JMIR bioinformatics and biotechnology最新文献

Background: The emergence of SARS-CoV-2 variants with mutations associated with increased transmissibility and virulence is a public health concern in Ontario, Canada. Characterizing how the mutational patterns of the SARS-CoV-2 genome have changed over time can shed light on the driving factors, including selection for increased fitness and host immune response, that may contribute to the emergence of novel variants. Moreover, the study of SARS-CoV-2 in the microcosm of Ontario, Canada can reveal how different province-specific public health policies over time may be associated with observed mutational patterns as a model system.

Objective: This study aimed to perform a comprehensive analysis of single base substitution (SBS) types, counts, and genomic locations observed in SARS-CoV-2 genomic sequences sampled in Ontario, Canada. Comparisons of mutational patterns were conducted between sequences sampled during 4 different epochs delimited by major public health events to track the evolution of the SARS-CoV-2 mutational landscape over 2 years.

Methods: In total, 24,244 SARS-CoV-2 genomic sequences and associated metadata sampled in Ontario, Canada from January 1, 2020, to December 31, 2021, were retrieved from the Global Initiative on Sharing All Influenza Data database. Sequences were assigned to 4 epochs delimited by major public health events based on the sampling date. SBSs from each SARS-CoV-2 sequence were identified relative to the MN996528.1 reference genome. Catalogues of SBS types and counts were generated to estimate the impact of selection in each open reading frame, and identify mutation clusters. The estimation of mutational fitness over time was performed using the Augur pipeline.

Results: The biases in SBS types and proportions observed support previous reports of host antiviral defense activity involving the SARS-CoV-2 genome. There was an increase in U>C substitutions associated with adenosine deaminase acting on RNA (ADAR) activity uniquely observed during Epoch 4. The burden of novel SBSs observed in SARS-CoV-2 genomic sequences was the greatest in Epoch 2 (median 5), followed by Epoch 3 (median 4). Clusters of SBSs were observed in the spike protein open reading frame, ORF1a, and ORF3a. The high proportion of nonsynonymous SBSs and increasing dN/dS metric (ratio of nonsynonymous to synonymous mutations in a given open reading frame) to above 1 in Epoch 4 indicate positive selection of the spike protein open reading frame.

Conclusions: Quantitative analysis of the mutational patterns of the SARS-CoV-2 genome in the microcosm of Ontario, Canada within early consecutive epochs of the pandemic tracked the mutational dynamics in the context of public health events that instigate significant shifts in selection and mutagenesis. Continued genomic surveillance of emergent variants will be useful for the design of public he

Background: The autonomic nervous system (ANS) plays a central role in pregnancy-induced adaptations, and failure in the required adaptations is associated with adverse neonatal and maternal outcomes. Mapping maternal ANS function in healthy pregnancy may help to understand ANS function.

Objective: This study aimed to systematically review studies on the use of heart rate variability (HRV) monitoring to measure ANS function during pregnancy and determine whether specific HRV patterns representing normal ANS function have been identified during pregnancy.

Methods: The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guideline was used to guide the systematic review. The CINAHL, PubMed, SCOPUS, and Web of Science databases were searched to comprehensively identify articles without a time span limitation. Studies were included if they assessed HRV in healthy pregnant individuals at least once during pregnancy or labor, with or without a comparison group (eg, complicated pregnancy). Quality assessment of the included literature was performed using the National Heart, Lung, and Blood Institute (NHLBI) tool. A narrative synthesis approach was used for data extraction and analysis, as the articles were heterogenous in scope, approaches, methods, and variables assessed, which precluded traditional meta-analysis approaches being used.

