AIM: To determine the prevalence of Helicobacter pylori (H. pylon) infection, the serum anti-H. pylori immunoglobulin G (IgG) and IgA antibody responses, and the value of clinical presentations in diagnosis of H. pylo...AIM: To determine the prevalence of Helicobacter pylori (H. pylon) infection, the serum anti-H. pylori immunoglobulin G (IgG) and IgA antibody responses, and the value of clinical presentations in diagnosis of H. pylori infection in patients with gastric atrophy, intestinal metaplasia and dysplasia.METHODS: H. pylori infection was detected by histology in 209 patients with mild chronic atrophic gastritis (CAG, n=76),severe CAG (n=22), mild intestinal metaplasia (IM, n=22),severe IM (n=58), or dysplasia (DYS, n=31). Serum antiH. pylori IgG and IgA were double sampled and evaluated by enzyme-linked immunoadsordent assays. 35 clinical presentations were observed and their relationship with H.pylori infection was analyzed by the k-means cluster method.RESULTS: Both IgG and IgA levels in H. pylori positive patients were significantly higher than those negative for H.pylori(P＜0.001-0.01). The prevalence of H. pylori was highest in severe IM (84.5%), and lowest in mild CAG (51.3%)(P＜0.01). They were similar in severe CAG (68.2%), mild IN (72.7%), and DYS (67.7%). In H.pylori positive patients,the IgG levels in severe CAG were significantly higher than those in mild CAG (P＜0.01). In H.pylori negative patients,both IgG and IgA levels increased remarkably in severe IM,compared to those in mild IM (P＜0.01-0.05).H. pylori infection exhibited no association with patient′s gender (62.1% in males; 71.7 % in females) and age (r=0.0814, P=0.241).The diagnostic accuracy based on 35 clinical presentations was 65.7 %. It could be improved by 5.7% when only the assemblage of digestive symptoms were engaged, or by 8.6 % when the pathogenic factors, general status and grossoscopy were combined. The diagnostic accuracy could be decreased when only the general symptoms were engaged, or when the pathogenic factors were accompanied with some common digestive symptoms.CONCLUSION: H. pylori infection is a major risk factor for the process from atrophy, IM to DYS of gastric mucosa.Serum IgG and IgA are good indicators to evaluate this progress with a certain arrearage. Investigation on the effective assemblages of clinical presentations may provide a better understanding in the pathogenesis, diagnosis and treatment for H. pylori infection.展开更多
Motivation: It was found that high accuracy splicing-site recognitio n of rice (Oryza sativa L.) DNA sequence is especially difficult. We describe d a new method for the splicing-site recognition of rice DNA sequences...Motivation: It was found that high accuracy splicing-site recognitio n of rice (Oryza sativa L.) DNA sequence is especially difficult. We describe d a new method for the splicing-site recognition of rice DNA sequences. Method: Bas e d on the intron in eukaryotic organisms conforming to the principle of GT-AG,w e used support vector machines (SVM) to predict the splicing sites. By machine l earning,we built a model and used it to test the effect of the test data set of true and pseudo splicing sites. Results: The prediction accuracy we obtained wa s 87.53% at the true 5' end splicing site and 87.37% at the true 3' end splicing sites. The results suggested that the SVM approach could achieve higher accuracy than the previous approaches.展开更多
By scanning the whole genomic sequence of japonica rice using 45 known plant disease resistance (R) genes, we identified 2119 resistance gene homologs or ana- logs (RGAs) and verified that RGAs are not randomly dis- t...By scanning the whole genomic sequence of japonica rice using 45 known plant disease resistance (R) genes, we identified 2119 resistance gene homologs or ana- logs (RGAs) and verified that RGAs are not randomly dis- tributed but tend to cluster in the rice genome. The RGAs were classified into 21 families according to their functional domain based on Hidden Markov model (HMM). By com- paring the RGAs of japonica rice with the whole genomic sequence of indica rice, we found 702 RGAs allelic between the two subspecies and revealed that 671 (95.6%) of them have length difference (InDels) in their genomic sequences (including coding and non-coding regions) between the two subspecies, suggesting that RGAs are highly polymorphic between the two subspecies in rice. We also exploited 402 PCR-based and co-dominant candidate RGA markers by designing primer pairs on the regions flanking the InDels and validating them via e-PCR. The length differences of the candidate RGA markers between the two subspecies are from 1 to 742 bp, with an average of 10.26 bp. All related information of the RGAs is available from our web site (http://ibi.zju.edu.cn/RGAs/index.html).展开更多
A hybrid GA (genetic algorithm)-based clustering (HGACLUS) schema, combining merits of the Simulated Annealing, was described for finding an optimal or near-optimal set of medoids. This schema maximized the clustering...A hybrid GA (genetic algorithm)-based clustering (HGACLUS) schema, combining merits of the Simulated Annealing, was described for finding an optimal or near-optimal set of medoids. This schema maximized the clustering success by achieving internal cluster cohesion and external cluster isolation. The performance of HGACLUS and other methods was compared by using simulated data and open microarray gene-expression datasets. HGACLUS was generally found to be more accurate and robust than other methods discussed in this paper by the exact validation strategy and the explicit cluster number.展开更多
