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Sample records for investigate strain variation

  1. Use of restriction fragment length polymorphisms to investigate strain variation within Neisseria meningitidis

    SciTech Connect

    Williams, S.D.

    1989-01-01

    Similarity within bacterial populations is difficult to assess due to the limited number of characters available for evaluation and the heterogeneity of bacterial species. Currently, the preferred method used to evaluate the structure of bacterial populations is multilocus enzyme electrophoresis. However, this method is extremely cumbersome and only offers an indirect measure of genetic similarities. The development of a more direct and less cumbersome method for this purpose is warranted. Restriction fragment length polymorphism analysis was evaluated as a tool for use in the study of bacterial population structures and in the epidemiology and surveillance of infectious disease. A collection of Neisseria meningitidis was available for use in the investigation of this technique. Neisseria meningitidis is the causative agent of epidemic cerebrospinal meningitis and septicemia as well as a variety of other clinical manifestations. Each isolate in the collection was defined in terms of serogroup specificity, clinical history, geographic source, and date of isolation. Forty-six strains were chosen for this study. The DNA from each strain was restricted with Pst1 and EcoR1 and electrophoresed on agarose gels. The DNA was transferred to nylon filters and hybridized with P{sup 32} labeled DNA probes. Two randomly generated probes and a gene-specific probe were used to estimate the genetic similarities between and among the strains in the study population. A total of 28 different restriction fragment migration types were detected by the probes used. Data obtained from the RFLP analysis was analyzed by cluster analysis and multivariate statistical methods. A total of 7 clones groups were detected. Two of these appear to be major clones that comprise 35% of the population.

  2. Use of Restriction Fragment Length Polymorphisms to Investigate Strain Variation Within Neisseria Meningitidis.

    NASA Astrophysics Data System (ADS)

    Williams, Shelley Diane

    Similarity within bacterial populations is difficult to assess due to the limited number of characters available for evaluation and the heterogeneity of bacterial species. Currently, the preferred method used to evaluate the structure of bacterial populations is multilocus enzyme electrophoresis. However, this method is extremely cumbersome and only offers an indirect measure of genetic similarities. The development of a more direct and less cumbersome method for this purpose is warranted. Restriction fragment length polymorphism analysis was evaluated as a tool for use in the study of bacterial population structures and in the epidemiology and surveillance of infectious disease. A collection of Neisseria meningitidis was available for use in the investigation of this technique. Neisseria meningitidis is the causative agent of epidemic cerebrospinal meningitis and septicemia as well as a variety of other clinical manifestations. Each isolate in the collection was defined in terms of serogroup specificity, clinical history, geographic source, and date of isolation. Forty -six strains were chosen for this study. The DNA from each strain was restricted with Pst1 and EcoR1 and electrophoresed on agarose gels. The DNA was transferred to nylon filters and hybridized with P ^{32} labeled DNA probes. Two randomly generated probes and a gene-specific probe were used to estimate the genetic similarities between and among the strains in the study population. A total of 28 different restriction fragment migration types were detected by the probes used. Data obtained from the RFLP analysis was analysed by cluster analysis and multivariate statistical methods. A total of 7 clones groups were detected. Two of these appear to be major clones that comprise 35% of the population. This analysis demonstrates the lack of structure within Neisseria meningitidis due primarily to a heterogenous population and the lack of geographic segregation. The potential utility of this technique as a

  3. Epstein-Barr Virus Strain Variation.

    PubMed

    Farrell, Paul J

    2015-01-01

    What is wild-type Epstein-Barr virus and are there genetic differences in EBV strains that contribute to some of the EBV-associated diseases? Recent progress in DNA sequencing has resulted in many new Epstein-Barr virus (EBV) genome sequences becoming available. EBV isolates worldwide can be grouped into type 1 and type 2, a classification based on the EBNA2 gene sequence. Type 1 transforms human B cells into lymphoblastoid cell lines much more efficiently than type 2 EBV and molecular mechanisms that may account for this difference in cell transformation are now becoming understood. Study of geographic variation of EBV strains independent of the type 1/type 2 classification and systematic investigation of the relationship between viral strains, infection and disease are now becoming possible. So we should consider more directly whether viral sequence variation might play a role in the incidence of some EBV-associated diseases.

  4. Comparative Investigation of the Genomic Regions Involved in Antigenic Variation of the TprK Antigen among Treponemal Species, Subspecies, and Strains

    PubMed Central

    Brandt, Stephanie L.; Puray-Chavez, Maritza; Reid, Tara Brinck; Godornes, Charmie; Molini, Barbara J.; Benzler, Martin; Hartig, Jörg S.; Lukehart, Sheila A.; Centurion-Lara, Arturo

    2012-01-01

    Although the three Treponema pallidum subspecies (T. pallidum subsp. pallidum, T. pallidum subsp. pertenue, and T. pallidum subsp. endemicum), Treponema paraluiscuniculi, and the unclassified Fribourg-Blanc treponeme cause clinically distinct diseases, these pathogens are genetically and antigenically highly related and are able to cause persistent infection. Recent evidence suggests that the putative surface-exposed variable antigen TprK plays an important role in both treponemal immune evasion and persistence. tprK heterogeneity is generated by nonreciprocal gene conversion between the tprK expression site and donor sites. Although each of the above-mentioned species and subspecies has a functional tprK antigenic variation system, it is still unclear why the level of expression and the rate at which tprK diversifies during infection can differ significantly among isolates. To identify genomic differences that might affect the generation and expression of TprK variants among these pathogens, we performed comparative sequence analysis of the donor sites, as well as the tprK expression sites, among eight T. pallidum subsp. pallidum isolates (Nichols Gen, Nichols Sea, Chicago, Sea81-4, Dal-1, Street14, UW104, and UW126), three T. pallidum subsp. pertenue isolates (Gauthier, CDC2, and Samoa D), one T. pallidum subsp. endemicum isolate (Iraq B), the unclassified Fribourg-Blanc isolate, and the Cuniculi A strain of T. paraluiscuniculi. Synteny and sequence conservation, as well as deletions and insertions, were found in the regions harboring the donor sites. These data suggest that the tprK recombination system is harbored within dynamic genomic regions and that genomic differences might be an important key to explain discrepancies in generation and expression of tprK variants among these Treponema isolates. PMID:22661689

  5. Investigation of a noncontact strain measurement technique

    SciTech Connect

    Damiano, B.; Talarico, L.J.

    1996-05-01

    The goal of this project was to investigate the feasibility of a new noncontact technique for directly and continuously monitoring peak strain in rotating components. The technique utilizes the unique strain-sensitive magnetic material properties of transformation Induced Plasticity (TRIP) steel alloys to measure strain. These alloys are weakly magnetic when unstrained but become strongly ferromagnetic after mechanical deformation. A computer study was performed to determine whether the strain-induced change in the magnetic material properties of a TRIP steel gage bonded to a rotating component would cause significant perturbations in the magnetic flux of a stationary electromagnet. The effects of strain level, distance between the rotating component and the stationary electromagnet, and motion-induced eddy currents on flux perturbation magnitude were investigated. The calculated results indicate that a TRIP steel strain sensing element can cause a significant perturbation in the magnetic flux of a stationary electromagnet. The magnetic flux perturbation magnitude was found to be inversely proportional to the distance between the magnet face and the TRIP steel element and directly proportional to the TRIP steel strain level. The effect of motion-induced eddy currents on the magnetic flux was found to be negligible. It appears that the technique can be successfully applied to measure peak strain in rotating components; however, the sensitivity of the magnetic flux perturbation magnitude to the distance between the strain sensing element and the electromagnet may require making an independent proximity measurement.

  6. Strain variation in bacteriocuprein superoxide dismutase from symbiotic Photobacterium leiognathi.

    PubMed

    Dunlap, P V; Steinman, H M

    1986-02-01

    Photobacterium leiognathi ATCC 25521 (the type strain and light-organ symbiont of ponyfish) is one of the few bacteria that produces a copper-zinc superoxide dismutase, termed bacteriocuprein. We enzymologically and immunologically characterized the bacteriocuprein superoxide dismutases in sonicates from the type strain and nine additional strains of P. leiognathi, each isolated from the light organ of a separate ponyfish specimen, representing seven ponyfish species. The results indicate considerable strain variation. (i) The level of bacteriocuprein enzymatic activity varied greatly among strains from different species of ponyfish. In four of the nine strains, activity was low or undetectable, while in five strains it was comparable to that in the type strain. (ii) The bacteriocuprein in one strain had a specific activity much lower than that of the type strain, and in another strain, no bacteriocuprein activity and no cross-reactive polypeptide were detectable. (iii) A new electrophoretic variant, which migrated slower than that of strains from fish captured in Thailand and Japan, was identified in strains from fish captured in the Philippine Islands. (iv) Enzymological and immunological differences were observed in bacteriocupreins of strains from male and female specimens of the same ponyfish species, for the two species in which specimens of both sexes were examined. These observations raise the possibility that specific variations in the bacteriocupreins of P. leiognathi might be characteristic of the species, geographical source, or sex of the ponyfish host. Thus, the data indicate that the possibility of strain variation should be considered when other species are screened for bacteriocupreins.

  7. Phenotypic variation of fluoride responses between inbred strains of mice.

    PubMed

    Yan, Dong; Willett, Thomas L; Gu, Xiao-Mei; Martinez-Mier, E Angeles; Sardone, Laura; McShane, Lauren; Grynpas, Marc; Everett, Eric T

    2011-01-01

    Excessive systemic exposure to fluoride (F) can lead to disturbances in bone homeostasis and dental enamel development. We have previously shown strain-specific responses to F in the development of dental fluorosis (DF) and in bone formation/mineralization. The current study was undertaken to further investigate F responsive variations in bone metabolism and to determine possible relationships with DF susceptibility. Seven-week-old male mice from FVB/NJ, C57BL/6J, C3H/HeJ, A/J, 129S1/SvImJ, AKR/J, DBA/2J, and BALB/cByJ inbred strains were exposed to NaF (0 or 50 ppm as F(-)) in drinking water for 60 days. Sera were collected for F, Ca, Mg, PO(4), iPTH, sRANKL, and ALP levels. Bone marrow cells were subjected to ex vivo cell culture for osteoclast potential and CFU colony assays (CFU-fibroblast, CFU-osteoblast, CFU-erythrocyte/granulocyte/macrophage/megakaryocyte, CFU-granulocyte/macrophage, CFU-macrophage, and CFU-granulocyte). Femurs and vertebrae were subjected to micro-CT analyses, biomechanical testing, and F, Mg, and Ca content assays. DF was evaluated using quantitative fluorescence and clinical criteria. Strain-specific responses to F were observed for DF, serum studies, ex vivo cell culture studies, and bone quality. Among the strains, there were no patterns or significant correlations between DF severity and the actions of F on bone homeostasis (serum studies, ex vivo assays, or bone quality parameters). The genetic background continues to play a role in the actions of F on tooth enamel development and bone homeostasis. F exposure led to variable phenotypic responses between strains involving dental enamel development and bone metabolism.

  8. Phenotypic Variation of Fluoride Responses between Inbred Strains of Mice

    PubMed Central

    Yan, Dong; Willett, Thomas L.; Gu, Xiao-Mei; Martinez-Mier, E. Angeles; Sardone, Laura; McShane, Lauren; Grynpas, Marc; Everett, Eric T.

    2011-01-01

    Excessive systemic exposure to fluoride (F) can lead to disturbances in bone homeostasis and dental enamel development. We have previously shown strain-specific responses to F in the development of dental fluorosis (DF) and in bone formation/mineralization. The current study was undertaken to further investigate F responsive variations in bone metabolism and to determine possible relationships with DF susceptibility. Seven-week-old male mice from FVB/NJ, C57BL/6J, C3H/HeJ, A/J, 129S1/SvImJ, AKR/J, DBA/2J, and BALB/cByJ inbred strains were exposed to NaF (0 or 50 ppm as F–) in drinking water for 60 days. Sera were collected for F, Ca, Mg, PO4, iPTH, sRANKL, and ALP levels. Bone marrow cells were subjected to ex vivo cell culture for osteoclast potential and CFU colony assays (CFU-fibroblast, CFU-osteoblast, CFU-erythrocyte/granulocyte/macrophage/megakaryocyte, CFU-granulocyte/macrophage, CFU-macrophage, and CFU-granulocyte). Femurs and vertebrae were subjected to micro-CT analyses, biomechanical testing, and F, Mg, and Ca content assays. DF was evaluated using quantitative fluorescence and clinical criteria. Strain-specific responses to F were observed for DF, serum studies, ex vivo cell culture studies, and bone quality. Among the strains, there were no patterns or significant correlations between DF severity and the actions of F on bone homeostasis (serum studies, ex vivo assays, or bone quality parameters). The genetic background continues to play a role in the actions of F on tooth enamel development and bone homeostasis. F exposure led to variable phenotypic responses between strains involving dental enamel development and bone metabolism. PMID:21555858

  9. Genetic Variation in Virulence among Chalkbrood Strains Infecting Honeybees

    PubMed Central

    Vojvodic, Svjetlana; Jensen, Annette B.; Markussen, Bo; Eilenberg, Jørgen; Boomsma, Jacobus J.

    2011-01-01

    Ascosphaera apis causes chalkbrood in honeybees, a chronic disease that reduces the number of viable offspring in the nest. Although lethal for larvae, the disease normally has relatively low virulence at the colony level. A recent study showed that there is genetic variation for host susceptibility, but whether Ascosphaera apis strains differ in virulence is unknown. We exploited a recently modified in vitro rearing technique to infect honeybee larvae from three colonies with naturally mated queens under strictly controlled laboratory conditions, using four strains from two distinct A. apis clades. We found that both strain and colony of larval origin affected mortality rates. The strains from one clade caused 12–14% mortality while those from the other clade induced 71–92% mortality. Larvae from one colony showed significantly higher susceptibility to chalkbrood infection than larvae from the other two colonies, confirming the existence of genetic variation in susceptibility across colonies. Our results are consistent with antagonistic coevolution between a specialized fungal pathogen and its host, and suggest that beekeeping industries would benefit from more systematic monitoring of this chronic stress factor of their colonies. PMID:21966406

  10. Brain strain uncertainty due to shape variation in and simplification of head angular velocity profiles.

    PubMed

    Zhao, Wei; Ji, Songbai

    2017-04-01

    Head angular velocity, instead of acceleration, is more predictive of brain strains. Surprisingly, no study exists that investigates how shape variation in angular velocity profiles affects brain strains, beyond characteristics such as peak magnitude and impulse duration. In this study, we evaluated brain strain uncertainty due to variation in angular velocity profiles and further compared with that resulting from simplifying the profiles into idealized shapes. To do so, we used reconstructed head impacts from American National Football League for shape extraction and simulated head uniaxial coronal rotations from onset to full stop. The velocity profiles were scaled to maintain an identical peak velocity magnitude and duration in order to isolate the shape for investigation. Element-wise peak maximum principal strains from 44 selected impacts were obtained. We found that the shape of angular velocity profile could significantly affect brain strain magnitude (e.g., percentage difference of 4.29-17.89 % in the whole brain relative to the group average, with cumulative strain damage measure (CSDM) uncertainty range of 23.9 %) but not pattern (correlation coefficient of 0.94-0.99). Strain differences resulting from simplifying angular velocity profiles into idealized shapes were largely within the range due to shape variation, in both percentage difference and CSDM (signed difference of 3.91 % on average, with a typical range of 0-6 %). These findings provide important insight into the uncertainty or confidence in the performance of kinematics-based injury metrics. More importantly, they suggest the feasibility to simplify head angular velocity profiles into idealized shapes, at least within the confinements of the profiles evaluated, to enable real-time strain estimation via pre-computation in the future.

  11. Tectonic strain and paleomagnetism: experimental investigation

    NASA Astrophysics Data System (ADS)

    Borradaile, G.; Mothersill, J.

    1989-09-01

    A porous, clay-rich sandstone with a natural remanent magnetisation shows complex changes in the orientation of the remanence vector when the sandstone is subjected to experimental deformation, at 100 MPa, room temperature and constant natural strain rates of 1 × 10 -5 s -1. The paleomagnetic vector does not simply rotate away from the axis of compression. When the rock is shortened perpendicular to bedding the remanence vector rotates toward the bedding, as expected, but the remanence also rotates toward bedding when the rock is shortened parallel to bedding. Moreover, in some cases the remanence vector changes azimuth within the specimen during experimental deformation. Thus bedding anisotropy and the accompanying mineral-fabric anisotropy are more influential than strain in controlling deflections of the paleomagnetic vector in this study. This anisotropy also influences the post-deformational behaviour of remanence: 4 months after deformation, some cores shortened perpendicular to bedding relaxed their remanence vectors back towards the pre-deformational attitude whereas some other cores continued to show progressive changes. Intragranular, recoverable elastic strains in the magnetic grains may be partly responsible for the experimentally induced deflections of remanence.

  12. Molecular Basis for Strain Variation in the Saccharomyces cerevisiae Adhesin Flo11p

    PubMed Central

    Li, Li; Lipke, Peter N.; Dranginis, Anne M.

    2016-01-01

    ABSTRACT FLO11 encodes a yeast cell wall flocculin that mediates a variety of adhesive phenotypes in Saccharomyces cerevisiae. Flo11p is implicated in many developmental processes, including flocculation, formation of pseudohyphae, agar invasion, and formation of microbial mats and biofilms. However, Flo11p mediates different processes in different yeast strains. To investigate the mechanisms by which FLO11 determines these differences in colony morphology, flocculation, and invasion, we studied gene structure, function, and expression levels. Nonflocculent Saccharomyces cerevisiae Σ1278b cells exhibited significantly higher FLO11 mRNA expression, especially in the stationary phase, than highly flocculent S. cerevisiae var. diastaticus. The two strains varied in cell surface hydrophobicity, and Flo11p contributed significantly to surface hydrophobicity in S. cerevisiae var. diastaticus but not in strain Σ1278b. Sequencing of the FLO11 gene in S. cerevisiae var. diastaticus revealed strain-specific differences, including a 15-amino-acid insertion in the adhesion domain. Flo11p adhesion domains from strain Σ1278b and S. cerevisiae var. diastaticus were expressed and used to coat magnetic beads. The adhesion domain from each strain bound preferentially to homologous cells, and the preferences were independent of the cells in which the adhesion domains were produced. These results are consistent with the idea that strain-specific variations in the amino acid sequences in the adhesion domains cause different Flo11p flocculation activities. The results also imply that strain-specific differences in expression levels, posttranslational modifications, and allelic differences outside the adhesion domains have little effect on flocculation. IMPORTANCE As a nonmotile organism, Saccharomyces cerevisiae employs the cell surface flocculin Flo11/Muc1 as an important means of adapting to environmental change. However, there is a great deal of strain variation in the

  13. Sensing sheet: the response of full-bridge strain sensors to thermal variations for detecting and characterizing cracks

    NASA Astrophysics Data System (ADS)

    Tung, S.-T.; Glisic, B.

    2016-12-01

    Sensing sheets based on large-area electronics consist of a dense array of unit strain sensors. This new technology has potential for becoming an effective and affordable monitoring tool that can identify, localize and quantify surface damage in structures. This research contributes to their development by investigating the response of full-bridge unit strain sensors to thermal variations. Overall, this investigation quantifies the effects of temperature on thin-film full-bridge strain sensors monitoring uncracked and cracked concrete. Additionally, an empirical formula is developed to estimate crack width given an observed strain change and a measured temperature change. This research led to the understanding of the behavior of full-bridge strain sensors installed on cracked concrete and exposed to temperature variations. It proves the concept of the sensing sheet and its suitability for application in environments with variable temperature.

  14. Two-dimensional surface strain measurement based on a variation of Yamaguchi's laser-speckle strain gauge

    NASA Technical Reports Server (NTRS)

    Barranger, John P.

    1990-01-01

    A novel optical method of measuring 2-D surface strain is proposed. Two linear strains along orthogonal axes and the shear strain between those axes is determined by a variation of Yamaguchi's laser-speckle strain gage technique. It offers the advantages of shorter data acquisition times, less stringent alignment requirements, and reduced decorrelation effects when compared to a previously implemented optical strain rosette technique. The method automatically cancels the translational and rotational components of rigid body motion while simplifying the optical system and improving the speed of response.

  15. Investigation of a non-contact strain measurement technique

    SciTech Connect

    Talarico, L.J.; Damiano, B.

    1997-03-01

    The goal of this project was to investigate the feasibility of a new non-contact technique for directly and continuously monitoring peak strain in rotating components. The technique utilizes the unique strain-sensitive magnetic material properties of TRansformation Induced Plasticity (TRIP) steel alloys to measure strain. These alloys are weakly magnetic when unstrained but become strongly ferromagnetic after mechanical deformation. A computer study was performed to determine whether the strain-induced change in the magnetic material properties of a TRIP steel gage bonded to a rotating component would cause significant perturbations in the magnetic flux of a stationary electromagnet. The effects of strain level, distance between the rotating component and the stationary electromagnet, and motion-induced eddy currents on flux perturbation magnitude were investigated. The calculated results indicate that a TRIP steel strain sensing element can cause a significant perturbation in the magnetic flux of a stationary electromagnet. The magnetic flux perturbation magnitude was found to be inversely proportional to the distance between the magnet face and the TRIP steel element and directly proportional to the TRIP steel strain level. The effect of motion-induced eddy currents on the magnetic flux was found to be negligible. It appears that the technique can be successfully applied to measure peak strain in rotating components, however, the sensitivity of the magnetic flux perturbation magnitude to the distance between the strain sensing element and the electromagnet may require making an independent proximity measurement.

  16. Regional Variations in Mechanical Strain in the Posterior Human Sclera

    PubMed Central

    Fazio, Massimo A.; Grytz, Rafael; Bruno, Luigi; Girard, Michael J. A.; Gardiner, Stuart; Girkin, Christopher A.; Downs, J. Crawford

    2012-01-01

    Purpose. The goal of this study was to establish sectorial and regional variability in the mechanical strain of peripapillary and mid-peripheral sclera in normal eyes from elderly human donors. Methods. Ten pairs of normal eyes from human donors aged 57 to 90 years old were mechanically inflation-tested within 48 hours post mortem. The intact posterior scleral shells were pressurized from 5 to 45 mm Hg while the full-field three-dimensional displacements of the scleral surface were measured using laser speckle interferometry. The displacement field was fit to continuous and differentiable analytical functions, from which the full strain tensor of the outer scleral surface was calculated. Mean maximum principal (tensile) strain was computed for eight circumferential sectors (45° wide) within the peripapillary and mid-peripheral regions surrounding the optic nerve head (ONH). Results. Overall, the peripapillary sclera exhibited significantly higher tensile strain (1.2%) than mid-peripheral sclera (0.95%) for a 40 mm Hg IOP elevation (P < 0.00001). In the peripapillary region, the inferotemporal sector exhibited the highest tensile strain (1.45%) while the superior sector had the lowest (1.19%; P < 0.00001). Mid-peripheral scleral strains were lower but exhibited a similar sectorial pattern. Conclusions. Human posterior sclera exhibits complex regional mechanical behavior in response to acute IOP elevations from 5 to 45 mm Hg. Results indicate 1) the peripapillary sclera is subjected to significantly higher tensile strain than the adjacent mid-peripheral sclera, and 2) strains are significantly higher in the temporal and inferior quadrants of the peripapillary sclera, which may contribute to the increased prevalence of glaucomatous damage associated with these regions of the ONH. PMID:22700704

  17. Variation in genotype and higher virulence of a strain of Sporothrix schenckii causing disseminated cutaneous sporotrichosis.

    PubMed

    Zhang, Zhenying; Liu, Xiaoming; Lv, Xuelian; Lin, Jingrong

    2011-12-01

    Sporotrichosis is usually a localized, lymphocutaneous disease, but its disseminated type was rarely reported. The main objective of this study was to identify specific DNA sequence variation and virulence of a strain of Sporothrix schenckii isolated from the lesion of disseminated cutaneous sporotrichosis. We confirmed this strain to be S. schenckii by(®) tubulin and chitin synthase gene sequence analysis in addition to the routine mycological and partial ITS and NTS sequencing. We found a 10-bp deletion in the ribosomal NTS region of this strain, in reference to the sequence of control strains isolated from fixed cutaneous sporotrichosis. After inoculated into immunosuppressed mice, this strain caused more extensive system involvement and showed stronger virulence than the control strain isolated from a fixed cutaneous sporotrichosis. Our study thus suggests that different clinical manifestation of sporotrichosis may be associated with variation in genotype and virulence of the strain, independent of effects due to the immune status of the host.

  18. A variational justification of the assumed natural strain formulation of finite elements

    NASA Technical Reports Server (NTRS)

    Militello, Carmelo; Felippa, Carlos A.

    1991-01-01

    The objective is to study the assumed natural strain (ANS) formulation of finite elements from a variational standpoint. The study is based on two hybrid extensions of the Reissner-type functional that uses strains and displacements as independent fields. One of the forms is a genuine variational principle that contains an independent boundary traction field, whereas the other one represents a restricted variational principle. Two procedures for element level elimination of the strain field are discussed, and one of them is shown to be equivalent to the inclusion of incompatible displacement modes. Also, the 4-node C(exp 0) plate bending quadrilateral element is used to illustrate applications of this theory.

  19. (90377) Sedna: Investigation of Surface Compositional Variation

    NASA Astrophysics Data System (ADS)

    Barucci, M. A.; Morea Dalle Ore, C.; Alvarez-Candal, A.; de Bergh, C.; Merlin, F.; Dumas, C.; Cruikshank, D.

    2010-12-01

    The dwarf planet (90377) Sedna is one of the most remote solar system objects accessible to investigations. To better constrain its surface composition and to investigate the possible heterogeneity of the surface of Sedna, several observations have been carried out at ESO-VLT with the powerful spectrometer SINFONI observing simultaneously the H and K bands. The analyzed spectra (obtained in 2005, 2007, and 2008) show a non-uniform spectral signature, particularly in the K band. Spectral modeling using the Shkuratov radiative transfer code for surface scattering has been performed using the various sets of data, including previous observations at visible wavelengths and photometry at 3.6 and 4.5 μm by the Spitzer Space Telescope. The visible and near-infrared spectra can be modeled with organic materials (triton and titan tholin), serpentine, and H2O ice in fairly significant amounts, and CH4, N2, and C2H6 in varying trace amounts. One of the spectra obtained in 2005 October shows a different signature in the K band and is best modeled with CH3OH in place of CH4, with reduced amounts of serpentine and with the addition of olivine. The compositional surface heterogeneity can give input on the past history as well clues to the origin of this peculiar, distant object. Based on observations obtained at the VLT Observatory Cerro Paranal of European Southern Observatory, ESO, Chile, in the framework of proposal 275.C-5055 and Large Program 178-C-0036/0867.

  20. (90377) SEDNA: INVESTIGATION OF SURFACE COMPOSITIONAL VARIATION

    SciTech Connect

    Barucci, M. A.; De Bergh, C.; Merlin, F.; Morea Dalle Ore, C.; Cruikshank, D.; Alvarez-Candal, A.; Dumas, C.

    2010-12-15

    The dwarf planet (90377) Sedna is one of the most remote solar system objects accessible to investigations. To better constrain its surface composition and to investigate the possible heterogeneity of the surface of Sedna, several observations have been carried out at ESO-VLT with the powerful spectrometer SINFONI observing simultaneously the H and K bands. The analyzed spectra (obtained in 2005, 2007, and 2008) show a non-uniform spectral signature, particularly in the K band. Spectral modeling using the Shkuratov radiative transfer code for surface scattering has been performed using the various sets of data, including previous observations at visible wavelengths and photometry at 3.6 and 4.5 {mu}m by the Spitzer Space Telescope. The visible and near-infrared spectra can be modeled with organic materials (triton and titan tholin), serpentine, and H{sub 2}O ice in fairly significant amounts, and CH{sub 4}, N{sub 2}, and C{sub 2}H{sub 6} in varying trace amounts. One of the spectra obtained in 2005 October shows a different signature in the K band and is best modeled with CH{sub 3}OH in place of CH{sub 4}, with reduced amounts of serpentine and with the addition of olivine. The compositional surface heterogeneity can give input on the past history as well clues to the origin of this peculiar, distant object.

  1. A damage detection model for unbonded post-tensioning tendons based on relative strain variation in multi-strand anchors

    NASA Astrophysics Data System (ADS)

    Abdullah, A. B. M.; Rice, Jennifer A.; Hamilton, H. R.

    2014-03-01

    Post-tensioned segmental bridges are common throughout the US; however, in recent years, the incidence of tendon failure in bonded post-tensioned bridges has raised questions regarding their design, construction, and maintenance. These failures have led to the investigation of the applicability of using replaceable unbonded tendons in segmental construction and new methods for monitoring their condition. This paper presents a damage detection algorithm to identify strand breakage in unbonded tendons based on the relative variation of strains in the anchorage. In unbonded construction, the anchorage assembly usually undergoes a severe stress-state condition as the entire prestressing force only passes through the deviator and end anchorage locations. The strain distribution in the anchorage mechanism, therefore, goes through significant changes in response to the breakage of an individual wire or an entire strand in a multi-strand arrangement. In this way, breakage of a post-tensioning strand can be identified by observing a non-uniform variation of the strain field over the anchorage region in contrast to a uniform variation of strains due to environmental or traffic loading. A reduced scale laboratory experiment is performed followed by an extensive finite element simulation to conduct a parametric study with wire/strand breakages at different locations on multi-strand anchorages commonly used in industry. Based on the observed strain variations from simulation, a damage detection model is proposed that enables the adoption of an automated monitoring strategy to characterize the breakage programmatically.

  2. GENETIC VARIATION AMONG STRAINS OF PSEUDOPFIESTERIA SHUMWAYAE AND PFIESTERIA PISCICIDA (DINOPHYCEAE)(1).

    PubMed

    Small, Hamish J; Shields, Jeffrey D; Haas, Leonard W; Vogelbein, Wolfgang K; Moss, Jessica; Reece, Kimberly S

    2009-12-01

    The putatively toxic dinoflagellates Pseudopfiesteria shumwayae (Glasgow et J. M. Burkh.) Litaker, Steid., P. L. Mason, Shields et P. A. Tester and Pfiesteria piscicida Steid. et J. M. Burkh. have been implicated in massive fish kills and of having negative impacts on human health along the mid-Atlantic seaboard of the USA. Considerable debate still remains as to the mechanisms responsible for fish mortality (toxicity vs. micropredation) caused by these dinoflagellates. Genetic differences among these cultures have not been adequately investigated and may account for or correlate with phenotypic variability among strains within each species. Genetic variation among strains of Ps. shumwayae and P. piscicida was examined by PCR-RFLP analysis using cultures obtained from the Provasoli-Guillard National Center for Culture of Marine Phytoplankton (CCMP), as well as those from our own and other colleagues' collection efforts. Examination of restriction digest banding profiles for 22 strains of Ps. shumwayae revealed the presence of 10 polymorphic restriction endonuclease sites within the first and second internal transcribed spacers (ITS1 and ITS2) and the 5.8S gene of the rDNA complex, and the cytochrome oxidase subunit I (COI) gene. Three compound genotypes were represented within the 22 Ps. shumwayae strains. Conversely, PCR-RFLP examination of 14 strains of P. piscicida at the same ITS1, 5.8S, and ITS2 regions revealed only one variable restriction endonuclease site, located in the ITS1 region. In addition, a dinoflagellate culture listed as P. piscicida (CCMP 1928) and analyzed as part of this study was identified as closely related to Luciella masanensis P. L. Mason, H. J. Jeong, Litaker, Reece et Steid.

  3. Variation of the internal transcribed spacer 1 sequence within individual strains and among different strains of Neospora caninum.

    PubMed

    Gondim, Luis F P; Laski, Paul; Gao, Liying; McAllister, Milton M

    2004-02-01

    Small differences have been reported in the internal transcribed spacer 1 (ITS1) region among strains of Neospora caninum. We compared ITS1 sequences among 6 N. caninum strains analyzed in our laboratory, including 2 strains that have not been examined previously (NC-Illinois and NC-Bahia). Five sequences showed 100% similarity and also were identical to 7 of 11 sequences that were previously reported by others. In contrast, initial attempts to sequence the ITS1 of NC-Bahia generated 12 nucleotide differences compared with the other 5 strains, and several ambiguous bases. However, the single band containing the ITS1 region, as observed after electrophoresis on a 2% agarose gel, became divided into 2 distinct bands when reanalyzed using 5 or 10% polyacrylamide gel electrophoresis (PAGE), and the ITS1 within these separate bands were sequenced without ambiguity. The other 5 N. caninum strains were also reexamined using PAGE, and in each strain 2 distinct bands were discovered. In comparison, 2 strains of Toxoplasma gondii continued to show only 1 band when examined using PAGE. The ITS1 sequence of NC-Bahia, from Brazil, differs in several base pairs from those of North American and European strains of N. caninum. Intrastrain variation of the ITS1 region appears to be common in N. caninum, in contrast to T. gondii.

  4. Mapping QTL Contributing to Variation in Posterior Lobe Morphology between Strains of Drosophila melanogaster

    PubMed Central

    Hackett, Jennifer L.; Wang, Xiaofei; Smith, Brittny R.

    2016-01-01

    Closely-related, and otherwise morphologically similar insect species frequently show striking divergence in the shape and/or size of male genital structures, a phenomenon thought to be driven by sexual selection. Comparative interspecific studies can help elucidate the evolutionary forces acting on genital structures to drive this rapid differentiation. However, genetic dissection of sexual trait divergence between species is frequently hampered by the difficulty generating interspecific recombinants. Intraspecific variation can be leveraged to investigate the genetics of rapidly-evolving sexual traits, and here we carry out a genetic analysis of variation in the posterior lobe within D. melanogaster. The lobe is a male-specific process emerging from the genital arch of D. melanogaster and three closely-related species, is essential for copulation, and shows radical divergence in form across species. There is also abundant variation within species in the shape and size of the lobe, and while this variation is considerably more subtle than that seen among species, it nonetheless provides the raw material for QTL mapping. We created an advanced intercross population from a pair of phenotypically-different inbred strains, and after phenotyping and genotyping-by-sequencing the recombinants, mapped several QTL contributing to various measures of lobe morphology. The additional generations of crossing over in our mapping population led to QTL intervals that are smaller than is typical for an F2 mapping design. The intervals we map overlap with a pair of lobe QTL we previously identified in an independent mapping cross, potentially suggesting a level of shared genetic control of trait variation. Our QTL additionally implicate a suite of genes that have been shown to contribute to the development of the posterior lobe. These loci are strong candidates to harbor naturally-segregating sites contributing to phenotypic variation within D. melanogaster, and may also be those

  5. Utilization of Genomic Variations Among Xylella fastidiosa Strains for Improved Diagnostic Design

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Gram-negative, xylem-limited phytopathogenic bacterium Xylella fastidiosa causes economically important diseases in grapevine, citrus and many other plant species. Our recent whole genome comparative analysis of the four sequenced strains has identified genomic variation among these strains. The...

  6. Investigation of cyanobacteria in a controlled hyperbolic straining flow

    NASA Astrophysics Data System (ADS)

    Akbaridoust, Farzan; Philip, Jimmy; Marusic, Ivan

    2016-11-01

    Here we report a systematic study on the effect of straining flow on cyanobacteria, which are a cause of significant water contamination issues worldwide. We focus on the species Anaebena Circinalis. A micro-cross channel equipped with two online computer-controlled on-chip membrane valves was designed and fabricated using standard soft-lithography. The device produces a hyperbolic straining flow on a micron-scaled region similar to G. I. Taylor's four-roll mill at larger scale. It was used to investigate the behaviour of a single filament of cynobacteria in a crowded medium under an increasing uniform strain rate flow. The velocity field and the resulting uniform strain-rate was measured in the absence of bacteria filaments using micro-PIV. A large number of single filaments of bacteria were trapped and exposed to stain-rates over 2 to 15 s-1. Previous studies have reported anecdotal evidence of suspected mechanical damage to Anaebena Circinalis for strain rates considerably lower than the maximum values studied here. In our case, no mechanical damage was observed. This work was performed in part at the Melbourne Centre for Nanofabrication (MCN) in the Victorian Node of the Australian National Fabrication Facility (ANFF).

  7. Inbred strains of zebrafish exhibit variation in growth performance and myostatin expression following fasting.

    PubMed

    Meyer, Ben M; Froehlich, Jacob M; Galt, Nicholas J; Biga, Peggy R

    2013-01-01

    Although the zebrafish (Danio rerio) has been widely utilized as a model organism for several decades, there is little information available on physiological variation underlying genetic variation among the most commonly used inbred strains. This study evaluated growth performance using physiological and molecular markers of growth in response to fasting in six commonly used zebrafish strains [AB, TU, TL, SJA, WIK, and petstore (PET) zebrafish]. Fasting resulted in a standard decrease in whole blood glucose levels, a typical vertebrate glucose metabolism pattern, in AB, PET, TL, and TU zebrafish strains. Alternatively, fasting did not affect glucose levels in SJA and WIK zebrafish strains. Similarly, fasting had no effect on myostatin mRNA levels in AB, PET, TU, and WIK zebrafish strains, but decreased myostatin-1 and -2 mRNA levels in SJA zebrafish. Consistent with previous work, fasting increased myostatin-2 mRNA levels in TL zebrafish. These data demonstrate that variation is present in growth performance between commonly used inbred strains of zebrafish. These data can help future research endeavors by highlighting the attributes of each strain with regard to growth performance so that the most fitting strain may be utilized.

  8. Inbred strains of zebrafish exhibit variation in growth performance and myostatin expression following fasting

    PubMed Central

    Meyer, Ben M.; Froehlich, Jacob M.; Galt, Nicholas J.; Biga, Peggy R.

    2012-01-01

    Although the zebrafish (Danio rerio) has been widely utilized as a model organism for several decades, there is little information available on physiological variation underlying genetic variation among the most commonly used inbred strains. This study evaluated growth performance using physiological and molecular markers of growth in response to fasting in six commonly used zebrafish strains [AB, TU, TL, SJA, WIK, and petstore (PET) zebrafish]. Fasting resulted in a standard decrease in whole blood glucose levels, typical vertebrate glucose metabolism pattern, in AB, PET, TL, and TU zebrafish strains. Alternatively, fasting did not affect glucose levels in SJA and WIK zebrafish strains. Similarly, fasting had no effect on myostatin mRNA levels in AB, PET, TU, and WIK zebrafish strains, but decreased myostatin-1 and -2 mRNA levels in SJA zebrafish. Consistent with previous work, fasting increased myostatin-2 mRNA levels in TL zebrafish. These data demonstrate that variation is present in growth performance between commonly used inbred strains of zebrafish. These data can help future research endeavors by highlighting the attributes of each strain with regard to growth performance so that the most fitting strain may be utilized. PMID:23047051

  9. Genome-scale investigation of phenotypically distinct but nearly clonal Trichoderma strains

    PubMed Central

    Weld, Richard J.; Cox, Murray P.; Bradshaw, Rosie E.; McLean, Kirstin L.; Stewart, Alison; Steyaert, Johanna M.

    2016-01-01

    Biological control agents (BCA) are beneficial organisms that are applied to protect plants from pests. Many fungi of the genus Trichoderma are successful BCAs but the underlying mechanisms are not yet fully understood. Trichoderma cf. atroviride strain LU132 is a remarkably effective BCA compared to T. cf. atroviride strain LU140 but these strains were found to be highly similar at the DNA sequence level. This unusual combination of phenotypic variability and high DNA sequence similarity between separately isolated strains prompted us to undertake a genome comparison study in order to identify DNA polymorphisms. We further investigated if the polymorphisms had functional effects on the phenotypes. The two strains were clearly identified as individuals, exhibiting different growth rates, conidiation and metabolism. Superior pathogen control demonstrated by LU132 depended on its faster growth, which is a prerequisite for successful distribution and competition. Genome sequencing identified only one non-synonymous single nucleotide polymorphism (SNP) between the strains. Based on this SNP, we successfully designed and validated an RFLP protocol that can be used to differentiate LU132 from LU140 and other Trichoderma strains. This SNP changed the amino acid sequence of SERF, encoded by the previously undescribed single copy gene “small EDRK-rich factor” (serf). A deletion of serf in the two strains did not lead to identical phenotypes, suggesting that, in addition to the single functional SNP between the nearly clonal Trichoderma cf. atroviride strains, other non-genomic factors contribute to their phenotypic variation. This finding is significant as it shows that genomics is an extremely useful but not exhaustive tool for the study of biocontrol complexity and for strain typing. PMID:27190719

  10. Chlamydomonas Genome Resource for Laboratory Strains Reveals a Mosaic of Sequence Variation, Identifies True Strain Histories, and Enables Strain-Specific Studies

    PubMed Central

    2015-01-01

    Chlamydomonas reinhardtii is a widely used reference organism in studies of photosynthesis, cilia, and biofuels. Most research in this field uses a few dozen standard laboratory strains that are reported to share a common ancestry, but exhibit substantial phenotypic differences. In order to facilitate ongoing Chlamydomonas research and explain the phenotypic variation, we mapped the genetic diversity within these strains using whole-genome resequencing. We identified 524,640 single nucleotide variants and 4812 structural variants among 39 commonly used laboratory strains. Nearly all (98.2%) of the total observed genetic diversity was attributable to the presence of two, previously unrecognized, alternate haplotypes that are distributed in a mosaic pattern among the extant laboratory strains. We propose that these two haplotypes are the remnants of an ancestral cross between two strains with ∼2% relative divergence. These haplotype patterns create a fingerprint for each strain that facilitates the positive identification of that strain and reveals its relatedness to other strains. The presence of these alternate haplotype regions affects phenotype scoring and gene expression measurements. Here, we present a rich set of genetic differences as a community resource to allow researchers to more accurately conduct and interpret their experiments with Chlamydomonas. PMID:26307380

  11. Sequence analysis of pooled bacterial samples enables identification of strain variation in group A streptococcus

    PubMed Central

    Weldatsadik, Rigbe G.; Wang, Jingwen; Puhakainen, Kai; Jiao, Hong; Jalava, Jari; Räisänen, Kati; Datta, Neeta; Skoog, Tiina; Vuopio, Jaana; Jokiranta, T. Sakari; Kere, Juha

    2017-01-01

    Knowledge of the genomic variation among different strains of a pathogenic microbial species can help in selecting optimal candidates for diagnostic assays and vaccine development. Pooled sequencing (Pool-seq) is a cost effective approach for population level genetic studies that require large numbers of samples such as various strains of a microbe. To test the use of Pool-seq in identifying variation, we pooled DNA of 100 Streptococcus pyogenes strains of different emm types in two pools, each containing 50 strains. We used four variant calling tools (Freebayes, UnifiedGenotyper, SNVer, and SAMtools) and one emm1 strain, SF370, as a reference genome. In total 63719 SNPs and 164 INDELs were identified in the two pools concordantly by at least two of the tools. Majority of the variants (93.4%) from six individually sequenced strains used in the pools could be identified from the two pools and 72.3% and 97.4% of the variants in the pools could be mined from the analysis of the 44 complete Str. pyogenes genomes and 3407 sequence runs deposited in the European Nucleotide Archive respectively. We conclude that DNA sequencing of pooled samples of large numbers of bacterial strains is a robust, rapid and cost-efficient way to discover sequence variation. PMID:28361960

  12. Peculiar Features of Microstructure Formation and Microhardness Variations During Torsional Straining of Tantalum Specimens in Bridgman Anvils

    NASA Astrophysics Data System (ADS)

    Ditenberg, I. A.; Tymentsev, A. N.; Korznikov, A. V.

    2015-04-01

    Using the method of transmission electron microscopy, peculiar features of evolution of microstructure and variations in microhardness of Та are investigated under torsional loading in the Bridgman anvil as a function of plastic deformation at room temperature. A quantitative examination of grain and defect's structure of the material under study and the values of local internal stresses is performed in different loading stages. The mechanisms of formation of submicrocrystalline and nanostructured states are analyzed and so is the microstructure variation as a function of the defect-structure characteristics, strain level, and spacing from the axis of torsion.

  13. Whole Genome Analysis of 132 Clinical Saccharomyces cerevisiae Strains Reveals Extensive Ploidy Variation

    PubMed Central

    Zhu, Yuan O.; Sherlock, Gavin; Petrov, Dmitri A.

    2016-01-01

    Budding yeast has undergone several independent transitions from commercial to clinical lifestyles. The frequency of such transitions suggests that clinical yeast strains are derived from environmentally available yeast populations, including commercial sources. However, despite their important role in adaptive evolution, the prevalence of polyploidy and aneuploidy has not been extensively analyzed in clinical strains. In this study, we have looked for patterns governing the transition to clinical invasion in the largest screen of clinical yeast isolates to date. In particular, we have focused on the hypothesis that ploidy changes have influenced adaptive processes. We sequenced 144 yeast strains, 132 of which are clinical isolates. We found pervasive large-scale genomic variation in both overall ploidy (34% of strains identified as 3n/4n) and individual chromosomal copy numbers (36% of strains identified as aneuploid). We also found evidence for the highly dynamic nature of yeast genomes, with 35 strains showing partial chromosomal copy number changes and eight strains showing multiple independent chromosomal events. Intriguingly, a lineage identified to be baker’s/commercial derived with a unique damaging mutation in NDC80 was particularly prone to polyploidy, with 83% of its members being triploid or tetraploid. Polyploidy was in turn associated with a >2× increase in aneuploidy rates as compared to other lineages. This dataset provides a rich source of information on the genomics of clinical yeast strains and highlights the potential importance of large-scale genomic copy variation in yeast adaptation. PMID:27317778

  14. Chromosomal Copy Number Variation in Saccharomyces pastorianus Is Evidence for Extensive Genome Dynamics in Industrial Lager Brewing Strains

    PubMed Central

    van den Broek, M.; Bolat, I.; Nijkamp, J. F.; Ramos, E.; Luttik, M. A. H.; Koopman, F.; Geertman, J. M.; de Ridder, D.; Pronk, J. T.

    2015-01-01

    Lager brewing strains of Saccharomyces pastorianus are natural interspecific hybrids originating from the spontaneous hybridization of Saccharomyces cerevisiae and Saccharomyces eubayanus. Over the past 500 years, S. pastorianus has been domesticated to become one of the most important industrial microorganisms. Production of lager-type beers requires a set of essential phenotypes, including the ability to ferment maltose and maltotriose at low temperature, the production of flavors and aromas, and the ability to flocculate. Understanding of the molecular basis of complex brewing-related phenotypic traits is a prerequisite for rational strain improvement. While genome sequences have been reported, the variability and dynamics of S. pastorianus genomes have not been investigated in detail. Here, using deep sequencing and chromosome copy number analysis, we showed that S. pastorianus strain CBS1483 exhibited extensive aneuploidy. This was confirmed by quantitative PCR and by flow cytometry. As a direct consequence of this aneuploidy, a massive number of sequence variants was identified, leading to at least 1,800 additional protein variants in S. pastorianus CBS1483. Analysis of eight additional S. pastorianus strains revealed that the previously defined group I strains showed comparable karyotypes, while group II strains showed large interstrain karyotypic variability. Comparison of three strains with nearly identical genome sequences revealed substantial chromosome copy number variation, which may contribute to strain-specific phenotypic traits. The observed variability of lager yeast genomes demonstrates that systematic linking of genotype to phenotype requires a three-dimensional genome analysis encompassing physical chromosomal structures, the copy number of individual chromosomes or chromosomal regions, and the allelic variation of copies of individual genes. PMID:26150454

  15. Chromosomal Copy Number Variation in Saccharomyces pastorianus Is Evidence for Extensive Genome Dynamics in Industrial Lager Brewing Strains.

    PubMed

    van den Broek, M; Bolat, I; Nijkamp, J F; Ramos, E; Luttik, M A H; Koopman, F; Geertman, J M; de Ridder, D; Pronk, J T; Daran, J-M

    2015-09-01

    Lager brewing strains of Saccharomyces pastorianus are natural interspecific hybrids originating from the spontaneous hybridization of Saccharomyces cerevisiae and Saccharomyces eubayanus. Over the past 500 years, S. pastorianus has been domesticated to become one of the most important industrial microorganisms. Production of lager-type beers requires a set of essential phenotypes, including the ability to ferment maltose and maltotriose at low temperature, the production of flavors and aromas, and the ability to flocculate. Understanding of the molecular basis of complex brewing-related phenotypic traits is a prerequisite for rational strain improvement. While genome sequences have been reported, the variability and dynamics of S. pastorianus genomes have not been investigated in detail. Here, using deep sequencing and chromosome copy number analysis, we showed that S. pastorianus strain CBS1483 exhibited extensive aneuploidy. This was confirmed by quantitative PCR and by flow cytometry. As a direct consequence of this aneuploidy, a massive number of sequence variants was identified, leading to at least 1,800 additional protein variants in S. pastorianus CBS1483. Analysis of eight additional S. pastorianus strains revealed that the previously defined group I strains showed comparable karyotypes, while group II strains showed large interstrain karyotypic variability. Comparison of three strains with nearly identical genome sequences revealed substantial chromosome copy number variation, which may contribute to strain-specific phenotypic traits. The observed variability of lager yeast genomes demonstrates that systematic linking of genotype to phenotype requires a three-dimensional genome analysis encompassing physical chromosomal structures, the copy number of individual chromosomes or chromosomal regions, and the allelic variation of copies of individual genes.

  16. Stress Tolerance Variations in Saccharomyces cerevisiae Strains from Diverse Ecological Sources and Geographical Locations

    PubMed Central

    Zheng, Yan-Lin; Wang, Shi-An

    2015-01-01

    The budding yeast Saccharomyces cerevisiae is a platform organism for bioethanol production from various feedstocks and robust strains are desirable for efficient fermentation because yeast cells inevitably encounter stressors during the process. Recently, diverse S. cerevisiae lineages were identified, which provided novel resources for understanding stress tolerance variations and related shaping factors in the yeast. This study characterized the tolerance of diverse S. cerevisiae strains to the stressors of high ethanol concentrations, temperature shocks, and osmotic stress. The results showed that the isolates from human-associated environments overall presented a higher level of stress tolerance compared with those from forests spared anthropogenic influences. Statistical analyses indicated that the variations of stress tolerance were significantly correlated with both ecological sources and geographical locations of the strains. This study provides guidelines for selection of robust S. cerevisiae strains for bioethanol production from nature. PMID:26244846

  17. Population genomics and transcriptional consequences of regulatory motif variation in globally diverse Saccharomyces cerevisiae strains.

    PubMed

    Connelly, Caitlin F; Skelly, Daniel A; Dunham, Maitreya J; Akey, Joshua M

    2013-07-01

    Noncoding genetic variation is known to significantly influence gene expression levels in a growing number of specific cases; however, the patterns of genome-wide noncoding variation present within populations, the evolutionary forces acting on noncoding variants, and the relative effects of regulatory polymorphisms on transcript abundance are not well characterized. Here, we address these questions by analyzing patterns of regulatory variation in motifs for 177 DNA binding proteins in 37 strains of Saccharomyces cerevisiae. Between S. cerevisiae strains, we found considerable polymorphism in regulatory motifs across strains (mean π = 0.005) as well as diversity in regulatory motifs (mean 0.91 motifs differences per regulatory region). Population genetics analyses reveal that motifs are under purifying selection, and there is considerable heterogeneity in the magnitude of selection across different motifs. Finally, we obtained RNA-Seq data in 22 strains and identified 49 polymorphic DNA sequence motifs in 30 distinct genes that are significantly associated with transcriptional differences between strains. In 22 of these genes, there was a single polymorphic motif associated with expression in the upstream region. Our results provide comprehensive insights into the evolutionary trajectory of regulatory variation in yeast and the characteristics of a compendium of regulatory alleles.

  18. Population Genomics and Transcriptional Consequences of Regulatory Motif Variation in Globally Diverse Saccharomyces cerevisiae Strains

    PubMed Central

    Connelly, Caitlin F.; Skelly, Daniel A.; Dunham, Maitreya J.; Akey, Joshua M.

    2013-01-01

    Noncoding genetic variation is known to significantly influence gene expression levels in a growing number of specific cases; however, the patterns of genome-wide noncoding variation present within populations, the evolutionary forces acting on noncoding variants, and the relative effects of regulatory polymorphisms on transcript abundance are not well characterized. Here, we address these questions by analyzing patterns of regulatory variation in motifs for 177 DNA binding proteins in 37 strains of Saccharomyces cerevisiae. Between S. cerevisiae strains, we found considerable polymorphism in regulatory motifs across strains (mean π = 0.005) as well as diversity in regulatory motifs (mean 0.91 motifs differences per regulatory region). Population genetics analyses reveal that motifs are under purifying selection, and there is considerable heterogeneity in the magnitude of selection across different motifs. Finally, we obtained RNA-Seq data in 22 strains and identified 49 polymorphic DNA sequence motifs in 30 distinct genes that are significantly associated with transcriptional differences between strains. In 22 of these genes, there was a single polymorphic motif associated with expression in the upstream region. Our results provide comprehensive insights into the evolutionary trajectory of regulatory variation in yeast and the characteristics of a compendium of regulatory alleles. PMID:23619145

  19. Bond-length variation in InxGa1-xAs/InP strained epitaxial layers

    NASA Astrophysics Data System (ADS)

    Romanato, F.; de Salvador, D.; Berti, M.; Drigo, A.; Natali, M.; Tormen, M.; Rossetto, G.; Pascarelli, S.; Boscherini, F.; Lamberti, C.; Mobilio, S.

    1998-06-01

    Tensile and compressive InxGa1-xAs epilayers grown on [001] InP substrates have been analyzed by fluorescence-detected x-ray-absorption fine structure in order to investigate the length variation suffered by Ga-As and In-As atomic bonds under epitaxial strain. A morphological and structural analysis had previously been performed in order to select only pseudomorphic samples with high lattice quality. A clear variation of the nearest-neighbor distances proportional to the tetragonal distortion of the film has been detected. We discuss the relationship between the long- and short-range descriptions of strain accommodation in the framework of an analytical model.

  20. The generation gap: Proteome changes and strain variation during encystation in Giardia duodenalis.

    PubMed

    Emery, Samantha J; Pascovi, Dana; Lacey, Ernest; Haynes, Paul A

    2015-05-01

    The prevalence of Giardia duodenalis in humans is partly owed to its direct and simple life cycle, as well as the formation of the environmentally resistant and infective cysts. Proteomic and transcriptomic studies have previously analysed the encystation process using the well-characterised laboratory genomic strain, WB C6. This study presents the first quantitative study of encystation using pathogenically relevant and alternative assemblage A strains: the human-derived BRIS/82/HEPU/106 (H-106)and avian-derived BRIS/95/HEPU/2041 (B-2041). We utilised tandem MS/MS with a label-free quantitative approach to compare cysts and trophozoite life stages for strain variation, as well as confirm universal encystation markers of assemblage A. A total of 1061 non-redundant proteins were identified from both strains, including trophozoite- and cyst-specific proteomes and life-stage differentially expressed proteins. Additionally, 24 proteins previously classified in the literature as encystation-specific were confirmed as strain-independent markers of encystation. Functional cluster analysis of differentially expressed proteins saw significant overlap between strains, including protein trafficking and localisation in cysts, NEK kinase function, and carbohydrate metabolism in trophozoites. Two significant points of strain specific adaptations in cysts were also identified. B-2041 possessed major up-regulation of the ankyrin repeat protein 21.1 family compared to H-106. Furthermore, cysts of B-2041 retained near-complete VSP variant diversity between cysts and trophozoites, while H-106 lost 45% of its VSP variant diversity between life cycle stages, a constriction previously observed in studies of WB C6. This is the first report of strain variation in the cyst stage in G. duodenalis, and highlights cyst variation and its impacts on reinfection and life cycle success.

  1. Variation in intake of sweet and bitter solutions by inbred strains of golden hamsters.

    PubMed

    Frank, Marion E; Wada, Yumiko; Makino, Junshiro; Mizutani, Makoto; Umezawa, Hidehiko; Katsuie, Yasutomi; Hettinger, Thomas P; Blizard, David A

    2004-07-01

    Variation in intake of sweet and bitter solutions by inbred strains of laboratory mice has helped identify genes related to taste behaviors; but similar information is not available for golden hamsters (Mesocricetus auratus ), a species used much in taste research. Thus, 6-hour, 1-bottle intake by water-replete hamsters of 7 inbred strains was measured for water and 2 concentrations of sucrose, maltose, D-phenylalanine (D-Phe), and sodium saccharin, which are sweet; and quinine.HCl, L-phenylalanine (L-Phe), caffeine, and sucrose octaacetate (SOA), which are bitter to humans. Difference scores (DIF), calculated as solution intake minus mean baseline water intake (mL) for each animal, were evaluated by analysis of variance. Compared to ACN, CN, APA, APG, and CBN, five strains with similar DIF for all compounds, GN, an ancestral strain of ACNT, and ACNT preferred sucrose, caffeine, and SOA more strongly; ACNT also preferred saccharin and maltose more strongly and rejected quinine more strongly. Narrow sense heritabilities for the 6 compounds for which strain differences were revealed ranged from 0.31 to 0.57. Genetic correlations indicated the strain variations in intake of sucrose, saccharin, SOA, and caffeine were coupled; a statistical association with several possible interpretations. Intakes of the two amino acids, preferred D-Phe and aversive L-Phe, did not reveal strain differences, and heritability ranged from 0.13 to 0.23 for the two optical isomers. Thus, although, compared to mice, genetic variation in laboratory hamsters may be small, genetic differences that influence taste behaviors in existing strains may help identify relevant genes.

  2. Investigation on strain sensing properties of carbon-based nanocomposites for structural aircraft applications

    NASA Astrophysics Data System (ADS)

    Lamberti, Patrizia; Spinelli, Giovanni; Tucci, Vincenzo; Guadagno, Liberata; Vertuccio, Luigi; Russo, Salvatore

    2016-05-01

    The mechanical and electrical properties of a thermosetting epoxy resin particularly indicated for the realization of structural aeronautic components and reinforced with multiwalled carbon nanotubes (MWCNTs, at 0.3 wt%) are investigated for specimens subjected to cycles and different levels of applied strain (i.e. ɛ) loaded both in axial tension and flexural mode. It is found that the piezoresistive behavior of the resulting nanocomposite evaluated in terms of variation of the electrical resistance is strongly affected by the applied mechanical stress mainly due to the high sensibility and consequent rearrangement of the electrical percolating network formed by MWCNTs in the composite at rest or even under a small strain. In fact, the variations in electrical resistance that occur during the mechanical stress are correlated to the deformation exhibited by the nanocomposites. In particular, the overall response of electrical resistance of the composite is characterized by a linear increase with the strain at least in the region of elastic deformation of the material in which the gauge factor (i.e. G.F.) of the sensor is usually evaluated. Therefore, the present study aims at investigating the possible use of the nanotechnology for application of embedded sensor systems in composite structures thus having capability of self-sensing and of responding to the surrounding environmental changes, which are some fundamental requirements especially for structural aircraft monitoring applications.

  3. Derivation of a variational principle for plane strain elastic-plastic silk biopolymers

    NASA Astrophysics Data System (ADS)

    He, J. H.; Liu, F. J.; Cao, J. H.; Zhang, L.

    2014-01-01

    Silk biopolymers, such as spider silk and Bombyx mori silk, behave always elastic-plastically. An elastic-plastic model is adopted and a variational principle for the small strain, rate plasticity problem is established by semi-inverse method. A trial Lagrangian is constructed where an unknown function is included which can be identified step by step.

  4. Measurements of Local Strain Variation in Si(1-x)Ge(x)/Si Heterostructures

    NASA Technical Reports Server (NTRS)

    Bell, L. D.; Kaiser, W. J.; Manion, S. J.; Milliken, S. J.; Pike, W. T.; Fathauer, R. W.

    1995-01-01

    The energy splitting of the conduction-band minimum of Si(1-x), Ge(x), due to strain has been directly measured by the application of ballistic-electron-emission microscope (BEEM) spectroscopy to Ag/Si(1-x), Ge(x) structures. Experimental values for this conduction-band splitting agree well with calculations. For Au/Si(1-x), Ge(x), however, heterogeneity in the strain of the Si(1-x), Ge(x) layer is introduced by deposition of the Au. This variation is attributed to species interdiffusion, which produces a rough Si(1-x)Ge(x) surface. Preliminary modeling indicates that the observed roughness is consistent with the strain variation measured by BEEM.

  5. Immunological variation between inbred laboratory mouse strains: points to consider in phenotyping genetically immunomodified mice.

    PubMed

    Sellers, R S; Clifford, C B; Treuting, P M; Brayton, C

    2012-01-01

    Inbred laboratory mouse strains are highly divergent in their immune response patterns as a result of genetic mutations and polymorphisms. The generation of genetically engineered mice (GEM) has, in the past, used embryonic stem (ES) cells for gene targeting from various 129 substrains followed by backcrossing into more fecund mouse strains. Although common inbred mice are considered "immune competent," many have variations in their immune system-some of which have been described-that may affect the phenotype. Recognition of these immune variations among commonly used inbred mouse strains is essential for the accurate interpretation of expected phenotypes or those that may arise unexpectedly. In GEM developed to study specific components of the immune system, accurate evaluation of immune responses must take into consideration not only the gene of interest but also how the background strain and microbial milieu contribute to the manifestation of findings in these mice. This article discusses points to consider regarding immunological differences between the common inbred laboratory mouse strains, particularly in their use as background strains in GEM.

  6. Genetic Architecture of Ethanol-Responsive Transcriptome Variation in Saccharomyces cerevisiae Strains

    PubMed Central

    Lewis, Jeffrey A.; Broman, Aimee T.; Will, Jessica; Gasch, Audrey P.

    2014-01-01

    Natural variation in gene expression is pervasive within and between species, and it likely explains a significant fraction of phenotypic variation between individuals. Phenotypic variation in acute systemic responses can also be leveraged to reveal physiological differences in how individuals perceive and respond to environmental perturbations. We previously found extensive variation in the transcriptomic response to acute ethanol exposure in two wild isolates and a common laboratory strain of Saccharomyces cerevisiae. Many expression differences persisted across several modules of coregulated genes, implicating trans-acting systemic differences in ethanol sensing and/or response. Here, we conducted expression QTL mapping of the ethanol response in two strain crosses to identify the genetic basis for these differences. To understand systemic differences, we focused on “hotspot” loci that affect many transcripts in trans. Candidate causal regulators contained within hotspots implicate upstream regulators as well as downstream effectors of the ethanol response. Overlap in hotspot targets revealed additive genetic effects of trans-acting loci as well as “epi-hotspots,” in which epistatic interactions between two loci affected the same suites of downstream targets. One epi-hotspot implicated interactions between Mkt1p and proteins linked to translational regulation, prompting us to show that Mkt1p localizes to P bodies upon ethanol stress in a strain-specific manner. Our results provide a glimpse into the genetic architecture underlying natural variation in a stress response and present new details on how yeast respond to ethanol stress. PMID:24970865

  7. The variation of the yield stress of Ti alloys with strain rate at high temperatures

    SciTech Connect

    Rosen, R.S.; Paddon, S.P.; Kassner, M.E.

    1999-06-01

    This study extended investigation on the elevated-temperature yield-strength dependence of beta-phase titanium alloys on strain rate and temperature. Yield stresses were found to increase substantially with increasing strain rate at elevated temperatures due to the high strain-rate sensitivity of titanium at high temperatures. Above 1000 C, the strain-rate sensitivities were found to increase substantially with increasing temperature and/or decreasing strain rate. The six alloys examined were TIMETAL 21S, Ti-15-3-, Ti-6-4, Ti-13-11-3, Beta C, and Beta III. There was particular interest in determining the strain-rate sensitivity of these alloys through strain-rate change tests above 1000 C. The yield stresses of all the titanium alloys at temperatures above 1093 C were less than 1% of their ambient temperature values. strain hardening was negligible in the alloys tested at these high temperatures. Extended tensile ductilities of 100 to 200% were observed due to the pronounced strain-rare sensitivity. The rate controlling mechanism for plasticity, based on activation energy and the strain-rate sensitivity measurements, is discussed.

  8. Durability investigation of a group of strain gage pressure transducers

    NASA Technical Reports Server (NTRS)

    Lederer, P. S.; Hilten, J. S.

    1972-01-01

    A durability investigation was conducted on a group of eighteen bonded-wire strain gage pressure transducers with ranges of 0 to 15 psig and 0 to 100 psig using an improved version of a previously developed technique. Some of the transducers were subjected to 40 million pressure cycles at a 5-Hz rate at laboratory ambient conditions, others were cycled at a temperature of 150 F (65.6 C). The largest change in sensitivity observed was 0.22% for a 100-psig transducer subjected to 40 million pressure cycles at 150 F. The largest change in zero pressure output observed was 0.91% FS for the same transducer. None of the transducers failed completely as a result of cycling at or below full scale pressure.

  9. Genomic variations associated with attenuation in Mycobacterium avium subsp. paratuberculosis vaccine strains

    PubMed Central

    2013-01-01

    Background Mycobacterium avium subspecies paratuberculosis (MAP) whole cell vaccines have been widely used tools in the control of Johne’s disease in animals despite being unable to provide complete protection. Current vaccine strains derive from stocks created many decades ago; however their genotypes, underlying mechanisms and relative degree of their attenuation are largely unknown. Results Using mouse virulence studies we confirm that MAP vaccine strains 316 F, II and 2e have diverse but clearly attenuated survival and persistence characteristics compared with wild type strains. Using a pan genomic microarray we characterise the genomic variations in a panel of vaccine strains sourced from stocks spanning over 40 years of maintenance. We describe multiple genomic variations specific for individual vaccine stocks in both deletion (26–32 Kbp) and tandem duplicated (11–40 Kbp) large variable genomic islands and insertion sequence copy numbers. We show individual differences suitable for diagnostic differentiation between vaccine and wild type genotypes and provide evidence for functionality of some of the deleted MAP-specific genes and their possible relation to attenuation. Conclusions This study shows how culture environments have influenced MAP genome diversity resulting in large tandem genomic duplications, deletions and transposable element activity. In combination with classical selective systematic subculture this has led to fixation of specific MAP genomic alterations in some vaccine strain lineages which link the resulting attenuated phenotypes with deficiencies in high reactive oxygen species handling. PMID:23339684

  10. Geoelectrical, strain and tilt investigations of hydrological processes at the broadband Geodynamical Observatory Moxa, Germany

    NASA Astrophysics Data System (ADS)

    Hermann, Tobias; Kroner, Corinna; Jahr, Thomas

    2013-11-01

    The Geodynamic Observatory Moxa, located in Thuringia/Germany, is dedicated to studies of temporal deformations of the earth's crust and of variations of the gravity field. One of the essential issues with respect to these investigations is the reduction of the hydrological impact on the data of the gravimeters, strainmeters and tiltmeters. In order to optimise the reductions, we investigated the changes in the hydrological conditions in the woody mountain slope above the observatory with time-lapse electrical resistivity tomography (ERT), and analysed the strain and tilt measurements for prominent signatures of pore pressure induced subsurface deformations. Here we present the results for two profiles - parallel and perpendicular to the slope - measured with ERT during 33 campaigns between June 2007 and April 2010. Resistivity changes and variations of apparent soil moisture, inferred from ERT sections, were found to primarily occur in the first two metres of the subsurface. These variations can be related to subsurface flow in the upper two metres induced by precipitation events and snowmelts. Trees close to the profiles only show a minimum impact on the resistivity and soil moisture changes. Furthermore, systematic hydrologically induced deformations can be observed in hodographs of strain and tilt measurements for large precipitation events (> 80 mm) and snowmelts. In the strain data a short-term (< 3 days) dilatational signal is found with an amplitude of 20 nstrain to 60 nstrain and a long-term (> 7 days) compressional signal between 40 nstrain and 180 nstrain. The preferential N-S direction of long-term deformational signals (> 1 week) is also observed in the tilt data. The direction of tilt changes (25 nrad-120 nrad) is nearly parallel to the drainage direction of the nearby Silberleite creek indicating variations of pore pressure gradients during hydrological events. The results of these hydrological studies at the Geodynamic Observatory Moxa can be used

  11. Genetic structure and natural variation associated with host of origin in Penicillium expansum strains causing blue mould.

    PubMed

    Sanzani, S M; Montemurro, C; Di Rienzo, V; Solfrizzo, M; Ippolito, A

    2013-07-15

    Blue mould, caused by Penicillium expansum, is one of the most economically damaging postharvest diseases of pome fruits, although it may affect a wider host range, including sweet cherries and table grapes. Several reports on the role of mycotoxins in plant pathogenesis have been published, but few focussed on the influence of mycotoxins on the variation in host preference amongst producing fungi. In the present study the influence of the host on P. expansum pathogenicity/virulence was investigated, focussing mainly on the relationship with patulin production. Three P. expansum strain groups, originating from apples, sweet cherries, and table grapes (7 strains per host) were grown on their hosts of isolation and on artificial media derived from them. Strains within each P. expansum group proved to be more aggressive and produced more patulin than the other two groups under evaluation when grown on the host from which they originated. Table grape strains were the most aggressive (81% disease incidence) and strongest patulin producers (up to 554μg/g). The difference in aggressiveness amongst strains was appreciable only in the presence of a living host, suggesting that the complex pathogen-host interaction significantly influenced the ability of P. expansum to cause the disease. Incidence/severity of the disease and patulin production proved to be positively correlated, supporting the role of patulin as virulence/pathogenicity factor. The existence of genetic variation amongst isolates was confirmed by the High Resolution Melting method that was set up herein, which permitted discrimination of P. expansum from other species (P. chrysogenum and P. crustosum) and, within the same species, amongst the host of origin. Host effect on toxin production appeared to be exerted at a transcriptional level.

  12. Significant gene content variation characterizes the genomes of inbred mouse strains

    PubMed Central

    Cutler, Gene; Marshall, Lisa A.; Chin, Ni; Baribault, Helene; Kassner, Paul D.

    2007-01-01

    The contribution to genetic diversity of genomic segmental copy number variations (CNVs) is less well understood than that of single-nucleotide polymorphisms (SNPs). While less frequent than SNPs, CNVs have greater potential to affect phenotype. In this study, we have performed the most comprehensive survey to date of CNVs in mice, analyzing the genomes of 42 Mouse Phenome Consortium priority strains. This microarray comparative genomic hybridization (CGH)-based analysis has identified 2094 putative CNVs, with an average of 10 Mb of DNA in 51 CNVs when individual mouse strains were compared to the reference strain C57BL/6J. This amount of variation results in gene content that can differ by hundreds of genes between strains. These genes include members of large families such as the major histocompatibility and pheromone receptor genes, but there are also many singleton genes including genes with expected phenotypic consequences from their deletion or amplification. Using a whole-genome association analysis, we demonstrate that complex multigenic phenotypes, such as food intake, can be associated with specific copy number changes. PMID:17989247

  13. Gene Expression Variation Resolves Species and Individual Strains among Coral-Associated Dinoflagellates within the Genus Symbiodinium

    PubMed Central

    Parkinson, John E.; Baumgarten, Sebastian; Michell, Craig T.; Baums, Iliana B.; LaJeunesse, Todd C.; Voolstra, Christian R.

    2016-01-01

    Reef-building corals depend on symbiotic mutualisms with photosynthetic dinoflagellates in the genus Symbiodinium. This large microalgal group comprises many highly divergent lineages (“Clades A–I”) and hundreds of undescribed species. Given their ecological importance, efforts have turned to genomic approaches to characterize the functional ecology of Symbiodinium. To date, investigators have only compared gene expression between representatives from separate clades—the equivalent of contrasting genera or families in other dinoflagellate groups—making it impossible to distinguish between clade-level and species-level functional differences. Here, we examined the transcriptomes of four species within one Symbiodinium clade (Clade B) at ∼20,000 orthologous genes, as well as multiple isoclonal cell lines within species (i.e., cultured strains). These species span two major adaptive radiations within Clade B, each encompassing both host-specialized and ecologically cryptic taxa. Species-specific expression differences were consistently enriched for photosynthesis-related genes, likely reflecting selection pressures driving niche diversification. Transcriptional variation among strains involved fatty acid metabolism and biosynthesis pathways. Such differences among individuals are potentially a major source of physiological variation, contributing to the functional diversity of coral holobionts composed of unique host–symbiont genotype pairings. Our findings expand the genomic resources available for this important symbiont group and emphasize the power of comparative transcriptomics as a method for studying speciation processes and interindividual variation in nonmodel organisms. PMID:26868597

  14. Dissecting the Effect of Genetic Variation on the Hepatic Expression of Drug Disposition Genes across the Collaborative Cross Mouse Strains

    PubMed Central

    Nachshon, Aharon; Abu-Toamih Atamni, Hanifa J.; Steuerman, Yael; Sheikh-Hamed, Roa'a; Dorman, Alexandra; Mott, Richard; Dohm, Juliane C.; Lehrach, Hans; Sultan, Marc; Shamir, Ron; Sauer, Sascha; Himmelbauer, Heinz; Iraqi, Fuad A.; Gat-Viks, Irit

    2016-01-01

    A central challenge in pharmaceutical research is to investigate genetic variation in response to drugs. The Collaborative Cross (CC) mouse reference population is a promising model for pharmacogenomic studies because of its large amount of genetic variation, genetic reproducibility, and dense recombination sites. While the CC lines are phenotypically diverse, their genetic diversity in drug disposition processes, such as detoxification reactions, is still largely uncharacterized. Here we systematically measured RNA-sequencing expression profiles from livers of 29 CC lines under baseline conditions. We then leveraged a reference collection of metabolic biotransformation pathways to map potential relations between drugs and their underlying expression quantitative trait loci (eQTLs). By applying this approach on proximal eQTLs, including eQTLs acting on the overall expression of genes and on the expression of particular transcript isoforms, we were able to construct the organization of hepatic eQTL-drug connectivity across the CC population. The analysis revealed a substantial impact of genetic variation acting on drug biotransformation, allowed mapping of potential joint genetic effects in the context of individual drugs, and demonstrated crosstalk between drug metabolism and lipid metabolism. Our findings provide a resource for investigating drug disposition in the CC strains, and offer a new paradigm for integrating biotransformation reactions to corresponding variations in DNA sequences. PMID:27761138

  15. Additional Investigations of Ice Shape Sensitivity to Parameter Variations

    NASA Technical Reports Server (NTRS)

    Miller, Dean R.; Potapczuk, Mark G.; Langhals, Tammy J.

    2006-01-01

    A second parameter sensitivity study was conducted at the NASA Glenn Research Center's Icing Research Tunnel (IRT) using a 36 in. chord (0.91 m) NACA-0012 airfoil. The objective of this work was to further investigate the feasibility of using ice shape feature changes to define requirements for the simulation and measurement of SLD and appendix C icing conditions. A previous study concluded that it was feasible to use changes in ice shape features (e.g., ice horn angle, ice horn thickness, and ice shape mass) to detect relatively small variations in icing spray condition parameters (LWC, MVD, and temperature). The subject of this current investigation extends the scope of this previous work, by also examining the effect of icing tunnel spray-bar parameter variations (water pressure, air pressure) on ice shape feature changes. The approach was to vary spray-bar water pressure and air pressure, and then evaluate the effects of these parameter changes on the resulting ice shapes. This paper will provide a description of the experimental method, present selected experimental results, and conclude with an evaluation of these results.

  16. Variational Monte Carlo investigation of SU (N ) Heisenberg chains

    NASA Astrophysics Data System (ADS)

    Dufour, Jérôme; Nataf, Pierre; Mila, Frédéric

    2015-05-01

    Motivated by recent experimental progress in the context of ultracold multicolor fermionic atoms in optical lattices, we have investigated the properties of the SU (N) Heisenberg chain with totally antisymmetric irreducible representations, the effective model of Mott phases with m variational Monte Carlo based on Gutzwiller projected fermionic wave functions, we have been able to verify these predictions for a representative number of cases with N ≤10 and m ≤N /2 , and we have shown that the opening of a gap is associated to a spontaneous dimerization or trimerization depending on the value of m and N . We have also investigated the marginal cases where Abelian bosonization did not lead to any prediction. In these cases, variational Monte Carlo predicts that the ground state is critical with exponents consistent with conformal field theory.

  17. Arterial blood gases, electrolytes, and metabolic indices associated with hemorrhagic shock: inter- and intrainbred rat strain variation.

