Tag: pubmed

Environ Microbiome. 2025 May 5;20(1):47. doi: 10.1186/s40793-025-00704-7.

ABSTRACT

INTRODUCTION: Metagenomics, the genomic analysis of all species present within a mixed population, is an important tool used for the exploration of microbiomes in clinical and environmental microbiology. Whilst the development of next-generation sequencing, and more recently third generation long-read approaches such as nanopore sequencing, have greatly advanced the study of metagenomics, recovery of unbiased material from microbial populations remains challenging. One promising advancement in genomic sequencing from Oxford Nanopore Technologies (ONT) is adaptive sampling, which enables real-time enrichment or depletion of target sequences. As sequencing technologies continue to develop, and advances such as adaptive sampling become common techniques within the microbiological toolkit, it is essential to evaluate the benefits of such advancements to metagenomic studies, and the impact of methodological choices on research outcomes.

AIM AND METHODS: Given the rapid development of sequencing tools and chemistry, this study aimed to demonstrate the impacts of choice of DNA extraction kit and sequencing chemistry on downstream metagenomic analyses. We first explored the quality and accuracy of 16S rRNA amplicon sequencing for DNA extracted from the ZymoBIOMICS Microbial Community Standard, using a range of commercially available DNA extraction kits to understand the effects of different kit biases on assessment of microbiome composition. We next compared the quality and accuracy of metagenomic analyses for two nanopore-based ligation chemistry kits with differing levels of base-calling error; the older and more error-prone (~ 97% accuracy) LSK109 chemistry, and newer more accurate (~ 99% accuracy) LSK112 Q20 + chemistry. Finally, we assessed the impact of the nanopore sequencing chemistry version on the output of the novel adaptive sampling approach for real-time enrichment of the genome for the yeast Saccharomyces cerevisiae from the microbial community.

RESULTS: Firstly, DNA extraction kit methodology impacted the composition of the yield, with mechanical bead-beating methodologies providing the least biased picture due to efficient lysis of Gram-positive microbes present in the community standard, with differences in bead-beating methodologies also producing variation in composition. Secondly, whilst use of the Q20 + nanopore sequencing kit chemistry improved the base-calling data quality, the resulting metagenomic assemblies were not significantly improved based on common metrics and assembly statistics. Most importantly, we demonstrated the effective application of adaptive sampling for enriching a low-abundance genome within a metagenomic sample. This resulted in a 5-7-fold increase in target enrichment compared to non-adaptive sequencing, despite a reduction in overall sequencing throughput due to strand-rejection processes. Interestingly, no significant differences in adaptive sampling enrichment efficiency were observed between the older and newer ONT sequencing chemistries, suggesting that adaptive sampling performs consistently across different library preparation kits.

CONCLUSION: Our findings underscore the importance of selecting a DNA extraction methodology that minimises bias to ensure an accurate representation of microbial diversity in metagenomic studies. Additionally, despite the improved base-calling accuracy provided by newer Q20 + sequencing chemistry, we demonstrate that even older ONT sequencing chemistries can achieve reliable metagenomic sequencing results, enabling researchers to confidently use these approaches depending on their specific experimental needs. Critically, we highlight the significant potential of ONT’s adaptive sampling technology for targeted enrichment of specific genomes within metagenomic samples. This approach offers broad applicability for enriching target organisms or genetic elements (e.g., pathogens or plasmids) or depleting unwanted DNA (e.g., host DNA) in diverse sample types from environmental and clinical studies. However, researchers should carefully weigh the benefits of adaptive sampling against the potential trade-offs in sequencing throughput, particularly for low-abundance targets, where strand rejection can lead to pore blocking. These results provide valuable guidance for optimising adaptive sampling in metagenomic workflows to achieve specific research objectives.

PMID:40325409 | DOI:10.1186/s40793-025-00704-7

BMC Public Health. 2025 May 5;25(1):1654. doi: 10.1186/s12889-025-22923-w.

ABSTRACT

BACKGROUND: People with disabilities (PWD) may be more vulnerable to the adverse health effects of air pollution than the general population. This study examined the association between long-term exposure to ambient fine particulate matter (PM_2.5) and mortality risk in PWD considering disability type and severity.

