Search

Abstract Urinary Tract Infections (UTIs) are one of the most prevalent bacterial infections in older adults and a significant contributor to unplanned hospital admissions in People Living with Dementia (PLWD), with early detection being crucial due to the predicament of reporting symptoms and limited help-seeking behaviour. The most common diagnostic tool is urine sample analysis, which can be time-consuming and is only employed where UTI clinical suspicion exists. In this method development and proof-of-concept study, participants living with dementia were monitored via low-cost devices in the home that passively measure activity, sleep, and nocturnal physiology. Using 27828 person-days of remote monitoring data (from 117 participants), we engineered features representing symptoms used for diagnosing a UTI. We then evaluate explainable machine learning techniques in passively calculating UTI risk and perform stratification on scores to support clinical translation and allow control over the balance between alert rate and sensitivity and specificity. The proposed UTI algorithm achieves a sensitivity of 65.3% (95% Confidence Interval (CI) = 64.3–66.2) and specificity of 70.9% (68.6–73.1) when predicting UTIs on unseen participants and after risk stratification, a sensitivity of 74.7% (67.9–81.5) and specificity of 87.9% (85.0–90.9). In addition, feature importance methods reveal that the largest contributions to the predictions were bathroom visit statistics, night-time respiratory rate, and the number of previous UTI events, aligning with the literature. Our machine learning method alerts clinicians of UTI risk in subjects, enabling earlier detection and enhanced screening when considering treatment.

Abstract Dementia is a progressive condition that affects cognitive and functional abilities. There is a need for reliable and continuous health monitoring of People Living with Dementia (PLWD) to improve their quality of life and support their independent living. Healthcare services often focus on addressing and treating already established health conditions that affect PLWD. Managing these conditions continuously can inform better decision-making earlier for higher-quality care management for PLWD. The Technology Integrated Health Management (TIHM) project developed a new digital platform to routinely collect longitudinal, observational, and measurement data, within the home and apply machine learning and analytical models for the detection and prediction of adverse health events affecting the well-being of PLWD. This work describes the TIHM dataset collected during the second phase (i.e., feasibility study) of the TIHM project. The data was collected from homes of 56 PLWD and associated with events and clinical observations (daily activity, physiological monitoring, and labels for health-related conditions). The study recorded an average of 50 days of data per participant, totalling 2803 days.

Patient care and management have entered a new arena, where intelligent technology can assist clinicians in both diagnosis and treatment [...]

Abstract Oncology patients experience numerous co-occurring symptoms during their treatment. The identification of sentinel/core symptoms is a vital prerequisite for therapeutic interventions. In this study, using Network Analysis, we investigated the inter-relationships among 38 common symptoms over time (i.e., a total of six time points over two cycles of chemotherapy) in 987 oncology patients with four different types of cancer (i.e., breast, gastrointestinal, gynaecological, and lung). In addition, we evaluated the associations between and among symptoms and symptoms clusters and examined the strength of these interactions over time. Eight unique symptom clusters were identified within the networks. Findings from this research suggest that changes occur in the relationships and interconnections between and among co-occurring symptoms and symptoms clusters that depend on the time point in the chemotherapy cycle and the type of cancer. The evaluation of the centrality measures provides new insights into the relative importance of individual symptoms within various networks that can be considered as potential targets for symptom management interventions.

Introduction The prevalence of traumatic brain injury (TBI) among older adults is increasing exponentially. The sequelae can be severe in older adults and interact with age-related conditions such as multimorbidity. Despite this, TBI research in older adults is sparse. Minder, an in-home monitoring system developed by the UK Dementia Research Institute Centre for Care Research and Technology, uses infrared sensors and a bed mat to passively collect sleep and activity data. Similar systems have been used to monitor the health of older adults living with dementia. We will assess the feasibility of using this system to study changes in the health status of older adults in the early period post-TBI.Methods and analysis The study will recruit 15 inpatients (>60 years) with a moderate-severe TBI, who will have their daily activity and sleep patterns monitored using passive and wearable sensors over 6 months. Participants will report on their health during weekly calls, which will be used to validate sensor data. Physical, functional and cognitive assessments will be conducted across the duration of the study. Activity levels and sleep patterns derived from sensor data will be calculated and visualised using activity maps. Within-participant analysis will be performed to determine if participants are deviating from their own routines. We will apply machine learning approaches to activity and sleep data to assess whether the changes in these data can predict clinical events. Qualitative analysis of interviews conducted with participants, carers and clinical staff will assess acceptability and utility of the system.Ethics and dissemination Ethical approval for this study has been granted by the London-Camberwell St Giles Research Ethics Committee (REC) (REC number: 17/LO/2066). Results will be submitted for publication in peer-reviewed journals, presented at conferences and inform the design of a larger trial assessing recovery after TBI.

