Molecular genetic characterization analysis of a novel HIV-1 circulating recombinant form (CRF156_0755) in Guangdong, China.

Introduction: The characteristic of human immunodeficiency virus type 1 (HIV-1) is its susceptibility to erroneous replication and recombination, which plays a crucial role in the diverse and dynamic variation of HIV-1. The spread of different subtypes in the same population often leads to the emergence of circulating recombination forms (CRFs). At present, the main recombinant subtypes of HIV-1 in China are CRF07_BC, CRF01_AE, CRF08_BC and B' subtypes, while CRF55_01B has become the fifth major epidemic strain in China after rapid growth in recent years since it was first reported in 2013. In this study, we obtained five nearly full-length genomes (NFLGs) and one half-length genome from five different cities in Guangdong. Here, we focused on analyzing their characteristics, parental origin and drug resistance. Methods: Plasma samples were collected from six HIV-1 infected patients in Guangdong Province who had no epidemiological association with each other. The NFLGs of HIV-1 were amplified in two overlapping segments by the near-terminal dilution method. The positive products were sequenced directly to obtain genomic sequences. The recombinant patterns and breakpoints of the NFLGs were determined using the Simplot software and confirmed by the maximum likelihood trees for segments using the IQ-TREE and BEAST software. The genotypic resistance profiles of the protease reverse transcriptase and integrase were resolved by the Stanford HIV drug resistance database. Results: The six genomes shared highly similar recombinant pattern, with the CRF55_01B backbone substituted by CRF07_BC segments, therefore assigned as CRF156_0755. The evolutionary analysis of the segments showed that CRF07_BC segments were not clustered with the Chinese MSM variants in the CRF07_BC lineage. All the five NFLGs were identified with the non-nucleoside reverse-transcription inhibitors (NNRTIs) resistance mutation V179E. Discussion: With the accumulation and evolution of recombination between CRF55_01B and CRF 07_BC, the prevalence of more recombinant strains of CRF55_01B and CRF 07_BC may occur. Therefore, it is necessary to strengthen the identification and monitoring of the recombination of CRF55_01B and CRF 07_BC.

Exploring the mechanism of dendrobine in treating metabolic associated fatty liver disease based on network pharmacology and experimental validation.

BACKGROUND: This study investigates the therapeutic mechanisms of dendrobine, a primary bioactive compound in Dendrobium nobile, for Metabolic Associated Fatty Liver Disease (MASLD) management. Utilizing network pharmacology combined with experimental validation, the clinical effectiveness of dendrobine in MASLD treatment was assessed and analyzed. RESULTS: The study demonstrates significant improvement in liver function among MASLD patients treated with Dendrobium nobile. Network pharmacology identified key targets such as Peroxisome Proliferator-Activated Receptor Gamma (PPARG), Interleukin 6 (IL6), Tumor Necrosis Factor (TNF), Interleukin 1 Beta (IL1B), and AKT Serine/Threonine Kinase 1 (AKT1), with molecular docking confirming their interactions. Additionally, dendrobine significantly reduced ALT and AST levels in palmitic acid-treated HepG2 cells, indicating hepatoprotective properties and amelioration of oxidative stress through decreased Malondialdehyde (MDA) levels and increased Superoxide Dismutase (SOD) levels. CONCLUSION: Dendrobine mitigates liver damage in MASLD through modulating inflammatory and immune responses and affecting lipid metabolism, potentially by downregulating inflammatory mediators like TNF, IL6, IL1B, and inhibiting AKT1 and Signal Transducer and Activator of Transcription 3 (STAT3). This study provides a theoretical basis for the application of dendrobine in MASLD treatment, highlighting its potential as a therapeutic agent.

A Fusion Learning Model Based on Deep Learning for Single-Cell RNA Sequencing Data Clustering.

