ABSTRACT
The chicken embryo chorioallantoic membrane (CAM) model has played a crucial role in various aspects of cancer research. The purpose of this study is to help researchers clarify the research direction and prospects of the CAM model. A bibliometric analysis was conducted on the top 100 most cited articles on use of the CAM model in tumour research, retrieved from the Web of Science Core Collection database. Tools such as Bibliometrix, VOSviewer, CiteSpace and Excel were utilized for the visualization network analysis. The 100 articles analysed were mainly from the USA, China and European countries such as Germany and France. Tumour research involving CAM model experiments demonstrated reliability and scientific rigor (average citation count = 156.2). The analysis of keywords, topics and subject areas revealed that the applications of this model ranged from the biological characteristics of tumours to molecular mechanisms and signaling pathways, to recent developments in nanotechnology and clinical applications. Additionally, nude mouse experiments have been more frequently performed in recent years. We conclude that the CAM model is efficient, simple and cost-effective, and has irreplaceable value in various aspects of cancer research. In the future, the CAM model can further contribute to nanotechnology research.
ABSTRACT
BACKGROUND: The quality of low-light endoscopic images involves applications in medical disciplines such as physiology and anatomy for the identification and judgement of tissue structures. Due to the use of point light sources and the constraints of narrow physiological structures, medical endoscopic images display uneven brightness, low contrast, and a lack of texture information, presenting diagnostic challenges for physicians. METHODS: In this paper, a nonlinear brightness enhancement and denoising network based on Retinex theory is designed to improve the brightness and details of low-light endoscopic images. The nonlinear luminance enhancement module uses higher-order curvilinear functions to improve overall brightness; the dual-attention denoising module captures detailed features of anatomical structures; and the color loss function mitigates color distortion. RESULTS: Experimental results on the Endo4IE dataset demonstrate that the proposed method outperforms existing state-of-the-art methods in terms of Peak Signal-to-Noise Ratio (PSNR), Structural Similarity (SSIM), and Learned Perceptual Image Patch Similarity (LPIPS). The PSNR is 27.2202, SSIM is 0.8342, and the LPIPS is 0.1492. It provides a method to enhance image quality in clinical diagnosis and treatment. CONCLUSIONS: It offers an efficient method to enhance images captured by endoscopes and offers valuable insights into intricate human physiological structures, which can effectively assist clinical diagnosis and treatment.
Subject(s)
Signal-To-Noise Ratio , Humans , Endoscopy/methods , Image Enhancement/methods , Algorithms , Nonlinear Dynamics , Image Processing, Computer-Assisted/methodsABSTRACT
Bedaquiline (BDQ), a first-in-class diarylquinoline anti-tuberculosis drug, and its analogue, TBAJ-587, prevent the growth and proliferation of Mycobacterium tuberculosis by inhibiting ATP synthase1,2. However, BDQ also inhibits human ATP synthase3. At present, how these compounds interact with either M. tuberculosis ATP synthase or human ATP synthase is unclear. Here we present cryogenic electron microscopy structures of M. tuberculosis ATP synthase with and without BDQ and TBAJ-587 bound, and human ATP synthase bound to BDQ. The two inhibitors interact with subunit a and the c-ring at the leading site, c-only sites and lagging site in M. tuberculosis ATP synthase, showing that BDQ and TBAJ-587 have similar modes of action. The quinolinyl and dimethylamino units of the compounds make extensive contacts with the protein. The structure of human ATP synthase in complex with BDQ reveals that the BDQ-binding site is similar to that observed for the leading site in M. tuberculosis ATP synthase, and that the quinolinyl unit also interacts extensively with the human enzyme. This study will improve researchers' understanding of the similarities and differences between human ATP synthase and M. tuberculosis ATP synthase in terms of the mode of BDQ binding, and will allow the rational design of novel diarylquinolines as anti-tuberculosis drugs.
