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Simple Summary: The nematode Caenorhabditis elegans, which is only 1 mm long, is used as a model to study the effects of irradiation on tissues (organs) of living organisms. This paper reviews the development of irradiation techniques using charged-particle microbeams in Japan, the U.S., China, and France, in which heavy-ion and proton beams (types of ionizing radiation) are targeted to specific cells or regions of C. elegans, and outlines the progress made over the past 20 years and where we are today. An essential part of irradiating the targeted cell/tissue of microscopic animals is having an immobilization method which does not damage the animals' physiological activity. This article introduces some technical difficulties that differ from those concerning the irradiation of cultured cells, which have been the main target of irradiation in the past. Charged-particle microbeam irradiation devices, which can convert heavy-ion or proton beams into microbeams and irradiate individual animal cells and tissues, have been developed and used for bioirradiation in Japan, the United States, China, and France. Microbeam irradiation technology has been used to analyze the effects of irradiation on mammalian cancer cells, especially bystander effects. In 2006, individual-level microbeam irradiation of the nematode Caenorhabditis elegans was first realized using JAEA-Takasaki's (now QST-TIAQS's) TIARA collimated microbeam irradiation device. As of 2023, microbeam irradiation of C. elegans has been achieved at five sites worldwide (one in Japan, one in the United States, one in China, and two in France). This paper summarizes the global progress in the field of microbeam biology using C. elegans, while focusing on issues unique to microbeam irradiation of live C. elegans, such as the method of immobilizing C. elegans for microbeam experiments. [ABSTRACT FROM AUTHOR]

Simple Summary: In this study, we ask whether the invasive paper mulberry (Broussonetia papyrifera) has a competitive advantage over neighbor trees in a native area. We determined the competitive capacity of paper mulberry in three deciduous broad-leaved forests using structural indices including the mixing index, the tree–tree interval index, and the diameter/height differentiation index. It was found that the reference paper mulberry had a slight competitive advantage over neighboring trees in both the horizontal and vertical planes. Such a competitive ability may play a significant role in the ecological invasion of paper mulberry. Our findings not only help to reveal the invasion mechanism of paper mulberry, but also provide an important reference for the management and utilization of paper mulberry in invaded areas. Paper mulberry (Broussonetia papyrifera) is currently an invasive species on several continents. However, little is known about whether paper mulberry has a competitive advantage over its surrounding trees in its native distribution range, subtropical regions of China. Here, we determined the relative intraspecific and interspecific competitive capacity of paper mulberry in three subtropical deciduous broad-leaved forests using the indices of structural diversity including the mixing index, the tree–tree interval index, and the diameter/height differentiation index. It was found that more than 80% of mingling index values were not greater than 0.25, suggesting a stronger competitiveness of paper mulberry relative to other tree species. The tree–tree interval index values ranged between 1 m and 2 m, suggesting a strong competition between paper mulberry and its neighbors. Moreover, more than 60% of the height differentiation index and diameter differentiation index values were positive, suggesting that the reference paper mulberry had a slight competitive advantage over neighboring trees in both the horizontal and vertical planes. These collectively suggest a competitive advantage over other tree species in the native distribution range, which may play a significant role in the ecological invasion of paper mulberry. Our findings not only help to reveal the invasion mechanism of paper mulberry, but also provide an important reference for the management and utilization of paper mulberry in invaded areas. [ABSTRACT FROM AUTHOR]

Simple Summary: Phenylpropanoids are specialized metabolites playing crucial roles in plant developmental processes and in plant defense towards pathogens. The attachment of sugar moieties to these small hydrophobic molecules renders them more hydrophilic and increases their solubility. The UDP-glycosyltransferase 72 family (UGT72) of plants has been shown to glycosylate mainly two classes of phenylpropanoids, (i) the monolignols that are the building blocks of lignin, the second most abundant polymer after cellulose, and (ii) the flavonoids, which play determinant roles in plant interactions with other organisms and in response to stress. The purpose of this review is to bring an overview of the current knowledge of the UGT72 family and to highlight its role in the homeostasis of these molecules. Potential applications in pharmacology and in wood, paper pulp, and bioethanol production are given within the perspectives. Plants have developed the capacity to produce a diversified range of specialized metabolites. The glycosylation of those metabolites potentially decreases their toxicity while increasing their stability and their solubility, modifying their transport and their storage. The UGT, forming the largest glycosyltransferase superfamily in plants, combine enzymes that glycosylate mainly hormones and phenylpropanoids by using UDP-sugar as a sugar donor. Particularly, members of the UGT72 family have been shown to glycosylate the monolignols and the flavonoids, thereby being involved in their homeostasis. First, we explore primitive UGTs in algae and liverworts that are related to the angiosperm UGT72 family and their role in flavonoid homeostasis. Second, we describe the role of several UGT72s glycosylating monolignols, some of which have been associated with lignification. In addition, the role of other UGT72 members that glycosylate flavonoids and are involved in the development and/or stress response is depicted. Finally, the importance to explore the subcellular localization of UGTs to study their roles in planta is discussed. [ABSTRACT FROM AUTHOR]

Simple Summary: Zebrafish form an ideal model for studying a wide range of ophthalmological and neurological conditions. The optokinetic reflex (OKR) assays in zebrafish models are proven to be a valuable tool for investigating these conditions. Despite its increasing popularity in recent years, the field lacks clear reporting guidelines for the assay. To better understand optimal reporting standards for an OKR assay in zebrafish, we performed a systematic literature review of 109 research papers exploring the animal, environmental, and technical factors that should be considered. In this article, we highlight multiple crucial factors, such as larval characteristics, sample size, fixing method, assay set-up, detailed stimulus parameters, eye recording, and eye movement analysis, necessary for preforming the assay. We have created the zebrafish optokinetic (ZOK) reflex minimal reporting guideline that will allow researchers to avoid future errors and create more reliable and transparent research. Optokinetic reflex (OKR) assays in zebrafish models are a valuable tool for studying a diverse range of ophthalmological and neurological conditions. Despite its increasing popularity in recent years, there are no clear reporting guidelines for the assay. Following reporting guidelines in research enhances reproducibility, reduces bias, and mitigates underreporting and poor methodologies in published works. To better understand optimal reporting standards for an OKR assay in zebrafish, we performed a systematic literature review exploring the animal, environmental, and technical factors that should be considered. Using search criteria from three online databases, a total of 109 research papers were selected for review. Multiple crucial factors were identified, including larval characteristics, sample size, fixing method, OKR set-up, distance of stimulus, detailed stimulus parameters, eye recording, and eye movement analysis. The outcome of the literature analysis highlighted the insufficient information provided in past research papers and the lack of a systematic way to present the parameters related to each of the experimental factors. To circumvent any future errors and champion robust transparent research, we have created the zebrafish optokinetic (ZOK) reflex minimal reporting guideline. [ABSTRACT FROM AUTHOR]

Simple Summary: The study of cell features has historically been key for the progress of biological sciences and its relevance remains intact. In recent years, mass cytometry has emerged as a promising and powerful technology, capable of studying multiple parameters of cells in the same sample. Mass cytometry has been quickly applied to many research areas, particularly to the study of the immune system for different purposes, in which the simultaneous analysis of a large number of proteins is crucial. However, despite being a technique that is on the rise, its performance in scientific publications has not yet been evaluated. In this work, a bibliometric methodology known as H-Classics was applied to analyse the most relevant articles, known as highly cited papers (HCPs), and determine the main scientific producers (authors, institutions, and countries) and trends around mass cytometry research field. The results confirmed a high interest and application in immunological studies. The identified HCPs came from prestigious institutions and were published in high impact journals. These results may help researchers to expand their knowledge and to establish new valuable collaborative networks around mass cytometry. Mass cytometry (CyTOF) is a relatively novel technique for the multiparametric analysis of single-cell features with an increasing central role in cell biology, immunology, pharmacology, and biomedicine. This technique mixes the fundamentals of flow cytometry with mass spectrometry and is mainly used for in-depth studies of the immune system and diseases with a significant immune load, such as cancer, autoimmune diseases, and viral diseases like HIV or the recently emerged COVID-19, produced by the SARS-CoV-2 coronavirus. The objective of this study was to provide a useful insight into the evolution of the mass cytometry research field, revealing the knowledge structure (conceptual and social) and authors, countries, sources, documents, and organizations that have made the most significant contribution to its development. We retrieved 937 articles from the Web of Science (2010–2019), analysed 71 Highly Cited Papers (HCP) through the H-Classics methodology and computed the data by using Bibliometrix R package. HCP sources corresponded to high-impact journals, such as Nature Biotechnology and Cell, and its production was concentrated in the US, and specifically Stanford University, affiliation of the most relevant authors in the field. HCPs analysis confirmed great interest in the study of the immune system and complex data processing in the mass cytometry research field. [ABSTRACT FROM AUTHOR]

Simple Summary: The evolutionary process can be seen as a process of acquisition, storage, and updating of information by a population about the environment in which it lives. In this paper, I propose a model that starts with the distribution of mating that occurs according to mutual mating fitness and ends with the distribution of viable adult genotypes obtained after this mating. The result of the evolutionary dynamics associated with each stage of the model can be described in terms of information. This informational description facilitates the connection between cause and effect, as well as the development of statistics to test the null model of zero information, i.e., random mating and/or no effect of natural selection. Incorporating the informational perspective into the mathematical formalism of population genetics/genomics contributes to clarifying, expanding, and deepening the mathematical description of evolutionary theory. Population genetics describes evolutionary processes, focusing on the variation within and between species and the forces shaping this diversity. Evolution reflects information accumulated in genomes, enhancing organisms' adaptation to their environment. In this paper, I propose a model that begins with the distribution of mating based on mutual fitness and progresses to viable adult genotype distribution. At each stage, the changes result in different measures of information. The evolutionary dynamics at each stage of the model correspond to certain aspects of interest, such as the type of mating, the distribution of genotypes in regard to mating, and the distribution of genotypes and haplotypes in the next generation. Changes to these distributions are caused by variations in fitness and result in Jeffrey's divergence values other than zero. As an example, a model of hybrid sterility is developed of a biallelic locus, comparing the information indices associated with each stage of the evolutionary process. In conclusion, the informational perspective seems to facilitate the connection between cause and effect and allows the development of statistical tests to perform hypothesis testing against zero-information null models (random mating, no selection, etc.). The informational perspective could contribute to clarify, deepen, and expand the mathematical foundations of evolutionary theory. [ABSTRACT FROM AUTHOR]

Simple Summary: Uncertainty in biology refers to situations in which information is imperfect or unknown. Variability is measured by the frequency distribution of observed data, allowing for an understanding of the fundamental principles influencing diversity across different levels of biological organization. Biological variability adds to the uncertainty. The Constrained Disorder Principle (CDP) defines all systems in the universe by their inherent variability. Per the CDP, while variability differs from uncertainty, it can be viewed as a regulated mechanism for efficient functionality rather than uncertainty. This paper examines the different aspects of uncertainty in biology. It specifically looks at using CDP-based platforms to improve fuzzy algorithms and tackle some of the challenges related to biological and medical uncertainties. The goal is to produce algorithm outputs more relevant to biology and clinical applications. Uncertainty in biology refers to situations in which information is imperfect or unknown. Variability, on the other hand, is measured by the frequency distribution of observed data. Biological variability adds to the uncertainty. The Constrained Disorder Principle (CDP) defines all systems in the universe by their inherent variability. According to the CDP, systems exhibit a degree of variability necessary for their proper function, allowing them to adapt to changes in their environments. Per the CDP, while variability differs from uncertainty, it can be viewed as a regulated mechanism for efficient functionality rather than uncertainty. This paper explores the various aspects of un-certainties in biology. It focuses on using CDP-based platforms for refining fuzzy algorithms to address some of the challenges associated with biological and medical uncertainties. Developing a fuzzy decision tree that considers the natural variability of systems can help minimize uncertainty. This method can reveal previously unidentified classes, reduce the number of unknowns, improve the accuracy of modeling results, and generate algorithm outputs that are more biologically and clinically relevant. [ABSTRACT FROM AUTHOR]