Single-cell RNA sequencing (scRNA-seq) technology provides a means for studying biology from a cellular perspective. The fundamental goal of scRNA-seq data analysis is to discriminate single-cell types using unsupervised clustering. Few single-cell clustering algorithms have taken into account both deep and surface information, despite the recent slew of suggestions. Consequently, this article constructs a fusion learning framework based on deep learning, namely scGASI. For learning a clustering similarity matrix, scGASI integrates data affinity recovery and deep feature embedding in a unified scheme based on various top feature sets. Next, scGASI learns the low-dimensional latent representation underlying the data using a graph autoencoder to mine the hidden information residing in the data. To efficiently merge the surface information from raw area and the deeper potential information from underlying area, we then construct a fusion learning model based on self-expression. scGASI uses this fusion learning model to learn the similarity matrix of an individual feature set as well as the clustering similarity matrix of all feature sets. Lastly, gene marker identification, visualization, and clustering are accomplished using the clustering similarity matrix. Extensive verification on actual data sets demonstrates that scGASI outperforms many widely used clustering techniques in terms of clustering accuracy.

Clinicopathological and molecular genetic analysis of 13 cases of primary retroperitoneal Ewing sarcoma.

Retroperitoneal Ewing sarcomas (RES) are very rare and mostly described in case reports. The purpose of this study was to retrospectively analyze the clinicopathology, molecular characteristics, biological behavior, and therapeutic information of 13 cases of primary RES with immunohistochemical staining, fluorescence in situ hybridization, RT-PCR and NGS sequencing detection techniques. The thirteen patients included eight males and five females with a mean age of 34 years. Morphologically, the tumors were comprised of small round or epithelial-like cells with vacuolated cytoplasm (6/13,46 %) arranged in diffuse, nested (8/13,62 %) and perivascular (7/13,54 %) patterns. Unusual morphologic patterns, such as meningioma-like swirling structures and sieve-like structures were relatively novel findings. Immunohistochemical studies showed CD99 (12/13; 92 %), CD56 (11/13; 85 %), NKX2.2 (9/13; 69 %), PAX7 (10/11;91 %) and CD117(6/9;67 %) to be positive.12 cases (92 %) demonstrated EWSR1 rearrangement and 3 cases displayed EWSR1::FLI1 fusion by FISH. ERCC4 splice-site variant, a novel pathogenic variant, was discovered for the first time via RNA sequencing. With a median follow-up duration of 14 months (6 to 79 months), 8/13 (62 %) patients died, while 5/13(38 %) survived. Three cases recurred, and five patients developed metastasis to the liver (2 cases), lung (2 cases) and bone (1 case). RES is an aggressive, high-grade tumor, prone to multiple recurrences and metastases, with distinctive morphologic, immunohistochemical, and molecular genetic features. ERCC4 splicing mutation, which is a novel pathogenic variant discovered for the first time, with possible significance for understanding the disease, as well as the development of targeted drugs.

The effect of telephone and short-message follow-ups on compliance and efficacy in asthmatic children treated with inhaled corticosteroid: A randomized controlled trial.

BACKGROUND: This study aims to evaluate the effect of telephone and short-message follow-ups on compliance and efficacy in asthmatic children treated with inhaled corticosteroids. METHODS: A total of 120 children with moderate bronchial asthma who visited the Asthma Outpatient Department of the Affiliated Hospital of Qingdao University were enrolled in the study. They were divided randomly into 3 groups based on the type of follow-up given: a combined telephone and short-message service (Tel + SMS) group, a SMS group, and a control group. After being followed up for 12 weeks, each child's asthma control level was assessed and their lung function was measured. RESULTS: The compliance rates of children in the Tel + SMS group and SMS group were 86.49% and 56.25%, respectively. The total effective rates of these 2 groups (94.59% and 75.0%, respectively) were significantly higher than the rate of the control group (P < .01). The lung function indicators of the children in all 3 groups were better than those before treatment, although only the Tel + SMS group and SMS group improved significantly (P < .05). The lung function indicators of the large and small airways in the Tel + SMS group and the SMS group were also significantly better than those of the control group (P < .01). The results of the study suggest that 1 of the causes of poor compliance in asthmatic children is fear of an adverse reaction to inhaled corticosteroids. CONCLUSION: Telephone and short-message follow-ups can increase compliance with inhaled corticosteroid treatment and improve the asthma control levels and lung function of asthmatic children.

