An ensemble method for predicting subnuclear localizations from primary protein structures

Background Predicting protein subnuclear localization is a challenging problem. Some previous works based on non-sequence information including Gene Ontology annotations and kernel fusion have respective limitations. The aim of this work is twofold: one is to propose a novel individual feature extraction method; another is to develop an ensemble method to improve prediction performance using comprehensive information represented in the form of high dimensional feature vector obtained by 11 feature extraction methods. Methodology/Principal Findings A novel two-stage multiclass support vector machine is proposed to predict protein subnuclear localizations. It only considers those feature extraction methods based on amino acid classifications and physicochemical properties. In order to speed up our system, an automatic search method for the kernel parameter is used. The prediction performance of our method is evaluated on four datasets: Lei dataset, multi-localization dataset, SNL9 dataset and a new independent dataset. The overall accuracy of prediction for 6 localizations on Lei dataset is 75.2% and that for 9 localizations on SNL9 dataset is 72.1% in the leave-one-out cross validation, 71.7% for the multi-localization dataset and 69.8% for the new independent dataset, respectively. Comparisons with those existing methods show that our method performs better for both single-localization and multi-localization proteins and achieves more balanced sensitivities and specificities on large-size and small-size subcellular localizations. The overall accuracy improvements are 4.0% and 4.7% for single-localization proteins and 6.5% for multi-localization proteins. The reliability and stability of our classification model are further confirmed by permutation analysis. Conclusions It can be concluded that our method is effective and valuable for predicting protein subnuclear localizations. A web server has been designed to implement the proposed method. It is freely available at http://bioinformatics.awowshop.com/snlpr​ed_page.php.

Language affects length of stay in emergency departments in Queensland public hospitals

BACKGROUND: A long length of stay (LOS) in the emergency department (ED) associated with overcrowding has been found to adversely affect the quality of ED care. The objective of this study is to determine whether patients who speak a language other than English at home have a longer LOS in EDs compared to those whose speak only English at home. METHODS: A secondary data analysis of a Queensland state-wide hospital EDs dataset (Emergency Department Information System) was conducted for the period, 1 January 2008 to 31 December 2010. RESULTS: The interpreter requirement was the highest among Vietnamese speakers (23.1%) followed by Chinese (19.8%) and Arabic speakers (18.7%). There were significant differences in the distributions of the departure statuses among the language groups (Chi-squared=3236.88, P<0.001). Compared with English speakers, the Beta coeffi cient for the LOS in the EDs measured in minutes was among Vietnamese, 26.3 (95%CI: 22.1–30.5); Arabic, 10.3 (95%CI: 7.3–13.2); Spanish, 9.4 (95%CI: 7.1–11.7); Chinese, 8.6 (95%CI: 2.6–14.6); Hindi, 4.0 (95%CI: 2.2–5.7); Italian, 3.5 (95%CI: 1.6–5.4); and German, 2.7 (95%CI: 1.0–4.4). The fi nal regression model explained 17% of the variability in LOS. CONCLUSION: There is a close relationship between the language spoken at home and the LOS at EDs, indicating that language could be an important predictor of prolonged LOS in EDs and improving language services might reduce LOS and ease overcrowding in EDs in Queensland's public hospitals.

Characteristics of Chinese drivers attending a mandatory training course following license suspension

