KinomeMETA: a web platform for kinome-wide polypharmacology profiling with meta-learning.

Kinase-targeted inhibitors hold promise for new therapeutic options, with multi-target inhibitors offering the potential for broader efficacy while minimizing polypharmacology risks. However, comprehensive experimental profiling of kinome-wide activity is expensive, and existing computational approaches often lack scalability or accuracy for understudied kinases. We introduce KinomeMETA, an artificial intelligence (AI)-powered web platform that significantly expands the predictive range with scalability for predicting the polypharmacological effects of small molecules across the kinome. By leveraging a novel meta-learning algorithm, KinomeMETA efficiently utilizes sparse activity data, enabling rapid generalization to new kinase tasks even with limited information. This significantly expands the repertoire of accurately predictable kinases to 661 wild-type and clinically-relevant mutant kinases, far exceeding existing methods. Additionally, KinomeMETA empowers users to customize models with their proprietary data for specific research needs. Case studies demonstrate its ability to discover new active compounds by quickly adapting to small dataset. Overall, KinomeMETA offers enhanced kinome virtual profiling capabilities and is positioned as a powerful tool for developing new kinase inhibitors and advancing kinase research. The KinomeMETA server is freely accessible without registration at https://kinomemeta.alphama.com.cn/.

Nomogram Based on US and Clinicopathologic Characteristics: Axillary Nodal Evaluation Following Neoadjuvant Chemotherapy in Patients With Node-Positive Breast Cancer.

BACKGROUND: To develop a convenient modality to predict axillary response to neoadjuvant chemotherapy (NAC) in breast cancer patients. MATERIALS AND METHODS: In this multi-center study, a total of 1019 breast cancer patients with biopsy-proven positive lymph node (LN) receiving NAC were randomly assigned to the training and validation groups at a ratio of 7:3. Clinicopathologic and ultrasound (US) characteristics of both primary tumors and LNs were used to develop corresponding prediction models, and a nomogram integrating clinicopathologic and US predictors was generated to predict the axillary response to NAC. RESULTS: Axillary pathological complete response (pCR) was achieved in 47.79% of the patients. The expression of estrogen receptor, human epidermal growth factor receptor -2, Ki-67 score, and clinical nodal stage were independent predictors for nodal response to NAC. Location and radiological response of primary tumors, cortical thickness and shape of LNs on US were also significantly associated with nodal pCR. In the validation cohort, the discrimination of US model (area under the curve [AUC], 0.76) was superior to clinicopathologic model (AUC, 0.68); the combined model (AUC, 0.85) demonstrates strong discriminatory power in predicting nodal pCR. Calibration curves of the nomogram based on the combined model demonstrated that substantial agreement can be observed between the predictions and observations. This nomogram showed a false-negative rates of 16.67% in all patients and 10.53% in patients with triple negative breast cancer. CONCLUSION: Nomogram incorporating routine clinicopathologic and US characteristics can predict nodal pCR and represents a tool to aid in treatment decisions for the axilla after NAC in breast cancer patients.

Apoptotic Bodies Derived from Fibroblast-Like Cells in Subcutaneous Connective Tissue Inhibit Ferroptosis in Ischaemic Flaps via the miR-339-5p/KEAP1/Nrf2 Axis.

Preventing and treating avascular necrosis at the distal end of the flaps are critical to surgery success, but current treatments are not ideal. A recent study shows that apoptotic bodies (ABs) generated near the site of apoptosis can be taken up and promote cell proliferation. The study reveals that ABs derived from fibroblast-like cells in the subcutaneous connective tissue (FSCT cells) of skin flaps promoted ischaemic flap survival. It is also found that ABs inhibited cell death and oxidative stress and promoted M1-to-M2 polarization in macrophages. Transcriptome sequencing and protein level testing demonstrated that ABs promoted ischaemic flap survival in endothelial cells and macrophages by inhibiting ferroptosis via the KEAP1-Nrf2 axis. Furthermore, microRNA (miR) sequencing data and in vitro and in vivo experiments demonstrated that ABs inhibited KEAP1 by delivering miR-339-5p to exert therapeutic effects. In conclusion, FSCT cell-derived ABs inhibited ferroptosis, promoted the macrophage M1-to-M2 transition via the miR-339-5p/KEAP1/Nrf2 axis and promoted ischaemic flap survival. These results provide a potential therapeutic strategy to promote ischaemic flap survival by administering ABs.

