Machine-learning methods for structure prediction of β-barrel membrane proteins

Different types of proteins exist with diverse functions that are essential for living organisms. An important class of proteins is represented by transmembrane proteins which are specifically designed to be inserted into biological membranes and devised to perform very important functions in the cell such as cell communication and active transport across the membrane. Transmembrane β-barrels (TMBBs) are a sub-class of membrane proteins largely under-represented in structure databases because of the extreme difficulty in experimental structure determination. For this reason, computational tools that are able to predict the structure of TMBBs are needed. In this thesis, two computational problems related to TMBBs were addressed: the detection of TMBBs in large datasets of proteins and the prediction of the topology of TMBB proteins. Firstly, a method for TMBB detection was presented based on a novel neural network framework for variable-length sequence classification. The proposed approach was validated on a non-redundant dataset of proteins. Furthermore, we carried-out genome-wide detection using the entire Escherichia coli proteome. In both experiments, the method significantly outperformed other existing state-of-the-art approaches, reaching very high PPV (92%) and MCC (0.82). Secondly, a method was also introduced for TMBB topology prediction. The proposed approach is based on grammatical modelling and probabilistic discriminative models for sequence data labeling. The method was evaluated using a newly generated dataset of 38 TMBB proteins obtained from high-resolution data in the PDB. Results have shown that the model is able to correctly predict topologies of 25 out of 38 protein chains in the dataset. When tested on previously released datasets, the performances of the proposed approach were measured as comparable or superior to the current state-of-the-art of TMBB topology prediction.

Learning Methods and Algorithms for Semantic Text Classification across Multiple Domains

Information is nowadays a key resource: machine learning and data mining techniques have been developed to extract high-level information from great amounts of data. As most data comes in form of unstructured text in natural languages, research on text mining is currently very active and dealing with practical problems. Among these, text categorization deals with the automatic organization of large quantities of documents in priorly defined taxonomies of topic categories, possibly arranged in large hierarchies. In commonly proposed machine learning approaches, classifiers are automatically trained from pre-labeled documents: they can perform very accurate classification, but often require a consistent training set and notable computational effort. Methods for cross-domain text categorization have been proposed, allowing to leverage a set of labeled documents of one domain to classify those of another one. Most methods use advanced statistical techniques, usually involving tuning of parameters. A first contribution presented here is a method based on nearest centroid classification, where profiles of categories are generated from the known domain and then iteratively adapted to the unknown one. Despite being conceptually simple and having easily tuned parameters, this method achieves state-of-the-art accuracy in most benchmark datasets with fast running times. A second, deeper contribution involves the design of a domain-independent model to distinguish the degree and type of relatedness between arbitrary documents and topics, inferred from the different types of semantic relationships between respective representative words, identified by specific search algorithms. The application of this model is tested on both flat and hierarchical text categorization, where it potentially allows the efficient addition of new categories during classification. Results show that classification accuracy still requires improvements, but models generated from one domain are shown to be effectively able to be reused in a different one.

A Fast Platform for Interactive E-Learning Systems

Modern e-learning systems represent a special type of web information systems. By definition, information systems are special computerized systems used to perform data operations by multiple users simultaneously. Each active user consumes an amount of hardware resources. A shortage of hardware resources can be caused by growing number of simultaneous users. Such situation can result in overall malfunctioning or slowed-down system. In order to avoid this problem, the underlying hardware system gets usually continuously upgraded. These upgrades, typically accompanied with various software updates, usually result in a temporarily increased amount of available resources. This work deals with the problem in a different way by proposing an implementation of a web e-learning system with a modified software architecture reducing resource usage of the server part to the bare minimum. In order to implement a full-scale e-learning system that could be used as a substitute to a conventional web e-learning system, a Rich Internet Application framework was used as basis. The technology allowed implementation of advanced interactivity features and provided an easy transfer of a substantial part of the application logic from server to clients. In combination with a special server application, the server part of the new system is able to run with a reasonable performance on a hardware with very limited computing resources.

