| 1. |
- Abazov, V. M., et al.
(författare)
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The upgraded DO detector
- 2006
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Ingår i: Nuclear Instruments and Methods in Physics Research Section A. - : Elsevier BV. - 0168-9002 .- 1872-9576. ; 565:2, s. 463-537
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Tidskriftsartikel (refereegranskat)abstract
- The DO experiment enjoyed a very successful data-collection run at the Fermilab Tevatron collider between 1992 and 1996. Since then, the detector has been upgraded to take advantage of improvements to the Tevatron and to enhance its physics capabilities. We describe the new elements of the detector, including the silicon microstrip tracker, central fiber tracker, solenoidal magnet, preshower detectors, forward muon detector, and forward proton detector. The uranium/liquid -argon calorimeters and central muon detector, remaining from Run 1, are discussed briefly. We also present the associated electronics, triggering, and data acquisition systems, along with the design and implementation of software specific to DO.
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| 2. |
- Abazov, V. M., et al.
(författare)
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Measurement of the isolated photon cross section in p(p)over-bar collisions at root s=1.96 TeV
- 2006
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Ingår i: Physics Letters B. - : Elsevier BV. - 0370-2693 .- 1873-2445. ; 639:3-4, s. 151-158
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Tidskriftsartikel (refereegranskat)abstract
- The cross section for the inclusive production of isolated photons has been measured in p (p) over bar collisions at root s = 1.96 TeV with the DO detector at the Fermilab Tevatron Collider. The photons span transverse momenta 23 to 300 GeV and have pseudorapidity vertical bar n vertical bar < 0.9. The cross section is compared with the results from two next-to-leading order perturbative QCD calculations. The theoretical predictions agree with the measurement within uncertainties.
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| 3. |
- Leebens-Mack, James H., et al.
(författare)
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One thousand plant transcriptomes and the phylogenomics of green plants
- 2019
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Ingår i: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 574:7780, s. 679-
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Tidskriftsartikel (refereegranskat)abstract
- Green plants (Viridiplantae) include around 450,000-500,000 species(1,2) of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.
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| 4. |
- Curtis, Bruce A., et al.
(författare)
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Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs
- 2012
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 492:7427, s. 59-65
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Tidskriftsartikel (refereegranskat)abstract
- Cryptophyte and chlorarachniophyte algae are transitional forms in the widespread secondary endosymbiotic acquisition of photosynthesis by engulfment of eukaryotic algae. Unlike most secondary plastid-bearing algae, miniaturized versions of the endosymbiont nuclei (nucleomorphs) persist in cryptophytes and chlorarachniophytes. To determine why, and to address other fundamental questions about eukaryote-eukaryote endosymbiosis, we sequenced the nuclear genomes of the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans. Both genomes have >21,000 protein genes and are intron rich, and B. natans exhibits unprecedented alternative splicing for a single-celled organism. Phylogenomic analyses and subcellular targeting predictions reveal extensive genetic and biochemical mosaicism, with both host-and endosymbiont-derived genes servicing the mitochondrion, the host cell cytosol, the plastid and the remnant endosymbiont cytosol of both algae. Mitochondrion-to-nucleus gene transfer still occurs in both organisms but plastid-to-nucleus and nucleomorph-to-nucleus transfers do not, which explains why a small residue of essential genes remains locked in each nucleomorph.
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| 5. |
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| 6. |
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| 7. |
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| 8. |
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| 9. |
- Robinson, N. A., et al.
(författare)
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Applying genetic technologies to combat infectious diseases in aquaculture
- 2022
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Ingår i: Reviews in Aquaculture. - : Wiley. - 1753-5123 .- 1753-5131. ; 15:2, s. 491-535
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Tidskriftsartikel (refereegranskat)abstract
- Disease and parasitism cause major welfare, environmental and economic concerns for global aquaculture. In this review, we examine the status and potential of technologies that exploit genetic variation in host resistance to tackle this problem. We argue that there is an urgent need to improve understanding of the genetic mechanisms involved, leading to the development of tools that can be applied to boost host resistance and reduce the disease burden. We draw on two pressing global disease problems as case studies—sea lice infestations in salmonids and white spot syndrome in shrimp. We review how the latest genetic technologies can be capitalised upon to determine the mechanisms underlying inter- and intra-species variation in pathogen/parasite resistance, and how the derived knowledge could be applied to boost disease resistance using selective breeding, gene editing and/or with targeted feed treatments and vaccines. Gene editing brings novel opportunities, but also implementation and dissemination challenges, and necessitates new protocols to integrate the technology into aquaculture breeding programmes. There is also an ongoing need to minimise risks of disease agents evolving to overcome genetic improvements to host resistance, and insights from epidemiological and evolutionary models of pathogen infestation in wild and cultured host populations are explored. Ethical issues around the different approaches for achieving genetic resistance are discussed. Application of genetic technologies and approaches has potential to improve fundamental knowledge of mechanisms affecting genetic resistance and provide effective pathways for implementation that could lead to more resistant aquaculture stocks, transforming global aquaculture. © 2022 The Authors. Reviews in Aquaculture published by John Wiley & Sons Australia, Ltd.
