Do protein–protein interaction databases identify moonlighting proteins?

One of the most striking results of the human (and mammalian) genomes is the low number of protein-coding genes. To-date, the main molecular mechanism to increase the number of different protein isoforms and functions is alternative splicing. However, a less-known way to increase the number of protein functions is the existence of multifunctional, multitask, or ‘‘moonlighting’’, proteins. By and large, moonlighting proteins are experimentally disclosed by serendipity. Proteomics is becoming one of the very active areas of biomedical research, which permits researchers to identify previously unseen connections among proteins and pathways. In principle, protein–protein interaction (PPI) databases should contain information on moonlighting proteins and could provide suggestions to further analysis in order to prove the multifunctionality. As far as we know, nobody has verified whether PPI databases actually disclose moonlighting proteins. In the present work we check whether well-established moonlighting proteins present in PPI databases connect with their known partners and, therefore, a careful inspection of these databases could help to suggest their different functions. The results of our research suggest that PPI databases could be a valuable tool to suggest multifunctionality.

Gene Promoter Evolution Targets the Center of the Human Protein Interaction Network

Assessing the contribution of promoters and coding sequences to gene evolution is an important step toward discovering the major genetic determinants of human evolution. Many specific examples have revealed the evolutionary importance of cis-regulatory regions. However, the relative contribution of regulatory and coding regions to the evolutionary process and whether systemic factors differentially influence their evolution remains unclear. To address these questions, we carried out an analysis at the genome scale to identify signatures of positive selection in human proximal promoters. Next, we examined whether genes with positively selected promoters (Prom+ genes) show systemic differences with respect to a set of genes with positively selected protein-coding regions (Cod+ genes). We found that the number of genes in each set was not significantly different (8.1% and 8.5%, respectively). Furthermore, a functional analysis showed that, in both cases, positive selection affects almost all biological processes and only a few genes of each group are located in enriched categories, indicating that promoters and coding regions are not evolutionarily specialized with respect to gene function. On the other hand, we show that the topology of the human protein network has a different influence on the molecular evolution of proximal promoters and coding regions. Notably, Prom+ genes have an unexpectedly high centrality when compared with a reference distribution (P = 0.008, for Eigenvalue centrality). Moreover, the frequency of Prom+ genes increases from the periphery to the center of the protein network (P = 0.02, for the logistic regression coefficient). This means that gene centrality does not constrain the evolution of proximal promoters, unlike the case with coding regions, and further indicates that the evolution of proximal promoters is more efficient in the center of the protein network than in the periphery. These results show that proximal promoters have had a systemic contribution to human evolution by increasing the participation of central genes in the evolutionary process.

Remote collaborative multi-user informal learning experiences: design and evaluation

This paper presents a customizable system used to develop a collaborative multi-user problem solving game. It addresses the increasing demand for appealing informal learning experiences in museum-like settings. The system facilitates remote collaboration by allowing groups of learners tocommunicate through a videoconferencing system and by allowing them to simultaneously interact through a shared multi-touch interactive surface. A user study with 20 user groups indicates that the game facilitates collaboration between local and remote groups of learners. The videoconference and multitouch surface acted as communication channels, attracted students’ interest, facilitated engagement, and promoted inter- and intra-group collaboration—favoring intra-group collaboration. Our findings suggest that augmentingvideoconferencing systems with a shared multitouch space offers newpossibilities and scenarios for remote collaborative environments and collaborative learning.

Remote Control of Mobile Devices in Android Platform

Remote control systems are a very useful element to control and monitor devices quickly and easily. This paper proposes a new architecture for remote control of Android mobile devices, analyzing the different alternatives and seeking the optimal solution in each case. Although the area of remote control, in case of mobile devices, has been little explored, it may provide important advantages for testing software and hardware developments in several real devices. It can also allow an efficient management of various devices of different types, perform forensic security tasks, etc ... The main idea behind the proposed architecture was the design of a system to be used as a platform which provides the services needed to perform remote control of mobile devices. As a result of this research, a proof of concept was implemented. An Android application running a group of server programs on the device, connected to the network or USB interface, depending on availability. This servers can be controlled through a small client written in Java and runnable both on desktop and web systems.

