Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information

Background The majority of peptide bonds in proteins are found to occur in the trans conformation. However, for proline residues, a considerable fraction of Prolyl peptide bonds adopt the cis form. Proline cis/trans isomerization is known to play a critical role in protein folding, splicing, cell signaling and transmembrane active transport. Accurate prediction of proline cis/trans isomerization in proteins would have many important applications towards the understanding of protein structure and function. Results In this paper, we propose a new approach to predict the proline cis/trans isomerization in proteins using support vector machine (SVM). The preliminary results indicated that using Radial Basis Function (RBF) kernels could lead to better prediction performance than that of polynomial and linear kernel functions. We used single sequence information of different local window sizes, amino acid compositions of different local sequences, multiple sequence alignment obtained from PSI-BLAST and the secondary structure information predicted by PSIPRED. We explored these different sequence encoding schemes in order to investigate their effects on the prediction performance. The training and testing of this approach was performed on a newly enlarged dataset of 2424 non-homologous proteins determined by X-Ray diffraction method using 5-fold cross-validation. Selecting the window size 11 provided the best performance for determining the proline cis/trans isomerization based on the single amino acid sequence. It was found that using multiple sequence alignments in the form of PSI-BLAST profiles could significantly improve the prediction performance, the prediction accuracy increased from 62.8% with single sequence to 69.8% and Matthews Correlation Coefficient (MCC) improved from 0.26 with single local sequence to 0.40. Furthermore, if coupled with the predicted secondary structure information by PSIPRED, our method yielded a prediction accuracy of 71.5% and MCC of 0.43, 9% and 0.17 higher than the accuracy achieved based on the singe sequence information, respectively. Conclusion A new method has been developed to predict the proline cis/trans isomerization in proteins based on support vector machine, which used the single amino acid sequence with different local window sizes, the amino acid compositions of local sequence flanking centered proline residues, the position-specific scoring matrices (PSSMs) extracted by PSI-BLAST and the predicted secondary structures generated by PSIPRED. The successful application of SVM approach in this study reinforced that SVM is a powerful tool in predicting proline cis/trans isomerization in proteins and biological sequence analysis.

Speech recognition in adverse environments using lip information

The performance of automatic speech recognition systems deteriorates in the presence of noise. One known solution is to incorporate video information with an existing acoustic speech recognition system. We investigate the performance of the individual acoustic and visual sub-systems and then examine different ways in which the integration of the two systems may be performed. The system is to be implemented in real time on a Texas Instruments' TMS320C80 DSP.

The use of temporal speech and lip information for multi-modal speaker identification via multi-stream HMMs

Investigates the use of temporal lip information, in conjunction with speech information, for robust, text-dependent speaker identification. We propose that significant speaker-dependent information can be obtained from moving lips, enabling speaker recognition systems to be highly robust in the presence of noise. The fusion structure for the audio and visual information is based around the use of multi-stream hidden Markov models (MSHMM), with audio and visual features forming two independent data streams. Recent work with multi-modal MSHMMs has been performed successfully for the task of speech recognition. The use of temporal lip information for speaker identification has been performed previously (T.J. Wark et al., 1998), however this has been restricted to output fusion via single-stream HMMs. We present an extension to this previous work, and show that a MSHMM is a valid structure for multi-modal speaker identification

Factors that influence Information Systems decisions and outcomes: A summary of key themes from four case studies" (2006). ACIS 2006 Proceedings. Paper 43.

This paper reports a summary of key findings from an examination of Information Systems decision making in four organisations. The study focused on what factors influenced decision makers during the critical preimplementation phase of Information Systems projects when systems were evaluated, selected and acquired. Using data gathered from interviews and organisational documentation, a critical hermeneutic analysis was performed in order to build an understanding of how informational and contextual influences acted on decision makers. Eight broad themes of factors were identified as having influence on decision makers and outcomes.

The measurement of information system use: preliminary considerations

The concept of system use has suffered from a "too simplistic definition" (DeLone and McLean [9], p. 16). This paper reviews various attempts at conceptualization and measurement of system use and then proposes a re-conceptualization of it as "the level of incorporation of an information system within a user's processes." We then go on to develop the concept of a Functional Interface Point and four dimensions of system usage: automation level, the proportion of the business process encoded by the information system; extent, the proportion of the FIPs used by the business process; frequency, the rate at which FIPs are used by the participants in the process; and thoroughness, the level of use of information/functionality provided by the system at an FIP. The article concludes with a discussion of some implications of this re-conceptualization and areas for follow on research.

Library and information science education 2.0: guiding principles and models of best practice. Interview with Sue Reynolds.