Results: After full screening, 8 studies met the inclusion criteria. In 88% (7/8) of the studies, HRV was measured using electrocardiogram and operationalized in 3 different ways: linear frequency domain (FD), linear time domain (TD), and nonlinear methods. FD was measured in all (8/8), TD in 75% (6/8), and nonlinear methods in 25% (2/8) of the studies. The assessment duration varied from 5 minutes to 24 hours. TD indexes and most of the FD indexes decreased from the first to the third trimesters in the majority (5/7, 71%) of the studies. Of the FD indexes, low frequency (LF [nu]) and the LF/high frequency (HF) ratio showed an ascending trend from early to late pregnancy, indicating an increase in sympathetic activity toward the end of the pregnancy.

Conclusions: We identified 3 HRV operationalization methods along with potentially indicative HRV patterns. However, we found no justification for the selection of measurement tools, measurement time frames, and operationalization methods, which threaten the generalizability and reliability of pattern findings. More research is needed to determine the criteria and methods for determining HRV patterns corresponding to ANS functioning in healthy pregnant persons.

Background: Chronic kidney disease is a major public health issue, with about 13% of the general adult population and 30% of the elderly affected. Patients in the last stage of this disease have an almost uniquely high risk of death and cardiovascular events, with reduced adherence to therapy representing an additional risk factor for cardiovascular morbidity and mortality. Considering the increased penetration of mobile phones, a mobile app could educate patients to autonomously monitor cardiorenal risk factors.

Objective: With this background in mind, we developed an integrated system of a server and app with the aim of improving self-monitoring of cardiovascular and renal risk factors and adherence to therapy.

Methods: The software infrastructure for both the Smit-CKD server and Smit-CKD app was developed using standard web-oriented development methodologies preferring open source tools when available. To make the Smit-CKD app suitable for Android and iOS, platforms that allow the development of a multiplatform app starting from a single source code were used. The integrated system was field tested with the help of 22 participants. User satisfaction and adherence to therapy were measured by questionnaires specifically designed for this study; regular use of the app was measured using the daily reports available on the platform.

Results: The Smit-CKD app allows the monitoring of cardiorenal risk factors, such as blood pressure, weight, and blood glucose. Collected data are transmitted in real time to the referring general practitioner. In addition, special reminders improve adherence to the medication regimen. Via the Smit-CKD server, general practitioners can monitor the clinical status of their patients and their adherence to therapy. During the test phase, 73% (16/22) of subjects entered all the required data regularly and sent feedback on drug intake. After 6 months of use, the percentage of regular intake of medications rose from 64% (14/22) to 82% (18/22). Analysis of the evaluation questionnaires showed that both the app and server components were well accepted by the users.

Conclusions: Our study demonstrated that a simple mobile app, created to self-monitor modifiable cardiorenal risk factors and adherence to therapy, is well tolerated by patients affected by chronic kidney disease. Further studies are required to clarify if the use of this integrated system will have long-term effects on therapy adherence and if self-monitoring of risk factors will improve clinical outcomes in this population.

Background: The mammalian immune system is able to generate antibodies against a huge variety of antigens, including bacteria, viruses, and toxins. The ultradeep DNA sequencing of rearranged immunoglobulin genes has considerable potential in furthering our understanding of the immune response, but it is limited by the lack of a high-throughput, sequence-based method for predicting the antigen(s) that a given immunoglobulin recognizes.

Objective: As a step toward the prediction of antibody-antigen binding from sequence data alone, we aimed to compare a range of machine learning approaches that were applied to a collated data set of antibody-antigen pairs in order to predict antibody-antigen binding from sequence data.

Methods: Data for training and testing were extracted from the Protein Data Bank and the Coronavirus Antibody Database, and additional antibody-antigen pair data were generated by using a molecular docking protocol. Several machine learning methods, including the weighted nearest neighbor method, the nearest neighbor method with the BLOSUM62 matrix, and the random forest method, were applied to the problem.

Results: The final data set contained 1157 antibodies and 57 antigens that were combined in 5041 antibody-antigen pairs. The best performance for the prediction of interactions was obtained by using the nearest neighbor method with the BLOSUM62 matrix, which resulted in around 82% accuracy on the full data set. These results provide a useful frame of reference, as well as protocols and considerations, for machine learning and data set creation in the prediction of antibody-antigen binding.

