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1.
Mol Carcinog ; 2024 Jun 05.
Article En | MEDLINE | ID: mdl-38837427

Regorafenib is a second-line standard treatment for hepatocellular carcinoma (HCC). However, the efficacy of regorafenib is often limited due to drug resistance, individual differences among patients, and irrational drug use. Radiotherapy (RT) is an important method of localized HCC treatment, and combining RT with other therapies may exert a synergetic antitumor effect. Platelet-derived growth factor receptor-like (PDGFRL) is a tumor suppressor in various solid tumors. However, the function of PDGFRL in HCC is still unknown. In this study, we explored whether regorafenib and RT exert a synergetic effect on the treatment of HCC. The antitumor effect and mechanisms of the combination of regorafenib and RT were verified in a xenograft mouse model in vivo and in HCC cells in vitro. The combination treatment significantly inhibited cell proliferation and promoted apoptosis both in vitro and in vivo. PDGFRL, a potential target of regorafenib, was increased after cumulative treatment in HCC cells, and PDGFRL suppressed HCC cell proliferation and promoted apoptosis by inhibiting STAT3 pathway activation. Furthermore, the cumulative antitumor effect was dependent on the upregulated expression of PDGFRL and inhibition of STAT3 signaling pathway activation in HCC cells. This study increased the understanding of the molecular mechanism underlying the effect of regorafenib plus RT on HCC and provided a theoretical basis for the clinical practice of HCC.

2.
Comput Struct Biotechnol J ; 23: 2173-2189, 2024 Dec.
Article En | MEDLINE | ID: mdl-38827229

The vast neuronal diversity in the human neocortex is vital for high-order brain functions, necessitating elucidation of the regulatory mechanisms underlying such unparalleled diversity. However, recent studies have yet to comprehensively reveal the diversity of neurons and the molecular logic of neocortical origin in humans at single-cell resolution through profiling transcriptomic or epigenomic landscapes, owing to the application of unimodal data alone to depict exceedingly heterogeneous populations of neurons. In this study, we generated a comprehensive compendium of the developing human neocortex by simultaneously profiling gene expression and open chromatin from the same cell. We computationally reconstructed the differentiation trajectories of excitatory projection neurons of cortical origin and inferred the regulatory logic governing lineage bifurcation decisions for neuronal diversification. We demonstrated that neuronal diversity arises from progenitor cell lineage specificity and postmitotic differentiation at distinct stages. Our data paves the way for understanding the primarily coordinated regulatory logic for neuronal diversification in the neocortex.

3.
Adv Mater ; : e2404618, 2024 Jun 09.
Article En | MEDLINE | ID: mdl-38853427

Photocatalytic solar hydrogen generation, encompassing both overall water splitting and organic reforming, presents a promising avenue for green hydrogen production. This technology holds the potential for reduced capital costs in comparison to competing methods like photovoltaic-electrocatalysis and photoelectrocatalysis, owing to its simplicity and fewer auxiliary components. However, the current solar-to-hydrogen efficiency of photocatalytic solar hydrogen production has predominantly remained low at around 1-2% or lower, mainly due to curtailed access to the entire solar spectrum, thus impeding practical application of photocatalytic solar hydrogen production. This review offers an integrated, multidisciplinary perspective on photocatalytic solar hydrogen production. Specifically, the review presents the existing approaches in photocatalyst and system designs aimed at significantly boosting the solar-to-hydrogen efficiency, while also considering factors of cost and scalability of each approach. In-depth discussions extending beyond the efficacy of material and system design strategies are particularly vital to identify potential hurdles in translating photocatalysis research to large-scale applications. Ultimately, this review aims to provide understanding and perspective of feasible pathways for commercialising photocatalytic solar hydrogen production technology, considering both engineering and economic standpoints. This article is protected by copyright. All rights reserved.

4.
ACS Appl Mater Interfaces ; 16(20): 25686-25697, 2024 May 22.
Article En | MEDLINE | ID: mdl-38739862

Polypropylene (PP) mesh is commonly used in repairing abdominal wall hernia (AWH). However, the use of synthetic prosthesis comes with the risk of developing a prosthetic infection, resulting in delayed healing, secondary surgery, and potentially increased mortality. To address these issues, a facile surface functionalization strategy for PP mesh based on phytic acid (PA) and polyhexamethylene guanidine (PHMG) was constructed through a one-step co-deposition process, referred to as the PA/PHMG coating. The development of PA/PHMG coating is mainly attributed to the surface affinity of PA and the electrostatic interactions between PA and PHMG. The PA/PHMG coating could be completed within 4 h under mild conditions. The prepared PA/PHMG coatings on PP mesh surfaces exhibited desirable biocompatibility toward mammalian cells and excellent antibacterial properties against the notorious "superbug" methicillin-resistant Staphylococcus aureus (MRSA) and tetracycline-resistant Escherichia coli (TRE). The PA/PHMG-coated PP meshes showed killing ratios of over 99% against MRSA in an infected abdominal wall hernia repair model. Furthermore, histological and immunohistochemical analysis revealed a significantly attenuated degree of neutrophil infiltration in the PA/PHMG coating group, attributed to the decreased bacterial numbers alleviating the inflammatory response at the implant sites. Meanwhile, the pristine PP and PA/PHMG-coated meshes showed effective tissue repair, with the PA/PHMG coating group exhibiting enhanced angiogenesis compared with pristine PP meshes, suggesting superior tissue restoration. Additionally, PP meshes with the highest PHMG weight ratio (PA/PHMG(3)) exhibited excellent long-term robustness under phosphate-buffered saline (PBS) immersion with a killing ratio against MRSA still exceeding 95% after 60 days of PBS immersion. The present work provides a facile and promising approach for developing antibacterial implants.


