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1.
PLoS One ; 18(5): e0286034, 2023.
Article in English | MEDLINE | ID: covidwho-2326982

ABSTRACT

The coronavirus disease 2019 pandemic has impacted and changed consumer behavior because of a prolonged quarantine and lockdown. This study proposed a theoretical framework to explore and define the influencing factors of online consumer purchasing behavior (OCPB) based on electronic word-of-mouth (e-WOM) data mining and analysis. Data pertaining to e-WOM were crawled from smartphone product reviews from the two most popular online shopping platforms in China, Jingdong.com and Taobao.com. Data processing aimed to filter noise and translate unstructured data from complex text reviews into structured data. The machine learning based K-means clustering method was utilized to cluster the influencing factors of OCPB. Comparing the clustering results and Kotler's five products level, the influencing factors of OCPB were clustered around four categories: perceived emergency context, product, innovation, and function attributes. This study contributes to OCPB research by data mining and analysis that can adequately identify the influencing factors based on e-WOM. The definition and explanation of these categories may have important implications for both OCPB and e-commerce.


Subject(s)
COVID-19 , Consumer Behavior , Humans , COVID-19/epidemiology , Communicable Disease Control , Models, Theoretical , Data Mining/methods
2.
J Emerg Manag ; 21(7): 133-151, 2023.
Article in English | MEDLINE | ID: covidwho-2303469

ABSTRACT

COVID-19, a novel coronavirus, is an ongoing global pandemic that has outbroken recently and spread to almost every part of the world. Several factors of this pandemic are still unknown to the world, which causes uncertainty to prepare a strategic plan to cope with this disease effectively and securing the future. A large number of research is in progress or expected to start shortly on the basis of the publicly available datasets of this deadly pandemic. The data are available in multiple formats that include geospatial data, medical data, demographic data, and time-series data. In this study, we propose a data mining method to classify and forecast the time-series pandemic data in an attempt to predict the expected end of this pandemic in a particular region. Based on the COVID-19 data obtained from several countries around the world, a naïve Bayes classifier is built, which may classify the affected countries into one of the following four categories: critical, unsustainable, sustainable, and closed. The pandemic data collected from online sources are preprocessed, labeled, and classified by using different data mining techniques. A new clustering technique is also proposed to predict the expected end of the pandemic in different countries. A method to preprocess the data before applying the clustering technique is also proposed. The results of naïve Bayes classification and clustering techniques are validated based on accuracy, execution time, and other statistical measures.


Subject(s)
COVID-19 , Humans , COVID-19/epidemiology , Pandemics , Bayes Theorem , Algorithms , Data Mining/methods
3.
Int J Mol Sci ; 23(23)2022 Nov 29.
Article in English | MEDLINE | ID: covidwho-2296973

ABSTRACT

The body of scientific literature continues to grow annually. Over 1.5 million abstracts of biomedical publications were added to the PubMed database in 2021. Therefore, developing cognitive systems that provide a specialized search for information in scientific publications based on subject area ontology and modern artificial intelligence methods is urgently needed. We previously developed a web-based information retrieval system, ANDDigest, designed to search and analyze information in the PubMed database using a customized domain ontology. This paper presents an improved ANDDigest version that uses fine-tuned PubMedBERT classifiers to enhance the quality of short name recognition for molecular-genetics entities in PubMed abstracts on eight biological object types: cell components, diseases, side effects, genes, proteins, pathways, drugs, and metabolites. This approach increased average short name recognition accuracy by 13%.


