Microarray data mining using Bioconductor packages

BACKGROUND: This paper describes the results of a Gene Ontology (GO) term enrichment analysis of chicken microarray data using the Bioconductor packages. By checking the enriched GO terms in three contrasts, MM8-PM8, MM8-MA8, and MM8-MM24, of the provided microarray data during this workshop, this analysis aimed to investigate the host reactions in chickens occurring shortly after a secondary challenge with either a homologous or heterologous species of Eimeria. The results of GO enrichment analysis using GO terms annotated to chicken genes and GO terms annotated to chicken-human orthologous genes were also compared. Furthermore, a locally adaptive statistical procedure (LAP) was performed to test differentially expressed chromosomal regions, rather than individual genes, in the chicken genome after Eimeria challenge. RESULTS: GO enrichment analysis identified significant (raw p-value < 0.05) GO terms for all three contrasts included in the analysis. Some of the GO terms linked to, generally, primary immune responses or secondary immune responses indicating the GO enrichment analysis is a useful approach to analyze microarray data. The comparisons of GO enrichment results using chicken gene information and chicken-human orthologous gene information showed more refined GO terms related to immune responses when using chicken-human orthologous gene information, this suggests that using chicken-human orthologous gene information has higher power to detect significant GO terms with more refined functionality. Furthermore, three chromosome regions were identified to be significantly up-regulated in contrast MM8-PM8 (q-value < 0.01). CONCLUSION: Overall, this paper describes a practical approach to analyze microarray data in farm animals where the genome information is still incomplete. For farm animals, such as chicken, with currently limited gene annotation, borrowing gene annotation information from orthologous genes in well-annotated species, such as human, will help improve the pathway analysis results substantially. Furthermore, LAP analysis approach is a relatively new and very useful way to be applied in microarray analysis

A cloud-based robot system for long-term interaction: principles, implementation, lessons learned

Making the transition to long-term interaction with social-robot systems has been identified as one of the main challenges in human-robot interaction. This article identifies four design principles to address this challenge and applies them in a real-world implementation: cloud-based robot control, a modular design, one common knowledge base for all applications, and hybrid artificial intelligence for decision making and reasoning. The control architecture for this robot includes a common Knowledge-base (ontologies), Data-base, “Hybrid Artificial Brain” (dialogue manager, action selection and explainable AI), Activities Centre (Timeline, Quiz, Break and Sort, Memory, Tip of the Day, ), Embodied Conversational Agent (ECA, i.e., robot and avatar), and Dashboards (for authoring and monitoring the interaction). Further, the ECA is integrated with an expandable set of (mobile) health applications. The resulting system is a Personal Assistant for a healthy Lifestyle (PAL), which supports diabetic children with self-management and educates them on health-related issues (48 children, aged 6–14, recruited via hospitals in the Netherlands and in Italy). It is capable of autonomous interaction “in the wild” for prolonged periods of time without the need for a “Wizard-of-Oz” (up until 6 months online). PAL is an exemplary system that provides personalised, stable and diverse, long-term human-robot interaction

Conversational Interfaces for Explainable AI: A Human-Centered Approach

One major goal of Explainable Artificial Intelligence (XAI), in order to enhance trust in technology, is to enable the user to enquire information and explanation about its functionality directly from an intelligent agent. We propose conversational interfaces (CI) to be the perfect setting, since they are intuitive for humans and computationally processible. While there are many approaches addressing technical issues of this human-agent communication problem, the user perspective appears to be widely neglected. With the purpose of better requirement understanding and identification of implicit expectations from a human-centered view, a Wizard of Oz experiment was conducted, where participants tried to elicit basic information from a pretended artificial agent (What are your capabilities?). The hypothesis that users pursue fundamentally different strategies could be verified with the help of Conversation Analysis. Results illustrate the vast variety in human communication and disclose both requirements of users and obstacles in the implementation of protocols for interacting agents. Finally, we infer essential indications for the implementation of such a CI

