Whole-proteome phylogeny of large dsDNA viruses and parvoviruses through a composition vector method related to dynamical language model

Background The vast sequence divergence among different virus groups has presented a great challenge to alignment-based analysis of virus phylogeny. Due to the problems caused by the uncertainty in alignment, existing tools for phylogenetic analysis based on multiple alignment could not be directly applied to the whole-genome comparison and phylogenomic studies of viruses. There has been a growing interest in alignment-free methods for phylogenetic analysis using complete genome data. Among the alignment-free methods, a dynamical language (DL) method proposed by our group has successfully been applied to the phylogenetic analysis of bacteria and chloroplast genomes. Results In this paper, the DL method is used to analyze the whole-proteome phylogeny of 124 large dsDNA viruses and 30 parvoviruses, two data sets with large difference in genome size. The trees from our analyses are in good agreement to the latest classification of large dsDNA viruses and parvoviruses by the International Committee on Taxonomy of Viruses (ICTV). Conclusions The present method provides a new way for recovering the phylogeny of large dsDNA viruses and parvoviruses, and also some insights on the affiliation of a number of unclassified viruses. In comparison, some alignment-free methods such as the CV Tree method can be used for recovering the phylogeny of large dsDNA viruses, but they are not suitable for resolving the phylogeny of parvoviruses with a much smaller genome size.

The role of gender and framing in shaping community activists' perceptions of environmental risks

campaign to oppose projects proposed in their local community. The social constructionist perspective advocates that these motivations are driven by activists’ interpretation of reality, such that activists will assign multiple meanings to and frame environmental issues in a way that reflects their view of reality. Past research suggest that these are also influenced by patterns of shared meaning and interpretation that develop over time in protest movements that shape activists’ perceptions of the environmental risks and impacts associated with construction activity. This paper explores the role of gender distinctions in shaping perceptions of environmental risk and how this affects their framing of the environmental, social, cultural/ historical impacts associated with a construction project. Using Snow and Benford’s (1988) 3-prong analytical tool for framing: diagnostic framing, prognostic framing and motivational framing, this paper presents findings from the content analysis of in-depth interviews of 24 activists protesting against a highly controversial housing project in the greater Sydney metropolitan area. The research adopts a single case study approach, and is particularly significant as it investigates an extensive and on-going community-based protest campaign (dating back almost 20 years) that has generated the longest standing 24-hour community picket in Australia.

A people-to-people recommendation system using Tensor Space Models

Existing recommendation systems often recommend products to users by capturing the item-to-item and user-to-user similarity measures. These types of recommendation systems become inefficient in people-to-people networks for people to people recommendation that require two way relationship. Also, existing recommendation methods use traditional two dimensional models to find inter relationships between alike users and items. It is not efficient enough to model the people-to-people network with two-dimensional models as the latent correlations between the people and their attributes are not utilized. In this paper, we propose a novel tensor decomposition-based recommendation method for recommending people-to-people based on users profiles and their interactions. The people-to-people network data is multi-dimensional data which when modeled using vector based methods tend to result in information loss as they capture either the interactions or the attributes of the users but not both the information. This paper utilizes tensor models that have the ability to correlate and find latent relationships between similar users based on both information, user interactions and user attributes, in order to generate recommendations. Empirical analysis is conducted on a real-life online dating dataset. As demonstrated in results, the use of tensor modeling and decomposition has enabled the identification of latent correlations between people based on their attributes and interactions in the network and quality recommendations have been derived using the 'alike' users concept.

