Molecular epidemiology of respiratory viruses in a paediatric cohort from Indonesia

Acute lower respiratory tract infections (ALRTIs) are a common cause of morbidity and mortality among children under 5 years of age and are found worldwide, with pneumonia as the most severe manifestation. Although the incidence of severe disease varies both between individuals and countries, there is still no clear understanding of what causes this variation. Studies of community-acquired pneumonia (CAP) have traditionally not focused on viral causes of disease due to a paucity of diagnostic tools. However, with the emergence of molecular techniques, it is now known that viruses outnumber bacteria as the etiological agents of childhood CAP, especially in children under 2 years of age. The main objective of this study was to investigate viruses contributing to disease severity in cases of childhood ALRTI, using a two year cohort study following 2014 infants and children enrolled in Bandung, Indonesia. A total of 352 nasopharyngeal washes collected from 256 paediatric ALRTI patients were used for analysis. A subset of samples was screened using a novel microarray pathogen detection method that identified respiratory syncytial virus (RSV), human metapneumovirus (hMPV) and human rhinovirus (HRV) in the samples. Real-time RT-PCR was used both for confirming and quantifying viruses found in the nasopharyngeal samples. Viral copy numbers were determined and normalised to the numbers of human cells collected with the use of 18S rRNA. Molecular epidemiology was performed for RSV A and hMPV using sequences to the glycoprotein gene and nucleoprotein gene respectively, to determine genotypes circulating in this Indonesian paediatric cohort. This study found that HRV (119/352; 33.8%) was the most common virus detected as the cause of respiratory tract infections in this cohort, followed by the viral pathogens RSV A (73/352; 20.7%), hMPV (30/352; 8.5%) and RSV B (12/352; 3.4%). Co-infections of more than two viruses were detected in 31 episodes (defined as an infection which occurred more than two weeks apart), accounting for 8.8% of the 352 samples tested or 15.4% of the 201 episodes with at least one virus detected. RSV A genotypes circulating in this population were predominantly GA2, GA5 and GA7, while hMPV genotypes circulating were mainly A2a (27/30; 90.0%), B2 (2/30; 6.7%) and A1 (1/30; 3.3%). This study found no evidence of disease severity associated either with a specific virus or viral strain, or with viral load. However, this study did find a significant association with co-infection of RSV A and HRV with severe disease (P = 0.006), suggesting that this may be a novel cause of severe disease.

Genetic Analysis of Tolerance to Rice Tungro Bacilliform Virus in Rice (Oryza sativa L.) Through Agroinoculation

Balimau Putih [an Indonesian cultivar tolerant to rice tungro bacilliform virus (RTBV)] was crossed with IR64 (RTBV, susceptible variety) to produce the three filial generations F1, F2 and F3. Agroinoculation was used to introduce RTBV into the test plants. RTBV tolerance was based on the RTBV level in plants by analysis of coat protein using enzyme-linked immunosorbent assay. The level of RTBV in cv. Balimau Putih was significantly lower than that of IR64 and the susceptible control, Taichung Native 1. Mean RTBV levels of the F1, F2 and F3 populations were comparable with one another and with the average of the parents. Results indicate that there was no dominance and an additive gene action may control the expression of tolerance to RTBV. Tolerance based on the level of RTBV coat protein was highly heritable (0.67) as estimated using the mean values of F3 lines, suggesting that selection for tolerance to RTBV can be performed in the early selfing generations using the technique employed in this study. The RTBV level had a negative correlation with plant height, but positive relationship with disease index value

The Biology, Epidemiology, and Management of Rice Tungro Disease in Asia

Many farmers in South and Southeast Asia describe rice tungro disease as a cancer disease because of the severe damage it causes and the difficulty of controlling it (121). As the most important of the 14 rice viral diseases, tungro was first recognized as a leafhopper-transmitted virus disease in 1963 (88). However, tungro, which means “degenerated growth” in a Filipino dialect, has a much longer history. It is almost certain that tungro was responsible for a disease outbreak that occurred in 1859 in Indonesia, which was referred to at the time as mentek (83). In the past, a variety of names has been given to tungro, including accep na pula in the Philippines, penyakit merah in Malaysia, and yelloworange leaf in Thailand (83).

Optimization of long rural feeders using a genetic algorithm

This paper describes the optimization of conductor size and the voltage regulator location & magnitude of long rural distribution lines. The optimization minimizes the lifetime cost of the lines, including capital costs and losses while observing voltage drop and operational constraints using a Genetic Algorithm (GA). The GA optimization is applied to a real Single Wire Earth Return (SWER) network in regional Queensland and results are presented.

Dynamic coast control of train movement with genetic algorithm

The railway service is now the major transportation means in most of the countries around the world. With the increasing population and expanding commercial and industrial activities, a high quality of railway service is the most desirable. Train service usually varies with the population activities throughout a day and train coordination and service regulation are then expected to meet the daily passengers' demand. Dwell time control at stations and fixed coasting point in an inter-station run are the current practices to regulate train service in most metro railway systems. However, a flexible and efficient train control and operation is not always possible. To minimize energy consumption of train operation and make certain compromises on the train schedule, coast control is an economical approach to balance run-time and energy consumption in railway operation if time is not an important issue, particularly at off-peak hours. The capability to identify the starting point for coasting according to the current traffic conditions provides the necessary flexibility for train operation. This paper presents an application of genetic algorithms (GA) to search for the appropriate coasting point(s) and investigates the possible improvement on fitness of genes. Single and multiple coasting point control with simple GA are developed to attain the solutions and their corresponding train movement is examined. Further, a hierarchical genetic algorithm (HGA) is introduced here to identify the number of coasting points required according to the traffic conditions, and Minimum-Allele-Reserve-Keeper (MARK) is adopted as a genetic operator to achieve fitter solutions.