Subject(s)
Artificial Intelligence , Data Mining , Data Mining/methods , PubMed , Databases, Factual , Proteins
4.
IEEE/ACM Trans Comput Biol Bioinform ; 20(3): 2101-2111, 2023.
Article in English | MEDLINE | ID: covidwho-2228811

ABSTRACT

Rapid and effective utilization of biomedical literature is paramount to combat diseases like COVID19. Biomedical named entity recognition (BioNER) is a fundamental task in text mining that can help physicians accelerate knowledge discovery to curb the spread of the COVID-19 epidemic. Recent approaches have shown that casting entity extraction as the machine reading comprehension task can significantly improve model performance. However, two major drawbacks impede higher success in identifying entities (1) ignoring the use of domain knowledge to capture the context beyond sentences and (2) lacking the ability to deeper understand the intent of questions. In this paper, to remedy this, we introduce and explore external domain knowledge which cannot be implicitly learned in text sequence. Previous works have focused more on text sequence and explored little of the domain knowledge. To better incorporate domain knowledge, a multi-way matching reader mechanism is devised to model representations of interaction between sequence, question and knowledge retrieved from Unified Medical Language System (UMLS). Benefiting from these, our model can better understand the intent of questions in complex contexts. Experimental results indicate that incorporating domain knowledge can help to obtain competitive results across 10 BioNER datasets, achieving absolute improvement of up to 2.02% in the f1 score.


Subject(s)
COVID-19 , Comprehension , Humans , Data Mining/methods , Unified Medical Language System
5.
Comput Biol Chem ; 102: 107808, 2023 Feb.
Article in English | MEDLINE | ID: covidwho-2165189

ABSTRACT

The number of biomedical articles published is increasing rapidly over the years. Currently there are about 30 million articles in PubMed and over 25 million mentions in Medline. Among these fundamentals, Biomedical Named Entity Recognition (BioNER) and Biomedical Relation Extraction (BioRE) are the most essential in analysing the literature. In the biomedical domain, Knowledge Graph is used to visualize the relationships between various entities such as proteins, chemicals and diseases. Scientific publications have increased dramatically as a result of the search for treatments and potential cures for the new Coronavirus, but efficiently analysing, integrating, and utilising related sources of information remains a difficulty. In order to effectively combat the disease during pandemics like COVID-19, literature must be used quickly and effectively. In this paper, we introduced a fully automated framework consists of BERT-BiLSTM, Knowledge graph, and Representation Learning model to extract the top diseases, chemicals, and proteins related to COVID-19 from the literature. The proposed framework uses Named Entity Recognition models for disease recognition, chemical recognition, and protein recognition. Then the system uses the Chemical - Disease Relation Extraction and Chemical - Protein Relation Extraction models. And the system extracts the entities and relations from the CORD-19 dataset using the models. The system then creates a Knowledge Graph for the extracted relations and entities. The system performs Representation Learning on this KG to get the embeddings of all entities and get the top related diseases, chemicals, and proteins with respect to COVID-19.


Subject(s)
COVID-19 , Pattern Recognition, Automated , Humans , Data Mining/methods
6.
Int J Environ Res Public Health ; 19(20)2022 Oct 18.
Article in English | MEDLINE | ID: covidwho-2142998

ABSTRACT

Doctor-patient relationships (DPRs) in China have been straining. With the emergence of the COVID-19 pandemic, the relationships and interactions between patients and doctors are changing. This study investigated how patients' attitudes toward physicians changed during the pandemic and what factors were associated with these changes, leading to insights for improving management in the healthcare sector. This paper collected 58,600 comments regarding Chinese doctors from three regions from the online health platform Good Doctors Online (haodf.com, accessed on 13 October 2022). These comments were analyzed using text mining techniques, such as sentiment and word frequency analyses. The results showed improvements in DPRs after the pandemic, and the degree of improvement was related to the extent to which a location was affected. The findings also suggest that administrative services in the healthcare sector need further improvement. Based on these results, we summarize relevant recommendations at the end of this paper.