In 2005, Stephen Abram, vice president of Innovation at SirsiDynix, challenged library and information science (LIS) professionals to start becoming “librarian 2.0.” In the last few years, discussion and debate about the “core competencies” needed by librarian 2.0 have appeared in the “biblioblogosphere” (blogs written by LIS professionals). However, beyond these informal blog discussions few systematic and empirically based studies have taken place. A project funded by the Australian Learning and Teaching Council fills this gap. The project identifies the key skills, knowledge, and attributes required by “librarian 2.0.” Eighty-one members of the Australian LIS profession participated in a series of focus groups. Eight themes emerged as being critical to “librarian 2.0”: technology, communication, teamwork, user focus, business savvy, evidence based practice, learning and education, and personal traits. Guided by these findings interviews with 36 LIS educators explored the current approaches used within contemporary LIS education to prepare graduates to become “librarian 2.0”. This video presents an example of ‘great practice’ in current LIS educative practice in helping to foster web 2.0 professionals.

Library and information science education 2.0 : guiding principles and models of best practice : interview with John Terrell

In 2005, Stephen Abram, vice president of Innovation at SirsiDynix, challenged library and information science (LIS) professionals to start becoming “librarian 2.0.” In the last few years, discussion and debate about the “core competencies” needed by librarian 2.0 have appeared in the “biblioblogosphere” (blogs written by LIS professionals). However, beyond these informal blog discussions few systematic and empirically based studies have taken place. A project funded by the Australian Learning and Teaching Council fills this gap. The project identifies the key skills, knowledge, and attributes required by “librarian 2.0.” Eighty-one members of the Australian LIS profession participated in a series of focus groups. Eight themes emerged as being critical to “librarian 2.0”: technology, communication, teamwork, user focus, business savvy, evidence based practice, learning and education, and personal traits. Guided by these findings interviews with 36 LIS educators explored the current approaches used within contemporary LIS education to prepare graduates to become “librarian 2.0”. This video presents an example of ‘great practice’ in current LIS education as it strives to foster web 2.0 professionals.

Library and information science education 2.0 : guiding principles and models of best practice : interview with Kate Davis.

In 2005, Stephen Abram, vice president of Innovation at SirsiDynix, challenged library and information science (LIS) professionals to start becoming “librarian 2.0.” In the last few years, discussion and debate about the “core competencies” needed by librarian 2.0 have appeared in the “biblioblogosphere” (blogs written by LIS professionals). However, beyond these informal blog discussions few systematic and empirically based studies have taken place. A project funded by the Australian Learning and Teaching Council fills this gap. The project identifies the key skills, knowledge, and attributes required by “librarian 2.0.” Eighty-one members of the Australian LIS profession participated in a series of focus groups. Eight themes emerged as being critical to “librarian 2.0”: technology, communication, teamwork, user focus, business savvy, evidence based practice, learning and education, and personal traits. Guided by these findings interviews with 36 LIS educators explored the current approaches used within contemporary LIS education to prepare graduates to become “librarian 2.0”. This video presents an example of ‘great practice’ in current LIS education as it strives to foster web 2.0 professionals.

Improving information security management in nonprofit organisations

All organisations, irrespective of size and type, need effective information security management (ISM) practices to protect vital organisational in- formation assets. However, little is known about the information security management practices of nonprofit organisations. Australian nonprofit organisations (NPOs) employed 889,900 people, managed 4.6 million volunteers and contributed $40,959 million to the economy during 2006-2007 (Australian Bureau of Statistics, 2009). This thesis describes the perceptions of information security management in two Australian NPOs and examines the appropriateness of the ISO 27002 information security management standard in an NPO context. The overall approach to the research is interpretive. A collective case study has been performed, consisting of two instrumental case studies with the researcher being embedded within two NPOs for extended periods of time. Data gathering and analysis was informed by grounded theory and action research, and the Technology Acceptance Model was utilised as a lens to explore the findings and provide limited generalisability to other contexts. The major findings include a distinct lack of information security management best practice in both organisations. ISM Governance and risk management was lacking and ISM policy was either outdated or non- existent. While some user focused ISM practices were evident, reference to standards, such as ISO 27002, were absent. The main factor that negatively impacted on ISM practices was the lack of resources available for ISM in the NPOs studied. Two novel aspects of information security dis- covered in this research were the importance of accuracy and consistency of information. The contribution of this research is a preliminary understanding of ISM practices and perceptions in NPOs. Recommendations for a new approach to managing information security management in nonprofit organisations have been proposed.

CAT Detect (Computer Activity Timeline Detection) : a tool for detecting inconsistency in computer activity timelines

The construction of timelines of computer activity is a part of many digital investigations. These timelines of events are composed of traces of historical activity drawn from system logs and potentially from evidence of events found in the computer file system. A potential problem with the use of such information is that some of it may be inconsistent and contradictory thus compromising its value. This work introduces a software tool (CAT Detect) for the detection of inconsistency within timelines of computer activity. We examine the impact of deliberate tampering through experiments conducted with our prototype software tool. Based on the results of these experiments, we discuss techniques which can be employed to deal with such temporal inconsistencies.

