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1.
JMIR Public Health Surveill ; 7(3): e26719, 2021 03 24.
Article in English | MEDLINE | ID: covidwho-2197901

ABSTRACT

BACKGROUND: Patient travel history can be crucial in evaluating evolving infectious disease events. Such information can be challenging to acquire in electronic health records, as it is often available only in unstructured text. OBJECTIVE: This study aims to assess the feasibility of annotating and automatically extracting travel history mentions from unstructured clinical documents in the Department of Veterans Affairs across disparate health care facilities and among millions of patients. Information about travel exposure augments existing surveillance applications for increased preparedness in responding quickly to public health threats. METHODS: Clinical documents related to arboviral disease were annotated following selection using a semiautomated bootstrapping process. Using annotated instances as training data, models were developed to extract from unstructured clinical text any mention of affirmed travel locations outside of the continental United States. Automated text processing models were evaluated, involving machine learning and neural language models for extraction accuracy. RESULTS: Among 4584 annotated instances, 2659 (58%) contained an affirmed mention of travel history, while 347 (7.6%) were negated. Interannotator agreement resulted in a document-level Cohen kappa of 0.776. Automated text processing accuracy (F1 85.6, 95% CI 82.5-87.9) and computational burden were acceptable such that the system can provide a rapid screen for public health events. CONCLUSIONS: Automated extraction of patient travel history from clinical documents is feasible for enhanced passive surveillance public health systems. Without such a system, it would usually be necessary to manually review charts to identify recent travel or lack of travel, use an electronic health record that enforces travel history documentation, or ignore this potential source of information altogether. The development of this tool was initially motivated by emergent arboviral diseases. More recently, this system was used in the early phases of response to COVID-19 in the United States, although its utility was limited to a relatively brief window due to the rapid domestic spread of the virus. Such systems may aid future efforts to prevent and contain the spread of infectious diseases.


Subject(s)
Communicable Diseases, Emerging/diagnosis , Electronic Health Records , Information Storage and Retrieval/methods , Public Health Surveillance/methods , Travel/statistics & numerical data , Algorithms , COVID-19/epidemiology , Communicable Diseases, Emerging/epidemiology , Feasibility Studies , Female , Humans , Machine Learning , Male , Middle Aged , Natural Language Processing , Reproducibility of Results , United States/epidemiology
2.
Medicine (Baltimore) ; 100(36): e26855, 2021 Sep 10.
Article in English | MEDLINE | ID: covidwho-2191052

ABSTRACT

ABSTRACT: Coronavirus disease (COVID-19) has spread worldwide. X-ray and computed tomography (CT) are 2 technologies widely used in image acquisition, segmentation, diagnosis, and evaluation. Artificial intelligence can accurately segment infected parts in X-ray and CT images, assist doctors in improving diagnosis efficiency, and facilitate the subsequent assessment of the severity of the patient infection. The medical assistant platform based on machine learning can help radiologists make clinical decisions and helper in screening, diagnosis, and treatment. By providing scientific methods for image recognition, segmentation, and evaluation, we summarized the latest developments in the application of artificial intelligence in COVID-19 lung imaging, and provided guidance and inspiration to researchers and doctors who are fighting the COVID-19 virus.


Subject(s)
COVID-19/diagnostic imaging , Machine Learning , Pneumonia, Viral/diagnostic imaging , SARS-CoV-2 , Humans , Radiography , Tomography, X-Ray Computed
3.
Front Public Health ; 10: 920849, 2022.
Article in English | MEDLINE | ID: covidwho-2154835

ABSTRACT

At present, COVID-19 is spreading widely around the world. It causes many health problems, namely, respiratory failure and acute respiratory distress syndrome. Wearable devices have gained popularity by allowing remote COVID-19 detection, contact tracing, and monitoring. In this study, the correlation of photoplethysmogram (PPG) morphology between patients with COVID-19 infection and healthy subjects was investigated. Then, machine learning was used to classify the extracted features between 43 cases and 43 control subjects. The PPG data were collected from 86 subjects based on inclusion and exclusion criteria. The systolic-onset amplitude was 3.72% higher for the case group. However, the time interval of systolic-systolic was 7.69% shorter in the case than in control subjects. In addition, 12 out of 20 features exhibited a significant difference. The top three features included dicrotic-systolic time interval, onset-dicrotic amplitude, and systolic-onset time interval. Nine features extracted by heatmap based on the correlation matrix were fed to discriminant analysis, k-nearest neighbor, decision tree, support vector machine, and artificial neural network (ANN). The ANN showed the best performance with 95.45% accuracy, 100% sensitivity, and 90.91% specificity by using six input features. In this study, a COVID-19 prediction model was developed using multiple PPG features extracted using a low-cost pulse oximeter.