Simple Summary: Fluctuations of physiological characteristics play an important role in a living organisms' normal existence and adaptation to environmental conditions. An important feature of oscillations in living systems is their ability to form (synchronization) or break links (desynchronization) with each other. For example, synchronization/desynchronization in the brain's electrical activity plays a role in memory and learning; synchronization changes cause epilepsy and other diseases. The task of quantifying the synchronization of signaling events in cells is currently unsolved. No universal, informative and accurate method has been found for assessing the synchronization of large cell groups. For the first time, we have tested the possibility of applying a mathematical method called bispectral analysis (applied earlier on the whole organism) to assess the coupling of signaling molecules and the level of fluctuations in cells. This method allows for a highly accurate estimation of the connection of oscillations between all pairs of cells in a studied population, the magnitude and frequency of these coupled oscillations, and which cells create and receive a "signal to form a connection of oscillations". We have shown that stress (overheating and excessive glucose concentration) changes the synchronization of oscillations of signaling molecules in cells. The obtained data can be applied in medicine and human economic activity. The oscillation synchronization analysis in biological systems will expand our knowledge about the response of living systems to changes in environmental conditions. This knowledge can be used in medicine (diagnosis, therapy, monitoring) and agriculture (increasing productivity, resistance to adverse effects). Currently, the search is underway for an informative, accurate and sensitive method for analyzing the synchronization of oscillatory processes in cell biology. It is especially pronounced in analyzing the concentration oscillations of intracellular signaling molecules in electrically nonexcitable cells. The bispectral analysis method could be applied to assess the characteristics of synchronized oscillations of intracellular mediators. We chose endothelial cells from mouse microvessels as model cells. Concentrations of well-studied calcium and nitric oxide (NO) were selected for study in control conditions and well-described stress: heating to 40 °C and hyperglycemia. The bispectral analysis allows us to accurately evaluate the proportion of synchronized cells, their synchronization degree, and the amplitude and frequency of synchronized calcium and NO oscillations. Heating to 40 °C increased cell synchronization for calcium but decreased for NO oscillations. Hyperglycemia abolished this effect. Heating to 40 °C changed the frequencies and increased the amplitudes of synchronized oscillations of calcium concentration and the NO synthesis rate. The first part of this paper describes the principles of the bispectral analysis method and equations and modifications of the method we propose. In the second part of this paper, specific examples of the application of bispectral analysis to assess the synchronization of living cells in vitro are presented. The discussion compares the capabilities of bispectral analysis with other analytical methods in this field. [ABSTRACT FROM AUTHOR]

Simple Summary: Due to the rapid development of single-cell RNA sequencing technology, the volume of single-cell RNA sequencing data has grown exponentially. Traditional clustering methods have proven increasingly difficult to cluster this large-scale and highly complex single-cell RNA sequencing data. Although many unsupervised clustering methods based on deep neural networks have been developed to cluster cell subpopulations, these methods are complex in models and poor in scalability. In this paper, we propose a novel clustering method for single-cell RNA sequencing, which successfully combines the advantages of these two clustering models, maintaining high clustering performance while also preserving the stable computational efficiency of traditional clustering methods. Experiments conducted on nine public datasets have demonstrated that our proposed novel clustering method for single-cell RNA sequencing outperforms both classic and state-of-the-art clustering methods. Single-cell RNA sequencing (scRNA-seq) is now a successful technology for identifying cell heterogeneity, revealing new cell subpopulations, and predicting developmental trajectories. A crucial component in scRNA-seq is the precise identification of cell subsets. Although many unsupervised clustering methods have been developed for clustering cell subpopulations, the performance of these methods is prone to be affected by dropout, high dimensionality, and technical noise. Additionally, most existing methods are time-consuming and fail to fully consider the potential correlations between cells. In this paper, we propose a novel unsupervised clustering method called scVGATAE (Single-cell Variational Graph Attention Autoencoder) for scRNA-seq data. This method constructs a reliable cell graph through network denoising, utilizes a novel variational graph autoencoder model integrated with graph attention networks to aggregate neighbor information and learn the distribution of the low-dimensional representations of cells, and adaptively determines the model training iterations for various datasets. Finally, the obtained low-dimensional representations of cells are clustered using kmeans. Experiments on nine public datasets show that scVGATAE outperforms classical and state-of-the-art clustering methods. [ABSTRACT FROM AUTHOR]

Simple Summary: The spread of invasive wild pigs across the United States has been successfully slowed due to the establishment of a national management program. In this paper, we study the effectiveness of the national program by modeling the spread of wild pigs in the absence of intervention. Further, we use the models to assess the value of resources safeguarded from the threat of wild pigs. Our findings indicate that, on average, invasive wild pigs were prevented from spreading to 724 counties, and USD 40.2 billion in resource value was safeguarded over the first eight years of the program. Continuation of the program will deliver additional benefits and further research is critical to understand its comprehensive economic effects. Wild pigs (Sus scrofa) are one of the most destructive invasive species in the US, known for causing extensive damage to agricultural commodities, natural resources, and property, and for transmitting diseases to livestock. Following the establishment of the National Feral Swine Damage Management Program (NFSDMP) in 2014, the expansion of wild pig populations has been successfully slowed. This paper combines two modeling approaches across eight separate models to characterize the expansion of wild pig populations in the absence of intervention by the NFSDMP and forecasts the value of a subset of resources safeguarded from the threat of wild pigs. The results indicate that if wild pigs had continued spreading at pre-program levels, they would have spread extensively across the US, with significant geographic variation across modeling scenarios. Further, by averting the threat of wild pigs, a substantial amount of crops, land, property, and livestock was safeguarded by the NFSDMP. Cumulatively, between 2014 and 2021, wild pig populations were prevented from spreading to an average of 724 counties and an average of USD 40.2 billion in field crops, pasture, grasses, and hay was safeguarded. The results demonstrate that intervention by the NFSDMP has delivered significant ecological and economic benefits that were not previously known. [ABSTRACT FROM AUTHOR]

Simple Summary: The main challenge in libraries, archives, and museums is the fungal deterioration of historical manuscripts (paper and leather), and an eco-friendly approach can be used to reduce or stop biodeterioration. Therefore, the current study examines the green synthesis of titanium oxide nanoparticles (TiO2-NPs) using a green method to inhibit the growth of fungal strains isolated from deteriorated historical manuscripts. Fifteen fungal strains were involved in the deterioration of historical manuscripts dating back to the 16th century that were identified by traditional and molecular identification. In addition, their potential in biodeterioration was investigated by hydrolytic enzymatic activities. TiO2-NPs were synthesized using a probiotic bacterial extract as a safe method and characterized by UV-Vis spectroscopy, X-ray diffraction (XRD), transmission electron microscopy (TEM), energy dispersive X-ray (EDX), and Fourier-transform infrared (FT-IR). The safe concentration of synthesized TiO2-NPs that was used as a coating agent for leather to inhibit fungal growth was detected via the investigation of in vitro cytotoxicity against two normal cell lines (skin and lung). The experimental study showed that the leather without NP treatment and inoculated with the most potent fungal strain exhibited high deterioration compared with those coated with NPs and inoculated with fungal strain. The main hypothesis of the present research is investigating the efficacy of titanium oxide nanoparticles (TiO2-NPs) to prevent the growth of fungal strains when applied on leather under an experimental study. Therefore, fifteen fungal strains were isolated from a deteriorated historical manuscript (papers and leathers) and identified by traditional methods and ITS sequence analysis, including Aspergillus chevalieri (one isolate), A. nidulans (two strains), A. flavus (four strains), A. cristatus (one strain), A. niger (one strain), Paecilomyces fulvus (two strains), Penicillium expansum (two strains), and P. citrinum (two strains). The enzymes cellulase, amylase, pectinase, and gelatinase, which play a crucial role in biodegradation, were highly active in these fungal strains. TiO2-NPs were formed using the cell-free filtrate of the probiotic bacterial strain, Lactobacillus plantarum, and characterized. Data showed that the TiO2-NPs were successfully formed with a spherical shape and anatase phase with sizes of 2–8 nm. Moreover, the EDX analysis revealed that the Ti and O ions occupied the main component with weight percentages of 41.66 and 31.76%, respectively. The in vitro cytotoxicity of TiO2-NPs toward two normal cell lines, WI38 and HFB4, showed a low toxicity effect against normal cells (IC50 = 114.1 ± 8.1µg mL−1 for Wi38, and 237.5 ± 3.5µg mL−1 for HFB4). Therefore, concentrations of 100 μg mL−1 were used to load on prepared leather samples before inoculation with fungal strain P. expansum AL1. The experimental study revealed that the loaded TiO2-NPs have the efficacy to inhibit fungal growth with percentages of 73.2 ± 2.5%, 84.2 ± 1.8%, and 88.8 ± 0.6% after 7, 14, and 21 days, respectively. Also, the analyses including SEM, FTIR-ART, color change, and mechanical properties for leather inoculated with fungal strain AL1 in the absence of NPs showed high damage aspects compared to those inoculated with fungal strains in the presence of TiO2-NPs. [ABSTRACT FROM AUTHOR]

Simple Summary: A bibliometric analysis of studies on the topic of earthworm in the soil ecosystem was conducted to reveal the research advances and trends in the field. The ecological effects of earthworms, the impact of agricultural activities on earthworms, earthworm ecotoxicology and earthworm invasion were four research hotspots on the topic and "impact", ''biodiversity", "oxidative stress", "diversity", "response", "Eisenia fetida" and "exposure" have been the emerging active topics. The earthworm, as a soil engineer, plays highly important roles in the soil ecosystem for shaping soil structure, promoting soil fertility, regulating microbial community composition and activities and decomposing soil pollutants. However, the research progresses on this important soil fauna have rarely been reviewed so far. Therefore, we conducted a bibliometric analysis of the literature published during 1900–2022, which was collected from the Web of Science Core Collection (WoS). The results showed that three periods (1900–1990, 1991–2005 and 2006–2022) could be identified in terms of the intensity of publications on the topic, and the number of publications kept increasing since 2006. The United States produced the highest publication record at the country scale, whereas Chinese Academy of Sciences was the most productive institution. Chinese institutions and authors played an active and prominent role during 2018–2022. Soil Biology & Biochemistry was the most popular journal for the topic-related research. In these publications, Professor Lavelle P was the most influential author. Based on a citation network of the top 50 cited papers, four hotspots were identified, i.e., the ecological effects of earthworms, the impact of agricultural activities on earthworms, earthworm ecotoxicology and earthworm invasion. Moreover, "impact", "biodiversity", "oxidative stress", "diversity", "response", "Eisenia fetida" and "exposure" were the emerging and active topics in recent years. This study can help us to better understand the relevant subject categories, journals, countries, institutions, authors and articles and identify the research hotspots and emerging trends in the field of soil earthworm research. [ABSTRACT FROM AUTHOR]

Simple Summary: Leaves often turn red during senescence, providing us with a colorful life. Anthocyanin accumulation is the main cause of the coloration and its biosynthesis during leaf senescence is an important biological process, which might contain different mechanisms from other tissues. It is essential to understand the molecular mechanism of anthocyanin accumulation during leaf senescence, which would provide new insight into leaf coloration and molecular breeding for more colorful plants in spring or autumn. In this review, we focused on leaf coloration during senescence. We emphatically discussed several networks linked to genetic, hormonal, environmental, and nutritional factors in regulating anthocyanin accumulation during leaf senescence. This paper aims to provide a regulatory model for leaf coloration and to put forward some prospects for future studies. Leaf senescence is the last stage of leaf development, and it is accompanied by a leaf color change. In some species, anthocyanins are accumulated during leaf senescence, which are vital indicators for both ornamental and commercial value. Therefore, it is essential to understand the molecular mechanism of anthocyanin accumulation during leaf senescence, which would provide new insight into autumn coloration and molecular breeding for more colorful plants. Anthocyanin accumulation is a surprisingly complex process, and significant advances have been made in the past decades. In this review, we focused on leaf coloration during senescence. We emphatically discussed several networks linked to genetic, hormonal, environmental, and nutritional factors in regulating anthocyanin accumulation during leaf senescence. This paper aims to provide a regulatory model for leaf coloration and to put forward some prospects for future development. [ABSTRACT FROM AUTHOR]

