| 1. |
- Abdeldaim, Guma, et al.
(författare)
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Duplex detection of the Mycobacterium tuberculosis complex and medically important non-tuberculosis mycobacteria by real-time PCR based on the rnpB gene
- 2016
-
Ingår i: Acta Pathologica, Microbiologica et Immunologica Scandinavica (APMIS). - : Wiley. - 0903-4641 .- 1600-0463. ; 124:11, s. 991-995
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Tidskriftsartikel (refereegranskat)abstract
- A duplex real-time PCR based on the rnpB gene was developed for Mycobacterium spp. The assay was specific for the Mycobacterium tuberculosis complex (MTB) and also detected all 19 tested species of non-tuberculous mycobacteria (NTM). The assay was evaluated on 404 clinical samples: 290 respiratory samples and 114 from tissue and other nonrespiratory body sites. M. tuberculosis was detected by culture in 40 samples and in 30 samples by the assay. The MTB assay showed a sensitivity similar to Roche Cobas Amplicor MTB-PCR (Roche Molecular Systems, Pleasanton, CA, USA). There were only nine samples with non-tuberculous mycobacteria detected by culture. Six of them were detected by the PCR assay.
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| 2. |
- Abdeldaim, Guma, et al.
(författare)
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Is quantitative PCR for the pneumolysin (ply) gene useful for detection of pneumococcal lower respiratory tract infection?
- 2009
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Ingår i: Clinical Microbiology and Infection. - : Elsevier BV. - 1198-743X .- 1469-0691. ; 15:6, s. 565-570
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Tidskriftsartikel (refereegranskat)abstract
- The pneumolysin (ply) gene is widely used as a target in PCR assays for Streptococcus pneumoniae in respiratory secretions. However, false-positive results with conventional ply-based PCR have been reported. The aim here was to study the performance of a quantitative ply-based PCR for the identification of pneumococcal lower respiratory tract infection (LRTI). In a prospective study, fibreoptic bronchoscopy was performed in 156 hospitalized adult patients with LRTI and 31 controls who underwent bronchoscopy because of suspicion of malignancy. Among the LRTI patients and controls, the quantitative ply-based PCR applied to bronchoalveolar lavage (BAL) fluid was positive at >/=10(3) genome copies/mL in 61% and 71% of the subjects, at >/=10(5) genome copies/mL in 40% and 58% of the subjects, and at >/=10(7) genome copies/mL in 15% and 3.2% of the subjects, respectively. Using BAL fluid culture, blood culture, and/or a urinary antigen test, S. pneumoniae was identified in 19 LRTI patients. As compared with these diagnostic methods used in combination, quantitative ply-based PCR showed sensitivities and specificities of 89% and 43% at a cut-off of 10(3) genome copies/mL, of 84% and 66% at a cut-off of 10(5) genome copies/mL, and of 53% and 90% at a cut-off of 10(7) genome copies/mL, respectively. In conclusion, a high cut-off with the quantitative ply-based PCR was required to reach acceptable specificity. However, as a high cut-off resulted in low sensitivity, quantitative ply-based PCR does not appear to be clinically useful. Quantitative PCR methods for S. pneumoniae using alternative gene targets should be evaluated.
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| 3. |
- Abdeldaim, Guma M. K., et al.
(författare)
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Detection of Haemophilus influenzae in respiratory secretions from pneumonia patients by quantitative real-time polymerase chain reaction
- 2009
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Ingår i: Diagnostic microbiology and infectious disease. - : Elsevier. - 0732-8893 .- 1879-0070. ; 64:4, s. 366-373
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Tidskriftsartikel (refereegranskat)abstract
- A quantitative real-time polymerase chain reaction (PCR) based on the omp P6 gene was developed to detect Haemophilus influenzae. Its specificity was determined by analysis of 29 strains of 11 different Haemophilus spp. and was compared with PCR assays having other target genes: rnpB, 16S rRNA, and bexA. The method was evaluated on nasopharyngeal aspirates from 166 adult patients with community-acquired pneumonia. When 104 DNA copies/mL was used as cutoff limit for the method, P6 PCR had a sensitivity of 97.5% and a specificity of 96.0% compared with the culture. Of 20 culture-negative but P6 PCR-positive cases, 18 were confirmed by fucK PCR as H. influenzae. Five (5.9%) of 84 nasopharyngeal aspirates from adult controls tested PCR positive. We conclude that the P6 real-time PCR is both sensitive and specific for identification of H. influenzae in respiratory secretions. Quantification facilitates discrimination between disease-causing H. influenzae strains and commensal colonization.
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| 4. |
- Abdeldaim, Guma M. K.
(författare)
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PCR detection of Streptococcus pneumoniae and Haemophilus influenzae in pneumonia patients
- 2009
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- PCR is a rapid, reproducible method for nucleic acid detection. However, this technology displays significant deficiencies when applied in clinical microbiology. This work’s aim was to improve current diagnostics and provide sensitive and quantitative real-time PCRs. Paper I describes the development of a sensitive and specific quantitative real-time PCR for the detection of Streptococcus pneumoniae, based on the Spn9802 DNA fragment. Applied to nasopharyngeal aspirates from 166 pneumonia patients, Spn9802 PCR had a sensitivity of 94% and a specificity of 98%. In Paper II the performance of a ply gene PCR for identification of pneumococcal lower respiratory tract infection (LRTI) was evaluated on bronchoalveloar lavage fluids. At the detection limit 103 genome copies/mL, 89% sensitivity but only 43% specificity was achieved. Paper III shows that S. pneumoniae DNA is detectable in plasma from acutely febrile patients. Sensitivities were low (26-42%) for detection of pneumococcal pneumonia, for bacteraemic pneumococcal pneumonia they were 60-70%. Paper IV describes evaluation of four PCR targets for Haemophilus influenzae detection. A real-time PCR based on the P6 gene was developed and applied to 166 CAP patients, using cut-off of 104 genome copies/mL the assay had a sensitivity of 97% and a specificity of 96%. In paper V, the two real-time PCRs presented in papers I and IV were combined with a PCR for detection of Neisseriae meningitidis. The analytical sensitivity of this multiplex real-time PCR was not affected by using a mixture of reagents and a combined DNA standard (S. pneumoniae/H. influenzae) in single tubes. Applied to 156 LRTI patients, this PCR had sensitivities over 90% for S. pneumoniae and H. influenzae, and specificities of 89% and 96%, respectively. In conclusion, real-time PCR assays are useful for the diagnosis of S. pneumoniae and H. influenzae. They enable detection after antibiotic installation, and quantification increases the etiological specificity of pneumonia.
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| 5. |
- Abdeldaim, Guma M. K., et al.