METHODS: Data from the Korean National Health Insurance Service and Statistics Korea were analyzed in this retrospective cohort study, including 2,880,265 individuals (41,501,709 person-years), of which 176,410 were PWD (2,011,231 person-years). PM_2.5 exposure was estimated using simulated data from 2006 to 2019. Causes of death included all causes, non-accidental causes, respiratory disease, lung cancer, and cardiovascular disease. Cox proportional hazard models were used to estimate hazard ratios (HRs) for mortality associated with PM_2.5 stratified by disability type and severity.

RESULTS: PWD, particularly those with severe disabilities or specific impairments such as kidney problems or brain lesions, showed significantly high mortality risks from all causes, non-accidental causes, and cardiovascular diseases due to PM_2.5 exposure. For individuals with kidney impairment, the HR (95% confidence interval) for mortality on increasing PM_2.5 by 10 µg/m³ was 1.79 (1.27-2.52) from all causes, while for those with brain lesions, it was 1.10 (1.00-1.22) from cardiovascular disease. PWD were not susceptible to mortality from respiratory causes.

CONCLUSIONS: This study highlights the increased vulnerability of PWD, especially those with severe disabilities or specific impairments, to the adverse effects of PM_2.5 exposure. Targeted interventions tailored to disability type and severity, along with stricter air quality standards and specialized healthcare approaches, are needed.

PMID:40325394 | DOI:10.1186/s12889-025-22923-w

BMC Med Educ. 2025 May 5;25(1):648. doi: 10.1186/s12909-025-07029-6.

ABSTRACT

The aim of this study was to introduce and validate an Objective Structured Clinical Examination (OSCE) as a robust assessment tool for evaluating clinical skills in audiology among third-year audiology and speech-language students. Drawing on guidelines for OSCE development, key competencies and clinical skills in audiology were identified through expert consultation. Four OSCE stations were designed comprising one theoretical and three practical stations covering essential clinical tasks. Content validity was measured using the Content Validity Coefficient (CVC), while inter-rater reliability was assessed using the Kappa coefficient and Intraclass Correlation Coefficient (ICC). The study involved 33 audiology students and eight audiologist expert evaluators. The study demonstrated high content validity of the OSCE, with CVC scores ranging from 0.97 to 1 across all stations. Inter-rater reliability analysis revealed substantial to almost perfect agreement among evaluators, with ICC values ranging from 0.94 to 0.99. Comparison of scores between evaluators revealed minimal statistically significant differences, indicating overall consistency in assessment. The results provide substantial evidence supporting the content validity, inter-rater agreement, and reliability of the Objective Structured Clinical Examination (OSCE) as an effective tool for assessing the clinical skills of audiology and speech-language pathology students in the area of audiology.

PMID:40325386 | DOI:10.1186/s12909-025-07029-6

Int J Equity Health. 2025 May 5;24(1):120. doi: 10.1186/s12939-025-02492-5.

ABSTRACT

BACKGROUND: HIV care continuum engagement is inadequate among African American/Black and Latine (AABL) young/emerging adults living with HIV in the United States. Within this population, some subgroups face barriers to research and are under-studied. Grounded in social action theory, the present study focuses on a diverse community-recruited cohort including those with non-suppressed HIV viral load. Using a sequential explanatory mixed methods design, we describe contextual self-regulatory resources (e.g., substance use, mental health), and their relationships to HIV management.

METHODS: Participants (N = 271) engaged in structured baseline assessments and biomarker testing (HIV viral load, drug screening). Being well-engaged in HIV care and HIV viral suppression were the primary outcomes. We purposively sampled a subset for maximum variability for in-depth interviews (N = 41). Quantitative data were analyzed via descriptive statistics and logistic regression, and results were used to develop qualitative research questions. Then, qualitative data were analyzed via directed content analysis. The joint display method was used to integrate results.

RESULTS: Participants’ mean age was 25 years (SD = 2). The majority (59%) were Latine/Hispanic and 41% were African American/Black. Nearly all were assigned male sex at birth (96%) and identified as gay/bisexual/queer (93%). The average HIV diagnosis was 4 years prior (SD = 3). The majority were well-engaged in HIV care (72%) and evidenced viral suppression (81%). Substance use (tobacco, marijuana, alcohol) was prevalent, mainly at low- and moderate-risk levels. Drug screening indicated marijuana, methamphetamine, and MDMA were the most common recent substances. Symptoms of depression and PTSD were associated with decreased odds of engagement in care. High-risk cannabis use was associated with decreased odds of HIV viral suppression. Qualitative results highlighted the prevalence of substance use in social networks and venues, and the importance of substances as a coping strategy, including for mental health distress. Tobacco and methamphetamine (but not marijuana) were described as problematic, and marijuana was used as harm reduction. Substance use was more common among those with non-suppressed versus suppressed HIV viral load. However, overall, substance use did not commonly interfere substantially with HIV management.

