Decoding neural activity in sulcal and white matter areas of the brain to accurately predict individual finger movement and tactile stimuli of the human hand

Millions of people worldwide suffer motor or sensory impairment due to stroke, spinal cord injury, multiple sclerosis, traumatic brain injury, diabetes, and motor neuron diseases such as ALS (amyotrophic lateral sclerosis). A brain-computer interface (BCI), which links the brain directly to a computer, offers a new way to study the brain and potentially restore impairments in patients living with these debilitating conditions. One of the challenges currently facing BCI technology, however, is to minimize surgical risk while maintaining efficacy. Minimally invasive techniques, such as stereoelectroencephalography (SEEG) have become more widely used in clinical applications in epilepsy patients since they can lead to fewer complications. SEEG depth electrodes also give access to sulcal and white matter areas of the brain but have not been widely studied in brain-computer interfaces. Here we show the first demonstration of decoding sulcal and subcortical activity related to both movement and tactile sensation in the human hand. Furthermore, we have compared decoding performance in SEEG-based depth recordings versus those obtained with electrocorticography electrodes (ECoG) placed on gyri. Initial poor decoding performance and the observation that most neural modulation patterns varied in amplitude trial-to-trial and were transient (significantly shorter than the sustained finger movements studied), led to the development of a feature selection method based on a repeatability metric using temporal correlation. An algorithm based on temporal correlation was developed to isolate features that consistently repeated (required for accurate decoding) and possessed information content related to movement or touch-related stimuli. We subsequently used these features, along with deep learning methods, to automatically classify various motor and sensory events for individual fingers with high accuracy. Repeating features were found in sulcal, gyral, and white matter areas and were predominantly phasic or phasic-tonic across a wide frequency range for both HD (high density) ECoG and SEEG recordings. These findings motivated the use of long short-term memory (LSTM) recurrent neural networks (RNNs) which are well-suited to handling transient input features. Combining temporal correlation-based feature selection with LSTM yielded decoding accuracies of up to 92.04 ± 1.51% for hand movements, up to 91.69 ± 0.49% for individual finger movements, and up to 83.49 ± 0.72% for focal tactile stimuli to individual finger pads while using a relatively small number of SEEG electrodes. These findings may lead to a new class of minimally invasive brain-computer interface systems in the future, increasing its applicability to a wide variety of conditions

A Comprehensive Survey on Applications of Transformers for Deep Learning Tasks

Transformer is a deep neural network that employs a self-attention mechanism to comprehend the contextual relationships within sequential data. Unlike conventional neural networks or updated versions of Recurrent Neural Networks (RNNs) such as Long Short-Term Memory (LSTM), transformer models excel in handling long dependencies between input sequence elements and enable parallel processing. As a result, transformer-based models have attracted substantial interest among researchers in the field of artificial intelligence. This can be attributed to their immense potential and remarkable achievements, not only in Natural Language Processing (NLP) tasks but also in a wide range of domains, including computer vision, audio and speech processing, healthcare, and the Internet of Things (IoT). Although several survey papers have been published highlighting the transformer's contributions in specific fields, architectural differences, or performance evaluations, there is still a significant absence of a comprehensive survey paper encompassing its major applications across various domains. Therefore, we undertook the task of filling this gap by conducting an extensive survey of proposed transformer models from 2017 to 2022. Our survey encompasses the identification of the top five application domains for transformer-based models, namely: NLP, Computer Vision, Multi-Modality, Audio and Speech Processing, and Signal Processing. We analyze the impact of highly influential transformer-based models in these domains and subsequently classify them based on their respective tasks using a proposed taxonomy. Our aim is to shed light on the existing potential and future possibilities of transformers for enthusiastic researchers, thus contributing to the broader understanding of this groundbreaking technology

Meta Heuristics based Machine Learning and Neural Mass Modelling Allied to Brain Machine Interface