Spin crossover of a Fe(II) mononuclear complex induced by intermolecular factors involving chloride and solvent ordering.

Two new salts of a mononuclear tripodal Fe(II) complex were prepared, using ClO4- and Cl-. The ClO4- sample (1) remained HS at low temperatures, similar to the previously reported BF4- analogue. Crystallising with the Cl- anion (2) led to a markedly different crystal packing arrangement, and engendered SCO activity. This has been correlated to the lower crystal packing density in 2 and the coordination complex conformational differences arising due to the packing motifs of 1 and 2. Further, solvent ordering effects have been proposed to facilitate spin transition behaviour in 2.

Health and Community Care workers' Knowledge and Perceptions of Social Prescribing in Singapore.

Objectives: This study aimed to survey knowledge and perceptions of social prescribing (SP) amongst health and community care workers. Study design: Cross sectional online survey conducted in November 2023. Methods: The survey on basic demographics, awareness, knowledge, and practices of SP was completed by 123 health and community care workers. Results: The mean age of respondents was 39.0 years. Nearly two-thirds had heard of SP. A lower proportion of acute hospital doctors (55.6%) and nurses (56.8%) had heard of SP compared with primary and subacute care doctors (75.0%). The majority agreed that SP is beneficial for patients' mental health and reducing healthcare utilisation. Primary care physicians, community nurses and active ageing centres were the top three professionals selected as most responsible for SP by survey respondents. The most commonly cited barriers to SP were seniors' reluctance (63.4%), lacking knowledge on how to refer (59.3%), lack of time (44.7%) and cost to seniors (44.7%). Conclusion: Overall, health and community care workers demonstrated positive attitudes toward SP and were keen to refer patients for SP. However, additional efforts are needed to improve knowledge about how to refer for and provide training on SP.

Yiqigubiao pill treatment regulates Sirtuin 5 expression and mitochondrial function in chronic obstructive pulmonary disease.

Background: Chronic obstructive pulmonary disease (COPD) is a heterogeneous group of pathophysiological bases of airway inflammation and its anti-inflammatory response. Aberrant mitochondrial signaling and mitochondrial dysfunction underlie the pathomechanisms leading to COPD. This study aims to investigate the effects of the Yiqigubiao (YQGB) pill, a traditional Chinese medicine (TCM), on Sirtuin 5 (SIRT5) and mitochondrial function in patients with COPD. Methods: Thirty-four patients with COPD were randomized into oral YQGB or placebo groups concurrent with a 24-week routine treatment. The pulmonary function was assessed by examining the levels of forced expiratory volume in one second (FEV1)/forced vital capacity (FVC), FEV1, and FVC. Quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot were used to detect SIRT5 expression in mitochondria isolated from peripheral blood. Flow cytometry was used to detect changes in mitochondrial membrane potential and reactive oxygen species (ROS) in peripheral blood lymphocytes. Human bronchial epithelial (HBE) cells stimulated by cigarette smoke extract (CSE) were treated with YQGB. After SIRT5 was knocked down in cells, the changes in mitochondrial membrane potential, levels of adenosine triphosphate (ATP), and ROS were detected. Results: YQGB treatment significantly improved lung function in patients with COPD. The expression of SIRT5 and the mitochondrial membrane potential significantly increased and ROS decreased in patients with COPD after YQGB treatment. The CSE decreased cell proliferation and SIRT5 expression, which was alleviated after YQGB treatment. Furthermore, SIRT5 was knocked down in CSE-stimulated HBE cells, and its expression was elevated upon YQGB treatment. The knockdown of SIRT5 significantly altered the CSE-stimulation-induced dysregulation of mitochondrial membrane potential, ATP levels, and ROS. This was also restored after YQGB treatment. Conclusions: YQGB treatment can elevate SIRT5 expression, restore mitochondrial function in COPD, and exert protective effects.

mRNA Delivery Systems Based on Protein Nanocages: How Far Can We Go?

