Category: Nevin Manimala

Front Aging Neurosci. 2025 Mar 21;17:1532470. doi: 10.3389/fnagi.2025.1532470. eCollection 2025.

ABSTRACT

Conventional computer-aided diagnostic techniques for Alzheimer’s disease (AD) predominantly rely on magnetic resonance imaging (MRI) in isolation. Genetic imaging methods, by establishing the link between genes and brain structures in disease progression, facilitate early prediction of AD development. While deep learning methods based on MRI have demonstrated promising results for early AD diagnosis, the limited dataset size has led most AD studies to lean on statistical approaches within the realm of imaging genetics. Existing deep-learning approaches typically utilize pre-defined regions of interest and risk variants from known susceptibility genes, employing relatively straightforward feature fusion methods that fail to fully capture the relationship between images and genes. To address these limitations, we proposed a multi-modal deep learning classification network based on MRI and single nucleotide polymorphism (SNP) data for AD diagnosis and mild cognitive impairment (MCI) progression prediction. Our model leveraged a convolutional neural network (CNN) to extract whole-brain structural features, a Transformer network to capture genetic features, and employed a cross-transformer-based network for comprehensive feature fusion. Furthermore, we incorporated an attention-map-based interpretability method to analyze and elucidate the structural and risk variants associated with AD and their interrelationships. The proposed model was trained and evaluated using 1,541 subjects from the ADNI database. Experimental results underscored the superior performance of our model in effectively integrating and leveraging information from both modalities, thus enhancing the accuracy of AD diagnosis and prediction.

PMID:40191788 | PMC:PMC11968703 | DOI:10.3389/fnagi.2025.1532470

Stoch Process Their Appl. 2025 Apr;182:104565. doi: 10.1016/j.spa.2025.104565. Epub 2025 Jan 11.

ABSTRACT

The site frequency spectrum (SFS) is a widely used summary statistic of genomic data. Motivated by recent evidence for the role of neutral evolution in cancer, we investigate the SFS of neutral mutations in an exponentially growing population. Using branching process techniques, we establish (first-order) almost sure convergence results for the SFS of a Galton-Watson process, evaluated either at a fixed time or at the stochastic time at which the population first reaches a certain size. We finally use our results to construct consistent estimators for the extinction probability and the effective mutation rate of a birth-death process.

PMID:40191782 | PMC:PMC11970945 | DOI:10.1016/j.spa.2025.104565

PeerJ. 2025 Apr 3;13:e19137. doi: 10.7717/peerj.19137. eCollection 2025.

ABSTRACT

BACKGROUND: B-Raf proto-oncogene, serine/threonine kinase (BRAF) V600E mutation stands as a pivotal genetic alteration strongly associated with several neoplasms and contributes significantly to their pathogenesis as well as potential targeted treatment strategies.

OBJECTIVE: This cross-sectional study aimed to determine the frequency of BRAF V600E mutation in ameloblastoma in a multi-center of Thailand.

METHOD: Anti-BRAF V600E (clone VE1) immunohistochemistry was performed on 227 conventional ameloblastoma (AM) and 113 unicystic ameloblastoma (UA) samples collected from four major dental schools located in the Central, North, South, and Northeast regions of Thailand. Tumor cells from randomly chosen AM cases were also micro-dissected from the FFPE sections and subjected to DNA sequencing to confirm the immunohistochemical results.

RESULTS: BRAF V600E mutation was detected in 71.8% of the AM samples, while 65.5% of samples with UAs demonstrated BRAF V600E positivity. The BRAF V600E mutation was significantly different in the histological subtypes of AMs in the four centers (p = 0.012) and the location of UA in three centers (p = 0.013). There was no significant association between the BRAF V600E mutation and the location of ameloblastoma in the overall prevalence of our multi-center study; nonetheless, a statistically significant association was found between the BRAF V600E mutation and the mandible location of AMs from the Central Faculty of Dentistry, Mahidol University (MU) center (p = 0.033), as well as with the histological subtypes of AMs from the Southern Faculty of Dentistry, Prince of Songkla University (PSU) center (p = 0.009). No statistical association was observed between the BRAF V600E mutation and AM and UA recurrence (p = 0.920 and p = 0.312), respectively. The results of DNA sequencing performed in randomly selected 40 BRAF V600E-positive and 20 BRAF V600E-negative ameloblastoma tissues were in accordance with the immunohistochemical findings.