Subject(s)
Antitubercular Agents , Diarylquinolines , Imidazoles , Mitochondrial Proton-Translocating ATPases , Mycobacterium tuberculosis , Piperidines , Pyridines , Humans , Antitubercular Agents/pharmacology , Antitubercular Agents/chemistry , Binding Sites , Cryoelectron Microscopy , Diarylquinolines/chemistry , Diarylquinolines/pharmacology , Imidazoles/chemistry , Imidazoles/pharmacology , Mitochondrial Proton-Translocating ATPases/antagonists & inhibitors , Mitochondrial Proton-Translocating ATPases/chemistry , Mitochondrial Proton-Translocating ATPases/metabolism , Mitochondrial Proton-Translocating ATPases/ultrastructure , Models, Molecular , Mycobacterium tuberculosis/enzymology , Mycobacterium tuberculosis/drug effects , Piperidines/chemistry , Piperidines/pharmacology , Protein Subunits/metabolism , Protein Subunits/chemistry , Protein Subunits/antagonists & inhibitors , Pyridines/chemistry , Pyridines/pharmacologyABSTRACT
Chitosan exhibits good biocompatibility and some antibacterial activity, making it a popular choice in biomedicine, personal care products, and food packaging. Despite its advantages, the limited antibacterial effectiveness of chitosan hinders its widespread use. Introducing a six-membered heterocyclic structure through chemical modification can significantly enhance its antimicrobial properties and broaden its potential applications. In order to explore the effect of six-membered heterocyclic structure on the antibacterial and antibiofilm activities of chitosan. In this study, seven chitosan derivatives containing six-membered heterocyclics were prepared. They were characterized using Fourier transform infrared (FT-IR) spectroscopy, nuclear magnetic resonance (NMR) spectroscopy, and elemental analysis. Cell viability assay showed that they were non-toxic. The antibacterial and antibiofilm activities against Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) were evaluated. Our research findings demonstrate that increasing the hydrophobicity, alkalinity and charge density of the substitute groups improved the antibacterial and antibiofilm activities of chitosan. This study also offers valuable insights into the quantitative structure-activity relationships of chitosan derivatives in terms of antibacterial and antibiofilm activities.
ABSTRACT
In this study, three types of dodecyl chitosan quaternary ammonium salts, each with different spacer groups were synthesized. These chitosan derivatives are N',N'-dimethyl-N'-dodecyl-ammonium chloride-N-amino-acetyl chitosan (DMDAC), N'-dodecyl-N-isonicotinyl chitosan chloride (DINCC) and N',N'-dimethyl-N'-dodecyl-ammonium chloride-N-benzoyl chitosan (DMDBC). The synthesized products were characterized using Fourier transform infrared spectrometers, nuclear magnetic resonance, thermogravimetric analysis, and elemental analysis. The antibacterial and antibiofilm activities against Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) were investigated. The experimental results indicated that the introduction of hydrophobic groups of spacer groups could enhance the antibacterial and antibiofilm activities of the chitosan derivatives. The antibacterial rates of the chitosan derivatives were over 90 % for both E. coli and S. aureus at a concentration of 0.5 mg/mL. The chitosan derivatives removed >50 % of the mature biofilm of E. coli and over 90 % of the mature biofilm of S. aureus at a concentration of 2.5 mg/mL. Further, the synthesized chitosan derivatives were determined to be non-toxic to L929 cells. Among them, DMDBC exhibited the most promising overall performance and show potential for wide-ranging applications in food preservation, disinfectants, medical, and other fields.
ABSTRACT
Chronic infections, including Mycobacterium tuberculosis (Mtb)-caused tuberculosis (TB), can induce host immune exhaustion. However, the key checkpoint molecules involved in this process and the underlying regulatory mechanisms remain largely undefined, which impede the application of checkpoint-based immunotherapy in infectious diseases. Here, through adopting time-of-flight mass cytometry and transcriptional profiling to systematically analyze natural killer (NK) cell surface receptors, we identify leukocyte immunoglobulin like receptor B1 (LILRB1) as a critical checkpoint receptor that defines a TB-associated cell subset (LILRB1+ NK cells) and drives NK cell exhaustion in TB. Mechanistically, Mtb-infected macrophages display high expression of human leukocyte antigen-G (HLA-G), which upregulates and activates LILRB1 on NK cells to impair their functions by inhibiting mitogen-activated protein kinase (MAPK) signaling via tyrosine phosphatases SHP1/2. Furthermore, LILRB1 blockade restores NK cell-dependent anti-Mtb immunity in immuno-humanized mice. Thus, LILRB1-HLA-G axis constitutes a NK cell immune checkpoint in TB and serves as a promising immunotherapy target.
