Accelerating Flow Simulations using Online Dynamic Mode Decomposition

We develop an on-the-fly reduced-order model (ROM) integrated with a flow simulation, gradually replacing a corresponding full-order model (FOM) of a physics solver. Unlike offline methods requiring a separate FOM-only simulation prior to model reduction, our approach constructs a ROM dynamically during the simulation, replacing the FOM when deemed credible. Dynamic mode decomposition (DMD) is employed for online ROM construction, with a single snapshot vector used for rank-1 updates in each iteration. Demonstrated on a flow over a cylinder with Re = 100, our hybrid FOM/ROM simulation is verified in terms of the Strouhal number, resulting in a 4.4 times speedup compared to the FOM solver.Comment: Presented at Machine Learning and the Physical Sciences Workshop, NeurIPS 202

Molecular characteristics of reiterative DNA unwinding by the Caenorhabditis elegans RecQ helicase

The RecQ family of helicases is highly conserved both structurally and functionally from bacteria to humans. Defects in human RecQ helicases are associated with genetic diseases that are characterized by cancer predisposition and/or premature aging. RecQ proteins exhibit 3'-5' helicase activity and play critical roles in genome maintenance. Recent advances in single-molecule techniques have revealed the reiterative unwinding behavior of RecQ helicases. However, the molecular mechanisms involved in this process remain unclear, with contradicting reports. Here, we characterized the unwinding dynamics of the Caenorhabditis elegans RecQ helicase HIM-6 using single-molecule fluorescence resonance energy transfer measurements. We found that HIM-6 exhibits reiterative DNA unwinding and the length of DNA unwound by the helicase is sharply defined at 25-31 bp. Experiments using various DNA substrates revealed that HIM-6 utilizes the mode of 'sliding back' on the translocated strand, without strand-switching for rewinding. Furthermore, we found that Caenorhabditis elegans replication protein A, a single-stranded DNA binding protein, suppresses the reiterative behavior of HIM-6 and induces unidirectional, processive unwinding, possibly through a direct interaction between the proteins. Our findings shed new light on the mechanism of DNA unwinding by RecQ family helicases and their co-operation with RPA in processing DNA

植物細胞のエンドサイトーシスにおけるトランスゴルジ網とRAB11ファミリーの機能の研究

学位の種別:課程博士University of Tokyo(東京大学

Multi-frame-based Cross-domain Image Denoising for Low-dose Computed Tomography

Computed tomography (CT) has been used worldwide for decades as one of the most important non-invasive tests in assisting diagnosis. However, the ionizing nature of X-ray exposure raises concerns about potential health risks such as cancer. The desire for lower radiation dose has driven researchers to improve the reconstruction quality, especially by removing noise and artifacts. Although previous studies on low-dose computed tomography (LDCT) denoising have demonstrated the effectiveness of learning-based methods, most of them were developed on the simulated data collected using Radon transform. However, the real-world scenario significantly differs from the simulation domain, and the joint optimization of denoising with modern CT image reconstruction pipeline is still missing. In this paper, for the commercially available third-generation multi-slice spiral CT scanners, we propose a two-stage method that better exploits the complete reconstruction pipeline for LDCT denoising across different domains. Our method makes good use of the high redundancy of both the multi-slice projections and the volumetric reconstructions while avoiding the collapse of information in conventional cascaded frameworks. The dedicated design also provides a clearer interpretation of the workflow. Through extensive evaluations, we demonstrate its superior performance against state-of-the-art methods

The value of type IV collagen immunohistochemical staining in the differential diagnosis of autoimmune subepidermal bullous diseases

