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.

Copyright and creative innovation in China : an evolutionary approach?

China has made great progress in constructing comprehensive legislative and judicial infrastructures to protect intellectual property rights. But levels of enforcement remain low. Estimates suggest that 90% of film and music products consumed in China are ‘pirated’ and in 2009 81% of the infringing goods seized at the US border originated from China. Despite of heavy criticism over its failure to enforce IPRs, key areas of China’s creative industries, including film, mobile-music, fashion and animation, are developing rapidly. This paper explores how the rapid expansion of China’s creative economy might be reconciled with conceptual approaches that view the CIs in terms of creativity inputs and IP outputs. It argues that an evolutionary understanding of copyright’s role in creative innovation might better explain China’s experiences and provide more general insights into the nature of the creative industries and the policies most likely to promote growth in this sector of the economy.

Patterns, heuristics for architectural design support: making use of evolutionary modelling in design

Software used by architectural and industrial designers – has moved from becoming a tool for drafting, towards use in verification, simulation, project management and project sharing remotely. In more advanced models, parameters for the designed object can be adjusted so a family of variations can be produced rapidly. With advances in computer aided design technology, numerous design options can now be generated and analyzed in real time. However the use of digital tools to support design as an activity is still at an early stage and has largely been limited in functionality with regard to the design process. To date, major CAD vendors have not developed an integrated tool that is able to both leverage specialized design knowledge from various discipline domains (known as expert knowledge systems) and support the creation of design alternatives that satisfy different forms of constraints. We propose that evolutionary computing and machine learning be linked with parametric design techniques to record and respond to a designer’s own way of working and design history. It is expected that this will lead to results that impact on future work on design support systems-(ergonomics and interface) as well as implicit constraint and problem definition for problems that are difficult to quantify.

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.

V2V/V2I augmented maps : state-of-the-art and contribution to real-time crash risk assessment

A number of advanced driver assistance systems (ADAS) are currently being released on the market, providing safety functions to the drivers such as collision avoidance, adaptive cruise control or enhanced night-vision. These systems however are inherently limited by their sensory range: they cannot gather information from outside this range, also called their “perceptive horizon”. Cooperative systems are a developing research avenue that aims at providing extended safety and comfort functionalities by introducing vehicle-to-vehicle (V2V) and vehicle-to-infrastructure (V2I) wireless communications to the road actors. This paper presents the problematic of cooperative systems, their advantages and contributions to road safety and exposes some limitations related to market penetration, sensors accuracy and communications scalability. It explains the issues of how to implement extended perception, a central contribution of cooperative systems. The initial steps of an evaluation of data fusion architectures for extended perception are exposed.

Genetic resources in wild and cultured stocks of the Asian mud crab, Scylla paramamosain

