Biology subjects

Suda, S.

Publications and source records attributed to Suda, S..

4 recordsLinked to original sources

bioRxiv2025

Excellent agreement between automated deep learning-based and manual DWI infarct volume measurement in hyperacute stroke

BackgroundDiffusion-weighted imaging (DWI) lesion volume and infarct growth are important imaging markers in acute ischemic stroke, but manual volume measurement is time-consuming and resource-intensive. Deep learning (DL)-based automated segmentation may facilitate rapid assessment; however, its performance on hyperacute DWI has not been sufficiently assessed. The aim was to evaluate the agreement between DL-based automated and manual infarct volume measurements and to compare their ability to predict clinical outcomes in patients treated with mechanical thrombectomy (MT). MethodConsecutive MT-treated patients (September 2014-December 2019) who underwent DWI at admission and at approximately 24 hours were retrospectively analyzed. Manual infarct volume was measured by stroke neurologists. Automated measurements were obtained using DL-based software. Agreement was assessed using Pearsons correlation, Bland-Altman analysis, and intraclass correlation coefficients (ICC 2,1). Inter- and intra-rater reliabilities were evaluated in a randomly selected subgroup of 150 patients. Predictive ability for a good outcome at 3 months (modified Rankin Scale score 0-2 or stable/improved from premorbid status) was compared using C-statistics and DeLongs test. ResultsA total of 371 patients (677 DWI scans) were included. Manual and automated measurements showed very strong correlation (r = 0.96) with minimal bias (-1.77 mL). The ICC for manual-automated agreement was 0.959 (95% CI, 0.952-0.965), comparable to inter- and intra-rater ICCs. Agreement remained high across onset-to-imaging times and lesion sizes. Predictive abilities for a good outcome were similar for manual and automated admission DWI volume (C-statistics 0.867 vs. 0.861) and infarct growth (0.859 vs. 0.853). Manual follow-up DWI volume showed slightly better predictive ability than automated measurement (0.880 vs. 0.866). ConclusionDL-based automated infarct volume measurement shows excellent agreement with experienced clinicians, with predictive performance comparable to manual assessment. Automated DWI-based quantification is reliable and feasible for use in hyperacute stroke management.

neuroscience↗

bioRxiv2022

Targeted single-cell genomics reveals novel host adaptation strategies of the symbiotic bacteria Endozoicomonas in Acropora tenuis coral

Endozoicomonas bacteria symbiose with various marine organisms and are known to be beneficial for coral health. However, genome analysis of coral-associated Endozoicomonas has been limited owing to the difficulty in cultivation and metagenomic approach by contamination of host-derived sequences. In this study, we applied a novel single-cell genomics technique using droplet microfluidics to obtain single-cell amplified genome (SAGs) for coral-associated Endozoicomonas spp. genome. We obtained seven novel Endozoicomonas genomes from Acropora tenuis coral. These genomes revealed that Endozoicomonas bacteria played host-associated functions in host corals and had undergone independent host-adaptive evolution in different clades. These adaptive evolutions were mediated by host-derived eukaryotic-like genes, some of which were speculated to influence host immune mechanisms. These genes are speculated to enhance coral tolerance to environmental stresses. This study suggests the possibility of host adaptation of Endozoicomonas spp. in symbiosis with corals and their contribution to coral bleaching tolerance.

microbiology↗

bioRxiv2021

Multi-omics analysis reveals cross-organism interactions in coral holobiont

Corals create an ecosystem, called a holobiont, with intracellular algae (zooxanthellae) and resident bacteria. Zooxanthellae and some bacteria play major roles in the physiological properties of the coral host. However, because of the difficulties in experimental verification of cross-organism interactions, the mechanisms underpinning these interactions are largely unknown. To address this, we here generated and then analyzed multi-omics datasets for corals, zooxanthellae, and bacteria collected at Okinawa, Japan, from November 2014 to September 2016. Using cross-organism co-expression analysis, we successfully characterized the host-alga relationship in the coral holobiont. Specifically, we observed that the coral host dominates the zooxanthellae. The multi-omics analysis also suggested that infection with coral-associated bacteria Endozoicomonas likely involves coral-like ephrin ligands, triggering an immune response of the coral host. This study highlights the potential of the multi-omics approach to elucidate coral-microbe interactions.

systems biology↗

bioRxiv2020

Hidden introductions of freshwater red algae via the aquarium trade exposed by DNA barcodes

ABSTRACTThe global aquarium trade can introduce alien freshwater invaders, potentially impacting local aquatic ecosystems and their biodiversity. The role of the aquarium trade in spreading freshwater red macroalgae that hitchhike on ornamental aquatic plants and animals is unassessed. We investigated this human-mediated phenomenon via a broad biodiversity survey and genetic analysis of freshwater red algae in the field and aquarium shops in East Asia. Using rbcL-based DNA barcoding, we surveyed 125 samples from 46 field sites and 88 samples from 53 aquarium shops (213 samples in total) mostly across Taiwan – a key hub in the global aquarium trade – as well as in Hong Kong, Okinawa (Japan), the Philippines, and Thailand. We augmented our rbcL sequences with GenBank rbcL sequences that represent 40 additional countries globally. We found 26 molecular operational taxonomic units (mOTUs) in Taiwan, some of which are cryptic. Phylogeographical analysis revealed three potential introduced mOTUs in Taiwan, which exhibit no local genetic variation in Taiwan and are distributed across continents. Also, we posit that some presumably endangered freshwater red algae may be preserved in aquaria, an unintentional ex situ conservation site for these organisms that are vulnerable to water pollution from anthropogenic disturbances. Collectively, these data suggest that freshwater red algae have been hitchhiking and dispersed via the aquarium trade, an important and overlooked mechanism of introduction of these organisms across the globe.Competing Interest StatementThe authors have declared no competing interest.View Full Text

ecology↗