Design of a novel gamma camera with large field of view for 16N diagnosis in the primary loop of nuclear reactor

The assessment of the concentration and distribution of l6N, derived from 16O in the cooling water exposed to neutron irradiation, is essential for ensuring radiation safety during nuclear reactor operation. The imaging method allows for the visualization of the intensity distribution of these l6N by capturing gamma-rays emitted during their decay process. However, the existing gamma camera is exclusively compatible with gamma-rays below 2 MeV. In this paper, a novel gamma camera featuring a thick double-conical penumbra aperture, a pixelated Lu1.8Y0.2SiO5:Ce scintillator array, and a position-sensitive photomultiplier tube is proposed to address this limitation. This innovative design offers a large field of view (FOV) and is suitable for high energy extended gamma source imaging. The optimization of key parameters of the camera was conducted, and a FOV of 60° and an angular resolution of up to 4.57° were achieved. Imaging simulations, including a simplified model of the primary loop of the pressurized-water reactor by GEANT4 code and image reconstruction using the expectation maximum algorithm, demonstrated that the proposed gamma camera could obtain a satisfactory spatial resolution for diagnosing the distribution of 16N in the primary loop of a nuclear reactor.

SPARC stabilizes ApoE to induce cholesterol-dependent invasion and sorafenib resistance in hepatocellular carcinoma

Dysregulation of cholesterol homeostasis is implicated in the development and progression of hepatocellular carcinoma (HCC) that is characterized by intrahepatic and early extrahepatic metastasis. A better understanding of the underlying mechanisms regulating cholesterol metabolism in HCC could help identify strategies to circumvent the aggressive phenotype. Here, we found that high expression of intracellular SPARC was significantly associated with elevated cholesterol levels and an enhanced invasive phenotype in HCC. SPARC potentiated cholesterol accumulation in HCC cells during tumor progression by stabilizing the ApoE protein. Mechanistically, SPARC competitively bound to ApoE, impairing its interaction with the E3 ligase tripartite motif containing 21 (TRIM21) and preventing its ubiquitylation and subsequent degradation. ApoE accumulation led to cholesterol enrichment in HCC cells, stimulating PI3K-AKT signaling and inducing epithelial-mesenchymal transition (EMT). Importantly, sorafenib-resistant HCC cells were characterized by increased expression of intracellular SPARC, elevated cholesterol levels, and enhanced invasive capacity. Inhibiting SPARC expression or reducing cholesterol levels enhanced the sensitivity of HCC cells to sorafenib treatment. Together, these findings unveil interplay between SPARC and cholesterol homeostasis. Targeting SPARC-triggered cholesterol-dependent oncogenic signaling is a potential therapeutic strategy for advanced HCC.

Development of Injectable Thermosensitive Nanocomposite Hydrogel for Ratiometric Drug Delivery to Treat Drug Resistant Chondrosarcoma In Vivo

Chondrosarcoma(CS), a prevalent primary malignant bone tumor, frequently exhibits chemotherapy resistance attributed to upregulated anti-apoptosis pathways such as the Bcl-2 family. In this manuscript, a new strategy is presented to augment chemosensitivity and mitigate systemic toxicity by harnessing a nano-enabled drug delivery hydrogel platform. The platform utilizes "PLGA-PEG-PLGA", an amphiphilic triblock copolymer combining hydrophilic polyethylene glycol (PEG) and hydrophobic polylactide glycolide (PLGA) blocks, renowned for its properties conducive to crafting a biodegradable, temperature-sensitive hydrogel. This platform is tailored to encapsulate a ratiometrically designed dual-loaded liposomes containing a first-line chemo option for CS, Doxorubicin (Dox), plus a calculated amount of small molecule inhibitor for anti-apoptotic Bcl-2 pathway, ABT-737. In vitro and in vivo evaluations demonstrate successful Bcl-2 suppression, resulting in the restoration of Dox sensitivity, evident through impeded tumor growth and amplified necrosis rates at the tumor site. This delivery system showcases remarkable thermal responsiveness, injectability, and biodegradability, all finely aligned with the clinical demands of CS treatment. Collectively, this study introduces a transformative avenue for tackling drug resistance in CS chemotherapy, offering significant clinical potential.

Is polyethylene glycol loxenatide 100 μg the preferred glucagon-like peptide-1 receptor agonist for type 2 diabetes mellitus? A meta-analysis and trial sequential analysis

OBJECTIVE

This study aimed to systematically evaluate the efficacy, safety and optimal dose of polyethylene glycol loxenatide (PEX168) for treating type 2 diabetes mellitus (T2DM).

MATERIALS AND METHODS

Clinical trials of PEX168 for T2DM were identified in 8 databases, with a build time limit of January 2023. Included studies were subjected to meta-analysis and trial sequential analysis (TSA).

RESULTS

On the efficacy endpoint, the meta-analysis showed that PEX168 100 μg significantly reduced 0.86% glycated hemoglobin type A1c (HbA1c) (MD -0.86, 95% CI -1.02 - -0.70,  p<0.00001), 1.11 mmol/L fasting plasma glucose (FPG) (MD -1.11, 95% CI -1.49 - -0.74, p<0.00001) and 1.91 mmol/L 2h postprandial glucose (PPG) (MD -1.91, 95% CI -3.35 - -0.46, p=0.01) compared with placebo. The TSA showed that all these benefits were conclusive. On safety endpoints, total adverse events (AEs), gastrointestinal (GI) AEs, serious AEs, and hypoglycemia were comparable to placebo for PEX168 100 μg (p>0.05). In the dose comparison, the HbA1c, FPG, and 2h PPG of PEX168 200 μg were comparable to 100 μg (p>0.05), while GI AEs were significantly higher than 100 μg (RR=2.84, 95% CI 1.64-4.93,  p=0.0002).

CONCLUSIONS

PEX168 100 μg can significantly lower blood glucose and does not increase the risk of total AEs, GI AEs, and hypoglycemia, which may be a preferred glucagon-like peptide-1 receptor agonist for type 2 diabetes mellitus.

Histone lactylation inhibits RARγ expression in macrophages to promote colorectal tumorigenesis through activation of TRAF6-IL-6-STAT3 signaling

Macrophages are phenotypically and functionally diverse in the tumor microenvironment (TME). However, how to remodel macrophages with a protumor phenotype and how to manipulate them for therapeutic purposes remain to be explored. Here, we show that in the TME, RARγ is downregulated in macrophages, and its expression correlates with poor prognosis in patients with colorectal cancer (CRC). In macrophages, RARγ interacts with tumor necrosis factor receptor-associated factor 6 (TRAF6), which prevents TRAF6 oligomerization and autoubiquitination, leading to inhibition of nuclear factor κB signaling. However, tumor-derived lactate fuels H3K18 lactylation to prohibit RARγ gene transcription in macrophages, consequently enhancing interleukin-6 (IL-6) levels in the TME and endowing macrophages with tumor-promoting functions via activation of signal transducer and activator of transcription 3 (STAT3) signaling in CRC cells. We identified that nordihydroguaiaretic acid (NDGA) exerts effective antitumor action by directly binding to RARγ to inhibit TRAF6-IL-6-STAT3 signaling. This study unravels lactate-driven macrophage function remodeling by inhibition of RARγ expression and highlights NDGA as a candidate compound for treating CRC.

Genetic screen identified PRMT5 as a neuroprotection target against cerebral ischemia

Epigenetic regulators present novel opportunities for both ischemic stroke research and therapeutic interventions. While previous work has implicated that they may provide neuroprotection by potentially influencing coordinated sets of genes and pathways, most of them remain largely uncharacterized in ischemic conditions. In this study, we used the oxygen-glucose deprivation (OGD) model in the immortalized mouse hippocampal neuronal cell line HT-22 and carried out an RNAi screen on epigenetic regulators. PRMT5 was identified as a novel negative regulator of neuronal cell survival after OGD, which presented a phenotype of translocation from the cytosol to the nucleus upon oxygen and energy depletion both in vitro and in vivo. PRMT5 bound to the chromatin and a large number of promoter regions to repress downstream gene expression. Silencing Prmt5 significantly dampened the OGD-induced changes for a large-scale of genes, and gene ontology analysis showed that PRMT5-target genes were highly enriched for Hedgehog signaling. Encouraged by the above observation, mice were treated with middle cerebral artery occlusion with the PRMT5 inhibitor EPZ015666 and found that PRMT5 inhibition sustains protection against neuronal death in vivo. Together, these findings revealed a novel epigenetic mechanism of PRMT5 in cerebral ischemia and uncovered a potential target for neuroprotection.

Unraveling the mechanism of ethyl acetate extract from Prismatomeris connata Y. Z. Ruan root in treating pulmonary fibrosis: insights from bioinformatics, network pharmacology, and experimental validation

Introduction

Pulmonary fibrosis is a terminal lung disease characterized by fibroblast proliferation, extracellular matrix accumulation, inflammatory damage, and tissue structure destruction. The pathogenesis of this disease, particularly idiopathic pulmonary fibrosis (IPF), remains unknown. Macrophages play major roles in organ fibrosis diseases, including pulmonary fibrosis. The phenotype and polarization of macrophages are closely associated with pulmonary fibrosis. A new direction in research on anti-pulmonary fibrosis is focused on developing drugs that maintain the stability of the pulmonary microenvironment.