    PubMed

    Rose, Rajiv; Kheirabadi, Bijan S; Klemcke, Harold G

    2013-05-01

    We have previously shown interstrain variation (indicating a genetic basis), and intrastrain variation in survival time after hemorrhage (STaH) among inbred rat strains. To assist in understanding physiological mechanisms associated with STaH, we analyzed various arterial blood measures (ABM; pH, Paco2, oxygen content, sodium, potassium, glucose, bicarbonate, base excess, total CO2, and ionized calcium) in inbred rats. Rats from five inbred strains (n = 8-10/strain) were catheterized and, ≈ 24 h later, subjected to a conscious, controlled, 47% hemorrhage. ABM were measured at the start (initial) and end (final) of hemorrhage. Inter- and intrainbred strain variations of ABM were quantified and compared, and correlations of ABM with STaH were determined. All final ABM values and some initial ABM values were different among strains. Most ABM changed (Δ) during hemorrhage, and these changes differed among strains (P <0.03). Some strain-dependent correlations (r ≥ 0.7; P ≤ 0.05) existed between ΔABM and STaH (e.g., BN/Mcwi, ΔK(+), r = -0.84). Dark Agouti rats (longest STaH) had the smallest ΔPaco2, ΔHCO3(-), and Δbase excess, and the highest final glucose. High coefficients of variation (CVs, >10%), strain-specific CVs, and low intraclass correlation coefficients (rI < 0.5) defined the large intrastrain ABM variation that exceeded interstrain variation for most ABM. These results suggest that some ABM (K(+), Paco2, glucose, oxygen content) could predict subsequent STaH in an inbred rat strain-dependent manner. We speculate that whereas genetic differences may be responsible for interstrain variation, individual-specific epigenetic processes (e.g., DNA methylation) may be partly responsible for both inter- and intrastrain ABM variation.

  18. Variations in life tables of geographically isolated strains of the mosquito Culex quinquefasciatus.

    PubMed

    Suman, D S; Tikar, S N; Mendki, M J; Sukumaran, D; Agrawal, O P; Parashar, B D; Prakash, S

    2011-09-01

    Variations in the life tables and other biological attributes of four strains of Culex quinquefasciatus Say (Diptera: Culicidae) from geographically isolated regions of India that had been reared to the fifth generation in the laboratory were assessed under a standardized rearing regime under constant laboratory conditions. Two strains from arid habitats [Jodhpur (JD) and Bikaner (BKN)], one from a semi-arid inland habitat [Bathinda (BTH)], one from a semi-arid coastal habitat [Jamnagar (JMN)] and a standard laboratory strain (LAB) were compared. Horizontal life-table parameters were measured for each strain. Egg mortality ranged from 4.4% (JD and BTH) to 19.5% (BKN). The lowest rate of adult emergence and highest female : male ratio were found in BKN, and the highest rate of adult emergence and lowest female : male ratio were recorded in BTH. The egg-hatching period was longest in BTH and shortest in LAB. The duration from oviposition to adult emergence was longest in JD and shortest in LAB. Females lived longer than males in all strains. The net reproductive rates (R(0) ) of all field-derived strains (122.9-162.2) differed significantly between strains and were significantly greater than that of LAB (107.6). Similarly, both the intrinsic rate of increase (r(m) ) and finite rate of increase (λ) were found to be lower in LAB than in the field strains, but the mean generation time (T) and doubling time (DT) were longest in LAB. For several life-table attributes, JD and BTH clustered together and were more similar to JMN than to BKN and LAB. The results indicate that BTH, BKN and JD can be characterized as r-strategists, more so than JMN. Overall fecundity increased with age. Differences in annual temperature ranges and mean annual rainfall between locations were positively correlated (r = 0.46-0.97) with egg production, female life expectancy, R(0) , r(m) , λ and T. The results suggest that strains of Cx. quinquefasciatus from different geographical areas with

  19. Phylogeny and Strain Typing of Escherichia coli, Inferred from Variation at Mononucleotide Repeat Loci

    PubMed Central

    Diamant, Eran; Palti, Yniv; Gur-Arie, Riva; Cohen, Helit; Hallerman, Eric M.; Kashi, Yechezkel

    2004-01-01

    Multilocus sequencing of housekeeping genes has been used previously for bacterial strain typing and for inferring evolutionary relationships among strains of Escherichia coli. In this study, we used shorter intergenic sequences that contained simple sequence repeats (SSRs) of repeating mononucleotide motifs (mononucleotide repeats [MNRs]) to infer the phylogeny of pathogenic and commensal E. coli strains. Seven noncoding loci (four MNRs and three non-SSRs) were sequenced in 27 strains, including enterohemorrhagic (six isolates of O157:H7), enteropathogenic, enterotoxigenic, B, and K-12 strains. The four MNRs were also sequenced in 20 representative strains of the E. coli reference (ECOR) collection. Sequence polymorphism was significantly higher at the MNR loci, including the flanking sequences, indicating a higher mutation rate in the sequences flanking the MNR tracts. The four MNR loci were amplifiable by PCR in the standard ECOR A, B1, and D groups, but only one (yaiN) in the B2 group was amplified, which is consistent with previous studies that suggested that B2 is the most ancient group. High sequence compatibility was found between the four MNR loci, indicating that they are in the same clonal frame. The phylogenetic trees that were constructed from the sequence data were in good agreement with those of previous studies that used multilocus enzyme electrophoresis. The results demonstrate that MNR loci are useful for inferring phylogenetic relationships and provide much higher sequence variation than housekeeping genes. Therefore, the use of MNR loci for multilocus sequence typing should prove efficient for clinical diagnostics, epidemiology, and evolutionary study of bacteria. PMID:15066845

  20. Variation.

    ERIC Educational Resources Information Center

    Hamilton City Board of Education (Ontario).

    Suggestions for studying the topic of variation of individuals and objects (balls) to help develop elementary school students' measurement, comparison, classification, evaluation, and data collection and recording skills are made. General suggestions of variables that can be investigated are made for the study of human variation. Twelve specific…

  1. Molecular Characterization of Trichomonas vaginalis Strains Based on Identifying Their Probable Variations in Asymptomatic Patients

    PubMed Central

    SPOTIN, Adel; EGHTEDAR, Sanaz TAGHIZADEH; SHAHBAZI, Abbas; SALEHPOUR, Asghar; SARAFRAZ, Seddigheh; SHARIATZADEH, Seyyed Ali; MAHAMI-OSKOUEI, Mahmoud

    2016-01-01

    Background: The aim of this study was to identify the Trichomonas vaginalis strains/haplotypes based on identifying their probable variations in asymptomatic patients referred to Tabriz health centers, northwestern Iran. Methods: Sampling was taken from 50-suspected women to T. vaginalis in northwestern Iran. The obtained samples were smeared and cultured. Fifty DNA samples were extracted, amplified and identified by nested polymerase chain reaction and PCR-RFLP of actin gene using two endonuclease enzymes: MseI and RsaI. To reconfirm, the amplicons of actin gene were directly sequenced in order to identify the strains/haplotypes. Results: PCR-RFLP patterns, sequencing and phylogenetic analyses revealed definitely the presence of the G (n=22; 73.4%) and E (n=8; 26.6%) strains. Multiple alignments findings of genotype G showed five haplotypes and two amino acid substitutions in codons 192 and 211 although, no remarkable unique haplotype was found in genotype E. Conclusion: The accurate identification of T. vaginalis strains based on discrimination of their unknown haplotypes particularly those which are impacted on protein translation should be considered in parasite status, drug resistance, mixed infection with HIV and monitoring of asymptomatic trichomoniasis in the region. PMID:28127362

  2. The impact of anaerobiosis on strain-dependent phenotypic variations in Pseudomonas aeruginosa.

    PubMed

    Fang, Hao; Toyofuku, Masanori; Kiyokawa, Tatsunori; Ichihashi, Akihiro; Tateda, Kazuhiro; Nomura, Nobuhiko

    2013-01-01

    Bacteria participate in social behaviors by communicating with each other and forming surface-associated biofilms. In Pseudomonas aeruginosa, such social behaviors are affected greatly by the environment. Although P. aeruginosa survive under anaerobic conditions, previous studies indicate that quorum sensing is attenuated under such conditions, and that this leads to decreased activity of extracellular virulence factors as compared to aerobic conditions. Hence it has come into question whether P. aeruginosa are virulent under anaerobic conditions. Here, we compared various phenotypes between PAO1 and clinical isolates under anaerobic conditions. Our data revealed that when grown anaerobically, growth and cell morphology greatly differed among the strains. One of the clinical isolates produced comparable amounts of quorum-sensing signaling molecules and extracellular virulence factors under aerobic and anaerobic conditions, while the other strains showed low production under anaerobic conditions. Biofilm formation also exhibited strain-dependent variations, suggesting that there are several mechanisms that lead to biofilm formation under anaerobic conditions. Taken together, these results indicate that the impact of anaerobiosis on the social interactions of P. aeruginosa is strain dependent, and suggest that multiple regulatory mechanisms are involved in the regulation of quorum sensing and biofilm formation under anaerobic conditions.

  3. Theory of bond-length variations in relaxed, strained, and amorphous silicon-germanium alloys

    NASA Astrophysics Data System (ADS)

    Tzoumanekas, C.; Kelires, P. C.

    2002-11-01

    We present a theoretical study of bond-length and angle variations in relaxed, epitaxially strained, and amorphous Si1-xGex alloys. Our approach is based on Monte Carlo simulations, within the semigrand-canonical ensemble utilizing Ising-like identity flips, and in conjuction with energies calculated using the empirical potential of Tersoff [Phys. Rev. B 39, 5566 (1989)]. The method offers great statistical precision enabling us to extract clear variations through the whole composition range and for all types of bonds. Our simulations show that in relaxed crystalline alloys, where the lattice constant takes its natural value, bond lengths depend on composition x and that these variations are type specific, in agreement with recent experimental studies. Similar type-specific variations are found for the angles and the second-nearest-neighbor distances. This analysis also reveals that the negative deviation of the lattice constant from Vegard's law is mainly due to radial, and not angular, relaxations. In the epitaxially strained alloys, bond lengths decrease with x due to the two-dimensional confinement in the growth layers, in good agreement with predictions based on the macroscopic theory of elasticity. The dimer bond lengths at the (100)-(2×1)-reconstructed alloy surface remain nearly constant, and they are elongated with respect to the bulk values. In the amorphous alloys, we unravel a remarkable behavior of bond lengths at the dilute low-x alloy limit, characterized by strong relaxations and elongation. Furthermore, the bond lengths decrease with increasing Ge content. We offer an explanation of this effect based on the analysis of the enthalpy of formation of the amorphous alloy.

  4. Estimation of Myocardial Strain and Contraction Phase From Cine MRI Using Variational Data Assimilation.

    PubMed

    Tuyisenge, Viateur; Sarry, Laurent; Corpetti, Thomas; Innorta-Coupez, Elisabeth; Ouchchane, Lemlih; Cassagnes, Lucie

    2016-02-01

    This paper presents a new method to estimate left ventricle deformations using variational data assimilation that combines image observations from cine MRI and a dynamic evolution model of the heart. The main contribution of the model is that it embeds parameters modeling the contraction / relaxation process. It estimates myocardial motion and contraction parameters simultaneously, providing accurate complementary information for diagnosis. The method was applied to synthetic datasets with known ground truth motion and to 47 patients MRI datasets acquired at three slice locations (base, mid-ventricle and apex). Radial and circumferential strain components were compared to those obtained with a reference tag tracking software, exhibiting good agreement with intraclass correlation coefficients (ICC) above 0.8. Results were also evaluated against wall motion score indices used to assess cardiac kinetics in clinical practice. The assimilation process overcame issues caused by temporal artifacts as a result of the dynamic model, compared to using the observation term alone. Moreover we found that the new dynamic model, consisting of a piecewise transport model acting independently on systole and diastole performed better than the standard continuous transport model, which oversmooths temporal variations. Estimated strain and contraction parameters significantly correlated to clinical scores, making them promising features for diagnosing not only hypokinesia but also dyskinesia.

  5. Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow.

    PubMed

    Brunk, Elizabeth; George, Kevin W; Alonso-Gutierrez, Jorge; Thompson, Mitchell; Baidoo, Edward; Wang, George; Petzold, Christopher J; McCloskey, Douglas; Monk, Jonathan; Yang, Laurence; O'Brien, Edward J; Batth, Tanveer S; Martin, Hector Garcia; Feist, Adam; Adams, Paul D; Keasling, Jay D; Palsson, Bernhard O; Lee, Taek Soon

    2016-05-25

    Understanding the complex interactions that occur between heterologous and native biochemical pathways represents a major challenge in metabolic engineering and synthetic biology. We present a workflow that integrates metabolomics, proteomics, and genome-scale models of Escherichia coli metabolism to study the effects of introducing a heterologous pathway into a microbial host. This workflow incorporates complementary approaches from computational systems biology, metabolic engineering, and synthetic biology; provides molecular insight into how the host organism microenvironment changes due to pathway engineering; and demonstrates how biological mechanisms underlying strain variation can be exploited as an engineering strategy to increase product yield. As a proof of concept, we present the analysis of eight engineered strains producing three biofuels: isopentenol, limonene, and bisabolene. Application of this workflow identified the roles of candidate genes, pathways, and biochemical reactions in observed experimental phenomena and facilitated the construction of a mutant strain with improved productivity. The contributed workflow is available as an open-source tool in the form of iPython notebooks.

  6. Phenotypic variation amongst genotypically homogeneous Legionella pneumophila serogroup 1 isolates: implications for the investigation of outbreaks of Legionnaires' disease.

    PubMed Central

    Harrison, T. G.; Saunders, N. A.; Haththotuwa, A.; Hallas, G.; Birtles, R. J.; Taylor, A. G.

    1990-01-01

    One hundred and seventy-nine isolates of Legionella pneumophila serogroup 1, obtained from a site associated with an outbreak of Legionnaires' disease, were examined by monoclonal antibody subgrouping, restriction fragment length polymorphism typing, restriction endonuclease analysis and plasmid content. Nine distinct phenotypes were detected but at the genotypic level all strains were closely related. The data presented indicate that phenotypic variation of a single parent strain can occur within an environmental site. The implications of these findings are discussed in relation to the investigation of outbreaks of Legionnaires' disease. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 PMID:1969803

  7. Investigations on color variations of Morpho rhetenor butterfly wing scales

    NASA Astrophysics Data System (ADS)

    Liao, Guanglan; Zuo, Haibo; Jiang, Xuan; Yang, Xuefeng; Shi, Tielin

    2012-12-01

    Experiments and simulations are carried out to investigate the optical properties of Morpho rhetenor butterfly wing scales. The upper surface of a male Morpho rhetenor butterfly wing presents a single-layer of scales, the microstructures of which are responsible for the brilliant blue color. The color varies from cyan blue to yellow green and soon afterwards returns back to cyan blue when some ethanol is dropped on the upper surface. At the start of the ethanol volatilization process, the reflection spectrum remains stable. As the ethanol further volatilizes, the peak reflectance decreases slightly, then increases dramatically. Meanwhile, the peak wavelength keeps approximately constant, then decreases, and keeps almost stable at the end of the process. Therefore, the optical properties depend strongly on the varying ambient conditions, including the refractive index and the thickness of the packing medium. Moreover, the possible causes for the scales in dark green region after several dropping ethanol experiments are clarified. This research benefits our understanding of the color variation mechanisms of the wing scales, and provides inspiration for further studies and applications.

  8. Laboratory investigation of hospital outbreak caused by two different multiresistant Acinetobacter calcoaceticus subsp. anitratus strains.

    PubMed Central

    Vila, J; Almela, M; Jimenez de Anta, M T

    1989-01-01

    During a 7-month period, from December 1986 to June 1987, multiresistant strains of Acinetobacter calcoaceticus subsp. anitratus were isolated from 25 patients in a respiratory intensive care unit. The biochemical characteristics defined two groups of strains, group 1 (14 strains) and group 2 (11 strains). Both groups had the same biochemical characteristics, but group 2 strains could assimilate adipate and phenyl acetate. Moreover, of 16 antibiotics tested only netilmicin and imipenem had some inhibitory activity for group 1 strains; group 2 strains were susceptible to mezlocillin, piperacillin, and ticarcillin. Plasmid profiles of the groups were also different. The results of a laboratory investigation (biochemical characteristics, antibiotic susceptibility, and plasmid isolation) identified two different A. calcoaceticus subsp. anitratus strains as the causes of the outbreak. Images PMID:2745682

  9. The influence of climatically-driven surface loading variations on continental strain and seismicity

    NASA Astrophysics Data System (ADS)

    Craig, Tim; Calais, Eric; Fleitout, Luce; Bollinger, Laurent; Scotti, Oona

    2016-04-01

    In slowly deforming regions of plate interiors, secondary sources of stress and strain can result in transient deformation rates comparable to, or greater than, the background tectonic rates. Highly variable in space and time, these transients have the potential to influence the spatio-temporal distribution of seismicity, interfering with any background tectonic effects to either promote or inhibit the failure of pre-existing faults, and potentially leading to a clustered, or 'pulse-like', seismic history. Here, we investigate the ways in which the large-scale deformation field resulting from climatically-controlled changes in surface ice mass over the Pleistocene and Holocene may have influenced not only the seismicity of glaciated regions, but also the wider seismicity around the ice periphery. We first use a set of geodynamic models to demonstrate that a major pulse of seismic activity occurring in Fennoscandia, coincident with the time of end-glaciation, occurred in a setting where the contemporaneous horizontal strain-rate resulting from the changing ice mass, was extensional - opposite to the reverse sense of coseismic displacement accommodated on these faults. Therefore, faulting did not release extensional elastic strain that was building up at the time of failure, but compressional elastic strain that had accumulated in the lithosphere on timescales longer than the glacial cycle, illustrating the potential for a non-tectonic trigger to tap in to the background tectonic stress-state. We then move on to investigate the more distal influence that changing ice (and ocean) volumes may have had on the evolving strain field across intraplate Europe, how this is reflected in the seismicity across intraplate Europe, and what impact this might have on the paleoseismic record.

  10. Metabolic response of Alicycliphilus denitrificans strain BC toward electron acceptor variation.

    PubMed

    Oosterkamp, Margreet J; Boeren, Sjef; Plugge, Caroline M; Schaap, Peter J; Stams, Alfons J M

    2013-10-01

    Alicycliphilus denitrificans is a versatile, ubiquitous, facultative anaerobic bacterium. Alicycliphilus denitrificans strain BC can use chlorate, nitrate, and oxygen as electron acceptor for growth. Cells display a prolonged lag-phase when transferred from nitrate to chlorate and vice versa. Furthermore, cells adapted to aerobic growth do not easily use nitrate or chlorate as electron acceptor. We further investigated these responses of strain BC by differential proteomics, transcript analysis, and enzyme activity assays. In nitrate-adapted cells transferred to chlorate and vice versa, appropriate electron acceptor reduction pathways need to be activated. In oxygen-adapted cells, adaptation to the use of chlorate or nitrate is likely difficult due to the poorly active nitrate reduction pathway and low active chlorate reduction pathway. We deduce that the Nar-type nitrate reductase of strain BC also reduces chlorate, which may result in toxic levels of chlorite if cells are transferred to chlorate. Furthermore, the activities of nitrate reductase and nitrite reductase appear to be not balanced when oxygen-adapted cells are shifted to nitrate as electron acceptor, leading to the production of a toxic amount of nitrite. These data suggest that strain BC encounters metabolic challenges in environments with fluctuations in the availability of electron acceptors. All MS data have been deposited in the ProteomeXchange with identifier PXD000258.

  11. Experimental Investigations of Woven Textile Tape as Strain Sensor

    NASA Astrophysics Data System (ADS)

    Kannaian, T.; Naveen, V. S.; Muthukumar, N.; Thilagavathi, G.

    2015-10-01

    In this article, a strain sensitive textile based elastomeric tape sensor has been developed and process parameters for sensor development are optimized. Polyester yarns are used as base threads and rubber threads are used as elastomer for the sensor development. The sensor has been developed with the help of narrow width tape loom by introducing the silver coated nylon yarn in the middle of the tape structure. The influence of weave structure, number of conductive threads and rubber thread tension on sensor development has been optimized by using the Box-Behnken method and the results are analyzed using the Design expert software. From the results, it is found that six numbers of conductive threads in a plain weave structure with rubber thread tension of 750 g is suitable for the sensor to give high gauge factor of 1.626.

  12. Brain transcriptome variation among behaviorally distinct strains of zebrafish (Danio rerio)

    PubMed Central

    2012-01-01

    Background Domesticated animal populations often show profound reductions in predator avoidance and fear-related behavior compared to wild populations. These reductions are remarkably consistent and have been observed in a diverse array of taxa including fish, birds, and mammals. Experiments conducted in common environments indicate that these behavioral differences have a genetic basis. In this study, we quantified differences in fear-related behavior between wild and domesticated zebrafish strains and used microarray analysis to identify genes that may be associated with this variation. Results Compared to wild zebrafish, domesticated zebrafish spent more time near the water surface and were more likely to occupy the front of the aquarium nearest a human observer. Microarray analysis of the brain transcriptome identified high levels of population variation in gene expression, with 1,749 genes significantly differentially expressed among populations. Genes that varied among populations belonged to functional categories that included DNA repair, DNA photolyase activity, response to light stimulus, neuron development and axon guidance, cell death, iron-binding, chromatin reorganization, and homeobox genes. Comparatively fewer genes (112) differed between domesticated and wild strains with notable genes including gpr177 (wntless), selenoprotein P1a, synaptophysin and synaptoporin, and acyl-CoA binding domain containing proteins (acbd3 and acbd4). Conclusions Microarray analysis identified a large number of genes that differed among zebrafish populations and may underlie behavioral domestication. Comparisons with similar microarray studies of domestication in rainbow trout and canids identified sixteen evolutionarily or functionally related genes that may represent components of shared molecular mechanisms underlying convergent behavioral evolution during vertebrate domestication. However, this conclusion must be tempered by limitations associated with comparisons

  13. Linearization of CMOS Hot-Electron Injectors for Self-Powered Monitoring of Biomechanical Strain Variations.

    PubMed

    Zhou, Liang; Chakrabartty, Shantanu

    2017-04-01

    In our previous work we demonstrated that by eliminating regulation and rectification modules from the energy harvesting pathway, the minimum activation power of a piezoelectricity-driven hot-electron injector (p-HEI) can be reduced down to a few nanowatts. As a result the p-HEI device could be used for self-powered, in-vivo recording of biomechanical strain variations. However, for large magnitudes of input strain energy, the response of the modified p-HEI sensor was found to be quasi-linear with respect to the number of loading cycles, which made the calibration of the sensor difficult across a wide variety of biomedical applications. In this paper we propose a compensation circuit that is able to linearize the response of the p-HEI injector over a wide range of input power while maintaining a low activation threshold. The compensation circuit uses a combination of a storage capacitor and a non-linear resistor which produces a compressive input-output response required for linearization. Using prototypes fabricated in a 0.5-μm bulk CMOS process we validate the functionality of the injector and demonstrate that it can achieve a linear injection response for input power ranging from 5 nW to 1.5 μW.

  14. Along-strike Variations in Active Strain Accumulation in the Northwest Himalaya

    NASA Astrophysics Data System (ADS)

    Morell, K. D.; Ahmad, T.; Sandiford, M.; Codilean, A. T.; Fulop, R. H.

    2015-12-01

    The spatial distribution of channel steepness, erosion rate, and physiographic data highlight pronounced along-strike changes in active strain accumulation in the northwest Himalaya. In particular, the data suggest that the mid-crustal ramp of the Main Himalayan Thrust could merge along-strike with an active portion of the Main Boundary Thrust near longitude ~77º E. This along-strike change in active fault geometry also coincides with the lateral termination of both lesser and greater Himalayan sequences, a significant reduction in total shortening within the wedge, and pronounced variations in regional seismicity. Recent activity along extensional structures in the high Himalaya of this same region appears to have led to significant reorganization, modification and capture of the Sutlej River basin, one of the largest Himalayan river systems. Given the recent 2015 Gorkha earthquake along a comparable section ~500-km along strike, these new constraints on active fault architecture could have regional implications for how strain is partitioned along seismogenic faults in the northwest Himalaya.

  15. Cellular basis of morphological variation and temperature-related plasticity in Drosophila melanogaster strains with divergent wing shapes.

    PubMed

    Torquato, Libéria Souza; Mattos, Daniel; Matta, Bruna Palma; Bitner-Mathé, Blanche Christine

    2014-12-01

    Organ shape evolves through cross-generational changes in developmental patterns at cellular and/or tissue levels that ultimately alter tissue dimensions and final adult proportions. Here, we investigated the cellular basis of an artificially selected divergence in the outline shape of Drosophila melanogaster wings, by comparing flies with elongated or rounded wing shapes but with remarkably similar wing sizes. We also tested whether cellular plasticity in response to developmental temperature was altered by such selection. Results show that variation in cellular traits is associated with wing shape differences, and that cell number may play an important role in wing shape response to selection. Regarding the effects of developmental temperature, a size-related plastic response was observed, in that flies reared at 16 °C developed larger wings with larger and more numerous cells across all intervein regions relative to flies reared at 25 °C. Nevertheless, no conclusive indication of altered phenotypic plasticity was found between selection strains for any wing or cellular trait. We also described how cell area is distributed across different intervein regions. It follows that cell area tends to decrease along the anterior wing compartment and increase along the posterior one. Remarkably, such pattern was observed not only in the selected strains but also in the natural baseline population, suggesting that it might be canalized during development and was not altered by the intense program of artificial selection for divergent wing shapes.

  16. Intraspecific Phenotypic Variation and Morphological Divergence of Strains of Folsomia candida (Willem) (Collembola: Isotomidae), the "Standard" Test Springtaill

    PubMed Central

    Tully, Thomas; Potapov, Mikhail

    2015-01-01

    We describe and compare the external morphology of eleven clonal strains and one sexual lineage of the globally distributed Folsomia candida, known as “standard” test Collembola. Of the 18 morphological characters studied, we measured 14 to have significant between-strains genetic variations, 9 of these had high heritabilities (>78%). The quantified morphological polymorphism was used to analyse the within-species relationships between strains by using both a parsimony analysis and a distance tree. These two detailed morphological phylogenies have revealed that the parthenogenetic strains grouped themselves into two major clades. However the exact position of the sexual strain remains unclear and further analysis is needed to confirm its exact relationship with the parthenogenetic ones. The two morphologically based clades were found to be the same as the ones previously described using molecular analysis. This shows that despite large within-strain variations, morphological characters can be used to differentiate some strains that have diverged within a single morphospecies. We discuss the potential evolutionary interpretations and consequences of these different levels of phenotypic variability. PMID:26355293

  17. Variation of consumer contact with household products: a preliminary investigation.

    PubMed

    Weegels, M E; van Veen, M P

    2001-06-01

    Little information is available on product use by consumers, which severely hampers exposure estimation for consumer products. This article describes actual contact with several consumer products, specifically dishwashing detergents, cleaning products, and hair styling products. How and where products are handled, as well as the duration, frequency, and amount of use were studied by means of diaries, in-home observations, and measurements. This study addressed the question, "To what extent are frequency, duration, and amount of use associated?" Findings showed that there was a large intra- as well as interindividual variation in frequency, duration, and amount of use, with the interindividual variation being considerably larger. At the same time, results showed that, for a given activity, users tended to follow their own routine. Few relations were found among frequency, duration, and amount of use. It was concluded that among persons, frequency, duration, and amount of product act in practice as independent parameters. Diaries appear to be quite suitable for gaining insight into frequently used products. Observations of usage, recorded on video, were indispensable for obtaining particular information on product use. In addition, home visits enabled the collection of specific measurements. Although diaries and home visits are time-consuming, the combination provided insight into variation as well as relations among frequency, duration, and amount of use.

  18. Evidence of horizontal transfer as origin of strain to strain variation of the tyramine production trait in Lactobacillus brevis.

    PubMed

    Coton, Emmanuel; Coton, Monika

    2009-02-01

    Lactobacillus brevis strains with the ability to decarboxylate tyrosine to tyramine have been described and the involvement of several genes constituting a tyrdc operon at the chromosomal level has been demonstrated in this species. In this study, the existence of Lb. brevis strains unable to form tyramine was observed. In order to evaluate if the tyramine-producing ability was strain-dependent or if it could be correlated to the existence of a new species or subspecies, different isolates were analysed. Analysis by M13-RAPD and sequencing of 16S rDNA, 16S-23S ISR and house-keeping gene recA confirmed that all the isolates belonged to the Lb. brevis species. Analysis of the TyrDC pathway encoding operon region in representative strains indicated the existence of a polymorphism. The genetic differences observed showed that the tyrosine decarboxylating ability is not a Lb. brevis species trait but that it is strain-dependent within this species and suggest that the genes encoding the tyramine-producing pathway constitute a genomic island.

  19. Investigation of the mechanical behavior of kangaroo humeral head cartilage tissue by a porohyperelastic model based on the strain-rate-dependent permeability.

    PubMed

    Thibbotuwawa, Namal; Oloyede, Adekunle; Senadeera, Wijitha; Li, Tong; Gu, YuanTong

    2015-11-01

    Solid-interstitial fluid interaction, which depends on tissue permeability, is significant to the strain-rate-dependent mechanical behavior of humeral head (shoulder) cartilage. Due to anatomical and biomechanical similarities to that of the human shoulder, kangaroos present a suitable animal model. Therefore, indentation experiments were conducted on kangaroo shoulder cartilage tissues from low (10(-4)/s) to moderately high (10(-2)/s) strain-rates. A porohyperelastic model was developed based on the experimental characterization; and a permeability function that takes into account the effect of strain-rate on permeability (strain-rate-dependent permeability) was introduced into the model to investigate the effect of rate-dependent fluid flow on tissue response. The prediction of the model with the strain-rate-dependent permeability was compared with those of the models using constant permeability and strain-dependent permeability. Compared to the model with constant permeability, the models with strain-dependent and strain-rate-dependent permeability were able to better capture the experimental variation at all strain-rates (p < 0.05). Significant differences were not identified between models with strain-dependent and strain-rate-dependent permeability at strain-rate of 5 × 10(-3)/s (p = 0.179). However, at strain-rate of 10(-2)/s, the model with strain-rate-dependent permeability was significantly better at capturing the experimental results (p < 0.005). The findings thus revealed the significance of rate-dependent fluid flow on tissue behavior at large strain-rates, which provides insights into the mechanical deformation mechanisms of cartilage tissues.

  20. Investigating time patterns of variation in radiation cancer associations

    PubMed Central

    Richardson, D; Ashmore, J

    2005-01-01

    Aims: In occupational settings, carcinogenic exposures are often repeated or protracted over time. The time pattern of exposure accrual may influence subsequent temporal patterns of cancer risk. The authors present several simple models that may be used to evaluate the influence of time since exposure or age at exposure on cancer incidence or mortality in an occupational cohort. Methods: A cohort of 40 415 nuclear industry workers was identified via the Canadian National Dose Registry. Vital status and cause of death were ascertained through 1994. Associations between ionising radiation and mortality due to lung cancer, leukaemia, and cancers other than lung and leukaemia were quantified using conditional logistic regression models with risk sets constructed by incidence density sampling. A step function, a bilinear function, and a sigmoid function were used to evaluate temporal variation in exposure effects. Results: Step and sigmoid functions were used to explore latency and morbidity periods. For analyses of lung cancer, leukaemia, and other cancers the best fitting models were obtained when exposure assignment was lagged by 13, 0, and 5 years, respectively. A bilinear function was used to evaluate whether exposure effects diminished with time since exposure. In analyses of lung cancer and leukaemia, there was evidence that radiation effects attenuated with protracted time since exposure. In analyses of age at exposure, there was evidence of variation in radiation mortality associations for analyses of lung cancer and leukaemia; discounting radiation doses accrued at younger ages (for example, 15–35 years) led to significant improvements in model fit. Conclusions: This paper illustrates empirical approaches to evaluating temporal variation in the effect of a protracted exposure on disease risk. PMID:16046608

  1. Investigation of the Dynamic Strain Aging and Mechanical Properties in Alloy-625 with Different Microstructures

    NASA Astrophysics Data System (ADS)

    Chatterjee, Arnomitra; Sharma, Garima; Tewari, R.; Chakravartty, J. K.

    2015-03-01

    Tensile tests were carried out on service exposed Alloy 625 ammonia cracker tube used at heavy water production plant to study the effect of microstructure on the serrated yielding and mechanical properties of the material. Owing to temperature gradient during service exposure, the microstructure was different in top, middle, and bottom sections of the tube. Variation of flow stress, ductility, and average work hardening were monitored with temperature. In the present work, emphasis was given on the study of serrated yielding in the service exposed Alloy 625. Detail investigations were made to study the effect of microstructure on the underlying mechanism of dynamic strain aging of the material. The study revealed that both the normal and the inverse Portevin-Le Chatelier effect (PLC) occured in the material at lower and higher temperature regime, respectively. While the normal PLC dynamics was associated with locking of dislocations by interstitial carbon atoms, the inverse one was accomplished by the dislocation pinning by substitutional Mo atoms. Further analyses identified that the basic deformation mechanism was different in middle and bottom samples as that in the top samples which was reflected in the difference in their respective activation energy and stress drop magnitude.

  2. Variations in mitochondrial membrane potential correlate with malic acid production by natural isolates of Saccharomyces cerevisiae sake strains.

    PubMed

    Oba, Takahiro; Kusumoto, Kenichi; Kichise, Yuki; Izumoto, Eiji; Nakayama, Shunichi; Tashiro, Kosuke; Kuhara, Satoru; Kitagaki, Hiroshi

    2014-08-01

    Research on the relationship between mitochondrial membrane potential and fermentation profile is being intensely pursued because of the potential for developing advanced fermentation technologies. In the present study, we isolated naturally occurring strains of yeast from sake mash that produce high levels of malic acid and demonstrate that variations in mitochondrial membrane potential correlate with malic acid production. To define the underlying biochemical mechanism, we determined the activities of enzymes required for malic acid synthesis and found that pyruvate carboxylase and malate dehydrogenase activities in strains that produce high levels of malic acid were elevated compared with the standard sake strain K901. These results inspired us to hypothesize that decreased mitochondrial membrane potential was responsible for increased malic acid synthesis, and we present data supporting this hypothesis. Thus, the mitochondrial membrane potential of high malic acid producers was lower compared with standard strains. We conclude that mitochondrial membrane potential correlates with malic acid production.

  3. [Investigation of variation of the production of biological and chemical compounds of Hyssopus officinalis L].

    PubMed

    Varga, E; Hajdú, Z; Veres, K; Máthé, I; Németh, E; Pluhár, Z; Bernáth, J

    1998-05-01

    Hyssopus officinalis L. (Lamiaceae family) has been cultivated in Central Europe for a long time. This essential oil containing species serves not only as spice but in many countries including Hungary, it is used as a folk medicine against certain respiratory diseases. Despite this fact, little is known about the variation of its productivity under Central European climatic conditions. The cultivated populations of hyssop can be characterised by a significant heterogenity. In the course of its breeding the uniformity of flower colour (e.g. blue form), and increase in the oil content are the main achievable purposes. The purpose of this work was to investigate both the variability of strains of different crigin and the time-dependent variations of its production parameters. The optimum of phytomass was obtained at the beginning of July. The essential oil content as well as compounds of the non volatile fractions were also investigated. The non volatile fractions for rosmarinic, caffeic acids were analysed mainly by TLC and densitometry. Both compounds were present in all samples and they are suitable for the characterisation of the plant. The essential oils were gained with Water Steam Distillation (WSD) and Supercritical Fluid Extraction (SFE) with CO2. The oils were analysed by GC, GC-MS techniques. In the essential oil composition of the populations studied significant heterogenity could be observed. In the case of applying SFE extraction the oil composition is more uniform, similarly to the obtained by WSD adding hexane. The heterogenity can be experienced in the offsprings, too. If only the main four components (beta-pinene, limonene, pinocamphone, isopinocamphone) are regarded, among the offsprings clear and mixed lines alike can be found. Results of these experiments justify the necessity and usefulness of selection which is going on.

  4. Investigation of molecular penetration depth variation with SMBI fluxes

    NASA Astrophysics Data System (ADS)

    Zhou, Yu-Lin; Wang, Zhan-Hui; Xu, Min; Wang, Qi; Nie, Lin; Feng, Hao; Sun, Wei-Guo

    2016-09-01

    We study the molecular penetration depth variation with the SMBI fluxes. The molecular transport process and the penetration depth during SMBI with various injection velocities and densities are simulated and compared. It is found that the penetration depth of molecules strongly depends on the radial convective transport of SMBI and it increases with the increase of the injection velocity. The penetration depth does not vary much once the SMBI injection density is larger than a critical value due to the dramatic increase of the dissociation rate on the fueling path. An effective way to improve the SMBI penetration depth has been predicted, which is SMBI with a large radial injection velocity and a lower molecule injection density than the critical density. Project supported by the National Natural Science Foundation of China (Grant Nos. 11375053, 11575055, 11405022, and 11405112), the Chinese National Fusion Project for ITER (Grant Nos. 2013GB107001 and 2013GB112005), the International S&T Cooperation Program of China (Grant No. 2015DFA61760), and the Funds of the Youth Innovation Team of Science and Technology in Sichuan Province of China (Grant No. 2014TD0023).

  5. Experimental Investigations on Anisotropic Evolution of 304 Stainless Sheets under Tensile Pre-Strains

    NASA Astrophysics Data System (ADS)

    Teng, Lai; Guo, Cheng

    2011-08-01

    The anisotropic evolution of cold rolled 304 stainless steel sheets under pre-strains is investigated experimentally. Uni-axial tensile yield stress and r-value are measured in experiments to represent the anisotropy. The tensile pre-strains under plane stress are achieved by cutting large specimens into small one at different angles to rolling direction. Then the uni-axial tensile tests are performed on the small specimens to investigate the anisotropic evolution. It is found that the yield stress increases with the increase of the pre-strains and decreases with the increase of the angles. However, the changes of r-value are hardly affected by the pre-strains, the small changes of r-value show that the material may remember the rolling direction even after the pre-strains. The sigmoidal shape can be observed in the tensile curves, and its shape depends on the pre-strains and angles. The change of hardening rate can be divided into three stages, and is the most significant at 90° to the rolling direction in the three stages, at the same time the pre-strains cause noncoincidence of the hardening rate curves at the same angle. Moreover, the hardening rate depends on the directions of tensile loading. Second derivative of the hardening rate also can be divided into three stages, and the differences of three stages may mainly be controlled by the different volume fraction of martensite.

  6. Investigation of osteogenic activity of primary rabbit periosteal cells stimulated by multi-axial tensile strain.

    PubMed

    Chiu, Chih-Hao; Liu, Jun-Liang; Chang, Chih-Hsuan; Lei, Kin Fong; Chen, Alvin Chao-Yu

    2017-03-01

    Periosteum-derived cells was indicated to respond to mechanical force and have stem cell potential capable of differentiating into multiple tissue. Investigation of osteogenic activity under mechanical stimulation is important to understand the therapeutic conditions of fracture healing. In this work, a cell culture platform was developed for respectively providing isotropic and anisotropic axial strain. Primary rabbit periosteal cells were isolated and cultured in the chamber. Multi-axial tensile strain was received and osteogenic activity was investigated by mRNA expressions of CBFA1 and OPN. The highest mRNA expression was found in moderate strain (5-8%) under anisotropic axial strain. These results provided important foundation for further in vivo studies and development of tailor-made stretching rehabilitation equipment.

  7. [Isolation and characterization of wild Sporothrix schenkii strains and investigation of sporototrichin reactors].

    PubMed

    Sánchez-Alemán, Miguel Angel; Araiza, Javier; Bonifaz, Alexandro

    2004-01-01

    We conducted a study in the southern mountains of the Mexican State of Oaxaca that consisted of isolation of wild Sporothrix schenckii strains obtained from soil samples and investigation of positive reactors to skin test reaction with sprotrichin antigen. The study was conducted by means of recollection of soil samples and processing of these with dilution methods and fungal isolation in ordinary culture media Sabouraud simple Agar with and without antibiotics (SS, SA). Suspected strains underwent dimorphism, melanin formation, and virulence confirmation tests. Investigation of positive reactors to sporotrichin Y (yeast) was also conducted. Three supposed strains were identified due to their reproductive characteristics, melanin production, and virulence. In the community, 144 individuals were studied, of whom 6.25% were positive to sporotichin. Isolation of virulent strains of Sporothrix schenkii from nature (soil) and primoinfection of a percentage of the studied population were confirmed.

  8. Investigating Molecular Kinetics by Variationally Optimized Diffusion Maps.

    PubMed

    Boninsegna, Lorenzo; Gobbo, Gianpaolo; Noé, Frank; Clementi, Cecilia

    2015-12-08

    Identification of the collective coordinates that describe rare events in complex molecular transitions such as protein folding has been a key challenge in the theoretical molecular sciences. In the Diffusion Map approach, one assumes that the molecular configurations sampled have been generated by a diffusion process, and one uses the eigenfunctions of the corresponding diffusion operator as reaction coordinates. While diffusion coordinates (DCs) appear to provide a good approximation to the true dynamical reaction coordinates, they are not parametrized using dynamical information. Thus, their approximation quality could not, as yet, be validated, nor could the diffusion map eigenvalues be used to compute relaxation rate constants of the system. Here we combine the Diffusion Map approach with the recently proposed Variational Approach for Conformation Dynamics (VAC). Diffusion Map coordinates are used as a basis set, and their optimal linear combination is sought using the VAC, which employs time-correlation information on the molecular dynamics (MD) trajectories. We have applied this approach to ultra-long MD simulations of the Fip35 WW domain and found that the first DCs are indeed a good approximation to the true reaction coordinates of the system, but they could be further improved using the VAC. Using the Diffusion Map basis, excellent approximations to the relaxation rates of the system are obtained. Finally, we evaluate the quality of different metric spaces and find that pairwise minimal root-mean-square deviation performs poorly, while operating in the recently introduced kinetic maps based on the time-lagged independent component analysis gives the best performance.

  9. Genetic variations of live attenuated plague vaccine strains (Yersinia pestis EV76 lineage) during laboratory passages in different countries.

    PubMed

    Cui, Yujun; Yang, Xianwei; Xiao, Xiao; Anisimov, Andrey P; Li, Dongfang; Yan, Yanfeng; Zhou, Dongsheng; Rajerison, Minoarisoa; Carniel, Elisabeth; Achtman, Mark; Yang, Ruifu; Song, Yajun

    2014-08-01

    Plague, one of the most devastating infectious diseases in human history, is caused by the bacterial species Yersinia pestis. A live attenuated Y. pestis strain (EV76) has been widely used as a plague vaccine in various countries around the world. Here we compared the whole genome sequence of an EV76 strain used in China (EV76-CN) with the genomes of Y. pestis wild isolates to identify genetic variations specific to the EV76 lineage. We identified 6 SNPs and 6 Indels (insertions and deletions) differentiating EV76-CN from its counterparts. Then, we screened these polymorphic sites in 28 other strains of EV76 lineage that were stored in different countries. Based on the profiles of SNPs and Indels, we reconstructed the parsimonious dissemination history of EV76 lineage. This analysis revealed that there have been at least three independent imports of EV76 strains into China. Additionally, we observed that the pyrE gene is a mutation hotspot in EV76 lineages. The fine comparison results based on whole genome sequence in this study provide better understanding of the effects of laboratory passages on the accumulation of genetic polymorphisms in plague vaccine strains. These variations identified here will also be helpful in discriminating different EV76 derivatives.

  10. Seasonal variations in bacterial communities and antibiotic-resistant strains associated with green bottle flies (Diptera: Calliphoridae).

    PubMed

    Wei, Ting; Ishida, Ryuichi; Miyanaga, Kazuhiko; Tanji, Yasunori

    2014-05-01

    Green bottle flies occur frequently around human environments in Japan. Many species of green bottle flies have been studied with regard to their importance in forensic examinations or clinical therapies, but the bacterial communities associated with this group of flies have not been comprehensively investigated. In this research, 454 pyrosequencing was used to reveal the bacterial communities in green bottle flies collected in different seasons. Meanwhile, the bacteria were screened with selective media and tested for antibiotic susceptibility. Samples collected in three different seasons harbored distinctive bacterial communities. The predominant genera associated with green bottles flies were Staphylococcus in spring, Ignatzschineria in summer, and Vagococcus, Dysgonomonas, and an unclassified Acetobacteraceae in autumn. An upward trend in bacterial community diversity was observed from spring to autumn. Changes in climatic conditions could be the cause of these seasonal variations in fly-associated bacterial communities. The species of isolated antibiotic-resistant bacteria also differed across seasons, but it was difficult to correlate seasonal changes in antibiotic-resistant bacteria with changes in whole communities. A number of multiple-antibiotic-resistant bacteria were isolated, and some of these strains were closely affiliated with pathogens such as Enterococcus faecalis and Enterococcus faecium, which could cause serious threats to public health. Overall, this research provided us with information about the composition and seasonality of bacterial communities in green bottle flies, and highlighted the risks of fly-mediated dissemination of antibiotic-resistant pathogens.

  11. Estimation of Staphylococcus aureus growth parameters from turbidity data: characterization of strain variation and comparison of methods.

    PubMed

    Lindqvist, R

    2006-07-01

    Turbidity methods offer possibilities for generating data required for addressing microorganism variability in risk modeling given that the results of these methods correspond to those of viable count methods. The objectives of this study were to identify the best approach for determining growth parameters based on turbidity data and use of a Bioscreen instrument and to characterize variability in growth parameters of 34 Staphylococcus aureus strains of different biotypes isolated from broiler carcasses. Growth parameters were estimated by fitting primary growth models to turbidity growth curves or to detection times of serially diluted cultures either directly or by using an analysis of variance (ANOVA) approach. The maximum specific growth rates in chicken broth at 17 degrees C estimated by time to detection methods were in good agreement with viable count estimates, whereas growth models (exponential and Richards) underestimated growth rates. Time to detection methods were selected for strain characterization. The variation of growth parameters among strains was best described by either the logistic or lognormal distribution, but definitive conclusions require a larger data set. The distribution of the physiological state parameter ranged from 0.01 to 0.92 and was not significantly different from a normal distribution. Strain variability was important, and the coefficient of variation of growth parameters was up to six times larger among strains than within strains. It is suggested to apply a time to detection (ANOVA) approach using turbidity measurements for convenient and accurate estimation of growth parameters. The results emphasize the need to consider implications of strain variability for predictive modeling and risk assessment.

  12. Investigations of paleoclimate variations using accelerator mass spectrometry

    SciTech Connect

    Southon, J R; Kashgarian, M; Brown, T A

    2000-08-24

    This project has used Accelerator Mass Spectrometry (AMS) {sup 14}C measurements to study climate and carbon cycle variations on time scales from decades to millennia over the past 30,000 years, primarily in the western US and the North Pacific. {sup 14}C dates provide a temporal framework for records of climate change, and natural radiocarbon acts as a carbon cycle tracer in independently dated records. The overall basis for the study is the observation that attempts to model future climate and carbon cycle changes cannot be taken seriously if the models have not been adequately tested. Paleoclimate studies are unique because they provide realistic test data under climate conditions significantly different from those of the present, whereas instrumental results can only sample the system as it is today. The aim of this project has been to better establish the extent, timing, and causes of past climate perturbations, and the carbon cycle changes with which they are linked. This provides real-world data for model testing, both for the development of individual models and also for inter-model diagnosis and comparison activities such as those of LLNL's PCMDI program; it helps us achieve a better basic understanding of how the climate system works so that models can be improved; and it gives an indication of the natural variability in the climate system underlying any anthropogenically-driven changes. The research has involved four projects which test hypotheses concerning the overall behavior of the North Pacific climate system. All are aspects of an overall theme that climate linkages are strong and direct, so that regional climate records are correlated, details of fine structure are important, and accurate and precise dating is critical for establishing correlations and even causality. An important requirement for such studies is the requirement for an accurate and precise radiocarbon calibration, to allow better correlation of radiocarbon-dated records with

  13. Investigations on fracture curves in strain and stress space for advanced high strength steel forming

    NASA Astrophysics Data System (ADS)

    Panich, S.; Drotleff, K.; Liewald, M.; Uthaisangsuk, V.

    2016-08-01

    Conventional forming limit curves (FLCs) are inappropriate for describing formability for advanced high strength (AHS) steel sheets, since such steel grades experience fracture without localized necking occurrence. The aim of this work was to develop a fracture curve (FC) for the AHS steel grade DP980. The FC was determined by means of the Nakajima stretch forming test and tensile tests of various sample geometries, by which shear fracture governed. An optical strain measurement system was used to capture strain histories of deformed samples up to failure. From these results, fracture strains were gathered and plotted in a strain space. Subsequently, the strain based curve was transformed to space between stress triaxiality and plastic strain. Hereby, effects of anisotropic yield function, namely, the Hill’48 model on obtained stress fracture loci were investigated. In order to verify applicability of the determined limit curves, a Mini-tunnel part was pressed and simulated. It was found that the stress based FC do predict failure of the DP980 steel sheet more accurately than the strain based F C.

  14. Resiliency to social defeat stress relates to the inter-strain social interaction and is influenced by season variation.

    PubMed

    Han, Qiuqin; Yang, Liu; Liu, Yan; Lv, Ning; Yu, Jin; Wu, Gencheng; Zhang, Yuqiu

    2014-02-21

    Exposure to social defeat (SD) stress exerts social avoidance and depressive disorders. Little is known about the relationship between resiliency to stressors and the inter-strain social interaction (SI) level. We hypothesized that SD resiliency is correlated with a high SI between the same strain. C57BL/6J mice experienced a 10-day period of SD stress by repeated CD-1 mice offensive. The susceptible mice exhibited significant social-avoidance behaviors with less time in interaction-zone (IZ) and lower social interaction ratio (SIR) toward the Target (CD-1 mice), while resilient ones exhibited similar social interaction to control mice. When the Target was C57BL/6J mouse, either susceptible or resilient mice spent more time in IZ and the inter-strain SI in the resilient group was significantly higher than the susceptible. Correlation analysis revealed a significantly non-zero slope of the linear relationship between SIRs toward two strains. But different groups had a similar baseline of the inter-strain SI before stress, indicating a SD-induced defect in both types of SI. In addition, in four different seasons, animals exhibited a significant resiliency to the stress in summer. These data suggest that SD resiliency is related to a higher SI toward the same-strain, and may be regulated by seasonal variations.

  15. Experimental investigation of crustacean swimming with variation of limb structures

    NASA Astrophysics Data System (ADS)

    Lai, Hong Kuan; Samaee, Milad; Donnell, Geoffrey; Santhanakrishnan, Arvind; Guy, Robert; Lewis, Timothy

    2015-11-01

    Crustaceans such as crayfish and krill swim by rhythmically paddling a set of four to five limbs (known as swimmerets or pleopods) originating from their abdomen. The limb motion in these animals has been observed to follow tail-to-head metachronal wave pattern with an approximate quarter-period inter-limb phase difference. The goal of this study is to investigate the hydrodynamics of this swimming mechanism as a function of inter-limb phase difference, inclusion of hinges in the limbs, and Reynolds number (Re). 2D PIV measurements were conducted on a scaled robotic model of metachronal paddling, consisting of a rectangular tank fitted with stepper motors coupled to a four-bar linkage that actuated four paddles immersed in water-glycerin fluid medium. The inter-limb phase difference was varied from 0% (synchronous paddling) through 50% across Re range of O(10-1000). Two types of limb models were used, including a simple flat plate and a `split-paddle' structure with two flat plates connected halfway with hinges. The results of the study show that limb models with hinges generated increased horizontal (thrust-producing direction) fluid velocity compared to the simple flat plate paddles, suggesting that asymmetry between power and return strokes is important to augment thrust.

  16. Latitudinal and Seasonal Investigations of Storm-Time TEC Variation

    NASA Astrophysics Data System (ADS)

    Adimula, I. A.; Oladipo, O. A.; Adebiyi, S. J.

    2016-07-01

    The ionosphere responds markedly and unpredictably to varying magnetospheric energy inputs caused by solar disturbances on the geospace. Knowledge of the impact of the space weather events on the ionosphere is important to assess the environmental effect on the operations of ground- and space-based technologies. Thus, global positioning system (GPS) measurements from the international GNSS service (IGS) database were used to investigate the ionospheric response to 56 geomagnetic storm events at six different latitudes comprising the northern and southern hemispheres in the Afro-European sector. Statistical distributions of total electron content (TEC) response show that during the main phase of the storms, enhancement of TEC is more pronounced in most of the seasons, regardless of the latitude and hemisphere. However, a strong seasonal dependence appears in the TEC response during the recovery phase. Depletion of TEC is majorly observed at the high latitude stations, and its appearance at lower latitudes is seasonally dependent. In summer hemisphere, the depletion of TEC is more pronounced in nearly all the latitudinal bands. In winter hemisphere, enhancement as well as depletion of TEC is observed over the high latitude, while enhancement is majorly observed over the mid and low latitudes. In equinoxes, the storm-time TEC distribution shows a fairly consistent characteristic with the summer distribution, particularly in the northern hemisphere.

  17. Investigation of Staphylococcus strains with heterogeneous resistance to glycopeptides in a Turkish university hospital

    PubMed Central

    Nakipoglu, Yasar; Derbentli, Sengul; Cagatay, Atahan A; Katranci, Handan

    2005-01-01

    Background The hetero-glycopeptide intermediate staphylococci is considered to be the precursor of glycopeptide intermediate staphylococci especially vancomycin intermediate Staphylococcus aureus (VISA). For this purpose, we aimed to investigate the heterogeneous resistance to glycopeptide and their frequencies in 135 Staphylococcus strains. Methods Heterogeneous resistance of Staphylococcus strains was detected by inoculating the strains onto Brain Heart Infusion agar supplemented with 4 mg/L of vancomycin (BHA-V4). Agar dilution method was used for determining MICs of glycopeptides and population analysis profile was performed for detecting frequency of heterogeneous resistance for the parents of selected strains on BHA-4. Results Eight (6%) out of 135 Staphylococcus strains were exhibited heterogeneous resistance to at least one glycopeptide. One (1.2%) out of 81 S. aureus was found intermediate resistance to teicoplanin (MIC 16 mg/L). Other seven strains were Staphylococcus haemolyticus (13%) out of 54 coagulase negative staphylococci (CoNS). Six of the seven strains were detected heterogeneously reducing susceptibility to vancomycin (MICs ranged between 5–8 mg/L) and teicoplanin (MICs ranged between 32–64 mg/L), and one S. haemolyticus was found heterogeneous resistance to teicoplanin (MIC 32 mg/L). Frequencies of heterogeneous resistance were measured being one in 106 – 107 cfu/ml. MICs of vancomycin and teicoplanin for hetero-staphylococci were determined as 2–6 folds and 3–16 folds higher than their parents, respectively. These strains were isolated from six patients (7%) and two (4%) of health care wokers hands. Hetero-VISA strain was not detected. Conclusion Heterogeneous resistance to glycopeptide in CoNS strains was observed to be significantly more emergent than those of S. aureus strains (vancomycin P 0.001, teicoplanin, P 0.007). The increase MICs of glycopeptide resistance for subpopulations of staphylococci comparing with their parents

  18. Chlorine inactivation of Salmonella Kentucky isolated from chicken carcasses: evaluation of strain variation.

    PubMed

    Mohamed, T M; Parveen, S; Ludwig, J B; Oscar, T P

    2015-02-01

    The current study was undertaken to evaluate chlorine resistance among strains of Salmonella Kentucky isolated from chicken carcasses. Selected strains (n = 8) were exposed to 30 ppm of chlorine in 10% buffered peptone water (pH 7.4) for 0 to 10 min at 4°C and 150 rpm. The initial level (mean ± SD) of Salmonella Kentucky was 6.18 ± 0.09 log CFU/ml and did not differ (P > 0.05) among strains. A two-way analysis of variance indicated that the level of Salmonella Kentucky in chlorinated water was affected (P < 0.05) by a time by strain interaction. Differences among strains increased as a function of chlorine exposure time. After 10 min of chlorine exposure, the most resistant strain (SK145) was 5.63 ± 0.54 log CFU/ml, whereas the least resistant strain (SK275) was 3.07 ± 0.29 log CFU/ml. Significant differences in chlorine resistance were observed for most strain comparisons. Death of Salmonella Kentucky was nonlinear over time and fitted well to a power law model with a shape parameter of 0.34 (concave upward). Time (minutes) for a 1-log reduction of Salmonella Kentucky differed (P < 0.05) among strains: >10 min for SK145, 6.0 min for SK254, 1.5 min for SK179, and 0.3 to 0.65 min for other strains. Results of this study indicate that strain is an important variable to include in models that predict changes in levels of Salmonella Kentucky in chlorinated water.

  19. The Epstein-Barr virus EBNA-2 gene in oral hairy leukoplakia: strain variation, genetic recombination, and transcriptional expression.

    PubMed Central

    Walling, D M; Perkins, A G; Webster-Cyriaque, J; Resnick, L; Raab-Traub, N

    1994-01-01

    Oral hairy leukoplakia (HLP) lesions frequently contain defective Epstein-Barr virus (EBV) genomes with deletions in the EBNA-2 gene that abundantly replicate and persist within the lesion. To characterize these viral strains and recombinant variants, the EBNA-2 gene in EBV DNA from several different HLP biopsy specimens was analyzed. Amplification of EBNA-2 coding sequences by PCR demonstrated the presence in HLP of intact EBNA-2 genes as well as a variety of internally deleted variants of both EBNA-2A and EBNA-2B. Some of the deletion variants evolved within the HLP lesion from intact EBNA-2 genes, while other variants appeared to be transmissible strains that directly infected the lesion. Intrastrain recombination within the HLP lesion also generated variation within the EBNA-2 polyproline region. Cloning and sequencing of HLP cDNA demonstrated transcription from the internally deleted EBNA-2 open reading frame, indicating that these variant genes are expressed in HLP. Comparative analysis of the HLP EBNA-2 sequences confirmed previous findings of EBV coinfection with multiple types and strains. Sequence variation of these wild-type genes demonstrated that EBNA-2A sequences distinguish at least two separate strains and a variety of substrains of EBV type 1. Two of the HLP EBNA-2A sequences contained amino acid changes in a cytotoxic T-cell epitope within an otherwise highly conserved region of the gene. These data indicate that EBV coinfection, strain variation, and recombination within the EBNA-2 gene are common features of HLP and suggest that the expression of internally deleted EBNA-2 variants could contribute to EBV pathogenesis in permissive infection. Images PMID:7966582

  20. Variations of whole genome sequences of Xylella fastidiosa strains within the same pathotype

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Xylella fastidiosa is a Gram negative and nutritionally fastidious plant pathogenic bacterium that causes almond leaf scorch disease (ALSD) and Pierce's disease (PD) of grapevine. X. fastidiosa strains from almond can be divided into two pathotypes: ALSD-PD, represented by strain M23, and ALSD-only,...

  1. Genetic diversity and host range variation of Ralstonia solanacearum strains entering North America.

    PubMed

    Norman, David J; Zapata, Mildred; Gabriel, Dean W; Duan, Y P; Yuen, Jeanne M F; Mangravita-Novo, Arianna; Donahoo, Ryan S

    2009-09-01

    Each year, large volumes of ornamental and food plant propagative stock are imported into the North America; occasionally, Ralstonia solanacearum is found systemically infecting this plant material. In this study, 107 new R. solanacearum strains were collected over a 10-year period from imported propagative stock and compared with 32 previously characterized R. solanacearum strains using repetitive polymerase chain reaction (rep-PCR) element (BOX, ERIC, and REP) primers. Additional strain comparisons were made by sequencing the endoglucanase and the cytochrome b561 genes. Using rep-PCR primers, populations could be distinguished by biovar and, to a limited extent, country of origin and original host. Similarity coefficients among rep-PCR clusters within biovars were relatively low in many cases, indicating that disease outbreaks over time may have been caused by different clonal populations. Similar population differentiations of R. solanacearum were obtained when comparing strain sequences using either the endoglucanase or cytochrome b561 genes. We found that most of the new biovar 1 strains of R. solanacearum entering the United States were genetically distinct from the biovar 1 strains currently found infecting vegetable production. These introduced biovar 1 strains also had a broader host range and could infect not only tomato, tobacco, and potato but also anthurium and pothos and cause symptoms on banana. All introductions into North America of race 3, biovar 2 strains in the last few years have been linked to geranium production and appeared to be clonal.

  2. Strain-induced optical band gap variation of SnO2 films

    DOE PAGES

    Rus, Stefania Florina; Ward, Thomas Zac; Herklotz, Andreas

    2016-06-29

    In this paper, thickness dependent strain relaxation effects are utilized to study the impact of crystal anisotropy on the optical band gap of epitaxial SnO2 films grown by pulsed laser deposition on (0001)-oriented sapphire substrates. An X-ray diffraction analysis reveals that all films are under tensile biaxial in-plane strain and that strain relaxation occurs with increasing thickness. Variable angle spectroscopic ellipsometry shows that the optical band gap of the SnO2 films continuously increases with increasing film thickness. This increase in the band gap is linearly related to the strain state of the films, which indicates that the main origin ofmore » the band gap change is strain relaxation. The experimental observation is in excellent agreement with results from density functional theory for biaxial in-plane strain. Our research demonstrates that strain is an effective way to tune the band gap of SnO2 films and suggests that strain engineering is an appealing route to tailor the optical properties of oxide semiconductors.« less

  3. Strain-induced optical band gap variation of SnO2 films

    SciTech Connect

    Rus, Stefania Florina; Ward, Thomas Zac; Herklotz, Andreas

    2016-06-29

    In this paper, thickness dependent strain relaxation effects are utilized to study the impact of crystal anisotropy on the optical band gap of epitaxial SnO2 films grown by pulsed laser deposition on (0001)-oriented sapphire substrates. An X-ray diffraction analysis reveals that all films are under tensile biaxial in-plane strain and that strain relaxation occurs with increasing thickness. Variable angle spectroscopic ellipsometry shows that the optical band gap of the SnO2 films continuously increases with increasing film thickness. This increase in the band gap is linearly related to the strain state of the films, which indicates that the main origin of the band gap change is strain relaxation. The experimental observation is in excellent agreement with results from density functional theory for biaxial in-plane strain. Our research demonstrates that strain is an effective way to tune the band gap of SnO2 films and suggests that strain engineering is an appealing route to tailor the optical properties of oxide semiconductors.

  4. Variations in Virulence and Molecular Biology among Emerging Strains of Clostridium difficile

    PubMed Central

    Hunt, Jonathan J.

    2013-01-01

    SUMMARY Clostridium difficile is a Gram-positive, spore-forming organism which infects and colonizes the large intestine, produces potent toxins, triggers inflammation, and causes significant systemic complications. Treating C. difficile infection (CDI) has always been difficult, because the disease is both caused and resolved by antibiotic treatment. For three and a half decades, C. difficile has presented a treatment challenge to clinicians, and the situation took a turn for the worse about 10 years ago. An increase in epidemic outbreaks related to CDI was first noticed around 2003, and these outbreaks correlated with a sudden increase in the mortality rate of this illness. Further studies discovered that these changes in CDI epidemiology were associated with the rapid emergence of hypervirulent strains of C. difficile, now collectively referred to as NAP1/BI/027 strains. The discovery of new epidemic strains of C. difficile has provided a unique opportunity for retrospective and prospective studies that have sought to understand how these strains have essentially replaced more historical strains as a major cause of CDI. Moreover, detailed studies on the pathogenesis of NAP1/BI/027 strains are leading to new hypotheses on how this emerging strain causes severe disease and is more commonly associated with epidemics. In this review, we provide an overview of CDI, discuss critical mechanisms of C. difficile virulence, and explain how differences in virulence-associated factors between historical and newly emerging strains might explain the hypervirulence exhibited by this pathogen during the past decade. PMID:24296572

  5. Strain-specific variations in Toxoplasma gondii GRA1, GRA5, GRA6, GRA8, and GRA14

    NASA Astrophysics Data System (ADS)

    Haryati, S.; Sari, Y.; Prasetyo, A. A.; Sariyatun, R.

    2016-02-01

    Diagnosis and identification of the genetic group of T. gondii (Toxoplasma gondii) are important to control better the T. gondii infection, particularly in immunocompromised people as HIV patients. This study aimed to identify strain-specific variations in T. gondii GRA1, GRA5, GRA6, GRA8, and GRA14 in order to help design such diagnostic tool to detect and characterize the parasite. Forty-three T. gondii GRA1, GRA5, GRA6, GRA8, and GRA14 sequences deposited in GenBank were aligned. A number of positions in the gene sequences were highly conserved. All GRA sequences had strain-specific positions, however, only GRA1, GRA5, and GRA6, which contained specific variations for each T. gondii lineage. In conclusion, T. gondii GRA1, GRA5, GRA6, GRA8, and GRA14 are predicted to contain highly conserved regions and positions with strain-specific variation, which might be useful for the design of diagnostic tools detecting and distinguishing T. gondiistrains.

  6. Investigation of the dominance behavior of Saccharomyces cerevisiae strains during wine fermentation.

    PubMed

    Perrone, Benedetta; Giacosa, Simone; Rolle, Luca; Cocolin, Luca; Rantsiou, Kalliopi

    2013-07-15

    During wine fermentation, different strains of Saccharomyces cerevisiae compete in the same fermenting must and dominance takes place when one strain overcomes all the others. The purpose of this study was to investigate this phenomenon by identifying S. cerevisiae strains endowed with this feature and to test them in laboratory fermentations. First, autochthonous S. cerevisiae from Nebbiolo fermentations were isolated, molecularly identified and characterized. Genetically diverse S. cerevisiae strains were subsequently subjected to physiological characterization and to micro-scale fermentation, the weight loss kinetics was measured and HPLC analysis was performed at the end of the fermentation. Then, the strains that presented good fermentation characteristics were chosen for further analysis and to determine the dominance feature. For this purpose, couples of strains were co-inoculated in Nebbiolo must and the fermentations were monitored by microbiological and chemical analysis. Two different inoculation approaches were used: co-fermentations in flasks with mixed cells and reactor co-fermentations, in which the cells from the two different strains were kept separate by means of a 0.45 μm filter membrane, which allowed the fermenting must to move freely between the two compartments. During the flask co-fermentations, a minisatellite PCR protocol was applied, in order to differentiate the two strains and determine which one was able to dominate. The protocol included a culture-dependent approach and an independent one. In the first case, DNA extraction was performed on all the colonies scraped off the plates after sampling. In the second case, DNA extraction was performed directly on the fermenting must. The strains that were able to dominate were tested against several S. cerevisiae in order to confirm this dominance behavior. Dominance was observed in the early stages of fermentation, as early as 3days. Combinations of dominant and not-dominant strains were

  7. Understanding the rise of the superbug: investigation of the evolution and genomic variation of Staphylococcus aureus.

    PubMed

    Lindsay, Jodi A; Holden, Matthew T G

    2006-07-01

    The bacterium Staphylococcus aureus is a common cause of human infection, and it is becoming increasingly virulent and resistant to antibiotics. Our understanding of the evolution of this species has been greatly enhanced by the recent sequencing of the genomes of seven strains of S. aureus. Comparative genomic analysis allows us to identify variation in the chromosomes and understand the mechanisms by which this versatile bacterium has accumulated diversity within its genome structure.

  8. Strain relaxation of metastable SiGe/Si: Investigation with two complementary X-ray techniques

    SciTech Connect

    Kasper, E.; Werner, J.; Oehme, M.; Lyutovich, K.; Burle, N.; Escoubas, S.

    2012-03-15

    Metastable and strain relaxed SiGe layers with about 20% Ge content have been grown by molecular beam epitaxy on Si substrates at 550 deg. C. The thickness regime of metastability and the onset of strain relaxation were investigated on dust particle free surfaces obtained by careful chemical cleaning and epitaxy loading under clean room conditions. Compared to earlier results true metastable regime without misfit dislocations was obtained up to 140 nm thickness. The onset of strain relaxation started with heterogeneous nucleation sites of misfit dislocations. X-ray topography proved to be a unique monitoring tool to observe a low density of single dislocations. From these results we suggested to define a critical thickness band with lower bound t{sub cl} from dislocation nucleation to an upper bound t{sub co} (600 nm in our case) defined by the onset of considerable strain relaxation. The strain relief was measured by X-ray diffraction (reciprocal space mapping) and found to be very abrupt (76% strain relaxation at 800 nm thickness).

  9. A new look at the drug-resistance investigation of uropathogenic E. coli strains.

    PubMed

    Adamus-Białek, Wioletta; Lechowicz, Łukasz; Kubiak-Szeligowska, Anna B; Wawszczak, Monika; Kamińska, Ewelina; Chrapek, Magdalena

    2017-02-01

    Bacterial drug resistance and uropathogenic tract infections are among the most important issues of current medicine. Uropathogenic Escherichia coli strains are the primary factor of this issue. This article is the continuation of the previous study, where we used Kohonen relations to predict the direction of drug resistance. The characterized collection of uropathogenic E. coli strains was used for microbiological (the disc diffusion method for antimicrobial susceptibility testing), chemical (ATR/FT-IR) and mathematical (artificial neural networks, Ward's hierarchical clustering method, the analysis of distributions of inhibition zone diameters for antibiotics, Cohen's kappa measure of agreement) analysis. This study presents other potential tools for the epidemiological differentiation of E. coli strains. It is noteworthy that ATR/FT-IR technique has turned out to be useful for the quick and simple identification of MDR strains. Also, diameter zones of resistance of this E. coli population were compared to the population of E. coli strains published by EUCAST. We observed the bacterial behaviors toward particular antibiotics in comparison to EUCAST bacterial collections. Additionally, we used Cohen's kappa to show which antibiotics from the same class are closely related to each other and which are not. The presented associations between antibiotics may be helpful in selecting the proper therapy directions. Here we present an adaptation of interdisciplinary studies of drug resistance of E. coli strains for epidemiological and clinical investigations. The obtained results may be some indication in deciding on antibiotic therapy.

  10. Effects of strain variations on aging response and corrosion properties of third generation Al-Li alloys

    NASA Astrophysics Data System (ADS)

    Wright, Ellen E.

    Due to their high specific strength (strength/density) and specific stiffness (elastic modulus/density), Al-Li alloys are attractive alloys for structural aircraft applications. To produce contoured aircraft components from Al-Li wrought products, stretch forming prior to aging is a common manufacturing technique. The effects of different amounts of tensile straining (0-9%) on the mechanical, microstructural, and corrosion properties of two third generation Al-Li alloys (2099 and 2196) were investigated. In addition to typical characterization techniques, electron backscatter diffraction (EBSD), 2D micro-digital image correlation (DIC), and scanning Kelvin probe force microscopy (SKPFM) were used to examine site-specific effects of orientation, micro-strain evolution during straining, and surface potential on corrosion, respectively. Tapping mode atomic force microscopy (AFM) was also performed to study galvanic corrosion in artificial seawater (3.5% NaCl) as it occurred in-situ. There was evidence of intergranular corrosion for 0% strain conditions, but the dominant form of corrosion was localized pitting for all specimens except Alloy 2196 strained 0%. Pitting initiated at grain boundaries and triple points. In many cases, pitting extended into particular grains and was elongated in the extrusion direction. Regions of high micro-strain preferentially corroded, and large, recrystallized grains in mostly unrecrystallized microstructures were detrimental to corrosion properties. Recommendations for improved thermomechanical processing and/or alloying to promote corrosion resistance of 2XXX series Al-Li alloys were investigated.

  11. Investigation of Strain-Induced Martensitic Transformation in Metastable Austenite using Nanoindentation

    SciTech Connect

    Ahn, T.-H.; Oh, C.-S.; Kim, D. H.; Oh, K. H.; Bei, Hongbin; George, Easo P; Han, H. N.

    2010-01-01

    Strain-induced martensitic transformation of metastable austenite was investigated by nanoindentation of individual austenite grains in multi-phase steel. A cross-section prepared through one of these indented regions using focused ion beam milling was examined by transmission electron microscopy. The presence of martensite underneath the indent indicates that the pop-ins observed on the load-displacement curve during nanoindentation correspond to the onset of strain-induced martensitic transformation. The pop-ins can be understood as resulting from the selection of a favorable martensite variant during nanoindentation.

  12. An investigation of the potential causes for the seasonal and annual variations in indoor radon concentrations.

    PubMed

    Barazza, F; Gfeller, W; Palacios, M; Murith, C

    2015-11-01

    Indoor radon concentrations exhibit strong variations on short and long timescales. Besides human influences, meteorological factors significantly affect the radon concentrations indoors as well as outdoors. In this article, long-term measurements showing strong annual variations are presented, which take a very similar course in different buildings located in largely separated regions in Switzerland. Also, seasonal variations can be very significant. In general, variations in indoor radon levels can primarily be attributed to human influences. On the other hand, specific weather conditions can have a significant impact on indoor radon levels. In order to further investigate the connection between indoor radon levels and meteorological factors, a measuring campaign has been started in two buildings located in two different regions in Switzerland exhibiting different climatic characteristics. Preliminary results of these investigations are presented, which provide evidence for correlations between indoor radon levels and in particular outdoor temperatures, contributing to seasonal and annual as well as short-term variations in indoor radon concentrations.

  13. [Investigation of the virulence genes in methicillin-resistant Staphylococcus aureus strains isolated from biomaterial surfaces].

    PubMed

    Sudağidan, Mert; Cavuşoğlu, Cengiz; Bacakoğlu, Feza

    2008-01-01

    Staphylococci are the most important agents of nosocomial infections originating from biomaterials. The aim of this study was to investigate the presence of virulence genes and their phenotypic expressions in 11 methicillin-resistant Staphylococcus aureus strains isolated from the surfaces of clinically used biomaterials of 48 thorasic intensive-care unit patients. By the use of specific primers, the presence of genes encoding the attachment and biofilm production (icaA, icaC, bap), methicillin resistance (mecA), enterotoxins A-E (sea, seb, sec, sed, see), toxic shock syndrome toxin (tst), exfoliative toxins A and B (eta and etb), alpha- and beta-hemolysins (hla and hlb), staphylococcal exotoxin-like protein-1 (set1), proteases (sspA, sspB, aur, serine proteaz gene), lipase (geh) and the regulatory genes (sarA and agrCA) were investigated by polymerase chain reaction (PCR). The phenotypic properties of the isolates such as biofilm formation, antibiotic susceptibility, extracellular protease and lipase production were also evaluated. None of the isolates were found to be biofilm and/or slime producers, however, all strains were found to have icaA gene which is responsible for biofilm formation. Nevertheless the presence of icaC and bap genes that are also responsible for biofilm formation were not detected. All the strains have had mecA gene and were resistant to oxacillin, penicilin G and gentamicin, while 10 were also resistant to erythromycin and nine were also resistant to ofloxacin. The isolates were susceptible to vancomycin, teicoplanin and co-trimoxazole. Screening of toxin and regulatory genes revealed that all the strains harboured sea, set1, hla, hlb and sarA genes. The phenotypic tests for the determination of extracellular protease production revealed that all the strains formed very weak zones on skim milk and milk agar plates, and yielded negative results on casein agar plates. Furthermore, all strains were found to harbour sspA, sspB, aur and serine

  14. ATR-FTIR spectroscopic investigation of imipenem-susceptible and -resistant Pseudomonas aeruginosa isogenic strains.

    PubMed

    Sockalingum, G D; Bouhedja, W; Pina, P; Allouch, P; Mandray, C; Labia, R; Millot, J M; Manfait, M

    1997-03-06

    The primary mechanism of imipenem resistance in Pseudomonas aeruginosa has been ascribed to an outer membrane impermeability owing to a loss of expression of protein D2. Attenuated total reflection-Fourier transform infrared spectroscopy in conjunction with statistical methods has been used as a new approach to rapidly discriminate four isogenic strains of P. aeruginosa--susceptible, less susceptible, and highly resistant to imipenem-- and to follow the structural modifications related to this low permeability. Decomposition of the broad protein and carbohydrate contours into underlying Gaussians and comparison of the susceptible and highly resistant strain provided quantitative and ultrastructural information on these strains. This methodology allows for discrimination not of the mutation itself but of its consequences observed in the protein and carbohydrate absorption regions. Its association with other existing biochemical methods may be envisaged since it may allow for rapid orientation of investigations in the field of bacterial resistance diagnosis.

