| 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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| 10. |
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| 11. |
- 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
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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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| 12. |
- Muradrasoli, Shaman, et al.
(författare)
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Broadly targeted triplex real-time PCR detection of influenza A, B and C viruses based on the nucleoprotein gene and a novel "MegaBeacon" probe strategy
- 2010
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Ingår i: Journal of Virological Methods. - : Elsevier BV. - 0166-0934 .- 1879-0984. ; 163:2, s. 313-322
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Tidskriftsartikel (refereegranskat)abstract
- A PCR assay that covers animal and human influenza A, B and C viruses, i.e., most of Orthomyxoviridae, is needed. Influenza types are distinguished based on differences in the nucleoprotein (NP) present in the virus. Conserved NP regions were therefore used to design a TaqMan (R)-based triplex reverse transcription real-time PCR method. Variability of influenza A within the probe target region mandated the development of a novel molecular beacon, the "Mega" molecular beacon (MegaBeacon: MegB), for the detection of influenza A with this method. MegaBeacon is a mismatch-tolerant molecular beacon that is also a TaqMan (R) probe. The triplex method (3QPCR-MegB) was evaluated with influenza A isolates covering 18 HxNx combinations, two influenza B isolates, and five Japanese influenza C isolates, as well as influenza A, B and C synthetic DNA targets. One to ten viral RNA and cDNA genome equivalents were detected per PCR reaction for influenza A, B and C. Seventy-one human nasopharyngeal aspirates from respiratory infections yielded 30 influenza A, 11 influenza B and 0 influenza C with 3QPCR-MegB, where immunofluorescence (IF) found 28 influenza A and 10 influenza B. 3QPCR-MegB was more mismatch-tolerant than a variant PCR with an influenza A TaqMan (R) probe (3QPCR) and is a sensitive and rational method to detect influenza viruses of animal and human origin. MegaBeacon probes hold promise for variable target nucleic acids.
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| 13. |
- Muradrasoli, Shaman, et al.
(författare)
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Prevalence and phylogeny of coronaviruses in wild birds from the Bering Strait area (Beringia)
- 2010
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 5:10
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Tidskriftsartikel (refereegranskat)abstract
- Coronaviruses (CoVs) can cause mild to severe disease in humans and animals, their host range and environmental spread seem to have been largely underestimated, and they are currently being investigated for their potential medical relevance. Infectious bronchitis virus (IBV) belongs to gamma-coronaviruses and causes a costly respiratory viral disease in chickens. The role of wild birds in the epidemiology of IBV is poorly understood. In the present study, we examined 1,002 cloacal and faecal samples collected from 26 wild bird species in the Beringia area for the presence of CoVs, and then we performed statistical and phylogenetic analyses. We detected diverse CoVs by RT-PCR in wild birds in the Beringia area. Sequence analysis showed that the detected viruses are gamma-coronaviruses related to IBV. These findings suggest that wild birds are able to carry gamma-coronaviruses asymptomatically. We concluded that CoVs are widespread among wild birds in Beringia, and their geographic spread and frequency is higher than previously realised. Thus, Avian CoV can be efficiently disseminated over large distances and could be a genetic reservoir for future emerging pathogenic CoVs. Considering the great animal health and economic impact of IBV as well as the recent emergence of novel coronaviruses such as SARS-coronavirus, it is important to investigate the role of wildlife reservoirs in CoV infection biology and epidemiology.