CONCLUSION: As a result of a notable prevalence of BRAF V600E in Thai individuals diagnosed with ameloblastoma, they may benefit from the utilization of adjunctive anti-BRAF targeted therapy for treatment.

PMID:40191760 | PMC:PMC11972564 | DOI:10.7717/peerj.19137

PeerJ. 2025 Apr 3;13:e19257. doi: 10.7717/peerj.19257. eCollection 2025.

ABSTRACT

INTRODUCTION/PURPOSE: In the radiology department, where advanced technologies and multidisciplinary collaboration are crucial, establishing a strong safety culture is particularly challenging. The present cross-sectional study examines the challenges of establishing a safety culture in radiology, focusing on how Saudi radiology trainees perceive and respond to safety and unprofessional conduct. It evaluates their willingness to voice concerns and the influencing factors, including workplace culture, potential patient risks, and demographics.

METHODS: The present study surveyed Saudi radiology residents and interns at two tertiary hospitals using a validated questionnaire. A non-probability total population purposive sampling method was employed. Descriptive statistics, Mann-Whitney U test, and Kruskal-Wallis H test were used to analyze differences in willingness to speak up across demographic groups.

RESULTS: Participants felt encouraged by colleagues to address patient safety and unprofessional behavior, with over 70% and 56% respectively agreeing. Residents demonstrated significantly greater support for raising concerns about safety and unprofessional conduct compared to interns (mean rank = 47.58 vs. 33.91, p = 0.009). Furthermore, residents expressed a stronger belief that speaking up leads to meaningful changes (mean rank = 46.24 vs. 35.36, p = 0.033) and reported observing others addressing these issues more frequently (mean rank = 46.98 vs. 34.56, p = 0.015). Trainees from different hospitals exhibited significantly varied perceptions regarding support from colleagues in addressing patient safety and unprofessional behavior (mean rank = KAMC 54.53 vs. KSMC 33.04, p < 0.0001), the perceived impact of raising concerns (mean rank = KAMC 50.50 vs. KSMC 35.41, p = 0.004), and the frequency of observing these concerns being addressed (mean rank = KAMC 55.28 vs. KSMC 32.60, p < 0.0001). Radiology trainees are particularly vigilant about unintentional breaches of sterile technique, often addressing these issues with nurses (66.7%).

CONCLUSION: The clinical environment supports safety concerns but less so for unprofessional behavior, with residents being more proactive. Promoting open communication in radiology requires leadership education, multifaceted strategies, alternative channels for concerns, and future research to assess and track cultural attitudes. The findings highlight the need to cultivate a supportive culture for speaking up in clinical settings, particularly in radiology, where trainee involvement can enhance patient safety and professional conduct. The present study lays the groundwork for future research and interventions to strengthen safety and professionalism among medical trainees in Saudi Arabia.

PMID:40191757 | PMC:PMC11972563 | DOI:10.7717/peerj.19257

Proc IEEE Int Symp Biomed Imaging. 2024 May;2024. doi: 10.1109/isbi56570.2024.10635543. Epub 2024 Aug 22.

ABSTRACT

Given the complex geometry of white matter streamlines, Autoencoders have been proposed as a dimension-reduction tool to simplify the analysis streamlines in a low-dimensional latent spaces. However, despite these recent successes, the majority of encoder architectures only perform dimension reduction on single streamlines as opposed to a full bundle of streamlines. This is a severe limitation of the encoder architecture that completely disregards the global geometric structure of streamlines at the expense of individual fibers. Moreover, the latent space may not be well structured which leads to doubt into their interpretability. In this paper we propose a novel Differentiable Vector Quantized Variational Autoencoder, which are engineered to ingest entire bundles of streamlines as single data-point and provides reliable trustworthy encodings that can then be later used to analyze streamlines in the latent space. Comparisons with several state of the art Autoencoders demonstrate superior performance in both encoding and synthesis.

