| 1. |
- Blixt, Y., et al.
(författare)
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Interlaboratory random amplified polymorphic DNA typing of Yersinia enterocolitica and Y. enterocolitica-like bacteria
- 2003
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Ingår i: International Journal of Food Microbiology. - 0168-1605 .- 1879-3460. ; 83:1, s. 15-26
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Tidskriftsartikel (refereegranskat)abstract
- A random amplified polymorphic DNA (RAPD) protocol was developed for interlaboratory use to discriminate food-borne Yersinia enterocolitica O:3 from other serogroups of Y. enterocolitica and from Y. enterocolitica-like species. Factors that were studied regarding the RAPD performance were choice of primers and concentration of PCR reagents (template DNA, MgCl 2, primer and Taq DNA polymerase). A factorial design experiment was performed to identify the optimal concentrations of the PCR reagents. The experiment showed that the concentration of the PCR reagents tested significantly affected the number of distinct RAPD products. The RAPD protocol developed was evaluated regarding its discrimination ability using 70 different Yersinia strains. Cluster analysis of the RAPD patterns obtained revealed three main groups representing (i) Y. pseudotuberculosis, (ii) Y. enterocolitica and (iii) Y. kristensenii, Y. frederiksenii, Y. intermedia and Y. ruckeri. Within the Y. enterocolitica group, the European serovar (O:3) and the North American serovar (O:8) could be clearly separated from each other. All Y. enterocolitica O:3 strains were found in one cluster which could be further divided into two subclusters, representing the geographical origin of the isolates. Thus, one of the subclusters contained Y. enterocolitica O:3 strains originating from Sweden, Finland and Norway, while Danish and English O:3 strains were found in another subcluster together with O:9 and O:5,27 strains. The repeatability (intralaboratory) and reproducibility (interlaboratory) of the RAPD protocol were tested using 15 Yersinia strains representing different RAPD patterns. The intralaboratory and the interlaboratory studies gave similarity coefficients of the same magnitude (generally >70%) for the individual strains. In the present study, it was shown that interreproducible RAPD results could be achieved by appropriate optimisation of the RAPD protocol. Furthermore, the study reflects the heterogeneous genetic diversity of the Y. enterocolitica species. © 2002 Elsevier Science B.V. All rights reserved.
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| 2. |
- Carlberger, Johan, et al.
(författare)
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The development and performance of a grammar checker for Swedish : A language engineering perspective
- 2004
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Ingår i: Natural Language Engineering. - 1351-3249 .- 1469-8110. ; 1:1
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Tidskriftsartikel (refereegranskat)abstract
- This article describes the construction and performance of Granska – a surface-oriented system for grammar checking of Swedish text. With the use of carefully constructed error detection rules, written in a new structured rule language, the system can detect and suggest corrections for a number of grammatical errors in Swedish texts. In this article, we specifically focus on how erroneously split compounds and disagreement are handled in the rules. The system combines probabilistic and rule-based methods to achieve high efficiency and robustness. The error detection rules are optimized using statistics of part-of-speech bigrams and words in a way that each rule needs to be checked as seldom as possible. We have found that the Granska system with higher efficiency can achieve the same or better results than systems with conventional technology.
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| 3. |
- Domeij, Rickard, et al.
(författare)
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Different ways of evaluating a Swedish grammar checker
- 2002
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Ingår i: Proceedings of the third international conference on language resources and evaluation (LREC). ; , s. 262-267
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Three different ways of evaluating a Swedish grammar checker are presented and discussed in this article. The first evaluationconcerns measuring the program's detection capacity on five text genres. The measures (precision and recall) are often used inevaluating grammar checkers. However, in order to test and improve the usability of grammar checking software, they need to becomplemented with user-oriented methods. Consequently, the second and the third evaluations presented in the article both involveusers. The second evaluation focuses on user reactions to grammar error presentations, especially with regard to false alarms anderroneous error identification. The third and last evaluation focuses on problems in supporting users' cognitive revision processes. Italso examines user motives behind choosing to correct or not to correct problems highlighted by the program. Advantages anddisadvantages of the different evaluation methods are discussed.