Penalties and sanctions to deter risky/illegal behaviours are important components of traffic law enforcement. Sanctions can be applied to the vehicle (e.g., impoundment), the person (e.g., remedial programs or jail), or the licence (e.g., disqualification). For licence sanctions, some offences attract automatic suspension while others attract demerit points which can indirectly lead to licence loss. In China, a licence is suspended when a driver accrues twelve demerit points within one year. When this occurs, the person must undertake a one-week retraining course at their own expense and successfully pass an examination to become relicensed. Little is known about the effectiveness of this program. A pilot study was conducted in Zhejiang Province to examine basic information about participants of a retraining course. The aim was to gather baseline data for future comparison. Participants were recruited at a driver retraining centre in a large city in Zhejiang Province. In total, 239 suspended drivers completed an anonymous questionnaire which included demographic information, driving history, and crash involvement. Overall, 87% were male with an overall mean age of 35.02 years (SD=8.77; range 21-60 years). A large proportion (83.3%) of participants owned a vehicle. Commuting to work was reported by 64% as their main reason for driving, while 16.3% reported driving for work. Only 6.4% reported holding a licence for 1 year or less (M=8.14 years, SD=6.5, range 1-31 years) and people reported driving an average of 18.06 hours/week (SD=14.4, range 1-86 hours). This represents a relatively experienced group, especially given the increase in new drivers in China. The number of infringements reportedly received in the previous year ranged from 2 to 18 (M=4.6, SD=3.18); one third of participants reported having received 5 or more infringements. Approximately one third also reported having received infringements in the previous year but not paid them. Various strategies for avoiding penalties were reported. The most commonly reported traffic violations were: drink driving (DUI; 0.02-0.08 mg/100ml) with 61.5% reporting 1 such violation; and speeding (47.7% reported 1-10 violations). Only 2.2% of participants reported the more serious drunk driving violation (DWI; above 0.08mg/100ml). Other violations included disobeying traffic rules, using inappropriate licence, and licence plate destroyed/not displayed. Two-thirds of participants reported no crash involvement in the previous year while 14.2% reported involvement in 2-5 crashes. The relationship between infringements and crashes was limited, however there was a small, positive significant correlation between crashes and speeding infringements (r=.2, p=.004). Overall, these results indicate the need for improved compliance with the law among this sample of traffic offenders. For example, lower level drink driving (DUI) and speeding were the most commonly reported violations with some drivers having committed a large number in the previous year. It is encouraging that the more serious offence of drunk driving (DWI) was rarely reported. The effectiveness of this driver retraining program and the demerit point penalty system in China is currently unclear. Future research including driver follow up via longitudinal study is recommended to determine program effectiveness to enhance road safety in China.

Shear capacity of reinforced concrete columns strengthened with CFRP sheet

This paper discusses the results of tests on the shear capacity of reinforced concrete columns strengthened with carbon fiber reinforced plastic (CFRP) sheet. The shear transfer mechanism of the specimens reinforced with CFRP sheet was studied. The factors affecting the shear capacity of reinforced concrete columns strengthened with CFRP sheet were analyzed. Several suggestions such as the number of layers, width and tensile strength of the CFRP sheet are proposed for this new strengthening technique. Finally, a simple and practical design method is presented in the paper. The calculated results of the suggested method are shown to be in good agreement with the test results. The suggested design method can be used in evaluating the shear capacity of reinforced concrete columns strengthened with CFRP sheet.

The potential contributions of traditional Chinese medicine to emergency medicine

BACKGROUND: Despite the fact that traditional Chinese medicine (TCM) has been developed and used to treat acute and urgent illness for many thousands of years. TCM has been widely perceived in western societies that TCM may only be effective to treat chronic diseases. The aim of this article is to provide some scientific evidence regarding the application of TCM in emergency medicine and its future potential. METHODS: Multiple databases (PubMed, ProQuest, Academic Search Elite and Science Direct) were searched using the terms: Traditional Chinese Medicine/ Chinese Medicine, Emergency Medicine, China. In addition, three leading TCM Journals in China were searched via Oriprobe Information Services for relevant articles (published from 1990—2012). Particular attention was paid to those articles that are related to TCM treatments or combined medicine in dealing with intensive and critical care. RESULTS: TCM is a systematic traditional macro medicine. The clinical practice of TCM is guided by the TCM theoretical framework – a methodology founded thousands of years ago. As the methodologies between TCM and Biomedicine are significantly different, it provides an opportunity to combine two medicines, in order to achieve clinical efficacy. Nowadays, combined medicine has become a common clinical model particular in TCM hospitals in China. CONCLUSIONS: It is evident that TCM can provide some assistance in emergency although to combine them in practice is stillits infant form and is mainly at TCM hospitals in China. The future effort could be put into TCM research, both in laboratories and clinics, with high quality designs, so that TCM could be better understood and then applied in emergency medicine.

Putative full-length clones of the genomic DNA segments of subterranean clover stunt virus and identification of the segment coding for the viral coat protein

Subterranean clover stunt disease is an economically important aphid-borne virus disease affecting certain pasture and grain legumes in Australia. The virus associated with the disease, subterranean clover stunt virus (SCSV), was previously found to be representative of a new type of single-stranded DNA virus. Analysis of the virion DNA and restriction mapping of double-stranded cDNA synthesized from virion DNA suggested that SCSV has a segmented genome composed of 3 or 4 different species of circular ssDNA each of about 850-880 nucleotides. To further investigate the complexity of the SCSV genome, we have isolated the replicative form DNA from infected pea and from it prepared putative full-length clones representing the SCSV genome segments. Analysis of these clones by restriction mapping indicated that clones representing at least 4 distinct genomic segments were obtained. This method is thus suitable for generating an extensive genomic library of novel ssDNA viruses containing multiple genome segments such as SCSV and banana bunchy top virus. The N-terminal amino acid sequence and amino acid composition of the coat protein of SCSV were determined. Comparison of the amino acid sequence with partial DNA sequence data, and the distinctly different restriction maps obtained for the full-length clones suggested that only one of these clones contained the coat protein gene. The results confirmed that SCSV has a functionally divided genome composed of several distinct ssDNA circles each of about 1 kb.

