The smarty4covid dataset and knowledge base: a framework enabling interpretable analysis of audio signals

Harnessing the power of Artificial Intelligence (AI) and m-health towards detecting new bio-markers indicative of the onset and progress of respiratory abnormalities/conditions has greatly attracted the scientific and research interest especially during COVID-19 pandemic. The smarty4covid dataset contains audio signals of cough (4,676), regular breathing (4,665), deep breathing (4,695) and voice (4,291) as recorded by means of mobile devices following a crowd-sourcing approach. Other self reported information is also included (e.g. COVID-19 virus tests), thus providing a comprehensive dataset for the development of COVID-19 risk detection models. The smarty4covid dataset is released in the form of a web-ontology language (OWL) knowledge base enabling data consolidation from other relevant datasets, complex queries and reasoning. It has been utilized towards the development of models able to: (i) extract clinically informative respiratory indicators from regular breathing records, and (ii) identify cough, breath and voice segments in crowd-sourced audio recordings. A new framework utilizing the smarty4covid OWL knowledge base towards generating counterfactual explanations in opaque AI-based COVID-19 risk detection models is proposed and validated.Comment: Submitted for publication in Nature Scientific Dat

Treatment of Exercise-induced Laryngeal Obstruction : Exploring modalities in short and long term

Background: Exercise-induced laryngeal obstruction (EILO) is an umbrella term describing inappropriate and transient closure of laryngeal structures during exercise, causing breathlessness and/or noisy respiration (stridor). EILO is a relatively prevalent entity, affecting adolescents or young adults in all activity levels. The condition has been reported to have a considerable functional impact, particularly as a limitation of physical activity in an effort to minimize the occurrence and severity of inspiratory symptoms. Objective visualization of the laryngeal obstruction and determining the level of obstruction within the larynx (supraglottic and/or glottic) during ongoing exercise is considered gold-standard for diagnosing EILO and seems of importance for subsequent treatment planning. Treatment options are based on weak evidence, with evaluation of different modalities mainly based on subjective outcomes. Information about the diagnosis and breathing advice (IBA) seems to be fundamental elements. Small studies and case reports suggests effect from speech therapy, biofeedback, inspiratory muscle training (IMT) and surgical supraglottoplasty. Robust treatment algorithms and follow-up streams are yet to be established. Aims: The overall aim of the thesis was to explore improvement of symptoms and laryngeal obstruction in EILO patients treated with IMT and supraglottoplasty in short- and long term. Study #I: To investigate laryngeal response pattern(s) during inspiratory muscle training (IMT) in healthy subjects using laryngoscopic evaluation and imaging. Study #II: To expand our knowledge and to explore possible effects from inspiratory muscle training in patients diagnosed with EILO. Study #III: To investigate the efficacy and safety of laser supraglottoplasty for patients with supraglottic EILO, using continuous laryngoscopy exercise (CLE) tests before and after surgery. Study #IV: To assess changes of self-reported symptoms and laryngeal outcomes shortly after IMT, and to compare self-reported symptoms with a control group 4-6 years later. Methods: Study design: An explorative approach with combined descriptive and quasi-experimental observational design. Study #I: cross-sectional study, Study #II: prospective pre-post study Study #III: retrospective pre-post study. Study #IV: follow-up study. Subjects and study procedures: Study #I: Twenty healthy volunteers examined with laryngoscopy during inspiratory muscle training (IMT). The laryngeal movements were retrospectively assessed from video files. Study# II and #III: EILO patients examined with continuous laryngoscopy exercise (CLE)-test before and after a treatment; six-week training program with IMT or supraglottoplasty. Outcome data were self-reported symptom scores and laryngeal obstruction (by CLE-scores from video recordings). Study #IV: Two groups were retrospectively identified from the EILO-register; one group receiving IBA only at diagnosis, and the other additionally receiving six weeks of IMT (IBA+IMT). Laryngeal outcome was assessed shortly after IMT, and the two groups’ self-reported symptoms were compared with a new questionnaire 4-6 years later. Results: Study #I: IMT facilitated laryngeal abduction in the investigated healthy subjects and application of medium intensity resistance seemed superior to higher resistance in opening of the laryngeal aperture. Study #II: IMT was safe and the perceived symptoms and laryngeal obstruction improved in subgroups of EILO after IMT, with improvement mainly observed at the glottic level. Study #III: Supraglottoplasty improved symptoms and reduced laryngeal obstruction in the investigated patients with predominantly supraglottic EILO and appeared safe in highly selected severe cases. Notably, supraglottoplasty might improve also glottic obstruction in patients with combined supraglottic and glottic obstruction. Study #IV: The response rate after 4-6 years was 40 % in the IBA-group and 55% in IBA+IMT-group. After 2-4 weeks, 23/32 in the IBA+IMT-group reported symptom improvements, associated mainly with glottic changes, contrasting unchanged laryngeal scores in 9/32 without symptom improvements. After 4-6 years, self-reported exercise-related symptoms and activity had decreased to similar levels in both groups. Full symptom resolution was reported by 8/55. Conclusion: Self-reported symptoms and laryngeal obstruction as observed and rated in CLE-tests can improve in EILO patients treated with IBA, IMT or supraglottoplasty. Heterogeneous responses to treatment were observed and substantiates that EILO is a heterogeneous condition, thus it is unlikely that one mode of treatment will work in all. Individual treatment and follow-up based on laryngeal findings seems essential. Future controlled studies with longer follow-up time are needed to establish effects from the treatment modalities applied in EILO patients. This work provides hypotheses that may serve as a basis in doing so.Doktorgradsavhandlin