Subject(s)
COVID-19 , Physicians , Humans , Physician-Patient Relations , COVID-19/epidemiology , Pandemics , Data Mining/methods , China/epidemiology
7.
Brief Bioinform ; 23(6)2022 Nov 19.
Article in English | MEDLINE | ID: covidwho-2107362

ABSTRACT

Target discovery and identification processes are driven by the increasing amount of biomedical data. The vast numbers of unstructured texts of biomedical publications provide a rich source of knowledge for drug target discovery research and demand the development of specific algorithms or tools to facilitate finding disease genes and proteins. Text mining is a method that can automatically mine helpful information related to drug target discovery from massive biomedical literature. However, there is a substantial lag between biomedical publications and the subsequent abstraction of information extracted by text mining to databases. The knowledge graph is introduced to integrate heterogeneous biomedical data. Here, we describe e-TSN (Target significance and novelty explorer, http://www.lilab-ecust.cn/etsn/), a knowledge visualization web server integrating the largest database of associations between targets and diseases from the full scientific literature by constructing significance and novelty scoring methods based on bibliometric statistics. The platform aims to visualize target-disease knowledge graphs to assist in prioritizing candidate disease-related proteins. Approved drugs and associated bioactivities for each interested target are also provided to facilitate the visualization of drug-target relationships. In summary, e-TSN is a fast and customizable visualization resource for investigating and analyzing the intricate target-disease networks, which could help researchers understand the mechanisms underlying complex disease phenotypes and improve the drug discovery and development efficiency, especially for the unexpected outbreak of infectious disease pandemics like COVID-19.


Subject(s)
COVID-19 , Humans , Data Mining/methods , Publications , Knowledge , Algorithms , Proteins
8.
J Biomed Semantics ; 13(1): 26, 2022 10 27.
Article in English | MEDLINE | ID: covidwho-2089233

ABSTRACT

BACKGROUND: Intense research has been done in the area of biomedical natural language processing. Since the breakthrough of transfer learning-based methods, BERT models are used in a variety of biomedical and clinical applications. For the available data sets, these models show excellent results - partly exceeding the inter-annotator agreements. However, biomedical named entity recognition applied on COVID-19 preprints shows a performance drop compared to the results on test data. The question arises how well trained models are able to predict on completely new data, i.e. to generalize. RESULTS: Based on the example of disease named entity recognition, we investigate the robustness of different machine learning-based methods - thereof transfer learning - and show that current state-of-the-art methods work well for a given training and the corresponding test set but experience a significant lack of generalization when applying to new data. CONCLUSIONS: We argue that there is a need for larger annotated data sets for training and testing. Therefore, we foresee the curation of further data sets and, moreover, the investigation of continual learning processes for machine learning-based models.


Subject(s)
COVID-19 , Data Mining , Humans , Data Mining/methods , Natural Language Processing , Machine Learning
9.
Database (Oxford) ; 20222022 10 05.
Article in English | MEDLINE | ID: covidwho-2051371

ABSTRACT

The coronavirus disease 2019 (COVID-19) pandemic has compelled biomedical researchers to communicate data in real time to establish more effective medical treatments and public health policies. Nontraditional sources such as preprint publications, i.e. articles not yet validated by peer review, have become crucial hubs for the dissemination of scientific results. Natural language processing (NLP) systems have been recently developed to extract and organize COVID-19 data in reasoning systems. Given this scenario, the BioCreative COVID-19 text mining tool interactive demonstration track was created to assess the landscape of the available tools and to gauge user interest, thereby providing a two-way communication channel between NLP system developers and potential end users. The goal was to inform system designers about the performance and usability of their products and to suggest new additional features. Considering the exploratory nature of this track, the call for participation solicited teams to apply for the track, based on their system's ability to perform COVID-19-related tasks and interest in receiving user feedback. We also recruited volunteer users to test systems. Seven teams registered systems for the track, and >30 individuals volunteered as test users; these volunteer users covered a broad range of specialties, including bench scientists, bioinformaticians and biocurators. The users, who had the option to participate anonymously, were provided with written and video documentation to familiarize themselves with the NLP tools and completed a survey to record their evaluation. Additional feedback was also provided by NLP system developers. The track was well received as shown by the overall positive feedback from the participating teams and the users. Database URL: https://biocreative.bioinformatics.udel.edu/tasks/biocreative-vii/track-4/.


