Splicing-site recognition of rice (Oryza sativa L.)DNA sequences by support vector machines

Motivation: It was found that high accuracy splicing-site recognition of rice (Oryza sativa L.) DNA sequence is especially difficult. We described a new method for the splicing-site recognition of rice DNA sequences. Method: Based on the intron in eukaryotic organisms conforming to the principle of GT-AG, we used support vector machines (SVM) to predict the splicing sites. By machine learning, 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 was 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.     

Splicing-site recognition of rice (Oryza sativa L.)DNA sequences

INTRODUCTIONCorrectlypinpointingsplicing sitesingenomicDNAsequencesisnotaneasytask ,whichisofgreatimportancetothegenomeannotationandgenefinding .Intronsaregenerallydividedinto3classes,namelycalssI,classIIandcommonnu cleuspre mRNA .IntronofclassIandIIcango…     

The estimation of the IRT reliability coefficient and its lower and upper bounds, with comparisons to CTT reliability statistics

The primary purpose of this study is to investigate the mathematical characteristics of the test reliability coefficient ρ _XX′ as a function of item response theory (IRT) parameters and present the lower and upper bounds of the coefficient. Another purpose is to examine relative performances of the IRT reliability statistics and two classical test theory (CTT) reliability statistics (Cronbach’s alpha and Feldt–Gilmer congeneric coefficients) under various testing conditions that result from manipulating large-scale real data. For the first purpose, two alternative ways of exactly quantifying ρ _XX′ are compared in terms of computational efficiency and statistical usefulness. In addition, the lower and upper bounds for ρ _XX′ are presented in line with the assumptions of essential tau-equivalence and congeneric similarity, respectively. Empirical studies conducted for the second purpose showed across all testing conditions that (1) the IRT reliability coefficient was higher than the CTT reliability statistics; (2) the IRT reliability coefficient was closer to the Feldt–Gilmer coefficient than to the Cronbach’s alpha coefficient; and (3) the alpha coefficient was close to the lower bound of IRT reliability. Some advantages of the IRT approach to estimating test-score reliability over the CTT approaches are discussed in the end.     

<Emphasis Type="Italic">Agrobacterium</Emphasis>-mediated transformation of herbicide resistance in creeping bentgrass and colonial bentgrass

Embryogenic calli were induced from the seeds of creeping bentgrass (Agrostis palustris Huds.) cv. Regent and colonial bentgrass (Agrostis Tenuis Sibth. Fl. Oxen.) cv. Tiger. The embryogenic calli were precultured on fresh medium for 4–7 days and then co-cultivated withAgrobacterium tumefaciens, LBA4404. which contains plasmid vector-pSBGM harboring bar coding region, synthetic green fluorescent protein (sGFP) coding region and matrix attachment region (MAR). After 3 days of co-cultivation, the calli were washed thoroughly and transferred to MS medium containing 2 mg/L of 2, 4-D, 12–15 mg/L phosphinothricin (PPT) and 250 mg/L of cefotaxime. After 2–3 months of selection, the actively growing calli of ‘Regent’ and ‘Tiger’ were transferred to MS medium with 12–15 mg/L PPT and 250 mg/L cefotazime for regeneration. The putative transformants were maintained on MS medium with 3 mg/L PPT for long period but control died within 1 month. After establishing in greenhouse, the transformants also showed strong resistance to 0.4% of herbicide Basta but control plants died within 2 weeks. Under confocal microscope, both young leaves and roots showed significant GFP expression. PCR analysis revealed the presence of a DNA fragment of GFP gene at the expected size (380 bp) in the transformants and its absence in a randomly selected control plant.     

Improved production of spiramycin by mutant<Emphasis Type="Italic">Streptomyces ambofaciens</Emphasis>

Strain improvement and medium optimization to increase the productivity of spiramycin were carried out. Of oil tolerant mutant strains screened, one mutant,Streptomyces ambofaciens XC 2–37, produced 9% more spiramycin than the parent strainS. ambofaciens XC 1–29. The effects of soybean oil and propyl alcohol on spiramycin production withS. ambofaciens XC 2–37 were studied. The potency ofS. ambofaciens XC 2–37 was improved by 61.8% with addition of 2% soybean oil in the fermentation medium and 0.4% propyl alcohol at 24 hours after incubation. The suitable time for feeding propyl alcohol is at 24 hours after incubation in flask fermentation and at 20 hours after incubation in fermentor fermentation. The new process withS. ambofaciens XC 2–37 was scaled up for industrial scale production of spiramycin in a 60 m³ fermentor in Xinchang Pharmaceutical Factory, Zhejiang Medicine Company, Ltd., China, and the potency and productivity of fermentation were improved by 42.9%.     