PMID:40191735 | PMC:PMC11968768 | DOI:10.1109/isbi56570.2024.10635543

Qual Quant. 2025;59(Suppl 1):389-412. doi: 10.1007/s11135-024-01983-x. Epub 2024 Oct 8.

ABSTRACT

Digital trace data form a rich, growing source of data for social sciences and humanities. Data donation offers an innovative and ethical approach to collect these digital trace data. In data donation studies, participants request a copy of the digital trace data a data controller (e.g., large digital social media or video platforms) collected about them. The European Union’s General Data Protection Regulation obliges platforms to provide such a copy. Next, the participant can choose to share (part of) this data copy with the researcher. This way, the researcher can obtain the digital trace data of interest with active consent of the participant. Setting up a data donation study involves several steps and considerations. If executed poorly, these steps might threaten a study’s quality. In this paper, we introduce a workflow for setting up a robust data donation study. This workflow is based on error sources identified in the Total Error Framework for data donation by Boeschoten et al. (2022a) as well as on experiences in earlier data donation studies by the authors. The workflow is discussed in detail and linked to challenges and considerations for each step. We aim to provide a starting point with guidelines for researchers seeking to set up and conduct a data donation study.

PMID:40191694 | PMC:PMC11971172 | DOI:10.1007/s11135-024-01983-x

SSM Popul Health. 2025 Mar 12;30:101776. doi: 10.1016/j.ssmph.2025.101776. eCollection 2025 Jun.

ABSTRACT

Having a sense of meaning in life supports adolescent health but is affected by experiences of wealth or poverty. We examined its associations with relative advantage (RA) and relative deprivation (RD) in a sample of Canadian adolescents (n = 17,634) using survey data from the Health Behaviour in School-aged Children study. We calculated RA and RD using all other schoolmates as reference groups in 238 schools. Descriptively, RA was associated with greater meaning and purpose and RD was associated with less. Regression-based estimates of prevalence ratios (PR) revealed more nuanced patterns. RD was associated with less of a sense of meaning and purpose in females and gender-diverse youth only. RA was associated with a reduced risk of low meaning and purpose in females (PR 0.77; 95 % CI: 0.61 to 0.98), with similar trends in males and gender diverse students that did not achieve significance. Although the association was not pronounced at the ecological (school) level, the negative associations with RD were stronger in more unequal schools. To illustrate, in schools of high wealth inequality, RD was most strongly associated with having low meaning and purpose in females (PR 1.59; 95 % CI: 1.20 to 2.11) and gender diverse adolescents (PR 1.97, 95 % CI: 0.90 to 4.33), with no statistically significant effect in males. These patterns reveal the salience of proximal socioeconomic reference cues for adolescents and offer new insights into why inequalities in health and wellbeing are so challenging to address in youth populations. They also underscore the importance of both socioeconomic position and wealth distribution within school settings, providing impetus for thought and change.

PMID:40191600 | PMC:PMC11968296 | DOI:10.1016/j.ssmph.2025.101776

Front Neurol. 2025 Mar 21;16:1553263. doi: 10.3389/fneur.2025.1553263. eCollection 2025.

ABSTRACT

OBJECTIVE: To evaluate the predictive value of the neutrophil-to-lymphocyte ratio (NLR) for prognosis spontaneous intracerebral hemorrhage (ICH) patients.

METHODS: PubMed, EMBASE, Cochrane Library, Web of Science were used for screening literature on NLR predicting ICH prognosis from database up to January 2024. Case-control or cohort studies that provided statistical analysis data on NLR predicting ICH prognosis were included. Data were combined using odds ratio (OR) and standard mean differences (SMD) for categorical variables and continuous variables, respectively. Meta-analysis, subgroup analyses, and sensitivity analyses were performed by Review Manager 5.4 and Stata 15.0.

