Constrained models of evolution lead to improved prediction of functional linkage from correlated gain and loss of genes

Motivation: We compare phylogenetic approaches for inferring functional gene links. The approaches detect independent instances of the correlated gain and loss of pairs of genes from species' genomes. We investigate the effect on results of basing evidence of correlations on two phylogenetic approaches, Dollo parsminony and maximum likelihood (ML). We further examine the effect of constraining the ML model by fixing the rate of gene gain at a low value, rather than estimating it from the data. Results: We detect correlated evolution among a test set of pairs of yeast (Saccharomyces cerevisiae) genes, with a case study of 21 eukaryotic genomes and test data derived from known yeast protein complexes. If the rate at which genes are gained is constrained to be low, ML achieves by far the best results at detecting known functional links. The model then has fewer parameters but it is more realistic by preventing genes from being gained more than once. Availability: BayesTraits by M. Pagel and A. Meade, and a script to configure and repeatedly launch it by D. Barker and M. Pagel, are available at http://www.evolution.reading.ac.uk .

An extensible automated protein annotation tool: standardizing input and output using validated XML

Motivation: There is a frequent need to apply a large range of local or remote prediction and annotation tools to one or more sequences. We have created a tool able to dispatch one or more sequences to assorted services by defining a consistent XML format for data and annotations. Results: By analyzing annotation tools, we have determined that annotations can be described using one or more of the six forms of data: numeric or textual annotation of residues, domains (residue ranges) or whole sequences. With this in mind, XML DTDs have been designed to store the input and output of any server. Plug-in wrappers to a number of services have been written which are called from a master script. The resulting APATML is then formatted for display in HTML. Alternatively further tools may be written to perform post-analysis.

Theory and practice in value management: a reply to Ellis et al (2005)

The constructivist model of 'soft' value management (VM) is contrasted with the VM discourse appropriated by cost consultants who operate from within UK quantity surveying (QS) practices. The enactment of VM by cost consultants is shaped by the institutional context within which they operate and is not necessarily representative of VM practice per se. Opportunities to perform VM during the formative stages of design are further constrained by the positivistic rhetoric that such practitioners use to conceptualize and promote their services. The complex interplay between VM theory and practice is highlighted and analysed from a non-deterministic perspective. Codified models of 'best practice' are seen to be socially constructed and legitimized through human interaction in the context of interorganizational networks. Published methodologies are seen to inform practice in only a loose and indirect manner, with extensive scope for localized improvization. New insights into the relationship between VM theory and practice are derived from the dramaturgical metaphor. The social reality of VM is seen to be constituted through scripts and performances, both of which are continuously contested across organizational arenas. It is concluded that VM defies universal definition and is conceptualized and enacted differently across different localized contexts.

Partnering in flight: From being to becoming

Current literature offers little understanding about how procurement methods are enacted in practice. Developments in procurement are often viewed as the result of responding to recommendations from particular constituents within the sector. The research seeks to remove itself from such deterministic leaning, counselling instead that procurement should not be viewed in static terms, but dynamically manifesting over time within a complex web of interconnections between various actors, their situated context and the broader industrial structure. Attention is given to how a client and construction firm engaged in a collusive interaction to realise an innovative procurement method that derived its legitimacy from a backcloth of initiatives promoted by various commentators. A case study of a medium-size regional contractor demonstrates how the first partnering arrangement was enacted within the UK affordable housing maintenance sector in the UK. The case study finds that the enactment of new procurement methods strongly relies on iterative learning between clients and contractors. It is further suggested that construction firms need to initiate new procurement in order to remain competitive within the sector. The findings point towards a pro-active initiative by the contractor and client to enact a ‘procurement first’. Encouragement may be drawn from this example by other contractors seeking to offer more than simply responsive procurement solutions.