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| 4. |
- Domeij, Rickard, et al.
(författare)
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Workshop on NLP for Reading and Writing : Resources, algorithms and tools
- 2008
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Ingår i: Swedish Conference of Language Technology, 2008. - 1736-6305. ; VOL. 3
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Konferensbidrag (refereegranskat)abstract
- New tools and media are creating new possibilities for people to communicate and find information over the Internet in a multilingual, global society. This is reflected in the fact that writers now write more in everyday life, typically create text directly on the computer and on the Internet (e.g. on blogs and other Web 2.0 technologies), and use new forms of writing in e-mails, web chats or SMS-messages on mobile phones. This concerns not only adults at work, but also children and youth. However, the new possibilities also put higher demands on our skills in using language for achieving our communicative goals in different situations. If the demands are not met, a great number of people will risk being excluded from participation in the emerging information society. Of course, this will have unfortunate consequences not only for the individual, but also for society at large. Therefore, there is a growing need for support in reading and writing. Certainly, there already exists writing tools such as authoring aids in word processors and instructional support in writing education. However, existing solutions have great difficulties meeting the growing need of support. In part, this is due to technical limitations of the tools in processing language, but also to the fact that these tools are poorly adjusted to different tasks, target user groups, genres and media.
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| 5. |
- Hedman, Johannes, et al.
(författare)
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Pre-PCR processing in bioterrorism preparedness : improved diagnostic capabilities for laboratory response networks
- 2013
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Ingår i: Biosecurity and bioterrorism. - : Mary Ann Liebert. - 1538-7135 .- 1557-850X. ; 11:S1, s. S87-S101
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Tidskriftsartikel (refereegranskat)abstract
- Diagnostic DNA analysis using polymerase chain reaction (PCR) has become a valuable tool for rapid detection of biothreat agents. However, analysis is often challenging because of the limited size, quality, and purity of the biological target. Pre-PCR processing is an integrated concept in which the issues of analytical limit of detection and simplicity for automation are addressed in all steps leading up to PCR amplification—that is, sampling, sample treatment, and the chemical composition of PCR. The sampling method should maximize target uptake and minimize uptake of extraneous substances that could impair the analysis—so-called PCR inhibitors. In sample treatment, there is a trade-off between yield and purity, as extensive purification leads to DNA loss. A cornerstone of pre-PCR processing is to apply DNA polymerase-buffer systems that are tolerant to specific sample impurities, thereby lowering the need for expensive purification steps and maximizing DNA recovery. Improved awareness among Laboratory Response Networks (LRNs) regarding pre-PCR processing is important, as ineffective sample processing leads to increased cost and possibly false-negative or ambiguous results, hindering the decision-making process in a bioterrorism crisis. This article covers the nature and mechanisms of PCR-inhibitory substances relevant for agroterrorism and bioterrorism preparedness, methods for quality control of PCR reactions, and applications of pre-PCR processing to optimize and simplify the analysis of various biothreat agents. Knowledge about pre-PCR processing will improve diagnostic capabilities of LRNs involved in the response to bioterrorism incidents.
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| 6. |
- Knutsson, Per, 1971, et al.
(författare)
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Simulating the implementation of Coastal Management Mechanisms (CMM) in the Municipality of Vellinge, Malmö Metropolitan Area : Swedish report for SECOA deliverable 3.4
- 2012
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- The report accounts for the forecasting of future developments (2050) in Skanör and Falsterbo, Vellinge Municapality, Sweden, according to two different scenarios. In the Coastal Defense Scenario we model the urban development in 2050 in relation to the implementation of inner and outer sea walls as already proposed by Vellinge Municipality. In the Development Limitation Scenario we situate the urban development 2050 in relation to the implementation of a three meter minimum elevation requirement for new development. The comparison of the two scenarios shows that while coastal defenses look attractive due to their capacity to protect existing land use, it will simultaneously interfere with protected natural and cultural areas and it will change a unique cultural landscape. It has a capacity to protect both existing human settlements and new urban development, but may increase the impact of flooding if the walls are not effective enough. On the other hand, minimum elevation requirement provides an alternative with less interference with existing protected areas and less changes in the landscape. In the short time perspective it is a low cost alternative to enhance the resilience of future urban development structures in the face of new conditions. However, it needs to be combined with other measures in order to offer protections for existing human settlements and activities in low lying areas. Furthermore, even though elevation requirements do not infer directly with the existing landscape, it will not protect the landscape from potentially permanent changes caused by inundation, soil erosion and flooding.
