Sequential Sampling of the Gastrointestinal Tract to Characterize the Entire Digestive Microbiome in Japanese Subjects.

The gastrointestinal (GI) tract harbors trillions of microorganisms known to influence human health and disease, and next-generation sequencing (NGS) now enables the in-depth analysis of their diversity and functions. Although a significant amount of research has been conducted on the GI microbiome, comprehensive metagenomic datasets covering the entire tract are scarce due to cost and technical challenges. Despite the widespread use of fecal samples, integrated datasets encompassing the entire digestive process, beginning at the mouth and ending with feces, are lacking.

Highly regio- and stereoselective (3 + 2) annulation reaction of allenoates with 3-methyleneindolin-2-ones catalyzed by a planar chiral [2.2]paracyclophane-based bifunctional phosphine-phenol catalyst.

A planar chiral [2.2]paracyclophane-based phosphine-phenol catalyst catalyzed the (3 + 2) annulation reaction of ethyl 2,3-butadienoate with 3-methyleneindolin-2-ones to produce 2,5-disubstituted cyclopentene-fused C3-spirooxindoles in high yields with high regio-, diastereo-, and enantioselectivities. This catalyst was suitable for reactions of not only benzylideneindolinones but also alkylideneindolinones, the chiral phosphine-catalyzed reactions of which have not yet been reported.

Identifying critical age and gender-based metabolomic shifts in a Japanese population of the Tohoku Medical Megabank cohort.

Understanding the physiological changes associated with aging and the associated disease risks is essential to establish biomarkers as indicators of biological aging. This study used the NMR-measured plasma metabolome to calculate age-specific metabolite indices. In doing so, the scope of the study was deliberately simplified to capture general trends and insights into age-related changes in metabolic patterns.

A Principal Component Analysis of Metabolome and Cognitive Decline Among Japanese Older Adults: Cross-sectional Analysis Using Tohoku Medical Megabank Cohort Study Data.

Background: Dementia is the leading cause of disability and imposes a significant burden on society. Previous studies have suggested an association between metabolites and cognitive decline. Although the metabolite composition differs between Western and Asian populations, studies targeting Asian populations remain scarce.

Engineered polyethylene terephthalate hydrolases: perspectives and limits.

Polyethylene terephthalate (PET) is a major component of plastic waste. Enzymatic PET hydrolysis is the most ecofriendly recycling technology. The biorecycling of PET waste requires the complete depolymerization of PET to terephthalate and ethylene glycol.

Two-stage strategy using denoising autoencoders for robust reference-free genotype imputation with missing input genotypes.

Widely used genotype imputation methods are based on the Li and Stephens model, which assumes that new haplotypes can be represented by modifying existing haplotypes in a reference panel through mutations and recombinations. These methods use genotypes from SNP arrays as inputs to estimate haplotypes that align with the input genotypes by analyzing recombination patterns within a reference panel, and then infer unobserved variants. While these methods require reference panels in an identifiable form, their public use is limited due to privacy and consent concerns.

Intermediate multidomain state in single-crystalline Mn-doped BiFeO thin films during ferroelectric polarization switching.

A intermediate multidomain state and large crystallographic tilting of 1.78° for the (hh0) planes of a (001)-oriented single-domain Mn-doped BiFeO (BFMO) thin film were found when an electric field was applied along the [110] direction. The anomalous crystallographic tilting was caused by ferroelastic domain switching of the 109° domain switching.

Pilot study of the relation between various dynamics of avatar experience and perceptual characteristics.

In recent years, due to the prevalence of virtual reality (VR) and human-computer interaction (HCI) research, along with the expectation that understanding the process of establishing sense of ownership, sense of agency, and limb heaviness (in this study, limb heaviness is replaced with comfort level) will contribute to the development of various medical rehabilitation, various studies have been actively conducted in these fields. Previous studies have indicated that each perceptual characteristics decrease in response to positive delay. However, it is still unclear how each perceptual characteristic changes in response to negative delay.

PNPO-PLP axis senses prolonged hypoxia in macrophages by regulating lysosomal activity.

Oxygen is critical for all metazoan organisms on the earth and impacts various biological processes in physiological and pathological conditions. While oxygen-sensing systems inducing acute hypoxic responses, including the hypoxia-inducible factor pathway, have been identified, those operating in prolonged hypoxia remain to be elucidated. Here we show that pyridoxine 5'-phosphate oxidase (PNPO), which catalyses bioactivation of vitamin B6, serves as an oxygen sensor and regulates lysosomal activity in macrophages.

The role of the STAS domain in SLC26A9 for chloride ion transporter function.

The anion exchanger solute carrier family 26 (SLC26)A9, consisting of the transmembrane (TM) domain and the cytoplasmic STAS domain, plays an essential role in regulating chloride transport across cell membranes. Recent studies have indicated that C-terminal helices block the entrance of the putative ion transport pathway. However, the precise functions of the STAS domain and C-terminal helix, as well as the underlying molecular mechanisms governing the transport process, remain poorly understood.

Superstructure of FeGeTe Determined by Te K-Edge Extended X-ray Absorption Fine Structure and Te Kα X-ray Fluorescence Holography.