Due to the inevitable role of emotions in human learning and decision-making, different types of emotions in the form of emotional weights/neurons have also been considered in shallow neural networks. Emotional neural networks suffer from a low convergence rate as well as batch learning instability mainly because of the improper tuning of learning coefficients. To overcome these drawbacks, we introduced two solutions: (i) a heuristic upgrading method, inspiring by the behavior of dopamine secretion in the human brain, to adaptively regulate the learning rate based on positive and negative emotional states at each epoch and (ii) a stochastic learning technique to stabilize the learning process. The proposed dopamine based adaptive emotional neural network statistically outperforms state-of-the-art methods like emotional neural network, prototype-incorporated emotional neural network, multi-layer perceptron, and deep convolutional neural networks such as LeNet, AlexNet, DenseNet, MobileNet and EfficientNet in terms of different measures such as accuracy and convergence rate on several high dimensional and big datasets.

Abstract COVID‐19 is a major, urgent, and ongoing threat to global health. Globally more than 24 million have been infected and the disease has claimed more than a million lives as of November 2020. Predicting which patients will need respiratory support is important to guiding individual patient treatment and also to ensuring sufficient resources are available. The ability of six common Early Warning Scores (EWS) to identify respiratory deterioration defined as the need for advanced respiratory support (high‐flow nasal oxygen, continuous positive airways pressure, non‐invasive ventilation, intubation) within a prediction window of 24 h is evaluated. It is shown that these scores perform sub‐optimally at this specific task. Therefore, an alternative EWS based on the Gradient Boosting Trees (GBT) algorithm is developed that is able to predict deterioration within the next 24 h with high AUROC 94% and an accuracy, sensitivity, and specificity of 70%, 96%, 70%, respectively. The GBT model outperformed the best EWS (LDTEWS:NEWS), increasing the AUROC by 14%. Our GBT model makes the prediction based on the current and baseline measures of routinely available vital signs and blood tests.

BackgroundSensor-based remote health monitoring can be used for the timely detection of health deterioration in people living with dementia with minimal impact on their day-to-day living. Anomaly detection approaches have been widely applied in various domains, including remote health monitoring. However, current approaches are challenged by noisy, multivariate data and low generalizability. ObjectiveThis study aims to develop an online, lightweight unsupervised learning–based approach to detect anomalies representing adverse health conditions using activity changes in people living with dementia. We demonstrated its effectiveness over state-of-the-art methods on a real-world data set of 9363 days collected from 15 participant households by the UK Dementia Research Institute between August 2019 and July 2021. Our approach was applied to household movement data to detect urinary tract infections (UTIs) and hospitalizations. MethodsWe propose and evaluate a solution based on Contextual Matrix Profile (CMP), an exact, ultrafast distance-based anomaly detection algorithm. Using daily aggregated household movement data collected via passive infrared sensors, we generated CMPs for location-wise sensor counts, duration, and change in hourly movement patterns for each patient. We computed a normalized anomaly score in 2 ways: by combining univariate CMPs and by developing a multidimensional CMP. The performance of our method was evaluated relative to Angle-Based Outlier Detection, Copula-Based Outlier Detection, and Lightweight Online Detector of Anomalies. We used the multidimensional CMP to discover and present the important features associated with adverse health conditions in people living with dementia. ResultsThe multidimensional CMP yielded, on average, 84.3% recall with 32.1 alerts, or a 5.1% alert rate, offering the best balance of recall and relative precision compared with Copula-Based and Angle-Based Outlier Detection and Lightweight Online Detector of Anomalies when evaluated for UTI and hospitalization. Midnight to 6 AM bathroom activity was shown to be the most important cross-patient digital biomarker of anomalies indicative of UTI, contributing approximately 30% to the anomaly score. We also demonstrated how CMP-based anomaly scoring can be used for a cross-patient view of anomaly patterns. ConclusionsTo the best of our knowledge, this is the first real-world study to adapt the CMP to continuous anomaly detection in a health care scenario. The CMP inherits the speed, accuracy, and simplicity of the Matrix Profile, providing configurability, the ability to denoise and detect patterns, and explainability to clinical practitioners. We addressed the need for anomaly scoring in multivariate time series health care data by developing the multidimensional CMP. With high sensitivity, a low alert rate, better overall performance than state-of-the-art methods, and the ability to discover digital biomarkers of anomalies, the CMP is a clinically meaningful unsupervised anomaly detection technique extensible to multimodal data for dementia and other health care scenarios.

