Biology subjects

Miyazaki, A.

Publications and source records attributed to Miyazaki, A..

4 recordsLinked to original sources

bioRxiv2026

A plasma metabolomics workflow for breast cancer detection using quantitative GC/MS and machine learning

Blood-based metabolomic profiling has been widely investigated for breast cancer (BC) detection; however, clinical implementation remains limited due to variability in sample handling, analytical reproducibility, and overfitting during statistical analysis. We established a plasma GC/MS metabolomics workflow for discriminating BC from healthy controls (HC) using conventional machine-learning algorithms. Plasma samples (n = 360; BC = 180, HC = 180) were collected prospectively under standardized preanalytical conditions before surgery and the initiation of systematic anticancer therapy and analyzed using a quantitative GC/MS platform with automated derivatization. Feature selection and model development were conducted using three machine-learning (ML) algorithms (Lasso logistic regression (LR), random forest classifier (RFC), and support vector machine (SVM)). A total of 45 metabolite candidate biomarkers were identified, and the optimal number of metabolite features for each algorithm was estimated by a recursive feature elimination (RFE)-based strategy. The best-performing models achieved area under the ROC curve values (AUC) of 0.910 (LR), 0.893 (RFC), and 0.843 (SVM). We selected prioritizing candidate biomarkers consistently expressed across the multi-algorithm pipeline. A bagging ensemble model improved stability (AUC = 0.911) and reduced false-positive predictions in the independent HC dataset. In addition, model stability with respect to false-positive predictions was assessed using an independent HC cohort (n = 15) that was collected at a separate institution. These results indicate that a plasma metabolomics workflow combined with conventional multi-algorithm ML, algorithm-specific feature selection, and independent assessment provides stable discrimination between BC and HC in a moderately sized cohort.

cancer biology↗

bioRxiv2023

Gut microbiota and faecal cytokine profiles of rural Cambodian infants and links to early life nutrition and diarrhoeal episodes.

The gut microbiota of infants in low-middle income countries like Cambodia remain underrepresented in microbiome research. This study aimed to explore the faecal gut microbiota composition and faecal cytokine profiles in a cohort of infants living in a rural province of Cambodia and explore the impact of sample storage conditions and infant environment on microbiota composition. Faecal samples collected at three time points from 32 infants (96 samples in total) after 7 months of age were analysed using 16S rRNA amplicon sequencing to determine the composition of the microbiota. Bacterial strains were isolated and subjected to whole genome sequencing and genomic analysis and concentrations of faecal cytokines were also measured. Initially, we compared the effects of two sample collection methods due to the challenges of faecal sample collection and storage in a rural location. Storage of faecal samples in a DNA preservation solution retained a greater abundance of Bacteroides. Analyses of microbiota composition of samples stored in DNA preservation solution indicated that Bifidobacterium was the most abundant genus with Bifidobacterium longum the most abundant species, particularly in breastfed infants. Most infants had detectable pathogenic taxa indicating frequent pathogen exposure, with Shigella and Klebsiella more abundant in infants with recent diarrheal illness. We did not detect antibiotic-associated perturbations in the gut microbiota, and no associations were found between the gut microbiota and infant growth. Genomic analysis of isolated strains indicated the presence of gene clusters encoding the ability to digest human milk oligosaccharides in B. longum and Bifidobacterium breve isolates. The presence of antibiotic-resistant genes was also identified in potentially pathogenic species, as well as in beneficial genera including Bifidobacterium. Faecal cytokine analysis showed higher concentrations of Interlukin-1alpha and vascular endothelial growth factor in breastfed infants, which may influence the infant gut mucosal immune system. This study provides insights into an underrepresented population of rural Cambodian infants, emphasising the impact of pathogen exposure and breastfeeding on gut microbiota composition and faecal immune profiles.

microbiology↗

bioRxiv2020

Brain/MINDS Beyond Human Brain MRI Study: Multi-Site Harmonization for Brain Disorders Throughout the Lifespan

Psychiatric and neurological disorders are afflictions of the brain that can affect individuals throughout their lifespan. Many brain magnetic resonance imaging (MRI) studies have been conducted; however, imaging-based biomarkers are not yet well established for diagnostic and therapeutic use. This article describes an outline of the planned study, the Brain/MINDS Beyond human brain MRI project (FY2018 [~] FY2023), which aims to establish clinically-relevant imaging biomarkers with multi-site harmonization by collecting data from healthy traveling subjects (TS) at 13 research sites. Collection of data in psychiatric and neurological disorders across the lifespan is also scheduled at 13 sites, whereas designing measurement procedures, developing and analyzing neuroimaging protocols, and databasing are done at three research sites. The Harmonization protocol (HARP) was established for five high-quality 3T scanners to obtain multimodal brain images including T1 and T2-weighted, resting state and task functional and diffusion-weighted MRI. Data are preprocessed and analyzed using approaches developed by the Human Connectome Project. Preliminary results in 30 TS demonstrated cortical thickness, myelin, functional connectivity measures are comparable across 5 scanners, providing high reproducibility and sensitivity to subject-specific connectome. A total of 75 TS, as well as patients with various psychiatric and neurological disorders, are scheduled to participate in the project, allowing a mixed model statistical harmonization. The HARP protocols are publicly available online, and all the imaging, demographic and clinical information, harmonizing database will also be made available by 2024. To the best of our knowledge, this is the first project to implement a rigorous, prospective harmonization protocol with multi-site TS data. It explores intractable brain disorders across the lifespan and may help to identify the disease-specific pathophysiology and imaging biomarkers for clinical practice.

neuroscience↗

bioRxiv2018

Age-related macular degeneration affects the optic radiation white matter projecting to locations of retinal damage

PurposeWe investigated the impact of age-related macular degeneration (AMD) on visual acuity and the visual white matter.\n\nMethodsWe combined an adaptive cortical atlas and diffusion-weighted magnetic resonance imaging (dMRI) and tractography to separate optic radiation (OR) projections to different retinal eccentricities in human primary visual cortex. We exploited the known anatomical organization of the OR and clinically relevant data to segment the OR into three primary components projecting to fovea, mid- and far-periphery. We measured white matter tissue properties - (fractional anisotropy, linearity, planarity, sphericity) along the aforementioned three components of the optic radiation to compare AMD patients and controls.\n\nResultsWe found differences in white matter properties specific to OR white matter fascicles projecting to primary visual cortex locations corresponding to the location of retinal damage (fovea). Additionally, we show that the magnitude of white matter properties in AMD patients correlates with visual acuity. In sum, we demonstrate a specific relation between visual loss, anatomical location of retinal damage and white matter damage in AMD patients. Importantly, we demonstrate that these changes are so profound that can be detected using magnetic resonance imaging data with clinical resolution. The conserved mapping between retinal and white matter damage suggests that retinal neurodegeneration might be a primary cause of white matter degeneration in AMD patients.\n\nConclusionsThe results highlight the impact of eye disease on brain tissue, a process that may become an important target to monitor during the course of treatment.

neuroscience↗