The local structure of the two-dimensional van der Waals material, FeGeTe, which exhibits unique structural/magnetic phase transitions, was investigated by Te K-edge extended X-ray absorption fine structure (EXAFS) and Te Kα X-ray fluorescence holography (XFH) over a wide temperature range. The formation of a trimer of Te atoms at low temperatures has been fully explored using these methods. An increase in the Te-Fe distance at approximately 150 K was suggested by EXAFS and presumably indicates the formation of a Te trimer.

Computational Estimation of Residues Involving Resistance to the SARS-CoV-2 Main Protease Inhibitor Ensitrelvir Based on Virtual Alanine Scan of the Active Site.

Ensitrelvir is a noncovalent inhibitor of the main protease (Mpro) of severe acute respiratory syndrome coronavirus 2. Acquisition of drug resistance in virus-derived proteins is a serious therapeutic concern, and drug resistance occurs due to amino acid mutations. In this study, we computationally constructed 24 mutants, in which one residue around the active site was replaced with alanine and performed molecular dynamics simulations to the complex of Mpro and ensitrelvir to predict the residues involved in drug resistance.

Theoretical Studies on the Reaction Mechanism of Schiff Base Formation from Hexoses.

The Maillard reaction is one of the nonenzymatic post-translational modifications of proteins. Products of this reaction are considered to be related to aging diseases and the sensation of taste. In the initial stage of the Maillard reaction, Schiff base formation first occurs by the nucleophilic attack of amine nitrogen in proteins, and then, the reaction proceeds through the formation of 1,2-eminal and Amadori compounds.

Automated escape system: identifying prey's kinematic and behavioral features critical for predator evasion.

Identifying the kinematic and behavioral variables of prey that influence evasion from predator attacks remains challenging. To address this challenge, we have developed an automated escape system that responds quickly to an approaching predator and pulls the prey away from the predator rapidly, similar to real prey. Reaction distance, response latency, escape speed and other variables can be adjusted in the system.

Multi-Omics Profiling Reveals Phenotypic and Functional Heterogeneity of Neutrophils in COVID-19.

Accumulating evidence has revealed unexpected phenotypic heterogeneity and diverse functions of neutrophils in several diseases. Coronavirus disease (COVID-19) can alter the leukocyte phenotype based on disease severity, including neutrophil activation in severe cases. However, the plasticity of neutrophil phenotypes and their relative impact on COVID-19 pathogenesis has not been well addressed.

Neural Radiance Field-Inspired Depth Map Refinement for Accurate Multi-View Stereo.

In this paper, we propose a method to refine the depth maps obtained by Multi-View Stereo (MVS) through iterative optimization of the Neural Radiance Field (NeRF). MVS accurately estimates the depths on object surfaces, and NeRF accurately estimates the depths at object boundaries. The key ideas of the proposed method are to combine MVS and NeRF to utilize the advantages of both in depth map estimation and to use NeRF for depth map refinement.

Photoemission Orbital Tomography Using a Robust Sparse PhaseLift.

Photoemission orbital tomography (POT) from photoelectron momentum maps (PMMs) is a powerful technique that visualizes the shape of the molecular orbitals (MOs) of molecular films. For further utilization of POT, a simple and low-cost method of POT is highly required. Here, we propose a new POT method based on the PhaseLift algorithm (PhaseLift POT).

Dietary habits and plasma lipid concentrations in a general Japanese population.

Introduction: Accumulating data on the associations between food consumption and lipid composition in the body is essential for understanding the effects of dietary habits on health.

Objectives: As part of omics research in the Tohoku Medical Megabank Community-Based Cohort Study, this study sought to reveal the dietary impact on plasma lipid concentration in a Japanese population.

Methods: We conducted a correlation analysis of food consumption and plasma lipid concentrations measured using mass spectrometry, for 4032 participants in Miyagi Prefecture, Japan.

Structural Perspective of NR4A Nuclear Receptor Family and Their Potential Endogenous Ligands.

There are 48 nuclear receptors in the human genome, and many members of this superfamily have been implicated in human diseases. The NR4A nuclear receptor family consisting of three members, NR4A1, NR4A2, and NR4A3 (formerly annotated as Nur77, Nurr1, and NOR1, respectively), are still orphan receptors but exert pathological effects on immune-related and neurological diseases. We previously reported that prostaglandin A (PGA) and prostaglandin A (PGA) are potent activators of NR4A3, which bind directly to the ligand-binding domain (LBD) of the receptor.

What Influence Could the Acceptance of Visitors Cause on the Epidemic Dynamics of a Reinfectious Disease?: A Mathematical Model.

The globalization in business and tourism becomes crucial more and more for the economical sustainability of local communities. In the presence of an epidemic outbreak, there must be such a decision on the policy by the host community as whether to accept visitors or not, the number of acceptable visitors, or the condition for acceptable visitors. Making use of an SIRI type of mathematical model, we consider the influence of visitors on the spread of a reinfectious disease in a community, especially assuming that a certain proportion of accepted visitors are immune.

Collective Relaxation Dynamics in a Three-Dimensional Lattice Glass Model.

We numerically elucidate the microscopic mechanisms controlling the relaxation dynamics of a three-dimensional lattice glass model that has static properties compatible with the approach to a random first-order transition. At low temperatures, the relaxation is triggered by a small population of particles with low-energy barriers forming mobile clusters. These emerging quasiparticles act as facilitating defects responsible for the spatially heterogeneous dynamics of the system, whose characteristic length scales remain strongly coupled to thermodynamic fluctuations.