Web services for transcriptomics

Transcriptomics is part of a family of disciplines focussing on high throughput molecular biology experiments. In the case of transcriptomics, scientists study the expression of genes resulting in transcripts. These transcripts can either perform a biological function themselves or function as messenger molecules containing a copy of the genetic code, which can be used by the ribosomes as templates to synthesise proteins. Over the past decade microarray technology has become the dominant technology for performing high throughput gene expression experiments. A microarray contains short sequences (oligos or probes), which are the reverse complement of fragments of the targets (transcripts or sequences derived thereof). When genes are expressed, their transcripts (or sequences derived thereof) can hybridise to these probes. Many thousand copies of a probe are immobilised in a small region on a support. These regions are called spots and a typical microarray contains thousands or sometimes even more than a million spots. When the transcripts (or sequences derived thereof) are fluorescently labelled and it is known which spots are located where on the support, a fluorescent signal in a certain region represents expression of a certain gene. For interpretation of microarray data it is essential to make sure the oligos are specific for their targets. Hence for proper probe design one needs to know all transcripts that may be expressed and how well they can hybridise with candidate oligos. Therefore oligo design requires: 1. A complete reference genome assembly. 2. Complete annotation of the genome to know which parts may be transcribed. 3. Insight in the amount of natural variation in the genomes of different individuals. 4. Knowledge on how experimental conditions influence the ability of probes to hybridise with certain transcripts. Unfortunately such complete information does not exist, but many microarrays were designed based on incomplete data nevertheless. This can lead to a variety of problems including cross-hybridisation (non-specific binding), erroneously annotated and therefore misleading probes, missing probes and orphan probes. Fortunately the amount of information on genes and their transcripts increases rapidly. Therefore, it is possible to improve the reliability of microarray data analysis by regular updates of the probe annotation using updated databases for genomes and their annotation. Several tools have been developed for this purpose, but these either used simplistic annotation strategies or did not support our species and/ or microarray platforms of interest. Therefore, we developed OligoRAP (Oligo Re- Annotation Pipeline), which is described in chapter 2. OligoRAP was designed to take advantage of amongst others annotation provided by Ensembl, which is the largest genome annotation effort in the world. Thereby OligoRAP supports most of the major animal model organisms including farm animals like chicken and cow. In addition to support for our species and array platforms of interest OligoRAP employs a new annotation strategy combining information from genome and transcript databases in a non-redundant way to get the most complete annotation possible. In chapter 3 we compared annotation generated with 3 oligo annotation pipelines including OligoRAP and investigated the effect on functional analysis of a microarray experiment involving chickens infected with Eimeria bacteria. As an example of functional analysis we investigated if up- or downregulated genes were enriched for Terms from the Gene Ontology (GO). We discovered that small differences in annotation strategy could lead to alarmingly large differences in enriched GO terms. Therefore it is important to know, which annotation strategy works best, but it was not possible to assess this due to the lack of a good reference or benchmark dataset. There are a few limited studies investigating the hybridisation potential of imperfect alignments of oligos with potential targets, but in general such data is scarce. In addition it is difficult to compare these studies due to differences in experimental setup including different hybridisation temperatures and different probe lengths. As result we cannot determine exact thresholds for the alignments of oligos with non-targets to prevent cross-hybridisation, but from these different studies we can get an idea of the range for the thresholds that would be required for optimal target specificity. Note that in these studies experimental conditions were first optimised for an optimal signal to noise ratio for hybridisation of oligos with targets. Then these conditions were used to determine the thresholds for alignments of oligos with non-targets to prevent cross-hybridisation. Chapter 4 describes a parameter sweep using OligoRAP to explore hybridisation potential thresholds from a different perspective. Given the mouse genome thresholds were determined for the largest amount of gene specific probes. Using those thresholds we then determined thresholds for optimal signal to noise ratios. Unfortunately the annotation-based thresholds we found did not fall within the range of experimentally determined thresholds; in fact they were not even close. Hence what was experimentally determined to be optimal for the technology was not in sync with what was determined to be optimal for the mouse genome. Further research will be required to determine whether microarray technology can be modified in such a way that it is better suited for gene expression experiments. The requirement of a priori information on possible targets and the lack of sufficient knowledge on how experimental conditions influence hybridisation potential can be considered the Achiles’ heels of microarray technology. Chapter 5 is a collection of 3 application notes describing other tools that can aid in analysis of transcriptomics data. Firstly, RShell, which is a plugin for the Taverna workbench allowing users to execute statistical computations remotely on R-servers. Secondly, MADMAX services, which provide quality control and normalisation of microarray data for AffyMetrix arrays. Finally, GeneIlluminator, which is a tool to disambiguate gene symbols allowing researchers to specifically retrieve literature for their genes of interest even if the gene symbols for those genes had many synonyms and homonyms. Web services High throughput experiments like those performed in transcriptomics usually require subsequent analysis with many different tools to make biological sense of the data. Installing all these tools on a single, local computer and making them compatible so users can build analysis pipelines can be very cumbersome. Therefore distributed analysis strategies have been explored extensively over the past decades. In a distributed system providers offer remote access to tools and data via the Internet allowing users to create pipelines from modules from all over the globe. Chapter 1 provides an overview of the evolution of web services, which represent the latest breed in technology for creating distributed systems. The major advantage of web services over older technology is that web services are programming language independent, Internet communication protocol independent and operating system independent. Therefore web services are very flexible and most of them are firewall-proof. Web services play a major role in the remaining chapters of this thesis: OligoRAP is a workflow entirely made from web services and the tools described in chapter 5 all provide remote programmatic access via web service interfaces. Although web services can be used to build relatively complex workflows like OligoRAP, a lack of mainly de facto standards and of user-friendly clients has limited the use of web services to bioinformaticians. A semantic web where biologists can easily link web services into complex workflows does n <br/

