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| 2. |
- Allander, Erik, et al.
(författare)
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Why is Prevention So Difficult and Slow?
- 1997
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Ingår i: Scandinavian Journal of Social Medicine. ; 25:3, s. 145-148
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The abundance of perceived 'possibilities' for prevention contrasts sharply with the difficulties that face preventive programmes. We argue that this situation has emerged from an incomplete understanding of the process of prevention, involving a mixture of biological factors, human decision making and time perspectives. Based on examples, an analysis of the factors in the prevention process is presented.
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| 3. |
- Barrientos-Somarribas, Mauricio, et al.
(författare)
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Discovering viral genomes in human metagenomic data by predicting unknown protein families
- 2018
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Massive amounts of metagenomics data are currently being produced, and in all such projects a sizeable fraction of the resulting data shows no or little homology to known sequences. It is likely that this fraction contains novel viruses, but identification is challenging since they frequently lack homology to known viruses. To overcome this problem, we developed a strategy to detect ORFan protein families in shotgun metagenomics data, using similarity-based clustering and a set of filters to extract bona fide protein families. We applied this method to 17 virus-enriched libraries originating from human nasopharyngeal aspirates, serum, feces, and cerebrospinal fluid samples. This resulted in 32 predicted putative novel gene families. Some families showed detectable homology to sequences in metagenomics datasets and protein databases after reannotation. Notably, one predicted family matches an ORF from the highly variable Torque Teno virus (TTV). Furthermore, follow-up from a predicted ORFan resulted in the complete reconstruction of a novel circular genome. Its organisation suggests that it most likely corresponds to a novel bacteriophage in the microviridae family, hence it was named bacteriophage HFM.
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| 4. |
- Gustafsson, Britt, et al.
(författare)
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KI, WU, and Merkel Cell Polyomavirus DNA was not Detected in Guthrie Cards of Children who Later Developed Acute Lymphoblastic Leukemia
- 2012
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Ingår i: Journal of pediatric hematology/oncology (Print). - 1077-4114 .- 1536-3678. ; 34:5, s. 364-367
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Tidskriftsartikel (refereegranskat)abstract
- Background: Neonatal dried blood spots (Guthrie cards) have been used to demonstrate a prenatal origin of clonal leukemia-specific genetic aberrations in several subgroups of childhood acute lymphoblastic leukemia (ALL). One hypothesis suggests that an infectious agent could initiate genetic transformation already in utero. In search for a possible viral agent, Guthrie cards were analyzed for the presence of 3 newly discovered polyomavirus Karolinska Institutet polymavirus (KIPyV), Washington University polyomavirus (WUPyV), and Merkel cell polyomavirus (MCPyV). Methods: Guthrie cards from 50 children who later developed ALL and 100 matched controls were collected and analyzed by standard or real-time polymerase chain reaction for the presence of the VP1 region of KIPyV, WUPyV, and MCPyV, and the LT region for MCPyV. Results and Conclusions: DNA from KIPyV, WUPyV, and MCPyV was not detected in neonatal blood samples from children with ALL or controls. Prenatal infections with these viruses are not likely to be etiological drivers for childhood leukemogenesis.
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| 6. |
- Messina, David, 1974-, et al.
(författare)
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Discovery of novel protein families in metagenomic samples
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Despite the steady rise in gene sequence information, there is a persistent, significant fraction of genes which do not match any previously known sequence. These genes are called ORFans, and metagenomic samples, where DNA is extracted from a mixed population of unknown and often uncultivable species, are a rich source of ORFans. Viral infections cause significant morbidity and mortality, and identifying ORFan viral gene families from human metagenomic samples represents a route to understanding molecular processes that affect human health. Few methods exist for metagenomic gene-finding, and most of them rely on sequence similarity, which cannot be used to detect ORFans. Furthermore, nonsimilarity-based methods are hard to apply to the complex mixture of short, higherror-rate sequence fragments which are typical of metagenomic projects. Here we present an approach to detect ORFan protein families in short-read data, and apply it to 937 Mbp (megabase pairs) of sequence from 17 virus-enriched libraries made from human nasopharyngeal aspirates, serum, feces, and cerebrospinal fluid samples. After isolating approximately 450 putative ORFan families from clusters of sequence contigs, we applied RNAcode, a gene finder developed for use on high-quality genome sequences, and calibrated it for errorprone short sequence reads. Additional predictive measures such as sequence complexity and length were then used to rank and filter candidates into a high-quality set of 32 putative novel gene families, only two of which show significant similarity to known genes.
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