[Forecasting the burden of disease from diabetes under the scenarios of specific risk factors control in China in 2030]

Objective: To forecast mortality, age-standardized mortality, and probability of premature mortality from diabetes, and to simulate the impact of controlling risk factors by 2030 in China. Methods: We simulated the burden of disease from diabetes in six scenarios according to the development goals of risk factors control by the WHO and Chinese government. Based on the theory of comparative risk assessment and the estimates of the burden of disease for China from the Global Burden of Disease Study 2015, we used the proportional change model to project the number of deaths, age-standardized mortality, and probability of premature mortality from diabetes under different scenarios of risk factors control in 2030. Results: If the trends in exposures to risk factors from 1990 to 2015 continued. Mortality, age-standardized mortality, and probability of premature mortality from diabetes would increase to 32.57/100 000, 17.32/100 000, and 0.84% by 2030, respectively. During that time, mortality, age-standardized mortality and probability of premature mortality for males would all be higher than for females. If the goals of controlling risk factors were all achieved, the number of deaths from diabetes in 2030 would decrease by 62.10% compared to the predicted numbers based on the historical trends in exposure to risk factors, and the probability of premature mortality would drop to 0.29%. If only the exposure to a single risk factor were achieved by 2030, high fasting plasma glucose control would have the greatest impact on diabetes, resulting in a 56.00% reduction in deaths compared to the predicted numbers based on the historical trends, followed by high BMI (4.92%), smoking (0.65%), and low physical activity (0.53%). Conclusions: Risk factors control plays an important role in reducing the number of deaths, age-standardized mortality rate, and probability of premature mortality from diabetes. We suggest taking comprehensive measures to control relevant risk factors for certain populations and regions, to achieve the goal of reducing the burden of disease from diabetes as expected.

[Investigate of the etiology and prevention status of liver cirrhosis]

Objective: To investigate the etiology, prevention and treatment status, and their corresponding regional differences of the patients with liver cirrhosis in China, in order to provide scientific basis for the development of diagnosis and control strategies in China. Methods: Clinical data of patients diagnosed with liver cirrhosis for the first time through January 1, 2018 to December 31, 2020 from 50 hospitals in seven different regions of China were collected and analyzed retrospectively, and the difference of etiology, treatment, and their differences in various regions were analyzed. Results: A total of 11 861 cases with liver cirrhosis were included in the study. Thereinto, 5 093 cases (42.94%) were diagnosed as compensated cirrhosis, and 6 768 cases (57.06%) had decompensated cirrhosis. Notably, 8 439 cases (71.15%) were determined as chronic hepatitis B-caused cirrhosis, 1 337 cases (11.27%) were alcoholic liver disease, 963 cases (8.12%) were chronic hepatitis C, 698 cases (5.88%) were autoimmune liver disease, 367 cases (3.09%) were schistosomiasis, 177 cases (1.49%) were nonalcoholic fatty liver, and 743 cases (6.26%) of other types of liver disease. There were significant differences in the incidence of chronic hepatitis B, chronic hepatitis C, alcoholic liver disease, fatty liver, schistosomiasis liver disease, and autoimmune liver disease among the seven regions (P<0.001). Only 1 139 cases (9.60%) underwent endoscopic therapy, thereinto, 718 cases (6.05%) underwent surgical therapy, and 456 cases (3.84%) underwent interventional therapy treatment. In patients with compensated liver cirrhosis, 60 cases (0.51%) underwent non-selective β receptor blockers(NSBB), including 59 cases (0.50%) underwent propranolol and 1 case (0.01%) underwent carvedilol treatment. In patients with decompensated liver cirrhosis, 310 cases (2.61%) underwent NSBB treatment, including 303 cases (2.55%) underwent propranolol treatment and 7 cases (0.06%) underwent carvedilol treatment. Interestingly, there were significant differences in receiving endoscopic therapy, interventional therapy, NSBB therapy, splenectomy and other surgical treatments among the seven regions (P<0.001). Conclusion: Currently, chronic hepatitis B is the main cause (71.15%) of liver cirrhosis in several regions of China, and alcoholic liver disease has become the second cause (11.27%) of liver cirrhosis in China. The three-level prevention and control of cirrhosis in China should be further strengthened.