Arousal and Valence Prediction in Spontaneous Emotional Speech: Felt versus Perceived Emotion

In this paper, we describe emotion recognition experiments carried out for spontaneous affective speech with the aim to compare the added value of annotation of felt emotion versus annotation of perceived emotion. Using speech material available in the TNO-GAMING corpus (a corpus containing audiovisual recordings of people playing videogames), speech-based affect recognizers were developed that can predict Arousal and Valence scalar values. Two types of recognizers were developed in parallel: one trained with felt emotion annotations (generated by the gamers themselves) and one trained with perceived/observed emotion annotations (generated by a group of observers). The experiments showed that, in speech, with the methods and features currently used, observed emotions are easier to predict than felt emotions. The results suggest that recognition performance strongly depends on how and by whom the emotion annotations are carried out. \u

Modeling the Cognitive Task Load and Performance of Naval Operators

Abstract. Operators on naval ships have to act in dynamic, critical and highdemand task environments. For these environments, a cognitive task load (CTL) model has been proposed as foundation of three operator support functions: adaptive task allocation, cognitive aids and resource feedback. This paper presents the construction of such a model as a Bayesian network with probability relationships between CTL and performance. The network is trained and tested with two datasets: operator performance with an adaptive user interface in a lab-setting and operator performance on a high-tech sailing ship. The “Naïve Bayesian network ” tuned out to be the best choice, providing performance estimations with 86 % and 74 % accuracy for respectively the lab and ship data. Overall, the resulting model nicely generalizes over the two datasets. It will be used to estimate operator performance under momentary CTL-conditions, and to set the thresholds of the load-mitigation strategies for the three support functions

How should a virtual agent present psychoeducation?

BACKGROUND AND OBJECTIVE: With the rise of autonomous e-mental health applications, virtual agents can play a major role in improving trustworthiness, therapy outcome and adherence. In these applications, it is important that patients adhere in the sense that they perform the tasks, but also that they adhere to the specific recommendations on how to do them well. One important construct in improving adherence is psychoeducation, information on the why and how of therapeutic interventions. In an e-mental health context, this can be delivered in two different ways: verbally by a (virtual) embodied conversational agent or just via text on the scree

Growing-up hand in hand with robots: Designing and evaluating child-robot interaction from a developmental perspective

Robots are becoming part of children's care, entertainment, education, social assistance and therapy. A steadily growing body of Human-Robot Interaction (HRI) research shows that child-robot interaction (CRI) holds promises to support children's development in novel ways. However, research has shown that technologies that do not take into account children's needs, abilities, interests, and developmental characteristics may have a limited or even negative impact on their physical, cognitive, social, emotional, and moral development. As a result, robotic technology that aims to support children via means of social interaction has to take the developmental perspective into consideration. With this workshop (the third of a series of workshops focusing CRI research), we aim to bring together researchers to discuss how a developmental perspective play a role for smart and natural interaction between robots and children. We invite participants to share their experiences on the challenges of taking the developmental perspective in CRI, such as long-term sustained interactions in the wild, involving children and other stakeholders in the design process and more. Looking across disciplinary boundaries, we hope to stimulate thought-provoking discussions on epistemology, methods, approaches, techniques, interaction scenarios and design principles focused on supporting children's development through interaction with robotic technology. Our goal does not only focus on the conception and formulation of the outcomes in the context of the workshop venue, but also on their establishment and availability for the HRI community in different forms