Subject(s)
COVID-19 , Photoplethysmography , COVID-19/diagnosis , Humans , Machine Learning , Neural Networks, Computer , Photoplethysmography/methods , Support Vector Machine
4.
Front Immunol ; 13: 960985, 2022.
Article in English | MEDLINE | ID: covidwho-2154722

ABSTRACT

One of the primary tasks in vaccine design and development of immunotherapeutic drugs is to predict conformational B-cell epitopes corresponding to primary antibody binding sites within the antigen tertiary structure. To date, multiple approaches have been developed to address this issue. However, for a wide range of antigens their accuracy is limited. In this paper, we applied the transfer learning approach using pretrained deep learning models to develop a model that predicts conformational B-cell epitopes based on the primary antigen sequence and tertiary structure. A pretrained protein language model, ESM-1v, and an inverse folding model, ESM-IF1, were fine-tuned to quantitatively predict antibody-antigen interaction features and distinguish between epitope and non-epitope residues. The resulting model called SEMA demonstrated the best performance on an independent test set with ROC AUC of 0.76 compared to peer-reviewed tools. We show that SEMA can quantitatively rank the immunodominant regions within the SARS-CoV-2 RBD domain. SEMA is available at https://github.com/AIRI-Institute/SEMAi and the web-interface http://sema.airi.net.


Subject(s)
COVID-19 , Vaccines , Antigens , Epitopes, B-Lymphocyte , Humans , Immunodominant Epitopes , Machine Learning , SARS-CoV-2
5.
Technol Health Care ; 30(6): 1299-1314, 2022.
Article in English | MEDLINE | ID: covidwho-2154631

ABSTRACT

BACKGROUND: Coronavirus disease 2019 (COVID-19) is a deadly viral infection spreading rapidly around the world since its outbreak in 2019. In the worst case a patient's organ may fail leading to death. Therefore, early diagnosis is crucial to provide patients with adequate and effective treatment. OBJECTIVE: This paper aims to build machine learning prediction models to automatically diagnose COVID-19 severity with clinical and computed tomography (CT) radiomics features. METHOD: P-V-Net was used to segment the lung parenchyma and then radiomics was used to extract CT radiomics features from the segmented lung parenchyma regions. Over-sampling, under-sampling, and a combination of over- and under-sampling methods were used to solve the data imbalance problem. RandomForest was used to screen out the optimal number of features. Eight different machine learning classification algorithms were used to analyze the data. RESULTS: The experimental results showed that the COVID-19 mild-severe prediction model trained with clinical and CT radiomics features had the best prediction results. The accuracy of the GBDT classifier was 0.931, the ROUAUC 0.942, and the AUCPRC 0.694, which indicated it was better than other classifiers. CONCLUSION: This study can help clinicians identify patients at risk of severe COVID-19 deterioration early on and provide some treatment for these patients as soon as possible. It can also assist physicians in prognostic efficacy assessment and decision making.


Subject(s)
COVID-19 , Humans , COVID-19/diagnostic imaging , Tomography, X-Ray Computed/methods , Machine Learning , Lung/diagnostic imaging , Algorithms , Retrospective Studies
6.
Nat Methods ; 19(11): 1376-1382, 2022 11.
Article in English | MEDLINE | ID: covidwho-2151063

ABSTRACT

Machine-learning prediction algorithms such as AlphaFold and RoseTTAFold can create remarkably accurate protein models, but these models usually have some regions that are predicted with low confidence or poor accuracy. We hypothesized that by implicitly including new experimental information such as a density map, a greater portion of a model could be predicted accurately, and that this might synergistically improve parts of the model that were not fully addressed by either machine learning or experiment alone. An iterative procedure was developed in which AlphaFold models are automatically rebuilt on the basis of experimental density maps and the rebuilt models are used as templates in new AlphaFold predictions. We show that including experimental information improves prediction beyond the improvement obtained with simple rebuilding guided by the experimental data. This procedure for AlphaFold modeling with density has been incorporated into an automated procedure for interpretation of crystallographic and electron cryo-microscopy maps.


