Transcriptomic Insights into Post-Spawning Death and Muscle Atrophy in Ayu ().

In semelparous species like the ayu (), spawning is followed by rapid physiological decline and death; yet, the underlying molecular mechanisms remain largely unexplored. This study examines transcriptomic changes in ayu skeletal muscle before and after spawning, with a focus on key genes and pathways contributing to muscle atrophy and metabolic dysfunction. Through RNA sequencing and DEG analysis, we identified over 3000 DEGs, and GSEA and KEGG pathway analysis revealed significant downregulation of energy metabolism and protein degradation.

Nodular-bronchiectatic pattern in pulmonary nocardiosis: Immune status and treatment outcomes in a multicenter retrospective study.

Background: Pulmonary nocardiosis is a rare opportunistic infection, with approximately 15 % of patients being immunocompetent. The isolation rate of Nocardia spp. has recently increased, indicating rising clinical concern.

Metagenomic sequencing of CRISPRs as a new marker to aid in personal identification with low-biomass samples.

The high specificity of the human skin microbiome is expected to provide a new marker for personal identification. Metagenomic sequencing of clustered regularly interspaced short palindromic repeats (CRISPRs), which we call metaCRISPR typing, was shown to achieve personal identification accurately. However, the intra-individual variability observed in previous studies, which may be due to poor DNA yields from skin samples, has resulted in non-reproducible results.

Unsupervised Dual Deep Hashing with Semantic-Index and Content-Code for Cross-Modal Retrieval.

Hashing technology has exhibited great cross-modal retrieval potential due to its appealing retrieval efficiency and storage effectiveness. Most current supervised cross-modal retrieval methods heavily rely on accurate semantic supervision, which is intractable for annotations with ever-growing sample sizes. By comparison, the existing unsupervised methods rely on accurate sample similarity preservation strategies with intensive computational costs to compensate for the lack of semantic guidance, which causes these methods to lose the power to bridge the semantic gap.

A Method for Inferring Polymers Based on Linear Regression and Integer Programming.

A novel framework has recently been proposed for designing the molecular structure of chemical compounds with a desired chemical property using both artificial neural networks and mixed integer linear programming. In this paper, we design a new method for inferring a polymer based on the framework. For this, we introduce a new way of representing a polymer as a form of monomer and define new descriptors that feature the structure of polymers.

Endoscopic Total Maxillectomy Without Facial Skin Incision.

This study presents a pioneering report on an endoscopic assisted total maxillectomy that allows for en bloc resection without a facial skin incision. Laryngoscope, 135:124-129, 2025.

A practically efficient algorithm for identifying critical control proteins in directed probabilistic biological networks.

Network controllability is unifying the traditional control theory with the structural network information rooted in many large-scale biological systems of interest, from intracellular networks in molecular biology to brain neuronal networks. In controllability approaches, the set of minimum driver nodes is not unique, and critical nodes are the most important control elements because they appear in all possible solution sets. On the other hand, a common but largely unexplored feature in network control approaches is the probabilistic failure of edges or the uncertainty in the determination of interactions between molecules.

Analysis of Carcinogenic Involvement of MicroRNA Pattern in Peripheral Non-Cancerous Tissues and Chronic Viral Liver Injury.

Risk factors for hepatocarcinogenesis include chronic inflammation due to viral infection, liver fibrosis, and aging. In this study, we separated carcinogenic and non-carcinogenic cases due to hepatitis C virus (HCV) infection, aiming to comprehensively analyze miRNA expression in liver tissues by age, and identify factors that contribute to carcinogenesis. Total RNA was extracted from 360 chronic hepatitis C (CH), 43 HCV infected hepatocellular carcinoma (HCC), and surrounding non-tumor (SNT) tissues.

Target control of linear directed networks based on the path cover problem.

Securing complete control of complex systems comprised of tens of thousands of interconnected nodes holds immense significance across various fields, spanning from cell biology and brain science to human-engineered systems. However, depending on specific functional requirements, it can be more practical and efficient to focus on a pre-defined subset of nodes for control, a concept known as target control. While some methods have been proposed to find the smallest driver node set for target control, they either rely on heuristic approaches based on k-walk theory, lacking a guarantee of optimal solutions, or they are overly complex and challenging to implement in real-world networks.

A well-managed case of discontinuous anorectal injury caused by a personal watercraft treated by combining surgery and colonoscopy.

Background: Anorectal injury caused by personal watercraft (PWC)-related trauma is rare. However, PWC accidents have increased recently, and since patients tend to be younger, treatment strategies should consider anal function preservation in addition to saving lives.

Case Presentation: A 30-year-old female patient who fell into the water when a PWC suddenly accelerated and injured her perineum with a forceful water jet was transported to our hospital.

Distributed Pinning Control: Stabilizing Large Boolean Networks Subjected to Perturbations.

Stability maintenance in systems refers to the capacity to preserve inherent stability characteristics. In this article, stability maintenance of large boolean networks (BNs) subjected to perturbations is investigated using a distributed pinning control (PC) strategy. The concept of edge removal as a form of perturbation is introduced, and several criteria for achieving global stability are established.

Molecular Design Based on Integer Programming and Splitting Data Sets by Hyperplanes.

