therefore a very desirable investigation. In this paper, we compare three such HMIs employed in the detection of finger forces, namely sEMG, ultrasound imaging, and pressure sensing. The comparison is performed along four main lines: the accuracy in the prediction, the stability over time, the wearability, and the cost. A psychophysical experiment involving ten intact subjects engaged in a simple finger-flexion task was set up. Our results show that, at least in this experiment, pressure sensing and sEMG yield comparably good prediction accuracies as opposed to ultrasound imaging; and that pressure sensing enjoys a much better stability than sEMG. Given that pressure sensors are as wearable as sEMG electrodes but way cheaper, we claim that this HMI could represent a valid alternative/augmentation to sEMG to control a multi-fingered hand prosthesis. PMID:25386135

  15. Comparative Analysis of Behavioral Models for Adaptive Learning in Changing Environments

    PubMed Central

    Marković, Dimitrije; Kiebel, Stefan J.

    2016-01-01

    Probabilistic models of decision making under various forms of uncertainty have been applied in recent years to numerous behavioral and model-based fMRI studies. These studies were highly successful in enabling a better understanding of behavior and delineating the functional properties of brain areas involved in decision making under uncertainty. However, as different studies considered different models of decision making under uncertainty, it is unclear which of these computational models provides the best account of the observed behavioral and neuroimaging data. This is an important issue, as not performing model comparison may tempt researchers to over-interpret results based on a single model. Here we describe how in practice one can compare different behavioral models and test the accuracy of model comparison and parameter estimation of Bayesian and maximum-likelihood based methods. We focus our analysis on two well-established hierarchical probabilistic models that aim at capturing the evolution of beliefs in changing environments: Hierarchical Gaussian Filters and Change Point Models. To our knowledge, these two, well-established models have never been compared on the same data. We demonstrate, using simulated behavioral experiments, that one can accurately disambiguate between these two models, and accurately infer free model parameters and hidden belief trajectories (e.g., posterior expectations, posterior uncertainties, and prediction errors) even when using noisy and highly correlated behavioral measurements. Importantly, we found several advantages of Bayesian inference and Bayesian model comparison compared to often-used Maximum-Likelihood schemes combined with the Bayesian Information Criterion. These results stress the relevance of Bayesian data analysis for model-based neuroimaging studies that investigate human decision making under uncertainty. PMID:27148030

  16. Controlling for non-independence in comparative analysis of patterns across populations within species

    PubMed Central

    Stone, Graham N.; Nee, Sean; Felsenstein, Joseph

    2011-01-01

    How do we quantify patterns (such as responses to local selection) sampled across multiple populations within a single species? Key to this question is the extent to which populations within species represent statistically independent data points in our analysis. Comparative analyses across species and higher taxa have long recognized the need to control for the non-independence of species data that arises through patterns of shared common ancestry among them (phylogenetic non-independence), as have quantitative genetic studies of individuals linked by a pedigree. Analyses across populations lacking pedigree information fall in the middle, and not only have to deal with shared common ancestry, but also the impact of exchange of migrants between populations (gene flow). As a result, phenotypes measured in one population are influenced by processes acting on others, and may not be a good guide to either the strength or direction of local selection. Although many studies examine patterns across populations within species, few consider such non-independence. Here, we discuss the sources of non-independence in comparative analysis, and show why the phylogeny-based approaches widely used in cross-species analyses are unlikely to be useful in analyses across populations within species. We outline the approaches (intraspecific contrasts, generalized least squares, generalized linear mixed models and autoregression) that have been used in this context, and explain their specific assumptions. We highlight the power of ‘mixed models’ in many contexts where problems of non-independence arise, and show that these allow incorporation of both shared common ancestry and gene flow. We suggest what can be done when ideal solutions are inaccessible, highlight the need for incorporation of a wider range of population models in intraspecific comparative methods and call for simulation studies of the error rates associated with alternative approaches. PMID:21444315

  17. Controlling for non-independence in comparative analysis of patterns across populations within species.

    PubMed

    Stone, Graham N; Nee, Sean; Felsenstein, Joseph

    2011-05-12

    How do we quantify patterns (such as responses to local selection) sampled across multiple populations within a single species? Key to this question is the extent to which populations within species represent statistically independent data points in our analysis. Comparative analyses across species and higher taxa have long recognized the need to control for the non-independence of species data that arises through patterns of shared common ancestry among them (phylogenetic non-independence), as have quantitative genetic studies of individuals linked by a pedigree. Analyses across populations lacking pedigree information fall in the middle, and not only have to deal with shared common ancestry, but also the impact of exchange of migrants between populations (gene flow). As a result, phenotypes measured in one population are influenced by processes acting on others, and may not be a good guide to either the strength or direction of local selection. Although many studies examine patterns across populations within species, few consider such non-independence. Here, we discuss the sources of non-independence in comparative analysis, and show why the phylogeny-based approaches widely used in cross-species analyses are unlikely to be useful in analyses across populations within species. We outline the approaches (intraspecific contrasts, generalized least squares, generalized linear mixed models and autoregression) that have been used in this context, and explain their specific assumptions. We highlight the power of 'mixed models' in many contexts where problems of non-independence arise, and show that these allow incorporation of both shared common ancestry and gene flow. We suggest what can be done when ideal solutions are inaccessible, highlight the need for incorporation of a wider range of population models in intraspecific comparative methods and call for simulation studies of the error rates associated with alternative approaches.

