Identifying DNA-binding proteins by combining support vector machine and PSSM distance transformation

Background: DNA-binding proteins play a pivotal role in various intra- and extra-cellular activities ranging from DNA replication to gene expression control. Identification of DNA-binding proteins is one of the major challenges in the field of genome annotation. There have been several computational methods proposed in the literature to deal with the DNA-binding protein identification. However, most of them can't provide an invaluable knowledge base for our understanding of DNA-protein interactions. Results: We firstly presented a new protein sequence encoding method called PSSM Distance Transformation, and then constructed a DNA-binding protein identification method (SVM-PSSM-DT) by combining PSSM Distance Transformation with support vector machine (SVM). First, the PSSM profiles are generated by using the PSI-BLAST program to search the non-redundant (NR) database. Next, the PSSM profiles are transformed into uniform numeric representations appropriately by distance transformation scheme. Lastly, the resulting uniform numeric representations are inputted into a SVM classifier for prediction. Thus whether a sequence can bind to DNA or not can be determined. In benchmark test on 525 DNA-binding and 550 non DNA-binding proteins using jackknife validation, the present model achieved an ACC of 79.96%, MCC of 0.622 and AUC of 86.50%. This performance is considerably better than most of the existing state-of-the-art predictive methods. When tested on a recently constructed independent dataset PDB186, SVM-PSSM-DT also achieved the best performance with ACC of 80.00%, MCC of 0.647 and AUC of 87.40%, and outperformed some existing state-of-the-art methods. Conclusions: The experiment results demonstrate that PSSM Distance Transformation is an available protein sequence encoding method and SVM-PSSM-DT is a useful tool for identifying the DNA-binding proteins. A user-friendly web-server of SVM-PSSM-DT was constructed, which is freely accessible to the public at the web-site on http://bioinformatics.hitsz.edu.cn/PSSM-DT/.

Self-contained encrypted image folding

The recently introduced approach for Encrypted Image Folding is generalized to make it self-contained. The goal is achieved by enlarging the folded image so as to embed all the necessary information for the image recovery. The need for extra size is somewhat compensated by considering a transformation with higher folding capacity. Numerical examples show that the size of the resulting cipher image may be significantly smaller than the plain text one. The implementation of the approach is further extended to deal also with color images.

Technology enhanced learning in Higher Education

Technology-Enhanced Learning in Higher Education is an anthology produced by the international association, Learning in Higher Education (LiHE). LiHE, whose scope includes the activities of colleges, universities and other institutions of higher education, has been one of the leading organisations supporting a shift in the education process from a transmission-based philosophy to a student-centred, learning-based approach. Traditionally education has been envisaged as a process in which the teacher disseminates knowledge and information to the student, and directs them to perform – instructing, cajoling, encouraging them as appropriate – despite different students’ abilities. Yet higher education is currently experiencing rapid transformation, with the introduction of a broad range of technologies which have the potential to enhance student learning. This anthology draws upon the experiences of those practitioners who have been pioneering new applications of technology in higher education, highlighting not only the technologies themselves but also the impact which they have had on student learning. The anthology illustrates how new technologies – which are increasingly well-known and accepted by today’s ‘digital natives’ undertaking higher education – can be adopted and incorporated. One key conclusion is that learning remains a social process even in technology-enhanced learning contexts. So the technology-based proxies we construct need to retain and reflect the agency of the teacher. Technology-Enhanced Learning in Higher Education showcases some of the latest pedagogical technologies and their most creative, state-of-the-art applications to learning in higher education from around the world. Each of the chapters explores technology-enhanced learning in higher education in terms of either policy or practice. They contain detailed descriptions of approaches taken in very different curriculum areas, and demonstrate clearly that technology may and can enhance learning only if it is designed with the learning process of students at its core. So the use of technology in education is more linked to pedagogy than it is to bits and bytes.

