Advances in point process filters and their application to sympathetic neural activity

This thesis is concerned with the development of techniques for analyzing the sequences of stereotypical electrical impulses within neurons known as spikes. Sequences of spikes, also called spike trains, transmit neural information; decoding them often provides details about the physiological processes generating the neural activity. Here, the statistical theory of event arrivals, called point processes, is applied to human muscle sympathetic spike trains, a peripheral nerve signal responsible for cardiovascular regulation. A novel technique that uses observed spike trains to dynamically derive information about the physiological processes generating them is also introduced. Despite the emerging usage of individual spikes in the analysis of human muscle sympathetic nerve activity, the majority of studies in this field remain focused on bursts of activity at or below cardiac rhythm frequencies. Point process theory applied to multi-neuron spike trains captured both fast and slow spiking rhythms. First, analysis of high-frequency spiking patterns within cardiac cycles was performed and, surprisingly, revealed fibers with no cardiac rhythmicity. Modeling spikes as a function of average firing rates showed that individual nerves contribute substantially to the differences in the sympathetic stressor response across experimental conditions. Subsequent investigation of low-frequency spiking identified two physiologically relevant frequency bands, and modeling spike trains as a function of hemodynamic variables uncovered complex associations between spiking activity and biophysical covariates at these two frequencies. For example, exercise-induced neural activation enhances the relationship of spikes to respiration but does not affect the extremely precise alignment of spikes to diastolic blood pressure. Additionally, a novel method of utilizing point process observations to estimate an internal state process with partially linear dynamics was introduced. Separation of the linear components of the process model and reduction of the sampled space dimensionality improved the computational efficiency of the estimator. The method was tested on an established biophysical model by concurrently computing the dynamic electrical currents of a simulated neuron and estimating its conductance properties. Computational load reduction, improved accuracy, and applicability outside neuroscience establish the new technique as a valuable tool for decoding large dynamical systems with linear substructure and point process observations

Extraction and Detection of Fetal Electrocardiograms from Abdominal Recordings

The non-invasive fetal ECG (NIFECG), derived from abdominal surface electrodes, offers novel diagnostic possibilities for prenatal medicine. Despite its straightforward applicability, NIFECG signals are usually corrupted by many interfering sources. Most significantly, by the maternal ECG (MECG), whose amplitude usually exceeds that of the fetal ECG (FECG) by multiple times. The presence of additional noise sources (e.g. muscular/uterine noise, electrode motion, etc.) further affects the signal-to-noise ratio (SNR) of the FECG. These interfering sources, which typically show a strong non-stationary behavior, render the FECG extraction and fetal QRS (FQRS) detection demanding signal processing tasks. In this thesis, several of the challenges regarding NIFECG signal analysis were addressed. In order to improve NIFECG extraction, the dynamic model of a Kalman filter approach was extended, thus, providing a more adequate representation of the mixture of FECG, MECG, and noise. In addition, aiming at the FECG signal quality assessment, novel metrics were proposed and evaluated. Further, these quality metrics were applied in improving FQRS detection and fetal heart rate estimation based on an innovative evolutionary algorithm and Kalman filtering signal fusion, respectively. The elaborated methods were characterized in depth using both simulated and clinical data, produced throughout this thesis. To stress-test extraction algorithms under ideal circumstances, a comprehensive benchmark protocol was created and contributed to an extensively improved NIFECG simulation toolbox. The developed toolbox and a large simulated dataset were released under an open-source license, allowing researchers to compare results in a reproducible manner. Furthermore, to validate the developed approaches under more realistic and challenging situations, a clinical trial was performed in collaboration with the University Hospital of Leipzig. Aside from serving as a test set for the developed algorithms, the clinical trial enabled an exploratory research. This enables a better understanding about the pathophysiological variables and measurement setup configurations that lead to changes in the abdominal signal's SNR. With such broad scope, this dissertation addresses many of the current aspects of NIFECG analysis and provides future suggestions to establish NIFECG in clinical settings.:Abstract Acknowledgment Contents List of Figures List of Tables List of Abbreviations List of Symbols (1)Introduction 1.1)Background and Motivation 1.2)Aim of this Work 1.3)Dissertation Outline 1.4)Collaborators and Conflicts of Interest (2)Clinical Background 2.1)Physiology 2.1.1)Changes in the maternal circulatory system 2.1.2)Intrauterine structures and feto-maternal connection 2.1.3)Fetal growth and presentation 2.1.4)Fetal circulatory system 2.1.5)Fetal autonomic nervous system 2.1.6)Fetal heart activity and underlying factors 2.2)Pathology 2.2.1)Premature rupture of membrane 2.2.2)Intrauterine growth restriction 2.2.3)Fetal anemia 2.3)Interpretation of Fetal Heart Activity 2.3.1)Summary of clinical studies on FHR/FHRV 2.3.2)Summary of studies on heart conduction 2.4)Chapter Summary (3)Technical State of the Art 3.1)Prenatal Diagnostic and Measuring Technique 3.1.1)Fetal heart monitoring 3.1.2)Related metrics 3.2)Non-Invasive Fetal ECG Acquisition 3.2.1)Overview 3.2.2)Commercial equipment 3.2.3)Electrode configurations 3.2.4)Available NIFECG databases 3.2.5)Validity and usability of the non-invasive fetal ECG 3.3)Non-Invasive Fetal ECG Extraction Methods 3.3.1)Overview on the non-invasive fetal ECG extraction methods 3.3.2)Kalman filtering basics 3.3.3)Nonlinear Kalman filtering 3.3.4)Extended Kalman filter for FECG estimation 3.4)Fetal QRS Detection 3.4.1)Merging multichannel fetal QRS detections 3.4.2)Detection performance 3.5)Fetal Heart Rate Estimation 3.5.1)Preprocessing the fetal heart rate 3.5.2)Fetal heart rate statistics 3.6)Fetal ECG Morphological Analysis 3.7)Problem Description 3.8)Chapter Summary (4)Novel Approaches for Fetal ECG Analysis 4.1)Preliminary Considerations 4.2)Fetal ECG Extraction by means of Kalman Filtering 4.2.1)Optimized Gaussian approximation 4.2.2)Time-varying covariance matrices 4.2.3)Extended Kalman filter with unknown inputs 4.2.4)Filter calibration 4.3)Accurate Fetal QRS and Heart Rate Detection 4.3.1)Multichannel evolutionary QRS correction 4.3.2)Multichannel fetal heart rate estimation using Kalman filters 4.4)Chapter Summary (5)Data Material 5.1)Simulated Data 5.1.1)The FECG Synthetic Generator (FECGSYN) 5.1.2)The FECG Synthetic Database (FECGSYNDB) 5.2)Clinical Data 5.2.1)Clinical NIFECG recording 5.2.2)Scope and limitations of this study 5.2.3)Data annotation: signal quality and fetal amplitude 5.2.4)Data annotation: fetal QRS annotation 5.3)Chapter Summary (6)Results for Data Analysis 6.1)Simulated Data 6.1.1)Fetal QRS detection 6.1.2)Morphological analysis 6.2)Own Clinical Data 6.2.1)FQRS correction using the evolutionary algorithm 6.2.2)FHR correction by means of Kalman filtering (7)Discussion and Prospective 7.1)Data Availability 7.1.1)New measurement protocol 7.2)Signal Quality 7.3)Extraction Methods 7.4)FQRS and FHR Correction Algorithms (8)Conclusion References (A)Appendix A - Signal Quality Annotation (B)Appendix B - Fetal QRS Annotation (C)Appendix C - Data Recording GU