Simple Summary: The use of sound wave technology on different plant species has revealed that variations in the Hz, sound pressure intensity, treatment time, and type of setup of the sound source significantly impact the plant performance. For example, a study conducted on cotton plants treated by Plant Acoustic Frequency Technology (PAFT) highlighted improvements across various growth parameters. In particular, the treated samples showed increases in the height, leaf area, and number of boll-bearing branches, as well as other plant anatomical parts. In other cases, such as in transgenic rice plants, GUS expression was upregulated or downregulated concerning the Hz employed. This paper presents a complete, rationalized and updated review of the literature on the effects of sound waves on the physiology and growth parameters of sound-treated plants. The application of sound wave technology to different plant species has revealed that variations in the Hz, sound pressure intensity, treatment duration, and type of setup of the sound source significantly impact the plant performance. A study conducted on cotton plants treated with Plant Acoustic Frequency Technology (PAFT) highlighted improvements across various growth metrics. In particular, the treated samples showed increases in the height, size of the fourth expanded leaf from the final one, count of branches carrying bolls, quantity of bolls, and weight of individual bolls. Another study showed how the impact of a 4 kHz sound stimulus positively promoted plant drought tolerance. In other cases, such as in transgenic rice plants, GUS expression was upregulated at 250 Hz but downregulated at 50 Hz. In the same way, sound frequencies have been found to enhance the osmotic potential, with the highest observed in samples treated with frequencies of 0.5 and 0.8 kHz compared to the control. Furthermore, a sound treatment with a frequency of 0.4 kHz and a sound pressure level (SPL) of 106 dB significantly increased the paddy rice germination index, as evidenced by an increase in the stem height and relative fresh weight. This paper presents a complete, rationalized and updated review of the literature on the effects of sound waves on the physiology and growth parameters of sound-treated plants. [ABSTRACT FROM AUTHOR]

Simple Summary: Yaks, which are ruminant animals primarily distributed in the Qinghai–Tibet Plateau, have an unclear skeletal muscle development process. This paper investigates the changes of muscle satellite cells and their epigenetic modifications in yak skeletal muscles during the developmental process. These data provide a theoretical basis for the growth and development of yak skeletal muscles. To investigate prenatal muscle satellite cell (MuSC) development and the associated epigenetic modifications in yak. Here, we conducted morphological and protein co-localization analyses of fetal longissimus dorsi muscle at various developmental stages using histology and immunofluorescence staining methods. Our study observed that primary muscle fibers began forming at 40 days of gestation, fully developed by 11 weeks, and secondary muscle fibers were predominantly formed by around 105 days. Throughout development, MuSCs were mainly located between the muscle fiber membrane and the basement membrane, acting as a reserve for the stem cell pool. MuSCs appeared within myotubes only during critical phases of primary and secondary muscle fiber formation. The proliferation of MuSCs gradually decreases until birth. MuSCs with 5mC modification show a trend of increasing first and then decreasing. MuSCs with 5hmC modification also present a dynamic change trend. The 41st day and 11th week are the critical periods for the changes of both. From the 11th week to around the 110th day of gestation, the modification effect of histone H3K4me3 is crucial for MuSCs during the development of the fetal longissimus dorsi muscle. Combined, our data identify key time points for yak fetal skeletal muscle growth and development and demonstrate that DNA methylation and histone modifications in MuSCs are closely related to this process, offering a valuable basis for future research into the molecular mechanisms underlying yak muscle development. [ABSTRACT FROM AUTHOR]

Simple Summary: Microbial communities living at a depth of 450 m in a granitoid massif (Krasnoyarsk Krai, Russia), potentially suitable for the construction of a radioactive waste storage facility, were studied. It has been established that their activation by organic matter, molecular hydrogen, can cause copper corrosion, which is significantly accelerated in the presence of sulfate ions. Microbial biofilms including sulfate-reducing and fermentative bacteria are resistant to copper ions and can reduce their toxicity during the formation of sulfide minerals. This paper presents the results of microbial corrosion tests on M0-grade copper under conditions simulating a geological repository for radioactive waste at the Yeniseisky site (Krasnoyarsk Krai, Russia). The work used a microbial community sampled from a depth of 450 m and stimulated with glucose, hydrogen and sulfate under anaerobic conditions. It was shown that the maximum corrosion rate, reaching 9.8 µm/y, was achieved with the addition of sulfate (1 g/L) with the participation of microorganisms from the families Desulfomicrobiaceae, Desulfovibrionaceae and Desulfuromonadaceae. It was noted that the most important factor leading to copper corrosion was the accumulation of hydrogen sulfide during the activation of sulfate-reducing microorganisms of the genera Desulfomicrobium, Desulfovibrio and Desulfuromonas. During the development of the microbial community under these conditions, the content of copper can have a significant toxic effect at a concentration of more than 250 mg/L. [ABSTRACT FROM AUTHOR]

Simple Summary: By analyzing inflammatory scores (INFLA-score, Systemic Inflammation Response Index—SIRI) and the Aging-Related Immune Phenotype (ARIP) in 249 participants aged 19–111 years, this study investigates the role of immune-inflammatory responses in semi- and supercentenarians who have survived significant challenges like pandemics. Statistical analyses indicated that the INFLA-score and SIRI increase with age, but no significant differences were observed between semi- and supercentenarians and other age groups. Moreover, ARIP values, specifically CD8 Naïve/Effector scores, calculated from a subcohort of 54 individuals, showed no notable differences across groups. These findings suggest that effective management of immune-inflammatory responses may play a role in achieving extreme longevity. Studying models of healthy aging and exceptional longevity is crucial to understanding a possible longevity signature, as most show resistance to age-related diseases. In particular, semi- and supercentenarians are a highly selected group, having survived significant adversities, including the Spanish flu and COVID-19 pandemics, indicating distinctive immune system characteristics. This paper analyzes the inflammatory scores (INFLA-score, Systemic Inflammation Response Index (SIRI)) and Aging-Related Immune Phenotype (ARIP) indicators calculated from the dataset of the DESIGN project, including 249 participants aged 19–111 years, aiming to understand the immune-inflammatory (IMFLAM) role in achieving longevity. Statistical analyses, including linear regression and one-way ANOVA, were performed to explore the correlations between these parameters and age. Both INFLA-score and SIRI showed a significant increase with age. However, no statistical differences were found when comparing the values of semi- and supercentenarians to other age groups, which are similar to adults and lower than younger centenarians. Regarding ARIP values, it is noteworthy that when comparing the CD8+ Naïve/Effector scores between groups, no significant differences were observed between the semi- and supercentenarian group and the other groups. These results support the idea that the control of IMFLAM response can promote extreme longevity. [ABSTRACT FROM AUTHOR]

Simple Summary: Salt challenges many cultivated plants by altering their growth, development, and composition. However, little is known about the influence of salt on medicinal plants that normally grow in low-salinity soils. Scutellaria baicalensis Georgi (Baikal skullcap) is an important medicinal plant rich in beneficial flavones. In this paper, we report the influence of NaCl addition to soil on the composition of these flavones in green parts and in the roots. It turned out that moderate doses of salt do not harm the plants and even increase the content of certain root constituents in favor of the most pharmacologically active. At the same time, we observed some alterations in the amino acid compositions which indicate physiological processes of adaptation of the plants to the stress related to excessive salinity. Scutellaria baicalensis Georgi is a valuable medicinal plant of the Lamiaceae family. Its roots have been used in Traditional Chinese Medicine (under the name Huang-qin) since antiquity and are nowadays included in Chinese and European Pharmacopoeias. It is abundant in bioactive compounds which constitute up to 20% of dried root mass. These substances are lipophilic flavones with unsubstituted B-ring, baicalein, and wogonin and their respective glucuronides–baicalin and wogonoside being the most abundant. The content of these compounds is variable and the environmental factors causing this remain partially unknown. The role of these compounds in stress response is still being investigated and in our efforts to measure the effect of NaCl treatment on S. baicalensis growth and metabolic profile, we hope to contribute to this research. Short-term exposure to salt stress (50, 100, and 150 mM NaCl) resulted in a marked increase of baicalein from 1.55 mg to 2.55 mg/g DM (1.6-fold), baicalin from 8.2 mg to 14.7 mg (1.8-fold), wogonin from 4.9 to 6.8 (1.4-fold), and wogonoside from 3.3 to 6.8 mg/g DM (2-fold) in the roots. Conversely, in the aerial parts, the content of individual major flavonoids: carthamidine-7-O-glucuronide and scutellarein-7-O-glucuronide decreased the most by 10–50% from 18.6 mg to 11.3 mg/g (1.6-fold less) and from 6.5 mg to 3.4 mg/g DM (0.52-fold less), respectively. The amino acid profile was also altered with an increase in root concentrations of the following amino acids: arginine from 0.19 to 0.33 mg/g (1.7-fold), glutamate from 0.09 to 0.16 mg/g DM (1.6-fold), alanine from 0.009 to 0.06 mg/g (6.8-fold), proline from 0.011 to 0.029 (2.4-fold) and lysine from 0.016 to 0.063 mg/g (3.9-fold). Aspartate concentration decreased from 0.01 to 0.002 mg/g (4.8-fold less) at 150 mM NaCl. In the aerial parts, the concentration and variation in levels of specific amino acids differed among groups. For instance, the glutamate content exhibited a significant increase exclusively in the treatment group, rising from 0.031 to 0.034 mg/g, representing a 1.2-fold increase. Proline concentration showed a marked increase across all treated groups with the highest from 0.011 to 0.11 mg/g (10-fold). In conclusion, moderate salt stress was shown to increase S. baicalensis root biomass and flavonoid content which is rarely observed in a glycophyte species and provides a foundation for further studies on the mechanisms of osmotic stress adaptation on the specialized metabolism level. [ABSTRACT FROM AUTHOR]

Simple Summary: A range of fruits and vegetables including tomatoes, cucumbers, peppers, and lettuce are grown in hydroponic systems. These systems do not contain soil and instead use a circulating nutrient solution to grow the plants. Removing soil from the growing systems changes the microscopic organisms that are present at the root of the plants. Fungi and oomycetes, a fungal-like organism, are both present in these systems. Some of these organisms promote plant growth, while others cause disease and crop loss. This paper reviews current literature on seven organisms that cause disease in plants, as well as four beneficial organisms. We explain the strategies beneficial fungi use to help plants grow, including direct killing of pathogens, strengthening the plant's immune system, and enabling the plant to gain more nutrients from the environment. Additionally, we explain how phytopathogens spread throughout hydroponic systems and destroy plant tissue. The aim of this review is to provide readers with management strategies to reduce harmful plant diseases in hydroponic operations, as well as beneficial options to increase crop yields. Both scientists and growers can benefit from a complete understanding of the interactions between plants, fungi, and oomycetes. Hydroponic systems are examples of controlled environment agriculture (CEA) and present a promising alternative to traditional farming methods by increasing productivity, profitability, and sustainability. In hydroponic systems, crops are grown in the absence of soil and thus lack the native soil microbial community. This review focuses on fungi and oomycetes, both beneficial and pathogenic, that can colonize crops and persist in hydroponic systems. The symptomatology and mechanisms of pathogenesis for Botrytis, Colletotrichum, Fulvia, Fusarium, Phytophthora, Pythium, and Sclerotinia are explored for phytopathogenic fungi that target floral organs, leaves, roots, and vasculature of economically important hydroponic crops. Additionally, this review thoroughly explores the use of plant growth-promoting fungi (PGPF) to combat phytopathogens and increase hydroponic crop productivity; details of PGP strategies and mechanisms are discussed. The benefits of Aspergillus, Penicillium, Taloromyces, and Trichoderma to hydroponics systems are explored in detail. The culmination of these areas of research serves to improve the current understanding of the role of beneficial and pathogenic fungi, specifically in the hydroponic microbiome. [ABSTRACT FROM AUTHOR]