Towards using Cough for Respiratory Disease Diagnosis by leveraging Artificial Intelligence: A Survey

Cough acoustics contain multitudes of vital information about pathomorphological alterations in the respiratory system. Reliable and accurate detection of cough events by investigating the underlying cough latent features and disease diagnosis can play an indispensable role in revitalizing the healthcare practices. The recent application of Artificial Intelligence (AI) and advances of ubiquitous computing for respiratory disease prediction has created an auspicious trend and myriad of future possibilities in the medical domain. In particular, there is an expeditiously emerging trend of Machine learning (ML) and Deep Learning (DL)-based diagnostic algorithms exploiting cough signatures. The enormous body of literature on cough-based AI algorithms demonstrate that these models can play a significant role for detecting the onset of a specific respiratory disease. However, it is pertinent to collect the information from all relevant studies in an exhaustive manner for the medical experts and AI scientists to analyze the decisive role of AI/ML. This survey offers a comprehensive overview of the cough data-driven ML/DL detection and preliminary diagnosis frameworks, along with a detailed list of significant features. We investigate the mechanism that causes cough and the latent cough features of the respiratory modalities. We also analyze the customized cough monitoring application, and their AI-powered recognition algorithms. Challenges and prospective future research directions to develop practical, robust, and ubiquitous solutions are also discussed in detail.Comment: 30 pages, 12 figures, 9 table

A comparison of acoustic and linguistics methodologies for Alzheimer’s dementia recognition

In the light of the current COVID-19 pandemic, the need for remote digital health assessment tools is greater than ever. This statement is especially pertinent for elderly and vulnerable populations. In this regard, the INTERSPEECH 2020 Alzheimer’s Dementia Recognition through Spontaneous Speech (ADReSS) Challenge offers competitors the opportunity to develop speech and language-based systems for the task of Alzheimer’s Dementia (AD) recognition. The challenge data consists of speech recordings and their transcripts, the work presented herein is an assessment of different contemporary approaches on these modalities. Specifically, we compared a hierarchical neural network with an attention mechanism trained on linguistic features with three acoustic-based systems: (i) Bag-of-Audio-Words (BoAW) quantising different low-level descriptors, (ii) a Siamese Network trained on log-Mel spectrograms, and (iii) a Convolutional Neural Network (CNN) end-to-end system trained on raw waveforms. Key results indicate the strength of the linguistic approach over the acoustics systems. Our strongest test-set result was achieved using a late fusion combination of BoAW, End-to-End CNN, and hierarchical-attention networks, which outperformed the challenge baseline in both the classification and regression tasks

Work Capability and physiological effects predictive studies. 4: In He-O2 excursions to pressures of 400- 800- 1200- and 1600 feet of sea water