Improving land surface models with FLUXNET data

There is a growing consensus that land surface models (LSMs) that simulate terrestrial biosphere exchanges of matter and energy must be better constrained with data to quantify and address their uncertainties. FLUXNET, an international network of sites that measure the land surface exchanges of carbon, water and energy using the eddy covariance technique, is a prime source of data for model improvement. Here we outline a multi-stage process for "fusing" (i.e. linking) LSMs with FLUXNET data to generate better models with quantifiable uncertainty. First, we describe FLUXNET data availability, and its random and systematic biases. We then introduce methods for assessing LSM model runs against FLUXNET observations in temporal and spatial domains. These assessments are a prelude to more formal model-data fusion (MDF). MDF links model to data, based on error weightings. In theory, MDF produces optimal analyses of the modelled system, but there are practical problems. We first discuss how to set model errors and initial conditions. In both cases incorrect assumptions will affect the outcome of the MDF. We then review the problem of equifinality, whereby multiple combinations of parameters can produce similar model output. Fusing multiple independent and orthogonal data provides a means to limit equifinality. We then show how parameter probability density functions (PDFs) from MDF can be used to interpret model validity, and to propagate errors into model outputs. Posterior parameter distributions are a useful way to assess the success of MDF, combined with a determination of whether model residuals are Gaussian. If the MDF scheme provides evidence for temporal variation in parameters, then that is indicative of a critical missing dynamic process. A comparison of parameter PDFs generated with the same model from multiple FLUXNET sites can provide insights into the concept and validity of plant functional types (PFT) – we would expect similar parameter estimates among sites sharing a single PFT. We conclude by identifying five major model-data fusion challenges for the FLUXNET and LSM communities: (1) to determine appropriate use of current data and to explore the information gained in using longer time series; (2) to avoid confounding effects of missing process representation on parameter estimation; (3) to assimilate more data types, including those from earth observation; (4) to fully quantify uncertainties arising from data bias, model structure, and initial conditions problems; and (5) to carefully test current model concepts (e.g. PFTs) and guide development of new concepts

Breathing Rate Estimation From the Electrocardiogram and Photoplethysmogram: A Review.