[Progress of research on evaluation indicators and standards about high-speed train comfort]

The rapid development of high-speed railway in China has proposed higher requests for the comfort level of high-speed trains. However, there is no internationally unified evaluation criterion for high-speed train comfort currently, which therefore substantially affects the comparability and standardization of research results for high-speed train comfort. This paper systematically reviews the research literature about evaluation indicators and standards related to high-speed train comfort, and finds that there is currently no unified definition, evaluation indicators, as well as evaluation criterion for high-speed train comfort. Most current evaluation criteria are based on a single indicator. Some indicators are simultaneously developed by different apartments and differ between each other, and there is no comprehensive indicator or criteria for high-speed train comfort, restricting the comparison of high-speed train comfort across regions. It is recommended that the administrative department of high-speed railroad in China should organize experts to establish a unified definition of high-speed train comfort, comprehensive evaluation indicators and relevant judgment criteria for high-speed train comfort, in face of the rapid development and globalization of high-speed trains.

[Prediction on the cardio-cerebrovascular death and probability of premature death caused by common risk factors in China in 2030]

Objective: Predictive models were used to evaluate the impact of common risk factors on the number of cardio-cerebrovascular deaths and the probability of premature death. Methods: Using the data for China estimated by the Global Burden of Disease study 2015 (GBD 2015), we calculated the population attribution fraction (PAF) of risk factors. The proportional change model was used to estimate the number of unattributable deaths by 2030, and to predict the number of deaths, mortality, standardized mortality and probability of premature death by 2030. Results: According to the natural change trend of risk factors from 1990 to 2015, the number of deaths and mortality would reach 6.12 million and 428.53/100 000 by 2030, with an increase of 59.92% and 52.87%. By 2030, the probability of premature death from cardio-cerebrovascular diseases among Chinese aged 30-70 years old would continue to decline, from 11.43% to 11.28% for men, and from 5.79% to 4.43% for women. If the goals of all included risk factors were reached by 2030, 2 289 200 cardio-cerebrovascular deaths would be avoided. If only the exposure to a single risk factor was achieved by 2030, blood pressure, total cholesterol, and fine particulate matter exposure were the three most important factors affecting cardio-cerebrovascular deaths, which would reduce 1 332 800, 609 100 and 306 800 deaths, respectively. Among the involved risk factors, the control of blood pressure would mostly decrease the number of deaths due to ischemic heart disease and hemorrhagic stroke, about 677 300 and 391 100 deaths, accordingly. Conclusion: The control of risk factors is of great significance in reducing deaths and probability of premature death due to cardio-cerebrovascular diseases. If the control targets of all risk factors could be achieved by 2030, the burden of cardio-cerebrovascular diseases would be reduced greatly.

[Progress on epidemiological characteristics and interventions of pedestrian distraction]

Pedestrian distraction is one of the important risk factors of road injury. This review summarized the epidemiological characteristics, influencing factors, safety implications, and the published intervention measures. The review found that: a) the prevalence of pedestrian distraction poses a serious threat to pedestrian safety, but most epidemiological studies on pedestrian distraction focus on mobile phone use, and the incidence of pedestrian distraction varied greatly across studies using various research methods and from different countries; b) demographic characteristics, social psychology, and environment are the three main influencing factors of pedestrian distraction; c) distraction differently affected physiology, cognition, motion control, efficiency and behavior of pedestrian's street-crossing to some degrees, threatening the safety of pedestrian; d) engineering interventions and education were the most common interventions to prevent pedestrian distraction currently, but the effectiveness of most measures was not assessed rigorously. In the future, multidisciplinary and systematic epidemiological studies are recommended to design interventions purposely and evaluate the effectiveness of interventions through rigorous designs, providing scientific evidence for reducing pedestrian distraction and improving road safety of pedestrians.