  18. 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

  19. Phylogenetic and Comparative Sequence Analysis of Thermostable Alpha Amylases of kingdom Archea, Prokaryotes and Eukaryotes.

    PubMed

    Huma, Tayyaba; Maryam, Arooma; Rehman, Shahid Ur; Qamar, Muhammad Tahir Ul; Shaheen, Tayyaba; Haque, Asma; Shaheen, Bushra

    2014-01-01

    Alpha amylase family is generally defined as a group of enzymes that can hydrolyse and transglycosylase α-(1, 4) or α-(1, 6) glycosidic bonds along with the preservation of anomeric configuration. For the comparative analysis of alpha amylase family, nucleotide sequences of seven thermo stable organisms of Kingdom Archea i.e. Pyrococcus furiosus (100-105°C), Kingdom Prokaryotes i.e. Bacillus licheniformis (90-95°C), Geobacillus stearothermophilus (75°C), Bacillus amyloliquefaciens (72°C), Bacillus subtilis (70°C) and Bacillus KSM K38 (55°C) and Eukaryotes i.e. Aspergillus oryzae (60°C) were selected from NCBI. Primary structure composition analysis and Conserved sequence analysis were conducted through Bio Edit tools. Results from BioEdit shown only three conserved regions of base pairs and least similarity in MSA of the above mentioned alpha amylases. In Mega 5.1 Phylogeny of thermo stable alpha amylases of Kingdom Archea, Prokaryotes and Eukaryote was handled by Neighbor-Joining (NJ) algorithm. Mega 5.1 phylogenetic results suggested that alpha amylases of thermo stable organisms i.e. Pyrococcus furiosus (100-105°C), Bacillus licheniformis (90-95°C), Geobacillus stearothermophilus (75°C) and Bacillus amyloliquefaciens (72°C) are more distantly related as compared to less thermo stable organisms. By keeping in mind the characteristics of most thermo stable alpha amylases novel and improved features can be introduced in less thermo stable alpha amylases so that they become more thermo tolerant and productive for industry.

  20. Threat to the point: improving the value of comparative extinction risk analysis for conservation action.

    PubMed

    Murray, Kris A; Verde Arregoitia, Luis D; Davidson, Ana; Di Marco, Moreno; Di Fonzo, Martina M I

    2014-02-01

    Comparative extinction risk analysis is a common approach for assessing the relative plight of biodiversity and making conservation recommendations. However, the usefulness of such analyses for conservation practice has been questioned. One reason for underperformance may be that threats arising from global environmental changes (e.g., habitat loss, invasive species, climate change) are often overlooked, despite being widely regarded as proximal drivers of species' endangerment. We explore this problem by (i) reviewing the use of threats in this field and (ii) quantitatively investigating the effects of threat exclusion on the interpretation and potential application of extinction risk model results. We show that threat variables are routinely (59%) identified as significant predictors of extinction risk, yet while most studies (78%) include extrinsic factors of some kind (e.g., geographic or bioclimatic information), the majority (63%) do not include threats. Despite low overall usage, studies are increasingly employing threats to explain patterns of extinction risk. However, most continue to employ methods developed for the analysis of heritable traits (e.g., body size, fecundity), which may be poorly suited to the treatment of nonheritable predictors including threats. In our global mammal and continental amphibian extinction risk case studies, omitting threats reduced model predictive performance, but more importantly (i) reduced mechanistic information relevant to management; (ii) resulted in considerable disagreement in species classifications (12% and 5% for amphibians and mammals, respectively, translating to dozens and hundreds of species); and (iii) caused even greater disagreement (20-60%) in a downstream conservation application (species ranking). We conclude that the use of threats in comparative extinction risk analysis is important and increasing but currently in the early stages of development. Priorities for future studies include improving uptake

  1. Comparative transcriptome analysis of embryonic and adult stem cells with extended and limited differentiation capacity

    PubMed Central

    Ulloa-Montoya, Fernando; Kidder, Benjamin L; Pauwelyn, Karen A; Chase, Lucas G; Luttun, Aernout; Crabbe, Annelies; Geraerts, Martine; Sharov, Alexei A; Piao, Yulan; Ko, Minoru SH; Hu, Wei-Shou; Verfaillie, Catherine M