Tests of syntactic comprehension in aphasia: an investigation of task effects

Background: Consistency of performance across tasks that assess syntactic comprehension in aphasia has clinical and theoretical relevance. In this paper we add to the relatively sparse previous work on how sentence comprehension abilities are influenced by the nature of the assessment task. Aims: Our aims are: (1) to compare linguistic performance across sentence-picture matching, enactment, and truth-value judgement tasks; (2) to investigate the impact of pictorial stimuli on syntactic comprehension. Methods Procedures: We tested a group of 10 aphasic speakers (3 with fluent and 7 with non-fluent aphasia) in three tasks (Experiment 1): (i) sentence-picture matching with four pictures, (ii) sentence-picture matching with two pictures, and (iii) enactment. A further task of truth-value judgement was given to a subgroup of those speakers (n=5, Experiment 2). Similar sentence types across all tasks were used and included canonical (actives, subject clefts) and non-canonical (passives, object clefts) sentences. We undertook two types of analyses: (a) we compared canonical and non-canonical sentences in each task; (b) we compared performance between (i) actives and passives, (ii) subject and object clefts in each task. We examined the results of all participants as a group and as case-series. Outcomes Results: Several task effects emerged. Overall, the two-picture sentence-picture matching and enactment tasks were more discriminating than the four-picture condition. Group performance in the truth-value judgement task was similar to two-picture sentence-picture matching and enactment. At the individual level performance across tasks contrasted to some group results. Conclusions: Our findings revealed task effects across participants. We discuss reasons that could explain the diverse profiles of performance and the implications for clinical practice.

The representation of delayed intentions: a prospective subject-performed task?

To-be-enacted material is more accessible in tests of recognition and lexical decision than material not intended for action (T. Goschke J. Kuhl, 1993; R. L. Marsh, J. L. Hicks, & M. L. Bink, 1998). This finding has been attributed to the superior status of intention-related information. The current article explores an alternative (action-superiority) account that draws parallels between the intended enactment effect (IEE) and the subject-performed task effect. Using 2 paradigms, the authors observed faster recognition latencies for both enacted and to-be-enacted material. It is crucial to note that there was no evidence of an IEE for items that had already been executed during encoding. The IEE was also eliminated when motor processing was prevented after verbal encoding. These findings suggest an overlap between overt and intended enactment and indicate that motor information may be activated for verbal material in preparation for subsequent execution.

Aging and the accessibility of performed and to-be-performed actions

In young adults information designated for future enactment is more readily accessible from memory than information not intended for enactment (e.g. Goschke & Kuhl, 1993). We examined whether this advantage for to-be-enacted material is reduced in older adults and thus whether attenuated action accessibility could underlie age-associated declines in prospective remembering. Young and older adults showed an equivalent increase in accessibility (faster recognition latencies) for to-be-enacted items over items intended for verbal report. Both age groups also showed increased accessibility for actions performed at encoding compared with verbally encoded items. Moreover, these effects were non-additive, suggesting similarities in the representation of completed and to-be-completed actions.

Motor brain regions are involved in the encoding of delayed intentions: a fMRI study

In studies of prospective memory, recall of the content of delayed intentions is normally excellent, probably because they contain actions that have to be enacted at a later time. Action words encoded for later enactment are more accessible from memory than those encoded for later verbal report [Freeman, J.E., and Ellis, J.A. 2003a. The representation of delayed intentions: A prospective subject-performed task? Journal of Experimental Psychology: Learning, Memory, and Cognition, 29, 976-992.]. As this higher assessibility is lost when the intended actions have to be enacted during encoding, or when a motor interference task is introduced concurrent to intention encoding, Freeman and Ellis suggested that the advantage of to-be-enacted actions is due to additional preparatory motor operations during encoding. Accordingly, in a fMRI study with 10 healthy young participants, we investigated whether motor brain regions are differentially activated during verbal encoding of actions for later enactment with the right hand in contrast to verbal encoding of actions for later verbal report. We included an additional condition of verbal encoding of abstract verbs for later verbal report to investigate whether the semantic motor information inherent in action verbs in contrast to abstract verbs activates motor brain regions different from those involved in the verbal encoding of actions for later enactment. Differential activation for the verbal encoding of to-be-enacted actions in contrast to to-be-reported actions was found in brain regions known to be involved in covert motor preparation for hand movements, i.e. the postcentral gyrus, the precuneus, the dorsal and ventral premotor cortex, the posterior middle temporal gyrus and the inferior parietal lobule. There was no overlap between these brain regions and those differentially activated during the verbal encoding of actions in contrast to abstract verbs for later verbal report. Consequently, the results of this fMRI study suggest the presence of preparatory motor operations during the encoding of delayed intentions requiring a future motor response, which cannot be attributed to semantic information inherent to action verbs. (c) 2006 Elsevier B.V. All rights reserved.