Interaction of Spiral Waves in the Complex Ginzburg-Landau Equation

Solutions of the general cubic complex Ginzburg-Landau equation comprising multiple spiral waves are considered, and laws of motion for the centers are derived. The direction of the motion changes from along the line of centers to perpendicular to the line of centers as the separation increases, with the strength of the interaction algebraic at small separations and exponentially small at large separations. The corresponding asymptotic wave number and frequency are also determined, which evolve slowly as the spirals move

Beaming into the rat world: enabling real-time intereaction between rat and human each at their own scale

Immersive virtual reality (IVR) typically generates the illusion in participants that they are in the displayed virtual scene where they can experience and interact in events as if they were really happening. Teleoperator (TO) systems place people at a remote physical destination embodied as a robotic device, and where typically participants have the sensation of being at the destination, with the ability to interact with entities there. In this paper, we show how to combine IVR and TO to allow a new class of application. The participant in the IVR is represented in the destination by a physical robot (TO) and simultaneously the remote place and entities within it are represented to the participant in the IVR. Hence, the IVR participant has a normal virtual reality experience, but where his or her actions and behaviour control the remote robot and can therefore have physical consequences. Here, we show how such a system can be deployed to allow a human and a rat to operate together, but the human interacting with the rat on a human scale, and the rat interacting with the human on the rat scale. The human is represented in a rat arena by a small robot that is slaved to the human"s movements, whereas the tracked rat is represented to the human in the virtual reality by a humanoid avatar. We describe the system and also a study that was designed to test whether humans can successfully play a game with the rat. The results show that the system functioned well and that the humans were able to interact with the rat to fulfil the tasks of the game. This system opens up the possibility of new applications in the life sciences involving participant observation of and interaction with animals but at human scale.

Acting Rehearsal in Collaborative Multimodal Mixed Reality Environments

This paper presents the use of our multimodal mixed reality telecommunication system to support remote acting rehearsal. The rehearsals involved two actors, located in London and Barcelona, and a director in another location in London. This triadic audiovisual telecommunication was performed in a spatial and multimodal collaborative mixed reality environment based on the 'destination-visitor' paradigm, which we define and put into use. We detail our heterogeneous system architecture, which spans the three distributed and technologically asymmetric sites, and features a range of capture, display, and transmission technologies. The actors' and director's experience of rehearsing a scene via the system are then discussed, exploring successes and failures of this heterogeneous form of telecollaboration. Overall, the common spatial frame of reference presented by the system to all parties was highly conducive to theatrical acting and directing, allowing blocking, gross gesture, and unambiguous instruction to be issued. The relative inexpressivity of the actors' embodiments was identified as the central limitation of the telecommunication, meaning that moments relying on performing and reacting to consequential facial expression and subtle gesture were less successful.

Technology educational affordance: Bridging the gap between patterns of interaction and technology usage

Peer-reviewed

A novel semi-fragile forensic watermarking scheme for remote sensing images

Peer-reviewed

Sea state effect on the sea surface emissivity at L-band

In May 1999, the European Space Agency (ESA) selected the Earth Explorer Opportunity Soil Moisture and Ocean Salinity (SMOS) mission to obtain global and frequent soil moisture and ocean salinity maps. SMOS' single payload is the Microwave Imaging Radiometer by Aperture Synthesis (MIRAS), an L-band two-dimensional aperture synthesis radiometer with multiangular observation capabilities. At L-band, the brightness temperature sensitivity to the sea surface salinity (SSS) is low, approximately 0.5 K/psu at 20/spl deg/C, decreasing to 0.25 K/psu at 0/spl deg/C, comparable to that to the wind speed /spl sim/0.2 K/(m/s) at nadir. However, at a given time, the sea state does not depend only on local winds, but on the local wind history and the presence of waves traveling from far distances. The Wind and Salinity Experiment (WISE) 2000 and 2001 campaigns were sponsored by ESA to determine the impact of oceanographic and atmospheric variables on the L-band brightness temperature at vertical and horizontal polarizations. This paper presents the results of the analysis of three nonstationary sea state conditions: growing and decreasing sea, and the presence of swell. Measured sea surface spectra are compared with the theoretical ones, computed using the instantaneous wind speed. Differences can be minimized using an "effective wind speed" that makes the theoretical spectrum best match the measured one. The impact on the predicted brightness temperatures is then assessed using the small slope approximation/small perturbation method (SSA/SPM).

A model of the wind direction signature in the Stokes emission vector from the ocean surface at microwave frequencies

This paper presents a model of the Stokes emission vector from the ocean surface. The ocean surface is described as an ensemble of facets with Cox and Munk's (1954) Gram-Charlier slope distribution. The study discusses the impact of different up-wind and cross-wind rms slopes, skewness, peakedness, foam cover models and atmospheric effects on the azimuthal variation of the Stokes vector, as well as the limitations of the model. Simulation results compare favorably, both in mean value and azimuthal dependence, with SSM/I data at 53° incidence angle and with JPL's WINDRAD measurements at incidence angles from 30° to 65°, and at wind speeds from 2.5 to 11 m/s.