    2007-01-01

    Background Recently, several populations of postnatal stem cells, such as multipotent adult progenitor cells (MAPCs), have been described that have broader differentiation ability than classical adult stem cells. Here we compare the transcriptome of pluripotent embryonic stem cells (ESCs), MAPCs, and lineage-restricted mesenchymal stem cells (MSCs) to determine their relationship. Results Applying principal component analysis, non-negative matrix factorization and k-means clustering algorithms to the gene-expression data, we identified a unique gene-expression profile for MAPCs. Apart from the ESC-specific transcription factor Oct4 and other ESC transcripts, some of them associated with maintaining ESC pluripotency, MAPCs also express transcripts characteristic of early endoderm and mesoderm. MAPCs do not, however, express Nanog or Sox2, two other key transcription factors involved in maintaining ESC properties. This unique molecular signature was seen irrespective of the microarray platform used and was very similar for both mouse and rat MAPCs. As MSC-like cells isolated under MAPC conditions are virtually identical to MSCs, and MSCs cultured in MAPC conditions do not upregulate MAPC-expressed transcripts, the MAPC signature is cell-type specific and not merely the result of differing culture conditions. Conclusion Multivariate analysis techniques clustered stem cells on the basis of their expressed gene profile, and the genes determining this clustering reflected the stem cells' differentiation potential in vitro. This comparative transcriptome analysis should significantly aid the isolation and culture of MAPCs and MAPC-like cells, and form the basis for studies to gain insights into genes that confer on these cells their greater developmental potency. PMID:17683608

  2. Comparative analysis of genome-wide Mlo gene family in Cajanus cajan and Phaseolus vulgaris.

    PubMed

    Deshmukh, Reena; Singh, V K; Singh, B D

    2016-04-01

    The Mlo gene was discovered in barley because the mutant 'mlo' allele conferred broad-spectrum, non-race-specific resistance to powdery mildew caused by Blumeria graminis f. sp. hordei. The Mlo genes also play important roles in growth and development of plants, and in responses to biotic and abiotic stresses. The Mlo gene family has been characterized in several crop species, but only a single legume species, soybean (Glycine max L.), has been investigated so far. The present report describes in silico identification of 18 CcMlo and 20 PvMlo genes in the important legume crops Cajanus cajan (L.) Millsp. and Phaseolus vulgaris L., respectively. In silico analysis of gene organization, protein properties and conserved domains revealed that the C. cajan and P. vulgaris Mlo gene paralogs are more divergent from each other than from their orthologous pairs. The comparative phylogenetic analysis classified CcMlo and PvMlo genes into three major clades. A comparative analysis of CcMlo and PvMlo proteins with the G. max Mlo proteins indicated close association of one CcMlo, one PvMlo with two GmMlo genes, indicating that there was no further expansion of the Mlo gene family after the separation of these species. Thus, most of the diploid species of eudicots might be expected to contain 15-20 Mlo genes. The genes CcMlo12 and 14, and PvMlo11 and 12 are predicted to participate in powdery mildew resistance. If this prediction were verified, these genes could be targeted by TILLING or CRISPR to isolate powdery mildew resistant mutants.

  3. Comparative Gene Expression Analysis of the Human Periodontal Ligament in Deciduous and Permanent Teeth

    PubMed Central

    Kim, Seong-Oh; Jeon, Mijeong; Choi, Byung-Jai; Jung, Han-Sung; Moon, Seok Jun; Park, Wonse; Choi, Hyung-Jun

    2013-01-01

    There are histological and functional differences between human deciduous and permanent periodontal ligament (PDL) tissues. The aim of this study was to determine the differences between these two types of tissue at the molecular level by comparing their gene expression patterns. PDL samples were obtained from permanent premolars (n = 38) and anterior deciduous teeth (n = 31) extracted from 40 healthy persons. Comparative cDNA microarray analysis revealed several differences in gene expression between the deciduous and permanent PDL tissues. These findings were verified by qRT-PCR (quantitative reverse-transcription–polymerase chain reaction) analysis, and the areas where genes are expressed were revealed by immunohistochemical staining. The expressions of 21 genes were up-regulated in deciduous relative to PDL tissues, and those of 30 genes were up-regulated in permanent relative to deciduous PDL tissues. The genes that were up-regulated in deciduous PDL tissues were those involved in the formation of the extracellular matrix (LAMC2, LAMB3, and COMP), tissue development (IGF2BP, MAB21L2, and PAX3), and inflammatory or immune reactions leading to tissue degradation (IL1A, CCL21, and CCL18). The up-regulated genes in permanent PDL tissues were related to tissue degradation (IL6 and ADAMTS18), myocontraction (PDE3B, CASQ2, and MYH10), and neurological responses (FOS, NCAM2, SYT1, SLC22A3, DOCK3, LRRTM1, LRRTM3, PRSS12, and ARPP21). The analysis of differential gene expressions between deciduous and permanent PDL tissues aids our understanding of histological and functional differences between them at the molecular level. PMID:23593441

