The significance of recurrent de novo amino acid substitutions that emerged during chronic SARS-CoV-2 infection: an observational study.

BACKGROUND: De novo amino acid substitutions (DNS) frequently emerge among immunocompromised patients with chronic SARS-CoV-2 infection. While previous studies have reported these DNS, their significance has not been systematically studied. METHODS: We performed a review of DNS that emerged during chronic SARS-CoV-2 infection. We searched PubMed until June 2023 using the keywords "(SARS-CoV-2 or COVID-19) and (mutation or sequencing) and ((prolonged infection) or (chronic infection) or (long term))". We included patients with chronic SARS-CoV-2 infection who had SARS-CoV-2 sequencing performed for at least 3 time points over at least 60 days. We also included 4 additional SARS-CoV-2 patients with chronic infection of our hospital not reported previously. We determined recurrent DNS that has appeared in multiple patients and determined the significance of these mutations among epidemiologically-significant variants. FINDINGS: A total of 34 cases were analyzed, including 30 that were published previously and 4 from our hospital. Twenty two DNS appeared in ≥3 patients, with 14 (64%) belonging to lineage-defining mutations (LDMs) of epidemiologically-significant variants and 10 (45%) emerging among chronically-infected patients before the appearance of the corresponding variant. Notably, nsp9-T35I substitution (Orf1a T4175I) emerged in all three patients with BA.2.2 infection in 2022 before the appearance of Variants of Interest that carry nsp9-T35I as LDM (EG.5 and BA.2.86/JN.1). Structural analysis suggests that nsp9-T35I substitution may affect nsp9-nsp12 interaction, which could be critical for the function of the replication and transcription complex. INTERPRETATION: DNS that emerges recurrently in different chronically-infected patients may be used as a marker for potential epidemiologically-significant variants. FUNDING: Theme-Based Research Scheme [T11/709/21-N] of the Research Grants Council (See acknowledgements for full list).

Kinetically Controlled Preparation of Worm-like Micelles with Tunable Diameter/Length and Structural Stability.

Anisotropic nanoparticles such as worm-like micelles have aroused much attention due to their promising applications from templates to drug delivery. The fabrication of worm-like micelles with tunable structural stability and control over their diameter and length is of great importance but still challenging. Herein, we report a kinetically controlled ring-opening metathesis polymerization-induced self-assembly (ROMPISA) for the robust preparation of kinetically trapped worm-like micelles with tunable diameter/length at enlarged experimental windows by the rational manipulation of kinetic factors, including solvent property, temperature, and π-π stacking effects. The resultant worm structures were thermodynamically metastable and capable of excellent structural stability at room temperature due to the kinetic trapping effect. At elevated temperatures, these thermodynamically metastable worms could undergo morphology evolution into vesicular structures in a controlled manner. Moreover, the structural stability of worms could also be significantly enhanced by in situ cross-linking. Overall, this kinetically controlled ROMPISA opens a new avenue for PISA chemistry that is expected to prepare "smart" polymer materials by manipulating kinetic factors.

The First-in-class Deubiquitinase-targeting Chimera Stabilizes and Activates cGAS.

Deubiquitinase-targeting chimera (DUBTAC) is a promising technology for inducing targeted protein stabilization (TPS). Despite its therapeutic potential, very few proteins have been stabilized by DUBTACs to date. The limited applicability of this technology is likely due to the modest DUBTAC-induced protein stabilization effect, and the scarcity of effective deubiquitinase ligands that can be harnessed for DUBTAC development. Here, we report the discovery of MS7829 and MS8588, the first-in-class DUBTACs of cGAS, a key component of the cGAS-STING pathway. While these DUBTACs are based on a cGAS inhibitor, they effectively stabilized cGAS and activated the cGAS/STING/IRF3 signaling. To develop these cGAS DUBTACs, we optimized EN523, an OTUB1 covalent ligand, into an improved ligand, MS5105. We validated MS5105 by generating a MS5105-based CFTR DUBTAC, which was approximately 10-fold more effective in stabilizing the ΔF508-CFTR mutant protein than the previously reported EN523-based CFTR DUBTAC. Overall, this work advances the DUBTAC technology for TPS.