Simple Summary: For many decades, human identification by DNA has used the difference in the length of certain loci in the human genome—the so-called fragment analysis. Their main drawback is that they are too long, which interferes with the analysis if the DNA is damaged by environmental factors (rotting, sunlight, or chemical agents). Another drawback of using these regions for human identification is their high mutability, which leads to errors in determining kinship. The interest of forensic researchers in short polymorphisms like InDels has been attracted because of their potential advantages, such as low mutation rates and improved application in the analysis of degraded samples. We selected 99 InDels from the entire human genome in such a way as to create a universal set of markers that have the same identification potential regardless of the population in which it is used. In order to experimentally verify the correctness of our calculations, we examined two populations located on different continents: Russian and Ecuadorian. The results confirmed the correctness of our choice of markers. In this paper, we propose a set of markers and a biochip method for their genotyping which can be used for human identification in any population. The aim of this work was to select InDel markers sufficient for human identification and to create a routine method for their genotyping. We analyzed the allele distribution of all known InDels in European, East Asian, South Asian, African, and American populations and selected markers whose minor allele frequency, MAF, was ≥ 0.30. Thus, a set of 99 polymorphisms was formed with an average MAF for all five populations of 0.397 and a distance between markers of ≥3 million bp. The expected values of combined random match probability differ very little between the five superpopulations and are in the range of 1.44 × 10−41–3.68 × 10−41. For the genotyping of this set of markers, we have developed a method that includes single-step multiplex PCR followed by hybridization on a biochip. The average amplicon length was 72 bp. Aiming to verify the usefulness of 99 biallelic InDels in genetic identification and kinship testing, two phylogenetically distant populations were studied: Russian and Ecuadorian. For the Russian population, the combined random match probability was 2.09 × 10−40, and the combined power of exclusion, CPE, was 0.999999989. For the Ecuadorian population, the combined random match probability was 1.02 × 10−40, and the combined power of exclusion was 0.999999978. The proposed method is intended to become an alternative to human identification based on differences in the length of STR loci. [ABSTRACT FROM AUTHOR]

Simple Summary: This review paper aims to summarize, for the first time, the current state of knowledge on the potential value of the Integrated Multi-Trophic Aquaculture (IMTA) system to positively influence the zootechnical performance, animal welfare, and flesh nutritional quality of the co-cultivated species. The crucial role that the characteristic nutritional (i.e., greater availability of food and nutrients) and environmental factors (i.e., better water quality) of the IMTA system play in shaping the physiological responses of aquatic organisms produced at different trophic levels, i.e., growth, survival, stress responses, and welfare, is highlighted. Given the still-limited diffusion of this valuable fish farm system in many European areas, we believe that emphasizing the economic and market value of IMTA products could contribute to improve public perception and interest in the concrete adoption of IMTA on a commercial scale and constitute a basis to encourage further studies in order to explore new IMTA opportunities. IMTA is one of the most innovative and sustainable farming systems, exhibiting the best technique available in rearing aquatic organisms belonging to different positions along the trophic levels. In the literature and in legislation, the environmental benefits of IMTA protocols have been extensively recognized, mainly for its capability to reduce the ecological footprint of intensive aquaculture systems and concretely address the Sustainable Development Goal no. 14 (SDG 14). However, lesser attention is given to the assessments of its role in enhancing the zootechnical performance, animal welfare, and flesh quality of the species involved. To the best of our knowledge, this is the first review that aims to offer a systematic analysis of the existing literature on the main commercial motivations that could draw the attention of stakeholders, including consumers and fish farmers, towards a greater social acceptability and implementation of the IMTA system on a large scale. The findings suggest that, beyond its environmental advantages, IMTA systems can positively influence the productivity, growth, survival, feed efficiency, and animal health and welfare (AH&W), as well as the nutritional quality of the harvested species, thus offering significant economic and market value both in terms of Environmental, Societal and Governance (ESG) parameters and One Health. [ABSTRACT FROM AUTHOR]

Simple Summary: Zebrafish have emerged as invaluable model organisms in biological research, offering a cost-effective alternative to rodents. However, the absence of standardized feeding protocols and nutritional requirements poses a significant challenge, potentially compromising the validity of experimental outcomes, particularly in preclinical studies. Our systematic review analyzes a plethora of studies focused on zebrafish feed intake, feeding regimes, and diet compositions. We uncover substantial variability in dietary parameters, notably in crude protein and lipid content. Despite this diversity, energy levels remain quite consistent across zebrafish diets. By using these insights, we propose a novel feeding protocol for zebrafish of different developmental stages, based on a formulated feed optimized for protein and energy content. This protocol might represent the first step towards standardizing zebrafish feeding practices, thereby enhancing experimental reproducibility and data reliability. Zebrafish are one of the most used animal models in biological research and a cost-effective alternative to rodents. Despite this, nutritional requirements and standardized feeding protocols have not yet been established for this species. This is important to avoid nutritional effects on experimental outcomes, and especially when zebrafish models are used in preclinical studies, as many diseases have nutritional confounding factors. A key aspect of zebrafish nutrition is related to feed intake, the amount of feed ingested by each fish daily. With the goal of standardizing feeding protocols among the zebrafish community, this paper systematically reviews the available data from 73 studies on zebrafish feed intake, feeding regimes (levels), and diet composition. Great variability was observed regarding diet composition, especially regarding crude protein (mean 44.98 ± 9.87%) and lipid content (9.91 ± 5.40%). Interestingly, the gross energy levels of the zebrafish diets were similar across the reviewed studies (20.39 ± 2.10 kilojoules/g of feed). In most of the reviewed papers, fish received a predetermined quantity of feed (feed supplied). The authors fed the fish according to the voluntary intake and then calculated feed intake (FI) in only 17 papers. From a quantitative point of view, FI was higher than when a fixed quantity (pre-defined) of feed was supplied. Also, the literature showed that many biotic and abiotic factors may affect zebrafish FI. Finally, based on the FI data gathered from the literature, a new feeding protocol is proposed. In summary, a daily feeding rate of 9–10% of body weight is proposed for larvae, whereas these values are equal to 6–8% for juveniles and 5% for adults when a dry feed with a proper protein and energy content is used. [ABSTRACT FROM AUTHOR]

Simple Summary: Diagnosing glioblastoma multiforme (GBM), solitary brain metastases (SBM), and primary central nervous system lymphoma (PCNSL) in malignant tumors of the central nervous system using multi-modal magnetic resonance imaging (MRI) is significantly important in helping physicians develop treatment plans and enhance patient prognosis. In this paper, MFFC-Net is developed and validated using deep learning methods to predict these three tumor categories from multi-modal MRI without the manual region of interest (ROI). MFFC-Net first uses a multi-encoder with DenseBlocks to extract deep features from multi-modal MRI. Then, the feature fusion layer fuses the deep information between different modalities and tissues. Finally, the spatial-channel attention module suppresses redundant new information and activates tumor classification-related features. Compared with radiomics models, MFFC-Net demonstrated higher accuracy. In addition, the results in the different sequences provide important references for future clinical work on MRI image acquisition. We believe that MFFC-Net has the potential to assist in the diagnosis and treatment of brain tumors in the future. (1) Background: Diagnosis of glioblastoma (GBM), solitary brain metastases (SBM), and primary central nervous system lymphoma (PCNSL) plays a decisive role in the development of personalized treatment plans. Constructing a deep learning classification network to diagnose GBM, SBM, and PCNSL with multi-modal MRI is important and necessary. (2) Subjects: GBM, SBM, and PCNSL were confirmed by histopathology with the multi-modal MRI examination (study from 1225 subjects, average age 53 years, 671 males), 3.0 T T2 fluid-attenuated inversion recovery (T2-Flair), and Contrast-enhanced T1-weighted imaging (CE-T1WI). (3) Methods: This paper introduces MFFC-Net, a classification model based on the fusion of multi-modal MRIs, for the classification of GBM, SBM, and PCNSL. The network architecture consists of parallel encoders using DenseBlocks to extract features from different modalities of MRI images. Subsequently, an L 1 − n o r m feature fusion module is applied to enhance the interrelationships among tumor tissues. Then, a spatial-channel self-attention weighting operation is performed after the feature fusion. Finally, the classification results are obtained using the full convolutional layer (FC) and Soft-max. (4) Results: The ACC of MFFC-Net based on feature fusion was 0.920, better than the radiomics model (ACC of 0.829). There was no significant difference in the ACC compared to the expert radiologist (0.920 vs. 0.924, p = 0.774). (5) Conclusions: Our MFFC-Net model could distinguish GBM, SBM, and PCNSL preoperatively based on multi-modal MRI, with a higher performance than the radiomics model and was comparable to radiologists. [ABSTRACT FROM AUTHOR]

Simple Summary: This paper is mainly based on the tea disease leaves for image classification research, using a combination of convolution, iterative module and transformer in the form of a combination of the traditional convolution for local feature extraction advantage and transformer for global feature extraction potential. The optimal cut size, small sample training ability, anti-interference ability and generalization ability of the model are demonstrated through five sets of experiments respectively. Also at the end of the class activation map visualization was performed to clearly see the model's classification basis on tea leaves. The results show that the model in this paper is able to accurately capture the location of leaf diseases, which further validates the effectiveness of the model. Tea diseases are one of the main causes of tea yield reduction, and the use of computer vision for classification and diagnosis is an effective means of tea disease management. However, the random location of lesions, high symptom similarity, and complex background make the recognition and classification of tea images difficult. Therefore, this paper proposes a tea disease IterationVIT diagnosis model that integrates a convolution and iterative transformer. The convolution consists of a superimposed bottleneck layer for extracting the local features of tea leaves. The iterative algorithm incorporates the attention mechanism and bilinear interpolation operation to obtain disease location information by continuously updating the region of interest in location information. The transformer module uses a multi-head attention mechanism for global feature extraction. A total of 3544 images of red leaf spot, algal leaf spot, bird's eye disease, gray wilt, white spot, anthracnose, brown wilt, and healthy tea leaves collected under natural light were used as samples and input into the IterationVIT model for training. The results show that when the patch size is 16, the model performed better with an IterationVIT classification accuracy of 98% and F1 measure of 96.5%, which is superior to mainstream methods such as VIT, Efficient, Shuffle, Mobile, Vgg, etc. In order to verify the robustness of the model, the original images of the test set were blurred, noise- was added and highlighted, and then the images were input into the IterationVIT model. The classification accuracy still reached over 80%. When 60% of the training set was randomly selected, the classification accuracy of the IterationVIT model test set was 8% higher than that of mainstream models, with the ability to analyze fewer samples. Model generalizability was performed using three sets of plant leaf public datasets, and the experimental results were all able to achieve comparable levels of generalizability to the data in this paper. Finally, this paper visualized and interpreted the model using the CAM method to obtain the pixel-level thermal map of tea diseases, and the results show that the established IterationVIT model can accurately capture the location of diseases, which further verifies the effectiveness of the model. [ABSTRACT FROM AUTHOR]