RESULTS: Meta-analysis of 21 studies with a total of 7,176 patients confirmed that NLR has a significant predictive value for mortality (SMD: 0.80, 95% CI: 0.58-1.02; OR: 1.10, 95% CI: 1.04-1.17) and neurological function outcomes (SMD: 0.66, 95% CI: 0.50-0.81; OR: 1.29, 95% CI: 1.17-1.41). NLR also significantly predicted the occurrence of stroke-associated pneumonia (SAP) (SMD: 0.54, 95% CI: 0.21-0.87). Subgroup analysis suggested that NLR had good predictive value for mortality in ICH patients aged ≥60 years, with hematoma volume > 15 mL, and NLR cut-off >7.5, and for neurological function in ICH patients, Asian patients, and those with NLR cut-off >7.5. The stability of the results was confirmed by sensitivity analysis.

CONCLUSION: NLR can significantly predict mortality, neurological function outcomes, and SAP occurrence in ICH patients. NLR cut-off >7.5 has good predictive value for both mortality and neurological function in ICH patients. Considering the limitations of this study, such as small sample size and potential heterogeneity, prospective studies with larger sample sizes are needed to confirm the findings of this article.

SYSTEMATIC REVIEW REGISTRATION: https://www.crd.york.ac.uk/PROSPERO/, identifier CRD42024544506.

PMID:40191597 | PMC:PMC11968378 | DOI:10.3389/fneur.2025.1553263

Front Neurol. 2025 Mar 21;16:1550250. doi: 10.3389/fneur.2025.1550250. eCollection 2025.

ABSTRACT

OBJECTIVE: This pilot study aims to assess the feasibility and preliminary effectiveness. of acupuncture as an adjunct therapy for improving sleep quality in patients with Parkinson’s Disease (PD) who are experiencing fragmented sleep disorders.

METHOD: This pilot study recruited a small cohort of 11 patients diagnosed. With PD, each undergoing a structured 4-week acupuncture intervention comprising three sessions per week. Outcome measures included polysomnography (PSG) and the Pittsburgh Sleep Quality Index (PSQI), both of which were evaluated at baseline and following the completion of the 4-week acupuncture regimen.

RESULT: Post-intervention analysis showed trends toward improved sleep continuity with statistical significance in the sleep arousal index (p = 0.001), sleep arousal frequency (p = 0.001), and PSQI scores (p = 0.026) compared to baseline measurements. Importantly, no adverse events or complications were reported throughout the study period.

CONCLUSION: The results indicate that acupuncture provides preliminary evidence supporting its use as a feasible adjunctive therapy for improving sleep quality in individuals with PD. Further research is required to evaluate the long-term efficacy of acupuncture and to examine its practicality and feasibility for integration into established PD management protocols.

PMID:40191590 | PMC:PMC11968347 | DOI:10.3389/fneur.2025.1550250

Biomater Investig Dent. 2025 Mar 31;12:43372. doi: 10.2340/biid.v12.43372. eCollection 2025.

ABSTRACT

OBJECTIVE: Considering the effect of bone resorption-inhibiting drugs, such as bisphosphonates, on bone density, the present study evaluated the stability of implants coated with polylactic-co-glycolic acid (PLGA)-alendronate sodium.

METHODOLOGY: Ten healthy Swiss rabbits were selected (mean weight: 3.5 kg). Two titanium implants were inserted in each rabbit’s tibia bone, one implant coated with PLGA-alendronate sodium and the other functioning as control. Torque meter equipment measured the amount of torque while inserting the implants. Insertion torque was measured during the initial insertion of the implants, and after 4 weeks, the rabbits were anesthetized again, the implants were exposed, and resistance torques were measured and recorded. Using a trephine bur, all implants and the surrounding bone structure were then removed for histological evaluation. Fourier transform infrared spectroscopy was used to investigate alendronate and PLGA biologically. Data analysis was performed using SPSS.v23 software with a significance level of p < 0.05.

RESULTS: The results showed that the difference between insertion torque and final resistance torque after 4 weeks was statistically significant (p = 0.024). The mean number of osteoclasts and macrophages differed substantially between the experimental and control groups (p < 0.001). The ratio of woven bone to lamellar bone and the number of osteoblasts did not differ significantly between the two groups (p > 0.05).

CONCLUSION: The use of PLGA-alendronate sodium coating decreased the number of osteoclasts and macrophages and increased the stability of implant anchorage.

PMID:40191582 | PMC:PMC11971944 | DOI:10.2340/biid.v12.43372