Subject(s)
COVID-19 , COVID-19/epidemiology , Data Mining/methods , Databases, Factual , Documentation , Humans , Natural Language Processing
10.
J Environ Public Health ; 2022: 6294436, 2022.
Article in English | MEDLINE | ID: covidwho-2020519

ABSTRACT

Climate change is a serious threat to humankind. As broad public participation is required in climate change mitigation efforts, it is critical to understand how the public talk about climate change on social media. This study sets out to increase the understanding of Chinese public awareness of climate change, as well as explore the potential and limitations of social media for public engagement on climate change issues. It examines the Chinese public's discussion about climate change on social media Weibo during the last six years through data mining and text analysis. The analyses include volume analysis, keyword extraction, topic modeling, and sentiment analysis. The results indicate three main aspects of public awareness and concern regarding climate change. First, public awareness of climate change is growing in China. Second, the sentiment analysis shows that the general sentiment toward climate change is becoming more positive over time. Third, based on keyword extraction and topic modeling, the discussion on climate change shows a top-down perspective, an optimistic economic perspective, and a preference for celebrity content. The study provides a comprehensive picture of Chinese social media users' views on climate change issues, based on large-scale research data. It contributes to a better understanding of what Chinese people think about climate change on social media generally. These findings may provide government and environmental organizations with valuable insights for better climate change campaigns on social media.


Subject(s)
Social Media , China , Climate Change , Data Mining/methods , Humans , Public Opinion
11.
Database (Oxford) ; 20222022 08 31.
Article in English | MEDLINE | ID: covidwho-2017881

ABSTRACT

The coronavirus disease 2019 (COVID-19) pandemic has been severely impacting global society since December 2019. The related findings such as vaccine and drug development have been reported in biomedical literature-at a rate of about 10 000 articles on COVID-19 per month. Such rapid growth significantly challenges manual curation and interpretation. For instance, LitCovid is a literature database of COVID-19-related articles in PubMed, which has accumulated more than 200 000 articles with millions of accesses each month by users worldwide. One primary curation task is to assign up to eight topics (e.g. Diagnosis and Treatment) to the articles in LitCovid. The annotated topics have been widely used for navigating the COVID literature, rapidly locating articles of interest and other downstream studies. However, annotating the topics has been the bottleneck of manual curation. Despite the continuing advances in biomedical text-mining methods, few have been dedicated to topic annotations in COVID-19 literature. To close the gap, we organized the BioCreative LitCovid track to call for a community effort to tackle automated topic annotation for COVID-19 literature. The BioCreative LitCovid dataset-consisting of over 30 000 articles with manually reviewed topics-was created for training and testing. It is one of the largest multi-label classification datasets in biomedical scientific literature. Nineteen teams worldwide participated and made 80 submissions in total. Most teams used hybrid systems based on transformers. The highest performing submissions achieved 0.8875, 0.9181 and 0.9394 for macro-F1-score, micro-F1-score and instance-based F1-score, respectively. Notably, these scores are substantially higher (e.g. 12%, higher for macro F1-score) than the corresponding scores of the state-of-art multi-label classification method. The level of participation and results demonstrate a successful track and help close the gap between dataset curation and method development. The dataset is publicly available via https://ftp.ncbi.nlm.nih.gov/pub/lu/LitCovid/biocreative/ for benchmarking and further development. Database URL https://ftp.ncbi.nlm.nih.gov/pub/lu/LitCovid/biocreative/.