New understanding of the brain function and increasing availability of low-cost-non-invasive electroencephalograms (EEGs) recording devices have made brain-computer-interface (BCI) as an alternative option to augmentation of human capabilities by providing a new non-muscular channel for sending commands, which could be used to activate electronic or mechanical devices based on modulation of thoughts. In this project, our emphasis will be on how to develop such a BCI using fuzzy rule-based systems (FRBSs), metaheuristics and Neural Mass Models (NMMs). In particular, we treat the BCI system as an integrated problem consisting of mathematical modelling, machine learning and classification. Four main steps are involved in designing a BCI system: 1) data acquisition, 2) feature extraction, 3) classification and 4) transferring the classification outcome into control commands for extended peripheral capability. Our focus has been placed on the first three steps. This research project aims to investigate and develop a novel BCI framework encompassing classification based on machine learning, optimisation and neural mass modelling. The primary aim in this project is to bridge the gap of these three different areas in a bid to design a more reliable and accurate communication path between the brain and external world. To achieve this goal, the following objectives have been investigated: 1) Steady-State Visual Evoked Potential (SSVEP) EEG data are collected from human subjects and pre-processed; 2) Feature extraction procedure is implemented to detect and quantify the characteristics of brain activities which indicates the intention of the subject.; 3) a classification mechanism called an Immune Inspired Multi-Objective Fuzzy Modelling Classification algorithm (IMOFM-C), is adapted as a binary classification approach for classifying binary EEG data. Then, the DDAG-Distance aggregation approach is proposed to aggregate the outcomes of IMOFM-C based binary classifiers for multi-class classification; 4) building on IMOFM-C, a preference-based ensemble classification framework known as IMOFM-CP is proposed to enhance the convergence performance and diversity of each individual component classifier, leading to an improved overall classification accuracy of multi-class EEG data; and 5) finally a robust parameterising approach which combines a single-objective GA and a clustering algorithm with a set of newly devised objective and penalty functions is proposed to obtain robust sets of synaptic connectivity parameters of a thalamic neural mass model (NMM). The parametrisation approach aims to cope with nonlinearity nature normally involved in describing multifarious features of brain signals

Hardware-efficient data compression in wireless intracortical brain-machine interfaces

Brain-Machine Interfaces (BMI) have emerged as a promising technology for restoring lost motor function in patients with neurological disorders and/or motor impairments, e.g. paraplegia, amputation, stroke, spinal cord injury, amyotrophic lateral sclerosis, etc. The past 2 decades have seen significant advances in BMI performance. This has largely been driven by the invention and uptake of intracortical microelectrode arrays that can isolate the activity of individual neurons. However, the current paradigm involves the use of percutaneous connections, i.e. wires. These wires carry the information from the intracortical array implanted in the brain to outside of the body, where the information is used for neural decoding. These wires carry significant long-term risks ranging from infection, to mechanical injury, to impaired mobility and quality of life for the individual. Therefore, there is a desire to make intracortical BMIs (iBMI) wireless, where the data is communicated out wirelessly, either with the use of electromagnetic or acoustic waves. Unfortunately, this consumes a significant amount of power, which is dissipated from the implant in the form of heat. Heating tissue can cause irreparable damage, and so there are strict limits on heat flux from implants to cortical tissue. Given the ever-increasing number of channels per implant, the required communication power is now exceeding the acceptable cortical heat transfer limits. This cortical heating issue is hampering widespread clinical use. As such, effective data compression would bring Wireless iBMIs (WI-BMI) into alignment with heat transfer limits, enabling large channel counts and small implant sizes without risking tissue damage via heating. This thesis addresses the aforementioned communication power problem from a signal processing and data compression perspective, and is composed of two parts. In the first part, we investigate hardware-efficient ways to compress the Multi-Unit Activity (MUA) signal, which is the most common signal in modern iBMIs. In the second and final part, we look at efficient ways to extract and compress the high-bandwidth Entire Spiking Activity signal, which, while underexplored as a signal, has been the subject of significant interest given its ability to outperform the MUA signal in neural decoding. Overall, this thesis introduces hardware-efficient methods of extracting high-performing neural features, and compressing them by an order of magnitude or more beyond the state-of-the-art in ultra-low power ways. This enables many more recording channels to be fit onto intracortical implants, while remaining within cortical heat transfer safety and channel capacity limits.Open Acces