Messenger RNA (mRNA) therapeutics hold great potential in the prevention and treatment of many diseases owing to several unique advantages. Delivery of mRNA into target cells is a critical step in mRNA therapy. Efficient and safe delivery systems remain an urgent need. Here, we provide an overview of the current applications of protein nanocages (PNCs), which include different types of PNCs, such as viral capsids, nonviral PNCs, and artificial PNCs, in mRNA delivery. PNCs have the features of uniform size, controllable assembly, modifiable inner and outer surfaces, good biocompatibility, and biodegradability, making them ideal candidates for mRNA delivery. In this review, the properties, loading strategies, and delivery outcomes of each tested PNC are introduced. The challenges faced by PNC-based mRNA carriers are discussed. We also share our perspectives on possible strategies to address these challenges, emphasizing the opportunities brought by emerging technologies and disciplinary convergence.

Targeting KRASG12D mutation in non-small cell lung cancer: molecular mechanisms and therapeutic potential.

Lung malignant tumors are a type of cancer with high incidence and mortality rates worldwide. Non-small cell lung cancer (NSCLC) accounts for over 80% of all lung malignant tumors, and most patients are diagnosed at advanced stages, leading to poor prognosis. Over the past decades, various oncogenic driver alterations associated with lung cancer have been identified, each of which can potentially serve as a therapeutic target. Rat sarcoma (RAS) genes are the most commonly mutated oncogenes in human cancers, with Kirsten rat sarcoma (KRAS) being the most common subtype. The role of KRAS oncogene in NSCLC is still not fully understood, and its impact on prognosis remains controversial. Despite the significant advancements in targeted therapy and immune checkpoint inhibitors (ICI) that have transformed the treatment landscape of advanced NSCLC in recent years, targeting KRAS (both directly and indirectly) remains challenging and is still under intensive research. In recent years, significant progress has been made in the development of targeted drugs targeting the NSCLC KRASG12C mutant subtype. However, research progress on target drugs for the more common KRASG12D subtype has been slow, and currently, no specific drugs have been approved for clinical use, and many questions remain to be answered, such as the mechanisms of resistance in this subtype of NSCLC, how to better utilize combination strategies with multiple treatment modalities, and whether KRASG12D inhibitors offer substantial efficacy in the treatment of advanced NSCLC patients.

Long-term residue returning increased subsoil carbon quality in a rice-wheat cropping system.

Residue returning (RR) was widely implemented to increase soil organic carbon (SOC) in farmland. Extensive studies concentrated on the effects of RR on SOC quantity instead of SOC fractions at aggregate scales. This study investigated the effects of 20-year RR on the distribution of labile (e.g., dissolved, microbial biomass, and permanganate oxidizable organic) and stable (e.g., microbial necromass) carbon fractions at aggregate scales, as well as their contribution to SOC accumulation and mineralization. The findings indicated a synchronized variation in the carbon content of bacterial and fungal necromass. Residue retention (RR) notably elevated the concentration of bacterial and fungal necromass carbon, while it did not amplify the microbial necromass carbon (MNC) contribution to SOC when compared to residue removal (R0) in the topsoil (0-5 cm). In the subsoil (5-15 cm), RR increased the MNC contribution to SOC concentration by 21.2%-33.4% and mitigated SOC mineralization by 12.6% in micro-aggregates (P < 0.05). Besides, RR increased soil ß-glucosidase and peroxidase activities but decreased soil phenol oxidase activity in micro-aggregates (P < 0.05). These indicated that RR might accelerate cellulose degradation and conversion to stable microbial necromass C, and thus RR improved SOC stability because SOC occluded in micro-aggregates were more stable. Interestingly, SOC concentration was mainly regulated by MNC, while SOC mineralization was by dissolved organic carbon under RR, both of which were affected by soil carbon, nitrogen, and phosphorus associated nutrients and enzyme activities. The findings of this study emphasize that the paths of RR-induced SOC accumulation and mineralization were different, and depended on stable and labile C, respectively. Overall, long-term RR increased topsoil carbon quantity and subsoil carbon quality.

Erratum: A Novel Pak1/ATF2/miR-132 Signaling Axis Is Involved in the Hematogenous Metastasis of Gastric Cancer Cells.