Subject(s)
Algorithms , Proteins , Models, Molecular , Cryoelectron Microscopy/methods , Proteins/chemistry , Machine Learning , Protein Conformation
7.
JMIR Public Health Surveill ; 7(4): e26780, 2021 04 05.
Article in English | MEDLINE | ID: covidwho-2141318

ABSTRACT

BACKGROUND: Despite scientific evidence supporting the importance of wearing masks to curtail the spread of COVID-19, wearing masks has stirred up a significant debate particularly on social media. OBJECTIVE: This study aimed to investigate the topics associated with the public discourse against wearing masks in the United States. We also studied the relationship between the anti-mask discourse on social media and the number of new COVID-19 cases. METHODS: We collected a total of 51,170 English tweets between January 1, 2020, and October 27, 2020, by searching for hashtags against wearing masks. We used machine learning techniques to analyze the data collected. We investigated the relationship between the volume of tweets against mask-wearing and the daily volume of new COVID-19 cases using a Pearson correlation analysis between the two-time series. RESULTS: The results and analysis showed that social media could help identify important insights related to wearing masks. The results of topic mining identified 10 categories or themes of user concerns dominated by (1) constitutional rights and freedom of choice; (2) conspiracy theory, population control, and big pharma; and (3) fake news, fake numbers, and fake pandemic. Altogether, these three categories represent almost 65% of the volume of tweets against wearing masks. The relationship between the volume of tweets against wearing masks and newly reported COVID-19 cases depicted a strong correlation wherein the rise in the volume of negative tweets led the rise in the number of new cases by 9 days. CONCLUSIONS: These findings demonstrated the potential of mining social media for understanding the public discourse about public health issues such as wearing masks during the COVID-19 pandemic. The results emphasized the relationship between the discourse on social media and the potential impact on real events such as changing the course of the pandemic. Policy makers are advised to proactively address public perception and work on shaping this perception through raising awareness, debunking negative sentiments, and prioritizing early policy intervention toward the most prevalent topics.


Subject(s)
COVID-19/epidemiology , COVID-19/prevention & control , Masks , Public Opinion , Social Media/statistics & numerical data , Data Mining , Humans , Machine Learning , United States/epidemiology
8.
Front Immunol ; 13: 1001070, 2022.
Article in English | MEDLINE | ID: covidwho-2142020

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS- CoV-2) is the causative virus of the pandemic coronavirus disease 2019 (COVID-19). Evaluating the immunological factors and other implicated processes underlying the progression of COVID-19 is essential for the recognition and then the design of efficacious therapies. Therefore, we analyzed RNAseq data obtained from PBMCs of the COVID-19 patients to explore coding and non-coding RNA diagnostic immunological panels. For this purpose, we integrated multiple RNAseq data and analyzed them overall as well as by considering the state of disease including severe and non-severe conditions. Afterward, we utilized a co-expressed-based machine learning procedure comprising weighted-gene co-expression analysis and differential expression gene as filter phase and recursive feature elimination-support vector machine as wrapper phase. This procedure led to the identification of two modules containing 5 and 84 genes which are mostly involved in cell dysregulation and innate immune suppression, respectively. Moreover, the role of vitamin D in regulating some classifiers was highlighted. Further analysis disclosed the role of discriminant miRNAs including miR-197-3p, miR-150-5p, miR-340-5p, miR-122-5p, miR-1307-3p, miR-34a-5p, miR-98-5p and their target genes comprising GAN, VWC2, TNFRSF6B, and CHST3 in the metabolic pathways. These classifiers differentiate the final fate of infection toward severe or non-severe COVID-19. The identified classifier genes and miRNAs may help in the proper design of therapeutic procedures considering their involvement in the immune and metabolic pathways.