Characterization of enhancer trap and gene trap harboring<Emphasis Type="Italic">Ac/Ds</Emphasis> transposon in transgenic rice

Insertion mutagenesis has become one of the most popular methods for gene functions analysis. Here we report a two-elementAc/Ds transposon system containing enhancer trap and gene trap for gene tagging in rice. The excision ofDs element was examined by PCR amplification. The excision frequency ofDs element varied from 0% to 40% among 20 F₂ populations derived from 11 differentDs parents. Southern blot analysis revealed that more than 70% of excisedDs elements reinserted into rice genome and above 70% of the reinsertedDs elements were located at different positions of the chromosome in rice. The result of histochemical GUS analysis indicated that 28% of enhancer trap and 22% of gene trap tagging plants displayed GUS activity in leaves, roots, flowers or seeds. The GUS positive lines will be useful for identifying gene function in rice. Project supported by the Hi-Tech Research and Development Program (863) of China (No. 2002AA2Z1003)     

Lovastatin production by Aspergillus terreus in solid-state fermentation

Lovastatin production by Aspergillus terreus ATCC 20542 in solid-state fermentation (SSF) was studied. Various substrates were used to evaluate the ability of A. terreus to produce lovastatin. The results showed that either rice or wheat bran was suitable substrate for lovastatin production in SSF. The maximum yield of lovastatin (2.9 mg/g dry substrate) using rice as substrate was achieved after incubating for 11 d at the following optimized process parameters: 50%～60% initial moisture content,pH 5.5,incubation temperature 28 °C.     

Statistical estimates of learners�� judgments about knowledge in calibration of achievement

In theoretical models of self-regulated learning, calibration is one important component in successful learning. Two issues of calibration are explored. First, Nelson (1987) suggested the G (gamma) coefficient is the most appropriate measure of calibration (judgment accuracy) and rejected signal detection theory’s d′ statistic because data commonly challenge distributional assumptions. We empirically examined this issue, comparing G and d′. Second, we examined whether a learner’s calibration varies across three domains of knowledge: general, word, and mathematics. A sample of 266 university students volunteered to participate in the study. Participants were selected from various undergraduate and graduate courses. Participants first answered demographic items. Then they completed three knowledge tests (general, word, and mathematics) and judged correctness for each answer provided. Order of domains was randomly counterbalanced among participants. Results show that d′ is a valid measure of calibration, that assumptions about underlying distributions can be tested, and that preliminary evidence suggests that d′ may be a superior measure of accuracy compared to G. Finally, calibration varied by domain.     

Distribution of<Emphasis Type="Italic">H. pylori</Emphasis> antigens in gastric mucosa and its significance

Objective: To investigate the distribution ofH. pylori antigens in the gastric mucosa in patients withH. pylori infection, and the relationship between the distribution and gastric cancer. Methods: Of 112 patients confirmed by pathological study to have chronic superficial gastritis, precancerous changes (chronic atrophic gastritis, intestinal metaplasia or atypical hyperplasia) and gastric cancer, 28 wereH. pylori negative and 84 wereH. pylori positive.H. pylori antigens in the gastric mucosa were detected by immunohistochemistry. Results: TheH. pylori positive group, comprised 12 of 22 (50.0%) in the chronic superficial gastritis group, 22 of 25 (88.0%) in the precancerous changes group and 13 of 35 (37.1%) in the gastric cancer group. The positive rates ofH. pylori antigens in the cytoplasm progressively increased, respectively at 0.0% (0/12), 63.6% (14/22) and 84.6% (11/13) for the same groups (χ ²=19.76,P=0.000);H. pylori antigens were located in the mucus layer and above the neck of the mucosal gland in 9 of 12 (75.0%) cases with chronic superficial gastritis, at the neck of the mucosal gland and the isthmus in 12 of 22 (54.5%) cases with precancerous changes, below the isthmus in 9 of 13 (69.2%) cases with gastric cancer (χ ²=25.30,P=0.000). In theH. pylori negative group, noH. pylori antigen was observed. Conclusion: With the progression of chronic superficial gastritis→precancerous changes→gastric cancer,H. pylori antigens progressively migrated from the outer part to the inner part of the cell, and from the superficial to the deep gastric mucosa.     