Methods

We obtained gene sequencing data and clinical information for patients with IPF from the GEO datasets GSE110147, GSE15197, GSE24988, GSE31934, GSE32537, GSE35145, GSE53845, GSE49072, GSE70864, and GSE90010. We performed GO, KEGG enrichment analysis and GSEA analysis, and conducted weighted gene co-expression network analysis. In addition, we performed proteomic analysis of mouse lung tissue. To verify the results of bioinformatics analysis and proteomic analysis, mice were induced by intratracheal instillation of bleomycin (BLM), and gavaged for 14 days after modeling. Respiratory function of mice in different groups was measured. Lung tissues were retained for histopathological examination, Western Blot and real-time quantitative PCR, etc. In addition, lipopolysaccharide, interferon-γ and interleukin-4 were used to induce RAW264.7 cells for 12h in vitro to establish macrophage inflammation and polarization model. At the same time, HG2 intervention was given. The phenotype transformation and cytokine secretion of macrophages were investigated by Western Blot, RT-qPCR and flow cytometry, etc.

Results

Through bioinformatics analysis and experiments involving bleomycin-induced pulmonary fibrosis in mice, we confirmed the importance of macrophage polarization in IPF. The analysis revealed that macrophage polarization in IPF involves a change in the phenotypic spectrum. Furthermore, experiments demonstrated high expression of M2-type macrophage-associated biomarkers and inducible nitric oxide synthase, thus indicating an imbalance in M1/M2 polarization of pulmonary macrophages in mice with pulmonary fibrosis.

Discussion

Our investigation revealed that the ethyl acetate extract (HG2) obtained from the roots of Prismatomeris connata Y. Z. Ruan exhibits therapeutic efficacy against bleomycin-induced pulmonary fibrosis. HG2 modulates macrophage polarization, alterations in the TGF-β/Smad pathway, and downstream protein expression in the context of pulmonary fibrosis. On the basis of our findings, we believe that HG2 has potential as a novel traditional Chinese medicine component for treating pulmonary fibrosis.

Profiling targets and potential target pairs of CAR-T cell therapy in clinical trials

Since the approval of the first chimeric antigen receptor (CAR)-T product in 2017, the number of new CAR-T clinical trials worldwide exceeds 100 per year. 1649 clinical studies have been conducted to explore possible future clinical applications of targets or target pairs through different biotechnologies. In this study, we aim to take a data-driven analytical approach to explore potential dual-target pairs based on clinical trial information. We screened 1283 non-withdrawal interventional CAR-T clinical trials spanning 96 different targets and 74 target pairs from clinicaltrials.gov. Through the Circos plot and temporal network plots, the information between targets and indications was visualized. Based on the assumption that two targets of a target pair must target the same indication, five new target pairs were inferred, including CD19/CD7, CD19/CD5, CD19/CD37, and CD19/BAFFR and validated by expression pattern, literature and patent information. This study provides novel support for target profiling of CAR-T from the perspective of clinical trials and also provides a reference for researchers and developers to select new targets or target pairs of CAR-T cell therapy.

Dissecting the Role of the Ccr4-Not Deadenylase Complex in Pluripotency and Differentiation

In this chapter, we describe methods and assays to examine the role of the Ccr4-Not mRNA deadenylase complex in regulating mouse embryonic stem cell (ESC) pluripotency and differentiation. We present the following procedures: sgRNA design and cloning, the culture of mouse ESCs, transfection and colony picking, genotyping, generation of Cnot3 conditional deletion ESCs, assessment of Cnot3 deletion efficiency, and examination of the impact on ESC maintenance and differentiation. The above approach and protocols can also be readily applied to study other Ccr4-Not subunits in ESC fate regulation, thereby facilitating the systematic dissection of Ccr4-Not function in stem cells and development.

Circulating miRNAs act as potential biomarkers for asthma

Background

Identification of new clinical markers contributes to a better understanding of the pathogenesis of asthma. Considering the crucial role of LIGHT in asthma, it may become a potential target for asthma. The aim of current study was to determine if circulating microRNAs (miRNAs) targeting LIGHT may be used as diagnostic biomarkers to distinguish asthma.

Methods

Blood serum from a cohort of 60 subjects, including 20 cases with mild asthma, 20 cases with moderate-to-severe asthma, and 20 healthy controls were included. Serum was analyzed for circulating miRNAs profiles through miRNAs microarray. Real Time PCR was conducted to verify the results of miRNA microarray. Correlations between circulating miRNAs targeting LIGHT and clinical characteristics were investigated.

Results

A total of 365 miRNAs were differentially expressed in asthma patients. Among them, miR-107 and miR-140-5p were found to target LIGHT, and varied in asthmatics. Additionally, miR-107 and miR-140-5p expressions were positively correlated with the absolute value of peripheral eosinophils. Finally, miR-140-5p and miR-107 were demonstrated to have good diagnostic efficacy for asthma (AUC= 0.8667 and 0.9400) with good sensitivity (0.8000 and 0.8667,respectively) and specificity (0.8667 and 0.867). Thus, circulating miRNAs expressed differentially between healthy control and asthma patients.

Conclusion

Plasma miR-140-5p and miR-107 can be used as diagnostic biomarkers to distinguish patients with asthma from healthy control, and may take part in asthma pathogenesis by negatively regulating LIGHT. Further research was needed to evaluate their roles as potential biomarkers in the diagnosis of asthma.

Case report: Differential diagnosis of highly amplified anti-CD5 CAR T cells and relapsed lymphoma cells in a patient with refractory ALK positive anaplastic large cell lymphoma

Background

Anaplastic Large Cell Lymphoma (ALCL) is one of the most common subtypes of T-cell lymphoma. Among these, refractory and relapsed (r/r) ALK positive ALCL lacks effective therapies. The chimeric antigen receptor-modified T (CAR-T) cell therapy holds great promise as a therapeutic strategy for this disease. However, it is not known yet whether anti-CD5 CAR-T cells are sufficient for the definitive treatment of relapsed ALK+ ALCL, nor the role of accurate laboratory-based diagnoses during CAR-T treatment.

Case presentation

The adolescent patient received autologous T cells containing sequences encoding VH domains specific to CD5. Following the infusion, there was an increase in both the copy number and proportion of CAR-T cells in peripheral blood. IL-6 and ferritin levels in the patient exhibited significant fluctuations, with increases of 13 and 70 folds respectively, compared to baseline after the treatment. Additionally, adverse effects were observed, including grade 4 rash, grade 1 headache, nausea, and neck-pain. Surprisingly, a relapsed disease phenotype was identified based on the results of PET/CT and histopathological analysis of the inguinal lymph node biopsy. After conducting a thorough diagnostic assessment, which included flow cytometry, next-generation sequencing (NGS), examination of immune-related gene rearrangements, and analysis of the immune repertoire of T-cell receptors (TCR), we conclusively determined that the hyperplastic T cells identified in the lymph node were the result of an expansion of CAR-T cells. Ultimately, the patient has attained complete remission (CR) and has sustained a disease-free survival state for 815 days as of the cutoff date on August 30, 2023.

Conclusion

Taken together, the results demonstrate that anti-CD5 CAR-T cells can induce a clinical response in r/r ALK+ ALCL patient. Furthermore, this case underscores the importance of utilizing advanced technologies with high sensitivity and accuracy for biological detection in clinical laboratory diagnosis and prognosis in CAR-T cell treatment.

Trial registration number

NCT04767308.

Differential expression of circular RNAs in interleukin 6-promoted osteogenic differentiation of human stem cells from apical papilla

INTRODUCTION

Studies have shown that interleukin 6 (IL-6) can regulate stem cell osteogenic differentiation; however, the exact mechanism is not clear. Circular RNAs (circRNAs) are closed circular non-coding RNAs that are involved in the process of stem cell osteogenic differentiation. Therefore, the purpose of this present study was to investigate the effect of IL-6 treatment on osteogenic differentiation of human apical tooth papillae stem cells (hSCAPs), and to detect the difference in circRNA expression using gene microarray technology.

METHODS

After extraction and identification of hSCAPs, alkaline phosphatase (ALP) activity, alizarin red staining, and calcium ion quantitative assay were used to determine the changes of ALP enzyme, mineralized nodules, and matrix calcium levels before and after IL-6 treatment of hSCAPs gene microarray technology was used to analyze the changes in circRNA expression levels before and after IL-6 induction of mineralization. The four selected circRNAs were validated by qRT-PCR. Moreover, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to predict the potential functions and biological signaling pathways of circRNAs. Finally, these data are integrated and analyzed to construct circRNA-microRNA-mRNA networks.

RESULTS

Alp and Alizarin red staining confirmed that IL-6 promoted the osteogenic differentiation of hSCAPs. The gene microarray results identified 132 differentially expressed circRNAs, of which 117 were upregulated and 15 were downregulated. Bioinformatic analysis predicted that the circRNA-406620/miR-103a-3p/FAT atypical cadherin 4 (FAT4) pathway might be involved in regulating IL-6 to promote osteogenic differentiation of hSCAPs.