Subject(s)
COVID-19 , MicroRNAs , Humans , COVID-19/diagnosis , COVID-19/genetics , MicroRNAs/genetics , MicroRNAs/metabolism , SARS-CoV-2/genetics , Machine Learning
9.
PLoS One ; 17(11): e0276970, 2022.
Article in English | MEDLINE | ID: covidwho-2140622

ABSTRACT

Voluntary isolation is one of the most effective methods for individuals to help prevent the transmission of diseases such as COVID-19. Understanding why people leave their homes when advised not to do so and identifying what contextual factors predict this non-compliant behavior is essential for policymakers and public health officials. To provide insight on these factors, we collected data from 42,169 individuals across 16 countries. Participants responded to items inquiring about their socio-cultural environment, such as the adherence of fellow citizens, as well as their mental states, such as their level of loneliness and boredom. We trained random forest models to predict whether someone had left their home during a one week period during which they were asked to voluntarily isolate themselves. The analyses indicated that overall, an increase in the feeling of being caged leads to an increased probability of leaving home. In addition, an increased feeling of responsibility and an increased fear of getting infected decreased the probability of leaving home. The models predicted compliance behavior with between 54% and 91% accuracy within each country's sample. In addition, we modeled factors leading to risky behavior in the pandemic context. We observed an increased probability of visiting risky places as both the anticipated number of people and the importance of the activity increased. Conversely, the probability of visiting risky places increased as the perceived putative effectiveness of social distancing decreased. The variance explained in our models predicting risk ranged from < .01 to .54 by country. Together, our findings can inform behavioral interventions to increase adherence to lockdown recommendations in pandemic conditions.


Subject(s)
COVID-19 , Humans , COVID-19/epidemiology , COVID-19/prevention & control , Pandemics , Communicable Disease Control , Machine Learning , Physical Distancing
10.
BMC Med Inform Decis Mak ; 22(1): 309, 2022 Nov 28.
Article in English | MEDLINE | ID: covidwho-2139266

ABSTRACT

BACKGROUND: Machine learning (ML) algorithms have been trained to early predict critical in-hospital events from COVID-19 using patient data at admission, but little is known on how their performance compares with each other and/or with statistical logistic regression (LR). This prospective multicentre cohort study compares the performance of a LR and five ML models on the contribution of influencing predictors and predictor-to-event relationships on prediction model´s performance. METHODS: We used 25 baseline variables of 490 COVID-19 patients admitted to 8 hospitals in Germany (March-November 2020) to develop and validate (75/25 random-split) 3 linear (L1 and L2 penalty, elastic net [EN]) and 2 non-linear (support vector machine [SVM] with radial kernel, random forest [RF]) ML approaches for predicting critical events defined by intensive care unit transfer, invasive ventilation and/or death (composite end-point: 181 patients). Models were compared for performance (area-under-the-receiver-operating characteristic-curve [AUC], Brier score) and predictor importance (performance-loss metrics, partial-dependence profiles). RESULTS: Models performed close with a small benefit for LR (utilizing restricted cubic splines for non-linearity) and RF (AUC means: 0.763-0.731 [RF-L1]); Brier scores: 0.184-0.197 [LR-L1]). Top ranked predictor variables (consistently highest importance: C-reactive protein) were largely identical across models, except creatinine, which exhibited marginal (L1, L2, EN, SVM) or high/non-linear effects (LR, RF) on events. CONCLUSIONS: Although the LR and ML models analysed showed no strong differences in performance and the most influencing predictors for COVID-19-related event prediction, our results indicate a predictive benefit from taking account for non-linear predictor-to-event relationships and effects. Future efforts should focus on leveraging data-driven ML technologies from static towards dynamic modelling solutions that continuously learn and adapt to changes in data environments during the evolving pandemic. TRIAL REGISTRATION NUMBER: NCT04659187.