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| 7. |
- Knutsson, Rickard, et al.
(författare)
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Bio-Agro Defense Collaboration : The Need of Joint Leadership Education and Training of Strategic Analysts and Decision Makers
- 2015
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Ingår i: Journal of Defense Resources Management. - : OMICS Publishing Group. - 2068-9403 .- 2247-6466 .- 2167-0374. ; 5:2
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Forskningsöversikt (refereegranskat)abstract
- Bioweapons deliberately spread to humans and animals is one of the most complex and intersectoral CBRNE threats. It requires multi-sectoral collaboration between law enforcement, public and animal health and in severe cases civil-military collaboration. By building a collaborative management culture between these sectors, through joint education, training and exercise activities, better methods and tools will be obtained in order to reach interoperability and an integrated preparedness approach. Lessons learned and experiences from previous projects, courses, workshops, and simulation exercises require a rationale knowledge transfer. Horison scanning is one example of a method that can be recommended to educate strategic analysts jointly from various sectors and the “Decision Theater” is a dynamic and flexible tool that is useful to train decision makers to examine complex bio-agro defense and biosecurity problems.
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| 8. |
- Knutsson, Rickard, et al.
(författare)
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Development of a PCR-compatible enrichment medium for Yersinia enterocolitica: amplification precision and dynamic detection range during cultivation
- 2002
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Ingår i: International Journal of Food Microbiology. - 0168-1605. ; 72:3, s. 185-201
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Tidskriftsartikel (refereegranskat)abstract
- A Yersinia PCR-Compatible Enrichment (YPCE) medium was developed, which removes the necessity for sample pretreatment before PCR-based detection of Yersinia enterocolitica. The medium was designed through a sequence of independent screening and factorial design experiments to study the PCR inhibition and growth characteristics of medium components. The compatibility of the YPCE medium was evaluated using real-time PCR. The real-time PCR assay, based on the fluorescent double-stranded DNA binding dye SYBR green, generated approximately a 4-log linear range of amplification and in the range of 10(5)-10(8) (CFU/ml), the coefficient of variation <5%. When a background flora was present at concentrations greater than or equal to10(6) (CFU/ml), the DNA amplification was influenced and a change in the log-linear slope leading to a lower amplification efficiency was observed. To study the dynamic detection range and relative amplification precision during enrichment, Y. enterocolitica and background flora were inoculated at various concentrations. It was possible to detect inoculation concentrations of 10(1) (CFU/ml) Y enterocolitica in the presence of at least an inoculation concentration of 10(3) (CFU/ml) of an undefined background flora and the optimal conditions for sample withdrawal was in the range of 9 to 18 h enrichment. The YPCE medium can, especially for swab samples, form part of a simple analysis procedure allowing high throughput PCR. (C) 2002 Elsevier Science B.V. All rights reserved.