Simple Summary: The ongoing advancements in deep learning, notably its use in predicting cancer survival through genomic data analysis, calls for an up-to-date review. This paper inspects notable works from 2021 to 2023, underlining essential developments and their implications in the field. We offer a comprehensive review of the research, selective paper choice, and thorough analysis of prevailing trends, contributing to a better understanding of deep learning's potential in this vital domain. Deep learning has brought about a significant transformation in machine learning, leading to an array of novel methodologies and consequently broadening its influence. The application of deep learning in various sectors, especially biomedical data analysis, has initiated a period filled with noteworthy scientific developments. This trend has majorly influenced cancer prognosis, where the interpretation of genomic data for survival analysis has become a central research focus. The capacity of deep learning to decode intricate patterns embedded within high-dimensional genomic data has provoked a paradigm shift in our understanding of cancer survival. Given the swift progression in this field, there is an urgent need for a comprehensive review that focuses on the most influential studies from 2021 to 2023. This review, through its careful selection and thorough exploration of dominant trends and methodologies, strives to fulfill this need. The paper aims to enhance our existing understanding of applications of deep learning in cancer survival analysis, while also highlighting promising directions for future research. This paper undertakes aims to enrich our existing grasp of the application of deep learning in cancer survival analysis, while concurrently shedding light on promising directions for future research in this vibrant and rapidly proliferating field. [ABSTRACT FROM AUTHOR]

Cellulases are a set of lignocellulolytic enzymes, capable of producing eco-friendly low-cost renewable bioethanol. However, low stability and hydrolytic activity limit their wide-scale applicability at the industrial scale. In this work, we report the domain engineering of endoglucanase (cel6A) of Thermobifida fusca to improve their catalytic activity and thermal stability. Later, enzymatic activity and thermostability of the most efficient variant named as cel6A.CBC was analyzed by molecular dynamics simulations. This variant demonstrated profound activity against soluble and insoluble cellulosic substrates like filter paper, alkali-treated bagasse, regenerated amorphous cellulose (RAC), and bacterial microcrystalline cellulose. The variant cel6A.CBC showed the highest catalysis of carboxymethyl cellulose (CMC) and other related insoluble substrates at a pH of 6.0 and a temperature of 60 °C. Furthermore, a sound rationale was observed between experimental findings and molecular modeling of cel6A.CBC which revealed thermostability of cel6A.CBC at 26.85, 60.85, and 74.85 °C as well as structural flexibility at 126.85 °C. Therefore, a thermostable derivative of cel6A engineered in the present work has enhanced biological performance and can be a useful construct for the mass production of bioethanol from plant biomass. [ABSTRACT FROM AUTHOR]

This editorial discusses the prevalence of heart failure worldwide and the advancements in molecular and cellular biology that are transforming our understanding and treatment of the condition. The special issue includes nine papers that highlight recent advances in understanding the transcriptome profile in cardiovascular diseases and providing novel treatments for promoting cardiac repair. The papers cover topics such as the transcriptomic profile of endothelial cells in Duchenne muscular dystrophy, the impact of inflammation in remote zones after myocardial infarction, the effectiveness of manganese porphyrin compound for cardiac arrest, the role of HIF2α and ARNT signaling in endothelial cells, strategies to induce cardiomyocyte proliferation, the characterization of the common marmoset as a primate model for cardiovascular disease, and the link between heart failure and cognitive impairment. The authors express their gratitude to the contributors and reviewers of the special issue. [Extracted from the article]

Simple Summary: Protected areas are essential for the conservation of biodiversity. (i) Ecological connectivity is essential for the maintenance and support of migratory bird habitats. Enhancing control measures to expand ecological corridors can effectively safeguard flagship and umbrella species, thereby promoting biodiversity conservation. (ii) The establishment of ecological corridors can facilitate the reconciliation of conflicts between conservation efforts and development goals, thereby yielding significant theoretical implications for achieving a harmonious coexistence between humans and birds within the migratory bird sanctuary of Poyang Lake. Protected areas are essential for the conservation of biodiversity. However, the rapid expansion of urbanization and the intensification of human activities have significantly disrupted environmental integrity, leading to a continuous deterioration in both the quantity and quality of large ecological patches. This has further diminished the connectivity among ecological patches, leading to significant consequences for regional biodiversity conservation. Taking Poyang Lake as a case study, which serves as a crucial wintering habitat for migratory birds along the East Asia–Australasia flyway, this research employs ArcMap technology. It considers various factors including land use type, slope, and elevation to evaluate habitat quality and degradation through the application of the InVEST model. Additionally, the study utilizes the minimum cumulative resistance (MCR) model alongside circuit theory to delineate ecological corridors within the area and to establish a comprehensive ecological network system. The research results in this paper are as follows. (i) During the period from 2000 to 2020, there was an overall decline in habitat quality within the study area, indicating a clear trend of habitat degradation. However, it is worth noting that there was an increase in habitat quality in certain local areas within the protected area. (ii) The ecological resistance values in the core area of the migratory bird reserve in Poyang Lake are generally low. However, the ecological resistance values of the habitats have shown a consistent increase from 2000 to 2020. Additionally, there has been a significant decrease in the density of ecological corridors during this time period. (iii) Over the period from 2000 to 2020, both the number and connectivity of ecological corridors decreased and their integrity and functionality degraded. Consequently, this weakened role of the ecological network has had implications for maintaining regional biodiversity and ecosystem service functions. The findings indicate two conclusions. (i) Ecological connectivity is essential for the conservation of migratory bird habitats. Strengthening control measures aimed at expanding ecological corridors can effectively safeguard flagship and umbrella species, thereby promoting biodiversity conservation. (ii) The establishment of ecological corridors can help reconcile conflicts between conservation efforts and development objectives. This reconciliation carries significant theoretical implications for fostering a harmonious coexistence between humans and birds in Poyang Lake's migratory bird sanctuary. [ABSTRACT FROM AUTHOR]

Simple Summary: This paper presents a meta-analysis of currently available single-cell RNA sequencing (scRNAseq) datasets from zebrafish kidneys. Our work aims to identify key marker genes for various immune cell types and transcription factors (TFs) involved in fish myelopoiesis. Our results validate previous studies and expand them; newly discovered markers and TFs have experimental confirmation of their roles in complementary cell types of mammals and fish species. Reconstructed gene networks of macrophage- and neutrophil-specific genes revealed the potential interactions of identified TFs and marker genes. Obtained results could be taken into account during the design of immunogenetics experiments (e.g., creating zebrafish lines with TF knockouts) and serve as a basis for novel applications for zebrafish. The revealed cell-specific markers could help in the accurate determination of fish cell types in the future. Our methodology of data integration showed its reliability and could be further adapted to meta-analyses of various scRNAseq datasets. The innate immune system (IIS) is an ancient and essential defense mechanism that protects animals against a wide range of pathogens and diseases. Although extensively studied in mammals, our understanding of the IIS in other taxa remains limited. The zebrafish (Danio rerio) serves as a promising model organism for investigating IIS-related processes, yet the immunogenetics of fish are not fully elucidated. To address this gap, we conducted a meta-analysis of single-cell RNA sequencing (scRNA-seq) datasets from zebrafish kidney marrow, encompassing approximately 250,000 immune cells. Our analysis confirms the presence of key genetic pathways in zebrafish innate immune cells that are similar to those identified in mammals. Zebrafish macrophages specifically express genes encoding cathepsins, major histocompatibility complex class II proteins, integral membrane proteins, and the V-ATPase complex and demonstrate the enrichment of oxidative phosphorylation ferroptosis processes. Neutrophils are characterized by the significant expression of genes encoding actins, cytoskeleton organizing proteins, the Arp2/3 complex, and glycolysis enzymes and have demonstrated their involvement in GnRH and CLR signaling pathways, adherents, and tight junctions. Both macrophages and neutrophils highly express genes of NOD-like receptors, phagosomes, and lysosome pathways and genes involved in apoptosis. Our findings reinforce the idea about the existence of a wide spectrum of immune cell phenotypes in fish since we found only a small number of cells with clear pro- or anti-inflammatory signatures. [ABSTRACT FROM AUTHOR]

Simple Summary: The protein α-zein from corn has been studied both in vivo and in vitro for its potential to target treatments for non-communicable chronic diseases. This biological activity is achieved through the hydrolysis of the protein, which produces bioactive peptides. The study involved scientific research and a literature review to gather evidence of the biological activity of corn peptides. Additionally, databases and bioinformatics tools were utilized to simulate the enzymatic digestion of α-zein and confirm the bioactivity of the resulting peptides. The study discovered that the primary bioactivity is the inhibition of ACE, followed by the inhibition of DPP-IV and DPP-III, which are targets for treating hypertension and type-2 diabetes. In conclusion, conducting an in silico evaluation before proceeding to in vitro or in vivo studies can be efficient and cost-effective and contribute to better usage of corn gluten meals. Studies have shown that corn (Zea mays L.) proteins, mainly α-zein, have the potential to act on therapeutic targets related to non-communicable chronic diseases, such as high blood pressure and type 2 diabetes. Enzymatic hydrolysis of proteins present in foods can result in a great diversity of peptides with different structures and possible bioactivities. A review of recent scientific research papers was performed to show evidence of the bioactive properties of corn peptides by in vitro assays. The α-zein amino acid sequences were identified in the UniProtKB protein database and then analyzed in the BIOPEP database to simulate enzymatic digestion and verify the potential biological action of the resulting peptides. The peptides found in the BIOPEP database were categorized according to the probability of presenting biological action using the PeptideRanker database. The aim was to use existing data to identify in silico the potential for obtaining biologically active peptides from α-zein, the main storage protein of corn. The analysis showed that the majority of peptide fragments were related to the inhibition of angiotensin-converting enzyme, followed by the inhibition of dipeptidyl peptidase IV and dipeptidyl peptidase III. Many drugs used to treat high blood pressure and type 2 diabetes work by inhibiting these enzymes, suggesting that corn peptides could be potential alternative agents. In vitro studies found that the primary bioactivity observed was antioxidative action. Both in vitro and in silico approaches are valuable for evaluating the bioactive properties resulting from protein hydrolysis, such as those found in α-zein. However, conducting in vitro studies based on prior in silico evaluation can be more efficient and cost-effective. [ABSTRACT FROM AUTHOR]

Simple Summary: The molecular heterogeneity of hepatocellular carcinoma (HCC) and its range of potential etiologies contribute to the complexities in treating this disease. Additionally, inter-sample molecular variability can mean the involvement of different prognostic genes or utilization of distinct molecular pathways in HCC development. This paper examines the genes and pathways most involved in different histological grades of HCC across various pre-cancer risk factors using publicly available bulk transcriptomics data and a systems biology approach. It identifies shared pathways among HCCs of varying grades and risk factors, as well as genes common to these pathways. Furthermore, this study highlights gene clusters preserved across risk factors, which may indicate shared targets for general treatment and gene clusters specific to viral or non-viral etiologies. Overall, this research reveals common and differing molecular pathways across risk factors and similarities in gene expression between histological grades. It provides a framework for understanding HCC development respective of risk factors and underscores the molecular pathways and genes involved. Hepatocellular carcinoma (HCC) has the highest mortality rate and is the most frequent of liver cancers. The heterogeneity of HCC in its etiology and molecular expression increases the difficulty in identifying possible treatments. To elucidate the molecular mechanisms of HCC across grades, data from The Cancer Genome Atlas (TCGA) were used for gene co-expression analysis, categorizing each sample into its pre-existing risk factors. The R library BioNERO was used for preprocessing and gene co-expression network construction. For those modules most correlated with a grade, functional enrichments from different databases were then tested, which appeared to have relatively consistent patterns when grouped by G1/G2 and G3/G4. G1/G2 exhibited the involvement of pathways related to metabolism and the PI3K/Akt pathway, which regulates cell proliferation and related pathways, whereas G3/G4 showed the activation of cell adhesion genes and the p53 signaling pathway, which regulates apoptosis, cell cycle arrest, and similar processes. Module preservation analysis was then used with the no history dataset as the reference network, which found cell adhesion molecules and cell cycle genes to be preserved across all risk factors, suggesting they are imperative in the development of HCC regardless of potential etiology. Through hierarchical clustering, modules related to the cell cycle, cell adhesion, the immune system, and the ribosome were found to be consistently present across all risk factors, with distinct clusters linked to oxidative phosphorylation in viral HCC and pentose and glucuronate interconversions in non-viral HCC, underscoring their potential roles in cancer progression. [ABSTRACT FROM AUTHOR]

