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- Rydén, Patrik, 1969-, et al.
(författare)
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Outbreaks of tularemia in a boreal forest region depends on mosquito prevalence
- 2012
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Ingår i: Journal of Infectious Diseases. - : Oxford University Press (OUP). - 0022-1899 .- 1537-6613. ; 205:2, s. 297-304
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Tidskriftsartikel (refereegranskat)abstract
- Background. We aimed to evaluate the potential association of mosquito prevalence in a boreal forest area with transmission of the bacterial disease tularemia to humans, and model the annual variation of disease using local weather data.Methods. A prediction model for mosquito abundance was built using weather and mosquito catch data. Then a negative binomial regression model based on the predicted mosquito abundance and local weather data was built to predict annual numbers of humans contracting tularemia in Dalarna County, Sweden.Results. Three hundred seventy humans were diagnosed with tularemia between 1981 and 2007, 94% of them during 7 summer outbreaks. Disease transmission was concentrated along rivers in the area. The predicted mosquito abundance was correlated (0.41, P < .05) with the annual number of human cases. The predicted mosquito peaks consistently preceded the median onset time of human tularemia (temporal correlation, 0.76; P < .05). Our final predictive model included 5 environmental variables and identified 6 of the 7 outbreaks.Conclusions. This work suggests that a high prevalence of mosquitoes in late summer is a prerequisite for outbreaks of tularemia in a tularemia-endemic boreal forest area of Sweden and that environmental variables can be used as risk indicators.
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- Lindgren, Petter, et al.
(författare)
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A likelihood ratio-based approach for improved source attribution in microbiological forensic investigations
- 2019
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Ingår i: Forensic Science International. - : Elsevier. - 0379-0738 .- 1872-6283. ; 302
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Tidskriftsartikel (refereegranskat)abstract
- A common objective in microbial forensic investigations is to identify the origin of a recovered pathogenic bacterium by DNA sequencing. However, there is currently no consensus about how degrees of belief in such origin hypotheses should be quantified, interpreted, and communicated to wider audiences. To fill this gap, we have developed a concept based on calculating probabilistic evidential values for microbial forensic hypotheses. The likelihood-ratio method underpinning this concept is widely used in other forensic fields, such as human DNA matching, where results are readily interpretable and have been successfully communicated in juridical hearings. The concept was applied to two case scenarios of interest in microbial forensics: (1) identifying source cultures among series of very similar cultures generated by parallel serial passage of the Tier 1 pathogen Francisella tularensis, and (2) finding the production facilities of strains isolated in a real disease outbreak caused by the human pathogen Listeria monocytogenes. Evidence values for the studied hypotheses were computed based on signatures derived from whole genome sequencing data, including deep-sequenced low-frequency variants and structural variants such as duplications and deletions acquired during serial passages. In the F. tularensis case study, we were able to correctly assign fictive evidence samples to the correct culture batches of origin on the basis of structural variant data. By setting up relevant hypotheses and using data on cultivated batch sources to define the reference populations under each hypothesis, evidential values could be calculated. The results show that extremely similar strains can be separated on the basis of amplified mutational patterns identified by high-throughput sequencing. In the L. monocytogenes scenario, analyses of whole genome sequence data conclusively assigned the clinical samples to specific sources of origin, and conclusions were formulated to facilitate communication of the findings. Taken together, these findings demonstrate the potential of using bacterial whole genome sequencing data, including data on both low frequency SNP signatures and structural variants, to calculate evidence values that facilitate interpretation and communication of the results. The concept could be applied in diverse scenarios, including both epidemiological and forensic source tracking of bacterial infectious disease outbreaks.
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| 7. |
- Reneland-Forsman, Linda, 1962-, et al.
(författare)
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Training doctoral supervisors to train researchers of tomorrow : a Swedish example
- 2024
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Ingår i: INTED2024 Proceedings. - : IATED Academy. - 9788409592159 ; , s. 2928-2932
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Konferensbidrag (refereegranskat)abstract
- Doctoral education is more important than ever, and PhD-student enrolment numbers are continually climbing, as is the demand for more graduates with high-level research skills. This mobilization can only be realized if there are sufficient well-trained researchers able to take on the challenge of supervision in a world where science is both more important than ever but also debated and mistrusted. But how do you train for supervising an individual, unique project preparing the student for an independent research career? At Linnaeus university with roughly 30 different PhD-programs, we have for six years now practiced and developed a 9-month special university-wide course for doctoral supervisors. The program balances between training for an individual unique project but preparing for a broader research career within what is in comparison a highly regulated education. In Sweden there is a requirement of a full four-years institutional financing before admittance, there are exam objectives, and all programs have course parts (including mandatory courses) in the span of 15-120 ECTS. There is also a national requirement for supervisors training for being a main supervisor, all this together constitute the framing of doctorates. The program aims to promote border-crossing exchanges of experiences between doctoral supervisors from different disciplines and collaborative learning where doctoral supervisors create a reflective community of practice together with seniors. Applicants for the supervision program are expected to have started an independent research career after their own Viva, published nationally and internationally, to have the necessary required higher education pedagogical training, and have supervision experience at advanced level.