CONCLUSIONS: The present study advances knowledge on AABL young/emerging adults living with HIV and highlights ways to improve screening and services.

PMID:40325383 | DOI:10.1186/s12939-025-02492-5

BMC Med Imaging. 2025 May 5;25(1):152. doi: 10.1186/s12880-025-01685-2.

ABSTRACT

OBJECTIVE: This study aimed to develop a nomogram integrating radiomics features derived from contrast-enhanced ultrasound (CEUS) and B-mode ultrasound (B-US) with clinical features to improve preoperative differentiation between follicular thyroid carcinoma (FTC) and follicular thyroid adenoma (FTA). Accurate preoperative diagnosis is critical for guiding appropriate treatment strategies and reducing unnecessary interventions.

METHODS: We retrospectively included 201 patients with histopathologically confirmed FTC (n = 133) or FTA (n = 68). Radiomics features were extracted from B-US and CEUS images, followed by feature selection and machine-learning model development. Five models were evaluated, and the one with the highest area under the curve (AUC) was used to construct a radiomics signature. A Clinical Risk model was developed using statistically significant clinical features, which outperformed the conventional Chinese Thyroid Imaging Reporting and Data System (C-TIRADS) in both training and test groups. The radiomics signature and Clinical Risk model were integrated into a nomogram, whose diagnostic performance, calibration and clinical utility were assessed.

RESULTS: The Clinical Risk model achieved superior diagnostic performance compared to the C-TIRADS model, with AUCs of 0.802 vs. 0.719 in the training group and 0.745 vs. 0.703 in the test group. The nomogram further improved diagnostic efficacy, with AUCs of 0.867 (95% CI, 0.800-0.933) in the training group and 0.833 (95% CI, 0.729-0.937) in the test group. It also demonstrated excellent calibration. Decision curve analysis (DCA) also indicated that the nomogram showed good clinical utility.

CONCLUSION: By combining CEUS and B-US radiomics features with clinical data, we developed a robust nomogram for distinguishing FTC from FTA. The model demonstrated superior diagnostic performance compared to existing methods and holds promise for enhancing clinical decision-making in thyroid nodule management.

CLINICAL TRIAL NUMBER: Not applicable.

PMID:40325381 | DOI:10.1186/s12880-025-01685-2

BMC Med. 2025 May 6;23(1):262. doi: 10.1186/s12916-025-04090-2.

ABSTRACT

BACKGROUND: People living with dementia (PlwD) have a 1.4 times higher risk of hospitalization than people living without dementia. Hospital admissions lead to negative consequences for PlwD and people living with mild cognitive impairment (PlwMCI). Housing models such as shared-housing arrangements (SHAs), which are predominantly used by PlwD, enable care-dependent people to experience daily life as ordinary as possible. However, studies are needed to show how complex non-pharmacological interventions affect hospital admissions, especially in the SHAs setting.

METHODS: The longitudinal, multicenter, cluster-randomized, controlled, and prospective mixed methods study from April 1, 2019, to December 31, 2022, was part of the German DemWG study and included a waitlist control group design. The multicomponent complex intervention consisted of (a) education of nursing staff in the SHAs-at the beginning of the study, (b) digital education of general practitioners-at the beginning of the study, and (c) the multimodal, psychosocial group intervention MAKS-mk + -structured application of MAKS-mk + between t0 (baseline) and t1 (after 6 months). Longitudinal data were collected at three survey times t0-t2 (t2 at another 6 months follow-up). The primary outcome parameter-hospital admission-was assessed using the nursing documentation. Poisson-models with hierarchical random effects were used for statistical analysis.