Global insights into endophytic bacterial communities of terrestrial plants: Exploring the potential applications of endophytic microbiota in sustainable agriculture.

Endophytic microorganisms are indispensable symbionts during plant growth and development and often serve functions such as growth promotion and stress resistance in plants. Therefore, an increasing number of researchers have applied endophytes for multifaceted phytoremediation (e.g., organic pollutants and heavy metals) in recent years. With the availability of next-generation sequencing technologies, an increasing number of studies have shifted the focus from culturable bacteria to total communities. However, information on the composition, structure, and function of bacterial endophytic communities is still not widely synthesized. To explore the general patterns of variation in bacterial communities between plant niches, we reanalyzed data from 1499 samples in 30 individual studies from different continents and provided comprehensive insights. A group of bacterial genera were commonly found in most plant roots and shoots. Our analysis revealed distinct variations in the diversity, composition, structure, and function of endophytic bacterial communities between plant roots and shoots. These variations underscore the sophisticated mechanisms by which plants engage with their endophytic microbiota, optimizing these interactions to bolster growth, health, and resilience against stress. Highlighting the strategic role of endophytic bacteria in promoting sustainable agricultural practices and environmental stewardship, our study not only offers global insights into the endophytic bacterial communities of terrestrial plants but also underscores the untapped potential of these communities as invaluable resources for future research.

Phosphocholine-induced energy source shift alleviates mitochondrial dysfunction in lung cells caused by geospecific PM2.5 components.

Fine particulate matter (PM2.5) is globally recognized for its adverse implications on human health. Yet, remain limited the individual contribution of particular PM2.5 components to its toxicity, especially considering regional disparities. Moreover, prevention solutions for PM2.5-associated health effects are scarce. In the present study, we comprehensively characterized and compared the primary PM2.5 constituents and their altered metabolites from two locations: Taiyuan and Guangzhou. Analysis of year-long PM2.5 samples revealed 84 major components, encompassing organic carbon, elemental carbon, ions, metals, and organic chemicals. PM2.5 from Taiyuan exhibited higher contamination, associated health risks, dithiothreitol activity, and cytotoxicities than Guangzhou's counterpart. Applying metabolomics, BEAS-2B lung cells exposed to PM2.5 from both cities were screened for significant alterations. A correlation analysis revealed the metabolites altered by PM2.5 and the critical toxic PM2.5 components in both regions. Among the PM2.5-down-regulated metabolites, phosphocholine emerged as a promising intervention for PM2.5 cytotoxicities. Its supplementation effectively attenuated PM2.5-induced energy metabolism disorder and cell death via activating fatty acid oxidation and inhibiting Phospho1 expression. The highlighted toxic chemicals displayed combined toxicities, potentially counteracted by phosphocholine. Our study offered a promising functional metabolite to alleviate PM2.5-induced cellular disorder and provided insights into the geo-based variability in toxic PM2.5 components.

Straightforward Creation of Multishell Hollow Hybrids for an Integrated Metabolic Monitoring System in Disease Management.

Multidimensional metabolic analysis has become a new trend in establishing efficient disease monitoring systems, as the constraints associated with relying solely on a single dimension in refined monitoring are increasingly pronounced. Here, coordination polymers are employed as derivative precursors to create multishell hollow hybrids, developing an integrated metabolic monitoring system. Briefly, metabolic fingerprints are extracted from hundreds of serum samples and urine samples, encompassing not only membranous nephropathy but also related diseases, using high-throughput mass spectrometry. With optimized algorithm and initial feature selection, the established combined panel demonstrates enhanced accuracy in both subtype differentiation (over 98.1%) and prognostic monitoring (over 95.6%), even during double blind test. This surpasses the serum biomarker panel (≈90.7% for subtyping, ≈89.7% for prognosis) and urine biomarker panel (≈94.4% for subtyping, ≈76.5% for prognosis). Moreover, after attempting to further refine the marker panel, the blind test maintains equal sensitivity, specificity, and accuracy, showcasing a comprehensive improvement over the single-fluid approach. This underscores the remarkable effectiveness and superiority of the integrated strategy in discriminating between MN and other groups. This work has the potential to significantly advance diagnostic medicine, leading to the establishment of more effective strategies for patient management.