  4. Array comparative genomic hybridization and cytogenetic analysis in pediatric acute leukemias.

    PubMed

    Dawson, A J; Yanofsky, R; Vallente, R; Bal, S; Schroedter, I; Liang, L; Mai, S

    2011-10-01

    Most patients with acute lymphocytic leukemia (all) are reported to have acquired chromosomal abnormalities in their leukemic bone marrow cells. Many established chromosome rearrangements have been described, and their associations with specific clinical, biologic, and prognostic features are well defined. However, approximately 30% of pediatric and 50% of adult patients with all do not have cytogenetic abnormalities of clinical significance. Despite significant improvements in outcome for pediatric all, therapy fails in approximately 25% of patients, and these failures often occur unpredictably in patients with a favorable prognosis and "good" cytogenetics at diagnosis.It is well known that karyotype analysis in hematologic malignancies, although genome-wide, is limited because of altered cell kinetics (mitotic rate), a propensity of leukemic blasts to undergo apoptosis in culture, overgrowth by normal cells, and chromosomes of poor quality in the abnormal clone. Array comparative genomic hybridization (acgh-"microarray") has a greatly increased genomic resolution over classical cytogenetics. Cytogenetic microarray, which uses genomic dna, is a powerful tool in the analysis of unbalanced chromosome rearrangements, such as copy number gains and losses, and it is the method of choice when the mitotic index is low and the quality of metaphases is suboptimal. The copy number profile obtained by microarray is often called a "molecular karyotype."In the present study, microarray was applied to 9 retrospective cases of pediatric all either with initial high-risk features or with at least 1 relapse. The conventional karyotype was compared to the "molecular karyotype" to assess abnormalities as interpreted by classical cytogenetics. Not only were previously undetected chromosome losses and gains identified by microarray, but several karyotypes interpreted by classical cytogenetics were shown to be discordant with the microarray results. The complementary use of microarray

  5. Comparative genome analysis: selection pressure on the Borrelia vls cassettes is essential for infectivity

    PubMed Central

    Glöckner, Gernot; Schulte-Spechtel, Ulrike; Schilhabel, Markus; Felder, Marius; Sühnel, Jürgen; Wilske, Bettina; Platzer, Matthias

    2006-01-01

    Background At least three species of Borrelia burgdorferi sensu lato (Bbsl) cause tick-borne Lyme disease. Previous work including the genome analysis of B. burgdorferi B31 and B. garinii PBi suggested a highly variable plasmid part. The frequent occurrence of duplicated sequence stretches, the observed plasmid redundancy, as well as the mainly unknown function and variability of plasmid encoded genes rendered the relationships between plasmids within and between species largely unresolvable. Results To gain further insight into Borreliae genome properties we completed the plasmid sequences of B. garinii PBi, added the genome of a further species, B. afzelii PKo, to our analysis, and compared for both species the genomes of pathogenic and apathogenic strains. The core of all Bbsl genomes consists of the chromosome and two plasmids collinear between all species. We also found additional groups of plasmids, which share large parts of their sequences. This makes it very likely that these plasmids are relatively stable and share common ancestors before the diversification of Borrelia species. The analysis of the differences between B. garinii PBi and B. afzelii PKo genomes of low and high passages revealed that the loss of infectivity is accompanied in both species by a loss of similar genetic material. Whereas B. garinii PBi suffered only from the break-off of a plasmid end, B. afzelii PKo lost more material, probably an entire plasmid. In both cases the vls gene locus encoding for variable surface proteins is affected. Conclusion The complete genome sequences of a B. garinii and a B. afzelii strain facilitate further comparative studies within the genus Borrellia. Our study shows that loss of infectivity can be traced back to only one single event in B. garinii PBi: the loss of the vls cassettes possibly due to error prone gene conversion. Similar albeit extended losses in B. afzelii PKo support the hypothesis that infectivity of Borrelia species depends heavily on

  6. Comparative efficacy of combination bronchodilator therapies in COPD: a network meta-analysis

    PubMed Central

    Huisman, Eline L; Cockle, Sarah M; Ismaila, Afisi S; Karabis, Andreas; Punekar, Yogesh Suresh

    2015-01-01

    Background Several new fixed-dose combination bronchodilators have been recently launched, and assessing their efficacy relative to each other, and with open dual combinations is desirable. This network meta-analysis (NMA) assessed the efficacy of umeclidinium and vilanterol (UMEC/VI) with that of available dual bronchodilators in single/separate inhalers. Methods A systematic literature review identified randomized controlled trials of ≥10 weeks among chronic obstructive pulmonary disease patients (≥40 years), assessing the efficacy of combination bronchodilators in single or separate inhalers. Comparative assessment was conducted on change from baseline in trough forced expiratory volume in 1 second (FEV1), St George’s Respiratory Questionnaire (SGRQ) total scores, transitional dyspnea index (TDI) focal scores, and rescue medication use at 12 weeks and 24 weeks using an NMA within a Bayesian framework. Results A systematic literature review identified 77 articles of 26 trials comparing UMEC/VI, indacaterol/glycopyrronium (QVA149), formoterol plus tiotropium (TIO) 18 μg, salmeterol plus TIO, or indacaterol plus TIO, with TIO and placebo as common comparators at 12 weeks and approximately 24 weeks. The NMA showed that at 24 weeks, efficacy of UMEC/VI was not significantly different compared with QVA149 on trough FEV1 (14.1 mL [95% credible interval: −14.2, 42.3]), SGRQ total score (0.18 [−1.28, 1.63]), TDI focal score (−0.30 [−0.73, 0.13]), and rescue medication use (0.02 [−0.27, 0.32]); compared with salmeterol plus TIO on trough FEV1 (67.4 mL [−25.3, 159.4]), SGRQ total score (−0.11 [−1.84, 1.61]), and TDI focal score (0.58 [−0.33, 1.50]); and compared with formoterol plus TIO 18 μg on SGRQ total score (−0.68 [−1.77, 0.39]). Results at week 12 were consistent with week 24 outcomes. Due to lack of availability of evidence, no comparison was made with formoterol plus TIO on FEV1 or TDI at 24 weeks. Conclusion UMEC/VI has comparable