  15. [Investigation on strains of Legionella pneumophila, isolated from a hospital of Milano, with three genotyping methods].

    PubMed

    Bianchi, A; Tesauro, M; Consonni, M; Galli, M G

    2009-01-01

    Various techniques have been developed in recent years for the molecular typing of microorganisms. Remains particularly difficult to isolate clinical strains for the low availability of cases and even more problematic matching clinical / environmental strains. We investigated 13 strains of Legionella pneumophila of clinical and environmental origin, isolated in 3 Health Facilities in Milan (2003-2006), using three molecular typing methods: Pulse-Field Gel Electrophoresis, Amplified Fragment Length Polymorphism and Sequence-Based Typing. PFGE and AFLP showed the correlation between a clinical case with only one of the environmental isolates taken from the places frequented by the patient, demonstrating with certainty the nosocomial origin of the case and identifying the source of infection in the shower water (Clin. 1 and Env. 1N). Two clinical samples from patients admitted to different wards presented an identical profile, which suggests that the nosocomial origin assumed an epidemic form, even without having isolated the environmental strain due to the absence of samples drawn during the period under consideration (Clin. 2 and 3). Finally, the comparison between the isolated environmental strains demonstrated a heterogeneous presence of strains, not correlated to each other although they belong to the same serum-group, having profiles that are clearly different regarding number and position of bands (Env. 2 and 4). The profile 2,10,18,10,1,1 had never been isolated and typed previously in Europe. The SBT has proved a better technique for reproducibility and interpretation of results than PFGE and AFLP To complete studies on SBT method, now considered gold standard, is currently being the EWGLI 5th Proficiency Panel, in which we are actively involved with the genotyping of five strains according to the latest version of the protocol (4.1).

  16. Variation along ITS markers across strains of Fibrocapsa japonica (Raphidophyceae) suggests hybridisation events and recent range expansion

    NASA Astrophysics Data System (ADS)

    Kooistra, Wiebe H. C. F.; de Boer, M. Karin; Vrieling, Engel G.; Connell, Laurie B.; Gieskes, Winfried W. C.

    2001-12-01

    The flagellate micro-alga Fibrocapsa japonica can form harmful algal blooms along all temperate coastal regions of the world. The species was first observed in coastal waters of Japan and the western US in the 1970s; it has been reported regularly worldwide since. To unravel whether this apparent range expansion can be tracked, we assessed genetic variation among nuclear ribosomal DNA ITS sequences, obtained from sixteen global strains collected over the course of three decades. Ten sequence positions showed polymorphism across the strains. Nine out of these revealed ambiguities in several or most sequences sampled. The oldest strain collected (LB-2161) was the only one without such intra-individual polymorphism. In the others, the proportion of ambiguities at variable sites increased with more recent collection date. The pattern does not result from loss of variation due to sexual reproduction and random drift in culture because sister cultures CS-332 and NIES-136 showed virtually the same ITS-pattern after seven years of separation. Neither are the patterns explained by recent range expansion of a single genotype, because in that case one would expect lowest genetic diversity in the recently invaded North Sea; instead, polymorphism is highest there. Recent ballast-water-mediated mixing of formerly isolated populations and subsequent ongoing sexual reproduction among them can explain the increase in ambiguities. The species' capacity to form harmful blooms may well have been enhanced through increased genetic diversity of regional populations.

  17. The time variations in the parameters of the volumetric strain response to the tidal and baric impacts

    NASA Astrophysics Data System (ADS)

    Cherepantsev, A. S.

    2016-07-01

    The parameters describing the state of the geological medium include its response to the continuous external impacts, which characterizes the structure of the medium and the stresses accumulated in it. In the present paper, through analyzing the long time series of the volumetric strain monitoring data in the nearsurface crustal layer, which were obtained by the American geophysicists under the Plate Boundary Observatory (PBO) project within the Parkfield segment of the San Andreas fault, the time behavior of the volumetric strain response to the separate components of the tides and the air pressure impacts is considered. The analysis of the response regime at the different observational stations suggests a significant influence of the local structural features and tectonic processes at the considered sites of the volumetric strain observations. The estimate of the variations in the partial information from the individual observations (values) is used for improving the reliability of identifying the amplitude peculiarities of the response when synchronizing the variations of the set of the tidal components. It is established that at the PKDLT observation point, a synchronous increase in the transfer coefficient of the tidal impact of the M 2, O 1, and L 2 components two years before the Parkfield earthquake of 2004 took place.

  18. Investigation of the Influence of Tool Geometry on Effective Strain Distribution in Full Forward Extrusion

    NASA Astrophysics Data System (ADS)

    Merklein, Marion; Ndzomssi, Franck; Engel, Ulf

    2011-05-01

    Due to strain hardening of the material, the hardness of cold forged parts is considerably improved. It is well known that the hardness of cold forged parts is closely related to its deformation, and that this relation is not dependent on the deformation process. The effective strain defines the local deformation, and can be determined in simulation of the cold forming process. In order to reach the required or to set specific hardness distribution with cold forging without any heat treatment processes, it is necessary to find out which manufacturing parameters influence the effective strain, and determine the effects of these parameters. The research work covered in this paper investigates the influence of the die geometry (as manufacturing parameter) on the effective strain. For that, a full forward extrusion process was modeled using the FE-software Simufact. Forming and three parameters of the die geometry, namely the deformation ratio, the shoulder radius and the opening angle were varied. The maximum effective strain from each combination is determined, and the effects of each considered parameter as well as the effects of interactions between these factors are checked.

  19. Bonding dynamics of compliant microbump during ultrasonic bonding investigated by using Si strain gauge

    NASA Astrophysics Data System (ADS)

    Iwanabe, Keiichiro; Nakadozono, Kenichi; Senda, Yousuke; Asano, Tanemasa

    2016-06-01

    The bonding dynamics of a cone-shaped microbump during ultrasonic bonding are investigated by in situ measurements of the strain generated in a substrate using a piezoresistance strain sensor. The strain sensor is composed of a pair of p- and n-type piezoresistance gauges to extract strain components in the ultrasonic vibration along the plane parallel to the substrate surface and along the direction perpendicular to the surface. Flip-chip bonding is performed at room-temperature. The time evolution of the strain generated in the substrate according to the load-up of pressing force and application of ultrasonic vibration is clearly detected. The softening of the bump metal during the application of ultrasonic vibration is clearly observed. Results of a comparative study between the bonding of a cone-shaped microbump and that of a flat-top microbump suggest mechanical stress concentration near the top end of the cone-shaped microbump, which results in the transformation of the crystal texture of the bump from grains to fine crystallites.

  20. Sporadic Distribution and Distinctive Variations of Cylindrospermopsin Genes in Cyanobacterial Strains and Environmental Samples from Chinese Freshwater Bodies

    PubMed Central

    Jiang, Yongguang; Xiao, Peng; Yu, Gongliang; Shao, Jihai; Liu, Deming; Azevedo, Sandra M. F. O.

    2014-01-01

    Increasing reports of cylindrospermopsins (CYNs) in freshwater ecosystems have promoted the demand for identifying all of the potential CYN-producing cyanobacterial species. The present study explored the phylogenetic distribution and evolution of cyr genes in cyanobacterial strains and water samples from China. Four Cylindrospermopsis strains and two Raphidiopsis strains were confirmed to produce CYNs. Mutant cyrI and cyrK genes were observed in these strains. Cloned cyr gene sequences from eight water bodies were clustered with cyr genes from Cylindrospermopsis and Raphidiopsis (C/R group) in the phylogenetic trees with high similarities (99%). Four cyrI sequence types and three cyrJ sequence types were observed to have different sequence insertions and repeats. Phylogenetic analysis of the rpoC1 sequences of the C/R group revealed four conserved clades, namely, clade I, clade II, clade III, and clade V. High sequence similarities (>97%) in each clade and a divergent clade IV were observed. Therefore, CYN producers were sporadically distributed in congeneric and paraphyletic C/R group species in Chinese freshwater ecosystems. In the evolution of cyr genes, intragenomic translocations and intergenomic transfer between local Cylindrospermopsis and Raphidiopsis were emphasized and probably mediated by transposases. This research confirms the existence of CYN-producing Cylindrospermopsis in China and reveals the distinctive variations of cyr genes. PMID:24928879

  1. Metabolic and genomic analysis elucidates strain-level variation in Microbacterium spp. isolated from chromate contaminated sediment

    PubMed Central

    Henson, Michael W.; Santo Domingo, Jorge W.; Kourtev, Peter S.; Jensen, Roderick V.; Dunn, James A.

    2015-01-01

    Hexavalent chromium [Cr(VI)] is a soluble carcinogen that has caused widespread contamination of soil and water in many industrial nations. Bacteria have the potential to aid remediation as certain strains can catalyze the reduction of Cr(VI) to insoluble and less toxic Cr(III). Here, we examine Cr(VI) reducing Microbacterium spp. (Cr-K1W, Cr-K20, Cr-K29, and Cr-K32) isolated from contaminated sediment (Seymore, Indiana) and show varying chromate responses despite the isolates’ phylogenetic similarity (i.e., identical 16S rRNA gene sequences). Detailed analysis identified differences based on genomic metabolic potential, growth and general metabolic capabilities, and capacity to resist and reduce Cr(VI). Taken together, the discrepancies between the isolates demonstrate the complexity inter-strain variation can have on microbial physiology and related biogeochemical processes. PMID:26587353

  2. Variation in hormone autonomy and regenerative potential of cells transformed by strain A66 of Agrobacterium tumefaciens

    SciTech Connect

    Binns, A.N.; Sciaky, D.; Wood, H.N.

    1982-12-01

    Mutant Agrobacterium tumefaciens strain A66 is shown to differ from its wild-type progenitor (strain A6) by a spontaneous 2.7 kb DNA insert into the T-DNA region of its Ti plasmid. Tobacco stems transformed by A66 exhibit an attenuated response characterized by slow growth and shoot proliferation. Clonal analysis demonstrates that this response is due to an alteration in the growth and regenerative potential of transformed cells, rather than to variation in the frequency of fully autonomous cells within the primary tumor. Cloned A66 transformed tobacco cells exhibit an auxin requirement for growth that can be overcome by shoot proliferation. Other host species, however, may complement the A66 mutation yielding fully auxin-independent tumors when transformed by this bacterium.

  3. Impact of Strain Variation on the Ability of Biosensor Technology to Detect Salmonella enterica

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Introduction: It is important to develop methods that can quickly and accurately detect the presence of bacteria in the food supply that cause disease. Salmonella enterica is a bacteria that is often associated with contamination of food. Strains vary in their ability to cause illness and to spread...

  4. Genetic diversity and host range variation of Ralstonia solanacearum strains entering the United States

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Each year, large volumes of plant propagative stock are imported into the United States; occasionally, Ralstonia solanacearum is found systemically infecting this plant material. In this study, 106 R. solanacearum strains were collected over a 10-year period from imported ornamental propagative sto...

  5. Composition, variation, and dynamics of major osmotic solutes in Methanohalophilus strain FDF1

    SciTech Connect

    Robertson, D.E.; Roberts, M.F. ); Meichin Lai; Gunsalus, R.P. )

    1992-08-01

    Methanohalophilus strain FDF1, a member of the halophilic genus of methanogens, can grow over a range of external NaCl concentrations from 1.2 to 2.9 M and utilize methanol, trimethylamine, and dimethyl sulfide as substrates for methanogenesis. It produces the osmolytes glycine betaine, [beta]-glutamine, and N[sup [epsilon

  6. Geographic variation in sexual attraction of Spodoptera frugiperda corn- and rice-strain males to pheromone lures

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The corn- and rice-strains of Spodoptera frugiperda exhibit several genetic and behavioral differences and appear to be undergoing ecological speciation in sympatry. Previous studies reported conflicting results when investigating male attraction to pheromone lures in different regions, but this cou...

  7. Investigation of thermomechanical couplings, strain localization and shape memory properties in a shape memory polymer subjected to loading at various strain rates

    NASA Astrophysics Data System (ADS)

    Pieczyska, E. A.; Staszczak, M.; Maj, M.; Kowalczyk-Gajewska, K.; Golasiński, K.; Cristea, M.; Tobushi, H.; Hayashi, S.

    2016-08-01

    This paper presents experimental and modeling results of the effects of thermomechanical couplings occurring in a polyurethane shape memory polymer (SMP) subjected to tension at various strain rates within large strains. The SMP mechanical curves, recorded using a testing machine, and the related temperature changes, measured in a contactless manner using an IR camera, were used to investigate the polymer deformation process at various loading stages. The effects of thermomechanical couplings allowed the determination of the material yield point in the initial loading stage, the investigation of nucleation and development of the strain localization at larger strains and the estimation of the effects of thermoelastic behavior during the unloading process. The obtained stress-strain and thermal characteristics, the results of the dynamic mechanical analysis and estimated values of the shape fixity and shape recovery parameters confirmed that the shape memory polymer (T g = 45 °C) is characterized by good mechanical and shape memory properties, as well as high sensitivity to the strain rate. The mechanical response of the SMP subjected to tension was simulated using the finite element method and applying the large strain, two-phase model. Strain localization observed in the experiment was well reproduced in simulations and the temperature spots were correlated with the accumulated viscoplastic deformation of the SMP glassy phase.

  8. Systematic investigation on topological properties of layered GaS and GaSe under strain

    SciTech Connect

    An, Wei; Tian, Guang-Shan; Wu, Feng; Jiang, Hong; Li, Xin-Zheng

    2014-08-28

    The topological properties of layered β-GaS and ε-GaSe under strain are systematically investigated by ab initio calculations with the electronic exchange-correlation interactions treated beyond the generalized gradient approximation (GGA). Based on the GW method and the Tran-Blaha modified Becke-Johnson potential approach, we find that while ε-GaSe can be strain-engineered to become a topological insulator, β-GaS remains a trivial one even under strong strain, which is different from the prediction based on GGA. The reliability of the fixed volume assumption rooted in nearly all the previous calculations is discussed. By comparing to strain calculations with optimized inter-layer distance, we find that the fixed volume assumption is qualitatively valid for β-GaS and ε-GaSe, but there are quantitative differences between the results from the fixed volume treatment and those from more realistic treatments. This work indicates that it is risky to use theoretical approaches like GGA that suffer from the band gap problem to address physical properties, including, in particular, the topological nature of band structures, for which the band gap plays a crucial role. In the latter case, careful calibration against more reliable methods like the GW approach is strongly recommended.

  9. Investigation on grain size effect in high strain rate ductility of 1100 pure aluminum

    NASA Astrophysics Data System (ADS)

    Bonora, N.; Bourne, N.; Ruggiero, A.; Iannitti, G.; Testa, G.

    2017-01-01

    The effect of the initial grain size on the material ductility at high strain rates in 1100 pure aluminum was investigated. Dynamic tensile extrusion (DTE) tests, at different impact velocities, were performed. Samples have been annealed at 350°C for different exposure times to induce grain growth. Extruded fragments were soft-recovered and the overall length of the extruded jets was used as a measure of material ductility at high strain rates. Numerical simulation of DTE test at different velocity was performed using the modified Rusinek-Klepaczko constitutive model. Results indicates that, as reported for pure copper, the overall ductility of the aluminum increases when grain size decreases. Numerical simulation results were in quite good agreement with experimental data.

  10. Investigation of Strain/Vorticity and Large-Scale Flow Structure in Turbulent Nonpremixed Jet Flames

    NASA Technical Reports Server (NTRS)

    Clemens, N. T.

    1999-01-01

    Our study will use the microgravity environment to investigate the underlying flow structure of turbulent nonpremixed round jet flames. In particular, we aim to investigate the large-scale turbulent structure using planar laser Mie scattering (PLMS), and the strain rate and vorticity fields using particle image velocimetry (PIV). This work is motivated by recent studies in our laboratory that have led to several interesting observations of nominally momentum-driven turbulent nonpremixed planar flames. First of all, the organized large-scale turbulent structures that are observed in nonreacting planar jets may be substantially modified or suppressed in nonpremixed planar jet flames. Furthermore, a recent study using PIV and planar laser-induced fluorescence of OH has shown that in transitional and turbulent nonpremixed planar jet flames the presence of the flame seems to greatly influence the underlying vorticity and strain fields, as compared to nonreacting jets. For example, the reaction zones in the jet flames are strongly correlated with regions of high vorticity. A related study has demonstrated that vorticity is not correlated in the same way with either iso-scalar surfaces or scalar dissipation layers in nonreacting planar jets. Furthermore, the relationship between strain and the reaction zone appears to be modified by the presence of high levels of heat release. In particular, the strain rate field in planar jet flames exhibits a preferred direction of principal compressive strain that apparently is related to strong shear across the reaction zone. This preferred direction of strain was not observed in nonreacting jets. One of the major problems encountered when conducting these types of studies is that it is difficult to know to what extent buoyancy influences the results. Therefore, the microgravity environment provides us with an excellent opportunity to explore these issues without the complicating effects of buoyancy. This is particularly the case when

  11. Regulatory gene mutation: a driving force behind group a Streptococcus strain- and serotype-specific variation.

    PubMed

    Sarkar, Poulomee; Sumby, Paul

    2017-02-01

    Data from multiple bacterial pathogens are consistent with regulator-encoding genes having higher mutation frequencies than the genome average. Such mutations drive both strain- and type- (e.g., serotype, haplotype) specific phenotypic heterogeneity, and may challenge public health due to the potential of variants to circumvent established treatment and/or preventative regimes. Here, using the human bacterial pathogen the group A Streptococcus (GAS; S. pyogenes) as a model organism, we review the types and regulatory-, phenotypic-, and disease-specific consequences of naturally occurring regulatory gene mutations. Strain-specific regulator mutations that will be discussed include examples that transform isolates into hyper-invasive forms by enhancing expression of immunomodulatory virulence factors, and examples that promote asymptomatic carriage of the organism. The discussion of serotype-specific regulator mutations focuses on serotype M3 GAS isolates, and how the identified rewiring of regulatory networks in this serotype may be contributing to a decades old epidemiological association of M3 isolates with particularly severe invasive infections. We conclude that mutation plays an outsized role in GAS pathogenesis and has clinical relevance. Given the phenotypic variability associated with regulatory gene mutations, the rapid examination of these genes in infecting isolates may inform with respect to potential patient complications and treatment options.

  12. Feasibility Study of Ex Ovo Chick Chorioallantoic Artery Model for Investigating Pulsatile Variation of Arterial Geometry.

    PubMed

    Nam, Kweon-Ho; Kim, Juho; Ra, Gicheol; Lee, Chong Hyun; Paeng, Dong-Guk

    2015-01-01

    Despite considerable research efforts on the relationship between arterial geometry and cardiovascular pathology, information is lacking on the pulsatile geometrical variation caused by arterial distensibility and cardiomotility because of the lack of suitable in vivo experimental models and the methodological difficulties in examining the arterial dynamics. We aimed to investigate the feasibility of using a chick embryo system as an experimental model for basic research on the pulsatile variation of arterial geometry. Optical microscope video images of various arterial shapes in chick chorioallantoic circulation were recorded from different locations and different embryo samples. The high optical transparency of the chorioallantoic membrane (CAM) allowed clear observation of tiny vessels and their movements. Systolic and diastolic changes in arterial geometry were visualized by detecting the wall boundaries from binary images. Several to hundreds of microns of wall displacement variations were recognized during a pulsatile cycle. The spatial maps of the wall motion harmonics and magnitude ratio of harmonic components were obtained by analyzing the temporal brightness variation at each pixel in sequential grayscale images using spectral analysis techniques. The local variations in the spectral characteristics of the arterial wall motion were reflected well in the analysis results. In addition, mapping the phase angle of the fundamental frequency identified the regional variations in the wall motion directivity and phase shift. Regional variations in wall motion phase angle and fundamental-to-second harmonic ratio were remarkable near the bifurcation area. In summary, wall motion in various arterial geometry including straight, curved and bifurcated shapes was well observed in the CAM artery model, and their local and cyclic variations could be characterized by Fourier and wavelet transforms of the acquired video images. The CAM artery model with the spectral

  13. Variation of strain energy release rate with plate thickness. [fracture mode transition

    NASA Technical Reports Server (NTRS)

    Sih, G. C.; Hartranft, R. J.

    1973-01-01

    An analytical model of a through-thickness crack in a statically stretched plate is presented in which the crack front stress state is permitted to vary in the direction of the plate thickness. The amplitude or intensity of this stress field can be made nearly constant over a major portion of the interior crack front which is in a state of plane strain. The average amount of work available for extending a small segment of the crack across the thickness is associated with an energy release rate quantity in a manner similar to the two-dimensional Griffith crack model. The theoretically calculated energy release rate is shown to increase with increasing plate thickness, indicating that available work for crack extension is higher in a thicker plate.

  14. Investigation of the Antimicrobial Activity of Bacillus licheniformis Strains Isolated from Retail Powdered Infant Milk Formulae.

    PubMed

    Alvarez-Ordóñez, Avelino; Begley, Máire; Clifford, Tanya; Deasy, Thérèse; Considine, Kiera; O'Connor, Paula; Ross, R Paul; Hill, Colin

    2014-03-01

    This study investigated the potential antimicrobial activity of ten Bacillus licheniformis strains isolated from retail infant milk formulae against a range of indicator (Lactococcus lactis, Lactobacillus bulgaricus and Listeria innocua) and clinically relevant (Listeria monocytogenes, Staphylococcus aureus, Streptococcus agalactiae, Salmonella Typhimurium and Escherichia coli) microorganisms. Deferred antagonism assays confirmed that all B. licheniformis isolates show antimicrobial activity against the Gram-positive target organisms. PCR and matrix-assisted laser desorption ionization time-of-flight mass spectrometry analyses indicated that four of the B. licheniformis isolates produce the bacteriocin lichenicidin. The remaining six isolates demonstrated a higher antimicrobial potency than lichenicidin-producing strains. Further analyses identified a peptide of ~1,422 Da as the most likely bioactive responsible for the antibacterial activity of these six isolates. N-terminal sequencing of the ~1,422 Da peptide from one strain identified it as ILPEITXIFHD. This peptide shows a high homology to the non-ribosomal peptides bacitracin and subpeptin, known to be produced by Bacillus spp. Subsequent PCR analyses demonstrated that the six B. licheniformis isolates may harbor the genetic machinery needed for the synthesis of a non-ribosomal peptide synthetase similar to those involved in production of subpeptin and bacitracin, which suggests that the ~1,422 Da peptide might be a variant of subpeptin and bacitracin.

  15. Investigation of VIM, IMP, NDM-1, KPC AND OXA-48 enzymes in Enterobacteriaceae strains.

    PubMed

    Demir, Yelda; Zer, Yasemin; Karaoglan, Ilkay

    2015-05-01

    Gram-negative bacteria especially Enterobacteriaceae species have become an increasing etiologic agent of nosocomial infections. The development of resistance to carbapenems have become an increasing problem in the treatment of nosocomial infections. Especially carbapenamases are common for Enterobacteriaceae strains. This study was performed to detect the types of carbapenemases in Enterobacteriaceae strains isolated from various clinical samples. Enterobacteriaceae species were isolated from urine, blood, tracheal aspirates, wound, and other respiratory samples. Susceptibility of isolates to imipenem, meropenem and ertapenem was tested. Carbapenemase genes were studied using HyplexSuperBug ID kit. VIM (1-13), IMP (1-22), NDM-1, KPC(1-10) and OXA-48 genes were investigated. Ninety-five isolates of Enterobacteriaceae spp. were included in the study. Sixty isolates were resistant to imipenem, meropenem and ertapenem and 20 isolates were found resistant to imipenem or ertapenem while 15 were susceptible to all carbapenems. Among the isolates with carbapenem resistance, 57 were positive for one carbapenemase gene and susceptible isolates did not have carbapenemase gene. OXA-48 was found in 49 of the isolates (86%), NDM-1 in 6 (10.5%) isolates, VIM in 2 isolates. IMP and KPC gene loci were not identified. Carbapenemase genes play a crucial role in the development and spread of resistant strains.

  16. Precise measurement of seismic traveltimes-investigation of variation from tidal stress in shallow crust

    SciTech Connect

    Liu, H.; Westerlund, R.E.; Fletcher, J.B.

    1983-05-01

    We have conducted 8 precise seismic surveys near Hollister, CA, over a period of 1 y in an attempt to detect the traveltime variation caused by the solid-earth tidal stress. The surveys were conducted along a 600 m baseline located in quartz monzonite hills 2 km west of the San Andreas fault. A 656 cm/sup 3/ air gun fired in a mud-filled pit 2 m deep provided a repeatable seismic source. The signals from two 2.3 Hz vertical-component geophones 600 m apart were digitized at a nominal rate of 600 samples/s by two cassette recorders modified for precise synchronization of data sampling against a master clock. Each survey consists of approx.100 traveltime measurements over the 12 h period between 6 p.m. and 6 a.m. local time; the time frame of each experiment was limited by daytime cultural noises. Analysis of traveltime variation is done either by timing of amplitude extrema or by cross-correlation of a waveform contructed from the digital data by a cubic-spline interpolation. Fractional error of the repeatablility of traveltime measurement is typically +- 3.3 x 10/sup -4/ for the first high-frequency, large amplitude arrival following the direct body waves. The first survey, conducted at a spring tide in August, 1981, showed a variation of ..delta..t/t -2 x 10/sup -3/ and correlated in time with the extensional tidal strain component along the baseline direction. The next two surveys, conducted at two neap tides, showed variation of ..delta..t/t approx.6 x 10/sup -4/ and also correlated with the same tidal strain component. However, the other 5 surveys conducted after the onset of 1981 rainy season and into the 1982 dry season, 4 at spring tides and 1 between a spring and a neap tide, showed traveltime constant to within 1 standard deviation. These results corroborate only partially the previously reported tidal stress variation of traveltimes in the shallow crust.

  17. Micromagnetic and Moessbauer spectroscopic investigation of strain-induced martensite in austenitic stainless steel

    SciTech Connect

    Meszaros, I.; Kaldor, M.; Hidasi, B.; Vertes, A.; Czako-Nagy, I.

    1996-08-01

    Strain-induced martensite in 18/8 austenitic stainless steel was studied. Magnetic measurements and Moessbauer spectroscopic investigations were performed to characterize the amount of {alpha}{prime}-martensite due to room-temperature plastic tensile loading. The effects of cold work and annealing heat treatment were explored using magnetic Barkhausen noise, saturation polarization, coercive force, hardness, and conversion electron Moessbauer spectroscopy. The suggested Barkhausen noise measurement technique proved to be a useful quantitative and nondestructive method for determining the ferromagnetic phase ratio of the studied alloy.

  18. Temporal Variation of Strain Field Around the Dedana Fault in NE Japan, Before and After the 2008 Iwate-Miyagi Nairiku Earthquake (M7.2)

    NASA Astrophysics Data System (ADS)

    Ohzono, M.; Miura, S.; Ohta, Y.; Iinuma, T.; Tachibana, K.; Sato, T.; Ueki, S.; Tsushima, H.; Miyao, K.; Takasuka, K.

    2008-12-01

    The Dedana fault (DF) is a southern part of the Kitakami-teichi-seien fault zone (KTSFZ), which consists of some typical active thrust faults along the eastern margin of Ou backbone range (OBR) in northeastern Japan. Based on the recent GPS studies, Miura et al. [EPS04] have found a strain concentration zone with EW contraction along OBR. In order to clarify more detailed strain field around the KTSFZ, we have installed 7 new continuous GPS sites along the EW line crossing the DF to complement the pre-existing sites operated by the Geographical Survey Institute (GSI) and the National Astronomical Observatory (NAO) in October 2007. Ohzono et al. [JPGU08] have pointed out a possibility of abrupt strain rate increase in OBR bounded by the DF from the time series of the site coordinates by March 2008. The Iwate-Miyagi Nairiku (inland) earthquake (M7.2) occurred beneath OBR on 13 June 2008 (UT). Its hypocenter is located at the southwest about 20 km away from the DF. This earthquake caused the large coseismic displacement around the source area. Ohta et al. [in review to EPS] proposed a fault model to explain the coseismic deformation observed by GPS. Soon after the earthquake, additional 14 GPS sites were deployed by the Japanese University Consortium for GPS (JUNCO) to reveal the postseismic deformation, which is distributed in the shallower part of the coseismic fault and the DF [Iinuma et al., submitted to ASC08]. Examining the time series of the site coordinates before and after the earthquake, we can summarize the temporal variation of the strain field around the DF as follows: 1) Before the earthquake, 8 months GPS data provide the clear strain increase in OBR around the west of the DF. However, this may be caused by the long-term strain accumulation as already suggested. We should investigate the data more carefully. 2) During the earthquake, the DF does not seem to be displaced because the EW profile of the coseismic displacement cannot be explained by the

  19. A Numerical Investigation of the Strain Effect on Saturation Optical Intensity in Electroabsorption Modulators Based on Asymmetric Intra-step-barrier Coupled Double Strained Quantum Wells

    NASA Astrophysics Data System (ADS)

    Abedi, Kambiz

    2011-12-01

    In this paper, the strain effect on saturation optical intensity in electroabsorption modulators (EAMs) based on asymmetric intra-step-barrier coupled double strained quantum well (AICD-SQWs) active region is theoretically investigated and compared with intra-step quantum well (IQW) structure. For this purpose, the thermionic emission and tunneling escape processes are taken into account and the escape times of photogenerated carriers are calculated. Then, the electroabsorption coefficient is calculated for different well strains for TE input light polarization. Finally, the saturation optical intensity of electroabsorption modulators with AICD-SQW structures in comparison with IQW structure is evaluated. Numerical results show that the tensile strain of well has the most significant effect on the saturation optical intensity of electroabsorption modulators with AICD-SQW structures due to reduction in escape times.

  20. Investigation of Copy Number Variation in Children with Conotruncal Heart Defects

    PubMed Central

    Campos, Carla Marques Rondon; Zanardo, Evelin Aline; Dutra, Roberta Lelis; Kulikowski, Leslie Domenici; Kim, Chong Ae

    2015-01-01

    Background Congenital heart defects (CHD) are the most prevalent group of structural abnormalities at birth and one of the main causes of infant morbidity and mortality. Studies have shown a contribution of the copy number variation in the genesis of cardiac malformations. Objectives Investigate gene copy number variation (CNV) in children with conotruncal heart defect. Methods Multiplex ligation-dependent probe amplification (MLPA) was performed in 39 patients with conotruncal heart defect. Clinical and laboratory assessments were conducted in all patients. The parents of the probands who presented abnormal findings were also investigated. Results Gene copy number variation was detected in 7/39 patients: 22q11.2 deletion, 22q11.2 duplication, 15q11.2 duplication, 20p12.2 duplication, 19p deletion, 15q and 8p23.2 duplication with 10p12.31 duplication. The clinical characteristics were consistent with those reported in the literature associated with the encountered microdeletion/microduplication. None of these changes was inherited from the parents. Conclusions Our results demonstrate that the technique of MLPA is useful in the investigation of microdeletions and microduplications in conotruncal congenital heart defects. Early diagnosis of the copy number variation in patients with congenital heart defect assists in the prevention of morbidity and decreased mortality in these patients. PMID:25387403

  1. Computational classification of different wild-type zebrafish strains based on their variation in light-induced locomotor response.

    PubMed

    Gao, Yuan; Zhang, Gaonan; Jelfs, Beth; Carmer, Robert; Venkatraman, Prahatha; Ghadami, Mohammad; Brown, Skye A; Pang, Chi Pui; Leung, Yuk Fai; Chan, Rosa H M; Zhang, Mingzhi

    2016-02-01

    Zebrafish larvae display a rapid and characteristic swimming behaviour after abrupt light onset or offset. This light-induced locomotor response (LLR) has been widely used for behavioural research and drug screening. However, the locomotor responses have long been shown to be different between different wild-type (WT) strains. Thus, it is critical to define the differences in the WT LLR to facilitate accurate interpretation of behavioural data. In this investigation, we used support vector machine (SVM) models to classify LLR data collected from three WT strains: AB, TL and TLAB (a hybrid of AB and TL), during early embryogenesis, from 3 to 9 days post-fertilisation (dpf). We analysed both the complete dataset and a subset of the data during the first 30after light change. This initial period of activity is substantially driven by vision, and is also known as the visual motor response (VMR). The analyses have resulted in three major conclusions: First, the LLR is different between the three WT strains, and at different developmental stages. Second, the distinguishable information in the VMR is comparable to, if not better than, the full dataset for classification purposes. Third, the distinguishable information of WT strains in the light-onset response differs from that in the light-offset response. While the classification accuracies were higher for the light-offset than light-onset response when using the complete LLR dataset, a reverse trend was observed when using a shorter VMR dataset. Together, our results indicate that one should use caution when extrapolating interpretations of LLR/VMR obtained from one WT strain to another.

  2. Genomic variations of Oenococcus oeni strains and the potential to impact on malolactic fermentation and aroma compounds in wine.

    PubMed

    Bartowsky, Eveline J; Borneman, Anthony R

    2011-11-01

    Malolactic fermentation (MLF) is the bacterially driven decarboxylation of L-malic acid to L-lactic acid and carbon dioxide, and brings about deacidification, flavour modification and microbial stability of wine. The main objective of MLF is to decrease wine sourness by a small increase in wine pH via the metabolism of L-malic acid. Oenococcus oeni is the main lactic acid bacterium to conduct MLF in virtually all red wine and an increasing number of white and sparkling wine bases. Over the last decade, it is becoming increasingly recognized that O. oeni exhibits a diverse array of secondary metabolic activities during MLF which can modify the sensory properties of wine. These secondary activities include the metabolism of organic acids, carbohydrates, polysaccharides and amino acids, and numerous enzymes such as glycosidases, esterases and proteases, which generate volatile compounds well above their odour detection threshold. Phenotypic variation between O. oeni strains is central for producing different wine styles. Recent studies using array-based comparative genome hybridization and genome sequencing of three O. oeni strains have revealed the large genomic diversity within this species. This review will explore the links between O. oeni metabolism, genomic diversity and wine sensory attributes.

  3. Chlorine inactivation of Salmonella Kentucky isolated from chicken carcasses: Evaluation of strain variation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The inactivation behavior of antibiotic resistant and non-resistant Salmonella Kentucky recovered from pre- and post-chill whole broiler carcasses in a large poultry plant was investigated by the exposure to 30 ppm chlorine for selected time intervals. The antibiotic resistance profiles were non-res...

  4. Investigation of geometric uncertainty introduced dosimetric variation in intensity modulated proton therapy (IMPT) and its intervention

    NASA Astrophysics Data System (ADS)

    Zhang, Miao

    The intensity modulated proton therapy (IMPT) can generate plans with reduced normal tissue toxicity and increased target dose conformity. However, geometric uncertainty associated with the treatment process could introduce large dose variations between the delivered dose distribution and the planned. There are three common types of geometric uncertainty: setup uncertainty, inter-, and intra-fractional organ motion. This thesis work will investigate setup uncertainty and inter-fractional organ motion introduced dose variation and find solutions to minimize such variations. A proton treatment planning system was developed by using Geant4 Monte Carlo toolbox as the dose calculation engine. The setup uncertainty was studied on the head and neck cancer site. Plan delivery simulation shown large dose variation occurred even with small amount of setup uncertainty. Two intervention strategies were investigated: (i) different proton pencil beam sizes, and (ii) the energy margin. By varying proton pencil beam size, we found the larger the beam size the less the dose variation, nevertheless the higher normal tissue dose. The energy margin is a planning strategy incorporating the possible motion effect into the planning stage by assigning proton pencil beams an energy value large enough to guarantee protons will travel to where they are planned. The energy margin solution was tested to be effective to minimize the dose variation in the distal edge tracking (DET) based IMPT. The inter-fractional motion was studied by looking at the daily prostate shift in the prostate cancer treatment. Delivery simulation for prostate cancer IMPT shown large dose variation would result even if the image guidance (IG) technique was used to realign the prostate back to its original location on the planning CT. A novel on-line adaptive image guided IMPT (A-IG-IMPT) technique was proposed to minimize the dose variation. By updating the energy value for individual proton pencil beam from the on

  5. Microstructures and strain variation: Evidence of multiple splays in the North Almora Thrust Zone, Kumaun Lesser Himalaya, Uttarakhand, India

    NASA Astrophysics Data System (ADS)

    Joshi, Gaurav; Agarwal, Amar; Agarwal, K. K.; Srivastava, Samriddhi; Alva Valdivia, L. M.

    2017-01-01

    The North Almora Thrust zone (NATZ) marks the boundary of the Almora Crystalline Complex (ACC) against the Lesser Himalayan Sedimentary sequence (LHS) in the north. Its southern counterpart, the South Almora Thrust (SAT), is a sharply marked contact between the ACC and the LHS in the south. Published studies argue various contradictory emplacement modes of the North Almora Thrust. Recent studies have implied splays of smaller back thrusts in the NATZ. The present study investigates meso- and microstructures, and strain distribution in the NATZ and compares it with strain distribution across the SAT. In the NATZ, field evidence reveals repeated sequence of 10-500 m thick slices of proto- to ultra-mylonite, thrust over the Lesser Himalayan Rautgara quartzite. In accordance with the field evidence, the strain analysis reveals effects of splays of smaller thrust in the NATZ. The study therefore, argues that contrary to popular nomenclature the northern contact of the ACC with the LHS is not a single thrust plane, but a thrust zone marked by numerous thrust splays.

  6. Investigating the effect of lateral viscosity variations in the Earth's mantle

    NASA Astrophysics Data System (ADS)

    O'Farrell, K. A.; Lithgow-Bertelloni, C. R.

    2015-12-01

    Seismic tomography can be used to investigate radial viscosity variations on instantaneous flow models by predicting the global geoid and comparing with the observed geoid. This method is one of many that has been used to constrain viscosity structure in the Earth's mantle in the last few decades. Using the 3D mantle convection model, Stag-YY (e.g., Hernlund and Tackley, 2008), we are further able to explore the effect of lateral variations in viscosity in addition to the radial variations. Examining over 50 tomographic models we found notable differences by comparing a synthetically produced geoid with the observed geoid. Comparing S- and P-wave tomographic models, the S-wave models provided a better fit to the observed geoid. Using this large suite of 50 tomographic models, we have been able to constrain the radial viscosity structure of the Earth. We found that two types of viscosity profiles yielded equally good fits. A viscosity profile with a low transition zone viscosity and a lower mantle viscosity equal to the upper mantle, or a profile with a large lower mantle viscosity and a transition zone viscosity similar to the upper mantle. Using the set of radial viscosity profiles that gave the best fit to the observed geoid, we can explore a range of lateral viscosity variations and see how they affect the different types of tomographic models. Improving on previous studies of lateral viscosity variations (e.g. Ghosh, Becker and Zhong, 2010), we systematically explore a large range of tomographic models and density-velocity conversion factors. We explore which type of tomographic model (S- or P- wave) is more strongly affected by lateral viscosity variations, as well as the effect on isotropic and anisotropic models. We constrain the strength of lateral viscosity variations necessary to produce a high correlation between observed and predicted geoid anomalies. We will discuss the wavelength of flow that is most affected by the lateral viscosity variations

  7. Investigation of Harper-Dorn creep under the condition of large strains

    NASA Astrophysics Data System (ADS)

    Cheng, Yu-Ching

    The purpose of this investigation is to identify and clarify the perspective of the nature and origin of necessary procedures and requirements for Harper-Dorn creep. Harper-Dorn creep represents to the anomalous high temperature deformation behavior, which is first reported by Harper and Dorn in aluminum under the condition of small strains about 0.01. To accomplish the purpose of this investigation, four types of large grained materials are selected: commercial purity grade lead, high purity grade lead, high purity grade polycrystalline aluminum, and high purity grade single crystalline aluminum. Creep experiments are conducted under 0.98 melting temperature of the selected materials in long term tests. Microstructures are examed by optical microscope, scanning electron microscope and transmission electron microscope. Mechanical results represent that creep curves of commercial purity grade lead are smooth and stress exponents obeys the five-power-law at both high and low stress areas. Micro-structural results show that dynamic recovery is the proper restoration mechanism for commercial purity grade lead. Mechanical results represent that creep curves of high purity grade aluminum and lead show periodic accelerations in strain. The creep results of high purity grade aluminum verify that the present test conditions correspond to the priors. Furthermore, under the condition of large strains about 0.05, it was determined that the stress exponent of Harper-Dorn creep is about 2.6 and does not reveal Newtonian behavior. Micro-structural results indicate that dynamic re-crystallization is a dominate restoration mechanism for Harper-Dorn creep in large grain size, low dislocation density, and high purity grade materials. Therefore, this investigation provides new evidence that dynamic re-crystallization occurs during Harper-Dorn creep. The evidence is proved by the occurrence of periodic accelerations in creep curves and the transition of the stress exponents

  8. Quantitative investigation of ligament strains during physical tests for sacroiliac joint pain using finite element analysis.

    PubMed

    Kim, Yoon Hyuk; Yao, Zhidong; Kim, Kyungsoo; Park, Won Man

    2014-06-01

    It may be assumed that the stability is affected when some ligaments are injured or loosened, and this joint instability causes sacroiliac joint pain. Several physical examinations have been used to diagnose sacroiliac pain and to isolate the source of the pain. However, more quantitative and objective information may be necessary to identify unstable or injured ligaments during these tests due to the lack of understanding of the quantitative relationship between the physical tests and the biomechanical parameters that may be related to pains in the sacroiliac joint and the surrounding ligaments. In this study, a three-dimensional finite element model of the sacroiliac joint was developed and the biomechanical conditions for six typical physical tests such as the compression test, distraction test, sacral apex pressure test, thigh thrust test, Patrick's test, and Gaenslen's test were modelled. The sacroiliac joint contact pressure and ligament strain were investigated for each test. The values of contact pressure and the combination of most highly strained ligaments differed markedly among the tests. Therefore, these findings in combination with the physical tests would be helpful to identify the pain source and to understand the pain mechanism. Moreover, the technology provided in this study might be a useful tool to evaluate the physical tests, to improve the present test protocols, or to develop a new physical test protocol.

  9. Community Genomic Analysis of Strain Variation of a Novel Archaeon in an Acid Mine Drainage Environment

    NASA Astrophysics Data System (ADS)

    Yelton, P.; Banfield, J.; Wilmes, P.

    2006-12-01

    Microorganisms play a significant role in acid mine drainage (AMD) generation within the Richmond Mine, Iron Mountain, California. To better understand the contributions of individual microbial species to this process, the assemblies of community genomic data from AMD biofilms were manually curated. Not reported previously is detailed analysis of genomic sequence from G-plasma, an archaeal population from a sample collected from the 5-way location in 2002. The G-plasma population exhibits a small number of differing nucleotide sequences at most genomic locations and comprises multiple genome types. Linkage between these sequence types indicates frequent homologous recombination. As the near complete genome is still in many fragments, the current investigation focused on the 25% of the genome in large, confidently linked pieces. Many predicted proteins from this organism were detected via proteomic analysis. In combination, information about genome heterogeneity and protein expression is providing clues to the role of this population in the biofilm community.

  10. Occurrence of 20S RNA and 23S RNA replicons in industrial yeast strains and their variation under nutritional stress conditions.

    PubMed

    López, Victoria; Gil, Rosario; Vicente Carbonell, José; Navarro, Alfonso

    2002-04-01

    We have characterized industrial yeast strains used in the brewing, baking, and winemaking industries for the presence or absence of cytoplasmic single-stranded 20S and 23S RNAs. Furthermore, the variation of intracellular concentrations of these replicons in brewing and laboratory strains under nutritional stress conditions was determined. Our results show a correlation between the relative abundance of these replicons and exposure of yeast to nutritionally stressful conditions, indicating that these RNAs could be employed as molecular probes to evaluate the exposure of 20S(+) and/or 23S(+) yeast strains to stress situations during industrial manipulation. During this study, several 20S(-)23S(+) Saccharomyces cerevisiae strains were isolated and identified. This is the first time that a yeast strain containing only 23S RNA has been reported, demonstrating that 20S RNA is not required for 23S RNA replication.

  11. Investigation of the Enteric Pathogenic Potential of Oral Campylobacter concisus Strains Isolated from Patients with Inflammatory Bowel Disease

    PubMed Central

    Octavia, Sophie; Day, Andrew S.; Riordan, Stephen M.; Grimm, Michael C.; Lan, Ruiting; Lemberg, Daniel; Tran, Thi Anh Tuyet; Zhang, Li

    2012-01-01

    Background Campylobacter concisus, a bacterium colonizing the human oral cavity, has been shown to be associated with inflammatory bowel disease (IBD). This study investigated if patients with IBD are colonized with specific oral C. concisus strains that have potential to cause enteric diseases. Methodology Seventy oral and enteric C. concisus isolates obtained from eight patients with IBD and six controls were examined for housekeeping genes by multilocus sequence typing (MLST), Caco2 cell invasion by gentamicin-protection-assay, protein analysis by mass spectrometry and SDS-PAGE, and morphology by scanning electron microscopy. The whole genome sequenced C. concisus strain 13826 which was isolated from an individual with bloody diarrhea was included in MLST analysis. Principal Findings MLST analysis showed that 87.5% of individuals whose C. concisus belonged to Cluster I had inflammatory enteric diseases (six IBD and one with bloody diarrhea), which was significantly higher than that in the remaining individuals (28.6%) (P<0.05). Enteric invasive C. concisus (EICC) oral strain was detected in 50% of patients with IBD and none of the controls. All EICC strains were in Cluster 1. The C. concisus strain colonizing intestinal tissues of patient No. 1 was closely related to the oral C. concisus strain from patient No. 6 and had gene recombination with the patient’s own oral C. concisus. The oral and intestinal C. concisus strains of patient No. 3 were the same strain. Some individuals were colonized with multiple oral C. concisus strains that have undergone natural recombination. Conclusions This study provides the first evidence that patients with IBD are colonized with specific oral C. concisus strains, with some being EICC strains. C. concisus colonizing intestinal tissues of patients with IBD at least in some instances results from an endogenous colonization of the patient’s oral C. concisus and that C. concisus strains undergo natural recombination. PMID

  12. The 100-genomes strains, an S. cerevisiae resource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen.

    PubMed

    Strope, Pooja K; Skelly, Daniel A; Kozmin, Stanislav G; Mahadevan, Gayathri; Stone, Eric A; Magwene, Paul M; Dietrich, Fred S; McCusker, John H

    2015-05-01

    Saccharomyces cerevisiae, a well-established model for species as diverse as humans and pathogenic fungi, is more recently a model for population and quantitative genetics. S. cerevisiae is found in multiple environments-one of which is the human body-as an opportunistic pathogen. To aid in the understanding of the S. cerevisiae population and quantitative genetics, as well as its emergence as an opportunistic pathogen, we sequenced, de novo assembled, and extensively manually edited and annotated the genomes of 93 S. cerevisiae strains from multiple geographic and environmental origins, including many clinical origin strains. These 93 S. cerevisiae strains, the genomes of which are near-reference quality, together with seven previously sequenced strains, constitute a novel genetic resource, the "100-genomes" strains. Our sequencing coverage, high-quality assemblies, and annotation provide unprecedented opportunities for detailed interrogation of complex genomic loci, examples of which we demonstrate. We found most phenotypic variation to be quantitative and identified population, genotype, and phenotype associations. Importantly, we identified clinical origin associations. For example, we found that an introgressed PDR5 was present exclusively in clinical origin mosaic group strains; that the mosaic group was significantly enriched for clinical origin strains; and that clinical origin strains were much more copper resistant, suggesting that copper resistance contributes to fitness in the human host. The 100-genomes strains are a novel, multipurpose resource to advance the study of S. cerevisiae population genetics, quantitative genetics, and the emergence of an opportunistic pathogen.

  13. Investigation of flaw geometry and loading effects on plane strain fracture in metallic structures

    NASA Technical Reports Server (NTRS)

    Hall, L. R.; Finger, R. W.

    1971-01-01

    The effects on fracture and flaw growth of weld-induced residual stresses, combined bending and tension stresses, and stress fields adjacent to circular holes in 2219-T87 aluminum and 5AI-2.5Sn(ELI) titanium alloys were evaluated. Static fracture tests were conducted in liquid nitrogen; fatigue tests were performed in room air, liquid nitrogen, and liquid hydrogen. Evaluation of results was based on linear elastic fracture mechanics concepts and was directed to improving existing methods of estimating minimum fracture strength and fatigue lives for pressurized structure in spacecraft and booster systems. Effects of specimen design in plane-strain fracture toughness testing were investigated. Four different specimen types were tested in room air, liquid nitrogen and liquid hydrogen environments using the aluminum and titanium alloys. Interferometry and holograph were used to measure crack-opening displacements in surface-flawed plexiglass test specimens. Comparisons were made between stress intensities calculated using displacement measurements, and approximate analytical solutions.

  14. Investigation of the stress distribution around a mode 1 crack with a novel strain gradient theory

    NASA Astrophysics Data System (ADS)

    Lederer, M.; Khatibi, G.

    2017-01-01

    Stress concentrations at the tip of a sharp crack have extensively been investigated in the past century. According to the calculations of Inglis, the stress ahead of a mode 1 crack shows the characteristics of a singularity. This solution is exact in the framework of linear elastic fracture mechanics (LEFM). From the viewpoint of multiscale modelling, however, it is evident that the stress at the tip of a stable crack cannot be infinite, because the strengths of atomic bonds are finite. In order to prevent the problem of this singularity, a new version of strain gradient elasticity is employed here. This theory is implemented in the commercial FEM code ABAQUS through user subroutine UEL. Convergence of the model is proved through consecutive mesh refinement. In consequence, the stresses ahead of a mode 1 crack become finite. Furthermore, the model predicts a size effect in the sense “smaller is stronger”.

  15. Strain-specific variation of the decorin-binding adhesin DbpA influences the tissue tropism of the lyme disease spirochete.

    PubMed

    Lin, Yi-Pin; Benoit, Vivian; Yang, Xiuli; Martínez-Herranz, Raúl; Pal, Utpal; Leong, John M

    2014-07-01

    Lyme disease spirochetes demonstrate strain- and species-specific differences in tissue tropism. For example, the three major Lyme disease spirochete species, Borrelia burgdorferi sensu stricto, B. garinii, and B. afzelii, are each most commonly associated with overlapping but distinct spectra of clinical manifestations. Borrelia burgdorferi sensu stricto, the most common Lyme spirochete in the U.S., is closely associated with arthritis. The attachment of microbial pathogens to cells or to the extracellular matrix of target tissues may promote colonization and disease, and the Lyme disease spirochete encodes several surface proteins, including the decorin- and dermatan sulfate-binding adhesin DbpA, which vary among strains and have been postulated to contribute to strain-specific differences in tissue tropism. DbpA variants differ in their ability to bind to its host ligands and to cultured mammalian cells. To directly test whether variation in dbpA influences tissue tropism, we analyzed murine infection by isogenic B. burgdorferi strains that encode different dbpA alleles. Compared to dbpA alleles of B. afzelii strain VS461 or B. burgdorferi strain N40-D10/E9, dbpA of B. garinii strain PBr conferred the greatest decorin- and dermatan sulfate-binding activity, promoted the greatest colonization at the inoculation site and heart, and caused the most severe carditis. The dbpA of strain N40-D10/E9 conferred the weakest decorin- and GAG-binding activity, but the most robust joint colonization and was the only dbpA allele capable of conferring significant joint disease. Thus, dbpA mediates colonization and disease by the Lyme disease spirochete in an allele-dependent manner and may contribute to the etiology of distinct clinical manifestations associated with different Lyme disease strains. This study provides important support for the long-postulated model that strain-specific variations of Borrelia surface proteins influence tissue tropism.

  16. Investigation of TEC Variations over Mid-Latitude during Quit and Disturbed Days of March 2015

    NASA Astrophysics Data System (ADS)

    Atıcı, Ramazan; Saǧır, Selçuk; Güzel, Esat

    2016-07-01

    The variations during 09-14-March-2015 quit days and 15-20 March 2015 disturbed days of Total Electron Content (TEC) values (provided by IONOLAB group) obtained by analysis the data from Ankara Global Position System (GPS) station of Turkey located at mid-latitude, IRI -2012 model the and IRI-PLUS model are investigated. Also, the variations of the geomagnetic, interplanetary and solar wind parameters are examined. As a result of investigations, TEC values from all three models are not change too much at quit days. Unlike, at the disturbed days, although IRI-2012 and IRI-PLUS TEC values are not change too much, a noticeable change in GPS-TEC values is occurred. GPS-TEC values are rapidly increased on 17-March 2015 to be severe magnetic storm (Dst = -124 nT). Then, on following days it was observed to significantly decrease. Thus, it is said that GPS-TEC values are more sensitive than IRI-2012 and IRI-PLUS models to variations occurred on disturbed days.

  17. Investigation of photospheric temperature gradient variations using limb darkening measurements and simulations

    NASA Astrophysics Data System (ADS)

    Criscuoli, Serena; Foukal, Peter V.

    2016-05-01

    The temperature stratifications of magnetic elements and unmagnetized plasma are different, so that changes of the facular and network filling factor over the cycle modify the average temperature gradient in the photosphere.Such variations have been suggested to explain irradiance measurements obtained by the SIM spectrometers in he visible and infrared spectral ranges. On the other hand, limb darkening measurements show no dependence upon activity level. We investigate the sensitivity of limb darkening to changes in network area filling factor using a 3-D MHD model of the magnetized photosphere. We find that the expected limb darkening change due to the measured 11- yr variation in filling factor lies outside the formal 99% confidence limit of the limb darkening measurements. This poses important constraints for observational validation of 3D-MHD simulations.

  18. Investigation of Strain Aging in the Ordered Intermetallic Compound beta-NiAl. Ph.D. Thesis Final Contractor Report

    NASA Technical Reports Server (NTRS)

    Weaver, Mark Lovell

    1995-01-01

    The phenomenon of strain aging has been investigated in polycrystalline and single crystal NiAl alloys at temperatures between 300 and 1200 K. Static strain aging studies revealed that after annealing at 1100 K for 7200 s (i.e., 2h) followed by furnace cooling, high purity, nitrogen-doped and titanium-doped polycrystalline alloys exhibited continuous yielding, while conventional-purity and carbon-doped alloys exhibited distinct yield points and Luders strains. Prestraining by hydrostatic pressurization removed the yield points, but they could be reintroduced by further annealing treatments. Yield points could be reintroduced more rapidly if the specimens were prestrained uniaxially rather than hydrostatically, owing to the arrangement of dislocations into cell structures during uniaxial deformation. The time dependence of the strain aging events followed at t(exp 2/3) relationship suggesting that the yield points observed in polycrystalline NiAl were the result of the pinning of mobile dislocations by interstitials, specifically carbon. Between 700 and 800 K, yield stress plateaus, yield stress transients upon a ten-fold increase in strain rate, work hardening peaks, and dips in the strain rate sensitivity (SRS) have been observed in conventional-purity and carbon-doped polycrystals. In single crystals, similar behavior was observed; in conventional-purity single crystals, however, the strain rate sensitivity became negative resulting in serrated yielding, whereas, the strain rate sensitivity stayed positive in high purity and in molybdenum-doped NiAl. These observations are indicative of dynamic strain aging (DSA) and are discussed in terms of conventional strain aging theories. The impact of these phenomena on the composition-structure-property relations are discerned. Finally, a good correlation has been demonstrated between the properties of NiAl alloys and a recently developed model for strain aging in metals and alloys developed by Reed-Hill et al.

  19. An Evaluation of Constitutive Laws and their Ability to Predict Flow Stress over Large Variations in Temperature, Strain, and Strain Rate Characteristic of Friction Stir Welding

    NASA Astrophysics Data System (ADS)

    Kuykendall, Katherine

    2011-07-01

    Constitutive laws commonly used to model friction stir welding have been evaluated, both qualitatively and quantitatively, and a new application of a constitutive law which can be extended to materials commonly used in FSW is presented. Existing constitutive laws have been classified as path-dependent or path-independent. Path-independent laws have been further classified according to the physical phenomena they capture: strain hardening, strain rate hardening, and/or thermal softening. Path-dependent laws can track gradients in temperature and strain rate characteristic to friction stir welding; however, path-independent laws cannot. None of the path-independent constitutive laws evaluated has been validated over the full range of strain, strain rate, and temperature in friction stir welding. Holding all parameters other than constitutive law constant in a friction stir weld model resulted in temperature differences of up to 21%. Varying locations for maximum temperature difference indicate that the constitutive laws resulted in different temperature profiles. The Sheppard and Wright law is capable of capturing saturation but incapable of capturing strain hardening with errors as large as 57% near yield. The Johnson-Cook law is capable of capturing strain hardening; however, its inability to capture saturation causes over-predictions of stress at large strains with errors as large as 37% near saturation. The Kocks and Mecking model is capable of capturing strain hardening and saturation with errors less than 5% over the entire range of plastic strain. The Sheppard and Wright and Johnson-Cook laws are incapable of capturing transients characteristic of material behavior under interrupted temperature or strain rate. The use of a state variable in the Kocks and Mecking law allows it to predict such transients. Constants for the Kocks and Mecking model for AA 5083, AA 3004, and Inconel 600 were determined from Atlas of Formability data. Constants for AA 5083 and AA

  20. [Investigation of plasmid-mediated quinolone resistance in Escherichia coli strains].

    PubMed

    Aktepe, Orhan Cem; Aşık, Gülşah; Cetinkol, Yeliz; Biçmen, Meral; Gülay, Zeynep

    2012-01-01

    Quinolones are widely used antimicrobial agents, particularly for the treatment of infections caused by gram-negative bacilli such as E.coli. As a consequence, quinolone resistance has been increasing among this species in recent years. Bacterial resistance to quinolones usually results from mutations in the chromosomal genes which encode topoisomerases and also the expression of efflux pumps and loss of porines contributed to development of quinolone resistance. However, recent studies have shown that the spread and increase of quinolone resistance may be due to the transfer of plasmid-mediated genes. To date, three groups of plasmid-mediated quinolone resistance genes, namely qnr, aac(6')-Ib-cr, and qepA, have been described. The aim of this study was to investigate the presence of plasmid-mediated quinolone resistance genes in E.coli clinical isolates. A total of 112 quinolone-resistant E.coli strains isolated from different clinical specimens (84 urine, 16 blood, 10 wound, 2 bronchoalveolar lavage) of which 78 (69.6%) were extended-spectrum beta-lactamase (ESBL) positive, in Afyon Kocatepe University Hospital, Microbiology Laboratory were included in the study. In the isolates, qnrA, qnrB, qnrS, qnrC, qepA, and aac(6')-1b-cr plasmid genes were analysed by polymerase chain reaction (PCR). After aac(6')- 1b determinant was amplified by PCR, all aac(6')-1b positive amplicons were analyzed by digestion with BseGI restriction enzyme to identify aac(6')-1b-cr variant. It was found that, none of the strains horboured qnrA, qnrB, qnrS, qnrC and qepA genes, however, plasmid-mediated quinolone resistance gene aac(6')-1b-cr was found positive in 59.8% (67/112) of the strains. It was notable that 86.6% (58/67) of those isolates were ESBL producers. The rates of quinolone resistance among E.coli isolates infections were high in our region and an increasing trend has been observed in recent years. Our data indicated that the presence of plasmid- mediated resistance genes

  1. In-situ x-ray scattering investigation of strain in thin-film morphological evolution of homoepitaxial Ag(001)

    NASA Astrophysics Data System (ADS)

    Hayden, S. T.; Kim, C.; Conrad, E. H.; Gramlich, M. W.; Miceli, P. F.

    2010-03-01

    Because it escapes detection in most experimental probes of surfaces, the role of strain during film growth has not been widely investigated. However, large strain fields arise from vacancy nano-clusters [C. Kim et al., APL 91, 093131 (2007)] that can be incorporated during film growth at lower temperatures. It has also been suggested that extreme surface morphologies, resulting from a deposition flux at grazing angles, might lead to significant strain [Y. Shim et. al., PRL 101, 11601 (2008)]. Because of its simultaneous sensitivity to both the surface and the subsurface, x-ray scattering is a particularly valuable technique for exploring the role of strain in epitaxial crystal growth. This talk will discuss our recent in-situ x-ray diffuse scattering and reflectivity measurements, performed at the Advanced Photon Source, which investigate the low temperature homoepitaxial growth of Ag(001).

  2. Full-Field Strain Methods for Investigating Failure Mechanisms in Triaxial Braided Composites

    NASA Technical Reports Server (NTRS)

    Littell, Justin D.; Binienda, Wieslaw K.; Goldberg, Robert K.; Roberts, Gary D.

    2008-01-01

    Recent advancements in braiding technology have led to commercially viable manufacturing approaches for making large structures with complex shape out of triaxial braided composite materials. In some cases, the static load capability of structures made using these materials has been higher than expected based on material strength properties measured using standard coupon tests. A more detailed investigation of deformation and failure processes in large-unit-cell-size triaxial braid composites is needed to evaluate the applicability of standard test methods for these materials and to develop alternative testing approaches. This report presents some new techniques that have been developed to investigate local deformation and failure using digital image correlation techniques. The methods were used to measure both local and global strains during standard straight-sided coupon tensile tests on composite materials made with 12- and 24-k yarns and a 0 /+60 /-60 triaxial braid architecture. Local deformation and failure within fiber bundles was observed and correlations were made between these local failures and global composite deformation and strength.

  3. National survey of prevalent HIV strains: limited genetic variation of Korean HIV-1 clade B within the population of Korean men who have sex with men.

    PubMed

    Kim, Gab Jung; Nam, Jeong-Gu; Shin, Bo Gyeong; Kee, Mee Kyeong; Kim, Eun-Jin; Lee, Joo-Shil; Kim, Sung Soon

    2008-06-01

    The evolution of HIV is the result of an explosive combination of factors-a high rate of mutation, replication dynamics, frequent recombination, and natural selection. To understand the evolution of the distinctive Korean HIV-1 B clade, we investigated the characteristics of the genetic variation of the HIV-1 subtype B env gene within the group of Korean men who have sex with men (MSM). From 1985 to 2005, 700 HIV-1-infected Koreans were sequenced at the V1 to V5 region of the HIV-1 env gene. In the phylogenetic analysis, 560 isolates were identified as HIV-1 subtype B, and 489 of the 560 isolates were HIV-1 Korean clade B. Based on epidemiologic investigation, 249 of 700 HIV-1-infected patients were HIV-1 subtype B-infected MSM. Interestingly, the proportion of the GPGS motif in MSM infected by Koreans was 1.6 times higher than in MSM infected by foreigners, and the genetic expansions of diversity and divergence for HIV-1 subtype B in Korean MSM were 2.1% and 2.5%, respectively. This was much lower than those observed in other countries. Therefore, our findings imply that the HIV strains in this group were closely related. This result may be helpful for understanding the evolution of the distinct HIV-1 Korean B clade.

  4. Quantitative susceptibility mapping for investigating subtle susceptibility variations in the human brain.

    PubMed

    Schweser, Ferdinand; Sommer, Karsten; Deistung, Andreas; Reichenbach, Jürgen Rainer

    2012-09-01

    Quantitative susceptibility mapping (QSM) is a novel magnetic resonance-based technique that determines tissue magnetic susceptibility from measurements of the magnetic field perturbation. Due to the ill-posed nature of this problem, regularization strategies are generally required to reduce streaking artifacts on the computed maps. The present study introduces a new algorithm for calculating the susceptibility distribution utilizing a priori information on its regional homogeneity derived from gradient echo phase images and analyzes the impact of erroneous a priori information on susceptibility map fidelity. The algorithm, Homogeneity Enabled Incremental Dipole Inversion (HEIDI), was investigated with a special focus on the reconstruction of subtle susceptibility variations in a numerical model and in volunteer data and was compared with two recently published approaches, Thresholded K-space Division (TKD) and Morphology Enabled Dipole Inversion (MEDI). HEIDI resulted in susceptibility maps without streaking artifacts and excellent depiction of subtle susceptibility variations in most regions. By investigating HEIDI susceptibility maps acquired with the volunteers' heads in different orientations, it was demonstrated that the apparent magnetic susceptibility distribution of human brain tissue considerably depends on the direction of the main magnetic field.

  5. Investigation of S3-2 satellite data for local time variation of energetic electron precipitation

    NASA Technical Reports Server (NTRS)

    Robbe, S.; Sheldon, W. R.; Benbrook, J. R.; Bering, E. A.; Vampola, A. L.

    1994-01-01

    Data on precipitating electrons from the S3-2 satellite were investigated for local time variation at four L = 4 stations in the southern hemisphere. The equatorial pitch angles of electrons mirroring at 100 km, assumed to be the edge of the bounce loss cone, are calculated for L = 4 using the International Geomagnetic Reference Field for the epoch of the S3-2 data, along with the variation in mirror altitude per degree of equatorial pitch angle. The largest obstacle to the investigation was uneven sampling in terms of local time for all of the stations. However, this situation was improved upon by the use of S3-2 measurements at the conjugate locations of the four stations which provided additional data on electrons in the southern hemisphere bounce loss cone. Evidence for an effect of the dawn-to-dusk geoelectric field was found at two of the stations, Halley Bay and Siple, in the form of a minimum in electron precipitation at dusk. However, the present study does not completely resolve the question of local time modulation of electron precipitation at L = 4 in the southern hemisphere. Furthermore, while the average precipitation was lowest at the Kerguelen site, as would be expected on the basis of drift loss cone (DLC) theories, the intensity at that site exceeds the level that is expected on the basis of these DLC theories.

  6. Investigation of cycle-to-cycle variations in an engine-like geometry

    NASA Astrophysics Data System (ADS)

    Schmitt, M.; Frouzakis, C. E.; Wright, Y. M.; Tomboulides, A. G.; Boulouchos, K.

    2014-12-01

    The multiple-cycle direct numerical simulation data of the flow in the valve/piston assembly investigated in Schmitt et al. ["Direct numerical simulation of multiple cycles in a valve/piston assembly," Phys. Fluids 26, 035105 (2014)] is revisited to identify the relevant flow features leading to the observed cyclic variations. These are found to be the radial velocity at top dead center (TDC) remaining from the previous cycle, the location of the center of the hollow jet during intake and the strength and orientation of the vortex ring at bottom dead center. Comparisons between these features showed strong correlations in the flow field within a cycle and between two consecutive cycles. The trajectory of the hollow jet during intake is strongly influenced by the remaining radial velocity from the previous cycle. Subsequently, the hollow jet forms a vortex ring whose orientation and strength influences the radial velocity at TDC of the next cycle. This has in turn an effect on the jet trajectory of the following cycle. The results in this simplified geometry are a first attempt to understand the origin of cause-and-effect relationships of cycle-to-cycle variations (CCVs) in the flow field and can serve as a base for investigating CCVs in more realistic engine geometries. Moreover, the reported correlations are a useful validation platform for large Eddy simulation models.

  7. Super Profile analysis of socioeconomic variations in coronary investigation and revascularisation rates

    PubMed Central

    Manson-Siddle, C. J.; Robinson, M. B.

    1998-01-01

    OBJECTIVES: To investigate socioeconomic variations in the utilisation of tertiary cardiology services. DESIGN: Cross sectional ecological study, using the Super Profile classification of enumeration districts, and ischaemic heart disease standardised mortality ratios as a proxy for needs. SETTING: The former Yorkshire Regional Health Authority area in England and its seven constituent district health authority areas. SUBJECTS: Patients with a primary diagnosis of ischaemic heart disease aged > or = 25 years who underwent investigation by angiography, or treatment by coronary artery bypass grafting (CABG) or percutaneous transluminal coronary angioplasty (PTCA), as a primary procedure between April 1992 and March 1994 in an NHS hospital. MAIN RESULTS: There is an overall increasing trend in investigation and revascularisation rates from the affluent to the deprived in the region suggesting equity. However, the gradient is slight compared with the corresponding mortality gradient. Age specific analysis shows a more appropriate trend in rates for the under 65s, but a downward trend from affluence to deprivation for the elderly. Much of the regional trend is caused by very high rates in one geographically small but densely populated district that has two tertiary cardiology centres. In other districts, with higher heart disease mortality but much lower procedure rates, there is a decreasing trend from the affluent to the deprived suggesting considerable inequity. CONCLUSIONS: This study confirms wide socioeconomic variations in coronary investigation and revascularisation within the former Yorkshire Region, suggesting that in some districts need is not being met and that service utilisation is inequitable. Such inequities are over and above those that result from proximity to tertiary cardiology centres.   PMID:9876362

  8. Investigation of mycoviruses in endophytic and phytopathogenic strains of Colletotrichum from different hosts.

    PubMed

    Rosseto, P; Costa, A T; Polonio, J C; da Silva, A A; Pamphile, J A; Azevedo, J L

    2016-02-26

    Fungi belonging to the Colletotrichum genus can be categorized as endophytic or phytopathogenic. These fungi can be infected by viruses, termed mycoviruses, which are know to promote hypovirulence in infected fungi. However, there are few studies that have described mycoviral infections of endophytes. The production of secondary metabolites by endophytes with antimicrobial potential in inhibiting numerous pathogens has gained increasing attention. The aim of the current study was to investigate the presence of mycoviruses in endophytic and phytopathogenic fungi of the Colletotrichum genus, as well as to analyze the antimicrobial activity of crude extracts obtained from these samples. To detect the presence of mycoviruses in the samples, dsRNA was extracted, treated with enzymes, and analyzed following electrophoresis in agarose gel. Furthermore, isometric mycoviral particles were observed by transmission electron microscopy. Serial microdilution methodology was used to test crude extracts of Colletotrichum spp for antibacterial activity against Escherichia coli and Staphylococcus aureus, and antifungal activity against Fusarium solani. The results of the molecular and microscopic analyses indicated that a phytopathogenic strain presented infection by mycovirus. The antibacterial activity analysis revealed that the minimum inhibitory concentrations and minimum bactericidal concentrations were low for the fungal extracts of the two endophytes, indicating that these extracts were effective antibacterial agents. However, their antifungal activity against F. solani was not statistically different compared to that of the negative control.

  9. Genomic Investigation into Strain Heterogeneity and Pathogenic Potential of the Emerging Gastrointestinal Pathogen Campylobacter ureolyticus

    PubMed Central

    Bullman, Susan; Lucid, Alan; Corcoran, Daniel; Sleator, Roy D.; Lucey, Brigid

    2013-01-01

    The recent detection and isolation of C. ureolyticus from patients with diarrhoeal illness and inflammatory bowel diseases warrants further investigation into its role as an emerging pathogen of the human gastrointestinal tract. Regarding the pathogenic mechanisms employed by this species we provide the first whole genome analysis of two C. ureolyticus isolates including the type strain. Comparative analysis, subtractive hybridisation and gene ontology searches against other Campylobacter species identifies the high degree of heterogenicity between C. ureolyticus isolates, in addition to the identification of 106 putative virulence associated factors, 52 of which are predicted to be secreted. Such factors encompass each of the known virulence tactics of pathogenic Campylobacter spp. including adhesion and colonisation (CadF, PEB1, IcmF and FlpA), invasion (ciaB and 16 virB-virD4 genes) and toxin production (S-layer RTX and ZOT). Herein, we provide the first virulence catalogue for C. ureolyticus, the components of which theoretically provide this emerging species with sufficient arsenal to establish pathology. PMID:24023611

  10. Investigating the non-classical boundary conditions relevant to strain gradient theories

    NASA Astrophysics Data System (ADS)

    Jafari, Akbar; Ezzati, Meysam

    2017-02-01

    In the present study, two classes of non-classical constitutive equations consisting of the first and the second order strain gradients theories (FSG and SSG) were applied in order to develop the governing equations of static and free vibrational behavior of beam structures. The governing equations in orders of six and eight were constructed for FSG and SSG theories, respectively. Therefore, higher order or in other words non-classical boundary conditions (HOBCs or NCBCs) came into play in addition to the classical ones (CBCs). Some explanations were presented about the concept of the non-classical boundary conditions. Analytical and finite element (FE) approaches were employed to solve the governing equations. The analytical solutions were utilized in validation and convergence study of FE results. Comparisons were made with the relevant data reported in the open literature; however, to the best of the authors' knowledge, few references have been published on SSG theory and HOBCs. In the numerical studies, the effects of applying different combinations of CBCs and HOBCs to the static and free vibration behaviors of the beam were investigated. Moreover, the impacts of non-classical elastic constants and the beam size on its behavior were also studied.

  11. Full-field Strain Methods for Investigating Failure Mechanisms in Triaxial Braided Composites

    NASA Technical Reports Server (NTRS)

    Littell, Justin D.; Binienda, Wieslaw K.; Goldberg, Robert K.; Roberts, Gary D.

    2008-01-01

    Composite materials made with triaxial braid architecture and large tow size carbon fibers are beginning to be used in many applications, including composite aircraft and engine structures. Recent advancements in braiding technology have led to commercially viable manufacturing approaches for making large structures with complex shape. Although the large unit cell size of these materials is an advantage for manufacturing efficiency, the fiber architecture presents some challenges for materials characterization, design, and analysis. In some cases, the static load capability of structures made using these materials has been higher than expected based on material strength properties measured using standard coupon tests. A potential problem with using standard tests methods for these materials is that the unit cell size can be an unacceptably large fraction of the specimen dimensions. More detailed investigation of deformation and failure processes in large unit cell size triaxial braid composites is needed to evaluate the applicability of standard test methods for these materials and to develop alternative testing approaches. In recent years, commercial equipment has become available that enables digital image correlation to be used on a more routine basis for investigation of full field 3D deformation in materials and structures. In this paper, some new techniques that have been developed to investigate local deformation and failure using digital image correlation techniques are presented. The methods were used to measure both local and global strains during standard straight-sided coupon tensile tests on composite materials made with 12 and 24 k yarns and a 0/+60/-60 triaxial braid architecture. Local deformation and failure within fiber bundles was observed, and this local failure had a significant effect on global stiffness and strength. The matrix material had a large effect on local damage initiation for the two matrix materials used in this investigation

  12. Investigating strength of materials at very high strain rates using magnetically driven expanding cylinders

    NASA Astrophysics Data System (ADS)

    Lovinger, Zev; Nemirovsky, Ron; Avriel, Eyal; Dorogoy, Avraham; Ashuach, Yehezkel; Rittel, Daniel

    2015-09-01

    Dynamic characterization of strength properties is done, in common practice by the means of a Split-Hopkinson Pressure Bar (also named Kolsky-Bar) apparatus. In such systems, strain rates are limited up to ˜ 5 ṡ 103 sec-1. For higher strain rates, the strain rate hardening is assumed to be the same as that measured at lower rates, with no direct measurement to validate the assumptions used for this extrapolation. In this work we are using a pulsed current generator (PCG) to create electro-magnetic (EM) driving forces on expanding cylinders. Most standard techniques for creating EM driving forces on cylinders or rings, as reported in the literature, reach strain rates of 1e3-1e4. Using our PCG, characterized by a fast rise time, we reach strain rates of ˜1e5, thus paving the way to a standard technique to measure strength at very high strain rates. To establish the experimental technique, we conducted a numerical study of the expanding cylinder set up using 2D hydrodynamic simulations to reach the desired high strain rates.

  13. Variation in Indole-3-Acetic Acid Production by Wild Saccharomyces cerevisiae and S. paradoxus Strains from Diverse Ecological Sources and Its Effect on Growth

    PubMed Central

    Liu, Yen-Yu; Chen, Hung-Wei; Chou, Jui-Yu

    2016-01-01

    Phytohormone indole-3-acetic acid (IAA) is the most common naturally occurring and most thoroughly studied plant growth regulator. Microbial synthesis of IAA has long been known. Microbial IAA biosynthesis has been proposed as possibly occurring through multiple pathways, as has been proven in plants. However, the biosynthetic pathways of IAA and the ecological roles of IAA in yeast have not been widely studied. In this study, we investigated the variation in IAA production and its effect on the growth of Saccharomyces cerevisiae and its closest relative Saccharomyces paradoxus yeasts from diverse ecological sources. We found that almost all Saccharomyces yeasts produced IAA when cultured in medium supplemented with the primary precursor of IAA, L-tryptophan (L-Trp). However, when cultured in medium without L-Trp, IAA production was only detected in three strains. Furthermore, exogenous added IAA exerted stimulatory and inhibitory effects on yeast growth. Interestingly, a negative correlation was observed between the amount of IAA production in the yeast cultures and the IAA inhibition ratio of their growth. PMID:27483373

  14. A preliminary investigation into the genetic variation and population structure of Taenia hydatigena from Sardinia, Italy.