(författare)
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Quantitative fucK gene polymerase chain reaction on sputum and nasopharyngeal secretions to detect Haemophilus influenzae pneumonia
- 2013
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Ingår i: Diagnostic microbiology and infectious disease. - : Elsevier. - 0732-8893 .- 1879-0070. ; 76:2, s. 141-146
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Tidskriftsartikel (refereegranskat)abstract
- A quantitative polymerase chain reaction (PCR) for the fucK gene was developed for specific detection of Haemophilus influenzae. The method was tested on sputum and nasopharyngeal aspirate (NPA) from 78 patients with community-acquired pneumonia (CAP). With a reference standard of sputum culture and/or serology against the patient's own nasopharyngeal isolate, H. influenzae etiology was detected in 20 patients. Compared with the reference standard, fucK PCR (using the detection limit 10(5) DNA copies/mL) on sputum and NPA showed a sensitivity of 95.0% (19/20) in both cases, and specificities of 87.9% (51/58) and 89.5% (52/58), respectively. In a receiver operating characteristic curve analysis, sputum fucK PCR was found to be significantly superior to sputum P6 PCR for detection of H. influenzae CAP. NPA fucK PCR was positive in 3 of 54 adult controls without respiratory symptoms. In conclusion, quantitative fucK real-time PCR provides a sensitive and specific identification of H. influenzae in respiratory secretions.
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| 6. |
- Abdeldaim, Guma M. K., et al.
(författare)
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Toward a quantitative DNA-based definition of pneumococcal pneumonia : a comparison of Streptococcus pneumoniae target genes, with special reference to the Spn9802 fragment
- 2008
-
Ingår i: Diagnostic microbiology and infectious disease. - : Elsevier BV. - 0732-8893 .- 1879-0070. ; 60:2, s. 143-150
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Tidskriftsartikel (refereegranskat)abstract
- The current shift from phenotypically toward genotypically based microbial diagnosis is not unproblematic. A novel quantitative real-time polymerase chain reaction (PCR) assay based on the Spn9802 DNA fragment was therefore developed for detection of Streptococcus pneumoniae. Out of 44 bacterial species, only S. pneumoniae and Streptococcus pseudopneumoniae were positive in Spn9802 PCR. In an evaluation on nasopharyngeal aspirates from 166 patients with community-acquired pneumonia, the assay was positive in 49 of 50 culture-positive cases. Of 19 culture-negative but Spn9802 PCR-positive cases, 12 were confirmed as S. pneumoniae by rnpB sequence analysis. With an expanded reference standard, including culture and rnpB sequencing, Spn9802 had a sensitivity of 94% and a specificity of 98%. A cutoff for clinically significant positivity was 10(4) DNA copies/mL, giving 71% sensitivity and 100% specificity. In conclusion, Spn9802 real-time PCR is highly sensitive and specific. The quantification it provides enables differentiation between pneumococcal pathogenicity and commensalism.
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| 7. |
- Abdeldaim, Guma, 1969-, et al.
(författare)
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Multiplex quantitative PCR for detection of lower respiratory tract infection and meningitis caused by Streptococcus pneumoniae, Haemophilus influenzae and Neisseria meningitidis
- 2010
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Ingår i: BMC Microbiology. - : Springer Science and Business Media LLC. - 1471-2180. ; 10, s. 310-
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Tidskriftsartikel (refereegranskat)abstract
- Background. Streptococcus pneumoniae and Haemophilus influenzae cause pneumonia and as Neisseria meningitidis they are important agents of meningitis. Although several PCR methods have been described for these bacteria the specificity is an underestimated problem. Here we present a quantitative multiplex real-time PCR (qmPCR) for detection of S. pneumoniae (9802 gene fragment), H. influenzae (omp P6 gene) and N. meningitidis (ctrA gene). The method was evaluated on bronchoalveolar lavage (BAL) samples from 156 adults with lower respiratory tract infection (LRTI) and 31 controls, and on 87 cerebrospinal fluid (CSF) samples from meningitis patients. Results. The analytical sensitivity was not affected by using a combined mixture of reagents and a combined DNA standard (S. pneumoniae/H. influenzae/N. meningitidis) in single tubes. By blood- and BAL-culture and S. pneumoniae urinary antigen test, S. pneumoniae and H. influenzae were aetiological agents in 21 and 31 of the LTRI patients, respectively. These pathogens were identified by qmPCR in 52 and 72 of the cases, respectively, yielding sensitivities and specificities of 95% and 75% for S. pneumoniae, and 90% and 65% for H. influenzae, respectively. When using a cut-off of 105 genome copies/mL for clinical positivity the sensitivities and specificities were 90% and 80% for S. pneumoniae, and 81% and 85% for H. influenzae, respectively. Of 44 culture negative but qmPCR positive for H. influenzae, 41 were confirmed by fucK PCR as H. influenzae. Of the 103 patients who had taken antibiotics prior to sampling, S. pneumoniae and H. influenzae were identified by culture in 6% and 20% of the cases, respectively, and by the qmPCR in 36% and 53% of the cases, respectively. In 87 CSF samples S. pneumoniae and N. meningitidis were identified by culture and/or 16 S rRNA in 14 and 10 samples and by qmPCR in 14 and 10 samples, respectively, giving a sensitivity of 100% and a specificity of 100% for both bacteria. Conclusions. The PCR provides increased sensitivity and the multiplex format facilitates diagnosis of S. pneumoniae, H. influenzae and N. meningitidis and the assay enable detection after antibiotic treatment has been installed. Quantification increases the specificity of the etiology for pneumonia.
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| 8. |
- Abdeldaim, Guma, et al.
(författare)
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Usefulness of real-time PCR for lytA, ply, and Spn9802 on plasma samples for the diagnosis of pneumococcal pneumonia
- 2010
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Ingår i: Clinical Microbiology and Infection. - : Elsevier BV. - 1198-743X .- 1469-0691. ; 16:8, s. 1135-1141
-
Tidskriftsartikel (refereegranskat)abstract
- In the present study, we evaluated rapid real-time PCR assays for ply, Spn9802, and lytA applied to plasma samples for the detection of Streptococcus pneumoniae in patients with community-acquired pneumonia (CAP). In a prospective study of CAP aetiology, an EDTA plasma sample was collected together with blood culture in 92 adult CAP patients and 91 adult controls. Among the 92 CAP patients, lytA PCR was positive in eight (9%), Spn9802 PCR was positive in 11 (12%) and ply PCR was positive in 19 (21%) cases. Of 91 controls, the ply PCR was positive in eight cases (9%), but no positive cases were noted by Spn9802 or lytA PCRs. Ten CAP patients had pneumococcal bacteraemia. Compared to blood culture, PCR for lytA, Spn9802 and ply had sensitivities of 70% (7/10), 60% (6/10) and 70% (7/10), and specificities of 96% (79/82), 94% (77/82) and 85% (70/82) respectively. With blood culture and/or culture of representative sputum, and/or urinary antigen detection, S. pneumoniae was identified in 31 CAP patients. Compared to these tests in combination, PCR for lytA, Spn9802 and ply showed sensitivities of 26% (8/31), 32% (10/31) and 42% (13/31), and specificities of 100% (61/61), 98% (60/61) and 90% (55/61) respectively. We conclude that Spn9802 and lytA PCRs may be useful for the rapid detection of bacteraemic pneumococcal pneumonia, whereas ply PCR is not specific enough for routine use and blood PCR with small plasma volumes is not useful for the detection of nonbacteraemic pneumococcal pneumonia.