Free surface flow past topography : a beyond-all-orders approach

The problem of steady subcritical free surface flow past a submerged inclined step is considered. The asymptotic limit of small Froude number is treated, with particular emphasis on the effect that changing the angle of the step face has on the surface waves. As demonstrated by Chapman & Vanden-Broeck (2006), the divergence of a power series expansion in powers of the square of the Froude number is caused by singularities in the analytic continuation of the free surface; for an inclined step, these singularities may correspond to either the corners or stagnation points of the step, or both, depending on the angle of incline. Stokes lines emanate from these singularities, and exponentially small waves are switched on at the point the Stokes lines intersect with the free surface. Our results suggest that for a certain range of step angles, two wavetrains are switched on, but the exponentially subdominant one is switched on first, leading to an intermediate wavetrain not previously noted. We extend these ideas to the problem of flow over a submerged bump or trench, again with inclined sides. This time there may be two, three or four active Stokes lines, depending on the inclination angles. We demonstrate how to construct a base topography such that wave contributions from separate Stokes lines are of equal magnitude but opposite phase, thus cancelling out. Our asymptotic results are complemented by numerical solutions to the fully nonlinear equations.

Community protest groups' perceptions of environmental risks using social contagion theory

Local communities are vulnerable to the potential environmental risks associated with construction activity. Currently, little is understood about how perceptions of environmental risks are shaped and spread within a community. A better understanding of this process can help bridge the gap between developers and communities and bring about more sustainable development practices. This paper reports a research methodology which uses social contagion theory to investigate this process. The research adopts a single case study approach of a highly controversial housing project in the greater Sydney metropolitan area. The case study is particularly significant as it investigates an extensive and on-going community-based protest campaign (dating back almost 20 years) that has generated the longest standing 24 hour community picket in the New South Wales.

Conflict or consensus : an investigation of stakeholder concerns during the participation process of major infrastructure and construction projects in Hong Kong

Public participate in the planning and design of major public infrastructure and construction (PIC) projects is crucial to their success, as the interests of different stakeholders can be systematically captured and built into the finalised scheme. However, public participation may not always yield a mutually acceptable solution, especially when the interests of stakeholders are diverse and conflicting. Confrontations and disputes can arise unless the concerns or needs of the community are carefully analysed and addressed. The aim of the paper is to propose a systematic method of analysing stakeholder concerns relating to PIC projects by examining the degree of consensus and/or conflict involved. The results of a questionnaire survey and a series of interviews with different entities are provided, which indicate the existence of a significant divergence of views among stakeholder groups and that conflicts arise when there is a mismatch between peoples’ perception concerning money and happiness on the one hand and development and damages on the other. Policy and decision-makers should strive to resolve at least the majority of conflicts that arise throughout the lifecycle of major PIC projects so as to maximise their chance of success.

Limestone and speleothem trace element geochemistry as tools for palaeoclimatic reconstruction, Mount Etna region, central-coastal Queensland