Subject(s)
HLA-G Antigens , Killer Cells, Natural , Leukocyte Immunoglobulin-like Receptor B1 , Mycobacterium tuberculosis , Tuberculosis , Leukocyte Immunoglobulin-like Receptor B1/metabolism , Killer Cells, Natural/immunology , Killer Cells, Natural/metabolism , HLA-G Antigens/metabolism , HLA-G Antigens/genetics , HLA-G Antigens/immunology , Humans , Animals , Tuberculosis/immunology , Tuberculosis/microbiology , Mice , Mycobacterium tuberculosis/immunology , Macrophages/immunology , Macrophages/metabolism , Receptors, Immunologic/metabolism , Receptors, Immunologic/genetics , Antigens, CDABSTRACT
In the process of human aging, significant age-related changes occur in brain tissue. To assist individuals in assessing the degree of brain aging, screening for disease risks, and further diagnosing age-related diseases, it is crucial to develop an accurate method for predicting brain age. This paper proposes a multi-scale feature fusion method called Tri-UNet based on the U-Net network structure, as well as a brain region information fusion method based on multi-channel input networks. These methods address the issue of insufficient image feature learning in brain neuroimaging data. They can effectively utilize features at different scales of MRI and fully leverage feature information from different regions of the brain. In the end, experiments were conducted on the Cam-CAN dataset, resulting in a minimum Mean Absolute Error (MAE) of 7.46. The results demonstrate that this method provides a new approach to feature learning at different scales in brain age prediction tasks, contributing to the advancement of the field and holding significance for practical applications in the context of elderly education.
Subject(s)
Aging , Brain , Magnetic Resonance Imaging , Humans , Magnetic Resonance Imaging/methods , Brain/diagnostic imaging , Aging/physiology , Aged , Middle Aged , Adult , Male , Female , Neuroimaging/methods , Aged, 80 and over , Image Processing, Computer-Assisted/methods , Young Adult , AlgorithmsABSTRACT
BACKGROUND: A long-term follow-up of close contacts to monitor their infection status is essential to formulate a promising screening strategy. The study aimed to assess the dynamics of tuberculosis (TB) infection using Interferon-γ release assay (IGRA) and determine risk factors associated with TB infection. METHODS: Definite TB patients were interviewed and their household contacts were screened for TB infection by IGRA during 12-month longitudinal investigation. RESULTS: We included in our analyses 184 household contacts of 92 index TB patients. 87 individuals (47.3%) in contact group progressed to TB infection, of whom 86 developed into IGRA positive within 24 weeks. Close contacts with a higher age and comorbidities are easier to exhibit TB infection. Analysis showed that risk factors for becoming IGRA-positive individuals included residence, older age, comorbidities, BCG scar and high bacterial load. Contacts with BCG scar had a lower IGRA-positive rate. CONCLUSION: IGRA conversion generally occurs within 24 weeks after exposure. The TB transmission happens since subclinical TB stage and the presence of BCG scar is an independent protective factor reducing risk of TB infection among close contacts. Repeated IGRA tests are sensible to conducted among close contacts at 24 weeks after exposure to identify the IGRA-positive individuals.
Subject(s)
Contact Tracing , Interferon-gamma Release Tests , Tuberculosis , Humans , Male , Female , Adult , Prospective Studies , Middle Aged , Risk Factors , Tuberculosis/epidemiology , Tuberculosis/transmission , Young Adult , Aged , Adolescent , Mycobacterium tuberculosis , Longitudinal Studies , Family CharacteristicsABSTRACT
The most frequent adverse event associated with bedaquiline (BDQ) is the QTc interval prolongation; however, there was no biomarkers that could be used to predict the occurrence of QTc prolongation in BDQ-treated patients. In this study, we employed the ultra-high performance liquid chromatography-MS/MS (UHPLC-MS/MS) to generate metabolic profiling for the discovery of potential predictive urine biomarkers of QTc prolongation in these patients. Untargeted metabolomic technique was used to concentrate the differential metabolic pathway, and targeted metabolomic technique was subsequently performed to identify predictive biomarkers for QTc prolongation. A total of 45 rifampicin-resistant TB (RR-TB) and multidrug-resistant TB (MDR-TB) patients were enrolled in our study, including 15 RR/MDR-TB patients with QTc interval prolongation (QIP) and 30 RR/MDR-TB patients with QTc interval un-prolongations (QIU). Untargeted technique revealed that the lipid metabolism was the most differential metabolic pathway between two groups. Further targeted technique identified four differential metabolites, including betaine, LPE (18:2), LPE (20:3), and LPE (20:4). The combined analysis of metabolisms revealed that the combined use of LPE (20:3) and LPE (20:4) had the best performance for predicting the occurrence of QTc prolongation in TB patients, yielding a sensitivity of 87.4% and a specificity of 78.5%. In addition, with the progression of BDQ treatment, the LPEs exhibited persistent difference in the BDQ-treated TB patients experiencing QTc interval prolongation. In conclusion, our data demonstrate that the combined use of LPE (20:3) and LPE (20:4) yields promising performance for predicting the occurrence of QTc interval prolongation in BDQ-treated patients.
