| 1. |
- Nystedt, Björn, et al.
(författare)
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The Norway spruce genome sequence and conifer genome evolution
- 2013
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Ingår i: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 497:7451, s. 579-584
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Tidskriftsartikel (refereegranskat)abstract
- Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the >100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism. Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon reveals that the transposable element diversity is shared among extant conifers. Expression of 24-nucleotide small RNAs, previously implicated in transposable element silencing, is tissue-specific and much lower than in other plants. We further identify numerous long (>10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding.
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| 2. |
- Gillman, Anna, et al.
(författare)
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Oseltamivir-Resistant Influenza A (H1N1) Virus Strain with an H274Y Mutation in Neuraminidase Persists without Drug Pressure in Infected Mallards
- 2015
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Ingår i: Applied and Environmental Microbiology. - : American Society for Microbiology. - 0099-2240 .- 1098-5336. ; 81:7, s. 2378-2383
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Tidskriftsartikel (refereegranskat)abstract
- Influenza A virus (IAV) has its natural reservoir in wild waterfowl and emerging human IAVs often contain gene segments from avian viruses. The active drug metabolite of oseltamivir (oseltamivir carboxylate (OC)), stockpiled as Tamiflu® for influenza pandemic preparedness, is not removed by conventional sewage treatment and has been detected in river water. There, it may there exert evolutionary pressure on avian IAV in waterfowl, resulting in development of resistant viral variants. A resistant avian IAV can circulate among wild birds only if resistance does not restrict viral fitness and if the resistant virus can persist without continuous drug pressure. In this in vivo Mallard (Anas platyrhynchos) study we tested if an OC-resistant avian IAV strain (A(H1N1)/NA-H274Y) could retain resistance while drug pressure was gradually removed. Successively infected Mallards were exposed to decreasing levels of OC, and fecal samples were analyzed for neuraminidase sequence and phenotypic resistance. No reversion to wild-type virus was observed during the experiment, which included 17 days of viral transmission in 10 ducks exposed to OC concentrations below resistance induction levels. We conclude that resistance in avian IAV, induced by OC exposure of the natural host, can persist in absence of the drug. Thus, there is a risk that human pathogenic IAVs that evolve from IAVs circulating among wild birds may contain resistance mutations. An oseltamivir resistant pandemic IAV would be a substantial public health threat. Therefore, our observations underscore the need for prudent oseltamivir use, upgraded sewage treatment and resistance surveillance of IAV in wild birds.
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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. |
- Alfonzo, Emilia, et al.
(författare)
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Colposcopic assessment by Swedescore, evaluation of effectiveness in the Swedish screening programme: a cross-sectional study.
- 2022
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Ingår i: BJOG : an international journal of obstetrics and gynaecology. - : Wiley. - 1471-0528 .- 1470-0328. ; 129:8, s. 1261-1267
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Tidskriftsartikel (refereegranskat)abstract
- To evaluate the effectiveness and performance of Swedescore in the Swedish screening programme.Cross-sectional register study.All Swedish women aged over 18years with a colposcopic assessment linked to a biopsy in the Swedish National Cervical Screening Registry, 2015-20.Colposcopies with Swedescore were compared with the histopathological diagnosis of cervical intraepithelial neoplasia grade 2 or higher (CIN2+). The respective influence of cytology and human papillomavirus (HPV) testing, at referral for colposcopy and concurrently with colposcopy, were investigated in regression models.CIN2+.A total of 11317 colposcopic assessments with Swedescore were included. Odds ratios for CIN2+ increased for every step in the Swedescore scale. At Swedescore ≥0-1, the proportion of CIN2+ was 9.8%. At Swedescore ≥8, the specificity was 93.3% and the positive predictive value was 60.1%, Area under the receiver operating characteristics curve (AUC) was 0.71. If the smear had been abnormal at referral, a normal colposcopy (Swedescore 0-1) was still associated with a CIN2+ risk of more than 5%. In the regression model, cytology and HPV had higher odds ratio for CIN2+ than colposcopy; the combination resulted in an AUC of 0.88.Swedescore works well in a routine clinical setting but colposcopy assessed with Swedescore was inferior to that reported in previous clinical studies. No safe cutoff level was identified for refraining from biopsy. See-and-treat at Swedescore 8-10 is feasible only if referral cytology showed high-grade squamous intraepithelial lesion.No safe cutoff level for refraining from biopsy nor for see-and-treat with Swedescore.
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| 5. |
- Alfonzo, Emilia, et al.