Asymptomatic Incidence of Monoclonal Gammopathy of Undetermined Significance and Preclinical Duration to Myeloma Diagnosis: A Modeling Study.

Background Monoclonal gammopathy of undetermined significance (MGUS) is the premalignant condition of multiple myeloma (MM). Given a lack of population-based screening for MGUS and its asymptomatic nature, the epidemiology of MGUS remains unknown. This study estimated age- and race/ethnicity-specific MGUS incidence and preclinical duration from MGUS to MM in the United States. Methods A previously published modeling approach was used to calculate national MGUS incidence using estimates of MGUS prevalence, MM incidence, MM-specific and all-cause mortality, and population age distribution from the National Health and Nutrition Examination Survey, 1999-2004, and Surveillance, Epidemiology, and End Results, 2000-2021. The estimated MGUS prevalence was divided by MGUS incidence to obtain preclinical duration of MM. Results MGUS incidence for non-Hispanic white (NHW) populations was 52, 86, 142, and 181 and for non-Hispanic black (NHB) population was 110, 212, 392, and 570 per 100,000 person-years at ages 50, 60, 70, and 80, respectively. The average preclinical duration was 20.5 (95% confidence interval, CI: 16.5, 26.1) years for the NHW population and 14.2 (95% CI: 11.5, 17.6) years for the NHB population. The cumulative risk of developing MGUS in age 50-85 was 2.8% (95% CI: 1.7%, 4.2%) for the NHW population and 6.1% (95% CI: 3.8%, 10.0%) for the NHB population. Conclusion NHB populations had a higher MGUS incidence rate at all ages and a shorter preclinical duration of MM compared to their NHW counterparts. Impact This study provides insights into the epidemiology of MGUS and enhances our understanding of the natural history of MM.

Severe Adenovirus Pneumonia Masked by Influenza Virus in an 11-Year-Old Child: A Case Report.

Background: Adenovirus pneumonia progresses rapidly, with a high rate of progression to severe pneumonia, but the early clinical manifestations lack specificity and are not easy to be recognized. Methods: Reviewing the relevant literatures, we studied and summarized the early recognition, clinical features and treatment outlook of severe adenovirus pneumonia Case Presentation: An 11-year-old child with community-acquired pneumonia, with influenza A antigen positive by colloidal gold, which further developed into acute respiratory distress syndrome after hospitalization. Three days later, adenovirus was detected positively by PCR of throat swab and diagnosed as severe adenovirus pneumonia. After aggressive treatment, her condition improved and was discharged from the hospital. Conclusion: Clinically, adenovirus combined with influenza virus infection is uncommon, and adenovirus infection is even rarer in adolescent children.

Mechanism research of non-coding RNA in immune checkpoint inhibitors therapy.

Immune checkpoint inhibitor (ICI) therapies for tumors of different systems have attained significant achievements and have changed the current situation of tumor treatment due to their therapeutic characteristics of high specificity and low side effects. The immune checkpoint Programmed death 1/Programmed cell death-Ligand 1 (PD-1/PD-L1) axis exerts a vital role in the immune escape of tumor cells. As a result, it has become a key target for tumor immunotherapy. Therefore, to perfect research into potential regulatory factors for the PD-1/PD-L1 axis, in order to understand and illustrate tumor ICI therapy mechanisms, is a significant goal. Moreover, ncRNA has been verified to regulate the PD-1/PD-L1 axis in the tumor immune microenvironment to regulate tumor genesis and development. ncRNAs can improve or decrease the efficacy of ICI therapy by modulating PD-L1 expression. This review aimed to investigate the mechanisms of action of ncRNA in regulating the PD-1/PD-L1 axis in ICI therapy, to provide more efficient immunotherapy for tumors of different systems.

Tumor Cell-Derived Exosomal Hybrid Nanosystems Loaded with Rhubarbic Acid and Tanshinone IIA for Sepsis Treatment.