  7. Comparative Analysis of Urinary Total Proteins by Bicinchoninic Acid and Pyrogallol Red Molybdate Methods

    PubMed Central

    Bhongir, Aparna Varma; Karra, Madhulatha; Beedu, Sashidhar Rao

    2015-01-01

    Background The concentration of total proteins in urine is a good index of renal function, but its determination is found to be unreliable. The pyrogallol red molybdate (PRM) method for urine total proteins is being widely used in most of the hospitals because of its high sensitivity, better precision and its practicability. Bicinchoninic acid method (BCA) is also used for protein estimation and there have been no studies comparing this method with the PRM method in human urine samples. BCA method overestimates the urinary protein concentration in the presence of interfering substances. After removing the interfering substances present in the human urine samples the results of BCA method were compared with the PRM method. Aim The purpose of the study is to identify whether the results of urine total proteins by BCA method are comparable to PRM method and can be used as an alternative to the PRM method. Setting and Design This is a cross-sectional study done on fresh urine specimens from the hospital laboratory, covering a wide range of protein concentrations. Material and Methods Fresh urine specimens covering a wide range of protein concentrations (urine dipstick: nil, trace, 1+, 2+ and ≥ 3+) of 36 patients were analysed by both the methods. Statistical Analysis Imprecision was determined by repeated analysis study and Inaccuracy was assessed by comparing the results of the patient’s urine samples by both the methods using correlation plots, Bland and Altman, and Passing and Bablok regression analyses. Results The coefficient of variation and mean (SD) for the BCA method were 4.6% and 799.1 (882.5) mg/L and for the PRM method were 5.1% and 802.1 (911.9) mg/L. The Pearson correlation coefficient, r was 0.93 (p < 0.0001). Method agreement studies showed no significant constant and proportional bias between both the methods. Conclusion In urine which is subjected to removal of interfering substances, the BCA results are comparable to PRM method. PMID:26435938

  8. Comparative Analysis of Nuclear Transfer Embryo-Derived Mouse Embryonic Stem Cells. Part I: Cellular Characterization

    PubMed Central

    Kobolak, Julianna; Mamo, Solomon; Rungsiwiwut, Ruttachuk; Ujhelly, Olga; Csonka, Erika; Hadlaczky, Gyula

    2012-01-01

    Abstract Embryonic stem cells derived from nuclear transfer embryos (ntESCs) are particularly valuable for regenerative medicine, as they are a patient-specific and histocompatible cell source for the treatment of varying diseases. However, currently, little is known about their cellular and molecular profile. In the present study, in a mouse model different donor cell-derived ntESCs from various genetic backgrounds were compared with reference ESCs and analyzed comprehensively at the cellular level. A number of pluripotency marker genes were compared by flow cytometry and immunocytochemistry analysis. Significant differences at the protein level were observed for POU5F1, SOX2, FGF4, NANOG, and SSEA-1. However, such differences had no effect on in vitro cell differentiation and cell fate: derivatives of the three germ layers were detected in all ntESC lines. The neural and cardiac in vitro differentiation revealed minor differences between the cell lines, both at the mRNA and protein level. Karyotype analyses and cell growth studies did not reveal any significant variations. Despite some differences observed, the present study revealed that ntESC lines had similar differentiation competences compared to other ESCs. The results indicate that the observed differences may be related to the genotype rather than to the nuclear transfer technology. PMID:22204592

  9. Comparative genomic analysis of Lactobacillus plantarum ZJ316 reveals its genetic adaptation and potential probiotic profiles* #

    PubMed Central

    Li, Ping; Li, Xuan; Gu, Qing; Lou, Xiu-yu; Zhang, Xiao-mei; Song, Da-feng; Zhang, Chen

    2016-01-01

    Objective: In previous studies, Lactobacillus plantarum ZJ316 showed probiotic properties, such as antimicrobial activity against various pathogens and the capacity to significantly improve pig growth and pork quality. The purpose of this study was to reveal the genes potentially related to its genetic adaptation and probiotic profiles based on comparative genomic analysis. Methods: The genome sequence of L. plantarum ZJ316 was compared with those of eight L. plantarum strains deposited in GenBank. BLASTN, Mauve, and MUMmer programs were used for genome alignment and comparison. CRISPRFinder was applied for searching the clustered regularly interspaced short palindromic repeats (CRISPRs). Results: We identified genes that encode proteins related to genetic adaptation and probiotic profiles, including carbohydrate transport and metabolism, proteolytic enzyme systems and amino acid biosynthesis, CRISPR adaptive immunity, stress responses, bile salt resistance, ability to adhere to the host intestinal wall, exopolysaccharide (EPS) biosynthesis, and bacteriocin biosynthesis. Conclusions: Comparative characterization of the L. plantarum ZJ316 genome provided the genetic basis for further elucidating the functional mechanisms of its probiotic properties. ZJ316 could be considered a potential probiotic candidate. PMID:27487802

