Biology subjects

Hashimoto, Y.

Publications and source records attributed to Hashimoto, Y..

4 recordsLinked to original sources

bioRxiv2020

Three-dimensional convolutional autoencoder extracts features of structural brain images with a diagnostic label-free approach: Application to schizophrenia datasets

There has been increasing interest in performing psychiatric brain imaging studies using deep learning. However, most studies in this field disregard three-dimensional (3D) spatial information and targeted disease discrimination, without considering the genetic and clinical heterogeneity of psychiatric disorders. The purpose of this study was to investigate the efficacy of a 3D convolutional autoencoder (CAE) for extracting features related to psychiatric disorders without diagnostic labels. The network was trained using a Kyoto University dataset including 82 patients with schizophrenia (SZ) and 90 healthy subjects (HS), and was evaluated using Center for Biomedical Research Excellence (COBRE) datasets including 71 SZ patients and 71 HS. The proposed 3D-CAEs were successfully reconstructed into high-resolution 3D structural magnetic resonance imaging (MRI) scans with sufficiently low errors. In addition, the features extracted using 3D-CAE retained the relevant clinical information. We explored the appropriate hyper parameter range of 3D-CAE, and it was suggested that a model with eight convolution layers might be relevant to extract features for predicting the dose of medication and symptom severity in schizophrenia.

neuroscience↗

bioRxiv2020

Deep Feature Extraction for Resting-State Functional MRI by Self-Supervised Learning and Application to Schizophrenia Diagnosis

In this study, we propose a novel deep-learning technique for functional MRI analysis. We introduced an "identity feature" by a self-supervised learning schema, in which a neural network is trained solely based on the MRI-scans; furthermore, training does not require any explicit labels. The proposed method demonstrated that each temporal slice of resting state functional MRI contains enough information to identify the subject. The network learned a feature space in which the features were clustered per subject for the test data as well as for the training data; this is unlike the features extracted by conventional methods including region of interests pooling signals and principle component analysis. In addition, using a simple linear classifier for the identity features, we demonstrated that the extracted features could contribute to schizophrenia diagnosis. The classification accuracy of our identity features was higher than that of the conventional functional connectivity. Our results suggested that our proposed training scheme of the neural network captured brain functioning related to the diagnosis of psychiatric disorders as well as the identity of the subject. Our results together highlight the validity of our proposed technique as a design for self-supervised learning.

neuroscience↗

bioRxiv2020

Coronatine contributes Pseudomonas cannabina pv. alisalensis virulence by overcoming both stomatal and apoplastic defenses in dicot and monocot plants

P. cannabina pv. alisalensis (Pcal) is a causative agent of bacterial blight of crucifer including cabbage, radish, and broccoli. Importantly, Pcal can infect not only a wide range of Brassicaceae, but also green manure crops such as oat. However, Pcal virulence mechanisms have not been investigated and are not fully understood. We focused on coronatine (COR) function, which is one of the well-known P. syringae pv. tomato DC3000 virulence factors, in Pcal infection processes on both dicot and monocot plants. Cabbage and oat plants dip-inoculated with a Pcal KB211 COR mutant ({Delta}cmaA) exhibited reduced virulence compared to Pcal WT. Moreover, {Delta}cmaA failed to reopen stomata on both cabbage and oat, suggesting that COR facilitates Pcal entry through stomata into both plants. Furthermore, cabbage and oat plants syringe-infiltrated with {Delta}cmaA also showed reduced virulence, suggesting that COR is involved in overcoming not only stomatal-based defense, but also apoplastic defense. Indeed, defense related genes, including PR1 and PR2, were highly expressed in plants inoculated with {Delta}cmaA compared to Pcal WT, indicating that COR suppresses defense-related genes of both cabbage and oat. Additionally, SA accumulation increases after {Delta}cmaA inoculation compared to Pcal WT. Taken together, COR contributes to cause disease by suppressing stomatal-based defense and apoplastic defense in both dicot and monocot plants. This is the first study to investigate COR functions in the interaction of Pcal and different host plants (dicot and monocot plants) using genetically and biochemically defined COR deletion mutants. Author summaryDisease outbreaks caused by new Pseudomonas syringae isolates are problems worldwide. P. cannabina pv. alisalensis (Pcal) causes bacterial blight on a wide range of cruciferous plants and bacterial brown spot on oat plants. Although P. syringae deploys a variety of virulence factors, Pcal virulence factors have not been investigated. We focused on coronatine (COR) function, which is one of the well-known P. syringae virulence factors. COR is a non-host-specific phytotoxin and contributes to P. syringae growth and lesion formation or expansion in several host plants. COR function has been mainly studied in the model pathogen P. syringae pv. tomato DC3000 and model the plant Arabidopsis thaliana. Thus, COR roles in Pcal infection especially on monocot plants have not been well studied. Therefore, we investigated COR role in Pcal interaction with both dicot and monocot plants. Here, we revealed that COR functions as a multifunctional suppressor to manage Pcal virulence on both plants.

plant biology↗

bioRxiv2020

In vivo recellularization of xenogeneic vascular grafts decellularized with high hydrostatic pressure method in a porcine carotid arterial interpose model

Autologous vascular grafts are widely used in revascularization surgeries for small caliber targets. However, the availability of autologous conduits might be limited due to prior surgeries or the quality of vessels. Xenogeneic decellularized vascular grafts from animals potentially substitute for autologous vascular grafts. Decellularization with high hydrostatic pressure (HHP) is reported to highly preserve extracellular matrix (ECM) which would be feasible for recellularization and vascular remodeling after implantation. In the present study, we conducted xenogeneic implantation of HHP-decellularized bovine vascular grafts from dorsalis pedis arteries to porcine carotid arteries then evaluated graft patency, ECM preservation and recellularization. Surgical procedure not to damage luminal surface of the grafts from drying significantly increased the graft patency at 4 weeks after implantation (P = 0.0079). After the technical improvement, all grafts (N = 5) were patent with mild stenosis due to intimal hyperplasia at 4 weeks after implantation. Neither aneurysmal change nor massive thrombosis was observed even without administration of anticoagulants nor anti-platelet agents. Elastica van Gieson and Sirius-red stainings revealed fair preservation of ECM proteins including elastin and collagen after implantation. Luminal surface of grafts was thoroughly covered with von Willebrand factor-positive endothelium. Scanning electron microscopy on luminal surface of implanted grafts exhibited cobblestone-like endothelial cell layer which is similar to native vascular endothelium. Recellularization of tunica media with alpha-smooth muscle actin-positive smooth muscle cells was partly observed. Thus, we confirmed that HHP-decellularized grafts are feasible for xenogeneic implantation accompanied by recellularization by recipient cells.

bioengineering↗