| 1. |
- Richards, Stephen, et al.
(författare)
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Genome Sequence of the Pea Aphid Acyrthosiphon pisum
- 2010
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Ingår i: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 8:2, s. e1000313-
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Tidskriftsartikel (refereegranskat)abstract
- Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.
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| 2. |
- Ask, Erik, et al.
(författare)
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Tractable and Reliable Registration of 2D Point Sets
- 2014
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Ingår i: Lecture Notes in Computer Science (Computer Vision - ECCV 2014, 13th European Conference, Zurich, Switzerland, September 6-12, 2014, Proceedings, Part I). - Cham : Springer International Publishing. - 0302-9743 .- 1611-3349. - 9783319105895 - 9783319105901 ; 8689, s. 393-406
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Konferensbidrag (refereegranskat)abstract
- This paper introduces two new methods of registering 2D point sets over rigid transformations when the registration error is based on a robust loss function. In contrast to previous work, our methods are guaranteed to compute the optimal transformation, and at the same time, the worst-case running times are bounded by a low-degree polynomial in the number of correspondences. In practical terms, this means that there is no need to resort to ad-hoc procedures such as random sampling or local descent methods that cannot guarantee the quality of their solutions. We have tested the methods in several different settings, in particular, a thorough evaluation on two benchmarks of microscopic images used for histologic analysis of prostate cancer has been performed. Compared to the state-of-the-art, our results show that the methods are both tractable and reliable despite the presence of a significant amount of outliers.
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| 4. |
- Mira Veiga, Joana, et al.
(författare)
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Identifying Sources of Marine Litter
- 2016
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Marine litter is a global problem causing harm to marine wildlife, coastal communities and maritime activities. It also embodies an emerging concern for human health and safety. The reduction of marine litter pollution poses a complex challenge for humankind, requiring adjustments in human behaviour as well as in the different phases of the life- cycle of products and across multiple economic sectors. The Marine Strategy Framework Directive (MSFD) requires European Member States to monitor marine litter and implement programmes of measures to reduce its occurrence. A crucial step in monitoring and effectively addressing marine litter is the identification of the origin and the pathways that lead to litter entering the marine environment. A given site or region can be subject to litter pollution from a number of sources, which can be local, regional or even distant, as litter can be transported to a specific area by ocean currents and wind drift. For this reason, pinpointing the origin of the different items that make up marine litter is a difficult task and will always have an inherent degree of associated uncertainty. Plastic food packaging recorded in the marine environment, for example, can consist of a diverse selection of items, which can be generated from a number of sources, which in turn can be sea-based or land-based and originate from near or distant regions. A wide variety of methods have been used over the years to determine the sources of marine litter, from simple counts of items believed to originate from a given source to more complex statistical methods. This report provides a brief overview of the main methods used and outlines one of the most promising approaches for determining sources – a Matrix Score Technique based on likelihoods, which considers the possibility that specific items originate from more than one source. Furthermore, it presents a series of other parameters that can be used to analyse data-sets, with regard to the use, origin and risk of items recorded in the marine or coastal environments. These can further support decision-making when considering preventive measures. Finally, recommendations to help the process of identification of sources are given, from the early stage of data collection and site characterization to bringing in the knowledge of local stakeholders to better determine where litter is coming from and what needs to be done to prevent it.
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| 6. |
- Sattui, Sebastian E., et al.
(författare)
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Outcomes of COVID-19 in patients with primary systemic vasculitis or polymyalgia rheumatica from the COVID-19 Global Rheumatology Alliance physician registry : a retrospective cohort study
- 2021
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Ingår i: The Lancet Rheumatology. - : Elsevier. - 2665-9913. ; 3:12, s. E855-E864
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Tidskriftsartikel (refereegranskat)abstract
- Background Patients with primary systemic vasculitis or polymyalgia rheumatica might be at a high risk for poor COVID-19 outcomes due to the treatments used, the potential organ damage cause by primary systemic vasculitis, and the demographic factors associated with these conditions. We therefore aimed to investigate factors associated with COVID-19 outcomes in patients with primary systemic vasculitis or polymyalgia rheumatica. Methods In this retrospective cohort study, adult patients (aged >= 18 years) diagnosed with COVID-19 between March 12, 2020, and April 12, 2021, who had a history of primary systemic vasculitis (antineutrophil cytoplasmic antibody [ANCA]-associated vasculitis, giant cell arteritis, Behcet's syndrome, or other vasculitis) or polymyalgia rheumatica, and were reported to the COVID-19 Global Rheumatology Alliance registry were included. To assess COVID-19 outcomes in patients, we used an ordinal COVID-19 severity scale, defined as: (1) no hospitalisation; (2) hospitalisation without supplemental oxygen; (3) hospitalisation with any supplemental oxygen or ventilation; or (4) death. Multivariable ordinal logistic regression analyses were used to estimate odds ratios (ORs), adjusting for age, sex, time period, number of comorbidities, smoking status, obesity, glucocorticoid use, disease activity, region, and medication category. Analyses were also stratified by type of rheumatic disease. Findings Of 1202 eligible patients identified in the registry, 733 (61.0%) were women arid 469 (39.0%) were men, and their mean age was 63.8 years (SD 17.1). A total of 374 (31.1%) patients had polymyalgia rheumatica, 353 (29.4%) had ANCA-associated vasculitis, 183 (15.2%) had giant cell arteritis, 112 (9.3%) had Behcet's syndrome, and 180 (15.0%) had other vasculitis. Of 1020 (84. 9%) patients with outcome data, 512 (S0.2%) were not hospitalised, 114 (11.2%) were hospitalised and did not receive supplemental oxygen, 239 (23 - 4%) were hospitalised and received ventilation or supplemental oxygen, and 155 (15.2%) died. A higher odds of poor COVID-19 outcomes were observed in patients who were older (per each additional decade of life OR 1.44 [95% CI 1. 31-1- 571), were male compared with female (1.38 [1.05-1.801), had more comorbidities (per each additional comorbidity 1.39 [1- 23-1- 581), were taking 10 mg/day or more of prednisolone compared with none (2.14 [1.50-3.04J), or had moderate, or high or severe disease activity compared with those who had disease remission or low disease activity (2.12 [1.49-3.021). Risk factors varied among different disease subtypes. Interpretation Among patients with primary systemic vasculitis and polymyalgia rheumatica, severe COVID-19 outcomes were associated with variable and largely unmodifiable risk factors, such as age, sex, and number of comorbidities, as well as treatments, including high-dose glucocorticoids. Our results could be used to info rm mitigation strategies for patients with these diseases.
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