    PubMed

    Boufana, Belgees; Scala, Antonio; Lahmar, Samia; Pointing, Steve; Craig, Philip S; Dessì, Giorgia; Zidda, Antonella; Pipia, Anna Paola; Varcasia, Antonio

    2015-11-30

    Cysticercosis caused by the metacestode stage of Taenia hydatigena is endemic in Sardinia. Information on the genetic variation of this parasite is important for epidemiological studies and implementation of control programs. Using two mitochondrial genes, the cytochrome c oxidase subunit 1 (cox1) and the NADH dehydrogenase subunit 1 (ND1) we investigated the genetic variation and population structure of Cysticercus tenuicollis from Sardinian intermediate hosts and compared it to that from other hosts from various geographical regions. The parsimony cox1 network analysis indicated the existence of a common lineage for T. hydatigena and the overall diversity and neutrality indices indicated demographic expansion. Using the cox1 sequences, low pairwise fixation index (Fst) values were recorded for Sardinian, Iranian and Palestinian sheep C. tenuicollis which suggested the absence of genetic differentiation. Using the ND1 sequences, C. tenuicollis from Sardinian sheep appeared to be differentiated from those of goat and pig origin. In addition, goat C. tenuicollis were genetically different from adult T. hydatigena as indicated by the statistically significant Fst value. Our results are consistent with biochemical and morphological studies that suggest the existence of variants of T. hydatigena.

  15. Investigation of dielectric pocket induced variations in tunnel field effect transistor

    NASA Astrophysics Data System (ADS)

    Upasana; Narang, Rakhi; Saxena, Manoj; Gupta, Mridula

    2016-04-01

    The performance of conventional Tunnel FETs struggling from ambipolar issues, insufficient on-current, lower transconductance value, higher delay and lower cut off frequency has been improved by introducing several material and device engineering concepts in past few years. Keeping this in view, another interesting and reliable option i.e. Dielectric Pocket TFET (featuring a dielectric pocket placement near tunneling junction) has been comprehensively and qualitatively demonstrated using ATLAS device simulator. The architecture has been explored in terms of various device electrostatic parameters such as potential, energy band profile, electron and hole concentration, electric field variation and band to band generation rate (GBTB) near the tunneling junction where the Dielectric Pocket (DP) has been introduced. Subsequently, a detailed investigation by changing the position and dielectric constant of pocket at respective junctions has been made where DP induced variations in drain current, transconductance and parasitic capacitance have been examined. The work highlights major improvements over conventional TFET in terms of lower subthreshold swing and threshold voltage, higher drain current and transconductance, improved on-to-off current ratio, suppressed ambipolar conduction and improved dynamic power dissipation issues for low voltage analog and digital applications.

  16. The Photoelastic Investigation of Three-dimensional Stress and Strain Conditions

    NASA Technical Reports Server (NTRS)

    Oppel, G

    1937-01-01

    The present report contains the description and typical application of two photoelastic methods which are suitable for the study of stress and strain conditions in three dimensions, namely: the fixation method and the immersion method.

  17. Virulence variation among epidemic and non-epidemic strains of Saint Louis encephalitis virus circulating in Argentina

    PubMed Central

    Rivarola, María Elisa; Tauro, Laura Beatriz; Llinás, Guillermo Albrieu; Contigiani, Marta Silvia

    2014-01-01

    Saint Louis encephalitis virus caused an outbreak of febrile illness and encephalitis cases in Córdoba, Argentina, in 2005. During this outbreak, the strain CbaAr-4005 was isolated from Culex quinquefasciatus mosquitoes. We hypothesised that this epidemic variant would be more virulent in a mouse model than two other non-epidemic strains (78V-6507 and CorAn-9275) isolated under different epidemiological conditions. To test this hypothesis, we performed a biological characterisation in a murine model, including mortality, morbidity and infection percentages and lethal infection indices using the three strains. Mice were separated into age groups (7, 10 and 21-day-old mice) and analysed after infection. The strain CbaAr-4005 was the most infective and lethal of the three variants, whereas the other two strains exhibited a decreasing mortality percentage with increasing animal age. The strain CbaAr-4005 produced the highest morbidity percentages and no significant differences among age groups were observed. The epidemic strain caused signs of illness in all inoculated animals and showed narrower ranges from the onset of symptoms than the other strains. CbaAr-4005 was the most virulent for Swiss albino mice. Our results highlight the importance of performing biological characterisations of arbovirus strains likely to be responsible for emerging or reemerging human diseases. PMID:24810175

  18. Investigation of strain birefringence and wavefront distortion in 001 plates of KD sub 2 PO sub 4

    SciTech Connect

    De Yoreo, J.J.; Woods, B.W.

    1991-08-26

    When 001 plates of KD{sub 2}PO{sub 4} (KD*P) are used in Pockels cells, strain induced refractive index variations result in beam depolarization and transmitted wavefront distortion. The depolarization is determined by the induced birefringence while the wavefront distortion is controlled by the average index shift. Here we show that the birefringence is determined by the shear stress in the xy-plane of the crystal while the average index shift depends only on the normal stresses. Furthermore, for depolarization losses of 0.1 to 1.0% and wavefront distortion of 0.1 to 1.0{lambda}, the critical range of stress is 10{sup 5} to 10{sup 6} Pa. We also present measured depolarization loss and wavefront distortion profiles for 5, 16 and 27cm, 95% deuterated, KD*P crystals. Using the analysis described above we show that the maximum internal stresses in the crystals are within the critical range, but that the area averaged stresses are substantially lower. We find that crystals from different locations along the length of a boule have similar strain birefringence and wavefront distortion profiles indicating that the growth conditions which generate the internal strain persist throughout much of the growth history of the boule. Finally, we discuss potential sources of strain in KD*P. 8 refs., 3 figs.

  19. A novel platform for in situ investigation of cells and tissues under mechanical strain.

    PubMed

    Ahmed, W W; Kural, M H; Saif, T A

    2010-08-01

    The mechanical micro-environment influences cellular responses such as migration, proliferation, differentiation and apoptosis. Cells are subjected to mechanical stretching in vivo, e.g., epithelial cells during embryogenesis. Current methodologies do not allow high-resolution in situ observation of cells and tissues under applied strain, which may reveal intracellular dynamics and the origin of cell mechanosensitivity. A novel polydimethylsiloxane substrate was developed, capable of applying tensile and compressive strain (up to 45%) to cells and tissues while allowing in situ observation with high-resolution optics. The strain field of the substrate was characterized experimentally using digital image correlation, and the deformation was modeled by the finite element method, using a Mooney-Rivlin hyperelastic constitutive relation. The substrate strain was found to be uniform for >95% of the substrate area. As a demonstration of the system, mechanical strain was applied to single fibroblasts transfected with GFP-actin and whole transgenic Drosophila embryos expressing GFP in all neurons during live imaging. Three observations of biological responses due to applied strain are reported: (1) dynamic rotation of intact actin stress fibers in fibroblasts; (2) lamellipodia activity and actin polymerization in fibroblasts; (3) active axonal contraction in Drosophila embryo motor neurons. The novel platform may serve as an important tool in studying the mechanoresponse of cells and tissues, including whole embryos.

  20. Investigation of genes involved in nisin production in Enterococcus spp. strains isolated from raw goat milk.

    PubMed

    Perin, Luana Martins; Todorov, Svetoslav Dimitrov; Nero, Luís Augusto

    2016-09-01

    Different strains of Lactococcus lactis are capable of producing the bacteriocin nisin. However, genetic transfer mechanisms allow the natural occurrence of genes involved in nisin production in members of other bacterial genera, such as Enterococcus spp. In a previous study, nisA was identified in eight enterococci capable of producing antimicrobial substances. The aim of this study was to verify the presence of genes involved in nisin production in Enterococcus spp. strains, as well as nisin expression. The nisA genes from eight Enterococcus spp. strains were sequenced and the translated amino acid sequences were compared to nisin amino-acid sequences previously described in databases. Although containing nisin structural and maturation related genes, the enterococci strains tested in the present study did not present the immunity related genes (nisFEG and nisI). The translated sequences of nisA showed some point mutations, identical to those presented by Lactococcus strains isolated from goat milk. All enterococci were inhibited by nisin, indicating the absence of immunity and thus that nisin cannot be expressed. This study demonstrated for the first time the natural occurrence of nisin structural genes in Enterococcus strains and highlights the importance of providing evidence of a link between the presence of bacteriocin genes and their expression.

  1. Influences of vowel and tone variation on emergent word knowledge: a cross-linguistic investigation.

    PubMed

    Singh, Leher; Hui, Tam Jun; Chan, Calista; Golinkoff, Roberta Michnick

    2014-01-01

    To learn words, infants must be sensitive to native phonological contrast. While lexical tone predominates as a source of phonemic contrast in human languages, there has been little investigation of the influences of lexical tone on word learning. The present study investigates infants' sensitivity to tone mispronunciations in two groups of infants. For one group (Chinese learners), tone is phonemic in their native language, and for the second group (English learners), tone is non-phonemic and constituted suprasegmental variation. In Experiment 1, English learners were trained on novel word-object pairings and tested on their recognition of correct pronunciations, tone and vowel mispronunciations of these words at 18 and 24 months. In Experiment 2a, bilingual English-Chinese learners were tested on a similar task translated into Chinese at the same age intervals. Results demonstrate that non-tonal learners treated tonal and vowel substitutions alike as mispronunciations at 18 months but only treated vowel substitutions as mispronunciations at 24 months. Tonal learners treated both tonal and vowel substitutions as mispronunciations at both ages. In Experiment 2b, bilingual non-tone language learners were tested on the same set of tasks replicating a similar set of results as monolingual non-tone language learners (Experiment 1). Findings point to an early predisposition to treat tone as a defining characteristic of words regardless of its lexical relevance at 18 months. Between 18 and 24 months, learners appear to ascribe lexical relevance to tone in a language-specific manner. The current study identifies the influences of tone variation on memories for newly learned words and the time period during which lexical tone - a highly frequent constituent of human languages - actually becomes lexical for early learners. Findings are contextualized with prevailing models of the developing lexicon.

  2. Investigations of the structural stability of highly strained [(Al)GaIn]As/Ga (PAs) multiple quantum wells

    NASA Astrophysics Data System (ADS)

    Marschner, T.; Lutgen, S.; Volk, M.; Stolz, W.; Göbel, E. O.

    1996-10-01

    The structural stability of highly strained [(Al)GaIn]As/Ga (PAs) strained layer superlattice (SLS) structures as a function of the average lattice mismatch is investigated. The SLS structures, grown by metalorganic vapor-phase epitaxy, are studied by using high-resolution x-ray diffraction. The range of stable SLS structures obtained experimentally is compared to a recent theoretical model assuming strain relaxation by formation of misfit dislocations [D. C. Houghton, M. Davies, and M. Dion, Appl. Phys. Lett. 64, 505 (1994)]. In particular, the influence of the surface migration length of the group-III species on the growth surface is investigated by varying the Al concentration in the compressively strained [(Al)GaIn]As layers. Structurally stable [(Al)GaIn]As/Ga(PAs) SLS structures having a total layer thickness of 1 μm and an average lattice mismatch of up to (Δd/d)⊥=1.2×10-2 have been realized. These values exceed by far the values of the misfit dislocation model. This behavior indicates that surface morphology changes rather than misfit dislocation formation are the primary cause for the instability of highly strained SLSs.

  3. Investigation of seasonal Be-7 variation near the Martian Poles using Mars Odyssey GRS data

    NASA Astrophysics Data System (ADS)

    Kim, Kyeong Ja; Boynton, William; Hamara, Dave

    (7) Be variation near the Martian Poles using Mars Odyssey has been investigated for about two Martian years. (7) Be is a cosmogenic nuclide produced via nuclear spallation interaction with carbon and oxygen in the atmosphere of the Mars. Because CO _{2} is main constituent of the atmosphere of the Mars and it condenses during winter season and sublimes in spring, and also it is transferred from the northern hemisphere to southern hemisphere. We assumed that the pattern of air movement could be monitored by the (7) Be production in the atmosphere. Since (7) Be peak is superimposed with (10) B which has a wide peak area and is from the background material of HPGe crystal. For this study, (7) Be peak area is defined using the thick target experiment and the influenced region due to (10) B is eliminated for (7) Be peak analysis. Our results show that the variation of (7) Be activity at 15 degree gives a lot of noise except the time associated with (7) Be spike due to solar particle event. However, the variations of (7) Be activity for 30 degree show that there is a peak rise at L _{s}100 for North Pole and L _{s}180 for South Pole. In the case of (7) Be activities at mid latitudes for L _{s}125 and L _{s}190 are distinctively higher than the rest of the seasonal zones. This implies that (7) Be activity was higher at the summer of northern hemisphere and fall season of southern hemisphere. This could be a significant and real effect associated with air density increase; therefore, the production of (7) Be increases for these seasons. Our results also show that there were two (7) Be spikes due to solar particle events observed. These spikes are distinctively high compared to the effect from the Martian atmospheric density changes. Our result of (7) Be activity of Mars could be less significant in understanding air circulation. However, this result indicated that a possible study where atmospheric density is high could be investigated with this technique including the

  4. Investigation of differences in sensitivity between 3 strains of Daphnia magna (crustacean Cladocera) exposed to malathion (organophosphorous pesticide).

    PubMed

    Toumi, Hela; Boumaiza, Moncef; Millet, Maurice; Radetski, Claudemir M; Camara, Baba I; Felten, Vincent; Ferard, Jean-François

    2015-01-01

    Acute and chronic ecotoxic effects of organophosphorous insecticide malathion (Fyfanon 50 EC 500 g L(-1)) were investigated on three strains of Daphnia magna. The nominal effective concentrations immobilizing 50% (EC50) of Daphnia after 24 and 48 h were 0.53 and 0.36 μg L(-1), 0.70 and 0.44 μg L(-1), and 0.75 and 0.46 μg L(-1) for the strains 1, 2, and 3 respectively. There was an increase in malathion ecotoxicity with time of exposure as confirmed by chronic studies. In fact, after 21 days of exposure, significant effects on survival (lowest observed effect concentration or LOECs) were recorded at malathion concentrations of 22, 220 and 230 ng L(-1) for strains 1, 2 and 3 respectively. Other endpoints were also examined, including reproduction (with different parameters), body length and embryo toxicity. ICs10 and ICs20 were calculated for these different parameters. ICs10 ranged from 4.7 to more than 220 ng L(-1) for the three tested strains. The most sensitive parameter was the number of neonates per adult (ICs10 = 4.7 and 10.8 ng L(-1) for strains 1 and 2 respectively) or the number of broods (IC10 = 10 ng L(-1) for strain 3). Moreover, an increase in embryo development abnormalities was observed at the two highest tested malathion concentrations. Abnormalities comprised undeveloped second antennae, curved or unextended shell spines, and curved post-abdomen spines in live neonates. Results suggest that malathion could act as an endocrine disruptor in D. magna as it interferes with development. It also induces a significant decrease in acetylcholinesterase (AChE) activities for the three strains. Both strains 2 and 3 seemed more sensitive (LOECs = 60 ng L(-1)) than strain 1 (LOEC = 120 ng L(-1)). Our results suggest that the AChE activity response can also be used as a biomarker of inter-strain (or inter-clonal) susceptibility (i.e. strain (or clone)-specific response).

  5. Use of variations in staphylococcal interspersed repeat units for molecular typing of methicillin-resistant Staphylococcus aureus strains.

    PubMed

    Hardy, Katherine J; Oppenheim, Beryl A; Gossain, Savita; Gao, Fang; Hawkey, Peter M

    2006-01-01

    Staphylococcal interspersed repeat unit typing has previously been shown to have the ability to discriminate between epidemic methicillin-resistant Staphylococcus aureus strains in the United Kingdom. The current study illustrates its ability to distinguish between strains within an endemic setting thereby providing a rapid transportable typing method for the identification of transmission events.

  6. Arterial Blood Gases, Electrolytes and Metabolic Indices Associated with Hemorrhagic Shock: Inter-and Intrainbred Rat Strain Variation

    DTIC Science & Technology

    2013-03-07

    intake postsurgery became a part of the model. Such alterations may result in some baseline changes in a strain-dependent manner. As expected, strain...Lancet 1: 521–527, 1963. 9. Carey LC, Lowery BD, Cloutier CT. Blood sugar and insulin response of humans in shock. Ann Surg 172: 342–350, 1970. 10

  7. Can low-level ethanol exposure during pregnancy influence maternal care? An investigation using two strains of rat across two generations.

    PubMed

    Popoola, Daniel O; Borrow, Amanda P; Sanders, Julia E; Nizhnikov, Michael E; Cameron, Nicole M

    2015-09-01

    Gestational alcohol use is well documented as detrimental to both maternal and fetal health, producing an increase in offspring's tendency for alcoholism, as well as in behavioral and neuropsychological disorders. In both rodents and in humans, parental care can influence the development of offspring physiology and behavior. Animal studies that have investigated gestational alcohol use on parental care and/or their interaction mostly employ heavy alcohol use and single strains. This study aimed at investigating the effects of low gestational ethanol dose on parental behavior and its transgenerational transmission, with comparison between two rat strains. Pregnant Sprague Dawley (SD) and Long Evans (LE) progenitor dams (F0) received 1g/kg ethanol or water through gestational days 17-20 via gavage, or remained untreated in their home cages. At maturity, F1 female offspring were mated with males of the same strain and treatment and were left undisturbed through gestation. Maternal behavior was scored in both generations during the first six postnatal days. Arch-back nursing (ABN) was categorized as: 1, when the dam demonstrated minimal kyphosis; 2, when the dam demonstrated moderate kyphosis; and 3, when the dam displayed maximal kyphosis. Overall, SD showed greater amounts of ABN than LE dams and spent more time in contact with their pups. In the F0 generation, water and ethanol gavage increased ABN1 and contact with pups in SD, behaviors which decreased in treated LE. For ABN2, ethanol-treated SD dams showed more ABN2 than water-treated dams, with no effect of treatment on LE animals. In the F1 generation, prenatal exposure affected retrieval. Transgenerational transmission of LG was observed only in the untreated LE group. Strain-specific differences in maternal behavior were also observed. This study provides evidence that gestational gavage can influence maternal behavior in a strain-specific manner. Our results also suggest that the experimental procedure during

  8. Investigations of segregation phenomena in highly strained Mn-doped Ge wetting layers and Ge quantum dots embedded in silicon

    SciTech Connect

    Prestat, E. Porret, C.; Favre-Nicolin, V.; Tainoff, D.; Boukhari, M.; Bayle-Guillemaud, P.; Jamet, M.; Barski, A.

    2014-03-10

    In this Letter, we investigate manganese diffusion and the formation of Mn precipitates in highly strained, few monolayer thick, Mn-doped Ge wetting layers and nanometric size Ge quantum dot heterostructures embedded in silicon. We show that in this Ge(Mn)/Si system manganese always precipitates and that the size and the position of Mn clusters (precipitates) depend on the growth temperature. At high growth temperature, manganese strongly diffuses from germanium to silicon, whereas decreasing the growth temperature reduces the manganese diffusion. In the germanium quantum dots layers, Mn precipitates are detected, not only in partially relaxed quantum dots but also in fully strained germanium wetting layers between the dots.

  9. The bandgap distribution investigated across the strain-induced bending ZnO nanowire

    NASA Astrophysics Data System (ADS)

    Tse, Geoffrey; Yu, Dapeng

    2016-12-01

    In this work, the strain dependence of electronic and optical properties in wurtzite zinc oxide (ZnO) lattice were explored. Ab initio density functional theory (DFT) was used in evaluating the energy bandgap and the dielectric tensor, respectively. The influence on the bandgap due to the shear distortion was so small that the reducing linear trends on uniaxial compressive/tensile strain were reported, in which the evolution of the absorption curve with uniaxial strain agrees well with the experimental results across the bending section. This study provides a set of useful data in analyzing the evolution of the optical adsorption across the bending ZnO nanowire, and gives a systematic explanation to the available experiments from the electronic structure’s perspective.

  10. Determining horizontal displacement and strains due to subsidence. Rept. of Investigations/1991

    SciTech Connect

    Tandanand, S.; Powell, L.R.

    1991-01-01

    Horizontal displacements and ground strains induced by mine subsidence are significant information needed for calculating damage and developing precautions against subsidence effects on surface structures. To devise a simple method for determining the surface horizontal displacements and strains simultaneously with the subsidence prediction, the U.S. Bureau of Mines examined the significance of the tilt number, which is the proportionality constant in the relationship between the horizontal displacement and the slope of the subsidence profile. The ratio of the tilt number to the critical radius of the subsidence trough is identical to the ratio of the maximum possible horizontal displacement to the full subsidence, which is found to be constant in most European coalfields. If this ratio is known for a particular minesite in the United States, then horizontal displacement and ground strains can be readily obtained from the primary subsidence data.

  11. Investigation of optimization-based reconstruction with an image-total-variation constraint in PET

    NASA Astrophysics Data System (ADS)

    Zhang, Zheng; Ye, Jinghan; Chen, Buxin; Perkins, Amy E.; Rose, Sean; Sidky, Emil Y.; Kao, Chien-Min; Xia, Dan; Tung, Chi-Hua; Pan, Xiaochuan

    2016-08-01

    Interest remains in reconstruction-algorithm research and development for possible improvement of image quality in current PET imaging and for enabling innovative PET systems to enhance existing, and facilitate new, preclinical and clinical applications. Optimization-based image reconstruction has been demonstrated in recent years of potential utility for CT imaging applications. In this work, we investigate tailoring the optimization-based techniques to image reconstruction for PET systems with standard and non-standard scan configurations. Specifically, given an image-total-variation (TV) constraint, we investigated how the selection of different data divergences and associated parameters impacts the optimization-based reconstruction of PET images. The reconstruction robustness was explored also with respect to different data conditions and activity up-takes of practical relevance. A study was conducted particularly for image reconstruction from data collected by use of a PET configuration with sparsely populated detectors. Overall, the study demonstrates the robustness of the TV-constrained, optimization-based reconstruction for considerably different data conditions in PET imaging, as well as its potential to enable PET configurations with reduced numbers of detectors. Insights gained in the study may be exploited for developing algorithms for PET-image reconstruction and for enabling PET-configuration design of practical usefulness in preclinical and clinical applications.

  12. Investigation of Helium Isotope Variations of Alkaline Volcanic Rocks in Kutahya Region

    NASA Astrophysics Data System (ADS)

    Cesur, Duru; Mutlu, Halim; Aldanmaz, Ercan; Güleç, Nilgün; Stuart, Finlay M.

    2016-04-01

    The noble gases, in particular helium isotopes, provide valuable information on the mantle source of recent basaltic volcanism, especially when linked to trace elements and radiogenic isotopes. Although the alkaline volcanics in the Kütahya region have been studied in detail by several works by means of trace element variations, radiogenic dating and isotope systematics, noble gas isotope compositions that could significantly contribute to dynamics of volcanism have not been investigated yet. In this study which aims to fill the deficiency of such data, helium isotope compositions of olivine-basalts in Kütahya region are measured. In this study we report helium isotope compositions of olivine from basalts. In olivine-basalts in alkaline volcanic rocks from the Kütahya region, western Turkey, are investigated. 3He/4He range from 3.0 to 5.19 Ra. These low helium isotope values are most probably indicative of a lithospheric mantle source. Kütahya alkaline volcanics are enriched in incompatible elements and show prominent negative Ti, Nd and Ta anomaly. Primitive mantle normalized trace element concentration patterns clearly display continental crustal contamination. Chemical compositions and helium isotope systematics imply contribution of a lithospheric mantle source and contamination of continental crust in the genesis of the Kütahya alkaline lavas. Keywords: Kütahya alkaline rocks, olivine, helium isotope, crust-mantle interaction Acknowledgement: This study has been supported by TUBITAK (Project No. 112Y366)

  13. Investigation of passive blade cyclic pitch variation using an automatic yaw control system. Final report

    SciTech Connect

    Hohenemser, K.H.; Swift, A.H.P.

    1982-08-01

    The investigation of passive cyclic pitch variation using an automatic yaw control system made use of the test equipment and of the results of an earlier study. The atmospheric test equipment consisted of a horizontal axis wind turbine with vane controlled upwind two-bladed rotor of 7.6 m (25 ft) diameter having passive cyclic pitch variation. An automatically triggered electric furl actuator prevented over-speeds and over-torques by furling the rotor which means yawing the rotor out of the winds. The atmospheric test equipment was modified to accept two alternative fully automatic yaw or furl control systems. The first system was of the active type and included a hydraulic single acting constant speed governor as it is used for aircraft propeller controls. Upon reaching the rotor speed limit, the governor delivered pressurized oil to a hydraulic furl actuator which then overcame the unfurling spring force and furled the rotor. When the rotor speed fell below the set value, the governor admitted oil flow from the hydraulic actuator into the oil reservoir and the rotor was unfurled by the spring. The second automatic control system was of a purely mechanical passive type. The rotor thrust, which was laterally off-set from the yaw axis, in combination with a yawing component of the rotor torque due to uptilt of the rotor axis overcame at rated power the unfurling spring and furled the rotor. The analytically predicted and experimentally substantiated negative rotor yaw damping would cause excessive furling rates unless alleviated by a furl damper. The tests were supported by a specially developed dynamic yawing analysis. Both analysis and tests indicated that the two-bladed passive cyclic pitch wind rotor can be effectively torque or speed limited by rotor yaw control systems which are less costly and more reliable than the conventional blade feathering control systems.

  14. Investigation on seasonal variations of Be-7 and H-3 in the rainwater of Korea

    NASA Astrophysics Data System (ADS)

    Kim, K. J.; Choi, Y.; Yoon, Y. Y.; Sohn, J.

    2014-12-01

    Both Beryllium-7 (Be-7) and Tritium (H-3) are produced by cosmic ray interactions in upper atmosphere by spallation reactions. We investigated these nuclides in rainwater along with sodium concentration in the region of Deajeon, Korea (36.32°N, 127.41°E) for 7 months during 2007 and 2008. The results of our study demonstrate that Be-7 in rainwater is inversely propotional to the amount of sodium, proportional to the amount of rainwater and air mixing of the stratosphere in sping. Both isotopes show their peaks during fall and spring seasons. The trend of H-3 variation is shifted about a month compared to that of Be-7. This could be due to the different residence time between H-3 and Be-7 in the atmosphere. The detection efficiency of uncorrected Be-7 concentrations in this area ranged from 0.06 to 14.13 Bq/L which is lower than the reference values of New Zealand (0.5 ~ 4.3 x 107 (atoms/kg rain)) and Japan. The H-3 concentrations of this study ranged from 4.8±0.10 and 18.6±0.3 (TU). This range is well compared to the H-3 concentration of the Northern Hemisphere. Also, sodium variation of the rainwater is found to be inversely proportaional to Be-7 concentrations. This could be associated with air mixing phenomenon involved in the movement of salt in land of Korea. This presentation demonstrates details in both chemistry and data analysis along with other previously published data. This study will provide reference values of Be-7 for the Korean region and will guide a prospective geolgical application associated with atmospheric cosmogenic nuclide production.

  15. An experimental investigation of strain rate, temperature and humidity effects on the mechanical behavior of a perfluorosulfonic acid membrane

    NASA Astrophysics Data System (ADS)

    Lu, Zongwen; Lugo, Melissa; Santare, Michael H.; Karlsson, Anette M.; Busby, F. Colin; Walsh, Peter

    2012-09-01

    The time-dependent hygro-thermal mechanical behavior of a perfluorosulfonic acid (PFSA) membrane (Nafion® 211 membrane) commonly used in Proton Exchange Membrane Fuel Cells (PEMFCs) is investigated at selected strain rates for a broad range of temperatures and humidities. Tensile tests and relaxation tests are conducted to determine Young's modulus and proportional limit stress as functions of strain rate, temperature and humidity. The results show that Young's modulus and proportional limit stress increase as the strain rate increases, and decrease as the temperature or humidity increases. The results also show that the mechanical response of Nafion® 211 membrane is more sensitive to typical changes in strain rate or temperature than to typical changes in humidity. In addition, two temperature/humidity cycles are conducted to determine the steady state swelling behavior of Nafion® 211 membrane as a function of temperature and humidity. The results show that the membrane swells with increasing temperature and humidity, and that there is little or no hygro-thermal history effect for the swelling strains.

  16. [Investigation of the presence of panton-valentin leucocidin (PVL) in Staphylococcus aureus strains isolated from clinical samples].

    PubMed

    Ozkul, Hilal; Oktem, I M Ali; Gülay, Zeynep

    2007-07-01

    Panton-Valentin leucocidin (PVL) is a cytotoxin which causes tissue necrosis by degradating leucocytes and other cell types. PVL has recently become very up to date as it has been shown to be the major virulance factor of community acquired methicillin resistant Staphylococcus aureus strains. In this study, the presence of PVL was investigated in methicillin sensitive and resistant S. aureus (MSSA and MRSA, respectively) strains which were isolated from clinical samples between January 2005-May 2006 at Dokuz Eylul University Hospital, Izmir. Fifty five MRSA and 79 MSSA strains which were isolated from blood, wound and respiratory tract samples were randomly included to the study. The presence of PVL was evaluated by multiplex polymerase chain reaction (PCR) which detects pvl and S. aureus-specific nuc genes. As a result, PVL positivities were detected in two (5%) of 40 MSSA and four (10.3%) of 39 MSSA strains isolated in the years 2005 and 2006, respectively. None of the MRSA isolates had pvl gene. Although this cytotoxin was rarely detected among MSSA isolates, it was interesting to note that the prevalence of PVL was twice more in the year 2006 compared to 2005. It was also worth to notify that four of six (66.7%) PVL positive strains had been isolated from the patients of general surgery inpatient or outpatient clinics.

  17. Effect of straining graphene on nanopore creation using Si cluster bombardment: A reactive atomistic investigation

    NASA Astrophysics Data System (ADS)

    Berdiyorov, G. R.; Mortazavi, B.; Ahzi, S.; Peeters, F. M.; Khraisheh, M. K.

    2016-12-01

    Graphene nanosheets have recently received a revival of interest as a new class of ultrathin, high-flux, and energy-efficient sieving membranes because of their unique two-dimensional and atomically thin structure, good flexibility, and outstanding mechanical properties. However, for practical applications of graphene for advanced water purification and desalination technologies, the creation of well controlled, high-density, and subnanometer diameter pores becomes a key factor. Here, we conduct reactive force-field molecular dynamics simulations to study the effect of external strain on nanopore creation in the suspended graphene by bombardment with Si clusters. Depending on the size and energy of the clusters, different kinds of topography were observed in the graphene sheet. In all the considered conditions, tensile strain results in the creation of nanopores with regular shape and smooth edges. On the contrary, compressive strain increases the elastic response of graphene to irradiation that leads to the formation of net-like defective structures with predominantly carbon atom chains. Our findings show the possibility of creating controlled nanopores in strained graphene by bombardment with Si clusters.

  18. Comparative phenomics and targeted use of genomics reveals variation in carbon and nitrogen assimilation among different Brettanomyces bruxellensis strains.

    PubMed

    Crauwels, S; Van Assche, A; de Jonge, R; Borneman, A R; Verreth, C; Troels, P; De Samblanx, G; Marchal, K; Van de Peer, Y; Willems, K A; Verstrepen, K J; Curtin, C D; Lievens, B

    2015-11-01

    Recent studies have suggested a correlation between genotype groups of Brettanomyces bruxellensis and their source of isolation. To further explore this relationship, the objective of this study was to assess metabolic differences in carbon and nitrogen assimilation between different B. bruxellensis strains from three beverages, including beer, wine, and soft drink, using Biolog Phenotype Microarrays. While some similarities of physiology were noted, many traits were variable among strains. Interestingly, some phenotypes were found that could be linked to strain origin, especially for the assimilation of particular α- and β-glycosides as well as α- and β-substituted monosaccharides. Based upon gene presence or absence, an α-glucosidase and β-glucosidase were found explaining the observed phenotypes. Further, using a PCR screen on a large number of isolates, we have been able to specifically link a genomic deletion to the beer strains, suggesting that this region may have a fitness cost for B. bruxellensis in certain fermentation systems such as brewing. More specifically, none of the beer strains were found to contain a β-glucosidase, which may have direct impacts on the ability for these strains to compete with other microbes or on flavor production.

  19. Experimental investigation of the behaviour of tungsten and molybdenum alloys at high strain-rate and temperature

    NASA Astrophysics Data System (ADS)

    Scapin, Martina; Fichera, Claudio; Carra, Federico; Peroni, Lorenzo

    2015-09-01

    The introduction in recent years of new, extremely energetic particle accelerators such as the Large Hadron Collider (LHC) gives impulse to the development and testing of refractory metals and alloys based on molybdenum and tungsten to be used as structural materials. In this perspective, in this work the experimental results of a tests campaign on Inermet® IT180 and pure Molybdenum (sintered by two different producers) are presented. The investigation of the mechanical behaviour was performed in tension varying the strain-rates, the temperatures and both of them. Overall six orders of magnitude in strain-rate (between 10-3 and 103 s-1) were covered, starting from quasi-static up to high dynamic loading conditions. The high strain-rate tests were performed using a direct Hopkinson Bar setup. Both in quasi-static and high strain-rate conditions, the heating of the specimens was obtained with an induction coil system, controlled in feedback loop, based on measurements from thermocouples directly welded on the specimen. The temperature range varied between 25 and 1000°C. The experimental data were, finally, used to extract the parameters of the Zerilli-Armstrong model used to reproduce the mechanical behaviour of the investigated materials.

  20. Structural and optical investigation of InAsxP1-x/InP strained superlattices

    NASA Astrophysics Data System (ADS)

    Lamberti, C.; Bordiga, S.; Boscherini, F.; Mobilio, S.; Pascarelli, S.; Gastaldi, L.; Madella, M.; Papuzza, C.; Rigo, C.; Soldani, D.; Ferrari, C.; Lazzarini, L.; Salviati, G.

    1998-01-01

    We report a complete characterization of InAsxP1-x/InP (0.05variations, which accommodate the nearly constant As-In bond length. In our investigation we characterize not only very high quality heterostructures but also samples showing serious interface problems such as nonplanarity and/or a consistent chemical spread along the growth axis. In the study presented here we thus propose a general method, based on

  1. Nanoindentation of lemur enamel: an ecological investigation of mechanical property variations within and between sympatric species.

    PubMed

    Campbell, Sara E; Cuozzo, Frank P; Sauther, Michelle L; Sponheimer, Matt; Ferguson, Virginia L

    2012-06-01

    The common morphological metrics of size, shape, and enamel thickness of teeth are believed to reflect the functional requirements of a primate's diet. However, the mechanical and material properties of enamel also contribute to tooth function, yet are rarely studied. Substantial wear and tooth loss previously documented in Lemur catta at the Beza Mahafaly Special Reserve suggests that their dental morphology, structure, and possibly their enamel are not adapted for their current fallback food (the mechanically challenging tamarind fruit). In this study, we investigate the nanomechanical properties, mineralization, and microstructure of the enamel of three sympatric lemur species to provide insight into their dietary functional adaptations. Mechanical properties measured by nanoindentation were compared to measurements of mineral content, prism orientation, prism size, and enamel thickness using electron microscopy. Mechanical properties of all species were similar near the enamel dentin junction and variations correlated with changes in microstructure (e.g., prism size) and mineral content. Severe wear and microcracking within L. catta's enamel were associated with up to a 43% reduction in nanomechanical properties in regions of cracking versus intact enamel. The mechanical and material properties of L. catta's enamel are similar to those of sympatric folivores and suggest that they are not uniquely mechanically adapted to consume the physically challenging tamarind fruit. An understanding of the material and mechanical properties of enamel is required to fully elucidate the functional and ecological adaptations of primate teeth.

  2. Investigation variation of carbon dioxide based on GOSAT data in peninsular Malaysia

    NASA Astrophysics Data System (ADS)

    Sim, C. K.; Lim, H. S.; MatJafri, M. Z.

    2015-10-01

    Carbon dioxide (CO2) is an inodorous and transparent gas, and naturally originates in our atmosphere. Due to its optical characteristics, CO2 is the most important greenhouse gas and play a key role in climate change due to an effective thermal infrared (IR) radiation absorber. Satellite observations of atmospheric carbon dioxide (CO2) can significantly improve our knowledge about the sources and sinks of CO2. The remote sensing satellite, namely Greenhouse Gases Observing Satellite (GOSAT) was employed to investigate the spatial and variations of CO2 column-averaged dry airmole fractions, denoted XCO2 over Peninsular Malaysia from January 2013 to December 2013. The analysis of CO2 in the study area shows the significant differences between northeast monsoon (NEM) and the southwest monsoon (SWM). During NEM season, cold air outbreaks from Siberia spreads to equatorial region in the form of north-easterly cold surge winds and associated with a low-level anticyclone over Southeast Asia. Inversely, air masses from the southwest contribute to long-range air pollution due to transportation of atmospheric CO2 by wind is associated with biomass burning in Sumatra, Indonesia. The GOSAT data and the Satellite measurements are able to measure the increase of the atmosphere CO2 values over different regions.

  3. A theoretical investigation of orientation relationships and transformation strains in steels.

    PubMed

    Koumatos, K; Muehlemann, A

    2017-03-01

    The identification of orientation relationships (ORs) plays a crucial role in the understanding of solid phase transformations. In steels, the most common models of ORs are the ones by Nishiyama-Wassermann (NW) and Kurdjumov-Sachs (KS). The defining feature of these and other OR models is the matching of directions and planes in the parent face-centred cubic γ phase to ones in the product body-centred cubic/tetragonal α/α' phase. In this article a novel method that identifies transformation strains with ORs is introduced and used to develop a new strain-based approach to phase-transformation models in steels. Using this approach, it is shown that the transformation strains that leave a close-packed plane in the γ phase and a close-packed direction within that plane unrotated are precisely those giving rise to the NW and KS ORs when a cubic product phase is considered. Further, it is outlined how, by choosing different pairs of unrotated planes and directions, other common ORs such as the ones by Pitsch and Greninger-Troiano can be derived. One of the advantages of our approach is that it leads to a natural generalization of the NW, KS and other ORs for different ratios of tetragonality r of the product body-centred tetragonal α' phase. These generalized ORs predict a sharpening of the transformation textures with increasing tetragonality and are thus in qualitative agreement with experiments on steels with varying alloy concentration.

  4. A Modeling Investigation of Thermal and Strain Induced Recovery and Nonlinear Hardening in Potential Based Viscoplasticity

    NASA Technical Reports Server (NTRS)

    Arnold, S. M.; Saleeb, A. F.; Wilt, T. E.

    1993-01-01

    Specific forms for both the Gibb's and the complementary dissipation potentials were chosen such that a complete potential based multiaxial, isothermal, viscoplastic model was obtained. This model in general possesses three internal state variables (two scalars associated with dislocation density and one tensor associated with dislocation motion) both thermal and dynamic recovery mechanisms, and nonlinear kinematic hardening. This general model, although possessing associated flow and evolutionary laws, is shown to emulate three distinct classes of theories found in the literature, by modification of the driving threshold function F. A parametric study was performed on a specialized nondimensional multiaxial form containing only a single tensorial internal state variable (i.e., internal stress). The study was conducted with the idea of examining the impact of including a strain-induced recovery mechanism and the compliance operator, derived from the Gibb's potential, on the uniaxial and multiaxial response. One important finding was that inclusion of strain recovery provided the needed flexibility in modeling stress-strain and creep response of metals at low homologous temperatures, without adversely affecting the high temperature response. Furthermore, for nonproportional loading paths, the inclusion of the compliance operator had a significant influence on the multiaxial response, but had no influence on either uniaxial or proportional load histories.

  5. An Investigation into the Gravity Current Aspects of a Cold Air Outbreak Using Variational Analysis Techniques

    DTIC Science & Technology

    1988-01-01

    temperatures dropped 30 degrees in a matter of hours in central Florida with dramatic drops in dewpoint as well. A method is developed using variational ... calculus to decompose observed gridded radiosonde data from this period into component fields. Three variational filters are used iteratively to extract

  6. Numerical Investigation of the Dynamic Compressive Behaviour of Rock Materials at High Strain Rate

    NASA Astrophysics Data System (ADS)

    Hao, Y.; Hao, H.

    2013-03-01

    The dynamic compressive strength of rock materials increases with the strain rate. They are usually obtained by conducting laboratory tests such as split Hopkinson pressure bar (SHPB) test or drop-weight test. It is commonly agreed now that the dynamic increase factor (DIF) obtained from impact test is affected by lateral inertia confinement, friction confinement between the specimen and impact materials and the specimen sizes and geometries. Therefore, those derived directly from testing data do not necessarily reflect the true dynamic material properties. The influences of these parameters, however, are not straightforward to be quantified in laboratory tests. Therefore, the empirical DIF relations of rock materials obtained directly from impact tests consist of contributions from lateral inertia and end friction confinements, which need be eliminated to reflect the true dynamic material properties. Moreover, different rocks, such as granite, limestone and tuff have different material parameters, e.g., equation of state (EOS) and strength, which may also affect the DIF of materials but are not explicitly studied in the open literature. In the present study, numerical models of granite, limestone and tuff materials with different EOS and strength under impact loads are developed to simulate SHPB tests and to study the influences of EOS and strength, lateral inertia confinement and end friction confinement effects on their respective DIFs in the strain rate range between 1 and 1,000 s-1. The commercial software AUTODYN with user-provided subroutines is used to perform the numerical simulations of SHPB tests. Numerical simulation results indicate that the lateral inertia confinement, friction confinement and specimen aspect ( L/ D) ratio significantly influence DIF obtained from impact tests and the inertia confinement effect is different for different rocks. Based on the numerical results, quantifications on the relative contributions from the lateral inertia

  7. Use of genome sequencing to assess nucleotide structure variation of Staphylococcus aureus strains cultured in spaceflight on Shenzhou-X, under simulated microgravity and on the ground.

    PubMed

    Guo, Jun; Han, Na; Zhang, Yuanyuan; Wang, Haiyin; Zhang, Xuelin; Su, Longxiang; Liu, Chao; Li, Jia; Chen, Chen; Liu, Changting

    2015-01-01

    nucleotide structure variation of S. aureus strains in a spaceflight environment and also provide a valuable insight for understanding the mutation strategies of MRSA on earth.

  8. Variation in host specificity and gene content in strains from genetically isolated lineages of the ectomycorrhizal fungus Paxillus involutus s. lat.

    PubMed

    Hedh, Jenny; Johansson, Tomas; Tunlid, Anders

    2009-10-01

    Ectomycorrhizal fungi are known to vary in host range. Some fungi can enter into symbiosis with multiple plant species, while others have restricted host ranges. The aim of this study was to examine variation in host specificity among strains from the basidiomycete Paxillus involutus s. lat. Recent studies have shown that this fungus consists of at least four genetically isolated lineages, phylogenetic species (PS) I (which corresponds to the morphological species Paxillus obscurosporus), PS II (P. involutus s. str.), PS III (Paxillus validus), and PS IV (not yet supported by any reference material). Thirty-five Paxillus strains of PS I to IV were examined in microcosms for their capacity to infect birch (Betula pendula) and spruce (Picea abies). Seventeen strains were compatible and formed mycorrhizae with both tree species. Seven strains were incompatible with both birch and spruce. The gene content in three pairs of incompatible and compatible strains PS I, II, and III were compared using microarray-based comparative genomic hybridizations. Of 4,113 P. involutus gene representatives analyzed, 390 varied in copy numbers in at least one of the three pairwise comparisons. Only three reporters showed significant changes in all three pairwise comparisons, and none of these were changed in a similar way in three comparisons. Our data indicate that changes in host range have occurred frequently and independently among strains in P. obscurosporus, P. involutus s. str., and P. validus. No evidence was obtained demonstrating that these changes have been associated with the gain or loss of similar genes in these three species.

  9. Spatial variation of crustal strain in the Kachchh region, India: Implication on the Bhuj earthquake of 2001

    NASA Astrophysics Data System (ADS)

    Sinha, Sushmita; Mohanty, S.

    2012-10-01

    The Kachchh province of Western India is a major seismic domain in an intraplate set-up. This seismic zone is located in a rift basin, which was developed during the early Jurassic break-up of the Gondwanaland. The crustal strain determined from the GPS velocity data of post-seismic time period following the 2001 Bhuj earthquake indicates a maximum strain rate of ˜266 × 10-9 per year along N013°. Focal mechanism solutions of the main event of 26 January 2001 and the aftershocks show that the maximum principal stress axis is close to this high strain direction. Maximum shear strain rate determined from the GPS data of the area has similar orientation. The unusually high strain rate is comparable in magnitude to the continental rift systems. The partitioning of the regional NE-SW horizontal stress (SHmax) by the pre-existing EW-striking boundary fault developed the strike-slip components parallel to the regional faults, the normal components perpendicular to the faults, NE-striking conjugate Riedel shear fractures and tension fractures. The partitioned normal component of the stress is considered to be the major cause for compression across the regional EW faults and development of the second-order conjugate shear fractures striking NE-SW and NW-SE. The NE-striking transverse faults parallel to the anti-Riedel shear planes have become critical under these conditions. These anti-Riedel planes are interpreted to be critical for the seismicity of the Kachchh region. The high strain rate in this area of low to moderate surface heat flow is responsible for deeper position of the brittle-ductile transition and development of deep seated seismic events in this intraplate region.

  10. Analysis of copy-number variation, insertional polymorphism, and methylation status of the tiniest class I (TRIM) and class II (MITE) transposable element families in various rice strains.

    PubMed

    Baruch, Omer; Kashkush, Khalil

    2012-05-01

    Transposable elements (TEs) dominate the genetic capacity of most eukaryotes, especially plants, where they may compose up to 90% of the genome. Many studies, both in plants and animals reported that in fact non-autonomous elements that have lost their protein-coding sequences and became miniature elements were highly associated with genes, and showed a high level of transpositional activity such as mPing family in rice. In this study, we have investigated in detail the copy number, insertional polymorphism and the methylation status of the tiniest LTR retrotransposon family, termed TRIM, in nine rice strains, in comparison with mPing. While TRIM showed similar copy numbers (average of 79 insertions) in all the nine rice strains, the copy number of mPing varied dramatically (ranging from 6 to 203 insertions) in the same strains. Site-specific PCR analysis revealed that ~58% of the TRIM elements have identical insertion sites among the nine rice strains, while none of the mPing elements (100% polymorphism) have identical insertion sites in the same strains. Finally, over 65% of the TRIM insertion sites were cytosine methylated in all nine rice strains, while the level of the methylated mPing insertion sites ranged between 43 and 81.5%. The findings of this study indicate that unlike mPing, TRIM is most probably a fossil TE family in rice. In addition, the data shows that there might be a strong correlation between TE methylation and copy number.

  11. On the origin of residual strain in shape memory alloys: experimental investigation on evolutions in the microstructure of CuAlBe during complex thermomechanical loadings

    NASA Astrophysics Data System (ADS)

    Barati, M.; Arbab Chirani, S.; Kadkhodaei, M.; Saint-Sulpice, L.; Calloch, S.

    2017-02-01

    The behaviors of shape memory alloys (SMAs) strongly depend on the presence of different phases: austenite, thermally-induced martensite and stress-induced martensite. Consequently, it is important to know the phase volume fraction of each phases and their evolution during thermomechanical loadings. In this work, a three-phase proportioning method based on electric resistivity variation of a CuAlBe SMA is proposed. Simple thermomechanical loadings (i. e. pseudoplasticity and pseudoelasticity), one-way shape memory effect, recovery stress, assisted two-way memory effect at different level of stress and cyclic pseudoelasticity tests are investigated. Based on the electric resistivity results, during each loading path, evolution of the microstructure is determined. The origin of residual strain observed during the considered thermomechanical loadings is discussed. A special attention is paid to two-way shape memory effect generated after considered cyclic loadings and its relation with the developed residual strain. These results permit to identify and to validate the macroscopic models of SMAs behaviors.

  12. Investigating the impact of oxygen concentration and blood flow variation on photodynamic therapy

    PubMed Central

    Penjweini, Rozhin; Kim, Michele M.; Finlay, Jarod C.; Zhu, Timothy C.

    2016-01-01

    Type II photodynamic therapy (PDT) is used for cancer treatment based on the combined action of a photosensitizer, a special wavelength of light, oxygen (3O2) and generation of singlet oxygen (1O2). Intra-patient and inter-patient variability of oxygen concentration ([3O2]) before and after the treatment as well as photosensitizer concentration and hemodynamic parameters such as blood flow during PDT has been reported. Simulation of these variations is valuable, as it would be a means for the rapid assessment of treatment effect. A mathematical model has been previously developed to incorporate the diffusion equation for light transport in tissue and the macroscopic kinetic equations for simulation of [3O2], photosensitizers in ground and triplet states and concentration of the reacted singlet oxygen ([1O2]rx) during PDT. In this study, the finite-element based calculation of the macroscopic kinetic equations is done for 2-(1-Hexyloxyethyl)-2-devinyl pyropheophorbide (HPPH)-mediated PDT by incorporating the information of the photosensitizer photochemical parameters as well as the tissue optical properties, photosensitizer concentration, initial oxygen concentration ([3O2]0), blood flow changes and ϕ that have been measured in mice bearing radiation-induced fibrosarcoma (RIF) tumors. Then, [1O2]rx calculated by using the measured [3O2] during the PDT is compared with [1O2]rx calculated based on the simulated [3O2]; both calculations showed a reasonably good agreement. Moreover, the impacts of the blood flow changes and [3O2]0 on [1O2]rx have been investigated, which showed no pronounced effect of the blood flow changes on the long-term 1O2 generation. When [3O2]0 becomes limiting, small changes in [3O2] have large effects on [1O2]rx. PMID:27453622

  13. Investigating the impact of oxygen concentration and blood flow variation on photodynamic therapy

    NASA Astrophysics Data System (ADS)

    Penjweini, Rozhin; Kim, Michele M.; Finlay, Jarod C.; Zhu, Timothy C.

    2016-03-01

    Type II photodynamic therapy (PDT) is used for cancer treatment based on the combined action of a photosensitizer, a special wavelength of light, oxygen (3O2) and generation of singlet oxygen (1O2). Intra-patient and inter-patient variability of oxygen concentration ([3O2]) before and after the treatment as well as photosensitizer concentration and hemodynamic parameters such as blood flow during PDT has been reported. Simulation of these variations is valuable, as it would be a means for the rapid assessment of treatment effect. A mathematical model has been previously developed to incorporate the diffusion equation for light transport in tissue and the macroscopic kinetic equations for simulation of [3O2], photosensitizers in ground and triplet states and concentration of the reacted singlet oxygen ([1O₂]rx) during PDT. In this study, the finite-element based calculation of the macroscopic kinetic equations is done for 2-(1- Hexyloxyethyl)-2-devinyl pyropheophorbide (HPPH)-mediated PDT by incorporating the information of the photosensitizer photochemical parameters as well as the tissue optical properties, photosensitizer concentration, initial oxygen concentration ([3O2]0), blood flow changes and Φ that have been measured in mice bearing radiation-induced fibrosarcoma (RIF) tumors. Then, [1O2]rx calculated by using the measured [3O2] during the PDT is compared with [1O2]rx calculated based on the simulated [3O₂]; both calculations showed a reasonably good agreement. Moreover, the impacts of the blood flow changes and [3O2]0 on [1O2]rx have been investigated, which showed no pronounced effect of the blood flow changes on the long-term 1O2 generation. When [3O2]0 becomes limiting, small changes in [3O₂] have large effects on [1O2]rx.

  14. Comparative genomics analysis of five Psychrobacter strains isolated from world-wide habitats reveal high intra-genus variations.

    PubMed

    Zhang, Shan; Song, Weizhi; Yu, Min; Lin, Xuezheng

    2017-03-17

    Psychrobacter has been regarded as an important genus for bacterial cold adaptation studies. However, members of this genus are highly varied in terms of both cold adaptability and genome content. To get an understanding of the diversity of members of this genus, five Psychrobacter strains (G, K5, 273-4, PAMC21119 and PRwf-1), with publicly available complete/draft genome, were selected and comprehensive comparative genomics analyses were performed among them. The closest phylogenetic relationship, highest average nucleotide identity (96.78%) and best sequence synteny were identified between strains G and K5. These findings suggest they belong to the same species, despite the long geographic distance between them (Antarctic and Siberia). 4542 gene clusters in total were identified from the five genomes, and of which 1424 were shared by all of them. The number of genes unique to strains G, K5, 273-4, PAMC21119 and PRwf-1 are 183, 188, 300, 637 and 665, respectively. COG assignment revealed their differences in gene content related to stress response. The extensive sequence rearrangements and the large number of genes unique to strain PAMC21119 and PRwf-1 suggest they may have experienced a high level of gene exchanges in the permafrost soil and the surface of fish skin.

  15. Lactobacillus kefiri shows inter-strain variations in the amino acid sequence of the S-layer proteins.

    PubMed

    Malamud, Mariano; Carasi, Paula; Bronsoms, Sílvia; Trejo, Sebastián A; Serradell, María de Los Angeles

    2017-04-01

    The S-layer is a proteinaceous envelope constituted by subunits that self-assemble to form a two-dimensional lattice that covers the surface of different species of Bacteria and Archaea, and it could be involved in cell recognition of microbes among other several distinct functions. In this work, both proteomic and genomic approaches were used to gain knowledge about the sequences of the S-layer protein (SLPs) encoding genes expressed by six aggregative and sixteen non-aggregative strains of potentially probiotic Lactobacillus kefiri. Peptide mass fingerprint (PMF) analysis confirmed the identity of SLPs extracted from L. kefiri, and based on the homology with phylogenetically related species, primers located outside and inside the SLP-genes were employed to amplify genomic DNA. The O-glycosylation site SASSAS was found in all L. kefiri SLPs. Ten strains were selected for sequencing of the complete genes. The total length of the mature proteins varies from 492 to 576 amino acids, and all SLPs have a calculated pI between 9.37 and 9.60. The N-terminal region is relatively conserved and shows a high percentage of positively charged amino acids. Major differences among strains are found in the C-terminal region. Different groups could be distinguished regarding the mature SLPs and the similarities observed in the PMF spectra. Interestingly, SLPs of the aggregative strains are 100% homologous, although these strains were isolated from different kefir grains. This knowledge provides relevant data for better understanding of the mechanisms involved in SLPs functionality and could contribute to the development of products of biotechnological interest from potentially probiotic bacteria.

  16. A Review of the Properties of Nb3Sn and Their Variation with A15Composition, Morphology and Strain State

    SciTech Connect

    Godeke, Arno

    2006-03-27

    Significant efforts can be found throughout the literature to optimize the current carrying capacity of Nb{sub 3}Sn superconducting wires. The achievable transport current density in wires depends on the A15 composition, morphology and strain state. The A15 sections in wires contain, due to compositional inhomogeneities resulting from solid state diffusion A15 formation reactions, a distribution of superconducting properties. The A15 grain size can be different from wire to wire and is also not necessarily homogeneous across the A15 regions. Strain is always present in composite wires, and the strain state changes as a result of thermal contraction differences and Lorentz forces in magnet systems. To optimize the transport properties it is thus required to identify how composition, grain size and strain state influence the superconducting properties. This is not accurately possible in inhomogeneous and spatially complex systems such as wires. This article therefore gives an overview of the available literature on simplified, well defined(quasi--)homogeneous laboratory samples. After more than 50 years of research on superconductivity in Nb{sub 3}Sn, a significant amount of results are available, but these are scattered over a multitude of publications. Two reviews exist on the basic properties of A15 materials in general, but no specific review for Nb{sub 3}Sn is available. This article is intended to provide such an overview. It starts with a basic description of the Niobium--Tin intermetallic. After this it maps the influence of Sn content on the electron--phonon interaction strength and on the field-temperature phase boundary. The literature on the influence of Cu, Ti and Ta additions will then be briefly summarized.This is followed by a review on the effects of grain size and strain. The article is concluded with a summary of the main results.

  17. Head impact accelerations for brain strain-related responses in contact sports: a model-based investigation.

    PubMed

    Ji, Songbai; Zhao, Wei; Li, Zhigang; McAllister, Thomas W

    2014-10-01

    Both linear [Formula: see text] and rotational [Formula: see text] accelerations contribute to head impacts on the field in contact sports; however, they are often isolated in injury studies. It is critical to evaluate the feasibility of estimating brain responses using isolated instead of full degrees-of-freedom (DOFs) accelerations. In this study, we investigated the sensitivities of regional brain strain-related responses to resultant [Formula: see text] and [Formula: see text] as well as the relative contributions of these acceleration components to the responses via random sampling and linear regression using parameterized, triangulated head impacts with kinematic variable values based on on-field measurements. Two independently established and validated finite element models of the human head were employed to evaluate model-consistency and dependency in results: the Dartmouth Head Injury Model and Simulated Injury Monitor. For the majority of the brain, volume-weighted regional peak strain, strain rate, and von Mises stress accumulated from the simulation significantly correlated with the product of the magnitude and duration of [Formula: see text], or effectively, the rotational velocity, but not to [Formula: see text]. Responses from [Formula: see text]-only were comparable to the full-DOF counterparts especially when normalized by injury-causing thresholds (e.g., volume fractions of large differences virtually diminished (i.e., [Formula: see text]1 %) at typical difference percentage levels of 1-4 % on average). These model-consistent results support the inclusion of both rotational acceleration magnitude and duration into kinematics-based injury metrics and demonstrate the feasibility of estimating strain-related responses from isolated [Formula: see text] for analyses of strain-induced injury relevant to contact sports without significant loss of accuracy, especially for the cerebrum.

  18. Large-insert genome analysis technology detects structural variation in Pseudomonas aeruginosa clinical strains from cystic fibrosis patients.

    PubMed

    Hayden, Hillary S; Gillett, Will; Saenphimmachak, Channakhone; Lim, Regina; Zhou, Yang; Jacobs, Michael A; Chang, Jean; Rohmer, Laurence; D'Argenio, David A; Palmieri, Anthony; Levy, Ruth; Haugen, Eric; Wong, Gane K S; Brittnacher, Mitch J; Burns, Jane L; Miller, Samuel I; Olson, Maynard V; Kaul, Rajinder

    2008-06-01

    Large-insert genome analysis (LIGAN) is a broadly applicable, high-throughput technology designed to characterize genome-scale structural variation. Fosmid paired-end sequences and DNA fingerprints from a query genome are compared to a reference sequence using the Genomic Variation Analysis (GenVal) suite of software tools to pinpoint locations of insertions, deletions, and rearrangements. Fosmids spanning regions that contain new structural variants can then be sequenced. Clonal pairs of Pseudomonas aeruginosa isolates from four cystic fibrosis patients were used to validate the LIGAN technology. Approximately 1.5 Mb of inserted sequences were identified, including 743 kb containing 615 ORFs that are absent from published P. aeruginosa genomes. Six rearrangement breakpoints and 220 kb of deleted sequences were also identified. Our study expands the "genome universe" of P. aeruginosa and validates a technology that complements emerging, short-read sequencing methods that are better suited to characterizing single-nucleotide polymorphisms than structural variation.

  19. Sequence variation in CYP51A from the Y strain of Trypanosoma cruzi alters its sensitivity to inhibition

    PubMed Central

    Cherkesova, Tatiana S.; Hargrove, Tatiana Y.; Vanrell, M. Cristina; Ges, Igor; Usanov, Sergey A.; Romano, Patricia S.; Lepesheva, Galina I.

    2014-01-01

    CYP51 (sterol 14α-demethylase) is an efficient target for clinical and agricultural antifungals and an emerging target for treatment of Chagas disease, the infection that is caused by multiple strains of a protozoan pathogen Trypanosoma cruzi. Here, we analyze CYP51A from the Y strain T. cruzi. In this protein, proline 355, a residue highly conserved across the CYP51 family, is replaced with serine. The purified enzyme retains its catalytic activity, yet has been found less susceptible to inhibition. These biochemical data are consistent with cellular experiments, both in insect and human stages of the pathogen. Comparative structural analysis of CYP51 complexes with VNI and two derivatives suggests that broad-spectrum CYP51 inhibitors are likely to be preferable as antichagasic drug candidates. PMID:25217832

  20. [Investigation of hydrophobicity of Proteus vulgaris strains and ability of Proteus vulgaris and Proteus penneri strains to penetrate bladder membrane HCV T-29 cells ].

    PubMed

    Bartodziejska, Beata; Błaszczyk, Aleksandra; Wykrota, Marianna; Kwil, Iwona; Babicka, Dorota; Rózalski, Antoni

    2002-01-01

    Proteus bacilli play a particularly important role in urinary tract infections (UTI). Fimbriae and adherence ability and hemolysins production (HpmA, HlyA) are one of the factors of pathogenicity of these bacteria. In this paper we describe the invasion of HCV T-29 transitional bladder urothelial cells carcinoma strains of P. penneri, as well as P. vulgaris strains belonging to different serogroups. The cytotoxic effect was observed at 8 hour of incubation of the tested cells with P. vulgaris O21 and the same effect (complete lysis) at 6 hours by P. vulgaris O4 (this strain manifests maximal activity in the production of HlyA hemolysin). P. penneri strains, produce different types of fimbriae, expressed similar bacterial invasiveness. The hydrophobic properties of 25 P. vulgaris strains were also tested and only 3 strains occur to have hydrophobic cell surface.

  1. Genetic Variation among Staphylococcus aureus Strains from Bovine Milk and Their Relevance to Methicillin-Resistant Isolates from Humans ▿

    PubMed Central

    Hata, Eiji; Katsuda, Ken; Kobayashi, Hideki; Uchida, Ikuo; Tanaka, Kiyoshi; Eguchi, Masashi

    2010-01-01

    In genetic analysis of bovine Staphylococcus aureus isolates that are recognized as an important pathogenic bacterium in bovine mastitis, multilocus sequence typing (MLST) showed strong correlation to the results of pulsed-field gel electrophoresis, coa PCR-restriction fragment length polymorphism (RFLP), spa typing, and the coagulase serotyping method. According to MLST results, strains derived from sequence type 97 (ST97) and ST705 were suggested as not only dominant bovine S. aureus lineages in Japan but also pandemic bovine S. aureus lineages. Although both lineages seem to be distantly related to each other by phylogenetic analysis, both had common characteristics, i.e., lukM/lukF′-PV and coagulase serotype VI. These characteristics were very rare among minor bovine strains and human strains and may contribute to the host specificity of these lineages. Four methicillin-resistant S. aureus (MRSA) isolates were first confirmed from bovine milk in Japan; these isolates showed geno- and serotypes that were identical or similar to those of human MRSA isolates in Japan (ST5, staphylococcal cassette chromosome mec type II [SCCmec II], Spa type t002 or t375, and coagulase serotype II, and ST89, SCCmec IIIa, Spa type t5266, and coagulase serotype I). ST5 and ST89 are uncommon among bovine isolates in the world, whereas these STs are common among human MRSA isolates in Japan. PMID:20392913

  2. CFD investigation of the influence of volute geometrical variations on hydrodynamic characteristics of circulator pump

    NASA Astrophysics Data System (ADS)

    Wu, Denghao; Yuan, Shouqi; Ren, Yun; Mu, Jiegang; Yang, Youdong; Liu, Jian

    2016-03-01

    Improper design of volute geometry can be the main cause that leads to unsteady pressure pulsation and radial force in pumps. Therefore, it is important to understand the influence of volute geometrical parameters on hydrodynamic characteristics of pump and the mechanism. However, the existing studies are limited to investigate the influence of only one or two volute geometrical parameters each time, and a systematic study of the influence of the combinations of different volute geometrical parameters on the pump's hydrodynamic characteristics is missing. In this paper, a study on the understanding of the influence of volute geometrical variations on hydrodynamic characteristics of a high speed circulator pump by using computational fluid dynamics(CFD) technology is presented. Five main volute geometrical parameters D 3, A 8, α 0, φ 0 and R t are selected and 25 different volute configurations are generated by using design of experiments(DOE) method. The 3D unsteady flow numerical simulations, which are based on the SST k- w turbulence model and sliding mesh technique provided by CFX, are executed on the 25 different volute configurations. The hydraulic performance, pressure pulsation and unsteady radial force inside the pump at design condition are obtained and analyzed. It has been found that volute geometrical parameters D 3 and A 8 are major influence factors on hydrodynamic characteristics of the pump, while α 0, φ 0 and R t are minor influence factors. The minimum contribution from both D 3 and A 8 is 58% on head, and maximum contribution from both D 3 and A 8 is 90% on pressure pulsation. Regarding the pressure pulsation intensity, two peaks can be found. One is in the tongue area and the other is in the diffusor area. The contributions are around 60% from tongue and 25% from diffusor, respectively. The amplitude of pressure pulsation has a quadratic polynomial functional relationship with respect to D 3/ D 2 and A 8/ A 10, and fluctuating level of

  3. Investigation of a Cross-Correlation Based Optical Strain Measurement Technique for Detecting radial Growth on a Rotating Disk

    NASA Technical Reports Server (NTRS)

    Clem, Michelle M.; Woike, Mark R.

    2013-01-01

    The Aeronautical Sciences Project under NASA`s Fundamental Aeronautics Program is extremely interested in the development of novel measurement technologies, such as optical surface measurements in the internal parts of a flow path, for in situ health monitoring of gas turbine engines. In situ health monitoring has the potential to detect flaws, i.e. cracks in key components, such as engine turbine disks, before the flaws lead to catastrophic failure. In the present study, a cross-correlation imaging technique is investigated in a proof-of-concept study as a possible optical technique to measure the radial growth and strain field on an already cracked sub-scale turbine engine disk under loaded conditions in the NASA Glenn Research Center`s High Precision Rotordynamics Laboratory. The optical strain measurement technique under investigation offers potential fault detection using an applied high-contrast random speckle pattern and imaging the pattern under unloaded and loaded conditions with a CCD camera. Spinning the cracked disk at high speeds induces an external load, resulting in a radial growth of the disk of approximately 50.0-im in the flawed region and hence, a localized strain field. When imaging the cracked disk under static conditions, the disk will be undistorted; however, during rotation the cracked region will grow radially, thus causing the applied particle pattern to be .shifted`. The resulting particle displacements between the two images will then be measured using the two-dimensional cross-correlation algorithms implemented in standard Particle Image Velocimetry (PIV) software to track the disk growth, which facilitates calculation of the localized strain field. In order to develop and validate this optical strain measurement technique an initial proof-of-concept experiment is carried out in a controlled environment. Using PIV optimization principles and guidelines, three potential speckle patterns, for future use on the rotating disk, are developed

  4. Fluconazole susceptibility and strain variation of Candida albicans isolates from HIV-infected patients with oropharyngeal candidosis.

    PubMed

    Barchiesi, F; Arzeni, D; Del Prete, M S; Sinicco, A; Falconi Di Francesco, L; Pasticci, M B; Lamura, L; Nuzzo, M M; Burzacchini, F; Coppola, S; Chiodo, F; Scalise, G

    1998-05-01

    Over a 16 month period we conducted a prospective study in a cohort of 45 HIV-positive patients to detect the development of resistance to fluconazole and to analyse the epidemiology of oropharyngeal candidosis (OPC). Each episode was treated with fluconazole 100 mg/day po for 10 days. All yeast isolates were tested for their in-vitro susceptibility to fluconazole. Multiple strains of Candida albicans simultaneously isolated from a given patient were typed by electrophoretic karyotyping. Overall, 106 episodes of OPC were diagnosed among the 45 patients: 18/45 patients (40%) had only one episode, 11/45 (24%) had two episodes, and the remaining 16/45 (36%) had three or more episodes (range 3-7). Cure (complete resolution of signs and symptoms and negative post-treatment cultures) and improvement (complete resolution of signs and symptoms but positive post-treatment cultures) were observed in 30/106 (28%) and 69/106 (65%) episodes of OPC, respectively. Failure (absence of improvement or exacerbation of signs and symptoms) was observed in seven episodes (7%) from four patients. In two of these four patients a significant and progressive increase in fluconazole MICs was observed: from 0.25 to 16 mg/L in one patient, and from < or = 0.125 to 32 mg/L in the second one. Tests on multiple colonies from individual isolation plates showed that it was not unusual to obtain different fluconazole MICs, indicating that, in order to avoid misleading results, one should perform in-vitro susceptibility testing by using a multiple colony inoculum rather than an inoculum made from a single colony. A total of 213 strains of C. albicans isolated from seven patients who suffered from four or more episodes of OPC through the course of the study were typed by electrophoretic karyotyping. Five individuals (71%) were infected with yeasts with only one DNA type, while the other two patients showed the presence of two or three different DNA types. The simultaneous presence of multiple types

  5. Dynamic investigations on the influence of epitaxial strain on the superconducting transition in YBa2Cu3O7-x

    NASA Astrophysics Data System (ADS)

    Hühne, R.; Okai, D.; Dörr, K.; Trommler, S.; Herklotz, A.; Holzapfel, B.; Schultz, L.

    2008-07-01

    YBa2Cu3O7-x (YBCO) films have been prepared on piezoelectric (001) Pb(Mg1/3Nb2/3)0.72Ti0.28O3 (PMN-PT) substrates for dynamic investigations on the influence of strain on the superconducting transition temperature. The YBCO films deposited by off-axis pulsed laser deposition showed a perfect epitaxial growth on the piezocrystals but also significant surface roughness due to the miscut of the substrate. The in-plane lattice constant of the PMN-PT substrate was varied dynamically by the application of an electric field of <=10 kV cm-1. As a result, a reversible shift of the superconducting transition by about 0.1 K was found on an optimally doped YBCO film for an applied strain of 0.05%. The results show for the first time that this approach is suitable for studying the strain dependence of superconducting properties in detail.

  6. Investigation of pre-pubertal sex differences in wheel running and social behavior in three mouse strains

    PubMed Central

    Gordon, Elizabeth A.; Corbitt, Cynthia

    2015-01-01

    Sex differences in social behaviors exist in mammals during adulthood, and further evidence suggests that sex differences in behavior are present before sexual maturity. In order to model behavioral disorders in animals, it is important to assess baseline sex-related behavioral differences, especially when studying disorders for which sex-related behavioral effects are expected. We investigated the effect of sex on behavior in 3 strains of pre-pubertal mice (C57BL/6, CFW, and CF1) using a wheel-running assay. We found no significant sex differences in latency to run on the wheel or total duration of wheel running within each strain. During the social interaction test, there were no differences between sexes in latency or total duration of contact or following between a subject and novel mouse. We also evaluated behavioral patterns of wheel running and stereotypical behaviors, such as burrowing and grooming. Both sexes showed characteristic wheel running behavior, spending the majority of each trial interacting with the wheel when it was free and more time performing other activities (e.g., stereotypical behaviors, general locomotion) when it was jammed. These results provide evidence that, among various strains of pre-pubertal mice, baseline sex-related behavioral differences are not strong enough to influence the measured behaviors. PMID:26316671

  7. Investigation of Spatial Variation of Sea States Offshore of Humboldt Bay CA Using a Hindcast Model.

    SciTech Connect

    Dallman, Ann Renee; Neary, Vincent Sinclair

    2014-10-01

    Spatial variability of sea states is an important consideration when performing wave resource assessments and wave resource characterization studies for wave energy converter (WEC) test sites and commercial WEC deployments. This report examines the spatial variation of sea states offshore of Humboldt Bay, CA, using the wave model SWAN . The effect of depth and shoaling on bulk wave parameters is well resolved using the model SWAN with a 200 m grid. At this site, the degree of spatial variation of these bulk wave parameters, with shoaling generally perpendicular to the depth contours, is found to depend on the season. The variation in wave height , for example, was higher in the summer due to the wind and wave sheltering from the protruding land on the coastline north of the model domain. Ho wever, the spatial variation within an area of a potential Tier 1 WEC test site at 45 m depth and 1 square nautical mile is almost negligible; at most about 0.1 m in both winter and summer. The six wave characterization parameters recommended by the IEC 6 2600 - 101 TS were compared at several points along a line perpendicular to shore from the WEC test site . As expected, these parameters varied based on depth , but showed very similar seasonal trends.

  8. Biochemical analysis and investigation on the prospective applications of alkaline protease from a Bacillus cereus strain.

    PubMed

    Saleem, Mahjabeen; Rehman, Atiqa; Yasmin, Riffat; Munir, Bushra

    2012-06-01

    Proteases have prospective financial and environment-friendly applications; hence attention is focused currently on the finding of new protease producing microorganism so as to meet the requirements of industry. A thermophilic bacterial strain producing extracellular protease activity was isolated from soil and identified as Bacillus cereus by analysis of 16S rRNA. Protease production by the microorganism was improved by studying the impact of the type of nitrogen and carbon source, fermentation period, growth temperature and initial pH of the culture medium in cultivation optimization experiments. The enzyme was purified to homogeneity in two step procedure involving Sephadex G-75 and Q-Sepharose chromatography. The molecular weight of purified enzyme was found to be 58 kDa by SDS-PAGE. Protease exhibited a pH and temperature optima of 7.5 and 60°, respectively. The enzyme was active in the pH range of 6.0-9.0 and stable up to 70°C. Histological analysis of protease treated goat and cow skin pelts showed complete removal of non leather forming structures such as hair shaft, hair follicles and glandular structures. The protease showed the stain removing property from blood stained cotton cloth and found to be compatible with six commercially available detergents. The protease could release peptides from natural proteins after digestion of coagulated egg albumin and blood clot.

  9. Antimicrobial resistance investigation on Staphylococcus strains in a local hospital in Guangzhou, China, 2001-2010.

    PubMed

    Deng, Yang; Liu, Junyan; Peters, Brian M; Chen, Lei; Miao, Jian; Li, Bing; Li, Lin; Chen, Dingqiang; Yu, Guangchao; Xu, Zhenbo; Shirtliff, Mark E

    2015-02-01

    A retrospective study was conducted on 1,739 Staphylococcus isolates from the First Affiliated Hospital of Jinan University (FAHJU) in Guangzhou during 2001-2010. With the exception of teicoplanin and vancomycin, antimicrobial resistance was commonly observed among the isolates examined, with high resistance rates for β-lactamases (94.0% and 73.7% for penicillin and oxacillin) and resistance percentages for cefoxitin, chloramphenicol, ciprofloxacin, clindamycin, erythromycin, gentamicin, trimethoprim-sulfamethoxazole, and tetracycline ranging from 83.9% to 19.4%. Two hundred sixty-three of the 1,739 isolates were subjected to SCCmec typing and 42 to MLST, spaA, and coa typing. ST239-MRSA-III was prevalently identified along with one distinct coa type HIJKL and 2 spaA types (WGKAOMQ-t037 and WGKAQQ-t030). Class 1 integrons were commonly detected (31.6%), although none of the integron-positive MRSA strains had been isolated since 2009. The widespread detection of integron-based antimicrobial resistance determinants may further contribute to the emergence of superbugs.

  10. Variation in lipid extractability by solvent in microalgae. Additional criterion for selecting species and strains for biofuel production from microalgae.

    PubMed

    Mendoza, Héctor; Carmona, Laura; Assunção, Patricia; Freijanes, Karen; de la Jara, Adelina; Portillo, Eduardo; Torres, Alicia

    2015-12-01

    The lipid extractability of 14 microalgae species and strains was assessed using organic solvents (methanol and chloroform). The high variability detected indicated the potential for applying this parameter as an additional criterion for microalgae screening in industrial processes such as biofuel production from microalgae. Species without cell walls presented higher extractability than species with cell walls. Analysis of cell integrity by flow cytometry and staining with propidium iodide showed a significant correlation between higher resistance to the physical treatments of cell rupture by sonication and the lipid extractability of the microalgae. The results highlight the cell wall as a determining factor in the inter- and intraspecific variability in lipid extraction treatments.

  11. Variability among Rhizobium Strains Originating from Nodules of Vicia faba

    PubMed Central

    van Berkum, P.; Beyene, D.; Vera, F. T.; Keyser, H. H.

