Mixture models of nucleotide sequence evolution that account for heterogeneity in the substitution process across sites and across lineages

Molecular phylogenetic studies of homologous sequences of nucleotides often assume that the underlying evolutionary process was globally stationary, reversible, and homogeneous (SRH), and that a model of evolution with one or more site-specific and time-reversible rate matrices (e.g., the GTR rate matrix) is enough to accurately model the evolution of data over the whole tree. However, an increasing body of data suggests that evolution under these conditions is an exception, rather than the norm. To address this issue, several non-SRH models of molecular evolution have been proposed, but they either ignore heterogeneity in the substitution process across sites (HAS) or assume it can be modeled accurately using the distribution. As an alternative to these models of evolution, we introduce a family of mixture models that approximate HAS without the assumption of an underlying predefined statistical distribution. This family of mixture models is combined with non-SRH models of evolution that account for heterogeneity in the substitution process across lineages (HAL). We also present two algorithms for searching model space and identifying an optimal model of evolution that is less likely to over- or underparameterize the data. The performance of the two new algorithms was evaluated using alignments of nucleotides with 10 000 sites simulated under complex non-SRH conditions on a 25-tipped tree. The algorithms were found to be very successful, identifying the correct HAL model with a 75% success rate (the average success rate for assigning rate matrices to the tree's 48 edges was 99.25%) and, for the correct HAL model, identifying the correct HAS model with a 98% success rate. Finally, parameter estimates obtained under the correct HAL-HAS model were found to be accurate and precise. The merits of our new algorithms were illustrated with an analysis of 42 337 second codon sites extracted from a concatenation of 106 alignments of orthologous genes encoded by the nuclear genomes of Saccharomyces cerevisiae, S. paradoxus, S. mikatae, S. kudriavzevii, S. castellii, S. kluyveri, S. bayanus, and Candida albicans. Our results show that second codon sites in the ancestral genome of these species contained 49.1% invariable sites, 39.6% variable sites belonging to one rate category (V1), and 11.3% variable sites belonging to a second rate category (V2). The ancestral nucleotide content was found to differ markedly across these three sets of sites, and the evolutionary processes operating at the variable sites were found to be non-SRH and best modeled by a combination of eight edge-specific rate matrices (four for V1 and four for V2). The number of substitutions per site at the variable sites also differed markedly, with sites belonging to V1 evolving slower than those belonging to V2 along the lineages separating the seven species of Saccharomyces. Finally, sites belonging to V1 appeared to have ceased evolving along the lineages separating S. cerevisiae, S. paradoxus, S. mikatae, S. kudriavzevii, and S. bayanus, implying that they might have become so selectively constrained that they could be considered invariable sites in these species.

Evidence of gene conversion in the evolutionary process of the codon 41/42 (-CTTT) mutation causing beta-thalassemia in southern China

The 4-bp deletion (-CTTT) at codon 41/42 (CD41/42) of the human beta-globin gene represents one of the most common beta-thalassemia mutations in East Asia and Southeast Asia, which is historically afflicted with endemic malaria, thus hypothetically evolvi

Perception of brazilian citizens about Darwinism and the (Non) Influence of God in the evolutionary process

The current context is unique in relation to the teaching of evolution in Brazil and the population's perception of evolution. On the one hand, it is said often about Darwinism in various media, especially due to the relatively recent commemoration of the two hundred years of the birth of Charles Darwin and one hundred and fifty years of the launch of the book The Origin of Species. On the other hand, it is clear, in recent years, a timid movement, more worryingly, in favor of equitable approach of creationist and evolutionist theories in the classroom. This article is a part of a research whose goal is to raise the design that Brazilian respondents have about the Darwinian view (which disregards the divine influence in the evolution of the species). The instrument used for data collection is a questionnaire, type Likert scale, which consists of a series of statements in which respondents must express their degree of agreement or disagreement with each statement. In this study, we present the results of the statement. "The thought of Darwin, which does not consider God as a participant in the process of evolution, is...". Analysis correlated with data on religion and education of the respondents are also held. The results point to a tendency of respondents not to accept the Darwinian view that disregards God's interference in the evolutionary process. The data also show that respondents' choices are influenced by religion and education. The frequency of responses that tend to accept the Darwinian view (which disregards the divine participation in the evolution of the species) is higher among respondents with higher levels of education. Adherents to religions "evangelical" tend to deny this view more often than followers of other religions. Given the potential risks of inserting creationist approaches in school education, it is necessary a discussion of the possible impacts of this rejection of Darwin's thinking (which does not consider God as a participant in the evolutionary process), indicated here, in the teaching of evolution. This work was supported by FAPEMIG.