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| 10. |
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| 11. |
- Barrenäs, Fredrik, et al.
(författare)
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Interleukin-15 response signature predicts RhCMV/SIV vaccine efficacy
- 2021
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Ingår i: PLoS Pathogens. - : Public Library of Science (PLoS). - 1553-7366 .- 1553-7374. ; 17:7
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Tidskriftsartikel (refereegranskat)abstract
- Simian immunodeficiency virus (SIV) challenge of rhesus macaques (RMs) vaccinated with strain 68-1 Rhesus Cytomegalovirus (RhCMV) vectors expressing SIV proteins (RhCMV/SIV) results in a binary outcome: stringent control and subsequent clearance of highly pathogenic SIV in similar to 55% of vaccinated RMs with no protection in the remaining 45%. Although previous work indicates that unconventionally restricted, SIV-specific, effector-memory (EM)-biased CD8(+) T cell responses are necessary for efficacy, the magnitude of these responses does not predict efficacy, and the basis of protection vs. non-protection in 68-1 RhCMV/SIV vector-vaccinated RMs has not been elucidated. Here, we report that 68-1 RhCMV/SIV vector administration strikingly alters the whole blood transcriptome of vaccinated RMs, with the sustained induction of specific immune-related pathways, including immune cell, toll-like receptor (TLR), inflammasome/cell death, and interleukin-15 (IL-15) signaling, significantly correlating with subsequent vaccine efficacy. Treatment of a separate RM cohort with IL-15 confirmed the central involvement of this cytokine in the protection signature, linking the major innate and adaptive immune gene expression networks that correlate with RhCMV/SIV vaccine efficacy. This change-from-baseline IL-15 response signature was also demonstrated to significantly correlate with vaccine efficacy in an independent validation cohort of vaccinated and challenged RMs. The differential IL-15 gene set response to vaccination strongly correlated with the pre-vaccination activity of this pathway, with reduced baseline expression of IL-15 response genes significantly correlating with higher vaccine-induced induction of IL-15 signaling and subsequent vaccine protection, suggesting that a robust de novo vaccine-induced IL-15 signaling response is needed to program vaccine efficacy. Thus, the RhCMV/SIV vaccine imparts a coordinated and persistent induction of innate and adaptive immune pathways featuring IL-15, a known regulator of CD8(+) T cell function, that support the ability of vaccine-elicited unconventionally restricted CD8(+) T cells to mediate protection against SIV challenge.
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| 12. |
- de Laat, A. T. J., et al.