Background: Sepsis continues to exert a significant impact on morbidity and mortality in clinical settings, with immunosuppression, multi-organ failure, and disruptions in gut microbiota being key features. Although rheinic acid and tanshinone IIA show promise in mitigating macrophage apoptosis in sepsis treatment, their precise targeting of macrophages remains limited. Additionally, the evaluation of intestinal flora changes following treatment, which plays a significant role in subsequent cytokine storms, has been overlooked. Leveraging the innate inflammation chemotaxis of tumor cell-derived exosomes allows for their rapid recognition and uptake by activated macrophages, facilitating phenotypic changes and harnessing anti-inflammatory effects. Methods: We extracted exosomes from H1299 cells using a precipitation method. Then we developed a tumor cell-derived exosomal hybrid nanosystem loaded with rhubarbic acid and tanshinone IIA (R+T/Lipo/EXO) for sepsis treatment. In vitro studies, we verify the anti-inflammatory effect and the mechanism of inhibiting cell apoptosis of nano drug delivery system. The anti-inflammatory effects, safety, and modulation of intestinal microbiota by the nanoformulations were further validated in the in vivo study. Results: Nanoformulation demonstrated enhanced macrophage internalization, reduced TNF-α expression, inhibited apoptosis, modulated intestinal flora, and alleviated immunosuppression. Conclusion: R+T/Lipo/EXO presents a promising approach using exosomal hybrid nanosystems for treating sepsis.

Exploring the predictive ability of the CA-Markov model for urban functional area in Nanjing old city.

With advancements in sustainable urban development, research on urban functional areas has garnered significant attention. In recent years, Point-of-Interest, with their large volume of information and ease of acquisition, have been widely applied in research on urban functional domains. However, scholars currently focus on the identification of urban functional areas, usually relying on data from a single period, whereas research on the prediction of functional areas has not yet been well validated. Therefore, in this study, we propose a new method based on several years of POI data to predict urban functional areas. Taking Nanjing City, Jiangsu Province, as an example, we first identified the functional area distribution of the old city of Nanjing over several years using POI data and then designed multiple sets of experiments to explore the CA-Markov model's ability to predict functional areas from various aspects, including model overall accuracy, robustness, and comparison analysis between predictions and actual situations. The results show that (1) for mixed or single functional areas, the model's predictions over several years tend to be stable, and the accuracy of the predictions over many years indicates the robustness of the model in predicting urban functional areas. (2) For mixed functional areas in cities, model predictions largely rely on the distribution of the base years used for prediction, leading to inaccurate results; thus, it is still not applicable for simulating and predicting mixed functional areas. (3) For single functional areas in cities or primary functions within an area, the model's predicted degree of change was close to the actual degree of change, making the results referable.

Decontamination promotes the release of incorporated organic contaminants in hair: Novel insights into non-invasive biomonitoring.

Human hair is increasingly employed as a non-invasive biomonitoring matrix for exposure to organic contaminants (OCs). Decontamination procedures are generally needed to remove external contamination from hair prior to analysis of OCs. Despite various existing decontamination protocols, their impacts on internally incorporated (endogenous) OCs in hair remain poorly understood. This study aims to quantitatively assess the impact of decontamination procedures on endogenous OCs in hair, and investigate optimal decontamination processes and factors influencing the removal of endogenous OCs. In this study, guinea pig was exposed to 6 OCs (triphenyl phosphate (TPHP), tris(1,3-dichloro-2-propyl) phosphate (TDCPP), and tri-n-butyl phosphate (TNBP), bisphenol A (BPA), perfluorooctanoic acid (PFOA), and phenanthrene (PHE)), and 6 decontamination procedures with different solvents (methanol, n-hexane, acetone, ultrapure water, Triton X-100, and sodium dodecyl sulfate) were used to rinse exposed guinea pig hair. All OCs and three metabolites (diphenyl phosphate (DPHP), dibutyl phosphate (DBP), and bis(1,3-dichloro-2-propyl) phosphate (BDCPP)) were detected in the majority of washing solutions. The decontamination procedures apparently resulted in the release of endogenous OCs from hair. The percentages of residual OCs in hair exhibited a linear or exponential decrease with more washing cycles. Furthermore, the residuals of OCs in hair washed with organic and aqueous solvents showed negative correlations with molecular weight, polarizability, and their initial concentrations. Although these findings need to be validated with a broader range of OCs, the results obtained in this study provide compelling evidence that current hair decontamination procedures have significant impacts on the analysis of endogenous OCs in hair. Therefore, it is important to interpret quantitative data on hair OC concentrations with caution and to thoroughly consider each decontamination procedure during analysis.