[This corrects the article DOI: 10.1016/j.omtn.2017.07.005.].

Identification of potent pan-ephrin receptor kinase inhibitors using DNA-encoded chemistry technology.

EPH receptors (EPHs), the largest family of tyrosine kinases, phosphorylate downstream substrates upon binding of ephrin cell surface-associated ligands. In a large cohort of endometriotic lesions from individuals with endometriosis, we found that EPHA2 and EPHA4 expressions are increased in endometriotic lesions relative to normal eutopic endometrium. Because signaling through EPHs is associated with increased cell migration and invasion, we hypothesized that chemical inhibition of EPHA2/4 could have therapeutic value. We screened DNA-encoded chemical libraries (DECL) to rapidly identify EPHA2/4 kinase inhibitors. Hit compound, CDD-2693, exhibited picomolar/nanomolar kinase activity against EPHA2 (Ki: 4.0 nM) and EPHA4 (Ki: 0.81 nM). Kinome profiling revealed that CDD-2693 bound to most EPH family and SRC family kinases. Using NanoBRET target engagement assays, CDD-2693 had nanomolar activity versus EPHA2 (IC50: 461 nM) and EPHA4 (IC50: 40 nM) but was a micromolar inhibitor of SRC, YES, and FGR. Chemical optimization produced CDD-3167, having picomolar biochemical activity toward EPHA2 (Ki: 0.13 nM) and EPHA4 (Ki: 0.38 nM) with excellent cell-based potency EPHA2 (IC50: 8.0 nM) and EPHA4 (IC50: 2.3 nM). Moreover, CDD-3167 maintained superior off-target cellular selectivity. In 12Z endometriotic epithelial cells, CDD-2693 and CDD-3167 significantly decreased EFNA5 (ligand) induced phosphorylation of EPHA2/4, decreased 12Z cell viability, and decreased IL-1ß-mediated expression of prostaglandin synthase 2 (PTGS2). CDD-2693 and CDD-3167 decreased expansion of primary endometrial epithelial organoids from patients with endometriosis and decreased Ewing's sarcoma viability. Thus, using DECL, we identified potent pan-EPH inhibitors that show specificity and activity in cellular models of endometriosis and cancer.

Portable and Flexible Hydrogel Sensor for On-Site Atrazine Assay on Agricultural Products.

There is growing attention focused toward the problems of ecological sustainability and food safety raised from the abuse of herbicides, which underscores the need for the development of a portable and reliable sensor for simple, rapid, and user-friendly on-site analysis of herbicide residues. Herein, a novel multifunctional hydrogel composite is explored to serve as a portable and flexible sensor for the facile and efficient analysis of atrazine (ATZ) residues. The hydrogel electrode is fabricated by doping graphite-phase carbon nitride (g-C3N4) into the aramid nanofiber reinforced poly(vinyl alcohol) hydrogel via a simple solution-casting procedure. Benefiting from the excellent electroactivity and large specific surface area of the solid nanoscale component, the prepared hydrogel sensor is capable of simple, rapid, and sensitive detection of ATZ with a detection limit down to 0.002 ng/mL and per test time less than 1 min. After combination with a smartphone-controlled portable electrochemical analyzer, the flexible sensor exhibited satisfactory analytical performance for the ATZ assay. We further demonstrated the applications of the sensor in the evaluation of the ATZ residues in real water and soil samples as well as the user-friendly on-site point-of-need detection of ATZ residues on various agricultural products. We envision that this flexible and portable sensor will open a new avenue on the development of next-generation analytical tools for herbicide monitoring in the environment and agricultural products.

Programmable spin and transport of a living shrimp egg through photoacoustic pressure.

