Comparing genotyping algorithms for Illumina's Infinium whole-genome SNP BeadChips

Background Illumina's Infinium SNP BeadChips are extensively used in both small and large-scale genetic studies. A fundamental step in any analysis is the processing of raw allele A and allele B intensities from each SNP into genotype calls (AA, AB, BB). Various algorithms which make use of different statistical models are available for this task. We compare four methods (GenCall, Illuminus, GenoSNP and CRLMM) on data where the true genotypes are known in advance and data from a recently published genome-wide association study. Results In general, differences in accuracy are relatively small between the methods evaluated, although CRLMM and GenoSNP were found to consistently outperform GenCall. The performance of Illuminus is heavily dependent on sample size, with lower no call rates and improved accuracy as the number of samples available increases. For X chromosome SNPs, methods with sex-dependent models (Illuminus, CRLMM) perform better than methods which ignore gender information (GenCall, GenoSNP). We observe that CRLMM and GenoSNP are more accurate at calling SNPs with low minor allele frequency than GenCall or Illuminus. The sample quality metrics from each of the four methods were found to have a high level of agreement at flagging samples with unusual signal characteristics. Conclusions CRLMM, GenoSNP and GenCall can be applied with confidence in studies of any size, as their performance was shown to be invariant to the number of samples available. Illuminus on the other hand requires a larger number of samples to achieve comparable levels of accuracy and its use in smaller studies (50 or fewer individuals) is not recommended.

A novel hybrid evolutionary algorithm based on ACO and SA for distribution feeder reconfiguration with regard to DGs

This paper presents an efficient hybrid evolutionary optimization algorithm based on combining Ant Colony Optimization (ACO) and Simulated Annealing (SA), called ACO-SA, for distribution feeder reconfiguration (DFR) considering Distributed Generators (DGs). Due to private ownership of DGs, a cost based compensation method is used to encourage DGs in active and reactive power generation. The objective function is summation of electrical energy generated by DGs and substation bus (main bus) in the next day. The approach is tested on a real distribution feeder. The simulation results show that the proposed evolutionary optimization algorithm is robust and suitable for solving DFR problem.

A hybrid evolutionary algorithm based on ACO and SA for distribution feeder reconfiguration

This paper deals with an efficient hybrid evolutionary optimization algorithm in accordance with combining the ant colony optimization (ACO) and the simulated annealing (SA), so called ACO-SA. The distribution feeder reconfiguration (DFR) is known as one of the most important control schemes in the distribution networks, which can be affected by distributed generations (DGs) for the multi-objective DFR. In such a case, DGs is used to minimize the real power loss, the deviation of nodes voltage and the number of switching operations. The approach is carried out on a real distribution feeder, where the simulation results show that the proposed evolutionary optimization algorithm is robust and suitable for solving the DFR problem.

Evolutionary Perspectives

The standard approach to industrial economics starts with the industry’s basic conditions, then runs through the structure–conduct–performance paradigm of industrial organization, and finally considers government regulation and policy. Most creative industries segments have been studied in this way, for example in Albarran (2002) and Caves (2000). These approaches use standard economic analysis to explain the particular properties and characteristics of a specific industrial sector. The overview presented here is different again. It focuses on the creative industries and examines their economic effect, specifically their contribution to economic evolu -tion. This is an evolutionary systems approach to industrial analysis, where we seek to understand how a sector fits into a broader system of production, consumption, technology, trade and institutions. The evolutionary approach focuses on innovation, economic growth and endogenous transformation. So, rather than using economics to explain static or industrial-organization features of the creative industries, we are using an open systems view of the creative industries to explain dynamic ‘Schumpeterian’ features of the broader economy. The creative industries are drivers of economic transformation through their role in the origination of new ideas, in consumer adoption, and in facilitating the institutional embedding of new ideas into the economic order. This is not a novel idea, as economists have long understood that particular activities are drivers of economic growth and development, for example research and development, and also that particular sectors are instrumental to this process, for example high-technology sectors. What is new is the argument that cultural and creative sectors are also a key part of this process of economic evolution. We will review the case for that claim, and outline purported mechanisms. We will also consider why policy settings in the creative industries should be more in line with innovation and growth policy than with industry policy.