Cellular Components of the Blood-Brain Barrier and Their Involvement in Aging-Associated Cognitive Impairment.

Human life expectancy has been significantly extended, which poses major challenges to our healthcare and social systems. Aging-associated cognitive impairment is attributed to endothelial dysfunction in the cardiovascular system and neurological dysfunction in the central nervous system. The central nervous system is considered an immune-privileged tissue due to the exquisite protection provided by the blood-brain barrier. The present review provides an overview of the structure and function of blood-brain barrier, extending the cell components of blood-brain barrier from endothelial cells and pericytes to astrocytes, perivascular macrophages and oligodendrocyte progenitor cells. In particular, the pathological changes in the blood-brain barrier in aging, with special focus on the underlying mechanisms and molecular changes, are presented. Furthermore, the potential preventive/therapeutic strategies against aging-associated blood-brain barrier disruption are discussed.

Helical polyisocyanide-based macroporous organic catalysts for asymmetric Michael addition with high efficiency and stereoselectivity.

Porous materials have attracted interest due to their high specific surface area and rich functionality. Immobilizing organocatalysts onto porous polymers not only boosts enantioselectivity but also improves the reaction rates. In this work, a series of porous polymers C-poly-3ms with rigid polyisocyanide-carrying secondary amine pendants as building blocks were successfully prepared. And the pore size and optical activity of C-poly-3ms can be controlled by the length of the polyisocyanide blocks due to their rigid and helical backbone. C-poly-3150 demonstrated a preferred left-handed helix with a θ 364 value of -8.21 × 103. The pore size and S BET of C-poly-3150 were 17.52 nm and 7.98 m2 g-1, respectively. The porous C-poly-3150 catalyzes the asymmetric Michael addition reaction efficiently and generates the target products in satisfactory yield and excellent enantioselectivity. For 6ab, an enantiomeric excess (ee) and a diastereomeric ratio (dr) up to 99% and 99/1 could be achieved, respectively. The recovered catalyst can be recycled at least 6 times in the asymmetric Michael addition reaction while maintaining activity and stereoselectivity.

Novel EGFR inhibitors against resistant L858R/T790M/C797S mutant for intervention of non-small cell lung cancer.

To overcome C797S mutation, the latest and most common resistance mechanism in the clinical treatment of third-generation EGFR inhibitor, a novel series of substituted 6-(2-aminopyrimidine)-indole derivatives were designed and synthesized. Through the structure-activity relationship (SAR) study, compound 11eg was identified as a novel and potent EGFR L858R/T790M/C797S inhibitor (IC50 = 0.053 µM) but had a weak effect on EGFRWT (IC50 = 1.05 µM). 11eg significantly inhibited the proliferation of the non-small cell lung cancer (NSCLC) cells harboring EGFRL858R/T790M/C797S with an IC50 of 0.052 µM. 11eg also showed potent inhibitory activity against other NSCLC cell lines harboring main EGFR mutants. Furthermore, 11eg exhibited much superior activity in arresting cell cycle and inducing apoptosis of NSCLC cells with mutant EGFRC797S. It blocked cellular EGFR signaling. Importantly, 11eg markedly suppressed the tumor growth in in vivo xenograft mouse model with good safety. Additionally, 11eg displayed good microsomal stability. These results demonstrated the potential of 11eg with novel scaffold as a promising lead compound targeting EGFRC797S to guide in-depth structural optimization.

The molecular architecture of the nuclear basket.