CONCLUSION

Differentially expressed circRNAs might be closely involved in regulating IL-6 to promote osteogenic differentiation of hSCAPs.

Identifying Lymph Node Metastasis-Related Factors in Breast Cancer Using Differential Modular and Mutational Structural Analysis

Complex diseases are generally caused by disorders of biological networks and/or mutations in multiple genes. Comparisons of network topologies between different disease states can highlight key factors in their dynamic processes. Here, we propose a differential modular analysis approach that integrates protein-protein interactions with gene expression profiles for modular analysis, and introduces inter-modular edges and date hubs to identify the "core network module" that quantifies the significant phenotypic variation. Then, based on this core network module, key factors, including functional protein-protein interactions, pathways, and driver mutations, are predicted by the topological-functional connection score and structural modeling. We applied this approach to analyze the lymph node metastasis (LNM) process in breast cancer. The functional enrichment analysis showed that both inter-modular edges and date hubs play important roles in cancer metastasis and invasion, and in metastasis hallmarks. The structural mutation analysis suggested that the LNM of breast cancer may be the outcome of the dysfunction of rearranged during transfection (RET) proto-oncogene-related interactions and the non-canonical calcium signaling pathway via an allosteric mutation of RET. We believe that the proposed method can provide new insights into disease progression such as cancer metastasis.

Molecular Mechanism Analysis of Protopine Against Triple Negative Breast Cancer

In this study, we utilized a pharmacological network and bioinformatics approach to investigate the molecular mechanism underlying the resistance of Protopine (PRO) against Triple Negative Breast Cancer (TNBC). To uncover the underlying mechanism of PRO, we employed network pharmacology analysis. We collected and enriched targets using various databases such as TCMSP, SwissTargetPrediction, PubChem, Genecards, and DAVID. Furthermore, we constructed Potential targets network and components-disease-core targets network by STRING 11.5 and Cytoscape 3.7.1 to investigate the association of targets of PRO with disease targets of TNBC. The results of the network pharmacology approach indicated that PRO may play a key role in protein phosphorylation, protein autophosphorylation, Progesterone-mediated oocyte maturation signaling pathway, PI3K-Akt signaling pathway, and acting as targets such as PRKACA, JAK2, CDK2, LRRK2, CCNE1, KDR, JAK1. Our findings suggest that PRO exerts its effects against TNBC through multi-channel and multi-target mechanisms. Therefore, this study provides a basis for further research on the mechanism of action of PRO.

GAABind: a geometry-aware attention-based network for accurate protein-ligand binding pose and binding affinity prediction

Protein-ligand interactions are increasingly profiled at high-throughput, playing a vital role in lead compound discovery and drug optimization. Accurate prediction of binding pose and binding affinity constitutes a pivotal challenge in advancing our computational understanding of protein-ligand interactions. However, inherent limitations still exist, including high computational cost for conformational search sampling in traditional molecular docking tools, and the unsatisfactory molecular representation learning and intermolecular interaction modeling in deep learning-based methods. Here we propose a geometry-aware attention-based deep learning model, GAABind, which effectively predicts the pocket-ligand binding pose and binding affinity within a multi-task learning framework. Specifically, GAABind comprehensively captures the geometric and topological properties of both binding pockets and ligands, and employs expressive molecular representation learning to model intramolecular interactions. Moreover, GAABind proficiently learns the intermolecular many-body interactions and simulates the dynamic conformational adaptations of the ligand during its interaction with the protein through meticulously designed networks. We trained GAABind on the PDBbindv2020 and evaluated it on the CASF2016 dataset; the results indicate that GAABind achieves state-of-the-art performance in binding pose prediction and shows comparable binding affinity prediction performance. Notably, GAABind achieves a success rate of 82.8% in binding pose prediction, and the Pearson correlation between predicted and experimental binding affinities reaches up to 0.803. Additionally, we assessed GAABind's performance on the severe acute respiratory syndrome coronavirus 2 main protease cross-docking dataset. In this evaluation, GAABind demonstrates a notable success rate of 76.5% in binding pose prediction and achieves the highest Pearson correlation coefficient in binding affinity prediction compared with all baseline methods.

A novel two-step administration of XPO-1 inhibitor may enhance the effect of anti-BCMA CAR-T in relapsed/refractory extramedullary multiple myeloma

BACKGROUND

Extramedullary disease usually implies a dismal outcome in relapsed/refractory multiple myeloma patients, and requires novel treatment approaches. We designed a trial using Selinexor, a nuclear export protein 1 inhibitor, together with anti-B cell maturation antigen (BCMA) chimeric antigen receptor (CAR)-T cell product CT103A to treat these patients, and describe the first two cases in this report.

METHODS

Selinexor was administered with a novel two-step schedule in bridging therapy and in maintenance. The clinical responses and adverse events were recorded after CAR-T infusion and Selinexor administration. In vitro analysis of the influence of Selinexor on CAR-T cell function was performed using myeloma cell lines.

RESULTS

After infusion, both patients achieved stringent complete remission (sCR), and were maintained in sCR at data-cutoff, with survival over 13 and 10 months, respectively. Neither immune effector cell-associated neurotoxicity syndrome nor over grade 2 cytokine release syndrome was observed. Meanwhile, the patients showed good tolerance to the combination. In addition, we demonstrated that low dose of Selinexor could upregulate the expression of BCMA on plasma cell lines and subsequently enhance the function of CAR-T cell in vitro.

CONCLUSIONS

The combination of Selinexor and CT103A exerts preliminary synergistic effect, and can be developed as a promising strategy for relapsed/refractory extramedullary myeloma.

Comparative study on main compounds and hypoglycemic effects of dispensing granules of Coptidis Rhizoma and Scutellaria-Coptis herb couple with traditional decoction

BACKGROUND

The clinical applications of dispensing granules (DG) have increased dramatically. However, it is controversial whether the DG has the same quality and efficacy compared with traditional decoction (TD). In this study, the contents of main compounds, hypoglycemic effects, and potential mechanism of Coptidis Rhizoma (CR) and Scutellaria-coptis (SC), constituted of a 1:1 mixture of CR and Scutellariae Radix (SR), in the forms of TD and DG were compared.

METHODS

The quantitative analysis was performed on an UPLC-PDA method. The 6-weeks-old male db/db mice were used as Type 2 Diabetes Mellitus (T2DM) mouse modle to investigate the antidiabetic effects of CR and SC in TD form (CR TD and SC TD), as well as CR and SC in DG form (CR DG and SC DG).

RESULTS

The total content of five alkaloids in CR TD ranged from 71.00 to 78.62 mg, whereas in CR DG it ranged from 38.77 to 53.68 mg in CR DG per 1 g of decoction pieces. Compared to CR TD, CR DG exhibited a 36% reduction on average. For SC samples, the precipitation occurred in the processing of TD but not in the DG, and the relative ratio of alkaloids to flavonoids was determined to be 1:1 in TD and 1:2 in DG. Furthermore, the animal experiments showed that the CR DG (equivalent to 3 g decoction pieces/kg) had almost the same hypoglycemic effect as CR TD when they were administered for 6 weeks. Compared with SC DG (equivalent to 6 g decoction pieces/kg), SC TD showed a better trend in ameliorating T2DM via ameliorating pancreatic structure and function, and activating Akt/AMPK/GLUT4 signaling pathways.

CONCLUSION

This study indicated that the contents of main compounds were generally higher in CR TD than CR DG originated from the same raw materials. Additionally, changes in the contents of the primary components validated that the compound interactions are exclusive to SC TD during co-decoction, rather than SC DG. The disparate prossing of SC DG and SC TD caused differences both in chemical composition and hypoglycemic effect, suggesting that the substitutability of DG and TD requires further research.

Research on the 3D Reverse Time Migration Technique for Internal Defects Imaging and Sensor Settings of Pressure Pipelines

Although pressure pipelines serve as a secure and energy-efficient means of transporting oil, gas, and chemicals, they are susceptible to fatigue cracks over extended periods of cyclic loading due to the challenging operational conditions. Their quality and efficiency directly affect the safe operation of the project. Therefore, a thorough and precise characterization approach towards pressure pipelines can proactively mitigate safety risks and yield substantial economic and societal benefits. At present, the current mainstream 2D ultrasound imaging technology faces challenges in fully visualizing the internal defects and topography of pressure pipelines. Reverse time migration (RTM), widely employed in geophysical exploration, has the capability to visualize intricate geological structures. In this paper, we introduced the RTM into the realm of ultrasonic non-destructive testing, and proposed a 3D ultrasonic RTM imaging method for internal defects and sensor settings of pressure pipelines. To accurately simulate the extrapolation of wave field in 3D pressure pipelines, we set the absorbing boundary and double free boundary in cylindrical coordinates. Subsequently, using the 3D ultrasonic RTM approach, we attained higher-precision 3D imaging of internal defects in the pressure pipelines through suppressing imaging artifacts. By comparing and analyzing the imaging results of different sensor settings, the design of the observation system is optimized to provide a basis for the imaging and interpretation of actual data. Both simulations and actual field data demonstrate that our approach delivers top-notch 3D imaging of pipeline defects (with an imaging range accuracy up to 97.85%). This method takes into consideration the complexities of multiple scattering and mode conversions occurring at the base of the defects as well as the optimal sensor settings.

