Objectives In this study, we performed comparative genomic and transcriptomic analysis of clinical isolates of Mycobacterium tuberculosis collected from patients with drug-susceptible tuberculosis (DS-TB). The clinical isolates were categorized based on treatment duration: standard 6 months or >6 months.
Methods Study participants were recruited from a 2016 to 2018 tuberculosis cohort, and clinical M. tuberculosis isolates were collected from the sputum of patients with tuberculosis. We analyzed the genome and transcriptome of the isolated M. tuberculosis.
Results Genomic analysis revealed a specific non-synonymous single-nucleotide polymorphism in pe_pgrs9 and ppe34, exclusive to the group treated for >6 months. Transcriptomic analysis revealed increased expression of various virulence-associated protein family genes and decreased expression of ribosomal protein genes and ppe38 genes in the group treated for >6 months.
Conclusion The identified genetic variation and gene expression patterns may influence treatment outcomes by modulating host immune responses, increasing virulence, and potentially contributing to persister cell formation in M. tuberculosis. This study provides insights into the genetic and transcriptomic factors associated with prolonged DS-TB treatment. However, our study identified molecular characteristics using a small sample size, and further detailed studies are warranted.
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Transcriptomic and genomic analysis of successful Ethiopian Mycobacterium tuberculosis sub-lineage 4.2.2.2 reveals differential expression of DosR-regulated genes Tesfaye Gebreyohannis Hailemariam, Abaysew Ayele, Tesfaye Gelanew, Michael Brennan, Kayleigh Floyd, Zemedkun Abebe Debella, Workineh Shibeshi, Kidist Bobosha, Yonas K. Hirutu, Simon J. Waddell, Ephrem Engidawork Scientific Reports.2026;[Epub] CrossRef
RNA extraction and RNA-sequencing method for transcriptomic analysis of
Mycobacterium tuberculosis
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Objectives This study aimed to comprehensively outline the methodological approaches used in published research comparing the vaccine effectiveness (VE) of coronavirus disease 2019 (COVID-19) vaccines.
Methods A systematic search was conducted on June 13, 2024, to identify comparative studies evaluating the effectiveness of mRNA versus non-mRNA and monovalent versus bivalent COVID-19 vaccines. We screened titles, abstracts, and full texts, collecting data on publication year, country, sample size, study population composition, study design, VE estimates, outcomes, and covariates. Studies that reported relative VE (rVE) were analyzed separately from those that did not.
Results We identified 25 articles comparing rVE between mRNA and non-mRNA COVID-19 vaccines, as well as between monovalent and bivalent formulations. Among the studies assessing VE by vaccine type, 126 did not provide rVE estimates. Comparative VE studies frequently employed retrospective cohort designs. Among the definitions of rVE used, the most common were hazard ratio and absolute VE, calculated as (1−odds ratio)×100. Studies were most frequently conducted in the United Kingdom and the United States, and the most common outcome was infection. Most targeted the general population and assessed the VE of mRNA vaccines using the AstraZeneca vaccine as a reference. A small proportion, 7.3% (n=11), did not adjust for any variables. Only 3 studies (2.0%) adjusted for all core confounding variables recommended by the World Health Organization.
Conclusion Few comparative studies of COVID-19 vaccines have incorporated rVE methodologies. Reporting rVE and employing a consistent set of covariates can broaden our understanding of COVID-19 vaccines.
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Objectives Breast cancer poses a significant global health challenge, characterized by complex origins and the potential for life-threatening metastasis. The critical need for early and accurate detection is underscored by the 685,000 lives claimed by the disease worldwide in 2020. Deep learning has made strides in advancing the prompt diagnosis of breast cancer. However, obstacles persist, such as dealing with high-dimensional data and the risk of overfitting, necessitating fresh approaches to improve accuracy and real-world applicability.
Methods In response to these challenges, we propose BCED-Net, which stands for Breast Cancer Ensemble Diagnosis Network. This innovative framework leverages transfer learning and the extreme gradient boosting (XGBoost) classifier on the Breast Cancer RSNA dataset. Our methodology involved feature extraction using pre-trained models—namely, Resnet50, EfficientnetB3, VGG19, Densenet121, and ConvNeXtTiny—followed by the concatenation of the extracted features. Our most promising configuration combined features extracted from deep convolutional neural networks—namely Resnet50, EfficientnetB3, and ConvNeXtTiny—that were classified using the XGBoost classifier.
Results The ensemble approach demonstrated strong overall performance with an accuracy of 0.89. The precision, recall, and F1-score values, which were all at 0.86, highlight a balanced trade-off between correctly identified positive instances and the ability to capture all actual positive samples.
Conclusion BCED-Net represents a significant leap forward in addressing persistent issues such as the high dimensionality of features and the risk of overfitting.
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Objectives This study aimed to summarize the results of coronavirus disease 2019 (COVID-19) risk assessments and to examine the associations between risk levels and various indicators, including COVID-19 incidence, risk perception, community mobility, and government policy.
Methods The results of the risk assessment and the indicators utilized were summarized. From November 2021 to May 2022, the COVID-19 risk level was evaluated on a weekly basis, and its correlation with these indicators was analyzed. Data were obtained from press releases by the Korea Disease Control and Prevention Agency, regular surveys conducted by Hankook Research, and information available on the Google and Oxford websites.
