A Multi-facetted Visual Analytics Tool for Exploratory Analysis of Human Brain and Function Datasets

Brain research typically requires large amounts of data from different sources, and often of different nature. The use of different software tools adapted to the nature of each data source can make research work cumbersome and time consuming. It follows that data is not often used to its fullest potential thus limiting exploratory analysis. This paper presents an ancillary software tool called BRAVIZ that integrates interactive visualization with real-time statistical analyses, facilitating access to multi-facetted neuroscience data and automating many cumbersome and error-prone tasks required to explore such data. Rather than relying on abstract numerical indicators, BRAVIZ emphasizes brain images as the main object of the analysis process of individuals or groups. BRAVIZ facilitates exploration of trends or relationships to gain an integrated view of the phenomena studied, thus motivating discovery of new hypotheses. A case study is presented that incorporates brain structure and function outcomes together with different types of clinical data

An Uncertainty Visual Analytics Framework for Functional Magnetic Resonance Imaging

Improving understanding of the human brain is one of the leading pursuits of modern scientific research. Functional magnetic resonance imaging (fMRI) is a foundational technique for advanced analysis and exploration of the human brain. The modality scans the brain in a series of temporal frames which provide an indication of the brain activity either at rest or during a task. The images can be used to study the workings of the brain, leading to the development of an understanding of healthy brain function, as well as characterising diseases such as schizophrenia and bipolar disorder. Extracting meaning from fMRI relies on an analysis pipeline which can be broadly categorised into three phases: (i) data acquisition and image processing; (ii) image analysis; and (iii) visualisation and human interpretation. The modality and analysis pipeline, however, are hampered by a range of uncertainties which can greatly impact the study of the brain function. Each phase contains a set of required and optional steps, containing inherent limitations and complex parameter selection. These aspects lead to the uncertainty that impacts the outcome of studies. Moreover, the uncertainties that arise early in the pipeline, are compounded by decisions and limitations further along in the process. While a large amount of research has been undertaken to examine the limitations and variable parameter selection, statistical approaches designed to address the uncertainty have not managed to mitigate the issues. Visual analytics, meanwhile, is a research domain which seeks to combine advanced visual interfaces with specialised interaction and automated statistical processing designed to exploit human expertise and understanding. Uncertainty visual analytics (UVA) tools, which aim to minimise and mitigate uncertainties, have been proposed for a variety of data, including astronomical, financial, weather and crime. Importantly, UVA approaches have also seen success in medical imaging and analysis. However, there are many challenges surrounding the application of UVA to each research domain. Principally, these involve understanding what the uncertainties are and the possible effects so they may be connected to visualisation and interaction approaches. With fMRI, the breadth of uncertainty arising in multiple stages along the pipeline and the compound effects, make it challenging to propose UVAs which meaningfully integrate into pipeline. In this thesis, we seek to address this challenge by proposing a unified UVA framework for fMRI. To do so, we first examine the state-of-the-art landscape of fMRI uncertainties, including the compound effects, and explore how they are currently addressed. This forms the basis of a field we term fMRI-UVA. We then present our overall framework, which is designed to meet the requirements of fMRI visual analysis, while also providing an indication and understanding of the effects of uncertainties on the data. Our framework consists of components designed for the spatial, temporal and processed imaging data. Alongside the framework, we propose two visual extensions which can be used as standalone UVA applications or be integrated into the framework. Finally, we describe a conceptual algorithmic approach which incorporates more data into an existing measure used in the fMRI analysis pipeline

Kangaroo mother care had a protective effect on the volume of brain structures in young adults born preterm

Q1Q1Jóvenes adultosAim: The protective effects of Kangaroo mother care (KMC) on the neurodevelop-ment of preterm infants are well established, but we do not know whether the ben-efits persist beyond infancy. Our aim was to determine whether providing KMC in infancy affected brain volumes in young adulthood. Method: Standardised cognitive, memory and motor skills tests were used to determine the brain volumes of 20-year-old adults who had formed part of a randomised controlled trial of KMC versus incubator care. Multivariate analysis of brain volumes was conducted according to KMC exposure. Results: The study comprised 178 adults born preterm: 97 had received KMC and 81 were incubator care controls. Bivariate analysis showed larger volumes of total grey matter, basal nuclei and cerebellum in those who had received KMC, and the white matter was better organised. This means that the volumes of the main brain structures associated with intelligence, attention, memory and coordination were larger in the KMC group. Multivariate lineal regression analysis demonstrated the direct rela-tionship between brain volumes and duration of KMC, after controlling for potential confounders. Conclusion: Our findings suggest that the neuroprotective effects of KMC for pre-term infants persisted beyond childhood and improved their lifetime functionality and quality of life.https://orcid.org/0000-0001-6697-5837https://orcid.org/0000-0002-1923-3934https://orcid.org/0000-0001-5464-2701Revista Internacional - IndexadaA1N

