Expanding the concept of ID conversion in TogoID by introducing multi-semantic and label features.

Background: TogoID ( https://togoid.dbcls.jp/ ) is an identifier (ID) conversion service designed to link IDs across diverse categories of life science databases.

jPOST environment accelerates the reuse and reanalysis of public proteome mass spectrometry data.

jPOST (https://jpostdb.org/) comprises jPOSTrepo (https://repository.jpostdb.

Enteropathway: the metabolic pathway database for the human gut microbiota.

The human gut microbiota produces diverse, extensive metabolites that have the potential to affect host physiology. Despite significant efforts to identify metabolic pathways for producing these microbial metabolites, a comprehensive metabolic pathway database for the human gut microbiota is still lacking. Here, we present Enteropathway, a metabolic pathway database that integrates 3269 compounds, 3677 reactions, and 876 modules that were obtained from 1012 manually curated scientific literature.

Characterizing Small-Scale Dynamics of Navier-Stokes Turbulence with Transverse Lyapunov Exponents: A Data Assimilation Approach.

Data assimilation (DA) of turbulence, which involves reconstructing small-scale turbulent structures based on observational data from large-scale ones, is crucial not only for practical forecasting but also for gaining a deeper understanding of turbulent dynamics. We propose a theoretical framework for DA of turbulence based on the transverse Lyapunov exponents (TLEs) in synchronization theory. Through stability analysis using TLEs, we identify a critical length scale as a key condition for DA; turbulent dynamics smaller than this scale are synchronized with larger-scale turbulent dynamics.

Divergent mechanisms of reduced growth performance in Betula ermanii saplings from high-altitude and low-latitude range edges.

The reduced growth performance of individuals from range edges is a common phenomenon in various taxa, and considered to be an evolutionary factor that limits the species' range. However, most studies did not distinguish between two mechanisms that can lead to this reduction: genetic load and adaptive selection to harsh conditions. To address this lack of understanding, we investigated the climatic and genetic factors underlying the growth performance of Betula ermanii saplings transplanted from 11 populations including high-altitude edge and low-latitude edge population.

Effect of scission on alignment of nonionic surfactant micelles under shear flow.

We investigate the alignment of wormlike micelles under shear flow with dissipative particle dynamics simulations of nonionic surfactant solutions. To reveal the effect of micellar scission on alignment, we evaluate the shear-rate dependence of the mean orientation angle and the average lifetime of micelles for fixed aggregation numbers. Our numerical results demonstrate the presence of two distinct shear-rate regimes of micellar alignment.

Flow-induced scission of wormlike micelles in nonionic surfactant solutions under shear flow.

We investigate flow-induced scission of wormlike micelles with dissipative particle dynamics simulations of nonionic surfactant solutions under shear flow. To understand flow-induced scission in terms of micellar timescales, we propose a method to evaluate the longest relaxation time of unentangled surfactant micelles from the rotational relaxation time and the average lifetime at equilibrium. The mean squared displacement of surfactant molecules provides evidence that the longest relaxation time estimated by the proposed method serves as the characteristic timescale at equilibrium.

Fluid mixing optimization with reinforcement learning.

Fluid mixing is crucial in various industrial processes. In this study, focusing on the characteristics that reinforcement learning (RL) is suitable for global-in-time optimization, we propose utilizing RL for fluid mixing optimization of passive scalar fields. For the two-dimensional fluid mixing problem described by the advection-diffusion equations, a trained mixer realizes an exponentially fast mixing without any prior knowledge.

TogoID: an exploratory ID converter to bridge biological datasets.

Motivation: Understanding life cannot be accomplished without making full use of biological data, which are scattered across databases of diverse categories in life sciences. To connect such data seamlessly, identifier (ID) conversion plays a key role. However, existing ID conversion services have disadvantages, such as covering only a limited range of biological categories of databases, not keeping up with the updates of the original databases and outputs being hard to interpret in the context of biological relations, especially when converting IDs in multiple steps.