Breathing rate (BR) is a key physiological parameter used in a range of clinical settings. Despite its diagnostic and prognostic value, it is still widely measured by counting breaths manually. A plethora of algorithms have been proposed to estimate BR from the electrocardiogram (ECG) and pulse oximetry (photoplethysmogram, PPG) signals. These BR algorithms provide opportunity for automated, electronic, and unobtrusive measurement of BR in both healthcare and fitness monitoring. This paper presents a review of the literature on BR estimation from the ECG and PPG. First, the structure of BR algorithms and the mathematical techniques used at each stage are described. Second, the experimental methodologies that have been used to assess the performance of BR algorithms are reviewed, and a methodological framework for the assessment of BR algorithms is presented. Third, we outline the most pressing directions for future research, including the steps required to use BR algorithms in wearable sensors, remote video monitoring, and clinical practice

Detecting Pilot's Engagement Using fNIRS Connectivity Features in an Automated vs. Manual Landing Scenario

Monitoring pilot's mental states is a relevant approach to mitigate human error and enhance human machine interaction. A promising brain imaging technique to perform such a continuous measure of human mental state under ecological settings is Functional Near-InfraRed Spectroscopy (fNIRS). However, to our knowledge no study has yet assessed the potential of fNIRS connectivity metrics as long as passive Brain Computer Interfaces (BCI) are concerned. Therefore, we designed an experimental scenario in a realistic simulator in which 12 pilots had to perform landings under two contrasted levels of engagement (manual vs. automated). The collected data were used to benchmark the performance of classical oxygenation features (i.e., Average, Peak, Variance, Skewness, Kurtosis, Area Under the Curve, and Slope) and connectivity features (i.e., Covariance, Pearson's, and Spearman's Correlation, Spectral Coherence, and Wavelet Coherence) to discriminate these two landing conditions. Classification performance was obtained by using a shrinkage Linear Discriminant Analysis (sLDA) and a stratified cross validation using each feature alone or by combining them. Our findings disclosed that the connectivity features performed significantly better than the classical concentration metrics with a higher accuracy for the wavelet coherence (average: 65.3/59.9 %, min: 45.3/45.0, max: 80.5/74.7 computed for HbO/HbR signals respectively). A maximum classification performance was obtained by combining the area under the curve with the wavelet coherence (average: 66.9/61.6 %, min: 57.3/44.8, max: 80.0/81.3 computed for HbO/HbR signals respectively). In a general manner all connectivity measures allowed an efficient classification when computed over HbO signals. Those promising results provide methodological cues for further implementation of fNIRS-based passive BCIs

Sensor fusion for tangible acoustic interfaces for human computer intreraction

This thesis presents the development of tangible acoustic interfaces for human computer interaction. The method adopted was to position sensors on the surface of a solid object to detect acoustic waves generated during an interaction, process the sensor signals and estimate either the location of a discrete impact or the trajectory of a moving point of contact on the surface. Higher accuracy and reliability were achieved by employing sensor fusion to combine the information collected from redundant sensors electively positioned on the solid object. Two different localisation approaches are proposed in the thesis. The learning-based approach is employed to detect discrete impact positions. With this approach, a signature vector representation of time-series patterns from a single sensor is matched with database signatures for known impact locations. For improved reliability, a criterion is proposed to extract the location signature from two vectors. The other approach is based on the Time Difference of Arrival (TDOA) of a source signal captured by a spatially distributed array of sensors. Enhanced positioning algorithms that consider near-field scenario, dispersion, optimisation and filtration are proposed to tackle the problems of passive acoustic localisation in solid objects. A computationally efficient algorithm for tracking a continuously moving source is presented. Spatial filtering of the estimated trajectory has been performed using Kalman filtering with automated initialisation

When fish are not poisson :modelling the migration of Atlantic salmon (Salmo salar) and sea trout (Salmo trutta) at multiple time scales

PhD ThesisMigratory species undertake prolonged seasonal journeys; monitoring these movements is challenging but can sometimes be achieved by observations that taken locally and, ideally, using remote methods. Amongst the best known examples of migrating fish in Europe, are Atlantic salmon (Salmo salar) and sea trout (Salmo trutta) that migrate between river and seawater. Characteristics of habitat suitability, feeding opportunities, predation, as well as salmonid sensitivity and needs, vary throughout successive stages of their anadromous life cycle. Since the marine stage is the longest but is also challenging to monitor, in-river fish counters are of increasing importance in understanding salmonid patterns in abundance. The original contribution of this thesis lies in the use of modelling techniques to investigate salmonid migration, based on temporal observations produced by an electronic fish counter triggered by salmonid passage, as they return to spawn in the River Tyne. Small scale observation revealed seasonal differences; aggregation behaviour intensified during the middle of the migration season, and explanatory covariates varied in both their effect size and relevance to salmonid abundance. At the population scale, migration was highly driven by annual periodicity, abundance increased with river temperature and there was an NAO effect with a four year lag, underlining the importance of marine conditions to parent population and/or post-smolts. Differences between distinct populations of S. salar and S. trutta appeared related to a species-specific annual periodicity and oceanic conditions as salmonids return (more so for S. salar). State-space models suggested a complex demographic structure for the two species. There was a species identification learning curve that affected the data by 2007. A classification algorithm determined that observations are more likely to be S. salar for larger signal amplitude, within a higher river flow and earlier in the year; characteristics were too similar between the two species to reach a useful classification success rate (69%). The project overall suggests specificities relating to both species and age-class that cannot be addressed in depth with the collected data; emerging limitations and recommendations are discussed.Environment Agenc