Subject(s)
COVID-19 , COVID-19/epidemiology , Data Mining/methods , Databases, Factual , Humans , PubMed , Publications
12.
Database (Oxford) ; 20222022 08 11.
Article in English | MEDLINE | ID: covidwho-1992163

ABSTRACT

TopEx is a natural language processing application developed to facilitate the exploration of topics and key words in a set of texts through a user interface that requires no programming or natural language processing knowledge, thus enhancing the ability of nontechnical researchers to explore and analyze textual data. The underlying algorithm groups semantically similar sentences together followed by a topic analysis on each group to identify the key topics discussed in a collection of texts. Implementation is achieved via a Python library back end and a web application front end built with React and D3.js for visualizations. TopEx has been successfully used to identify themes, topics and key words in a variety of corpora, including Coronavirus disease 2019 (COVID-19) discharge summaries and tweets. Feedback from the BioCreative VII Challenge Track 4 concludes that TopEx is a useful tool for text exploration for a variety of users and tasks. DATABSE URL: http://topex.cctr.vcu.edu.


Subject(s)
COVID-19 , Algorithms , Data Mining/methods , Humans , Natural Language Processing , Software
13.
J Med Internet Res ; 24(8): e38776, 2022 08 09.
Article in English | MEDLINE | ID: covidwho-1987335

ABSTRACT

BACKGROUND: The COVID-19 pandemic caused a critical public health crisis worldwide, and policymakers are using lockdowns to control the virus. However, there has been a noticeable increase in aggressive social behaviors that threaten social stability. Lockdown measures might negatively affect mental health and lead to an increase in aggressive emotions. Discovering the relationship between lockdown and increased aggression is crucial for formulating appropriate policies that address these adverse societal effects. We applied natural language processing (NLP) technology to internet data, so as to investigate the social and emotional impacts of lockdowns. OBJECTIVE: This research aimed to understand the relationship between lockdown and increased aggression using NLP technology to analyze the following 3 kinds of aggressive emotions: anger, offensive language, and hate speech, in spatiotemporal ranges of tweets in the United States. METHODS: We conducted a longitudinal internet study of 11,455 Twitter users by analyzing aggressive emotions in 1,281,362 tweets they posted from 2019 to 2020. We selected 3 common aggressive emotions (anger, offensive language, and hate speech) on the internet as the subject of analysis. To detect the emotions in the tweets, we trained a Bidirectional Encoder Representations from Transformers (BERT) model to analyze the percentage of aggressive tweets in every state and every week. Then, we used the difference-in-differences estimation to measure the impact of lockdown status on increasing aggressive tweets. Since most other independent factors that might affect the results, such as seasonal and regional factors, have been ruled out by time and state fixed effects, a significant result in this difference-in-differences analysis can not only indicate a concrete positive correlation but also point to a causal relationship. RESULTS: In the first 6 months of lockdown in 2020, aggression levels in all users increased compared to the same period in 2019. Notably, users under lockdown demonstrated greater levels of aggression than those not under lockdown. Our difference-in-differences estimation discovered a statistically significant positive correlation between lockdown and increased aggression (anger: P=.002, offensive language: P<.001, hate speech: P=.005). It can be inferred from such results that there exist causal relations. CONCLUSIONS: Understanding the relationship between lockdown and aggression can help policymakers address the personal and societal impacts of lockdown. Applying NLP technology and using big data on social media can provide crucial and timely information for this effort.


Subject(s)
COVID-19 , Social Media , Aggression , COVID-19/prevention & control , Communicable Disease Control , Data Mining/methods , Humans , Pandemics , United States/epidemiology
14.
Database (Oxford) ; 20222022 07 15.
Article in English | MEDLINE | ID: covidwho-1948247