Learning processes in student teaching: Analyses from a study using learning diaries

The present study seeks to obtain deeper insight into the learning processes in practical training in primary teacher education in Upper Austria. Based on the offer-and-use model of instruction, 230 diary entries of 46 student teachers (28 students in their third semester, 18 students in their fifth semester) were analysed with legard to the learning topics, learning sourcesJ and Ìealning processes involved in practical training. The results show a variety of learning forms, ranging from the unreflective imitation of school mentors' practices to active knowledge construction. In addition, they illustrate that the available learning offers were suboptimally utilized by stuclent teachers who failed to work systernatically and continuously on their professional development.

A characterisation of passive and active interactions and their influence on student's achievement using Moodle LMS Logs

During the last years, there has been much concern about learning management systems' (LMS) effectiveness when compared to traditional learning and about how to assess students' participation during the course. The tracking and monitoring capabilities of most recent LMS have made it possible to analyse every interaction in the system. The issues addressed on this study are: a) Is LMS student's interaction an indicator of academic performance?; b) Are different results in performance expected between distance and in-class LMS-supported education?; c) How can LMS interactions from logs be categorised?; d) May this categorisation detect 'learning witnesses'? To answer these questions, a set of interaction types from Moodle LMS activity record logs has been analysed during two years in online and in-class Master's degrees at the UPM. The results show partial or no evidence of influence between interaction indicators and academic performance, although the proposed categorisation may help detect learning witnesses.

Reaching the unreached: An initiative to bridge the gap between the gap by active role of management institutes/schools

There are large numbers of business communities in India which neither had any formal education nor they took any professional training but still they contribute in successful business formation. Their presence can be felt in all areas of business. Still there is a big professional gap between the educational institutes, specially the B-Schools and this independent business community. With the help of this paper an effort is made to develop a Two-Way learning relationship for the mutual benefit of both entities. It will also highlight the role of an educational institute beyond academics for the well being of society. This may lead to derive and develop the exchange of innovative business ideas and framing the suitable policies for long term sustainability in today´s competitive arena. The study conducted by researcher with a sample size of 100 which includes a mix of well known academic professionals, MBA students and non academic business professionals has revealed that there is a need of an exchange program for the mutual benefits. There exists a big professional gap in this area which can be filled with the active and effective initiative by management institutes. An effort is made in this paper to highlight this gap and to suggest some framework to bridge the gap

Using online presence to improve online collaborative learning

Social software tools have become an integral part of students? personal lives and their primary communication medium. Likewise, these tools are increasingly entering the enterprise world (within the recent trend known as Enterprise 2.0) and becoming a part of everyday work routines. Aiming to keep the pace with the job requirements and also to position learning as an integral part of students? life, the field of education is challenged to embrace social software. Personal Learning Environments (PLEs) emerged as a concept that makes use of social software to facilitate collaboration, knowledge sharing, group formation around common interests, active participation and reflective thinking in online learning settings. Furthermore, social software allows for establishing and maintaining one?s presence in the online world. By being aware of a student's online presence, a PLE is better able to personalize the learning settings, e.g., through recommendation of content to use or people to collaborate with. Aiming to explore the potentials of online presence for the provision of recommendations in PLEs, in the scope of the OP4L project, we have develop a software solution that is based on a synergy of Semantic Web technologies, online presence and socially-oriented learning theories. In this paper we present the current results of this research work.

Learning Analytics and Interactions in Virtual Learning Environments. A Comparative Study of Typologies and their Relationship with Academic Performance

Analysis of learning data (learning analytics) is a new research field with high growth potential. The main objective of Learning analytics is the analysis of data (interactions being the basic data unit) generated in virtual learning environments, in order to maximize the outcomes of the learning process; however, a consensus has not been reached yet on which interactions must be measured and what is their influence on learning outcomes. This research is grounded on the study of e-learning interaction typologies and their relationship with students? academic performance, by means of a comparative study between different interaction typologies (based on the agents involved, frequency of use and participation mode). The main conclusions are a) that classifications based on agents offer a better explanation of academic performance; and b) that each of the three typologies are able to explain academic performance in terms of some of their components (student-teacher and student-student interactions, evaluating students interactions and active interactions, respectively), with the other components being nonrelevant.