Experiments which exposed men in chambers, breathing helium with oxygen, to progressive increases of pressure equivalent to 400-800-1200-1600 feet of sea water (fsw) were conducted. Rates of compression and exposure to stable high pressure. Goals included: 1) determination of the specific character and time course of onset of physiological and performance decrements during the intentionally rapid compressions, and determination of rates of adaptation on reaching stable elevated pressure; 2) investigation of accelerated methods for decompression in deep saturation excursion diving; and 3) determination of competence in practical work performed in water at pressures equivalent to the extreme diving depths of 1200 and 1600 fsw

Music for physical rehabilitation (1987-1996): a literature review and analysis

1998 Spring.Includes bibliographical references.A comprehensive literature review and analysis was conducted on the use of music for physical rehabilitation from 1987-1996. An earlier literature review and analysis of music for physical rehabilitation was published by Staum (1988), which covered the literature from 1950 -1986. The purpose of the current study was to provide music therapists with an updated and comprehensive resource to aid them in choosing effective treatment strategies for clients in need of physical rehabilitation. Pertinent music therapy sources, such as the Journal of Music Therapy, and pertinent non-music sources, specifically electronic bibliographic databases such as Medline, were consulted. Relevant sources were discussed in two chapters; Chapter 4 - An Overview of the Use of Music in the Treatment of Physical Rehabilitation, and Chapter 5- Clinical Implications for the Use of Music in Physical Rehabilitation . Tables containing frequency data supplement the discussion of the findings on treatment modalities, research settings, clinical population, musical applications, and literature sources. An overview of the methodology of all experimental and single-subject studies is provided in Table 8

Studies on the impact of assistive communication devices on the quality of life of patients with amyotrophic lateral sclerosis

Tese de doutoramento, Ciências Biomédicas (Neurociências), Universidade de Lisboa, Faculdade de Medicina, 2016Amyotrophic Lateral Sclerosis (ALS) is a progressive neuromuscular disease with rapid and generalized degeneration of motor neurons. Patients with ALS experiment a relentless decline in functions that affect performance of most activities of daily living (ADL), such as speaking, eating, walking or writing. For this reason, dependence on caregivers grows as the disease progresses. Management of the respiratory system is one of the main concerns of medical support, since respiratory failure is the most common cause of death in ALS. Due to increasing muscle weakness, most patients experience dramatic decrease of speech intelligibility and difficulties in using upper limbs (UL) for writing. There is growing evidence that mild cognitive impairment is common in ALS, but most patients are self-conscious of their difficulties in communicating and, in very severe stages, locked-in syndrome can occur. When no other resources than speech and writing are used to assist communication, patients are deprived of expressing needs or feelings, making decisions and keeping social relationships. Further, caregivers feel increased dependence due to difficulties in communication with others and get frustrated about difficulties in understanding partners’ needs. Support for communication is then very important to improve quality of life of both patients and caregivers; however, this has been poorly investigated in ALS. Assistive communication devices (ACD) can support patients by providing a diversity of tools for communication, as they progressively lose speech. ALS, in common with other degenerative conditions, introduces an additional challenge for the field of ACD: as the disease progresses, technologies must adapt to different conditions of the user. In early stages, patients may need speech synthesis in a mobile device, if dysarthria is one of the initial symptoms, or keyboard modifications, as weakness in UL increases. When upper limbs’ dysfunction is high, different input technologies may be adapted to capture voluntary control (for example, eye-tracking devices). Despite the enormous advances in the field of Assistive Technologies, in the last decade, difficulties in clinical support for the use of assistive communication devices (ACD) persist. Among the main reasons for these difficulties are lack of assessment tools to evaluate communication needs and determine proper input devices and to indicate changes over disease progression, and absence of clinical evidence that ACD has relevant impact on the quality of life of affected patients. For this set of reasons, support with communication tools is delayed to stages where patients are severely disabled. Often in these stages, patients face additional clinical complications and increased dependence on their caregivers’ decisions, which increase the difficulty in adaptation to new communication tools. This thesis addresses the role of assistive technologies in the quality of life of early-affected patients with ALS. Also, it includes the study of assessment tools that can improve longitudinal evaluation of communication needs of patients with ALS. We longitudinally evaluated a group of 30 patients with bulbar-onset ALS and 17 caregivers, during 2 to 29 months. Patients were assessed during their regular clinical appointments, in the Hospital de Santa Maria-Centro Hospitalar Lisboa_Norte. Evaluation of patients was based on validated instruments for assessing the Quality of Life (QoL) of patients and caregivers, and on methodologies for recording communication and measuring its performance (including speech, handwriting and typing). We tested the impact of early support with ACD on the QoL of patients with ALS, using a randomized, prospective, longitudinal design. Patients were able to learn and improve their skills to use communication tools based on electronic assistive devices. We found a positive impact of ACD in psychological and wellbeing domains of quality of life in patients, as well as in the support and psychological domains in caregivers. We also studied performance of communication (words per minute) using UL. Performance in handwriting may decline faster than performance in typing, supporting the idea that the use of touchscreen-based ACD supports communication for longer than handwriting. From longitudinal recordings of speech and typing activity we could observe that ACD can support tools to detect early markers of bulbar and UL dysfunction in ALS. Methodologies that were used in this research for recording and assessing function in communication can be replicated in the home environment and form part of the original contributions of this research. Implementation of remote monitoring tools in daily use of ACD, based on these methodologies, is discussed. Considering those patients who receive late support for the use of ACD, lack of time or daily support to learn how to control complex input devices may hinder its use. We developed a novel device to explore the detection and control of various residual movements, based on sensors of accelerometry, electromyography and force, as input signals for communication. The aim of this input device was to develop a tool to explore new communication channels in patients with generalized muscle weakness. This research contributed with novel tools from the Engineering field to the study of assistive communication in patients with ALS. Methodologies that were developed in this work can be further applied to the study of the impact of ACD in other neurodegenerative diseases that affect speech and motor control of UL

