Genesis and expansion of metazoan transcription factor gene classes

We know little about the genomic events that led to the advent of a multicellular grade of organization in animals, one of the most dramatic transitions in evolution. Metazoan multicellularity is correlated with the evolution of embryogenesis, which presumably was underpinned by a gene regulatory network reliant on the differential activation of signaling pathways and transcription factors. Many transcription factor genes that play critical roles in bilaterian development largely appear to have evolved before the divergence of cnidarian and bilaterian lineages. In contrast, sponges seem to have a more limited suite of transcription factors, suggesting that the developmental regulatory gene repertoire changed markedly during early metazoan evolution. Using whole- genome information from the sponge Amphimedon queenslandica, a range of eumetazoans, and the choanoflagellate Monosiga brevicollis, we investigate the genesis and expansion of homeobox, Sox, T- box, and Fox transcription factor genes. Comparative analyses reveal that novel transcription factor domains ( such as Paired, POU, and T- box) arose very early in metazoan evolution, prior to the separation of extant metazoan phyla but after the divergence of choanoflagellate and metazoan lineages. Phylogenetic analyses indicate that transcription factor classes then gradually expanded at the base of Metazoa before the bilaterian radiation, with each class following a different evolutionary trajectory. Based on the limited number of transcription factors in the Amphimedon genome, we infer that the genome of the metazoan last common ancestor included fewer gene members in each class than are present in extant eumetazoans. Transcription factor orthologues present in sponge, cnidarian, and bilaterian genomes may represent part of the core metazoan regulatory network underlying the origin of animal development and multicellularity.

The effects of maternal depression and parental conflict on children's peer play

Background Little is known about the relative effects of exposure to postnatal depression and parental conflict on the social functioning of school-aged children. This is, in part, because of a lack of specificity in the measurement of child and parental behaviour and a reliance on children's reports of their hypothetical responses to conflict in play. Methods In the course of a prospective longitudinal study of children of postnatally depressed and well women, 5-year-old children were videotaped at home with a friend in a naturalistic dressing-up play setting. As well as examining possible associations between the occurrence of postnatal depression and the quality of the children's interactions, we investigated the influence of parental conflict and co-operation, and the continuity of maternal depression. The quality of the current mother-child relationship was considered as a possible mediating factor. Results Exposure to postnatal depression was associated with increased likelihood, among boys, of displaying physical aggression in play with their friend. However, parental conflict mediated the effects of postnatal depression on active aggression during play, and was also associated with displays of autonomy and intense conflict. While there were no gender effects in terms of the degree or intensity of aggressive behaviours, girls were more likely to express aggression verbally using denigration and gloating whereas boys were more likely to display physical aggression via interpersonal and object struggles. Conclusions The study provided evidence for the specificity of effects, with strong links between parental and child peer conflict. These effects appear to arise from direct exposure to parental conflict, rather than indirectly, through mother-child interactions.

Supporting ad hoc collaborations in peer-to-peer networks

Traditionally, applications and tools supporting collaborative computing have been designed only with personal computers in mind and support a limited range of computing and network platforms. These applications are therefore not well equipped to deal with network heterogeneity and, in particular, do not cope well with dynamic network topologies. Progress in this area must be made if we are to fulfil the needs of users and support the diversity, mobility, and portability that are likely to characterise group work in future. This paper describes a groupware platform called Coco that is designed to support collaboration in a heterogeneous network environment. The work demonstrates that progress in the p development of a generic supporting groupware is achievable, even in the context of heterogeneous and dynamic networks. The work demonstrates the progress made in the development of an underlying communications infrastructure, building on peer-to-peer concept and topologies to improve scalability and robustness.

A peer-to-peer approach to content dissemination and search in collaborative networks

There are three key driving forces behind the development of Internet Content Management Systems (CMS) - a desire to manage the explosion of content, a desire to provide structure and meaning to content in order to make it accessible, and a desire to work collaboratively to manipulate content in some meaningful way. Yet the traditional CMS has been unable to meet the latter of these requirements, often failing to provide sufficient tools for collaboration in a distributed context. Peer-to-Peer (P2P) systems are networks in which every node is an equal participant (whether transmitting data, exchanging content, or invoking services) and there is an absence of any centralised administrative or coordinating authorities. P2P systems are inherently more scalable than equivalent client-server implementations as they tend to use resources at the edge of the network much more effectively. This paper details the rationale and design of a P2P middleware for collaborative content management.

Identifying problematic classes in text classification

Real-world text classification tasks often suffer from poor class structure with many overlapping classes and blurred boundaries. Training data pooled from multiple sources tend to be inconsistent and contain erroneous labelling, leading to poor performance of standard text classifiers. The classification of health service products to specialized procurement classes is used to examine and quantify the extent of these problems. A novel method is presented to analyze the labelled data by selectively merging classes where there is not enough information for the classifier to distinguish them. Initial results show the method can identify the most problematic classes, which can be used either as a focus to improve the training data or to merge classes to increase confidence in the predicted results of the classifier.

