The genome of Vicia sativa ssp. amphicarpa provides insights into the role of terpenoids in antimicrobial resistance within subterranean fruits.

Vicia sativa ssp. amphicarpa is a unique forage crop capable of simultaneously producing fruits above and below ground, representing a typical amphicarpic plant. In this study, we sequenced and assembled seven pseudo-chromosomes of the genome of V. sativa ssp. amphicarpa (n = 7) yielding a genome size of 1.59 Gb, with a total annotation of 48 932 protein-coding genes. Long terminal repeat (LTR) elements constituted 62.28% of the genome, significantly contributing to the expansion of genome size. Phylogenetic analysis revealed that the divergence between V. sativa ssp. amphicarpa and V. sativa was around 0.88 million years ago (MYA). Comparative transcriptomic and metabolomic analysis of aerial and subterranean pod shells showed biosynthesis of terpenoids in the subterranean pod shells indicating a correlation between the antimicrobial activity of subterranean pod shells and the biosynthesis of terpenoids. Furthermore, functional validation indicates that overexpression of VsTPS5 and VsTPS16 enhances terpenoid biosynthesis for antibacterial activity. Metabolomic analysis suggests the involvement of terpenoids in the antimicrobial properties of subterranean pod shells. Deciphering the genome of V. sativa ssp. amphicarpa elucidated the molecular mechanisms behind the antimicrobial properties of subterranean fruits in amphicarpic plants, providing valuable insights for the study of amphicarpic plant biology.

Hybrid mRMR and multi-objective particle swarm feature selection methods and application to metabolomics of traditional Chinese medicine.

Metabolomics data has high-dimensional features and a small sample size, which is typical of high-dimensional small sample (HDSS) data. Too high a dimensionality leads to the curse of dimensionality, and too small a sample size tends to trigger overfitting, which poses a challenge to deeper mining in metabolomics. Feature selection is a valuable technique for effectively handling the challenges HDSS data poses. For the feature selection problem of HDSS data in metabolomics, a hybrid Max-Relevance and Min-Redundancy (mRMR) and multi-objective particle swarm feature selection method (MCMOPSO) is proposed. Experimental results using metabolomics data and various University of California, Irvine (UCI) public datasets demonstrate the effectiveness of MCMOPSO in selecting feature subsets with a limited number of high-quality features. MCMOPSO achieves this by efficiently eliminating irrelevant and redundant features, showcasing its efficacy. Therefore, MCMOPSO is a powerful approach for selecting features from high-dimensional metabolomics data with limited sample sizes.

Exploring cerebral structural and functional abnormalities in a mouse model of post-traumatic headache induced by mild traumatic brain injury.

Mild traumatic brain injury (mTBI)-induced post-traumatic headache (PTH) is a pressing public health concern and leading cause of disability worldwide. Although PTH is often accompanied by neurological disorders, the exact underlying mechanism remains largely unknown. Identifying potential biomarkers may prompt the diagnosis and development of effective treatments for mTBI-induced PTH. In this study, a mouse model of mTBI-induced PTH was established to investigate its effects on cerebral structure and function during short-term recovery. Results indicated that mice with mTBI-induced PTH exhibited balance deficits during the early post-injury stage. Metabolic kinetics revealed that variations in neurotransmitters were most prominent in the cerebellum, temporal lobe/cortex, and hippocampal regions during the early stages of PTH. Additionally, variations in brain functional activities and connectivity were further detected in the early stage of PTH, particularly in the cerebellum and temporal cortex, suggesting that these regions play central roles in the mechanism underlying PTH. Moreover, our results suggested that GABA and glutamate may serve as potential diagnostic or prognostic biomarkers for PTH. Future studies should explore the specific neural circuits involved in the regulation of PTH by the cerebellum and temporal cortex, with these two regions potentially utilized as targets for non-invasive stimulation in future clinical treatment.

Comparison of Complications between Total Intravenous Anaesthesia and Combined Intravenous and Inhalation Anaesthesia after Renal Biopsy in Children.