Subject(s)
COVID-19 , Humans , Logistic Models , Cohort Studies , Prospective Studies , Machine Learning , Hospitals
11.
Comput Intell Neurosci ; 2022: 4307708, 2022.
Article in English | MEDLINE | ID: covidwho-2138230

ABSTRACT

The COVID-19 virus continues to generate waves of infections around the world. With major areas in developing countries still lagging behind in vaccination campaigns, the risk of new variants that can cause re-infections worldwide makes the monitoring and forecasting of the evolution of the virus a high priority. Having accurate models able to forecast the incidence of the spread of the virus provides help to policymakers and health professionals in managing the scarce resources in an optimal way. In this paper, a new machine learning model is proposed to forecast the spread of the virus one-week ahead in a geographic area which combines mobility and COVID-19 incidence data. The area is divided into zones or districts according to the location of the COVID-19 measuring points. A traffic-driven mobility estimate among adjacent districts is proposed to capture the spatial spread of the virus. Traffic-driven mobility in adjacent districts will be used together with COVID-19 incidence data to feed a new deep learning LSTM-based model which will extract patterns from mobility-modulated COVID-19 incidence spatiotemporal data in order to optimize one-week ahead estimations. The model is trained and validated with open data available for the city of Madrid (Spain) for 3 different validation scenarios. A baseline model based on previous literature able to extract temporal patterns in COVID-19 incidence time series is also trained with the same dataset. The results show that the proposed model, based on the combination of traffic and COVID-19 incidence data, is able to outperform the baseline model in all the validation scenarios.


Subject(s)
COVID-19 , Humans , Incidence , COVID-19/epidemiology , Machine Learning , Forecasting , Cities
12.
Database (Oxford) ; 20222022 Nov 25.
Article in English | MEDLINE | ID: covidwho-2135127

ABSTRACT

The Coronavirus Disease 2019 (COVID-19) pandemic has shifted the focus of research worldwide, and more than 10 000 new articles per month have concentrated on COVID-19-related topics. Considering this rapidly growing literature, the efficient and precise extraction of the main topics of COVID-19-relevant articles is of great importance. The manual curation of this information for biomedical literature is labor-intensive and time-consuming, and as such the procedure is insufficient and difficult to maintain. In response to these complications, the BioCreative VII community has proposed a challenging task, LitCovid Track, calling for a global effort to automatically extract semantic topics for COVID-19 literature. This article describes our work on the BioCreative VII LitCovid Track. We proposed the LitCovid Ensemble Learning (LCEL) method for the tasks and integrated multiple biomedical pretrained models to address the COVID-19 multi-label classification problem. Specifically, seven different transformer-based pretrained models were ensembled for the initialization and fine-tuning processes independently. To enhance the representation abilities of the deep neural models, diverse additional biomedical knowledge was utilized to facilitate the fruitfulness of the semantic expressions. Simple yet effective data augmentation was also leveraged to address the learning deficiency during the training phase. In addition, given the imbalanced label distribution of the challenging task, a novel asymmetric loss function was applied to the LCEL model, which explicitly adjusted the negative-positive importance by assigning different exponential decay factors and helped the model focus on the positive samples. After the training phase, an ensemble bagging strategy was adopted to merge the outputs from each model for final predictions. The experimental results show the effectiveness of our proposed approach, as LCEL obtains the state-of-the-art performance on the LitCovid dataset. Database URL: https://github.com/JHnlp/LCEL.


Subject(s)
COVID-19 , Humans , COVID-19/epidemiology , Databases, Factual , Semantics , Machine Learning
13.
Sci Rep ; 12(1): 20499, 2022 Nov 28.
Article in English | MEDLINE | ID: covidwho-2133631

ABSTRACT

The contact and interaction of human is considered to be one of the important factors affecting the epidemic transmission, and it is critical to model the heterogeneity of individual activities in epidemiological risk assessment. In digital society, massive data makes it possible to implement this idea on large scale. Here, we use the mobile phone signaling to track the users' trajectories and construct contact network to describe the topology of daily contact between individuals dynamically. We show the spatiotemporal contact features of about 7.5 million mobile phone users during the outbreak of COVID-19 in Shanghai, China. Furthermore, the individual feature matrix extracted from contact network enables us to carry out the extreme event learning and predict the regional transmission risk, which can be further decomposed into the risk due to the inflow of people from epidemic hot zones and the risk due to people close contacts within the observing area. This method is much more flexible and adaptive, and can be taken as one of the epidemic precautions before the large-scale outbreak with high efficiency and low cost.