Tuberculosis is a respiratory disease that is treatable with antibiotics. An increasing prevalence of resistance means that to ensure a good treatment outcome it is desirable to test the susceptibility of each infection to different antibiotics. Conventionally, this is done by culturing a clinical sample and then exposing aliquots to a panel of antibiotics, each being present at a pre-determined concentration, thereby determining if the sample isresistant or susceptible to each sample. The minimum inhibitory concentration (MIC) of a drug is the lowestconcentration that inhibits growth and is a more useful quantity but requires each sample to be tested at a range ofconcentrations for each drug. Using 96-well broth micro dilution plates with each well containing a lyophilised pre-determined amount of an antibiotic is a convenient and cost-effective way to measure the MICs of several drugs at once for a clinical sample. Although accurate, this is still an expensive and slow process that requires highly-skilled and experienced laboratory scientists. Here we show that, through the BashTheBug project hosted on the Zooniverse citizen science platform, a crowd of volunteers can reproducibly and accurately determine the MICs for 13 drugs and that simply taking the median or mode of 11–17 independent classifications is sufficient. There is therefore a potential role for crowds to support (but not supplant) the role of experts in antibiotic susceptibility testing.

Summary: Background: Molecular diagnostics are considered the most promising route to achievement of rapid, universal drug susceptibility testing for Mycobacterium tuberculosis complex (MTBC). We aimed to generate a WHO-endorsed catalogue of mutations to serve as a global standard for interpreting molecular information for drug resistance prediction. Methods: In this systematic analysis, we used a candidate gene approach to identify mutations associated with resistance or consistent with susceptibility for 13 WHO-endorsed antituberculosis drugs. We collected existing worldwide MTBC whole-genome sequencing data and phenotypic data from academic groups and consortia, reference laboratories, public health organisations, and published literature. We categorised phenotypes as follows: methods and critical concentrations currently endorsed by WHO (category 1); critical concentrations previously endorsed by WHO for those methods (category 2); methods or critical concentrations not currently endorsed by WHO (category 3). For each mutation, we used a contingency table of binary phenotypes and presence or absence of the mutation to compute positive predictive value, and we used Fisher's exact tests to generate odds ratios and Benjamini-Hochberg corrected p values. Mutations were graded as associated with resistance if present in at least five isolates, if the odds ratio was more than 1 with a statistically significant corrected p value, and if the lower bound of the 95% CI on the positive predictive value for phenotypic resistance was greater than 25%. A series of expert rules were applied for final confidence grading of each mutation. Findings: We analysed 41 137 MTBC isolates with phenotypic and whole-genome sequencing data from 45 countries. 38 215 MTBC isolates passed quality control steps and were included in the final analysis. 15 667 associations were computed for 13 211 unique mutations linked to one or more drugs. 1149 (7·3%) of 15 667 mutations were classified as associated with phenotypic resistance and 107 (0·7%) were deemed consistent with susceptibility. For rifampicin, isoniazid, ethambutol, fluoroquinolones, and streptomycin, the mutations' pooled sensitivity was more than 80%. Specificity was over 95% for all drugs except ethionamide (91·4%), moxifloxacin (91·6%) and ethambutol (93·3%). Only two resistance mutations were identified for bedaquiline, delamanid, clofazimine, and linezolid as prevalence of phenotypic resistance was low for these drugs. Interpretation: We present the first WHO-endorsed catalogue of molecular targets for MTBC drug susceptibility testing, which is intended to provide a global standard for resistance interpretation. The existence of this catalogue should encourage the implementation of molecular diagnostics by national tuberculosis programmes. Funding: Unitaid, Wellcome Trust, UK Medical Research Council, and Bill and Melinda Gates Foundation.