ABSTRACT

In this research, we explored various state-of-the-art biomedical-specific pre-trained Bidirectional Encoder Representations from Transformers (BERT) models for the National Library of Medicine - Chemistry (NLM CHEM) and LitCovid tracks in the BioCreative VII Challenge, and propose a BERT-based ensemble learning approach to integrate the advantages of various models to improve the system's performance. The experimental results of the NLM-CHEM track demonstrate that our method can achieve remarkable performance, with F1-scores of 85% and 91.8% in strict and approximate evaluations, respectively. Moreover, the proposed Medical Subject Headings identifier (MeSH ID) normalization algorithm is effective in entity normalization, which achieved a F1-score of about 80% in both strict and approximate evaluations. For the LitCovid track, the proposed method is also effective in detecting topics in the Coronavirus disease 2019 (COVID-19) literature, which outperformed the compared methods and achieve state-of-the-art performance in the LitCovid corpus. Database URL: https://www.ncbi.nlm.nih.gov/research/coronavirus/.


Subject(s)
COVID-19 , Data Mining , Data Mining/methods , Humans , Machine Learning , Medical Subject Headings , PubMed
15.
J Clin Epidemiol ; 149: 53-59, 2022 09.
Article in English | MEDLINE | ID: covidwho-1873129

ABSTRACT

BACKGROUND AND OBJECTIVES: Text-mining tool, Abstrackr, may potentially reduce the workload burden of title and abstract screening (Stage 1), using screening prioritization and truncation. This study aimed to evaluate the performance of Abstrackr's text-mining functions ('Abstrackr-assisted screening'; screening undertaken by a single-human screener and Abstrackr) vs. Single-human screening. METHODS: A systematic review of treatments for relapsed/refractory diffuse large B cell lymphoma (n = 7,723) was used. Citations, uploaded to Abstrackr, were screened by a human screener until a pre-specified maximum prediction score of 0.39540 was reached. Abstrackr's predictions were compared with the judgments of a second, human screener (who screened all citations in Covidence). The performance metrics were sensitivity, specificity, precision, false negative rate, proportion of relevant citations missed, workload savings, and time savings. RESULTS: Abstrackr reduced Stage 1 workload by 67% (5.4 days), when compared with Single-human screening. Sensitivity was high (91%). The false negative rate at Stage 1 was 9%; however, none of those citations were included following full-text screening. The high proportion of false positives (n = 2,001) resulted in low specificity (72%) and precision (15.5%). CONCLUSION: Abstrackr-assisted screening provided Stage 1 workload savings that did not come at the expense of omitting relevant citations. However, Abstrackr overestimated citation relevance, which may have negative workload implications at full-text screening.


Subject(s)
Data Mining , Workload , Humans , Data Mining/methods , Mass Screening , Research
16.
IEEE/ACM Trans Comput Biol Bioinform ; 19(5): 2584-2595, 2022.
Article in English | MEDLINE | ID: covidwho-1831866

ABSTRACT

The rapid growth of biomedical literature poses a significant challenge for curation and interpretation. This has become more evident during the COVID-19 pandemic. LitCovid, a literature database of COVID-19 related papers in PubMed, has accumulated over 200,000 articles with millions of accesses. Approximately 10,000 new articles are added to LitCovid every month. A main curation task in LitCovid is topic annotation where an article is assigned with up to eight topics, e.g., Treatment and Diagnosis. The annotated topics have been widely used both in LitCovid (e.g., accounting for ∼18% of total uses) and downstream studies such as network generation. However, it has been a primary curation bottleneck due to the nature of the task and the rapid literature growth. This study proposes LITMC-BERT, a transformer-based multi-label classification method in biomedical literature. It uses a shared transformer backbone for all the labels while also captures label-specific features and the correlations between label pairs. We compare LITMC-BERT with three baseline models on two datasets. Its micro-F1 and instance-based F1 are 5% and 4% higher than the current best results, respectively, and only requires ∼18% of the inference time than the Binary BERT baseline. The related datasets and models are available via https://github.com/ncbi/ml-transformer.