RESULTS: Nationwide, 97 SHAs with 341 residents participated at t0. Within the longitudinal observation period (12 months, t0-t2), data from 236 participants at t1 and 168 participants at t2 with mild cognitive impairment or mild to moderate dementia were evaluated. In the intention-to-treat sample, the adjusted Poisson-model showed that participants in the intervention group (IG, n = 201) had a significantly lower number of hospital admissions at t1 than participants in the control group (CG, n = 140) (p-value = 0.048; CI = 0.22; 0.99). Beyond t1-“open phase” of the study, no further statistically significant long-term effects of the IG could be identified (p-value ≤ 0.498; CI = 0.25; 1.98).

CONCLUSIONS: The complex intervention significantly reduced the number of hospital admissions for PlwD and PlwMCI in the “structured phase” of DemWG. This leads to significant improvements in the nursing care and living situation for PlwD and PlwMCI. Since the intervention has been proven to have positive effects and can be easily integrated into SHAs, regular and nationwide integration into everyday care should be given greater consideration.

TRIAL REGISTRATION: ISRCTN89825211 (Registered prospectively, 16 July 2019).

PMID:40325380 | DOI:10.1186/s12916-025-04090-2

BMC Health Serv Res. 2025 May 5;25(1):643. doi: 10.1186/s12913-025-12816-4.

ABSTRACT

BACKGROUND: In the Netherlands, the annual expenditure on HIV care was reported as €202 million in 2019, with about 70% allocated to antiretroviral therapy (ART). The introduction of generic antiretroviral medications (ARVs) in 2017 has offered potential cost-saving opportunities in healthcare. Understanding the financial implications of incorporating generic ART into the Dutch healthcare system is crucial to determine its impact.

METHODS: We used data from the Foundation for Pharmaceutical Statistics (SFK), covering 98% of all community and outpatient clinic pharmacies across the Netherlands. This dataset contained medication information from 2016 to 2022. Medication data were classified using the Anatomical Therapeutic Chemical Classification with Defined Daily Dose (ATC/DDD) system. Cost analysis was based on Dutch drug prices ( www.medicijnkosten.nl ) for a specified period, and the data were processed using IBM SPSS.

RESULTS: In the Netherlands, people with HIV receiving ART increased from 20,072 to 24,573 between 2016 and 2022. HIV medication expenditure was €190 million euros in 2016, with generic medication at 6% DDDs. After an increase in 2017, a subsequent decrease in total HIV medication expenditure led to an overall cost of €181 million in 2022 (-5.1% compared to 2016). Simultaneously, the proportion of DDDs dispensed as a generic increased to 16-32% over the years. This could be linked to 97% compliance with generic substitutions for ARVs where a generic equivalent was available. Notably, the cost per patient per year has declined from €9,488 in 2016 to €7,352 in 2022 (-22.5% compared to 2016). Some of the potential cost-savings through generic substitution were not utilized because of the 20% point increase in the use of novel branded single-tablet regimens (STRs).

CONCLUSIONS: Our analysis showed high compliance with generic substitution of ARVs in the Netherlands. The increased use of generic ARVs was accompanied by an almost 10% reduction in overall expenditure on ART despite a significant increase in the number of patients in care in the Netherlands during this period. A significant contributing factor to ART costs appears to be the high percentage of prescribed patented Single-Tablet Regimens (STRs). These findings underscore the complex dynamics of pharmaceutical expenditures in the Dutch healthcare system.

PMID:40325377 | DOI:10.1186/s12913-025-12816-4

Gen Hosp Psychiatry. 2025 Apr 30;95:80-92. doi: 10.1016/j.genhosppsych.2025.04.008. Online ahead of print.

ABSTRACT

INTRODUCTION: Multimorbidity, the co-occurrence of multiple health conditions, is increasingly recognised as a significant public health concern. While the association between multimorbidity and suicidal thoughts is well-documented, its relationship with suicidal behaviour remains underexplored. This study aims to quantify the association between multimorbidity and both suicide attempts and suicide mortality.

METHODS: We searched Medline, PsycINFO, and Scopus databases for studies published from January 1990 up to July 2024. We applied prespecified eligibility criteria to select studies for inclusion. To assess the risk of bias, we used the Mixed Methods Appraisal Tool. We conducted meta-analyses using random-effects models and assessed heterogeneity with Cochran’s Q and I² statistics. We evaluated publication bias using funnel plots and Egger’s test. Sub-group analysis was conducted incorporating potential moderator variables.