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| 9. |
- Ahonen, Pasi, et al.
(författare)
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Writing resistance together
- 2020
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Ingår i: Gender, Work and Organization. - : John Wiley & Sons. - 0968-6673 .- 1468-0432. ; 27:4, s. 447-470
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Tidskriftsartikel (refereegranskat)abstract
- This piece of writing is a joint initiative by the participants in the Gender, Work and Organization writing workshop organized in Helsinki, Finland, in June 2019. This is a particular form of writing differently. We engage in collective writing and embody what it means to write resistance to established academic practices and conventions together. This is a form of emancipatory initiative where we care for each other as writers and as human beings. There are many author voices and we aim to keep the text open and dialogical. As such, this piece of writing is about suppressed thoughts and feelings that our collective picket line allows us to express. In order to maintain the open-ended nature of the text, and perhaps also to retain some 'dirtiness' that is essential to writing, the article has not been language checked throughout by a native speaker of English.
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| 10. |
- Al Moubayed, Samer, et al.
(författare)
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Talking with Furhat - multi-party interaction with a back-projected robot head
- 2012
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Ingår i: Proceedings of Fonetik 2012. - Gothenberg, Sweden. ; , s. 109-112
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- This is a condensed presentation of some recent work on a back-projected robotic head for multi-party interaction in public settings. We will describe some of the design strategies and give some preliminary analysis of an interaction database collected at the Robotville exhibition at the London Science Museum
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| 11. |
- Alm Rosenblad, Magnus, 1957, et al.
(författare)
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Genomic Characterization of the Barnacle Balanus improvisus Reveals Extreme Nucleotide Diversity in Coding Regions
- 2021
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Ingår i: Marine Biotechnology. - : Springer Science and Business Media LLC. - 1436-2228 .- 1436-2236. ; 23, s. 402-416
-
Tidskriftsartikel (refereegranskat)abstract
- Barnacles are key marine crustaceans in several habitats, and they constitute a common practical problem by causing biofouling on man-made marine constructions and ships. Despite causing considerable ecological and economic impacts, there is a surprising void of basic genomic knowledge, and a barnacle reference genome is lacking. We here set out to characterize the genome of the baybarnacle Balanus improvisus (= Amphibalanus improvisus) based on short-read whole-genome sequencing and experimental genome size estimation. We show both experimentally (DNA staining and flow cytometry) and computationally (k-mer analysis) that B. improvisus has a haploid genome size of ~ 740 Mbp. A pilot genome assembly rendered a total assembly size of ~ 600 Mbp and was highly fragmented with an N50 of only 2.2 kbp. Further assembly-based and assembly-free analyses revealed that the very limited assembly contiguity is due to the B. improvisus genome having an extremely high nucleotide diversity (π) in coding regions (average π ≈ 5% and average π in fourfold degenerate sites ≈ 20%), and an overall high repeat content (at least 40%). We also report on high variation in the α-octopamine receptor OctA (average π = 3.6%), which might increase the risk that barnacle populations evolve resistance toward antifouling agents. The genomic features described here can help in planning for a future high-quality reference genome, which is urgently needed to properly explore and understand proteins of interest in barnacle biology and marine biotechnology and for developing better antifouling strategies. © 2021, The Author(s).
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| 12. |
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| 13. |
- Bergström, Göran, 1964, et al.
(författare)
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Prevalence of Subclinical Coronary Artery Atherosclerosis in the General Population
- 2021
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Ingår i: Circulation. - Philadelphia : American Heart Association. - 0009-7322 .- 1524-4539. ; 144:12, s. 916-929
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Tidskriftsartikel (refereegranskat)abstract
- Background: Early detection of coronary atherosclerosis using coronary computed tomography angiography (CCTA), in addition to coronary artery calcification (CAC) scoring, may help inform prevention strategies. We used CCTA to determine the prevalence, severity, and characteristics of coronary atherosclerosis and its association with CAC scores in a general population.Methods: We recruited 30 154 randomly invited individuals age 50 to 64 years to SCAPIS (the Swedish Cardiopulmonary Bioimage Study). The study includes individuals without known coronary heart disease (ie, no previous myocardial infarctions or cardiac procedures) and with high-quality results from CCTA and CAC imaging performed using dedicated dual-source CT scanners. Noncontrast images were scored for CAC. CCTA images were visually read and scored for coronary atherosclerosis per segment (defined as no atherosclerosis, 1% to 49% stenosis, or ≥50% stenosis). External validity of prevalence estimates was evaluated using inverse probability for participation weighting and Swedish register data.Results: In total, 25 182 individuals without known coronary heart disease were included (50.6% women). Any CCTA-detected atherosclerosis was found in 42.1%; any significant stenosis (≥50%) in 5.2%; left main, proximal left anterior descending artery, or 3-vessel disease in 1.9%; and any noncalcified plaques in 8.3% of this population. Onset of atherosclerosis was delayed on average by 10 years in women. Atherosclerosis was more prevalent in older individuals and predominantly found in the proximal left anterior descending artery. Prevalence of CCTA-detected atherosclerosis increased with increasing CAC scores. Among those with a CAC score >400, all had atherosclerosis and 45.7% had significant stenosis. In those with 0 CAC, 5.5% had atherosclerosis and 0.4% had significant stenosis. In participants with 0 CAC and intermediate 10-year risk of atherosclerotic cardiovascular disease according to the pooled cohort equation, 9.2% had CCTA-verified atherosclerosis. Prevalence estimates had excellent external validity and changed marginally when adjusted to the age-matched Swedish background population.Conclusions: Using CCTA in a large, random sample of the general population without established disease, we showed that silent coronary atherosclerosis is common in this population. High CAC scores convey a significant probability of substantial stenosis, and 0 CAC does not exclude atherosclerosis, particularly in those at higher baseline risk.
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| 14. |
- Bergström, Göran, et al.