Oogenesis in summer females of the rice water weevil, Lissorhoptrus oryzophilus Kuschel （Coleoptera： Curculionidae）, in southern Zhejiang, China

The rice water weevil, Lissorhoptrus oryzophilus Kuschel, has two generations in southern Zhejiang, China. To determine oogenesis in first-generation females （summer females） and its relations to temperature, females were collected from a rice field in early and mid-July and reared on young rice plants at 28, 31 and 34 ℃ in the laboratory. Percentage of females having oocytes, number of oocytes of different stages （stage-Ⅰ, from early previtellogenesis to middle vitellogenesis; stage-Ⅱ, late vitellogenesis; and matute-oocyte stage）, and length of ovarioles were determined every 10 d of feeding. At each temperature, oogenesis took place in over 40% of females after 20-40 d of feeding, but only 0.0-3.3 stage-Ⅰ, 0.0-0.8 stage-Ⅱ and 0.0-1.1 mature oocytes were observed at each observation date. Temperature had significant effect on number of stage-Ⅰ oocytes but not on number of stage-Ⅱ and mature oocytes in early July females; temperature had no significant effect on number of oocytes of either stage in mid-July females. Conclusively, in southern Zhejiang, summer L. oryzophilus females have great potential to become reproductive on rice, but their oogenesis activity is very low, with the overall procedures little affected by temperature.     

On Turán type inequality with doubling weights andA * weights

LetH _n be the set of real algebraic polynomials of degreen, whose zeros all lie in the interval [−1,1]. The well known Turán type inequalities tell us that forf(x)∈H _n , it holds ‖f′‖≥C√n‖f‖. This note deals with the weighted Turán type inequalities with the weights having inner singularities underL ^p norm for 0<p≤∞. Our results essentially extend the result of Wang and Zhou (2002), and the method used in this paper is simpler and more direct than that of Wang and Zhou (2002). The results and methods have their own values in approximation theory and computation.     

A novel long-chain acyl-derivative of epigallocatechin-3-O-gallate prepared and purified from green tea polyphenols

Lipophilic tea polyphenols (LTP) were prepared by catalytic esterification of green tea polyphenols (GTP) with hexadecanoyl chloride. A novel long-chain acyl-derivative of epigallocatechin-3-o-gallate (EGCG) was first isolated from purification of LTP by high-speed countercurrent chromatography (HSCCC) using a solvent system composed of n-hexane-ethyl acetate-methanol-water (1∶1∶1∶1, v/v). The molecular structure of the acyl-derivative, Epigallocatechin-3-O-gallate-4′-O-hexadecanate, was elucidated by means of elemental analysis, IR,¹H-NMR and MS spectra. Project (No. 200010) supported by Zhejiang Provincial Natural Science Foundation, China     

Study of serum<Emphasis Type="Italic">Helicobacter pylori</Emphasis> soluble antigen

Objective: to explore a new serological method for detectingHelicobacter pylori (H. pylori) infection. Methods: Serum soluble antigen ofH. pylori was detected by using avidin-biotin ELISA technique to evaluate the status ofH. pylori infection and for comparison with rapid urease test (RUT), histologic examination and serology. Results: The sensitivity, specificity, positive predictive value and negative predictive value were 77.46%, 91.07%, 91.67% and 76.12%, respectively. The prevalence rate of serumH. pylori soluble antigen in 138 patients undergoing endoscopy was similar to the rate obtained by¹⁴C-UBT methods (P>0.05). Conclusions: The detection of serumH. pylori soluble antigen(HpSAg) could be used as a new serological method which is accurate, and convenient, not affected by the memorizing reaction of serum antibody; is more sensitive, more specific and suitable for clinical diagnosis, and evaluation of eradication and for follow-up ofH. pylori as well as for detection in children and pregnant women. Project supported by Zhejiang Provincial Health Bureau (No. 2000A118), China     

Diversity of Gram negative bacteria antagonistic against major pathogens of rice from rice seed in the tropic environment