Conclusions: Several machine learning approaches were compared to predict antibody-antigen interaction from protein sequences. Both the data set (in CSV format) and the machine learning program (coded in Python) are freely available for download on GitHub.

Background: The COVID-19 pandemic is becoming one of the largest, unprecedented health crises, and chest X-ray radiography (CXR) plays a vital role in diagnosing COVID-19. However, extracting and finding useful image features from CXRs demand a heavy workload for radiologists.

Objective: The aim of this study was to design a novel multiple-inputs (MI) convolutional neural network (CNN) for the classification of COVID-19 and extraction of critical regions from CXRs. We also investigated the effect of the number of inputs on the performance of our new MI-CNN model.

Methods: A total of 6205 CXR images (including 3021 COVID-19 CXRs and 3184 normal CXRs) were used to test our MI-CNN models. CXRs could be evenly segmented into different numbers (2, 4, and 16) of individual regions. Each region could individually serve as one of the MI-CNN inputs. The CNN features of these MI-CNN inputs would then be fused for COVID-19 classification. More importantly, the contributions of each CXR region could be evaluated through assessing the number of images that were accurately classified by their corresponding regions in the testing data sets.

Results: In both the whole-image and left- and right-lung region of interest (LR-ROI) data sets, MI-CNNs demonstrated good efficiency for COVID-19 classification. In particular, MI-CNNs with more inputs (2-, 4-, and 16-input MI-CNNs) had better efficiency in recognizing COVID-19 CXRs than the 1-input CNN. Compared to the whole-image data sets, the efficiency of LR-ROI data sets showed approximately 4% lower accuracy, sensitivity, specificity, and precision (over 91%). In considering the contributions of each region, one of the possible reasons for this reduced performance was that nonlung regions (eg, region 16) provided false-positive contributions to COVID-19 classification. The MI-CNN with the LR-ROI data set could provide a more accurate evaluation of the contribution of each region and COVID-19 classification. Additionally, the right-lung regions had higher contributions to the classification of COVID-19 CXRs, whereas the left-lung regions had higher contributions to identifying normal CXRs.

Conclusions: Overall, MI-CNNs could achieve higher accuracy with an increasing number of inputs (eg, 16-input MI-CNN). This approach could assist radiologists in identifying COVID-19 CXRs and in screening the critical regions related to COVID-19 classifications.

Background: Treatment discontinuation (TD) is one of the major prognostic issues in diabetes care, and several models have been proposed to predict a missed appointment that may lead to TD in patients with diabetes by using binary classification models for the early detection of TD and for providing intervention support for patients. However, as binary classification models output the probability of a missed appointment occurring within a predetermined period, they are limited in their ability to estimate the magnitude of TD risk in patients with inconsistent intervals between appointments, making it difficult to prioritize patients for whom intervention support should be provided.

Objective: This study aimed to develop a machine-learned prediction model that can output a TD risk score defined by the length of time until TD and prioritize patients for intervention according to their TD risk.

Methods: This model included patients with diagnostic codes indicative of diabetes at the University of Tokyo Hospital between September 3, 2012, and May 17, 2014. The model was internally validated with patients from the same hospital from May 18, 2014, to January 29, 2016. The data used in this study included 7551 patients who visited the hospital after January 1, 2004, and had diagnostic codes indicative of diabetes. In particular, data that were recorded in the electronic medical records between September 3, 2012, and January 29, 2016, were used. The main outcome was the TD of a patient, which was defined as missing a scheduled clinical appointment and having no hospital visits within 3 times the average number of days between the visits of the patient and within 60 days. The TD risk score was calculated by using the parameters derived from the machine-learned ranking model. The prediction capacity was evaluated by using test data with the C-index for the performance of ranking patients, area under the receiver operating characteristic curve, and area under the precision-recall curve for discrimination, in addition to a calibration plot.