(författare)
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Prevalence of Subclinical Coronary Artery Atherosclerosis in the General Population
- 2021
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Ingår i: Circulation. - : Wolters Kluwer. - 0009-7322 .- 1524-4539. ; 144:12, s. 916-929
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Early detection of coronary atherosclerosis using coronary computed tomography angiography (CCTA), in addition to coronary artery calcification (CAC) scoring, may help inform prevention strategies. We used CCTA to determine the prevalence, severity, and characteristics of coronary atherosclerosis and its association with CAC scores in a general population.Methods: We recruited 30 154 randomly invited individuals age 50 to 64 years to SCAPIS (the Swedish Cardiopulmonary Bioimage Study). The study includes individuals without known coronary heart disease (ie, no previous myocardial infarctions or cardiac procedures) and with high-quality results from CCTA and CAC imaging performed using dedicated dual-source CT scanners. Noncontrast images were scored for CAC. CCTA images were visually read and scored for coronary atherosclerosis per segment (defined as no atherosclerosis, 1% to 49% stenosis, or ≥50% stenosis). External validity of prevalence estimates was evaluated using inverse probability for participation weighting and Swedish register data.Results: In total, 25 182 individuals without known coronary heart disease were included (50.6% women). Any CCTA-detected atherosclerosis was found in 42.1%; any significant stenosis (≥50%) in 5.2%; left main, proximal left anterior descending artery, or 3-vessel disease in 1.9%; and any noncalcified plaques in 8.3% of this population. Onset of atherosclerosis was delayed on average by 10 years in women. Atherosclerosis was more prevalent in older individuals and predominantly found in the proximal left anterior descending artery. Prevalence of CCTA-detected atherosclerosis increased with increasing CAC scores. Among those with a CAC score >400, all had atherosclerosis and 45.7% had significant stenosis. In those with 0 CAC, 5.5% had atherosclerosis and 0.4% had significant stenosis. In participants with 0 CAC and intermediate 10-year risk of atherosclerotic cardiovascular disease according to the pooled cohort equation, 9.2% had CCTA-verified atherosclerosis. Prevalence estimates had excellent external validity and changed marginally when adjusted to the age-matched Swedish background population.Conclusions: Using CCTA in a large, random sample of the general population without established disease, we showed that silent coronary atherosclerosis is common in this population. High CAC scores convey a significant probability of substantial stenosis, and 0 CAC does not exclude atherosclerosis, particularly in those at higher baseline risk.
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| 15. |
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| 16. |
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| 17. |
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| 18. |
- Blomberg, Björn, 1948-
(författare)
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Helicobacter pylori : Prevalence, heterogeneity, and ulcerogenic properties
- 1993
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In 117. unselected patients H. pylori infection was found in 49.6% by combining culture and acndme orange stammg of hssue sections. Infection was equally common in the gastric body and antrum. The activity of gastritis was generally higher in the antrum. The overallagreement between acridine orange stain and culture was 0.93.Formalin treated H. pylori whole cells were used to immunize rabbits. With the aid of coagglutination and indirect immunofluorescence all H. pylori strains tested were shown to contain cross reactive antigens, but no serum cross-reacted with all strains tested. Multiple, antigenically different, isolates were found in some patients and a provisional serogrouping based on heat-stable antigens was proposed.Acid glycine extracts from four H. pylori strains were prepared. Rabbit antisera against these, and ten further, strains showed extensive cross-reactions with all four extracts. An EIA based on H. pylori strain NCTC 11637 had a sensitivity of 90 % and a specificity of 87 %.In 197 unselected patient culture, histopathology using acridine orange or Giemsa staining, and serology was evaluated. 33.5 % of patients were infected by H. pylori. The sensitivities for culture/acridine orange stain/Giemsa stain were 0.94/0.86/0.91 respectively. The specificities were 1.0/1.0/0.84. For two commercial serologic tests the negative predictive values were 0.93/0.95 respectively. A strategy of serologic screening to avoidunnecessary endoscopies was suggested, but that positive serology be confirmed by histopathology.Sixty-one human gastric isolates of H. pylori were tested for their ability to induce oxidative burst in human neutrophils. A cell bound, heat-labile, property able to induce a strong and rapid oxidative burst in neutrophils in the abscence of opsonins, was found in about one third of strains tested. This property was significantly associated with peptic ulcer disease(p=0.0261, Fisher's exact test).Fifty-four clinical isolates of H. pylori were tested for cytotoxin production and their ability to induce oxidative burst in human neutrophils. Nonopsonised, 20 strains showed a rapid and strong oxidative burst, 30 a slow and weak response, and four remaining gave inconclusive results. Cytotoxin production was seen in 10 of 20 rapid and strong inducers, but only in 3 of 30 with a slow and weak response (p=0.0027, Fisher's exact test). 11/15 of the cytotoxin producing strains (p=0.0135) and 13/20 of the rapid and strong inducers (p=0.0209) were from 22 patients with peptic ulcer disease. The ability of some nonopsonised H. pylori to activate neutrophils showed eo-variation with cytotoxin production, but the two properties seem to be independent markers of peptic ulcer disease.With theuse of electron microscopy the interactions of human neutrophils with four nonopsonised H. pylori strains, two rapid and strong, two slow and weak inducers of neutrophil oxidative burst were studied in morphologic detail. The rapid inducers were phagocytosed within minutes, whereas the slow inducers showed little reaction even after one hour.Conclusions: Histopathology using acridine orange or Giernsa stains correlates well with culture. Serologic screening might be of value to reduce unnecessary endoscopies. A cellbound heat-labile property of some H. pylori strains able to nonopsonised induce a rapid oxidative burst in neutrophils is significantly associated with peptic ulcer disease. This property is also associated with, but independent of, cytotoxin production.
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| 19. |
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| 20. |
- Blomberg, Mats, et al.
(författare)
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Children and adults in dialogue with the robot head Furhat - corpus collection and initial analysis
- 2012
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Ingår i: Proceedings of WOCCI. - Portland, OR : The International Society for Computers and Their Applications (ISCA).
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Konferensbidrag (refereegranskat)abstract
- This paper presents a large scale study in a public museum setting, where a back-projected robot head interacted with the visitors in multi-party dialogue. The exhibition was seen by almost 8000 visitors, out of which several thousand interacted with the system. A considerable portion of the visitors were children from around 4 years of age and adolescents. The collected corpus consists of about 10.000 user utterances. The head and a multi-party dialogue design allow the system to regulate the turn-taking behaviour, and help the robot to effectively obtain information from the general public. The commercial speech recognition component, supposedly designed for adult speakers, had considerably lower accuracy for the children. Methods are proposed for improving the performance for that speaker category.
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| 21. |
- Blomberg, Margareta R A, et al.