Subject(s)
COVID-19 , Epidemics , Names , Humans , COVID-19/epidemiology , China/epidemiology , Machine Learning
14.
Environ Sci Pollut Res Int ; 28(30): 40496-40506, 2021 Aug.
Article in English | MEDLINE | ID: covidwho-2115929

ABSTRACT

COVID-19 was first discovered in Wuhan, China in December 2019. It is one of the worst pandemics in human history. Recent studies reported that COVID-19 is transmitted among humans by droplet infection or direct contact. COVID-19 pandemic has invaded more than 210 countries around the world and as of February 18th, 2021, just after a year has passed, a total of 110,533,973 confirmed cases of COVID-19 were reported and its death toll reached about 2,443,091. COVID-19 is a new member of the family of corona viruses, its nature, behaviour, transmission, spread, prevention, and treatment are to be investigated. Generally, a huge amount of data is accumulating regarding the COVID-19 pandemic, which makes hot research topics for machine learning researchers. However, the panicked world's population is asking when the COVID-19 will be over? This study considered machine learning approaches to predict the spread of the COVID-19 in many countries. The experimental results of the proposed model showed that the overall R2 is 0.99 from the perspective of confirmed cases. A machine learning model has been developed to predict the estimation of the spread of the COVID-19 infection in many countries and the expected period after which the virus can be stopped. Globally, our results forecasted that the COVID-19 infections will greatly decline during the first week of September 2021 when it will be going to an end shortly afterward.


Subject(s)
COVID-19 , Pandemics , Forecasting , Humans , Machine Learning , SARS-CoV-2
15.
Sensors (Basel) ; 22(22)2022 Nov 12.
Article in English | MEDLINE | ID: covidwho-2110225

ABSTRACT

People with diabetes mellitus (DM) are at elevated risk of in-hospital mortality from coronavirus disease-2019 (COVID-19). This vulnerability has spurred efforts to pinpoint distinctive characteristics of COVID-19 patients with DM. In this context, the present article develops ML models equipped with interpretation modules for inpatient mortality risk assessments of COVID-19 patients with DM. To this end, a cohort of 156 hospitalised COVID-19 patients with pre-existing DM is studied. For creating risk assessment platforms, this work explores a pool of historical, on-admission, and during-admission data that are DM-related or, according to preliminary investigations, are exclusively attributed to the COVID-19 susceptibility of DM patients. First, a set of careful pre-modelling steps are executed on the clinical data, including cleaning, pre-processing, subdivision, and feature elimination. Subsequently, standard machine learning (ML) modelling analysis is performed on the cured data. Initially, a classifier is tasked with forecasting COVID-19 fatality from selected features. The model undergoes thorough evaluation analysis. The results achieved substantiate the efficacy of the undertaken data curation and modelling steps. Afterwards, SHapley Additive exPlanations (SHAP) technique is assigned to interpret the generated mortality risk prediction model by rating the predictors' global and local influence on the model's outputs. These interpretations advance the comprehensibility of the analysis by explaining the formation of outcomes and, in this way, foster the adoption of the proposed methodologies. Next, a clustering algorithm demarcates patients into four separate groups based on their SHAP values, providing a practical risk stratification method. Finally, a re-evaluation analysis is performed to verify the robustness of the proposed framework.


Subject(s)
COVID-19 , Diabetes Mellitus , Humans , Inpatients , Machine Learning , Hospital Mortality
16.
Sensors (Basel) ; 22(22)2022 Nov 08.
Article in English | MEDLINE | ID: covidwho-2110220