Simple Summary: This review explores how common sleep disorders, such as insomnia and sleep apnoea, can affect heart health, particularly by increasing the risk of a heart condition called atrial fibrillation (AF). Sleep is vital for overall health, and disruptions in sleep can lead to significant health issues. Insomnia and sleep apnoea are widespread problems that affect millions of people worldwide. This paper examines how these sleep issues might cause changes in the body that lead to heart problems, such as inflammation and stress. The review also discusses how treating sleep disorders, especially with therapies such as continuous positive airway pressure for sleep apnoea, can help reduce the risk of developing AF and improve overall heart health. These conclusions are important because they suggest that addressing sleep disorders could be a key part of preventing and managing heart conditions, ultimately helping to improve people's quality of life and reduce the burden of heart disease on society. Sleep is a complex biobehavioural process essential for overall health, with various dimensions including duration, continuity, timing, and satisfaction. This study investigated the intricate relationships between common sleep disorders such as insomnia and obstructive sleep apnoea (OSA) and their impact on atrial fibrillation (AF), a prevalent arrhythmia with significant health implications. Using a comprehensive review of the current literature, this study examined the pathophysiological mechanisms linking sleep disorders to cardiovascular risks, focusing on autonomic nervous system disturbances, inflammation, and oxidative stress associated with OSA. These findings indicate that sleep disorders significantly elevate the risk of AF through mechanisms such as increased sympathetic activity and structural cardiac remodelling. Additionally, this study highlights the potential benefits of treating sleep disorders, particularly with continuous positive airway pressure (CPAP) therapy, in reducing AF recurrence and improving cardiovascular outcomes. This conclusion emphasises the importance of integrated therapeutic approaches that address both sleep disorders and AF to enhance patient outcomes and quality of life. Future research should explore these connections to develop more effective and holistic treatment strategies. [ABSTRACT FROM AUTHOR]

Simple Summary: This paper reports the interaction between flavonoids, identified in the chemical matrix of açaí extract, and NLRP3 PYD through computational simulation, as well as the in vitro safety profile and anti-inflammatory effect in macrophages and monocytes of three flavonoids, isolated and combined, via the modulation of the NLRP3 inflammasome. Inflammation is a vital mechanism that defends the organism against infections and restores homeostasis. However, when inflammation becomes uncontrolled, it leads to chronic inflammation. The NLRP3 inflammasome is crucial in chronic inflammatory responses and has become a focal point in research for new anti-inflammatory therapies. Flavonoids like catechin, apigenin, and epicatechin are known for their bioactive properties (antioxidant, anti-inflammatory, etc.), but the mechanisms behind their anti-inflammatory actions remain unclear. This study aimed to explore the ability of various flavonoids (isolated and combined) to modulate the NLRP3 inflammasome using in silico and in vitro models. Computer simulations, such as molecular docking, molecular dynamics, and MM/GBSA calculations examined the interactions between bioactive molecules and NLRP3 PYD. THP1 cells were treated with LPS + nigericin to activate NLRP3, followed by flavonoid treatment at different concentrations. THP1-derived macrophages were also treated following NLRP3 activation protocols. The assays included colorimetric, fluorometric, microscopic, and molecular techniques. The results showed that catechin, apigenin, and epicatechin had high binding affinity to NLRP3 PYD, similar to the known NLRP3 inhibitor MCC950. These flavonoids, particularly at 1 µg/mL, 0.1 µg/mL, and 0.01 µg/mL, respectively, significantly reduced LPS + nigericin effects in both cell types and decreased pro-inflammatory cytokine, caspase-1, and NLRP3 gene expression, suggesting their potential as anti-inflammatory agents through NLRP3 modulation. [ABSTRACT FROM AUTHOR]

Simple Summary: 1. Three types of rice grown in Africa: The native African rice O. glaberrima, the Asian rice (O. sativa) and the new type of African rice (e.g., NERICA varieties). O. sativa has mostly supplanted O. glaberrima as the dominant crop in Africa. 2. There is no evidence of the existence of Asian weedy rice (O. sativa f. spontanea) in Africa, while African weedy rice (Oryza spp.) is a complex population which harbors both a native and Asian genetic background. The genomic approach is an ideal way to characterize the African weedy rice population structure. 3. There have been no genomics studies on African weedy rice yet, and the latest genomic study on African cultivated rice occurred five years ago. Rice is a staple crop in sub-Saharan Africa, and it is mostly produced by Asian cultivars of Oryza sativa that were introduced to the continent around the fifteenth or sixteenth century. O. glaberrima, the native African rice, has also been planted due to its valuable traits of insect and drought tolerance. Due to competition and resistance evolution, weedy rice has evolved from O. sativa and O. glaberrima, posing an increasing threat to rice production. This paper provides an overview of current knowledge on the introduction and domestication history of cultivated rice in Africa, as well as the genetic properties of African weedy rice that invades paddy fields. Recent developments in genome sequencing have made it possible to uncover findings about O. glaberrima's population structure, stress resilience genes, and domestication bottleneck. Future rice genomic research in Africa should prioritize producing more high-quality reference genomes, quantifying the impact of crop–wild hybridization, elucidating weed adaptation mechanisms through resequencing, and establishing a connection between genomic variation and stress tolerance phenotypes to accelerate breeding efforts. [ABSTRACT FROM AUTHOR]

Simple Summary: Anthracycline drugs, as a class of commonly used antitumor chemotherapeutics, play a significant role in the treatment of various cancers. However, they possess notable cardiotoxicity, which seriously undermines the quality of life for cancer patients. Therefore, early monitoring and mitigation of anthracycline-induced cardiotoxicity (AIC) have become urgent clinical issues to address. This study summarizes the mechanisms of AIC, encompassing oxidative stress, apoptosis, cardiac microenvironment remodeling, ferroptosis, and autophagy. Meanwhile, we have discovered that in addition to traditional medical imaging techniques that can monitor cardiotoxicity, emerging diagnostic tools such as advanced imaging technologies and human induced pluripotent stem cells demonstrate immense potential for early identification of subclinical toxicity and timely pharmacological intervention prior to the occurrence of irreversible cardiac damage. In terms of prevention and treatment of AIC, on the one hand, we can select appropriate drugs based on the molecular mechanisms of AIC to reduce cardiotoxicity. On the other hand, we can use derivatives with lesser cardiotoxicity, such as liposomes and nanoparticles, to prevent AIC, thereby improving the prognosis of cancer patients. Anthracyclines represent a highly efficacious class of chemotherapeutic agents employed extensively in antitumor therapy. They are universally recognized for their potency in treating diverse malignancies, encompassing breast cancer, gastrointestinal tumors, and lymphomas. Nevertheless, the accumulation of anthracyclines within the body can lead to significant cardiac toxicity, adversely impacting both the survival rates and quality of life for tumor patients. This limitation somewhat restricts their clinical utilization. Determining how to monitor and mitigate their cardiotoxicity at an early stage has become an urgent clinical problem to be solved. Therefore, this paper reviews the mechanism of action, early monitoring, and strategies for the prevention of anthracycline-induced cardiotoxicity for clinical reference. [ABSTRACT FROM AUTHOR]

Simple Summary: Salt, or sodium chloride, is a crucial component of a balanced diet. However, an excessive consumption of salt can lead to a range of adverse health effects that are often overlooked. Salt enters the body's digestive system through the ingestion of everyday foods and exerts an effect on a key component of the digestive system, namely the intestinal microbiota. Some studies have indicated that alterations in the composition of the intestinal microbiota may influence the functioning of the human body. This paper presents a review of the effects of a high-salt diet on the gut microbiome and, in turn, on the development of cardiovascular disease and inflammatory bowel disease. Furthermore, it synthesizes recent research on the effects of high-salt diets on the gut microbiome and the gut immune system. This further elucidates the mechanisms through which a high-salt diet affects the gut microbiome and associated diseases. Salt, or sodium chloride, is an essential component of the human diet. Recent studies have demonstrated that dietary patterns characterized by a high intake of salt can influence the abundance and diversity of the gut microbiota, and may play a pivotal role in the etiology and exacerbation of certain diseases, including inflammatory bowel disease and cardiovascular disease. The objective of this review is to synthesize the effects of elevated salt consumption on the gut microbiota, including its influence on gut microbial metabolites and the gut immune system. Additionally, this review will investigate the potential implications of these effects for the development of cardiovascular disease and inflammatory bowel disease. The findings of this study offer novel insights and avenues for the management of two common conditions with significant clinical implications. [ABSTRACT FROM AUTHOR]

Simple Summary: Rare earth elements (REEs) are widely used in various fields of human activity. However, data from many studies indicate the harmful effects of REEs on humans and animals, including the nervous system. In this study, we estimated the REE content in hair samples of children living on the Kola Peninsula (Murmansk region) in the vicinity of the Lovozersky REE Mining and Processing Plant, and we linked the REE content in children's bodies to the prevalence of the nervous system diseases in Lovozersky District. We observed a higher prevalence of nervous system diseases (episodic paroxysmal disorders (G40–G47), cerebral palsy (G80–G83), epilepsy and status epilepticus (G40–G41)) in children aged 15–17 years in Lovozersky District compared to other territories of the Murmansk region. Indirect evidence of the link between REE content in hair samples of children and nervous system diseases is provided by data in the literature. According to these data, REEs are deposited in the brain structures responsible for the function of the nervous system, thus impairing them. This investigation highlights the relevance of studying the role of REEs in nervous system diseases, and it points to the need for the further research in this area. The aim of this study is to assess the rare earth element (REE) content in hair samples of children living in Lovozero village, near an REE mining site, and the possible effects of REEs on the prevalence of nervous system diseases in Lovozersky District (Murmansk region, Kola Peninsula). Fifty-three school-age children were recruited for the analysis of REE content in hair samples. REE (Y, La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, and Lu) content was estimated by means of inductively coupled plasma mass spectrometry (ICP-MS). The analysis of REE content in the hair of children living in Russia, Kazakhstan, and China indicated REE intake from the environment. The possible contribution of REEs to nervous system disorders is supported by the link between the REE content in hair samples of children living near REE mining areas (China) and the manifestation of cognitive disorders in these children. It is also found that the prevalence of nervous system diseases in children aged 15–17 years is higher in Lovozersky District compared to the other districts of the Murmansk region. In this paper, the possible contribution of REEs to the prevalence of episodic paroxysmal disorders (G40–G47), cerebral palsy (G80–G83), and epilepsy and status epilepticus (G40–G41) is discussed. [ABSTRACT FROM AUTHOR]

Simple Summary: Functional studies of neuropeptides are of great significance in revealing the neuroendocrine regulation mechanism in crustaceans, and in guiding and developing artificial regulation techniques in economic species. In this paper, we investigated the effect of a crustacean neuropeptide corazonin (Crz) on ecdysteroid synthesis based on the high expression of Crz receptor in the Y-organ, the main site of ecdysteroid synthesis. By using Crz treatment and CrzR silencing, we found that Crz/CrzR signaling could cause up-regulation of ecdysteroid synthesis genes and an increase in ecdysteroid levels both in vitro and in vivo. In addition, it was also observed that Crz/CrzR signaling affects the expression level of ecdysis-triggering hormones. Our results provide new insights into the understanding of Crz function in crustaceans. The neuropeptide corazonin (Crz) exerts diverse physiological effects in insects, yet its role in crustaceans remains elusive. The abundant expression of Crz receptor (CrzR) in the Y-organs of several crustaceans suggests a potential involvement of Crz in regulating ecdysteroid synthesis. In this study, we examined the effects of PtCrz on ecdysteroid synthesis during the molting period of Portunus trituberculatus through PtCrz treatments and PtCrzR silencing. Our results showed that PtCrz peptide stimulates ecdysteroid levels and the gene expression involved in ecdysteroidogenesis both in vitro and in vivo, whereas dsPtCrzR treatments had opposite effects on ecdysteroid levels and associated gene expression. Thus, our study suggests that PtCrz may modulate ecdysteroid synthesis via Y-organ-expressed PtCrzR. Furthermore, we also discovered the involvement of PtCrz/PtCrzR signaling in regulating PtETH expression. Notably, the inhibitory effect of dsPtCrzR on ecdysteroid synthesis or PtETH expression can be reversed by PtCrz treatment, suggesting the potential existence of multiple receptors for PtCrz. This study provides new insights into the function of crustacean Crz and, for the first time, elucidates the presence of a neuropeptide that can stimulate ecdysteroid synthesis in crustaceans. [ABSTRACT FROM AUTHOR]