(författare)
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A Quantum Chemical Study of Hydrogen Abstraction from Manganese-Coordinated Water by a Tyrosyl Radical: A Model for Water Oxidation in Photosystem II
- 1997
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 1520-5126 .- 0002-7863. ; 119:35, s. 8285-8292
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Tidskriftsartikel (refereegranskat)abstract
- Recently, water oxidation in photosystem II was proposed to involve direct abstraction of hydrogen atoms from water molecules terminally ligated to manganese ions in the oxygen-evolving complex by the oxidized tyrosine radical, TyrZ. This model is tested here by performing quantum chemical calculations. An empirically parametrized hybrid density functional method is used, and both monomeric and dimeric manganese model systems are studied. It is found that, by coordination to a manganese center, the first O-H bond strength of water is lowered from 113.4 to 84.3 kcal/mol. This O-H bond strength is only 2.8 kcal/mol stronger than that in tyrosine. Using an extended basis set, we find that this difference decreases still further. The second hydrogen abstraction energy is quite similar. Since thermoneutrality in the reaction (or a weak exothermicity) is a requirement for the hydrogen abstraction model, the present calculations support this model. Possible functions of a coordinated chloride and a nearby calcium complex are suggested. Five- or six-coordination and ferro- or antiferromagnetic spin couplings of the manganese centers are discussed.
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| 22. |
- Blomberg, Olle, et al.
(författare)
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Plikt att kollektivisera?
- 2018
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Ingår i: Tidskrift för politisk filosofi. - 1402-2710. ; 22:2, s. 36-46
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- En del moraliska dilemman och samhällsproblem uppstår ur många sinsemellan orelaterade individuella handlingar eller underlåtelser, samtidigt som problemen bara kan åtgärdas genom kollektiv handling. Vi kritiserar tre sätt att resonera om ostrukturerade gruppers moraliska plikter och ansvar i sådana situationer. Därefter föreslår vi att intuitionen att en sådan grupp kan ha moraliska plikter och vara ansvarig bäst förklaras med utgångspunkt i att individer åtminstone i småskaliga fall kan identifiera sig med gruppen i en stark mening, och betrakta beslutssituationen ur gruppens perspektiv.
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| 23. |
- Blomberg, Olle, et al.
(författare)
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Team reasoning and collective moral obligation
- 2024
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Ingår i: Social Theory and Practice. - : Philosophy Documentation Center. - 0037-802X.
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Tidskriftsartikel (refereegranskat)abstract
- We propose a new account of collective moral obligation. We argue that several agents have a moral obligation together only if they each have (i) a context-specific capacity to view their situation from the group’s perspective, and (ii) at least a general capacity to deliberate about what they ought to do together. Such an obligation is irreducibly collective, in that it doesn’t imply that the individuals have any obligations to contribute to what is required of the group. We highlight various distinctive features of our account. One such feature is that moral obligations are always relative to an agential perspective.
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| 24. |
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| 25. |
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| 26. |
- Chaplin, John, et al.
(författare)
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Varför ska du använda PROMIS? : Nytt system för patientrapporterad utfallsmått
- 2018
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- PROMIS är ett itembanksystem för hälso- och sjukvården. Syftet är att erbjuda moderna, patientrapporterade mått som kan användas för flertalet patientgrupper till en mycket låg kostnad och med ett nationellt supportsystem.En itembankär en modern form av elektronisk enkät som kan innehålla ett stort antal enkätfrågor. Ett datorprogram väljer ut de mest lämpade frågorna till varje person utifrån dennes svar på föregående frågor, på så sätt enkäten individanpassas.
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| 27. |
- Crüts, Björn, et al.
(författare)
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Exposure to diesel exhaust induces changes in EEG in human volunteers.
- 2008
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Ingår i: Particle and Fibre Toxicology. - : Springer Science and Business Media LLC. - 1743-8977. ; 5, s. 4-
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Tidskriftsartikel (refereegranskat)abstract
- ABSTRACT: BACKGROUND: Ambient particulate matter and nanoparticles have been shown to translocate to the brain, and potentially influence the central nervous system. No data are available whether this may lead to functional changes in the brain. METHODS: We exposed 10 human volunteers to dilute diesel exhaust (DE, 300 mug/m3) as a model for ambient PM exposure and filtered air for one hour using a double blind randomized crossover design. Brain activity was monitored during and for one hour following each exposure using quantitative electroencephalography (QEEG) at 8 different sites on the scalp. The frequency spectrum of the EEG signals was used to calculate the median power frequency (MPF) and specific frequency bands of the QEEG. RESULTS: Our data demonstrate a significant increase in MPF in response to DE in the frontal cortex within 30 min into exposure. The increase in MPF is primarily caused by an increase in fast wave activity (beta2) and continues to rise during the 1 hour post-exposure interval. CONCLUSION: This study is the first to show a functional effect of DE exposure in the human brain, indicating a general cortical stress response. Further studies are required to determine whether this effect is mediated by the nanoparticles in DE and to define the precise pathways involved.
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| 28. |
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| 29. |
- Elenius, Daniel, 1975-
(författare)
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Accounting for Individual Speaker Properties in Automatic Speech Recognition
- 2010
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In this work, speaker characteristic modeling has been applied in the fields of automatic speech recognition (ASR) and automatic speaker verification (ASV). In ASR, a key problem is that acoustic mismatch between training and test conditions degrade classification per- formance. In this work, a child exemplifies a speaker not represented in training data and methods to reduce the spectral mismatch are devised and evaluated. To reduce the acoustic mismatch, predictive modeling based on spectral speech transformation is applied. Follow- ing this approach, a model suitable for a target speaker, not well represented in the training data, is estimated and synthesized by applying vocal tract predictive modeling (VTPM). In this thesis, the traditional static modeling on the utterance level is extended to dynamic modeling. This is accomplished by operating also on sub-utterance units, such as phonemes, phone-realizations, sub-phone realizations and sound frames. Initial experiments shows that adaptation of an acoustic model trained on adult speech significantly reduced the word error rate of ASR for children, but not to the level of a model trained on children’s speech. Multi-speaker-group training provided an acoustic model that performed recognition for both adults and children within the same model at almost the same accuracy as speaker-group dedicated models, with no added model complexity. In the analysis of the cause of errors, body height of the child was shown to be correlated to word error rate. A further result is that the computationally demanding iterative recognition process in standard VTLN can be replaced by synthetically extending the vocal tract length distribution in the training data. A multi-warp model is trained on the extended data and recognition is performed in a single pass. The accuracy is similar to that of the standard technique. A concluding experiment in ASR shows that the word error rate can be reduced by ex- tending a static vocal tract length compensation parameter into a temporal parameter track. A key component to reach this improvement was provided by a novel joint two-level opti- mization process. In the process, the track was determined as a composition of a static and a dynamic component, which were simultaneously optimized on the utterance and sub- utterance level respectively. This had the principal advantage of limiting the modulation am- plitude of the track to what is realistic for an individual speaker. The recognition error rate was reduced by 10% relative compared with that of a standard utterance-specific estimation technique. The techniques devised and evaluated can also be applied to other speaker characteristic properties, which exhibit a dynamic nature. An excursion into ASV led to the proposal of a statistical speaker population model. The model represents an alternative approach for determining the reject/accept threshold in an ASV system instead of the commonly used direct estimation on a set of client and impos- tor utterances. This is especially valuable in applications where a low false reject or false ac- cept rate is required. In these cases, the number of errors is often too few to estimate a reli- able threshold using the direct method. The results are encouraging but need to be verified on a larger database.