The mud crab (Scylla spp.) aquaculture industry has expanded rapidly in recent years in many countries in the Indo - West Pacific (IWP) region as an alternative to marine shrimp culture because of significant disease outbreaks and associated failures of many shrimp culture industries in the region. Currently, practices used to produce and manage breeding crabs in hatcheries may compromise levels of genetic diversity, ultimately compromising growth rates, disease resistance and stock productivity. Therefore, to avoid “genetic pollution” and its harmful effects and to promote further development of mud crab aquaculture and fisheries in a sustainable way, a greater understanding of the genetic attributes of wild and cultured mud crab stocks is required. Application of these results can provide benefits for managing wild and cultured Asian mud crab populations for multiple purposes including for commercial production, recreation and conservation and to increase profitability and sustainability of newly emerging crab culture industries. Phylogeographic patterns and the genetic structure of Asian mud crab populations across the IWP were assessed to determine if they were concordant with those of other widespread taxa possessing pelagic larvae of relatively long duration. A 597 bp fragment of the mitochondrial DNA COI gene was amplified and screened for variation in a total of 297 individuals of S. paramamosain from six sampling sites across the species’ natural geographical distribution in the IWP and 36 unique haplotypes were identified. Haplotype diversities per site ranged from 0.516 to 0.879. Nucleotide diversity estimates among haplotypes were 0.11% – 0.48%. Maximum divergence observed among S. paramamosain samples was 1.533% and samples formed essentially a single monophyletic group as no obvious clades were related to geographical location of sites. A weak positive relationship was observed however, between genetic distance and geographical distance among sites. Microsatellite markers were then used to assess contemporary gene flow and population structure in Asian mud crab populations sampled across their natural distribution in the IWP. Eight microsatellite loci were screened in sampled S. paramamosain populations and all showed high allelic diversity at all loci in sampled populations. In total, 344 individuals were analysed, and 304 microsatellite alleles were found across the 8 loci. The mean number of alleles per locus at each site ranged from 20.75 to 28.25. Mean allelic richness per site varied from 17.2 to 18.9. All sites showed high levels of heterozygosity as average expected heterozygosities for all loci ranged from 0.917 – 0.953 while mean observed heterozygosity ranged from 0.916 – 0.959. Allele diversities were similar at all sites and across all loci. The results did not show any evidence for major differences in allele frequencies among sites and patterns of allele frequencies were very similar in all populations across all loci. Estimates of population differentiation (FST) were relatively low and most probably largely reflect intra – individual variation for very highly variable loci. Results from nDNA analysis showed evidence for only very limited population genetic structure among sampled S. paramamosain, and a positive and significant association for genetic and geographical distance among sample sites. Microsatellite markers were then employed to determine if adequate levels of genetic diversity has been captured in crab hatcheries for the breeding cycle. The results showed that all microsatellite loci were polymorphic in hatchery samples. Culture populations were in general, highly genetically depauperate, compared with comparable wild populations, with only 3 to 8 alleles recorded for the same loci set per population. In contrast, very high numbers of alleles per locus were found in reference wild S. paramamosain populations, which ranged from 18 to 46 alleles per locus per population. In general, this translates into a 3 to 10 fold decline in mean allelic richness per locus in all culture stocks compared with wild reference counterparts. Furthermore, most loci in all cultured S. paramamosain samples showed departures from HWE equilibrium. Allele frequencies were very different in culture samples from that present in comparable wild reference samples and this in particular, was reflected in a large decline in allele diversity per locus. The pattern observed was best explained by significant impacts of breeding practices employed in hatcheries rather than natural differentiation among wild populations used as the source of brood stock. Recognition of current problems and management strategies for the species both for the medium and long-term development of the new culture industry are discussed. The priority research to be undertaken over the medium term for S. paramamosain should be to close the life cycle fully to allow individuals to be bred on demand and their offspring equalised to control broodstock reproductive contributions. Establishing a broodstock register and pedigree mating system will be required before any selection program is implemented. This will ensure that sufficient genetic variation will be available to allow genetic gains to be sustainably achieved in a future stock improvement program. A fundamental starting point to improve hatchery practices will be to encourage farmers and hatchery managers to spawn more females in their hatcheries as it will increase background genetic diversity in culture stocks. Combining crablet cohorts from multiple hatcheries into a single cohort for supply to farmers or rotation of breeding females regularly in hatcheries will help to address immediate genetic diversity problems in culture stocks. Application of these results can provide benefits for managing wild and cultured Asian mud crab populations more efficiently. Over the long-term, application of data on genetic diversity in wild and cultured stocks of Asian mud crab will contribute to development of sustainable and productive culture industries in Vietnam and other countries in the IWP and can contribute towards conservation of wild genetic resources.

Designing participation : Reconsidering agile ridesharing with evolutionary distributed design thinking

This paper explores design thinking from the perspective of designing new forms of interaction to engage people in community change initiatives. A case study of an agile ridesharing system is presented. We describe the fundamental premise of the design approach taken—deploying simple interactive prototypes for use by communities in order to test the design hypothesis, evolve the design in use and grow the community of participants. Real-time use data and feedback from participants influences our understanding of the design approach and feeds into the gradual evolution of the prototype while it continues to be used. We then reflect upon this form of evolutionary distributed design thinking. In contrast to the conventional IT wisdom of building systems to automate ride matching and fare calculation using structured forms, our initial phase of design revealed a preference for informal messaging, negotiation and caution in the sharing of specific location information.

Robust multidisciplinary design optimisation using CFD and advanced evolutionary algorithms

Computation Fluid Dynamics (CFD) has become an important tool in optimization and has seen successful in many real world applications. Most important among these is in the optimisation of aerodynamic surfaces which has become Multi-Objective (MO) and Multidisciplinary (MDO) in nature. Most of these have been carried out for a given set of input parameters such as free stream Mach number and angle of attack. One cannot ignore the fact that in aerospace engineering one frequently deals with situations where the design input parameters and flight/flow conditions have some amount of uncertainty attached to them. When the optimisation is carried out for fixed values of design variables and parameters however, one arrives at an optimised solution that results in good performance at design condition but poor drag or lift to drag ratio at slightly off-design conditions. The challenge is still to develop a robust design that accounts for uncertainty in the design in aerospace applications. In this paper this issue is taken up and an attempt is made to prevent the fluctuation of objective performance by using robust design technique or Uncertainty.