Simple Summary: Bacillus subtilis is a model organism used to study molecular processes in Gram-positive bacteria. Sigma factor B (σB, SigB) is a major regulator of gene expression in response to various stresses. SigB itself is controlled by a network involving several other factors. In this paper, I focused on computational modeling of their interactions and analyzed how these interactions influence the production of SigB and other components of the network. Understanding the detailed functioning of such a network and the concept of its analysis helps to comprehend molecular processes occurring in the cell. Bacillus subtilis is a model organism used to study molecular processes in Gram-positive bacteria. Sigma factor B, which associates with RNA polymerase, is one of the transcriptional regulators involved in the cell's response to environmental stress. Experiments have proven that the amounts of free σB (SigB) are controlled by a system of anti- (RsbW) and anti-anti-sigma (RsbV) factors expressed from the same operon as SigB. Moreover, the phosphorylation state of RsbV is controlled by phosphatases RsbP and RsbU, which directly dephosphorylate RsbV. A set of chemical equations describing the network controlling the levels of free SigB was converted to a set of differential equations quantifying the dynamics of the network. The solution of these equations allowed the simulation of the kinetic behavior of the network and its components under real conditions reflected in the time series of protein expression. In this study, the time series of protein expression measured by mass spectrometry were utilized to investigate the role of phosphatases RsbU/RsbP in transmitting the environmental signal. Additionally, the influence of kinetic constants and the amounts of other network components on the functioning of the network was investigated. A comparison with the same simulation performed using a transcriptomic dataset showed that while the time series between the proteomic and transcriptomic datasets are not correlated, the results are the same. This indicates that when modeling is performed within one dataset, it does not matter whether the data come from the mRNA or protein level. In summary, the computational results based on experimental data provide a quantitative insight into the functioning of the SigB-dependent circuit and offer a template for the quantitative study of similar systems. [ABSTRACT FROM AUTHOR]

Simple Summary: This paper reports on three new species and a new record of the lichen genus Peltula Nyl., highlighting research progress on lichen diversity in Helan Mountain. In this study, species were identified through a combination of morpho-anatomy, molecular systematics, and chemical substance detection. The results of the study enrich the data of Peltula and the study of lichens in Helan Mountain. In this study, a systematic taxonomic analysis was carried out on the lichen genus Peltula, collected from Helan Mountain in China; three new species (Peltula helanense, P. overlappine, and P. reticulata) and a new record (P. crispatula (Nyl.) Egea) for China were identified. Four species were identified by morph-anatomical, chemical, and phylogenetic analyses by combining two gene loci (ITS and LSU). Peltula helanense is with tiny individual thalli up to 1mm, attached by creamy-white cylindrical rhizoids and apothecia filling the whole squamule. Peltula overlappine is characterized by thallus squamulose forming rosette-shaped patches and squamules with distinctive thickened margins. Peltula reticulata is characterized by brownish brown thallus and squamules with densely reticulate upper surface. P. crispatula is characterized by irregular squamules attached to a tuft of hyphae. The four species are described in detail, compared, and discussed with similar species, and images of morpho-anatomical structures of the four species are also provided. Moreover, a key to the species of Peltula from Helan Mountain is provided. The results enrich the data of the genus Peltula and also indicate that the rich diversity of lichen species in Helan Mountain is worthy of in-depth study. [ABSTRACT FROM AUTHOR]

Simple Summary: Proteomics can be very useful in identifying proteins, which helps find potential markers for diseases. Managing endometrial cancer can be difficult and finding reliable markers can contribute to an early diagnosis, to manage its evolution, and even predict the response to treatment. This paper reviews the current research on the proteins involved in endometrial cancer. Most studies used tissue, serum, and plasma samples and found potential diagnostic and prognostic markers. Eight studies were examined closely, with three showing strong similarities, sharing forty-five proteins. This review also identified the 10 most commonly reported proteins in these studies. While proteomics shows promise in finding diagnostic and prognostic markers for endometrial cancer, there is still a need for more research on new therapeutic targets. Proteomics can be a robust tool in protein identification and regulation, allowing the discovery of potential biomarkers. In clinical practice, the management of endometrial cancer can be challenging. Thus, identifying promising markers could be beneficial, helping both in diagnosis and prognostic stratification, even predicting the response to therapy. Therefore, this manuscript systematically reviews the existing evidence of the proteomic profile of human endometrial cancer. The literature search was conducted via Medline (through PubMed) and the Web of Science. The inclusion criteria were clinical, in vitro, and in vivo original studies reporting proteomic analysis using all types of samples to map the human endometrial cancer proteome. A total of 55 publications were included in this review. Most of the articles carried out a proteomic analysis on endometrial tissue, serum and plasma samples, which enabled the identification of several potential diagnostic and prognostic biomarkers. In addition, eight articles were analyzed regarding the identified proteins, where three studies showed a strong correlation, sharing forty-five proteins. This analysis also allowed the identification of the 10 most frequently reported proteins in these studies: EGFR, PGRMC1, CSE1L, MYDGF, STMN1, CASP3 ANXA2, YBX1, ANXA1, and MYH11. Proteomics-based approaches pointed out potential diagnostic and prognostic candidates for endometrial cancer. However, there is a lack of studies exploring novel therapeutic targets. [ABSTRACT FROM AUTHOR]

Simple Summary: Cells continually sense and receive signals from the environment and respond accordingly. Due to biological noise, however, the response is not always as expected. Such a response can induce a different cell fate and may disrupt some cellular functions. In the presence of noise, cells may either mistakenly perceive non-existent signals and act accordingly, or may ignore the actual signals and do nothing. We label these two as false alarm and signal miss events, respectively. In this paper, we consider an important signaling system with one input and two outputs to show how the likelihood of false alarm and signal miss events can be computed, using the experimentally measured joint response of the two outputs of the signaling system. The two system outputs are the nuclear factor κB (NFκB) and the activating transcription factor-2 (ATF-2), whereas the system input is the tumor necrosis factor (TNF). These molecules are highly involved in essential processes such as cell survival, cell death, and viral replication. The introduced methodology and the measured false alarm and miss probabilities using experimental data can model complex cellular decision-making processes and provide insight into how they may contribute to the development of some pathological conditions. A cell constantly receives signals and takes different fates accordingly. Given the uncertainty rendered by signal transduction noise, a cell may incorrectly perceive these signals. It may mistakenly behave as if there is a signal, although there is none, or may miss the presence of a signal that actually exists. In this paper, we consider a signaling system with two outputs, and introduce and develop methods to model and compute key cell decision-making parameters based on the two outputs and in response to the input signal. In the considered system, the tumor necrosis factor (TNF) regulates the two transcription factors, the nuclear factor κB (NFκB) and the activating transcription factor-2 (ATF-2). These two system outputs are involved in important physiological functions such as cell death and survival, viral replication, and pathological conditions, such as autoimmune diseases and different types of cancer. Using the introduced methods, we compute and show what the decision thresholds are, based on the single-cell measured concentration levels of NFκB and ATF-2. We also define and compute the decision error probabilities, i.e., false alarm and miss probabilities, based on the concentration levels of the two outputs. By considering the joint response of the two outputs of the signaling system, one can learn more about complex cellular decision-making processes, the corresponding decision error rates, and their possible involvement in the development of some pathological conditions. [ABSTRACT FROM AUTHOR]

Simple Summary: The field of cell culture technology involves the cultivation of cells in a controlled environment, mimicking the natural conditions found in living organisms. This process is performed on a large scale, utilizing a specially designed culture medium. The goal is to create either undifferentiated individual cells or multicellular aggregates with minimal differentiation. The present paper offers a comprehensive overview of the advancements and applications of primary cell culture techniques in fish. It places a particular focus on revealing the physiological roles played by fish cells during their in vitro cultivation. Maintaining the functional characteristics of fish cells is of paramount importance, as it is essential for gaining a deeper understanding of the underlying mechanisms governing various physiological processes. To facilitate the use of fish cells in research and practical applications, it is crucial to standardize the separation techniques for these cells and optimize the conditions for their culture. This not only contributes to our knowledge of fish health, disease development, and drug discovery but also drives progress in the aquaculture industry. Fish primary cell culture has emerged as a valuable tool for investigating the physiological roles and responses of various cell types found in fish species. This review aims to provide an overview of the advancements and applications of fish primary cell culture techniques, focusing on the profiling of physiological roles exhibited by fish cells in vitro. Fish primary cell culture involves the isolation and cultivation of cells directly derived from fish tissues, maintaining their functional characteristics and enabling researchers to study their behavior and responses under controlled conditions. Over the years, significant progress has been made in optimizing the culture conditions, establishing standardized protocols, and improving the characterization techniques for fish primary cell cultures. The review highlights the diverse cell types that have been successfully cultured from different fish species, including gonad cells, pituitary cells, muscle cells, hepatocytes, kidney and immune cells, adipocyte cells and myeloid cells, brain cells, primary fin cells, gill cells, and other cells. Each cell type exhibits distinct physiological functions, contributing to vital processes such as metabolism, tissue regeneration, immune response, and toxin metabolism. Furthermore, this paper explores the pivotal role of fish primary cell culture in elucidating the mechanisms underlying various physiological processes. Researchers have utilized fish primary cell cultures to study the effects of environmental factors, toxins, pathogens, and pharmaceutical compounds on cellular functions, providing valuable insights into fish health, disease pathogenesis, and drug development. The paper also discusses the application of fish primary cell cultures in aquaculture research, particularly in investigating fish growth, nutrition, reproduction, and stress responses. By mimicking the in vivo conditions in vitro, primary cell culture has proven instrumental in identifying key factors influencing fish health and performance, thereby contributing to the development of sustainable aquaculture practices. [ABSTRACT FROM AUTHOR]

Simple Summary: This study systematically reviewed the literature on the bioactivities and phytochemical profile of Genista tridentata (L.) Willk, which is an edible plant used in folk medicine. Four databases (PubMed, GoogleScholar, Repositórios Cientificos de Acesso Aberto de Portugal (RCAAP), and ScienceDirect) were searched from inception up to 31 December 2022. Among 34 eligible papers, the flowers and aerial parts were extensively studied, with aqueous extracts being the most commonly used. The findings suggest that Genista tridentata has high potential as a natural source of antioxidants and preservatives for the food/cosmetic industry, offering health benefits. Additionally, its year-round collectability provides an advantage for industrial applications. Genista tridentata (L.) Willk., known as "prickled broom", is a Leguminosae (Fabaceae) species native to the Iberian Peninsula, Morocco, Algeria, and Tunisia. It is used in folk medicine as an anti-inflammatory, for gastrointestinal and respiratory disorders, rheumatism, and headaches, to lower blood pressure, against hypercholesterolemia and hyperglycemia. This study aimed to systematically review the literature on the bioactivities and phytochemical profile of Genista tridentata to understand its pharmacological potential. For this, four electronic databases (PubMed, GoogleScholar, Repositórios Cientificos de Acesso Aberto de Portugal (RCCAP), and ScienceDirect) were searched from inception up to 31 December 2022. From a total of 264 potentially eligible studies considered for screening, 34 papers were considered eligible for this systematic review. The sampling included 71 extracts, collected mainly in Portugal. Genista tridentata extracts present a high level of flavonoids and phenolic compounds. The flowers and aerial parts of the plant were the most studied, and aqueous extracts were the most used. The results predict a high potential for the application of Genista tridentata as a new source of natural antioxidants and preservatives for the food industry with subsequent health benefits, such as the production of nutraceuticals. Moreover, the results indicate that the plant can be collected at all seasons of the year, which represents a benefit for the industry. [ABSTRACT FROM AUTHOR]

