Gene Regulatory Network Analysis and Web-based Application Development

Microarray data is a valuable source for gene regulatory network analysis. Using earthworm microarray data analysis as an example, this dissertation demonstrates that a bioinformatics-guided reverse engineering approach can be applied to analyze time-series data to uncover the underlying molecular mechanism. My network reconstruction results reinforce previous findings that certain neurotransmitter pathways are the target of two chemicals - carbaryl and RDX. This study also concludes that perturbations to these pathways by sublethal concentrations of these two chemicals were temporary, and earthworms were capable of fully recovering. Moreover, differential networks (DNs) analysis indicates that many pathways other than those related to synaptic and neuronal activities were altered during the exposure phase. A novel differential networks (DNs) approach is developed in this dissertation to connect pathway perturbation with toxicity threshold setting from Live Cell Array (LCA) data. Findings from this proof-of-concept study suggest that this DNs approach has a great potential to provide a novel and sensitive tool for threshold setting in chemical risk assessment. In addition, a web-based tool “Web-BLOM” was developed for the reconstruction of gene regulatory networks from time-series gene expression profiles including microarray and LCA data. This tool consists of several modular components: a database, the gene network reconstruction model and a user interface. The Bayesian Learning and Optimization Model (BLOM), originally implemented in MATLAB, was adopted by Web-BLOM to provide an online reconstruction of large-scale gene regulation networks. Compared to other network reconstruction models, BLOM can infer larger networks with compatible accuracy, identify hub genes and is much more computationally efficient

User-centred design of flexible hypermedia for a mobile guide: Reflections on the hyperaudio experience

A user-centred design approach involves end-users from the very beginning. Considering users at the early stages compels designers to think in terms of utility and usability and helps develop the system on what is actually needed. This paper discusses the case of HyperAudio, a context-sensitive adaptive and mobile guide to museums developed in the late 90s. User requirements were collected via a survey to understand visitors’ profiles and visit styles in Natural Science museums. The knowledge acquired supported the specification of system requirements, helping defining user model, data structure and adaptive behaviour of the system. User requirements guided the design decisions on what could be implemented by using simple adaptable triggers and what instead needed more sophisticated adaptive techniques, a fundamental choice when all the computation must be done on a PDA. Graphical and interactive environments for developing and testing complex adaptive systems are discussed as a further step towards an iterative design that considers the user interaction a central point. The paper discusses how such an environment allows designers and developers to experiment with different system’s behaviours and to widely test it under realistic conditions by simulation of the actual context evolving over time. The understanding gained in HyperAudio is then considered in the perspective of the developments that followed that first experience: our findings seem still valid despite the passed time

A future of living machines? International trends and prospects in biomimetic and biohybrid systems

Research in the fields of biomimetic and biohybrid systems is developing at an accelerating rate. Biomimetics can be understood as the development of new technologies using principles abstracted from the study of biological systems, however, biomimetics can also be viewed from an alternate perspective as an important methodology for improving our understanding of the world we live in and of ourselves as biological organisms. A biohybrid entity comprises at least one artificial (engineered) component combined with a biological one. With technologies such as microscale mobile computing, prosthetics and implants, humankind is moving towards a more biohybrid future in which biomimetics helps us to engineer biocompatible technologies. This paper reviews recent progress in the development of biomimetic and biohybrid systems focusing particularly on technologies that emulate living organisms—living machines. Based on our recent bibliographic analysis [1] we examine how biomimetics is already creating life-like robots and identify some key unresolved challenges that constitute bottlenecks for the field. Drawing on our recent research in biomimetic mammalian robots, including humanoids, we review the future prospects for such machines and consider some of their likely impacts on society, including the existential risk of creating artifacts with significant autonomy that could come to match or exceed humankind in intelligence. We conclude that living machines are more likely to be a benefit than a threat but that we should also ensure that progress in biomimetics and biohybrid systems is made with broad societal consent. © (2014) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only

A cognitive ego-vision system for interactive assistance

With increasing computational power and decreasing size, computers nowadays are already wearable and mobile. They become attendant of peoples' everyday life. Personal digital assistants and mobile phones equipped with adequate software gain a lot of interest in public, although the functionality they provide in terms of assistance is little more than a mobile databases for appointments, addresses, to-do lists and photos. Compared to the assistance a human can provide, such systems are hardly to call real assistants. The motivation to construct more human-like assistance systems that develop a certain level of cognitive capabilities leads to the exploration of two central paradigms in this work. The first paradigm is termed cognitive vision systems. Such systems take human cognition as a design principle of underlying concepts and develop learning and adaptation capabilities to be more flexible in their application. They are embodied, active, and situated. Second, the ego-vision paradigm is introduced as a very tight interaction scheme between a user and a computer system that especially eases close collaboration and assistance between these two. Ego-vision systems (EVS) take a user's (visual) perspective and integrate the human in the system's processing loop by means of a shared perception and augmented reality. EVSs adopt techniques of cognitive vision to identify objects, interpret actions, and understand the user's visual perception. And they articulate their knowledge and interpretation by means of augmentations of the user's own view. These two paradigms are studied as rather general concepts, but always with the goal in mind to realize more flexible assistance systems that closely collaborate with its users. This work provides three major contributions. First, a definition and explanation of ego-vision as a novel paradigm is given. Benefits and challenges of this paradigm are discussed as well. Second, a configuration of different approaches that permit an ego-vision system to perceive its environment and its user is presented in terms of object and action recognition, head gesture recognition, and mosaicing. These account for the specific challenges identified for ego-vision systems, whose perception capabilities are based on wearable sensors only. Finally, a visual active memory (VAM) is introduced as a flexible conceptual architecture for cognitive vision systems in general, and for assistance systems in particular. It adopts principles of human cognition to develop a representation for information stored in this memory. So-called memory processes continuously analyze, modify, and extend the content of this VAM. The functionality of the integrated system emerges from their coordinated interplay of these memory processes. An integrated assistance system applying the approaches and concepts outlined before is implemented on the basis of the visual active memory. The system architecture is discussed and some exemplary processing paths in this system are presented and discussed. It assists users in object manipulation tasks and has reached a maturity level that allows to conduct user studies. Quantitative results of different integrated memory processes are as well presented as an assessment of the interactive system by means of these user studies