A new grouping genetic algorithm for the MapReduce placement problem in cloud computing

MapReduce is a computation model for processing large data sets in parallel on large clusters of machines, in a reliable, fault-tolerant manner. A MapReduce computation is broken down into a number of map tasks and reduce tasks, which are performed by so called mappers and reducers, respectively. The placement of the mappers and reducers on the machines directly affects the performance and cost of the MapReduce computation. From the computational point of view, the mappers/reducers placement problem is a generation of the classical bin packing problem, which is NPcomplete. Thus, in this paper we propose a new grouping genetic algorithm for the mappers/reducers placement problem in cloud computing. Compared with the original one, our grouping genetic algorithm uses an innovative coding scheme and also eliminates the inversion operator which is an essential operator in the original grouping genetic algorithm. The new grouping genetic algorithm is evaluated by experiments and the experimental results show that it is much more efficient than four popular algorithms for the problem, including the original grouping genetic algorithm.

Accelerometer data reduction : a comparison of four reduction algorithms on select outcome variables

Purpose Accelerometers are recognized as a valid and objective tool to assess free-living physical activity. Despite the widespread use of accelerometers, there is no standardized way to process and summarize data from them, which limits our ability to compare results across studies. This paper a) reviews decision rules researchers have used in the past, b) compares the impact of using different decision rules on a common data set, and c) identifies issues to consider for accelerometer data reduction. Methods The methods sections of studies published in 2003 and 2004 were reviewed to determine what decision rules previous researchers have used to identify wearing period, minimal wear requirement for a valid day, spurious data, number of days used to calculate the outcome variables, and extract bouts of moderate to vigorous physical activity (MVPA). For this study, four data reduction algorithms that employ different decision rules were used to analyze the same data set. Results The review showed that among studies that reported their decision rules, much variability was observed. Overall, the analyses suggested that using different algorithms impacted several important outcome variables. The most stringent algorithm yielded significantly lower wearing time, the lowest activity counts per minute and counts per day, and fewer minutes of MVPA per day. An exploratory sensitivity analysis revealed that the most stringent inclusion criterion had an impact on sample size and wearing time, which in turn affected many outcome variables. Conclusions These findings suggest that the decision rules employed to process accelerometer data have a significant impact on important outcome variables. Until guidelines are developed, it will remain difficult to compare findings across studies

Critical review of time-dependent shortest path algorithms: A multimodal trip planner perspective

A multimodal trip planner that produces optimal journeys involving both public transport and private vehicle legs has to solve a number of shortest path problems, both on the road network and the public transport network. The algorithms that are used to solve these shortest path problems have been researched since the late 1950s. However, in order to provide accurate journey plans that can be trusted by the user, the variability of travel times caused by traffic congestion must be taken into consideration. This requires the use of more sophisticated time-dependent shortest path algorithms, which have only been researched in depth over the last two decades, from the mid-1990s. This paper will review and compare nine algorithms that have been proposed in the literature, discussing the advantages and disadvantages of each algorithm on the basis of five important criteria that must be considered when choosing one or more of them to implement in a multimodal trip planner.

Исследования и испытания алгоритмов автоматической пилотажно-навигационной системы малогабаритного беспилотного летательного аппарата = Research and testing of automatic navigation management system’s algorithms for small unmanned aerial vehicle

В статье представлено развитие принципа построения автоматической пилотажно-навигационной системы (АПНС) для беспилотного летательного аппарата (БЛА). Принцип заключается в синтезе комплексных систем управления БПЛА не только на основе использования алгоритмов БИНС, но и алгоритмов, объединяющих в себе решение задач формирования и отработки сформированной траектории резервированной системой управления и навигации. Приведены результаты аналитического исследования и данные летных экспериментов разработанных алгоритмов АПНС БЛА, обеспечивающих дополнительное резервирование алгоритмов навигации и наделяющих БЛА новым функциональной способностью по выходу в заданную точку пространства с заданной скоростью в заданный момент времени с учетом атмосферных ветровых возмущений. Предложена и испытана методика идентификации параметров воздушной атмосферы: направления и скорости W ветра. Данные летных испытаний полученного решения задачи терминальной навигации демонстрируют устойчивую работу синтезированных алгоритмов управления в различных метеоусловиях. The article presents a progress in principle of development of automatic navigation management system (ANMS) for small unmanned aerial vehicle (UAV). The principle defines a development of integrated control systems for UAV based on tight coupling of strap down inertial navigation system algorithms and algorithms of redundant flight management system to form and control flight trajectory. The results of the research and flight testing of the developed ANMS UAV algorithms are presented. The system demonstrates advanced functional redundancy of UAV guidance. The system enables new UAV capability to perform autonomous multidimensional navigation along waypoints with controlled speed and time of arrival taking into account wind. The paper describes the technique for real-time identification of atmosphere parameters such as wind direction and wind speed. The flight test results demonstrate robustness of the algorithms in diverse meteorological conditions.