Are you thinking what I’m thinking? Peer group similarities in adolescent hostile attribution tendencies

A bias towards attributing hostile intent to others has been linked to aggression. In an adolescent sample, we investigated whether peer group homophily exists in the tendency towards attributing hostile intent. We assessed hostile attribution tendencies and self-reported aggressive behaviours in a normative sample of 910 adolescents, and computed average peer group scores based on nominated friend scores. Results indicated that adolescents showed significant correlations between their own level of hostile attributions and that of their peer group. Further analyses indicated that this effect occurred specifically in reciprocal friendships, and was retained even once own and peer group level of aggression were controlled.

Citation and peer review of data: moving towards formal data publication

This paper discusses many of the issues associated with formally publishing data in academia, focusing primarily on the structures that need to be put in place for peer review and formal citation of datasets. Data publication is becoming increasingly important to the scientific community, as it will provide a mechanism for those who create data to receive academic credit for their work and will allow the conclusions arising from an analysis to be more readily verifiable, thus promoting transparency in the scientific process. Peer review of data will also provide a mechanism for ensuring the quality of datasets, and we provide suggestions on the types of activities one expects to see in the peer review of data. A simple taxonomy of data publication methodologies is presented and evaluated, and the paper concludes with a discussion of dataset granularity, transience and semantics, along with a recommended human-readable citation syntax.

An experimental investigation of peer influences on hostile attributions in adolescents

Aggression in young people has been associated with a bias towards attributing hostile intent to others; however, little is known about the origin of biased social information processing. The current study explored the potential role of peer contagion in the emergence of hostile attribution in adolescents. 134 adolescents were assigned to one of two manipulated ‘chat-room’ conditions, where they believed they were communicating with online peers (e-confederates) who endorsed either hostile or benign intent attributions. Adolescents showed increased hostile attributions following exposure to hostile e-confederates and reduced hostility in the benign condition. Further analyses demonstrated that social anxiety was associated with a reduced tendency to take on hostile peer attitudes. Neither gender nor levels of aggression influenced individual susceptibility to peer influence, but aggressive adolescents reported greater affinity with hostile e-confederates.

Virtual landmarking for locality aware peer IDs

In Peer-to-Peer (P2P) networks, it is often desirable to assign node IDs which preserve locality relationships in the underlying topology. Node locality can be embedded into node IDs by utilizing a one dimensional mapping by a Hilbert space filling curve on a vector of network distances from each node to a subset of reference landmark nodes within the network. However this approach is fundamentally limited because while robustness and accuracy might be expected to improve with the number of landmarks, the effectiveness of 1 dimensional Hilbert Curve mapping falls for the curse of dimensionality. This work proposes an approach to solve this issue using Landmark Multidimensional Scaling (LMDS) to reduce a large set of landmarks to a smaller set of virtual landmarks. This smaller set of landmarks has been postulated to represent the intrinsic dimensionality of the network space and therefore a space filling curve applied to these virtual landmarks is expected to produce a better mapping of the node ID space. The proposed approach, the Virtual Landmarks Hilbert Curve (VLHC), is particularly suitable for decentralised systems like P2P networks. In the experimental simulations the effectiveness of the methods is measured by means of the locality preservation derived from node IDs in terms of latency to nearest neighbours. A variety of realistic network topologies are simulated and this work provides strong evidence to suggest that VLHC performs better than either Hilbert Curves or LMDS use independently of each other.

The global distribution of phytoplankton size spectrum and size classes from their light-absorption spectra derived from satellite data

The absorption spectra of phytoplankton in the visible domain hold implicit information on the phytoplankton community structure. Here we use this information to retrieve quantitative information on phytoplankton size structure by developing a novel method to compute the exponent of an assumed power-law for their particle-size spectrum. This quantity, in combination with total chlorophyll-a concentration, can be used to estimate the fractional concentration of chlorophyll in any arbitrarily-defined size class of phytoplankton. We further define and derive expressions for two distinct measures of cell size of mixed populations, namely, the average spherical diameter of a bio-optically equivalent homogeneous population of cells of equal size, and the average equivalent spherical diameter of a population of cells that follow a power-law particle-size distribution. The method relies on measurements of two quantities of a phytoplankton sample: the concentration of chlorophyll-a, which is an operational index of phytoplankton biomass, and the total absorption coefficient of phytoplankton in the red peak of visible spectrum at 676 nm. A sensitivity analysis confirms that the relative errors in the estimates of the exponent of particle size spectra are reasonably low. The exponents of phytoplankton size spectra, estimated for a large set of in situ data from a variety of oceanic environments (~ 2400 samples), are within a reasonable range; and the estimated fractions of chlorophyll in pico-, nano- and micro-phytoplankton are generally consistent with those obtained by an independent, indirect method based on diagnostic pigments determined using high-performance liquid chromatography. The estimates of cell size for in situ samples dominated by different phytoplankton types (diatoms, prymnesiophytes, Prochlorococcus, other cyanobacteria and green algae) yield nominal sizes consistent with the taxonomic classification. To estimate the same quantities from satellite-derived ocean-colour data, we combine our method with algorithms for obtaining inherent optical properties from remote sensing. The spatial distribution of the size-spectrum exponent and the chlorophyll fractions of pico-, nano- and micro-phytoplankton estimated from satellite remote sensing are in agreement with the current understanding of the biogeography of phytoplankton functional types in the global oceans. This study contributes to our understanding of the distribution and time evolution of phytoplankton size structure in the global oceans.