A novel framework for designing the molecular structure of chemical compounds with a desired chemical property has recently been proposed. The framework infers a desired chemical graph by solving a mixed integer linear program (MILP) that simulates the computation process of two functions: a feature function defined by a two-layered model on chemical graphs and a prediction function constructed by a machine learning method. To improve the learning performance of prediction functions in the framework, we design a method that splits a given data set C into two subsets C,i=1,2 by a hyperplane in a chemical space so that most compounds in the first (resp.

Quantitative evaluation of endometrium-expressed mRNAs for the purpose of discriminating between menstruation and traumatic vaginal injury in sexual assault cases.

In sexual assault cases, it is crucial to discriminate between peripheral blood and menstrual blood to provide evidence for vaginal intercourse with traumatic injury. In this study, the menstrual blood mRNA markers progestagen-associated endometrial protein (PAEP), matrix metallopeptidase 7 (MMP7), and left-right determination factor 2 (LEFTY2) were evaluated by quantitative RT-PCR (RT-qPCR) for the discrimination of menstrual blood from peripheral blood and vaginal fluid. As a result, all markers with cutoff delta cycle quantification (ΔCq) values were specifically determined in menstrual blood among forensically relevant body fluids.

Comparison of complications and functional outcomes following total or subtotal glossectomy with laryngeal preservation using a deep inferior epigastric artery perforator free flap versus a rectus abdominis musculocutaneous free flap.

Objective: Wide defects resulting from subtotal or total glossectomy are commonly reconstructed using a bulk flap to maintain oral and speech functions. The flap, including muscle tissue, diminishes with time. This study aimed to compare the surgical outcomes of deep inferior epigastric artery perforator and rectus abdominis musculocutaneous free flap reconstructions after glossectomy with laryngeal preservation.

The gene is required for the early stages of sporangium formation in .

Unlabelled: In , multiple paralogs of SsgA-like proteins (SALPs) are involved in spore formation from aerial hyphae. However, the functions of SALPs have not yet been elucidated in other actinobacterial genera. Here, we report the primary function of an SsgB ortholog (AmSsgB) in , which develops terminal sporangia on the substrate mycelia via short sporangiophores.

Measuring criticality in control of complex biological networks.

Recent controllability analyses have demonstrated that driver nodes tend to be associated to genes related to important biological functions as well as human diseases. While researchers have focused on identifying critical nodes, intermittent nodes have received much less attention. Here, we propose a new efficient algorithm based on the Hamming distance for computing the importance of intermittent nodes using a Minimum Dominating Set (MDS)-based control model.

DiCleave: a deep learning model for predicting human Dicer cleavage sites.

Background: MicroRNAs (miRNAs) are a class of non-coding RNAs that play a pivotal role as gene expression regulators. These miRNAs are typically approximately 20 to 25 nucleotides long. The maturation of miRNAs requires Dicer cleavage at specific sites within the precursor miRNAs (pre-miRNAs).

Development and comparison of forensic interval age prediction models by statistical and machine learning methods based on the methylation rates of ELOVL2 in blood DNA.

Age estimation can be useful information for narrowing down candidates of unidentified donors in criminal investigations. Various age estimation models based on DNA methylation biomarkers have been developed for forensic usage in the past decade. However, many of these models using ordinary least squares regression cannot generate an appropriate estimation due to the deterioration in prediction accuracy caused by an increased prediction error in older age groups.

On the Size and Width of the Decoder of a Boolean Threshold Autoencoder.

In this brief paper, we study the size and width of autoencoders consisting of Boolean threshold functions, where an autoencoder is a layered neural network whose structure can be viewed as consisting of an encoder, which compresses an input vector to a lower dimensional vector, and a decoder which transforms the low-dimensional vector back to the original input vector exactly (or approximately). We focus on the decoder part and show that [Formula: see text] and O(√{Dn}) nodes are required to transform n vectors in d -dimensional binary space to D -dimensional binary space. We also show that the width can be reduced if we allow small errors, where the error is defined as the average of the Hamming distance between each vector input to the encoder part and the resulting vector output by the decoder.

SMG: self-supervised masked graph learning for cancer gene identification.

Cancer genomics is dedicated to elucidating the genes and pathways that contribute to cancer progression and development. Identifying cancer genes (CGs) associated with the initiation and progression of cancer is critical for characterization of molecular-level mechanism in cancer research. In recent years, the growing availability of high-throughput molecular data and advancements in deep learning technologies has enabled the modelling of complex interactions and topological information within genomic data.

Multi-shelled ECIF: improved extended connectivity interaction features for accurate binding affinity prediction.

Motivation: Extended connectivity interaction features (ECIF) is a method developed to predict protein-ligand binding affinity, allowing for detailed atomic representation. It performed very well in terms of Comparative Assessment of Scoring Functions 2016 (CASF-2016) scoring power. However, ECIF has the limitation of not being able to adequately account for interatomic distances.

Whole-Brain Evaluation of Cortical Microconnectomes.

The brain is an organ that functions as a network of many elements connected in a nonuniform manner. In the brain, the neocortex is evolutionarily newest and is thought to be primarily responsible for the high intelligence of mammals. In the mature mammalian brain, all cortical regions are expected to have some degree of homology, but have some variations of local circuits to achieve specific functions performed by individual regions.