Physiological and transcriptional responses of the ectomycorrhizal fungus Cenococcum geophilum to salt stress.

Ectomycorrhizal (ECM) fungi improve the host plant's tolerance to abiotic and biotic stresses. Cenococcum geophilum (Cg) is among the most common ECM fungi worldwide and often grows in saline environments. However, the physiological and molecular mechanisms of salt tolerance in this fungus are largely unknown.

Self-similar hierarchy of coherent tubular vortices in turbulence.

Energy transfers from larger to smaller scales in turbulence. This energy cascade is a process of the creation of smaller-scale coherent vortices by larger ones. In our recent study (Yoneda, Goto and Tsuruhashi 2022 , 1380-1401), we reformulated the energy cascade in terms of this stretching process and derived the [Formula: see text] law of the energy spectrum under physically reasonable assumptions.

Genetic Dissection of Growth and Eco-Physiological Traits Associated with Altitudinal Adaptation in Sakhalin Fir () Based on QTL Mapping.

(1) Background: The genetic basis of local adaptation in conifers remains poorly understood because of limited research evidence and the lack of suitable genetic materials. Sakhalin fir () is an ideal organism for elucidating the genetic basis of local adaptation because its altitudinal adaptation has been demonstrated, and suitable materials for its linkage mapping are available. (2) Method: We constructed P336 and P236 linkage maps based on 486 and 516 single nucleotide polymorphisms, respectively, that were derived from double digest restriction site-associated DNA sequences.

Directional seed and pollen dispersal and their separate effects on anisotropy of fine-scale spatial genetic structure among seedlings in a dioecious, wind-pollinated, and wind-dispersed tree species, .

Prevailing directions of seed and pollen dispersal may induce anisotropy of the fine-scale spatial genetic structure (FSGS), particularly in wind-dispersed and wind-pollinated species. To examine the separate effects of directional seed and pollen dispersal on FSGS, we conducted a population genetics study for a dioecious, wind-pollinated, and wind-dispersed tree species, Sieb. et Zucc, based on genotypes at five microsatellite loci of 281 adults of a population distributed over a ca.

Transfer learning for nonlinear dynamics and its application to fluid turbulence.

We introduce transfer learning for nonlinear dynamics, which enables efficient predictions of chaotic dynamics by utilizing a small amount of data. For the Lorenz chaos, by optimizing the transfer rate, we accomplish more accurate inference than the conventional method by an order of magnitude. Moreover, a surprisingly small amount of learning is enough to infer the energy dissipation rate of the Navier-Stokes turbulence because we can, thanks to the small-scale universality of turbulence, transfer a large amount of the knowledge learned from turbulence data at lower Reynolds number.

Deficiency of Gankyrin in the small intestine is associated with augmented colitis accompanied by altered bacterial composition of intestinal microbiota.

Background: Gankyrin (GK) is an oncoprotein which regulates inflammatory responses and its inhibition is considered as a possible anti-inflammatory therapy for inflammatory bowel disease (IBD).

Methods: In this study, we investigated the role of GK in epithelial cells using mice with intestinal epithelial cell-specific GK deletion in (i) the entire small intestine and colon (Villin-Cre;Gankyrin) and (ii) the distal intestine and colon (Cdx2-Cre;Gankyrin).

Result: Unexpectedly, GK-deficiency in the upper small bowel augmented inflammatory activity compared with control mice when colitis was induced with dextran sodium sulfate.

KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold.

Summary: KofamKOALA is a web server to assign KEGG Orthologs (KOs) to protein sequences by homology search against a database of profile hidden Markov models (KOfam) with pre-computed adaptive score thresholds. KofamKOALA is faster than existing KO assignment tools with its accuracy being comparable to the best performing tools. Function annotation by KofamKOALA helps linking genes to KEGG resources such as the KEGG pathway maps and facilitates molecular network reconstruction.

Distinctions in Fine-Scale Spatial Genetic Structure Between Growth Stages of Carr.