[Comparison of training models for master of public health between China and other countries]

With the accelerating globalization and the implementation of "Belt and Road" initiative proposed by our government, communication and exchanges between China and foreign countries have become more and more frequent than before, and much more international students have chosen to study in China's universities as candidates of master of public health (MPH). However, because China only launched the MPH program in recent years, with the training models being highly similar to the program of master of science in China but quite different from those of main international MPH programs, hindering China's MPH program to become an international one. This paper systematically evaluated existing training models of MPH programs both at home and abroad through literature review and identified major differences and deficiencies of China's MPH program compared to those from other countries: (1) requirement for medical background only; (2) comparatively longer period to complete the program; (3) incomplete curriculum; (4) overemphasizing scientific research competencies but somewhat neglecting practical abilities; and (5) limited career choices, and put forward some suggestions to improve the MPH program of China, including removing requirement for medical background only, shortening the period of MPH program, improving the curriculum of MPH program, and enhancing the training of practical abilities.

[Progress in research of burden of disease attributed to population ageing]

Objective: To summarize recent progress in research of burden of disease attributed to population ageing and provide reference for relevant research in the future. Methods: We conducted a systematic literature review of quantitative studies about the impact of population ageing on burden of disease published from 2009 to 2019 according to the inclusion and exclusion criteria through PubMed, Web of Science, Embase, Cochrane Library, Wangfang database and China National Knowledge Infrastructure (CNKI) databases and extracted basic information and key results of the searched literature. Results: A total of 65 studies were included in the analysis, in which 29 (44.6%) studies used death number or mortality rate as outcome measures, 43 (66.2%) studies focused on a single country, such as China, United Kingdom and United States, 39 (60.0%) studies quantified the impact of population ageing on single disease, such as diabetes, lung cancer and coronary heart disease, 44 (67.7%) studies used decomposition methods to quantify the impact of population ageing, and 10 (15.4%) studies evaluated the effect of interventions on alleviating the impact of population ageing. Most studies found that population ageing increased the burden of some diseases, such as cancer, cardiovascular disease and dementia, while a few studies reported that population ageing decreased the burden of some diseases, such as neonatal disease and malaria. Various decomposition methods were adopted in 65 included studies, but several common methods were sensitive to the preconditions that were assumed, the decomposition order of three factors (population size, age structure, and age-specific rate) and the choice of control group, resulting incomparable and unstable results. Conclusions: The published decomposition studies adopted various methods and only evaluated the impact of population ageing in very limited countries and for several diseases. Therefore, a systematic evaluation using robust decomposition method is very necessary to evaluate the impact of population aging on disease burden across countries and diseases.

[Using multiple measure to promote injury prevention and control rapidly in China]

This paper highlights the grand significance of enhancing injury prevention and control through multiple measures currently, briefly summarizes the achievements, challenges of Chinese injury prevention and control in the past few decades and the core contents of current issue, and puts forward some suggestions, combined with the current challenges, to promote the development of injury prevention and control in China.

[Progress in cohort studies related to injury]

Objective: To summarize the progress of injury cohort studies over the world. Methods: Relevant information of injury cohort publications published before December 2017 were retrieved from PubMed, WanFang and China National Knowledge Infrastructure (CNKI) databases, consisting of the starting year, category of injury, study population, sample size, countries, follow-up duration, main exposure variables, outcome variables and method of data collection, and statistical methods. Results: A total of 295 studies were included in the analysis. The overall number of injury cohort studies increased with a peak in 2000, and then decreased. The top three countries that most frequently published cohort studies were the United States (52), Sweden (46) and the United Kingdom (37). A total of 29 published injury cohorts were identified in China, about 3, 23 and 3 cohort studies from the mainland of China, Taiwan Province, and Hong Kong Specific Administrative Region, respectively. The majority of cohort studies involved a single injury cause (93.6%); the most common injury causes included suicide/self-harm (46.1%), falls (17.3%) and road traffic injuries (14.6%). For the published cohort studies, exposure variables and outcome events varied with injury causes, primarily being collected through data registration system, national survey data, questionnaire survey, telephone interviews, and other means. Conclusion: A number of injury cohorts have been established worldwide, and few in the mainland of China. The existed cohort studies could offer important references for the design of large-scale, multi-center and high-quality injury cohort in China in the future.