INTEGRATED MANAGEMENT OF THE INVASIVE SPECIES CIRSIUM ARVENSE, CANADA THISTLE, AND PHRAGMITES AUSTRALIS, COMMON REED: USING ECOLOGICALLY BASED CONTROL MEASURES AT EACH STAGE OF THE INVASION PROCESS

Invasive plant species threaten natural areas by reducing biodiversity and altering ecosystem functions. They also impact agriculture by reducing crop and livestock productivity. Millions of dollars are spent on invasive species control each year, and traditionally, herbicides are used to manage invasive species. Herbicides have human and environmental health risks associated with them; therefore, it is essential that land managers and stakeholders attempt to reduce these risks by utilizing the principles of integrated weed management. Integrated weed management is a practice that incorporates a variety of measures and focuses on the ecology of the invasive plant to manage it. Roadways are high risk areas that have high incidence of invasive species. Roadways act as conduits for invasive species spread and are ideal harborages for population growth; therefore, roadways should be a primary target for invasive species control. There are four stages in the invasion process which an invasive species must overcome: transport, establishment, spread, and impact. The aim of this dissertation was to focus on these four stages and examine the mechanisms underlying the progression from one stage to the next, while also developing integrated weed management strategies. The target species were Phragmites australis, common reed, and Cisrium arvense, Canada thistle. The transport and establishment risks of P. australis can be reduced by removing rhizome fragments from soil when roadside maintenance is performed. The establishment and spread of C. arvense can be reduced by planting particular resistant species, e.g. Heterotheca villosa, especially those that can reduce light transmittance to the soil. Finally, the spread and impact of C. arvense can be mitigated on roadsides through the use of the herbicide aminopyralid. The risks associated with herbicide drift produced by application equipment can be reduced by using the Wet-Blade herbicide application system.

A natural model for architecture : the nature of the evolutionary model 1995

John Frazer's architectural work is inspired by living and generative processes. Both evolutionary and revolutionary, it explores informatin ecologies and the dynamics of the spaces between objects. Fuelled by an interest in the cybernetic work of Gordon Pask and Norbert Wiener, and the possibilities of the computer and the "new science" it has facilitated, Frazer and his team of collaborators have conducted a series of experiments that utilize genetic algorithms, cellular automata, emergent behaviour, complexity and feedback loops to create a truly dynamic architecture. Frazer studied at the Architectural Association (AA) in London from 1963 to 1969, and later became unit master of Diploma Unit 11 there. He was subsequently Director of Computer-Aided Design at the University of Ulter - a post he held while writing An Evolutionary Architecture in 1995 - and a lecturer at the University of Cambridge. In 1983 he co-founded Autographics Software Ltd, which pioneered microprocessor graphics. Frazer was awarded a person chair at the University of Ulster in 1984. In Frazer's hands, architecture becomes machine-readable, formally open-ended and responsive. His work as computer consultant to Cedric Price's Generator Project of 1976 (see P84)led to the development of a series of tools and processes; these have resulted in projects such as the Calbuild Kit (1985) and the Universal Constructor (1990). These subsequent computer-orientated architectural machines are makers of architectural form beyond the full control of the architect-programmer. Frazer makes much reference to the multi-celled relationships found in nature, and their ongoing morphosis in response to continually changing contextual criteria. He defines the elements that describe his evolutionary architectural model thus: "A genetic code script, rules for the development of the code, mapping of the code to a virtual model, the nature of the environment for the development of the model and, most importantly, the criteria for selection. In setting out these parameters for designing evolutionary architectures, Frazer goes beyond the usual notions of architectural beauty and aesthetics. Nevertheless his work is not without an aesthetic: some pieces are a frenzy of mad wire, while others have a modularity that is reminiscent of biological form. Algorithms form the basis of Frazer's designs. These algorithms determine a variety of formal results dependent on the nature of the information they are given. His work, therefore, is always dynamic, always evolving and always different. Designing with algorithms is also critical to other architects featured in this book, such as Marcos Novak (see p150). Frazer has made an unparalleled contribution to defining architectural possibilities for the twenty-first century, and remains an inspiration to architects seeking to create responsive environments. Architects were initially slow to pick up on the opportunities that the computer provides. These opportunities are both representational and spatial: computers can help architects draw buildings and, more importantly, they can help architects create varied spaces, both virtual and actual. Frazer's work was groundbreaking in this respect, and well before its time.

User-designer collaboration during the early stage of the design process

As user involvement becomes a necessary part of the product development process, various ways of accessing users' latent needs have been developed and studied. Reviews of literatures in user involvement and product development have revealed that accessing users' latent needs and transferring them into design process could be facilitated by effectively implementing user-designer collaboration during the early stage of the design process. In this paper, various types of user-designer collaboration were observed and then distinct characteristics of user-designer collaboration were classified into three categories. 1) Passive objectivity, 2) workplace democratisation, and 3) shared contexts were observed as strategies for better user-designer collaboration, which have been employed in the area of user-centred design, user participatory design and design for experiencing. Based on the literature review, this paper proposed a basic collaboration mechanism between the users and the designers during the early stage of the design process and then discussed how its mechanism will help to describe the interactions between the users and the designers during the user involvement sessions.