This study investigated potential palaeoclimate proxies provided by rare earth element (REE) geochemistry in speleothems and in clay mineralogy of cave sediments. Speleothem and sediment samples were collected from a series of cave fill deposits that occurred with rich vertebrate fossil assemblages in and around Mount Etna National Park, Rockhampton (central coastal Queensland). The fossil deposits range from Plio- Pleistocene to Holocene in age (based on uranium/thorium dating) and appear to represent depositional environments ranging from enclosed rainforest to semi-arid grasslands. Therefore, the Mount Etna cave deposits offer the perfect opportunity to test new palaeoclimate tools as they include deposits that span a known significant climate shift on the basis of independent faunal data. The first section of this study investigates the REE distribution of the host limestone to provide baseline geochemistry for subsequent speleothem investigations. The Devonian Mount Etna Beds were found to be more complex than previous literature had documented. The studied limestone massif is overturned, highly recrystallised in parts and consists of numerous allochthonous blocks with different spatial orientations. Despite the complex geologic history of the Mount Etna Beds, Devonian seawater-like REE patterns were recovered in some parts of the limestone and baseline geochemistry was determined for the bulk limestone for comparison with speleothem REE patterns. The second part of the study focused on REE distribution in the karst system and the palaeoclimatic implications of such records. It was found that REEs have a high affinity for calcite surfaces and that REE distributions in speleothems vary between growth bands much more than along growth bands, thus providing a temporal record that may relate to environmental changes. The morphology of different speleothems (i.e., stalactites, stalagmites, and flowstones) has little bearing on REE distributions provided they are not contaminated with particulate fines. Thus, baseline knowledge developed in the study suggested that speleothems were basically comparable for assessing palaeoclimatically controlled variations in REE distributions. Speleothems from rainforest and semi-arid phases were compared and it was found that there are definable differences in REE distribution that can be attributed to climate. In particular during semiarid phases, total REE concentration decreased, LREE became more depleted, Y/Ho increased, La anomalies were more positive and Ce anomalies were more negative. This may reflect more soil development during rainforest phases and more organic particles and colloids, which are known to transport REEs, in karst waters. However, on a finer temporal scale (i.e. growth bands) within speleothems from the same climate regime, no difference was seen. It is suggested that this may be due to inadequate time for soil development changes on the time frames represented by differences in growth band density. The third part of the study was a reconnaissance investigation focused on mineralogy of clay cave sediments, illite/kaolinite ratios in particular, and the potential palaeoclimatic implications of such records. Although the sample distribution was not optimal, the preliminary results suggest that the illite/kaolinite ratio increased during cold and dry intervals, consistent with decreased chemical weathering during those times. The study provides a basic framework for future studies at differing latitudes to further constrain the parameters of the proxy. The identification of such a proxy recorded in cave sediment has broad implications as clay ratios could potentially provide a basic local climate proxy in the absence of fossil faunas and speleothem material. This study suggests that REEs distributed in speleothems may provide information about water throughput and soil formation, thus providing a potential palaeoclimate proxy. It highlights the importance of understanding the host limestone geochemistry and broadens the distribution and potential number of cave field sites as palaeoclimate information no longer relies solely on the presence of fossil faunas and or speleothems. However, additional research is required to better understand the temporal scales required for the proxies to be recognised.

Finding and matching communities in social networks using data mining

The rapid growth in the number of users using social networks and the information that a social network requires about their users make the traditional matching systems insufficiently adept at matching users within social networks. This paper introduces the use of clustering to form communities of users and, then, uses these communities to generate matches. Forming communities within a social network helps to reduce the number of users that the matching system needs to consider, and helps to overcome other problems from which social networks suffer, such as the absence of user activities' information about a new user. The proposed system has been evaluated on a dataset obtained from an online dating website. Empirical analysis shows that accuracy of the matching process is increased using the community information.

The feeling

In this video, a thumping house-music track is accompanied by lines of rotating text, which resemble computer screen-savers. The text is sourced from websites offering tips for dating and seducing potential lovers. This work engages with the language of online forums. It reworks text from online advice forums and mixes them with visual codes of computer graphics. By extending on some of Nicolas Bourriaud’s ideas around ‘postproduction’ and the creative and critical strategies of ‘editing’, it offers new speculative perspectives on the relationship between screen realities, desire and romance.

Kiss

In an age of mobile phones, Facebook, Twitter and online dating, interactions in mediated environments often outnumber face to face encounters. Kiss is an interactive light artwork by artists Priscilla Bracks & Gavin Sade. Kiss reacts to people standing in front of the artwork looking at each other - the moment before kissing. Without interaction the work generates a seductive, ambient, red lighting display, that creates the restful sense of staring into a fire. A fleeting response of white light – like sparks flying in the air – occurs the moment before two faces touch. These sparks are visible in peripheral vision, but fade when the kissing couple turns to look at the work. This moment - as two people look at each other - is a primal moment when two people recognise each other. Face to face encounters with another person are a privileged phenomenon in which the other person's presence and proximity are strongly felt. Kiss does not respond to every instance of a kiss or a look. Its recognition algorithms are fussy, selecting some faces and not others. As in life it’s difficult to tell why sparks fly with some people but not with others. For some this will be felt as a glitch. “This machine should be part of my social life!” But it does promote trial and error, asking viewers to be intimate in public and look at each other for longer than otherwise socially normal. 10 minutes continuous eye contact is said in most cases to arouse sexual feelings in both parties. But even if we don’t look that long, a short time may be all that is needed to explore the face of the person we are looking at. We see that they are human like us. We experience beauty, difference, discomfort, perhaps even nervous laughing, before turning to a more intimate moment of recognition.