Mobile Phone-Delivered Cognitive Behavioral Therapy for Insomnia:A Randomized Waitlist Controlled Trial

Background: This study is one of the first randomized controlled trials investigating cognitive behavioral therapy for insomnia (CBT-I) delivered by a fully automated mobile phone app. Such an app can potentially increase the accessibility of insomnia treatment for the 10% of people who have insomnia. Objective: The objective of our study was to investigate the efficacy of CBT-I delivered via the Sleepcare mobile phone app, compared with a waitlist control group, in a randomized controlled trial. Methods: We recruited participants in the Netherlands with relatively mild insomnia disorder. After answering an online pretest questionnaire, they were randomly assigned to the app (n=74) or the waitlist condition (n=77). The app packaged a sleep diary, a relaxation exercise, sleep restriction exercise, and sleep hygiene and education. The app was fully automated and adjusted itself to a participant’s progress. Program duration was 6 to 7 weeks, after which participants received posttest measurements and a 3-month follow-up. The participants in the waitlist condition received the app after they completed the posttest questionnaire. The measurements consisted of questionnaires and 7-day online diaries. The questionnaires measured insomnia severity, dysfunctional beliefs about sleep, and anxiety and depression symptoms. The diary measured sleep variables such as sleep efficiency. We performed multilevel analyses to study the interaction effects between time and condition. Results: The results showed significant interaction effects (P<.01) favoring the app condition on the primary outcome measures of insomnia severity (d=–0.66) and sleep efficiency (d=0.71). Overall, these improvements were also retained in a 3-month follow-up. Conclusions: This study demonstrated the efficacy of a fully automated mobile phone app in the treatment of relatively mild insomnia. The effects were in the range of what is found for Web-based treatment in general. This supports the applicability of such technical tools in the treatment of insomnia. Future work should examine the generalizability to a more diverse population. Furthermore, the separate components of such an app should be investigated. It remains to be seen how this app can best be integrated into the current health regimens. Trial Registration: Netherlands Trial Register: NTR5560; http://www.trialregister.nl/trialreg/admin/rctview.asp?TC=5560 (Archived by WebCite at http://www.webcitation.org/6noLaUdJ4

Personal Assistants for Healthcare Treatment at Home

ABSTRACT This paper describes the research plans in the SuperAssist project, introducing personal assistants in the care of diabetes patients, assisting the patients themselves, the medical specialists looking after the patients&apos; healthcare, and the technical specialists responsible for maintaining the health of the devices involved. The paper discusses the issues of trust and cooperation as the critical success factors within this multi-user multi-agent (MUMA) project and within the future of agent-based healthcare attempting to increase the self-help abilities of individual patients

Methods for interpreting lists of affected genes obstained in a DNA microarray experiment

Background - The aim of this paper was to describe and compare the methods used and the results obtained by the participants in a joint EADGENE (European Animal Disease Genomic Network of Excellence) and SABRE (Cutting Edge Genomics for Sustainable Animal Breeding) workshop focusing on post analysis of microarray data. The participating groups were provided with identical lists of microarray probes, including test statistics for three different contrasts, and the normalised log-ratios for each array, to be used as the starting point for interpreting the affected probes. The data originated from a microarray experiment conducted to study the host reactions in broilers occurring shortly after a secondary challenge with either a homologous or heterologous species of Eimeria. Results - Several conceptually different analytical approaches, using both commercial and public available software, were applied by the participating groups. The following tools were used: Ingenuity Pathway Analysis, MAPPFinder, LIMMA, GOstats, GOEAST, GOTM, Globaltest, TopGO, ArrayUnlock, Pathway Studio, GIST and AnnotationDbi. The main focus of the approaches was to utilise the relation between probes/genes and their gene ontology and pathways to interpret the affected probes/genes. The lack of a well-annotated chicken genome did though limit the possibilities to fully explore the tools. The main results from these analyses showed that the biological interpretation is highly dependent on the statistical method used but that some common biological conclusions could be reached. Conclusion - It is highly recommended to test different analytical methods on the same data set and compare the results to obtain a reliable biological interpretation of the affected genes in a DNA microarray experimen