Early prediction of pathogen infestation is a key factor to reduce the disease spread in plants. Macrophomina phaseolina (Tassi) Goid, as one of the main causes of charcoal rot disease, suppresses the plant productivity significantly. Charcoal rot disease is one of the most severe threats to soybean productivity. Prediction of this disease in soybeans is very tedious and non-practical using traditional approaches. Machine learning (ML) techniques have recently gained substantial traction across numerous domains. ML methods can be applied to detect plant diseases, prior to the full appearance of symptoms. In this paper, several ML techniques were developed and examined for prediction of charcoal rot disease in soybean for a cohort of 2,000 healthy and infected plants. A hybrid set of physiological and morphological features were suggested as inputs to the ML models. All developed ML models were performed better than 90% in terms of accuracy. Gradient Tree Boosting (GBT) was the best performing classifier which obtained 96.25% and 97.33% in terms of sensitivity and specificity. Our findings supported the applicability of ML especially GBT for charcoal rot disease prediction in a real environment. Moreover, our analysis demonstrated the importance of including physiological featured in the learning. The collected dataset and source code can be found in https://github.com/Elham-khalili/Soybean-Charcoal-Rot-Disease-Prediction-Dataset-code.

Resistance prediction and mutation ranking are important tasks in the analysis of Tuberculosis sequence data. Due to standard regimens for the use of first-line antibiotics, resistance co-occurrence, in which samples are resistant to multiple drugs, is common. Analysing all drugs simultaneously should therefore enable patterns reflecting resistance co-occurrence to be exploited for resistance prediction. Here, multi-label random forest (MLRF) models are compared with single-label random forest (SLRF) for both predicting phenotypic resistance from whole genome sequences and identifying important mutations for better prediction of four first-line drugs in a dataset of 13402 Mycobacterium tuberculosis isolates. Results confirmed that MLRFs can improve performance compared to conventional clinical methods (by 18.10%) and SLRFs (by 0.91%). In addition, we identified a list of candidate mutations that are important for resistance prediction or that are related to resistance co-occurrence. Moreover, we found that retraining our analysis to a subset of top-ranked mutations was sufficient to achieve satisfactory performance. The source code can be found at http://www.robots.ox.ac.uk/~davidc/code.php.

Advances in DNA sequencing technology are facilitating genomic analyses of unprecedented scope and scale, widening the gap between our abilities to generate and fully exploit biological sequence data. Comparable analytical challenges are encountered in other data-intensive fields involving sequential data, such as signal processing, in which dimensionality reduction (i.e., compression) methods are routinely used to lessen the computational burden of analyses. In this work, we explored the application of dimensionality reduction methods to numerically represent high-throughput sequence data for three important biological applications of virus sequence data: reference-based mapping, short sequence classification and de novo assembly. Leveraging highly compressed sequence transformations to accelerate sequence comparison, our approach yielded comparable accuracy to existing approaches, further demonstrating its suitability for sequences originating from diverse virus populations. We assessed the application of our methodology using both synthetic and real viral pathogen sequences. Our results show that the use of highly compressed sequence approximations can provide accurate results, with analytical performance retained and even enhanced through appropriate dimensionality reduction of sequence data.

Purpose: Sleep is a complex physiological state and an indicator of the changes in the brain function similar to those occurring in many psychiatric and neurological conditions. Since visual sleep scoring consuming process, automatic sleep staging methods, also called scoring, hold promise in diagnosing alterations in the sleep process and the sleep EEG more effectively. Method: In this paper, a supervised approach for sleep scoring from single channel EEG signals is proposed. First, a supervised singular spectrum analysis (SSA) which is a subspace based method is used to extract the desired signal for each stage of sleep. Then, two recursive least squares (RLS) adaptive filters are trained and used to identify first and deep sleep stages. Result: The proposed system which can be considered as a filter bank for separating multiple signal subbands is tested using real EEG where the results verify the accuracy of the proposed method. Conclusion: The overall result show the effectiveness of algorithm for detection of sleep stages from EEG signals often characterised by a sharp increase in delta and a rapid decrease in alpha as sleep deepens.