ABSTRACT
Chitosan quaternary phosphine salts (NPCS) were synthesized with enhanced antimicrobial properties using a two-step method. Composite films (CNSP) were prepared by incorporating NPCS and polyvinyl alcohol (PVA) as the base material, citric acid as the crosslinker and functional additive, exhibiting antibacterial and UV-blocking properties. The composite film showed a maximum tensile strength of 20.4 MPa, an elongation at break of 677%, and a UV light barrier transmittance of 70%. Application of these composite membranes in preserving strawberries demonstrated effectiveness in maintaining freshness by preventing water loss, inhibiting microbial growth, and extending shelf life. In addition, the composite film demonstrated biosafety. These results indicate that CNSP composite films holds significant promise for safe and sustainable food packaging applications.
Subject(s)
Chitosan , Citric Acid , Food Packaging , Food Preservation , Fragaria , Polyvinyl Alcohol , Polyvinyl Alcohol/chemistry , Fragaria/chemistry , Chitosan/chemistry , Chitosan/pharmacology , Citric Acid/chemistry , Citric Acid/pharmacology , Food Packaging/instrumentation , Food Preservation/methods , Food Preservation/instrumentation , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/chemistry , Cross-Linking Reagents/chemistry , Tensile StrengthABSTRACT
Drought-induced xylem embolism is a primary cause of plant mortality. Although c. 70% of cycads are threatened by extinction and extant cycads diversified during a period of increasing aridification, the vulnerability of cycads to embolism spread has been overlooked. We quantified the vulnerability to drought-induced embolism, pressure-volume curves, in situ water potentials, and a suite of xylem anatomical traits of leaf pinnae and rachises for 20 cycad species. We tested whether anatomical traits were linked to hydraulic safety in cycads. Compared with other major vascular plant clades, cycads exhibited similar embolism resistance to angiosperms and pteridophytes but were more vulnerable to embolism than noncycad gymnosperms. All 20 cycads had both tracheids and vessels, the proportions of which were unrelated to embolism resistance. Only vessel pit membrane fraction was positively correlated to embolism resistance, contrary to angiosperms. Water potential at turgor loss was significantly correlated to embolism resistance among cycads. Our results show that cycads exhibit low resistance to xylem embolism and that xylem anatomical traits - particularly vessels - may influence embolism resistance together with tracheids. This study highlights the importance of understanding the mechanisms of drought resistance in evolutionarily unique and threatened lineages like the cycads.
Subject(s)
Cycadopsida , Droughts , Plant Leaves , Water , Xylem , Xylem/physiology , Xylem/anatomy & histology , Plant Leaves/anatomy & histology , Plant Leaves/physiology , Cycadopsida/physiology , Cycadopsida/anatomy & histology , Species SpecificityABSTRACT
N-(sodium 2-hydroxypropylsulfonate) chitosan (HSCS), N-sulfonate chitosan (SCS) and N-isonicotinic sulfonate chitosan (ISCS) were prepared. The structures of the prepared chitosan derivatives were characterized by nuclear magnetic resonance (1H NMR) spectroscopy, Fourier transform infrared (FTIR) spectroscopy, ultraviolet-visible (UV-vis) spectroscopy and elemental analysis (EA). Antibacterial and antibiofilm activities of these chitosan derivatives were evaluated in vitro. The minimum inhibitory concentration (MIC) of HSCS and SCS against Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) were 0.625 mg/mL and 0.156 mg/mL, respectively. ISCS exhibited MIC values of 0.313 mg/mL and 0.078 mg/mL against E. coli and S. aureus, respectively. ISCS demonstrated superior antibacterial and antibiofilm properties compared to SCS and HSCS. These findings suggest that the incorporation of a pyridine structure into sulfonate chitosan enhances its antibacterial and antibiofilm activities, and the prepared ISCS has a promising application prospect for controlling the reproduction of microorganisms in the field of food packaging.