Results: The means (95% confidence limits) of the C-index, area under the receiver operating characteristic curve, and area under the precision-recall curve for the TD risk score were 0.749 (0.655, 0.823), 0.758 (0.649, 0.857), and 0.713 (0.554, 0.841), respectively. The observed and predicted probabilities were correlated with the calibration plots.

Conclusions: A TD risk score was developed for patients with diabetes by combining a machine-learned method with electronic medical records. The score calculation can be integrated into medical records to identify patients at high risk of TD, which would be useful in supporting diabetes care and preventing TD.

Background: Since the start of the COVID-19 pandemic, health policymakers globally have been attempting to predict an impending wave of COVID-19. India experienced a devastating second wave of COVID-19 in the late first week of May 2021. We retrospectively analyzed the viral genomic sequences and epidemiological data reflecting the emergence and spread of the second wave of COVID-19 in India to construct a prediction model.

Objective: We aimed to develop a bioinformatics tool that can predict an impending COVID-19 wave.

Methods: We analyzed the time series distribution of genomic sequence data for SARS-CoV-2 and correlated it with epidemiological data for new cases and deaths for the corresponding period of the second wave. In addition, we analyzed the phylodynamics of circulating SARS-CoV-2 variants in the Indian population during the study period.

Results: Our prediction analysis showed that the first signs of the arrival of the second wave could be seen by the end of January 2021, about 2 months before its peak in May 2021. By the end of March 2021, it was distinct. B.1.617 lineage variants powered the wave, most notably B.1.617.2 (Delta variant).

Conclusions: Based on the observations of this study, we propose that genomic surveillance of SARS-CoV-2 variants, complemented with epidemiological data, can be a promising tool to predict impending COVID-19 waves.

Background: In recent years, thanks to the rapid development of next-generation sequencing (NGS) technology, an entire human genome can be sequenced in a short period. As a result, NGS technology is now being widely introduced into clinical diagnosis practice, especially for diagnosis of hereditary disorders. Although the exome data of single-nucleotide variant (SNV) can be generated using these approaches, processing the DNA sequence data of a patient requires multiple tools and complex bioinformatics pipelines.

Objective: This study aims to assist physicians to automatically interpret the genetic variation information generated by NGS in a short period. To determine the true causal variants of a patient with genetic disease, currently, physicians often need to view numerous features on every variant manually and search for literature in different databases to understand the effect of genetic variation.

Methods: We constructed a machine learning model for predicting disease-causing variants in exome data. We collected sequencing data from whole-exome sequencing (WES) and gene panel as training set, and then integrated variant annotations from multiple genetic databases for model training. The model built ranked SNVs and output the most possible disease-causing candidates. For model testing, we collected WES data from 108 patients with rare genetic disorders in National Taiwan University Hospital. We applied sequencing data and phenotypic information automatically extracted by a keyword extraction tool from patient's electronic medical records into our machine learning model.

Results: We succeeded in locating 92.5% (124/134) of the causative variant in the top 10 ranking list among an average of 741 candidate variants per person after filtering. AI Variant Prioritizer was able to assign the target gene to the top rank for around 61.1% (66/108) of the patients, followed by Variant Prioritizer, which assigned it for 44.4% (48/108) of the patients. The cumulative rank result revealed that our AI Variant Prioritizer has the highest accuracy at ranks 1, 5, 10, and 20. It also shows that AI Variant Prioritizer presents better performance than other tools. After adopting the Human Phenotype Ontology (HPO) terms by looking up the databases, the top 10 ranking list can be increased to 93.5% (101/108).