Acting rehearsal in collaborative multimodal mixed reality environments

This paper presents the use of our multimodal mixed reality telecommunication system to support remote acting rehearsal. The rehearsals involved two actors, located in London and Barcelona, and a director in another location in London. This triadic audiovisual telecommunication was performed in a spatial and multimodal collaborative mixed reality environment based on the 'destination-visitor' paradigm, which we define and put into use. We detail our heterogeneous system architecture, which spans the three distributed and technologically asymmetric sites, and features a range of capture, display, and transmission technologies. The actors' and director's experience of rehearsing a scene via the system are then discussed, exploring successes and failures of this heterogeneous form of telecollaboration. Overall, the common spatial frame of reference presented by the system to all parties was highly conducive to theatrical acting and directing, allowing blocking, gross gesture, and unambiguous instruction to be issued. The relative inexpressivity of the actors' embodiments was identified as the central limitation of the telecommunication, meaning that moments relying on performing and reacting to consequential facial expression and subtle gesture were less successful.

Beaming into the rat world: enabling real-time intereaction between rat and human each at their own scale

Immersive virtual reality (IVR) typically generates the illusion in participants that they are in the displayed virtual scene where they can experience and interact in events as if they were really happening. Teleoperator (TO) systems place people at a remote physical destination embodied as a robotic device, and where typically participants have the sensation of being at the destination, with the ability to interact with entities there. In this paper, we show how to combine IVR and TO to allow a new class of application. The participant in the IVR is represented in the destination by a physical robot (TO) and simultaneously the remote place and entities within it are represented to the participant in the IVR. Hence, the IVR participant has a normal virtual reality experience, but where his or her actions and behaviour control the remote robot and can therefore have physical consequences. Here, we show how such a system can be deployed to allow a human and a rat to operate together, but the human interacting with the rat on a human scale, and the rat interacting with the human on the rat scale. The human is represented in a rat arena by a small robot that is slaved to the human"s movements, whereas the tracked rat is represented to the human in the virtual reality by a humanoid avatar. We describe the system and also a study that was designed to test whether humans can successfully play a game with the rat. The results show that the system functioned well and that the humans were able to interact with the rat to fulfil the tasks of the game. This system opens up the possibility of new applications in the life sciences involving participant observation of and interaction with animals but at human scale.

Beaming into the rat world: enabling real-time intereaction between rat and human each at their own scale

Immersive virtual reality (IVR) typically generates the illusion in participants that they are in the displayed virtual scene where they can experience and interact in events as if they were really happening. Teleoperator (TO) systems place people at a remote physical destination embodied as a robotic device, and where typically participants have the sensation of being at the destination, with the ability to interact with entities there. In this paper, we show how to combine IVR and TO to allow a new class of application. The participant in the IVR is represented in the destination by a physical robot (TO) and simultaneously the remote place and entities within it are represented to the participant in the IVR. Hence, the IVR participant has a normal virtual reality experience, but where his or her actions and behaviour control the remote robot and can therefore have physical consequences. Here, we show how such a system can be deployed to allow a human and a rat to operate together, but the human interacting with the rat on a human scale, and the rat interacting with the human on the rat scale. The human is represented in a rat arena by a small robot that is slaved to the human"s movements, whereas the tracked rat is represented to the human in the virtual reality by a humanoid avatar. We describe the system and also a study that was designed to test whether humans can successfully play a game with the rat. The results show that the system functioned well and that the humans were able to interact with the rat to fulfil the tasks of the game. This system opens up the possibility of new applications in the life sciences involving participant observation of and interaction with animals but at human scale.

Designing online interaction to address disciplinary competencies: A cross-country comparison of faculty perspectives

This study was conducted at colleges in three countries (United States, Venezuela, and Spain) and across three academic disciplines (engineering, education, and business), to examine how experienced faculty define competencies for their discipline, and design instructional interaction for online courses. A qualitative research design employing in-depth interviews was selected. Results show that disciplinary knowledge takes precedence when faculty members select competencies to be developed in online courses for their respective professions. In all three disciplines, the design of interaction to correspond with disciplinary competencies was often influenced by contextual factors that modify faculty intention. Therefore, instructional design will vary across countries in the same discipline to address the local context, such as the needs and expectations of the learners, faculty perspectives, beliefs and values, and the needs of the institution, the community, and country. The three disciplines from the three countries agreed on the importance of the following competencies: knowledge of the field, higher order cognitive processes such as critical thinking, analysis, problem solving, transfer of knowledge, oral and written communication skills, team work, decision making, leadership and management skills, indicating far more similarities in competencies than differences between the three different applied disciplines. We found a lack of correspondence between faculty¿s intent to develop collaborative learning skills and the actual development of them. Contextual factors such as faculty prior experience in design, student reluctance to engage in collaborative learning, and institutional assessment systems that focus on individual performance were some of these reasons.