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- Bauer, Pavol, et al.
(författare)
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Fast event-based epidemiological simulations on national scales
- 2016
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Ingår i: The international journal of high performance computing applications. - : SAGE Publications. - 1094-3420 .- 1741-2846. ; 30, s. 438-453
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Tidskriftsartikel (refereegranskat)abstract
- We present a computational modeling framework for data-driven simulations and analysis of infectious disease spread in large populations. For the purpose of efficient simulations, we devise a parallel solution algorithm targeting multi-socket shared-memory architectures. The model integrates infectious dynamics as continuous-time Markov chains and available data such as animal movements or aging are incorporated as externally defined events. To bring out parallelism and accelerate the computations, we decompose the spatial domain and optimize cross-boundary communication using dependency-aware task scheduling. Using registered livestock data at a high spatiotemporal resolution, we demonstrate that our approach not only is resilient to varying model configurations but also scales on all physical cores at realistic workloads. Finally, we show that these very features enable the solution of inverse problems on national scales.
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| 2. |
- Engblom, Stefan, et al.
(författare)
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Bayesian epidemiological modeling over high-resolution network data
- 2020
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Ingår i: Epidemics. - : Elsevier BV. - 1755-4365 .- 1878-0067. ; 32
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Tidskriftsartikel (refereegranskat)abstract
- Mathematical epidemiological models have a broad use, including both qualitative and quantitative applications. With the increasing availability of data, large-scale quantitative disease spread models can nowadays be formulated. Such models have a great potential, e.g., in risk assessments in public health. Their main challenge is model parameterization given surveillance data, a problem which often limits their practical usage. We offer a solution to this problem by developing a Bayesian methodology suitable to epidemiological models driven by network data. The greatest difficulty in obtaining a concentrated parameter posterior is the quality of surveillance data; disease measurements are often scarce and carry little information about the parameters. The often overlooked problem of the model's identifiability therefore needs to be addressed, and we do so using a hierarchy of increasingly realistic known truth experiments. Our proposed Bayesian approach performs convincingly across all our synthetic tests. From pathogen measurements of shiga toxin-producing Escherichia coli O157 in Swedish cattle, we are able to produce an accurate statistical model of first-principles confronted with data. Within this model we explore the potential of a Bayesian public health framework by assessing the efficiency of disease detection and -intervention scenarios.
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| 8. |
- Widgren, Stefan, et al.
(författare)
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Spatio-temporal modelling of verotoxigenic Escherichia coli O157 in cattle in Sweden: exploring options for control
- 2018
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Ingår i: Veterinary Research. - : Springer Science and Business Media LLC. - 0928-4249 .- 1297-9716. ; 49
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Tidskriftsartikel (refereegranskat)abstract
- A spatial data-driven stochastic model was developed to explore the spread of verotoxigenic Escherichia coli O157 (VTEC O157) by livestock movements and local transmission among neighbouring holdings in the complete Swedish cattle population. Livestock data were incorporated to model the time-varying contact network between holdings and population demographics. Furthermore, meteorological data with the average temperature at the geographical location of each holding was used to incorporate season. The model was fitted against observed data and extensive numerical experiments were conducted to investigate the model's response to control strategies aimed at reducing shedding and susceptibility, as well as interventions informed by network measures. The results showed that including local spread and season improved agreement with prevalence studies. Also, control strategies aimed at reducing the average shedding rate were more efficient in reducing the VTEC O157 prevalence than strategies based on network measures. The methodology presented in this study could provide a basis for developing disease surveillance on regional and national scales, where observed data are combined with readily available high-resolution data in simulations to get an overview of potential disease spread in unobserved regions.
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| 9. |
- Antonson, Hans, 1963-
(författare)
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Landskap och ödesbölen : Jämtland före, under och efter den medeltida agrarkrisen
- 2004
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This study examines landscape change in the Province of Jämtland during c. 1000–1750 AD. Settlement and arable cultivation are two of the most important sources in this study. They are therefore treated in depth, particularly farmsteads that were deserted during the late medieval agrarian crisis, so-called ödesbölen, and their fossil field-traces. The dissertation contains four major investigations. In the first investigation 610 possible ödesbölen were identified. The desertion was estimated at 50 per cent. The second investigation had its focus on the geographic location, and the conclusion was that the ödesbölen may have been deserted when the climate turned colder in the 14th century. The third investigation concerned medieval agriculture. Using historical maps and detailed mapping of fossil field traces it was established that the annually cultivated acreage decreased from the High Middle Ages until early modern times. This probably means that the agrarian crisis caused a change in the agrarian regime, from predominant arable farming to predominant stock-raising. The fourth investigation was whether the ownership or the use of the ödesbölen created obstacles to recolonization when the crisis subsided. This turned out not to be so in the case of ownership, but may have been so with regard to communal forest grazing. According to historical maps the ödesbölen in Jämtland were finally recolonized about 200 years later than for example in southern Sweden. The reasons probably were wars and a worse climate. The dissertation is capped off with both a model and a description of landscape change in Jämtland. Characteristic for the development of the landscape has been fluctuations in settlement. The ödesbölen are part of a pattern in which they are colonized, deserted, recolonized and again deserted in a cyclical course of events. The openness of the landscape is not part of this course of events.
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| 10. |
- Bergström, Karin, et al.
(författare)
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Infection prevention and control interventions in the first outbreak of methicillin-resistant Staphylococcus aureus infections in an equine hospital in Sweden
- 2012
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Ingår i: Acta Veterinaria Scandinavica. - : Springer Science and Business Media LLC. - 0044-605X .- 1751-0147. ; 54, s. 1-14
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: The first outbreak of methicillin-resistant Staphylococcus aureus (MRSA) infection in horses in Sweden occurred in 2008 at the University Animal Hospital and highlighted the need for improved infection prevention and control. The present study describes interventions and infection prevention control in an equine hospital setting July 2008 - April 2010. METHOD: This descriptive study of interventions is based on examination of policy documents, medical records, notes from meetings and cost estimates. MRSA cases were identified through clinical sampling and telephone enquiries about horses post-surgery. Prospective sampling in the hospital environment with culture for MRSA and genotyping of isolates by spa-typing and pulsed-field gel electrophoresis (PFGE) were performed. RESULTS: Interventions focused on interruption of indirect contact spread of MRSA between horses via staff and equipment and included: Temporary suspension of elective surgery; and identification and isolation of MRSA-infected horses; collaboration was initiated between authorities in animal and human public health, human medicine infection control and the veterinary hospital; extensive cleaning and disinfection was performed; basic hygiene and cleaning policies, staff training, equipment modification and interior renovation were implemented over seven months.Ten (11%) of 92 surfaces sampled between July 2008 and April 2010 tested positive for MRSA spa-type 011, seven of which were from the first of nine sampling occasions. PFGE typing showed the isolates to be the outbreak strain (9 of 10) or a closely related strain. Two new cases of MRSA infection occurred 14 and 19 months later, but had no proven connections to the outbreak cases. CONCLUSIONS: Collaboration between relevant authorities and the veterinary hospital and formation of an infection control committee with an executive working group were required to move the intervention process forward. Support from hospital management and the dedication of staff were essential for the development and implementation of new, improved routines. Demonstration of the outbreak strain in the environment was useful for interventions such as improvement of cleaning routines and interior design, and increased compliance with basic hygienic precautions. The interventions led to a reduction in MRSA-positive samples and the outbreak was considered curbed as no new cases occurred for over a year.
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