OBJECTIVE: The objective of this study was to examine the influence of total intravenous anaesthesia (TIVA) compared to combined intravenous and inhalation anaesthesia (CIIA) in paediatric patients undergoing renal biopsy. METHODS: A total of 86 children with nephrotic syndrome, acute glomerulonephritis, chronic glomerulonephritis, IgG nephropathy, systemic lupus erythematosus and purpura nephritis were selected from January 2018 to January 2023 in our hospital. All children were divided into the total intravenous anaesthesia group and intravenous inhalational anaesthesia group according to the anaesthesia method. The experimental group comprised 46 children with renal diseases who underwent static aspiration compound anaesthesia during renal biopsy at our hospital from January 2018 to January 2023. Conversely, the control group included 40 children with renal diseases who underwent total intravenous anaesthesia during renal biopsy at the hospital within the same period. Hemodynamic parameters, such as mean arterial pressure (MAP), heart rate (HR), and oxygen saturation (SPO2), were assessed at four different time points: Before anesthesia induction (T0), during anesthesia induction (T1), after anesthesia induction (T2), and at the conclusion of the surgery (T3). Puncture success rate, time to renal puncture, time to get out of bed, postoperative recovery from anaesthesia (including time to postoperative awakening and time to return to spontaneous respiration) and incidence of adverse anaesthetic reactions were also included. RESULTS: We observed notable variations in HR and MAP at T2 and T3, as well as SPO2 levels, duration of awakening from anaesthesia and time taken to resume spontaneous respiration between the two groups at T2 (p < 0.05). No statistically significant variances were detected between the two groups concerning adverse reactions to anaesthesia, puncture success rate, duration to renal puncture and time to mobilisation from bed (p > 0.05). CONCLUSIONS: In conclusion, compared with the total intravenous anaesthesia, the implementation of the sedation-aspiration-combined anaesthesia in renal biopsy in children with renal disease features less haemodynamic fluctuation, better postoperative anaesthesia recovery and does not increase the incidence of adverse reactions.

A non-linear partial least squares based on monotonic inner relation.

A novel regression model, monotonic inner relation-based non-linear partial least squares (MIR-PLS), is proposed to address complex issues like limited observations, multicollinearity, and nonlinearity in Chinese Medicine (CM) dose-effect relationship experimental data. MIR-PLS uses a piecewise mapping function based on monotonic cubic splines to model the non-linear inner relations between input and output score vectors. Additionally, a new weight updating strategy (WUS) is developed by leveraging the properties of monotonic functions. The proposed MIR-PLS method was compared with five well-known PLS variants: standard PLS, quadratic PLS (QPLS), error-based QPLS (EB-QPLS), neural network PLS (NNPLS), and spline PLS (SPL-PLS), using CM dose-effect relationship datasets and near-infrared (NIR) spectroscopy datasets. Experimental results demonstrate that MIR-PLS exhibits general applicability, achieving excellent predictive performances in the presence or absence of significant non-linear relationships. Furthermore, the model is not limited to CM dose-effect relationship research and can be applied to other regression tasks.

Analysing pharmacodynamic interactions of traditional Chinese medicine in treating acute pancreatitis based on OPLS method.

Acute pancreatitis (AP) is a surgical abdominal disease for which the Dachengqi Decoction (DCQD) of traditional Chinese medicine (TCM) is widely used in China. This study aims to analyse the pharmacodynamic interactions and quantitative relationship of DCQD in the treatment of AP based on orthogonal partial least squares (OPLS) analysis. The experimental data show organic chemical components as candidate pharmacodynamic substances (PS) in the blood and include pharmacodynamic indicators (PIs). Taking each PI as the target and using OPLS method to construct three types of mathematical equations, including the mathematical relationship between the pharmacodynamic substances and each target pharmacodynamic indicator (PS-TPI); the mathematical relationship between the pharmacodynamic substances, the pharmacodynamics indicators and each target pharmacodynamic indicator (PS, PI-TPI); and the mathematical relationship between the pharmacodynamic indicators and each target pharmacodynamic indicator (PI-TPI). Through analysis, we find that the R2Y(cum) values and VIP values indicate that PS and PI are the follow-up factors of TPI; the coefficient value indicates that there is a quantitative relationship between the PS and the TPI; and there also is a quantitative relationship between PI and TPI. The results demonstrated that PS and other PIs are the important influencing factors of TPI, and that there are interactions and quantitative relationships among the PIs.

New research for detecting complex associations between variables with randomness.