(författare)
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Risk of vaginal cancer among hysterectomised women with cervical intraepithelial neoplasia: a population-based national cohort study.
- 2020
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Ingår i: BJOG : an international journal of obstetrics and gynaecology. - : Wiley. - 1471-0528 .- 1470-0328. ; 127:4, s. 448-454
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Tidskriftsartikel (refereegranskat)abstract
- To study the risk of vaginal cancer among hysterectomised women with and without CIN.Population-based national cohort study.All Swedish women, five million in total, aged 20 and up, 1987-2011 using national registries.The study cohort was subdivided into four exposure groups: hysterectomised with no previous history of CIN3 and without prevalent CIN at hysterectomy; hysterectomised with a history of CIN3/adenocarcinoma in situ (AIS); hysterectomised with prevalent CIN at hysterectomy; non-hysterectomised.Vaginal cancer.We identified 898 incident cases of vaginal cancer.Women with prevalent CIN at hysterectomy and those with CIN3/AIS history had incidence rates (IR) of vaginal cancer: 51.3 (34.3-76.5) and 17.1 (12.5-23-4) per 100000, respectively. Age-adjusted IR-ratios (IRRs) compared to hysterectomised with benign cervical history, were 21.0 (13.4-32.9) and 5.81(4.00-8.43), respectively. IR for non-hysterectomised women was 0.87 (0.81-0.93) and IRR 0.37 (0.30-0.46). In hysterectomised with prevalent CIN, the IR remained high after 15 years of follow-up: 65.7 (21.2-203.6).Our findings suggest that hysterectomised women with prevalent CIN at surgery should be offered surveillance. Hysterectomised women without the studied risk factors have a more than doubled risk of contracting vaginal cancer compared with non-hysterectomised women in the general population. Still, the incidence rate does not justify screening.
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| 6. |
- Alsmark, Cecilia M., et al.
(författare)
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The louse-borne human pathogen Bartonella quintana is a genomic derivative of the zoonotic agent Bartonella henselae
- 2004
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 101:26, s. 9716-9721
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Tidskriftsartikel (refereegranskat)abstract
- We present the complete genomes of two human pathogens, Bartonella quintana (1,581,384 bp) and Bartonella henselae (1,931,047 bp). The two pathogens maintain several similarities in being transmitted by insect vectors, using mammalian reservoirs, infecting similar cell types (endothelial cells and erythrocytes) and causing vasculoproliferative changes in immunocompromised hosts. A primary difference between the two pathogens is their reservoir ecology. Whereas B. quintana is a specialist, using only the human as a reservoir, B. henselae is more promiscuous and is frequently isolated from both cats and humans. Genome comparison elucidated a high degree of overall similarity with major differences being B. henselae specific genomic islands coding for filamentous hemagglutinin, and evidence of extensive genome reduction in B. quintana, reminiscent of that found in Rickettsia prowazekii. Both genomes are reduced versions of chromosome I from the highly related pathogen Brucella melitensis. Flanked by two rRNA operons is a segment with similarity to genes located on chromosome II of B. melitensis, suggesting that it was acquired by integration of megareplicon DNA in a common ancestor of the two Bartonella species. Comparisons of the vector-host ecology of these organisms suggest that the utilization of host-restricted vectors is associated with accelerated rates of genome degradation and may explain why human pathogens transmitted by specialist vectors are outnumbered by zoonotic agents, which use vectors of broad host ranges.
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| 7. |
- Andersson, Björn A., 1968, et al.
(författare)
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Materials constraints in a global energy scenario based on thin-film solar cells
- 1998
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Ingår i: Energy. - 0360-5442. ; 23, s. 407-411
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Tidskriftsartikel (refereegranskat)abstract
- Harnessing solar energy by using photovoltaic cells has the potential to become a major CO2-free energy source. Materials requirements for the solar cells based on four types of thin-film photovoltaics have been estimated and compared with global reserves, resources and annual refining. The use of solar cells based on Cd, Ga, Ge, In, Ru, Se and Te as a major energy-supply technology has severe resource constraints. Other systems such as a-Si without Ge and crystalline silicon do not involve such constraints. For some of these metals, there is the risk of enhanced, environmentally deleterious concentrations in the ecosphere due to leakage from manufacturing, use or waste handling.
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| 8. |
- Andreassen, Björn, 1975-, et al.