Elements pour adapter les systemes de recherche d'information aux dyslexiques [Elements to adapt information retrieval systems to dyslexic users]

RÉSUMÉ. La prise en compte des troubles de la communication dans l’utilisation des systèmes de recherche d’information tels qu’on peut en trouver sur le Web est généralement réalisée par des interfaces utilisant des modalités n’impliquant pas la lecture et l’écriture. Peu d’applications existent pour aider l’utilisateur en difficulté dans la modalité textuelle. Nous proposons la prise en compte de la conscience phonologique pour assister l’utilisateur en difficulté d’écriture de requêtes (dysorthographie) ou de lecture de documents (dyslexie). En premier lieu un système de réécriture et d’interprétation des requêtes entrées au clavier par l’utilisateur est proposé : en s’appuyant sur les causes de la dysorthographie et sur les exemples à notre disposition, il est apparu qu’un système combinant une approche éditoriale (type correcteur orthographique) et une approche orale (système de transcription automatique) était plus approprié. En second lieu une méthode d’apprentissage automatique utilise des critères spécifiques , tels que la cohésion grapho-phonémique, pour estimer la lisibilité d’une phrase, puis d’un texte. ABSTRACT. Most applications intend to help disabled users in the information retrieval process by proposing non-textual modalities. This paper introduces specific parameters linked to phonological awareness in the textual modality. This will enhance the ability of systems to deal with orthographic issues and with the adaptation of results to the reader when for example the reader is dyslexic. We propose a phonology based sentence level rewriting system that combines spelling correction, speech synthesis and automatic speech recognition. This has been evaluated on a corpus of questions we get from dyslexic children. We propose a specific sentence readability measure that involves phonetic parameters such as grapho-phonemic cohesion. This has been learned on a corpus of reading time of sentences read by dyslexic children.

Political information choices in a media saturated environment : credibility or convenience?

This thesis examines the ways in which citizens find out about socio-political issues. The project set out to discover how audience characteristics such as scepticism towards the media, gratifications sought, need for cognition and political interest influence information selection. While most previous information choice studies have focused on how individuals select from a narrow range of media types, this thesis considered a much wider sweep of the information landscape. This approach was taken to obtain an understanding of information choices in a more authentic context - in everyday life, people are not simply restricted to one or two news sources. Rather, they may obtain political information from a vast range of information sources, including media sources (e.g. radio, television, newspapers) and sources from beyond the media (eg. interpersonal sources, public speaking events, social networking websites). Thus, the study included both media and non-news media information sources. Data collection for the project consisted of a written, postal survey. The survey was administered to a probability sample in the greater Brisbane region, which is the third largest city in Australia. Data was collected during March and April 2008, approximately four months after the 2007 Australian Federal Election. Hence, the study was conducted in a non-election context. 585 usable surveys were obtained. In addition to measuring the attitudinal characteristics listed above, respondents were surveyed as to which information sources (eg. television shows, radio stations, websites and festivals) they usually use to find out about socio-political issues. Multiple linear regression analysis was conducted to explore patterns of influence between the audience characteristics and information consumption patterns. The results of this analysis indicated an apparent difference between the way citizens use news media sources and the way they use information sources from beyond the news media. In essence, it appears that non-news media information sources are used very deliberately to seek socio-political information, while media sources are used in a less purposeful way. If media use in a non-election context, such as that of the present study, is not primarily concerned with deliberate information seeking, media use must instead have other primary purposes, with political information acquisition as either a secondary driver, or a by-product of that primary purpose. It appears, then, that political information consumption in a media-saturated society is more about routine ‘practices’ than it is about ‘information seeking’. The suggestion that media use is no longer primarily concerned with information seeking, but rather, is simply a behaviour which occurs within the broader set of everyday practices reflects Couldry’s (2004) media as practice paradigm. These findings highlight the need for more authentic and holistic contexts for media research. It is insufficient to consider information choices in isolation, or even from a wider range of information sources, such as that incorporated in the present study. Future media research must take greater account of the broader social contexts and practices in which media-oriented behaviours occur. The findings also call into question the previously assumed centrality of trust to information selection decisions. Citizens regularly use media they do not trust to find out about politics. If people are willing to use information sources they do not trust for democratically important topics such as politics, it is important that citizens possess the media literacy skills to effectively understand and evaluate the information they are presented with. Without the application of such media literacy skills, a steady diet of ‘fast food’ media may result in uninformed or misinformed voting decisions, which have implications for the effectiveness of democratic processes. This research has emphasized the need for further holistic and authentically contextualised media use research, to better understand how citizens use information sources to find out about important topics such as politics.