Railway junction conflict resolution by genetic algorithm

In general, simple and traditional methods are applied to resolve traffic conflicts at railway junctions. They are, however, either inefficient or computationally demanding. A simple genetic algorithm is presented to enable a search for a near optimal resolution to be carried out while meeting the constraints on generation evolution and minimising the search time.

Signalling layout for fixed-block railway lines with real-coded genetic algorithms.

Signalling layout design is one of the keys to railway operations with fixed-block signalling system and it also carries direct effect on overall train efficiency and safety. Based on an analysis to system objectives, this paper presents an optimization model with two objectives in order to devise an efficient signalling layout scheme. Taking into account the present railway line design practices in China, the paper describes steps of the computer-based signalling layout optimisation with real-coded genetic algorithms. A computer-aided system, based on train movement simulator, has also been employed to assist the optimisation process. A case study on a practical railway line has been conducted to make comparisons between the proposed GA-based approach and the current practices. The results illustrate the improved performance of the proposed approach in reducing signal block joints and shortening minimum train service headway.

Coast control of train movement with genetic algorithms

Railway service is now the major transportation means in most of the countries around the world. With the increasing population and expanding commercial and industrial activities, a high quality of railway service is the most desirable. We present an application of genetic algorithms (GA) to search for the appropriate coasting point(s) and investigate the possible improvement on fitness of genes. Single and multiple coasting point control with simple GA are developed to attain the solutions and their corresponding train movement is examined. The multiple coasting point control with hierarchical genetic algorithm (HGA) is then proposed to integrate the determination of the number of coasting points.

Coasting control of train operation by genetic algorithm

Balancing between the provision of high quality of service and running within a tight budget is one of the biggest challenges for most metro railway operators around the world. Conventionally, one possible approach for the operator to adjust the time schedule is to alter the stop time at stations, if other system constraints, such as traction equipment characteristic, are not taken into account. Yet it is not an effective, flexible and economical method because the run-time of a train simply cannot be extended without limitation, and a balance between run-time and energy consumption has to be maintained. Modification or installation of a new signalling system not only increases the capital cost, but also affects the normal train service. Therefore, in order to procure a more effective, flexible and economical means to improve the quality of service, optimisation of train performance by coasting point identification has become more attractive and popular. However, identifying the necessary starting points for coasting under the constraints of current service conditions is no simple task because train movement is attributed by a large number of factors, most of which are non-linear and inter-dependent. This paper presents an application of genetic algorithms (GA) to search for the appropriate coasting points and investigates the possible improvement on computation time and fitness of genes.

Hierarchical fuzzy logic traffic control at a road junction using genetic algorithms

Traffic control at a road junction by a complex fuzzy logic controller is investigated. The increase in the complexity of junction means more number of input variables must be taken into account, which will increase the number of fuzzy rules in the system. A hierarchical fuzzy logic controller is introduced to reduce the number of rules. Besides, the increase in the complexity of the controller makes formulation of the fuzzy rules difficult. A genetic algorithm based off-line leaning algorithm is employed to generate the fuzzy rules. The learning algorithm uses constant flow-rates as training sets. The system is tested by both constant and time-varying flow-rates. Simulation results show that the proposed controller produces lower average delay than a fixed-time controller does under various traffic conditions.

Optimisation of a class of transportation problems using genetic algorithms

This paper presents a Genetic Algorithms (GA) approach to search the optimized path for a class of transportation problems. The formulation of the problems for suitable application of GA will be discussed. Exchanging genetic information in the sense of neighborhoods will be introduced for generation reproduction. The performance of the GA will be evaluated by computer simulation. The proposed algorithm use simple coding with population size 1 converged in reasonable optimality within several minutes.

12 fingers or one, it’s how you play? Genetic discrimination in the Australian workforce

For quite some time, debate has raged about what the human race can and should do with its knowledge of genetics. We are now nearly 60 years removed from the work of Watson and Crick who determined the structure of deoxyribonucleic acid (DNA), yet our opinions as how best to employ scientific knowledge of the human genome, remain as diverse and polarised as ever. Human judgment is often shaped and coloured by popular media and culture, so it should come as no surprise that box office movies such as Gattaca (1997) continue to play a role in informing public opinion on genetics. In order to perform well at the box office, movies such as Gattaca take great liberty in sensationalising (and even distorting) the implications that may result from genetic screening and testing. If the public’s opinion on human genetics is strongly derived from the box office and popular media, then it is no wonder that the discourse on human genetics is couched in the polar parlances of future utopias or future dystopias. When legislating in an area like genetic discrimination in the workforce, we must be mindful of not overplaying the causal link between genetic predisposition towards a disability and an employee’s ability to perform the inherent requirements of their job. Genetic information is ultimately about people, it is not about genes. Genetic discrimination is ultimately about actions, it is not about the intrinsic value of genetic information.