  10. A comparative immunological analysis of CoCl2 treated cells with in vitro hypoxic exposure.

    PubMed

    Shweta; Mishra, K P; Chanda, S; Singh, S B; Ganju, L

    2015-02-01

    The hypoxic preconditioning of mammalian cells has been shown to have beneficial effects against hypoxic injuries. However, very little information is available on the comparative analysis of immunological responses to hypoxic and hypoxia mimetic exposure. Therefore, in the present study, mouse peritoneal macrophages and splenocytes were subjected to hypoxia exposure (0.5 % O2) and hypoxia mimetic Cobalt chloride (CoCl2) treatment to evaluate their effect on immune response and delineate the underlying signaling mechanisms. The results obtained indicated that super oxide generation increased while TLR4 expression and cell surface markers like CD25, CD40 and CD69 were suppressed in both the treatments as compared to normoxia. Cobalt chloride treatment increased NF-κB expression, nitric oxide (NO) and iNOS expression, cytokines TNF-α and IL-6 as compared to hypoxia exposure. Our study showed that CoCl2 stabilizes HIF-1α to create hypoxia like conditions but it mainly influences the inflammatory response via NF-κB signaling pathway by skewing the production of proinflammatory molecules like TNF-α, IL-6 and NO.

  11. Comparison of Discectomy versus Sequestrectomy in Lumbar Disc Herniation: A Meta-Analysis of Comparative Studies

    PubMed Central

    Ran, Jisheng; Hu, Yejun; Zheng, Zefeng; Zhu, Ting; Zheng, Huawei; Jing, Yibiao; Xu, Kan

    2015-01-01

    Background Lumbar disc removal is currently the standard treatment for lumbar disc herniation. No consensus has been achieved whether aggressive disc resection with curettage (discectomy) versus conservative removal of the offending disc fragment alone (sequestrectomy) provides better outcomes. This study aims to compare the reherniation rate and clinical outcomes between discectomy and sequestrectomy by literature review and a meta-analysis. Methods A systematic search of PubMed, Medline, Embase and the Cochrane Library was performed up to June 1, 2014. Outcomes of interest assessing the two techniques included demographic and clinical baseline characteristics, perioperative variables, complications, recurrent herniation rate and post-operative functional outcomes. Results Twelve eligible trials evaluating discectomy vs sequestrectomy were identified including one randomized controlled study, five prospective and six retrospective comparative studies. By contrast to discectomy, sequestrectomy was associated with significantly less operative time (p<0.001), lower visual analogue scale (VAS) for low back pain (p<0.05), less post-operative analgesic usage (p<0.05) and better patients’ satisfaction (p<0.05). Recurrent herniation rate, reoperation rate, intraoperative blood loss, hospitalization duration and VAS for sciatica were without significant difference. Conclusions According to our pooled data, sequestrectomy entails equivalent reherniation rate and complications compared with discectomy but maintains a lower incidence of recurrent low back pain and higher satisfactory rate. High-quality prospective randomized controlled trials are needed to firmly assess these two procedures. PMID:25815514

  12. Comparative analysis of female physicists in the physical sciences: Motivation and background variables

    NASA Astrophysics Data System (ADS)

    Dabney, Katherine P.; Tai, Robert H.

    2014-06-01

    The majority of existing science, technology, engineering, and mathematics (STEM) research studies compare women to men, yet a paucity of research exists that examines what differentiates female career choice within the physical sciences. In light of these research trends and recommendations, this study examines the following question: On average, do females who select physics as compared to chemistry doctoral programs differ in their reported personal motivations and background factors prior to entering the field? This question is analyzed using variables from the Project Crossover Survey data set through a subset of female physical science doctoral students and scientists (n =1137). A logistic regression analysis and prototypical odds ratio uncover what differentiates women in the physical sciences based on their academic achievement and experiences ranging from high school through undergraduate education. Results indicate that females who have negative undergraduate chemistry experiences as well as higher grades and positive experiences in undergraduate physics are more likely to pursue a career in physics as opposed to chemistry. Conclusions suggest that a greater emphasis should be placed on the classroom experiences that are provided to females in gateway physics courses. Analyses show that women are not a single entity that should only be examined as a whole group or in comparison to men. Instead women can be compared to one another to see what influences their differences in educational experiences and career choice in STEM-based fields as well as other academic areas of study.

