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- Forrest, ARR, et al.
(författare)
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A promoter-level mammalian expression atlas
- 2014
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 507:7493, s. 462-
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Tidskriftsartikel (refereegranskat)
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| 2. |
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| 3. |
- Yarza, P., et al.
(författare)
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Sequencing orphan species initiative (SOS): Filling the gaps in the 16S rRNA gene sequence database for all species with validly published names
- 2013
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Ingår i: Systematic and Applied Microbiology. - : Elsevier BV. - 0723-2020. ; 36:1, s. 69-73
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Tidskriftsartikel (refereegranskat)abstract
- High quality 16S ribosomal RNA (rRNA) gene sequences from the type strains of all species with validly published names, as defined by the International Code of Nomenclature of Bacteria, are a prerequisite for their accurate affiliations within the global genealogical classification and for the recognition of potential new taxa. During the last few years, the Living Tree Project (LTP) has taken care to create a high quality, aligned 16S and 23S rRNA gene sequence database of all type strains. However, the manual curation of the sequence dataset and type strain information revealed that a total of 552 “orphan” species (about 5.7% of the currently classified species) had to be excluded from the reference trees. Among them, 322 type strains were not represented by an SSU entry in the public sequence repositories. The remaining 230 type strains had to be discarded due to bad sequence quality. Since 2010, the LTP team has coordinated a network of researchers and culture collections in order to improve the situation by (re)-sequencing the type strains of these “orphan” species. As a result, we can now report 351 16S rRNA gene sequences of type strains. Nevertheless, 201 species could not be sequenced because cultivable type strains were not available (121), the cultures had either been lost or were never deposited in the first place (66), or it was not possible due to other constraints (14). The International Code of Nomenclature of Bacteria provides a number of mechanisms to deal with the problem of missing type strains and we recommend that due consideration be given to the appropriate mechanisms in order to help solve some of these issues.
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| 5. |
- Sihver, Lembit, 1962, et al.
(författare)
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Current status of the "Hybrid Kurotama model" for total reaction cross sections
- 2014
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Ingår i: Nuclear Instruments and Methods in Physics Research, Section B: Beam Interactions with Materials and Atoms. - : Elsevier BV. - 0168-583X. ; 334, s. 34-39
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Tidskriftsartikel (refereegranskat)abstract
- To be able to calculate the nucleon + nucleus and nucleus + nucleus total reaction cross sections with precision is of great importance for studies of fundamental nuclear properties, e.g., the nuclear structure. This is also very important for particle and heavy ion transport calculations since in all particle and heavy ion transport codes, the probability function according to which a projectile particle will collide within a certain distance in a matter depends on the total reaction cross sections. This will also scale the calculated partial fragmentation cross sections. It is therefore crucial that accurate total reaction cross section models are used in the transport calculations. In this paper, a new general purpose total reaction cross section model/subroutine called "Hybrid Kurotama" is presented. The model has been tested against available p + He, p + nucleus, and nucleus + nucleus total reaction cross sections and an overall better agreement has been found than for earlier published models. This model is therefore very suitable to be used in any deterministic or Monte Carlo particle and heavy ion transport code.
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