Conifers in northern forests, such as fir and spruce, preferably regenerate on coarse woody debris, including fallen logs, stumps, and snags. In northern Japan, the sub-boreal conifer species is completely dependent on coarse woody debris for seedling establishment. To understand the fine-scale spatial genetic structure (FSGS) of this species, a 5-ha plot was established in central Hokkaido, and 531 individual trees were categorized into four life-stages (seedling, sapling, juvenile, and mature) on the basis of age and size.

The jPOST environment: an integrated proteomics data repository and database.

Rapid progress is being made in mass spectrometry (MS)-based proteomics, yielding an increasing number of larger datasets with higher quality and higher throughput. To integrate proteomics datasets generated from various projects and institutions, we launched a project named jPOST (Japan ProteOme STandard Repository/Database, https://jpostdb.org/) in 2015.

Correction: Locality and diel cycling of viral production revealed by a 24 h time course cross-omics analysis in a coastal region of Japan.

The original version of this Article contained an error in the main text citations and reference list. These errors have now been corrected in both the PDF and HTML versions of the Article.

Collective Motion of Repulsive Brownian Particles in Single-File Diffusion with and without Overtaking.

Subdiffusion is commonly observed in liquids with high density or in restricted geometries, as the particles are constantly pushed back by their neighbors. Since this "cage effect" emerges from many-body dynamics involving spatiotemporally correlated motions, the slow diffusion should be understood not simply as a one-body problem but as a part of collective dynamics, described in terms of space-time correlations. Such collective dynamics are illustrated here by calculations of the two-particle displacement correlation in a system of repulsive Brownian particles confined in a (quasi-)one-dimensional channel, whose subdiffusive behavior is known as the single-file diffusion (SFD).

Taxon Richness of "Megaviridae" Exceeds those of Bacteria and Archaea in the Ocean.

Since the discovery of the giant mimivirus, evolutionarily related viruses have been isolated or identified from various environments. Phylogenetic analyses of this group of viruses, tentatively referred to as the family "Megaviridae", suggest that it has an ancient origin that may predate the emergence of major eukaryotic lineages. Environmental genomics has since revealed that Megaviridae represents one of the most abundant and diverse groups of viruses in the ocean.

MAPLE 2.3.0: an improved system for evaluating the functionomes of genomes and metagenomes.

MAPLE is an automated system for inferring the potential comprehensive functions harbored by genomes and metagenomes. To reduce runtime in MAPLE analyzing the massive amino acid datasets of over 1 million sequences, we improved it by adapting the KEGG automatic annotation server to use GHOSTX and verified no substantial difference in the MAPLE results between the original and new implementations.

TodoFirGene: Developing Transcriptome Resources for Genetic Analysis of Abies sachalinensis.

Todo-matsu (Abies sachalinensis) is one of the most important forestry species in Hokkaido, Japan and is distributed from near sea level to the alpine zone. Due to its wide spatial distribution, the species adapts to its environment, displaying phenotypes of ecological relevance. In order to identify candidate genes under natural selection, we collected the transcriptome from the female and male flower, leaf and inner bark.

Locality and diel cycling of viral production revealed by a 24 h time course cross-omics analysis in a coastal region of Japan.

Viruses infecting microorganisms are ubiquitous and abundant in the ocean. However, it is unclear when and where the numerous viral particles we observe in the sea are produced and whether they are active. To address these questions, we performed time-series analyses of viral metagenomes and microbial metatranscriptomes collected over a period of 24 h at a Japanese coastal site.

Supplementation of pancreatic digestive enzymes alters the composition of intestinal microbiota in mice.

Although pancreatic enzyme replacement therapy (PERT) is effective in the alleviation of pancreatic exocrine insufficiency (PEI)-related symptoms in patients with chronic pancreatitis, its mechanism of action is poorly understood. Recent studies suggest that the intestinal microbiota is associated with the pathogenesis of chronic pancreatitis. Therefore, we hypothesized that PERT exerts its effect by modifying the intestinal microbiota in addition to its presumed role in promoting fat and protein absorption.