Subject(s)
COVID-19 , Data Mining , Data Mining/methods , Databases, Factual , Humans , Pandemics , Publications
17.
J Biomed Inform ; 130: 104081, 2022 06.
Article in English | MEDLINE | ID: covidwho-1819520

ABSTRACT

Process mining is a discipline sitting between data mining and process science, whose goal is to provide theoretical methods and software tools to analyse process execution data, known as event logs. Although process mining was originally conceived to facilitate business process management activities, research studies have shown the benefit of leveraging process mining in healthcare contexts. However, applying process mining tools to analyse healthcare process execution data is not straightforward. In this paper, we show a methodology to: i) prepare general practice healthcare process data for conducting a process mining analysis; ii) select and apply suitable process mining solutions for successfully executing the analysis; and iii) extract valuable insights from the obtained results, alongside leads for traditional data mining analysis. By doing so, we identified two major challenges when using process mining solutions for analysing healthcare process data, and highlighted benefits and limitations of the state-of-the-art process mining techniques when dealing with highly variable processes and large data-sets. While we provide solutions to the identified challenges, the overarching goal of this study was to detect differences between the patients' health services utilization pattern observed in 2020-during the COVID-19 pandemic and mandatory lock-downs -and the one observed in the prior four years, 2016 to 2019. By using a combination of process mining techniques and traditional data mining, we were able to demonstrate that vaccinations in Victoria did not drop drastically-as other interactions did. On the contrary, we observed a surge of influenza and pneumococcus vaccinations in 2020, as opposed to other research findings of similar studies conducted in different geographical areas.


Subject(s)
COVID-19 , COVID-19/epidemiology , COVID-19/prevention & control , Communicable Disease Control , Data Mining/methods , Humans , Pandemics/prevention & control , Vaccination
18.
Elife ; 102021 11 23.
Article in English | MEDLINE | ID: covidwho-1622815

ABSTRACT

Background: Potential therapy and confounding factors including typical co-administered medications, patient's disease states, disease prevalence, patient demographics, medical histories, and reasons for prescribing a drug often are incomplete, conflicting, missing, or uncharacterized in spontaneous adverse drug event (ADE) reporting systems. These missing or incomplete features can affect and limit the application of quantitative methods in pharmacovigilance for meta-analyses of data during randomized clinical trials. Methods: Data from patients with hypertension were retrieved and integrated from the FDA Adverse Event Reporting System; 134 antihypertensive drugs out of 1131 drugs were filtered and then evaluated using the empirical Bayes geometric mean (EBGM) of the posterior distribution to build ADE-drug profiles with an emphasis on the pulmonary ADEs. Afterward, the graphical least absolute shrinkage and selection operator (GLASSO) captured drug associations based on pulmonary ADEs by correcting hidden factors and confounder misclassification. Selected drugs were then compared using the Friedman test in drug classes and clusters obtained from GLASSO. Results: Following multiple filtering stages to exclude insignificant and noise-driven reports, we found that drugs from antihypertensives agents, urologicals, and antithrombotic agents (macitentan, bosentan, epoprostenol, selexipag, sildenafil, tadalafil, and beraprost) form a similar class with a significantly higher incidence of pulmonary ADEs. Macitentan and bosentan were associated with 64% and 56% of pulmonary ADEs, respectively. Because these two medications are prescribed in diseases affecting pulmonary function and may be likely to emerge among the highest reported pulmonary ADEs, in fact, they serve to validate the methods utilized here. Conversely, doxazosin and rilmenidine were found to have the least pulmonary ADEs in selected drugs from hypertension patients. Nifedipine and candesartan were also found by signal detection methods to form a drug cluster, shown by several studies an effective combination of these drugs on lowering blood pressure and appeared an improved side effect profile in comparison with single-agent monotherapy. Conclusions: We consider pulmonary ADE profiles in multiple long-standing groups of therapeutics including antihypertensive agents, antithrombotic agents, beta-blocking agents, calcium channel blockers, or agents acting on the renin-angiotensin system, in patients with hypertension associated with high risk for coronavirus disease 2019 (COVID-19). We found that several individual drugs have significant differences between their drug classes and compared to other drug classes. For instance, macitentan and bosentan from endothelin receptor antagonists show major concern while doxazosin and rilmenidine exhibited the least pulmonary ADEs compared to the outcomes of other drugs. Using techniques in this study, we assessed and confirmed the hypothesis that drugs from the same drug class could have very different pulmonary ADE profiles affecting outcomes in acute respiratory illness. Funding: GJW and MJD accepted funding from BioNexus KC for funding on this project, but BioNexus KC had no direct role in this article.