POST-OPERATIVE VENTILATION PATTERNS AND THE EFFECTS OF NON-INVASIVE POSITIVE PRESSURE THERAPY ON VENTILATORY CHANGES AS MEASURED BY A NON-INVASIVE IMPEDANCE DEVICE IN PATIENTS WITH OBSTRUCTIVE SLEEP APNEA

Patients undergoing general anesthesia who have or are suspected of obstructive sleep apnea (OSA) may be at increased risk for ventilatory complications, including respiratory depression, airway obstructions, and apnea events. The increased prevalence of OSA in the surgical population has led clinicians and researchers to explore strategies to screen for OSA and employ best management practices to minimize perioperative respiratory events. Standardized monitors in the postoperative anesthesia care unit (PACU) may have limited utility in this patient population to readily detect real or potential airway complications. The purposes of this prospective observational study were: to further explore the relationship of OSA risk to perioperative events in participants undergoing laparoscopic gastric bypass surgery (GBS); explore the utility of using an innovate respiratory volume monitor (RVM, ExSpironTM, Waltham, MA, USA) to identify reduced ventilatory function before standard postoperative monitors alert nurses of hypoventilation or apnea events; measure the ventilatory changes when noninvasive positive pressure therapy (NPPV) was applied in the PACU using the RVM. A prospective convenience sample of 50 adult participants with 25 assigned as "mild OSA" (M-OSA) and 25 in the "moderate/severe OSA" (S-OSA) were selected and observed in the PACU to explore the research questions. Findings included no differences perioperative outcomes with the exception of longer PACU stay mean times for the M-OSA, despite S-OSA group being older, having larger neck circumferences, and receiving more opioids in the PACU. The RVM identified respiratory depression events earlier and more often than decreases in pulse oximetry. Thirteen participants who received NPPV and had no significant change in minute ventilation (MV) during use, however a mean decrease of 25% in tidal volume (TV) was measured from mask removal time to five-minute post removal period. This supports the effects of NPPV on maintaining MV when measured by RVM. Findings of the study help support the need to further explore the utility of using RVM to measure ventilatory function, guide therapies, and incorporate RVM into practice settings where patient populations are at risk for respiratory complications. The use of postoperative NPPV therapy needs further exploration in randomized studies to identify optimal NPPV type, pressure settings, and duration of use to help improve ventilatory function in patients known to or suspected of having OSA