[Review on the progress regarding the intervention mapping protocol]

Along with the significant development on both theory and practice of health promotion programs, the application of behavioral and social science theories has also been advanced in the fields of design and evaluation regarding the intervention-related studies. Intervention mapping is a new planning protocol, efficiently used to develop, implement, and evaluate health promotion related intervention programs. In this article, we are briefly introducing the basic concepts, implementation steps, specific requirements, as well as reviewing the current progress in methodologies, application that are related to intervention mapping, so as to provide reference for health intervention research studies, domestically.

[Progress in research of mobile health intervention]

With the rapid development of mobile communication technology and the growing popularity of smartphones worldwide, mobile health has become an extension of e-Health and Tele-Health, and is of value in the research and practice of public health. In this paper, we systematically assessed research literature of mobile health' s application on disease prevention and control as well as health promotion. Based on the characteristics of current literature, this paper focused on the application of mobile health in maternal health promotion, chronic disease management, and communicable disease prevention and control to provide reference for the mobile health intervention research in China.

[Efficacy of the treatment of pharyngeal fistula through pectoralis major myocutaneous flap combined with fistula local skin inversion in 20 cases]

OBJECTIVE

To sum up the efficacy of treatment of pharyngeal fistula through pectoralis major myocutaneous flap combined with fistula local skin inversion in 20 patients.

METHODS

A retrospective analysis of the therapeutic efficacy in 20 cases of laryngeal and laryngopharyngeal cancer with postoperative pharyngeal fistula, to whom double-deck repairing were operated on through pectoralis major myocutaneous island flap combined with inversion of skin around fistula from January 2010 to December 2013.

RESULTS

20 patients were treated by improved pharyngeal fistula inverting suture of pectoralis major myocutaneous flap combined with the skin around the pharyngeal fistula. Flap around the fistula were sutured without tension formation. The pectoralis major myocutaneous flaps were sutured without tension formation covering the inner flanging flap wound. 20 patients were on a nasogastric liquid diet after operation for one week and received antibiotics to prevent infection. Then they all took liquid diet after one week, and had extubation safely later. Stitches were removed 10 more days later. All the twenty patients were recovered successfully, among them, 16 cases recovered in stage Ⅰ and left the hospital 10 days later, 4 cases recovered in stage Ⅱ and left the hospital 20 days later. All the 4 cases recovered in stage Ⅱ were treated with radiotherapy. Fistulas less than 1 cm occurred near their anastomotic stomas at 7 to 14 days after operation. They were healed well by dressing change and pressure dressing. No recurrence was observed during the six months follow-up.

CONCLUSIONS

Pectoralis major myocutaneous flap combined with fistula local skin inversion is a good way to repair pharyngeal fistula, and it is suitable for the laryngeal and laryngopharynx cancer patients with postoperative throat fistula in an internal diameter larger than 2 cm.

Leaderless genes in bacteria: clue to the evolution of translation initiation mechanisms in prokaryotes

Background

Shine-Dalgarno (SD) signal has long been viewed as the dominant translation initiation signal in prokaryotes. Recently, leaderless genes, which lack 5'-untranslated regions (5'-UTR) on their mRNAs, have been shown abundant in archaea. However, current large-scale in silico analyses on initiation mechanisms in bacteria are mainly based on the SD-led initiation way, other than the leaderless one. The study of leaderless genes in bacteria remains open, which causes uncertain understanding of translation initiation mechanisms for prokaryotes.

Results

Here, we study signals in translation initiation regions of all genes over 953 bacterial and 72 archaeal genomes, then make an effort to construct an evolutionary scenario in view of leaderless genes in bacteria. With an algorithm designed to identify multi-signal in upstream regions of genes for a genome, we classify all genes into SD-led, TA-led and atypical genes according to the category of the most probable signal in their upstream sequences. Particularly, occurrence of TA-like signals about 10 bp upstream to translation initiation site (TIS) in bacteria most probably means leaderless genes.