Study on the Thermal Stability of the Sweet-Tasting Protein Brazzein Based on Its Structure-Sweetness Relationship.

Brazzein (Brz) is a sweet-tasting protein composed of 54 amino acids and is considered as a potential sugar substitute. The current methods for obtaining brazzein are complicated, and limited information is available regarding its thermal stability. In this study, we successfully expressed recombinant brazzein, achieving a sweetness threshold of 15.2 µg/mL. Subsequently, we conducted heat treatments at temperatures of 80, 90, 95, and 100 °C for a duration of 2 h to investigate the structural changes in the protein. Furthermore, we employed hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS) to analyze the effect of heating on the protein structure-sweetness relationships. Our results indicated that the thermal inactivation process primarily affects residues 6-14 and 36-45 of brazzein, especially key residues Tyr8, Tyr11, Ser14, Glu36, and Arg43, which are closely associated with its sweetness. These findings have significant implications for improving the thermal stability of brazzein.

Designed Directional Growth of Ti-Metal-Organic Frameworks for Decoding Alzheimer's Disease-Specific Exosome Metabolites.

Exosomes, a growing focus for liquid biopsies, contain diverse molecular cargos. In particular, exosome metabolites with valuable information have exhibited great potential for improving the efficiency of liquid biopsies for addressing complex medical conditions. In this work, we design the directional growth of Ti-metal-organic frameworks on polar-functionalized magnetic particles. This design facilitates the rapid synergistic capture of exosomes with the assistance of an external magnetic field and additionally synergistically enhances the ionization of their metabolites during mass spectrometry detection. Benefiting from this dual synergistic effect, we identified three high-performance exosome metabolites through the differential comparison of a large number of serum samples from individuals with Alzheimer's disease (AD) and normal cognition. Notably, the accuracy of AD identification ranges from 93.18 to 100% using a single exosome metabolite and reaches a flawless 100% with three metabolites. These findings emphasize the transformative potential of this work to enhance the precision and reliability of AD diagnosis, ushering in a new era of improved diagnostic accuracy.

Effect of early dexamethasone on outcomes of COVID-19: A quasi-experimental study using propensity score matching.

BACKGROUND: The RECOVERY trial demonstrated that the use of dexamethasone is associated with a 36% lower 28-day mortality in hospitalized patients with COVID-19 on invasive mechanical ventilation. Nevertheless, the optimal timing to start dexamethasone remains uncertain. METHODS: We conducted a quasi-experimental study at National Taiwan University Hospital (Taipei, Taiwan) using propensity score matching to simulate a randomized controlled trial to receive or not to receive early dexamethasone (6 mg/day) during the first 7 days following the onset of symptoms. Treatment was standard protocol-based, except for the timing to start dexamethasone, which was left to physicians' decision. The primary outcome is 28-day mortality. Secondary outcomes include secondary infection within 60 days and fulfilling the criteria of de-isolation within 20 days. RESULTS: A total of 377 patients with COVID-19 were enrolled. Early dexamethasone did not decrease 28-day mortality in all patients (adjusted odds ratio [aOR], 1.03; 95% confidence interval [CI], 0.97-1.10) or in patients who required O2 for severe/critical disease at admission (aOR, 1.05; 95%CI, 0.94-1.18); but is associated with a 24% increase in superinfection in all patients (aOR, 1.24; 95% CI, 1.12-1.37) and a 23% increase in superinfection in patients of O2 for several/critical disease at admission (aOR, 1.23; 95% CI, 1.02-1.47). Moreover, early dexamethasone is associated with a 42% increase in likelihood of delayed clearance of SARS-CoV-2 virus (adjusted hazard ratio, 1.42; 95% CI, 1.01-1.98). CONCLUSION: An early start of dexamethasone (within 7 days after the onset of symptoms) could be harmful to hospitalized patients with COVID-19.

Physicochemical Quantitative Analysis of the Oil-Water Interface as Affected by the Mutual Interactions between Pea Protein Isolate and Mono- and Diglycerides.

