PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information

As the number of protein folds is quite limited, a mode of analysis that will be increasingly common in the future, especially with the advent of structural genomics, is to survey and re-survey the finite parts list of folds from an expanding number of perspectives. We have developed a new resource, called PartsList, that lets one dynamically perform these comparative fold surveys. It is available on the web at http://bioinfo.mbb.yale.edu/partslist and http://www.partslist.org. The system is based on the existing fold classifications and functions as a form of companion annotation for them, providing ‘global views’ of many already completed fold surveys. The central idea in the system is that of comparison through ranking; PartsList will rank the approximately 420 folds based on more than 180 attributes. These include: (i) occurrence in a number of completely sequenced genomes (e.g. it will show the most common folds in the worm versus yeast); (ii) occurrence in the structure databank (e.g. most common folds in the PDB); (iii) both absolute and relative gene expression information (e.g. most changing folds in expression over the cell cycle); (iv) protein–protein interactions, based on experimental data in yeast and comprehensive PDB surveys (e.g. most interacting fold); (v) sensitivity to inserted transposons; (vi) the number of functions associated with the fold (e.g. most multi-functional folds); (vii) amino acid composition (e.g. most Cys-rich folds); (viii) protein motions (e.g. most mobile folds); and (ix) the level of similarity based on a comprehensive set of structural alignments (e.g. most structurally variable folds). The integration of whole-genome expression and protein–protein interaction data with structural information is a particularly novel feature of our system. We provide three ways of visualizing the rankings: a profiler emphasizing the progression of high and low ranks across many pre-selected attributes, a dynamic comparer for custom comparisons and a numerical rankings correlator. These allow one to directly compare very different attributes of a fold (e.g. expression level, genome occurrence and maximum motion) in the uniform numerical format of ranks. This uniform framework, in turn, highlights the way that the frequency of many of the attributes falls off with approximate power-law behavior (i.e. according to V–b, for attribute value V and constant exponent b), with a few folds having large values and most having small values.

Tema 6, parte 3: Frameworks web para dispositivos móviles

Se describen las ventajas de usar un framework para desarrollar aplicaciones web para móviles, y en concreto se ve el funcionamiento de jQuery Mobile.

El Mobile Learning en el aula de ELE. Propuestas para el alumnado italófono

Los dispositivos móviles se han convertido en una herramienta irrenunciable en la vida de los seres humanos, principalmente como instrumento para estar en contacto con cualquier persona en cualquier lugar y en cualquier momento. La introducción de los smartphone y las tabletas en las aulas de Educación Secundaria favorece la motivación y la autonomía del alumnado, puesto que las aplicaciones digitales (Apps) son el mundo en el que nace y vive. Sin embargo, el concepto de Mobile Learning se puede aplicar tanto al aula de lengua y literatura para hispanohablantes como al aula de español para extranjeros, empleando el móvil no como sustituto del material en papel, sino como elemento que fomenta las habilidades comunicativas. Teniendo en cuenta la utilidad de las app para dispositivos móviles en las aulas de Español como Lengua Extranjera (ELE), en el presente trabajo se desarrolla una propuesta didáctica desde el área de lengua y literatura española para el alumnado italófono: estos estudiantes constituyen un grupo particular de aprendices de español ya que, como los dos idiomas se parecen, surgen dificultades inesperadas al descubrir las divergencias durante el estudio de la lengua.

Towards Automation in Digital Investigations : Seeking Efficiency in Digital Forensics in Mobile and Cloud Environments

Cybercrime and related malicious activity in our increasingly digital world has become more prevalent and sophisticated, evading traditional security mechanisms. Digital forensics has been proposed to help investigate, understand and eventually mitigate such attacks. The practice of digital forensics, however, is still fraught with various challenges. Some of the most prominent of these challenges include the increasing amounts of data and the diversity of digital evidence sources appearing in digital investigations. Mobile devices and cloud infrastructures are an interesting specimen, as they inherently exhibit these challenging circumstances and are becoming more prevalent in digital investigations today. Additionally they embody further characteristics such as large volumes of data from multiple sources, dynamic sharing of resources, limited individual device capabilities and the presence of sensitive data. These combined set of circumstances make digital investigations in mobile and cloud environments particularly challenging. This is not aided by the fact that digital forensics today still involves manual, time consuming tasks within the processes of identifying evidence, performing evidence acquisition and correlating multiple diverse sources of evidence in the analysis phase. Furthermore, industry standard tools developed are largely evidence-oriented, have limited support for evidence integration and only automate certain precursory tasks, such as indexing and text searching. In this study, efficiency, in the form of reducing the time and human labour effort expended, is sought after in digital investigations in highly networked environments through the automation of certain activities in the digital forensic process. To this end requirements are outlined and an architecture designed for an automated system that performs digital forensics in highly networked mobile and cloud environments. Part of the remote evidence acquisition activity of this architecture is built and tested on several mobile devices in terms of speed and reliability. A method for integrating multiple diverse evidence sources in an automated manner, supporting correlation and automated reasoning is developed and tested. Finally the proposed architecture is reviewed and enhancements proposed in order to further automate the architecture by introducing decentralization particularly within the storage and processing functionality. This decentralization also improves machine to machine communication supporting several digital investigation processes enabled by the architecture through harnessing the properties of various peer-to-peer overlays. Remote evidence acquisition helps to improve the efficiency (time and effort involved) in digital investigations by removing the need for proximity to the evidence. Experiments show that a single TCP connection client-server paradigm does not offer the required scalability and reliability for remote evidence acquisition and that a multi-TCP connection paradigm is required. The automated integration, correlation and reasoning on multiple diverse evidence sources demonstrated in the experiments improves speed and reduces the human effort needed in the analysis phase by removing the need for time-consuming manual correlation. Finally, informed by published scientific literature, the proposed enhancements for further decentralizing the Live Evidence Information Aggregator (LEIA) architecture offer a platform for increased machine-to-machine communication thereby enabling automation and reducing the need for manual human intervention.