In the fields of biomedicine and microfluidics, the non-contact capture, manipulation, and spin of micro-particles hold great importance. In this study, we propose a programmable non-contact manipulation technique that utilizes photoacoustic effect to spin and transport living shrimp eggs. By directing a modulated pulsed laser toward a liquid-covered stainless-steel membrane, we can excite patterned Lamb waves within the membrane. These Lamb waves occur at the interface between the membrane and the liquid, enabling the manipulation of nearby particles. Experimental results demonstrate the successful capture, spin, and transport of shrimp eggs in diameter of 220 µm over a distance of about 5 mm. Calculations indicate that the acoustic radiation force and torque generated by our photoacoustic manipulation system are more than 299.5 nN and 41.0 nN·mm, respectively. The system surpasses traditional optical tweezers in terms of force and traditional acoustic tweezers in terms of flexibility. Consequently, this non-contact manipulation system significantly expands the possibilities for applications in various fields, including embryo screening, cell manipulation, and microfluidics.

The Application of Problem-Based Learning Combined With Case-Based Learning in EEG Teaching.

OBJECTIVE: The aim of this study is to explore the application effectiveness and value of combining problem-based learning (PBL) and case-based learning (CBL) in clinical electroencephalography (EEG) education. METHODS: A total of 104 standardized training for residents and refresher physicians from the Neurology Department of the First Affiliated Hospital of Chongqing Medical University, Neurology Department of Chongqing Yubei Hospital, and Neurology Department of Banan Hospital of Chongqing Medical University were enrolled. According to randomization principles, 52 participants were assigned into the PBL-CBL combination group and 52 subjects were assigned into the control group. We used statistical methods to compare the differences between the 2 groups in basic theory, case analysis, practical assessment scores, and teaching satisfaction. RESULTS: In terms of basic theory, case analysis, practical assessment scores, and teaching satisfaction, there were significant differences between the 2 groups, and the PBL-CBL combination group was superior to the control group (P < .05). CONCLUSION: In clinical EEG education, the teaching model of combining PBL and CBL has certain application effects and value.

Efficacy of intestinal microorganisms on immunotherapy of non-small cell lung cancer.

While the 5-year survival rate of patients with advanced non-small cell lung cancer (NSCLC) has seen some improvement, the majority of NSCLC patients fail to respond to immunotherapy with immune checkpoint inhibitors (ICIs). It is critical to identify effective biomarkers that can enhance the efficacy of immunotherapy. The clinical data in the current study were collected from NSCLC patients treated with ICIs, and two groups were classified according to treatment effect: good group with consistent efficacy, poor group with only progressiveness. Differences in intestinal microbiota between the two groups were analyzed using 16s rRNA sequencing. Beta diversity analysis indicated differences between the two groups that were available for differentiation. Comparison of the number of common or unique operational taxonomic units (OTUs) among different groups suggested that there were 53 unique OTUs in the good group and 51 unique OTUs in the poor group. At the phylum level, there was a difference between the two groups for several bacterial groups with the highest abundance values, among which Firmicutes, Actinobacteria and Fusobacteria were more abundant in the good group. Members of the genera Bifidobacterium and Lactobacillus were abundant in the good group, while the abundance of Bacteroides was low. Biomarkers in the poor group included Bacteroides, Bacteroidetes, Bacteroidia, Bacteroidales, Bacteroidaceae and Veillonellaceae. The intestinal microbiota composition affected the immunotherapy process for NSCLC, which might offer more rational instructions for the clinical application of ICIs in NSCLC patients.

PanDepth, an ultrafast and efficient genomic tool for coverage calculation.

Coverage quantification is required in many sequencing datasets within the field of genomics research. However, most existing tools fail to provide comprehensive statistical results and exhibit limited performance gains from multithreading. Here, we present PanDepth, an ultra-fast and efficient tool for calculating coverage and depth from sequencing alignments. PanDepth outperforms other tools in computation time and memory efficiency for both BAM and CRAM-format alignment files from sequencing data, regardless of read length. It employs chromosome parallel computation and optimized data structures, resulting in ultrafast computation speeds and memory efficiency. It accepts sorted or unsorted BAM and CRAM-format alignment files as well as GTF, GFF and BED-formatted interval files or a specific window size. When provided with a reference genome sequence and the option to enable GC content calculation, PanDepth includes GC content statistics, enhancing the accuracy and reliability of copy number variation analysis. Overall, PanDepth is a powerful tool that accelerates scientific discovery in genomics research.