Copyright and research: an archivangelist's perspective

Conflation of academic copyright issues with respect to books (whether text books, research monographs or popularisations) and research articles, is rife in the academic publishing industry. A charitable interpretation is that this is because to publishers they are all effectively the same: a product produced for commercial benefit. An uncharitable interpretation is that this is a classic Fear Uncertainty and Doubt approach, in an attempt to delay the inevitable move to Open Access (OA) to research articles. To authors, however, research articles and books are generally very different things. Research articles are produced without the expectation of direct financial return, whereas books generally include some consideration of financial return. Taylor’s “Copyright and research: an academic publisher’s perspective” (SCRIPT-ed 4:2) falls wholesale into this mental trap and in particular his lauding of the position paper of the Association of American Professional and Scholarly Publishers, shows a lack of understanding of the continuing huge loss to scholarship of a lack of OA to research articles. It should be regarded as a categorical imperative for scholars to embrace OA to research articles.

Adobe Garamond Premier Pro Greek

In 2003, through a conference presentation in Vancouver and a series of exchanges with Lemon, Leonidas convinced Adobe to substantially extend the coverage of the Greek script in forthcoming Adobe typefaces. The revised brief for Garamond was extended to include, for the first time in a digital typeface, extensive polytonic support, full archaic characters, and small capitals with optional polytonic diacritics; these features should be implemented with respect for the Greek language’s complex rules for case conversion, allowing full dictionary support regardless of the features applied. This project was the first where these issues were addressed, both from a documentation and a development point of view. Leonidas’ responsibilities lay with researching historical and current conventions, developing specifications for the appearance and behaviour of the typefaces, editing glyph outlines, and testing of development versions.

Adobe Devanagari typeface

Typeface design: collaborative work commissioned by Adobe Inc. Published but unreleased. The Adobe Devanagari typefaces were commissioned from Tiro Typeworks and collaboratively designed by Tim Holloway, Fiona Ross and John Hudson, beginning in 2005. The types were officially released in 2009. The design brief was to produce a typeface for modern business communications in Hindi and other languages, to be legible both in print and on screen. Adobe Devanagari was designed to be highly readable in a range of situations including quite small sizes in spreadsheets and in continuous text setting, as well as at display sizes, where the full character of the typeface reveals itself. The construction of the letters is based on traditional penmanship but possesses less stroke contrast than many Devanagari types, in order to maintain strong, legible forms at smaller sizes. To achieve a dynamic, fluid style the design features a rounded treatment of distinguishing terminals and stroke reversals, open counters that also aid legibility at smaller sizes, and delicately flaring strokes. Together, these details reveal an original hand and provide a contemporary approach that is clean, clear and comfortable to read whether in short or long passages of text. This new approach to a traditional script is intended to counter the dominance of rigid, staccato-like effects of straight verticals and horizontals in earlier types and many existing fonts. OpenType Layout features in the fonts provide both automated and discretionary access to an extensive glyph set, enabling sophisticated typography. Many conjuncts preferred in classical literary texts and particularly in some North Indian languages are included; these literary conjuncts may be substituted by specially designed alternative linear forms and fitted half forms. The length of the ikars—ि and ी—varies automatically according to adjacent letter or conjunct width. Regional variants of characters and numerals (e.g. Marathi forms) are included as alternates. Careful attention has been given to the placements of all vowel signs and modifiers. The fonts include both proportional and tabular numerals in Indian and European styles. Extensive kerning covers several thousand possible combinations of half forms and full forms to anticipate arbitrary conjuncts in foreign loan words. _____

Highly accurate detection of ovarian cancer using CA125 but limited improvement with serum matrix-assisted laser desorption/ionization time-of-flight mass spectrometry profiling