Numerical solution of the Dirichlet initial boundary value problem for the heat equation in exterior 3-dimensional domains using integral equations

A numerical method for the Dirichlet initial boundary value problem for the heat equation in the exterior and unbounded region of a smooth closed simply connected 3-dimensional domain is proposed and investigated. This method is based on a combination of a Laguerre transformation with respect to the time variable and an integral equation approach in the spatial variables. Using the Laguerre transformation in time reduces the parabolic problem to a sequence of stationary elliptic problems which are solved by a boundary layer approach giving a sequence of boundary integral equations of the first kind to solve. Under the assumption that the boundary surface of the solution domain has a one-to-one mapping onto the unit sphere, these integral equations are transformed and rewritten over this sphere. The numerical discretisation and solution are obtained by a discrete projection method involving spherical harmonic functions. Numerical results are included.

Modelling and improving maintenance decisions:Having foresight with simulation and artificial intelligence

Machine breakdowns are one of the main sources of disruption and throughput fluctuation in highly automated production facilities. One element in reducing this disruption is ensuring that the maintenance team responds correctly to machine failures. It is, however, difficult to determine the current practice employed by the maintenance team, let alone suggest improvements to it. 'Knowledge based improvement' is a methodology that aims to address this issue, by (a) eliciting knowledge on current practice, (b) evaluating that practice and (c) looking for improvements. The methodology, based on visual interactive simulation and artificial intelligence methods, and its application to a Ford engine assembly facility are described. Copyright © 2002 Society of Automotive Engineers, Inc.

Study of neutral Fe(III) complexes of pyridoxal-N-substituted thiosemicarbazone with desolvation induced spin-state transformation above room temperature

The preparation and characterization of two new neutral ferric complexes with desolvation-induced discontinuous spin-state transformation above room temperature are reported. The compounds, Fe(Hthpy)(thpy).CH3OH.3H2O (1) and Fe(Hmthpy)(mthpy).2H2O (2), are low-spin (LS) at room temperature and below, whereas their nonsolvated forms are high-spin (HS), exhibiting zero-field splitting. In these complexes, Hthpy, Hmthpy, and thpy, mthpy are the deprotonated forms of pyridoxal thiosemicarbazone and pyridoxal methylthiosemicarbazone, respectively; each is an O,N,S-tridentate ligand. The molecular structures have been determined at 100(1) K using single-crystal X-ray diffraction techniques and resulted in a triclinic system (space group P1) and monoclinic unit cell (space group P21/c) for 1 and 2, respectively. Structures were refined to the final error indices, where RF = 0.0560 for 1 and RF = 0.0522 for 2. The chemical inequivalence of the ligands was clearly established, for the "extra" hydrogen atom on the monodeprotonated ligands (Hthpy, Hmthpy) was found to be bound to the nitrogen of the pyridine ring. The ligands are all of the thiol form; the doubly deprotonated chelates (thpy, mthpy) have C-S bond lengths slightly longer than those of the singly deprotonated forms. There is a three-dimensional network of hydrogen bonds in both compounds. The discontinuous spin-state transformation is accompanied with liberation of solvate molecules. This is evidenced also from DSC analysis. Heat capacity data for the LS and HS phases are tabulated at selected temperatures, the values of the enthalpy and entropy changes connected with the change of spin state were reckoned at DeltaH = 12.5 0.3 kJ mol-1 and DeltaS = 33.3 0.8 J mol-1 K-1, respectively, for 1 and DeltaH = 6.5 0.3 kJ mol-1 and DeltaS = 17.6 0.8 J mol-1 K-1, respectively, for 2

The relationship between student-centred lectures, emotional intelligence, and study teams:a social telemetry study with mobile telephony

A student-centred approach to teaching has been conceptualized as a key driver in higher education to facilitate understanding of concepts and improve attainment. The occurrence of student study team behaviours is diagnostic of this approach to teaching. However, the extent to which team behaviours are performed outside the parameters of formal teacher-learner environments remains under-researched. This is problematic as it is unclear whether study teams are maintained outside the confines of lectures, and the extent to which they impact on individual student grades. A naturalistic observational study was carried out that utilized short message text service communication as a means to record the frequency of team behaviours within informal environments. The findings suggest the frequency of team behaviours: 1) were positively associated with student grades; 2) increased after lectures independently rated as low in employing a student-centred focus; and 3) were facilitated by students' trait emotional intelligence.