Autoimmune subepidermal bullous diseases (AISBDs) exhibit various clinical presentations, histological appearances, prognoses, and responses to treatment. Many diagnostic techniques, such as direct immunofluorescence (IF), indirect salt-split skin IF, and enzyme-linked immunosorbent assays, are used in the differential diagnoses of AISBDs. However, these techniques require fresh frozen tissue, expensive laboratory equipment, and sophisticated laboratory techniques. The purpose of this study was to evaluate the value of type IV collagen immunohistochemical (IHC) staining for the differential diagnosis of AISBDs. Paraffin-embedded blocks of skin biopsies were selected from 28 patients with autoimmune subepidermal bullous diseases. Among these 28 cases, 24 patients exhibited bullous pemphigoid (BP), 2 exhibited epidermolysis bullosa acquisita (EBA), 1 exhibited linear immunoglobulin A dermatosis (LAD), and 1 exhibited bullous systemic lupus erythematosus (BSLE). Sections were stained for type IV collagen and examined to determine the location of type IV collagen in the subepidermal blister. Type IV collagen positivity was observed on the base of the subepidermal blister in patients with BP (24 of 24 cases) and LAD (1 of 1 case). Staining was observed on the roof of the blister in patients with EBA (2 of 2 cases) and BSLE (1 of 1 case), and irregular staining was also observed on the base in patients with EBA. In conclusion, type IV collagen IHC staining is a simple and useful diagnostic technique for the differential diagnosis of AISBDs. .042) compared with controls. The filiform papillae had partially or completely regenerated in 85.7% of cases in the test group and in 23.1% of the controls (P=0.001). Red patches with raised keratotic rims may have healed spontaneously and reappeared in constantly changing patterns that are typical for MG. This phenomenon was not observed in patients supplemented with zinc, and new atrophy areas occurred in only one case. Low-dose zinc gluconate supplementation may have a positive therapeutic effect on tongue epithelium regeneration and symptomatology in patients with MG.   in our region were consistent with those from other studies. </p

The value of type IV collagen immunohistochemical staining in the differential diagnosis of autoimmune subepidermal bullous diseases

Autoimmune subepidermal bullous diseases (AISBDs) exhibit various clinical presentations, histological appearances, prognoses, and responses to treatment. Many diagnostic techniques, such as direct immunofluorescence (IF), indirect salt-split skin IF, and enzyme-linked immunosorbent assays, are used in the differential diagnoses of AISBDs. However, these techniques require fresh frozen tissue, expensive laboratory equipment, and sophisticated laboratory techniques. The purpose of this study was to evaluate the value of type IV collagen immunohistochemical (IHC) staining for the differential diagnosis of AISBDs. Paraffin-embedded blocks of skin biopsies were selected from 28 patients with autoimmune subepidermal bullous diseases. Among these 28 cases, 24 patients exhibited bullous pemphigoid (BP), 2 exhibited epidermolysis bullosa acquisita (EBA), 1 exhibited linear immunoglobulin A dermatosis (LAD), and 1 exhibited bullous systemic lupus erythematosus (BSLE). Sections were stained for type IV collagen and examined to determine the location of type IV collagen in the subepidermal blister. Type IV collagen positivity was observed on the base of the subepidermal blister in patients with BP (24 of 24 cases) and LAD (1 of 1 case). Staining was observed on the roof of the blister in patients with EBA (2 of 2 cases) and BSLE (1 of 1 case), and irregular staining was also observed on the base in patients with EBA. In conclusion, type IV collagen IHC staining is a simple and useful diagnostic technique for the differential diagnosis of AISBDs. .042) compared with controls. The filiform papillae had partially or completely regenerated in 85.7% of cases in the test group and in 23.1% of the controls (P=0.001). Red patches with raised keratotic rims may have healed spontaneously and reappeared in constantly changing patterns that are typical for MG. This phenomenon was not observed in patients supplemented with zinc, and new atrophy areas occurred in only one case. Low-dose zinc gluconate supplementation may have a positive therapeutic effect on tongue epithelium regeneration and symptomatology in patients with MG.   in our region were consistent with those from other studies. </p

Regulatory gaps between LNG carriers and LNG fuelled ships

Given a number of marine vessels treating the liquefied natural gas either as cargo or fuel, this paper examined the regulatory gaps of two different international Codes – the InternationalCodeof the Construction and Equipment of Ships Carrying Liquefied Gases in Bulk and the International Code of Safety for Ships Using Gases or Other Low-flashpoint Fuels – from the regulatory standpoint. Results of the gap analysis have identified and discussed the key areas encountered with regulatory discrepancies or ambiguities that might interrupt the proper design, construction and operation of LNG carrier and LNG fuelled ship. A systematic investigation and harmonisation process across the Codes was proposed to mitigate the potential issues that may arise from the discordant regulations. Also, the International Maritime Organization was suggested to take proactive action to improve such dissonances while a general insight into the importance of filling those gaps was provided for rule-makers and stakeholders