Large-scale ORF screening based on LC-MS to discover novel lncRNA-encoded peptides responding to ionizing radiation and microgravity

In the human genome, 98% of genes can be transcribed into non-coding RNAs (ncRNAs), among which lncRNAs and their encoded peptides play important roles in regulating various aspects of cellular processes and may serve as crucial factors in modulating the biological effects induced by ionizing radiation and microgravity. Unfortunately, there are few reports in space radiation biology on lncRNA-encoded peptides below 10kD due to limitations in detection techniques. To fill this gap, we integrated a variety of methods based on genomics and peptidomics, and discovered 22 lncRNA-encoded small peptides that are sensitive to space radiation and microgravity, which have never been reported before. We concurrently validated the transmembrane helix, subcellular localization, and biological function of these small peptides using bioinformatics and molecular biology techniques. More importantly, we found that these small peptides function independently of the lncRNAs that encode them. Our findings have uncovered a previously unknown human proteome encoded by 'non-coding' genes in response to space conditions and elucidated their involvement in biological processes, providing valuable strategies for individual protection mechanisms for astronauts who carry out deep space exploration missions in space radiation environments.

Cnot3 is required for male germ cell development and spermatogonial stem cell maintenance

The foundation of spermatogenesis and lifelong fertility is provided by spermatogonial stem cells (SSCs). SSCs divide asymmetrically to either replenish their numbers (self-renewal) or produce undifferentiated progenitors that proliferate before committing to differentiation. However, regulatory mechanisms governing SSC maintenance are poorly understood. Here, we show that the CCR4-NOT mRNA deadenylase complex subunit CNOT3 plays a critical role in maintaining spermatogonial populations in mice. Cnot3 is highly expressed in undifferentiated spermatogonia, and its deletion in spermatogonia resulted in germ cell loss and infertility. Single cell analyses revealed that Cnot3 deletion led to the de-repression of transcripts encoding factors involved in spermatogonial differentiation, including those in the glutathione redox pathway that are critical for SSC maintenance. Together, our study reveals that CNOT3 - likely via the CCR4-NOT complex - actively degrades transcripts encoding differentiation factors to sustain the spermatogonial pool and ensure the progression of spermatogenesis, highlighting the importance of CCR4-NOT-mediated post-transcriptional gene regulation during male germ cell development.

The bioceramic sealer iRoot SP promotes osteogenic differentiation of human stem cells from apical papilla via miR-141-3p/SPAG9/MAPK signalling pathway

AIM

The premixed bioceramic sealer iRoot SP that is widely used clinically has been reported to kill bacterial biofilms and promote osteogenic differentiation of human stem cells from the apical papilla (hSCAPs). Although miR-141-3p has been substantiated to be involved in the osteogenic process, the underlying mechanisms remain unclear. The aim of this study was to investigate the role of miR-141-3p in osteogenic differentiation and underlying mechanisms of iRoot SP-treated hSCAPs.

METHODOLOGY

hSCAPs were extracted from tissue blocks with enzyme digestion and identified by using immunofluorescence, flow cytometry and alizarin red staining. The mRNA expression level of miR-141-3p in hSCPAs after culture with iRoot SP was examined by quantitative real-time PCR (qRT-PCR) assay. SPAG9 was identified as a downstream target gene of miR-141-3p by dual-luciferase report assay. Alkaline phosphatase (ALP) staining and activity detection, alizarin red staining, calcium concentration assay, qRT-PCR and western blot were used to estimate osteogenic differentiation ability and involved protein expression levels of the osteogenic makers and signalling pathway-related factors in iRoot SP-treated hSCAPs. Data were analysed by one-way anova and post hoc Tukey's test to determine any statistical differences between the experimental groups and the control group. p < .05 was considered statistically significant.

RESULTS

Expression of miR-141-3p was reduced in iRoot SP-treated hSCAPs with the increased exposure time up to 7 days, and the western blot and qRT-PCR results revealed that the osteogenic markers osteocalcin (OCN), osterix (OSX), runt-related transcription factor 2 (RUNX2) and dentin sialophosphoprotein (DSPP) were inversely correlated with miR-141-3p. The negative regulatory relationship between miR-141-3p and SPAG9/ mitogen-activated protein kinases (MAPK) signalling axis was validated in this in vitro experiments.

CONCLUSIONS

The bioceramic sealer iRoot SP promoted osteogenic differentiation of hSCAPs by inhibiting miR-141-3p following down-regulated SPAG9 expression, and activated MAPK pathway. These findings proposed a novel therapeutic impact of bioceramic sealer iRoot SP inducing bone regeneration in refractory periapical periodontitis.

Pluripotent Stem Cell-derived Dopaminergic Neurons for Studying Developmental Neurotoxicity

With the vast number of chemicals in commerce, higher throughput strategies are needed to inform risk assessment. The field of toxicology is therefore moving away from traditional in vivo guideline studies towards in vitro new approach methodologies. There has been a great push for such a shift in the field of developmental neurotoxicity, where there is a particular lack of data. A battery of in vitro new approach methodologies has thus been developed to help fill this gap. Included in this battery are assays for numerous processes critical to neurodevelopment, such as proliferation, migration, and synaptogenesis. The current battery of developmental neurotoxicity new approach methodologies still lacks recapitulation of several critical neurodevelopmental processes, including development of neuronal subtypes. With their pluripotency, alongside other advantages, pluripotent stem cells (PSCs) are uniquely suited to address questions of developmental neurotoxicity, as they can recapitulate the different stages of human in vivo neurodevelopment. Among the various neuronal subtypes, development of dopaminergic neurons (DA) is perhaps the best understood and several approaches exist to differentiate PSCs into DA. Herein we review these approaches and propose utilizing PSCs for screening of the impact of environmental chemicals on development of DA. Related techniques and gaps in knowledge are also addressed.

Deciphering the functional landscape of phosphosites with deep neural network

Current biochemical approaches have only identified the most well-characterized kinases for a tiny fraction of the phosphoproteome, and the functional assignments of phosphosites are almost negligible. Herein, we analyze the substrate preference catalyzed by a specific kinase and present a novel integrated deep neural network model named FuncPhos-SEQ for functional assignment of human proteome-level phosphosites. FuncPhos-SEQ incorporates phosphosite motif information from a protein sequence using multiple convolutional neural network (CNN) channels and network features from protein-protein interactions (PPIs) using network embedding and deep neural network (DNN) channels. These concatenated features are jointly fed into a heterogeneous feature network to prioritize functional phosphosites. Combined with a series of in vitro and cellular biochemical assays, we confirm that NADK-S48/50 phosphorylation could activate its enzymatic activity. In addition, ERK1/2 are discovered as the primary kinases responsible for NADK-S48/50 phosphorylation. Moreover, FuncPhos-SEQ is developed as an online server.

WNK1 is required during male pachynema to sustain fertility

WNK1 is an important regulator in many physiological functions, yet its role in male reproduction is unexplored. In the male germline, WNK1 is upregulated in preleptotene spermatocytes indicating possible function(s) in spermatogenic meiosis. Indeed, deletion of Wnk1 in mid-pachytene spermatocytes using the Wnt7a-Cre mouse led to male sterility which resembled non-obstructive azoospermia in humans, where germ cells failed to complete spermatogenesis and produced no sperm. Mechanistically, we found elevated MTOR expression and signaling in the Wnk1-depleted spermatocytes. As MTOR is a central mediator of translation, we speculated that translation may be accelerated in these spermatocytes. Supporting this, we found the acrosome protein, ACRBP to be prematurely expressed in the spermatocytes with Wnk1 deletion. Our study uncovered an MTOR-regulating factor in the male germline with potential implications in translation, and future studies will aim to understand how WNK1 regulates MTOR activity and impact translation on a broader spectrum.

Bibliometric analysis of intestinal microbiota in diabetic nephropathy

OBJECTIVE

The purpose of this study is to use bibliometrics to explore the research overview and research hotspots.

MATERIALS AND METHODS

The relevant literature on intestinal flora and diabetic nephropathy in the Web of Science Core Collection was sorted out, and VOSviewer, CiteSpace, Scimago Graphica and other software were used to conduct data visualization analysis on the number of publications, countries, institutions, journals, authors, keywords and citations.

RESULTS

A total of 124 relevant literatures were included. From 2015 to 2022, the number of published papers increased every year. The countries, institutions and journals that published the most articles in this field are China, Isfahan University Medical Science and Frontiers in Pharmacology. Liu Bicheng and Mirlohi Maryam are the authors with the most published articles in this field. The main keywords of research in this field are obesity, inflammation, oxidative stress, indoxyl sulfate, short-chain fatty acids (SCFAs) and Chinese herbal medicine.

CONCLUSIONS

This is the first bibliometric analysis of diabetic nephropathy and gut microbiota, reporting hot spots and emerging trends. Obesity, inflammation, oxidative stress, indoxyl sulfate, SCFAs and Chinese herbal medicine are the main keywords of current research, and SCFAs and Chinese herbal medicine may be the hotspots of future research.