An efficient hybrid evolutionary optimization algorithm based on PSO and SA for clustering

The K-means algorithm is one of the most popular techniques in clustering. Nevertheless, the performance of the K-means algorithm depends highly on initial cluster centers and converges to local minima. This paper proposes a hybrid evolutionary programming based clustering algorithm, called PSO-SA, by combining particle swarm optimization (PSO) and simulated annealing (SA). The basic idea is to search around the global solution by SA and to increase the information exchange among particles using a mutation operator to escape local optima. Three datasets, Iris, Wisconsin Breast Cancer, and Ripley’s Glass, have been considered to show the effectiveness of the proposed clustering algorithm in providing optimal clusters. The simulation results show that the PSO-SA clustering algorithm not only has a better response but also converges more quickly than the K-means, PSO, and SA algorithms.

Health education and the control of intestinal worm infections in China : a new vision

Background: The transmission of soil-transmitted helminths (STHs) is associated with poverty, poor hygiene behaviour, lack of clean water and inadequate waste disposal and sanitation. Periodic administration of benzimidazole drugs is the mainstay for global STH control but it does not prevent re-infection, and is unlikely to interrupt transmission as a stand-alone intervention. Findings: We reported recently on the development and successful testing in Hunan province, PR China, of a health education package to prevent STH infections in Han Chinese primary school students. We have recently commenced a new trial of the package in the ethnically diverse Xishuangbanna autonomous prefecture in Yunnan province and the approach is also being tested in West Africa, with further expansion into the Philippines in 2015. Conclusions: The work in China illustrates well the direct impact that health education can have in improving knowledge and awareness, and in changing hygiene behaviour. Further, it can provide insight into the public health outcomes of a multi-component integrated control program, where health education prevents re-infection and periodic drug treatment reduces prevalence and morbidity.

The unequal distribution of road trauma in China : understanding risk factors to improve public health