Conclusions: We successfully applied sequencing data from WES and free-text phenotypic information of patient's disease automatically extracted by the keyword extraction tool for model training and testing. By interpreting our model, we identified which features of variants are important. Besides, we achieved a satisfactory result on finding the target variant in our testing data set. After adopting the HPO terms by looking up the databases, the top 10 ranking list can be increased to 93.5% (101/108). The performance of the model is similar to that

Background: Emergency department crowding continues to threaten patient safety and cause poor patient outcomes. Prior models designed to predict hospital admission have had biases. Predictive models that successfully estimate the probability of patient hospital admission would be useful in reducing or preventing emergency department "boarding" and hospital "exit block" and would reduce emergency department crowding by initiating earlier hospital admission and avoiding protracted bed procurement processes.

Objective: To develop a model to predict imminent adult patient hospital admission from the emergency department early in the patient visit by utilizing existing clinical descriptors (ie, patient biomarkers) that are routinely collected at triage and captured in the hospital's electronic medical records. Biomarkers are advantageous for modeling due to their early and routine collection at triage; instantaneous availability; standardized definition, measurement, and interpretation; and their freedom from the confines of patient histories (ie, they are not affected by inaccurate patient reports on medical history, unavailable reports, or delayed report retrieval).

Methods: This retrospective cohort study evaluated 1 year of consecutive data events among adult patients admitted to the emergency department and developed an algorithm that predicted which patients would require imminent hospital admission. Eight predictor variables were evaluated for their roles in the outcome of the patient emergency department visit. Logistic regression was used to model the study data.

Results: The 8-predictor model included the following biomarkers: age, systolic blood pressure, diastolic blood pressure, heart rate, respiration rate, temperature, gender, and acuity level. The model used these biomarkers to identify emergency department patients who required hospital admission. Our model performed well, with good agreement between observed and predicted admissions, indicating a well-fitting and well-calibrated model that showed good ability to discriminate between patients who would and would not be admitted.

Conclusions: This prediction model based on primary data identified emergency department patients with an increased risk of hospital admission. This actionable information can be used to improve patient care and hospital operations, especially by reducing emergency department crowding by looking ahead to predict which patients are likely to be admitted following triage, thereby providing needed information to initiate the complex admission and bed assignment processes much earlier in the care continuum.

Background: Hashimoto thyroiditis (HT) is an autoimmune thyroid disease and the leading cause of hypothyroidism in areas with sufficient iodine intake. The quality-of-life impact and financial burden of hypothyroidism and HT highlight the need for additional research investigating the disease etiology with the aim of revealing potential modifiable risk factors.

Objective: Implementation of measures against such risk factors, once identified, has the potential to lessen the financial burden while also improving the quality of life of many individuals. Therefore, we aimed to examine the potential seasonality of HT in Europe using the Google Trends data to explore whether there is a seasonal characteristic of Google searches regarding HT, examine the potential impact of the countries' geographic location on the potential seasonality, and identify potential modifiable risk factors for HT, thereby inspiring future research on the topic.

Methods: Monthly Google Trends data on the search topic "Hashimoto thyroiditis" were retrieved in a 17-year time frame from January 2004 to December 2020 for 36 European countries. A cosinor model analysis was conducted to evaluate potential seasonality. Simple linear regression was used to estimate the potential effect of latitude and longitude on seasonal amplitude and phase of the model outputs.

Results: Of 36 included European countries, significant seasonality was observed in 30 (83%) countries. Most phase peaks occurred in spring (14/30, 46.7%) and winter (8/30, 26.7%). A statistically significant effect was observed regarding the effect of geographical latitude on cosinor model amplitude (y = -3.23 + 0.13 x; R²=0.29; P=.002). Seasonal increases in HT search volume may therefore be a consequence of an increased incidence or higher disease activity. It is particularly interesting that in most countries, a seasonal peak occurred in spring and winter months; when viewed in the context of the statistically significant impact of geographical latitude on seasonality amplitude, this may indicate the potential role of vitamin D levels in the seasonality of HT.

Conclusions: Significant seasonality of HT Google Trends search volume was observed in our study, with seasonal peaks in most countries occurring in spring and winter and with a significant impact of latitude on seasonality amplitude. Further studies on the topic of seasonality in HT and factors impacting it are required.