Conclusions

Our analysis reveals that leaderless genes are totally widespread, although not dominant, in a variety of bacteria. Especially for Actinobacteria and Deinococcus-Thermus, more than twenty percent of genes are leaderless. Analyzed in closely related bacterial genomes, our results imply that the change of translation initiation mechanisms, which happens between the genes deriving from a common ancestor, is linearly dependent on the phylogenetic relationship. Analysis on the macroevolution of leaderless genes further shows that the proportion of leaderless genes in bacteria has a decreasing trend in evolution.

Histone H4K20/H3K9 demethylase PHF8 regulates zebrafish brain and craniofacial development

X-linked mental retardation (XLMR) is a complex human disease that causes intellectual disability. Causal mutations have been found in approximately 90 X-linked genes; however, molecular and biological functions of many of these genetically defined XLMR genes remain unknown. PHF8 (PHD (plant homeo domain) finger protein 8) is a JmjC domain-containing protein and its mutations have been found in patients with XLMR and craniofacial deformities. Here we provide multiple lines of evidence establishing PHF8 as the first mono-methyl histone H4 lysine 20 (H4K20me1) demethylase, with additional activities towards histone H3K9me1 and me2. PHF8 is located around the transcription start sites (TSS) of approximately 7,000 RefSeq genes and in gene bodies and intergenic regions (non-TSS). PHF8 depletion resulted in upregulation of H4K20me1 and H3K9me1 at the TSS and H3K9me2 in the non-TSS sites, respectively, demonstrating differential substrate specificities at different target locations. PHF8 positively regulates gene expression, which is dependent on its H3K4me3-binding PHD and catalytic domains. Importantly, patient mutations significantly compromised PHF8 catalytic function. PHF8 regulates cell survival in the zebrafish brain and jaw development, thus providing a potentially relevant biological context for understanding the clinical symptoms associated with PHF8 patients. Lastly, genetic and molecular evidence supports a model whereby PHF8 regulates zebrafish neuronal cell survival and jaw development in part by directly regulating the expression of the homeodomain transcription factor MSX1/MSXB, which functions downstream of multiple signalling and developmental pathways. Our findings indicate that an imbalance of histone methylation dynamics has a critical role in XLMR.

Genome reannotation of Escherichia coli CFT073 with new insights into virulence

Background

As one of human pathogens, the genome of Uropathogenic Escherichia coli strain CFT073 was sequenced and published in 2002, which was significant in pathogenetic bacterial genomics research. However, the current RefSeq annotation of this pathogen is now outdated to some degree, due to missing or misannotation of some essential genes associated with its virulence. We carried out a systematic reannotation by combining automated annotation tools with manual efforts to provide a comprehensive understanding of virulence for the CFT073 genome.

Results

The reannotation excluded 608 coding sequences from the RefSeq annotation. Meanwhile, a total of 299 coding sequences were newly added, about one third of them are found in genomic island (GI) regions while more than one fifth of them are located in virulence related regions pathogenicity islands (PAIs). Furthermore, there are totally 341 genes were relocated with their translational initiation sites (TISs), which resulted in a high quality of gene start annotation. In addition, 94 pseudogenes annotated in RefSeq were thoroughly inspected and updated. The number of miscellaneous genes (sRNAs) has been updated from 6 in RefSeq to 46 in the reannotation. Based on the adjustment in the reannotation, subsequent analysis were conducted by both general and case studies on new virulence factors or new virulence-associated genes that are crucial during the urinary tract infections (UTIs) process, including invasion, colonization, nutrition uptaking and population density control. Furthermore, miscellaneous RNAs collected in the reannotation are believed to contribute to the virulence of strain CFT073. The reannotation including the nucleotide data, the original RefSeq annotation, and all reannotated results is freely available via http://mech.ctb.pku.edu.cn/CFT073/.

Conclusion

As a result, the reannotation presents a more comprehensive picture of mechanisms of uropathogenicity of UPEC strain CFT073. The new genes change the view of its uropathogenicity in many respects, particularly by new genes in GI regions and new virulence-associated factors. The reannotation thus functions as an important source by providing new information about genomic structure and organization, and gene function. Moreover, we expect that the detailed analysis will facilitate the studies for exploration of novel virulence mechanisms and help guide experimental design.