  13. Atrazine Molecular Imprinted Polymers: Comparative Analysis by Far-Infrared and Ultraviolet Induced Polymerization

    PubMed Central

    Chen, Jun; Bai, Lian-Yang; Liu, Kun-Feng; Liu, Run-Qiang; Zhang, Yu-Ping

    2014-01-01

    Atrazine molecular imprinted polymers (MIPs) were comparatively synthesized using identical polymer formulation by far-infrared (FIR) radiation and ultraviolet (UV)-induced polymerization, respectively. Equilibrium binding experiments were carried out with the prepared MIPs; the results showed that MIPuv possessed specific binding to atrazine compared with their MIPFIR radiation counterparts. Scatchard plot’s of both MIPs indicated that the affinities of the binding sites in MIPs are heterogeneous and can be approximated by two dissociation-constants corresponding to the high-and low-affinity binding sites. Moreover, several common pesticides including atrazine, cyromazine, metamitron, simazine, ametryn, terbutryn were tested to determine their specificity, similar imprinting factor (IF) and different selectivity index (SI) for both MIPs. Physical characterization of the polymers revealed that the different polymerization methods led to slight differences in polymer structures and performance by scanning electron microscope (SEM), Fourier transform infrared absorption (FT-IR), and mercury analyzer (MA). Finally, both MIPs were used as selective sorbents for solid phase extraction (SPE) of atrazine from lake water, followed by high performance liquid chromatography (HPLC) analysis. Compared with commercial C18 SPE sorbent (86.4%–94.8%), higher recoveries of atrazine in spiked lake water were obtained in the range of 90.1%–97.1% and 94.4%–101.9%, for both MIPs, respectively. PMID:24398982

  14. Comparative genomic analysis of novel Acinetobacter symbionts: A combined systems biology and genomics approach

    PubMed Central

    Gupta, Vipin; Haider, Shazia; Sood, Utkarsh; Gilbert, Jack A.; Ramjee, Meenakshi; Forbes, Ken; Singh, Yogendra; Lopes, Bruno S.; Lal, Rup

    2016-01-01

    The increasing trend of antibiotic resistance in Acinetobacter drastically limits the range of therapeutic agents required to treat multidrug resistant (MDR) infections. This study focused on analysis of novel Acinetobacter strains using a genomics and systems biology approach. Here we used a network theory method for pathogenic and non-pathogenic Acinetobacter spp. to identify the key regulatory proteins (hubs) in each strain. We identified nine key regulatory proteins, guaA, guaB, rpsB, rpsI, rpsL, rpsE, rpsC, rplM and trmD, which have functional roles as hubs in a hierarchical scale-free fractal protein-protein interaction network. Two key hubs (guaA and guaB) were important for insect-associated strains, and comparative analysis identified guaA as more important than guaB due to its role in effective module regulation. rpsI played a significant role in all the novel strains, while rplM was unique to sheep-associated strains. rpsM, rpsB and rpsI were involved in the regulation of overall network topology across all Acinetobacter strains analyzed in this study. Future analysis will investigate whether these hubs are useful as drug targets for treating Acinetobacter infections. PMID:27378055

  15. Comparative proteomic analysis of horseweed (Conyza canadensis) biotypes identifies candidate proteins for glyphosate resistance

    PubMed Central

    González-Torralva, Fidel; Brown, Adrian P.; Chivasa, Stephen

    2017-01-01

    Emergence of glyphosate-resistant horseweed (Conyza canadensis) biotypes is an example of how unrelenting use of a single mode of action herbicide in agricultural weed control drives genetic adaptation in targeted species. While in other weeds glyphosate resistance arose from target site mutation or target gene amplification, the resistance mechanism in horseweed uses neither of these, being instead linked to reduced herbicide uptake and/or translocation. The molecular components underpinning horseweed glyphosate-resistance remain unknown. Here, we used an in vitro leaf disc system for comparative analysis of proteins extracted from control and glyphosate-treated tissues of glyphosate-resistant and glyphosate-susceptible biotypes. Analysis of shikimic acid accumulation, ABC-transporter gene expression, and cell death were used to select a suitable glyphosate concentration and sampling time for enriching proteins pivotal to glyphosate resistance. Protein gel analysis and mass spectrometry identified mainly chloroplast proteins differentially expressed between the biotypes before and after glyphosate treatment. Chloroplasts are the organelles in which the shikimate pathway, which is targeted by glyphosate, is located. Calvin cycle enzymes and proteins of unknown function were among the proteins identified. Our study provides candidate proteins that could be pivotal in engendering resistance and implicates chloroplasts as the primary sites driving glyphosate-resistance in horseweed. PMID:28198407

  16. Comparative Normal Mode Analysis of the Dynamics of DENV and ZIKV Capsids

    PubMed Central

    Hsieh, Yin-Chen; Poitevin, Frédéric; Delarue, Marc; Koehl, Patrice

    2016-01-01

    Key steps in the life cycle of a virus, such as the fusion event as the virus infects a host cell and its maturation process, relate to an intricate interplay between the structure and the dynamics of its constituent proteins, especially those that define its capsid, much akin to an envelope that protects its genomic material. We present a comprehensive, comparative analysis of such interplay for the capsids of two viruses from the flaviviridae family, Dengue (DENV) and Zika (ZIKV). We use for that purpose our own software suite, DD-NMA, which is based on normal mode analysis. We describe the elements of DD-NMA that are relevant to the analysis of large systems, such as virus capsids. In particular, we introduce our implementation of simplified elastic networks and justify their parametrization. Using DD-NMA, we illustrate the importance of packing interactions within the virus capsids on the dynamics of the E proteins of DENV and ZIKV. We identify differences between the computed atomic fluctuations of the E proteins in DENV and ZIKV and relate those differences to changes observed in their high resolution structures. We conclude with a discussion on additional analyses that are needed to fully characterize the dynamics of the two viruses. PMID:28083537

