Negatively selected genes (NSGs) and positively selected genes (PSGs) are the two types of most nuclear protein-coding genes in organisms. However, the evolutionary rates and characteristics of different types of genes have been rarely understood. In...
Laccases (EC 1.10.3.2) have been widely considered to participate in the metabolic processes of lignin synthesis, osmotic stress response, and flavonoid oxidation in higher plants. The research into Populus trichocarpa laccase focused on the synthesi...
Ascorbate peroxidase (APX) is an important antioxidant enzyme. APXs in maize are encoded by multiple genes and exist as isoenzymes. The evolutionary history and functional divergence of the maize APX gene family were analyzed through comparative geno...
Anthocyanin is the main pigment forming floral diversity. Several transcription factors that regulate the expression of anthocyanin biosynthetic genes belong to the R2R3-MYB family. Here we examined the transcriptomes of inflorescence buds of Scutel...
Alcohol dehydrogenases (ADHs) are critical enzymes involved in the oxidation of alcohols, contributing to various metabolic pathways across organisms. This study investigates type I functional divergence within three ADH1 families: Saccharomyces cere...
Sugars are critical for plant growth and development as suppliers of carbon and energy, as signal molecules, or as solute molecules for osmotic homeostasis. Monosaccharide transporter (MST) genes are involved in various processes of plant growth and...
Transferrin is an important iron-binding glycosylated protein and plays key roles in iron-binding and immune response. Here, a 2037-bp open reading frame was obtained from our previous transcriptome sequencing data of Amur stickleback, which encoded...
The five members of the mammalian G subfamily of ATP-binding cassette transporters differ greatly in their substrate specificity. Four members of the subfamily are important in lipid transport and the wide substrate specificity of one of the members,...
Using Taylor-type expansions, we obtain identity expressions for functions on three intervals and differences for two pairs of Csiszár
Inositol polyphosphate 5-phosphatase (5PTase), a key enzyme that hydrolyzes the 5′ position of the inositol ring, has essential functions in growth, development, and stress responses in plants, yeasts, and animals. However, the evolutionary his...
Research Highlights: Functional diversity studies help to better understand how organisms respond to different environmental conditions. Conditions in tropical flooded forests are highly variable, including levels of nutrient availability, pH, and fl...
The AGAMOUS-LIKE6 (AGL6) lineage is an important clade of MADS-box transcription factors that play essential roles in floral organ development. The genome of Prunus mume contains two homoeologous AGL6 genes that are replicated as gene fragments. In t...
Chemokine receptor Cxcr4 evolved two paralogs in the teleost lineage. However, cxcr4a and cxcr4b have been characterized only in a few species. In this study, we identified two cxcr4 paralogs from the orange-spotted grouper, Epinephelus coioides. The...
Invasive Alien Species (IAS) are a serious threat to biodiversity, severely affecting natural habitats and species assemblages. However, no consistent empirical evidence emerged on which functional traits or trait combination may foster community inv...
This study examined the unfolding in real time of original ideas during divergent thinking (DT) in five- to six-year-olds and related individual differences in DT to executive functions (EFs). The Alternative Uses Task was administered with verbal pr...
K-mer analysis is a powerful tool for understanding genome structure and evolution. A “k-mer” refers to a short DNA sequence made up of k nucleotides (where k is a specific integer), while an “m-mer” is a similar concept but w...
Inter- and intratumor heterogeneity is an important cause of treatment failure. In human pancreatic cancer (PC), heterogeneity has been investigated almost exclusively at the genomic and transcriptional level. Morphological heterogeneity, though prom...
SMYD5 belongs to a special class of protein lysine methyltransferases with an MYND (Myeloid-Nervy-DEAF1) domain inserted into a SET (Suppressor of variegation, Enhancer of Zeste, Trithorax) domain. Despite recent advances in its functional characteri...
Salmonella enterica is a leading cause of bacterial food-borne illness in humans and is responsible for millions of cases annually. A critical strategy for the survival of this pathogen is the translocation of bacterial virulence factors termed effec...
The WOX (WUSCHEL-related homeobox) is a plant-specific transcription factor involved in plant development and stress response. However, few studies have been reported on the WOX gene in woody plants. In this study, 10 BpWOX genes were isolated from p...
TPX2 (Targeting Protein for Xklp2) is an evolutionary conserved microtubule-associated protein important for microtubule nucleation and mitotic spindle assembly. The protein was described as an activator of the mitotic kinase Aurora A in humans and t...
Superoxide dismutases (SODs), a family of antioxidant enzymes, are the first line of defense against oxidative damage and are ubiquitous in every cell of all plant types. The Cu/Zn SOD, one of three types of SODs present in plant species, is involved...
In this paper, we introduce new divergences called Jensen–Sharma–Mittal and Jeffreys–Sharma–Mittal in relation to convex functions. Some theorems, which give the lower and upper bounds for two new introduced divergences, are p...