(författare)
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Validation of five years (2003-2007) of SCIAMACHY CO total column measurements using ground-based spectrometer observations
- 2010
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Ingår i: Atmospheric Measurement Techniques. - : Copernicus GmbH. - 1867-1381 .- 1867-8548. ; 3:5, s. 1457-1471
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Tidskriftsartikel (refereegranskat)abstract
- This paper presents a validation study of SCanning Imaging Absorption spectroMeter for Atmospheric CHartographY (SCIAMACHY) carbon monoxide (CO) total column measurements from the Iterative Maximum Likelihood Method (IMLM) algorithm using ground-based spectrometer observations from twenty surface stations for the five year time period of 2003-2007. Overall we find a good agreement between SCIAMACHY and ground-based observations for both mean values as well as seasonal variations. For high-latitude Northern Hemisphere stations absolute differences between SCIAMACHY and ground-based measurements are close to or fall within the SCIAMACHY CO 2 sigma precision of 0.2 x 10(18) molecules/cm(2) (similar to 10%) indicating that SCIAMACHY can observe CO accurately at high Northern Hemisphere latitudes. For Northern Hemisphere mid-latitude stations the validation is complicated due to the vicinity of emission sources for almost all stations, leading to higher ground-based measurements compared to SCIAMACHY CO within its typical sampling area of 8 degrees x 8 degrees. Comparisons with Northern Hemisphere mountain stations are hampered by elevation effects. After accounting for these effects, the validation provides satisfactory results. At Southern Hemisphere mid-to high latitudes SCIAMACHY is systematically lower than the ground-based measurements for 2003 and 2004, but for 2005 and later years the differences between SCIAMACHY and ground-based measurements fall within the SCIAMACHY precision. The 2003-2004 bias is consistent with previously reported results although its origin remains under investigation. No other systematic spatial or temporal biases could be identified based on the validation presented in this paper. Validation results are robust with regard to the choices of the instrument-noise error filter, sampling area, and time averaging required for the validation of SCIAMACHY CO total column measurements. Finally, our results show that the spatial coverage of the ground-based measurements available for the validation of the 2003-2007 SCIAMACHY CO columns is sub-optimal for validation purposes, and that the recent and ongoing expansion of the ground-based network by carefully selecting new locations may be very beneficial for SCIAMACHY CO and other satellite trace gas measurements validation efforts.
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| 13. |
- Schulz, A, et al.
(författare)
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Arctic ozone loss in threshold conditions: Match observations in 1997/1998 and 1998/1999
- 2001
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Ingår i: JOURNAL OF GEOPHYSICAL RESEARCH-ATMOSPHERES. - : AMER GEOPHYSICAL UNION. - 0747-7309. ; 106:D7, s. 7495-7503
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Tidskriftsartikel (refereegranskat)abstract
- Chemical ozone loss rates inside the Arctic polar vortex were determined in early 1998 and early 1999 by using the Match technique based on coordinated ozonesonde measurements. These two winters provide the only opportunities in recent years to investigat
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| 14. |
- Abaasa, A, et al.
(författare)
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Use of propensity score matching to create counterfactual group to assess potential HIV prevention interventions
- 2021
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Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 11:1, s. 7017-
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Tidskriftsartikel (refereegranskat)abstract
- The design of HIV prevention trials in the context of effective HIV preventive methods is a challenge. Alternate designs, including using non-randomised ‘observational control arms’ have been proposed. We used HIV simulated vaccine efficacy trials (SiVETs) to show pitfalls that may arise from using such observational controls and suggest how to conduct the analysis in the face of the pitfalls. Two SiVETs were nested within previously established observational cohorts of fisherfolk (FF) and female sex workers (FSW) in Uganda. SiVET participants received a licensed Hepatitis B vaccine in a schedule (0, 1 and 6 months) similar to that for a possible HIV vaccine efficacy trial. All participants received HIV counselling and testing every quarter for one year to assess HIV incidence rate ratio (IRR) between SiVET and non-SiVET (observational data). Propensity scores, conditional on baseline characteristics were calculated for SiVET participation and matched between SiVET and non-SiVET in the period before and during the SiVET study. We compared IRR before and after propensity score matching (PSM). In total, 3989 participants were enrolled into observational cohorts prior to SiVET, (1575 FF prior to Jul 2012 and 2414 FSW prior to Aug 2014). SiVET enrolled 572 participants (Jul 2012 to Apr 2014 in FF and Aug 2014 to Apr 2017 in FSW), with 953 non-SiVET participants observed in the SiVET concurrent period and 2928 from the pre-SiVET period (before Jul 2012 in FF or before Apr 2014 in FSW). Imbalances in baseline characteristics were observed between SiVET and non-SiVET participants in both periods before PSM. Similarly, HIV incidence was lower in SiVET than non-SiVET; SiVET-concurrent period, IRR = 0.59, 95% CI 0.31–0.68, p = 0.033 and pre-SiVET period, IRR = 0.77, 95% CI 0.43–1.29, p = 0.161. After PSM, participants baseline characteristics were comparable and there were minimal differences in HIV incidence between SiVET and non-SiVET participants. The process of screening for eligibility for efficacy trial selects participants with baseline characteristics different from the source population, confounding any observed differences in HIV incidence. Propensity score matching can be a useful tool to adjust the imbalance in the measured participants’ baseline characteristics creating a counterfactual group to estimate the effect of interventions on HIV incidence.