Predicting academic performance with learning analytics in virtual learning environments: A comparative study of three interaction classifications

Learning analytics is the analysis of static and dynamic data extracted from virtual learning environments, in order to understand and optimize the learning process. Generally, this dynamic data is generated by the interactions which take place in the virtual learning environment. At the present time, many implementations for grouping of data have been proposed, but there is no consensus yet on which interactions and groups must be measured and analyzed. There is also no agreement on what is the influence of these interactions, if any, on learning outcomes, academic performance or student success. This study presents three different extant interaction typologies in e-learning and analyzes the relation of their components with students? academic performance. The three different classifications are based on the agents involved in the learning process, the frequency of use and the participation mode, respectively. The main findings from the research are: a) that agent-based classifications offer a better explanation of student academic performance; b) that at least one component in each typology predicts academic performance; and c) that student-teacher and student-student, evaluating students, and active interactions, respectively, have a significant impact on academic performance, while the other interaction types are not significantly related to academic performance.

ASYTRAIN: a new methodology for teaching and learning antennas

This paper presents ASYTRAIN, a new tool to teach and learn antennas, based on the use of a modular building kit and a low cost portable antenna measurement system that lets the students design and build different types of antennas and observe their characteristics while learning the insights of the subjects. This tool has a methodology guide for try-and-test project development and, makes the students be active antenna engineers instead of passive learners. This experimental learning method arises their motivation during the antenna courses.

The educational learning lifecycle and the cloud computing

Currently, student dropout rates are a matter of concern among universities. Many research studies, aimed at discovering the causes, have been carried out. However, few solutions, that could serve all students and related problems, have been proposed so far. One such problem is caused by the lack of the "knowledge chain educational links" that occurs when students move onto higher studies without mastering their basic studies. Most regulated studies imparted at universities are designed so that some basic subjects serve as support for other, more complicated, subjects, thus forming a complicated knowledge network. When a link in this chain fails, student frustration occurs as it prevents him from fully understanding the following educational links. In this proposal we try to mitigate these disasters that stem, for the most part, the student?s frustration beyond his college stay. On one hand, we make a dissertation on the student?s learning process, which we divide into a series of phases that amount to what we call the "learning lifecycle." Also, we analyze at what stage the action by the stakeholders involved in this scenario: teachers and students; is most important. On the other hand, we consider that Information and Communication Technologies ICT, such as Cloud Computing, can help develop new ways, allowing for the teaching of higher education, while easing and facilitating the student?s learning process. But, methods and processes need to be defined as to direct the use of such technologies; in the teaching process in general, and within higher education in particular; in order to achieve optimum results. Our methodology integrates, as another actor, the ICT into the "Learning Lifecycle". We stimulate students to stop being merely spectators of their own education, and encourage them to take an active part in their training process. To do this, we offer a set of useful tools to determine not only academic failure causes, (for self assessment), but also to remedy these failures (with corrective actions); "discovered the causes it is easier to determine solutions?. We believe this study will be useful for both students and teachers. Students learn from their own experience and improve their learning process, while obtaining all of the "knowledge chain educational links? required in their studies. We stand by the motto "Studying to learn instead of studying to pass". Teachers will also be benefited by detecting where and how to strengthen their teaching proposals. All of this will also result in decreasing dropout rates.

Lack of tissue glucocorticoid reactivation in 11β-hydroxysteroid dehydrogenase type 1 knockout mice ameliorates age-related learning impairments