ABSTRACT

Extracting useful knowledge from proper data analysis is a very challenging task for efficient and timely decision-making. To achieve this, there exist a plethora of machine learning (ML) algorithms, while, especially in healthcare, this complexity increases due to the domain's requirements for analytics-based risk predictions. This manuscript proposes a data analysis mechanism experimented in diverse healthcare scenarios, towards constructing a catalogue of the most efficient ML algorithms to be used depending on the healthcare scenario's requirements and datasets, for efficiently predicting the onset of a disease. To this context, seven (7) different ML algorithms (Naïve Bayes, K-Nearest Neighbors, Decision Tree, Logistic Regression, Random Forest, Neural Networks, Stochastic Gradient Descent) have been executed on top of diverse healthcare scenarios (stroke, COVID-19, diabetes, breast cancer, kidney disease, heart failure). Based on a variety of performance metrics (accuracy, recall, precision, F1-score, specificity, confusion matrix), it has been identified that a sub-set of ML algorithms are more efficient for timely predictions under specific healthcare scenarios, and that is why the envisioned ML catalogue prioritizes the ML algorithms to be used, depending on the scenarios' nature and needed metrics. Further evaluation must be performed considering additional scenarios, involving state-of-the-art techniques (e.g., cloud deployment, federated ML) for improving the mechanism's efficiency.


Subject(s)
COVID-19 , Humans , Bayes Theorem , Machine Learning , Algorithms , Delivery of Health Care
17.
PLoS One ; 17(11): e0277438, 2022.
Article in English | MEDLINE | ID: covidwho-2119313

ABSTRACT

The COVID-19 pandemic has worsened the mental health and substance use challenges among many people who are Two Spirit, lesbian, gay, bisexual, transgender, queer, questioning, and intersex (2SLGBTQI+). We aimed to identify the important correlates and their effects on the predicted likelihood of wanting to seek help among 2SLGBTQI+ young adults for mental health or substance use concerns during the pandemic. A cross-sectional survey was conducted in 2020-2021 among 2SLGBTQI+ young adults aged 16-29 living in two Canadian provinces (Ontario and Quebec). Among 1414 participants, 77% (n = 1089) wanted to seek help for their mental health or substance use concerns during the pandemic, out of these, 69.8% (n = 760) reported delay in accessing care. We built a random forest (RF) model to predict the status of wanting to seek help, which achieved moderately high performance with an area under the receiver operating characteristic curve (AUC) of 0.85. The top 10 correlates of wanting to seek help were worsening mental health, age, stigma and discrimination, and adverse childhood experiences. The interactions of adequate housing with certain sexual orientations, gender identities and mental health challenges were found to increase the likelihood of wanting to seek help. We built another RF model for predicting risk of delay in accessing care among participants who wanted to seek help (n = 1089). The model identified a similar set of top 10 correlates of delay in accessing care but lacked adequate performance (AUC 0.61). These findings can direct future research and targeted prevention measures to reduce health disparities for 2SLGBTQI+ young adults.


Subject(s)
COVID-19 , Sexual and Gender Minorities , Substance-Related Disorders , Female , Young Adult , Humans , Mental Health , Pandemics , COVID-19/epidemiology , Cross-Sectional Studies , Substance-Related Disorders/epidemiology , Machine Learning , Ontario
18.
Anal Chem ; 94(47): 16361-16368, 2022 Nov 29.
Article in English | MEDLINE | ID: covidwho-2119248

ABSTRACT

The unstoppable spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has severely threatened public health over the past 2 years. The current ubiquitously accepted method for its diagnosis provides sensitive detection of the virus; however, it is relatively time-consuming and costly, not to mention the need for highly skilled personnel. There is a clear need to develop novel computer-based diagnostic tools to provide rapid, cost-efficient, and time-saving detection in places where massive traditional testing is not practical. Here, we develop an electrochemiluminescence (ECL)-based detection system whose results are quantified as reverse transcriptase polymerase chain reaction (RT-PCR) cyclic threshold (CT) values. A concentration-dependent signal is generated upon the introduction of the virus to the electrode and is recorded with a smartphone camera. The ECL images are used to train machine learning algorithms, and a model using artificial neural networks (ANNs) for 45 samples was developed. The model demonstrated more than 90% accuracy in the diagnosis of 50 unknown real samples, detecting up to a CT value of 32 and a limit of detection (LOD) of 10-12 g mL-1 in the testing of artificial samples.