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| 30. |
- Elfaitouri, Amal, et al.
(författare)
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Epitopes of Microbial and Human Heat Shock Protein 60 and Their Recognition in Myalgic Encephalomyelitis
- 2013
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8:11, s. 55-
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Tidskriftsartikel (refereegranskat)abstract
- Myalgic encephalomyelitis (ME, also called Chronic Fatigue Syndrome), a common disease with chronic fatigability, cognitive dysfunction and myalgia of unknown etiology, often starts with an infection. The chaperonin human heat shock protein 60 (HSP60) occurs in mitochondria and in bacteria, is highly conserved, antigenic and a major autoantigen. The anti-HSP60 humoral (IgG and IgM) immune response was studied in 69 ME patients and 76 blood donors (BD) (the Training set) with recombinant human and E coli HSP60, and 136 30-mer overlapping and targeted peptides from HSP60 of humans, Chlamydia, Mycoplasma and 26 other species in a multiplex suspension array. Peptides from HSP60 helix I had a chaperonin-like activity, but these and other HSP60 peptides also bound IgG and IgM with an ME preference, theoretically indicating a competition between HSP60 function and antibody binding. A HSP60-based panel of 25 antigens was selected. When evaluated with 61 other ME and 399 non-ME samples (331 BD, 20 Multiple Sclerosis and 48 Systemic Lupus Erythematosus patients), a peptide from Chlamydia pneumoniae HSP60 detected IgM in 15 of 61 (24%) of ME, and in 1 of 399 non-ME at a high cutoff (p<0.0001). IgM to specific cross-reactive epitopes of human and microbial HSP60 occurs in a subset of ME, compatible with infection-induced autoimmunity.
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| 31. |
- Engström, Gunnar, et al.
(författare)
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The Swedish CArdioPulmonary BioImage Study : objectives and design
- 2015
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Ingår i: Journal of Internal Medicine. - : Wiley. - 0954-6820 .- 1365-2796. ; 278:6, s. 645-659
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Tidskriftsartikel (refereegranskat)abstract
- Cardiopulmonary diseases are major causes of death worldwide, but currently recommended strategies for diagnosis and prevention may be outdated because of recent changes in risk factor patterns. The Swedish CArdioPulmonarybioImage Study (SCAPIS) combines the use of new imaging technologies, advances in large-scale 'omics' and epidemiological analyses to extensively characterize a Swedish cohort of 30 000 men and women aged between 50 and 64 years. The information obtained will be used to improve risk prediction of cardiopulmonary diseases and optimize the ability to study disease mechanisms. A comprehensive pilot study in 1111 individuals, which was completed in 2012, demonstrated the feasibility and financial and ethical consequences of SCAPIS. Recruitment to the national, multicentre study has recently started.
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| 32. |
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| 33. |
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| 34. |
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| 35. |
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| 36. |
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| 37. |
- Eriksson, Björn, et al.
(författare)
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In-line application of electric field in capillary separation systems Part I: Joule heating, pH and conductivity
- 2008
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Ingår i: Journal of Chromatography A. - : Elsevier BV. - 0021-9673 .- 1873-3778. ; 75:1, s. 83-90
-
Tidskriftsartikel (refereegranskat)abstract
- This study concerns the technique electric field-assisted capillary liquid chromatography. In this technique, an electric field is applied over the separation capillary in order to provide an additional selectivity. In this technique, the electric field is applied in-line in the separation capillary and here the electric current is the factor limiting the magnitude of applied electric field. The influence of Joule heating and other factors on the current in such systems has been investigated.The temperature in the capillary was first measured within a standard CE set-up, as function of effect per unit of length. Then the same cooling system was applied to an in-line set-up, to replicate the conditions between the two systems, and thus the temperature. Thus Joule heating effects could then be calculated within the in-line system. It was found that for systems applying an electric field in line, the direct influence from Joule heating was only relatively small.The pH in the capillary was measured in the in-line set-up using cresol red/TRIS solutions as pH probe. Significant changes in pH were observed and the results suggested that electrolysis of water is the dominant electrode reaction in the in-line system. In summary, the observed conductivity change in in-line systems was found to be mainly due to the pH change by hydrolysis of water, but primarily not due the temperature change in the capillary column.
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| 38. |
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| 39. |
- Eriksson, Björn, 1976-
(författare)
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In-line application of electric fields in capillary separation systems
- 2006
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The magnitude of an electric field possible to apply in a capillary separation system is limited, because a high electric field causes a too high current through the capillary. Application of the electric field in-line will give an increased conductivity in the column, further increasing the risk of too high currents. The conductivity changes were found to result from an overall increase in ionic strength within the electric field. The increase in ionic strength is caused by the increase in mobile phase ions with electrophoretic velocity against the flow, together with OH- or H3O+ ions (depending on polarity) formed at the inlet electrode. Further it was found that the use of a pressurized reservoir or splitting of the flow at the inlet electrode could significantly limit the conductivity changes and thereby the maximum applicable electric field strengths could be increased.
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| 40. |
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| 41. |
- Eriksson, Ronnie, et al.
(författare)
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Multiplex and quantifiable detection of nucleic acid from pathogenic fungi using padlock probes, generic real time PCR and specific suspension array readout
- 2009
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Ingår i: Journal of Microbiological Methods. - : Elsevier BV. - 0167-7012 .- 1872-8359. ; 78:2, s. 195-202
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Tidskriftsartikel (refereegranskat)abstract
- A new concept for multiplex detection and quantification of microbes is here demonstrated on a range of infectious fungal species. Padlock probe methodology in conjunction with qPCR and Luminex technology was used for simultaneous detection of ten fungal species in one single experiment. By combining the multiplexing properties of padlock probes and Luminex detection with the well established quantitative characteristics of qPCR, quantitative microbe detection was done in 10-plex mode. A padlock probe is an oligonucleotide that via a ligation reaction forms circular DNA when hybridizing to specific target DNA. The region of the padlock probe that does not participate in target DNA hybridization contains generic primer sequences for amplification and a tag sequence for Luminex detection. This was the fundament for well performing multiplexing. Circularized padlock probes were initially amplified by rolling circle amplification (RCA), followed by a SybrGreen real time PCR which allowed an additive quantitative assessment of target DNA in the sample. Detection and quantification of amplified padlock probes were then done on color coded Luminex microspheres carrying anti-tag sequences. A novel technique, using labeled oligonucleotides to prevent reannealing of amplimers by covering the flanks of the address sequence, improved the signal to noise ratio in the detection step considerably. The method correctly detected fungi in a variety of clinical samples and offered quantitative information on fungal nucleic acid.