A Closed-Loop Bidirectional Brain-Machine Interface System For Freely Behaving Animals

A brain-machine interface (BMI) creates an artificial pathway between the brain and the external world. The research and applications of BMI have received enormous attention among the scientific community as well as the public in the past decade. However, most research of BMI relies on experiments with tethered or sedated animals, using rack-mount equipment, which significantly restricts the experimental methods and paradigms. Moreover, most research to date has focused on neural signal recording or decoding in an open-loop method. Although the use of a closed-loop, wireless BMI is critical to the success of an extensive range of neuroscience research, it is an approach yet to be widely used, with the electronics design being one of the major bottlenecks. The key goal of this research is to address the design challenges of a closed-loop, bidirectional BMI by providing innovative solutions from the neuron-electronics interface up to the system level. Circuit design innovations have been proposed in the neural recording front-end, the neural feature extraction module, and the neural stimulator. Practical design issues of the bidirectional neural interface, the closed-loop controller and the overall system integration have been carefully studied and discussed.To the best of our knowledge, this work presents the first reported portable system to provide all required hardware for a closed-loop sensorimotor neural interface, the first wireless sensory encoding experiment conducted in freely swimming animals, and the first bidirectional study of the hippocampal field potentials in freely behaving animals from sedation to sleep. This thesis gives a comprehensive survey of bidirectional BMI designs, reviews the key design trade-offs in neural recorders and stimulators, and summarizes neural features and mechanisms for a successful closed-loop operation. The circuit and system design details are presented with bench testing and animal experimental results. The methods, circuit techniques, system topology, and experimental paradigms proposed in this work can be used in a wide range of relevant neurophysiology research and neuroprosthetic development, especially in experiments using freely behaving animals

Digital Traces of the Mind::Using Smartphones to Capture Signals of Well-Being in Individuals