The nuclear pore complex (NPC) is the sole mediator of nucleocytoplasmic transport. Despite great advances in understanding its conserved core architecture, the peripheral regions can exhibit considerable variation within and between species. One such structure is the cage-like nuclear basket. Despite its crucial roles in mRNA surveillance and chromatin organization, an architectural understanding has remained elusive. Using in-cell cryo-electron tomography and subtomogram analysis, we explored the NPC's structural variations and the nuclear basket across fungi (yeast; S. cerevisiae), mammals (mouse; M. musculus), and protozoa (T. gondii). Using integrative structural modeling, we computed a model of the basket in yeast and mammals that revealed how a hub of nucleoporins (Nups) in the nuclear ring binds to basket-forming Mlp/Tpr proteins: the coiled-coil domains of Mlp/Tpr form the struts of the basket, while their unstructured termini constitute the basket distal densities, which potentially serve as a docking site for mRNA preprocessing before nucleocytoplasmic transport.

Aerobic granular sludge for swine wastewater treatment: Implications for antibiotic and antibiotic resistance gene elimination.

Swine wastewater (SW) contains high levels of traditional pollutants, antibiotics, and antibiotic resistance genes (ARGs), necessitating effective elimination. Two parallel aerobic granular sludge (AGS) reactors, R1 and R2, were constructed and optimized for treating SW from two pig farms, identified as SW1 and SW2. R2 showed higher antibiotic removal efficiency, particularly in the removal of sulfonamides, while fluoroquinolones tended to adsorb onto the sludge. Process optimization by introducing an additional anoxic phase enhanced denitrification and reduced effluent ARG levels, also aiding in the improved removal of fluoroquinolones. The nitrite-oxidizing bacteria (NOB) Nitrospira accumulated after the treatment process, reaching 12.8 % in R1 and 14.1 % in R2, respectively. Mantel's test revealed that pH, NH4+-N, and Mg significantly affected ARGs and microbial community. Sulfadiazine and sulfamethazine were found to significantly impact ARGs and the microbial communities. This study provides innovative insights into the application of AGS for the treatment of real SW.

Reinforcing thermostability and pH robustness of exo-inulinase facilitated by ReverseTag/ReverseCatcher tagging system.

Enhancing protein stability is pivotal in the field of protein engineering. Protein self-cyclization using peptide a tagging system has emerged as an effective strategy for augmenting the thermostability of target proteins. In this study, we utilized a novel peptide tagging system, ReverseTag/ReverseCatcher, which leverages intramolecular ester bond formation. Initially, we employed GFP as a model to validate the feasibility of cyclization mediated by ReverseTag/ReverseCatcher in improving the protein thermostability. Cyclized GFP (cGFP) retained 30 % of its relative fluorescence after a 30-min incubation at 100 °C, while both GFP and linear GFP (lGFP) completely lost their fluorescence within 5 min. Additionally, we applied this method to exo-inulinase (EXINU), resulting in a variant named cyclized EXINU (cEXINU). The T50 and t1/2 values of cEXINU exhibited significant enhancements of 10 °C and 10 min, respectively, compared to EXINU. Furthermore, post-cyclization, EXINU demonstrated a broad operational pH range from 5 to 10 with sustained catalytic activity, and cEXINU maintained a half-life of 960 min at pH 5 and 9. Molecular dynamics simulations were conducted to elucidate the mechanisms underlying the enhanced thermostability and pH robustness of EXINU following cyclization. This study highlights that cyclization substanitially enhances the stability of both highly stable protein GFP and low-stable protein EXINU, mediated by the ReverseTag/ReverseCatcher tagging system. The ReverseTag/ReverseCatcher tagging system proves to be a potent conjugation method, with potential applications in improving thermostability, pH robustness, and other areas of protein engineering.

GPR50 regulates neuronal development as a mitophagy receptor.