Genetic and phenotypic evidence supports evolutionary divergence of the American flamingo (Phoenicopterus ruber) population in the Galapagos islands

The Galapagos archipelago is characterized by a high degree of endemism across many taxa, linked to the archpelago's oceanic origin and distance from other colonizing land masses. A population of ~ 500 American Flamingos (Phoenicopterus ruber) resides in Galapagos, which is thought to share an historical origin with the American Flamingo currently found in the Caribbean region. Genetic and phenotypic parameters in American Flamingos from Galapagos and from the Caribbean were investigated. Microsatellite and microchondrial DNA markers data showed that the American Flamingo population in Galapagos differs genetically from that in the Caribbean. American Flamingos in Galapagos form a clade which differs by a single common nucleotide substitution from American Flamingos in the Caribbean. The genetic differentiation is also evident from nuclear DNA in that microsatellite data reveal a number of private alleles for the American Flamingo in Galapagos. Analysis of skeletal measurements showed that American Flamingos in Galapagos are smaller than those in the Caribbean primarily due to shorter tarsus length, and differences in body shape sexual dimorphism. American Flamingo eggs from Galapagos have smaller linear dimensions and volumes than those from the Caribbean. The findings are consistent with reproductive isolation of American Flamingo population in Galapagos.

A review of modern computational algorithms for Bayesian optimal design

Bayesian experimental design is a fast growing area of research with many real-world applications. As computational power has increased over the years, so has the development of simulation-based design methods, which involve a number of algorithms, such as Markov chain Monte Carlo, sequential Monte Carlo and approximate Bayes methods, facilitating more complex design problems to be solved. The Bayesian framework provides a unified approach for incorporating prior information and/or uncertainties regarding the statistical model with a utility function which describes the experimental aims. In this paper, we provide a general overview on the concepts involved in Bayesian experimental design, and focus on describing some of the more commonly used Bayesian utility functions and methods for their estimation, as well as a number of algorithms that are used to search over the design space to find the Bayesian optimal design. We also discuss other computational strategies for further research in Bayesian optimal design.

Outbreak detection algorithms for seasonal disease data : a case study using Ross River virus disease

Background Detection of outbreaks is an important part of disease surveillance. Although many algorithms have been designed for detecting outbreaks, few have been specifically assessed against diseases that have distinct seasonal incidence patterns, such as those caused by vector-borne pathogens. Methods We applied five previously reported outbreak detection algorithms to Ross River virus (RRV) disease data (1991-2007) for the four local government areas (LGAs) of Brisbane, Emerald, Redland and Townsville in Queensland, Australia. The methods used were the Early Aberration Reporting System (EARS) C1, C2 and C3 methods, negative binomial cusum (NBC), historical limits method (HLM), Poisson outbreak detection (POD) method and the purely temporal SaTScan analysis. Seasonally-adjusted variants of the NBC and SaTScan methods were developed. Some of the algorithms were applied using a range of parameter values, resulting in 17 variants of the five algorithms. Results The 9,188 RRV disease notifications that occurred in the four selected regions over the study period showed marked seasonality, which adversely affected the performance of some of the outbreak detection algorithms. Most of the methods examined were able to detect the same major events. The exception was the seasonally-adjusted NBC methods that detected an excess of short signals. The NBC, POD and temporal SaTScan algorithms were the only methods that consistently had high true positive rates and low false positive and false negative rates across the four study areas. The timeliness of outbreak signals generated by each method was also compared but there was no consistency across outbreaks and LGAs. Conclusions This study has highlighted several issues associated with applying outbreak detection algorithms to seasonal disease data. In lieu of a true gold standard, a quantitative comparison is difficult and caution should be taken when interpreting the true positives, false positives, sensitivity and specificity.