Subject(s)
Anti-Bacterial Agents , Biofilms , Chitosan , Escherichia coli , Microbial Sensitivity Tests , Staphylococcus aureus , Chitosan/chemistry , Chitosan/pharmacology , Chitosan/chemical synthesis , Staphylococcus aureus/drug effects , Staphylococcus aureus/physiology , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/chemical synthesis , Anti-Bacterial Agents/chemistry , Biofilms/drug effects , Escherichia coli/drug effects , Sulfonic Acids/chemistry , Sulfonic Acids/pharmacology , Sulfonic Acids/antagonists & inhibitorsABSTRACT
AIM: To assess the performance of macular ganglion cell-inner plexiform layer thickness (mGCIPLT) and 10-2 visual field (VF) parameters in detecting early glaucoma and evaluating the severity of advanced glaucoma. METHODS: Totally 127 eyes from 89 participants (36 eyes of 19 healthy participants, 45 eyes of 31 early glaucoma patients and 46 eyes of 39 advanced glaucoma patients) were included. The relationships between the optical coherence tomography (OCT)-derived parameters and VF sensitivity were determined. Patients with early glaucoma were divided into eyes with or without central 10° of the VF damages (CVFDs), and the diagnostic performances of OCT-derived parameters were assessed. RESULTS: In early glaucoma, the mGCIPLT was significantly correlated with 10-2 VF pattern standard deviation (PSD; with average mGCIPLT: ß=-0.046, 95%CI, -0.067 to -0.024, P<0.001). In advanced glaucoma, the mGCIPLT was related to the 24-2 VF mean deviation (MD; with average mGCIPLT: ß=0.397, 95%CI, 0.199 to 0.595, P<0.001), 10-2 VF MD (with average mGCIPLT: ß=0.762, 95%CI, 0.485 to 1.038, P<0.001) and 24-2 VF PSD (with average mGCIPLT: ß=0.244, 95%CI, 0.124 to 0.364, P<0.001). Except for the minimum and superotemporal mGCIPLT, the decrease of mGCIPLT in early glaucomatous eyes with CVFDs was more severe than that of early glaucomatous eyes without CVFDs. The area under the curve (AUC) of the average mGCIPLT (AUC=0.949, 95%CI, 0.868 to 0.982) was greater than that of the average circumpapillary retinal nerve fiber layer thickness (cpRNFLT; AUC=0.827, 95%CI, 0.674 to 0.918) and rim area (AUC=0.799, 95%CI, 0.610 to 0.907) in early glaucomatous eyes with CVFDs versus normal eyes. CONCLUSION: The 10-2 VF and mGCIPLT parameters are complementary to 24-2 VF, cpRNFLT and ONH parameters, especially in detecting early glaucoma with CVFDs and evaluating the severity of advanced glaucoma in group level.
ABSTRACT
Proper timing of vigilance states serves fundamental brain functions. Although disturbance of sleep onset rapid eye movement (SOREM) sleep is frequently reported after orexin deficiency, their causal relationship still remains elusive. Here, we further study a specific subgroup of orexin neurons with convergent projection to the REM sleep promoting sublaterodorsal tegmental nucleus (OXSLD neurons). Intriguingly, although OXSLD and other projection-labeled orexin neurons exhibit similar activity dynamics during REM sleep, only the activation level of OXSLD neurons exhibits a significant positive correlation with the post-inter-REM sleep interval duration, revealing an essential role for the orexin-sublaterodorsal tegmental nucleus (SLD) neural pathway in relieving REM sleep pressure. Monosynaptic tracing reveals that multiple inputs may help shape this REM sleep-related dynamics of OXSLD neurons. Genetic ablation further shows that the homeostatic architecture of sleep/wakefulness cycles, especially avoidance of SOREM sleep-like transition, is dependent on this activity. A positive correlation between the SOREM sleep occurrence probability and depression states of narcoleptic patients further demonstrates the possible significance of the orexin-SLD pathway on REM sleep homeostasis.