Results Weekly risk assessments were conducted for 30 weeks, using different indices depending on the phases. Correlation analysis revealed the strongest positive correlation between risk level and risk perception (r=0.841). The risk level from “1-week lead” demonstrated a strong positive correlation with the time-varying reproduction number (Rt). Similarly, the risk level from “week lagged value” showed a strong positive correlation with the number of severe cases in the hospital.
Conclusion At the time of risk assessment, the Rt precedes the risk level, while severe cases in hospitals follow. Therefore, the assessed risk level functioned as an early warning system. Risk perception demonstrated the strongest correlation with the risk level, suggesting consistency throughout the assessment period. Contextual indicators (e.g., risk perception) that consider time lags and implementation scales, could improve the evaluation of future risk assessment results, particularly when there are challenges in reflecting specific situations in coordinated emergency response.
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Objectives Despite effective vaccination strategies, measles remains a global public health challenge. The study explored individual and contextual factors associated with measles infection in Malaysia from 2018 to 2022, informing the development of targeted public health interventions. Methods: This cross-sectional study utilised data from the Ministry of Health, the Department of Statistics, and the Department of Environment Malaysia. Multilevel logistic regression analysis was employed to examine individual-level factors, including age, sex, ethnicity, nationality, contact history, travel history, and vaccination status. Concurrently, contextual factors were assessed, encompassing district-level determinants such as population density, median household income, urbanisation, the number of health and rural clinics, vaccination rates, fine particulate matter less than 2.5 μm (PM2.5) levels, relative humidity, and temperature, to determine their impact on measles infection risk. Results: Measles infection was significantly associated with various individual factors. These included age (adjusted odds ratio [aOR], 1.02; 95% confidence interval [CI], 1.02–1.03), ethnicity, non-Malaysian nationality (aOR, 34.53; 95% CI, 8.42– 141.51), prior contact with a measles case (aOR, 2.36; 95% CI, 2.07–2.69), travel history (aOR, 2.30; 95% CI, 1.13–4.70), and vaccination status (aOR, 0.76; 95% CI, 0.72–0.79). Among contextual factors, urbanisation (aOR, 1.56; 95% CI, 1.16– 2.10) and the number of clinics (aOR, 0.98; 95% CI, 0.97–0.99) were significant determinants. Conclusion: This multilevel logistic regression analysis illuminates the complexities of measles transmission, advocating public health interventions tailored to individual and contextual vulnerabilities. The findings highlight the need for a synergistic approach that combines vaccination campaigns, healthcare accessibility improvements, and socioeconomic interventions to effectively combat measles.
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Objectives The onset of common mental disorders (CMDs) is most prevalent among youth; thus, mental health management is crucial. We examined differences in risk and risk factor determinants regarding CMDs prevalence among youth in rural and urban Indonesia. Methods: This cross-sectional study utilized data from the 2018 Indonesia National Health Survey. The population comprised 122,114 respondents, aged 15 to 24 years, who had completed the 20-item Self-Report Questionnaire along with providing demographic and health behavior data. Chi-square testing and logistic regression were employed for analysis. Results: The CMDs risk was higher among urban than rural youth. Risk factors impacting both populations included being female, having a lower education level, consuming fewer than 7 portions of vegetables weekly, smoking, and drinking alcohol (p<0.05). Consuming under 7 portions of fruit weekly and being in the highest or lowest wealth quintile were significant risk factors only in urban youth, while unemployment and divorce were significant only among rural respondents (p<0.05). Marriage was protective against CMDs among rural participants. Conclusion: Being male, possessing a college degree, consuming at least 7 portions of vegetables weekly, not smoking, and not consuming alcohol were associated with reduced CMDs risk in urban and rural youth. Among rural youth, marriage and employment were linked to decreased risk, whereas divorce displayed the opposite relationship. In urban populations, consuming at least 7 portions of fruit weekly and belonging to neither the highest nor the lowest economic quintile were protective factors. Management strategies for CMDs in young people must address these considerations.
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Objectives Social activities are important and influential factors for healthy aging. However, limited information is available regarding the associations of the type and intensity of social participation with health and well-being. This study aimed to investigate how various types of social activities are associated with several dimensions of health outcomes. Methods: This cross-sectional study utilized data from the Seventh Korean Longitudinal Study of Aging, which included 5,526 adults aged 60 years and older. Multivariate linear regression analysis was employed to analyze the associations of social activities with depression, self-rated health, and life satisfaction. Additionally, subgroup analyses by sex and age were performed. Results: Among the participants, 73.5% reported involvement in at least 1 of the 4 types of social engagement. After adjustment for all covariates, individuals who participated in any social activity reported better self-rated health and higher life satisfaction compared to those who did not participate. However, the intensity of engagement in different social activities had varying impacts on subjective health outcomes. An increased level of participation was associated with a lower rate of depression and improved self-rated health. However, no significant differences were observed in the relationship between the intensity of participation in activities (with the exception of alumni societies or family councils) and life satisfaction. Conclusion: This study suggests that to improve their health, older adults in the Republic of Korea should not only engage in social activities but also do so actively and regularly.
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