General context and questions Adolescents and young adults typically use their smartphone several hours a day. Although there are concerns about how such behaviour might affect their well-being, the popularity of these powerful devices also opens novel opportunities for monitoring well-being in daily life. If successful, monitoring well-being in daily life provides novel opportunities to develop future interventions that provide personalized support to individuals at the moment they require it (just-in-time adaptive interventions). Taking an interdisciplinary approach with insights from communication, computational, and psychological science, this dissertation investigated the relation between smartphone app use and well-being and developed machine learning models to estimate an individual’s well-being based on how they interact with their smartphone. To elucidate the relation between smartphone trace data and well-being and to contribute to the development of technologies for monitoring well-being in future clinical practice, this dissertation addressed two overarching questions:RQ1: Can we find empirical support for theoretically motivated relations between smartphone trace data and well-being in individuals? RQ2: Can we use smartphone trace data to monitor well-being in individuals?Aims The first aim of this dissertation was to quantify the relation between the collected smartphone trace data and momentary well-being at the sample level, but also for each individual, following recent conceptual insights and empirical findings in psychological, communication, and computational science. A strength of this personalized (or idiographic) approach is that it allows us to capture how individuals might differ in how smartphone app use is related to their well-being. Considering such interindividual differences is important to determine if some individuals might potentially benefit from spending more time on their smartphone apps whereas others do not or even experience adverse effects. The second aim of this dissertation was to develop models for monitoring well-being in daily life. The present work pursued this transdisciplinary aim by taking a machine learning approach and evaluating to what extent we might estimate an individual’s well-being based on their smartphone trace data. If such traces can be used for this purpose by helping to pinpoint when individuals are unwell, they might be a useful data source for developing future interventions that provide personalized support to individuals at the moment they require it (just-in-time adaptive interventions). With this aim, the dissertation follows current developments in psychoinformatics and psychiatry, where much research resources are invested in using smartphone traces and similar data (obtained with smartphone sensors and wearables) to develop technologies for detecting whether an individual is currently unwell or will be in the future. Data collection and analysis This work combined novel data collection techniques (digital phenotyping and experience sampling methodology) for measuring smartphone use and well-being in the daily lives of 247 student participants. For a period up to four months, a dedicated application installed on participants’ smartphones collected smartphone trace data. In the same time period, participants completed a brief smartphone-based well-being survey five times a day (for 30 days in the first month and 30 days in the fourth month; up to 300 assessments in total). At each measurement, this survey comprised questions about the participants’ momentary level of procrastination, stress, and fatigue, while sleep duration was measured in the morning. Taking a time-series and machine learning approach to analysing these data, I provide the following contributions: Chapter 2 investigates the person-specific relation between passively logged usage of different application types and momentary subjective procrastination, Chapter 3 develops machine learning methodology to estimate sleep duration using smartphone trace data, Chapter 4 combines machine learning and explainable artificial intelligence to discover smartphone-tracked digital markers of momentary subjective stress, Chapter 5 uses a personalized machine learning approach to evaluate if smartphone trace data contains behavioral signs of fatigue. Collectively, these empirical studies provide preliminary answers to the overarching questions of this dissertation.Summary of results With respect to the theoretically motivated relations between smartphone trace data and wellbeing (RQ1), we found that different patterns in smartphone trace data, from time spent on social network, messenger, video, and game applications to smartphone-tracked sleep proxies, are related to well-being in individuals. The strength and nature of this relation depends on the individual and app usage pattern under consideration. The relation between smartphone app use patterns and well-being is limited in most individuals, but relatively strong in a minority. Whereas some individuals might benefit from using specific app types, others might experience decreases in well-being when spending more time on these apps. With respect to the question whether we might use smartphone trace data to monitor well-being in individuals (RQ2), we found that smartphone trace data might be useful for this purpose in some individuals and to some extent. They appear most relevant in the context of sleep monitoring (Chapter 3) and have the potential to be included as one of several data sources for monitoring momentary procrastination (Chapter 2), stress (Chapter 4), and fatigue (Chapter 5) in daily life. Outlook Future interdisciplinary research is needed to investigate whether the relationship between smartphone use and well-being depends on the nature of the activities performed on these devices, the content they present, and the context in which they are used. Answering these questions is essential to unravel the complex puzzle of developing technologies for monitoring well-being in daily life.<br/

Neuroglia

This book is a compiled version of the journal Neuroglia. It was a peer-review Open Access journal by MDPI that investigated a wide range of glia related topics. Now the journal is published as a section of the journal Brain Sciences, with a new section Editor-in-Chief Prof. Sergey Kasparov

New Perspectives in Health

Gut microbiota are an area recently targeted by modern biomedical research. In fact, during the last five years, there has been increasing evidence related to the role of gut microbiota as remarkable symbiotic partners critical for the maintenance of good health. Several factors cause alterations in gut microbiota which are, indeed, accompanied by alterations in the quality of health. Accordingly, gut microbiota dysbiosis has been related to increased susceptibilities to intestinal, cardiovascular, and nervous pathologies. In this manual, you will find the latest studies carried out in the field of microbiota. Overall, the contributions published in this Special Issue further strengthen the essential function of gut microbiota in health and in various diseases

Clinical Utility of Applying PGx and Deprescribing-Based Decision Support in Polypharmacy

Polypharmacy is a necessary and important aspect of drug treatment; however, it becomes a challenge when the medication risks outweigh the benefits for an individual patient. Drug–drug interactions and the introduction of prescribing cascades are common features of polypharmacy, which can lead to ineffectiveness and increased risk of adverse drug reactions (ADR). Genes encoding CYP450 isozymes and other drug-related biomarkers have attracted considerable attention as targets for pharmacogenetic (PGx) testing due to their impact on drug metabolism and response. This Special Issue is devoted to explore the status and initiatives taken to circumvent ineffectiveness and to improve medication safety for polypharmacy patients. Specific areas include drug–drug interactions and consequences thereof in therapeutic management, including PK- and PD-profiling; the application of PGx-based guidance and/or decision tools for drug–gene and drug–drug gene interactions; medication reviews; development and application of deprescribing tools; and drivers and barriers to overcome for successful implementation in the healthcare system