Many correlation analysis methods can capture a wide range of functional types of variables. However, the influence of uncertainty and distribution status in data is not considered, which leads to the neglect of the regularity information between variables, so that the correlation of variables that contain functional relationship but subject to specific distributions cannot be well identified. Therefore, a novel correlation analysis framework for detecting associations between variables with randomness (RVCR-CA) is proposed. The new method calculates the normalized RMSE to evaluate the degree of functional relationship between variables, calculates entropy difference to measure the degree of uncertainty in variables and constructs the copula function to evaluate the degree of dependence on random variables with distributions. Then, the weighted sum method is performed to the above three indicators to obtain the final correlation coefficient R. In the study, which considers the degree of functional relationship between variables, the uncertainty in variables and the degree of dependence on the variables containing distributions, cannot only measure the correlation of functional relationship variables with specific distributions, but also can better evaluate the correlation of variables without clear functional relationships. In experiments on the data with functional relationship between variables that contain specific distributions, UCI data and synthetic data, the results show that the proposed method has more comprehensive evaluation ability and better evaluation effect than the traditional method of correlation analysis.

An improved particle swarm optimization combined with double-chaos search.

Particle swarm optimization (PSO) has been successfully applied to various complex optimization problems due to its simplicity and efficiency. However, the update strategy of the standard PSO algorithm is to learn from the global best particle, making it difficult to maintain diversity in the population and prone to premature convergence due to being trapped in local optima. Chaos search mechanism is an optimization technique based on chaotic dynamics, which utilizes the randomness and nonlinearity of a chaotic system for global search and can escape from local optima. To overcome the limitations of PSO, an improved particle swarm optimization combined with double-chaos search (DCS-PSO) is proposed in this paper. In DCS-PSO, we first introduce double-chaos search mechanism to narrow the search space, which enables PSO to focus on the neighborhood of the optimal solution and reduces the probability that the swarm gets trapped into a local optimum. Second, to enhance the population diversity, the logistic map is employed to perform a global search in the narrowed search space and the best solution found by both the logistic and population search guides the population to converge. Experimental results show that DCS-PSO can effectively narrow the search space and has better convergence accuracy and speed in most cases.

Systematic analysis of cuproptosis-related genes in immunological characterization and predictive drugs in Alzheimer's disease.

Objectives: This study aimed to make a systematic analysis of cuproptosis-related genes (CRGs) in immunological characterization and predictive drugs in Alzheimer's disease (AD) through bioinformatics and biological experiments. Methods: The molecular clusters related to CRGs and associated immune cell infiltrations in AD were investigated. The diagnostic models were constructed for AD and different AD subtypes. Moreover, drug prediction and molecular docking were also performed. Subsequently, a molecular dynamics (MD) simulation was conducted to further verify the findings. Finally, RT-qPCR validation was performed. Results: The characterization of 12 AD-related CRGs was evaluated in AD, and a diagnostic model for AD showed a satisfying discrimination power based on five CRGs by LASSO regression analysis. The dysregulated CRGs and activated immune responses partially differed between patients with AD and healthy subjects. Furthermore, two molecular subtypes (clusters A and B) with different immune infiltration characteristics in AD were identified. Similarly, a diagnostic model for different AD subtypes was built with nine CRGs, which achieved a good performance. Molecular docking revealed the optimum conformation of CHEMBL261454 and its target gene CSNK1D, which was further validated by MD simulation. The RT-qPCR results were consistent with those of the comprehensive analysis. Conclusion: This study systematically elucidated the complex relationship between cuproptosis and AD, providing novel molecular targets for treatment and diagnosis biomarkers of AD.

Adipose-derived stem cells repair radiation-induced chronic lung injury via inhibiting TGF-ß1/Smad 3 signaling pathway.