Using Q-methodology to study the metaphors of consumption for mobile phone users

Even before business has really come to grips with the intricacies of incorporating emarketing and e-commerce into their organisational strategies, they are now being encouraged to make significant investments in developing capabilities for mobile phone marketing. Fuelled once again by huge profit predictions reminiscent of the mid-1990s when speaking of e-commerce (Anckar and D’Incau 2002) marketers are tapping into this mobility. So, instead of having to drive consumers to web sites through the ‘sit and search’ context, marketers are now exploring ways to develop strategies to deliver relevant and timely information in a ‘roam and receive’ context directly to their potential customers anywhere, anytime, any place (Mort and Drennan 2002).

Towards a web-based progressive handwriting recognition environment for mathematical problem solving

The emergence of pen-based mobile devices such as PDAs and tablet PCs provides a new way to input mathematical expressions to computer by using handwriting which is much more natural and efficient for entering mathematics. This paper proposes a web-based handwriting mathematics system, called WebMath, for supporting mathematical problem solving. The proposed WebMath system is based on client-server architecture. It comprises four major components: a standard web server, handwriting mathematical expression editor, computation engine and web browser with Ajax-based communicator. The handwriting mathematical expression editor adopts a progressive recognition approach for dynamic recognition of handwritten mathematical expressions. The computation engine supports mathematical functions such as algebraic simplification and factorization, and integration and differentiation. The web browser provides a user-friendly interface for accessing the system using advanced Ajax-based communication. In this paper, we describe the different components of the WebMath system and its performance analysis.

Sensing presence (PreSense) ontology : user modelling in the semantic sensor web

Increasingly, people's digital identities are attached to, and expressed through, their mobile devices. At the same time digital sensors pervade smart environments in which people are immersed. This paper explores different perspectives in which users' modelling features can be expressed through the information obtained by their attached personal sensors. We introduce the PreSense Ontology, which is designed to assign meaning to sensors' observations in terms of user modelling features. We believe that the Sensing Presence ( PreSense ) Ontology is a first step toward the integration of user modelling and "smart environments". In order to motivate our work we present a scenario and demonstrate how the ontology could be applied in order to enable context-sensitive services. © 2012 Springer-Verlag.

Developments in technologies for human-centric mobile computing and applications

With recent expansions in technology, mobile computing continues to play a vital role in all aspects of our lives. Digital technology tools such as Web browsing, media tracking, social media, and emailing have made mobile technology more than just a means of communication but has widespread use in business and social networks. Developments in Technologies for Human-Centric Mobile Computing and Applications is a comprehensive collection of knowledge and practice in the development of technologies in human –centric mobile technology. This book focuses on the developmental aspects of mobile technology; bringing together researchers, educators, and practitioners to encourage readers to think outside of the box.

Sensing presence (PreSense) ontology:user modelling in the semantic sensor web

Increasingly, people's digital identities are attached to, and expressed through, their mobile devices. At the same time digital sensors pervade smart environments in which people are immersed. This paper explores different perspectives in which users' modelling features can be expressed through the information obtained by their attached personal sensors. We introduce the PreSense Ontology, which is designed to assign meaning to sensors' observations in terms of user modelling features. We believe that the Sensing Presence ( PreSense ) Ontology is a first step toward the integration of user modelling and "smart environments". In order to motivate our work we present a scenario and demonstrate how the ontology could be applied in order to enable context-sensitive services. © 2012 Springer-Verlag.

Emerging perspectives on the design, use, and evaluation of mobile and handheld devices

Human-computer interaction is a growing field of study in which researchers and professionals aim to understand and evaluate the impact of new technologies on human behavior. With the integration of smart phones, tablets, and other portable devices into everyday life, there is a greater need to understand the influence of such technology on the human experience. Emerging Perspectives on the Design, Use, and Evaluation of Mobile and Handheld Devices is an authoritative reference source consisting of the latest scholarly research and theories from international experts and professionals on the topic of human-computer interaction with mobile devices. Featuring a comprehensive collection of chapters on critical topics in this dynamic field, this publication is an essential reference source for researchers, educators, students, and practitioners interested in the use of mobile and handheld devices and their impact on individuals and society as a whole. This publication features timely, research-based chapters pertaining to topics in the design and evaluation of smart devices including, but not limited to, app stores, category-based interfaces, gamified mobility applications, mobile interaction, mobile learning, pervasive multimodal applications, smartphone interaction, and social media use.