Combined brain language connectivity and intraoperative neurophysiologic techniques in awake craniotomy for eloquent-area brain tumor resection

Speech processing can be disturbed by primary brain tumors (PBT). Improvement of presurgical planning techniques decrease neurological morbidity associated to tumor resection during awake craniotomy. The aims of this work were: 1. To perform Diffusion Kurtosis Imaging based tractography (DKI-tract) in the detection of brain tracts involved in language; 2. To investigate which factors contribute to functional magnetic resonance imaging (fMRI) maps in predicting eloquent language regional reorganization; 3. To determine the technical aspects of accelerometric (ACC) recording of speech during surgery. DKI-tracts were streamlined using a 1.5T magnetic resonance scanner. Number of tracts and fiber pathways were compared between DKI and standard Diffusion Tensor Imaging (DTI) in healthy subjects (HS) and PBT patients. fMRI data were acquired using task-specific and resting-state paradigms during language and motor tasks. After testing intraoperative fMRI’s influence on direct cortical stimulation (DCS) number of stimuli, graph-theory measures were extracted and analyzed. Regarding speech recording, ACC signals were recorded after evaluating neck positions and filter bandwidths. To test this method, language disturbances were recorded in patients with dysphonia and after applying DCS in the inferior frontal gyrus. In contrast, HS reaction time was recorded during speech execution. DKI-tract showed increased number of arcuate fascicle tracts in PBT patients. Lower spurious tracts were identified with DKI-tract. Intraoperative fMRI and DCS showed similar stimuli in comparison with DCS alone. Increased local centrality accompanied language ipsilateral and contralateral reorganization. ACC recordings showed minor artifact contamination when placed at the suprasternal notch using a 20-200 Hz filter bandwidth. Patients with dysphonia showed decreased amplitude and frequency in comparison with HS. ACC detected an additional 11% disturbances after DCS, and a shortening of latency within the presence of a loud stimuli during speech execution. This work improved current knowledge on presurgical planning techniques based on brain structural and functional neuroimaging connectivity, and speech recordingA função linguística do ser humano pode ser afetada pela presença de tumores cerebrais (TC) A melhoria de técnicas de planeamento pré-cirurgico diminui a morbilidade neurológica iatrogénica associada ao seu tratamento cirúrgico. O objetivo deste trabalho é: 1. Testar a fiabilidade da tractografia estimada por difusor de kurtose (tract-DKI), dos feixes cerebrais envolvidos na linguagem 2. Identificar os fatores que contribuem para o mapeamento linguagem por ressonância magnética funcional (RMf) na predição da neuroplasticidade. 3. Identificar aspetos técnicos do registo da linguagem por accelerometria (ACC). A DKI-tract foi estimada após realização de RM cerebral com 1.5T. O número e percurso das fibras foi avaliado. A RMf foi adquirida durante realização de tarefas linguísticas, motoras, e em repouso. Foi testada influência dos mapas de ativação calculados por RMf, no número de estímulos realizados durante a estimulação direta cortical (EDC) intraoperatória. Medidas de conectividade foram extraídas de regiões cerebrais. A posição e filtragem de sinal ACC foram estudadas após vocalização de palavras. O sinal ACC obtido em voluntários foi comparado com doentes disfónicos, após estimulação do giro inferior frontal, e após a adição de um estímulo sonoro perturbador durante vocalização. A tract-DKI estimou um elevado número de fascículos do feixe arcuato com menos falsos negativos. Os mapas linguísticos de RMf intraoperatória, não influenciou a EDC. Medidas de centralidade aumentaram após neuroplasticidade ipsilateral e contralateral. A posição supraesternal e a filtragem de sinal ACC entre 20-200Hz demonstrou menor ruido de contaminação. Este método identificou diminuição de frequência e amplitude em doentes com disfonia, 11% de erros linguísticos adicionais após estimulação e diminuição do tempo de latência quando presente o sinal sonoro perturbador. Este trabalho promoveu a utilização de novas técnicas no planeamento pré-cirúrgico do doente com tumor cerebral e alterações da linguagem através do estudo de conectividade estrutural, funcional e registo da linguagem