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- Hjelmevoll, Stig Ove, et al.
(författare)
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A fast real-time polymerase chain reaction method for sensitive and specific detection of the Neisseria gonorrhoeae porA pseudogene
- 2006
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Ingår i: Journal of Molecular Diagnostics. - : Elsevier BV. - 1525-1578 .- 1943-7811. ; 8:5, s. 574-581
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Tidskriftsartikel (refereegranskat)abstract
- Ever since the advent of molecular methods, the diagnostics of Neisseria gonorrhoeae has been troubled by false negative and false positive results compared with culture. Commensal Neisseria species and Neisseria meningitidis are closely related to N. gonorrhoeae and may cross-react when using molecular tests comprising too-low specificity. We have devised a real-time polymerase chain reaction (PCR), including an internal amplification control, that targets the N. gonorrhoeae porA pseudogene. DNA was automatically isolated on a BioRobot M48. Our subsequent PCR method amplified all of the different N. gonorrhoeae international reference strains (n = 34) and N. gonorrhoeae clinical isolates (n = 176) but not isolates of the 13 different nongonococcal Neisseria species (n = 68) that we tested. Furthermore, a panel of gram-negative bacterial (n = 18), gram-positive bacterial (n = 23), fungal (n = 1), and viral (n = 4) as well as human DNA did not amplify. The limit of detection was determined to be less than 7.5 genome equivalents/PCR reaction. In conclusion, the N. gonorrhoeae porA pseudogene real-time PCR developed in the present study is highly sensitive, specific, robust, rapid and reproducible, making it suitable for diagnosis of N. gonorrhoeae infection.
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- Hjelmevoll, Stig Ove, et al.
(författare)
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Clinical validation of a real-time polymerase chain reaction detection of Neisseria gonorrheae porA pseudogene versus culture techniques
- 2008
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Ingår i: Sexually Transmitted Diseases. - Philadelphia : American Venereal Disease Association. - 0148-5717 .- 1537-4521. ; 35:5, s. 517-520
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Tidskriftsartikel (refereegranskat)abstract
- Background: Diagnosing Neisseria gonorrheae using nucleic acid amplification tests (NAATs) might increase the sensitivity, compared to cultivation. However, using NAATs has also been problematic mainly due to the close genetic relationships between different Neisseria species, resulting in false positive diagnoses. This study was conducted to clinically validate a previously published real-time polymerase chain reaction (PCR) method targeting the porA pseudogene in N. gonorrheae in comparison to culture techniques.Methods: In total, 360 samples, urethra (n = 109), rectum (n = 84), pharynx (n = 119), and cervix (n = 48) from 185 males and 57 females, were analyzed using porA pseudogene PCR and cultivation. Sequencing of the entire porA pseudogene and the 16S rRNA gene were used to resolve discrepant results.Results: Of the 360 samples, 37 were positive by both culture and PCR, however, the PCR identified 15 additional confirmed positive samples. The PCR method showed a sensitivity, specificity, positive predictive value, and negative predictive value of 100% in a preselected population. The preselected population had a true gonorrhea prevalence of 17.4%.Conclusions: The present porA pseudogene real-time PCR comprises a valuable supplement to the traditional culture techniques for diagnosis of N. gonorrheae, especially for samples from extragenital sites such as pharynx and rectum.
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- Jarmar, T., et al.
(författare)
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Influence of germanium on the formation of NiSi1-xGex on (111)-oriented Si1-xGex
- 2005
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Ingår i: Journal of Applied Physics. - : AIP Publishing. - 0021-8979 .- 1089-7550. ; 98:5
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Tidskriftsartikel (refereegranskat)abstract
- The formation of NiSi1-xGex on Si1-xGex(111) substrates with x=0, 0.05, and 0.20 at an annealing temperature of 500 degrees C has been studied by x-ray diffraction, transmission electron microscopy, and pole-figure measurements. NiSi formed preferentially oriented on Si, with (100), (001), and (102) parallel to Si(111) and NiSi[010]parallel to Si < 211 >. In NiSi0.95Ge0.05, (001) and (102) maintained their preferential orientations, whereas NiSi0.95Ge0.05(100) was rotated by 30 degrees, so that NiSi0.95Ge0.05[010]parallel to Si0.95Ge0.05< 011 >. An epitaxial alignment in the form of a double axiotaxy, with NiSi0.95Ge0.05(2 +/- 11) as well as (20-2)parallel to Si0.95Ge0.05{220}, simultaneously with NiSi0.95Ge0.05(0 +/- 13) as well as (020)parallel to Si0.95Ge0.05{022}, caused NiSi0.95Ge0.05(100) to tilt over the range of 0 degrees-7.5 degrees. The Ge addition also enhanced the preferentially oriented structure by reinforcing NiSi0.95Ge0.05(123)parallel to Si0.95Ge0.05(111) through the axiotaxial alignments, NiSi0.95Ge0.05(211) and (-112)parallel to Si0.95Ge0.05{220}. Observed was also the presence of NiSi0.95Ge0.05(011)parallel to Si0.95Ge0.05(111), with NiSi0.95Ge0.05[100]parallel to Si0.95Ge0.05< 011 >. In the case of NiSi0.80Ge0.20, the preferential orientations were sharply reduced in favor of NiSi0.80Ge0.20(100)parallel to Si0.80Ge0.20(111), with NiSi0.80Ge0.20[010]parallel to Si0.80Ge0.20< 011 > and the 30 degrees rotation thus preserved. The observed Ge influence is shown to be consistent with a model suggested earlier for Si1-xGex(001) substrates, which is based on the nonexistence of Ni(Si1-xGex)(2) for all except the smallest values of x. High-resolution transmission electron microscopy was used to show that the surface steps typical of molecular-beam-deposited epitaxial Si1-xGex substrate films do not influence the growth of the NiSi1-xGex.
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