MetaTISA: Metagenomic Translation Initiation Site Annotator for improving gene start prediction

SUMMARY

We proposed a tool named MetaTISA with an aim to improve TIS prediction of current gene-finders for metagenomes. The method employs a two-step strategy to predict translation initiation sites (TISs) by first clustering metagenomic fragments into phylogenetic groups and then predicting TISs independently for each group in an unsupervised manner. As evaluated on experimentally verified TISs, MetaTISA greatly improves the accuracies of TIS prediction of current gene-finders.

AVAILABILITY

The C++ source code is freely available under the GNU GPL license via http://mech.ctb.pku.edu.cn/MetaTISA/.

Prediction of translation initiation site for microbial genomes with TriTISA

We report a new and simple method, TriTISA, for accurate prediction of translation initiation site (TIS) of microbial genomes. TriTISA classifies all candidate TISs into three categories based on evolutionary properties, and characterizes them in terms of Markov models. Then, it employs a Bayesian methodology for the selection of true TIS with a non-supervised, iterative procedure. Assessment on experimentally verified TIS data shows that TriTISA is overall better than all other methods of the state-of-the-art for microbial genome TIS prediction. In particular, TriTISA is shown to have a robust accuracy independent of the quality of initial annotation.

AVAILABILITY

The C++ source code is freely available under the GNU GPL license via http://mech.ctb.pku.edu.cn/protisa/TriTISA.

Computational evaluation of TIS annotation for prokaryotic genomes

Background

Accurate annotation of translation initiation sites (TISs) is essential for understanding the translation initiation mechanism. However, the reliability of TIS annotation in widely used databases such as RefSeq is uncertain due to the lack of experimental benchmarks.

Results

Based on a homogeneity assumption that gene translation-related signals are uniformly distributed across a genome, we have established a computational method for a large-scale quantitative assessment of the reliability of TIS annotations for any prokaryotic genome. The method consists of modeling a positional weight matrix (PWM) of aligned sequences around predicted TISs in terms of a linear combination of three elementary PWMs, one for true TIS and the two others for false TISs. The three elementary PWMs are obtained using a reference set with highly reliable TIS predictions. A generalized least square estimator determines the weighting of the true TIS in the observed PWM, from which the accuracy of the prediction is derived. The validity of the method and the extent of the limitation of the assumptions are explicitly addressed by testing on experimentally verified TISs with variable accuracy of the reference sets. The method is applied to estimate the accuracy of TIS annotations that are provided on public databases such as RefSeq and ProTISA and by programs such as EasyGene, GeneMarkS, Glimmer 3 and TiCo. It is shown that RefSeq's TIS prediction is significantly less accurate than two recent predictors, Tico and ProTISA. With convincing proofs, we show two general preferential biases in the RefSeq annotation, i.e. over-annotating the longest open reading frame (LORF) and under-annotating ATG start codon. Finally, we have established a new TIS database, SupTISA, based on the best prediction of all the predictors; SupTISA has achieved an average accuracy of 92% over all 532 complete genomes.

Conclusion

Large-scale computational evaluation of TIS annotation has been achieved. A new TIS database much better than RefSeq has been constructed, and it provides a valuable resource for further TIS studies.

ProTISA: a comprehensive resource for translation initiation site annotation in prokaryotic genomes

Correct annotation of translation initiation site (TIS) is essential for both experiments and bioinformatics studies of prokaryotic translation initiation mechanism as well as understanding of gene regulation and gene structure. Here we describe a comprehensive database ProTISA, which collects TIS confirmed through a variety of available evidences for prokaryotic genomes, including Swiss-Prot experiments record, literature, conserved domain hits and sequence alignment between orthologous genes. Moreover, by combining the predictions from our recently developed TIS post-processor, ProTISA provides a refined annotation for the public database RefSeq. Furthermore, the database annotates the potential regulatory signals associated with translation initiation at the TIS upstream region. As of July 2007, ProTISA includes 440 microbial genomes with more than 390 000 confirmed TISs. The database is available at http://mech.ctb.pku.edu.cn/protisa