Subject(s)
COVID-19 , Humans , COVID-19/diagnosis , Reverse Transcriptase Polymerase Chain Reaction , SARS-CoV-2/genetics , Smartphone , Sensitivity and Specificity , Machine Learning , Immunoassay , Tomography, X-Ray Computed
19.
Eur Rev Med Pharmacol Sci ; 26(21): 8129-8143, 2022 Nov.
Article in English | MEDLINE | ID: covidwho-2118079

ABSTRACT

OBJECTIVE: A lack of objective biomarkers is preventing the screening and diagnosis of COVID-19 combined with major depression disorder (COVID-19-MDD). The purpose of this study was to identify diagnostic biomarkers and gene regulatory mechanisms associated with autophagy; a crucial process significantly involved in the pathogenesis of COVID-19-MDD. MATERIALS AND METHODS: In this study, differentially expressed genes (DEGs) were screened using GSE98793 from the GEO2R analysis (GEO) database, and intersected with the COVID-19-related gene (CRGs) and autophagy-related genes (ARGs) to obtain common genes involved in. Then, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of these common genes were performed. Subsequently, the transcription factor (TF)-gene regulatory network and comorbidity network were constructed. In addition, 10 drug candidates were screened using the DSigDB database. To identify diagnostic markers, we used LASSO regression. RESULTS: In total, 13 common genes were screened, which were primarily enriched in lysosomes, endoplasmic reticulum membranes, and other endomembrane systems also associated with autophagy. Additionally, these genes were involved in neurological cell signaling and have a functional role in pathways related to vascular endothelial growth factor, tyrosine kinase, autophagy, inflammation, immunity, and carcinogenesis. Tumors and psychiatric disorders were the most highly linked diseases to COVID-19. Finally, ten drug candidates and eight diagnostic markers (STX17, NRG1, RRAGD, XPO1, HERC1, HSP90AB1, EPHB2, and S1PR3) were screened. CONCLUSIONS: This is the first study to screen eight diagnostic markers and construct a gene regulatory network for COVID-19-MDD from the perspective of autophagy. The findings of our study provide novel insights into the diagnosis and treatment of COVID-19-MDD.


Subject(s)
COVID-19 , Depressive Disorder, Major , Humans , Computational Biology , COVID-19/genetics , Vascular Endothelial Growth Factor A , Biomarkers , Machine Learning , Autophagy/genetics
20.
Sci Rep ; 12(1): 19165, 2022 Nov 10.
Article in English | MEDLINE | ID: covidwho-2118041

ABSTRACT

Machine learning methods are a novel way to predict and rank donors' willingness to donate blood and to achieve precision recruitment, which can improve the recruitment efficiency and meet the challenge of blood shortage. We collected information about experienced blood donors via short message service (SMS) recruitment and developed 7 machine learning-based recruitment models using PyCharm-Python Environment and 13 features which were described as a method for ranking and predicting donors' intentions to donate blood with a floating number between 0 and 1. Performance of the prediction models was assessed by the Area under the receiver operating characteristic curve (AUC), accuracy, precision, recall, and F1 score in the full dataset, and by the accuracy in the four sub-datasets. The developed models were applied to prospective validations of recruiting experienced blood donors during two COVID-19 pandemics, while the routine method was used as a control. Overall, a total of 95,476 recruitments via SMS and their donation results were enrolled in our modelling study. The strongest predictor features for the donation of experienced donors were blood donation interval, age, and donation frequency. Among the seven baseline models, the eXtreme Gradient Boosting (XGBoost) and Support vector machine models (SVM) achieved the best performance: mean (95%CI) with the highest AUC: 0.809 (0.806-0.811), accuracy: 0.815 (0.812-0.818), precision: 0.840 (0.835-0.845), and F1 score of XGBoost: 0.843 (0.840-0.845) and recall of SVM: 0.991 (0.988-0.994). The hit rate of the XGBoost model alone and the combined XGBoost and SVM models were 1.25 and 1.80 times higher than that of the conventional method as a control in 2 recruitments respectively, and the hit rate of the high willingness to donate group was 1.96 times higher than that of the low willingness to donate group. Our results suggested that the machine learning models could predict and determine the experienced donors with a strong willingness to donate blood by a ranking score based on personalized donation data and demographical details, significantly improve the recruitment rate of blood donors and help blood agencies to maintain the blood supply in emergencies.


Subject(s)
Blood Donors , COVID-19 , Humans , COVID-19/epidemiology , Machine Learning , Intention , Disease Outbreaks
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