As a commercially available ingredient, the mono- and diglycerides (MDG) were widely used in a plant protein-based emulsion to provide effective, functional, emulsifying properties. The simultaneous addition of the MDG and pea protein isolate (PPI) was investigated by the methods of interfacial rheology and quantitative protein proteomics. The physicochemical quantitative analysis of the oil-water interface revealed an interfacial stability mechanism for the protein adsorption layer. For a low MDG concentration, the interfacial quantities of vicilin and albumin were increased, which could be attributed to the adsorption rate. For a high MDG concentration, both vicilin and albumin were displaced by MDG and desorbed from the interface, while legumin was more difficult to displace due to its slow adsorption and the complex structure of protein molecules. The protein molecules with the structural rearrangement interacted with MDG, exhibiting potential effects on the interfacial film structure. Combined with some nanotechnologies, the new comprehension of protein-emulsifier interactions may promote food delivery systems. The research aims to develop an in-depth analysis of interfacial proteins, and provide more innovative and tailored functionalities for the application of the plant protein emulsion.

Formulations and assessments of structure, physical properties, and sensory attributes of soy yogurts: Effect of carboxymethyl cellulose content and degree of substitution.

Soy yogurts present challenges, including absence of tender and slipperiness mouthfeel, and poor stability. This study aimed to investigate the impacts of carboxymethyl cellulose (CMC) with degrees of substitution of 0.7 (CMC0.7) and 1.2 (CMC1.2) at concentrations ranging from 0 % to 1.1 % on the stability, microstructure, rheology, tribology, and mouthfeel of soy yogurts. As the CMC concentration increased from 0 % to 0.3 %, soy yogurts displayed a coarser microstructure, decreased stability, and increased gel strength. As the concentration of CMC further increased from 0.5 % to 1.1 %, soy yogurts exhibited trends of a smoother microstructure, increased stability, and softer gel strength. Notably, soy yogurts with CMC0.7 demonstrated a superior water holding capacity (WHC) than soy yogurts with CMC1.2. Tribological measurements indicated that soy yogurts with CMC0.7 at a 0.7 % concentration had the lowest coefficient of friction (COF) value among most sliding speeds, showing a 23 % reduction compared to soy yogurts without CMC at a sliding speed of 10 mm/s. Moreover, sensory evaluation showed that soy yogurts with CMC0.7 at a 0.7 % concentration had the highest total score in mouthfeel evaluation. Therefore, the addition of CMC0.7 within the concentration range of 0.5 % to 1.1 % may produce stable and delicate yogurts.

Expression of Ice Nucleation Protein in Bacillus amyloliquefaciens and Its Application in Food Freezing Process.

To produce food-grade ice nucleators, a 3.77 kb ice nucleation gene (iceE) isolated from Pantoea agglomerans (Erwinia herbicola) was introduced into the Gram-positive microorganism Bacillus amyloliquefaciens for the first time. The differential scanning calorimetry (DSC) results indicated that recombined strain B9-INP was an effective ice nucleator for controlling the supercooling point of distilled water at low concentrations. In the presence of B9-INP cells, model food systems, including sucrose solution and sodium chloride solution, different pH solutions froze at a relatively high subzero temperature, thus increasing the supercooling point by 5.8~16.7 °C. Moreover, B9-INP also facilitated model and real food systems to freeze at -6 °C. This recombinant strain not only improved the freezing temperature of food systems but also shortened the total freezing time, thus saving energy and reducing consumption. The results suggest that B9-INP has great application potential in the frozen food industry.

ESCO2 promotes hypopharyngeal carcinoma progression in a STAT1-dependent manner.

BACKGROUND: The establishment of sister chromatid cohesion N-acetyltransferase 2 (ESCO2) is involved in the development of multiple malignancies. However, its role in hypopharyngeal carcinoma (HPC) progression remains uncharacterized. METHODS: This study employed bioinformatics to determine the ESCO2 expression in head and neck squamous cell carcinoma (HNSC) and normal tissues. In vitro cell proliferation, migration, apoptosis, and/or cell cycle distribution assays were used to determine the function of ESCO2 and its relationship with STAT1. Xenograft models were established in nude mice to determine ESCO2 in HPC growth in vivo. Co-immunoprecipitation/mass spectrometry (Co-IP/MS) was conducted to identify the potential ESCO2 binding partners. RESULTS: We found that ESCO2 expression was elevated in HNSC tissues, and ESCO2 depletion suppressed tumor cell migration in vitro and inhibited tumor growth in vitro and in vivo. Co-IP/MS and immunoblotting assays revealed the interaction between ESCO2 and STAT1 in HPC cells. STAT1-overexpression compromised ESCO2-mediated suppressive effects on HPC cell proliferation, viability, and migration. CONCLUSIONS: These findings suggest that ESCO2 is crucial in promoting HPC malignant progression through the STAT1 pathway and provides novel therapeutic targets for HPC treatment.