  17. IMG/M: integrated genome and metagenome comparative data analysis system.

    PubMed

    Chen, I-Min A; Markowitz, Victor M; Chu, Ken; Palaniappan, Krishna; Szeto, Ernest; Pillay, Manoj; Ratner, Anna; Huang, Jinghua; Andersen, Evan; Huntemann, Marcel; Varghese, Neha; Hadjithomas, Michalis; Tennessen, Kristin; Nielsen, Torben; Ivanova, Natalia N; Kyrpides, Nikos C

    2017-01-04

    The Integrated Microbial Genomes with Microbiome Samples (IMG/M: https://img.jgi.doe.gov/m/) system contains annotated DNA and RNA sequence data of (i) archaeal, bacterial, eukaryotic and viral genomes from cultured organisms, (ii) single cell genomes (SCG) and genomes from metagenomes (GFM) from uncultured archaea, bacteria and viruses and (iii) metagenomes from environmental, host associated and engineered microbiome samples. Sequence data are generated by DOE's Joint Genome Institute (JGI), submitted by individual scientists, or collected from public sequence data archives. Structural and functional annotation is carried out by JGI's genome and metagenome annotation pipelines. A variety of analytical and visualization tools provide support for examining and comparing IMG/M's datasets. IMG/M allows open access interactive analysis of publicly available datasets, while manual curation, submission and access to private datasets and computationally intensive workspace-based analysis require login/password access to its expert review (ER) companion system (IMG/M ER: https://img.jgi.doe.gov/mer/). Since the last report published in the 2014 NAR Database Issue, IMG/M's dataset content has tripled in terms of number of datasets and overall protein coding genes, while its analysis tools have been extended to cope with the rapid growth in the number and size of datasets handled by the system.

  18. Bayesian uncertainty analysis compared with the application of the GUM and its supplements

    NASA Astrophysics Data System (ADS)

    Elster, Clemens

    2014-08-01

    The Guide to the Expression of Uncertainty in Measurement (GUM) has proven to be a major step towards the harmonization of uncertainty evaluation in metrology. Its procedures contain elements from both classical and Bayesian statistics. The recent supplements 1 and 2 to the GUM appear to move the guidelines towards the Bayesian point of view, and they produce a probability distribution that shall encode one's state of knowledge about the measurand. In contrast to a Bayesian uncertainty analysis, however, Bayes' theorem is not applied explicitly. Instead, a distribution is assigned for the input quantities which is then ‘propagated’ through a model that relates the input quantities to the measurand. The resulting distribution for the measurand may coincide with a distribution obtained by the application of Bayes' theorem, but this is not true in general. The relation between a Bayesian uncertainty analysis and the application of the GUM and its supplements is investigated. In terms of a simple example, similarities and differences in the approaches are illustrated. Then a general class of models is considered and conditions are specified for which the distribution obtained by supplement 1 to the GUM is equivalent to a posterior distribution resulting from the application of Bayes' theorem. The corresponding prior distribution is identified and assessed. Finally, we briefly compare the GUM approach with a Bayesian uncertainty analysis in the context of regression problems.

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

    PubMed Central

    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

  20. Does Postthyroidectomy Syndrome Really Exist Following Thyroidectomy? Prospective Comparative Analysis of Open vs. Endoscopic Thyroidectomy

    PubMed Central

    Park, Ki Nam; Mok, Ji Oh; Chung, Chan Hee

    2015-01-01

    Objectives This study prospectively evaluated postthyroidectomy syndrome (PTS) through objective and subjective voice changes following thyroidectomy of open vs. endoscopic thyroidectomy. Methods A prospective clinical trial (SCHBC IRB 09 26) was performed from Jan 2008 to Aug 2010 to compare the open thyroidectomy (OPEN group) and endoscopic thyroidectomy (ENDO group). Of the 110 patients, 75 completed the evaluation before and 1 and 6 months after surgery. Subjective parameters included perceptual analysis (GRBAS [grade, roughness, breathiness, asthenia, and strain] scale), stroboscopic or flexible fiberscopic analysis, voice handicap index, and 5-point visual analog scales for vocal fatigue, singing difficulty, difficulty with high-pitch phonation, and neck discomfort. Objective parameters included acoustic, aerodynamic analysis and the electroglottograph. Results For the ENDO group (n=36), the operation time was longer than in the OPEN group (n=39; P<0.01). For the OPEN group, two objective and five subjective parameters were worse 1 month postoperatively; of these, two subjective parameters persisted for 6 months (P<0.05). For the ENDO group, three objective and six subjective parameters were worse 1 month postoperatively, and three of the subjective parameters persisted 6 months postoperatively (P<0.05). Conclusion PTS really exists following simple thyroidectomy and are very common for both OPEN and ENDO groups. Most of the parameters improved gradually over time, but some subjective changes persisted 6 months postoperatively. PMID:25729500