To investigate the effect of adipose-derived stem cells (ASCs) transplantation on radiation-induced lung injury (RILI), Sprague-Dawley rats were divided into phosphate-buffered saline (PBS) group, ASCs group, Radiation + PBS group, and Radiation + ASCs group. Radiation + PBS and Radiation + ASCs groups received single dose of 30 Gy X-ray radiation to the right chest. The Radiation + PBS group received 1 mL PBS suspension and Radiation + ASCs group received 1 mL PBS suspension containing 1 × 107 CM-Dil-labeled ASCs. The right lung tissue was collected on Days 30, 90, and 180 after radiation. Hematoxylin-eosin and Masson staining were performed to observe the pathological changes and collagen fiber content in the lung tissue. Immunohistochemistry (IHC) and western blot (WB) were used to detect levels of fibrotic markers collagen I (Collal), fibronectin (FN), as well as transforming growth factor-ß1 (TGF-ß1), p-Smad 3, and Smad 3. Compared with the non-radiation groups, the radiation groups showed lymphocyte infiltration on Day 30 after irradiation and thickened incomplete alveolar walls, collagen deposition, and fibroplasia on Days 90 and 180. ASCs relieved these changes on Day 180 (Masson staining, P = 0.0022). Compared with Radiation + PBS group, on Day 180 after irradiation, the Radiation + ASCs group showed that ASCs could significantly decrease the expressions of fibrosis markers Collal (IHC: P = 0.0022; WB: P = 0.0087) and FN (IHC: P = 0.0152; WB: P = 0.026) and inhibit the expressions of TGF-ß1 (IHC: P = 0.026; WB: P = 0.0152) and p-Smad 3 (IHC: P = 0.0043; WB: P = 0.0087) in radiation-induced injured lung tissue. These indicated that ASCs could relieve RILI by inhibiting TGF-ß1/Smad 3 signaling pathway.

Monovalent Salt and pH-Stimulated Gelation of Scallop (Patinopecten yessoensis) Male Gonad Hydrolysates/κ-Carrageenan.

The gelation of scallop Patinopecten yessoensis male gonad hydrolysates (SMGHs) and κ-carrageenan (KC) subjected to pH (2-8, 3-9) and NaCl/KCl stimuli-response was investigated. SMGHs/KC gels subjected to a NaCl response exhibited an increasing storage modulus G'from 2028.6 to 3418.4 Pa as the pH decreased from pH 8 to 2, with corresponding T23 fluctuating from 966.40 to 365.64 ms. For the KCl-treated group, SMGHs/KC gels showed an even greater G' from 4646.7 to 10996.5 Pa, with T23 fluctuating from 622.2 to 276.98 ms as the pH decreased from 9 to 3. The improved gel strength could be ascribed to the blueshift and redshift of hydroxyl groups and amide I peaks, enhanced enthalpy and peak temperature, and gathered characteristic diffraction peaks from SMGHs, KC, NaCl, and KCl. The CLSM and cryo-SEM images further reflected that SMGHs/KC gels showed more flocculation formation and denser and more homogeneous networks with smaller pore sizes in more acidic domains, especially when subjected to the KCl response. This research gives a theoretical and methodological understanding of the construction of salt- and pH-responsive SMGHs/KC hydrogels as novel functional soft biomaterials applied in food and biological fields.

Global Trends and Performances of Acupuncture Therapy on Bell's Palsy from 2000 to 2023: A Bibliometric Analysis.

Purpose: Recent studies have shown that acupuncture may have great potential in the treatment of Bell's palsy. However, the bibliometric analysis of this field has not been summarized properly. Thus, the purpose of this study is to analyze the hotspot of acupuncture for Bell's Palsy. Methods: The core collection database of Web of Science was searched for relevant publications from 2000 to 2023, and countries, institutions, authors, keywords, and literature were analyzed and visualized by bibliometric softwareCiteSpace 5.1.R6, Vosviewer, BICOMB, and gCLUTO to explore the scientific achievements, research collaboration networks, research hot spots, and research trends. Results: 229 publications were included in this study. The most cited journal is Journal of Otolaryngology-Head & Neck Surgery; the most prolific country is China; the most prolific author is Li Ying, moreover, the collaboration among scholars is poor; Kyung Hee University is the most prolific institution studying acupuncture for Bell's Palsy. Reference burst detection indicates that traditional Chinese Medicine philosophy, the role of acupuncture in the prognosis of facial palsy, mechanism of acupuncture to improve facial nerve function, and the use of electroacupuncture are starting to become new research hotspots. Conclusion: The field of acupuncture for Bell's Palsy has developed rapidly in recent years, and new research trends are mainly: combination with traditional Chinese medicine, the role of acupuncture in the prognosis of facial palsy, mechanism of acupuncture to improve facial nerve function, and the use of electroacupuncture. However, research in this field is still dominated by case reports and clinical trials, and there is a lack of large-scale, multicenter clinical trials and animal experiments there are still many problems in institutional cooperation and experimental design, which requires relevant researchers to strengthen cooperation and improve experimental design.

