Tracking repeats using significance and transitivty.

transitivity; extreme value distribution Motivation: Internal repeats in coding sequences correspond to structural and functional units of proteins. Moreover, duplication of fragments of coding sequences is known to be a mechanism to facilitate evolution. Identification of repeats is crucial to shed light on the function and structure of proteins, and explain their evolutionary past. The task is difficult because during the course of evolution many repeats diverged beyond recognition. Results: We introduce a new method TRUST, for ab-initio determination of internal repeats in proteins. It provides an improvement in prediction quality as compared to alternative state-of-the-art methods. The increased sensitivity and accuracy of the method is achieved by exploiting the concept of transitivity of alignments. Starting from significant local suboptimal alignments, the application of transitivity allows us to: 1) identify distant repeat homologues for which no alignments were found; 2) gain confidence about consistently well-aligned regions; and 3) recognize and reduce the contribution of nonhomologous repeats. This reassessment step enables us to derive a virtually noise-free profile representing a generalized repeat with high fidelity. We also obtained superior specificity by employing rigid statistical testing for self-sequence and profile-sequence alignments. Assessment was done using a database of repeat annotations based on structural superpositioning. The results show that TRUST is a useful and reliable tool for mining tandem and non-tandem repeats in protein sequence databases, able to predict multiple repeat types with varying intervening segments within a single sequence

Ab initio detection of fuzzy amino acid tandem repeats in protein sequences

Background Tandem repetitions within protein amino acid sequences often correspond to regular secondary structures and form multi-repeat 3D assemblies of varied size and function. Developing internal repetitions is one of the evolutionary mechanisms that proteins employ to adapt their structure and function under evolutionary pressure. While there is keen interest in understanding such phenomena, detection of repeating structures based only on sequence analysis is considered an arduous task, since structure and function is often preserved even under considerable sequence divergence (fuzzy tandem repeats). Results In this paper we present PTRStalker, a new algorithm for ab-initio detection of fuzzy tandem repeats in protein amino acid sequences. In the reported results we show that by feeding PTRStalker with amino acid sequences from the UniProtKB/Swiss-Prot database we detect novel tandemly repeated structures not captured by other state-of-the-art tools. Experiments with membrane proteins indicate that PTRStalker can detect global symmetries in the primary structure which are then reflected in the tertiary structure. Conclusions PTRStalker is able to detect fuzzy tandem repeating structures in protein sequences, with performance beyond the current state-of-the art. Such a tool may be a valuable support to investigating protein structural properties when tertiary X-ray data is not available

How Many Poor People Should There Be? A Rejoinder to Ravallion

Greatly boosting the political importance of the $1/day poverty headcount statistics the World Bank had been supplying since 1990, the first Millennium Development Goal (MDG) then promised "to halve, by the year 2015, the proportion of the world's people whose income is less than one dollar a day and the proportion of people who suffer from hunger." The UN and its MDG administrators have since decided that this proportion is to be calculated as a percentage not of world population but of the faster-growing population of the less developed countries, and that the benchmark year for this and all MDGs should be not the year of their adoption (2000), but 1990. The fate of billions is gravely affected by these as well as by additional decisions about how the relevant calculations are performed by the World Bank. It is in this context that Sanjay Reddy and I have joined the poverty measurement debate

Symmetric Key Structural Residues in Symmetric Proteins with Beta-Trefoil Fold

To understand how symmetric structures of many proteins are formed from asymmetric sequences, the proteins with two repeated beta-trefoil domains in Plant Cytotoxin B-chain family and all presently known beta-trefoil proteins are analyzed by structure-based multi-sequence alignments. The results show that all these proteins have similar key structural residues that are distributed symmetrically in their structures. These symmetric key structural residues are further analyzed in terms of inter-residues interaction numbers and B-factors. It is found that they can be distinguished from other residues and have significant propensities for structural framework. This indicates that these key structural residues may conduct the formation of symmetric structures although the sequences are asymmetric

Mapping the pedagogic practice of grade ten English teachers: a qualitative multi-lensed study.

Doctoral Degree. University of KwaZulu-Natal, Pietermaritzburg.This study addresses the issue of how to track the classroom talk of subject English teachers in Grade Ten classrooms in KwaZulu-Natal. Subject English, as a horizontal knowledge structure, presents particular challenges of content and methodological specification: what may be included, and the means of teaching and assessment, are contested, wide-ranging, and frequently opaque. English teachers are central to the construal of the subject in the classroom and their classroom talk is central to their construal of the subject to their learners. Classroom observations were conducted in four purposively selected KwaZulu- Natal state high schools, spanning the socio-economic spectrum, across the period 2005-2009. Twenty-six lessons were analysed using code theory’s concepts of classification and framing. This analysis presented broadly similar categorisations of strong classification and framing for most of the lessons, apart from some framing differences with respect to evaluation. However, my field observations had identified differences between the teachers’ classroom talk that were not captured. This led to the quest of finding pedagogically well theorised languages of description of teacher talk capable of capturing the range of variation and flow with greater nuance. Application of the lenses of systemic functional linguistics (SFL), Jacklin’s tripartite typology extending code theory (2004), Brodie’s expansion of classic classroom discourse analysis (2008, 2010), Legitimation Code Theory (LCT) (2014), and conceptual integration theory (2015), were successful in describing and discriminating more fully the range of pedagogy. Detailed analysis of four literature lessons (two teaching novels, two teaching poetry) from the two schools at opposite ends of the socio-economic spectrum, are presented as exemplars of these lenses’ capacity as languages of description for subject English teacher classroom talk. The multi-lensed descriptions highlighted variations such as: o the degree of use of nominalised discourse (SFL); o more dominantly discursive pedagogy or more dominantly conventional pedagogy (Jacklin); o more overt or more implicit evaluations, greater use of insert moves versus greater use of elicit moves (Brodie); and o cultivation of a cognitively associative literary gaze versus cultivation of a decoding of the text gaze and intricate movements by the teachers between relatively stronger and weaker epistemic and social relations; more frequent and deeper versus less frequent and flatter semantic waving (LCT). A fifth lesson, focused on learner oral performances of infomercials, is analysed using conceptual integration theory, as the sole example in the data set, of pedagogic conceptual integration. These analyses highlight the potential of these lenses as tools for the unpacking and specification of teachers’ pedagogic practice, particularly their pedagogic content knowledge, an undertaking which has been protractedly difficult to achieve beyond localised, intuitive description. They also illuminated the intricate complexity of pedagogy, and the propensity for pedagogic meaning to disintegrate when the level of analysis shifts down to too small a micro-focus. This highlights the ongoing need for research to pinpoint the ‘sweet spot’ of the optimally smallest unit of a pedagogic act. Key components of the pedagogic process emerged that we need more refined understanding of in relation to what teachers do and the impact of this on the epistemic access of learners: teacher pedagogic mobility, pedagogic coherence and pedagogic flow. The study points to the Jacklinian and LCT lenses as offering the most potential for the ongoing investigation of these dimensions