The cotton miR171a-SCL6 module mediates plant resistance through regulating GhPR1 expression

Plants have developed intricate defense mechanisms in response to fluctuating environmental cues, including the use of microRNA (miRNA) as post-transcriptional regulators. However, the specific mechanisms through which miRNA contributes to disease resistance remain largely elusive. While the miR171-SCLs have been investigated in an eclectic array of plants, there has been a notable scarcity of research specifically focused on cotton (Gossypium hirsutum). In our previous miRNA-sequencing analysis, we found that ghr-miR171a displayed a differential response to infections by Verticillium dahliae. In this study, we further investigated the function of the miR171a-SCL6 module in cotton during V. dahliae infection. The ghr-miR171a was confirmed to direct the cleavage of GhSCL6 mRNA in the post-transcriptional process, as evidenced by 5' RLM-RACE, β-glucuronidase (GUS) histochemical staining and enzyme activity assay. Interestingly, we found that overexpressing ghr-miR171a reduced cotton plants' resistance to V. dahliae, while suppressing ghr-miR171a increased the plants' defense capacity. The GhSCL6 protein, when fused with green fluorescent protein (GFP), localizes in the cell nucleus, indicating its potential role in gene regulation. This was further corroborated by yeast two-hybrid assays, which verified GhSCL6's transcriptional activation ability. Through quantitative reverse transcriptase PCR (qRT-PCR), luciferase (LUC) fluorescence, and yeast one-hybrid assays, we found that GhSCL6 binds to the GT-box element of the GhPR1 promoter, activating its expression and thereby enhancing plant disease resistance. Taken together, our findings demonstrate that the cotton miR171a-SCL6 module regulates Verticillium wilt resistance in plants through the post-transcriptional process. This insight may offer new perspectives for disease resistance strategies in cotton.

Efficacy and safety of iguratimod combined with methylprednisolone for primary Sjögren's syndrome: a meta-analysis and trial sequential analysis

OBJECTIVE

The purpose of this study is to evaluate the combination of iguratimod (IGU) and methylprednisolone (MP) for the efficacy and safety of primary Sjögren's syndrome (pSS) by a meta-analysis and a trial sequential analysis (TSA).

MATERIALS AND METHODS

Clinical studies of IGU combined with MP for pSS were searched through eight databases. Revman 5.3 and TSA 0.9.5.10 Beta were used for the meta-analysis and TSA.

RESULTS

In terms of efficacy endpoints, compared with "HCQ+MP" group, "IGU+MP" group decreased erythrocyte sedimentation rate (ESR) [mean difference (MD)=-5.15, 95% confidence interval (CI)=(-7.37, -2.93), p<0.0001], immunoglobulin G (IgG) [MD=-3.38, 95% CI=(-4.13, -2.64), p<0.00001], immunoglobulin M (IgM) [MD=-0.64, 95% CI=(-1.19, -0.09), p=0.02], Immunoglobulin A (IgA) [MD=-1.16, 95% CI=(-1.92, -0.39), p=0.003], EULAR Sjögren's Syndrome Disease Activity Index (ESSDAI) [MD=-1.62, 95% CI=(-2.07, -1.17), p<0.0001], EULAR Sjögren's Syndrome Patient Reported Index (ESSPRI) [MD=-2.07, 95% CI=(-2.54, -1.59), p<0.0001], increase platelet (PLT) [MD=13.21, 95% CI=(9.77,16.65), p<0.00001], and improve Schirmer I test (SIT) [MD=1.86, 95% CI=(1.40, 2.32), p<0.0001]. TSA presented that these benefits observed with the current information volume were all conclusive, except for IgM. In terms of safety endpoints, the total adverse event rates (AEs), leucopenia, gastrointestinal (GI) AEs, skin diseases, and liver dysfunction of the "IGU+MP" group and the "HCQ+MP" group were comparable. And TSA indicated that the results need to be confirmed by additional studies. Harbord regression showed no publication bias (p=0.986).

CONCLUSIONS

IGU combined with MP effectively attenuates autoimmune responses (IgG, IgM, IgA), reduces clinical symptoms and disease activity (ESR, PLT, ESSPRI, ESSDAI), and improves the exocrine gland functional status (SIT) in patients with pSS. IGU combined with MP does not increase the risk of adverse events, which means that IGU combined with MP may be a safe and effective strategy for the treatment of pSS and has value for further research exploration.

Is tirzepatide 15 mg the preferred treatment strategy for type 2 diabetes? A meta-analysis and trial-sequence-analysis

OBJECTIVE

The study aims to evaluate tirzepatide's efficacy and safety in treating type 2 diabetes by meta-analysis and trial-sequential-analysis (TSA).

MATERIALS AND METHODS

Eight databases were searched for clinical trials on tirzepatide for type 2 diabetes with a time limit of November 2022. Revman5.3 and TSA 0.9.5.10 Beta were selected for meta-analysis and TSA.

RESULTS

Compared with placebo, the meta-analysis demonstrated that tirzepatide 15 mg reduced hemoglobin-type-A1C (HbA1c) (p<0.00001), fasting-serum-glucose (FSG) (p<0.00001), and weight (p<0.00001). Compared with insulin, tirzepatide 15 mg reduced HbA1c (p<0.00001), FSG (p<0.00007), and weight (p<0.00001). Compared with glucagon-like-peptide-1 receptor-agonist (GLP-1 RA), tirzepatide 15 mg reduced HbA1c (p=0.00004), FSG (p=0.001), and weight (p<0.00001). In safety endpoints, the meta-analysis revealed that adverse events (AEs) of placebo, insulin and GLP-1 RA were comparable to tirzepatide 15 mg. The total AEs (p=0.02) and gastrointestinal (GI) AEs (p=0.03) were higher in tirzepatide 15 mg than in the placebo, while hypoglycemia (<54 mg/dl) was comparable. The major adverse cardiovascular events-4 (MACE-4) (p=0.03) and hypoglycemia (<54 mg/dl) (p<0.00001) of tirzepatide 15 mg were lower when compared to insulin, while total AEs (p=0.03) were increased. Compared with GLP-1 RA, tirzepatide 15 mg was comparable in safety endpoints in total AEs and GI AEs, while hypoglycemia (<54 mg/dl) (p=0.04) was higher. TSA indicated that HgA1c, FSG, and weight benefits were conclusive. In safety endpoints, only MACE-4 and hypoglycemia (<54 mg/dl) of Tirzepatide 15 mg vs. Insulin were conclusive. Harbord regression of AEs suggested no evident publication bias (p=0.618).

CONCLUSIONS

Tirzepatide 15 mg reduced HbA1c and weight more effectively than placebo, insulin, and GLP-1 RA. Total AEs were higher than placebo and insulin but comparable to GLP-1 RA. Tirzepatide 15 mg is a kind of optimal strategy to treat type 2 diabetes. However, there is a need to focus on GI AEs.

Retinoic acid is dispensable for meiotic initiation but required for spermiogenesis in the mammalian testis

Retinoic acid (RA) is the proposed mammalian 'meiosis inducing substance'. However, evidence for this role comes from studies in the fetal ovary, where germ cell differentiation and meiotic initiation are temporally inseparable. In the postnatal testis, these events are separated by more than 1 week. Exploiting this difference, we discovered that, although RA is required for spermatogonial differentiation, it is dispensable for the subsequent initiation, progression and completion of meiosis. Indeed, in the absence of RA, the meiotic transcriptome program in both differentiating spermatogonia and spermatocytes entering meiosis was largely unaffected. Instead, transcripts encoding factors required during spermiogenesis were aberrant during preleptonema, and the subsequent spermatid morphogenesis program was disrupted such that no sperm were produced. Taken together, these data reveal a RA-independent model for male meiotic initiation.

A Nitro Functionalized MOF with Multi-Enzyme Mimetic Activities for the Colorimetric Sensing of Glucose at Neutral pH

Benefiting from the advantages like large surface area, flexible constitution, and diverse structure, metal-organic frameworks (MOFs) have been one of the most ideal candidates for nanozymes. In this study, a nitro-functionalized MOF, namely NO₂-MIL-53(Cu), was synthesized. Multi-enzyme mimetic activities were discovered on this MOF, including peroxidase-like, oxidase-like, and laccase-like activity. Compared to the non-functional counterpart (MIL-53(Cu)), NO₂-MIL-53(Cu) displayed superior enzyme mimetic activities, indicating a positive role of the nitro group in the MOF. Subsequently, the effects of reaction conditions on enzyme mimetic activities were investigated. Remarkably, NO₂-MIL-53(Cu) exhibited excellent peroxidase-like activity even at neutral pH. Based on this finding, a simple colorimetric sensing platform was developed for the detection of H₂O₂ and glucose, respectively. The detection liner range for H₂O₂ is 1-800 μM with a detection limit of 0.69 μM. The detection liner range for glucose is linear range 0.5-300 μM with a detection limit of 2.6 μM. Therefore, this work not only provides an applicable colorimetric platform for glucose detection in a physiological environment, but also offers guidance for the rational design of efficient nanozymes with multi-enzyme mimetic activities.