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| 42. |
- Filén, Finn, et al.
(författare)
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Duplex real-time polymerase chain reaction assay for detection and quantification of herpes simplex virus type 1 and herpes simplex virus type 2 in genital and cutaneous lesions
- 2004
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Ingår i: Sexually Transmitted Diseases. - 0148-5717 .- 1537-4521. ; 31:6, s. 331-6
-
Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: A sensitive and specific method for detecting herpes simplex virus type 1 (HSV-1) and herpes simplex virus type 2 (HSV-2) is important for diagnosing genital and cutaneous infections. GOAL: The goal of this study was to compare quantitative real-time polymerase chain reaction (qPCR) with virus culture for diagnosis of genital and cutaneous HSV-1 and HSV-2. STUDY DESIGN: A duplex qPCR system for quantification of DNA from HSV-1 and HSV-2 was developed. Duplicate swabs for PCR and virus culture were collected from 89 patients attending our sexually transmitted infection and dermatology clinic. RESULTS: The duplex qPCR had a linear measure interval of 10-10 copies/mL. The detection limit was between 1 and 5 copies per reaction. qPCR detected HSV in 57 (64%) specimens and virus was isolated in 45 (50%) cases. First-episode infections showed higher viral quantities with a median value of 4.2 x 10 copies per reaction compared with recurrent infections with 1.0 x 10 (P = 0.0002). HSV-1 was more likely to be the cause of first-episode genital infections (72%), and HSV-2 of recurrent and atypical genital manifestations (73%). CONCLUSION: Real-time PCR is a sensitive method for diagnosing genital herpes, and the duplex format is convenient for typing. The method increased the detection rate by 27% compared with virus culture.
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| 43. |
- Fischer, Alexandra, et al.
(författare)
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Adherence to a Mediterranean-like Diet as a Protective Factor Against COPD : A Nested Case-Control Study
- 2019
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Ingår i: COPD. - : Taylor & Francis. - 1541-2555 .- 1541-2563. ; 16:3–4, s. 272-277
-
Tidskriftsartikel (refereegranskat)abstract
- A diet rich in nutrients has been suggested to have protective effects against the development of chronic obstructive pulmonary disease (COPD). Since the traditional Mediterranean diet is high in nutrients, including antioxidants, vitamins, and minerals, it is of interest to study as a protective factor against COPD. Our aim was therefore to study its associations with development of COPD using population-based prospective data from the Vasterbotten Intervention Programme (VIP) cohort. Data on diet from 370 individuals, who later visited the Department of Medicine at the University Hospital, Umea, Sweden, with a diagnosis of COPD, were compared to 1432 controls. Adherence to a Mediterranean diet was assessed by a modified version of the Mediterranean diet score (MDS). Cases were diagnosed with COPD 11.1 years (mean) (standard deviation [SD] 4.5 years) after first stating their dietary habits in the VIP at a mean age of 55.5 years (SD 6.6 years). Higher MDS was associated with a higher level of education and not living alone. After adjustment for co-habiting and education level, individuals with an intermediate MDS and those with the highest MDS had a lower odds of developing COPD (odds ratio [OR] 0.73, 95% confidence interval [CI] 0.56-0.95; OR 0.56, 95% CI 0.37-0.86, respectively). These results remained also after adjustment for smoking intensity, i.e., numbers of cigarettes smoked per day (OR 0.73, 95% CI 0.53-0.99; OR 0.59, 95% CI 0.35-0.97), respectively). To conclude, adherence to a Mediterranean-like diet seems to be inversely associated with the development of COPD.
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| 44. |
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| 45. |
- Gross, Susanna, 1982, et al.
(författare)
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Optimization of a high-throughput phenotyping method for chain-forming phytoplankton species
- 2018
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Ingår i: Limnology and Oceanography : Methods. - : Wiley. - 1541-5856. ; 16:2, s. 57-67
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Tidskriftsartikel (refereegranskat)abstract
- Modern equipment facilitates phenotyping of hundreds of strains of unicellular organisms by culturing and monitoring growth in microplates. However, in the field of phytoplankton ecology, automated monitoring of growth is not often done and this method has not been tested for many species. To meet the demand for a high-throughput technique for monitoring growth of chain-forming phytoplankton species, we have assessed and optimized a method commonly used for other microorganisms. Skeletonema marinoi is a pelagic chain-forming diatom, and we have acquired growth patterns in four different treatments (i.e., low and high light, low and high nutrient concentrations) when cultured in multi-well plates. Due to the unexpected heterogeneity in growth rates and maximum cell densities observed between wells (spatial) and runs (temporal), a set of models was fitted to the obtained phenotypic data to correct for these biases. Models were tested for robustness on two replicate multi-strain experiments including 23 different strains. Using the model accounting for temporal and spatial bias, we could reliably determine changes in growth rate caused by nutrient treatments as well as differences in cell density as a response to nutrient availability and light treatment. This method can facilitate high-throughput phenotyping of hundreds of strains, which is often a bottleneck in characterizing the ecology and capacity for adaptation of chain-forming phytoplankton.
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| 46. |
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| 47. |
- Gustavsson, Anders, et al.
(författare)
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Smoking is a risk factor for recurrence of intestinal stricture after endoscopic dilation in Crohn’s disease
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Background: Endoscopic balloon dilation is an efficacious and safe alternative to surgery as treatment of short intestinal strictures in Crohn’s disease (CD). Factors predicting outcome of the procedure are not well described.Aim: To evaluate whether smoking at diagnosis, treatment with azathioprine, or other clinical variables may affect clinical outcome after endoscopic dilation.Endpoint was requirement of a new intervention such as dilation or surgerywith intestinal resection or strictureplasty.Methods: Retrospective study of 83 patients with CD who underwent endoscopic balloon dilation of an intestinal stricture between 1987 and 2009.Results: After index dilation 55/83 patients underwent a new intervention. Among current smokers, 31/32 (97%) underwent another intervention compared to 18/33 (55%) among never smokers (HR 2.18, 95%CI 1.22-3.93, P=0.009). After 5 years, cumulative probability of new intervention was 0.81 in smokers compared to 0.52 in never smokers; difference 0.29 (95 % CI 0.07–0.52, P = 0.01). In 16 patients, therapy with azathioprine was initiated before or shortly after the index dilation; 7/16 underwent a new intervention compared to 48/67of those without azathioprine (HR 0.46, 95%CI 0.21-1.03, P=0.06). After adjustment for other variables, the association was even weaker (HR 0.80, 95%CI 0.29-2.18, P=0.668). Sex, age atdiagnosis, age at first dilation, balloon size, location of stricture, and treatment period did not influence outcome.Conclusions: Smoking doubles the risk of recurrent stricture formation requiring a new intervention after index dilation. Maintenance therapy with azathioprine did not influence the subsequent course and need for a new intervention.