Study of carbon nanotube modified biosensor for monitoring total cholesterol in blood

A carbon nanotube modified biosensor for monitoring total cholesterol in blood was studied. This sensor consists of a carbon working electrode and a reference electrode screen-printed on a polycarbonate substrate. Cholesterol esterase, cholesterol oxidase, peroxidase and potassium ferrocyanide were immobilized on the screen-printed carbon electrodes. Multi-walled carbon nanotubes (MWCN) were added to prompt electron transfer. Experimental results show that the carbon nanotube modified biosensor offers a reliable calibration profile and stable electrochemical properties.

Accuracy improvement for identifying translation initiation sites in microbial genomes

MOTIVATION

At present the computational gene identification methods in microbial genomes have a high prediction accuracy of verified translation termination site (3' end), but a much lower accuracy of the translation initiation site (TIS, 5' end). The latter is important to the analysis and the understanding of the putative protein of a gene and the regulatory machinery of the translation. Improving the accuracy of prediction of TIS is one of the remaining open problems.

RESULTS

In this paper, we develop a four-component statistical model to describe the TIS of prokaryotic genes. The model incorporates several features with biological meanings, including the correlation between translation termination site and TIS of genes, the sequence content around the start codon; the sequence content of the consensus signal related to ribosomal binding sites (RBSs), and the correlation between TIS and the upstream consensus signal. An entirely non-supervised training system is constructed, which takes as input a set of annotated coding open reading frames (ORFs) by any gene finder, and gives as output a set of organism-specific parameters (without any prior knowledge or empirical constants and formulas). The novel algorithm is tested on a set of reliable datasets of genes from Escherichia coli and Bacillus subtillis. MED-Start may correctly predict 95.4% of the start sites of 195 experimentally confirmed E.coli genes, 96.6% of 58 reliable B.subtillis genes. Moreover, the test results indicate that the algorithm gives higher accuracy for more reliable datasets, and is robust to the variation of gene length. MED-Start may be used as a postprocessor for a gene finder. After processing by our program, the improvement of gene start prediction of gene finder system is remarkable, e.g. the accuracy of TIS predicted by MED 1.0 increases from 61.7 to 91.5% for 854 E.coli verified genes, while that by GLIMMER 2.02 increases from 63.2 to 92.0% for the same dataset. These results show that our algorithm is one of the most accurate methods to identify TIS of prokaryotic genomes.

AVAILABILITY

The program MED-Start can be accessed through the website of CTB at Peking University: http://ctb.pku.edu.cn/main/SheGroup/MED_Start.htm.

Some efficient strategies for improving the eigenstructure method in synthesis of feedback neural networks

Two efficient strategies are proposed for improving the eigenstructure method from the best approximation projector point of view. Interpreted as two complementary best approximation projectors, the method is reformulated in a much more simplified form. We develop a new synthesis procedure through constructing the related best approximation projectors by using a simple recursive formula, which improves on the existing eigenstructure method not only in the significant reduction of the computational complexity but also in the incorporation of the learning capability comparable to the outer product method. The networks designed by the present procedure outperform those designed by some other known methods. We also propose a new forgetting algorithm for deleting any specific existing memories in a synthesized network. The algorithm performs efficiently and reliably, which particularly eliminates the overforgetting drawback of the Yen-Michel algorithm (1991, 1992). The feasibility and effectiveness of the algorithm are supported by theoretical analysis and computer simulations.

Compact, magneto-optic Q-switched, neodymium-doped bismuth germinate crystal (Nd:BGO) laser pumped by a laser diode

The magneto-optic Q-switched operation of a neodymium-doped bismuth germinate crystal (Nd:BGO) laser that is end pumped by a cw 500-mW laser diode is reported. The crystal is a new host for Nd lasers. Here it acts as a magneto-optic modulator as well as a laser medium. A pulse energy of 2 µJ with a FWHM of 100 ns has been obtained. The device operates at a repetition rate of 1 kHz, and the fluctuation of the shot-to-shot intensity is less than ±1%.