Influence of historical landscapes, drainage evolution and ecological traits on patterns of genetic diversity in Southeast Asian freshwater snakehead fishes

Snakehead fishes in the family Channidae are obligate freshwater fishes represented by two extant genera, the African Parachannna and the Asian Channa. These species prefer still or slow flowing water bodies, where they are top predators that exercise high levels of parental care, have the ability to breathe air, can tolerate poor water quality, and interestingly, can aestivate or traverse terrestrial habitat in response to seasonal changes in freshwater habitat availability. These attributes suggest that snakehead fishes may possess high dispersal potential, irrespective of the terrestrial barriers that would otherwise constrain the distribution of most freshwater fishes. A number of biogeographical hypotheses have been developed to account for the modern distributions of snakehead fishes across two continents, including ancient vicariance during Gondwanan break-up, or recent colonisation tracking the formation of suitable climatic conditions. Taxonomic uncertainty also surrounds some members of the Channa genus, as geographical distributions for some taxa across southern and Southeast (SE) Asia are very large, and in one case is highly disjunct. The current study adopted a molecular genetics approach to gain an understanding of the evolution of this group of fishes, and in particular how the phylogeography of two Asian species may have been influenced by contemporary versus historical levels of dispersal and vicariance. First, a molecular phylogeny was constructed based on multiple DNA loci and calibrated with fossil evidence to provide a dated chronology of divergence events among extant species, and also within species with widespread geographical distributions. The data provide strong evidence that trans-continental distribution of the Channidae arose as a result of dispersal out of Asia and into Africa in the mid–Eocene. Among Asian Channa, deep divergence among lineages indicates that the Oligocene-Miocene boundary was a time of significant species radiation, potentially associated with historical changes in climate and drainage geomorphology. Mid-Miocene divergence among lineages suggests that a taxonomic revision is warranted for two taxa. Deep intra-specific divergence (~8Mya) was also detected between C. striata lineages that occur sympatrically in the Mekong River Basin. The study then examined the phylogeography and population structure of two major taxa, Channa striata (the chevron snakehead) and the C. micropeltes (the giant snakehead), across SE Asia. Species specific microsatellite loci were developed and used in addition to a mitochondrial DNA marker (Cyt b) to screen neutral genetic variation within and among wild populations. C. striata individuals were sampled across SE Asia (n=988), with the major focus being the Mekong Basin, which is the largest drainage basin in the region. The distributions of two divergent lineages were identified and admixture analysis showed that where they co-occur they are interbreeding, indicating that after long periods of evolution in isolation, divergence has not resulted in reproductive isolation. One lineage is predominantly confined to upland areas of northern Lao PDR to the north of the Khorat Plateau, while the other, which is more closely related to individuals from southern India, has a widespread distribution across mainland SE Asian and Sumatra. The phylogeographical pattern recovered is associated with past river networks, and high diversity and divergence among all populations sampled reveal that contemporary dispersal is very low for this taxon, even where populations occur in contiguous freshwater habitats. C. micropeltes (n=280) were also sampled from across the Mekong River Basin, focusing on the lower basin where it constitutes an important wild fishery resource. In comparison with C. striata, allelic diversity and genetic divergence among populations were extremely low, suggesting very recent colonisation of the greater Mekong region. Populations were significantly structured into at least three discrete populations in the lower Mekong. Results of this study have implications for establishing effective conservation plans for managing both species, that represent economically important wild fishery resources for the region. For C. micropeltes, it is likely that a single fisheries stock in the Tonle Sap Great Lake is being exploited by multiple fisheries operations, and future management initiatives for this species in this region will need to account for this. For C. striata, conservation of natural levels of genetic variation will require management initiatives designed to promote population persistence at very localised spatial scales, as the high level of population structuring uncovered for this species indicates that significant unique diversity is present at this fine spatial scale.

Comparison of Nucleotide Sequences between Northern and Southern Philippine Isolates of Rice Grassy Stunt Virus Indicates Occurrence of Natural Genetic Reassortment

Rice grassy stunt virus is a member of the genus Tenuivirus, is persistently transmitted by a brown planthopper, and has occurred in rice plants in South, Southeast, and East Asia (similar to North and South America). We determined the complete nucleotide (nt) sequences of RNAs 1 (9760 nt), 2 (4069 nt), 3 (3127 nt), 4 (2909 nt), 5 (2704 nt), and 6 (2590 nt) of a southern Philippine isolate from South Cotabato and compared them with those of a northern Philippine isolate from Laguna (Toriyama et al., 1997, 1998). The numbers of nucleotides in the terminal untranslated regions and open reading frames were identical between the two isolates except for the 5′ untranslated region of the complementary strand of RNA 4. Overall nucleotide differences between the two isolates were only 0.08% in RNA 1, 0.58% in RNA 4, and 0.26% in RNA 5, whereas they were 2.19% in RNA 2, 8.38% in RNA 3, and 3.63% in RNA 6. In the intergenic regions, the two isolates differed by 9.12% in RNA 2, 11.6% in RNA 3, and 6.86% in RNA 6 with multiple consecutive nucleotide deletion/insertions, whereas they differed by only 0.78% in RNA 4 and 0.34% in RNA 5. The nucleotide variation in the intergenic region of RNA 6 within the South Cotabato isolate was only 0.33%. These differences in accumulation of mutations among individual RNA segments indicate that there was genetic reassortment in the two geographical isolates; RNAs 1, 4, and 5 of the two isolates came from a common ancestor, whereas RNAs 2, 3, and 6 were from two different ancestors.