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| 15. |
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| 16. |
- Fast, Karin, et al.
(författare)
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Half of the children with overweight or obesity and attention-deficit/hyperactivity disorder reach normal weight with stimulants
- 2021
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Ingår i: Acta Paediatrica. - : Wiley-Blackwell. - 0803-5253 .- 1651-2227. ; 110:10, s. 2825-2832
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Tidskriftsartikel (refereegranskat)abstract
- Aim Treatment of childhood obesity is often insufficient and may be aggravated by high co-occurrence of attention-deficit/hyperactivity disorder (ADHD). We aimed to investigate whether children with overweight or obesity normalised in weight when receiving stimulant treatment for ADHD. Methods Growth data of 118 children were obtained from medical records at outpatient paediatric and children’s psychiatric services in the Gothenburg area, Sweden. The children were diagnosed with ADHD and were between 6 and 17 years at the start of stimulant treatment. The pre-treatment data act as an internal control where every child is their own control. Results At the start of treatment, 74 children had normal weight and 44 had either overweight or obesity. During the year with stimulants, the mean (SD) body mass index (BMI) in standard deviation score (SDS) decreased significantly: -0.72 (0.66) compared with 0.17 (0.43) during the year before treatment (p < 0.01). After one year with treatment, 43% of those with overweight or obesity had reached normal weight. Conclusions Stimulant treatment for ADHD yields significant weight loss. In children with overweight or obesity and ADHD, this is an important finding showing additional benefit in terms of weight management.
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| 17. |
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| 18. |
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| 19. |
- Hartlaub, J, et al.
(författare)
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Diagnosis and Pathogenesis of Nairobi Sheep Disease Orthonairovirus Infections in Sheep and Cattle
- 2021
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Ingår i: Viruses. - : MDPI AG. - 1999-4915. ; 13:7
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Tidskriftsartikel (refereegranskat)abstract
- Nairobi sheep disease orthonairovirus (NSDV) is a zoonotic tick-borne arbovirus, which causes severe gastroenteritis in small ruminants. To date, the virus is prevalent in East Africa and Asia. However, due to climate change, including the spread of transmitting tick vectors and increased animal movements, it is likely that the distribution range of NSDV is enlarging. In this project, sheep and cattle (hitherto classified as resistant to NSDV) were experimentally infected with NSDV for a comparative study of the species-specific pathogenesis. For this purpose, several new diagnostic assays (RT-qPCR, ELISA, iIFA, mVNT, PRNT) were developed, which will also be useful for future epidemiological investigations. All challenged sheep (three different doses groups) developed characteristic clinical signs, transient viremia and virus shedding—almost independent on the applied virus dose. Half of the sheep had to be euthanized due to severe clinical signs, including hemorrhagic diarrhea. In contrast, the course of infection in cattle was only subclinical. However, all ruminants showed seroconversion—implying that, indeed, both species are susceptible for NSDV. Hence, not only sheep but also cattle sera can be included in serological monitoring programs for the surveillance of NSDV occurrence and spread in the future.
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| 20. |
- Hartlaub, J, et al.
(författare)
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Experimental Challenge of Sheep and Cattle with Dugbe Orthonairovirus, a Neglected African Arbovirus Distantly Related to CCHFV
- 2021
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Ingår i: Viruses. - : MDPI AG. - 1999-4915. ; 13:3
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Tidskriftsartikel (refereegranskat)abstract
- Dugbe orthonairovirus (DUGV) is a tick-borne arbovirus within the order Bunyavirales. DUGV was first isolated in Nigeria, but virus isolations in ten further African countries indicate that DUGV is widespread throughout Africa. Humans can suffer from a mild febrile illness, hence, DUGV is classified as a biosafety level (BSL) 3 agent. In contrast, no disease has been described in animals, albeit serological evidence exists that ruminants are common hosts and may play an important role in the transmission cycle of this neglected arbovirus. In this study, young sheep and calves were experimentally inoculated with DUGV in order to determine their susceptibility and to study the course of infection. Moreover, potential antibody cross-reactivities in currently available diagnostic assays for Crimean-Congo hemorrhagic fever orthonairovirus (CCHFV) were assessed as DUGV is distantly related to CCHFV. Following subcutaneous inoculation, none of the animals developed clinical signs or viremia. However, all ruminants seroconverted, as demonstrated by two DUGV neutralization test formats (micro-virus neutralization test (mVNT), plaque reduction (PRNT)), by indirect immunofluorescence assays and in bovines by a newly developed DUGV recombinant N protein ELISA. Sera did not react in commercial CCHFV ELISAs, whereas cross-reactivities were observed by immunofluorescence and immunoblot assays.