Participatory research with older adults with AMD:co-designing a SMART diet diary app

The global population of people aged 60 years and older is growing rapidly. In the UK, there are currently around 10 million people aged 65 and over, and the number is projected to rise by 50% in the next 20 years (RNIB, 2013). While ongoing advances in information technology (IT) are undoubtedly increasing the scope for IT to enhance and support older adults' daily living, the digital divide between older and younger adults - 43% of people below the age of 55 own and use a smartphone, compared to only 3% of people aged 65 and over (AgeUK, 2013) - raises concerns about the suitability of technological solutions for older adults, especially for older adults with impairments. Evidence suggests that sympathetic design of mobile technology does render it useful and acceptable to older adults: the key issue is, however, how best to achieve such sympathetic design when working with impaired older adults. We report here on a case study in order to outline the practicalities and highlight the benefits of participatory research for the design of sympathetic technology for (and importantly with) older adults with impairments.

A longitudinal evaluation of the acceptability and impact of a diet diary app for older adults with age-related macular degeneration

Ongoing advances in technology are increasing the scope for enhancing and supporting older adults’ daily living. The digital divide between older and younger adults raises concerns, however, about the suitability of technological solutions for older adults, especially for those with impairments. Taking older adults with Age-Related Macular Degeneration (AMD) as a case study, we used user-centred and participatory design approaches to develop an assistive mobile app for self-monitoring their intake of food [12,13]. In this paper we report on findings of a longitudinal field evaluation of our app that was conducted to investigate how it was received and adopted by older adults with AMD and its impact on their lives. Demonstrating the benefit of applying inclusive design methods for technology for older adults, our findings reveal how the use of the app raises participants’ awareness and facilitates self-monitoring of diet, encourages positive (diet) behaviour change, and encourages learning.

Dynamic data retrieval on the World Wide Web

Methods for accessing data on the Web have been the focus of active research over the past few years. In this thesis we propose a method for representing Web sites as data sources. We designed a Data Extractor data retrieval solution that allows us to define queries to Web sites and process resulting data sets. Data Extractor is being integrated into the MSemODB heterogeneous database management system. With its help database queries can be distributed over both local and Web data sources within MSemODB framework. ^ Data Extractor treats Web sites as data sources, controlling query execution and data retrieval. It works as an intermediary between the applications and the sites. Data Extractor utilizes a twofold “custom wrapper” approach for information retrieval. Wrappers for the majority of sites are easily built using a powerful and expressive scripting language, while complex cases are processed using Java-based wrappers that utilize specially designed library of data retrieval, parsing and Web access routines. In addition to wrapper development we thoroughly investigate issues associated with Web site selection, analysis and processing. ^ Data Extractor is designed to act as a data retrieval server, as well as an embedded data retrieval solution. We also use it to create mobile agents that are shipped over the Internet to the client's computer to perform data retrieval on behalf of the user. This approach allows Data Extractor to distribute and scale well. ^ This study confirms feasibility of building custom wrappers for Web sites. This approach provides accuracy of data retrieval, and power and flexibility in handling of complex cases. ^

The Effect of Mobile Technology as an Active Student Response System on the Acquisition of U.S. History Content of Secondary Students with Specific Learning Disabilities

Students with specific learning disabilities (SLD) typically learn less history content than their peers without disabilities and show fewer learning gains. Even when they are provided with the same instructional strategies, many students with SLD struggle to grasp complex historical concepts and content area vocabulary. Many strategies involving technology have been used in the past to enhance learning for students with SLD in history classrooms. However, very few studies have explored the effectiveness of emerging mobile technology in K-12 history classrooms. This study investigated the effects of mobile devices (iPads) as an active student response (ASR) system on the acquisition of U.S. history content of middle school students with SLD. An alternating treatments single subject design was used to compare the effects of two interventions. There were two conditions and a series of pretest probesin this study. The conditions were: (a) direct instruction and studying from handwritten notes using the interactive notebook strategy and (b) direct instruction and studying using the Quizlet App on the iPad. There were three dependent variables in this study: (a) percent correct on tests, (b) rate of correct responses per minute, and (c) rate of errors per minute. A comparative analysis suggested that both interventions (studying from interactive notes and studying using Quizlet on the iPad) had varying degrees of effectiveness in increasing the learning gains of students with SLD. In most cases, both interventions were equally effective. During both interventions, all of the participants increased their percentage correct and increased their rate of correct responses. Most of the participants decreased their rate of errors. The results of this study suggest that teachers of students with SLD should consider a post lesson review in the form of mobile devices as an ASR system or studying from handwritten notes paired with existing evidence-based practices to facilitate students’ knowledge in U.S. history. Future research should focus on the use of other interactive applications on various mobile operating platforms, on other social studies subjects, and should explore various testing formats such as oral question-answer and multiple choice.