| 1. |
- 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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| 2. |
- 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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| 3. |
- 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
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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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| 4. |
- 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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| 5. |
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| 6. |
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| 7. |
- 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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| 8. |
- 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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| 9. |
- 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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