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| 21. |
- Hartlaub, J, et al.
(författare)
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Sheep and Cattle Are Not Susceptible to Experimental Inoculation with Hazara Orthonairovirus, a Tick-Borne Arbovirus Closely Related to CCHFV
- 2020
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Ingår i: Microorganisms. - : MDPI AG. - 2076-2607. ; 8:12
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Tidskriftsartikel (refereegranskat)abstract
- Hazara orthonairovirus (HAZV) is a tick-borne arbovirus closely related to Crimean–Congo hemorrhagic fever orthonairovirus (CCHFV). Whereas CCHFV is a biosafety level (BSL) 4 agent, HAZV is classified as BSL 2, as it is not known to cause any disease in humans. Belonging to the same serogroup as CCHFV, HAZV might act as a model which can provide a better understanding of this important zoonosis. Furthermore, the serological relatedness may cause diagnostic problems if antibodies against HAZV interfere with current CCHFV serological assays. Therefore, sheep and cattle—important natural hosts for CCHFV—were experimentally infected with HAZV to prove their susceptibility and evaluate potential antibody cross-reactivities. According to this study, neither sheep nor cattle are susceptible to experimental HAZV infections. Consequently, the HAZV infection in ruminants is clearly distinct from CCHFV infections. Sera of immunized animals weakly cross-reacted between HAZV and CCHFV in immunofluorescence and immunoblot assays, but not in commercial CCHFV ELISAs commonly used for field studies.
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| 22. |
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| 23. |
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| 24. |
- Pettersson, Pär, 1985, et al.
(författare)
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A proposal for an operating cycle description format for road transport missions
- 2018
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Ingår i: European Transport Research Review. - : Springer Science and Business Media LLC. - 1867-0717 .- 1866-8887. ; 10:2
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: This article presents a proposal for an operating cycle format for describing transport missions of road vehicles, for example a logging truck fetching its cargo. The primary application is in dynamic simulation models for evaluation of energy consumption and other costs of transportation. When applied to product development, the objective is an ensemble of components and functions optimised for specific tasks and environments. When applied to selection of vehicle configuration, the objective is a vehicle specification tailored for its task. Method: The proposal is presented and its four main parts: road, weather, traffic and mission, are thoroughly explained. Furthermore, we implement the proposal in an example of a dynamic forward simulation model. Results: The example model is used for two case studies: a synthetic example of a complex transport mission (a logging truck fetching its cargo) that shows some advanced format features, and an example from a real vehicle log file (cargo transport) that seeks to compare the resulting simulated speed profile to the measured one. Conclusion: The results show that the proposed format works in practice. It can represent complex transport missions and it can be used to reproduce the main features of a logged speed profile even when combined with simple driver and vehicle models.
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| 25. |
- Pettersson, Pär, 1985, et al.
(författare)
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A statistical operating cycle description for prediction of road vehicles’ energy consumption
- 2019
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Ingår i: Transportation Research Part D. - : Elsevier Ltd. - 1361-9209 .- 1879-2340. ; 73, s. 205-229
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Tidskriftsartikel (refereegranskat)abstract
- We propose a novel statistical description of the physical properties of road transport operations by using stochastic models arranged in a hierarchical structure. The description includes speed signs, stops, speed bumps, curvature, topography, road roughness and ground type, with a road type introduced at the top of the hierarchy to group characteristics that are often connected. Methods are described how to generate data on a form (the operating cycle format) that can be used in dynamic simulations to estimate energy usage and CO2 emissions. To showcase the behaviour of the description, two examples are presented using a modular vehicle model for a heavy-duty truck: a sensitivity study on impacts from changes in the environment, and a comparison study on a real goods transport operation with respect to energy usage. It is found that the stop intensity and topography amplitude have the greatest impact in the sensitivity study (8.3% and 9.5% respectively), and the comparison study implies that the statistical description is capable of capturing properties of the road that are significant for vehicular energy usage. Moreover, it is discussed how the statistical description can be used in a vehicle design process, and how the mean CO2 emissions and its variation can be estimated for a vehicle specification.
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