With the use of a seed washing technique, more than 4000 Gram negative bacteria were isolated by two improved isolation methods from 446 batches of 1 kg rice seed samples obtained from 22 provinces in the Philippines. They were initially characterized on the basis of colony morphology and results of biochemical and pathogenicity tests. Six hundred and fifty-two strains were further identified by Biolog, from which 133 were selected for fatty acid methyl ester (FAME) analysis together with 80 standard reference! strains. Six-teen species or types ofPseudomonas and 17 genera of non-pseudomonads were identified, more than one third of which have not been recorded in rice. The most predominant species observed wereP. putida andP. fulva. About 17% of the strains ofPseudomonas and 2% of the non-pseudomonads were antagonistic to one or more fungal or bacterial pathogens of rice. Rice seed is an important source of biological control agents. Project supported by Belgium government and Asia Development Bank. Part of the experiments conducted at the University of Gent, Belgium and IRRI during 1997–2000.     

An Empirical Assessment of Cooperative Groups in Large, Time-compressed, Introductory Courses

We measured student knowledge and motivation at the beginning and end of a three-week general psychology course. Two large lecture sections (N = 215 and N = 154) were compared; one used a cooperative learning process, and one did not. Student knowledge significantly improved in both sections, but there was no additional benefit derived from using cooperative learning. Interestingly, student motivation significantly decreased in the cooperative learning section. With recognition of the study’s limitations, we conclude that cooperative learning has limited efficacy in large enrollment, compressed courses. Dawn Vreven is an Assistant Professor of Psychology at the University of Wisconsin Oshkosh. She received her Ph.D. from Brown University. Her research interests include visual perception and cognition. Susan McFadden is a Professor of Psychology at the University of Wisconsin Oshkosh. She received her Ph.D. from Drew University. She co-edits the “Teaching Tips” column for the Association for Psychological Science’s Observer and has published a number of articles on teaching and learning. This work was supported by the University of Wisconsin Oshkosh’s Scholarship of Teaching and Learning Program.     

Effect of mineral admixtures and repeated loading on chloride migration through concrete

The effect of fly ash (FA) and ground granulated blast furnace slag (GGBFS) on chloride migration through concrete subjected to repeated loading was examined. Portland cement was replaced by three percentages (20%, 30%, and 40%) of mineral admixtures. Five repeated loadings were applied to concrete specimens using a WHY series fully automatic testing machine. The maximum loadings were 40% and 80% of the axial cylinder compressive strength (f′c). Chloride migration through concretes was evaluated using the rapid chloride migration test and the chloride concentration in the anode chamber was measured. The results showed that the replacement percentages of mineral admixtures, the curing time and repeated loading had a significant effect on chloride migration through concrete. The transport number of chloride through concrete cured for 28 d increased with increasing FA replacement and markedly decreased with extension of the curing time. 20% and 30% GGBFS replacement decreased the transport number of chloride through concrete, but 40% GGBFS replacement increased the transport number. Five repeated loadings at 40% or 80% f′c increased the transport number of chloride for all mixes.     

基于SVM的智能统分自学习系统设计与实现

为了解决传统纸质试卷人工统分过程存在工作量大、错误率高、统分效率低等问题,设计开发一款基于SVM的智能统分自学习系统。该系统由前端用户界面、后台手写分数识别子系统和自学习子系统构成。系统采用C#编程语言和Microsoft Visual Studio软件设计前端用户界面;使用Matlab作为系统运算后台,并构建SVM多分类器识别手写分数;使用C#编程语言设置定时器,在系统空闲时间定时启动Matlab执行自学习程序。经过MNIST数据集的训练和测试,SVM多分类器的测试精度达到97.74%。完成系统设计开发后,使用试卷统分栏图片测试系统。测试结果表明,该系统可以有效实现智能识别、统分栏内手写分数汇总以及自学习功能,并将运行结果清晰准确地显示在前端用户界面上。     

