| 1. |
- Borch, Kurt, 1944-, et al.
(författare)
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Prevalence of gastroduodenitis and Helicobacter priori infection in a general population sample : relations to symptomatology and life-style
- 2000
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Ingår i: Digestive Diseases and Sciences. - 0163-2116 .- 1573-2568. ; 45:7, s. 1322-1329
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Tidskriftsartikel (refereegranskat)abstract
- Some benign and malignant diseases develop on the background of chronic gastritis or duodenitis. The present study was performed in order to determine the magnitude of these background changes with relations to symptomatology and life style in the general population. Examinations were performed in 501 volunteers (age 35–85 years). Fifty percent had gastritis; this was associated with H. pylori in 87%. H. pylori-negative gastritis was associated with regular use of NSAIDs [odds ratio 3.8 (1.6–9.9)]. Duodenitis, observed in 32%, was associated with H. pylori infection [odds ratio 2.3 (1.3–4.6)], previous cholecystectomy [odds ratio 3.6 (1.1–16.1)], and regular use of NSAIDs [odds ratio 3.0 (1.4–7.1)]. Neither gastritis nor duodenitis was associated with smoking or alcohol consumption. The rate of digestive symptoms did not differ between subjects with and without uncomplicated gastritis or duodenitis. In conclusion, half of this adult population had gastritis strongly associated with H. pylori infection. Gastritis without H. pylori infection was frequently associated with regular NSAID intake. One third had duodenitis, which was associated with H. pylori infection as well as with regular use of NSAIDs and previous cholecystectomy. Digestive symptoms were not overrepresented in uncomplicated gastritis or duodenitis.
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| 2. |
- Eriksson, Gunnar, et al.
(författare)
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Exploiting Syntax when Detecting Protein Names in Text
- 2002. - 1
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Ingår i: Proceedings of FMI Workshop on Natural Language Processing in Biomedical Applications.
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Konferensbidrag (refereegranskat)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. |
- Eriksson, Gunnar, et al.
(författare)
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Using heuristics, syntax and a local dynamic dictionary for protein name tagging
- 2002. - 5
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Konferensbidrag (refereegranskat)abstract
- This paper presents work on a method to detect names of proteins in running text. The detection and categorisation of named entities, such as names of people, organisations and places, in classical MUC-style information extraction tasks (Borthwick 1998) might be regarded a solved problem. But names of proteins present a slightly different challenge because of their variant structural characteristics and the specifics of the text domains in which they appear. This certainly holds true for other biological substances, and probably for many other kinds of terminology as well. We will present the different steps involved in our approach to this problem, and show how combinations of them influence recall and precision.
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| 4. |
- Franzén, Kristofer, et al.
(författare)
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Protein names and how to find them
- 2002. - 1
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Ingår i: International Journal of Medical Informatics. - : Elsevier. - 1386-5056 .- 1872-8243. ; 67, s. 49-61
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Tidskriftsartikel (refereegranskat)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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| 5. |
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| 6. |
- Olsson, Fredrik, et al.
(författare)
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Notions of correctness when evaluating protein name taggers
- 2002. - 1
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Ingår i: Proceedings of the 19th International Conference on Computational Linguistics (COLING 2002): Vol. 1. - Morristown, NJ, USA : Association for Computational Linguistics.
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Konferensbidrag (refereegranskat)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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| 7. |
- Petersson, Fredrik, et al.
(författare)
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Gastric epithelial proliferation and p53 and p21 expression in a general population sample : relations to age, sex, and mucosal changes associated with H. pylori infection
- 2002
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Ingår i: Digestive Diseases and Sciences. - 0163-2116 .- 1573-2568. ; 47:7, s. 1558-1566
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Tidskriftsartikel (refereegranskat)abstract
- Helicobacter pylori infection is the main cause of chronic gastritis. The infection has been linked to altered proliferative activity and changes in various cell cycle regulating proteins. To determine, in a general population sample, the proliferative activity and expression of p53 and p21 in males and females of different age groups with and without H. pylori-associated chronic gastritis, gastric biopsies from 273 subjects (188 with and 85 without H. pylori infection) randomly selected from a general population were examined immunohistochemically for Ki-67, p53, and p21. One thousand epithelial cells, including the surface, neck, and glandular areas, were counted in both the corpus and the antrum. Results are expressed as the percentage of positive cells. Subjects with H. pylori infection showed significantly increased proliferative activity and expression of p53 compared to uninfected individuals. Regarding the expression of p21, no difference was detected. Multiple linear regression analysis showed significant associations between chronic inflammation or inflammatory activity, on the one hand, and the degree of proliferation in both the corpus and the antrum, on the other hand. In the antrum, the degree of H. pylori colonization was related to the expression of p53. H. pylori seems to cause increased proliferation and increased expression of p53 (but not p21) in the gastric mucosa, neither of which is age or sex dependent. The proliferative activity is related mainly to events associated with inflammation, while the expression of p53 in the antrum is associated with the degree of H. pylori infection. The action of p53 appears to be independent of p21 activity.
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| 8. |
- Petersson, Fredrik, et al.
(författare)
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Prevalence of subtypes of intestinal metaplasia in the general population and in patients with autoimmune chronic atrophic gastritis
- 2002
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Ingår i: Scandinavian Journal of Gastroenterology. - : Informa UK Limited. - 0036-5521 .- 1502-7708. ; 37:3, s. 262-266
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Tidskriftsartikel (refereegranskat)abstract
- Background: Gastric intestinal metaplasia (IM) is seen mostly in association with chronic gastritis, induced either by Helicobacter pylori infection or autoimmune mechanisms. IM can be categorized into three subtypes, where type III is associated with gastric carcinoma of intestinal type.Methods: Gastric biopsies from 475 subjects randomly selected from the general population and from 27 patients with autoimmune gastritis associated with pernicious anaemia were used. The criteria of Filipe & Jass were applied using different histochemical techniques in combination with haematoxylin and eosin stained material.Results: Twenty-three percent (109/475) of the subjects from the general population and 88% (24/27) in the group with autoimmune gastritis had IM. Type III IM occurred in 4% in both populations. Type III IM was located in the antrum in 90% in the general population. In the group with autoimmune gastritis, only one patient had type III IM, which was located in the corpus.Conclusions: This study reveals for the first time the prevalence and distribution of subtypes of IM in a general population from the Western world. The comparatively high prevalence of type III IM in the general population (4%) indicates that its role as a precursor of gastric carcinoma may have been overemphasized. A similar prevalence of type III IM in patients with autoimmune gastritis may be considered low and suggests that mechanisms for gastric carcinogenesis other than the atrophy - metaplasia-dysplasia sequence could also operate in this condition.
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