The mechanical heterogeneity of the hard callus influences local tissue strains during bone healing : a finite element study based on sheep experiments

During secondary fracture healing, various tissue types including new bone are formed. The local mechanical strains play an important role in tissue proliferation and differentiation. To further our mechanobiological understanding of fracture healing, a precise assessment of local strains is mandatory. Until now, static analyses using Finite Elements (FE) have assumed homogenous material properties. With the recent quantification of both the spatial tissue patterns (Vetter et al., 2010) and the development of elastic modulus of newly formed bone during healing (Manjubala et al., 2009), it is now possible to incorporate this heterogeneity. Therefore, the aim of this study is to investigate the effect of this heterogeneity on the strain patterns at six successive healing stages. The input data of the present work stemmed from a comprehensive cross-sectional study of sheep with a tibial osteotomy (Epari et al., 2006). In our FE model, each element containing bone was described by a bulk elastic modulus, which depended on both the local area fraction and the local elastic modulus of the bone material. The obtained strains were compared with the results of hypothetical FE models assuming homogeneous material properties. The differences in the spatial distributions of the strains between the heterogeneous and homogeneous FE models were interpreted using a current mechanobiological theory (Isakson et al., 2006). This interpretation showed that considering the heterogeneity of the hard callus is most important at the intermediate stages of healing, when cartilage transforms to bone via endochondral ossification.

Child Victims of Sexual Abuse: Children's Experience of the Investigative Process in the Criminal Justice System

This paper is a selected review of research on issues surrounding the investigation of intra-familial child sexual abuse for children aged eight and above, in the criminal justice system. Particular attention is paid to features of the investigative interview in relation to the child's level of understanding, ability to report and likely emotional response when the proceedings take place. Best practice by police and social care agencies involves establishing valid and reliable information from children while attending to their developmental level and emotional state. The review aims to distil principles optimising this process from both the investigative judicial perspective and the child's focus, as well as from the inter-agency perspective and information sharing. Recommendations are made for improving the interview process based on research and methods from a range of disciplines and to optimise information recording in a format easily shared between agencies. Updated and ongoing training procedures are key to successful practice with training shared across police and social work agencies. The focus of this review is informed by preliminary findings from pilot research in progress on behalf of the Metropolitan Police Child Abuse Investigation Command.

The use of an electrostatic lens to enhance the efficiency of the electrospinning process

Electrospun scaffolds manufactured using conventional electrospinning configurations have an intrinsic thickness limitation, due to a charge build-up at the collector. To overcome this limitation, an electrostatic lens has been developed that, at the same relative rate of deposition, focuses the polymer jet onto a smaller area of the collector, resulting in the fabrication of thick scaffolds within a shorter period of time. We also observed that a longer deposition time (up to 13 h, without the intervention of the operator) could be achieved when the electrostatic lens was utilised, compared to 9–10 h with a conventional processing set-up and also showed that fibre fusion was less likely to occur in the modified method. This had a significant impact on the mechanical properties, as the scaffolds obtained with the conventional process had a higher elastic modulus and ultimate stress and strain at short times. However, as the thickness of the scaffolds produced by the conventional electrospinning process increased, a 3-fold decrease in the mechanical properties was observed. This was in contrast to the modified method, which showed a continual increase in mechanical properties, with the properties of the scaffold finally having similar mechanical properties to the scaffolds obtained via the conventional process at longer times. This “focusing” device thus enabled the fabrication of thicker 3-dimensional electrospun scaffolds (of thicknesses up to 3.5 mm), representing an important step towards the production of scaffolds for tissue engineering large defect sites in a multitude of tissues.

Simplified computation and generalization of the refined process structure tree

A business process is often modeled using some kind of a directed flow graph, which we call a workflow graph. The Refined Process Structure Tree (RPST) is a technique for workflow graph parsing, i.e., for discovering the structure of a workflow graph, which has various applications. In this paper, we provide two improvements to the RPST. First, we propose an alternative way to compute the RPST that is simpler than the one developed originally. In particular, the computation reduces to constructing the tree of the triconnected components of a workflow graph in the special case when every node has at most one incoming or at most one outgoing edge. Such graphs occur frequently in applications. Secondly, we extend the applicability of the RPST. Originally, the RPST was applicable only to graphs with a single source and single sink such that the completed version of the graph is biconnected. We lift both restrictions. Therefore, the RPST is then applicable to arbitrary directed graphs such that every node is on a path from some source to some sink. This includes graphs with multiple sources and/or sinks and disconnected graphs.

Commitment to internationalisation : an extension of the internationalisation process model

Notwithstanding the interest over many years by scholars in modeling the internationalization of the firm, the initial transition for the firm from domestic to international operations remains under-researched. We identify the behavioral factors that are important at the pre-internationalization state and discuss how they may interrelate to influence a decision to commit to internationalization through export commencement. We study export commitment by proposing and constructing an index that incorporates the factors that influence a firm’s propensity to commit to export activities. Utilizing the items from this index in a logistic regression analysis, we distinguish between the pre-internationalization characteristics of exporting and non-exporting firms to better understand the key influences in export commitment. Implications are discussed.