Retrograde Approach via Ipsilateral Septal Collateral Channel in Percutaneous Coronary Intervention for Coronary Chronic Total Occlusion: A Single-Center Experience.

Background: The septal collateral channel (CC) is the preferred channel in retrograde percutaneous coronary intervention (PCI) for chronic total occlusion (CTO). However, reports on the utilization of the ipsilateral septal CC are limited. Objective: To evaluate the feasibility and safety of the ipsilateral septal CC in retrograde CTO PCI. Methods: Twenty-five patients with successful wire CC tracking via the ipsilateral septal CC in retrograde CTO PCI were retrospectively analyzed. All procedures were performed by experienced CTO operators. Procedures were divided into the left descending coronary artery (LAD)-septal-LAD group and the LAD-septal-left circumflex coronary artery (LCX) group. Procedural complications and in-hospital outcomes were ascertained. Results: Both groups were similar with respect to risk factors and angiographic characteristics of the CTO, except for the collateral tortuosity (86.7% vs 20%, p=0.002). The success rate of microcatheter CC tracking was 96%. Both technical success and procedural success rates were 92%. Procedural complications were found in one case (septal perforation, 4%), which happened in the LAD-septal-LAD group (p=0.250). One postoperative adverse event (Q-wave myocardial infarction, 4%) was observed before discharge. Conclusion: The retrograde approach via the ipsilateral septal CC was feasible, with high success rates and acceptable complications, in the hands of experienced operators.

IRE1α: from the function to the potential therapeutic target in atherosclerosis.

Inositol requiring enzyme 1 (IRE1) is generally thought to control the most conserved pathway in the unfolded protein response (UPR). Two isoforms of IRE1, IRE1α and IRE1ß, have been reported in mammals. IRE1α is a ubiquitously expressed protein whose knockout shows marked lethality. In contrast, the expression of IRE1ß is exclusively restricted in the epithelial cells of the respiratory and gastrointestinal tracts, and IRE1ß-knockout mice are phenotypically normal. As research continues to deepen, IRE1α was showed to be tightly linked to inflammation, lipid metabolism regulation, cell death and so on. Growing evidence also suggests an important role for IRE1α in promoting atherosclerosis (AS) progression and acute cardiovascular events through disrupting lipid metabolism balance, facilitating cells apoptosis, accelerating inflammatory responses and promoting foam cell formation. In addition, IRE1α was recognized as novel potential therapeutic target in AS prevention. This review provides some clues about the relationship between IRE1α and AS, hoping to contribute to further understanding roles of IRE1α in atherogenesis and to be helpful for the design of novel efficacious therapeutics agents targeting IRE1α-related pathways.

Characteristics of the Intestine Extracts and Their Effect on the Crude Collagen Fibers of the Body Wall from Sea Cucumber Apostichopus japonicus.

Sea cucumbers Apostichopus japonicus will vomit their intestines during certain stimulations, and the collagen of the body wall will then be degraded. To define the effect of the sea cucumber intestine extracts on the body wall, the intestinal extracts and crude collagen fibers (CCF) of sea cucumber A. japonicus were prepared. According to the gelatin zymography, the type of endogenous enzymes in intestinal extracts were mainly serine endopeptidases with optimal activities at pH 9.0 and 40 °C. According to the rheology results, the viscosity of 3% CCF decreased from 32.7 Pa·s to 5.3 Pa·s by adding intestine extracts. The serine protease inhibitor phenylmethanesulfonyl fluoride inhibited the activity of intestinal extracts and increased the viscosity of collagen fibers to 25.7 Pa·s. The results proved that serine protease in the intestinal extracts participated in the process of body wall softening in sea cucumbers.

MicroRNA-146a Improved Acute Lung Injury Induced by hepatic Ischemia-reperfusion Injury by Inhibiting PRDX1.