The World Health Organization identifies road trauma as a major public health issue in every country; most notably among low-to-middle income countries. More than 90% of all road fatalities occur in these countries, although they have only 48% of all registered vehicles [1]. Unprecedented focus has been placed on reducing the global road trauma burden through the United Nations Decade of Action for Road Safety (2011-2020). China is rapidly transitioning from a nation of bicycle riders and pedestrians to one where car ownership and use is increasing. This transition presents important public health, mobility, and safety challenges. Rapid motorisation has resulted in an increased road trauma burden, shouldered disproportionately among the population. Vulnerable road users (bicyclists, pedestrians, and motorcyclists) are of particular concern, representing 70% of all road-related fatalities [1]. Furthermore, those at greatest risk of sustaining a crash-related disability are: male, older, less educated, and earning a lower income [2] and residing in urban areas [3], with higher fatality rates in north-western poorer provinces [3]. Speeding is a key factor in road crashes in China [1, 4] and is one of two risk factors targeted in the Bloomberg Philanthropies-funded Global Road Safety Program operating in two Chinese cities over five year [5] to which the first author has provided expert advice. However, little evidence exists to help understand the factors underpinning speeding behaviour. Previous research conducted by the authors in Beijing and Hangzhou explored personal, social, and legal factors relating to speeding to assist in better understanding the motivations for non-compliance with speed limits. Qualitative and quantitative research findings indicated that speeding is relatively common, including self-reported travel speeds of greater than 30 km/hour above posted speed limits [6], and that the road safety laws and enforcement practices may, in some circumstances, contribute to this [7]. Normative factors were also evident; the role of friends, family members and driving instructors were influential. Additionally, using social networks to attempt to avoid detection and penalty was reported, thereby potentially reinforcing community perceptions that speeding is acceptable [8, 9]. The authors established strong collaborative links with the Chinese Academy of Sciences and Zhejiang Police College to conduct this research. The first author has worked in both institutions for extended time periods and recognises that research must include an understanding of culturally-relevant issues if road safety is to improve in China. Future collaborations to assist in enhancing our understanding of such issues are welcomed. References [1] World Health Organization. (2009). Global status report on road safety: Time for action; Geneva. [2] Chen, H., Du, W., & Li, N. (2013). The socioeconomic inequality in traffic-related disability among Chinese adults: the application of concentration index. Accident Analysis & Prevention, 55(101-106). [3] Wang, S. Y., Li, Y. H., Chi, G. B., Xiao, S. Y., Ozanne-Smith, J., Stevenson, M., & Phillips, M. (2008). Injury-related fatalities in China: an under-recognised public-health problem. The Lancet (British edition), 372(9651), 1765-1773. [4] He, J., King, M. J., Watson, B., Rakotonirainy, A., & Fleiter, J. J. (2013). Speed enforcement in China: National, provincial and city initiatives and their success. Accident Analysis & Prevention, 50, 282-288. [5] Bhalla, K., Li, Q., Duan, L., Wang, Y., Bishai, D., & Hyder, A. A. (2013). The prevalence of speeding and drink driving in two cities in China: a mid project evaluation of ongoing road safety interventions. Injury, 44, 49-56. doi:10.1016/S0020-1383(13)70213-4. [6] Fleiter, J. J., Watson, B., & Lennon, A. (2013). Awareness of risky behaviour among Chinese drivers. Peer-reviewed paper presented at 23rd Canadian Multidisciplinary Road Safety Conference, Montréal, Québec. [7] Fleiter, J. J., Watson, B., Lennon, A., King, M. J., & Shi, K. (2009). Speeding in Australia and China: A comparison of the influence of legal sanctions and enforcement practices on car drivers. Peer-reviewd paper presented at Australasian Road Safety Research Policing Education Conference, Sydney. [8] Fleiter, J. J., Watson, B., Lennon, A., King, M. J., & Shi, K. (2011). Social influences on drivers in China. Journal of the Australasian College of Road Safety, 22(2), 29-36. [9] Fleiter, J. J., Watson, B., Guan, M. Q., Ding, J. Y., & Xu, C. (2013). Characteristics of Chinese Drivers Attending a Mandatory Training Course Following Licence Suspension. Peer-reviewed paper presented at Road Safety on Four Continents, Beijing, China.

Fruit-feeding behaviour and use of olfactory cues by the fruit bat Rousettus leschenaulti: an experimental study

This paper describes the feeding behaviour ofRousettus leschenaulti Desmarest, 1820 on lychees, the preferred cultivated food of this bat in captive conditions. We found that feeding comprised 25–30% of the total activity of these animals in a flight cage and that feeding durations were not significantly different between two sexes. To evaluate the role of odor and vision in foraging behaviour, we provided animals with artificial lychees, real lychees and artificial lychees soaked in the juice of real lychees and we recorded the number of feeding approaches to the different “fruit” types. The results indicated that bats approached real fruit significantly more than artificial fruit, and that the number of approaches to the soaked artificial fruit was also significantly higher than to the unsoaked artificial fruit. There were no significant differences between sexes in approach rates to any “fruit” type. We discuss the role of different sensory cues in the foraging behaviour of these bats and emphasize that the olfactory cue is important in detecting food resources and discriminating between different kinds of food items.

Temporal and spatial patterns of seed dispersal of Musa acuminata by Cynopterus sphinx

The foraging behavior of greater short-nosed fruit bats (Cynopterus sphinx) on wild banana (Musa acuminata) and subsequent dispersal of seeds were studied in the Tropical Rainforest Conservation Area, Xishuangbanna Tropical Botanical Garden, Yunnan province, by direct observation of marked fruits, mist netting, and seed collection. The mean number (± SE) of individual C. sphinx captured by mist net were 2.2 ± 0.33/day and 1.4 ± 0.32/day in the rainy season (September to October) and dry season (November to December), respectively; the difference was not significant. The number of seed pellets expelled was 9.0 ± 1.12/day and 7.2 ± 1.37/day in the rainy and dry seasons respectively; again the difference was not significant. The removal curves for marked fruit were similar for 10 focal trees. Fruits were consumed heavily within two weeks after ripening and all the marked fruit were removed within one month. The difference in seed dispersal was significant between different feeding roosts indicating that patterns of seed dispersal may not be uniform. We found the seeds of M. acuminata can be dispersed by C. sphinx to a distance of about 200 m, and C. sphinx can be considered as an effective seed disperser of M. acuminata.