On Making in the Digital Humanities

On Making in the Digital Humanities fills a gap in our understanding of digital humanities projects and craft by exploring the processes of making as much as the products that arise from it. The volume draws focus to the interwoven layers of human and technological textures that constitute digital humanities scholarship. To do this, it assembles a group of well-known, experienced and emerging scholars in the digital humanities to reflect on various forms of making (we privilege here the creative and applied side of the digital humanities). The volume honours the work of John Bradley, as it is totemic of a practice of making that is deeply informed by critical perspectives. A special chapter also honours the profound contributions that this volume’s co-editor, Stéfan Sinclair, made to the creative, applied and intellectual praxis of making and the digital humanities. Stéfan Sinclair passed away on 6 August 2020. The chapters gathered here are individually important, but together provide a very human view on what it is to do the digital humanities, in the past, present and future. This book will accordingly be of interest to researchers, teachers and students of the digital humanities; creative humanities, including maker spaces and culture; information studies; the history of computing and technology; and the history of science and the humanities

Visual Analytics for Performing Complex Tasks with Electronic Health Records

Electronic health record systems (EHRs) facilitate the storage, retrieval, and sharing of patient health data; however, the availability of data does not directly translate to support for tasks that healthcare providers encounter every day. In recent years, healthcare providers employ a large volume of clinical data stored in EHRs to perform various complex data-intensive tasks. The overwhelming volume of clinical data stored in EHRs and a lack of support for the execution of EHR-driven tasks are, but a few problems healthcare providers face while working with EHR-based systems. Thus, there is a demand for computational systems that can facilitate the performance of complex tasks that involve the use and working with the vast amount of data stored in EHRs. Visual analytics (VA) offers great promise in handling such information overload challenges by integrating advanced analytics techniques with interactive visualizations. The user-controlled environment that VA systems provide allows healthcare providers to guide the analytics techniques on analyzing and managing EHR data through interactive visualizations. The goal of this research is to demonstrate how VA systems can be designed systematically to support the performance of complex EHR-driven tasks. In light of this, we present an activity and task analysis framework to analyze EHR-driven tasks in the context of interactive visualization systems. We also conduct a systematic literature review of EHR-based VA systems and identify the primary dimensions of the VA design space to evaluate these systems and identify the gaps. Two novel EHR-based VA systems (SUNRISE and VERONICA) are then designed to bridge the gaps. SUNRISE incorporates frequent itemset mining, extreme gradient boosting, and interactive visualizations to allow users to interactively explore the relationships between laboratory test results and a disease outcome. The other proposed system, VERONICA, uses a representative set of supervised machine learning techniques to find the group of features with the strongest predictive power and make the analytic results accessible through an interactive visual interface. We demonstrate the usefulness of these systems through a usage scenario with acute kidney injury using large provincial healthcare databases from Ontario, Canada, stored at ICES

Tools and theory to improve data analysis

This thesis proposes a scientific model to explain the data analysis process. I argue that data analysis is primarily a procedure to build un- derstanding and as such, it dovetails with the cognitive processes of the human mind. Data analysis tasks closely resemble the cognitive process known as sensemaking. I demonstrate how data analysis is a sensemaking task adapted to use quantitative data. This identification highlights a uni- versal structure within data analysis activities and provides a foundation for a theory of data analysis. The model identifies two competing chal- lenges within data analysis: the need to make sense of information that we cannot know and the need to make sense of information that we can- not attend to. Classical statistics provides solutions to the first challenge, but has little to say about the second. However, managing attention is the primary obstacle when analyzing big data. I introduce three tools for managing attention during data analysis. Each tool is built upon a different method for managing attention. ggsubplot creates embedded plots, which transform data into a format that can be easily processed by the human mind. lubridate helps users automate sensemaking out- side of the mind by improving the way computers handle date-time data. Visual Inference Tools develop expertise in young statisticians that can later be used to efficiently direct attention. The insights of this thesis are especially helpful for consultants, applied statisticians, and teachers of data analysis