Subject(s)
Antihypertensive Agents/adverse effects , COVID-19/complications , Data Mining/methods , Drug-Related Side Effects and Adverse Reactions , Hypertension/drug therapy , Pharmacovigilance , Adverse Drug Reaction Reporting Systems , Angiotensin-Converting Enzyme Inhibitors/adverse effects , Antihypertensive Agents/therapeutic use , Bayes Theorem , Calcium Channel Blockers/adverse effects , Fibrinolytic Agents/adverse effects , Humans , Hypertension/complications , SARS-CoV-2
19.
Sci Rep ; 11(1): 24491, 2021 12 29.
Article in English | MEDLINE | ID: covidwho-1591547

ABSTRACT

There is an ongoing need for scientific analysis to help governments and public health authorities make decisions regarding the COVID-19 pandemic. This article presents a methodology based on data mining that can offer support for coping with epidemic diseases. The methodological approach was applied in São Paulo, Rio de Janeiro and Manaus, the cities in Brazil with the most COVID-19 deaths until the first half of 2021. We aimed to predict the evolution of COVID-19 in metropolises and identify air quality and meteorological variables correlated with confirmed cases and deaths. The statistical analyses indicated the most important explanatory environmental variables, while the cluster analyses showed the potential best input variables for the forecasting models. The forecast models were built by two different algorithms and their results have been compared. The relationship between epidemiological and environmental variables was particular to each of the three cities studied. Low solar radiation periods predicted in Manaus can guide managers to likely increase deaths due to COVID-19. In São Paulo, an increase in the mortality rate can be indicated by drought periods. The developed models can predict new cases and deaths by COVID-19 in studied cities. Furthermore, the methodological approach can be applied in other cities and for other epidemic diseases.


Subject(s)
COVID-19/epidemiology , COVID-19/mortality , Data Mining/methods , Brazil/epidemiology , COVID-19/pathology , Cities/epidemiology , Epidemiological Models , Humans , Models, Theoretical , Morbidity , Pandemics/prevention & control , SARS-CoV-2/pathogenicity
20.
Int J Mol Sci ; 22(22)2021 Nov 12.
Article in English | MEDLINE | ID: covidwho-1534086

ABSTRACT

Transmembrane proteins (TMPs) play important roles in cells, ranging from transport processes and cell adhesion to communication. Many of these functions are mediated by intrinsically disordered regions (IDRs), flexible protein segments without a well-defined structure. Although a variety of prediction methods are available for predicting IDRs, their accuracy is very limited on TMPs due to their special physico-chemical properties. We prepared a dataset containing membrane proteins exclusively, using X-ray crystallography data. MemDis is a novel prediction method, utilizing convolutional neural network and long short-term memory networks for predicting disordered regions in TMPs. In addition to attributes commonly used in IDR predictors, we defined several TMP specific features to enhance the accuracy of our method further. MemDis achieved the highest prediction accuracy on TMP-specific dataset among other popular IDR prediction methods.


Subject(s)
Computational Biology/methods , Intrinsically Disordered Proteins/chemistry , Membrane Proteins/chemistry , Neural Networks, Computer , Amino Acid Sequence , Data Mining/methods , Databases, Protein/statistics & numerical data , Internet , Models, Molecular , Protein Conformation , Reproducibility of Results
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