AIG1 (avrRpt2-induced gene 1)-like proteins are a class of GTPases that play crucial roles in plants, functioning both in chloroplast protein import and disease resistance. However, their evolutionary history and the mechanisms driving this functiona...
Disparities in the functional classification of secretory genes among aphid taxa may be attributed to variations in coding sequences and gene expression profiles. However, the driving factors that regulate sequence evolution remain unclear. This stud...
In this paper, we propose a generalization of Rényi divergence, and then we investigate its induced geometry. This generalization is given in terms of a φ-function, the same function that is used in the definition of non-parametric φ-families. The pr...
Signalling activities are tightly regulated to control cellular responses. Heparan sulfate proteoglycans (HSPGs) at the cell membrane and extracellular matrix regulate ligand availability and interaction with a range of key receptors. SULF1 and SULF2...
Functional divergences of coding genes can be caused by divergences in their coding sequences and expression. However, whether and how expression divergences and coding sequence divergences coevolve is not clear. Gene expression divergences in differ...
In image and signal processing, the beta-divergence is well known as a similarity measure between two positive objects. However, it is unclear whether or not the distance-like structure of beta-divergence is preserved, if we extend the domain of the...
The evolution of robust DNA repair mechanisms was a prerequisite for the conquest of land by plants, a transition that exposed them to harsh new environmental stressors. The poly (ADP-ribose) polymerase (PARP) family is central to this adaptation, as...
Functional diversity is considered a key link between ecosystem functions and biodiversity, and forms the basis for making community diversity conservation strategies. Here, we chose a subtropical forest community in China as the research object, whi...
The mechanisms through which forest thinning influences the fine root foraging strategies of coexisting tree species in mixed forests remain unclear, limiting our ability to manage mixed forests for long-term productivity. We employed a space-for-tim...
The functional components in cereals (rice and barley), such as gamma-aminobutyric acid (GABA), resistant starch (RS), and alkaloids, play crucial roles in human health, offering benefits such as improved cardiovascular function, enhanced gut microbi...
Within exponential families, which may consist of multi-parameter and multivariate distributions, a variety of divergence measures, such as the Kullback–Leibler divergence, the Cressie–Read divergence, the Rényi divergence, and the Hellinger metric,...
Members of AP1/FUL subfamily genes play an essential role in the regulation of floral meristem transition, floral organ identity, and fruit ripping. At present, there have been insufficient studies to explain the function of the AP1/FUL-like subfamil...
Ionotropic receptors (IRs) are a divergent subfamily of ionotropic glutamate receptors (iGluRs) that detect olfactory and environmental cues, influencing behaviors such as foraging and adaptation. To explore the evolution of IRs in relation to feedin...
Dkks have inhibitory effects on the Wnt signaling pathway, which is involved in the development of skin and its appendages and the regulation of hair growth. The nucleotide sequences were compared and analyzed to further investigate the relationship...
Information geometry concerns the study of a dual structure
A unifying
In this paper, we use the generalized version of convex functions, known as strongly convex functions, to derive improvements to the Jensen–Mercer inequality. We achieve these improvements through the newly discovered characterizations of stron...
The domain of unknown function (DUF) superfamily encodes proteins of unknown functions in plants. Among them, DUF668 family members in plants possess a 29 amino-acid conserved domain, and this family has not been described previously. Here, we report...
The density power divergence (DPD) is a well-studied member of the Bregman divergence family and forms the basis of widely used minimum divergence estimators that balance efficiency and robustness. In this paper, we introduce and study a new sub-clas...
The divergence function in information geometry, and the discrete Lagrangian in discrete geometric mechanics each induce a differential geometric structure on the product manifold
Riparian forests are important for maintaining aquatic biodiversity, yet they face increasing pressure from logging activities. This study assessed the functional diversity of Ephemeroptera, Plecoptera, and Trichoptera (EPT) in 30 Amazonian first-ord...
RAC3 encodes a small Rho-family GTPase essential for cytoskeletal regulation and neurodevelopment, and de novo RAC3 variants typically act as gain-of-function alleles that cause severe neurodevelopmental disorders. In this study, we analyzed a fetus...
Generative modelling is an important unsupervised task in machine learning. In this work, we study a hybrid quantum-classical approach to this task, based on the use of a quantum circuit born machine. In particular, we consider training a quantum cir...
To address the unknown nature of probability-sampling models, in this paper we use information theoretic concepts and the Cressie-Read (CR) family of information divergence measures to produce a flexible family of probability distributions, likelihoo...
In this paper, we introduce a novel objective prior distribution levering on the connections between information, divergence and scoring rules. In particular, we do so from the starting point of convex functions representing information in density fu...
In this work, we define cumulative residual q-Fisher (CRQF) information measures for the survival function (SF) of the underlying random variables as well as for the model parameter. We also propose q-hazard rate (QHR) function via q-logarithmic func...
Axiomatic characterizations of Shannon entropy, Kullback I-divergence, and some generalized information measures are surveyed. Three directions are treated: (A) Characterization of functions of probability distributions suitable as information measur...
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