[Importance of comprehensive management of anastomotic site after ultra-low anal sphincter-preservation surgery]

Intersphincteric resection (ISR) surgery increases the rate of anal sphincter preservation in patients with ultra-low rectal cancers. However, the anastomotic site of ISR surgery is at risk for structural healing complications such as anastomotic leakage, anastomotic dehiscence, secondary anastomotic stenosis, chronic presacral sinus, rectovaginal fistula, and rectourethral fistula, which can lead to a persistent defunctioning ostomy or a secondary permanent colostomy. This article systematically describes the preoperative high-risk factors and characteristics of anastomotic site structural healing complications after ISR surgery, as well as the management of the anastomotic site during various stages including hospitalization, from discharge to one month after surgery, from one month after surgery to before stoma reversal, and after stoma reversal. This is to provide a clearer understanding of the risks associated with the anastomotic site at different stages of the healing process and to timely detect and actively manage related complications, thereby reducing the rate of permanent colostomy and truly achieving the dual goals of "survival benefit" and "quality of life improvement" in ISR surgery.

TRIM21 is a druggable target for the treatment of metastatic colorectal cancer through ubiquitination and activation of MST2

Metastatic colorectal cancer (mCRC) is characterized by poorer prognosis of patients and limited therapeutic approach, partly due to the lack of effective target. Using mouse models and tumor organoids, this study reported a tripartite motif 21 (TRIM21) protein, exerting potential inhibitory effects on the invasion and metastasis of CRC. Mechanistically, TRIM21 directly interacted with and ubiquitinated MST2 at lysine 473 (K473) via K63-linkage. This ubiquitination enabled the formation of MST2 homodimer and enhanced its kinase activity, ultimately resulting in the functional inactivation of yes-associated protein (YAP) and inhibition of an epithelial-mesenchymal transition (EMT) feature. We identified that vilazodone, an antidepressant, directly bound to TRIM21 to exert effective anti-metastatic action both in vitro and in vivo. Collectively, these findings revealed a previously unrecognized interplay between TRIM21 and the Hippo-YAP signaling. These results suggested that vilazodone could be repositioned as an anti-tumor drug to inhibit CRC metastasis by targeting TRIM21.

Functional insight into Cordyceps militaris sugar transporters by structure modeling, network analysis and allosteric regulation

Insights into the structures, functions and dynamics of Cordyceps militaris (C. militaris) sugar transporters are necessary for understanding their versatile metabolic capability for fungal growth. The sequence-function relationship study of 85 C. militaris sugar transporters showed that there is a gap between phylogenetic-based subfamily classification and their functions. Beyond protein sequences, structural modeling and principal component analysis of the structural ensemble revealed the different folds of the Car and Org subfamilies. Performing channel detection and network analysis found that the Alp and Hex subfamilies can be specifically distinguished from others by the betweenness of channel residues. Signature dynamics analysis further suggested that the Hex subfamily demonstrates different dynamics, with high flexibility at the H1 region in TM11. Furthermore, the H1 region as an allosteric site was examined by network parameter calculations that guided allosteric pathways between this region and the channel cavity. Together with gene expression data of C. militaris, e.g., Hex06741 in the Hex subfamily, it was promisingly expressed when sugar utilization was altered. This work demonstrates an in silico framework for investigating C. militaris sugar transporters as an example case study of the allosteric activity of the Hex subfamily and can facilitate sugar transporter engineering design that can further optimize the preferable sugar utilization and fermentation process of C. militaris.

The cotton miR530-SAP6 module activated by systemic acquired resistance mediates plant defense against Verticillium dahliae

Many cotton miRNAs in root responding to Verticillium dahliae infection have been identified. Conversely, the miRNAs in leaf distantly responding to this fungal infection from roots via systemic acquired resistance (SAR) remain to be explored. Here, we constructed two groups of leaf sRNA libraries in cotton treated with V. dahliae via root-dipped method at 7- and 10-day post inoculation. Analysis of high-throughput sRNA sequencing identified 75 known and 379 novel miRNAs, of which 41 miRNAs significantly differentially expressed in fungal treatment plant leaves compared to the mock treatment at two time points. Then we characterized the cotton miR530-SAP6 module as a representative in the distant response to V. dahliae infection in roots. Based on degradome data and a luciferase (LUC) fusion reporter analysis, ghr-miR530 directedly cleaved GhSAP6 mRNA during the post-transcriptional process. Silencing of ghr-miR530 increased plant defense to this fungus, while its overexpression attenuated plant resistance. In link with ghr-miR530 function, the knockdown of GhSAP6 also decreased the plant resistance, resulting from down-regulation of SA-relative gene expression including GhNPR1 and GhPR1. In all, these results demonstrated that there are numerous miRNAs in leaf distantly responding to V. dahliae infection in roots mediate plant immunity.

CMR validation of left ventricular volumes and ejection fraction measured by the IQ-SPECT system in patients with small heart size

BACKGROUND

The IQ-SPECT system is equipped with multifocal collimators and uses ordered-subset conjugate gradient minimization (OSCGM) as its reconstruction algorithm, achieving a shorter acquisition time than conventional SPECT. Left ventricular ejection fraction (LVEF) is overestimated by conventional SPECT in patients with small heart size. In this study, we compared IQ-SPECT with conventional SPECT and cardiovascular magnetic resonance (CMR) for the estimation of LVEF in patients with small hearts (males: EDV ≤ 60 ml, ESV ≤ 25 ml; females: EDV ≤ 45 ml, ESV ≤ 20 ml).

METHODS

The study consisted of 49 consecutive patients (20 normal and 29 with small heart size) undergoing gated myocardial perfusion imaging (GMPI) with a 99mTc-labelled agent during stress or rest to assess the risk of coronary artery disease (CAD). The data were reconstructed using filtered back-projection (FBP) for conventional SPECT and OSCGM for IQ-SPECT. ESV, EDV, and LVEF were calculated using quantitative gated SPECT (QGS). To determine the optimal ordered-subset reconstruction parameters, we compared the LVEF from SPECT to the corresponding measurement from CMR.

RESULTS

EDV, ESV, and LVEF values obtained from IQ-SPECT and conventional SPECT showed that the results of these two forms of SPECT were significantly correlated, although the EDV and ESV obtained by IQ-SPECT were higher than those obtained by conventional SPECT. IQ-SPECT yielded lower LVEF measurements than conventional SPECT (normal heart size: 50.6 ± 4.3% vs. 73.4 ± 8.4%, P = 0.002; small heart size: 62.1 ± 7.8% vs. 75.0 ± 11.4%, P < 0.001). There were no significant differences in LVEF measurements made by IQ-SPECT and CMR (normal heart size: 50.6 ± 4.3% vs. 53.2 ± 5.8%, P > 0.05; small heart size: 62.1 ± 7.8% vs. 64.6 ± 8.8%, P > 0.05). Five subsets (S) and 12 iterations (I) did not differ significantly in LVEF between CMR and IQ-SPECT for patients with small hearts (64.6 ± 8.8% vs. 62.1 ± 7.8%, P = 0.120), while 3 S and 10 I were the best parameters for patients with normal heart size (50.6 ± 4.3% vs. 53.1 ± 5.8%, P = 0.117).

CONCLUSION

With CMR as the standard, IQ-SPECT yields more reliable LVEF values than conventional SPECT for populations with small heart size. The best reconstruction parameters from IQ-SPECT were 5 S and 12 I for patients with small hearts.

EBD: an eye biomarker database

MOTIVATION

Many ophthalmic disease biomarkers have been identified through comprehensive multi-omics profiling, and hold significant potential in advancing the diagnosis, prognosis, and management of diseases. Meanwhile, the eye itself serves as a natural biomarker for several systemic diseases including neurological, renal and cardiovascular systems. We aimed to collect and standardize these eye biomarkers information and construct the eye biomarker database (EBD) to provide ophthalmologists with a platform to search, analyse and download these eye biomarker data.

RESULTS

Data were collected from published papers, and the database was constructed based on the MySQL server. Biological network and functional analysis were conducted to analyse biomarkers in-network and pathway levels. In this study, we present the Eye Biomarker Database (EBD) <http://www.eyeseeworld.com/ebd/index.html>, a world-first online compilation comprising 889 biomarkers for 26 ocular diseases and 939 eye biomarkers for 181 systemic diseases. The EBD also includes the information of 78 "non-biomarkers"-the objects that have been proven cannot be biomarkers. Biological function and network analysis were conducted for these ocular disease biomarkers, and several hub pathways and common network topology characteristics were newly identified, which may promote future ocular disease biomarker discovery and characterizes the landscape of biomarkers for eye diseases at the pathway and network level. The EBD is expected to yield broader utility among developmental biologists and clinical scientists in and outside of the eye field by assisting in the identification of biomarkers linked to eye disorders and related systemic diseases.

AVAILABILITY

EBD is available at http://www.eyeseeworld.com/ebd/index.html.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Rif1 Regulates Self-Renewal and Impedes Mesendodermal Differentiation of Mouse Embryonic Stem Cells

Background

RAP1 interacting factor 1 (Rif1) is highly expressed in mice embryos and mouse embryonic stem cells (mESCs). It plays critical roles in telomere length homeostasis, DNA damage, DNA replication timing and ERV silencing. However, whether Rif1 regulates early differentiation of mESC is still unclear.