Simple Summary: As COVID-19 shifts from pandemic to endemic, emerging variants may be more or less virulent. Predicting whether an emerging COVID-19 variant has of high risk of causing severe disease is needed to plan for potential burdens on hospital capacity and protecting vulnerable populations. However, it takes time to do laboratory and animal experiments to determine whether a new genetic variant might be more severe, and the results may not be representative of when the virus infects humans. By the time there is epidemiological data on the severity of disease associated with a new variant, it can be too late for designing an optimal public health response. There is a critical need for computer models that can predict severe disease risk from genetic sequence data, which can be obtained from just the first few infections in a potential incoming wave. Two key challenges make computer modeling difficult: (1) sequence changes are complex, and (2) using historical data to predict future disease requires accounting for the confounding effects of changing patient demographics, improving therapeutics, and increased vaccination. In this paper, we introduce a novel interpretable deep learning architecture to solve this problem, demonstrating that it can make robust predictions for emerging variants. Through the COVID-19 pandemic, SARS-CoV-2 has gained and lost multiple mutations in novel or unexpected combinations. Predicting how complex mutations affect COVID-19 disease severity is critical in planning public health responses as the virus continues to evolve. This paper presents a novel computational framework to complement conventional lineage classification and applies it to predict the severe disease potential of viral genetic variation. The transformer-based neural network model architecture has additional layers that provide sample embeddings and sequence-wide attention for interpretation and visualization. First, training a model to predict SARS-CoV-2 taxonomy validates the architecture's interpretability. Second, an interpretable predictive model of disease severity is trained on spike protein sequence and patient metadata from GISAID. Confounding effects of changing patient demographics, increasing vaccination rates, and improving treatment over time are addressed by including demographics and case date as independent input to the neural network model. The resulting model can be interpreted to identify potentially significant virus mutations and proves to be a robust predctive tool. Although trained on sequence data obtained entirely before the availability of empirical data for Omicron, the model can predict the Omicron's reduced risk of severe disease, in accord with epidemiological and experimental data. [ABSTRACT FROM AUTHOR]

Simple Summary: Gonadal tissue transplantation as a fertility preservation technique is highly conditioned by our current knowledge of functionality following transplantation, tissue cryodamage, and ischemia–reperfusion injury. This paper presents an updated review of the literature on mitochondrial dysfunction and oxidative stress in the context of gonadal tissue cryopreservation and transplantation. Advances in tissue preservation techniques have allowed reproductive medicine and assisted reproductive technologies (ARTs) to flourish in recent years. Because radio- and chemotherapy procedures are often gonadotoxic, irreversible damage can preclude future gamete production and endocrine support. Accordingly, in recent years, the freezing and storage of gonadal tissue fragments prior to the first oncological treatment appointment and autologous transplantation post-recovery have been considered improved solutions for fertility recovery in cancer survivors. Nevertheless, the cryopreservation and transplantation of thawed tissues is still very limited, and positive outcomes are relatively low. This review aims to discuss the limitations of oncofertility protocols with a focus on the impacts of mitochondrial dysfunction, oxidative stress, and the loss of antioxidant defense in graft integrity. [ABSTRACT FROM AUTHOR]

Simple Summary: The presence of secondary metabolites like flavonoids, alkaloids, and phenolic compounds in white mulberry (Morus alba) make it an ornamental tree mainly in the Asian subcontinent. These secondary metabolites are synthesized through various biosynthetic pathways. Flavonoids like rutin, quercetin, and kaempferol are produced via the phenylpropanoid and flavonoid biosynthetic pathways. The key enzymes responsible for this pathway include phenylalanine ammonia-lyase, chalcone synthase, and flavonoid hydroxylases. Phenolic compounds like resveratrol and oxyresveratrol are produced via the phenylpropanoid pathway using phenylalanine as a precursor. Presences of these secondary metabolites, like in the case of flavonoids (rutin and quercetin), in the mulberry tree have potential biological activities like antioxidant, anti-inflammatory and neuroprotective effects. Also, they have been found to have great medicinal importance, for example in treating diabetes, obesity and neurodegenerative diseases. Also, phenolic compounds like reservertrol exhibit cardio-protective, anticancer, and anti-aging properties. Traditional natural products have been the focus of research to explore their medicinal properties. One such medicinally important plant is the white mulberry, Morus alba, widely distributed in the Asian subcontinent. It is one of the most cultivated species of mulberry tree and has attracted more focus from researchers because of its abundance in phytochemicals as well as multipurpose uses. The leaves, fruits and other parts of the white mulberry plant act as a source of valuable bioactive compounds like flavonoids, phenolic acids, terpenoids and alkaloids. These secondary metabolites have manifold healthy uses as they possess antioxidant, anti-inflammatory, antidiabetic, neutrotrophic, and anticancer properties. Despite the increasing scientific interest in this plant, there are very few reviews that highlight the phytochemistry and biological potential of white mulberry for biomedical research. To this end, this review elaborates the phytochemistry, biosynthetic pathways and pharmacological activities of the glycoside flavonoids of Morus alba. A comprehensive analysis of the available literature indicates that Morus alba could emerge as a promising natural agent to combat diverse conditions including diabetes, cancer, inflammation and infectious diseases. To achieve such important objectives, it is crucial to elucidate the biosynthesis and regulation mechanisms of the bioactive compounds in white mulberry as well as the multifaceted pharmacological effects attributed to this plant resource. The present review paper is intended to present a summary of existing scientific data and a guide for further research in the phytochemistry and pharmacology of white mulberry. Further, a biosynthetic pathway analysis of the glycoside flavonoid in mulberry is also given. Lastly, we discuss the pros and cons of the current research to ensure the prudent and effective therapeutic value of mulberry for promoting human and animal health. [ABSTRACT FROM AUTHOR]

Simple Summary: Analyzing the immune mechanism of sea urchins against pathogens is the basis of disease-resistant breeding. When faced with pathogen invasion, the phagocytosis of sea urchin coelomocytes plays a major immune role. However, it is unclear how can phagocytosis-related immune indices change can help sea urchins resist disease. To answer this question, this study compared the differences in immune indices related to phagocytosis between susceptible and disease-resistant sea urchins after pathogen infection. We found that the apoptosis and necrosis rate of phagocytes, phagocytic index, ACP, ROS and T-AOC may be used as indicators of disease resistance in sea urchins. Disease resistance standards in immune indices can be summarized as phagocytosis increases greatly in the early infection stage and decreases timely to a normal level after killing the pathogen in a short period. The results of this paper can provide important references for disease-resistant breeding of sea urchins. To screen for immune indicators closely related to disease resistance, two species of sea urchin susceptible to black mouth disease (Strongylocentrotus intermedius, S. intermedius ♀ × Heliocidaris crassispina ♂) and three species of sea urchin resistant to black mouth disease (H. crassispina, H. crassispina ♀ × S. intermedius ♂ and Mesocentrotus nudus) were artificially infected with the black mouth pathogen Vibrio echinoideorum. The phagocytosis-related immune indices of the five sea urchin species were compared at different time points post-infection. The results demonstrated that the parameters such as apoptotic rate of phagocytes, mean contribution value (MCV) of single effective phagocyte on Acid Phosphatase (ACP), Reactive Oxygen Species (ROS), and Total Antioxidant Capacity (T-AOC) of the five sea urchin species first increased and then decreased after infection. The key time points were 3 h to 6 h and 48 h post-infection when the black mouth disease-resistant and susceptible sea urchins demonstrated differences. At 3 h or 6 h post-infection, the up-regulation folds in MCV of ACP, ROS and T-AOC of black mouth disease-resistant sea urchins were considerably higher than that of the susceptible sea urchins. At 6 h post-infection, the apoptosis rate and the phagocytic index (PI) of the black mouth disease-resistant sea urchins were significantly higher than those of the susceptible sea urchins (p < 0.05). At 48 h post-infection, the necrosis rate of phagocytes, MCV of ACP and MCV of ROS of the black mouth disease-resistant sea urchins were significantly lower than those of the susceptible sea urchins (p < 0.05). The apoptosis and necrosis rate of phagocytes, PI, and MCV on ACP, ROS may be used as indicators of disease resistance in sea urchins. Disease resistance standards in immune indices can be summarized as phagocytosis increases greatly in the early infection stage and decreases timely to a normal level after killing the pathogen in a short period. [ABSTRACT FROM AUTHOR]

Simple Summary: Eales' Disease, an ocular condition characterized by unknown pathophysiology, exhibits a higher prevalence among young males. Since the etiology of the disease remains unclear, a comprehensive exploration of clinical presentations and diagnostic approaches is undertaken to deepen insights into its current understanding. Furthermore, potential cofactors that may trigger Eales' Disease are reviewed, investigating the association between Eales' Disease and other ocular conditions such as diabetic retinopathy and glaucoma. Additionally, diverse therapeutic interventions across disease stages are examined to assess the efficacy and possibility of repurposing treatments from related conditions. Through this review, the aim is to extend and elucidate potential study areas to facilitate a comprehensive understanding of Eales' Disease and aid patients in preventing the disease or finding optimal treatment strategies. Eales' Disease is an idiopathic peripheral retinal vasculopathy first described by British ophthalmologist Henry Eales in 1880. Most prevalent in healthy young males, Eales' Disease often presents with symptoms of sudden blurry or decreased vision and floaters. Although no clear, standardized stage of the disease exists, it progresses through three overlapping phases—peripheral periphlebitis, ischemic capillary ischemia, and retinal neovascularization. The etiology of Eales' Disease is unknown and appears to be multifactorial, but post-TB hypersensitivity to tuberculoprotein and M. tuberculosis DNA is the most potential cause in the etiology of Eales' Disease. With a thorough examination of the clinical presentation and diagnosis of Eales' Disease—incorporating the latest clinical findings related to the condition—the investigation for Eales' Disease extends to explore recent potential connections with other ocular conditions or possible cofactors, such as glaucoma, uncontrolled diabetes, drug abuse, or inherited medical conditions. Moreover, focusing on critical insights into the treatment of Eales' Disease across its various stages of progression, the overarching goal of the paper is to refine and suggest possible future diagnostic and therapeutic strategies. Widening our understanding of pathophysiology and utilizing various treatment options for individual patients holds immense potential for advancing ocular medicine and optimizing patient care for people with this disease with unknown pathophysiology. [ABSTRACT FROM AUTHOR]

Simple Summary: This study examines how statins, which are drugs commonly used to lower cholesterol, affect the growth of liver cancer cells. Statins can be either lipophilic (lipid-soluble) or hydrophilic (water-soluble), and this characteristic influences how they enter cells. In our research, we compared the effects of lipophilic simvastatin and hydrophilic pravastatin. We found that simvastatin significantly reduces cancer cell growth and increases cell death depending on the dosage and duration of treatment. In contrast, pravastatin, due to its limited uptake, has a minimal impact on cancer cells. These findings suggest that the type of statin used could be crucial in cancer treatment, potentially offering better outcomes for patients with liver cancer. The HMG-CoA reductase inhibitors, statins, are drugs used globally for lowering the level of cholesterol in the blood. Different clinical studies of statins in cancer patients have indicated a decrease in cancer mortality, particularly in patients using lipophilic statins compared to those on hydrophilic statins. In this paper, we selected two structurally different statins (simvastatin and pravastatin) with different lipophilicities and investigated their effects on the proliferation and apoptosis of hepatocellular carcinoma cells. Lipophilic simvastatin highly influences cancer cell growth and survival in a time- and concentration-dependent manner, while pravastatin, due to its hydrophilic structure and limited cellular uptake, showed minimal cytotoxic effects. [ABSTRACT FROM AUTHOR]