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| 48. |
- Gustavsson, Anders, 1964-, et al.
(författare)
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Smoking is a risk factor for recurrence of intestinal stricture after endoscopic dilation in Crohn's disease
- 2013
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Ingår i: Alimentary Pharmacology and Therapeutics. - : Wiley-Blackwell. - 0269-2813 .- 1365-2036. ; 37:4, s. 430-437
-
Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Endoscopic balloon dilation is an efficacious and safe alternative to surgery as treatment of short intestinal strictures in Crohn's disease (CD). Factors predicting outcome of the procedure are not well described.AIM: To evaluate whether smoking at diagnosis, treatment with azathioprine, or other clinical variables may affect clinical outcome after endoscopic dilation. The endpoint was requirement of a new intervention such as dilation or surgery with intestinal resection or strictureplasty.METHODS: Retrospective study of 83 patients with CD who underwent endoscopic balloon dilation of an intestinal stricture between 1987 and 2009.RESULTS: After index dilation 55/83 patients underwent a new intervention. Among current smokers, 31/32 (97%) underwent another intervention compared to 18/33 (55%) among never smokers (adjusted HR: 2.50, 95% CI: 1.14-5.50, P = 0.022). After 5 years, cumulative probability of new intervention was 0.81 in smokers compared to 0.52 in never smokers; difference 0.29 (95% CI: 0.07-0.52, P = 0.01). In 16 patients, therapy with azathioprine was initiated before or shortly after the index dilation; 7/16 underwent a new intervention compared to 48/67 of those without azathioprine (HR: 0.46, 95% CI: 0.21-1.03, P = 0.06). After adjustment for other variables, the association was even weaker (HR: 0.80, 95% CI: 0.29-2.18, P = 0.668). Sex, age at diagnosis, age at first dilation, balloon size, location of stricture, and treatment period did not influence outcome.CONCLUSIONS: Smoking doubles the risk of recurrent stricture formation requiring a new intervention after index dilation. Maintenance therapy with azathioprine did not influence the subsequent course and need for a new intervention.
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| 49. |
- Haroun-Izquierdo, Alvaro, et al.
(författare)
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Adaptive single-KIR(+)NKG2C(+) NK cells expanded from select superdonors show potent missing-self reactivity and efficiently control HLA-mismatched acute myeloid leukemia
- 2022
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Ingår i: Journal for ImmunoTherapy of Cancer. - : BMJ. - 2051-1426. ; 10:11, s. e005577-
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundNatural killer (NK) cells hold great promise as a source for allogeneic cell therapy against hematological malignancies, including acute myeloid leukemia (AML). Current treatments are hampered by variability in NK cell subset responses, a limitation which could be circumvented by specific expansion of highly potent single killer immunoglobulin-like receptor (KIR)(+)NKG2C(+) adaptive NK cells to maximize missing-self reactivity.MethodsWe developed a GMP-compliant protocol to expand adaptive NK cells from cryopreserved cells derived from select third-party superdonors, that is, donors harboring large adaptive NK cell subsets with desired KIR specificities at baseline. We studied the adaptive state of the cell product (ADAPT-NK) by flow cytometry and mass cytometry as well as cellular indexing of transcriptomes and epitopes by sequencing (CITE-Seq). We investigated the functional responses of ADAPT-NK cells against a wide range of tumor target cell lines and primary AML samples using flow cytometry and IncuCyte as well as in a mouse model of AML.ResultsADAPT-NK cells were >90% pure with a homogeneous expression of a single self-HLA specific KIR and expanded a median of 470-fold. The ADAPT-NK cells largely retained their adaptive transcriptional signature with activation of effector programs without signs of exhaustion. ADAPT-NK cells showed high degranulation capacity and efficient killing of HLA-C/KIR mismatched tumor cell lines as well as primary leukemic blasts from AML patients. Finally, the expanded adaptive NK cells had preserved robust antibody-dependent cellular cytotoxicity potential and combination of ADAPT-NK cells with an anti-CD16/IL-15/anti-CD33 tri-specific engager led to near-complete killing of resistant CD45(dim) blast subtypes.ConclusionsThese preclinical data demonstrate the feasibility of off-the-shelf therapy with a non-engineered, yet highly specific, NK cell population with full missing-self recognition capability.
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| 50. |
- Herrmann, Björn, et al.
(författare)
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Comparison of a duplex quantitative real-time PCR assay and the COBAS Amplicor CMV Monitor test for detection of cytomegalovirus
- 2004
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Ingår i: Journal of Clinical Microbiology. - 0095-1137 .- 1098-660X. ; 42:5, s. 1909-14
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Tidskriftsartikel (refereegranskat)abstract
- A duplex quantitative real-time PCR (qPCR) assay was designed to detect both the polymerase gene (pol) and the glycoprotein gene (gB) of cytomegalovirus (CMV). The detection limit of the qPCR was determined to be 1 to 3 copies/reaction and the linear measure interval was 10(3) to 10(8) copies/ml. The qPCR system was compared to the COBAS Amplicor CMV Monitor test (COBAS) by an analysis of 138 plasma samples. Both systems detected CMV in 71 cases and had negative results for 33 samples. In addition, 34 samples were positive by qPCR and negative by the COBAS assay, but in no case was the COBAS result positive and the qPCR result negative. Thus, qPCR detected 48% more positive cases than the COBAS method. For samples with > or = 10(5) copies/ml by qPCR, a saturation effect was seen in the COBAS assay and quantification required dilution. Copy numbers for pol and gB by qPCR generally agreed. However, the reproducibility of qPCR assays and the need for an international standard are discussed. Discrepant copy numbers for pol and gB by qPCR were found for samples from two patients, and sequence analysis revealed that the corresponding CMV strains were mismatched at four nucleotide positions compared with the gB fragment primer sequences. In conclusion, a duplex qPCR assay in a real-time format facilitates quantitative measurements and minimizes the risk of false-negative results.
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