| 1. |
- Atteia, A., et al.
(author)
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Structure, organization and expression of the genes encoding mitochondrial cytochrome c1 and the Rieske iron-sulfur protein in Chlamydomonas reinhardtii
- 2003
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In: Molecular Genetics and Genomics. - : Springer Verlag. - 1617-4615 .- 1617-4623. ; 268:5, s. 637-644
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Journal article (peer-reviewed)abstract
- The sequence and organization of the Chlamydomonas reinhardtii genes encoding cytochrome c 1 ( Cyc1) and the Rieske-type iron-sulfur protein ( Isp), two key nucleus-encoded subunits of the mitochondrial cytochrome bc 1 complex, are presented. Southern hybridization analysis indicates that both Cyc1 and Isp are present as single-copy genes in C. reinhardtii. The Cyc1 gene spans 6404 bp and contains six introns, ranging from 178 to 1134 bp in size. The Isp gene spans 1238 bp and contains four smaller introns, ranging in length from 83 to 167 bp. In both genes, the intron/exon junctions follow the GT/AG rule. Internal conserved sequences were identified in only some of the introns in the Cyc1 gene. The levels of expression of Isp and Cyc1 genes are comparable in wild-type C. reinhardtii cells and in a mutant strain carrying a deletion in the mitochondrial gene for cytochrome b (dum-1). Nevertheless, no accumulation of the nucleus-encoded cytochrome c 1 or of core proteins I and II was observed in the membranes of the respiratory mutant. These data show that, in the green alga C. reinhardtii, the subunits of the cytochrome bc1 complex fail to assemble properly in the absence of cytochrome b.
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| 2. |
- Eriksson, Gunnar, et al.
(author)
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Exploiting Syntax when Detecting Protein Names in Text
- 2002. - 1
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In: Proceedings of FMI Workshop on Natural Language Processing in Biomedical Applications.
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Conference paper (peer-reviewed)abstract
- This paper presents work on a method to detect names of proteins in running text. Our system - Yapex - uses a combination of lexical and syntactic knowledge, heuristic filters and a local dynamic dictionary. The syntactic information given by a general-purpose off-the-shelf parser supports the correct identification of the boundaries of protein names, and the local dynamic dictionary finds protein names in positions incompletely analysed by the parser. We present the different steps involved in our approach to protein tagging, and show how combinations of them influence recall and precision. We evaluate the system on a corpus of MEDLINE abstracts and compare it with the KeX system (Fukuda et al., 1998) along four different notions of correctness.
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| 3. |
- Franzén, Kristofer, et al.
(author)
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Protein names and how to find them
- 2002. - 1
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In: International Journal of Medical Informatics. - : Elsevier. - 1386-5056 .- 1872-8243. ; 67, s. 49-61
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Journal article (peer-reviewed)abstract
- A prerequisite for all higher level information extraction tasks is the identification of unknown names in text. Today, when large corpora can consist of billions of words, it is of utmost importance to develop accurate techniques for the automatic detection, extraction and categorization of named entities in these corpora. Although named entity recognition might be regarded a solved problem in some domains, it still poses a significant challenge in others. In this work we focus on one of the more difficult tasks, the identification of protein names in text. This task presents several interesting difficulties because of the named entities' variant structural characteristics, their sometimes unclear status as names, the lack of common standards and fixed nomenclatures, and the specifics of the texts in the molecular biology domain in which they appear. We describe how we approached these and other difficulties in the implementation of Yapex, a system for the automatic identification of protein names in text. We also evaluate Yapex under four different notions of correctness and compare its performance to that of another publicly available system for protein name recognition.
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| 4. |
- Gisslén, Magnus, 1962, et al.
(author)
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Cerebrospinal fluid and plasma viral load in HIV-1-infected patients with various anti-retroviral treatment regimens
- 2000
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In: Scand J Infect Dis. ; 32:4, s. 365-9
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Journal article (peer-reviewed)abstract
- Highly active anti-retroviral therapy (HAART) effectively decreases HIV-1 RNA in cerebrospinal fluid (CSF) and plasma in controlled clinical trials. To study the virological effect in CSF and plasma achieved in routine practice, HIV-1 RNA levels were analysed retrospectively in 27 patients on mono-nucleoside reversed transcriptase inhibitor (NRTI) treatment, 27 on dual-NRTI-treatment and 45 on HAART using a Roche Amplicor HIV-1 monitor quantitative PCR. A significant difference was found in the proportion of patients with a CSF viral load below 20 copies/ml between patients treated with 1 (0%) and 2 NRTIs (41%) as well as between those treated with 2 NRTIs and HAART (69%). The proportion of patients with plasma viral load below 20 copies/ml differed significantly between patients on HAART (47%) and those on 2 NRTIs (0%), but not between those with 1 (0%) or 2 NRTIs. In multivariate regression analysis, treatment regimen and prior anti-retroviral experience (but not treatment time) were independently associated with the CSF viral load. Plasma viral load was independently associated with treatment regimen and treatment time, but not with anti-retroviral experience. Dual-NRTI-treatment affects the CSF viral load substantially, while HAART is required to achieve an essential decline in plasma viral load.
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| 5. |
- Olsson, Fredrik, et al.
(author)
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Notions of correctness when evaluating protein name taggers
- 2002. - 1
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In: Proceedings of the 19th International Conference on Computational Linguistics (COLING 2002): Vol. 1. - Morristown, NJ, USA : Association for Computational Linguistics.
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Conference paper (peer-reviewed)abstract
- This paper introduces four different notions of correctness to be used when measuring the performance of protein name taggers, each of which reflects certain characteristics of the tagger under evaluation. The discussion regarding the different notions is centered around the evaluation of two protein name taggers; Yapex, developed by the authors, and KeX developed by Fukuda et al (1998). For the purpose of illustrating the difference between the ways of evaluation, both taggers are applied to a corpus of 101 MEDLINE abstracts in which all occurrences of protein names have been marked up by domain experts.
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| 6. |
- Stevens, DR, et al.
(author)
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Cycloheximide resistance conferred by novel mutations in ribosomal protein L41 of Chlamydomonas reinhardtii
- 2001
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In: Molecular General Genetics. - Berlin : Springer-Verlag. - 0026-8925 .- 1432-1874. ; 264:6, s. 790-795
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Journal article (peer-reviewed)abstract
- Although most eukaryotic cells are sensitive to the 80S ribosome inhibitor cycloheximide (CYH), naturally occurring CYH resistance is widespread amongst yeast species. The primary determinant of resistance appears to be a single residue within ribosomal protein L41; resistance is acquired by the substitution of a conserved proline (P-56) by a glutamate residue. We have isolated the L41 gene (RPL41) from the green alga Chlamydomonas and investigated the molecular basis of CYH resistance in various mutant strains. In both the wild-type strain and the mutant act-1, a proline is found at the key position in L41.; However, analysis of six independently isolated act-2 mutants reveals that all have point mutations that replace the proline with either leucine or serine. Of the two changes, the leucine mutation confers significantly higher levels of CYH resistance. This work identifies the ACT-2 locus as RPL41 and provides a possible dominant marker for nuclear transformation of C. reinhardtii.
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