QTL Mapping of Soybean (Glycine max) Vine Growth Habit Trait.

The vine growth habit (VGH) is a notable property of wild soybean plants that also holds a high degree of importance in domestication as it can preclude using these wild cultivars for breeding and improving domesticated soybeans. Here, a bulked segregant analysis (BSA) approach was employed to study the genetic etiology of the VGH in soybean plants by integrating linkage mapping and population sequencing approaches. To develop a recombinant inbred line (RIL) population, the cultivated Zhongdou41 (ZD41) soybean cultivar was bred with ZYD02787, a wild soybean accession. The VGH status of each line in the resultant population was assessed, ultimately leading to the identification of six and nine QTLs from the BSA sequencing of the F4 population and F6-F8 population sequence mapping, respectively. One QTL shared across these analyzed generations was detected on chromosome 19. Three other QTLs detected by BSA-seq were validated and localized to the 90.93 kb, 2.9 Mb, and 602.08 kb regions of chromosomes 6 and 13, harboring 14, 53, and 4 genes, respectively. Three consistent VGH-related QTLs located on chromosomes 2 and 19 were detected in a minimum of three environments, while an additional six loci on chromosomes 2, 10, 13, and 18 were detected in at least two environments via ICIM mapping. Of all the detected loci, five had been reported previously whereas seven represent novel QTLs. Together, these data offer new insights into the genetic basis of the VGH in soybean plants, providing a rational basis to inform the use of wild accessions in future breeding efforts.

A combination of ultrasound and contrast-enhanced ultrasound improves diagnostic accuracy for the differentiation of cervical tuberculous lymphadenitis from primary lymphoma.

OBJECTIVES: To present a method combining ultrasound (US) and contrast-enhanced ultrasound (CEUS) features for differential diagnosis of cervical tuberculous lymphadenitis (CTL) and primary lymphoma. METHODS: A total of 155 patients with CTL (n = 49) and lymphoma (n = 106) who underwent US and CEUS were retrospectively included. The features extracted from US and CEUS and the significant clinical data were created three models using the least absolute shrinkage and selection operator and logistic regression analysis. The diagnostic performance of the models was assessed using the area under the curve (AUC). RESULTS: The combined model outperformed US model and CEUS model in distinguish CTL from lymphoma achieved favorable performances in training set and validation set with AUCs of 0.958 and 0.946 as well as high accuracies (91.7% and 87.2%), sensitivities (95.9% and 84.4%) and specificities (82.4% and 93.3%). Delong's test showed that among the three models, combined model was significantly different from the other two models in training set (p = 0.011 and 0.029, respectively) and validation set (p = 0.018 and 0.001, respectively). CONCLUSIONS: A combination of US and CEUS achieved good diagnostic performance in differentiating lymphoma and CTL, which might aid in clinical decision-making.

Ultrasonographic Findings and Prognosis of Metastases to the Thyroid Gland.

Metastases to the thyroid gland (MTT) are uncommon in clinical practice. The ultrasound (US) features are easily confused with primary thyroid malignancy, Hashimoto's thyroiditis, and other thyroid diseases. Therefore, this study aimed to assess the role of US and analysis of prognosis of MTT. A total of 45 patients with MTT in the database between July 2009 and February 2022 at the Fujian Cancer Hospital were reviewed. US examinations were performed only on 20 patients, who were finally included in our study. Among the 20 patients, nine were male, and eleven were female. According to US characteristics, metastases to the thyroid gland were divided into nodular and diffuse types (17 and 3 cases, respectively). Three lesions (17.6%) had circumscribed margins, and 14 (82.4%) were uncircumscribed. Three lesions (17.6%) were regular in shape, and 14 (82.4%) were irregular. Nine metastases (52.9%) were a taller-than-wide shape, and eight (47.1%) were not a taller-than-wide shape. Ten lesions (58.8%) had rich vascularity, and seven (41.2%) had absence/not rich vascularity. The mean overall survival (OS) from the time of MTT diagnosis was 22 months (95% confidence interval: 5.95-38.05). The 1-, 3-, and 5-year OS after metastasis was 68.1%, 25.5%, and 17%, respectively. The prognosis of MTT was poor, which is closely related to the characteristics of the primary tumor and metastatic disease. The US findings and US-guided core needle biopsy may be useful in diagnosing MTT in patients with a history of the malignant tumors.