基金National Natural Science Foundation of China,No. 30200365
文摘AIM: To determine the prevalence of Helicobacter pylori (H. pylon) infection, the serum anti-H. pylori immunoglobulin G (IgG) and IgA antibody responses, and the value of clinical presentations in diagnosis of H. pylori infection in patients with gastric atrophy, intestinal metaplasia and dysplasia.METHODS: H. pylori infection was detected by histology in 209 patients with mild chronic atrophic gastritis (CAG, n=76),severe CAG (n=22), mild intestinal metaplasia (IM, n=22),severe IM (n=58), or dysplasia (DYS, n=31). Serum antiH. pylori IgG and IgA were double sampled and evaluated by enzyme-linked immunoadsordent assays. 35 clinical presentations were observed and their relationship with H.pylori infection was analyzed by the k-means cluster method.RESULTS: Both IgG and IgA levels in H. pylori positive patients were significantly higher than those negative for H.pylori(P＜0.001-0.01). The prevalence of H. pylori was highest in severe IM (84.5%), and lowest in mild CAG (51.3%)(P＜0.01). They were similar in severe CAG (68.2%), mild IN (72.7%), and DYS (67.7%). In H.pylori positive patients,the IgG levels in severe CAG were significantly higher than those in mild CAG (P＜0.01). In H.pylori negative patients,both IgG and IgA levels increased remarkably in severe IM,compared to those in mild IM (P＜0.01-0.05).H. pylori infection exhibited no association with patient′s gender (62.1% in males; 71.7 % in females) and age (r=0.0814, P=0.241).The diagnostic accuracy based on 35 clinical presentations was 65.7 %. It could be improved by 5.7% when only the assemblage of digestive symptoms were engaged, or by 8.6 % when the pathogenic factors, general status and grossoscopy were combined. The diagnostic accuracy could be decreased when only the general symptoms were engaged, or when the pathogenic factors were accompanied with some common digestive symptoms.CONCLUSION: H. pylori infection is a major risk factor for the process from atrophy, IM to DYS of gastric mucosa.Serum IgG and IgA are good indicators to evaluate this progress with a certain arrearage. Investigation on the effective assemblages of clinical presentations may provide a better understanding in the pathogenesis, diagnosis and treatment for H. pylori infection.
文摘Motivation: It was found that high accuracy splicing-site recognitio n of rice (Oryza sativa L.) DNA sequence is especially difficult. We describe d a new method for the splicing-site recognition of rice DNA sequences. Method: Bas e d on the intron in eukaryotic organisms conforming to the principle of GT-AG,w e used support vector machines (SVM) to predict the splicing sites. By machine l earning,we built a model and used it to test the effect of the test data set of true and pseudo splicing sites. Results: The prediction accuracy we obtained wa s 87.53% at the true 5' end splicing site and 87.37% at the true 3' end splicing sites. The results suggested that the SVM approach could achieve higher accuracy than the previous approaches.
基金the National High-Tech Research and Development Program of China(Grant Nos.2003AA207160&2002AA234031) the Natural Science Foundationof Fujian Province(Grant No.B9910011).
文摘By scanning the whole genomic sequence of japonica rice using 45 known plant disease resistance (R) genes, we identified 2119 resistance gene homologs or ana- logs (RGAs) and verified that RGAs are not randomly dis- tributed but tend to cluster in the rice genome. The RGAs were classified into 21 families according to their functional domain based on Hidden Markov model (HMM). By com- paring the RGAs of japonica rice with the whole genomic sequence of indica rice, we found 702 RGAs allelic between the two subspecies and revealed that 671 (95.6%) of them have length difference (InDels) in their genomic sequences (including coding and non-coding regions) between the two subspecies, suggesting that RGAs are highly polymorphic between the two subspecies in rice. We also exploited 402 PCR-based and co-dominant candidate RGA markers by designing primer pairs on the regions flanking the InDels and validating them via e-PCR. The length differences of the candidate RGA markers between the two subspecies are from 1 to 742 bp, with an average of 10.26 bp. All related information of the RGAs is available from our web site (http://ibi.zju.edu.cn/RGAs/index.html).
文摘A hybrid GA (genetic algorithm)-based clustering (HGACLUS) schema, combining merits of the Simulated Annealing, was described for finding an optimal or near-optimal set of medoids. This schema maximized the clustering success by achieving internal cluster cohesion and external cluster isolation. The performance of HGACLUS and other methods was compared by using simulated data and open microarray gene-expression datasets. HGACLUS was generally found to be more accurate and robust than other methods discussed in this paper by the exact validation strategy and the explicit cluster number.