Hepatic ischemia-reperfusion injury (HIRI)-induced acute lung injury (ALI) is characterized by high incidence and poor prognosis. The regulatory role of microRNA-146a (miR-146a) in HIRI has been reported, but if miR-146a could affect the progression of HIRI-induced ALI has not been reported. The mice HIRI model was established by ligating left hepatic portal vein and hepatic artery for 60 minutes and then treating with reperfusion for 4 hours. Hypoxia-reoxygenation (HR) was performed to establish cell model. The binding site between miR-146a and Peroxidase 1 (PRDX1) was predicted and validated. The levels of inflammation factors and redox markers were detected with commercial kits. Significant lower expression of miR-146a and higher expression of PRDX1 in HIRI animal model were observed. miR-146a inhibited the liver injury after HIRI induction through targeting PRDX1. miR-146a inhibited the lung injury caused by HIRI via regulating PRDX1. The inhibition of cell apoptosis and inflammation factors by miR-146a were reversed by pcDNA-PRDX1. This research demonstrated that miR-146a improved ALI caused by HIRI by inhibiting apoptosis, inflammation, oxidative condition through targeting PRDX1. This study might provide a novel thought for the prevention and treatment of ALI caused by HIRI by regulating miR-146a/PRDX1 axis.

Leaf morphology, functional trait and altitude response in perennial vetch (Vicia unijuga A. Braun), alfalfa (Medicago sativa L.) and sainfoin (Onobrychis viciifolia Scop.).

MAIN CONCLUSION: Species have plasticity across altitude gradients in leaf morphology and function, and their response to high altitude conditions was mainly reflected in leaf cell metabolism and gas exchange. Leaf morphological and functional adaptation to altitude has received research attention in recent years, but there are no studies for forage legumes. Here we report differences in 39 leaf morphology and functional traits of three leguminous forages (alfalfa, sainfoin and perennial vetch) at three sites in Gansu Province, China, ranging from 1768 to 3074 m altitude to provide information for potential use in breeding programmes. With increasing altitude, plant water status increased, reflecting increase in soil water content and decreased average temperature, which lead to leaf intercellular CO2 concentration. Stomatal conductance and evapotranspiration increased significantly but water-use efficiency decreased. At high altitude, ΦPSII decreased but non-photochemical quenching and chlorophyll a:b ratio increased while spongy mesophyll tissue and leaf thickness increased. These changes may be due to UV or low-temperature damage of leaf protein and metabolic cost of plant protection or defence responses. Contrary to many other studies, leaf mass per area decreased significantly at higher altitude. This was consistent with predictions under the worldwide leaf economic spectrum on the basis that soil nutrients increased with increasing altitude. The key species differences were more irregularly shaped epidermal cells and larger stomatal size in perennial vetch compared to alfalfa or sainfoin that enhanced gas exchange and photosynthesis by generating mechanical force, increasing guard cell turgor, and promoting stomatal operation. The lower adaxial stomatal density also enhanced water-use efficiency. These adaptations might confer perennial vetch an advantage in environments with extreme diurnal temperature fluctuation or in frigid conditions.

Identification of key candidate genes and pathways in rheumatoid arthritis and osteoarthritis by integrated bioinformatical analysis.

Rheumatoid arthritis (RA) and osteoarthritis (OA) are the most common joint disorders. Although they have shown analogous clinical manifestations, the pathogenesis of RA and OA are different. In this study, we used the online Gene Expression Omnibus (GEO) microarray expression profiling dataset GSE153015 to identify gene signatures between RA and OA joints. The relevant data on 8 subjects obtained from large joints of RA patients (RA-LJ), 8 subjects obtained from small joints of RA patients (RA-SJ), and 4 subjects with OA were investigated. Differentially expressed genes (DEGs) were screened. Functional enrichment analysis of DEGs including the Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified, which were mainly associated with T cell activation or chemokine activity. Besides, protein-protein interaction (PPI) network analysis was performed, and key modules were identified. Hub genes of RA-LJ and OA groups were screened, they were CD8A, GZMB, CCL5, CD2, and CXCL9, whereas CD8A, CD2, IL7R, CD27, and GZMB were hub genes of RA-SJ and OA group. The novel DEGs and functional pathways between RA and OA identified in this study may provide new insight into the underlying molecular mechanisms and therapeutic strategies of RA and OA.