Neurons rely heavily on high mitochondrial metabolism to provide sufficient energy for proper development. However, it remains unclear how neurons maintain high oxidative phosphorylation (OXPHOS) during development. Mitophagy plays a pivotal role in maintaining mitochondrial quality and quantity. We herein describe that G protein-coupled receptor 50 (GPR50) is a novel mitophagy receptor, which harbors the LC3-interacting region (LIR) and is required in mitophagy under stress conditions. Although it does not localize in mitochondria under normal culturing conditions, GPR50 is recruited to the depolarized mitochondrial membrane upon mitophagy stress, which marks the mitochondrial portion and recruits the assembling autophagosomes, eventually facilitating the mitochondrial fragments to be engulfed by the autophagosomes. Mutations Δ502-505 and T532A attenuate GPR50-mediated mitophagy by disrupting the binding of GPR50 to LC3 and the mitochondrial recruitment of GPR50. Deficiency of GPR50 causes the accumulation of damaged mitochondria and disrupts OXPHOS, resulting in insufficient ATP production and excessive ROS generation, eventually impairing neuronal development. GPR50-deficient mice exhibit impaired social recognition, which is rescued by prenatal treatment with mitoQ, a mitochondrially antioxidant. The present study identifies GPR50 as a novel mitophagy receptor that is required to maintain mitochondrial OXPHOS in developing neurons.

Development and External Validation of an Artificial Intelligence-Based Method for Scalable Chest Radiograph Diagnosis: A Multi-Country Cross-Sectional Study.

Problem: Chest radiography is a crucial tool for diagnosing thoracic disorders, but interpretation errors and a lack of qualified practitioners can cause delays in treatment. Aim: This study aimed to develop a reliable multi-classification artificial intelligence (AI) tool to improve the accuracy and efficiency of chest radiograph diagnosis. Methods: We developed a convolutional neural network (CNN) capable of distinguishing among 26 thoracic diagnoses. The model was trained and externally validated using 795,055 chest radiographs from 13 datasets across 4 countries. Results: The CNN model achieved an average area under the curve (AUC) of 0.961 across all 26 diagnoses in the testing set. COVID-19 detection achieved perfect accuracy (AUC 1.000, [95% confidence interval {CI}, 1.000 to 1.000]), while effusion or pleural effusion detection showed the lowest accuracy (AUC 0.8453, [95% CI, 0.8417 to 0.8489]). In external validation, the model demonstrated strong reproducibility and generalizability within the local dataset, achieving an AUC of 0.9634 for lung opacity detection (95% CI, 0.9423 to 0.9702). The CNN outperformed both radiologists and nonradiological physicians, particularly in trans-device image recognition. Even for diseases not specifically trained on, such as aortic dissection, the AI model showed considerable scalability and enhanced diagnostic accuracy for physicians of varying experience levels (all P < 0.05). Additionally, our model exhibited no gender bias (P > 0.05). Conclusion: The developed AI algorithm, now available as professional web-based software, substantively improves chest radiograph interpretation. This research advances medical imaging and offers substantial diagnostic support in clinical settings.

[Quality control mode between Lonicera macranthoides and L. japonica based on multi-elemental difference through inductively coupled plasma mass spectrometry].

Numerous studies show that Lonicera macranthoides and L. japonica have significant differences in organic matter. However, there is still a lack of research on inorganic elements between them. In this study, a non-targeted elemental metabolomics method was established by inductively coupled plasma mass spectrometry(ICP-MS), so as to compare the overall differences of inorganic elements between L. macranthoides and L. japonica. In addition, the differential markers were screened, and these differential markers were quantitatively analyzed by the targeted method. The non-targeted elemental metabolomics showed that the established mathematical model could reflect the difference in element content between L. macranthoides and L. japonica. Four inorganic elements such as ~(55)Mn, ~(209)Bi, ~(111)Cd, and ~(85)Rb were confirmed as the differential markers of L. macranthoides and L. japonica based on the screening principles of variable importance in the projection(VIP) value>2.0, P<0.01 and fold change(FC) value>1.2 or <0.80. The targeted quantitative results showed that the content of ~(209)Bi in L. japonica was significantly higher than that in L. macranthoides, while ~(55)Mn, ~(111)Cd, and ~(85)Rb in L. macranthoides were significantly higher than that in L. japonica. The non-targeted and targeted elemental metabolomics methods based on ICP-MS can significantly reflect the overall differences in inorganic elements between L. macranthoides and L. japonica. Exploring the differences between them from the perspective of elements can partly reflect the differences in their drug properties and lay a foundation for further study on the quality control mode of inorganic elements in L. macranthoides and L. japonica and their pharmacological effects.