Objectives: Our objective was to test the performance of CA125 in classifying serum samples from a cohort of malignant and benign ovarian cancers and age-matched healthy controls and to assess whether combining information from matrix-assisted laser desorption/ionization (MALDI) time-of-flight profiling could improve diagnostic performance. Materials and Methods: Serum samples from women with ovarian neoplasms and healthy volunteers were subjected to CA125 assay and MALDI time-of-flight mass spectrometry (MS) profiling. Models were built from training data sets using discriminatory MALDI MS peaks in combination with CA125 values and tested their ability to classify blinded test samples. These were compared with models using CA125 threshold levels from 193 patients with ovarian cancer, 290 with benign neoplasm, and 2236 postmenopausal healthy controls. Results: Using a CA125 cutoff of 30 U/mL, an overall sensitivity of 94.8% (96.6% specificity) was obtained when comparing malignancies versus healthy postmenopausal controls, whereas a cutoff of 65 U/mL provided a sensitivity of 83.9% (99.6% specificity). High classification accuracies were obtained for early-stage cancers (93.5% sensitivity). Reasons for high accuracies include recruitment bias, restriction to postmenopausal women, and inclusion of only primary invasive epithelial ovarian cancer cases. The combination of MS profiling information with CA125 did not significantly improve the specificity/accuracy compared with classifications on the basis of CA125 alone. Conclusions: We report unexpectedly good performance of serum CA125 using threshold classification in discriminating healthy controls and women with benign masses from those with invasive ovarian cancer. This highlights the dependence of diagnostic tests on the characteristics of the study population and the crucial need for authors to provide sufficient relevant details to allow comparison. Our study also shows that MS profiling information adds little to diagnostic accuracy. This finding is in contrast with other reports and shows the limitations of serum MS profiling for biomarker discovery and as a diagnostic tool

Minimising the latency induced by consistency control, within a large scale multi-user distributed virtual reality system

Where users are interacting in a distributed virtual environment, the actions of each user must be observed by peers with sufficient consistency and within a limited delay so as not to be detrimental to the interaction. The consistency control issue may be split into three parts: update control; consistent enactment and evolution of events; and causal consistency. The delay in the presentation of events, termed latency, is primarily dependent on the network propagation delay and the consistency control algorithms. The latency induced by the consistency control algorithm, in particular causal ordering, is proportional to the number of participants. This paper describes how the effect of network delays may be reduced and introduces a scalable solution that provides sufficient consistency control while minimising its effect on latency. The principles described have been developed at Reading over the past five years. Similar principles are now emerging in the simulation community through the HLA standard. This paper attempts to validate the suggested principles within the schema of distributed simulation and virtual environments and to compare and contrast with those described by the HLA definition documents.

Critical Mass: Sermon for the Church of the Atom (part of A Theatre to Address at Arnolfini, Bristol and Late at Tate Britain)

A Theatre to Address explores the work of contemporary artists who use text as both a visual and sonic form. In this programme, text appears not primarily as a means of communication, but as something which has shape and structure of its own. The Reading Room will also be displaying work that looks at text as concrete or visual poetry, and the script in artists' practice. Clare Gasson presents a new work The traveller - walking walking walking through ... that explores the connection between the text, the rhythm and the action. Maryam Jafri presents a performance-lecture Death With Friends, a body of visual and textual material that forms the basis for her new film of the same name. Pil and Galia Kollectiv present a radical worship for the apocalypse, featuring a sermon for the Church of the Atom with live music by Gelbart.

Flatpack revolution

The project consists of a trilogy of films and a live performance. The Future trilogy takes IKEA riot of 2005 as the starting point for a speculative history of a fictional future, culminating in a choreographed re-enactment of the original event. Shot on 16mm and 8mm film, the series explores the possibility of collective action emerging from the capitalist relations inherent in the consumer riot. The live performance No Haus Like Bau, staged at the HAU 1 theatre in Berlin for the 5th Berlin Biennale, continues this research into re-enactment and post-1989 politics by dramatizing the rise and fall of the soviet union as a neo-Constructivist mime using a stage set made of flatpack furniture. Using the aesthetics of Modernism and the avant garde, from Constructivist and Futurist constumes to biomechanics and Bauhaus theatre theory, the project transposes early twentieth century utopian ideology to a present day setting where mass uprisings are motivated by cheap commodities. These explorations of consumerism and revolution have been widely exhibited internationally and supported by Film London, Arts Council England, Collective Gallery and the Berlin Biennale. The Future Trilogy formed the basis of a solo exhibition at the Te Tuhi Art Centre in Auckland, New Zealand and was screened as part of the Signal and Noise media art festival in Vancouver, as well as other exhibitions and screenings including “Roll it to Me” at Collective Gallery, Edinburgh, and Apocatopia, Castlefield Gallery, Manchester.