(författare)
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Development of an efficient scanning and purging magnet system for IMRT with narrow high energy photon beams
- 2009
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Ingår i: Nuclear Instruments and Methods in Physics Research Section A. - : Elsevier BV. - 0168-9002 .- 1872-9576. ; 612:1, s. 201-208
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Tidskriftsartikel (refereegranskat)abstract
- Due to the clinical advantages of Intensity Modulated Radiation Therapy (IMRT) high flexibility and accuracy in intensity modulated dose delivery is desirable to really maximize treatment outcome. Although it is possible to deliver IMRT by using broad beams in combination with dynamic multileaf collimation the process is rather time consuming and inefficient. By using narrow scanned high energy photon beams the treatment outcome can be improved, the treatment time reduced and accurate 3D in vivo dose delivery monitoring is possible by PET-CT based dose delivery imaging of photo nuclear reactions in human tissues. Narrow photon beams can be produced by directing a low emittance high energy electron beam on a thin target, and then cleaning the therapeutic photon beam from transmitted high energy electrons, and photon generated charged leptons, with a dedicated purging magnet placed directly downstream of the target. To have an effective scanning and purging magnet system the purging magnet should be placed immediately after the bremsstrahlung target to deflect the transmitted electrons to an efficient electron stopper. In the static electron stopper the electrons should be safely collected independent of the desired direction of the therapeutic scanned photon beam. The SID (Source to Isocentre Distance) should preferably be short while retaining the ability to scan over a large area on the patient and consequently there are severe requirements both on the strength and the geometry of the scanning and purging magnets. In the present study an efficient magnet configuration with a purging and scanning magnet assembly is developed for electron energies in the 50-75 MeV range and a SID of 75 cm. For a bremsstrahlung target of 3mm Be these electron energies produce a photon beam of 25-17 mm FWHM (Full Width Half Maximum) at a SID of 75 cm. The magnet system was examined both in terms of the efficiency in scanning the narrow bremsstrahlung beam and the deflection of transmitted and photon generated electrons. The simulations show that its is possible to have a scan area on the patient of up to 43 x 40 cm2 for an incident electron energy of 50 MeV and 28 x 40 cm2 at 75 MeV, while at the same time adequately deflecting the transmitted electron beam.
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| 9. |
- Andreassen, Björn, et al.
(författare)
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Fast IMRT with narrow high energy scanned photon beams
- 2011
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Ingår i: Medical physics (Lancaster). - : Wiley. - 0094-2405. ; 38:8, s. 4774-4784
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: Since the first publications on intensity modulated radiation therapy (IMRT) in the early 1980s almost all efforts have been focused on fairly time consuming dynamic or segmental multileaf collimation. With narrow fast scanned photon beams, the flexibility and accuracy in beam shaping increases, not least in combination with fast penumbra trimming multileaf collimators. Previously, experiments have been performed with full range targets, generating a broad bremsstrahlung beam, in combination with multileaf collimators or material compensators. In the present publication, the first measurements with fast narrow high energy (50 MV) scanned photon beams are presented indicating an interesting performance increase even though some of the hardware used were suboptimal. Methods: Inverse therapy planning was used to calculate optimal scanning patterns to generate dose distributions with interesting properties for fast IMRT. To fully utilize the dose distributional advantages with scanned beams, it is necessary to use narrow high energy beams from a thin bremsstrahlung target and a powerful purging magnet capable of deflecting the transmitted electron beam away from the generated photons onto a dedicated electron collector. During the present measurements the scanning system, purging magnet, and electron collimator in the treatment head of the MM50 racetrack accelerator was used with 3-6 mm thick bremsstrahlung targets of beryllium. The dose distributions were measured with diodes in water and with EDR2 film in PMMA. Monte Carlo simulations with GEANT4 were used to study the influence of the electrons transmitted through the target on the photon pencil beam kernel. Results: The full width at half-maximum (FWHM) of the scanned photon beam was 34 mm measured at isocenter, below 9.5 cm of water, 1 m from the 3 mm Be bremsstrahlung target. To generate a homogeneous dose distribution in a 10 x 10 cm(2) field, the authors used a spot matrix of 100 equal intensity beam spots resulting in a uniformity of collimated 80%-20% penumbra of 9 mm at a primary electron energy of 50 MeV. For the more complex cardioid shaped dose distribution, they used 270 spots, which at a pulse repetition frequency of 200 Hz is completed every 1.36 s. Conclusions: The present measurements indicate that the use of narrow scanned photon beams is a flexible and fast method to deliver advanced intensity modulated beams. Fast scanned photon IMRT should, therefore, be a very interesting modality in the delivery of biologically optimized radiation therapy with the possibility for in vivo treatment verification with PET-CT imaging.
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| 10. |
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