    1995-01-01

    Rhizobium strains from nodules of Vicia faba were diverse in plasmid content and serology. Results of multilocus gel electrophoresis and restriction fragment length polymorphism indicated several deep chromosomal lineages among the strains. Linkage disequilibrium among the chromosomal types was detected and may have reflected variation of Rhizobium strains in the different geographical locations from which the strains originated. An investigation of pea strains with antibodies prepared against fava bean strains and restriction fragment length polymorphism analyses, targeting DNA regions coding for rRNA and nodulation, indicated that Rhizobium strains from V. faba nodules were distinguishable from those from Pisum sativum, V. villosa, and Trifolium spp. PMID:16535075

  12. GNSS strain rate patterns and their application to investigate geodynamical credibility of the GNSS velocities

    NASA Astrophysics Data System (ADS)

    Araszkiewicz, Andrzej; Figurski, Mariusz

    2015-04-01

    The potential that lies in the use of GNSS measurements for crustal deformation studies have already noticed in the beginning of the first of such a system (GPS). Today thanks to the development of satellite positioning techniques it is possible to detect displacement on the Earth surface with an accuracy less than 1 cm. With long-term observations we can determine the velocities even more accurately. Growing demand in the last years for GNSS applications, both for scientific and civil use, meant that new networks of the reference stations were created. Such a dense GNSS networks allow to conduct research in the field of crust deformation at a higher spatial resolution than before. In Europe most of the research focuses on Mediterranean regions, where we can monitor events resulting from the tectonic plates collision. But even in Central Europe we can see effect of Africa push. In our research we focused on Polish territory, where in the past 5 years a nearly 300 reference stations were established. With minimal movements that have been observed in Poland, a key issue in this type of research is to determine the geodynamic reliability of the estimated stations velocities. While the long-term observations enable us to determine the very accurate velocities, it hard to indicate how reliably they reflect actual tectonic movements is. In this paper we proposed a method for testing the reliability of stations velocities based on the strain rate field analysis. The method is based on the analysis of the distribution of the rate of deformation tensor components obtained for triangular elements built on the basis of assessed station. The paper presents the results of numerical simulations and initial use of the method for the Polish network of reference stations: ASG-EUPOS

  13. Continuous Tuning of Phase Transition Temperature in VO2 Thin Films on c-Cut Sapphire Substrates via Strain Variation.

    PubMed

    Jian, Jie; Wang, Xuejing; Li, Leigang; Fan, Meng; Zhang, Wenrui; Huang, Jijie; Qi, Zhimin; Wang, Haiyan

    2017-02-15

    Vanadium dioxide (VO2) thin films with controlled thicknesses are deposited on c-cut sapphire substrates with Al-doped ZnO (AZO) buffer layers by pulsed laser deposition. The surface roughness of AZO buffer layers is varied by controlling oxygen pressure during growth. The strain in the VO2 lattice is found to be dependent on the VO2 thickness and the VO2/AZO interface roughness. The semiconductor-to-metal transition (SMT) properties of VO2 thin films are characterized and the transition temperature (Tc) is successfully tuned by the VO2 thickness as well as the VO2/AZO interface roughness. It shows that the Tc of VO2 decreases with the decrease of film thickness or VO2/AZO interface roughness. Other SMT properties of the VO2 films are maintained during the Tc tuning. The results suggest that the strain tuning induced by AZO buffer provides an effective approach for tuning Tc of VO2 continuously.

  14. Contribution of Gag and protease to variation in susceptibility to protease inhibitors between different strains of subtype B human immunodeficiency virus type 1.

    PubMed

    Sutherland, Katherine A; Mbisa, Jean L; Cane, Patricia A; Pillay, Deenan; Parry, Chris M

    2014-01-01

    Recent reports have shown that human immunodeficiency virus type 1 (HIV-1) Gag can directly affect susceptibility to protease inhibitors (PIs) in the absence of known resistance mutations in protease. Inclusion of co-evolved Gag alongside protease in phenotypic drug susceptibility assays can alter PI susceptibility in comparison with protease with a WT Gag. Using a single-replication-cycle assay encompassing full-length Gag together with protease we demonstrated significant variation in PI susceptibility between a number of PI-naïve subtype B viruses. Six publicly available subtype B molecular clones, namely HXB2, NL4-3, SF2, YU2, JRFL and 89.6, displayed up to nine-fold reduced PI susceptibility in comparison with the assay reference strain. For two molecular clones, YU2 and JRFL, Gag contributed solely to the observed reduction in susceptibility, with the N-terminal region of Gag contributing significantly. Gag and protease from treatment-naïve, patient-derived viruses also demonstrated significant variation in susceptibility, with up to a 17-fold reduction to atazanavir in comparison with the assay reference strain. In contrast to the molecular clones, protease was the main determinant of the reduced susceptibility. Common polymorphisms in protease, including I13V, L63P and A71T, were shown to contribute to this reduction in PI susceptibility, in the absence of major resistance mutations. This study demonstrated significant variation in PI susceptibility of treatment-naïve patient viruses, and provided further evidence of the independent role of Gag, the protease substrate and in particular the N-terminus of Gag in PI susceptibility. It also highlighted the importance of considering co-evolved Gag and protease when assessing PI susceptibility.

  15. Genetic variation responsible for mouse strain differences in integrin {alpha}{sub 2} expression is associated with altered platelet responses to collagen

    SciTech Connect

    Li, Tong-Tong; Larrucea, Susana; Souza, Shiloe; Leal, Suzanne M.; Lopez, Jose A.; Rubin, Edward M.; Nieswandt, Bernhard; Bray, Paul F.

    2003-11-01

    exert quantitative and qualitative alterations in human platelet adhesive receptors. Polymorphisms of both integrin {alpha}{sub 2} and GPIb have been associated with quantitative differences in receptor levels in healthy individuals. The variation of integrin {alpha}{sub 2} in the normal population is 5-fold, and some portion of this variability has been associated with a C/T polymorphism at nucleotide 807. Individuals homozygous for the 807C or 807T alleles have an average 2-fold difference in platelet {alpha}{sub 2} {beta}{sub 1} levels, and this difference has been linked to increased adhesion to collagen and clinical thrombotic events. Comparable alterations in platelet adhesion receptor expression have not been assessed in different mouse strains. Assessing the functional consequences of subtle genetic variations in humans is challenged by numerous gene-gene and gene environment interactions, and studies in mice can greatly minimize these confounding variables. In addition, comparative sequence analyses between species and between nonhuman primates have proved useful for identifying sequences that affect function and expression. Thus, in the case of platelet adhesion receptors, knowing mouse strain differences in expression levels might be valuable for defining the responsible quantitative trait loci as well as affecting strain choice for particular functional experiments.

  16. Microcosm investigations of stormwater pond sediment toxicity to embryonic and larval amphibians: variation in sensitivity among species.

    PubMed

    Snodgrass, Joel W; Casey, Ryan E; Joseph, Debra; Simon, Judith A

    2008-07-01

    Stormwater ponds have become common features of modern development and often represent significant amounts of open space in urbanized areas. Although stormwater ponds may provide habitat for wildlife, factors responsible for producing variation in wildlife use of ponds have received limited attention. To investigate the role of variation in species tolerances of pollutants in structuring pond-breeding amphibian assemblages, we exposed species tolerant (Bufo americanus) and not tolerant (Rana sylvatica) of urbanization to pond sediments in laboratory microcosms. Pond microcosms had elevated sediment metal levels and chloride water concentrations. Among R. sylvatica embryos, exposure to pond sediments resulted in 100% mortality. In contrast, B. americanus embryos and larvae experienced only sublethal effects (i.e., reduced size at metamorphosis) due to pond sediment exposure. Our results suggest variation in pollutant tolerance among early developmental stages of amphibians may act in concert with terrestrial habitat availability to structure amphibian assemblages associated with stormwater ponds.

  17. SU-E-T-636: Investigation of Dose Variation in High Dose Radiation Brachytherapy

    SciTech Connect

    Hyvarinen, M; Leventouri, T; Casey, C; Long, S; Pella, S; Dumitru, N; Herrera, R

    2014-06-15

    Purpose: The purpose of this study is to revise most of the HDR types of treatments with their applicators and their localization challenges. Since every millimeter of misplacement counts the study will look into the necessity of increasing the immobilization for several types of applicators Methods: The study took over 136 plans generated by the treatment planning system (TPS) looking into the applicator's placement in regard to the organs at risk (OR) and simulated the three possible displacements at the hottest dose point on the critical organ for several accessories to evaluate the variation of the delivered dose at the point due to the displacement. Results: Significant dose variation was obtained for the Contura, Savi, MLM and Prostate applicators. Conclusion: This study data indicates that an improvement of the immobilization devices for HDR is absolutely necessary. Better applicator fixation devices are required too. Developing new immobilization devices for all the applicators is recommended. Florida Atlantic University may provide Travel reimbursements.

  18. [Investigation of OXA type beta-lactamases and PFGE patterns in Acinetobacter baumannii strains resistant to carbapenems].

    PubMed

    Keyik, Serafettin; Arslan, Uğur; Türk Dağı, Hatice; Seyhan, Tuba; Fındık, Duygu

    2014-10-01

    Acinetobacter baumannii is an important opportunistic and multidrug-resistant pathogen leading to nosocomial infections. Over the last 10 years, a significant and threatening increase in resistance to carbapenems, mainly due to the dissemination of class D beta-lactamases, has been reported in A.baumannii worldwide. The most common types of beta-lactamases causing carbapenem resistance in A.baumannii are the OXA-23, OXA-24, OXA-40, OXA-58 and OXA-143 type serine beta-lactamases. The aim of this study was to investigate the presence of OXA type beta-lactamases in carbapenem-resistant A.baumannii strains and the clonal relationship between the strains. A total of 105 non-duplicate carbapenem-resistant A.baumannii strains isolated from various clinical samples (68 blood, 18 bronchoalveolar lavage, 13 drainage, 3 urine, 2 cerebrospinal fluid and 1 catheter samples) in the Microbiology Laboratories of Selcuk University, Meram (2009-2012) and Selcuklu (2007-2008) Medical School Hospitals, were included in the study. The isolates were identified by conventional methods and Phoenix 100 BD (BD Diagnostic, USA) and Vitek II (bioMerieux, France) automated systems. Carbapenem susceptibility test was performed by Kirby-Bauer disk diffusion method according to the CLSI standards. bla(OXA 23-like), bla(OXA 24-like), bla(OXA 58-like) and bla(OXA 51-like) genes were amplified by multiplex PCR assay and clonal relatedness was investigated by pulsed-field gel electrophoresis (PFGE) using ApaI enzyme. The bla(OXA 51-like) gene was determined in all carbapenem-resistant A.baumannii isolates, while the bla(OXA 23-like) and bla(OXA 58-like) genes were detected in 46.6% and 53.3% of isolates, respectively. However bla(OXA 24-like) gene was not demonstrated in any isolates. bla(OXA 23-like) gene was determined in both Meram and Selcuklu Medical School hospitals, but bla(OXA 58-like) gene was detected only in Meram Medical School hospital. PFGE analysis of the isolates revealed 32 different

  19. An investigation of the solar zenith angle variation of D-region ionization

    NASA Technical Reports Server (NTRS)

    Ratnasiri, P. A. J.; Sechrist, C. F., Jr.

    1975-01-01

    Model calculations are carried out with a view to interpreting the solar zenith angle variation of D-region ionization. A model is developed for the neutral chemistry including the transport terms relating to molecular and eddy diffusion. The diurnal behavior is described of the minor neutral constituents formed in an oxygen-hydrogen-nitrogen atmosphere, in the height interval between 30 and 120 km. Computations carried out for two cases of the eddy diffusion coefficients models indicate that the constituents which are important for the D-region positive-ion chemistry do not show a significant variation with zenith angle for values up to 75 deg over the D-region heights. In the ion chemistry model, ion-pair production rates are calculated for solar X-rays between 1 A and 100 A, EUV radiations from 100 A up to the Lyman-alpha line, precipitating electrons, and galactic cosmic rays. The solar zenith angle variation of the positive-ion composition, negative-ion composition, and the electron densities are described up to 75 deg zenith angle, in the height interval between 60 and 100 km.

  20. Origins of Tropospheric Ozone Interannual Variation (IAV) over Reunion: A Model Investigation

    NASA Technical Reports Server (NTRS)

    Liu, Junhua; Rodriguez, Jose M.; Thompson, Anne M.; Logan, Jennifer A.; Douglass, Anne R.; Olsen, Mark A.; Steenrod, Stephen D.; Posny, Francoise

    2016-01-01

    Observations from long-term ozonesonde measurements show robust variations and trends in the evolution of ozone in the middle and upper troposphere over Reunion Island (21.1 degrees South Latitude, 55.5 degrees East Longitude) in June-August. Here we examine possible causes of the observed ozone variation at Reunion Island using hindcast simulations by the stratosphere-troposphere Global Modeling Initiative chemical transport model for 1992-2014, driven by assimilated Modern-Era Retrospective Analysis for Research and Applications (MERRA) meteorological fields. Reunion Island is at the edge of the subtropical jet, a region of strong stratospheric-tropospheric exchange. Our analysis implies that the large interannual variation (IAV) of upper tropospheric ozone over Reunion is driven by the large IAV of the stratospheric influence. The IAV of the large-scale, quasi-horizontal wind patterns also contributes to the IAV of ozone in the upper troposphere. Comparison to a simulation with constant emissions indicates that increasing emissions do not lead to the maximum trend in the middle and upper troposphere over Reunion during austral winter implied by the sonde data. The effects of increasing emission over southern Africa are limited tothe lower troposphere near the surface in August-September.

  1. Origins of tropospheric ozone interannual variation over Réunion: A model investigation

    NASA Astrophysics Data System (ADS)

    Liu, Junhua; Rodriguez, Jose M.; Thompson, Anne M.; Logan, Jennifer A.; Douglass, Anne R.; Olsen, Mark A.; Steenrod, Stephen D.; Posny, Françoise

    2016-01-01

    Observations from long-term ozonesonde measurements show robust variations and trends in the evolution of ozone in the middle and upper troposphere over Réunion Island (21.1°S, 55.5°E) in June-August. Here we examine possible causes of the observed ozone variation at Réunion Island using hindcast simulations by the stratosphere-troposphere Global Modeling Initiative chemical transport model for 1992-2014, driven by assimilated Modern-Era Retrospective Analysis for Research and Applications meteorological fields. Réunion Island is at the edge of the subtropical jet, a region of strong stratospheric-tropospheric exchange. Our analysis implies that the large interannual variation (IAV) of upper tropospheric ozone over Réunion is driven by the large IAV of the stratospheric influence. The IAV of the large-scale, quasi-horizontal wind patterns also contributes to the IAV of ozone in the upper troposphere. Comparison to a simulation with constant emissions indicates that increasing emissions do not lead to the maximum trend in the middle and upper troposphere over Réunion during austral winter implied by the sonde data. The effects of increasing emission over southern Africa are limited to the lower troposphere near the surface in August-September.

  2. Phase variation of a Type IIG restriction-modification enzyme alters site-specific methylation patterns and gene expression in Campylobacter jejuni strain NCTC11168

    PubMed Central

    Anjum, Awais; Brathwaite, Kelly J.; Aidley, Jack; Connerton, Phillippa L.; Cummings, Nicola J.; Parkhill, Julian; Connerton, Ian; Bayliss, Christopher D.

    2016-01-01

    Phase-variable restriction-modification systems are a feature of a diverse range of bacterial species. Stochastic, reversible switches in expression of the methyltransferase produces variation in methylation of specific sequences. Phase-variable methylation by both Type I and Type III methyltransferases is associated with altered gene expression and phenotypic variation. One phase-variable gene of Campylobacter jejuni encodes a homologue of an unusual Type IIG restriction-modification system in which the endonuclease and methyltransferase are encoded by a single gene. Using both inhibition of restriction and PacBio-derived methylome analyses of mutants and phase-variants, the cj0031c allele in C. jejuni strain NCTC11168 was demonstrated to specifically methylate adenine in 5′CCCGA and 5′CCTGA sequences. Alterations in the levels of specific transcripts were detected using RNA-Seq in phase-variants and mutants of cj0031c but these changes did not correlate with observed differences in phenotypic behaviour. Alterations in restriction of phage growth were also associated with phase variation (PV) of cj0031c and correlated with presence of sites in the genomes of these phages. We conclude that PV of a Type IIG restriction-modification system causes changes in site-specific methylation patterns and gene expression patterns that may indirectly change adaptive traits. PMID:26786317

  3. Use of multiple molecular subtyping techniques to investigate a Legionnaires' disease outbreak due to identical strains at two tourist lodges.

    PubMed Central

    Mamolen, M; Breiman, R F; Barbaree, J M; Gunn, R A; Stone, K M; Spika, J S; Dennis, D T; Mao, S H; Vogt, R L

    1993-01-01

    A multistate outbreak of Legionnaires' disease occurred among nine tour groups of senior citizens returning from stays at one of two lodges in a Vermont resort in October 1987. Interviews and serologic studies of 383 (85%) of the tour members revealed 17 individuals (attack rate, 4.4%) with radiologically documented pneumonia and laboratory evidence of legionellosis. A survey of tour groups staying at four nearby lodges and of Vermont-area medical facilities revealed no additional cases. Environmental investigation of common tour stops revealed no likely aerosol source of Legionella infection outside the lodges. Legionella pneumophila serogroup 1 was isolated from water sources at both implicated lodges, and the monoclonal antibody subtype matched those of the isolates from six patients from whom clinical isolates were obtained. The cultures reacted with monoclonal antibodies MAB1, MAB2, 33G2, and 144C2 to yield a 1,2,5,7 or a Benidorm 030E pattern. The strains were also identical by alloenzyme electrophoresis and DNA ribotyping techniques. The epidemiologic and laboratory data suggest that concurrent outbreaks occurred following exposures to the same L. pneumophila serogroup 1 strain at two separate lodges. Multiple molecular subtyping techniques can provide essential information for epidemiologic investigations of Legionnaires' disease. PMID:8253953

  4. The investigation of short-term variations of Jupiter's Synchrotron Radiation with the large radio interferometer GMRT

    NASA Astrophysics Data System (ADS)

    Imai, Kota; Misawa, Hiroaki; Bhardwaj, Anil; Tsuchiya, Fuminori; Doi, Akihiro; Kondo, Tetsuro; Morioka, Akira

    The goal of this research is to investigate physical processes of short term variations of Jupiter's Synchrotron Radiation (JSR) which is important for revealing the origin of relativistic electrons at Jupiter's Radiation Belt (JRB). JSR has been frequently observed by radio interferometers and single dish radio telescopes to understand characteristics of the spatial distribution and variations inferring dynamics and energetics of the relativistic electrons. Observations with radio interferometers have showed JSR source structure (Dunn et al., 2003, etc), and contributed to modeling of JRB (Garrett et al., 2005, etc). On the other hand, observations of total intensity of JSR with a single dish radio telescope have revealed characteristics of time variable phenomena. The time variations are indispensable parameters giving clues to understand particle source and/or loss processes which characterize the formation of JRB. Recently, Miyoshi et al. (1999) and Bolton et al. (2002) confirmed the existence of short term (days to weeks) variations in JSR. The detection of short term variations makes a great impact on the study on JRB because it has been believed for a long time that the strong internal magnetic field and rapidly rotating magnetosphere of Jupiter protect the JRB region from solar wind variations and magnetospheric disturbances as theoretically suggested by de Pater and Goertz (1994). So far we have made the JSR observations to investigate the short term variations of mainly several hundreds MHz JSR which is emitted by low energy particles (< 10MeV) and has been observed systematically only few times (Miyoshi et al., 1999, Misawa et al., 2005, etc). The latter observation suggested that the short term variation is a general feature at low frequencies. Therefore, it is essential to study its detailed characteristics and the causalities. Theoretically expected physical processes which are responsible for the short term variation are enhanced radial diffusion

  5. Strain-Dependent Variations in Stress Coping Behavior Are Mediated by a 5-HT/GABA Interaction within the Prefrontal Corticolimbic System

    PubMed Central

    Maran, Dario; Viscomi, Maria Teresa; Puglisi-Allegra, Stefano

    2015-01-01

    Background: Serotonin and γ–aminobutyric acid (GABA) transmission is crucial in coping strategies. Methods: Here, using mice from 2 inbred strains widely exploited in behavioral neurochemistry, we investigated whether serotonin transmission in medial prefrontal cortex and GABA in basolateral amygdala determine strain-dependent liability to stress response and differences in coping. Results: C57BL/6J mice displayed greater immobility in the forced swimming test, higher serotonin outflow in medial prefrontal cortex, higher GABA outflow in basolateral amygdala induced by stress, and higher serotonin 1A receptor levels in medial prefrontal cortex accompanied by lower GABAb receptor levels in basolateral amygdala than DBA/2J mice. In assessing whether serotonin in medial prefrontal cortex determines GABA functioning in response to stress and passive coping behavior in C57BL/6J and DBA/2J mice, we observed that selective prefrontal serotonin depletion in C57BL/6J and DBA/2J reduced stress-induced GABA outflow in basolateral amygdala and immobility in the forced swimming test. Conclusions: These results show that strain-dependent prefrontal corticolimbic serotonin/GABA regulation determines the strain differences in stress-coping behavior in the forced swimming test and point to a role of a specific neuronal system in genetic susceptibility to stress that opens up new prospects for innovative therapies for stress disorders. PMID:25522413

  6. Investigating peptide sequence variations for 'double-click' stapled p53 peptides.

    PubMed

    Lau, Yu Heng; de Andrade, Peterson; Sköld, Niklas; McKenzie, Grahame J; Venkitaraman, Ashok R; Verma, Chandra; Lane, David P; Spring, David R

    2014-06-28

    Stapling peptides for inhibiting the p53/MDM2 interaction is a promising strategy for developing anti-cancer therapeutic leads. We evaluate double-click stapled peptides formed from p53-based diazidopeptides with different staple positions and azido amino acid side-chain lengths, determining the impact of these variations on MDM2 binding and cellular activity. We also demonstrate a K24R mutation, necessary for cellular activity in hydrocarbon-stapled p53 peptides, is not required for analogous 'double-click' peptides.

  7. An investigation of surface albedo variations during the recent sahel drought. [ats 3 observations

    NASA Technical Reports Server (NTRS)

    Norton, C. C.; Mosher, F. R.; Hinton, B.

    1978-01-01

    Applications Technology Satellite 3 green sensor data were used to measure surface reflectance variations in the Sahara/Sahel during the recent drought period; 1967 to 1974. The magnitude of the seasonal reflectance change is shown to be as much as 80% for years of normal precipitation and less than 50% for drought years. Year to year comparisons during both wet and dry seasons reveal the existence of a surface reflectance cycle coincident with the drought intensity. The relationship between the green reflectance and solar albedo is examined and estimated to be about 0.6 times the reflectance change observed by the green channel.

  8. Influences of Vowel and Tone Variation on Emergent Word Knowledge: A Cross-Linguistic Investigation

    ERIC Educational Resources Information Center

    Singh, Leher; Hui, Tam Jun; Chan, Calista; Golinkoff, Roberta Michnick

    2014-01-01

    To learn words, infants must be sensitive to native phonological contrast. While lexical tone predominates as a source of phonemic contrast in human languages, there has been little investigation of the influences of lexical tone on word learning. The present study investigates infants' sensitivity to tone mispronunciations in two groups of…

  9. Polar lipid fatty acids, LPS-hydroxy fatty acids, and respiratory quinones of three Geobacter strains, and variation with electron acceptor

    SciTech Connect

    Hedrick, David B.; Peacock, Aaron; Lovley, Derek; Woodard, Trevor L.; Nevin, Kelly P.; Long, Philip E.; White, David C.

    2009-02-01

    The polar lipid fatty acids, lipopolysaccharide hydroxy-fatty acids, and respiratory quinones of Geobacter metallireducens str. GS-15, Geobacter sulfurreducens str. PCA, and Geobacter bemidjiensis str. Bem are reported. Also, the lipids of G. metallireducens were compared when grown with Fe3+ or nitrate as electron acceptors and G. sulfurreducens with Fe3+ or fumarate. In all experiments, the most abundant polar lipid fatty acids were 14:0, i15:0, 16:1*7c, 16:1*5c, and 16:0; lipopolysaccharide hydroxyfatty acids were dominated by 3oh16:0, 3oh14:0, 9oh16:0, and 10oh16:0; and menaquinone-8 was the most abundant respiratory quinone. Some variation in lipid proWles with strain were observed, but not with electron acceptor.

  10. Individual variation in p53 and Cip1 expression profiles in normal human fibroblast strains following exposure to high-let radiation

    SciTech Connect

    Carpenter, T.R.; Johnson, N.F.; Gilliland, F.D.

    1995-12-01

    Exposure to {alpha}-particles emitted by radon progeny appears to be the second-leading cause of lung cancer mortality. However, individual susceptibility to the carcinogenic effects of {alpha}-particles remains poorly characterized. Variation in susceptibility to cancer produced by certian classes of DNA-damaging chemicals is suspected to involve differences in metabolic activation and detoxication. Susceptibility to {alpha}-particle-induced cancer may involve variations in capacity or opportunity to repair DNA damage. Subtle variations in DNA repair capacity would more likely explain radon-related lung cancer susceptibility. The p53 tumor suppressor protein accumulates as a cellular response to DNA damage from ionizing radiation and regulates arrest in the G{sub 1} portion of the cell cycle. Arrest in G{sub 1} portion of the cell cycle. While upstream regulation of p53 protein stability is poorly understood, variations in the ability to accumulate p53 following DNA damage represent potential variations in lung cancer susceptibility related to radon progeny. Further, transcription of the cell-cycle regulatory gene Cip1 is regulated by p53 and increases following ionizing radiation. Therefore, variations in the expression of Cip1 following {alpha}-particle exposure may also be a susceptibility factor in radon-related lung cancers. The purpose of the present investigation was to measure p53 and Cip1 protein induction following {alpha}-particle exposure of fibroblast lines from nine individuals to determine if there were significant variations. The expression of Cip1 protein indicates the differences in response are biologically relevant.

  11. Investigation of factors affecting the calibration of strain gage based transducers ( Goodzeit gages'') for SSC magnets

    SciTech Connect

    Davidson, M.; Gilbertson, A.; Dougherty, M.

    1991-03-01

    These transducers are designed to measure stresses on SSC collared coils. They are individually calibrated with a bonded ten-stack of SSC inner coil cable by applying a known load and reading corresponding output from the gages. The transducer is supported by a notched backing plate'' that allows for bending of the gage beam during calibration or in use with an actual coil. Several factors affecting the calibration and use of the transducers are: the number of times a backing plate'' is used, the similarities or difficulties between bonded ten-stacks, and the differences between the ten-stacks and the coil they represent. The latter is probably the most important because a calibration curve is a model of how a transducer should react within a coil. If the model is wrong, the calibration curve is wrong. Information will be presented regarding differences in calibrations between Brookhaven National Labs (also calibrating these transducers) and Fermilab -- what caused these differences, the investigation into the differences between coils and ten-stacks and how they relate to transducer calibration, and some suggestions for future calibrations.

  12. Coronary stent strut size dependent stress-strain response investigated using micromechanical finite element models.

    PubMed

    Savage, P; O'Donnell, B P; McHugh, P E; Murphy, B P; Quinn, D F

    2004-02-01

    Cardiovascular stents are metal scaffolds that are used in the treatment of atherosclerosis. These devices are typically composed of very thin struts (< or = 100 microm thickness, for coronary applications). At this size-scale the question arises as to the suitability of using bulk material properties in stent design. This paper investigates the use of finite element analysis to predict the mechanical failure of stent struts, typical of the strut size used in coronary stents. 316 L stainless steel in uniaxial loading was considered. To accurately represent the constitutive behavior of the material at this size-scale, a computational micromechanics approach was taken involving an explicit representation of the grain structure in the steel struts, and the use of crystal plasticity theory to represent the constitutive behavior of the individual grains. The development of the finite element models is discussed and results are presented for the predictions of tensile mechanical behavior as a function of strut thickness. The results showed that using this modelling approach, a size effect, already seen experimentally, is produced. This has significant implications for stent design, especially in the context of the desire to produce smaller stents for small bore neurovascular and peripheral artery applications.

  13. Investigation of the dynamic stress–strain response of compressible polymeric foam using a non-parametric analysis

    DOE PAGES

    Koohbor, Behrad; Kidane, Addis; Lu, Wei -Yang; ...

    2016-01-25

    Dynamic stress–strain response of rigid closed-cell polymeric foams is investigated in this work by subjecting high toughness polyurethane foam specimens to direct impact with different projectile velocities and quantifying their deformation response with high speed stereo-photography together with 3D digital image correlation. The measured transient displacement field developed in the specimens during high stain rate loading is used to calculate the transient axial acceleration field throughout the specimen. A simple mathematical formulation based on conservation of mass is also proposed to determine the local change of density in the specimen during deformation. By obtaining the full-field acceleration and density distributions,more » the inertia stresses at each point in the specimen are determined through a non-parametric analysis and superimposed on the stress magnitudes measured at specimen ends to obtain the full-field stress distribution. Furthermore, the process outlined above overcomes a major challenge in high strain rate experiments with low impedance polymeric foam specimens, i.e. the delayed equilibrium conditions can be quantified.« less

  14. Convergent beam electron diffraction investigation of strain induced by Ti self-aligned silicides in shallow trench Si isolation structures

    NASA Astrophysics Data System (ADS)

    Armigliato, Aldo; Spessot, Alessio; Balboni, Roberto; Benedetti, Alessandro; Carnevale, Gianpietro; Frabboni, Stefano; Mastracchio, Gianfranco; Pavia, Giuseppe

    2006-03-01

    The deformation induced onto silicon by the formation of Ti self-aligned silicides (salicides) in shallow trench isolation structures has been investigated by the convergent beam electron diffraction technique (CBED) in the transmission electron microscope (TEM). The splitting of the high order Laue zone (HOLZ) lines in the CBED patterns taken in TEM cross sections close to the salicide/silicon interface has been explained assuming that the salicide grains induce a local bending of the lattice planes of the underlying matrix. This bending, which affects in opposite sense the silicon areas below adjacent grains, decreases with the distance from the interface, eventually vanishing at a depth of 300-400 nm. The proposed strain field has been implemented into a fully dynamical simulation of the CBED patterns and has proved to be able to reproduce both the asymmetry of the HOLZ line splitting and the associated subsidiary fringes. This model is confirmed by the shift of a Bragg contour observed in large angle CBED patterns, taken in a cross section cut along a perpendicular direction. The whole experimental results cannot be explained by just a strain relaxation of the TEM cross section, induced by the salicide film onto the underlying silicon.

  15. Investigation of the dynamic stress–strain response of compressible polymeric foam using a non-parametric analysis

    SciTech Connect

    Koohbor, Behrad; Kidane, Addis; Lu, Wei -Yang; Sutton, Michael A.

    2016-01-25

    Dynamic stress–strain response of rigid closed-cell polymeric foams is investigated in this work by subjecting high toughness polyurethane foam specimens to direct impact with different projectile velocities and quantifying their deformation response with high speed stereo-photography together with 3D digital image correlation. The measured transient displacement field developed in the specimens during high stain rate loading is used to calculate the transient axial acceleration field throughout the specimen. A simple mathematical formulation based on conservation of mass is also proposed to determine the local change of density in the specimen during deformation. By obtaining the full-field acceleration and density distributions, the inertia stresses at each point in the specimen are determined through a non-parametric analysis and superimposed on the stress magnitudes measured at specimen ends to obtain the full-field stress distribution. Furthermore, the process outlined above overcomes a major challenge in high strain rate experiments with low impedance polymeric foam specimens, i.e. the delayed equilibrium conditions can be quantified.

  16. Outbreak investigation identifies a single Listeria monocytogenes strain in sheep with different clinical manifestations, soil and water.

    PubMed

    Dreyer, M; Thomann, A; Böttcher, S; Frey, J; Oevermann, A

    2015-08-31

    Listeria (L.) monocytogenes causes orally acquired infections and is of major importance in ruminants. Little is known about L. monocytogenes transmission between farm environment and ruminants. In order to determine potential sources of infection, we investigated the distribution of L. monocytogenes genetic subtypes in a sheep farm during a listeriosis outbreak by applying four subtyping methods (MALDI-TOF-MS, MLST, MLVA and PFGE). L. monocytogenes was isolated from a lamb with septicemia and from the brainstem of three sheep with encephalitis. Samples from the farm environment were screened for the presence of L. monocytogenes during the listeriosis outbreak, four weeks and eight months after. L. monocytogenes was found only in soil and water tank swabs during the outbreak. Four weeks later, following thorough cleaning of the barn, as well as eight months later, L. monocytogenes was absent in environmental samples. All environmental and clinical L. monocytogenes isolates were found to be the same strain. Our results show that the outbreak involving two different clinical syndromes was caused by a single L. monocytogenes strain and that soil and water tanks were potential infection sources during this outbreak. However, silage cannot be completely ruled out as the bales fed prior to the outbreak were not available for analysis. Faeces samples were negative, suggesting that sheep did not act as amplification hosts contributing to environmental contamination. In conclusion, farm management appears to be a crucial factor for the limitation of a listeriosis outbreak.

  17. Investigations of the Response of Swimming Paramecia to Variations in their Apparent Weight

    NASA Astrophysics Data System (ADS)

    Valles, James; Jung, Ilyong; Guevorkian, Karine; Mickalide, Harry; Wagman, Michael

    2011-11-01

    There is a set of micro-organisms that are small enough that they swim at low Reynolds number and large enough that gravity exerts an influence on their behavior Many protists, like paramecia, for example, exhibit negative gravi-taxis by orienting their swimming upward and negative gravi-kinesis by increasing their propulsion when swimming against their apparent weight. It is not clear whether these responses to a very weak force (about 100 pN) are active or passive. We have developed a technique, Magnetic Force Buoyancy Variation, which enables us to vary the apparent weight of the swimmers in situ. We will describe experiments on paramecia conducted at the National High Magnetic Field Laboratory. In particular, we will describe how increasing the apparent weight induces paramecia to accumulate at upper surfaces. A simple force model suggests that this accumulation is a passive response. Supported by NSF-PHY0750360 and a grant to the NHMFL, NSF DMR-0654118.

  18. Investigation of sulphur isotope variation due to different processes applied during uranium ore concentrate production.

    PubMed

    Krajkó, Judit; Varga, Zsolt; Wallenius, Maria; Mayer, Klaus; Konings, Rudy

    The applicability and limitations of sulphur isotope ratio as a nuclear forensic signature have been studied. The typically applied leaching methods in uranium mining processes were simulated for five uranium ore samples and the n((34)S)/n((32)S) ratios were measured. The sulphur isotope ratio variation during uranium ore concentrate (UOC) production was also followed using two real-life sample sets obtained from industrial UOC production facilities. Once the major source of sulphur is revealed, its appropriate application for origin assessment can be established. Our results confirm the previous assumption that process reagents have a significant effect on the n((34)S)/n((32)S) ratio, thus the sulphur isotope ratio is in most cases a process-related signature.

  19. Application of mobile sampling to investigate spatial variation in fine particle composition

    NASA Astrophysics Data System (ADS)

    Li, Hugh Z.; Dallmann, Timothy R.; Gu, Peishi; Presto, Albert A.

    2016-10-01

    Long-term exposure to particulate matter (PM) is a major contributor to air pollution related deaths. Evidence indicates that metals play an important role in harming human health due to their redox potential. We conducted a mobile sampling campaign in 2013 summer and winter in Pittsburgh, PA to characterize spatial variation in PM2.5 mass and composition. Thirty-six sites were chosen based on three stratification variables: traffic density, proximity to point sources, and elevation. We collected filters in three time sessions (morning, afternoon, and overnight) in each season. X-ray fluorescence (XRF) was used to analyze concentrations of 26 elements: Na, Mg, Al, Si, S, Cl, K, Ca, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Se, Br, Rb, Sr, Zr, Cd, Sb, and Pb. Trace elements had a broad range of concentrations from 0 to 300 ng/m3. Comparison of data from mobile sampling filters with stationary monitors suggested that the mobile sampling strategy did not lead to a biased dataset. We developed Land Use Regression (LUR) models to describe spatial variation of PM2.5, Si, S, Cl, K, Ca, Ti, Cr, Fe, Cu, and Zn. Using ArcGIS-10.3 (ESRI, Redlands, CA), we extracted different independent variables related to traffic influence, land-use type, and facility emissions based on the National Emission Inventory (NEI). To validate LUR models, we used regression diagnostics such as leave-one-out cross validation (LOOCV), mean studentized prediction residual (MSPR), and root mean square of studentized residuals (RMS). The number of predictors in final LUR models ranged from 1 to 6. Models had an average R2 of 0.57 (SD = 0.16). Traffic related variables explained the most variability with an average R2 contribution of 0.20 (SD = 0.20). Overall, these results demonstrated significant intra-urban spatial variability of fine particle composition.

  20. Extensive lava flow fields on Venus: Preliminary investigation of source elevation and regional slope variations

    NASA Technical Reports Server (NTRS)

    Magee-Roberts, K.; Head, James W., III; Lancaster, M. G.

    1992-01-01

    Large-volume lava flow fields have been identified on Venus, the most areally extensive of which are known as fluctus and have been subdivided into six morphologic types. Sheetlike flow fields (Type 1) lack the numerous, closely spaced, discrete lava flow lobes that characterize digitate flow fields. Transitional flow fields (Type 2) are similar to sheetlike flow fields but contain one or more broad flow lobes. Digitate flow fields are divided further into divergent (Types 3-5) and subparallel (Type 6) classes on the basis of variations in the amount of downstream flow divergence. As a result of our previous analysis of the detailed morphology, stratigraphy, and tectonic associations of Mylitta Fluctus, we have formulated a number of questions to apply to all large flow fields on Venus. In particular, we would like to address the following: (1) eruption conditions and style of flow emplacement (effusion rate, eruption duration), (2) the nature of magma storage zones (presence of neutral buoyancy zones, deep or shallow crustal magma chambers), (3) the origin of melt and possible link to mantle plumes, and (4) the importance of large flow fields in plains evolution. To answer these questions we have begun to examine variations in flow field dimension and morphology; the distribution of large flow fields in terms of elevation above the mean planetary radius; links to regional tectonic or volcanic structures (e.g., associations with large shield edifices, coronae, or rift zones); statigraphic relationships between large flow fields, volcanic plains, shields, and coronae; and various models of flow emplacement in order to estimate eruption parameters. In this particular study, we have examined the proximal elevations and topographic slopes of 16 of the most distinctive flow fields that represent each of the 6 morphologic types.

  1. Investigation of H2 Concentration and Combustion Instability Effects on the Kinetics of Strained Syngas Flames

    SciTech Connect

    Ahsan R. Choudhuri

    2006-08-07

    The flame extinction limits of syngas (H{sub 2}-CO) flames were measured using a twin-flame-counter-flow burner. Plots of Extinction limits vs. global stretch rates were generated at different mixture compositions and an extrapolation method was used to calculate the flame extinction limit corresponding to an experimentally unattainable zero-stretch condition. The zero-stretch extinction limit of H{sub 2}-CO mixtures decreases (from rich to lean) with the increase in H{sub 2} concentration in the mixture. The average difference between the measured flame extinction limit and the Le Chatelier's calculation is around {approx} 7%. The measured OH{sup -} chemiluminescent data indicates that regardless of mixture compositions the OH radical concentration reduces (within the experimental uncertainties) to an extinction value prior to the flame extinction. Flame extinction limits of H{sub 2}-CO mixtures measured in a flat-flame burner configuration also show a similar relation. Additionally, the measured laminar flame velocity close to the extinction indicates that regardless of fuel composition the premixed flame of hydrogen fuel blends extinguishes when the mixture laminar flame velocity falls below a critical value. The critical laminar flame velocity at extinction for H{sub 2}-CO premixed flames (measured in the flat flame burner configuration) is found to be 3.77({+-}0.38) cm/s. An externally perturbed H{sub 2}-CO twin flame was not experimentally achievable for the mixture conditions used in the present investigation. A slightest perturbation in the flow-field distorts the H{sub 2}-CO twin-flame. The flame becomes highly unstable with the introduction of an externally excited flow oscillation.

  2. A Computational Icing Effects Study for a Three-Dimensional Wing: Comparison with Experimental Data and Investigation of Spanwise Variation

    NASA Technical Reports Server (NTRS)

    Thompson, D.; Mogili, P.; Chalasani, S.; Addy, H.; Choo, Y.

    2004-01-01

    Steady-state solutions of the Reynolds-averaged Navier-Stokes (RANS) equations were computed using the Colbalt flow solver for a constant-section, rectangular wing based on an extruded two-dimensional glaze ice shape. The one equation Spalart-Allmaras turbulence model was used. The results were compared with data obtained from a recent wind tunnel test. Computed results indicate that the steady RANS solutions do not accurately capture the recirculating region downstream of the ice accretion, even after a mesh refinement. The resulting predicted reattachment is farther downstream than indicated by the experimental data. Additionally, the solutions computed on a relatively coarse baseline mesh had detailed flow characteristics that were different from those computed on the refined mesh or the experimental data. Steady RANS solutions were also computed to investigate the effects of spanwise variation in the ice shape. The spanwise variation was obtained via a bleeding function that merged the ice shape with the clean wing using a sinusoidal spanwise variation. For these configurations, the results predicted for the extruded shape provided conservative estimates for the performance degradation of the wing. Additionally, the spanwise variation in the ice shape and the resulting differences in the flow fields did not significantly change the location of the primary reattachment.

  3. MetaPalette: a k-mer Painting Approach for Metagenomic Taxonomic Profiling and Quantification of Novel Strain Variation

    PubMed Central

    Falush, Daniel

    2016-01-01

    ABSTRACT Metagenomic profiling is challenging in part because of the highly uneven sampling of the tree of life by genome sequencing projects and the limitations imposed by performing phylogenetic inference at fixed taxonomic ranks. We present the algorithm MetaPalette, which uses long k-mer sizes (k = 30, 50) to fit a k-mer “palette” of a given sample to the k-mer palette of reference organisms. By modeling the k-mer palettes of unknown organisms, the method also gives an indication of the presence, abundance, and evolutionary relatedness of novel organisms present in the sample. The method returns a traditional, fixed-rank taxonomic profile which is shown on independently simulated data to be one of the most accurate to date. Tree figures are also returned that quantify the relatedness of novel organisms to reference sequences, and the accuracy of such figures is demonstrated on simulated spike-ins and a metagenomic soil sample. The software implementing MetaPalette is available at: https://github.com/dkoslicki/MetaPalette. Pretrained databases are included for Archaea, Bacteria, Eukaryota, and viruses. IMPORTANCE Taxonomic profiling is a challenging first step when analyzing a metagenomic sample. This work presents a method that facilitates fine-scale characterization of the presence, abundance, and evolutionary relatedness of organisms present in a given sample but absent from the training database. We calculate a “k-mer palette” which summarizes the information from all reads, not just those in conserved genes or containing taxon-specific markers. The compositions of palettes are easy to model, allowing rapid inference of community composition. In addition to providing strain-level information where applicable, our approach provides taxonomic profiles that are more accurate than those of competing methods. Author Video: An author video summary of this article is available. PMID:27822531

  4. Effect of Rickettsia felis Strain Variation on Infection, Transmission, and Fitness in the Cat Flea (Siphonaptera: Pulicidae).

    PubMed

    Healy, Sean P; Brown, Lisa D; Hagstrom, Melena R; Foil, Lane D; Macaluso, Kevin R

    2017-03-02

    Rickettsia felis is a human pathogen transmitted by the cat flea, Ctenocephalides felis (Bouché) (str. LSU), as well as an obligate symbiont of the parthenogenic booklouse Liposcelis bostrychophila (Badonnel) (str. LSU-Lb). The influence of genetic variability in these two strains of R. felis on host specialization and fitness and possible resulting differences on infection and transmission kinetics in C. felis is unknown. Utilizing an artificial host system, cat fleas were exposed to a R. felis str. LSU-Lb-infected bloodmeal and monitored for infection at 7-d intervals for 28 d. Quantitative real-time PCR was used to determine rickettsial load and infection density in newly exposed cat fleas, and transmission frequency between cat fleas. The effect of persistent R. felis infection on cat flea F1 progeny was also assessed. At 7 d postexposure 76.7% of the cat fleas successfully acquired R. felis str. LSU-Lb. In R. felis str. LSU-Lb-exposed cat fleas, the mean infection load (6.15 × 106), infection density (0.76), and infection prevalence (91/114) were significantly greater than R. felis str. LSU infection load (3.09 × 106), infection density (0.68), and infection prevalence (76/113). A persistent R. felis str. LSU-Lb infection was detected for 28 d in adult cat fleas but neither female:male ratio distortion nor vertical transmission was observed in F1 progeny. While infection kinetics differed, with higher intensity associated with R. felis str. LSU-Lb, no distinct phenotype was observed in the F1 progeny.

  5. Investigating host dependence of xylose utilization in recombinant Saccharomyces cerevisiae strains using RNA-seq analysis

    PubMed Central

    2013-01-01

    Background Xylose-based ethanol production by recombinant S. cerevisiae is of great interest to basic and applied bioenergy research. By expressing three different fungal pathways in two S. cerevisiae hosts respectively, we found that the xylose utilization efficiency by recombinant S. cerevisiae depends not only on the choice of xylose pathway but also on the choice of host, exhibiting an obvious host or context dependence. To investigate molecular mechanisms of this context dependence, we applied RNA-seq analysis in this study for a systematic characterization of the xylose utilization via different pathways in different S. cerevisiae hosts. Results Based on the RNA-seq analysis, the transcripts that were regulated during xylose utilization have been identified. Three transcription factors involved in regulation of amino acid metabolism, responses to oxidative stresses, and degradation of aggregated proteins, respectively, were found to participate in xylose metabolism regulation regardless of which pathway was expressed and which host the xylose pathway was expressed in. Nine transcription factors, involved in homeostasis, regulation of amino acid metabolism, and stress responses, were identified as the key modules responsible for the host-specific responses to the same xylose pathway. In addition, the transcriptional regulations of xylose utilization in different yeast hosts were compared to two reference regulation patterns, which indicated that diverse regulation strategies were adopted by different hosts for improved xylose utilization. Conclusions This study provides the first transcriptomic study of the host dependence of xylose utilization in S. cerevisiae. Both the conserved regulatory modules for xylose metabolism and the key modules responsible for host dependence were identified. As indicated by the functions of the conserved transcription factors involved in xylose metabolism regulation, the xylose utilization in recombinant S. cerevisiae may be

  6. Investigating Müllerian mimicry: predator learning and variation in prey defences.

    PubMed

    Ihalainen, E; Lindström, L; Mappes, J

    2007-03-01

    Inexperienced predators are assumed to select for similarity of warning signals in aposematic species (Müllerian mimicry) when learning to avoid them. Recent theoretical work predicts that if co-mimic species have unequal defences, predators attack them according to their average unpalatability and mimicry may not be beneficial for the better defended co-mimic. In this study, we tested in a laboratory environment whether a uniform warning signal is superior to a variable one in promoting predator learning, and simultaneously whether co-mimics are preyed upon according to their average unpalatability. There was an interaction of signal variation and unpalatability but inexperienced birds did not select for signal similarity in artificial prey; when the prey was moderately defended a variable signal was even learnt faster than a uniform one. Due to slow avoidance learning, moderately defended prey had higher mortality than highly defended prey (although this was not straightforward), but mixing high and moderate unpalatability did not increase predation compared with high unpalatability. This does not support the view that predators are sensitive to varying unpalatability. The results suggest that inexperienced predators may neither strongly select for accurate Müllerian mimicry nor affect the benefits of mimicry when the co-mimics are unequally defended.

  7. Impacts of diurnal variation of ultraviolet-B and photosynthetically active radiation on phycobiliproteins of the hot-spring cyanobacterium Nostoc sp. strain HKAR-2.

    PubMed

    Kannaujiya, Vinod K; Sinha, Rajeshwar P

    2017-01-01

    The effects of diurnal variation of photosynthetically active radiation (PAR; 400-700 nm) and ultraviolet-B (UV-B; 280-315 nm) radiation on phycobiliproteins (PBPs) and photosynthetic pigments (PP) have been studied in the hot-spring cyanobacterium Nostoc sp. strain HKAR-2. The variations in PBPs and PP were monitored by alternating light and dark under PAR, UV-B, and PAR + UV-B radiations over a period of 25 h. There was a decline in the amount of Chl a and PBPs during light periods of UV-B and PAR + UV-B and an increase during dark periods showing a circadian rhythm by destruction and resynthesis of pigment-protein complex. However, a marked induction in carotenoids was recorded during light periods of the same radiations. Moreover, the ratio of Chl a/PE and Chl a/PC was increased in dark periods showing the resynthesis of bleached Chl a. The wavelength shift in emission fluorescence of PBPs toward shorter wavelengths further indicated the bleaching and destruction of PBPs during light periods. Oxidative damage upon exposure to PAR, UV-B, and PAR + UV-B was alleviated by induction of antioxidative enzymes such as superoxide dismutase (SOD), catalase (CAT), and ascorbate peroxidase (APX). The studied cyanobacterium exhibits a significant increase in the activities of SOD, CAT, and APX upon exposure to UV-B and PAR + UV-B radiations. The results indicate that pigment-protein composition of Nostoc sp. stain HKAR-2 was significantly altered during diurnal variation of light/radiation, which might play an important role in optimization for their productivity in a particular cyanobacterium.

  8. A Monte Carlo Investigation of the Analysis of Variance Applied to Non-Independent Bernoulli Variates.

    ERIC Educational Resources Information Center

    Draper, John F., Jr.

    The applicability of the Analysis of Variance, ANOVA, procedures to the analysis of dichotomous repeated measure data is described. The design models for which data were simulated in this investigation were chosen to represent simple cases of two experimental situations: situation one, in which subjects' responses to a single randomly selected set…

  9. Investigation into Risk and Uncertainty: Identifying Coefficient of Variation Benchmarks for Air Force ACAT I Programs

    DTIC Science & Technology

    2013-03-01

    with this approach is SAR data provides only a point estimate for budgeting purposes of a system . The uncertainty metrics: Monte Carlo 5... uncertainty including: mean, median, mode, confidence interval , standard deviation, cumulative distribution functions, correlation, and coefficient...USAF March 2013 APPROVED FOR PUBLIC RELEASE; DISTRIBUTION IS UNLIMITED AFIT-ENV-13-M-05 Investigation into Risk and Uncertainty

  10. A Genre-Based Investigation of Discussion Sections of Research Articles in Dentistry and Disciplinary Variation

    ERIC Educational Resources Information Center

    Basturkmen, Helen

    2012-01-01

    Outwardly the rhetorical organisation of sections of research reports in different disciplines can appear similar. Close examination, however, may reveal subtle differences. Numerous studies have drawn on the genre-based approach developed by Swales (1990, 2004) to investigate the schematic structure of sections of articles in a range of…

  11. High-resolution typing reveals distinct Chlamydia trachomatis strains in an at-risk population in Nanjing, China.

    PubMed

    Bom, Reinier J M; van den Hoek, Anneke; Wang, Qianqiu; Long, Fuquan; de Vries, Henry J C; Bruisten, Sylvia M

    2013-08-01

    We investigated Chlamydia trachomatis strains from Nanjing, China, and whether these strains differed from Amsterdam, the Netherlands. C. trachomatis type was determined with multilocus sequence typing. Most strains were specific to Nanjing, but some clustered with strains from Amsterdam. This demonstrates a geographical variation in C. trachomatis previously left undetected.

  12. Investigating the genetic basis of fever-associated syndromic epilepsies using copy number variation analysis.

    PubMed

    Hartmann, Corinna; von Spiczak, Sarah; Suls, Arvid; Weckhuysen, Sarah; Buyse, Gunnar; Vilain, Catheline; Van Bogaert, Patrick; De Jonghe, Peter; Cook, Joseph; Muhle, Hiltrud; Stephani, Ulrich; Helbig, Ingo; Mefford, Heather C

    2015-03-01

    Fever-associated syndromic epilepsies ranging from febrile seizures plus (FS+) to Dravet syndrome have a significant genetic component. However, apart from SCN1A mutations in >80% of patients with Dravet syndrome, the genetic underpinnings of these epilepsies remain largely unknown. Therefore, we performed a genome-wide screening for copy number variations (CNVs) in 36 patients with SCN1A-negative fever-associated syndromic epilepsies. Phenotypes included Dravet syndrome (n = 23; 64%), genetic epilepsy with febrile seizures plus (GEFS+) and febrile seizures plus (FS+) (n = 11; 31%) and unclassified fever-associated epilepsies (n = 2; 6%). Array comparative genomic hybridization (CGH) was performed using Agilent 4 × 180K arrays. We identified 13 rare CNVs in 8 (22%) of 36 individuals. These included known pathogenic CNVs in 4 (11%) of 36 patients: a 1q21.1 duplication in a proband with Dravet syndrome, a 14q23.3 deletion in a proband with FS+, and two deletions at 16p11.2 and 1q44 in two individuals with fever-associated epilepsy with concomitant autism and/or intellectual disability. In addition, a 3q13.11 duplication in a patient with FS+ and two de novo duplications at 7p14.2 and 18q12.2 in a patient with atypical Dravet syndrome were classified as likely pathogenic. Six CNVs were of unknown significance. The identified genomic aberrations overlap with known neurodevelopmental disorders, suggesting that fever-associated epilepsy syndromes may be a recurrent clinical presentation of known microdeletion syndromes.

  13. Investigation of the phase morphology of bacterial PHA inclusion bodies by contrast variation SANS

    NASA Astrophysics Data System (ADS)

    Russell, R. A.; Holden, P. J.; Garvey, C. J.; Wilde, K. L.; Hammerton, K. M.; Foster, L. J.

    2006-11-01

    Under growth-limiting conditions, many bacteria are able to metabolise excess organic acids into polyhydroxyalkanoates (PHA) and store these polymers as intracellular inclusions until the return of favourable conditions. Various models have been proposed for the macromolecular organisation of the boundary layer surrounding the polymer, and contrast-variation small-angle neutron scattering (SANS) was used to study its organisation. Inclusions formed by Pseudomonas oleovorans under hydrogenating conditions showed lowest scattering intensity at ca. 20% D 2O. The inclusions consist of protein and membrane lipids in the boundary layer and polyhydroxyoctanoate (lipid) in the inclusion body. At 20% D 2O the contributions of lipids were contrast matched with the solvent, indicating that lipids contributed the bulk of the scattering intensity observed at other D 2O/H 2O ratios. These results are inconsistent with a model of the boundary layer which proposed outer and inner layers of crystalline protein lattice sandwiching a membrane lipid membrane layer [E.S. Stuart, R.W. Lenz, R.C. Fuller, Can J Microbiol 41(Suppl 1) (1995) 84-93], and is more consistent with a model consisting of a lipid monolayer containing embedded proteins [U. Pieper-furst, M.H. Madkour, F. Mayer, A. Steinbuchel, J. Bacteriol. 176 (1994) 4328-4337.] By altering the H/D content of the precursors, we were able to collect SANS data from preparations of both deuterated and H/D copolymer inclusions, where initial PHA produced was hydrogenated followed by deuteration. Deuterated inclusions showed minimum intensity above 90% D 2O/H 2O whereas the sequentially produced copolymer (assumed to be in a core/shell arrangement) displayed minimum scattering some 20% lower, which is consistent with the increased hydrogenation of the boundary layer expected from its synthesis during supply of hydrogenated followed by deuterated precursors.

  14. Investigating different filter and rescaling methods on simulated GRACE-like TWS variations for hydrological applications

    NASA Astrophysics Data System (ADS)

    Zhang, Liangjing; Dahle, Christoph; Neumayer, Karl-Hans; Dobslaw, Henryk; Flechtner, Frank; Thomas, Maik

    2016-04-01

    Terrestrial water storage (TWS) variations obtained from GRACE play an increasingly important role in various hydrological and hydro-meteorological applications. Since monthly-mean gravity fields are contaminated by errors caused by a number of sources with distinct spatial correlation structures, filtering is needed to remove in particular high frequency noise. Subsequently, bias and leakage caused by the filtering need to be corrected before the final results are interpreted as GRACE-based observations of TWS. Knowledge about the reliability and performance of different post-processing methods is highly important for the GRACE users. In this contribution, we re-assess a number of commonly used post-processing methods using a simulated GRACE-like gravity field time-series based on realistic orbits and instrument error assumptions as well as background error assumptions out of the updated ESA Earth System Model. Two non-isotropic filter methods from Kusche (2007) and Swenson and Wahr (2006) are tested. Rescaling factors estimated from five different hydrological models and the ensemble median are applied to the post-processed simulated GRACE-like TWS estimates to correct the bias and leakage. Since TWS anomalies out of the post-processed simulation results can be readily compared to the time-variable Earth System Model initially used as "truth" during the forward simulation step, we are able to thoroughly check the plausibility of our error estimation assessment and will subsequently recommend a processing strategy that shall also be applied to planned GRACE and GRACE-FO Level-3 products for hydrological applications provided by GFZ. Kusche, J. (2007): Approximate decorrelation and non-isotropic smoothing of time-variable GRACE-type gravity field models. J. Geodesy, 81 (11), 733-749, doi:10.1007/s00190-007-0143-3. Swenson, S. and Wahr, J. (2006): Post-processing removal of correlated errors in GRACE data. Geophysical Research Letters, 33(8):L08402.

  15. Modeling of ground albedo neutrons to investigate seasonal cosmic ray-induced neutron variations measured at high-altitude stations

    NASA Astrophysics Data System (ADS)

    Hubert, G.; Pazianotto, M. T.; Federico, C. A.

    2016-12-01

    This paper investigates seasonal cosmic ray-induced neutron variations measured over a long-term period (from 2011 to 2016) in both the high-altitude stations located in medium geomagnetic latitude and Antarctica (Pic-du-Midi and Concordia, respectively). To reinforce analysis, modeling based on ground albedo neutrons simulations of extensive air showers and the solar modulation potential was performed. Because the local environment is well known and stable over time in Antarctica, data were used to validate the modeling approach. A modeled scene representative to the Pic-du-Midi was simulated with GEANT4 for various hydrogen properties (composition, density, and wet level) and snow thickness. The orders of magnitudes of calculated thermal fluence rates are consistent with measurements obtained during summers and winters. These variations are dominant in the thermal domain (i.e., En < 0.5 eV) and lesser degree in epithermal and evaporation domains (i.e., 0.5 eV < En < 0.1 MeV and 0.1 MeV < En < 20 MeV, respectively). Cascade neutron (En > 20 MeV) is weakly impacted. The role of hydrogen content on ground albedo neutron generation was investigated with GEANT4 simulations. These investigations focused to mountain environment; nevertheless, they demonstrate the complexity of the local influences on neutron fluence rates.

  16. Investigation of pressure variations over stepped spillways using smooth particle hydrodynamics

    NASA Astrophysics Data System (ADS)

    Husain, Sarhang M.; Muhammed, Jowhar R.; Karunarathna, Harshinie U.; Reeve, Dominic E.

    2014-04-01

    In this paper the smoothed particle hydrodynamics, (SPH), technique is used to investigate the pressure distribution on steps located in the non-aerated flow region of a stepped spillway for different discharges typical of skimming flow conditions. The open source code 2D SPHysics has been employed after being validated against the laboratory model studies of flow over broad crested weirs and flow over stepped spillways. The numerical results, in terms of the water surface and velocity profiles at different sections, are in good agreement with the corresponding experimental results. The code is then applied to determine the pressure distribution on the vertical and horizontal step faces. Also, the aspects of the pressure pattern are described and the positions/magnitudes of the maximum and minimum pressure values are presented.

  17. Investigation of Li/Ca variations in aragonitic shells of the ocean quahog Arctica islandica, northeast Iceland

    NASA Astrophysics Data System (ADS)

    ThéBault, Julien; SchöNe, Bernd R.; Hallmann, Nadine; Barth, Matthias; Nunn, Elizabeth V.

    2009-12-01

    Interannual and intra-annual variations in lithium-to-calcium ratio were investigated with high temporal resolution in the aragonitic outer shell layer of juvenile Arctica islandica (Mollusca; Bivalvia) collected alive in 2006 off northeast Iceland. Li/Cashell ranged between 7.00 and 11.12 μmol mol-1 and presented well-marked seasonal cycles with minimum values recorded at the annual growth lines; a general pattern was a progressive increase in Li/Cashell from March to May, followed by a plateau in June and a decrease down to minimum values in July-August. Li/Cashell was correlated with δ18Oshell-derived temperature, but the strength of this relationship was weak (r2 < 0.25 and p < 0.05). It covaried significantly with microgrowth increment width and with the discharge from one of the closest rivers. Seasonal variations of Li/Cashell in A. islandica may most likely be explained (1) by calcification rate and/or (2) by significant river inputs of Li-rich silicate particles flowing to the sea as soon as snow melts. In the first case, Li/Cashell may be a useful proxy for addressing seasonal variations of growth rate in bivalves that lack discernable microgrowth patterns. Abrupt decreases of Li/Cashell may, in turn, help identify growth retardations due to harsh environmental conditions. Alternatively, if Li/Cashell variations are linked to particulate Li inputs by rivers, this could be a new proxy for the intensity of mechanical weathering of Icelandic basalts, with interesting perspectives for the reconstruction of frequency and intensity of past jökulhlaups (subglacial outburst floods). Further works, including experimental studies, are needed to test these hypotheses.

  18. Investigating the use of liquisolid compacts technique to minimize the influence of pH variations on loratadine release.

    PubMed

    El-Hammadi, Mazen; Awad, Nisrine

    2012-03-01

    Loratadine is a class II water-insoluble drug and its dissolution rate and, consequently, absorption are dependent on the gastrointestinal pH. The resulting very high variability in bioavailability and related inter- and intra-subject absorption variations present a major challenge that hinders the realization of an effective and uniform therapy. Among the several techniques that have been used to minimize pH dependency of dissolution rate, liquisolid compacts technique can be suggested as a promising solution. In this study, it was hypothesized that the formulation of loratadine using liquisolid compacts technique may reduce the effect of pH variation on the drug dissolution rate. Solubilities of loratadine in propylene glycol, Tween 80, and polyethylene glycol 400 were first measured and propylene glycol was selected as for producing the highest solubility among the tested solvents. Several liquisolid tablet formulations containing various ratios of drug: propylene glycol (5%, 10%, and 20% w/w) were prepared. The ratio of microcrystalline cellulose (carrier) to silica (coating powder material) was kept constant in all formulations. The dissolution behavior of loratadine from liquisolid compacts was investigated in several buffered media with different pH values (pH 1.2, 2.5, and 5). The results showed that the drug release rates produced by liquisolid compacts were significantly higher and less affected by pH variation compared with conventionally made (direct compression) and commercial (Clarityn) tablets. In conclusion, liquisolid compacts technique may be used as a tool to minimize the effects of pH variation on the dissolution rate of drugs with poor water solubility.

  19. Corticomuscular coherence variation throughout the gait cycle during overground walking and ramp ascent: A preliminary investigation.

    PubMed

    Winslow, Anna T; Brantley, Justin; Zhu, Fangshi; Contreras Vidal, Jose L; Huang, He

    2016-08-01

    Recent designs of neural-machine interfaces (NMIs) incorporating electroencephalography (EEG) or electromyography (EMG) have been used in lower limb assistive devices. While the results of previous studies have shown promise, a NMI which takes advantage of early movement-related EEG activity preceding movement onset, as well as the improved signal-to-noise ratio of EMG, could prove to be more accurate and responsive than current NMI designs based solely on EEG or EMG. Previous studies have demonstrated that the activity of the sensorimotor cortex is coupled to the firing rate of motor units in lower limb muscles during voluntary contraction. However, the exploration of corticomuscular coherence during locomotive tasks has been limited. In this study, coupling between the motor cortex and right tibialis anterior muscle activity was preliminarily investigated during self-paced over-ground walking and ramp ascent. EEG at the motor cortex and surface EMG from the tibialis anterior were collected from one able-bodied subject. Coherence between the two signals was computed and studied across gait cycles. The EEG activity led the EMG activity in the low gamma band in swing phase of level ground walking and in stance phase of ramp ascent. These results may inform the future design of EEG-EMG multimodal NMIs for lower limb devices that assist locomotion of people with physical disabilities.

  20. Dielectric engineered symmetric underlap double gate tunnel FET (DGTFET): An investigation towards variation of dielectric materials

    NASA Astrophysics Data System (ADS)

    Mallikarjunarao; Ranjan, Rajeev; Pradhan, K. P.; Sahu, P. K.

    2016-08-01

    In this article, an underlap silicon n-channel Tunnel Field Effect Transistor (n-TFET) i.e., symmetric single-k spacer (SSS) Double Gate N-TFET (DGTFET) is proposed to improve the performance of the device by using different spacer materials. A detailed investigation has been made on the proposed device characteristics with the help of extensive 2-D TCAD simulations. It is demonstrated that an optimized underlap length is chosen for a significant on-state current (Ion) without deteriorating the off-state current (Ioff) and sub-threshold swing (SS). The proposed model with different spacer materials has been extensively analyzed by using transfer characteristics, output characteristics, and analog/RF characteristics. The structure is optimized based on the comparison among various performance metrics like Ion, Ioff, SS, on-off ratio (Ion/Ioff), threshold (or) cut-off frequency (fT), and intrinsic delay with considering different spacer materials like SiO2 (k = 3.9), Si3N4 (k = 7.5), and HfO2 (k = 25).

  1. Investigation of modifier genes within copy number variations in Rett syndrome.

    PubMed

    Artuso, Rosangela; Papa, Filomena T; Grillo, Elisa; Mucciolo, Mafalda; Yasui, Dag H; Dunaway, Keith W; Disciglio, Vittoria; Mencarelli, Maria A; Pollazzon, Marzia; Zappella, Michele; Hayek, Giuseppe; Mari, Francesca; Renieri, Alessandra; Lasalle, Janine M; Ariani, Francesca

    2011-07-01

    MECP2 mutations are responsible for two different phenotypes in females, classical Rett syndrome and the milder Zappella variant (Z-RTT). We investigated whether copy number variants (CNVs) may modulate the phenotype by comparison of array-CGH data from two discordant pairs of sisters and four additional discordant pairs of unrelated girls matched by mutation type. We also searched for potential MeCP2 targets within CNVs by chromatin immunopreceipitation microarray (ChIP-chip) analysis. We did not identify one major common gene/region, suggesting that modifiers may be complex and variable between cases. However, we detected CNVs correlating with disease severity that contain candidate modifiers. CROCC (1p36.13) is a potential MeCP2 target, in which a duplication in a Z-RTT and a deletion in a classic patient were observed. CROCC encodes a structural component of ciliary motility that is required for correct brain development. CFHR1 and CFHR3, on 1q31.3, may be involved in the regulation of complement during synapse elimination, and were found to be deleted in a Z-RTT but duplicated in two classic patients. The duplication of 10q11.22, present in two Z-RTT patients, includes GPRIN2, a regulator of neurite outgrowth and PPYR1, involved in energy homeostasis. Functional analyses are necessary to confirm candidates and to define targets for future therapies.

  2. Investigation of 3-D lateral variations on seismic waveform modeling, in preparation for the InSight mission to Mars

    NASA Astrophysics Data System (ADS)

    Drilleau, M.; Dubois, A.; Blanchette-Guertin, J. F.; Kawamura, T.; Lognonne, P. H.

    2015-12-01

    In 2016, the InSight mission will provide the very first seismic records from Mars after installing a seismometer on the surface of the Red Planet. Obtaining information on the deep 1-D seismic structure of Mars using a single geophysical station will be challenging. However, successful test inversions using body and surface waves have been presented in a preliminary study by Panning et al. (2015). Future investigations need now to focus on inversions making a complete use of the seismic waveform. An important challenge is to investigate the effects of 3-D lateral variations of seismic velocity structures on seismograms. The HOPT (Higher Order Perturbation Theory) code originally developed by P. Lognonné and E. Clévédé (Lognonné, 1991 ; Lognonné and Clévédé, 2002) and based on the perturbation theory allows for the computation of synthetic seismograms in a 3-D Earth. We adapted the code for Mars and computed surface wave synthetics in a 3-D planet, initially only considering the effects of the planet's ellipticity as well as the lateral variations in the depth of the Moho which are known through gravity measurements (e.g. Neumann et al., 2004). Additional constraints from lateral variations in topography will be the focus of future work. These synthetics can be compared to future seismic data in order to identify a suite of Martian internal structure models that best match the data. To do so, we first need to estimate the resolvable parameters concerning the Mars deep interior while considering the 3-D effects, which is the main goal of this study. Furthermore, in preparation for the InSight mission data return phase, the computation of these synthetic (but realistic) seismograms is primordial to test the softwares developed by the InSight Mars Quake and Mars Structure Services (in charge of locating the seismic events, and using them to assess the internal structure of Mars).

  3. Structural Variation in Bacterial Glyoxalase I Enzymes: Investigation of the Metalloenzyme Glyoxalase I from Clostridium acetobutylicum

    SciTech Connect

    Suttisansanee U.; Swaminathan S.; Lau, K.; Lagishetty, S.; Rao, K. N.; Sauder, J. M.; Burley, S. K.; Honek, J. F.

    2011-11-04

    The glyoxalase system catalyzes the conversion of toxic, metabolically produced {alpha}-ketoaldehydes, such as methylglyoxal, into their corresponding nontoxic 2-hydroxycarboxylic acids, leading to detoxification of these cellular metabolites. Previous studies on the first enzyme in the glyoxalase system, glyoxalase I (GlxI), from yeast, protozoa, animals, humans, plants, and Gram-negative bacteria, have suggested two metal activation classes, Zn{sup 2+} and non-Zn{sup 2+} activation. Here, we report a biochemical and structural investigation of the GlxI from Clostridium acetobutylicum, which is the first GlxI enzyme from Gram-positive bacteria that has been fully characterized as to its three-dimensional structure and its detailed metal specificity. It is a Ni{sup 2+}/Co{sup 2+}-activated enzyme, in which the active site geometry forms an octahedral coordination with one metal atom, two water molecules, and four metal-binding ligands, although its inactive Zn{sup 2+}-bound form possesses a trigonal bipyramidal geometry with only one water molecule liganded to the metal center. This enzyme also possesses a unique dimeric molecular structure. Unlike other small homodimeric GlxI where two active sites are located at the dimeric interface, the C. acetobutylicum dimeric GlxI enzyme also forms two active sites but each within single subunits. Interestingly, even though this enzyme possesses a different dimeric structure from previously studied GlxI, its metal activation characteristics are consistent with properties of other GlxI. These findings indicate that metal activation profiles in this class of enzyme hold true across diverse quaternary structure arrangements.

  4. Genome-wide genetic and transcriptomic investigation of variation in antibody response to dietary antigens

    PubMed Central

    Rubicz, Rohina; Yolken, Robert; Alaedini, Armin; Drigalenko, Eugene; Charlesworth, Jac C.; Carless, Melanie A.; Severance, Emily G.; Krivogorsky, Bogdana; Dyer, Thomas D.; Kent, Jack W.; Curran, Joanne E.; Johnson, Matthew P.; Cole, Shelley A.; Almasy, Laura; Moses, Eric K.; Blangero, John; Göring, Harald H.H.

    2014-01-01

    Increased immunoglobulin G (IgG) response to dietary antigens can be associated with gastrointestinal dysfunction and autoimmunity. The underlying processes contributing to these adverse reactions remain largely unknown, and it is likely that genetic factors play a role. Here we estimate heritability and attempt to localize genetic factors influencing IgG antibody levels against food-derived antigens using an integrative genomics approach. IgG antibody levels were determined by ELISA in >1300 Mexican Americans for the following food antigens: wheat gliadin; bovine casein; and two forms of bovine serum albumin (BSA-a and BSA-b). Pedigree-based variance components methods were used to estimate additive genetic heritability (h2), perform genome-wide association analyses, and identify transcriptional signatures (based on 19,858 transcripts from peripheral blood lymphocytes). Heritability estimates were significant for all traits (0.15-0.53), and shared environment (based on shared residency among study participants) was significant for casein (0.09) and BSA-a (0.33). Genome-wide significant evidence of association was obtained only for antibody to gliadin (p=8.57×10-8), mapping to the human leukocyte antigen II region, with HLA-DRA and BTNL2 as the best candidate genes. Lack of association of known celiac disease risk alleles HLA-DQ2.5 and -DQ8 with anti-gliadin antibodies in the studied population suggests a separate genetic etiology. Significant transcriptional signatures were found for all IgG levels except BSA-b. These results demonstrate that individual genetic differences contribute to food antigen antibody measures in this population. Further investigations may elucidate the underlying immunological processes involved. PMID:24962563

  5. Real time investigation of the effect of thermal expansion coefficient mismatch on film-substrate strain partitioning in Ag/Si systems

    NASA Astrophysics Data System (ADS)

    Das, Debolina; Banu, Nasrin; Bisi, Bhaskar; Mahato, J. C.; Srihari, V.; Halder, Rumu; Dev, B. N.

    2016-10-01

    We have used X-ray diffraction (XRD) to investigate strain partitioning between an epitaxial layer and the substrate as a function of temperature, where the substrate (Si) and the epilayer material (Ag) have large thermal expansion coefficient (α) mismatch. The Ag/Si(111) system undergoes morphological changes upon heating, and the larger and taller islands are formed exposing more substrate surfaces. Sample heating was carried out under nitrogen flow. At >300 °C, the Si(111) diffraction peak splits into three. One of these components conforms to the thermal expansion of bulk Si. The other two components correspond to a highly nonlinear decrease and increase of Si-d(111) planar spacing. The decreasing component has been associated with strained Si under Ag and the increasing component with strained Si under SiO2, which has been formed partly prior to the XRD experiment and partly during sample heating. The opposite trends of these two Si-d(111) components are because of the larger value of α for Ag (7 times) and smaller for SiO2 (1/5th) compared to Si. The out-of-plane strain partitioning has been such that at room temperature, the Si substrate is unstrained and the strain in Ag is ˜0.3%. At 800 °C, Ag is practically relaxed, while Si under Ag is ˜-0.7% strained. A temperature dependent strain partitioning factor has been introduced to fit the data.

  6. Investigating Transition Zone Thickness Variation under the Arabian Plate: Evidence Lacking for Deep Mantle Upwellings

    NASA Astrophysics Data System (ADS)

    Juliá, J.; Tang, Z.; Mai, P. M.; Zahran, H.

    2014-12-01

    Cenozoic volcanic outcrops in Arabia - locally known as harrats - span more than 2000 km along the western half of the Arabian plate, from eastern Yemen to southern Syria. The magmatism is bimodal in character, with older volcanics (30 to 20 My) being tholeiitic-to-transitional and paralleling the Red Sea margin, and younger volcanics (12 Ma to Recent) being transitional-to-strongly-alkalic and aligning in a more north-south direction. The bimodal character has been attributed to a two-stage rifting process along the Red Sea, where the old volcanics would have produced from shallow sources related to an initial passive rifting stage, and young volcanics would have originated from one or more deep-seated mantle plumes driving present active rifting. Early models suggested the harrats would have resulted from either lateral flow from the Afar plume in Ethiopia, or more locally from a separate mantle plume directly located under the shield. Most recently, tomographic images of the Arabian mantle have suggested the northern harrats could be resulting from flow originating at a deep plume under Jordan. In this work, we investigate the location of deep mantle plumes under the Arabian plate by mapping transition zone thickness with teleseismic receiver functions. The transition zone is bounded by seismic discontinuities, nominally at 410 and 660 km depth, originating from phase transitions in the olivine-normative component of the mantle. The precise depth of the discontinuities is strongly dependent on temperature and, due to the opposing signs of the corresponding Clapeyron slopes, positive temperature anomalies are expected to result in thinning of the transition zone. Our dataset consists of ~5000 low-frequency (fc < 0.25 Hz) receiver function waveforms obtained at ~110 broadband stations belonging to a number of permanent and temporary seismic networks in the region. The receiver functions were migrated to depth and stacked along a ~2000 km long record section

  7. Phylogenetic Identification, Phenotypic Variations, and Symbiotic Characteristics of the Peculiar Rhizobium, Strain CzR2, Isolated from Crotalaria zanzibarica in Taiwan

    PubMed Central

    Huang, Cheng-Tai; Liu, Chi-Te; Chen, Shiang-Jiuun; Kao, Wen-Yuan

    2016-01-01

    Crotalaria zanzibarica is an exotic and widely distributed leguminous plant in Taiwan. The relationship between C. zanzibarica and its rhizobial symbionts has been suggested to contribute to its successful invasion. A rhizobial strain (designed as CzR2) isolated from the root nodules of C. zanzibarica and cultivated in standard YEM medium displayed pleomorphism, with cells ranging between 2 and 10 μm in length and some branching. In the present study, we identified this rhizobial strain, investigated the causes of pleomorphism, and examined the nodules formed. The results of a multilocus sequence analysis of the atpD, dnaK, glnII, gyrB, recA, and rpoB genes revealed that CzR2 belongs to Bradyrhizobium arachidis, a peanut symbiont recently isolated from China. Cells of the strain were uniformly rod-shaped in basal HM medium, but displayed pleomorphism in the presence of yeast extract, mannitol, or fructose. These results indicate that the morphology of CzR2 in its free-living state is affected by nutrient conditions. Several highly pleomorphic bacteroids enclosed in symbiosomes were frequently detected in FM and TEM observations of sections of the indeterminate nodules induced by CzR2; however, no infection thread was identified. Flow cytometric analyses showed that CzR2 cells in YEM medium and in the nodules of C. zanzibarica had two or more than two peaks in relative DNA contents, respectively, suggesting that the elongated cells of CzR2 in its free-living state occur due to a cell cycle-delayed process, while those in its symbiotic state are from genomic endo-reduplication. PMID:27682803

  8. Investigation of the antitrypanosomal activity of Buchholzia coriacea seed extract against a field strain of Trypanosoma congolense.