The Contribution of Naming Speed to the Simple View of Reading

The purpose of this study was to investigate whether naming speed makes a contribution to the prediction of reading comprehension, after taking into account the product of word decoding and listening comprehension (i.e., the Simple View of Reading; [Gough, P.B. & Tunmer, W.E. (1986). Remedial and Special Education 7, 6–10]), and phonological awareness. In grade 3, word decoding was measured with the Woodcock [(1998). Woodcock Reading Mastery Tests – Revised. Circle Pines, MN: American Guidance Services]. Word Identification and Word Attack subtests, listening comprehension with the Woodcock (1991) [Woodcock Language Proficiency Battery – Revised. Chicago: Riverside Publishing Company] test of Listening Comprehension, naming speed with a picture naming task, and 4 measures assessed phonological awareness. Reading comprehension was assessed in grades 3, 4, and 5 with the Woodcock (1998) Passage Comprehension subtest and in grade 5 with the Gates–MacGinitie reading test. The Simple View was evaluated twice: first, with a pseudoword measure for decoding (Grapheme–Phoneme-conversion product) and, second, with a word identification measure for decoding (word recognition product). Hierarchical regression and commonality analyses indicated that the decoding and listening comprehension products accounted for considerable variance in reading comprehension. Naming speed had a small but significant effect after accounting for the Grapheme–Phoneme-conversion product (2–3%), but little effect after accounting for the word-recognition product (0–2%). Subgroup analyses indicated that naming speed had its primary effect for less able readers. Commonality analyses supported the interpretation that naming speed contributes after the Grapheme–Phoneme-conversion product but not after the word recognition product because naming speed has already had its effect upon word recognition. These results indicate that it is important how the Simple View decoding term is defined, and that the Simple View may be incomplete, especially for less able readers.     

Association between infection of different strains of <Emphasis Type="Italic">Porphyromonas gingivalis</Emphasis> and <Emphasis Type="Italic">Actinobacillus actinomycetemcomitans</Emphasis> in subgingival plaque and clinical parameters in chronic periodontitis

Objective： The aim of this study was to investigate subgingival infection frequencies ofPorphyromonas gingivalis and Actinobacillus actinomycetemcomitans strains with genetic variation in Chinese chronic periodontitis （CP） patients and to evaluate its correlation with clinical parameters. Methods： Two multiplex polymerase chain reaction （PCR） assays were developed to detect the 16SrDNA, collagenase （prtC） and fimbria （fimA） genes of P. gingivalis and the 16SrDNA, leukotoxin （lktA） and fimbria-associated protein （fap） genes ofA. actinomycetemcomitans in 60 sulcus samples from 30 periodontal healthy subjects and in 122 subgingival plaque samples from 61 patients with CP. The PCR products were further T-A cloned and sent for nucleotide sequence analysis. Results： The 16SrDNA,prtC andfimA genes ofP. gingivalis were detected in 92.6%, 85.2% and 80.3% of the subgingival plaque samples respectively, while the 16SrDNA, lktA andfap genes ofA. actinomycetemcomitans were in 84.4%, 75.4% and 50.0% respectively. Nucleotide sequence analysis showed 98.62%-100% homology of the PCR products in these genes with the reported sequences. P. gingivalis strains with prtC＋/fimA＋ and A. actinomycetemcomitans with lktA＋ were predominant in deep pockets （〉6 mm） or in sites with attachment loss 〉5 mm than in shallow pockets （3-4 mm） or in sites with attachment loss 〈2 mm （P〈0.05）. P. gingivalis strains withprtC＋/fimA＋ also showed higher frequency in gingival index （GI）=3 than in GI=1 group （P〈0.05）. Conclusion： Infection ofP. gingivalis with prtC＋/fimA＋ and A. actinomycetemcomitans with lktA＋ correlates with periodontal destruction of CP in Chinese. Nonetheless P. gingivalis fim4, prtC genes and A. actinomycetem- comitans lktA gene are closely associated with periodontal destruction, while A. actinomycetemcomitansfap gene is not.     

A CHASE domain containing protein kinaseOsCRL4, represents a newAtCRE1-like gene family in rice

AtCRE1 is known to be a cytokinin receptor inArabidopsis. TheAtCRE1 protein contains CHASE domain at the N-terminal part, followed by a transmitter (histidine kinase) domain and two receiver domains. The N-terminal CHASE domain ofAtCRE1 contains putative recognition sites for cytokinin. Five CHASE domains containing proteins were found in rice,osCRL1a,OsCRL1b,OsCRL2,OsCRL3, andOsCRL4.OsCRL1a,OsCRL1b,OsCRL2 andOsCRL3 contain the four domains existing inCRE1, whereasOsCRL4 only contains the CHASE domain and a putative Ser/Thr protein kinase domain. The authors cloned the encoding geneOsCRL4 and found that it represents a new member of the cytokinin receptor protein in rice. Project supported by the National Natural Science Foundation of China