A Study of feature extraction algorithms for optical flow tracking

Sparse optical flow algorithms, such as the Lucas-Kanade approach, provide more robustness to noise than dense optical flow algorithms and are the preferred approach in many scenarios. Sparse optical flow algorithms estimate the displacement for a selected number of pixels in the image. These pixels can be chosen randomly. However, pixels in regions with more variance between the neighbours will produce more reliable displacement estimates. The selected pixel locations should therefore be chosen wisely. In this study, the suitability of Harris corners, Shi-Tomasi's “Good features to track", SIFT and SURF interest point extractors, Canny edges, and random pixel selection for the purpose of frame-by-frame tracking using a pyramidical Lucas-Kanade algorithm is investigated. The evaluation considers the important factors of processing time, feature count, and feature trackability in indoor and outdoor scenarios using ground vehicles and unmanned aerial vehicles, and for the purpose of visual odometry estimation.

Document clustering algorithms, representations and evaluation for information retrieval

This thesis presents new methods for classification and thematic grouping of billions of web pages, at scales previously not achievable. This process is also known as document clustering, where similar documents are automatically associated with clusters that represent various distinct topic. These automatically discovered topics are in turn used to improve search engine performance by only searching the topics that are deemed relevant to particular user queries.

The plasticity of NBS resistance genes in sorghum is driven by multiple evolutionary processes

Background Increased disease resistance is a key target of cereal breeding programs, with disease outbreaks continuing to threaten global food production, particularly in Africa. Of the disease resistance gene families, the nucleotide-binding site plus leucine-rich repeat (NBS-LRR) family is the most prevalent and ancient and is also one of the largest gene families known in plants. The sequence diversity in NBS-encoding genes was explored in sorghum, a critical food staple in Africa, with comparisons to rice and maize and with comparisons to fungal pathogen resistance QTL. Results In sorghum, NBS-encoding genes had significantly higher diversity in comparison to non NBS-encoding genes and were significantly enriched in regions of the genome under purifying and balancing selection, both through domestication and improvement. Ancestral genes, pre-dating species divergence, were more abundant in regions with signatures of selection than in regions not under selection. Sorghum NBS-encoding genes were also significantly enriched in the regions of the genome containing fungal pathogen disease resistance QTL; with the diversity of the NBS-encoding genes influenced by the type of co-locating biotic stress resistance QTL. Conclusions NBS-encoding genes are under strong selection pressure in sorghum, through the contrasting evolutionary processes of purifying and balancing selection. Such contrasting evolutionary processes have impacted ancestral genes more than species-specific genes. Fungal disease resistance hot-spots in the genome, with resistance against multiple pathogens, provides further insight into the mechanisms that cereals use in the “arms race” with rapidly evolving pathogens in addition to providing plant breeders with selection targets for fast-tracking the development of high performing varieties with more durable pathogen resistance.

Not drowning, (hand)waving? Molecular phylogenetics, biogeography and evolutionary tempo of the ‘Gondwanan’ midge Stictocladius Edwards (Diptera: Chironomidae)

Many insect clades, especially within the Diptera (true flies), have been considered classically ‘Gondwanan’, with an inference that distributions derive from vicariance of the southern continents. Assessing the role that vicariance has played in the evolution of austral taxa requires testing the location and tempo of diversification and speciation against the well-established predictions of fragmentation of the ancient super-continent. Several early (anecdotal) hypotheses that current austral distributions originate from the breakup of Gondwana derive from studies of taxa within the family Chironomidae (non-biting midges). With the advent of molecular phylogenetics and biogeographic analytical software, these studies have been revisited and expanded to test such conclusions better. Here we studied the midge genus Stictocladius Edwards, from the subfamily Orthocladiinae, which contains austral-distributed clades that match vicariance-based expectations. We resolve several issues of systematic relationships among morphological species and reveal cryptic diversity within many taxa. Time-calibrated phylogenetic relationships among taxa accorded partially with the predicted tempo from geology. For these apparently vagile insects, vicariance-dated patterns persist for South America and Australia. However, as often found, divergence time estimates for New Zealand at c. 50 mya post-date separation of Zealandia from Antarctica and the remainder of Gondwana, but predate the proposed Oligocene ‘drowning’ of these islands. We detail other such ‘anomalous’ dates and suggest a single common explanation rather than stochastic processes. This could involve synchronous establishment following recovery from ‘drowning’ and/or deleteriously warming associated with the mid-Eocene climatic optimum (hence ‘waving’, which refers to cycles of drowning events) plus new availability of topography providing of cool running waters, or all these factors in combination. Alternatively a vicariance explanation remains available, given the uncertain duration of connectivity of Zealandia to Australia–Antarctic–South America via the Lord Howe and Norfolk ridges into the Eocene.