    PubMed

    Nweze, N E; Anene, B M; Asuzu, I U

    2011-01-01

    The antitrypanosomal activity of the methanol extract of Buchholzia coriacea seed against a field strain of Trypanosoma congolense was investigated using experimentally infected mice of both sexes. Monitoring of parasitaemia was by the rapid matching technique. When parasitaemia was approximately log 7.8 (63 × 10(6) parasites/ml), treatment with graded doses of the extract (250, 500 and 1000 mg/kg) was instituted for 5 consecutive days. Diminazene diaceturate (Dimivet SKM Pharma Pvt. Ltd.) was given at 3.5 mg/kg i.p. to the positive control mice. No significant differences in body weights were observed. The rectal temperatures of infected mice showed fluctuations. The PCV of infected mice were significantly (p < 0.05) lower than those of the uninfected controls. There was no significant difference between the PCV of the extract-treated and untreated animals. Parasitaemia increased steadily in the extract-treated and untreated mice groups till all the animals died. Three days post-treatment with diminazene diaceturate parasitaemia was cleared. Six days later, there was a relapse of infection. By the end of the experiment, a 50 % relapse rate was recorded in the diminazene diaceturate-treated group. The methanol extract of Buchholzia coriacea seeds did not show any antitrypanosomal activity in mice infected with Trypanosoma congolense at the doses tested.

  9. A Numerical Investigation of the Extinction of Low Strain Rate Diffusion Flames by an Agent in Microgravity

    NASA Technical Reports Server (NTRS)

    Puri, Ishwar K.

    2004-01-01

    Our goal has been to investigate the influence of both dilution and radiation on the extinction process of nonpremixed flames at low strain rates. Simulations have been performed by using a counterflow code and three radiation models have been included in it, namely, the optically thin, the narrowband, and discrete ordinate models. The counterflow flame code OPPDIFF was modified to account for heat transfer losses by radiation from the hot gases. The discrete ordinate method (DOM) approximation was first suggested by Chandrasekhar for solving problems in interstellar atmospheres. Carlson and Lathrop developed the method for solving multi-dimensional problem in neutron transport. Only recently has the method received attention in the field of heat transfer. Due to the applicability of the discrete ordinate method for thermal radiation problems involving flames, the narrowband code RADCAL was modified to calculate the radiative properties of the gases. A non-premixed counterflow flame was simulated with the discrete ordinate method for radiative emissions. In comparison with two other models, it was found that the heat losses were comparable with the optically thin and simple narrowband model. The optically thin model had the highest heat losses followed by the DOM model and the narrow-band model.

  10. Investigation and optimization of intraband electromagnetically induced transparency in strained InAs quantum dot/wetting layer structures

    NASA Astrophysics Data System (ADS)

    Parvizi, R.; Rezaei, G.

    2016-01-01

    In this work, effects of the shape and size on the optical properties and optimization of the intersubband electromagnetically induced transparency in the Infra-red region of three-dimensional strained truncated pyramid-shaped InAs/GaAs quantum dot (QD) were investigated in detail. More precisely, within the density matrix approach, the probe absorption and group velocity along with the refractive index of the medium were studied with respect to their dependence on the dephasing rates and the Rabi frequencies of the probe and coupling fields for different QD heights and wetting layer (WL) thicknesses. It is found that the slow-down factors, group index, and absorption coefficient are inversely proportional to the width of the transparency window and proportional to the depth of the transparency window. The optimized transparency window can be achieved by varying the dot height and the WL thickness such that the tall dots with thin WL thickness induce significant enhancements at a fixed resonant peak position of Rabi frequency of the coupling field. The physical reasons behind these interesting phenomena were also explained based on the polarized features of intersubband transitions.

  11. Study on biodegradation of Mazut by newly isolated strain Enterobacter cloacae BBRC10061: improving and kinetic investigation

    PubMed Central

    2013-01-01

    Mazut as a source content of various hydrocarbons is hard to be degraded and its cracking could turn mazut into useful materials. Nevertheless degradation of mazut by routine methods is too expensive but application of indigenous microorganisms as biocatalysts could be effective and important to lower the costs and expand its consumption. Mazut biodegradation can be improved using various strategies; Therefore in this study newly isolated strain Enterobacter cloacae BBRC 10061 was used in a method of gradual addition of mazut into medium and its results were compared with simple addition method. To investigate degradation of mazut by BBRC 10061, influence of increase of mazut concentration was assayed based on gradual addition method. Also different kinetic models were used to evaluate kinetics of the process. Results showed that gradual addition method has been a beneficial technique for improvement of mazut degradation because bacterial induction to produce biosurfactant and essential enzymes for cracking mazut was higher during process. Although addition of more mazut increased the rate of biodegradation but percentage of degradation decreased. pH of medium decreased during biodegradation period while electric potential increased. Also the biodegradation kinetics was not fitted with the biokinetic models; therefore kinetics of biodegradation of mazut has to be studied by new models. PMID:23369455

  12. Investigation of temperature and barometric pressure variation effects on radon concentration in the Sopronbánfalva Geodynamic Observatory, Hungary.

    PubMed

    Mentes, Gyula; Eper-Pápai, Ildikó

    2015-11-01

    Radon concentration variation has been monitored since 2009 in the artificial gallery of the Sopronbánfalva Geodynamic Observatory, Hungary. In the observatory, the radon concentration is extremely high, 100-600 kBq m(-3) in summer and some kBq m(-3) in winter. The relationships between radon concentration, temperature and barometric pressure were separately investigated in the summer and winter months by Fast Fourier Transform, Principal Component Analysis, Multivariable Regression and Partial Least Square analyses in different frequency bands. It was revealed that the long-period radon concentration variation is mainly governed by the temperature (20 kBq m(-1) °C(-1)) both in summer and winter. The regression coefficients between long-period radon concentration and barometric pressure are -1.5 kBq m(-3) hPa(-1) in the summer and 5 kBq m(-3) hPa(-1) in the winter months. In the 0.072-0.48 cpd (cycles per day) frequency band the effect of the temperature is about -1 kBq m(-3) °C(-1) and that of the barometric pressure is -5 kBq m(-3) hPa(-1) in summer and -0.5 kBq m(-3) hPa(-1) in winter. In the high frequency range (>0.48 cpd) all regression coefficients are one order of magnitude smaller than in the range of 0.072-0.48 cpd. Fast Fourier Transform of the radon concentration, temperature and barometric pressure time series revealed S1, K1, P1, S2, K2, M2 tidal constituents in the data and weak O1 components in the radon concentration and barometric pressure series. A detailed tidal analysis, however, showed that the radon tidal components are not directly driven by the gravitational force but rather by solar radiation and barometric tide. Principal Component Analysis of the raw data was performed to investigate the yearly, summer and winter variability of the radon concentration, temperature and barometric pressure. In the summer and winter periods the variability does not change. The higher variability of the radon concentration compared to the variability of

  13. Secular Variation in the Storage and Dissipation of Elastic Strain Energy Along the Central Altyn Tagh Fault (86-88.5°E), NW China

    NASA Astrophysics Data System (ADS)

    Cowgill, E.; Gold, R. D.; Arrowsmith, R.; Friedrich, A. M.

    2015-12-01

    In elastic rebound theory, hazard increases as interseismic strain rebuilds after rupture. This model is challenged by the temporal variation in the pacing of major earthquakes that is both predicted by mechanical models and suggested by some long paleoseismic records (e.g., 1-3). However, the extent of such behavior remains unclear due to a lack of long (5-25 ky) records of fault slip. Using Monte Carlo analysis of 11 offset landforms, we determined a 16-ky record of fault slip for the active, left-lateral Altyn Tagh fault, which bounds the NW margin of the Tibetan Plateau. This history reveals a pulse of accelerated slip between 6.4 and 6.0 ka, during which the fault slipped 9 +14/-2 m at a rate of 23 +35/-5 mm/y, or ~3x the 16 ky average of 8.1 +1.2/-0.9mm/y. These two modes of earthquake behavior suggest temporal variation in the rates of stress storage and release. The simplest explanation for the pulse is a cluster of 2-8 Mw > 7.5 earthquakes. Such supercyclicity has been reported for the Sunda (4) and Cascadia (3) megathrusts, but contrasts with steady slip along the strike-slip Alpine fault (5), for example. A second possibility is that the pulse reflects a single, unusually large rupture. However, this Black Swan event is unlikely: empirical scaling relationships require a Mw 8.2 rupture of the entire 1200-km-long ATF to produce 7 m of average slip. Likewise, Coulomb stress change from rupture on the adjacent North Altyn fault is of modest magnitude and overlap with the ATF. Poor temporal correlation between precipitation and the slip pulse argues against climatically modulated changes in surface loading (lakes/ice) or pore-fluid pressure. "Paleoslip" studies such as this sacrifice the single-event resolution of paleoseismology in exchange for long records that quantify both the timing and magnitude of fault slip averaged over multiple ruptures, and are essential for documenting temporal variations in fault slip as we begin to use calibrated physical

  14. Independent variation and positive selection in env V1 and V2 domains within maternal-infant strains of human immunodeficiency virus type 1 in vivo.

    PubMed Central

    Lamers, S L; Sleasman, J W; She, J X; Barrie, K A; Pomeroy, S M; Barrett, D J; Goodenow, M M

    1993-01-01

    Multiple targets for immune recognition and cellular tropism are localized to the V1 and V2 hypervariable regions in the amino portion of human immunodeficiency virus type 1 (HIV-1) gp120env. We have assessed genetic diversity in env V1 and V2 hypervariable domains in vivo within epidemiologically related strains of HIV-1. Our strategy was to analyze longitudinal samples from two seropositive mothers and multiple children infected by perinatal transmission. Although the V1 and V2 domains are closely linked in the HIV-1 genome, nucleotide sequences in V1 and in V2 evolved independently in maternal-infant viruses in vivo. A high proportion of the nucleotide substitutions would introduce amino acid diversity in V1 and in V2. A significant excess of nonsynonymous over synonymous substitutions was identified in HIV-1 env V1 and V2 peptides in the mothers and in two older children but was not generally apparent in HIV-1 sequences in infants. An excess of nonsynonymous over synonymous substitutions indicated that there is positive selection for independent genetic variation in the V1 and V2 domains in vivo. It is likely that there are host responses to complex determinants in the V1 or V2 hypervariable domain of HIV-1 gp120. PMID:8510212

  15. Haemophilus influenzae strains possess variations in the global transcriptional profile in response to oxygen levels and this influences sensitivity to environmental stresses.

    PubMed

    Jiang, Donald; Tikhomirova, Alexandra; Kidd, Stephen P

    2016-01-01

    An alcohol dehydrogenase, AdhC, is required for Haemophilus influenzae Rd KW20 growth with high oxygen. AdhC protects against both exogenous and metabolically generated, endogenous reactive aldehydes. However, adhC in the strain 86-028NP is a pseudogene. Unlike the Rd KW20 adhC mutant, 86-028NP does grow with high oxygen. This suggests the differences between Rd KW20 and 86-028NP include broader pathways, such as for the maintenance of redox and metabolism that avoids the toxicity related to oxygen. We hypothesized that these differences affect their resistance to relevant toxic chemicals, including reactive aldehydes. Across a range of oxygen concentrations, despite the growth profiles of Rd KW20 and 86-028NP being similar, there was a significant variation in their sensitivity to reactive aldehydes. 86-028NP is more sensitive to methylglyoxal, formaldehyde and glycolaldehyde under high oxygen than low oxygen as well as compared to Rd KW20. Also, as oxygen levels changed the whole genome gene expression profiles of Rd KW20 and 86-028NP revealed distinctions in their transcriptomes (the iron, FNR and ArcAB regulons). These were indicative of a difference in their intracellular redox properties and we show it is this that underpins their survival against reactive aldehydes.

  16. Investigation of Control System and Display Variations on Spacecraft Handling Qualities for Docking with Stationary and Rotating Targets

    NASA Technical Reports Server (NTRS)

    Jackson, E. Bruce; Goodrich, Kenneth H.; Bailey, Randall E.; Barnes, James R.; Ragsdale, William A.; Neuhaus, Jason R.

    2010-01-01

    This paper documents the investigation into the manual docking of a preliminary version of the Crew Exploration Vehicle with stationary and rotating targets in Low Earth Orbit. The investigation was conducted at NASA Langley Research Center in the summer of 2008 in a repurposed fixed-base transport aircraft cockpit and involved nine evaluation astronauts and research pilots. The investigation quantified the benefits of a feed-forward reaction control system thruster mixing scheme to reduce translation-into-rotation coupling, despite unmodeled variations in individual thruster force levels and off-axis center of mass locations up to 12 inches. A reduced rate dead-band in the phase-plane attitude controller also showed some promise. Candidate predictive symbology overlaid on a docking ring centerline camera image did not improve handling qualities, but an innovative attitude status indicator symbol was beneficial. The investigation also showed high workload and handling quality problems when manual dockings were performed with a rotating target. These concerns indicate achieving satisfactory handling quality ratings with a vehicle configuration similar to the nominal Crew Exploration Vehicle may require additional automation.

  17. Insight into proteomic investigations of Neisseria meningitidis serogroup C strain L91543 from analysis of its genome sequence.

    PubMed

    Karlyshev, Andrey V; Snyder, Lori A S; McFadden, Johnjoe; Griffin, Ruth

    2015-05-01

    Here, we describe the draft sequence of a virulent isolate of Neisseria meningitidis strain L91543, belonging to serogroup C. The findings from previous proteomic and metabolomic studies of this strain can now be further interpreted with genomic analysis. Comparative analysis of the genome sequence revealed close similarity and localized synteny with the genome sequence of N. meningitidis serogroup C strain, FAM18. Polymorphisms were identified in the signal peptide sequence of factor H binding protein, a target for new meningococcal vaccines, which may result in its inefficient translocation across the cytoplasmic membrane affecting its processing (lipidation and cleavage of the signal peptide) and transportation to the outer membrane in strain L91543. This would explain the unusual proteomic data for factor H binding protein for this strain. NadA, another target for new vaccines, and the MtrR regulator, which controls expression of NadA, both contain SNPs between strains L91543 and FAM18. The genome sequence data were generated using Ion Torrent PGM sequencing, assembled into 50 contigs with 64× coverage and annotated with 2262 genes, 14 rRNAs and 56 tRNAs. The availability of the genome of N. meningitidis strain L91543 will aid our understanding of the proteome of this organism, importantly its vaccine antigens.

  18. Design and performance investigation of a highly accurate apodized fiber Bragg grating-based strain sensor in single and quasi-distributed systems.

    PubMed

    Ali, Taha A; Shehata, Mohamed I; Mohamed, Nazmi A

    2015-06-01

    In this work, fiber Bragg grating (FBG) strain sensors in single and quasi-distributed systems are investigated, seeking high-accuracy measurement. Since FBG-based strain sensors of small lengths are preferred in medical applications, and that causes the full width at half-maximum (FWHM) to be larger, a new apodization profile is introduced for the first time, to the best of our knowledge, with a remarkable FWHM at small sensor lengths compared to the Gaussian and Nuttall profiles, in addition to a higher mainlobe slope at these lengths. A careful selection of apodization profiles with detailed investigation is performed-using sidelobe analysis and the FWHM, which are primary judgment factors especially in a quasi-distributed configuration. A comparison between the elite selection of apodization profiles (extracted from related literature) and the proposed new profile is carried out covering the reflectivity peak, FWHM, and sidelobe analysis. The optimization process concludes that the proposed new profile with a chosen small length (L) of 10 mm and Δnac of 1.4×10-4 is the optimum choice for single stage and quasi-distributed strain-sensor networks, even better than the Gaussian profile at small sensor lengths. The proposed profile achieves the smallest FWHM of 15 GHz (suitable for UDWDM), and the highest mainlobe slope of 130 dB/nm. For the quasi-distributed scenario, a noteworthy high isolation of 6.953 dB is achieved while applying a high strain value of 1500 μstrain (με) for a five-stage strain-sensing network. Further investigation was undertaken, proving that consistency in choosing the apodization profile in the quasi-distributed network is mandatory. A test was made of the inclusion of a uniform apodized sensor among other apodized sensors with the proposed profile in an FBG strain-sensor network.

  19. Strain gradient development in 3-dimensional extracellular matrix scaffolds during in vitro mechanical stimulation.

    PubMed

    Seifer, Benjamin J; Wagner, Christopher T

    2017-01-01

    This study analyzed strain variations in 3D ECM scaffolds using a membrane-adherent model (MM) and a direct elongation model (DM). Computational models were solved for target strains from 1 to 10% at varied scaffold thicknesses and intra-scaffold slices. DM strain profiles were uniform within the scaffold and independent of thickness. However, a wide range of strains developed with substantial volume experiencing significantly off-target strain. MM strain profiles varied throughout the scaffold, exhibiting significantly reduced average strain with increasing thickness. These findings are important for tissue engineering studies since biological responses are commonly attributed to a single strain level that only partially describes the mechanical condition, making it difficult to develop precise causal relationships. Spatial strain variations and reduced average strain may warrant targeted sampling for cell response and should be taken into consideration by investigators using large-volume 3D scaffolds when engineering mechanically sensitive tissues.

  20. Investigation of the spatiotemporal variation and influencing factors on fine particulate matter and carbon monoxide concentrations near a road intersection

    NASA Astrophysics Data System (ADS)

    Wang, Zhanyong; Lu, Qing-Chang; He, Hong-Di; Wang, Dongsheng; Gao, Ya; Peng, Zhong-Ren

    2017-03-01

    The minute-scale variations of fine particulate matter (PM2.5) and carbon monoxide (CO) concentrations near a road intersection in Shanghai, China were investigated to identify the influencing factors at three traffic periods. Measurement results demonstrate a synchronous variation of pollutant concentrations at the roadside and setbacks, and the average concentration of PM2.5 at the roadside is 7% (44% for CO) higher than that of setbacks within 500 m of the intersection. The pollution level at traffic peak periods is found to be higher than that of off-peak periods, and the morning peak period is found to be the most polluted due to a large amount of diesel vehicles and unfavorable dispersion conditions. Partial least square regressions were constructed for influencing factors and setback pollutant concentrations, and results indicate that meteorological factors are the most significant, followed by setback distance from the intersection and traffic factors. CO is found to be sensitive to distance from the traffic source and vehicle type, and highly dependent on local traffic conditions, whereas PM2.5 originates more from other sources and background levels. These findings demonstrate the importance of localized factors in understanding spatiotemporal patterns of air pollution at intersections, and support decision makers in roadside pollution management and control.

  1. Palaeomagnetic investigations on lake sediments from NE China: a new record of geomagnetic secular variations for the last 37 ka

    NASA Astrophysics Data System (ADS)

    Frank, Ute

    2007-04-01

    Detailed palaeomagnetic investigations were carried out on two 23 m long sediment cores from Erlongwan maar lake, NE China. The sediment composition of both cores is nearly identical. Based on a macroscopical inspection of the cores 410 graded layers intercalated into the laminated sediments were identified. Measurements of the anisotropy of the magnetic susceptibility revealed that these layers have not disturbed the sediment structure in general, but only in intervals where their thicknesses exceeds 50 cm. The age model for Erlongwan is based on 15 AMS 14C-datings on bulk sediment, showing that the sediment profile spans the last 37 ka cal BP. Although one of the sediment cores has been slightly deformed during core recovery, similar inclination and declination records could be obtained by standard palaeomagnetic methods. The stacked inclination and declination records show both variations similar to those known from palaeosecular variation records from Eastern China and Japan. Therefore, the presented study is a contribution to the ongoing process of compiling a PSV mastercurve for East Asia.

  2. Variation in susceptibility of field strains of three stored grain insect species to spinosad and chlorpyrifos-methyl plus deltamethrin on hard red winter wheat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Spinosad and chlorpyrifos-methyl plus deltamethrin efficacy at labeled rates on hard red winter wheat was evaluated against 11 strains of the red flour beetle, Tribolium castaneum (Herbst); six strains of the sawtoothed grain beetle, Oryzaephilus surinamensis (L.); and two strains of the lesser grai...

  3. Experimental investigation of the inlet detector configuration variation in the flow field at Mach 1.9

    NASA Technical Reports Server (NTRS)

    Hwang, Kyu C.; Tiwari, Surrendra N.; Miley, Stanley J.

    1995-01-01

    In recent years, active research has been conducted to study the technological feasibility of supersonic laminar flow control on the wing of the High Speed Civil Transport (HSCT). For this study, the F-16XL has been chosen due to its highly swept crank wing planform that closely resembles the HSCT configurations. During flights, it is discovered that the shock wave generated from the aircraft inlet introduces disturbances on the wing where the data acquisition is conducted. The flow field about a supersonic inlet is characterized by a complex three dimensional pattern of shock waves generated by the geometrical configuration of a deflector and a cowl lip. Hence, in this study, experimental method is employed to investigate the effects of the variation of deflector configuration on the flow field, and consequently, the possibility of diverting the incoming shock-disturbances away from the test section. In the present experiments, a model composed of a simple circular tube with a triangular deflector is designed to study the deflector length and the deflector base width variation in the flow field. Experimental results indicate that the lowest external pressure ratio is observed at the junction where the deflector lip and the inlet cowl lip merge. Also, it is noted that the external pressure ratio, the internal pressure ratio, the coefficient of spillage drag, and the shock standoff distance decrease as the deflector length increases. In addition, the Redefined Total Pressure Recovery Ratio (RTPRR) increases with an increase in the deflector length. Results from the study of the effect of the deflector's base width variation on the flow field indicate that the lowest external pressure ratio is observed at the junction between the inlet cowl lip and the deflector lip. As the base width of the deflector increases, the external pressure ratio at 0 rotation increases, whereas the external pressure ratio at 180 rotation decreases. In addition, the internal pressure ratio

  4. Verification of CH4 on Mars and investigation of its temporal and spatial variations by SOFIA/EXES

    NASA Astrophysics Data System (ADS)

    Aoki, Shohei

    2015-10-01

    Discovery of CH4 in the Martian atmosphere has led to much discussion since it could be a signature of on-going and/or past biological/geological activities on Mars. However, the presence of CH4 and its temporal and spatial variations are still under discussion because previous observations had large uncertainties. We propose sensitive measurements of the Martian CH4 by SOFIA/EXES in order to verify the presence and investigate its temporal and spatial variation. Our primal goal is to demonstrate the firm detection of CH4 on Mars. SOFIA/EXES allows us to perform sensitive observations of the Martian CH4 from the Earth using the 7.5 um band. The high altitude of SOFIA telescope (~12 km) enables us to significantly reduce the effects of terrestrial atmosphere, and high spectral resolution of EXES (R~90,000) enables us to detect the tiny lines of the Martian CH4. We request to perform weekly observations of CH4 by SOFIA/EXES during larger Doppler-shift period (between Feb./2016-March/2016). The large Doppler shift (-14.3 - -17.3 km/s) allows us to separate the Martian and terrestrial CH4 lines. In addition, owing to the relatively large diameter of the SOFIA telescope (~ 2.5 m), geographical distribution of CH4 (3 x 3 areas over the Martian disk) can be investigated. Last but not least, we plan to perform joint observations with (1) the spacecraft-borne MEX/PFS, (2) the ground-based T60/MILAHI, (3) ground-based IRTF/CSHELL, and (4) in-situ Curiosity/TLS. Combination of the current best instruments for the joint observations provide definitive confirmation of the presence (or absence) of CH4, and clues to search for the source.

  5. Investigation of the Amycolatopsis sp. strain ATCC 39116 vanillin dehydrogenase and its impact on the biotechnical production of vanillin.

    PubMed

    Fleige, Christian; Hansen, Gunda; Kroll, Jens; Steinbüchel, Alexander

    2013-01-01

    The actinomycete Amycolatopsis sp. strain ATCC 39116 is capable of synthesizing large amounts of vanillin from ferulic acid, which is a natural cell wall component of higher plants. The desired intermediate vanillin is subject to undesired catabolism caused by the metabolic activity of a hitherto unknown vanillin dehydrogenase (VDH(ATCC 39116)). In order to prevent the oxidation of vanillin to vanillic acid and thereby to obtain higher yields and concentrations of vanillin, the responsible vanillin dehydrogenase in Amycolatopsis sp. ATCC 39116 was investigated for the first time by using data from our genome sequence analysis and further bioinformatic approaches. The vdh gene was heterologously expressed in Escherichia coli, and the encoded vanillin dehydrogenase was characterized in detail. VDH(ATCC 39116) was purified to apparent electrophoretic homogeneity and exhibited NAD(+)-dependent activity toward vanillin, coniferylaldehyde, cinnamaldehyde, and benzaldehyde. The enzyme showed its highest level of activity toward vanillin at pH 8.0 and at a temperature of 44°C. In a next step, a precise vdh deletion mutant of Amycolatopsis sp. ATCC 39116 was generated. The mutant lost its ability to grow on vanillin and did not show vanillin dehydrogenase activity. A 2.3-times-higher vanillin concentration and a substantially reduced amount of vanillic acid occurred with the Amycolatopsis sp. ATCC 39116 Δvdh::Km(r) mutant when ferulic acid was provided for biotransformation in a cultivation experiment on a 2-liter-bioreactor scale. Based on these results and taking further metabolic engineering into account, the Amycolatopsis sp. ATCC 39116 Δvdh::Km(r) mutant represents an optimized and industrially applicable platform for the biotechnological production of natural vanillin.

  6. Investigation of the Workability and Response of Ti-6Al-4V Titanium alloys at Lower Elevated Temperature and Higher Strain Rate

    SciTech Connect

    Huang, Cindy Xiaohui; Lim, Chao Voon; Castagne, Sylvie

    2011-05-04

    Titanium and its alloys have a wide range of applications in various industries such as aerospace, medical, automotive and even commercial products. However, formability of titanium alloys has always been an issue. This study presents the results of an investigation on the workability and response of Ti-6Al-4V deformed at different strain rates and lower elevated temperatures with different initial microstructures. Compression tests of cylindrical specimens were performed at various temperatures (300 deg. C, 400 deg. C, 450 deg. C, 500 deg. C) and at different strain rates (0.001 s{sup -1}, 0.02 s{sup -1} and 0.1 s{sup -1}). The effects of strain rate, temperature and initial microstructure on the workability of the Ti alloy were investigated. Based on these experimental results, workability maps for the respective initial microstructures were developed. Results showed that temperature played an important role in the formability of Ti-6Al-4V titanium alloys unlike strain rate. In addition, feasibility study on Multi-Directional Forging (MDF) was performed and positive results were obtained. It was demonstrated that Ti-6Al-4V titanium alloys can undergo severe plastic deformation at lower elevated temperature (400-500 deg. C) and at a higher strain rate of 0.1 s{sup -1}.

  7. Investigating the Levels of Strain, from the Point of Various Variables, at Their Efforts of Obtain Information of Preservice Teachers' of Secondary Education

    ERIC Educational Resources Information Center

    Adiguzel, Abdullah

    2012-01-01

    The aim of this study is investigating the Levels of Strain, From the Point of Various Variables (according to gender, branch, working at a job which provides financial gain, the reason to prefer the teaching profession, the number of digests of related field which have been followed, the frequency of weekly using internet, the aim of using…

  8. Investigation of environmental factors on the prevalence of free bacteriophages against Shiga toxin-producing Escherichia coli strains in produce pre-harvest environment in Salinas, California

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Investigation of environmental factors on the prevalence of free bacteriophages against Shiga toxin-producing Escherichia coli strains in produce pre-harvest environment in Salinas, California Yen-Te Liaoa, Irwin Quintelab, Kimberly Nguyena, Alexandra Salvadora, Michael Cooleya, and Vivian C.H. Wu*a...

  9. Marked intra-strain variation in response of Listeria monocytogenes dairy isolates to acid or salt stress and the effect of acid or salt adaptation on adherence to abiotic surfaces.

    PubMed

    Adrião, A; Vieira, M; Fernandes, I; Barbosa, M; Sol, M; Tenreiro, R P; Chambel, L; Barata, B; Zilhao, I; Shama, G; Perni, S; Jordan, S J; Andrew, P W; Faleiro, M L

    2008-03-31

    During food processing, and particularly in cheese manufacturing processes, Listeria monocytogenes may be exposed routinely to environments of low pH or high salt concentration. It has been suggested that these environmental conditions may contribute to bacterial adherence to abiotic surfaces and increased resistance to disinfection. In this study strains isolated from the environment of artisanal cheese-making dairies were used to investigate the behaviour of L. monocytogenes in response to acid and salt stress and clear differences between strains was observed. In planktonic culture, strains varied in resistance to low pH or high NaCl concentration and in the occurrence of an adaptive response to moderate acid or NaCl. There was dislocation in responses to salt and acid. Strains resistant, or adaptive, to acid were not resistant or adaptive to NaCl. The reverse also was observed. Exposure to moderate acid did not promote adherence to polystyrene but survival, at low pH or high NaCl concentration, of cells adherent to stainless steel was increased, even for strains that had no adaptive response planktonically, but the detail of these observations varied between strains. In contrast to acid adaptation, with some strains salt adaptation enhanced adherence of L. monocytogenes to polystyrene but this was not true for all strains. For some strains salt- or acid adaptation may enhance the survival of sessile cells exposed to hypochlorite disinfection.

  10. Isolation and identification of new lactobacilli from goatling stomach and investigation of reuterin production in Lactobacillus reuteri strains.

    PubMed

    Kiňová Sepová, Hana; Bilková, Andrea

    2013-01-01

    Five new strains of lactobacilli isolated from goatling's stomach were identified by molecular-biological approaches. Profiles of fermentable saccharides, Gram staining, and cell morphology were also determined. They were identified as Lactobacillus reuteri (strains KO4b, KO4m, KO5) and as Lactobacillus plantarum (strains KG1z, KG4). In DNA samples of all newly isolated L. reuteri strains as well as in L. reuteri E (Lreu E; originated from lamb), the part of gldC gene, coding large subunit of glycerol dehydratase, that is necessary for 3-hydroxypropionaldehyde (3-HPA; reuterin) production, was amplified using two designed primer sets. However, the 3-HPA production was revealed only in the strain Lreu E. It produced five- or ten-fold lower amount of 3-HPA in comparison with probiotic L. reuteri ATCC 55730 in aerobic or anaerobic conditions, respectively. Moreover, Lreu E completely lost its production ability after ca. five passages in MRS medium. The co-incubation of Lreu E, but not other L. reuteri isolates, with Escherichia coli re-induced 3-HPA production. In the case of L. reuteri ATCC 55730, the 3-HPA production increased more than four times after co-incubation with E. coli.

  11. Child Maltreatment, Inflammation, and Internalizing Symptoms: Investigating the Roles of C-Reactive Protein, Gene Variation and Neuroendocrine Regulation

    PubMed Central

    Cicchetti, Dante; Handley, Elizabeth D.; Rogosch, Fred A.

    2015-01-01

    Prior research has found inconsistent evidence regarding the association among childhood adversity, inflammation, and internalizing symptoms, perhaps because previous studies have yet to adequately integrate important factors such as the timing of the adversity, genetic variation, and other relevant processes such as neuroendocrine regulation. The aims of the present study were threefold: 1) Determine whether the effect of the timing of child maltreatment on C-reactive protein (CRP), an inflammatory marker, varies by CRP gene variation; 2) Explore whether links between salivary CRP and childhood internalizing symptoms depend on the presence and timing of maltreatment experiences; 3) Investigate the role of CRP in the relations between child neuroendocrine regulation and internalizing symptoms and examine whether these associations are moderated by the presence and timing of child maltreatment. Participants included a sample of 267 maltreated and 222 nonmaltreated children (M age= 9.72, SD=0.99; 52.4% male; 66% African-American) who attended a summer day camp research program designed for school-aged low-income children. Department of Human Services records were examined to determine the onset and recency of maltreatment for children in the maltreated group. Results indicated that among children with recent onset maltreatment, those with at least one A allele from CRP SNP rs1417938 evidenced significantly higher CRP levels compared to recently maltreated children carrying the TT genotype. Moreover, higher levels of CRP were associated with higher levels of internalizing symptoms only for recently maltreated children. Finally, we did not find support for salivary CRP as a mechanism in the relation between neuroendocrine regulation and childhood internalizing symptoms. Our findings highlight the importance of the timing of child maltreatment and have important implications for characterizing variability in inflammation and internalizing symptoms among youth. PMID

  12. Child maltreatment, inflammation, and internalizing symptoms: Investigating the roles of C-reactive protein, gene variation, and neuroendocrine regulation.

    PubMed

    Cicchetti, Dante; Handley, Elizabeth D; Rogosch, Fred A

    2015-05-01

    Prior research has found inconsistent evidence regarding the association among childhood adversity, inflammation, and internalizing symptoms, perhaps because previous studies have yet to adequately integrate important factors such as the timing of the adversity, genetic variation, and other relevant processes such as neuroendocrine regulation. The aims of the present study were threefold: (a) to determine whether the effect of the timing of child maltreatment on C-reactive protein (CRP), an inflammatory marker, varies by CRP gene variation; (b) to explore whether links between salivary CRP and childhood internalizing symptoms depend on the presence and timing of maltreatment experiences; and (c) to investigate the role of CRP in the relations between child neuroendocrine regulation and internalizing symptoms and examine whether these associations are moderated by the presence and timing of child maltreatment. Participants included a sample of 267 maltreated and 222 nonmaltreated children (M age = 9.72, SD = 0.99; 52.4% male; 66% African American) who attended a summer day camp research program designed for school-aged low-income children. Department of Human Services records were examined to determine the onset and recency of maltreatment for children in the maltreated group. The results indicated that among children with recent onset maltreatment, those with at least one A allele from CRP single nucleotide polymorphism rs1417938 evidenced significantly higher CRP levels compared to recently maltreated children carrying the TT genotype. Moreover, higher levels of CRP were associated with higher levels of internalizing symptoms only for recently maltreated children. Finally, we did not find support for salivary CRP as a mechanism in the relation between neuroendocrine regulation and childhood internalizing symptoms. Our findings highlight the importance of the timing of child maltreatment and have important implications for characterizing variability in inflammation

  13. An investigation of regional tectonic strain on water levels in Devils Hole, Death Valley National Park, Nevada

    NASA Astrophysics Data System (ADS)

    Robertson, G. D.; Ge, S.; Cutillo, P. A.

    2007-12-01

    Changes in hydraulic head at Devils Hole due to regional tectonic deformation were estimated using aquifer properties and the volumetric strain field present through the Great Basin in the western United States. Devils Hole is a large fault cavern located along a 15 km spring discharge line in a carbonate-rock aquifer, 240 km west of Las Vegas, Nevada. Geodetic measurements indicate that extensional strain in the Devils Hole area is oriented N 65 W and has a rate of 8 nanostrain/yr. Changes in hydraulic head due to strain were calculated and then used as initial conditions in a calibrated numerical ground-water flow model. Results of this analysis show that tectonic deformation could produce up to 0.02 cm/yr of water-level decline in Devils Hole. However, this rate is relatively small in comparison to rates caused from other factors such as natural recharge and ground-water pumping.

  14. Common skin infection due to Panton-Valentine leucocidin-producing Staphylococcus aureus strains in asylum seekers from Eritrea: a genome-based investigation of a suspected outbreak.

    PubMed

    Jaton, L; Pillonel, T; Jaton, K; Dory, E; Prod'hom, G; Blanc, D S; Tissot, F; Bodenmann, P; Greub, G

    2016-08-01

    Since late 2014, multiple cases of abscesses and boils due to methicillin-susceptible Staphylococcus aureus (MSSA) expressing the Panton-Valentine leucocidin (PVL) were observed in Eritrean asylum seekers in Lausanne, Switzerland. Strains isolated from infected Eritrean and non-Eritrean patients were compared by whole genome sequencing to determine whether these numerous cases result from an outbreak. The genome of S. aureus PVL-producing strains were sequenced and compared. Clinical and epidemiological characteristics of patients infected by PVL-producing strains were investigated. This work reports 15 cases of infections due to PVL-producing strains affecting mostly asylum seekers (n = 10), people working with refugees and/or exposed to Africans (n = 3). Most infections were due to closely related strains of CC152 (n = 8) and CC15 (n = 3), two distantly related (>34 000 core single nucleotide polymorphisms) clonal complexes. An epidemiological link between the 15 cases could be ruled out by whole genome sequencing (33 to 172 core single nucleotide polymorphisms between the different strains of a given complex). Altogether, these results reflect the probable high incidence of CC15 and CC152 PVL-producing strains in eastern Africa. Clinicians facing unusual skin infections in African refugees (or in any person returning from this region of high endemicity) should consider S. aureus PVL-producer before suspecting rare infections such as leishmaniasis or rickettsiosis. Clinicians should also remember that PVL are frequently expressed by MSSA in some regions of the world and that antibiotics that are efficient on toxin expression, such as clindamycin, represent the best therapeutic option.

  15. Investigation of dosimetric variations of liver radiotherapy using deformable registration of planning CT and cone-beam CT.

    PubMed

    Huang, Pu; Yu, Gang; Chen, Jinhu; Ma, Changsheng; Qin, Shaohua; Yin, Yong; Liang, Yueqiang; Li, Hongsheng; Li, Dengwang

    2017-01-01

    Many patients with technically unresectable or medically inoperable hepatocellular carcinoma (HCC) had hepatic anatomy variations as a result of interfraction deformation during fractionated radiotherapy. We conducted this retrospective study to investigate interfractional normal liver dosimetric consequences via reconstructing weekly dose in HCC patients. Twenty-three patients with HCC received conventional fractionated three-dimensional conformal radiation therapy (3DCRT) were enrolled in this retrospective investigation. Among them, seven patients had been diagnosed of radiation-induced liver disease (RILD) and the other 16 patients had good prognosis after treatment course. The cone-beam CT (CBCT) scans were acquired once weekly for each patient throughout the treatment, deformable image registration (DIR) of planning CT (pCT) and CBCT was performed to acquire modified CBCT (mCBCT), and the structural contours were propagated by the DIR. The same plan was applied to mCBCT to perform dose calculation. Weekly dose distribution was displayed on the pCT dose space and compared using dose difference, target coverage, and dose volume histograms. Statistical analysis was performed to identify the significant dosimetric variations. Among the 23 patients, the three weekly normal liver D50 increased by 0.2 Gy, 4.2 Gy, and 4.7 Gy, respectively, for patients with RILD, and 1.0 Gy, 2.7 Gy, and 3.1 Gy, respectively, for patients without RILD. Mean dose to the normal liver (Dmean) increased by 0.5 Gy, 2.6 Gy, and 4.0 Gy, respectively, for patients with RILD, and 0.4 Gy, 3.1 Gy, and 3.4 Gy, respectively, for patients without RILD. Regarding patients with RILD, the average values of the third weekly D50 and Dmean were both over hepatic radiation tolerance, while the values of patients without RILD were below. The dosimetric consequence showed that the liver dose between patients with and without RILD were different relative to the planned dose, and the RILD patients suffered

  16. Using a DNA microarray to investigate the distribution of insect virulence factors in strains of photorhabdus bacteria.

    PubMed

    Marokhazi, Judit; Waterfield, Nicholas; LeGoff, Gaelle; Feil, Edward; Stabler, Richard; Hinds, Jason; Fodor, Andras; ffrench-Constant, Richard H

    2003-08-01

    Photorhabdus is an insect-pathogenic bacterium in which oral toxicity to insects is found in two distinct taxonomic groups. Using a DNA microarray and comparative genomics, we show that oral toxicity is associated with toxin complex genes tcaABC and that this locus can be mobilized or deleted within different strains.

  17. Using a DNA Microarray To Investigate the Distribution of Insect Virulence Factors in Strains of Photorhabdus Bacteria

    PubMed Central

    Marokhazi, Judit; Waterfield, Nicholas; LeGoff, Gaelle; Feil, Edward; Stabler, Richard; Hinds, Jason; Fodor, Andras; ffrench-Constant, Richard H.

    2003-01-01

    Photorhabdus is an insect-pathogenic bacterium in which oral toxicity to insects is found in two distinct taxonomic groups. Using a DNA microarray and comparative genomics, we show that oral toxicity is associated with toxin complex genes tcaABC and that this locus can be mobilized or deleted within different strains.   PMID:12867479

  18. Investigation of the types and characteristics of the proteolytic enzymes formed by diverse strains of Proteus species.

    PubMed

    Senior, B W

    1999-07-01

    Many diverse clinical isolates of Proteus mirabilis (48 strains), P. penneri (25), P. vulgaris biogroup 2 (48) and P. vulgaris biogroup 3 (21) from man were examined for their ability to produce proteolytic enzymes and the nature and characteristics of the proteases were studied. All the P. penneri isolates, most (94-90%) of the P. mirabilis and P. vulgaris biogroup 2 isolates, but only 71% of the P. vulgaris biogroup 3 isolates, secreted proteolytic enzymes. These were detected most readily at pH 8 with gelatin as substrate. A strong correlation was found between the ability of a strain to form swarming growth and its ability to secrete proteases. Non-swarming isolates invariably appeared to be non-proteolytic. However, some isolates, particularly of P. vulgaris biogroup 3, were non-proteolytic even when they formed swarming growth. Analysis of the secreted enzymes of the different Proteus spp. on polyacrylamide-gelatin gels under various constraints of pH and other factors showed that they were all EDTA-sensitive metalloproteinases. Analysis of the kinetics of production of the proteases revealed the formation of an additional protease of undefined type and function that was cell-associated and formed before the others were secreted. The secreted protease was subsequently modified to two isoforms whose mass (53-46 kDa) varied with the Proteus spp. and the strain. There was no evidence that the secreted proteases of strains of Proteus spp. were of types other than metalloproteinases.

  19. Characterization of group A Streptococcus strains recovered from Mexican children with pharyngitis by automated DNA sequencing of virulence-related genes: unexpectedly large variation in the gene (sic) encoding a complement-inhibiting protein.

    PubMed Central

    Mejia, L M; Stockbauer, K E; Pan, X; Cravioto, A; Musser, J M

    1997-01-01

    Sequence variation was studied in several target genes in 54 strains of group A Streptococcus (GAS) cultured from children with pharyngitis in Mexico City. Although 16 distinct emm alleles were identified, only 4 had not been previously described. Virtually all bacteria (31 of 33 [94%] with the streptococcal pyrogenic exotoxin gene (speA) had emm1-related, emm3, or emm6 alleles. The gene (sic) encoding an extracellular GAS protein that inhibits complement function was unusually variable among isolates with the emm1 family of alleles, with a total of seven variants identified. The data suggest that many GAS strains infecting Mexican children are genetically similar to organisms commonly encountered in the United States and western Europe. Sequence variation in the sic gene is useful for rapid differentiation among GAS isolates with the emm1 family of alleles. PMID:9399523

  20. Cold Tolerance of some Ralstonia solanacearum strains, including Race3 Biovar2, is conferred in part by variation in cold shock gene cspD3.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ralstonia solanacearum race 3 biovar 2 (R3B2) strains are one of only 10 USDA Select Agents, a category of quarantined pathogens reserved for the most serious threats to U.S. plant industry. The threat of R3B2 strains was not considered to be likely due to race (these are poorly defined) or biovar ...

  1. Hyper-variation of Tandem Repeats at the PD0218 (pspB) locus of Xylella fastidiosa Almond Leaf Scorch and Grape Pierce’s Disease Strains

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Xylella fastidiosa is a Gram negative plant pathogenic bacterium that causes almond leaf scorch disease (ALSD) and grape Pierce’s disease (PD) in California. A-genotype strains cause ALSD only. G-genotype strains cause both PD and ALSD. Little is known about how X. fastidiosa interacts with the envi...

  2. Investigating the Variation of Volatile Compound Composition in Maotai-Flavoured Liquor During Its Multiple Fermentation Steps Using Statistical Methods

    PubMed Central

    Wu, Zheng-Yun; Lei, Xue-Jun; Zhu, De-Wen

    2016-01-01

    Summary The use of multiple fermentations is one of the most specific characteristics of Maotai--flavoured liquor production. In this research, the variation of volatile composition of Maotai-flavoured liquor during its multiple fermentations is investigated using statistical approaches. Cluster analysis shows that the obtained samples are grouped mainly according to the fermentation steps rather than the distillery they originate from, and the samples from the first two fermentation steps show the greatest difference, suggesting that multiple fermentation and distillation steps result in the end in similar volatile composition of the liquor. Back-propagation neural network (BNN) models were developed that satisfactorily predict the number of fermentation steps and the organoleptic evaluation scores of liquor samples from their volatile compositions. Mean impact value (MIV) analysis shows that ethyl lactate, furfural and some high-boiling-point acids play important roles, while pyrazine contributes much less to the improvement of the flavour and taste of Maotai-flavoured liquor during its production. This study contributes to further understanding of the mechanisms of Maotai-flavoured liquor production. PMID:27904415

  3. An investigation of the role of gene copy number variations in sorafenib sensitivity in metastatic hepatocellular carcinoma patients

    PubMed Central

    Lee, Ji Yun; Hong, Mineui; Lee, Jeeyun; Lee, Sujin; Kim, Kyoung-Mee; Park, Cheolkeun; Lim, Ho Yeong

    2017-01-01

    Background: Metastatic hepatocellular carcinoma (HCC) is a highly aggressive tumor with limited treatment options. While sorafenib has recently been shown to provide a survival advantage in patients with advanced HCC, the overall outcomes such as time to progression (TTP) and overall survival (OS) ought to be further improved. To that end, several targeted agents aimed at amplified oncogenes such as HER2 and FGFR2 have recently been developed. In this study, we aimed to identify genetic markers in the form of copy number variations (CNVs) that influence clinical outcomes post-sorafenib treatment in advanced HCC patients. Methods: We surveyed 38 metastatic HCC patients who were treated with sorafenib for the presence of CNVs using the NanoString nCounter assay. Results: The median TTP and OS for all patients were 2.7 months (95% confidence interval [CI]: 2.0-3.3 months) and 13.4 months (95% CI: 8.4-18.4 months), respectively. Several genes previously implicated in liver cancer were amplified, including CCND1 (n = 4), CDKN1A (n = 2), KRAS (n = 2), MDM2 (n = 1), and ERBB2 (n = 1). However, we found no correlations between CNVs and survival in our sorafenib-treated patients. Conclusions: The clinical features and biomarkers that account for sensitivity to sorafenib in HCC are complicated and remain unclear. Further investigation to identify predictive biomarkers and therapeutic strategies, including combining sorafenib with other target agents, are warranted. PMID:28382134

  4. Comparison of Widely Used Listeria monocytogenes Strains EGD, 10403S, and EGD-e Highlights Genomic Differences Underlying Variations in Pathogenicity

    PubMed Central

    Bécavin, Christophe; Bouchier, Christiane; Lechat, Pierre; Archambaud, Cristel; Creno, Sophie; Gouin, Edith; Wu, Zongfu; Kühbacher, Andreas; Brisse, Sylvain; Pucciarelli, M. Graciela; García-del Portillo, Francisco; Hain, Torsten; Portnoy, Daniel A.; Chakraborty, Trinad; Lecuit, Marc; Pizarro-Cerdá, Javier; Moszer, Ivan; Bierne, Hélène; Cossart, Pascale

    2014-01-01

    ABSTRACT For nearly 3 decades, listeriologists and immunologists have used mainly three strains of the same serovar (1/2a) to analyze the virulence of the bacterial pathogen Listeria monocytogenes. The genomes of two of these strains, EGD-e and 10403S, were released in 2001 and 2008, respectively. Here we report the genome sequence of the third reference strain, EGD, and extensive genomic and phenotypic comparisons of the three strains. Strikingly, EGD-e is genetically highly distinct from EGD (29,016 single nucleotide polymorphisms [SNPs]) and 10403S (30,296 SNPs), and is more related to serovar 1/2c than 1/2a strains. We also found that while EGD and 10403S strains are genetically very close (317 SNPs), EGD has a point mutation in the transcriptional regulator PrfA (PrfA*), leading to constitutive expression of several major virulence genes. We generated an EGD-e PrfA* mutant and showed that EGD behaves like this strain in vitro, with slower growth in broth and higher invasiveness in human cells than those of EGD-e and 10403S. In contrast, bacterial counts in blood, liver, and spleen during infection in mice revealed that EGD and 10403S are less virulent than EGD-e, which is itself less virulent than EGD-e PrfA*. Thus, constitutive expression of PrfA-regulated virulence genes does not appear to provide a significant advantage to the EGD strain during infection in vivo, highlighting the fact that in vitro invasion assays are not sufficient for evaluating the pathogenic potential of L. monocytogenes strains. Together, our results pave the way for deciphering unexplained differences or discrepancies in experiments using different L. monocytogenes strains. PMID:24667708

  5. [Investigation of antitumorigenic effects of food-borne non-pathogenic and pathogenic Salmonella enterica strains on MEF, DU145 and HeLa cell lines].

    PubMed

    Altıntaş Kazar, Gamze; Şen, Ece

    2016-07-01

    Basic applications in cancer therapy may fail to eradicate cancer cells completely, they can show toxic affects to healthy cells and development of resistance to antitumor agents may increase tendency to metastasis. Bacterial therapies have the advantage of specific targetting of tumors by selective toxicity, responsiveness to external signals, self-propelling capacity, and the sense of microenvironment. The most interest on the bacterial cancer therapy is about Salmonella spp. with a special emphasis of S.Typhimurium. The aim of this study was to investigate the antitumorigenic effects of food-borne non-pathogenic and pathogenic Salmonella enterica strains on different cell cultures. Non-pathogenic Salmonella Enteriditis (A17) and pathogenic Salmonella Telaviv (A22) strains isolated from chicken carcasses which were put on the market in Edirne province (located at Thrace region of Turkey), and Salmonella Typhimurium ATCC 14028 strain were used in the study. ATCC-derived MEF (mouse embryonic fibroblasts), DU145 (human prostate cancer cells), and HeLa (human cervical cancer cells) cell lines were cocultivated with Salmonella strains of MOI (Multiplicity of infection; number of bacteria:number of cell) of 1000:1, 100:1, 10:1, 1:1, 0.1:1. The cell viability was measured by colorimetric MTT cytotoxicity assay, the percentage of apoptosis was assessed by Tali® Apoptosis Assay-Annexin V Alexa Fluor® 488 kit (Invitrogen, Molecular Probes, Life Technologies, USA), and the caspase-3 activity was determined by colorimetric protease ApoTarget™ kit (Invitrogen, BioSource International, USA). It was shown that non-pathogenic S.Enteriditis (A17) decreased cell viability approximately to 70%, wheras patogenic S.Telaviv (A22) and standart S.Typhimurium ATCC 14028 strains reduced cell viability approximately to 80%. Adversely, it was also observed that pathogenic S.Telaviv (A22) strain induces apoptosis more effectively than non-pathogenic S.Enteriditis (A17) and S

  6. Investigation of spatial and historical variations of air pollution around an industrial region using trace and macro elements in tree components.

    PubMed

    Odabasi, Mustafa; Tolunay, Doganay; Kara, Melik; Ozgunerge Falay, Ezgi; Tuna, Gizem; Altiok, Hasan; Dumanoglu, Yetkin; Bayram, Abdurrahman; Elbir, Tolga

    2016-04-15

    Several trace and macro elements (n=48) were measured in pine needle, branch, bark, tree ring, litter, and soil samples collected at 27 sites (21 industrial, 6 background) to investigate their spatial and historical variation in Aliaga industrial region in Turkey. Concentrations generally decreased with distance from the sources and the lowest ones were measured at background sites far from major sources. Spatial distribution of anthropogenic trace elements indicated that their major sources in the region are the iron-steel plants, ship-breaking activities and the petroleum refinery. Patterns of 40 elements that were detected in most of the samples were also evaluated to assess their suitability for investigation of historical variations. Observed increasing trends of several trace and macro elements (As, Cr, Fe, Mo, Ni, V, Cu, Pb, Sb, Sn, and Hg) in the tree-ring samples were representative for the variations in anthropogenic emissions and resulting atmospheric concentrations in Aliaga region. It was shown that lanthanides (La, Ce, Pr, Nd, Sm, Gd, Dy, Er, Yb) could also be used for the investigation of historical variations due to specific industrial emissions (i.e., petroleum refining). Results of the present study showed that tree components, litter, and soil could be used to determine the spatial variations of atmospheric pollution in a region while tree rings could be used to assess the historical variations.

  7. Genome-Scale Metabolic Reconstructions and Theoretical Investigation of Methane Conversion in Methylomicrobium buryatense Strain 5G(B1)

    SciTech Connect

    de la Torre, Andrea; Metivier, Aisha; Chu, Frances; Laurens, Lieve M. L.; Beck, David A. C.; Pienkos, Philip T.; Lidstrom, Mary E.; Kalyuzhnaya, Marina G.

    2015-11-25

    Methane-utilizing bacteria (methanotrophs) are capable of growth on methane and are attractive systems for bio-catalysis. However, the application of natural methanotrophic strains to large-scale production of value-added chemicals/biofuels requires a number of physiological and genetic alterations. An accurate metabolic model coupled with flux balance analysis can provide a solid interpretative framework for experimental data analyses and integration.

  8. The Use of NF1 and NF2 Mutant Mouse Strains in the Investigation of Gene Function and Disease Development

    DTIC Science & Technology

    1998-10-01

    percentage of which show features of malignant peripheral nerve sheath tumors ( MPNSTs ). Importantly, human NFl patients also develop MPNSTs at high...significant subset (at least 50%) are malignant peripheral nerve sheath tumors ( MPNSTs ). This evaluation is based on the presence of S 100 staining...percentage of MPNSTs that develop in NF1 patients have mutations in p53. Thus, the Nfl/p53 mutant strain represents an animal model of the more malignant

  9. Natural Variation in the Promoter of the Gene Encoding the Mga Regulator Alters Host-Pathogen Interactions in Group A Streptococcus Carrier Strains

    PubMed Central

    Flores, Anthony R.; Olsen, Randall J.; Wunsche, Andrea; Kumaraswami, Muthiah; Shelburne, Samuel A.; Carroll, Ronan K.

    2013-01-01

    Humans commonly carry pathogenic bacteria asymptomatically, but the molecular factors underlying microbial asymptomatic carriage are poorly understood. We previously reported that two epidemiologically unassociated serotype M3 group A Streptococcus (GAS) carrier strains had an identical 12-bp deletion in the promoter of the gene encoding Mga, a global positive gene regulator. Herein, we report on studies designed to test the hypothesis that the identified 12-bp deletion in the mga promoter alters GAS virulence, thereby potentially contributing to the asymptomatic carrier phenotype. Using allelic exchange, we introduced the variant promoter into a serotype M3 invasive strain and the wild-type promoter into an asymptomatic carrier strain. Compared to strains with the wild-type mga promoter, we discovered that strains containing the promoter with the 12-bp deletion produced significantly fewer mga and Mga-regulated gene transcripts. Consistent with decreased mga transcripts, strains containing the variant mga promoter were also significantly less virulent in in vivo and ex vivo models of GAS disease. Further, we provide evidence that the pleiotropic regulator protein CodY binds to the mga promoter and that the 12-bp deletion in the mga promoter reduces CodY-mediated mga transcription. We conclude that the naturally occurring 12-bp deletion in the mga promoter significantly alters the pathogen-host interaction of these asymptomatic carrier strains. Our findings provide new insight into the molecular basis of the carrier state of an important human pathogen. PMID:23980109

  10. Investigating late Holocene variations in hydroclimate and the stable isotope composition of precipitation using southern South American peatlands: a hypothesis

    NASA Astrophysics Data System (ADS)

    Daley, T. J.; Mauquoy, D.; Chambers, F. M.

    2012-02-01

    Ombrotrophic raised peatlands provide an ideal archive for integrating late Holocene records of variations in hydroclimate and the estimated stable isotope composition of precipitation with recent instrumental measurements. Modern measurements of mean monthly surface air temperature, precipitation and δD and δ18O values in precipitation from the late twentieth and early twenty-first centuries provide a short but invaluable record with which to investigate modern relationships between these variables, thereby enabling improved interpretation of the peatland palaeodata. Data from two stations in the Global Network for Isotopes in Precipitation (GNIP) from Tierra del Fuego (Punta Arenas, Chile and Ushuaia, Argentina) were analysed for the period 1982 to 2008. In both locations, δD and δ18O values have decreased in response to quite different trends in local surface air temperature and total precipitation amount. At Ushuaia, the fall in δ18O values is associated with an increase in the mean annual amount of precipitation. At Punta Arenas, the fall in δ18O values is weakly associated with decrease in the precipitation amount and an increase in local temperatures. The pattern in both records is consistent with an increase in the zonal intensity of the southern westerly wind belt. These regional differences, observed in response to a known driver, should be detectable in peatland sites close to the GNIP stations. There is currently insufficient availability of suitably temporally resolved data to test for these regional differences over the last 3000 yr. Existing peatland palaeoclimate data from two sites near Ushuaia, however, provide evidence for changes in the late Holocene that are consistent with the pattern observed in modern observations. Furthermore, the records suggest synchroneity in millennial-scale oscillations between the Northern and Southern Hemispheres.

  11. Investigation of low-molecular weight organic acids and their spatiotemporal variation characteristics in Hongfeng Lake, China.

    PubMed

    Xiao, Min; Wu, Fengchang; Wang, Liying; Li, Xinqing; Huang, Rongsheng

    2013-02-01

    The identities and concentrations of low-molecular-weight organic acids (LMWOAs) were determined by ion chromatography throughout a 20-m water column in Hongfeng Lake, China. The spatiotemporal variations of LMWOAs and their contributions to dissolved organic matter (DOM) in a research period of 24 hr were also investigated. The results demonstrated that five LMWOAs (lactic, acetic, pyruvic, sorbic, oxalic acid) were detected, and their total concentration and proportion in DOC were 6.55 micromol/L and 7.47%. Their average levels were 2.50, 0.65, 2.35, 0.96 and 0.09 micromol/L, respectively. LMWOAs were higher during daytime (10:00-18:00 on Jun 13, 2008) than nighttime (21:00-6:00 the next morning), in particular 4.99 micromol/L high in the epilimnion (< or = 1 m water depth), reflecting the fact that direct import from terrigenous sources and photochemical production from humic materials were dominant during LMWOAs' origin and accumulation. The same factors caused LMWOAs to be 0.63 micromol/L in the epilimnion higher than in the hypolimnion. The rapid decrease of total organic acid (TOA) up until 18:00 mainly resulted from bio-uptake and mineralization in the hypolimnion (>1 m water depth). Pyruvic acid increased with time in the epilimnion and decreased in the hypolimnion, largely related to the two contrary processes of continuous degradation and synthesis of macromolecular organic matter during life materials' cycle mediated by organisms. Simultaneously, plankton behavior and thermal stratification played a pivotal role in LMWOAs' behavior in the water column, causing decreasing and increasing profiles. The distribution of LMWOAs represents an interesting resource for biogeochemical research of DOM in aquatic ecosystems.

  12. Simulation of the isotopic composition of stratospheric water vapour - Part 2: Investigation of HDO / H2O variations

    NASA Astrophysics Data System (ADS)

    Eichinger, R.; Jöckel, P.; Lossow, S.

    2015-06-01

    Studying the isotopic composition of water vapour in the lower stratosphere can reveal the driving mechanisms of changes in the stratospheric water vapour budget and therefore help to explain the trends and variations of stratospheric water vapour during recent decades. We equipped a global chemistry climate model with a description of the water isotopologue HDO, comprising its physical and chemical fractionation effects throughout the hydrological cycle. We use this model to improve our understanding of the processes which determine the patterns in the stratospheric water isotope composition and in the water vapour budget itself. The link between the water vapour budget and its isotopic composition in the tropical stratosphere is presented through their correlation in a simulated 21-year time series. The two quantities depend on the same processes; however, they are influenced with different strengths. A sensitivity experiment shows that fractionation effects during the oxidation of methane have a damping effect on the stratospheric tape recorder signal in the water isotope ratio. Moreover, the chemically produced high water isotope ratios overshadow the tape recorder in the upper stratosphere. Investigating the origin of the boreal-summer signal of isotopically enriched water vapour reveals that in-mixing of old stratospheric air from the extratropics and the intrusion of tropospheric water vapour into the stratosphere complement each other in order to create the stratospheric isotope ratio tape recorder signal. For this, the effect of ice lofting in monsoon systems is shown to play a crucial role. Furthermore, we describe a possible pathway of isotopically enriched water vapour through the tropopause into the tropical stratosphere.

  13. Simulation of the isotopic composition of stratospheric water vapour - Part 2: Investigation of HDO/H2O variations

    NASA Astrophysics Data System (ADS)

    Eichinger, R.; Jöckel, P.; Lossow, S.

    2014-11-01

    Studying the isotopic composition of water vapour in the lower stratosphere can reveal the driving mechanisms of changes in the stratospheric water vapour budget and therefore help to explain the trends and variations of stratospheric water vapour during the recent decades. We equipped a global chemistry climate model with a description of the water isotopologue HDO, comprising its physical and chemical fractionation effects throughout the hydrological cycle. We use this model to improve our understanding of the processes, which determine the patterns in the stratospheric water isotope composition and in the water vapour budget, itself. The link between the water vapour budget and its isotopic composition in the tropical stratosphere is presented through their correlation in a simulated 21 year time series. The two quantities depend on the same processes, however, are influenced with different strengths. A sensitivity experiment shows that fractionation effects during the oxidation of methane has a damping effect on the stratospheric tape recorder signal in the water isotope ratio. Moreover, the chemically produced high water isotope ratios overshadow the tape recorder in the upper stratosphere. Investigating the origin of the boreal summer tape recorder signal in the lower stratosphere reveals isotopically enriched water vapour crossing the tropopause over the subtropical Western Pacific. A correlation analysis confirms this link, which identifies the Asian Summer Monsoon as the major contributor for the intrusion of isotopically enriched water vapour into the stratosphere during boreal summer. Furthermore, convective ice lofting is shown to have a substantial impact on the isotope ratios of water vapour in the upper troposphere and lower stratosphere.

  14. Dispersion-Corrected Density Functional Theory Investigations of Structural and Electronic Properties of Bulk MoS2: Effect of Uniaxial Strain.

    PubMed

    Nguyen, Chuong V; Hieu, Nguyen N; Nguyen, Duong T

    2015-12-01

    Strain-dependent structural and electronic properties of MoS2 materials are investigated using first principles calculations. The structural and electronic band structures of the MoS2 with relaxed unit cells are optimized and calculated by the dispersion-corrected density functional theory (DFT-D2). Calculations within the local density approximation (LDA) and GGA using PAW potentials were also performed for specific cases for the purpose of comparison. The effect of strain on the band gap and the dependence of formation energy on strain of MoS2 are also studied and discussed using the DFT-D2 method. In bulk MoS2, the orbitals shift towards the higher/lower energy area when strain is applied along the z/x direction, respectively. The energy splitting of Mo4d states is in the range from 0 to 2 eV, which is due to the reduction of the electronic band gap of MoS2.

  15. Phylogeography of Yersinia ruckeri reveals effects of past evolutionary events on the current strain distribution and explains variations in the global transmission of enteric redmouth (ERM) disease.

    PubMed

    Bastardo, Asmine; Ravelo, Carmen; Romalde, Jesús L

    2015-01-01

    Phylogeographic patterns and population genetic structure of Yersinia ruckeri, the pathological agent of enteric redmouth disease (ERM) in salmonids, were investigated on the basis of concatenated multiloci sequences from isolates of different phenotypes obtained between 1965 and 2009 from diverse areas and hosts. Sequence analyses revealed genetic differentiation among subpopulations with the largest genetic distance occurring between subpopulations of Europe and Canada and/or South America. Bayesian analysis indicated the presence of three ancestral population clusters. Mismatch distribution displayed signatures characteristic of changes in size due to demographic and spatial expansions in the overall Y. ruckeri population, and also in the geographically separate subpopulations. Furthermore, a weak signal of isolation by distance was determined. A significant positive correlation between genetic and geographical distances was observed. These results revealed that the population of Y. ruckeri has undergone both ancient and recent population changes that were probably induced by biogeography forces in the past and, much more recently, by adaptive processes forced by aquaculture expansion. These findings have important implications for future studies on Y. ruckeri population dynamics, on the potential role of genetic structure to explain variations in ERM transmission, and on the effect of past evolutionary events on current estimations of gene flow.

  16. Phylogeography of Yersinia ruckeri reveals effects of past evolutionary events on the current strain distribution and explains variations in the global transmission of enteric redmouth (ERM) disease

    PubMed Central

    Bastardo, Asmine; Ravelo, Carmen; Romalde, Jesús L.

    2015-01-01

    Phylogeographic patterns and population genetic structure of Yersinia ruckeri, the pathological agent of enteric redmouth disease (ERM) in salmonids, were investigated on the basis of concatenated multiloci sequences from isolates of different phenotypes obtained between 1965 and 2009 from diverse areas and hosts. Sequence analyses revealed genetic differentiation among subpopulations with the largest genetic distance occurring between subpopulations of Europe and Canada and/or South America. Bayesian analysis indicated the presence of three ancestral population clusters. Mismatch distribution displayed signatures characteristic of changes in size due to demographic and spatial expansions in the overall Y. ruckeri population, and also in the geographically separate subpopulations. Furthermore, a weak signal of isolation by distance was determined. A significant positive correlation between genetic and geographical distances was observed. These results revealed that the population of Y. ruckeri has undergone both ancient and recent population changes that were probably induced by biogeography forces in the past and, much more recently, by adaptive processes forced by aquaculture expansion. These findings have important implications for future studies on Y. ruckeri population dynamics, on the potential role of genetic structure to explain variations in ERM transmission, and on the effect of past evolutionary events on current estimations of gene flow. PMID:26579104

  17. Investigation of high-speed free shear flows using improved pressure-strain correlated Reynolds stress turbulence model

    NASA Technical Reports Server (NTRS)

    Tiwari, S. N.; Lakshmanan, B.

    1993-01-01

    A high-speed shear layer is studied using compressibility corrected Reynolds stress turbulence model which employs newly developed model for pressure-strain correlation. MacCormack explicit prediction-corrector method is used for solving the governing equations and the turbulence transport equations. The stiffness arising due to source terms in the turbulence equations is handled by a semi-implicit numerical technique. Results obtained using the new model show a sharper reduction in growth rate with increasing convective Mach number. Some improvements were also noted in the prediction of the normalized streamwise stress and Reynolds shear stress. The computed results are in good agreement with the experimental data.

  18. Strain induced directional coarsening in nickel based superalloys: Investigation on kinetics using the small angle neutron scattering (SANS) technique

    SciTech Connect

    Veron, M.; Bastie, P.

    1997-08-01

    Using the small angle neutron scattering technique, the authors have observed rafting in nickel based single crystal superalloys. Kinetics of morphological evolution of the precipitates have been studied in situ. Therefore the authors used a special furnace designed for the ageing of prestrained specimens under a neutron beam. The evolution of both the precipitate aspect ratio and the distance between precipitates confirms the importance of strain in the directional coarsening process. Results are presented and discussed regarding kinetics and microstructural aspects. In such conditions, rafts seem to be different from those obtained after a creep test.

  19. Investigations on the in vitro metacyclogenesis of a visceral and a cutaneous human strain of Leishmania infantum.

    PubMed

    Louassini, M; Adroher, F J; Foulquié, M R; Benítez, R

    1998-07-30

    The in vitro metacyclogenesis of a visceral (VL) and cutaneous (CL) human strain of Leishmania infantum was monitored in order to find out the kinetics of this process and the in vitro infective capacity for macrophages of the metacyclic promastigotes developed. To identify, enumerate, and separate the metacyclic population, the complement-dependent lysis by normal serum and the agglutination by peanut agglutinin (PNA) were used, as they were shown to be useful for the purpose of this study. Maximum percentage of metacyclics was detected by both techniques on the 4th day of growth for VL and the 6th day for CL, and was higher for the VL strain. The in vitro infectivity for macrophages of two strains was assayed, and the high parasitization data obtained were transformed in order to determine the increase of the parasite burden for macrophages throughout the incubation time of the experiments (2-72 h post-infection (p.i.)). This parameter is denominated the infectivity ratio (%I) and calculated as follows: (number of intracellular parasites per infected macrophage at 'x' time p.i./number of intracellular parasites per infected macrophage at 2 h p.i.) x 100. When %I was calculated for promastigotes unagglutinated by PNA (PNA-)--metacyclic or infective promastigotes--at any time of culture, the %I at 72 h p.i. was always much higher than for agglutinated promastigotes (2.1-12.5 times)--non-infective promastigotes--and unfractionated promastigotes from culture (1.7-9.5 times), especially with VL parasites. Likewise, the %I for VL PNA- promastigotes from the 4th day of culture was 1.9 times higher than for CL PNA- promastigotes from the 6th day of culture. The higher resistance to lysis by serum, percentage of metacyclics (PNA-), and infectivity ratio of VL than CL could be related to a higher spreading capability into the host body associated with higher pathogenic effects of the visceral strain than the cutaneous one.

  20. Emergence of a multidrug-resistant (ASSuTTm) strain of Salmonella enterica serovar Typhimurium DT120 in England in 2011 and the use of multiple-locus variable-number tandem-repeat analysis in supporting outbreak investigations.

    PubMed

    Paranthaman, Karthikeyan; Haroon, Sophie; Latif, Samia; Vinnyey, Natalie; de Souza, Valerie; Welfare, William; Tahir, Mamoona; Cooke, Edward; Stone, Kirsten; Lane, Chris; Peters, Tansy; Puleston, Richard

    2013-10-01

    In summer 2011, two outbreaks of a unique, multidrug-resistant strain of Salmonella enterica serovar Typhimurium phage type 120 (DT120) occurred mainly in the Midlands, England. The first outbreak occurred among guests attending a wedding in July 2011 ('Wedding outbreak'), followed by a more geographically dispersed outbreak in August and September 2011 ('Midlands outbreak'). Fifty-one cases were confirmed. Detailed epidemiological and environmental health investigations suggested that pork was the most likely source of both outbreaks. All human samples and one pork sample showed the specific multiple-locus variable-number tandem-repeat analysis (MLVA) profile 3-11-12-NA-0211, with at most two loci variations. Trace-back investigations suggested a link to a butcher's shop and a pig farm in the East Midlands. The investigations highlight the utility of molecular analysis (MLVA) in supporting epidemiological investigations of outbreaks caused by S. Typhimurium DT120. Safe handling and cooking of pork by food business operators and consumers are key interventions to prevent future outbreaks.

  1. Investigation of the osteometry of the skull of the one-humped camels. Part II: sex dimorphism and geographical variations in adults.

    PubMed

    Yahaya, Ahmed; Olopade, James O; Kwari, Hyelduku D; Wiam, Ibrahim M

    2012-01-01

    Sexual dimorphism in the skull of different species has been of importance in archaeological, forensic and anatomical studies; also, a variation in phenotypic and genetic traits across geographic space is a recurring phenomenon in biological species. This study investigated 10 adult camels from each of three geographical locations in northern Nigeria, for sex- and location-based variations in the skulls. In one location, male skulls had greater absolute osteometric values but there were no significance differences in relative proportions between sexes. Moreover, all index values (skull, cranial and facial) indicate no sexual dimorphism in all locations. There were some variations in the osteometry of the frontal region, and neurocranial volume between the locations. In addition it was observed that the skull index of Nigerian camels was similar to the Malha type documented in literature but wide variations exist in many other craniometric dimensions of the skull. This suggests a definite difference in phenotype and probable origin.

  2. Molecular investigation and phylogeny of Anaplasma spp. in Mediterranean ruminants reveal the presence of neutrophil-tropic strains closely related to A. platys.

    PubMed

    Zobba, Rosanna; Anfossi, Antonio G; Pinna Parpaglia, Maria Luisa; Dore, Gian Mario; Chessa, Bernardo; Spezzigu, Antonio; Rocca, Stefano; Visco, Stefano; Pittau, Marco; Alberti, Alberto

    2014-01-01

    Few data are available on the prevalence and molecular typing of species belonging to the genus Anaplasma in Mediterranean ruminants. In this study, PCR analysis and sequencing of both 16S rRNA and groEL genes were combined to investigate the presence, prevalence, and molecular traits of Anaplasma spp. in ruminants sampled on the Island of Sardinia, chosen as a subtropical representative area. The results demonstrate a high prevalence of Anaplasma spp. in ruminants, with animals infected by at least four of six Anaplasma species (Anaplasma marginale, A. bovis, A. ovis, and A. phagocytophilum). Moreover, ruminants host a number of neutrophil-tropic strains genetically closely related to the canine pathogen A. platys. The high Anaplasma spp. prevalence and the identification of as-yet-unclassified neutrophil-tropic strains raise concerns about the specificity of serological tests routinely used in ruminants and provide additional background for reconstructing the evolutionary history of species genetically related to A. phagocytophilum.

  3. Dependence of the elastic strain coefficient of copper on the pre-treatment

    NASA Technical Reports Server (NTRS)

    Kuntze, Wilhelm

    1950-01-01

    The effect of various pre-treatments on the elastic strain coefficient (alpha) (defined as the reciprocal of the modulus of elasticity E) (Epsilon) and on the mechanical hysteresis of copper has been investigated. Variables comprising the pre-treatments were pre-straining by stretching in a tensile testing machine and by drawing through a die, aging at room and elevated temperatures and annealing. The variation of the elastic strain coefficient with test stress was also investigated.

  4. Investigating late Holocene variations in hydroclimate and the stable isotope composition of precipitation using southern South American peatlands: an hypothesis

    NASA Astrophysics Data System (ADS)

    Daley, T. J.; Mauquoy, D.; Chambers, F. M.; Street-Perrott, F. A.; Hughes, P. D. M.; Loader, N. J.; Roland, T. P.; van Bellen, S.; Garcia-Meneses, P.; Lewin, S.