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| 9. |
- Knutsson, Rickard
(författare)
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Diagnostic PCR for the Detection of Yersinia enterocolitica and Salmonella in the Food-Chain: Reliability of PCR Performance
- 2001
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis deals with the methodological advances of diagnostic PCR including reliability of PCR and pre-PCR processing of food and feed samples. Diagnostic PCR has been greatly improved by the introduction of the second generation of PCR, so-called real-time PCR. Automated closed-tube quantitative real-time PCR favours the analysis of food-borne pathogenic bacteria. However, in common with conventional PCR, the real-time PCR technology requires pre-PCR processing of the food/feed sample (i) to remove PCR-inhibitory substances, (ii) facilitate detection of low concentrations of target bacteria, (iii) to convert a heterogeneous bulk sample to a more homogeneous PCR sample, and (iv) to restrict competitive background flora. The aim of the research presented in this thesis was to adapt microbiological food sampling to PCR by designing pre-PCR processing strategies for future routine analysis of Yersinia enterocolitica and Salmonella in complex samples from the food-chain. To enable the detection of low concentrations of Y. enterocolitica and Salmonella in PCR-inhibitory samples, such as pork and animal feed, enrichment PCR procedures have been employed. The reliability of PCR detection of pathogenic Y. enterocolitica using a developed multiplex PCR assay was studied using a logistic regression model for determination of the detection probability. The probability of detecting 1´104 CFU/ml Y. enterocolitica was estimated to be 85.4%. A Yersinia-PCR-compatible enrichment (YPCE) medium was developed to remove the necessity for sample preparation prior to PCR detection of Y. enterocolitica. The pre-PCR processing strategy allows detection of low concentrations (101 CFU/ml) in the presence of background flora in concentrations up to three orders of magnitude higher than Y. enterocolitica. The YPCE medium can, form part of integrated and automated pre-PCR processing protocol, especially for swab samples. To complement the Yersinia assay a RAPD protocol was developed for inter-laboratory use. The stringent RAPD protocol was evaluated on 70 Yersinia strains and allowed discrimination at serotype level, and the sub-clusters of Y. enterocolitica correlated with the geographic origin of isolates, where especially O:3 strains from Scandinavia formed a homogeneous sub-cluster. Enrichment PCR of Salmonella enterica was studied using real-time PCR. A model was developed to describe the 5' nuclease real-time PCR performance in the presence buffered peptone water (BPW) and brain heart infusion. Using the model it was found that the rTth DNA polymerase mixture was more resistant to the presence of BPW than AmpliTaq Gold. Accurate detection of 1 CFU/ml S. Enteritidis inoculated in BPW required 8.4 hours’ enrichment using the rTth DNA polymerase mixture, while AmpliTaq Gold required 11.6 h. Using an alternative DNA polymerase, Tth instead of Taq, facilitated the PCR detection of Salmonella in animal feed. The PCR protocol was more sensitive than the traditional culture-based standard method (NMKL-71), since out of 155 feed samples, 8% were positive for PCR detection of Salmonella in comparison with 3% with the NMKL-71 method.
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| 10. |
- Knutsson, Rickard, et al.
(författare)
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Evaluation of selective enrichment PCR procedures for Yersinia enterocolitica.
- 2002
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Ingår i: International Journal of Food Microbiology. - 0168-1605 .- 1879-3460. ; 73:1, s. 35-46
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Tidskriftsartikel (refereegranskat)abstract
- Four enrichment PCR protocols for detecting unlysed cells of pathogenic Yersinia enterocolitica were studied. First, the probability of detecting Y. enterocolitica cells of known concentrations by a multiplex PCR assay was determined, and it was found to follow a logistic regression model. From this model, the probability of detecting Y enterocolitica at a specific concentration could be estimated; for example, the detection probability of 10(4) CFU/ml was estimated to be 85.4%. The protocols were evaluated on enrichment cultures inoculated with 10(2) CFU/ml Y. enterocolitica and 10(2)-10(6) CFU/ml of a defined background flora. For each protocol, the time for sample withdrawal and the presence of background flora were studied with respect to PCR detection. The optimal point in time of sample withdrawal was found to be different for each protocol employed. Early detection was favoured by concentrating the target cells, and the most rapid PCR detection of Y. enterocolitica was achieved with enrichment in Yersinia-PCR-compatible-enrichment (YPCE) medium for 3 h at 25 degrees C, followed by a centrifugation prior to PCR analysis. For detection of Y. enterocolitica in the presence of high concentrations (10(6) CFU/ml) of background flora, a long incubation time followed by density centrifugation and a dilution step was most successful. The protocol that gave the most reliable PCR detection in the presence of 10(6) CFU/ml background flora included 24 h incubation in Yersinia-selective-enrichment (YSE) broth at 25 degrees C, followed by Percoll density centrifugation, and a 100 times dilution prior to PCR analysis.
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