Molecular modelling studies of binding of DACD derivatives into G-Quadruplex DNA: comparison of force field and quantum polarized ligand docking methods

The DNA G-qadruplexes are one of the targets being actively explored for anti-cancer therapy by inhibiting them through small molecules. This computational study was conducted to predict the binding strengths and orientations of a set of novel dimethyl-amino-ethyl-acridine (DACA) analogues that are designed and synthesized in our laboratory, but did not diffract in Synchrotron light.Thecrystal structure of DNA G-Quadruplex(TGGGGT)4(PDB: 1O0K) was used as target for their binding properties in our studies.We used both the force field (FF) and QM/MM derived atomic charge schemes simultaneously for comparing the predictions of drug binding modes and their energetics. This study evaluates the comparative performance of fixed point charge based Glide XP docking and the quantum polarized ligand docking schemes. These results will provide insights on the effects of including or ignoring the drug-receptor interfacial polarization events in molecular docking simulations, which in turn, will aid the rational selection of computational methods at different levels of theory in future drug design programs. Plenty of molecular modelling tools and methods currently exist for modelling drug-receptor or protein-protein, or DNA-protein interactionssat different levels of complexities.Yet, the capasity of such tools to describevarious physico-chemical propertiesmore accuratelyis the next step ahead in currentresearch.Especially, the usage of most accurate methods in quantum mechanics(QM) is severely restricted by theirtedious nature. Though the usage of massively parallel super computing environments resulted in a tremendous improvement in molecular mechanics (MM) calculations like molecular dynamics,they are still capable of dealing with only a couple of tens to hundreds of atoms for QM methods. One such efficient strategy that utilizes thepowers of both MM and QM are the QM/MM hybrid methods. Lately, attempts have been directed towards the goal of deploying several different QM methods for betterment of force field based simulations, but with practical restrictions in place. One of such methods utilizes the inclusion of charge polarization events at the drug-receptor interface, that is not explicitly present in the MM FF.

Evoked prior learning experience and approach to learning as predictors of academic achievement

Background. In separate studies and research from different perspectives, five factors are found to be among those related to higher quality outcomes of student learning (academic achievement). Those factors are higher self-efficacy, deeper approaches to learning, higher quality teaching, students’ perceptions that their workload is appropriate, and greater learning motivation. University learning improvement strategies have been built on these research results. Aim. To investigate how students’ evoked prior experience, perceptions of their learning environment, and their approaches to learning collectively contribute to academic achievement. This is the first study to investigate motivation and self-efficacy in the same educational context as conceptions of learning, approaches to learning and perceptions of the learning environment. Sample. Undergraduate students (773) from the full range of disciplines were part of a group of over 2,300 students who volunteered to complete a survey of their learning experience. On completing their degrees 6 and 18 months later, their academic achievement was matched with their learning experience survey data. Method. A 77-item questionnaire was used to gather students’ self-report of their evoked prior experience (self-efficacy, learning motivation, and conceptions of learning), perceptions of learning context (teaching quality and appropriate workload), and approaches to learning (deep and surface). Academic achievement was measured using the English honours degree classification system. Analyses were conducted using correlational and multi-variable (structural equation modelling) methods. Results. The results from the correlation methods confirmed those found in numerous earlier studies. The results from the multi-variable analyses indicated that surface approach to learning was the strongest predictor of academic achievement, with self-efficacy and motivation also found to be directly related. In contrast to the correlation results, a deep approach to learning was not related to academic achievement, and teaching quality and conceptions of learning were only indirectly related to achievement. Conclusions. Research aimed at understanding how students experience their learning environment and how that experience relates to the quality of their learning needs to be conducted using a wider range of variables and more sophisticated analytical methods. In this study of one context, some of the relations found in earlier bivariate studies, and on which learning intervention strategies have been built, are not confirmed when more holistic teaching–learning contexts are analysed using multi-variable methods.

‘That’s definite discrimination’: practice under the umbrella of inclusion

Inclusive practice is well embedded across society and has developed over time. However, although policy and public view have moved forward, the way organisations address the agenda for inclusion often represents a superficial interpretation of this concept. Qualitative data were gathered using new ethnography to explore the experiences of a library-based reading group for visually impaired readers. The voices of the individuals shed light on the individual and collective experience of reading. These insights challenge the traditional views of distinct provision that are designed to address targets for inclusion of individuals with disabilities. We argue for a clearer focus on the unintentional consequences of practice in the name of inclusion that leave individuals feeling marginalised. This paper suggests the alternative focus on social justice as offering a discourse that focuses on society and away from the individual.

What people study when they study Twitter: classifying Twitter related academic papers

PURPOSE: Since its introduction in 2006, messages posted to the microblogging system Twitter have provided a rich dataset for researchers, leading to the publication of over a thousand academic papers. This paper aims to identify this published work and to classify it in order to understand Twitter based research. DESIGN/METHODOLOGY/APPROACH: Firstly the papers on Twitter were identified. Secondly, following a review of the literature, a classification of the dimensions of microblogging research was established. Thirdly, papers were qualitatively classified using open coded content analysis, based on the paper’s title and abstract, in order to analyze method, subject, and approach. FINDINGS: The majority of published work relating to Twitter concentrates on aspects of the messages sent and details of the users. A variety of methodological approaches are used across a range of identified domains. RESEARCH LIMITATIONS/IMPLICATIONS: This work reviewed the abstracts of all papers available via database search on the term “Twitter” and this has two major implications: 1) the full papers are not considered and so works may be misclassified if their abstract is not clear, 2) publications not indexed by the databases, such as book chapters, are not included. ORIGINALITY/VALUE: To date there has not been an overarching study to look at the methods and purpose of those using Twitter as a research subject. Our major contribution is to scope out papers published on Twitter until the close of 2011. The classification derived here will provide a framework within which researchers studying Twitter related topics will be able to position and ground their work

Vocabulary size revisited: the link between vocabulary size and academic achievement

Many researchers have tried to assess the number of words adults know. A general conclusion which emerges from such studies is that vocabularies of English monolingual adults are very large with considerable variation. This variation is important given that the vocabulary size of schoolchildren in the early years of school is thought to materially affect subsequent educational attainment. The data is difficult to interpret, however, because of the different methodologies which researchers use. The study in this paper uses the frequency-based vocabulary size test from Goulden et al (1990) and investigates the vocabulary knowledge of undergraduates in three British universities. The results suggest that monolingual speaker vocabulary sizes may be much smaller than is generally thought with far less variation than is usually reported. An average figure of about 10,000 English words families emerges for entrants to university. This figure suggests that many students must struggle with the comprehension of university level texts.