Genetic Diversity of Rice Tungro Spherical Virus in Tungro-Endemic Provinces of the Philippines and Indonesia

The two adjacent genes of coat protein 1 and 2 of rice tungro spherical virus (RTSV) were amplified from total RNA extracts of serologically indistinguishable field isolates from the Philippines and Indonesia, using reverse transcriptase polymerase chain reaction (RT-PCR). Digestion with HindIII and BstYI restriction endonucleases differentiated the amplified DNA products into eight distinct coat protein genotypes. These genotypes were then used as indicators of virus diversity in the field. Inter- and intra-site diversities were determined over three cropping seasons. At each of the sites surveyed, one or two main genotypes prevailed together with other related minor or mixed genotypes that did not replace the main genotype over the sampling time. The cluster of genotypes found at the Philippines sites was significantly different from the one at the Indonesia sites, suggesting geographic isolation for virus populations. Phylogenetic studies based on the nucleotide sequences of 38 selected isolates confirm the spatial distribution of RTSV virus populations but show that gene flow may occur between populations. Under the present conditions, rice varieties do not seem to exert selective pressure on the virus populations. Based on the selective constraints in the coat protein amino acid sequences and the virus genetic composition per site, a negative selection model followed by random-sampling events due to vector transmissions is proposed to explain the inter-site diversity observed

Inter-and Intra-Site Genetic Diversity of Natural Field Populations of Rice Tungro Bacilliform Virus in the Philippines

The genetic structure of rice tungro bacilliform virus (RTBV) populations within and between growing sites was analyzed in a collection of natural field isolates from different rice varieties grown in eight tungro-endemic sites of the Philippines. Total DNA extracts from 345 isolates were digested with EcoRV restriction enzyme and hybridized with a full-length probe of RTBV, a procedure shown in preliminary experiments capable of revealing high levels of polymorphism in RTBV field isolates. In the total population, 17 distinct EcoRV-based genome profiles (genotypes) were identified and used as indicators for virus diversity. Distinct sets of genotypes occurred in Isabela and North Cotabato provinces suggesting a geographic isolation of virus populations. However, among the sites in each province, there were few significant differences in the genotype compositions of virus populations. The number of genotypes detected at a site varied from two to nine with a few genotypes dominating. In general the isolates at a site persisted from season to season indicating a genetic stability for the local virus population. Over the sampling time, IRRI rice varieties, which have green leafhopper resistance genes, supported similar virus populations to those supported by other varieties, indicating that the variety of the host exerted no apparent selection pressures. Insect transmission experiments on selected RTBV field isolates showed that dramatic shifts in genotype and phenotype distributions can occur in response to host /environmental shifts.

Genetic Composition and Complexity of Virus Populations at Tungro-Endemic and Outbreak Rice Sites

We have recently demonstrated the geographic isolation of rice tungro bacilliform virus (RTBV) populations in the tungro-endemic provinces of Isabela and North Cotabato, Philippines. In this study, we examined the genetic structure of the virus populations at the tungro-outbreak sites of Lanao del Norte, a province adjacent to North Cotabato. We also analyzed the virus populations at the tungro-endemic sites of Subang, Indonesia, and Dien Khanh, Vietnam. Total DNA extracts from 274 isolates were digested with EcoRV restriction enzyme and hybridized with a full-length probe of RTBV. In the total population, 22 EcoRV-restricted genome profiles (genotypes) were identified. Although overlapping genotypes could be observed, the outbreak sites of Lanao del Norte had a genotype combination distinct from that of Subang or Dien Khanh but a genotype combination similar to that identified earlier from North Cotabato, the adjacent endemic province. Sequence analysis of the intergenic region and part of the ORF1 RTBV genome from randomly selected genotypes confirms the geographic clustering of RTBV genotypes and, combined with restriction analysis, the results suggest a fragmented spatial distribution of RTBV local populations in the three countries. Because RTBV depends on rice tungro spherical virus (RTSV) for transmission, the population dynamics of both tungro viruses were then examined at the endemic and outbreak sites within the Philippines. The RTBV genotypes and the coat protein RTSV genotypes were used as indicators for virus diversity. A shift in population structure of both viruses was observed at the outbreak sites with a reduced RTBV but increased RTSV gene diversity