ABSTRACT
The study aimed to create a low loading, high retention, easier to apply O/W mometasone furoate (MF) cream using a chemical enhancer (CE) approach to provide more options for patients with atopic dermatitis (AD) and to investigate molecular mechanisms of its increased release and retention. A Box-Behnken design determined the optimal formulation based on stability and in vitro skin retention. Evaluations included appearance, rheological properties, irritation, in vivo tissue distribution and pharmacodynamics. Molecular mechanisms of enhanced release were studied using high-speed centrifugation, molecular dynamics and rheology. The interaction between the CE, MF and skin was studied by tape stripping, CLSM, ATR-FTIR and SAXS. The formulation was optimized to contain 0.05% MF and used 10% polyglyceryl-3 oleate (POCC) as the CE. There was no significant difference from Elocon® cream in in vivo retention and pharmacodynamics but increased in vivo retention by 3.14-fold and in vitro release by 1.77-fold compared to the basic formulation. POCC reduced oil phase cohesive energy density, enhancing drug mobility and release. It disrupted skin lipid phases, aiding drug entry and formed hydrogen bonds, prolonging retention. This study highlights POCC as a CE in the cream, offering insights for semi-solid formulation development.
Subject(s)
Drug Liberation , Mometasone Furoate , Skin Cream , Skin , Mometasone Furoate/administration & dosage , Mometasone Furoate/pharmacokinetics , Mometasone Furoate/chemistry , Animals , Skin Cream/administration & dosage , Skin Cream/chemistry , Skin/metabolism , Skin/drug effects , Administration, Cutaneous , Male , Skin Absorption/drug effects , Chemistry, Pharmaceutical/methods , Glycerol/chemistry , Glycerol/analogs & derivatives , Dermatitis, Atopic/drug therapy , Female , Excipients/chemistry , Anti-Inflammatory Agents/administration & dosage , Anti-Inflammatory Agents/chemistry , Anti-Inflammatory Agents/pharmacology , Anti-Inflammatory Agents/pharmacokinetics , Drug Compounding/methods , Oleic Acid/chemistry , Polymers/chemistryABSTRACT
Adherent-invasive Escherichia coli (AIEC) strain LF82, isolated from patients with Crohn's disease, invades gut epithelial cells, and replicates in macrophages contributing to chronic inflammation. In this study, we found that RstAB contributing to the colonization of LF82 in a mouse model of chronic colitis by promoting bacterial replication in macrophages. By comparing the transcriptomes of rstAB mutant- and wild-type when infected macrophages, 83 significant differentially expressed genes in LF82 were identified. And we identified two possible RstA target genes (csgD and asr) among the differentially expressed genes. The electrophoretic mobility shift assay and quantitative real-time PCR confirmed that RstA binds to the promoters of csgD and asr and activates their expression. csgD deletion attenuated LF82 intracellular biofilm formation, and asr deletion reduced acid tolerance compared with the wild-type. Acidic pH was shown by quantitative real-time PCR to be the signal sensed by RstAB to activate the expression of csgD and asr. We uncovered a signal transduction pathway whereby LF82, in response to the acidic environment within macrophages, activates transcription of the csgD to promote biofilm formation, and activates transcription of the asr to promote acid tolerance, promoting its replication within macrophages and colonization of the intestine. This finding deepens our understanding of the LF82 replication regulation mechanism in macrophages and offers new perspectives for further studies on AIEC virulence mechanisms.