RESULTS: Out of 2202 identified records, 38 studies were included in the analysis. Participants with multimorbidity were over five times more likely to attempt suicide compared to those without multimorbidity (pooled odds ratio [OR] = 5.31; 95 % confidence interval [CI] = 3.98, 7.09; I² = 94.9 %). Multimorbidity was associated with an 83 % increased likelihood of suicide mortality (pooled OR = 1.83; 95 % CI = 1.21, 2.77; I² = 99.9 %). Mental multimorbidity was associated with the highest odds of suicide attempts (OR = 6.96; 95 % CI = 4.94, 9.81; I² = 81.8 %), with higher odds also observed in studies with single disease comparator (OR = 6.16; 95 % CI = 3.68, 10.31; I² = 95.5 %), and across both high income and low-middle income regions. For suicide mortality, significant associations were found in studies assessing physical-mental multimorbidity (OR = 2.32; 95 % CI = 1.14, 4.71; I² = 99.8 %), studies from Europe/USA and Asia, and those using a mixed comparator group, with additional significant effects noted by study design, publication year, covariate adjustment, and risk of bias.

CONCLUSIONS: Multimorbidity significantly increases the risk of both suicide attempts and suicide mortality. We recommend enhanced suicide risk assessment among patients with multiple chronic conditions, especially when mental health diagnoses are present.

PMID:40324313 | DOI:10.1016/j.genhosppsych.2025.04.008

Comput Biol Med. 2025 May 4;192(Pt A):110230. doi: 10.1016/j.compbiomed.2025.110230. Online ahead of print.

ABSTRACT

A cardiac digital twin is a virtual replica of a patient-specific heart, mimicking its anatomy and physiology. A crucial step of building a cardiac digital twin is anatomical twinning, where the computational mesh of the digital twin is tailored to the patient-specific cardiac anatomy. In a number of studies, the effect of anatomical variation on clinically relevant functional measurements like electrocardiograms (ECGs) is investigated, using computational simulations. While such a simulation environment provides researchers with a carefully controlled ground truth, the impact of anatomical differences on functional measurements in real-world patients remains understudied. In this study, we develop a biventricular statistical shape model and use it to quantify the effect of biventricular anatomy on ECG-derived and demographic features, providing novel insights for the development of digital twins of cardiac electrophysiology. To this end, a dataset comprising high-resolution cardiac CT scans from 271 healthy individuals, including athletes, is utilized. Furthermore, a novel, universal, ventricular coordinate-based method is developed to establish lightweight shape correspondence. The performance of the shape model is rigorously established, focusing on its dimensionality reduction capabilities and the training data requirements. The most important variability in healthy ventricles captured by the model is their size, followed by their elongation. These anatomical factors are found to significantly correlate with ECG-derived and demographic features. Additionally, a comprehensive synthetic cohort is made available, featuring ready-to-use biventricular meshes with fiber structures and anatomical region annotations. These meshes are well-suited for electrophysiological simulations.

PMID:40324309 | DOI:10.1016/j.compbiomed.2025.110230

J Environ Radioact. 2025 May 4;287:107712. doi: 10.1016/j.jenvrad.2025.107712. Online ahead of print.

ABSTRACT

Radon is a by-product of decayed uranium and thorium isotopes, which are naturally occurring radionuclide with extremely long half-lives. It is rated as the second cause of lung cancer after tobacco cigarette smoking. This study assesses knowledge and awareness of health risks associated with radon among undergraduate students at Mkwawa University College of Education (MUCE) by using questionnaires. A structured questionnaire with 36 items was administered to 403 respondents at MUCE. Information was collected on the demographic variables of the respondents as well as knowledge and awareness of health risks associated with radon among undergraduates at MUCE. Data were analysed by using descriptive statistics. Respondents included 204 (50.6 %) females and 199 (49.4 %) males. Findings revealed that 257 (63.8 %) of the respondents had no knowledge of radon gas and had not even heard about it before this study, while only 146 (36.2 %) of the respondents had heard about radon gas. Moreover, 285 (70.7 %) of the respondents were not aware that radon gas can cause health effect, and only 118 (29.3 %) of the respondents were aware about health effect of radon gas. Likewise, only 145 (36 %) of the respondents were aware about the risks of radon gas, while 258 (64 %) of the respondents were not aware about the risk of radon as the second cause of lung cancer after tobacco smoking. This study suggests the need to increase public education and awareness campaigns on radon and its associated risks.

PMID:40324307 | DOI:10.1016/j.jenvrad.2025.107712