    2012-09-01

    Ombrotrophic raised peatlands provide an ideal archive for integrating late Holocene records of variations in hydroclimate and the estimated stable isotope composition of precipitation with recent instrumental measurements. Modern measurements of mean monthly surface air temperature, precipitation, and δD and δ18O-values in precipitation from the late twentieth and early twenty-first centuries provide a short but invaluable record with which to investigate modern relationships between these variables, thereby enabling improved interpretation of the peatland palaeodata. Stable isotope data from two stations in the Global Network for Isotopes in Precipitation (GNIP) from southern South America (Punta Arenas, Chile and Ushuaia, Argentina) were analysed for the period 1982 to 2008 and compared with longer-term meteorological data from the same locations (1890 to present and 1931 to present, respectively). δD and δ18O-values in precipitation have exhibited quite different trends in response to local surface air temperature and precipitation amount. At Punta Arenas, there has been a marked increase in the seasonal difference between summer and winter δ18O-values. A decline in the deuterium excess of summer precipitation at this station was associated with a general increase in relative humidity at 1000 mb over the surface of the Southeast Pacific Ocean, believed to be the major vapour source for the local precipitation. At Ushuaia, a fall in δ18O-values was associated with an increase in the mean annual amount of precipitation. Both records are consistent with a southward retraction and increase in zonal wind speed of the austral westerly wind belt. These regional differences, observed in response to a known driver, should be detectable in peatland sites close to the GNIP stations. Currently, insufficient data with suitable temporal resolution are available to test for these regional differences over the last 3000 yr. Existing peatland palaeoclimate data from two

  5. Using stable isotopes of carbon to investigate the seasonal variation of carbon transfer in a northwestern Arkansas cave

    USGS Publications Warehouse

    Knierim, Katherine J.; Pollock, Erik; Hays, Phillip D.; Khojasteh, Jam

    2015-01-01

    -to-month variations in temperature and precipitation and provided insight into the sources of carbon in the cave. Stable carbon isotope ratios provided an effective tool to explore carbon transfer from the soil zone and into the cave, identify carbon sources in the cave, and investigate how seasonality affected the transfer of carbon in a shallow karst system.

  6. Investigation of genetic variation in scavenger receptor class B, member 1 (SCARB1) and association with serum carotenoids

    PubMed Central

    McKay, Gareth J; Loane, Edward; Nolan, John M; Patterson, Christopher C; Meyers, Kristin J; Mares, Julie A; Yonova-Doing, Ekaterina; Hammond, Christopher J; Beatty, Stephen; Silvestri, Giuliana

    2013-01-01

    Objective To investigate association of scavenger receptor class B, member 1 (SCARB1) genetic variants with serum carotenoid levels of lutein (L) and zeaxanthin (Z) and macular pigment optical density (MPOD). Design A cross-sectional study of healthy adults aged 20-70. Participants 302 participants recruited following local advertisement. Methods MPOD was measured by customized heterochromatic flicker photometry. Fasting blood samples were taken for serum L and Z measurement by HPLC and lipoprotein analysis by spectrophotometric assay. Forty-seven single nucleotide polymorphisms (SNPs) across SCARB1 were genotyped using Sequenom technology. Association analyses were performed using PLINK to compare allele and haplotype means, with adjustment for potential confounding and correction for multiple comparisons by permutation testing. Replication analysis was performed in the TwinsUK and CAREDS cohorts. Main outcome measures Odds ratios (ORs) for macular pigment optical density area, serum lutein and zeaxanthin concentrations associated with genetic variations in SCARB1 and interactions between SCARB1 and sex. Results Following multiple regression analysis with adjustment for age, body mass index, sex, high-density lipoprotein cholesterol (HDLc), low-density lipoprotein cholesterol (LDLc), triglycerides, smoking, dietary L and Z levels, 5 SNPs were significantly associated with serum L concentration and 1 SNP with MPOD (P<0.01). Only the association between rs11057841 and serum L withstood correction for multiple comparisons by permutation testing (P<0.01) and replicated in the TwinsUK cohort (P=0.014). Independent replication was also observed in the CAREDS cohort with rs10846744 (P=2×10−4), a SNP in high linkage disequilibrium with rs11057841 (r2=0.93). No significant interactions by sex were found. Haplotype analysis revealed no stronger association than obtained with single SNP analyses. Conclusions Our study has identified association between rs11057841 and

  7. Investigation of interfacial shear stresses, shape fixity, and actuation strain in composites incorporating shape memory polymers and shape memory alloys

    NASA Astrophysics Data System (ADS)

    Park, Jungkyu; Headings, Leon; Dapino, Marcelo; Baur, Jeffery; Tandon, Gyaneshwar

    2015-03-01

    Shape memory composites (SMCs) based on shape memory alloys (SMAs) and shape memory polymers (SMPs) allow many design possibilities due to their controllable temperature-dependent mechanical properties. The complementary characteristics of SMAs and SMPs can be utilized in systems with shape recovery created by the SMA and shape fixity provided by the SMP. In this research, three SMC operating regimes are identified and the behavior of SMC structures is analyzed by focusing on composite shape fixity and interfacial stresses. Analytical models show that SMPs can be used to adequately fix the shape of SMA actuators and springs. COMSOL finite element simulations are in agreement with analytical expressions for shape fixity and interfacial stresses. Analytical models are developed for an end-coupled linear SMP-SMA two-way actuator and the predicted strain is shown to be in good agreement with experimental test results.

  8. Spontaneous orientation-tuning driven by the strain variation in self-assembled ZnO-SrRuO{sub 3} heteroepitaxy

    SciTech Connect

    Zhu, Yuanmin; Liu, Ruirui; Zhan, Qian; Chang, Wei Sea; Yu, Rong; Wei, Tzu-Chiao; He, Jr-Hau; Chu, Ying-Hao

    2015-11-09

    Heteroepitaxial ZnO and SrRuO{sub 3} were grown on SrTiO{sub 3} (111) substrates and formed a self-assembled wurtzite-perovskite nanostructure. Spontaneous orientation-tuning of the SrRuO{sub 3} pillars was observed, with the growth direction changing from [111]{sub SRO} to [011]{sub SRO} as the film thickness increased, which is attributed to a misfit strain transition from the biaxial strain imposed by the SrTiO{sub 3} substrate to the vertical strain provided by the ZnO matrix. The [011]-SrRuO{sub 3} and [0001]-ZnO combination presents a favorable matching in the nanocomposite films, resulting in higher charge carrier mobility. This vertically integrated configuration and regulation on the crystallographic orientations are expected to be employed in designing multi-functional nanocomposite systems for applications in electronic devices.

  9. Investigating the Impact of Temperature Changes, Material Aging, and Service Load on the Strain of a Reinforced Concrete Construction

    NASA Astrophysics Data System (ADS)

    Kanciruk, Adam

    2014-12-01

    Intensive exploitation of coal beds in the Upper Silesia Coal Basin led to the degradation of the Katowice-Muchowiec civilian/military airport. As a result, it became necessary to adapt the Pyrzowice military airport for use as a public transport facility. This involved reconstruction of a hangar located at the airport. As part of this process, a new hangar slab was constructed, designed in such a way as to bear the load of passenger aircraft. In the area of the greatest wheel load to the slab, three strain rosettes were installed for the purpose of monitoring the slab strain. The mointoring process - which has been automatically conducted for almost three years now - revealed deformations resulting from service load, the aging of reinforced concrete, and changes of its temperature. Intensywna eksploatacja górnośląskich złóż węgla doprowadziła do degradacji cywilno-wojskowego lotniska Katowice-Muchowiec. W związku z tym, wynikła konieczność przystosowania do celów komunikacyjnych lotniska wojskowego w Pyrzowicach, w tym przebudowy znajdującego się na jego terenie hangaru. W ramach przebudowy wykonano nową posadzkę, zdolną przenosić ciężar samolotów pasażerskich. W posadzce tej, w rejonie występowania największych nacisków zainstalowano 3 rozety tensometryczne w celu monitorowania jej odkształceń. Monitorowanie to, prowadzone w sposób automatyczny już niemal 3 lata, wykazało występowanie odkształceń będących skutkiem obciążeń eksploatacyjnych, starzenia się żelbetu oraz zmian jego temperatury.

  10. Comparative genome analysis of VSP-II and SNPs reveals heterogenic variation in contemporary strains of Vibrio cholerae O1 isolated from cholera patients in Kolkata, India.

    PubMed

    Imamura, Daisuke; Morita, Masatomo; Sekizuka, Tsuyoshi; Mizuno, Tamaki; Takemura, Taichiro; Yamashiro, Tetsu; Chowdhury, Goutam; Pazhani, Gururaja P; Mukhopadhyay, Asish K; Ramamurthy, Thandavarayan; Miyoshi, Shin-Ichi; Kuroda, Makoto; Shinoda, Sumio; Ohnishi, Makoto

    2017-02-13

    Cholera is an acute diarrheal disease and a major public health problem in many developing countries in Asia, Africa, and Latin America. Since the Bay of Bengal is considered the epicenter for the seventh cholera pandemic, it is important to understand the genetic dynamism of Vibrio cholerae from Kolkata, as a representative of the Bengal region. We analyzed whole genome sequence data of V. cholerae O1 isolated from cholera patients in Kolkata, India, from 2007 to 2014 and identified the heterogeneous genomic region in these strains. In addition, we carried out a phylogenetic analysis based on the whole genome single nucleotide polymorphisms to determine the genetic lineage of strains in Kolkata. This analysis revealed the heterogeneity of the Vibrio seventh pandemic island (VSP)-II in Kolkata strains. The ctxB genotype was also heterogeneous and was highly related to VSP-II types. In addition, phylogenetic analysis revealed the shifts in predominant strains in Kolkata. Two distinct lineages, 1 and 2, were found between 2007 and 2010. However, the proportion changed markedly in 2010 and lineage 2 strains were predominant thereafter. Lineage 2 can be divided into four sublineages, I, II, III and IV. The results of this study indicate that lineages 1 and 2-I were concurrently prevalent between 2007 and 2009, and lineage 2-III observed in 2010, followed by the predominance of lineage 2-IV in 2011 and continued until 2014. Our findings demonstrate that the epidemic of cholera in Kolkata was caused by several distinct strains that have been constantly changing within the genetic lineages of V. cholerae O1 in recent years.

  11. Comparative genome analysis of VSP-II and SNPs reveals heterogenic variation in contemporary strains of Vibrio cholerae O1 isolated from cholera patients in Kolkata, India

    PubMed Central

    Sekizuka, Tsuyoshi; Mizuno, Tamaki; Takemura, Taichiro; Yamashiro, Tetsu; Chowdhury, Goutam; Pazhani, Gururaja P.; Mukhopadhyay, Asish K.; Ramamurthy, Thandavarayan; Miyoshi, Shin-ichi; Kuroda, Makoto; Shinoda, Sumio; Ohnishi, Makoto

    2017-01-01

    Cholera is an acute diarrheal disease and a major public health problem in many developing countries in Asia, Africa, and Latin America. Since the Bay of Bengal is considered the epicenter for the seventh cholera pandemic, it is important to understand the genetic dynamism of Vibrio cholerae from Kolkata, as a representative of the Bengal region. We analyzed whole genome sequence data of V. cholerae O1 isolated from cholera patients in Kolkata, India, from 2007 to 2014 and identified the heterogeneous genomic region in these strains. In addition, we carried out a phylogenetic analysis based on the whole genome single nucleotide polymorphisms to determine the genetic lineage of strains in Kolkata. This analysis revealed the heterogeneity of the Vibrio seventh pandemic island (VSP)-II in Kolkata strains. The ctxB genotype was also heterogeneous and was highly related to VSP-II types. In addition, phylogenetic analysis revealed the shifts in predominant strains in Kolkata. Two distinct lineages, 1 and 2, were found between 2007 and 2010. However, the proportion changed markedly in 2010 and lineage 2 strains were predominant thereafter. Lineage 2 can be divided into four sublineages, I, II, III and IV. The results of this study indicate that lineages 1 and 2-I were concurrently prevalent between 2007 and 2009, and lineage 2-III observed in 2010, followed by the predominance of lineage 2-IV in 2011 and continued until 2014. Our findings demonstrate that the epidemic of cholera in Kolkata was caused by several distinct strains that have been constantly changing within the genetic lineages of V. cholerae O1 in recent years. PMID:28192431

  12. Investigating Variation in Teaching with Technology-Rich Intervention: What Matters in Teaching and Teacher Training at Scale?

    ERIC Educational Resources Information Center

    Dunn, Margaret Breslin

    2009-01-01

    A main question this dissertation addresses is: what variation in teaching and teacher training matter? This question is examined within a specific but important context: the scale-up of a technology-rich intervention focused on the algebra strand of 8th grade mathematics. I conducted a multi-level case study by gathering and analyzing data at…

  13. INVESTIGATION OF SYSTEMATIC EFFECTS IN KEPLER DATA: SEASONAL VARIATIONS IN THE LIGHT CURVE OF HAT-P-7b

    SciTech Connect

    Van Eylen, V.; Lindholm Nielsen, M.; Hinrup, B.; Tingley, B.; Kjeldsen, H.

    2013-09-10

    With years of Kepler data currently available, the measurement of variations in planetary transit depths over time can now be attempted. To do so, it is of primary importance to understand which systematic effects may affect the measurement of transits. We aim to measure the stability of Kepler measurements over years of observations. We present a study of the depth of about 500 transit events of the Hot Jupiter HAT-P-7b, using 14 quarters (Q0-Q13) of data from the Kepler satellite. We find a systematic variation in the depth of the primary transit, related to quarters of data and recurring yearly. These seasonal variations are about 1%. Within seasons, we find no evidence for trends. We speculate that the cause of the seasonal variations could be unknown field crowding or instrumental artifacts. Our results show that care must be taken when combining transits throughout different quarters of Kepler data. Measuring the relative planetary radius of HAT-P-7b without taking these systematic effects into account leads to unrealistically low error estimates. This effect could be present in all Kepler targets. If so, relative radius measurements of all Hot Jupiters to a precision much better than 1% are unrealistic.

  14. [Investigation of pathogenic phenotypes and virulence determinants of food-borne Salmonella enterica strains in Caenorhabditis elegans animal model].

    PubMed

    Aksoy, Deniz; Şen, Ece

    2015-10-01

    Salmonellosis, caused by non-typhoidal Salmonella enterica serovars with the consumption of contaminated food, is one of the leading food-borne disease that makes microbial food safety an important public health issue. This study was performed in order to determine the antibiotic resistance, serotyping, plasmid profiles and pathogenicity potentials of food-borne Salmonella isolates in Caenorhabditis elegans animal model system in Edirne province, located at Thrace region of Turkey. In this study, 32 Salmonella isolates, of which 26 belonged to Infantis, four to Enteritidis, one to Telaviv and one to Kentucky serovars, isolated from chicken carcasses were used. Antibiotic resistance profiles were determined by disc diffusion and broth microdilution methods. A new C.elegans nematode animal model system was used to determine the pathogenicity potential of the isolates. The antibiotic resistance profiles revealed that one (3.1%) isolate was resistant to gentamicin, two (6.2%) to ciprofloxacin, three (9.4%) to ampicillin, 18 (56.3%) to kanamycin, 19 (60.8%) to neomycin, 25 (78.1%) to tetracycline, 25 (78.1%) to trimethoprim, 26 (81.25%) to nalidixic acid, 27 (84.4%) to streptomycin and 32 (100%) to sulfonamide. All of the 32 strains were susceptible to chloramphenicol and ampicillin/sulbactam. High levels of resistance to streptomycin, nalidixic acid, tetracycline, trimethoprim, sulfonamide, kanamycin and neomycin was determined. According to the plasmid analysis, six isolates (18.75%) harboured 1-3 plasmids with sizes between 1.2 and 42.4 kb. In C.elegans nematode animal model system, the time (in days) required to kill 50% (TD50) of nematodes was calculated for each experimental group. TD50 values of the nematode group fed with S.Typhimurium ATCC 14028 that was used as the positive control and another group fed with E.coli OP50 as the negative control were 4.2 ± 0.5 days and 8.0 ± 0.02 days, respectively. TD50 of the groups fed with Salmonella isolates ranged

  15. Investigation of the seasonal variations of aerosol physicochemical properties and their impact on cloud condensation nuclei number concentration

    NASA Astrophysics Data System (ADS)

    Logan, Timothy S.

    Aerosols are among the most complex yet widely studied components of the atmosphere not only due to the seasonal variability of their physical and chemical properties but also their effects on climate change. The three main aerosol types that are known to affect the physics and chemistry of the atmosphere are: mineral dust, anthropogenic pollution, and biomass burning aerosols. In order to understand how these aerosols affect the atmosphere, this dissertation addresses the following three scientific questions through a combination of surface and satellite observations: SQ1: What are the seasonal and regional variations of aerosol physico-chemical properties at four selected Asian sites? SQ2: How do these aerosol properties change during transpacific and intra-continental long range transport? SQ3: What are the impacts of aerosol properties on marine boundary layer cloud condensation nuclei number concentration? This dissertation uses an innovative approach to classify aerosol properties by region and season to address SQ1. This is useful because this method provides an additional dimension when investigating the physico-chemical properties of aerosols by linking a regional and seasonal dependence to both the aerosol direct and indirect effects. This method involves isolating the aerosol physico-chemical properties into four separate regions using AERONET retrieved Angstrom exponent (AEAOD) and single scattering co-albedo (o oabs) to denote aerosol size and absorptive properties. The aerosols events are then clustered by season. The method is first applied to four AERONET sites representing single mode aerosol dominant regions: weakly absorbing pollution (NASA Goddard), strongly absorbing pollution (Mexico City), mineral dust (Solar Village), and biomass burning smoke (Alta Floresta). The method is then applied to four Asian sites that represent complicated aerosol components. There are strong regional and seasonal influences of the four aerosol types over the

  16. Extreme multi-millennial slip rate variations on the Garlock fault, California: Strain super-cycles, potentially time-variable fault strength, and implications for system-level earthquake occurrence

    NASA Astrophysics Data System (ADS)

    Dolan, James F.; McAuliffe, Lee J.; Rhodes, Edward J.; McGill, Sally F.; Zinke, Robert

    2016-07-01

    Pronounced variations in fault slip rate revealed by new measurements along the Garlock fault have basic implications for understanding how faults store and release strain energy in large earthquakes. Specifically, dating of a series of 26.0+3.5/-2.5 m fault offsets with a newly developed infrared-stimulated luminescence method shows that the fault was slipping at >14.0+2.2/-1.8 mm /yr, approximately twice as fast as the long-term average rate, during a previously documented cluster of four earthquakes 0.5-2.0 ka. This elevated late Holocene rate must be balanced by periods of slow or no slip such as that during the ca. 3300-yr-long seismic lull preceding the cluster. Moreover, whereas a comparison of paleoseismic data and stress modeling results suggests that individual Garlock earthquakes may be triggered by periods of rapid San Andreas fault slip or very large-slip events, the ;on-off; behavior of the Garlock suggests a longer-term mechanism that may involve changes in the rate of elastic strain accumulation on the fault over millennial time scales. This inference is consistent with most models of the geodetic velocity field, which yield slip-deficit rates that are much slower than the average latest Pleistocene-early Holocene (post-8-13 ka) Garlock slip rate of 6.5 ± 1.5 mm /yr. These observations indicate the occurrence of millennia-long strain ;super-cycles; on the Garlock fault that may be associated with temporal changes in elastic strain accumulation rate, which may in turn be controlled by variations in relative strength of the various faults in the Garlock-San Andreas-Eastern California Shear Zone fault system and/or changes in relative plate motion rates.

  17. Investigating a continuous shear strain function for depth-dependent properties of native and tissue engineering cartilage using pixel-size data.

    PubMed

    Motavalli, Mostafa; Whitney, G Adam; Dennis, James E; Mansour, Joseph M

    2013-12-01

    A previously developed novel imaging technique for determining the depth dependent properties of cartilage in simple shear is implemented. Shear displacement is determined from images of deformed lines photobleached on a sample, and shear strain is obtained from the derivative of the displacement. We investigated the feasibility of an alternative systematic approach to numerical differentiation for computing the shear strain that is based on fitting a continuous function to the shear displacement. Three models for a continuous shear displacement function are evaluated: polynomials, cubic splines, and non-parametric locally weighted scatter plot curves. Four independent approaches are then applied to identify the best-fit model and the accuracy of the first derivative. One approach is based on the Akaiki Information Criteria, and the Bayesian Information Criteria. The second is based on a method developed to smooth and differentiate digitized data from human motion. The third method is based on photobleaching a predefined circular area with a specific radius. Finally, we integrate the shear strain and compare it with the total shear deflection of the sample measured experimentally. Results show that 6th and 7th order polynomials are the best models for the shear displacement and its first derivative. In addition, failure of tissue-engineered cartilage, consistent with previous results, demonstrates the qualitative value of this imaging approach.

  18. Investigation of the biotransformation of pentachlorophenol and pulp paper mill effluent decolorisation by the bacterial strains in a mixed culture.

    PubMed

    Singh, Shail; Chandra, R; Patel, D K; Reddy, M M K; Rai, Vibhuti

    2008-09-01

    Mixed culture of two bacterial strains Bacillus sp. and Serratia marcescens showed potential pentachlorophenol (PCP) degradation and decolorisation of pulp paper mill effluent. The physico-chemical quality of pulp paper mill effluent has been analyzed after 168 h incubation period degraded by mixed culture. The study revealed that it has decreased high load of BOD, COD, TS, TDS, TSS, sulphate, phosphate, total nitrogen, total phenols, metals and different salts (i.e. chloride, sodium, nitrate, potassium) at 168 h incubation period. PCP degradation in pulp paper mill effluent was confirmed by HPLC analysis. Mixed culture was found to degrade PCP up to (94%) present in pulp paper mill effluent with 1% glucose and 0.5% peptone (w/v) at 30+/-1 degrees C, pH 8.0+/-0.2 at 120 rpm in 168 h incubation period. The simultaneous release of chloride ion up to 1,200 mg/l at 168 h emphasized the bacterial dechlorination in the medium. The pulp paper mill effluent degradation was also supported by decline in pH, AOX (absorbable organic halides), color, D.O., BOD, COD and PCP. The analysis of pulp paper mill effluent degradation products by GC-MS analysis revealed the formation of low molecular weight compound like 2-chlorophenol (RT=3.8 min) and tetrachlorohydroquinone (RT=11.86 min) from PCP extracted degraded sample. Further, mixed culture may be used for bioremediation of PCP containing pulp paper mill waste in the environment.

  19. Use of Taylor Rod-on-Anvil Impact Experiments to Investigate High Strain Rate Behaviour in Polyolefins

    NASA Astrophysics Data System (ADS)

    Bucknall, David; Luce, Amanda; Kannan, Abhiram; Breidenich, Jennifer; Thadhani, Naresh

    2015-06-01

    The high strain rate deformation and mechano-lumination of various polyethylenes and polypropylene is studied using Taylor rod-on-anvil impact testing. Polypropylene and low density (LDPE), high density (HDPE), and ultra high molecular weight (UHMWPE) polyethylene samples were impacted against a hardened steel anvil at velocities ranging from 50-500 m/s. High-speed imaging, time-resolved spectroscopy, and thermal imaging are employed to track the macroscopic shape change and observe mechano-lumination and heating during impact. Additionally, electron spin resonance (ESR) and gel permeation chromatography (GPC) measurements were performed on recovered impacted samples to explain the observed deformation behavior in the various polyolefins. Time-resolved spectroscopy, coupled with ESR and GPC measurements indicate that chain scission occurs during the first few microseconds of the impact event. The observed macroscopic deformation that occurs after the observed mechano-illumination event is therefore influenced by the loss of mechanical strength associated with a drop in the molecular weight of the polymer.

  20. Strain and Texture in Al-Interconnect Wires Measured by X-Ray Microbeam Diffraction

    SciTech Connect

    Budai, J.D.; Chung, J.-S.; Ice, G.E.; Larson, B.C.; Lowe, W.P.; Tamura, N.; Tischler, J.Z.; Williams, E.L.; Yoon, M.

    1999-04-05

    The local strain and texture in Al interconnect wires have been investigated using white and monochromatic x-ray microbeams on the MHATTCAT undulator beam line at the Advanced Photon Source. Intergrain and intragrain orientations were obtained with ~0.01 degree sensitivity using white beam measurements on wide Al pads (~100 Mu-m) and thin (2 Mu-m) Al wires. Orientation changes of up to 1 degree were found within individual grains of the (111) textured Al interconnects. Deviatoric strain measurements indicate small intragranular strain variations, but intergranular strain variations were found to be quite large.

  1. Investigating Long-Range Dependence in American Treasury Bills Variations and Volatilities during Stable and Unstable Periods

    NASA Astrophysics Data System (ADS)

    Lahmiri, Salim

    2016-05-01

    Detrended fluctuation analysis (DFA) is used to examine long-range dependence in variations and volatilities of American treasury bills (TB) during periods of low and high movements in TB rates. Volatility series are estimated by generalized autoregressive conditional heteroskedasticity (GARCH) model under Gaussian, Student, and the generalized error distribution (GED) assumptions. The DFA-based Hurst exponents from 3-month, 6-month, and 1-year TB data indicates that in general the dynamics of the TB variations process is characterized by persistence during stable time period (before 2008 international financial crisis) and anti-persistence during unstable time period (post-2008 international financial crisis). For volatility series, it is found that; for stable period; 3-month volatility process is more likely random, 6-month volatility process is anti-persistent, and 1-year volatility process is persistent. For unstable period, estimation results show that the generating process is persistent for all maturities and for all distributional assumptions.

  2. Nosocomial transmission of carbapenem-resistant Klebsiella pneumoniae elucidated by single-nucleotide variation analysis: a case investigation.

    PubMed

    Hagiya, Hideharu; Aoki, Kotaro; Akeda, Yukihiro; Sakamoto, Noriko; Yamamoto, Norihisa; Yoshida, Hisao; Nishi, Isao; Ishii, Yoshikazu; Tomono, Kazunori

    2017-04-01

    Identifying transmission route of antimicrobial-resistant pathogen is essential for appropriate infection control strategy in healthcare facilities. We report the utility of single-nucleotide variation analysis in tracing nosocomial transmission of antimicrobial-resistant pathogens by describing a pseudo-outbreak case of carbapenem-resistant Klebsiella pneumoniae. The present case highlights that infection control strategy should encompass pathological dissection rooms, neglected but potentially highly contaminated places in hospitals.

  3. An initial investigation of associations between dopamine-linked genetic variation and smoking motives in African Americans.

    PubMed

    Bidwell, L C; McGeary, J E; Gray, J C; Palmer, R H C; Knopik, V S; MacKillop, J

    2015-11-01

    Nicotine dependence (ND) is a heterogeneous phenotype with complex genetic influences that may vary across ethnicities. The use of intermediate phenotypes may clarify genetic influences and reveal specific etiological pathways. Prior work in European Americans has found that the four Primary Dependence Motives (PDM) subscales (Automaticity, Craving, Loss of Control, and Tolerance) of the Wisconsin Inventory of Smoking Motives represent core features of nicotine dependence and are promising intermediate phenotypes for understanding genetic pathways to ND. However, no studies have examined PDM as an intermediate phenotype in African American smokers, an ethnic population that displays unique patterns of smoking and genetic variation. In the current study, 268 African American daily smokers completed a phenotypic assessment and provided a sample of DNA. Associations among haplotypes in the NCAM1-TTC12-ANKK1-DRD2 gene cluster, a dopamine-related gene region associated with ND, PDM intermediate phenotypes, and ND were examined. Dopamine-related genetic variation in the DBH and COMT genes was also considered on an exploratory basis. Mediational analysis was used to test the indirect pathway from genetic variation to smoking motives to nicotine dependence. NCAM1-TTC12-ANKK1-DRD2 region variation was significantly associated with the Automaticity subscale and, further, Automaticity significantly mediated associations among NCAM1-TTC12-ANKK1-DRD2 cluster variants and ND. DBH was also significantly associated with Automaticity, Craving, and Tolerance; Automaticity and Tolerance also served as mediators of the DBH-ND relationship. These results suggest that PDM, Automaticity in particular, may be a viable intermediate phenotype for understanding dopamine-related genetic influences on ND in African American smokers. Findings support a model in which putatively dopaminergic variants exert influence on ND through an effect on patterns of automatic routinized smoking.

  4. Investigation of dynamic behind the seasonal variations of Es and sporadic Na layer near the turbopause of aurora free zone

    NASA Astrophysics Data System (ADS)

    Yuan, T.; Sojka, J. J.; Criddle, N.; Cai, X.; Rice, D.

    2013-12-01

    The dearth of experimental observations, as well as dynamics study, near the turbopause (100-120 km) is the culprit for the mystery of this critical layer in the lower thermosphere. The sporadic E layer (Es) and the sporadic Na layer, occurring within this region, provide unique tracers for such topic. It is believed that the downward transporting of Es, which is full with metal ions (such as Na+), enriches the Na reservoir in the lower E region that causes the occurrence of sporadic Na layer within. In this paper, a statistic study show strong positive correlation between Es and sporadic Na layer above 100 km, measured by Utah State University Na lidar at Logan, Utah and CADI (ionosonde) at Bear Lake Observatory nearby. Both of these two turbopause features indicate strong seasonal variation with peak occurrence rate in the summer and minimum during the winter. To explain the dynamics behind the variations in the aurora free zone, HAMMONIA model produced monthly zonal wind climatology and Climatological Tidal Model of the Thermospehre (CTMT) are joining together to reproduce the hourly zonal wind variation within the turbopause, along with the temperature prediction from the two models. Using the well accepted wind shear theory of the Es formation, we conclude that such seasonal behaviors of Es and sporadic Na layer are due to large negative zonal wind shear driven by tidal wave peaking near the turbopause during summer time in the early evening.

  5. Interclonal variations in the molecular karyotype of Trypanosoma cruzi: chromosome rearrangements in a single cell-derived clone of the G strain.

    PubMed

    Lima, Fabio Mitsuo; Souza, Renata Torres; Santori, Fábio Rinaldo; Santos, Michele Fernandes; Cortez, Danielle Rodrigues; Barros, Roberto Moraes; Cano, Maria Isabel; Valadares, Helder Magno Silva; Macedo, Andréa Mara; Mortara, Renato Arruda; da Silveira, José Franco

    2013-01-01

    Trypanosoma cruzi comprises a pool of populations which are genetically diverse in terms of DNA content, growth and infectivity. Inter- and intra-strain karyotype heterogeneities have been reported, suggesting that chromosomal rearrangements occurred during the evolution of this parasite. Clone D11 is a single-cell-derived clone of the T. cruzi G strain selected by the minimal dilution method and by infecting Vero cells with metacyclic trypomastigotes. Here we report that the karyotype of clone D11 differs from that of the G strain in both number and size of chromosomal bands. Large chromosomal rearrangement was observed in the chromosomes carrying the tubulin loci. However, most of the chromosome length polymorphisms were of small amplitude, and the absence of one band in clone D11 in relation to its reference position in the G strain could be correlated to the presence of a novel band migrating above or below this position. Despite the presence of chromosomal polymorphism, large syntenic groups were conserved between the isolates. The appearance of new chromosomal bands in clone D11 could be explained by chromosome fusion followed by a chromosome break or interchromosomal exchange of large DNA segments. Our results also suggest that telomeric regions are involved in this process. The variant represented by clone D11 could have been induced by the stress of the cloning procedure or could, as has been suggested for Leishmania infantum, have emerged from a multiclonal, mosaic parasite population submitted to frequent DNA amplification/deletion events, leading to a 'mosaic' structure with different individuals having differently sized versions of the same chromosomes. If this is the case, the variant represented by clone D11 would be better adapted to survive the stress induced by cloning, which includes intracellular development in the mammalian cell. Karyotype polymorphism could be part of the T. cruzi arsenal for responding to environmental pressure.

  6. Genetic variation in the free-living amoeba Naegleria fowleri.

    PubMed

    Pélandakis, M; De Jonckheere, J F; Pernin, P

    1998-08-01

    In this study, 30 strains of the pathogenic free-living amoeba Naegleria fowleri were investigated by using the randomly amplified polymorphic DNA (RAPD) method. The present study confirmed our previous finding that RAPD variation is not correlated with geographical origin. In particular, Mexican strains belong to the variant previously detected in Asia, Europe, and the United States. In France, surprisingly, strains from Cattenom gave RAPD patterns identical to those of the Japanese strains. In addition, all of these strains, together with an additional French strain from Chooz, exhibited similarities to South Pacific strains. The results also confirmed the presence of numerous variants in Europe, whereas only two variants were detected in the United States. The two variants found in the United States were different from the South Pacific variants. These findings do not support the previous hypothesis concerning the origin and modes of dispersal of N. fowleri.

  7. Genetic Variation in the Free-Living Amoeba Naegleria fowleri

    PubMed Central

    Pélandakis, Michel; De Jonckheere, Johan F.; Pernin, Pierre

    1998-01-01

    In this study, 30 strains of the pathogenic free-living amoeba Naegleria fowleri were investigated by using the randomly amplified polymorphic DNA (RAPD) method. The present study confirmed our previous finding that RAPD variation is not correlated with geographical origin. In particular, Mexican strains belong to the variant previously detected in Asia, Europe, and the United States. In France, surprisingly, strains from Cattenom gave RAPD patterns identical to those of the Japanese strains. In addition, all of these strains, together with an additional French strain from Chooz, exhibited similarities to South Pacific strains. The results also confirmed the presence of numerous variants in Europe, whereas only two variants were detected in the United States. The two variants found in the United States were different from the South Pacific variants. These findings do not support the previous hypothesis concerning the origin and modes of dispersal of N. fowleri. PMID:9687460

  8. Finite element analysis of equine incisor teeth. Part 2: investigation of stresses and strain energy densities in the periodontal ligament and surrounding bone during tooth movement.

    PubMed

    Schrock, P; Lüpke, M; Seifert, H; Staszyk, C

    2013-12-01

    This study investigated the hypothetical contribution of biomechanical loading to the onset of equine odontoclastic tooth resorption and hypercementosis (EOTRH) and to elucidate the physiological age-related positional changes of the equine incisors. Based on high resolution micro-computed tomography (μCT) datasets, 3-dimensional models of entire incisor arcades and the canine teeth were constructed representing a young and an old incisor dentition. Special attention was paid to constructing an anatomically correct model of the periodontal ligament (PDL). Using previously determined Young's moduli for the equine incisor PDL, finite element (FE) analysis was performed. Resulting strains, stresses and strain energy densities (SEDs), as well as the resulting regions of tension and compression within the PDL and the surrounding bone were investigated during occlusion. The results showed a distinct distribution pattern of high stresses and corresponding SEDs in the PDL and bone. Due to the tooth movement, peaks of SEDs were obtained in the PDL as well as in the bone on the labial and palatal/lingual sides of the alveolar crest. At the root, highest SEDs were detected in the PDL on the palatal/lingual side slightly occlusal of the root tip. This distribution pattern of high SEDs within the PDL coincides with the position of initial resorptive lesions in EOTRH affected teeth. The position of high SEDs in the bone can explain the typical age-related alteration of shape and angulation of equine incisors.

  9. Investigation of Photoluminescence and Photocurrent in InGaAsP/InP Strained Multiple Quantum Well Heterostructures

    NASA Technical Reports Server (NTRS)

    Raisky, O. Y.; Wang, W. B.; Alfano, R. R.; Reynolds, C. L., Jr.; Swaminathan, V.

    1997-01-01

    Multiple quantum well InGaAsP/InP p-i-n laser heterostructures with different barrier thicknesses have been investigated using photoluminescence (PL) and photocurrent (PC) measurements. The observed PL spectrum and peak positions are in good agreement with those obtained from transfer matrix calculations. Comparing the measured quantum well PC with calculated carrier escape rates, the photocurrent changes are found to be governed by the temperature dependence of the electron escape time.

  10. An investigation of spatial variation of suspended sediment concentration induced by a bay bridge based on Landsat TM and OLI data

    NASA Astrophysics Data System (ADS)

    Cai, LiNa; Tang, DanLing; Li, CongYing

    2015-07-01

    This study investigates the spatial variation of suspended sediment concentration (SSC) induced by Hangzhou Bay Bridge (HBB) in the coastal waters of the East China Sea. Based on Landsat Thematic Mapper (TM), Operational Land Imager (OLI) data and in-situ measurements, spectral characteristics of waters in Hangzhou Bay and SSC retrieved from near infrared single band have been analyzed. The results revealed significant difference of SSC in the water on two sides of HBB. SSC increases downstream of the bridge under conditions of low turbidity (SSC < 300 mg l-1) upstream water, while SSC decreases when high turbidity water (SSC > 400 mg l-1) upstream. This study shows that the interaction of bridge piers and currents has important influences on SSC distribution by inducing hydrodynamic factors and by changing suspended sediment transport. Remotely sensed data with high spatial resolution as TM and OLI can be applied to investigate SSC variations induced by a bridge in the bay area.

  11. Using BEEM To Probe Strains In Semiconductors

    NASA Technical Reports Server (NTRS)

    Bell, L. Douglas; Milliken, Autumn M.; Manion, Stephen J.; Kaiser, William J.

    1996-01-01

    Ballistic-electron-emission microscopy (BEEM) useful in determining strains in semiconductors under some conditions. More specifically, BEEM is variant of scanning tunneling microscopy and sensitive to electronic structure of probed material. In present approach, BEEM used to obtain data on those aspects of variations in electronic structures related to variations in strains. Then by use of mathematical modeling of relationships between electronic structures and strains, variations in strains deduced from BEEM data.

  12. Genetic variation in the 3’ untranslated region of dengue virus serotype 3 strains isolated from mosquitoes and humans in Brazil

    PubMed Central

    2013-01-01

    Summary Background Dengue, a mosquito-borne viral infection caused by one of the four dengue virus (DENV) serotypes (DENV-1 to 4), replicate alternately on the mosquito vector and human host and are responsible for infections throughout tropical and subtropical regions of the world. In Brazil, the disease has become a major public health problem and the introduction of DENV-3 in 2000 in Rio de Janeiro (RJ) was associated with severe dengue epidemics. The potential emergence of strains associated with severe disease highlights the need for the surveillance of DENV in human host and vectors. Methods Aiming to contribute for DENV phylogenetic and vector-virus-human host studies, we sequenced the entire genome of one DENV-3 isolated from naturally infected Aedes aegypti from RJ in 2001 and characterized the 3’ UTR from strains isolated from mosquitoes and humans. Mosquitoes were pooled and submitted to virus isolation in Ae. albopictus C6/36 cells and the infecting serotype was identified by immunofluorescence using type-specific monoclonal antibody. Sequence analysis was performed using BioEdit software, the multiple alignments were performed using CLUSTAL W and the phylogenetic analysis by MEGA 5, using the Neighbor-joining method. Secondary structure prediction was performed by using the MFOLD program. Results Exclusive substitutions and a substitution leading to a stop codon on the NS5 gene were observed in the DENV-3 isolated from a naturally infected Ae. aegypti and fully sequenced. As an 8- nucleotides deletion was observed within the 11- nucleotides (nts) insertion on the variable region (VR) from the 3′UTR in this isolate, we further sequenced other DENV-3 from both mosquitoes and humans. The majority of DENV-3 from RJ analyzed were characterized by the 11-nts insertion in the VR of the 3′UTR, despite the observation of strains carrying the 8-nts deletion. The latter presented similar secondary structures, however not all strains presenting the 11-nts

  13. Variation of B1 gene and AF146527 repeat element copy numbers according to Toxoplasma gondii strains assessed using real-time quantitative PCR.

    PubMed

    Costa, Jean-Marc; Bretagne, Stéphane

    2012-04-01

    Using the multicopy B1 gene and AF146527 element for the amplification of Toxoplasma gondii DNA raises the issue of reliable quantification for clinical diagnosis. We applied relative quantification to reference strains using the single-copy P30 gene as a reference. According to the parasite type, the copy numbers for the B1 gene and AF146527 element were found to be 5 to 12 and 4 to 8 times lower than the previous estimations of 35 and 230 copies, respectively.

  14. Rescue of the highly virulent classical swine fever virus strain "Koslov" from cloned cDNA and first insights into genome variations relevant for virulence.

    PubMed

    Fahnøe, Ulrik; Pedersen, Anders Gorm; Risager, Peter Christian; Nielsen, Jens; Belsham, Graham J; Höper, Dirk; Beer, Martin; Rasmussen, Thomas Bruun

    2014-11-01

    Classical swine fever virus (CSFV) strain "Koslov" is highly virulent with a mortality rate of up to 100% in pigs. In this study, we modified non-functional cDNAs generated from the blood of Koslov virus infected pigs by site-directed mutagenesis, removing non-synonymous mutations step-by-step, thereby producing genomes encoding the consensus amino acid sequence. Viruses rescued from the construct corresponding to the inferred parental form were highly virulent, when tested in pigs, with infected animals displaying pronounced clinical symptoms leading to high mortality. The reconstruction therefore gave rise to a functional cDNA corresponding to the highly virulent Koslov strain of CSFV. It could be demonstrated that two single amino acid changes (S763L and P968H) in the surface structural protein E2 resulted in attenuation in the porcine infection system while another single amino acid change within the nonstructural protein NS3 (D2183G) reduced virus growth within cells in vitro.

  15. PCR-RFLP of ribosomal internal transcribed spacers highlights inter and intra-species variation among Leishmania strains native to La Paz, Bolivia.

    PubMed

    Buitrago, Rosio; Cupolillo, Elisa; Bastrenta, Brigitte; Le Pont, Francois; Martinez, Eddy; Barnabé, Christian; Brenière, Simone Frédérique

    2011-04-01

    Human leishmaniasis is highly endemic in Bolivia and shows a growing incidence. This report reveals the genetic variability of 35 isolates mainly belonging to Leishmania braziliensis and Leishmania amazonensis species. Among them, 31 were from human patients with different clinical presentations, 3 strains from Lutzomya nuneztovari anglesi (the proven vector of L. amazonensis) and 1 strain of a mammal (Conepatus chinga). The isolates were analyzed by isoenzyme electrophoresis (MLEE) and PCR-RFLP of ITS rRNA genes, a genetic marker highly polymorphic and better adapted to sub-structuring of populations. MLEE and RFLP-ITS were in agreement to discriminate the species, 12 belong to L. (V.) braziliensis, 21 to L. (L.) amazonensis, 1 to Leishmania (V.) lainsoni and 1 to Leishmania (L.) chagasi. Among L. (V.) braziliensis the RFLP-ITS only highlights variability. Ten isolates from either cutaneous or mucocutaneous clinical forms, were grouped together (bootstrap value of 99.8%) apart from two others, one from a mammal (C. chinga), the other from a patient with a cutaneous form. Among L. (L.) amazonensis both markers detect variability but no significant sub-division was identified including isolates from different clinical forms. Moreover, the high frequency of several isolates from cutaneous forms occurred during an outbreak, with putative hybrid character (multiloci heterozygous patterns depicted by MLEE) could be linked to better fitness of these parasites. However, in the absence of observation of hypothetical parents, their hybrid status remains a question.

  16. Interspecific variation in metamorphic competence in marine invertebrates: the significance for comparative investigations into the timing of metamorphosis.

    PubMed

    Bishop, Cory D; Huggett, Megan J; Heyland, Andreas; Hodin, Jason; Brandhorst, Bruce P

    2006-12-01

    Metamorphosis in marine invertebrate larvae is a dynamic, environmentally dependent process that integrates ontogeny with habitat selection. The capacity of many marine invertebrate larvae to survive and maintain metamorphic competence in the absence of environmental cues has been hypothesized to be an adaptive convergence (Hadfield and others 2001). A survey of the literature reveals that a single generalized hypothesis about metamorphic competence as an adaptive convergence is not sufficient to account for interspecific variation in this character. In an attempt to capture this variation, we discuss the "desperate larva hypothesis" and propose two additional hypotheses called the "variable retention hypothesis" and the "death before dishonor hypothesis." To validate these additional hypotheses we collected data on taxa from the published literature and performed a contingency analysis to detect correlations between spontaneous metamorphosis, habitat specificity and/or larval life-history mode, three characters relevant to environmentally induced settlement and metamorphosis. In order to account for phylogenetic bias in these correlations, we also constructed a phylogeny of these taxa and again performed a character-correlation analysis. Both these tests suggest that juvenile habitat specificity is correlated to the capacity of individuals to retain the competent larval state in the absence of substrate cues and therefore validate the existence of more than one hypothesis about metamorphic competence. We provide new data from the sea urchin Lytechinus pictus that suggest that nitric oxide (NO) and thyroxine hormone signaling interact to determine the probability of settlement in response to a settlement cue. Similarly, we provide evidence that thyroxine signaling in the sand dollar Dendraster excentricus increases spontaneous metamorphosis in the absence of cues from adult conspecifics in a manner that is independent of larval age.

  17. Investigation of the morphology and Wait's parameter variations of the low-latitude D region ionosphere using the multiple harmonics of tweeks

    NASA Astrophysics Data System (ADS)

    Tan, Le Minh

    2016-06-01

    Recording the tweeks with a maximum up to eight harmonics using the receiver installed at Tay Nguyen University (12.65° N, 108.02° E) during 2013-2014, we investigated the morphology of the nighttime D-region ionosphere. Tweeks were recorded on 5 quiet nights per month. The results show that the mean reflection height in 2014 (Rz = 79.3) is lower by 3.3 km than that in 2013 (Rz = 64.9). The reflection height at low latitudes is higher than that at high latitudes. The mean reference height h‧ in 2013 is higher about 0.9 km than that in 2014 and the mean sharpness factor β in 2013 is higher by 0.07 km-1 than that in 2014. The short-term variation of reflection heights for tweeks with harmonics m = 1-3 and sunspot number have the negative correlation coefficients. However, the correlations between them are not clear. On some nights, from 19:00-21:00 LT, the reflection height temporal variability shows a moderate to strong negative correlation with the tweek occurrence. This suggests that the reflection height variation may be caused by QE fields generated by lightning discharges. The variations of tweek reflection heights observed during 2013-2014, at low latitudes could be significantly caused by the ionization effect by Lyman- α and Lyman- β coming from geocorona, variation of neutral density, particle precipitations, and by direct energy coupling between lightning and lower ionosphere.

  18. Differential 24-hour variation of alertness and subjective tension in process controllers: investigation of the relationship with body temperature and heart rate.

    PubMed

    Cariou, Magali; Galy, Edith; Mélan, Claudine

    2008-07-01

    The effects of shift and time-on-shift on alertness and perceived tension, as well as related physiological variables, were investigated in satellite controllers working a rapid forward rotating three-shift system. In controlled laboratory conditions, subjective tension and HR have been reported to display circadian variation and marked sensitivity to external factors. We examined whether circadian variations were masked for these particular variables in real-job conditions, unlike for alertness and body temperature, which have been repeatedly shown to display circadian variation in these conditions. This hypothesis was tested in a repeated-measures design by collecting alertness and tension self-reports and recording operators' sublingual temperature on three occasions on each shift and HR continuously throughout shifts. Alertness and body temperature varied according to a typical diurnal trend; subjective tension was only enhanced on the initial recording of each shift (compared to the remaining ones), while HR displayed an intermediary trend. Intra-subject correlations revealed a positive relationship between alertness, oral temperature, and HR, while no such relationship was found for subjective tension. These results support the hypothesis of a close dependence of alertness and temperature, and to a lesser extent for HR, on endogenous mechanisms in this job-situation. In addition, some situation-specific factors, such as job-demand, would affect subjective tension and partially mask the circadian variations in HR.

  19. Tetragonal-strain-induced local structural modifications in InAsxP1-x/InP superlattices: A detailed x-ray-absorption investigation

    NASA Astrophysics Data System (ADS)

    Pascarelli, S.; Boscherini, F.; Lamberti, C.; Mobilio, S.

    1997-07-01

    We report a comprehensive investigation of the local structure around As in thin InAsxP1-x strained layers in InAsxP1-x/InP superlattices by fluorescence-detected x-ray-absorption fine structure; seven superlattice samples are studied as a function of composition, and compared to six unstrained, bulk samples of similar composition. Contributions up to the third coordination shell around As are clearly visible in the spectra, and are analyzed taking into account important multiple-scattering contributions. Results show that structural modifications due to tetragonal distortion appear mainly in the second and third coordination shells, while nearest-neighbor bond lengths remain closer to the values in unstrained bulk alloys. This implies that in semiconductor alloys tetragonal strain accommodation is mainly obtained through bond-angle distortions, in analogy to the situation in bulk pseudobinary alloys. A model which combines macroscopic elastic theory and the known local structure in bulk pseudobinary alloys is presented, and is found to fit the data very well.

  20. [Investigation of the presence of mecC and Panton-Valentine leukocidin genes in Staphylococcus aureus strains isolated from clinical specimens during seven years period].

    PubMed

    Kılıç, Abdullah; Doğan, Eyüp; Kaya, Sinem; Baysallar, Mehmet

    2015-10-01

    Detection and identification of methicillin-resistant Staphylococcus aureus (MRSA) in clinical microbiology laboratories are important for the selection of appropriate treatment and obtaining epidemiological data. mecC gene, is a mecA homologue, showing almost 69% DNA similarity with the mecA gene and the encoded protein by this gene shows almost 63% similarity with the PBP2a/2' protein. Several studies indicated that mecC positive MRSA strains can be transmitted from the livestock to humans by cross contamination. Panton-Valentine leukocidin (PVL), a potent cytotoxin of S.aureus is also considered as an important virulence factor. The aim of this study was to determine the existence and prevalence of mecC and pvl genes among S.aureus strains isolated from clinical specimens. A total of 1700 S.aureus isolates including 1177 methicillin-susceptible S.aureus (MSSA) and 523 MRSA, isolated in our hospital between January 2007 to December 2014, were included in the study. The isolates were identified by both conventional methods and BD Phoenix automated system (BD Diagnostic Instrument Systems, USA). Antibiotic susceptibility testing was performed by Kirby-Bauer disk diffusion method with oxacillin (1 μg) and cefoxitin (30 μg) according to the CLSI standards. The presence of mecA gene was investigated by the use of real-time PCR, and the presence of pvl and mecC genes were detected by conventional PCR method. Among the patients, 44.6% (759/1700) were outpatients, 65.8% (1119/1700) were male and the mean age of of patients was 39.7 years. Of 1700 isolates evaluated in this study, 523 (30.7%) were positive for mecA gene, however all of them were negative for mecC gene. A total of 32 (1.8%) isolates were positive for pvl gene including 23 (1.9%) out of 1177 MSSA and nine (1.7%) out of 523 MRSA strains. Eighteen (56.2%) of the PVL-positive S.aureus strains were isolated from skin and soft tissue infections. The frequency of PVL detected in this study was similar to the

  1. Investigation of the effects of manufacturing variations and materials on fatigue crack detection methods in gear teeth

    NASA Technical Reports Server (NTRS)

    Wheitner, Jeffrey A.; Houser, Donald R.

    1994-01-01

    The fatigue life of a gear tooth can be thought of as the sum of the number of cycles required to initiate a crack, N(sub i), plus the number of cycles required to propagate the crack to such a length that fracture occurs, N(sub p). The factors that govern crack initiation are thought to be related to localized stress or strain at a point, while propagation of a fatigue crack is a function of the crack tip parameters such as crack shape, stress state, and stress intensity factor. During a test there is no clear transition between initiation and propagation. The mechanisms of initiation and propagation are quite different and modeling them separately produces a higher degree of accuracy, but then the question that continually arises is 'what is a crack?' The total life prediction in a fracture mechanics model presently hinges on the assumption of an initial crack length, and this length can significantly affect the total life prediction. The size of the initial crack is generally taken to be in the range of 0.01 in. to 0.2 in. Several researchers have used various techniques to determine the beginning of the crack propagation stage. Barhorst showed the relationship between dynamic stiffness changes and crack propagation. Acoustic emissions, which are stress waves produced by the sudden movement of stressed materials, have also been successfully used to monitor the growth of cracks in tensile and fatigue specimens. The purpose of this research is to determine whether acoustic emissions can be used to define the beginning of crack propagation in a gear using a single-tooth bending fatigue test.

  2. [Investigation of macrolide, lincosamide and streptogramin B resistance in Staphylococcus aureus strains isolated from clinical samples by phenotypical and genotypical methods].

    PubMed

    Aydeniz Ozansoy, Fatma; Cevahir, Nural; Kaleli, İlknur

    2015-01-01

    Staphylococcus aureus is one of the most common cause of both community and healthcare-associated infections. As staphylococci have developed resistance to various antibiotics, initially to penicillins then to methicillin and glycopeptides and have the ability to cause epidemics, they continue to be a major problem from past to present. Methicillin resistance gave rise to the use of alternative antibiotics such as macrolides, however worldwide development of macrolide resistance limited the use of these antibiotics. Macrolide resistance occurs either through target site modification (MLS(B) phenotype, encoded by erm genes), efflux pumps (MS phenotype, encoded by msrA/B genes) or decreased cell wall permeability. The aim of this study was to investigate the MLS(B) resistance of clinical S.aureus strains with phenotypic and genotypic methods. A total of 404 S.aureus strains isolated from different clinical samples (50% wound, 15% tracheal aspirate and 35% other samples) of inpatients (93.3%) and outpatients (6.7%) were included in the study. Double disc synergy test (D-test) was used for the phenotypical research and PCR was used for the genotypical research of MLS(B) resistance of isolates. One hundred fifty eight (39.1%) of the S.aureus isolates were methicillin-resistant (MRSA), and 246 (60.9%) were methicillin-susceptible (MSSA). By the use of D-test, constitutive (cMLS(B)) and inducible (iMLS(B)) clindamycin resistance were detected in 19 and 111 isolates, respectively, while five isolates were MS phenotype and 268 isolates were S phenotype (susceptible to erythromycin and clindamycin). The resistance genes of 136 isolates with MLS(B) resistance phenotype were determined genotypically and among 111 isolates showing iMLS(B) phenotype ermA gene was found in 81.9% (83 MRSA, 8 MSSA), ermC gene in 10.8% (7 MRSA, 5 MSSA), msrA gene in 10.8% (11 MRSA, 1 MSSA), msrB gene in 1.8% (2 MRSA) and ermB gene in 0.9% (1 MRSA). Among 19 strains with cMLS(B) phenotype, ermA was

  3. Investigation of Stress Memorization Process on Low-Frequency Noise Performance for Strained Si n-Type Metal-Oxide-Semiconductor Field-Effect Transistors

    NASA Astrophysics Data System (ADS)

    Kuo, Cheng-Wen; Wu, San-Lein; Lin, Hau-Yu; Huang, Yao-Tsung; Chang, Shoou-Jinn; Hong, De-Gong; Wu, Chung-Yi; Cheng, Yao-Chin; Cheng, Osbert

    2011-04-01

    The use of low-frequency (1/f) noise to evaluate low-cost stress-memorization technique (SMT) induced-stress in n-type metal-oxide-semiconductor field-effect transistors has been investigated. As compared to device without SMT process, the comparable 1/f noise level obtained for strained Si devices with the low-cost SMT process indicates that adding the low-cost SMT process will not affect the Si/SiO2 interface quality. Moreover, through observing experiment result and Hooge's parameter αH, the mechanism of 1/f noise in the both devices can be properly interpreted by the carrier number fluctuations correlated mobility fluctuations (unified model).

  4. Investigation of whether in-room CT-based adaptive intracavitary brachytherapy for uterine cervical cancer is robust against interfractional location variations of organs and/or applicators

    PubMed Central

    Oku, Yoshifumi; Arimura, Hidetaka; Nguyen, Tran Thi Thao; Hiraki, Yoshiyuki; Toyota, Masahiko; Saigo, Yasumasa; Yoshiura, Takashi; Hirata, Hideki

    2016-01-01

    This study investigates whether in-room computed tomography (CT)-based adaptive treatment planning (ATP) is robust against interfractional location variations, namely, interfractional organ motions and/or applicator displacements, in 3D intracavitary brachytherapy (ICBT) for uterine cervical cancer. In ATP, the radiation treatment plans, which have been designed based on planning CT images (and/or MR images) acquired just before the treatments, are adaptively applied for each fraction, taking into account the interfractional location variations. 2D and 3D plans with ATP for 14 patients were simulated for 56 fractions at a prescribed dose of 600 cGy per fraction. The standard deviations (SDs) of location displacements (interfractional location variations) of the target and organs at risk (OARs) with 3D ATP were significantly smaller than those with 2D ATP (P < 0.05). The homogeneity index (HI), conformity index (CI) and tumor control probability (TCP) in 3D ATP were significantly higher for high-risk clinical target volumes than those in 2D ATP. The SDs of the HI, CI, TCP, bladder and rectum D2cc, and the bladder and rectum normal tissue complication probability (NTCP) in 3D ATP were significantly smaller than those in 2D ATP. The results of this study suggest that the interfractional location variations give smaller impacts on the planning evaluation indices in 3D ATP than in 2D ATP. Therefore, the 3D plans with ATP are expected to be robust against interfractional location variations in each treatment fraction. PMID:27296250

  5. Investigation of effect of variations in bone fraction and red marrow cellularity on bone marrow dosimetry in radio-immunotherapy

    NASA Astrophysics Data System (ADS)

    Wilderman, S. J.; Roberson, P. L.; Bolch, W. E.; Dewaraja, Y. K.

    2013-07-01

    A method is described for computing patient-specific absorbed dose rates to active marrow which accounts for spatial variation in bone volume fraction and marrow cellularity. A module has been added to the 3D Monte Carlo dosimetry program DPM to treat energy deposition in the components of bone spongiosa distinctly. Homogeneous voxels in regions containing bone spongiosa (as defined on CT images) are assumed to be comprised only of bone, active (red) marrow and inactive (yellow) marrow. Cellularities are determined from biopsy, and bone volume fractions are computed from cellularities and CT-derived voxel densities. Electrons are assumed to deposit energy locally in the three constituent components in proportions determined by electron energy absorption fractions which depend on energy, cellularity, and bone volume fraction, and which are either taken from the literature or are derived from Monte Carlo simulations using EGS5. Separate algorithms are used to model primary β particles and secondary electrons generated after photon interactions. Treating energy deposition distinctly in bone spongiosa constituents leads to marrow dosimetry results which differ from homogeneous spongiosa dosimetry by up to 20%. Dose rates in active marrow regions with cellularities of 20, 50, and 80% can vary by up to 20%, and can differ by up to 10% as a function of bone volume fraction. Dose to bone marrow exhibits a strong dependence on marrow cellularity and a potentially significant dependence on bone volume fraction.

  6. Refining the Late Quaternary Paleomagnetic Secular Variation record in the Mediterranean Region as a Chronologic Tool for Marine Geology Investigations

    NASA Astrophysics Data System (ADS)

    Iorio, M.; Liddicoat, J. C.; Budillon, F.; Incoronato, A.; Coe, R.; Insinga, D.; Lubritto, C.; Cassata, W. S.; Tiano, P.; Petruccione, E.

    2011-12-01

    Together, piston cores C1067, C1201 and C1202 from the continental shelf and slope in the Salerno Gulf and Cilento offshore in the Eastern Tyrrhenian Sea record long-term change (Paleomagnetic Secular Variation - PSV) of Earth's magnetic field during the last approximately 115,000 years. Each core contains the last 24,000 years except for the interval from about 20,000 to 11,000 years that is absent in C1067 and C1202 because of erosion on the continental slope. The PSV for the Eastern Tyrrhenian Sea is correlated to curves of global relative paleomagnetic field intensity in other marine cores (Stoner et al., 2002) and dated lacustrine records of PSV for western Europe (Thouveny et al., 1990) and Great Britain (Turner and Thompson, 1981). Tephrochronolgy and radiometric dates (C14 and Ar/Ar) also are used for assigning an age to the record. Along with an improved record of PSV for the Mediterranean region, the PSV in the Salerno Gulf and Cilento offshore piston cores has application for placing time constraints on the marine geology and stratigraphy on the continental shelf and slope. The result is that catastrophic events such as large-scale submarine slumps, volcanic eruptions, turbidite deposition, and abrupt changes in sedimentation rate are dated. The changes in sedimentation rate seem to be linked to global rapid sea-level pulses and climate events that induced concurrent reduction and/or abundance in the sediment supply from the adjacent coastal margin.

  7. The interstitial nuclei of the human anterior hypothalamus: an investigation of variation with sex, sexual orientation, and HIV status.

    PubMed

    Byne, W; Tobet, S; Mattiace, L A; Lasco, M S; Kemether, E; Edgar, M A; Morgello, S; Buchsbaum, M S; Jones, L B

    2001-09-01

    The interstitial nuclei of the human anterior hypothalamus (INAH1-4) have been considered candidates for homology with the sexually dimorphic nucleus of the preoptic area of the rat. Volumetric sexual dimorphism has been described for three of these nuclei (INAH1-3), and INAH3 has been reported to be smaller in homosexual than heterosexual men. The current study measured the INAH in Nissl-stained coronal sections in autopsy material from 34 presumed heterosexual men (24 HIV- and 10 HIV+), 34 presumed heterosexual women (25 HIV- and 9 HIV+), and 14 HIV+ homosexual men. HIV status significantly influenced the volume of INAH1 (8% larger in HIV+ heterosexual men and women relative to HIV- individuals), but no other INAH. INAH3 contained significantly more neurons and occupied a greater volume in presumed heterosexual males than females. No sex difference in volume was detected for any other INAH. No sexual variation in neuronal size or density was observed in any INAH. Although there was a trend for INAH3 to occupy a smaller volume in homosexual men than in heterosexual men, there was no difference in the number of neurons within the nucleus based on sexual orientation.

  8. Preliminary investigation of the elemental variation and diagenesis of a tabular uranium deposit, La Sal Mine, San Juan County, Utah

    USGS Publications Warehouse

    Brooks, Robert A.; Campbell, John A.

    1976-01-01

    Ore in the La Sal mine, San Juan County, Utah, occurs as a typical tabular-type uranium deposit of the-Colorado Plateau. Uranium-vanadium occurs in the Salt Wash Member of the Jurassic Morrison Formation. Chemical and petrographic analyses were used to determine elemental variation and diagenetic aspects across the orebody. Vanadium is concentrated in the dark clay matrix, which constitutes visible ore. Uranium content is greater above the vanadium zone. Calcium, carbonate carbon, and lead show greater than fifty-fold increase across the ore zone, whereas copper and organic carbon show only a several-fold increase. Large molybdenum concentrations are present in and above the tabular layer, and large selenium concentrations occur below the uranium zone within the richest vanadium zone. Iron is enriched in the vanadium horizon. Chromium is depleted from above the ore and strongly enriched below. Elements that vary directly with the vanadium content include magnesium, iron, selenium, zirconium, strontium, titanium, lead, boron, yttrium, and scandium. The diagenetic sequence is as follows: (1) formation of secondary quartz overgrowths as cement; (2) infilling and lining of remaining pores with amber opaline material; (3) formation of vanadium-rich clay matrix, which has replaced overgrowths as well as quartz grains; (4) replacement of overgrowths and detrital grains by calcite; (5) infilling of pores with barite and the introduction of pyrite and marcasite.

  9. Investigation of effect of variations in bone fraction and red marrow cellularity on bone marrow dosimetry in radio-immunotherapy.

    PubMed

    Wilderman, S J; Roberson, P L; Bolch, W E; Dewaraja, Y K

    2013-07-21

    A method is described for computing patient-specific absorbed dose rates to active marrow which accounts for spatial variation in bone volume fraction and marrow cellularity. A module has been added to the 3D Monte Carlo dosimetry program DPM to treat energy deposition in the components of bone spongiosa distinctly. Homogeneous voxels in regions containing bone spongiosa (as defined on CT images) are assumed to be comprised only of bone, active (red) marrow and inactive (yellow) marrow. Cellularities are determined from biopsy, and bone volume fractions are computed from cellularities and CT-derived voxel densities. Electrons are assumed to deposit energy locally in the three constituent components in proportions determined by electron energy absorption fractions which depend on energy, cellularity, and bone volume fraction, and which are either taken from the literature or are derived from Monte Carlo simulations using EGS5. Separate algorithms are used to model primary β particles and secondary electrons generated after photon interactions. Treating energy deposition distinctly in bone spongiosa constituents leads to marrow dosimetry results which differ from homogeneous spongiosa dosimetry by up to 20%. Dose rates in active marrow regions with cellularities of 20, 50, and 80% can vary by up to 20%, and can differ by up to 10% as a function of bone volume fraction. Dose to bone marrow exhibits a strong dependence on marrow cellularity and a potentially significant dependence on bone volume fraction.

  10. Investigation of the physiological response to oxygen limited process conditions of Pichia pastoris Mut(+) strain using a two-compartment scale-down system.

    PubMed

    Lorantfy, Bettina; Jazini, Mohammadhadi; Herwig, Christoph

    2013-09-01

    Inhomogeneities in production-scale bioreactors influence microbial growth and product quality due to insufficient mixing and mass transfer. For this reason, lots of efforts are being made to investigate the effects of gradients that impose stress in large-scale reactors in laboratory scale. We have implemented a scale-down model which allows separating a homogeneous part, a stirred tank reactor (STR), and a plug flow reactor (PFR) which mimics the inhomogeneous regimes of the large-scale fermenters. This scale-down model shows solutions to trigger oxygen limited conditions in the PFR part of the scale-down setup for physiological analysis. The goal of the study was to investigate the scale-up relevant physiological responses of Pichia pastoris strain to oxygen limited process conditions in the above mentioned two-compartment bioreactor setup. Experimental results with non-induced cultures show that the specific growth rate significantly decreased with increasing the exposure time to oxygen limitation. In parallel more by-products were produced. Examining physiological scalable key parameters, multivariate data analyses solely using on-line data revealed that different exposures to the oxygen limitation significantly affected the culture performance. This work with the small scale-downs setup reflects new approaches for a valuable process development tool for accelerating strain characterization or for verifying CFD simulations of large-scale bioreactors. As a novel methodological achievement, the combination of the two-compartment scale-down system with the proposed multivariate techniques of solely using on-line data is a valuable tool for recognition of stress effects on the culture performance for physiological bioprocess scale-up issues.

  11. Investigation of carbon storage regulation network (csr genes) and phenotypic differences between acid sensitive and resistant Escherichia coli O157:H7 strains

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: Escherichia coli O157:H7 and related serotype strains have previously been shown to vary in acid resistance, however, little is known about strain specific mechanisms of acid resistance. We examined sensitive and resistant E. coli strains to determine the effects of growth in minimal and...

  12. A Study to Investigate Cloud Feedback Processes and Evaluate GCM Cloud Variations Using Statistical Cloud Property Composites From ARM Data

    SciTech Connect

    George Tselioudis

    2009-08-11

    cloud layering information into the context of large-scale dynamical regimes, such information can be used to study interactions among cloud vertical distributions and dynamical and microphysical processes and to evaluate the ability of models to simulate those interactions. The U.S. Department of Energy's Atmospheric Radiation Measurement (ARM) program has established several Climate Research Facilities (ACRF) that provide continuous, long-term observations of clouds and radiation. ARM, with its overall goal of improving the treatment of radiation and clouds in climate models has provided unique observing systems for accelerating progress on the representation of cloud processes. In this project, six and a half years (January 1998 to June 2004) of cloud observations collected at the Southern Great Plains (SGP) Oklahoma ACRF were used to produce a cloud-type climatology. The climatology provides cloud amounts for seven different cloud types as well as information on the detailed structure of multi-layer cloud occurrences. Furthermore, the European Centre for Medium-Range Weather Forecasts (ECMWF) model output was used to define the dynamic regimes present during the observations of the cloud conditions by the vertically pointing radars at the SGP ACRF. The cloud-type climatology and the ECMWF SGP data set were then analyzed to examine and map dynamical conditions that favor the creation of single-layer versus multi-layer cloud structures as well as dynamical conditions that favor the occurrence of drizzle in continental stratus clouds. In addition, output from the ECMWF weather model forecasts was analyzed with the objective to compare model and radar derived cloud type statistics, in order to identify the major model deficiencies in cloud vertical distribution and map their seasonal variations. The project included two primary goals. The first was to create a cloud type climatology over the Southern Great Planes site that will show how cloud vertical distribution

  13. A piloted simulation of helicopter air combat to investigate effects of variations in selected performance and control response characteristics

    NASA Technical Reports Server (NTRS)

    Lewis, Michael S.; Mansur, M. Hossein; Chen, Robert T. N.

    1987-01-01

    A piloted simulation study investigating handling qualities and flight characteristics required for helicopter air to air combat is presented. The Helicopter Air Combat system was used to investigate this role for Army rotorcraft. Experimental variables were the maneuver envelope size (load factor and sideslip), directional axis handling qualities, and pitch and roll control-response type. Over 450 simulated, low altitude, one-on-one engagements were conducted. Results from the experiment indicate that a well damped directional response, low sideforce caused by sideslip, and some effective dihedral are all desirable for weapon system performance, good handling qualities, and low pilot workload. An angular rate command system was favored over the attitude type pitch and roll response for most applications, and an enhanced maneuver envelope size over that of current generation aircraft was found to be advantageous. Pilot technique, background, and experience are additional factors which had a significant effect on performance in the air combat tasks investigated. The implication of these results on design requirements for future helicopters is presented.

  14. Investigation of lactic acid bacterial strains for meat fermentation and the product's antioxidant and angiotensin-I-converting-enzyme inhibitory activities.

    PubMed

    Takeda, Shiro; Matsufuji, Hisashi; Nakade, Koji; Takenoyama, Shin-Ichi; Ahhmed, Abdulatef; Sakata, Ryoichi; Kawahara, Satoshi; Muguruma, Michio

    2016-08-02

    In the lactic acid bacteria (LAB) strains screened from our LAB collection, Lactobacillus (L.) sakei strain no. 23 and L. curvatus strain no. 28 degraded meat protein and tolerated salt and nitrite in vitro. Fermented sausages inoculated strains no. 23 and no. 28 showed not only favorable increases in viable LAB counts and reduced pH, but also the degradation of meat protein. The sausages fermented with these strains showed significantly higher antioxidant activity than those without LAB or fermented by each LAB type strain. Angiotensin-I-converting-enzyme (ACE) inhibitory activity was also significantly higher in the sausages fermented with strain no. 23 than in those fermented with the type strain. Higher ACE inhibitory activity was also observed in the sausages fermented with strain no. 28, but did not differ significantly from those with the type strain. An analysis of the proteolysis and degradation products formed by each LAB in sausages suggested that those bioactivities yielded fermentation products such as peptides. Therefore, LAB starters that can adequately ferment meat, such as strains no. 23 and no. 28, should contribute to the production of bioactive compounds in meat products.

  15. Genetic diversity of Histoplasma capsulatum strains isolated from Argentina based on nucleotide sequence variations in the internal transcribed spacer regions of rDNA.

    PubMed

    Landaburu, Fernanda; Cuestas, María Luján; Rubio, Andrea; Elías, Nahuel Alejandro; Daneri, Gabriela Lopez; Veciño, Cecilia; Iovannitti, Cristina A; Mujica, María Teresa

    2014-05-01

    The internal transcribed spacer (ITS) regions of rDNA genes of 49 Histoplasma capsulatum (48 from clinical samples and one from soil) isolates were examined. Nucleotide sequence heterogeneity within this region was useful for phylogenetic classification of H. capsulatum and species identification. Thus, in 45 of 49 isolates we observed higher percentages of identity in the nucleotide sequences of ITS regions when the isolates studied herein were compared with those reported in our country in the South America B clade. Phylogenetic analyses of rDNA sequences corresponding to the 537 bp of the ITS region obtained from H. capsulatum isolates assigned South America type B clade (45 isolates), North America type 1 and Asia clade (2 isolates each one). H. capsulatum strains isolated from soil and from patients living in Argentina (45 of 49) clustered together with the H. capsulatum isolates of the South America B clade. The high level of genetic similarity among our isolates suggests that almost one genetic population is present in the microenvironment. Isolates described as H. capsulatum var. capsulatum or var. farciminosum (2 isolates) did not form a monophyletic group and were found in the Asia clade. Subsequent studies are needed to properly identify these isolates.

  16. Differences in the carriage and the ability to utilize the serotype associated virulence plasmid in strains of Salmonella enterica serotype Typhimurium investigated by use of a self-transferable virulence plasmid, pOG669.

    PubMed

    Olsen, John E; Brown, Derek J; Thomsen, Line E; Platt, David J; Chadfield, Mark S

    2004-06-01

    Most strains of Salmonella enterica subspecies enterica serotype typhimurium (S. typhimurium) naturally harbour a virulence plasmid which carries the salmonella plasmid virulence (spv) genes. However, isolates belonging to certain phage types are generally found without the plasmid. We have utilized a self-transferable virulence plasmid, pOG669 to investigate the effect of introduction of spv genes into strains of such phage types. The use of the co-integrate plasmid, pOG669, was validated on a diverse collection of strains. pOG669 was transferred into strains of serotypes that are normally associated with the possession of virulence plasmids. All strains maintained the wild type level of virulence in a mouse model, except that introduction of pOG669 restored normal virulence levels in an avirulent, plasmid free strain of S. dublin and resulted in a decrease in virulence in a strain of S. dublin from clonal line Du3. S. gallinarum did not become virulent in mice, but pOG669 was functionally interchangeable with the wild type plasmid when strains were tested in a chicken model. Strains of serotypes not normally associated with the carriage of a virulence plasmid did not increase in virulence upon the introduction of pOG669. An IncX plasmid pOG670 that was included as control was incompatible with the virulence plasmid in a strain of S. dublin, demonstrating that the common virulence plasmid of this serotype is of a different incompatibility group than other virulence plasmids. Strains of S. typhimurium from phage types that do not normally carry a virulence plasmid responded differently to attempts to introduce pOG669. No transconjugants were observed with the strains of DT5 and DT21. The introduction of pOG669 did not alter the virulence of JEO3942(DT10), DT35 and JEO3949(DT66) significantly, while DT1 and DT27 became more virulent. DT27 became as virulent as wild type C5, while logVC(10) of DT1 only increased from 4.1 to 5.7. The ability to express spv-genes was

  17. Investigations of nanoscale variations in spin and charge transport in manganites and organic semiconductors using spin polarized scanning tunneling spectroscopy

    NASA Astrophysics Data System (ADS)

    Hughes, Cameron Richard

    Analysis of DNA structure and behavior, up to and including full sequencing of a genome's bases, and of biological processes such as replication, transcription and translation, is essential for an understanding of genetic variation, heritable diseases and the effects of environmental factors. Recently, single-molecule techniques have been developed to study DNA properties in unprecedented detail. For a number of these techniques, controlled adsorption of linearly stretched DNA molecules on surfaces is necessary. In experiments where hybridization of adsorbed molecules to labeled probes is used to determine DNA structure, single-stranded DNA is needed. Conventionally, for long DNA's (up to Mbp), double-stranded DNA is deposited on a surface and denatured in-situ. While successful, this method has several disadvantages. This thesis reports efforts to directly adsorb long single-stranded DNA's out of solution as an alternative strategy. It consists of three parts: (1) Establishment of a simple method using Acridine Orange (AO) staining dye to determine whether DNA's are ss or ds on the surface. The method allows for the assessment of the degree of renaturation during deposition. Incubation of surface-adsorbed DNA in solutions of AO dye in the concentration range of 10--15uM were found to be effective for discriminating between ss DNA and ds DNA based on differences in the fluorescence emission spectra. (2) Deposition of ss DNA produced by heat denaturation on polymer-coated surfaces. Lambda DNA (48502bp) was adsorbed by drop evaporation or dipping/extraction of surface out of a buffered solution. The efficiency of deposition was optimized with respect to DNA concentration, buffer type and pH. (3) Separation of complementary single strands of Lambda, mono-cut digest and HindIII digest by gel electrophoresis. Using agarose gels in concentrations ranging from 0.4% to 1.4% (weight/volume), electric fields in the range 1--4V/cm in 1x Tris-Acetate-EDTA (TAE) buffer, good

  18. National investigation of semi-volatile organic compounds (PAHs, OCPs, and PCBs) in lake sediments of China: Occurrence, spatial variation and risk assessment.

    PubMed

    Li, Chaocan; Huo, Shouliang; Yu, Zhiqiang; Xi, Beidou; Yeager, Kevin M; He, Zhuoshi; Ma, Chunzi; Zhang, Jingtian; Wu, Fengchang

    2017-02-01

    In this study, a large scale investigation of semi-volatile organic compounds (SVOCs) in sediments from 52 lakes, located in five geographic regions across China, was conducted to assess sediment quality in terms of organic contaminants. Concentrations of polycyclic aromatic hydrocarbons (PAHs), organochlorine pesticides (OCPs), and polychlorinated biphenyls (PCBs) in sediment were found to range between 17.00-6,633, 0.12-45.24, and 0.03-13.99ngg(-1), respectively. Lake sediments from different regions exhibited variation in contamination levels, and in the compositions of isomers. The descending order of contamination levels for the three SVOCs groups (i.e., ∑PAHs, ∑OCPs, ∑PCBs) were as follows: the eastern plain region (EPR)>the Yunnan-Guizhou plateau (YGP)>the northeast China region (NCR)>the Qinghai-Tibet plateau (QTP)>the Mongolia-Xinjiang plateau (MXP). High molecular weight PAHs, OCPs and PCBs were found at high concentrations in parts of the EPR and YGP, while lighter isomers were likely to be atmospherically transported, resulting in their nationwide distribution. The sources and type variation (local input or atmospheric deposition) are the primary controls of spatial variation. Additionally, human related socio-economic factors, and geographic conditions also played important roles in influencing the spatial differentiation. According to simple sediment quality guidelines (SQG), the risks posed by PCBs in sediments were not as serious as those posed by PAHs and DDT.