Subject(s)
Bacterial Adhesion , Biofilms , Escherichia coli Infections , Escherichia coli Proteins , Escherichia coli , Gene Expression Regulation, Bacterial , Macrophages , Macrophages/microbiology , Animals , Mice , Escherichia coli/genetics , Escherichia coli/pathogenicity , Escherichia coli/metabolism , Escherichia coli Proteins/genetics , Escherichia coli Proteins/metabolism , Biofilms/growth & development , Escherichia coli Infections/microbiology , Humans , Hydrogen-Ion Concentration , Virulence , Colitis/microbiology , Crohn Disease/microbiology , Disease Models, Animal , Signal Transduction , Acids/metabolismABSTRACT
Combination therapy is a promising strategy for the successful treatment of cancer. The large number of possible combinations, however, mean that it is laborious and expensive to screen for synergistic drug combinations in vitro. Nevertheless, because of the availability of high-throughput screening data and advances in computational techniques, deep learning (DL) can be a useful tool for the prediction of synergistic drug combinations. In this study, we proposed a multimodal DL framework, MMSyn, for the prediction of synergistic drug combinations. First, features embedded in the drug molecules were extracted: structure, fingerprint, and string encoding. Then, gene expression data, DNA copy number, and pathway activity were used to describe cancer cell lines. Finally, these processed features were integrated using an attention mechanism and an interaction module and then input into a multilayer perceptron to predict drug synergy. Experimental results showed that our method outperformed five state-of-the-art DL methods and three traditional machine learning models for drug combination prediction. We verified that MMSyn achieved superior performance in stratified cross-validation settings using both the drug combination and cell line data. Moreover, we performed a set of ablation experiments to illustrate the effectiveness of each component and the efficacy of our model. In addition, our visual representation and case studies further confirmed the effectiveness of our model. All results showed that MMSyn can be used as a powerful tool for the prediction of synergistic drug combinations.
Subject(s)
Deep Learning , Drug Synergism , Humans , Cell Line, Tumor , Drug Combinations , Antineoplastic Agents/pharmacology , Antineoplastic Agents/chemistryABSTRACT
OBJECTIVE: Clinical trials involve the collection of a wealth of data, comprising multiple diverse measurements performed at baseline and follow-up visits over the course of a trial. The most common primary analysis is restricted to a single, potentially composite endpoint at one time point. While such an analytical focus promotes simple and replicable conclusions, it does not necessarily fully capture the multi-faceted effects of a drug in a complex disease setting. Therefore, to complement existing approaches, we set out here to design a longitudinal multivariate analytical framework that accepts as input an entire clinical trial database, comprising all measurements, patients, and time points across multiple trials. METHODS: Our framework composes probabilistic principal component analysis with a longitudinal linear mixed effects model, thereby enabling clinical interpretation of multivariate results, while handling data missing at random, and incorporating covariates and covariance structure in a computationally efficient and principled way. RESULTS: We illustrate our approach by applying it to four phase III clinical trials of secukinumab in Psoriatic Arthritis (PsA) and Rheumatoid Arthritis (RA). We identify three clinically plausible latent factors that collectively explain 74.5% of empirical variation in the longitudinal patient database. We estimate longitudinal trajectories of these factors, thereby enabling joint characterisation of disease progression and drug effect. We perform benchmarking experiments demonstrating our method's competitive performance at estimating average treatment effects compared to existing statistical and machine learning methods, and showing that our modular approach leads to relatively computationally efficient model fitting. CONCLUSION: Our multivariate longitudinal framework has the potential to illuminate the properties of existing composite endpoint methods, and to enable the development of novel clinical endpoints that provide enhanced and complementary perspectives on treatment response.
Subject(s)
Arthritis, Psoriatic , Arthritis, Rheumatoid , Humans , Arthritis, Rheumatoid/drug therapy , Arthritis, Psoriatic/drug therapy , Longitudinal Studies , Treatment Outcome , Antibodies, Monoclonal, Humanized/therapeutic use , Principal Component Analysis , Clinical Trials as Topic , Clinical Trials, Phase III as Topic , Models, StatisticalABSTRACT
Uropathogenic Escherichia coli (UPEC) is the most common causative agent of urinary tract infection (UTI). UPEC invades bladder epithelial cells (BECs) via fusiform vesicles, escapes into the cytosol, and establishes biofilm-like intracellular bacterial communities (IBCs). Nucleoside-diphosphate kinase (NDK) is secreted by pathogenic bacteria to enhance virulence. However, whether NDK is involved in UPEC pathogenesis remains unclear. Here, we find that the lack of ndk impairs the colonization of UPEC CFT073 in mouse bladders and kidneys owing to the impaired ability of UPEC to form IBCs. Furthermore, we demonstrate that NDK inhibits caspase-1-dependent pyroptosis by consuming extracellular ATP, preventing superficial BEC exfoliation, and promoting IBC formation. UPEC utilizes the reactive oxygen species (ROS) sensor OxyR to indirectly activate the regulator integration host factor, which then directly activates ndk expression in response to intracellular ROS. Here, we reveal a signaling transduction pathway that UPEC employs to inhibit superficial BEC exfoliation, thus facilitating acute UTI.