Estudio de la influencia de la automatización en el proyecto arquitectónico

Estudio de la influencia de la automatización en el proyecto arquitectónic

XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous web services

Background: Life sciences make heavily use of the web for both data provision and analysis. However, the increasing amount of available data and the diversity of analysis tools call for machine accessible interfaces in order to be effective. HTTP-based Web service technologies, like the Simple Object Access Protocol (SOAP) and REpresentational State Transfer (REST) services, are today the most common technologies for this in bioinformatics. However, these methods have severe drawbacks, including lack of discoverability, and the inability for services to send status notifications. Several complementary workarounds have been proposed, but the results are ad-hoc solutions of varying quality that can be difficult to use. Results: We present a novel approach based on the open standard Extensible Messaging and Presence Protocol (XMPP), consisting of an extension (IO Data) to comprise discovery, asynchronous invocation, and definition of data types in the service. That XMPP cloud services are capable of asynchronous communication implies that clients do not have to poll repetitively for status, but the service sends the results back to the client upon completion. Implementations for Bioclipse and Taverna are presented, as are various XMPP cloud services in bio- and cheminformatics. Conclusion: XMPP with its extensions is a powerful protocol for cloud services that demonstrate several advantages over traditional HTTP-based Web services: 1) services are discoverable without the need of an external registry, 2) asynchronous invocation eliminates the need for ad-hoc solutions like polling, and 3) input and output types defined in the service allows for generation of clients on the fly without the need of an external semantics description. The many advantages over existing technologies make XMPP a highly interesting candidate for next generation online services in bioinformatics

A cross-lingual adaptation approach for rapid development of speech recognizers for learning disabled users

Building a voice-operated system for learning disabled users is a difficult task that requires a considerable amount of time and effort. Due to the wide spectrum of disabilities and their different related phonopathies, most approaches available are targeted to a specific pathology. This may improve their accuracy for some users, but makes them unsuitable for others. In this paper, we present a cross-lingual approach to adapt a general-purpose modular speech recognizer for learning disabled people. The main advantage of this approach is that it allows rapid and cost-effective development by taking the already built speech recognition engine and its modules, and utilizing existing resources for standard speech in different languages for the recognition of the users’ atypical voices. Although the recognizers built with the proposed technique obtain lower accuracy rates than those trained for specific pathologies, they can be used by a wide population and developed more rapidly, which makes it possible to design various types of speech-based applications accessible to learning disabled users.This research was supported by the project ‘Favoreciendo la vida autónoma de discapacitados intelectuales con problemas de comunicación oral mediante interfaces personalizados de reconocimiento automático del habla’, financed by the Centre of Initiatives for Development Cooperation (Centro de Iniciativas de Cooperación al Desarrollo, CICODE), University of Granada, Spain. This research was supported by the Student Grant Scheme 2014 (SGS) at the Technical University of Liberec

Laser spectroscopy for breath analysis : towards clinical implementation

Detection and analysis of volatile compounds in exhaled breath represents an attractive tool for monitoring the metabolic status of a patient and disease diagnosis, since it is non-invasive and fast. Numerous studies have already demonstrated the benefit of breath analysis in clinical settings/applications and encouraged multidisciplinary research to reveal new insights regarding the origins, pathways, and pathophysiological roles of breath components. Many breath analysis methods are currently available to help explore these directions, ranging from mass spectrometry to laser-based spectroscopy and sensor arrays. This review presents an update of the current status of optical methods, using near and mid-infrared sources, for clinical breath gas analysis over the last decade and describes recent technological developments and their applications. The review includes: tunable diode laser absorption spectroscopy, cavity ring-down spectroscopy, integrated cavity output spectroscopy, cavity-enhanced absorption spectroscopy, photoacoustic spectroscopy, quartz-enhanced photoacoustic spectroscopy, and optical frequency comb spectroscopy. A SWOT analysis (strengths, weaknesses, opportunities, and threats) is presented that describes the laser-based techniques within the clinical framework of breath research and their appealing features for clinical use.Peer reviewe