Methods

In this study, we generated a Rif1 conditional knockout mouse embryonic stem (ES) cell line based on Cre-loxP system. Western blot, flow cytometry, quantitative real-time polymerase chain reaction (qRT-PCR), RNA high-throughput sequencing (RNA-Seq), chromatin immunoprecipitation followed high-throughput sequencing (ChIP-Seq), chromatin immunoprecipitation quantitative PCR (ChIP-qPCR), immunofluorescence, and immunoprecipitation were employed for phenotype and molecular mechanism assessment.

Results

Rif1 plays important roles in self-renewal and pluripotency of mESCs and loss of Rif1 promotes mESC differentiation toward the mesendodermal germ layers. We further show that Rif1 interacts with histone H3K27 methyltransferase EZH2, a subunit of PRC2, and regulates the expression of developmental genes by directly binding to their promoters. Rif1 deficiency reduces the occupancy of EZH2 and H3K27me3 on mesendodermal gene promoters and activates ERK1/2 activities.

Conclusion

Rif1 is a key factor in regulating the pluripotency, self-renewal, and lineage specification of mESCs. Our research provides new insights into the key roles of Rif1 in connecting epigenetic regulations and signaling pathways for cell fate determination and lineage specification of mESCs.

Graphical abstract

[Laparoscopic versus open pelvic exenteration for locally advanced rectal cancer: analysis of short- and long-term effects]

Objective: To explore the feasibility, safety, and short- and long-term efficacy of laparoscopic pelvic exenteration (LPE) in treating locally advanced rectal cancer. Methods: The clinical data of 173 patients who had undergone pelvic exenteration (PE) for locally advanced rectal cancer that had been shown by preoperative imaging or intraoperative exploration to have invaded beyond the mesorectal excision plane and adjacent organs in the Cancer Hospital, Chinese Academy of Medical Sciences (n=64) and Peking University First Hospital (n=109) from 2010 January to 2021 December were collected retrospectively. Laparoscopic PE (LPE) had been performed on 82 of these patients and open PE (OPE) on 91. Short- and long-term outcomes (1-, 3-, and 5-year overall and disease-free survival and 1- and 3-year cumulative local recurrence rates) were compared between these groups. Results: The only statistically significant difference in baseline data between the two groups (P>0.05) was administration of neoadjuvant therapy. Compared with OPE, LPE had a significantly shorter operative time (319.3±129.3 minutes versus 417.3±155.0 minutes, t=4.531, P<0.001) and less intraoperative blood loss (175 [20-2000] ml vs. 500 [20-4500] ml, U=2206.500, P<0.001). The R0 resection rates were 98.8% and 94.5%, respectively (χ²=2.355, P=0.214). At 18.3% (15/82), and the incidence of perioperative complications was lower in the LPE group than in the OPE group (37.4% [34/91], χ²=7.727, P=0.005). The rates of surgical site infection were 7.3% (6/82) and 23.1% (21/91) in the LPE and OPE group, respectively (χ²=8.134, P=0.004). The rates of abdominal wound infection were 0 and 12.1% (11/91) (χ²=10.585, P=0.001), respectively, and of urinary tract infection 0 and 6.6% (6/91) (χ²=5.601, P=0.030), respectively. Postoperative hospital stay was shorter in the LPE than OPE group (12 [4-60] days vs. 15 [7-87] days, U=2498.000, P<0.001). The median follow-up time was 40 (2-88) months in the LPE group and 59 (1-130) months in the OPE group. The 1-, 3-, and 5-year overall survival rates were 91.3%, 76.0%, and 62.5%, respectively, in the LPE group, and 91.2%, 68.9%, and 57.6%, respectively, in the OPE group. The 1, 3, and 5-year disease-free survival rates were 82.8%, 64.9%, and 59.7%, respectively, in the LPE group and 76.9%, 57.8%, and 52.7%, respectively, in the OPE group. The 1- and 3-year cumulative local recurrence rates were 5.1% and 14.1%, respectively, in the LPE group and 8.0% and 15.1%, respectively, in the OPE group (both P>0.05). Conclusions: In locally advanced rectal cancer patients, LPE is associated with shorter operative time, less intraoperative blood loss, fewer perioperative complications, and shorter hospital stay compared with OPE. It is safe and feasible without compromising oncological effect.

PPICT: an integrated deep neural network for predicting inter-protein PTM cross-talk

Post-translational modifications (PTMs) fine-tune various signaling pathways not only by the modification of a single residue, but also by the interplay of different modifications on residue pairs within or between proteins, defined as PTM cross-talk. As a challenging question, less attention has been given to PTM dynamics underlying cross-talk residue pairs and structural information underlying protein-protein interaction (PPI) graph, limiting the progress in this PTM functional research. Here we propose a novel integrated deep neural network PPICT (Predictor for PTM Inter-protein Cross-Talk), which predicts PTM cross-talk by combining protein sequence-structure-dynamics information and structural information for PPI graph. We find that cross-talk events preferentially occur among residues with high co-evolution and high potential in allosteric regulation. To make full use of the complex associations between protein evolutionary and biophysical features, and protein pair features, a heterogeneous feature combination net is introduced in the final prediction of PPICT. The comprehensive test results show that the proposed PPICT method significantly improves the prediction performance with an AUC value of 0.869, outperforming the existing state-of-the-art methods. Additionally, the PPICT method can capture the potential PTM cross-talks involved in the functional regulatory PTMs on modifying enzymes and their catalyzed PTM substrates. Therefore, PPICT represents an effective tool for identifying PTM cross-talk between proteins at the proteome level and highlights the hints for cross-talk between different signal pathways introduced by PTMs.

Preclinical development and evaluation of nanobody-based CD70-specific CAR T cells for the treatment of acute myeloid leukemia

BACKGROUND

Acute myeloid leukemia (AML) treatment remains challenging. CD70 was reported as a promising AML-specific antigen. Preclinically, CAR T-cell with single-chain-variable fragment (scFv) or truncated CD27 targeting CD70 has been reported to treat AML. However, various disadvantages including spontaneous exhaustion, proteinase-mediated loss of functional receptors, and high immunogenicity, limited its further application to clinical settings. Alternatively, the single-variable domain on heavy chain (VHH), also known as nanobodies, with comparable binding ability and specificity, provides an optional solution.

METHOD

We generated CD70 knocked-out novel nanobody-based anti-CD70-CAR T-cells (nb70CAR-T) with two different VHHs for antigen detection. Next, we detected the CD70 expression on primary AML blasts by flow cytometry and associated the efficacy of nb70CAR-T with the target antigen density. Finally, epigenetic modulators were investigated to regulate the CD70 expression on AML cells to promote the functionality of nb70CAR-T.

RESULTS

Our nb70CAR-T exhibited expected tumoricidal functionality against CD70-expressed cell lines and primary AML blasts. However, CD70 expression in primary AML blasts was not consistently high and nb70CAR-T potently respond to an estimated 40.4% of AML patients when the CD70 expression level was over a threshold of 1.6 (MFI ratio). Epigenetic modulators, Decitabine and Chidamide can up-regulate CD70 expression on AML cells, enhancing the treatment efficacy of nb70CAR-T.

CONCLUSION

CD70 expression in AML blasts was not fully supportive of its role in AML targeted therapy as reported. The combinational use of Chidamide and Decitabine with nb70CAR-T could provide a new potential for the treatment of AML.

Colorimetric Sensors for Chemical and Biological Sensing Applications

Colorimetric sensors have been widely used to detect numerous analytes due to their cost-effectiveness, high sensitivity and specificity, and clear visibility, even with the naked eye. In recent years, the emergence of advanced nanomaterials has greatly improved the development of colorimetric sensors. This review focuses on the recent (from the years 2015 to 2022) advances in the design, fabrication, and applications of colorimetric sensors. First, the classification and sensing mechanisms of colorimetric sensors are briefly described, and the design of colorimetric sensors based on several typical nanomaterials, including graphene and its derivatives, metal and metal oxide nanoparticles, DNA nanomaterials, quantum dots, and some other materials are discussed. Then the applications, especially for the detection of metallic and non-metallic ions, proteins, small molecules, gas, virus and bacteria, and DNA/RNA are summarized. Finally, the remaining challenges and future trends in the development of colorimetric sensors are also discussed.

MiR-200/183 family-mediated module biomarker for gastric cancer progression: an AI-assisted bioinformatics method with experimental functional survey

BACKGROUND

Gastric cancer (GC) is a major cancer burden throughout the world with a high mortality rate. The performance of current predictive and prognostic factors is still limited. Integrated analysis is required for accurate cancer progression predictive biomarker and prognostic biomarkers that help to guide therapy.

METHODS

An AI-assisted bioinformatics method that combines transcriptomic data and microRNA regulations were used to identify a key miRNA-mediated network module in GC progression. To reveal the module's function, we performed the gene expression analysis in 20 clinical samples by qRT-PCR, prognosis analysis by multi-variable Cox regression model, progression prediction by support vector machine, and in vitro studies to elaborate the roles in GC cells migration and invasion.

RESULTS

A robust microRNA regulated network module was identified to characterize GC progression, which consisted of seven miR-200/183 family members, five mRNAs and two long non-coding RNAs H19 and CLLU1. Their expression patterns and expression correlation patterns were consistent in public dataset and our cohort. Our findings suggest a two-fold biological potential of the module: GC patients with high-risk score exhibited a poor prognosis (p-value < 0.05) and the model achieved AUCs of 0.90 to predict GC progression in our cohort. In vitro cellular analyses shown that the module could influence the invasion and migration of GC cells.