  19. Large sedimentary aquifer system and sustainable management: investigations of hydrogeological and geochemical variations in Eocene sand aquifer, south western France

    NASA Astrophysics Data System (ADS)

    Malcuit, E.; Negrel, P. J.; Petelet-Giraud, E.; Durst, P.

    2010-12-01

    In the sedimentary Aquitaine Basin, the Eocene Sand Aquifer system, mostly confined, represents strategic resources for drinking water, irrigation, gas storage and geothermal resources. Therefore, its quantity and quality issues are essential for the sustainable management in this large region that extends over 116,000 km2 (i.e. one-fifth of the French territory). The Eocene Sand Aquifer system comprises at least five aquifers: Paleocene, Eocene infra-molassic sands, early Eocene, middle Eocene, and late Eocene. The extension and thickness of Eocene aquifer layers and negative confined layers vary throughout the basin, from several tens of metres to a hundred metres. The deposit sequences characterizing the Eocene Aquifer System are progradational westward from detrital deposits to carbonates. Eocene sands and Eocene limestones are hydraulically connected and covered by an aquiclude of up to several hundred metres thick of molassic sediments. The groundwater recharge is assumed to occur through the Eocene outcrops located in the north and north-east, and in the south east in contact with the Montagne Noire as well as by vertical leakage from the upper and lower aquifers. Another recharge is suspected in the south near the Petites Pyrenees. According to isotopic data, both present-day recharge and old recharge (16-35 ky) can be evidenced. The north and south evolutions of the piezometric surface are different. In the north, because of years of pumping, a trough in the potentiometric surface has been formed. The piezometric decline is roughly one meter per year in the depression centre. In the south, the decline of the water table is roughly half a meter per year. Furthermore, in the south part, around two sites of gas storage, significant fluctuations of the potentiometric surface are superimposed to the variations resulting from water abstraction, due to the injection and abstraction of gas. However, a major difficulty for the sustainable management is the lack of

  20. Investigation of defect structure of impurity-doped lithium niobate by combining thermodynamic constraints with lattice constant variations

    SciTech Connect

    Koyama, Chihiro; Nozawa, Jun Fujiwara, Kozo; Uda, Satoshi; Maeda, Kensaku

    2015-01-07

    The defect structures of impurity-doped congruent lithium niobates (c-LN) were determined for impurities with various valences, including divalent, trivalent, and tetravalent impurities, in a concentration range where antisite niobium (Nb{sub Li}) exists. On the basis of the “Li site vacancy model,” six kinds of defect structures in impurity-doped c-LN are possible. Using thermodynamic constraints, these can be narrowed down to two kinds. The first structure is that in which impurities, vacancies and Nb exist as defects in the Li site and no defects exist in the Nb site (structure A), described as ([Li{sub Li}] {sub 1-5x-jy}[Nb{sub Li}]{sub x}[M{sub Li}]{sub y}[V{sub Li}]{sub 4x+(j-1)y})[Nb{sub Nb}][O{sub O}] {sub 3} (V: vacancy, M: impurity, j: valence of impurity, x, y: compositional variable (≠0), Li/Nb = congruent ratio). ([Li{sub Li}{sup ×}] {sub 1-5x-2y}[Nb{sub Li}{sup ••••}]{sub x}[M{sub Li}{sup •}]{sub y}[V{sub Li}{sup ′}]{sub 4x+y})[Nb{sub Nb}{sup ×}][O{sub O}{sup ×}] {sub 3} is an example by the Kröger-Vink notation for divalent M. In the second structure, vacancies and Nb exist as defects in the Li site and impurities exist as defects in the Nb site (structure B), described as ([Li{sub Li}] {sub 1-5x-(j-5)y}[Nb{sub Li}]{sub x}[V{sub Li}]{sub 4x+(j-5)y})([Nb{sub Nb}] {sub 1-y}[M{sub Nb}]{sub y})[O{sub O}] {sub 3}. ([Li{sub Li}{sup ×}] {sub 1-5x+y}[Nb{sub Li}{sup ••••}]{sub x}[V{sub Li}{sup ′}]{sub 4x-y})([Nb{sub Nb}{sup ×}] {sub 1-y}[M{sub Nb}{sup ′}]{sub y})[O{sub O}{sup ×}] {sub 3} is an example for tetravalent M. Since the relationship between impurity concentration and lattice constants for structures A and B differs, the defect structures can be differentiated by analyzing lattice constant variations as a function of impurity concentration. The results show that the defect structure of divalent and trivalent impurity-doped c-LN is structure A and that of tetravalent impurity-doped c-LN is

  1. Cd hyperfine interactions in DNA bases and DNA of mouse strains infected with Trypanosoma cruzi investigated by perturbed angular correlation spectroscopy and ab initio calculations.

    PubMed

    Petersen, Philippe A D; Silva, Andreia S; Gonçalves, Marcos B; Lapolli, André L; Ferreira, Ana Maria C; Carbonari, Artur W; Petrilli, Helena M

    2014-06-03

    In this work, perturbed angular correlation (PAC) spectroscopy is used to study differences in the nuclear quadrupole interactions of Cd probes in DNA molecules of mice infected with the Y-strain of Trypanosoma cruzi. The possibility of investigating the local genetic alterations in DNA, which occur along generations of mice infected with T. cruzi, using hyperfine interactions obtained from PAC measurements and density functional theory (DFT) calculations in DNA bases is discussed. A comparison of DFT calculations with PAC measurements could determine the type of Cd coordination in the studied molecules. To the best of our knowledge, this is the first attempt to use DFT calculations and PAC measurements to investigate the local environment of Cd ions bound to DNA bases in mice infected with Chagas disease. The obtained results also allowed the detection of local changes occurring in the DNA molecules of different generations of mice infected with T. cruzi, opening the possibility of using this technique as a complementary tool in the characterization of complicated biological systems.

  2. Serotonin and Dopamine Gene Variation and Theory of Mind Decoding Accuracy in Major Depression: A Preliminary Investigation

    PubMed Central

    Zahavi, Arielle Y.; Sabbagh, Mark A.; Washburn, Dustin; Mazurka, Raegan; Bagby, R. Michael; Strauss, John; Kennedy, James L.; Ravindran, Arun; Harkness, Kate L.

    2016-01-01

    Theory of mind–the ability to decode and reason about others’ mental states–is a universal human skill and forms the basis of social cognition. Theory of mind accuracy is impaired in clinical conditions evidencing social impairment, including major depressive disorder. The current study is a preliminary investigation of the association of polymorphisms of the serotonin transporter (SLC6A4), dopamine transporter (DAT1), dopamine receptor D4 (DRD4), and catechol-O-methyl transferase (COMT) genes with theory of mind decoding in a sample of adults with major depression. Ninety-six young adults (38 depressed, 58 non-depressed) completed the ‘Reading the Mind in the Eyes task’ and a non-mentalistic control task. Genetic associations were only found for the depressed group. Specifically, superior accuracy in decoding mental states of a positive valence was seen in those homozygous for the long allele of the serotonin transporter gene, 9-allele carriers of DAT1, and long-allele carriers of DRD4. In contrast, superior accuracy in decoding mental states of a negative valence was seen in short-allele carriers of the serotonin transporter gene and 10/10 homozygotes of DAT1. Results are discussed in terms of their implications for integrating social cognitive and neurobiological models of etiology in major depression. PMID:26974654

  3. From genome-wide to candidate gene: an investigation of variation at the major histocompatibility complex in common bottlenose dolphins exposed to harmful algal blooms.

    PubMed

    Cammen, Kristina M; Wilcox, Lynsey A; Rosel, Patricia E; Wells, Randall S; Read, Andrew J

    2015-02-01

    The role the major histocompatibility complex (MHC) plays in response to exposure to environmental toxins is relatively poorly understood, particularly in comparison to its well-described role in pathogen immunity. We investigated associations between MHC diversity and resistance to brevetoxins in common bottlenose dolphins (Tursiops truncatus). A previous genome-wide association study investigating an apparent difference in harmful algal bloom (HAB) resistance among dolphin populations in the Gulf of Mexico identified genetic variation associated with survival in close genomic proximity to multiple MHC class II loci. Here, we characterized genetic variation at DQA, DQB, DRA, and DRB loci in dolphins from central-west Florida and the Florida Panhandle, including dolphins that died during HABs and dolphins presumed to have survived HAB exposure. We found that DRB and DQB exhibited patterns of genetic differentiation among geographic regions that differed from neutral microsatellite loci. In addition, genetic differentiation at DRB across multiple pairwise comparisons of live and dead dolphins was greater than differentiation observed at neutral loci. Our findings at these MHC loci did not approach the strength of association with survival previously described for a nearby genetic variant. However, the results provide evidence that selective pressures at the MHC vary among dolphin populations that differ in the frequency of HAB exposure and that the overall composition of DRB variants differs between dolphin survivors and non-survivors of HABs. These results may suggest a potential role of MHC diversity in variable survival of bottlenose dolphins exposed to HABs.

  4. Strain evaluation of strengthened concrete structures using FBG sensors

    NASA Astrophysics Data System (ADS)

    Lau, Kin-tak; Zhou, Li-min; Ye, Lin

    1999-12-01

    Fibre-optic Bragg Grating (FBG) sensor presents a great deal of potential in monitoring the internal status of the concrete structures after repairing or strengthening by an external adhered reinforcement. It can be used in a variety of configurations ranging from pointwise to multi-point strain measurement in order to investigate the strain distribution of the structures. In this paper, an experimental investigation on the rectangular notched-concrete beam, which was strengthened by glass fibre composites with the embedment of multiplexing FBG sensors is presented. Three point bending test was performed to investigate the strain profile of the specimen. Frequency modulated continuous wave (FMCW) technique was used to measure the strain variation of the fibre-grating regions. The results give a good agreement with the electrical resistance strain gauge in early loading condition. The difference of the strain-measuring results between the strain-gauge and FBG sensor was increased when further increasing the applied load. It was suspected that the micro/marco cracks occurred on the concrete surface and that the externally bonded strain-measuring device cannot be detected.

  5. Strain evaluation of strengthened concrete structures using FBG sensors

    SciTech Connect

    Lau Kintak; Zhou Limin; Ye Lin

    1999-12-02

    Fibre-optic Bragg Grating (FBG) sensor presents a great deal of potential in monitoring the internal status of the concrete structures after repairing or strengthening by an external adhered reinforcement. It can be used in a variety of configurations ranging from pointwise to multi-point strain measurement in order to investigate the strain distribution of the structures. In this paper, an experimental investigation on the rectangular notched-concrete beam, which was strengthened by glass fibre composites with the embedment of multiplexing FBG sensors is presented. Three point bending test was performed to investigate the strain profile of the specimen. Frequency modulated continuous wave (FMCW) technique was used to measure the strain variation of the fibre-grating regions. The results give a good agreement with the electrical resistance strain gauge in early loading condition. The difference of the strain-measuring results between the strain-gauge and FBG sensor was increased when further increasing the applied load. It was suspected that the micro/marco cracks occurred on the concrete surface and that the externally bonded strain-measuring device cannot be detected.

  6. Variations in aortic pressure affect the mechanics of the intra-aortic balloon: an in vitro investigation.

    PubMed

    Biglino, Giovanni; Kolyva, Christina; Whitehorne, Michael; Pepper, John R; Khir, Ashraf W

    2010-07-01

    This study aims to investigate the mechanics of the intra-aortic balloon (IAB) under different aortic pressure (P(ao)) and inclination (0-75 degrees). Pressure and flow were measured in an artificial aorta during IAB pumping with a frequency of 1:3. Volume displaced toward the "coronary arteries" during inflation (V(prox)) and "intra-aortic" pressure reduction during deflation (P(r)) were derived. IAB duration of inflation and deflation was determined with a high-speed camera visualization. When the aorta was horizontal, P(ao) raised from 45 mm Hg to 115 mm Hg, V(prox) reduced by 18% (25.0 +/- 1.0 mL vs. 30.4 +/- 1.9 mL) and P(r) increased by 117% (106.4 +/- 0.3 mm Hg vs. 48.9 +/- 0.6 mm Hg). When the aorta was inclined, at low P(ao) of 45 mm Hg, V(prox) was reduced by 30% from 0 degrees to 45 degrees (19.8 +/- 2.3 mL vs. 28.3 +/- 1.7 mL) and P(r) was reduced by 66% (16.5 +/- 0.1 mm Hg vs. 48.9 +/- 0.6 mm Hg). However, at high P(ao) of 115 mm Hg, V(prox) remained unchanged with increasing angle (20.0 +/- 1.0 mL) and P(r) was reduced by 24% (80.6 +/- 0.8 mm Hg vs. 106.4 +/- 0.3 mm Hg). Increasing P(ao) increased duration of inflation. At low P(ao), increasing angle resulted in increasing duration of inflation, but at high P(ao), increasing angle had the opposite effect. Duration of deflation generally decreased with P(ao) and increased with increasing angle. The IAB pump is affected by both P(ao) and angle, indicating that non-normotensive patients or patients in the semi-recumbent position might not receive the full benefits of IAB counterpulsation.

  7. Investigation of global variations in the in amplitude and frequency content of the PdP, SdS and Pds phases from common upper mantle discontinuities

    NASA Astrophysics Data System (ADS)

    Ainiwaer, A.; Gurrola, H.; Zou, Z.

    2013-12-01

    The global existence of transition zone discontinuities at 410 km and 660 km depths and both almost universally observed in PdP, SdS and Pds data but the 520 and 660 are usually not observed in PdP data.. Discontinuities at approximately 220 km and 520 km depth are observed in these types of data at many regions. The discontinuities at 410, 520 and 660 km are believed to be the polymorphic phase transition zone in olivine. At 410 km discontinuity, α-olivine transforms to β-wadsleyite while γ-ringwoodite decomposes into wusite and provskite at 660 discontinuity while the 220 is usually considered to be the LAB and caused by partial melt. The contrast of elastic properties and the thickness of discontinuity can be estimated by investigating the amplitude of reflected or converted seismic waves. Recent progress in our ability to image these discontinuities in PP and SS data have made it possible to image these PdP and SdS phases to a much as 4 Hz. This will make it possible to investigate the frequency response of these phases to frequencies previously not possible; analysis of which makes it possible add new insight as to the nature of these boundaries. For example beneath the regions beneath the Line Island and the Aleutian Trench The PdP phase has amplitudes of 0.04 to 0.08, which is significantly higher than beneath Hawaii(0.02-0.04) and the region near the Nazca Plate and South American subduction zone Plate where the PdP phase has amplitudes of 0.02-0.04. We interpret that the difference of reflection amplitudes is the result of variations in the impedance between layers due to variations in the velocity and density contrast and the sharpness thereof. For example in most region investigated the P510P is not present in our data but is present in some regions such as the Line Islands. But the phase change expected for the 520 is usually considered to occur over a wide range of depths in which case it should not be visible anywhere at such high frequencies

  8. Natural Strain

    NASA Technical Reports Server (NTRS)

    Freed, Alan D.

    1995-01-01

    The purpose of this paper is to present a consistent and thorough development of the strain and strain-rate measures affiliated with Hencky. Natural measures for strain and strain-rate, as I refer to them, are first expressed in terms of of the fundamental body-metric tensors of Lodge. These strain and strain-rate measures are mixed tensor fields. They are mapped from the body to space in both the Eulerian and Lagrangian configurations, and then transformed from general to Cartesian fields. There they are compared with the various strain and strain-rate measures found in the literature. A simple Cartesian description for Hencky strain-rate in the Lagrangian state is obtained.

  9. Beyond Punnett Squares: Student Word Association and Explanations of Phenotypic Variation through an Integrative Quantitative Genetics Unit Investigating Anthocyanin Inheritance and Expression in "Brassica rapa" Fast Plants

    ERIC Educational Resources Information Center

    Batzli, Janet M.; Smith, Amber R.; Williams, Paul H.; McGee, Seth A.; Dosa, Katalin; Pfammatter, Jesse

    2014-01-01

    Genetics instruction in introductory biology is often confined to Mendelian genetics and avoids the complexities of variation in quantitative traits. Given the driving question "What determines variation in phenotype (Pv)? (Pv=Genotypic variation Gv + environmental variation Ev)," we developed a 4-wk unit for an inquiry-based laboratory…

  10. Construction and preliminary investigation of a novel dengue serotype 4 chimeric virus using Japanese encephalitis vaccine strain SA14-14-2 as the backbone.

    PubMed

    Li, Zhushi; Yang, Huiqiang; Yang, Jian; Lin, Hua; Wang, Wei; Liu, Lina; Zhao, Yu; Liu, Li; Zeng, Xianwu; Yu, Yongxin; Li, Yuhua

    2014-10-13

    For the purpose of developing a novel dengue vaccine candidate, recombinant plasmids were constructed which contained the full length cDNA clone of Japanese encephalitis (JE) vaccine strain SA14-14-2 with its premembrane (PreM) and envelope (E) genes replaced by the counterparts of dengue virus type 4 (DENV4). By transfecting the in vitro transcription products of the recombinant plasmids into BHK-21 cells, a chimeric virus JEV/DENV4 was successfully recovered. The chimeric virus was identified by complete genome sequencing, Western blot and immunofluorescent staining. Growth characteristics revealed it was well adapted to primary hamster kidney (PHK) cells. Its genetic stability was investigated and only one unintentional mutation in 5'-untranslated region (5'-UTR) was found after 20 passages in PHK cells. Neurotropism, neurovirulence and immunogenicity of the chimeric virus were tested in mice. Besides, the influence of JE vaccine pre-immunization on the neutralizing antibody level induced by the chimeric virus was illuminated. To our knowledge, this is the first chimeric virus incorporating the JE vaccine stain SA14-14-2 and DENV4. It is probably a potential candidate to compose a tetravalent dengue chimeric vaccine.

  11. Assessment of analysis-of-variance-based methods to quantify the random variations of observers in medical imaging measurements: guidelines to the investigator.

    PubMed

    Zeggelink, William F A Klein; Hart, Augustinus A M; Gilhuijs, Kenneth G A

    2004-07-01

    The random variations of observers in medical imaging measurements negatively affect the outcome of cancer treatment, and should be taken into account during treatment by the application of safety margins that are derived from estimates of the random variations. Analysis-of-variance- (ANOVA-) based methods are the most preferable techniques to assess the true individual random variations of observers, but the number of observers and the number of cases must be taken into account to achieve meaningful results. Our aim in this study is twofold. First, to evaluate three representative ANOVA-based methods for typical numbers of observers and typical numbers of cases. Second, to establish guidelines to the investigator to determine which method, how many observers, and which number of cases are required to obtain the a priori chosen performance. The ANOVA-based methods evaluated in this study are an established technique (pairwise differences method: PWD), a new approach providing additional statistics (residuals method: RES), and a generic technique that uses restricted maximum likelihood (REML) estimation. Monte Carlo simulations were performed to assess the performance of the ANOVA-based methods, which is expressed by their accuracy (closeness of the estimates to the truth), their precision (standard error of the estimates), and the reliability of their statistical test for the significance of a difference in the random variation of an observer between two groups of cases. The highest accuracy is achieved using REML estimation, but for datasets of at least 50 cases or arrangements with 6 or more observers, the differences between the methods are negligible, with deviations from the truth well below +/-3%. For datasets up to 100 cases, it is most beneficial to increase the number of cases to improve the precision of the estimated random variations, whereas for datasets over 100 cases, an improvement in precision is most efficiently achieved by increasing the number of

  12. Use of transgenic GFP reporter strains of the nematode Caenorhabditis elegans to investigate the patterns of stress responses induced by pesticides and by organic extracts from agricultural soils.

    PubMed

    Anbalagan, Charumathi; Lafayette, Ivan; Antoniou-Kourounioti, Melissa; Gutierrez, Carmen; Martin, Jose Rodriguez; Chowdhuri, Debapratim K; De Pomerai, David I

    2013-01-01

    As a free-living nematode, C. elegans is exposed to various pesticides used in agriculture, as well as to persistent organic residues which may contaminate the soil for long periods. Following on from our previous study of metal effects on 24 GFP-reporter strains representing four different stress-response pathways in C. elegans (Anbalagan et al. Ecotoxicology 21:439-455, 2012), we now present parallel data on the responses of these same strains to several commonly used pesticides. Some of these, like dichlorvos, induced multiple stress genes in a concentration-dependent manner. Unusually, endosulfan induced only one gene (cyp-34A9) to very high levels (8-10-fold) even at the lowest test concentration, with a clear plateau at higher doses. Other pesticides, like diuron, did not alter reporter gene expression detectably even at the highest test concentration attainable, while others (such as glyphosate) did so only at very high concentrations. We have also used five responsive GFP reporters to investigate the toxicity of soil pore water from two agricultural sites in south-east Spain, designated P74 (used for cauliflower production, but significantly metal contaminated) and P73 (used for growing lettuce, but with only background levels of metals). Both soil pore water samples induced all five test genes to varying extents, yet artificial mixtures containing all major metals present had essentially no effect on these same transgenes. Soluble organic contaminants present in the pore water were extracted with acetone and dichloromethane, then after evaporation of the solvents, the organic residues were redissolved in ultrapure water to reconstitute the soluble organic components of the original soil pore water. These organic extracts induced transgene expression at similar or higher levels than the original pore water. Addition of the corresponding metal mixtures had either no effect, or reduced transgene expression towards the levels seen with soil pore water only. We

  13. Investigation on Raman spectral features of a coated tablet under variation of its orientation respective to laser illumination and measurement of nominal coating thickness of packed tablets.

    PubMed

    Kim, Jaejin; Hwang, Jinyoung; Woo, Young-Ah; Chung, Hoeil

    2016-11-30

    To investigate Raman spectral features of a coated biconvex tablet under variation of its orientation respective to laser illumination, spectra of the tablet were collected by illuminating laser on 12 different locations on the tablet with 3 different illumination angles of 45, 75 and 90°. The spectral variations were more substantial when the tablet faces with engraved letters and greater surface curvature were measured, since the sampled volume of coating relative to that of a core tablet changed significantly under these circumstances as the illumination angle varied. The preliminary examination confirmed that the acquisition of tablet-representative spectra was the requisite for reliable measurement of coating thickness. Then, to mimic real monitoring of coating process, Raman spectra were directly collected on a packing of 30 tablets with repetition of random tablet packing up to 15 times and univariate models utilizing the intensity of coating peak at 638cm(-1) were developed using the cumulatively averaged spectra with an average weight of the 30 tablets as a reference. To acquire less tablet orientation-sensitive spectra, a wide area illumination (WAI) scheme providing a large sampling area (28.3mm(2)) on a tablet with a long focal length (∼25cm) was employed. The averaging of the first to seventh spectra, equivalently utilizing more packing-representative spectra for quantitative analysis, made the measurement of nominal coating thickness of packed tablets accurate.

  14. Development of a method for simultaneously genotyping multiple horse coat colour loci and genetic investigation of basic colour variation in Thoroughbred and Misaki horses in Japan.

    PubMed

    Kakoi, H; Tozaki, T; Nagata, S; Gawahara, H; Kijima-Suda, I

    2009-12-01

    In order to develop a genotyping method that can be used in the registration procedure for Thoroughbreds, we developed a method for simultaneously genotyping multiple coat colour genes on the basis of single nucleotide polymorphism typing by using the SNaPshot(TM) technique. This method enabled precise and reasonable detection of causal mutations; it was effective for genotyping of MC1R, ASIP, and SLC45A2 at the Extension (E), Agouti (A), Cream dilution (C) loci, and the possibility of identification of rare variants of MC1R, EDNRB and KIT at the E, Overo (O) and Sabino 1 (SB1) loci, respectively, was also indicated. It was considered that this genotyping method would provide information not only for the registration of Thoroughbreds but also for the preservation of phenotypic characters, such as coat colour, of endangered Misaki native horses in Japan. Therefore, genetic variations at the five coat colour loci were investigated in 1111 Thoroughbred and 99 Misaki native horses. Allele frequencies at the polymorphic E and A loci were estimated, and the proportions of basic coat colours that could be expected in the Thoroughbred population were bay, 0.662; black, 0.070; chestnut, 0.268. In the Misaki population, they were bay, 0.792; black, 0.129; chestnut, 0.080. The data presented were the first of its kind on genetic coat colour variation, and will be important with regard to the registration of Thoroughbreds and the management of Misaki horses.

  15. Investigation into the Effect of Ethylcellulose Viscosity Variation on the Drug Release of Metoprolol Tartrate and Acetaminophen Extended Release Multiparticulates-Part I.

    PubMed

    Mehta, R; Teckoe, J; Schoener, C; Workentine, S; Ferrizzi, D; Rajabi-Siahboomi, A

    2016-12-01

    Ethylcellulose is one of the most commonly used polymers to develop reservoir type extended release multiparticulate dosage forms. For multiparticulate extended release dosage forms, the drug release is typically governed by the properties of the barrier membrane coating. The ICH Pharmaceutical Development Guideline (ICH Q8) requires an understanding of the influence of critical material attributes and critical process parameters on the drug release of a pharmaceutical product. Using this understanding, it is possible to develop robust formulations with consistent drug release characteristics. Critical material attributes for ethylcellulose were evaluated, and polymer molecular weight variation (viscosity) was considered to be the most critical attribute that can impact drug release. To investigate the effect of viscosity variation within the manufacturer's specifications of ethylcellulose, extended release multiparticulate formulations of two model drugs, metoprolol tartrate and acetaminophen, were developed using ETHOCEL™ as the rate controlling polymer. Quality by Design (QbD) samples of ETHOCEL Std. 10, 20, and 100 Premium grades representing the low, medium, and high molecular weight (viscosity) material were organically coated onto drug layered multiparticulates to a 15% weight gain (WG). The drug release was found to be similar (f 2 > 50) for both metoprolol tartrate and acetaminophen multiparticulates at different coating weight gains of ethylcellulose, highlighting consistent and robust drug release performance. The use of ETHOCEL QbD samples also serves as a means to develop multiparticulate dosage formulations according to regulatory guidelines.

  16. Genomic characterization and molecular investigation of VP7 epitopes of uncommon G10P[8] group A rotavirus strains detected in Italy in 2009.

    PubMed

    Ianiro, Giovanni; Delogu, Roberto; Fiore, Lucia; Ruggeri, Franco M

    2015-07-01

    Rotavirus strains with the uncommon genotype G10 have been detected sporadically in cases of acute gastroenteritis in humans and are thought to be transmitted zoonotically. During 2009, 10 G10P[8] rotavirus strains were detected in the stools of children hospitalized with acute diarrhoea in several paediatric hospitals in Italy. The phylogenetic analysis of the VP7 gene of the Italian G10P[8] strains analysed revealed nucleotide identities ranging from 94 to 99 %. Molecular characterization of the 11 genomic segments was performed for one of the G10 strains, which displayed a complete genomic constellation 1 for the non-G genes. The analysis of the deduced amino acid sequences of the G10 VP7 epitopes revealed low amino acid identity with common human strains of different G genotype and with the VP7 proteins included in both anti-rotavirus commercial vaccines (Rotarix and RotaTeq). Amongst the common G genotypes, the VP7 amino acid sequence of the G10 strains showed a high similarity with sequences from G9 strains. A hydrophobic cluster analysis (HCA) of the VP7 protein including aa 20-298 was performed for the G10 Italian sequences in comparison with the major human group A rotavirus G genotypes. The HCA analysis confirmed the findings obtained previously by amino acid analysis of the VP7 epitopes, detecting a genotype-specific pattern of hydrophobicity in the hypervariable regions of the major outer capsid protein.

  17. Screening of freshwater and seawater microalgae strains in fully controlled photobioreactors for biodiesel production.

    PubMed

    Taleb, A; Kandilian, R; Touchard, R; Montalescot, V; Rinaldi, T; Taha, S; Takache, H; Marchal, L; Legrand, J; Pruvost, J

    2016-10-01

    Strain selection is one of the primary hurdles facing cost-effective microalgal biodiesel production. Indeed, the strain used affects both upstream and downstream biodiesel production processes. This study presents a screening procedure that considers the most significant criteria in microalgal biodiesel production including TAG production and wet extraction and recovery of TAGs. Fourteen freshwater and seawater strains were investigated. Large variation was observed between the strains in all the screening criteria. The overall screening procedure ultimately led to the identification of Parachlorella kessleri UTEX2229 and Nannochloropsis gaditana CCMP527 as the best freshwater and seawater strains, respectively. They featured the largest areal TAG productivity equal to 2.7×10(-3) and 2.3×10(-3)kgm(-2)d(-1), respectively. These two strains also displayed encouraging cell fragility in a high pressure bead milling process with 69% and 98% cell disruption at 1750bar making them remarkable strains for TAG extraction in wet environment.

  18. M gene analysis of canine coronavirus strains detected in Korea

    PubMed Central

    Jeoung, Seok-Young; Ann, So-Yun; Kim, Hyun-Tae

    2014-01-01

    The purpose of this study was to investigate the genetic features of canine coronavirus (CCV) strains detected in Korea. M gene sequences obtained for isolates from 22 dogs with enteritis over a 5-year period were evaluated. Sequence comparison revealed that the 22 Korean CCV strains had an 87.2 to 100% nucleotide homology. Comparing to the typical reference CCV strains (type II), the nucleotide sequence of Korean strains had homology ranged from 86.3% to 98.3% (89.1% to 99.2% for the amino acid sequence) and 87.7% to 97.8% (92.4% to 100% for the amino acid sequence) when compared to FCoV-like CCV strains (type I). Three amino acid variations in the M gene were characteristic for the Korean CCV strains. Phylogenetic analysis demonstrated that the 22 Korean CCV strains belonged to four typical CCV clusters (i.e., a unique Korean CCV cluster, a type II and transmissible gastroenteritis virus cluster, an intermediate cluster between type I and II, and a type I cluster). This study was the first to identify genetic differences of the M gene from Korean CCV strains and provided a platform for molecular identification of different Korean CCV strains. PMID:25234323

  19. Investigation of carbon profiles for enhanced boron confinement and improved carrier transport in strained silicon germanium nanolayers for heterojunction bipolar transistors

    NASA Astrophysics Data System (ADS)

    Enicks, Darwin Gene

    This research covers a breadth of topics, in Chapters 1 through 7, ranging from the crystal lattice, to dopant diffusion in SiGe, to SiGe and SiGeC chemical vapor deposition, to the Si/SiGe and Si/SiGeC energy band structure, and NPN SiGeC HBT AC and DC characteristics. Chapters 8 and 9 contain the results of the research, which relates the film growth and carbon positioning to boron diffusion, sheet resistance, and device performance; specifically current gain, fmax, and noise figures of merit. The first objective of the dissertation was to investigate carbon doping profiles in nano-layers (≤32 nm) of silicon germanium (Si1-xGe x), and provide an understanding of "remote carbon boron confinement" (RCBC), which is demonstrated to exploit the advantages of carbon to increase NPN HBT (heterojunction bipolar transistor) performance, reduce base resistance, and improve overall noise figures of merit. The second objective was to investigate the noise characteristics of this method compared to the standard method of placing carbon throughout the lattice, which is known as "uniform carbon boron confinement" (UCBC). The current technological development towards smaller and faster devices has forced engineers and scientists to look into materials other than silicon, but which are highly compatible. A natural choice is the Si1-xGe x alloy, since Ge is also a Group IV. Si1-xGex has the same lattice structure as Si, but its lattice constant is 4.2% larger (aSi = 0.543nm, aGe = 0.567nm), and the bandgap is less than that of Si (Eg_Si = 1.11eV, Eg_Ge = 0.67eV). This opens the possibility of bandgap, strain, and dopant diffusion engineering, all of which affect the material and electronic properties of devices. The primary benefit of carbon is to reduce the diffusion of boron in Si1-xGex thus keeping the base narrow for significantly reduced electron transit times and increased unity gain cutoff frequencies (fT). However the utilization of carbon reduces base conductivity and

  20. Variation of dominance of newly arisen adaptive genes.

    PubMed

    Bourguet, D; Lenormand, T; Guillemaud, T; Marcel, V; Fournier, D; Raymond, M

    1997-11-01

    Newly arisen adaptive alleles such as insecticide resistance genes represent a good opportunity to investigate the theories put forth to explain the molecular basis of dominance and its possible evolution. Dominance levels of insecticide resistance conferred by insensitive alleles of the acetylcholinesterase gene were analyzed in five resistant strains of the mosquito Culex pipiens. Dominance levels were found to differ between strains, varying from partial recessivity to complete dominance. This variation was not explained by differences in catalytic properties of the enzyme, since four of the five resistant strains had identical inhibition properties for the insensitive acetylcholinesterase. Among these four laboratory strains and in individuals collected from natural populations, we found a correlation between increased acetylcholinesterase activities and higher dominance levels. We propose a molecular explanation for how variation in acetylcholinesterase activity may result in variation of dominance level. We also conjecture that the four resistant strains did not differ in their amino acid sequence in the catalytically active regions of acetylcholinesterase, but that the expression of the gene was regulated by either neighboring or distant sites, thereby modifying the dominance level. Under this interpretation, dominance levels may evolve in this system, since heritable variation in acetylcholinesterase activity was found.

  1. Sex and strain differences in the hepatocyte primary culture/DNA repair test

    SciTech Connect

    McQueen, C.A.; Way, B.M. )

    1991-01-01

    The hepatocyte primary culture (HPC)/DNA repair test was developed using hepatocytes isolated from male F-344 rats. A number of genetic polymorphisms have been shown to occur in inbred strains of rats, which may lead to variation in biotransformation of xenobiotics resulting in differences in susceptibility to genotoxins. The effect of the strain utilized as a source of hepatocytes was investigated with female Lewis, F-344, and DA rats. Variation was observed when hepatocytes from the three strains were exposed to aflatoxin B{sub 1} (AFB{sub 1}). No clearcut strain differences were seen when cells were exposed to diethylnitrosamine (DEN) or 2-acetylaminofluorene. These results demonstrate that both the strain and the sex of the animal used as a source of hepatocytes can affect the HPC/DNA repair test.

  2. Genetic Variations Strongly Influence Phenotypic Outcome in the Mouse Retina

    PubMed Central

    Jelcick, Austin S.; Yuan, Yang; Leehy, Barrett D.; Cox, Lakeisha C.; Silveira, Alexandra C.; Qiu, Fang; Schenk, Sarah; Sachs, Andrew J.; Morrison, Margaux A.; Nystuen, Arne M.; DeAngelis, Margaret M.; Haider, Neena B.

    2011-01-01

    Variation in genetic background can significantly influence the phenotypic outcome of both disease and non-disease associated traits. Additionally, differences in temporal and strain specific gene expression can also contribute to phenotypes in the mammalian retina. This is the first report of microarray based cross-strain analysis of gene expression in the retina investigating genetic background effects. Microarray analyses were performed on retinas from the following mouse strains: C57BL6/J, AKR/J, CAST/EiJ, and NOD.NON-H2-nb1 at embryonic day 18.5 (E18.5) and postnatal day 30.5 (P30.5). Over 3000 differentially expressed genes were identified between strains and developmental stages. Differential gene expression was confirmed by qRT-PCR, Western blot, and immunohistochemistry. Three major gene networks were identified that function to regulate retinal or photoreceptor development, visual perception, cellular transport, and signal transduction. Many of the genes in these networks are implicated in retinal diseases such as bradyopsia, night-blindness, and cone-rod dystrophy. Our analysis revealed strain specific variations in cone photoreceptor cell patterning and retinal function. This study highlights the substantial impact of genetic background on both development and function of the retina and the level of gene expression differences tolerated for normal retinal function. These strain specific genetic variations may also be present in other tissues. In addition, this study will provide valuable insight for the development of more accurate models for human retinal diseases. PMID:21779340

  3. [Investigation of SCCmec types and Panton-Valentine leukocidin in community-acquired and nosocomial Staphylococcus aureus strains: comparing skin and soft tissue infections to the other infections].

    PubMed

    Gülmez, Dolunay; Sancak, Banu; Ercis, Serpil; Karakaya, Jale; Hasçelik, Gülşen

    2012-07-01

    Infections due to methicillin-resistant Staphylococcus aureus (MRSA) are important health care problems since they are usually multidrug resistant. Although MRSA is isolated especially from nosocomial infections, community-acquired MRSA infections are increasing. Methicillin resistance is due to the expression of mecA gene, which is located on SCCmec gene cassette. Different SCCmec types can be detected in hospital-acquired and community-acquired (CA-) MRSA strains. CA-MRSA strains might harbour Panton-Valentine leukocidin (PVL), an important virulence factor in skin and soft tissue infections. Strains carrying PVL has the ability to penetrate undamaged skin and cause more severe infections. The aim of this study was to detect SCCmec types and PVL gene in S.aureus strains isolated from skin and soft tissue infections and to compare with strains isolated from other infections in a university hospital in Ankara, Turkey. S.aureus strains isolated from skin and soft tissue infections (n= 285) and a control group consisting of 161 strains isolated from other infections (53 blood, 48 lower respiratory tract samples, 30 sterile body fluids, 30 genitourinary tract samples) chosen by stratification and random selection method, were included in the study. Among skin and soft tissue infection strains 46.7% were from the hospitalized patients and 48.4% of skin and soft tissue infection strains were from female patients. The mean age of the skin and soft tissue infection patients was 45.5 years. Among the control strains 60.9% were from the hospitalized patients and 41.6% of the control patients were female. The mean age of the control patients was 50.2 years. Strains were identified by the Phoenix system (Becton Dickinson, USA) and identification was confirmed by tube coagulase test. Methicillin resistance was determined by the Phoenix system which determines both oxacillin and cefoxitin minimum inhibitor concentrations and, confirmed by oxacillin agar screening and

  4. How accurately can subject-specific finite element models predict strains and strength of human femora? Investigation using full-field measurements.

    PubMed

    Grassi, Lorenzo; Väänänen, Sami P; Ristinmaa, Matti; Jurvelin, Jukka S; Isaksson, Hanna

    2016-03-21

    Subject-specific finite element models have been proposed as a tool to improve fracture risk assessment in individuals. A thorough laboratory validation against experimental data is required before introducing such models in clinical practice. Results from digital image correlation can provide full-field strain distribution over the specimen surface during in vitro test, instead of at a few pre-defined locations as with strain gauges. The aim of this study was to validate finite element models of human femora against experimental data from three cadaver femora, both in terms of femoral strength and of the full-field strain distribution collected with digital image correlation. The results showed a high accuracy between predicted and measured principal strains (R(2)=0.93, RMSE=10%, 1600 validated data points per specimen). Femoral strength was predicted using a rate dependent material model with specific strain limit values for yield and failure. This provided an accurate prediction (<2% error) for two out of three specimens. In the third specimen, an accidental change in the boundary conditions occurred during the experiment, which compromised the femoral strength validation. The achieved strain accuracy was comparable to that obtained in state-of-the-art studies which validated their prediction accuracy against 10-16 strain gauge measurements. Fracture force was accurately predicted, with the predicted failure location being very close to the experimental fracture rim. Despite the low sample size and the single loading condition tested, the present combined numerical-experimental method showed that finite element models can predict femoral strength by providing a thorough description of the local bone mechanical response.

  5. Investigating the presence of post-perovskite and large-scale chemical variations in Earth's lower mantle using tomographic-geodynamic model comparisons.

    NASA Astrophysics Data System (ADS)

    Koelemeijer, Paula; Ritsema, Jeroen; Deuss, Arwen; Davies, Rhodri; Schuberth, Bernhard

    2016-04-01

    Tomographic models of the Earth's mantle consistently image two large provinces of low shear-wave velocities (LLSVPs) in the lowermost mantle beneath Africa and the Pacific. Seismic studies also find an increase in the ratio of shear-wave velocity (Vs) to compressional-wave velocity (Vp) variations, accompanied by a significant negative correlation between shear-wave and bulk-sound velocity (Vc) variations, both of which are also observed in the recent SP12RTS model. The LLSVPs have consequently been suggested to represent intrinsically dense piles of thermochemical material. Alternatively, they have been interpreted as poorly imaged clusters of thermal plumes, with the deep mantle post-perovskite (pPv) phase invoked as explanation for the high Vs/Vp ratios and Vs-Vc anti-correlation. Geodynamical calculations of thermal plumes and thermochemical piles predict a fundamentally different style of mantle convection, interface topographies and CMB heat flow. However, to interpret tomographic images using these high-resolution models, the limited resolving power of seismic tomography has to be accounted for. Here, we interpret the observed seismic characteristics of SP12RTS by comparing the velocity structures to synthetic tomography images derived from 3D mantle convection models. As in previous studies, geodynamic models are converted to seismic velocities using mineral physics constraints and subsequently convolved with the tomographic resolution operator. In contrast to these studies, where generally only the shear-wave velocity structure has been compared, we use both the Vs and Vp resolution operator of SP12RTS to allow direct comparisons of the resulting velocity ratios and correlations. We use geodynamic models with and without pPv and/or chemical variations to investigate the cause of the high Vs/Vp ratio and Vs-Vs anti-correlation. Although the tomographic filtering significantly affects the synthetic tomography images, we demonstrate that the patterns

  6. An initial investigation of the association between the SARS outbreak and weather: with the view of the environmental temperature and its variation

    PubMed Central

    Tan, J.; Mu, L.; Huang, J.; Yu, S.; Chen, B.; Yin, J.

    2005-01-01

    Objective: To understand the association between the SARS outbreak and the environmental temperature, and to provide a scientific basis for prevention and control measures against it. Methods: The daily numbers of the probable SARS patients and the daily meteorological factors during the SARS outbreak period in Hong Kong, Guangzhou, Beijing, and Taiyuan were used in the data analysis. Ecological analysis was conducted to explore the association between the daily numbers of probable SARS patients and the environmental temperature and its variations. Results: There was a significant correlation between the SARS cases and the environmental temperature seven days before the onset and the seven day time lag corresponds well with the known incubation period for SARS. The optimum environmental temperature associated with the SARS cases was between 16°C to 28°C, which may encourage virus growth. A sharp rise or decrease in the environmental temperature related to the cold spell led to an increase of the SARS cases because of the possible influence of the weather on the human immune system. This study provided some evidence that there is a higher possibility for SARS to reoccur in spring than that in autumn and winter. Conclusion: Current knowledge based on case studies of the SARS outbreak in the four cities suggested that the SARS outbreaks were significantly associated with the temperature and its variations. However, because the fallacy and the uncontrolled confounding effects might have biased the results, the possibility of other meteorological factors having an affect on the SARS outbreaks deserves further investigation. PMID:15709076

  7. Red shift, blue shift: investigating Doppler shifts, blubber thickness, and migration as explanations of seasonal variation in the tonality of Antarctic blue whale song.

    PubMed

    Miller, Brian S; Leaper, Russell; Calderan, Susannah; Gedamke, Jason

    2014-01-01

    The song of Antarctic blue whales (Balaenoptera musculus intermedia) comprises repeated, stereotyped, low-frequency calls. Measurements of these calls from recordings spanning many years have revealed a long-term linear decline as well as an intra-annual pattern in tonal frequency. While a number of hypotheses for this long-term decline have been investigated, including changes in population structure, changes in the physical environment, and changes in the behaviour of the whales, there have been relatively few attempts to explain the intra-annual pattern. An additional hypothesis that has not yet been investigated is that differences in the observed frequency from each call are due to the Doppler effect. The assumptions and implications of the Doppler effect on whale song are investigated using 1) vessel-based acoustic recordings of Antarctic blue whales with simultaneous observation of whale movement and 2) long-term acoustic recordings from both the subtropics and Antarctic. Results from vessel-based recordings of Antarctic blue whales indicate that variation in peak-frequency between calls produced by an individual whale was greater than would be expected by the movement of the whale alone. Furthermore, analysis of intra-annual frequency shift at Antarctic recording stations indicates that the Doppler effect is unlikely to fully explain the observations of intra-annual pattern in the frequency of Antarctic blue whale song. However, data do show cyclical changes in frequency in conjunction with season, thus suggesting that there might be a relationship among tonal frequency, body condition, and migration to and from Antarctic feeding grounds.

  8. Variation in susceptibility of laboratory and field strains of three stored-grain insect species to beta-cyfluthrin and chlorpyrifos-methyl plus deltamethrin applied to concrete surfaces

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The efficacy of beta-cyfluthrin and chlorpyrifos-methyl plus deltamethrin applied to clean, concrete floors of empty bins prior to grain storage against field strains of stored-grain insects is unknown. We exposed adults of 16 strains of the red flour beetle, Tribolium castaneum (Herbst); 8 strains ...

  9. Medically Complex Home Care and Caregiver Strain

    ERIC Educational Resources Information Center

    Moorman, Sara M.; Macdonald, Cameron

    2013-01-01

    Purpose of the study: To examine (a) whether the content of caregiving tasks (i.e., nursing vs. personal care) contributes to variation in caregivers' strain and (b) whether the level of complexity of nursing tasks contributes to variation in strain among caregivers providing help with such tasks. Design and methods: The data came from the Cash…

  10. Two dimensional WS2 lateral heterojunctions by strain modulation

    NASA Astrophysics Data System (ADS)

    Meng, Lan; Zhang, Yuhan; Hu, Song; Wang, Xiangfu; Liu, Chunsheng; Guo, Yandong; Wang, Xinran; Yan, Xiaohong

    2016-06-01

    "Strain engineering" has been widely used to tailor the physical properties of layered materials, like graphene, black phosphorus, and transition-metal dichalcogenides. Here, we exploit thermal strain engineering to construct two dimensional (2D) WS2 in-plane heterojunctions. Kelvin probe force microscopy is used to investigate the surface potentials and work functions of few-layer WS2 flakes, which are grown on SiO2/Si substrates by chemical vapor deposition, followed by a fast cooling process. In the interior regions of strained WS2 flakes, work functions are found to be much larger than that of the unstrained regions. The difference in work functions, together with the variation of band gaps, endows the formation of heterojunctions in the boundaries between inner and outer domains of WS2 flakes. This result reveals that the existence of strain offers a unique opportunity to modulate the electronic properties of 2D materials and construct 2D lateral heterojunctions.

  11. Maintenance of genetic variation in human personality: testing evolutionary models by estimating heritability due to common causal variants and investigating the effect of distant inbreeding.

    PubMed

    Verweij, Karin J H; Yang, Jian; Lahti, Jari; Veijola, Juha; Hintsanen, Mirka; Pulkki-Råback, Laura; Heinonen, Kati; Pouta, Anneli; Pesonen, Anu-Katriina; Widen, Elisabeth; Taanila, Anja; Isohanni, Matti; Miettunen, Jouko; Palotie, Aarno; Penke, Lars; Service, Susan K; Heath, Andrew C; Montgomery, Grant W; Raitakari, Olli; Kähönen, Mika; Viikari, Jorma; Räikkönen, Katri; Eriksson, Johan G; Keltikangas-Järvinen, Liisa; Lehtimäki, Terho; Martin, Nicholas G; Järvelin, Marjo-Riitta; Visscher, Peter M; Keller, Matthew C; Zietsch, Brendan P

    2012-10-01

    Personality traits are basic dimensions of behavioral variation, and twin, family, and adoption studies show that around 30% of the between-individual variation is due to genetic variation. There is rapidly growing interest in understanding the evolutionary basis of this genetic variation. Several evolutionary mechanisms could explain how genetic variation is maintained in traits, and each of these makes predictions in terms of the relative contribution of rare and common genetic variants to personality variation, the magnitude of nonadditive genetic influences, and whether personality is affected by inbreeding. Using genome-wide single nucleotide polymorphism (SNP) data from > 8000 individuals, we estimated that little variation in the Cloninger personality dimensions (7.2% on average) is due to the combined effect of common, additive genetic variants across the genome, suggesting that most heritable variation in personality is due to rare variant effects and/or a combination of dominance and epistasis. Furthermore, higher levels of inbreeding were associated with less socially desirable personality trait levels in three of the four personality dimensions. These findings are consistent with genetic variation in personality traits having been maintained by mutation-selection balance.

  12. Strain specificity in antimicrobial activity of silver and copper nanoparticles.

    PubMed

    Ruparelia, Jayesh P; Chatterjee, Arup Kumar; Duttagupta, Siddhartha P; Mukherji, Suparna

    2008-05-01

    The antimicrobial properties of silver and copper nanoparticles were investigated using Escherichia coli (four strains), Bacillus subtilis and Staphylococcus aureus (three strains). The average sizes of the silver and copper nanoparticles were 3 nm and 9 nm, respectively, as determined through transmission electron microscopy. Energy-dispersive X-ray spectra of silver and copper nanoparticles revealed that while silver was in its pure form, an oxide layer existed on the copper nanoparticles. The bactericidal effect of silver and copper nanoparticles were compared based on diameter of inhibition zone in disk diffusion tests and minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of nanoparticles dispersed in batch cultures. Bacterial sensitivity to nanoparticles was found to vary depending on the microbial species. Disk diffusion studies with E. coli and S. aureus revealed greater effectiveness of the silver nanoparticles compared to the copper nanoparticles. B. subtilis depicted the highest sensitivity to nanoparticles compared to the other strains and was more adversely affected by the copper nanoparticles. Good correlation was observed between MIC and MBC (r2=0.98) measured in liquid cultures. For copper nanoparticles a good negative correlation was observed between the inhibition zone observed in disk diffusion test and MIC/MBC determined based on liquid cultures with the various strains (r2=-0.75). Although strain-specific variation in MIC/MBC was negligible for S. aureus, some strain-specific variation was observed for E. coli.

  13. [Investigation of mutations in transcription factors of efflux pump genes in fluconazole-resistant Candida albicans strains overexpressing the efflux pumps].

    PubMed

    Kalkandelen, Kemal Turan; Doluca Dereli, Mine

    2015-10-01

    In recent years, a significant rise in the number of immunocompromised patients have been observed due to cancer chemotherapy, organ transplantation and HIV infection. As a result of this, the frequency of Candida albicans infections in the clinics have been increased. Fluconazole, as being a well tolerated, easy to use drug with minor side effects, is often the first choice antifungal agent for this patient group, both for therapy and prophylaxis. Especially the long-term use of this drug, causes the selection of resistant strains and leads to the development of fluconazole resistance. The most frequently observed resistance mechanism against fluconazole in C.albicans strains is the transportation of the drug out of the cell via efflux pumps. The efflux pumps mainly involved are Cdr1, Cdr2 ve Mdr1 encoded by CDR1, CDR2 and MDR1 genes. It has been shown that, the overexpression of these efflux pump genes was caused by functional mutations in TAC1 and MRR1 genes which encode the transcription factors Tac1p and Mrr1p. This study was aimed to analyze TAC1 and MRR1 genes of 15 C.albicans strains which consist of six fluconazole-susceptible, four susceptible with trailing effect and five fluconazole-resistant isolates plus one resistant strain (DSY292), known to overexpress Mdr1 efflux pump due to P683H mutation in MRR1 gene and one fluconazole-sensitive ATCC 14053 C.albicans strain in terms of mutations with polymerase chain reaction and sequence analysis. Two of the fluconazole-resistant isolates which had overexpression of Cdr1 and Cdr2 pumps known to have overexpression of TAC1 gene, revealed R673Q and A736V mutations. A P683H point mutation, that overexpressed the Mdr1 pump was detected in a fluconazole-resistant strain, which was known to cause MRR1 overexpression. In conclusion, mutations in the transcription factors of the efflux pump genes may play an important role in the resistance against fluconazole among our selected C.albicans strains.

  14. Timeline trend profile and seasonal variations in nicotine present in ambient PM10 samples: A four year investigation from Delhi region, India

    NASA Astrophysics Data System (ADS)

    Yadav, Shweta; Tandon, Ankit; Attri, Arun K.

    2014-12-01

    The detection of nicotine, an organic tracer for Environmental Tobacco Smoke (ETS), in the collected PM10 samples from Delhi region's ambient environment, in a appropriately designed investigation was initiated over four years (2006-2009) to: (1) Comprehend seasonal and inter-annual variations in the nicotine present in PM10; (2) Extract regression based linear trend profile manifested by nicotine in PM10; (3) Determine the non-linear trend timeline from the nicotine data, and compare it with the obtained linear trend; (4) Suggest the possible use of the designed experiment and analysis to have a qualitative appraisal of Tobacco Smoking activity in the sampling region. The PM10 samples were collected in a monthly time-series sequence at a known receptor site. Quantitative estimates of nicotine (ng m-3) were made by using a Thermal Desorption Gas Chromatography Mass Spectrometry (TD-GC/MS). The annual average concentrations of nicotine (ng m-3) were 516 ± 302 (2008) > 494 ± 301 (2009) > 438 ± 250 (2007) > 325 ± 149 (2006). The estimated linear trend of 5.4 ng m-3 month-1 corresponded to 16.3% per annum increase in the PM10 associated nicotine. The industrial production of India's tobacco index normalized to Delhi region's consumption, pegged an increase at 10.5% per annum over this period.

  15. Strain-induced modulation of perpendicular magnetic anisotropy in Ta/CoFeB/MgO structures investigated by ferromagnetic resonance

    NASA Astrophysics Data System (ADS)

    Yu, Guoqiang; Wang, Zhenxing; Abolfath-Beygi, Maryam; He, Congli; Li, Xiang; Wong, Kin L.; Nordeen, Paul; Wu, Hao; Carman, Gregory P.; Han, Xiufeng; Alhomoudi, Ibrahim A.; Amiri, Pedram Khalili; Wang, Kang L.

    2015-02-01

    We demonstrate strain-induced modulation of perpendicular magnetic anisotropy (PMA) in (001)-oriented [Pb(Mg1/3Nb2/3)O3](1-x)-[PbTiO3]x (PMN-PT) substrate/Ta/CoFeB/MgO/Ta structures using ferromagnetic resonance (FMR). An in-plane biaxial strain is produced by applying voltage between the two surfaces of the PMN-PT substrate, and is transferred to the ferromagnetic CoFeB layer, which results in tuning of the PMA of the CoFeB layer. The strain-induced change in PMA is quantitatively extracted from the experimental FMR spectra. It is shown that both first and second-order anisotropy terms are affected by the electric field, and that they have opposite voltage dependencies. A very large value of the voltage-induced perpendicular magnetic anisotropy modulation of ˜7000 fJ/V.m is obtained through this strain-mediated coupling. Using this FMR technique, the magnetostriction coefficient λ is extracted for the ultrathin 1.1 nm Co20Fe60B20 layer, and is found to be 3.7 × 10-5, which is approximately 4 times larger than the previously reported values for CoFeB films thicker than 5 nm. In addition, the effect of strain on the effective damping constant (αeff) is also studied and no obvious modulation of the αeff is observed. The results are relevant to the development of CoFeB-MgO magnetic tunnel junctions for memory applications.

  16. Genetic variation in the lactase gene, dairy product intake and risk for prostate cancer in the European Prospective Investigation into Cancer and Nutrition

    PubMed Central

    Travis, Ruth C; Appleby, Paul N; Siddiq, Afshan; Allen, Naomi E; Kaaks, Rudolf; Canzian, Federico; Feller, Silke; Tjønneland, Anne; Føns Johnsen, Nina; Overvad, Kim; Ramón Quirós, J; González, Carlos A; Sánchez, Maria-José; Larrañaga, Nerea; Chirlaque, Maria-Dolores; Barricarte, Aurelio; Khaw, Kay-Tee; Wareham, Nick; Trichopoulou, Antonia; Valanou, Elisavet; Oustoglou, Erifili; Palli, Domenico; Sieri, Sabina; Tumino, Rosario; Sacerdote, Carlotta; Bueno-de-Mesquita, H B(as); Stattin, Pär; Ferrari, Pietro; Johansson, Mattias; Norat, Teresa; Riboli, Elio; Key, Timothy J

    2013-01-01

    High dairy protein intake has been found to be associated with increased prostate cancer risk in the European Prospective Investigation into Cancer and Nutrition (EPIC). To further examine this possible relationship, we investigated the hypothesis that a genetic polymorphism in the lactase (LCT) gene might be associated with elevated dairy product intake and increased prostate cancer risk in a case–control study nested in EPIC. The C/T-13910 lactase variant (rs4988235) was genotyped in 630 men with prostate cancer and 873 matched control participants. Dairy product consumption was assessed by diet questionnaire. Odds ratios (ORs) for prostate cancer in relation to lactase genotype were estimated by conditional logistic regression. Lactase genotype frequency varied significantly between countries, with frequencies of the T (lactase persistence) allele ranging from 7% in Greece to 79% in Denmark. Intake of milk and total dairy products varied significantly by lactase genotype after adjustment for recruitment center; adjusted mean intakes of milk were 44.4, 69.8 and 82.3 g/day among men with CC, CT and TT genotypes, respectively. The lactase variant was not significantly associated with prostate cancer risk, both in our data (adjusted OR for TT vs. CC homozygotes: 1.10, 95% CI: 0.76–1.59) and in a meta-analysis of all the published data (combined OR for T allele carriers vs. CC homozygotes: 1.12, 0.96–1.32). These findings show that while variation in the lactase gene is associated with milk intake in men, the lactase polymorphism does not have a large effect on prostate cancer risk. What's new? High dairy protein intake has previously been found to be associated with increased prostate cancer risk in the European Prospective Investigation into Cancer and Nutrition (EPIC). The current study was nested in EPIC, and results from this first Europe-wide study suggest that while the C/T13910 lactase polymorphism is associated with milk intake, the variant has no

  17. Genetic variation in the lactase gene, dairy product intake and risk for prostate cancer in the European prospective investigation into cancer and nutrition.

    PubMed

    Travis, Ruth C; Appleby, Paul N; Siddiq, Afshan; Allen, Naomi E; Kaaks, Rudolf; Canzian, Federico; Feller, Silke; Tjønneland, Anne; Føns Johnsen, Nina; Overvad, Kim; Ramón Quirós, J; González, Carlos A; Sánchez, Maria-José; Larrañaga, Nerea; Chirlaque, Maria-Dolores; Barricarte, Aurelio; Khaw, Kay-Tee; Wareham, Nick; Trichopoulou, Antonia; Valanou, Elisavet; Oustoglou, Erifili; Palli, Domenico; Sieri, Sabina; Tumino, Rosario; Sacerdote, Carlotta; Bueno-de-Mesquita, H B as; Stattin, Pär; Ferrari, Pietro; Johansson, Mattias; Norat, Teresa; Riboli, Elio; Key, Timothy J

    2013-04-15

    High dairy protein intake has been found to be associated with increased prostate cancer risk in the European Prospective Investigation into Cancer and Nutrition (EPIC). To further examine this possible relationship, we investigated the hypothesis that a genetic polymorphism in the lactase (LCT) gene might be associated with elevated dairy product intake and increased prostate cancer risk in a case-control study nested in EPIC. The C/T-13910 lactase variant (rs4988235) was genotyped in 630 men with prostate cancer and 873 matched control participants. Dairy product consumption was assessed by diet questionnaire. Odds ratios (ORs) for prostate cancer in relation to lactase genotype were estimated by conditional logistic regression. Lactase genotype frequency varied significantly between countries, with frequencies of the T (lactase persistence) allele ranging from 7% in Greece to 79% in Denmark. Intake of milk and total dairy products varied significantly by lactase genotype after adjustment for recruitment center; adjusted mean intakes of milk were 44.4, 69.8 and 82.3 g/day among men with CC, CT and TT genotypes, respectively. The lactase variant was not significantly associated with prostate cancer risk, both in our data (adjusted OR for TT vs. CC homozygotes: 1.10, 95% CI: 0.76-1.59) and in a meta-analysis of all the published data (combined OR for T allele carriers vs. CC homozygotes: 1.12, 0.96-1.32). These findings show that while variation in the lactase gene is associated with milk intake in men, the lactase polymorphism does not have a large effect on prostate cancer risk.

  18. Strain Gage

    NASA Technical Reports Server (NTRS)

    1995-01-01

    HITEC Corporation developed a strain gage application for DanteII, a mobile robot developed for NASA. The gage measured bending forces on the robot's legs and warned human controllers when acceptable forces were exceeded. HITEC further developed the technology for strain gage services in creating transducers out of "Indy" racing car suspension pushrods, NASCAR suspension components and components used in motion control.

  19. Characterization of the time-dependent strain field at seismogenic depths using first-motion focal mechanisms: Observations of large-scale decadal variations in stress along the San Andrea fault system

    USGS Publications Warehouse

    Sipkin, S.A.; Silver, P.G.

    2003-01-01

    We present a method for summing moment tensors derived from first-motion focal mechanisms to study temporal dependence in features of the subsurface regional strain field. Time-dependent processes are inferred by comparing mechanisms summed over differing time periods. We apply this methodology to seismogenic zones in central and southern California using focal mechanisms produced by the Northern and Southern California Seismograph Networks for events during 1980-1999. We find a consistent pattern in both the style of deformation (strike-slip versus compressional) and seismicity rate across the entire region. If these temporal variations are causally related, it suggests a temporal change in the regional-scale stress field. One change consistent with the observations is a rotation in the regional maximum horizontal compressive stress direction, followed by a reversal to the original direction. Depending upon the dominant style of deformation locally, this change in orientation of the regional stress will tend to either enhance or hinder deformation. The mode of enhanced deformation can range from increased microseismicity and creep to major earthquakes. We hypothesize that these temporal changes in the regional stress field are the result of subtle changes in apparent relative plate motion between the Pacific and North American plates, perhaps due to long-range postseismic stress diffusion. Others have hypothesized that small changes in plate motion over thousands of years, and/or over decades, are responsible for changes in the style of deformation in southern California. We propose that such changes, over the course of just a few years, also affect the style of deformation.

  20. Strain-Dependent Transcriptome Signatures for Robustness in Lactococcus lactis

    PubMed Central

    Dijkstra, Annereinou R.; Alkema, Wynand; Starrenburg, Marjo J. C.; van Hijum, Sacha A. F. T.; Bron, Peter A.

    2016-01-01

    Recently, we demonstrated that fermentation conditions have a strong impact on subsequent survival of Lactococcus lactis strain MG1363 during heat and oxidative stress, two important parameters during spray drying. Moreover, employment of a transcriptome-phenotype matching approach revealed groups of genes associated with robustness towards heat and/or oxidative stress. To investigate if other strains have similar or distinct transcriptome signatures for robustness, we applied an identical transcriptome-robustness phenotype matching approach on the L. lactis strains IL1403, KF147 and SK11, which have previously been demonstrated to display highly diverse robustness phenotypes. These strains were subjected to an identical fermentation regime as was performed earlier for strain MG1363 and consisted of twelve conditions, varying in the level of salt and/or oxygen, as well as fermentation temperature and pH. In the exponential phase of growth, cells were harvested for transcriptome analysis and assessment of heat and oxidative stress survival phenotypes. The variation in fermentation conditions resulted in differences in heat and oxidative stress survival of up to five 10-log units. Effects of the fermentation conditions on stress survival of the L. lactis strains were typically strain-dependent, although the fermentation conditions had mainly similar effects on the growth characteristics of the different strains. By association of the transcriptomes and robustness phenotypes highly strain-specific transcriptome signatures for robustness towards heat and oxidative stress were identified, indicating that multiple mechanisms exist to increase robustness and, as a consequence, robustness of each strain requires individual optimization. However, a relatively small overlap in the transcriptome responses of the strains was also identified and this generic transcriptome signature included genes previously associated with stress (ctsR and lplL) and novel genes, including nan

  1. Strain-Dependent Transcriptome Signatures for Robustness in Lactococcus lactis.

    PubMed

    Dijkstra, Annereinou R; Alkema, Wynand; Starrenburg, Marjo J C; Hugenholtz, Jeroen; van Hijum, Sacha A F T; Bron, Peter A

    2016-01-01

    Recently, we demonstrated that fermentation conditions have a strong impact on subsequent survival of Lactococcus lactis strain MG1363 during heat and oxidative stress, two important parameters during spray drying. Moreover, employment of a transcriptome-phenotype matching approach revealed groups of genes associated with robustness towards heat and/or oxidative stress. To investigate if other strains have similar or distinct transcriptome signatures for robustness, we applied an identical transcriptome-robustness phenotype matching approach on the L. lactis strains IL1403, KF147 and SK11, which have previously been demonstrated to display highly diverse robustness phenotypes. These strains were subjected to an identical fermentation regime as was performed earlier for strain MG1363 and consisted of twelve conditions, varying in the level of salt and/or oxygen, as well as fermentation temperature and pH. In the exponential phase of growth, cells were harvested for transcriptome analysis and assessment of heat and oxidative stress survival phenotypes. The variation in fermentation conditions resulted in differences in heat and oxidative stress survival of up to five 10-log units. Effects of the fermentation conditions on stress survival of the L. lactis strains were typically strain-dependent, although the fermentation conditions had mainly similar effects on the growth characteristics of the different strains. By association of the transcriptomes and robustness phenotypes highly strain-specific transcriptome signatures for robustness towards heat and oxidative stress were identified, indicating that multiple mechanisms exist to increase robustness and, as a consequence, robustness of each strain requires individual optimization. However, a relatively small overlap in the transcriptome responses of the strains was also identified and this generic transcriptome signature included genes previously associated with stress (ctsR and lplL) and novel genes, including nan

  2. Analytical threshold voltage model for strained silicon GAA-TFET

    NASA Astrophysics Data System (ADS)

    Kang, Hai-Yan; Hu, Hui-Yong; Wang, Bin

    2016-11-01

    Tunnel field effect transistors (TFETs) are promising devices for low power applications. An analytical threshold voltage model, based on the channel surface potential and electric field obtained by solving the 2D Poisson’s equation, for strained silicon gate all around TFETs is proposed. The variation of the threshold voltage with device parameters, such as the strain (Ge mole fraction x), gate oxide thickness, gate oxide permittivity, and channel length has also been investigated. The threshold voltage model is extracted using the peak transconductance method and is verified by good agreement with the results obtained from the TCAD simulation. Project supported by the National Natural Science Foundation of China (Grant No. 61474085).

  3. Interrelationship between polymorphisms of incA, fusogenic properties of Chlamydia trachomatis strains, and clinical manifestations in patients in The Netherlands.

    PubMed

    Pannekoek, Yvonne; Spaargaren, Joke; Langerak, Ankie A J; Merks, Judith; Morré, Servaas A; van der Ende, Arie

    2005-05-01

    IncA variation among Dutch Chlamydia trachomatis isolates was investigated. Of 98 strains, two carried an incA with a premature stop codon, lacked IncA, and were nonfusogenic, while 96 contained an intact incA, expressed IncA, and were fusogenic. Among these 96 strains, nine IncA sequence types were found, of which the three most frequently encountered (88% of the strains) were randomly distributed among symptomatic and asymptomatic patients.

  4. Experimental and computational investigation of the response of an elastomer at pressures up to 18 GPa and strain rates of 105 -106 s-1

    NASA Astrophysics Data System (ADS)

    Jiao, T.; Clifton, Rodney J.

    2017-01-01

    Pressure-shear plate impact (PSPI) experiments have been conducted to study the mechanical response of an elastomer (polyurea) at high pressures and high strain rate. The previously determined isentrope has been extended to 18 GPa. At this pressure, the high-strain-rate shearing resistance of polyurea is approximately 1 GPa. From the PSPI tests, it is evident that the shearing resistance of polyurea is quite sensitive to pressure. Based on the experimental results, a quasilinear viscoelasticity model is introduced and implemented in ABAQUS to simulate the response of polyurea P1000 under the impact conditions of the various PSPI experiments. Results of these simulations are compared with the experimental results to gain insight into the viability of the proposed model.

  5. Investigation into the Combined Effects of Compaction, Strain Rate Sensitivity, and Anisotropic Damage of a Geologic Target on the Trajectory Stability of Rigid Penetrators

    DTIC Science & Technology

    2007-05-01

    class of compressible rigid viscoplastic models were pro- posed to capture the solid -fluid transition in behavior at high strain rates, account for...that depending on their dynamical state, particulate ma- terials may display both solid and fluid like behavior. Since at low deformation rates the...particulate systems are modeled using a solid mechanics approach. These models are gener- ally developed within the framework of plasticity theory

  6. Experimental and Computational Investigation of the Shearing Resistance of an Elastomer at Pressures Up to 18 GPa and Strain Rates of 105 -106s-1

    NASA Astrophysics Data System (ADS)

    Jiao, Tong; Clifton, Rodney

    2015-06-01

    Pressure-shear plate impact (PSPI) experiments have been conducted to study the mechanical response of an elastomer (polyurea) at high pressures and high strain rates. The previously determined isentrope has been extended to 18 GPa. At this pressure, the high-strain-rate shearing resistance of polyurea is approximately 1 GPa-comparable to, or greater than, that of high strength steels and at much lower weight. From the PSPI experiments it is evident that the shearing resistance of polyurea increases essentially proportionately with increasing pressure. Polyurea's response to volumetric changes is largely reversible whereas its response to distortional changes is largely dissipative. These effects are modeled by introducing a constitutive model that incorporates a finite deformation isotropic elasticity model for the instantaneous response and a quasilinear viscoelasticity model-with distributed relaxation times-to model relaxation from the instantaneous elastic response. In order to model a dependence of shear wave speed on pressure, the strain energy function for the instantaneous elastic response is comprised of a distortion-dependent term multiplied by a factor that depends only on the change in volume. This model has been implemented into Abaqus™ to simulate the response of polyurea P1000 under the impact conditions of a variety of PSPI experiments. Results of these simulations suggest that the main features of the experimental results can be explained by such a model.

  7. Investigation of the Booroola (FecB) and Inverdale (FecX(I)) mutations in 21 prolific breeds and strains of sheep sampled in 13 countries.

    PubMed

    Davis, G H; Balakrishnan, L; Ross, I K; Wilson, T; Galloway, S M; Lumsden, B M; Hanrahan, J P; Mullen, M; Mao, X Z; Wang, G L; Zhao, Z S; Zeng, Y Q; Robinson, J J; Mavrogenis, A P; Papachristoforou, C; Peter, C; Baumung, R; Cardyn, P; Boujenane, I; Cockett, N E; Eythorsdottir, E; Arranz, J J; Notter, D R

    2006-03-01

    Twenty-one of the world's prolific sheep breeds and strains were tested for the presence of the FecB mutation of BMPR1B and the FecX(I) mutation of BMP15. The breeds studied were Romanov (2 strains), Finn (2 strains), East Friesian, Teeswater, Blueface Leicester, Hu, Han, D'Man, Chios, Mountain Sheep (three breeds), German Whiteheaded Mutton, Lleyn, Loa, Galician, Barbados Blackbelly (pure and crossbred) and St. Croix. The FecB mutation was found in two breeds, Hu and Han from China, but not in any of the other breeds. The 12 Hu sheep sampled were all homozygous carriers of FecB (FecB(B)/FecB(B)) whereas the sample of 12 Han sheep included all three genotypes (FecB(B)/FecB(B), FecB(B)/FecB+, FecB+/FecB+) at frequencies of 0.33, 0.58 and 0.08, respectively. There was no evidence of FecX(I) in any of the breeds sampled.

  8. Beyond Punnett squares: Student word association and explanations of phenotypic variation through an integrative quantitative genetics unit investigating anthocyanin inheritance and expression in Brassica rapa Fast plants.

    PubMed

    Batzli, Janet M; Smith, Amber R; Williams, Paul H; McGee, Seth A; Dósa, Katalin; Pfammatter, Jesse

    2014-01-01

    Genetics instruction in introductory biology is often confined to Mendelian genetics and avoids the complexities of variation in quantitative traits. Given the driving question "What determines variation in phenotype (Pv)? (Pv=Genotypic variation Gv + environmental variation Ev)," we developed a 4-wk unit for an inquiry-based laboratory course focused on the inheritance and expression of a quantitative trait in varying environments. We utilized Brassica rapa Fast Plants as a model organism to study variation in the phenotype anthocyanin pigment intensity. As an initial curriculum assessment, we used free word association to examine students' cognitive structures before and after the unit and explanations in students' final research posters with particular focus on variation (Pv = Gv + Ev). Comparison of pre- and postunit word frequency revealed a shift in words and a pattern of co-occurring concepts indicative of change in cognitive structure, with particular focus on "variation" as a proposed threshold concept and primary goal for students' explanations. Given review of 53 posters, we found ∼50% of students capable of intermediate to high-level explanations combining both Gv and Ev influence on expression of anthocyanin intensity (Pv). While far from "plug and play," this conceptually rich, inquiry-based unit holds promise for effective integration of quantitative and Mendelian genetics.

  9. Diurnal pH variations of a Glacial Stream: a starting point for Inquiry-driven student and teacher Investigations of a Glacial Ecosystem

    NASA Astrophysics Data System (ADS)

    O'Brien, W. P.; Galbraith, J.; Fatland, D. R.; Heavner, M.

    2009-12-01

    Contemporary geoscience research often operates in a mode that generates huge repositories of data available on the internet to the scientific community and the general public. The SEAMONSTER (SM) online data browser of both archival and real-time data is an example of such a dynamic online ecosystem resource associated with the Juneau Icefield. Although newly developed database navigation tools and geobrowsers make it easy for non-experts to access data of interest, it nonetheless can be daunting to K-16 educators to fashion lesson plans that make effective use of these rich resources. In the following scenario, a student and associated teacher, operating outside the traditional didactic lecture/demo mode, explore and try to make sense of a tiny portion of SM data in a spirit of inquiry guided by curiosity, looking for features that catch their attention as they skim through interactive time-series graphs (96 samples/day) of data from Lemon Creek (which drains Lemon Glacier) for stream hydrological variables (temperature, pH, conductivity, dissolved oxygen, turbidity, discharge) and associated meteorological variables (precipitation, humidity, temperature). Amidst all the complex fluctuations that follow no immediately apparent pattern, one regular and continuous feature does stand out: a seemingly sinusoidal diurnal variation in pH of about 0.1 that peaks daily at noon. This high-frequency signal is superimposed on a slower signal characterized by multiple-day trends and larger fluctuations in pH. The resulting composite signal with its easily identifiable patterns is an ideal candidate for investigating Fourier signal decomposition. They hypothesize that photosynthesis could be a contributing factor to the diurnal signal and then design and run an experiment modeling bioactive streamwater with a blended chloroplast-rich slurry of fresh spinach leaves (spinach soup). They put a recording pH meter in the spinach soup and expose it to high and low levels of light

  10. Temperature and strain discrimination based on a temperature-insensitive birefringent interferometer incorporating an erbium-doped fiber.

    PubMed

    Han, Young-Geun; Chung, Youngjoo; Lee, Sang Bae; Kim, Chang-Seok; Jeong, Myung Yung; Kim, Moon Ki

    2009-04-20

    A simple configuration for simultaneous measurement of temperature and strain exploiting a temperature-insensitive birefringent interferometer based on a photonic crystal fiber incorporating an erbium-doped fiber (EDF) is investigated. The transmission peak power of the birefringent interferometer incorporating the EDF is changed by the temperature variation because the amplified spontaneous emission of the EDF strongly depends on temperature. The applied strain changes the peak wavelength of the birefringent interferometer connecting with the EDF, which can make it possible to discriminate concurrent sensitivities like temperature and strain. The temperature and strain sensitivities were -0.04 dB/ degrees C and 1.3 pm/microepsilon, respectively.

  11. Strain-specific variation in a soilborne phytopathogenic fungus for the expression of genes involved in pH signal transduction pathway, pathogenesis and saprophytic survival in response to environmental pH changes.

    PubMed

    Daval, Stéphanie; Lebreton, Lionel; Gracianne, Cécile; Guillerm-Erckelboudt, Anne-Yvonne; Boutin, Morgane; Marchi, Muriel; Gazengel, Kévin; Sarniguet, Alain

    2013-12-01

    The soilborne fungus Gaeumannomyces graminis var. tritici (Ggt) causes take-all, a wheat root disease. In an original strain-specific way, a previous study indicates that inside the Ggt species, some strains grow preferentially at acidic pH and other strains at neutral/alkaline pH. Th