Resol/triblock copolymer composite-guided smart fabrication of carbonized mesopores for efficiently decoding exosomal glycans.

Soft-template carbonized mesopores were developed for the purpose of enriching urinary exosomal glycans through organic-organic self-assembly using block copolymers and resol precursors. With a high surface area of 229 m2 g-1, a small pore size of 3.1 nm, and a significant amount of carbon that specifically interacts with oligosaccharides in glycans, this carbonized mesopore material exhibits high selectivity and low limits of detection (5 ng µL-1) towards glycans. Our analysis of complex urine samples from healthy volunteers and bladder carcinoma patients successfully profiled 48 and 56 exosomal glycans, respectively, and 16 of them were significantly changed. Moreover, one upregulated bisecting N-acetylglucosamine (GlcNAc)-type glycan with core fucose, two upregulated and two downregulated terminal-sialylated glycans were revealed to be linked to bladder carcinoma. This approach is of significant importance for understanding diseases that arise from protein glycosylation mutations, and it may contribute to the development of novel diagnostic and therapeutic strategies for bladder carcinoma.

Drug repurposing screens to identify potential drugs for chronic kidney disease by targeting prostaglandin E2 receptor.

Renal inflammation and fibrosis are significantly correlated with the deterioration of kidney function and result in chronic kidney disease (CKD). However, current therapies only delay disease progression and have limited treatment effects. Hence, the development of innovative therapeutic approaches to mitigate the progression of CKD has become an attractive issue. To date, the incidence of CKD is still increasing, and the biomarkers of the pathophysiologic processes of CKD are not clear. Therefore, the identification of novel therapeutic targets associated with the progression of CKD is an attractive issue. It is a critical necessity to discover new therapeutics as nephroprotective strategies to stop CKD progression. In this research, we focus on targeting a prostaglandin E2 receptor (EP2) as a nephroprotective strategy for the development of additional anti-inflammatory or antifibrotic strategies for CKD. The in silico study identified that ritodrine, dofetilide, dobutamine, and citalopram are highly related to EP2 from the results of chemical database virtual screening. Furthermore, we found that the above four candidate drugs increased the activation of autophagy in human kidney cells, which also reduced the expression level of fibrosis and NLRP3 inflammasome activation. It is hoped that these findings of the four candidates with anti-NLRP3 inflammasome activation and antifibrotic effects will lead to the development of novel therapies for patients with CKD in the future.

Three-Stage Global Channel Pruning for Resources-Limited Platform.

Deep neural networks (DNNs) have demonstrated remarkable performance in many fields, and deploying them on resource-limited devices has drawn more and more attention in industry and academia. Typically, there are great challenges for intelligent networked vehicles and drones to deploy object detection tasks due to the limited memory and computing power of embedded devices. To meet these challenges, hardware-friendly model compression approaches are required to reduce model parameters and computation. Three-stage global channel pruning, which involves sparsity training, channel pruning, and fine-tuning, is very popular in the field of model compression for its hardware-friendly structural pruning and ease of implementation. However, existing methods suffer from problems such as uneven sparsity, damage to the network structure, and reduced pruning ratio due to channel protection. To solve these issues, the present article makes the following significant contributions. First, we present an element-level heatmap-guided sparsity training method to achieve even sparsity, resulting in higher pruning ratio and improved performance. Second, we propose a global channel pruning method that fuses both global and local channel importance metrics to identify unimportant channels for pruning. Third, we present a channel replacement policy (CRP) to protect layers, ensuring that the pruning ratio can be guaranteed even under high pruning rate conditions. Evaluations show that our proposed method significantly outperforms the state-of-the-art (SOTA) methods in terms of pruning efficiency, making it more suitable for deployment on resource-limited devices.