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- Song, William Wei, 1960-, et al.
(författare)
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An Euclidean similarity measurement approach for hotel rating data analysis
- 2017
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Ingår i: Proceedings 2017 2nd IEEE International Conference on Cloud Computing and Big Data Analysis, ICCCBDA 2017. - 9781509044986 - 9781509044993 ; , s. 293-298
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Konferensbidrag (refereegranskat)abstract
- The most widely used method in recommendation systems is collaborative filtering, of which, a critical step is to analyze a user's preferences and make recommendations of products or services based on similarity analysis with other users' ratings. However, collaborative filtering is less usable for recommendation facing the 'cold start' problem, i.e. few comments being given to products or services. To tackle this problem, we propose an improved method that combines collaborative filtering and data classification. We use hotel recommendation data to test the proposed method. The accuracy of the recommendation is determined by the rankings. Evaluations regarding the accuracies of Top-3 and Top-10 recommendation lists using the 10-fold cross-validation method and ROC curves are conducted. The results show that the Top-3 hotel recommendation list proposed by the combined method has the superiority of the recommendation performance than the Top-10 list under the cold start condition in most of the times.
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- Song, William Wei, 1960-, et al.
(författare)
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Collaborative Filtering with Data Classification : A Combined Approach to Hotel Recommendation Systems
- 2016
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Ingår i: 25th International Conference on Information Systems Development (ISD2016 Poland).
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Konferensbidrag (refereegranskat)abstract
- Recommendation systems aim to help users make decisions more efficiently. The most widely used method in recommendation systems is collaborative filtering, of which, a critical step is to analyze a user's preferences and make recommendations of products or services based on similarity analysis with other users' ratings. However, collaborative filtering is less usable for recommendation facing the "cold start" problem, i.e. few comments being given to products or services. To tackle this problem, we propose an improved method that combines collaborative filtering and data classification. We use hotel recommendation data to test the proposed method. The accuracy of the recommendation is determined by the rankings. Evaluations regarding the accuracies of Top-3 and Top-10 recommendation lists using the 10-fold cross-validation method and ROC curves are conducted. The results show that the Top-3 hotel recommendation list proposed by the combined method has the superiority of the recommendation performance than the Top-10 list under the cold start condition in most of the times.
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| 10. |
- Twine, Susan, et al.
(författare)
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A mutant of Francisella tularensis strain SCHU S4 lacking the ability to express a 58-kilodalton protein is attenuated for virulence and is an effective live vaccine
- 2005
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Ingår i: Infection and Immunity. - 0019-9567 .- 1098-5522. ; 73:12, s. 8345-8352
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Tidskriftsartikel (refereegranskat)abstract
- Francisella tularensis subsp. tularensis (type A) strain SCHU S4 is a prototypic strain of the pathogen that is highly virulent for humans and other mammals. Its intradermal (i.d.) 50% lethal dose (LD50) for mice is <10 CFU. We discovered a spontaneous mutant, designated FSC043, of SCHU S4 with an i.d. LD50 of >10(8) CFU. FSC043 effectively vaccinated mice against challenge with a highly virulent type A strain, and the protective efficacy was at least as good as that of F. tularensis LVS, an empirically attenuated strain which has been used as an efficacious human vaccine. Comparative proteomics was used to identify two proteins of unknown function that were identified as defective in LVS and FSC043, and deletion mutants of SCHU S4 were created for each of the two encoding genes. One mutant, the DeltaFTT0918 strain, failed to express a 58-kDa protein, had an i.d. LD50 of approximately 10(5) CFU, and was found to be less capable than SCHU S4 of growing in peritoneal mouse macrophages. Mice that recovered from sublethal infection with the DeltaFTT0918 mutant survived when challenged 2 months later with >100 LD50s of the highly virulent type A strain FSC033. This is the first report of the generation of defined mutants of F. tularensis subsp. tularensis and their use as live vaccines.
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