The drift

In this video, text floats on screen amidst a field of swirling coloured orbs and a stock music soundtrack. The text is sourced from Internet dating websites and combine into a single animated portrait charting an array of likes, dislikes, influences, beliefs and hobbies. This work examines the nature of consciousness and identity in a contemporary context. It reworks the languages of Internet dating websites to question how we construct and communicate our sense of self. Drawing on Zygmunt Bauman’s theoretical work on “liquid modernity”, this work presents an exaggerated take on contemporary identity that emphasizes its construction through consumer tastes, lifestyle choices and relationships with popular culture.

Time-dependent rates of molecular evolution

For over half a century, it has been known that the rate of morphological evolution appears to vary with the time frame of measurement. Rates of microevolutionary change, measured between successive generations, were found to be far higher than rates of macroevolutionary change inferred from the fossil record. More recently, it has been suggested that rates of molecular evolution are also time dependent, with the estimated rate depending on the timescale of measurement. This followed surprising observations that estimates of mutation rates, obtained in studies of pedigrees and laboratory mutation-accumulation lines, exceeded long-term substitution rates by an order of magnitude or more. Although a range of studies have provided evidence for such a pattern, the hypothesis remains relatively contentious. Furthermore, there is ongoing discussion about the factors that can cause molecular rate estimates to be dependent on time. Here we present an overview of our current understanding of time-dependent rates. We provide a summary of the evidence for time-dependent rates in animals, bacteria and viruses. We review the various biological and methodological factors that can cause rates to be time dependent, including the effects of natural selection, calibration errors, model misspecification and other artefacts. We also describe the challenges in calibrating estimates of molecular rates, particularly on the intermediate timescales that are critical for an accurate characterization of time-dependent rates. This has important consequences for the use of molecular-clock methods to estimate timescales of recent evolutionary events.

Review ["Telling the Evolutionary Time : Molecular Clocks and the Fossil Record" edited by Philip C. J. Donoghue and M. Paul Smith]

Determining the temporal scale of biological evolution has traditionally been the preserve of paleontology, with the timing of species originations and major diversifications all being read from the fossil record. However, the ages of the earliest (correctly identified) records will underestimate actual origins due to the incomplete nature of the fossil record and the necessity for lineages to have evolved sufficiently divergent morphologies in order to be distinguished. The possibility of inferring divergence times more accurately has been promoted by the idea that the accumulation of genetic change between modern lineages can be used as a molecular clock (Zuckerkandl and Pauling, 1965). In practice, though, molecular dates have often been so old as to be incongruent even with liberal readings of the fossil record. Prominent examples include inferred diversifications of metazoan phyla hundreds of millions of years before their Cambrian fossil record appearances (e.g., Nei et al., 2001) and a basal split between modern birds (Neoaves) that is almost double the age of their earliest recognizable fossils (e.g., Cooper and Penny, 1997).

Reply to Camens : how recently did modern monotremes diversify?

Camens (1) responds to our analysis of morphological data (2) in which platypuses (Ornithorhynchidae) and echidnas (Tachyglossidae) were inferred to be each other's closest relatives, to the exclusion of Early Cretaceous forms, Teinolophos and Steropodon. Our phylogeny is consistent with the late appearance of undisputed fossil echidnas and platypuses. Molecular dating provided important independent corroboration, revealing that platypuses and echidnas diverged only 19–48 Ma, implying that Teinolophos and Steropodon (105–121 Ma) must lie outside the platypus–echidna dichotomy...