CONCLUSIONS

Our strategy which combines AI-assisted bioinformatics method with experimental and clinical validation suggested that the miR-200/183 family-mediated network module as a "pluripotent module", which could be potential marker for GC progression.

HNRNPA2B1 as a potential therapeutic target for thymic epithelial tumor recurrence: An integrative network analysis

Thymic epithelial tumors (TETs) are rare malignant tumors, and the molecular mechanisms of both primary and recurrent TETs are poorly understood. Here we established comprehensive proteomic signatures of 15 tumors (5 recurrent and 10 non-recurrent) and 15 pair wised tumor adjacent normal tissues. We then proposed an integrative network approach for studying the proteomics data by constructing protein-protein interaction networks based on differentially expressed proteins and a machine learning-based score, followed by network modular analysis, functional enrichment annotation and shortest path inference analysis. Network modular analysis revealed that primary and recurrent TETs shared certain common molecular mechanisms, including a spliceosome module consisting of RNA splicing and RNA processing, but the recurrent TET was specifically related to the ribosome pathway. Applying the shortest path inference to the collected seed gene module identified that the ribonucleoprotein hnRNPA2B1 probably serves as a potential target for recurrent TET therapy. The drug repositioning combined molecular dynamics simulations suggested that the compound ergotamine could potentially act as a repurposing drug to treat recurrent TETs by targeting hnRNPA2B1. Our study demonstrates the value of integrative network analysis to understand proteotype robustness and its relationships with genotype, and provides hits for further research on cancer therapeutics.

Role of tea plantations in the maintenance of bird diversity in Anji County, China

Background

Tea plantations support regional sustainable development and have the potential to support more biodiversity than urban open spaces. Numerous studies have shown the value of low-intensity agroecosystems for preserving biodiversity, however tea plantations have received less attention. The relationship between tea plantations and the diversity of macro-organisms, such as birds, is still not fully understood.

Methods

We investigated the bird diversity and vegetation conditions and calculated landscape metrics in 30 tea plantations in Anji County, Zhejiang Province, China. At these 30 sampling sites, we recorded 262 individuals belonging to 37 species, which were classified into two guilds: nature- and urban-dependent birds. We used cluster analysis to group the sampling sites based on the abundance of the birds. Then we evaluated the effects of associated plant diversity in tea plantations and the surrounding landscape composition on these bird guilds using species association computation and a generalized linear model.

Results

The results show that the maintenance of bird diversity by tea plantations benefits both nature- and urban-dependent birds. We found that landscape-scale factors surrounding the tea plantations mainly affected the bird richness due to their habitat selection. Landscape agglomeration and habitat quality were the dominant landscape-scale metrics. Patch-scale factors of tea plantations, especially the vegetation structure, had a strong influence on the abundance of the birds. Nature-dependent birds preferred to occur in tea plantations with perennial herbs, while urban-dependent birds were attracted by the general distributed plants, as annual herbs. Therefore, we concluded that tea plantations play an important role as a transitional zone between natural habitats and urban areas, thus reducing the impact of urbanization and maintaining bird diversity in low-quality habitats.

A New Method for Training CycleGAN to Enhance Images of Cold Seeps in the Qiongdongnan Sea

Clear underwater images can help researchers detect cold seeps, gas hydrates, and biological resources. However, the quality of these images suffers from nonuniform lighting, a limited range of visibility, and unwanted signals. CycleGAN has been broadly studied in regard to underwater image enhancement, but it is difficult to apply the model for the further detection of Haima cold seeps in the South China Sea because the model can be difficult to train if the dataset used is not appropriate. In this article, we devise a new method of building a dataset using MSRCR and choose the best images based on the widely used UIQM scheme to build the dataset. The experimental results show that a good CycleGAN could be trained with the dataset using the proposed method. The model has good potential for applications in detecting the Haima cold seeps and can be applied to other cold seeps, such as the cold seeps in the North Sea. We conclude that the method used for building the dataset can be applied to train CycleGAN when enhancing images from cold seeps.

Identification of ovarian endometriotic cysts in cystic lesions of the ovary by amide proton transfer-weighted imaging and R2∗ mapping

AIM

To investigate the value of amide proton transfer weighted (APTw) imaging and R2∗ mapping of cystic fluid in differentiating ovarian endometriotic cysts (OE) from other ovarian cystic (OOC) lesions.

MATERIALS AND METHODS

A total of 42 patients who underwent 3 T pelvic magnetic resonance imaging (MRI) were enrolled. Nineteen lesions were OE and 27 lesions were OOC. The APTw imaging and R2∗ values of the cystic fluid were measured and compared between the two groups using the independent sample t-test or Mann-Whitney U-test. Receiver operating characteristic (ROC) curves were used to evaluate the diagnostic efficacy of different parameters. The area under ROC curves (AUCs) was compared using the Delong test. Spearman's correlation analysis was used to assess the correlation between APTw imaging and R2∗ values.

RESULTS

APTw imaging values of OE were lower, while R2∗ values were higher in OE than those in OOC (p=0.001 and < 0.001). The AUCs of APTw imaging and R2∗ values to identify OE from OOC were 0.910 and 0.975. The AUC increased to 0.990 when combining APTw imaging and R2∗ values, yet without a significant difference to the APTw imaging or R2∗ value alone (p=0.229 and 0.082, respectively). APTw imaging values were negatively correlated with R2∗ values (r=-0.522, p<0.001).

CONCLUSION

Both APTw imaging and R2∗ values of OE are significantly different from other ovarian cystic lesions. APTw imaging combined with R2∗ values show excellent diagnostic efficacy to differentiate between OE and OOC.

Iris lactea var. chinensis plant drought tolerance depends on the response of proline metabolism, transcription factors, transporters and the ROS-scavenging system

BACKGROUND

Iris lactea var. chinensis, a perennial herbaceous species, is widely distributed and has good drought tolerance traits. However, there is little information in public databases concerning this herb, so it is difficult to understand the mechanism underlying its drought tolerance.

RESULTS

In this study, we used Illumina sequencing technology to conduct an RNA sequencing (RNA-seq) analysis of I. lactea var. chinensis plants under water-stressed conditions and rehydration to explore the potential mechanisms involved in plant drought tolerance. The resulting de novo assembled transcriptome revealed 126,979 unigenes, of which 44,247 were successfully annotated. Among these, 1187 differentially expressed genes (DEGs) were identified from a comparison of the water-stressed treatment and the control (CK) treatment (T/CK); there were 481 upregulated genes and 706 downregulated genes. Additionally, 275 DEGs were identified in the comparison of the rehydration treatment and the water-stressed treatment (R/T). Based on Quantitative Real-time Polymerase Chain Reaction (qRT-PCR) analysis, the expression levels of eight randomly selected unigenes were consistent with the transcriptomic data under water-stressed and rehydration treatment, as well as in the CK. According to Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, proline metabolism-related DEGs, including those involved in the 'proline catabolic process', the 'proline metabolic process', and 'arginine and proline metabolism', may play important roles in plant drought tolerance. Additionally, these DEGs encoded 43 transcription factors (TFs), 46 transporters, and 22 reactive oxygen species (ROS)-scavenging system-related proteins. Biochemical analysis and histochemical detection showed that proline and ROS were accumulated under water-stressed conditions, which is consistent with the result of the transcriptomic analysis.

CONCLUSIONS

In summary, our transcriptomic data revealed that the drought tolerance of I. lactea var. chinensis depends on proline metabolism, the action of TFs and transporters, and a strong ROS-scavenging system. The related genes found in this study could help us understand the mechanisms underlying the drought tolerance of I. lactea var. chinensis.

Surface integrity of laser-assisted turning of the GH4169 alloy

The unique properties of GH4169, such as low thermal conductivity, high strength at high temperatures, and work hardening characteristics, make it difficult to machine. As an effective way to improve the machinability of materials, laser-assisted machining (LAM) has the advantages of reducing the cutting force, restraining chatter, improving productivity, and prolonging tool life. This study investigates the surface integrity of GH4169 in LAM, including the surface roughness, surface defects, microhardness, residual stress, and white-layer formation. First, the depth of the heat-affected layer from 380 to 760 r/min was determined to ascertain the depth of cutting. Secondly, at different cutting parameters, the surface roughness was found to be significantly reduced. LAM leads to a more severe plastic deformation, producing a thicker hardened layer and higher surface hardness on the fabricated substrate, but its internal hardness is less than that of samples made by conventional machining (CM), owing to thermal softening. Both machining methods produce residual tensile stresses, which are larger in LAM. Thirdly, the results of a surface integrity experiment show that white-layer generation is a consequence of the combination of phase change, heat, and plastic deformation. Finally, a comprehensive fuzzy evaluation considering the surface roughness, surface defects, microhardness, residual stress, and thickness of the white layer is established, which verifies that LAM significantly improves the surface integrity of GH4169, setting up a theoretical foundation and technical reference for the laser-assisted turning of nickel-based superalloys.