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| 14. |
- Yalcin, Zeki, 1973-
(författare)
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Facklig gränspolitik : Landsorganisationens invandrings- och invandrarpolitik 1946 - 2009
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis concerns the trade union reaction to immigration as a phenomenon and toimmigrants as a labour force on the Swedish labour market. It concerns trade union politicsregarding immigration and immigrants, from the political decision taken in 1946 to recruitworkers from other countries because of the labour shortage in Sweden, to 2009 when theconflict in the Swedish town of Vaxholm, that was a consequence of the EU’s expansion to theeast and which received such enormous attention in the Swedish media, was given its finalverdict and the continued existence of the “Swedish model” was placed under question. Thestudy focuses on the labour movement’s central trade union organisation in Sweden, in otherwords the Swedish Trade Union Confederation (Landsorganisationen, or LO as it is commonlyabbreviated in Sweden).The basis for the thesis has been that the process of immigration must naturally in the longterm lead to the addition of workers on the labour market, and consequently increasedcompetition amongst workers. The question has been how the interest organisation LO, whoseprimary mission is to protect the wage rates and social conditions for its members, and whichhas the restriction of competition as an overriding strategy, would handle the phenomenon ofimmigration and the existence of immigrants as a labour force on the Swedish labour marketand within the trade union movement, during the course of the study. The choice of LO as afundamental starting point for the study, being as it is an interest organisation with the shorttermobjective of protecting its members’ interests, but also given the organisation’s more longtermobjectives of being an important actor on the labour market and within society, hasinfluenced the choice of the thesis’ central theoretical concepts; strategy, restriction ofcompetition, calculability, power and hegemony. This very starting point, but also the natureof the source materials and a reflection over the immigration process (from immigration toimmigrant workers on the labour market and finally to trade union members), has meant that Ihave chosen to structure the thesis and present my findings based on three different problemareas. I have chosen to refer to these problem areas as boundaries, there LO have dealt withvarious problems concerning the phenomena of immigration and immigrants on the Swedishlabour market, as well as problems related to some of its own members having foreignbackgrounds. These boundaries consist firstly of an outer boundary that is a physicalboundary, coincident with national boundaries and influencing immigration politics, there LOwas able to consider the scope of the immigration process and make calculations about whatthe resultant addition of new workers, that is a natural consequence of the immigrationprocess, would mean for the labour market. Secondly an inner boundary, that encompasses thelabour market but is more transparent to members of society and influences immigrant politics,there LO was able to consider the terms and conditions that should be made available to theimmigrant workers, in general within society and in particular on the labour market. Finally aninnermost boundary, encompassing the trade union membership, there LO was able to managethe terms and conditions for the immigrant workers within the trade union movement.The thesis’ overriding objective has been to examine LO’s strategies for these threeboundary areas and to see if there is a coherent pattern behind LO’s actions on these threevarying levels. A more theoretical objective with this thesis has been to examine if the possiblepatterns that would appear in LO’s actions within these three boundary areas, could bediscussed from the perspective of a power structure.
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| 15. |
- Öhrmalm, Christina, et al.
(författare)
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Variation-tolerant capture and multiplex detection of nucleic acids : application to detection of microbes
- 2012
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Ingår i: Journal of Clinical Microbiology. - 0095-1137 .- 1098-660X. ; 50:10, s. 3208-3215
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Tidskriftsartikel (refereegranskat)abstract
- In contrast to ordinary PCRs, which have a limited multiplex capacity and often return false-negative results due to target variation or inhibition, our new detection strategy, VOCMA (variation-tolerant capture multiplex assay), allows variation-tolerant, target-specific capture and detection of many nucleic acids in one test. Here we demonstrate the use of a single-tube, dual-step amplification strategy that overcomes the usual limitations of PCR multiplexing, allowing at least a 22-plex format with retained sensitivity. Variation tolerance was achieved using long primers and probes designed to withstand variation at known sites and a judicious mix of degeneration and universal bases. We tested VOCMA in situations where enrichment from a large sample volume with high sensitivity and multiplexity is important (sepsis; streptococci, enterococci, and staphylococci, several enterobacteria, candida, and the most important antibiotic resistance genes) and where variation tolerance and high multiplexity is important (gastroenteritis; astrovirus, adenovirus, rotavirus, norovirus genogroups I and II, and sapovirus, as well as enteroviruses, which are not associated with gastroenteritis). Detection sensitivities of 10 to 1,000 copies per reaction were achieved for many targets. VOCMA is a highly multiplex, variation-tolerant, general purpose nucleic acid detection concept. It is a specific and sensitive method for simultaneous detection of nucleic acids from viruses, bacteria, fungi, and protozoa, as well as host nucleic acid, in the same test. It can be run on an ordinary PCR and a Luminex machine and is suitable for both clinical diagnoses and microbial surveillance.
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