11β-hydroxysteroid dehydrogenase type 1 (11β-HSD-1) intracellularly regenerates active corticosterone from circulating inert 11-dehydrocorticosterone (11-DHC) in specific tissues. The hippocampus is a brain structure particularly vulnerable to glucocorticoid neurotoxicity with aging. In intact hippocampal cells in culture, 11β-HSD-1 acts as a functional 11β-reductase reactivating inert 11-DHC to corticosterone, thereby potentiating kainate neurotoxicity. We examined the functional significance of 11β-HSD-1 in the central nervous system by using knockout mice. Aged wild-type mice developed elevated plasma corticosterone levels that correlated with learning deficits in the watermaze. In contrast, despite elevated plasma corticosterone levels throughout life, this glucocorticoid-associated learning deficit was ameliorated in aged 11β-HSD-1 knockout mice, implicating lower intraneuronal corticosterone levels through lack of 11-DHC reactivation. Indeed, aged knockout mice showed significantly lower hippocampal tissue corticosterone levels than wild-type controls. These findings demonstrate that tissue corticosterone levels do not merely reflect plasma levels and appear to play a more important role in hippocampal functions than circulating blood levels. The data emphasize the crucial importance of local enzymes in determining intracellular glucocorticoid activity. Selective 11β-HSD-1 inhibitors may protect against hippocampal function decline with age.

The Influence of Space Layout, Technology and Teaching Approach on Student Learning: An Architectural Technology Perspective

Some would argue that there is a need for the traditional lecture format to be rethought in favour of a more active approach. However, this must form part of a bipartite strategy, considered in conjunction with the layout of any new space to facilitate alternative learning and teaching methods. With this in mind, this paper begins to examine the impact of the learning environment on the student learning experience, specifically focusing on students studying on the Architectural Technology and Management programme at Ulster University. The aim of this study is two-fold: to increase understanding of the impact of learning space layout, by taking a student centered approach; and to gain an appreciation of how technology can impact upon the learning space. The study forms part of a wider project being undertaken at Ulster University known as the Learning Landscape Transition Project, exploring the relationship between learning, teaching and space layout. Data collection was both qualitative and quantitative, with use of a case study supported by a questionnaire based on attitudinal scaling. A focus group was also used to further analyse the key trends resulting from the questionnaire. The initial results suggest that the learning environment, and the technology within it, can not only play an important part in the overall learning experience of the student, but also assist with preparation for the working environment to be experienced in professional life.

O sistema PBL, problem-based learning, no ensino de medicina no Brasil : análise bibliográfica sobre a sua execução

Introdução: Entre as estratégias de ensino e aprendizagem utilizadas nas práticas pedagógicas, a Problem Based Learning (PBL) (Aprendizagem Baseada em Problemas) é utilizada desde 1960, em especial nos cursos de Medicina. Mesmo sendo uma estratégia valiosa, um dos seus obstáculos é a pouca prática dos alunos em atividades autodirigidas, pesquisa e construção coletiva do conhecimento. Objetivo: Rastrear elementos constitutivos da PBL através de dados colhidos em artigos pesquisados em sítios de divulgação científica; Avaliar, nos estudos selecionados, os aspectos positivos e negativos que estejam relacionados com a metodologia do Sistema PBL aplicada ao ensino médico no Brasil. Metodologia: Estudo bibliográfico de 13 textos utilizando um modelo de desconstrução, denominada Análise Textual Discursiva (ATD) que consiste em: transformação dos artigos em pedaços menores; análise textual; identificação de padrões convergentes e divergentes em relação a PBL; organização e síntese dos dados, culminando com a elaboração de estratégia adaptativa da PBL para o curso de Medicina. Resultados: Foram encontradas 116 citações que convergiam para referências positivos acerca da metodologia PBL e 40 citações que divergiam acerca dos pontos positivos. Os aspectos positivos como o desenvolvimento de atitudes e habilidades; desenvolvimento de competências anteriores ao curso; efeitos positivos depois de terminada a graduação, como autonomia de estudo e a articulação entre currículo e realidade profissional, representam pontos a serem reforçados na aula. Em contraponto, foi observado que dentre os negativos a não compreensão do papel do professor como tutor; necessidade de conteúdo formal tradicional pelos alunos e a expectativa que o professor retire as suas dúvidas são pontos a serem evitados. Conclusões: A metodologia PBL deverá servir como metodologia ativa para aproveitar ao máximo as habilidades que os alunos já apresentam, potencializando o aprendizado na educação médica em sala de aula. Palavras-Chave: PBL; curso de medicina; metodologia ativa; educação médica.

Teaching College Writing in a High School Setting: The Impact of Concurrent Enrollment on Teacher Learning and Practice

Thesis (Ph.D.)--University of Washington, 2016-06