Anti-Bacterial Agents , Methicillin-Resistant Staphylococcus aureus , Polypropylenes , Surgical Mesh , Polypropylenes/chemistry , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/chemistry , Methicillin-Resistant Staphylococcus aureus/drug effects , Animals , Escherichia coli/drug effects , Herniorrhaphy/instrumentation , Abdominal Wall/surgery , Abdominal Wall/pathology , Coated Materials, Biocompatible/chemistry , Coated Materials, Biocompatible/pharmacology , Mice , Hernia, Abdominal/surgery , Humans , Microbial Sensitivity Tests
5.
Methods ; 226: 164-175, 2024 Jun.
Article En | MEDLINE | ID: mdl-38702021

Ensuring the safety and efficacy of chemical compounds is crucial in small-molecule drug development. In the later stages of drug development, toxic compounds pose a significant challenge, losing valuable resources and time. Early and accurate prediction of compound toxicity using deep learning models offers a promising solution to mitigate these risks during drug discovery. In this study, we present the development of several deep-learning models aimed at evaluating different types of compound toxicity, including acute toxicity, carcinogenicity, hERG_cardiotoxicity (the human ether-a-go-go related gene caused cardiotoxicity), hepatotoxicity, and mutagenicity. To address the inherent variations in data size, label type, and distribution across different types of toxicity, we employed diverse training strategies. Our first approach involved utilizing a graph convolutional network (GCN) regression model to predict acute toxicity, which achieved notable performance with Pearson R 0.76, 0.74, and 0.65 for intraperitoneal, intravenous, and oral administration routes, respectively. Furthermore, we trained multiple GCN binary classification models, each tailored to a specific type of toxicity. These models exhibited high area under the curve (AUC) scores, with an impressive AUC of 0.69, 0.77, 0.88, and 0.79 for predicting carcinogenicity, hERG_cardiotoxicity, mutagenicity, and hepatotoxicity, respectively. Additionally, we have used the approved drug dataset to determine the appropriate threshold value for the prediction score in model usage. We integrated these models into a virtual screening pipeline to assess their effectiveness in identifying potential low-toxicity drug candidates. Our findings indicate that this deep learning approach has the potential to significantly reduce the cost and risk associated with drug development by expediting the selection of compounds with low toxicity profiles. Therefore, the models developed in this study hold promise as critical tools for early drug candidate screening and selection.


Deep Learning , Humans , Drug Discovery/methods , Animals , Drug-Related Side Effects and Adverse Reactions , Cardiotoxicity/etiology
6.
PLoS Pathog ; 20(5): e1012214, 2024 May.
Article En | MEDLINE | ID: mdl-38722857

Epithelial cells function as the primary line of defense against invading pathogens. However, bacterial pathogens possess the ability to compromise this barrier and facilitate the transmigration of bacteria. Nonetheless, the specific molecular mechanism employed by Mycobacterium tuberculosis (M.tb) in this process is not fully understood. Here, we investigated the role of Rv2569c in M.tb translocation by assessing its ability to cleave E-cadherin, a crucial component of cell-cell adhesion junctions that are disrupted during bacterial invasion. By utilizing recombinant Rv2569c expressed in Escherichia coli and subsequently purified through affinity chromatography, we demonstrated that Rv2569c exhibited cell wall-associated serine protease activity. Furthermore, Rv2569c was capable of degrading a range of protein substrates, including casein, fibrinogen, fibronectin, and E-cadherin. We also determined that the optimal conditions for the protease activity of Rv2569c occurred at a temperature of 37°C and a pH of 9.0, in the presence of MgCl2. To investigate the function of Rv2569c in M.tb, a deletion mutant of Rv2569c and its complemented strains were generated and used to infect A549 cells and mice. The results of the A549-cell infection experiments revealed that Rv2569c had the ability to cleave E-cadherin and facilitate the transmigration of M.tb through polarized A549 epithelial cell layers. Furthermore, in vivo infection assays demonstrated that Rv2569c could disrupt E-cadherin, enhance the colonization of M.tb, and induce pathological damage in the lungs of C57BL/6 mice. Collectively, these results strongly suggest that M.tb employs the serine protease Rv2569c to disrupt epithelial defenses and facilitate its systemic dissemination by crossing the epithelial barrier.


Bacterial Proteins , Cadherins , Epithelial Cells , Mycobacterium tuberculosis , Serine Proteases , Cadherins/metabolism , Mycobacterium tuberculosis/pathogenicity , Mycobacterium tuberculosis/metabolism , Animals , Humans , Mice , Serine Proteases/metabolism , Serine Proteases/genetics , Epithelial Cells/metabolism , Epithelial Cells/microbiology , Bacterial Proteins/metabolism , Bacterial Proteins/genetics , A549 Cells , Tuberculosis/microbiology , Tuberculosis/metabolism , Female
7.
Epilepsy Behav ; 157: 109850, 2024 May 30.
Article En | MEDLINE | ID: mdl-38820682

BACKGROUND: Physical activity may be associated with health benefits for people with epilepsy. It remains unclear how the prevalence of physical activity has changed at a national level over the years and whether this prevalence varies between subgroups. METHODS: The National Health and Interview Survey, which was conducted from 2010 to 2017 and again in 2022, was used for our nationally representative study. This study explored the trends and disparities in meeting physical activity guidelines among US individuals with epilepsy and non-epilepsy adults. RESULTS: The prevalence of adults with epilepsy meeting physical activity guidelines was consistently lower and remained unchanged compared to those without epilepsy. Among the population with epilepsy, the prevalence of aerobic physical activity was 38.1 % (95 % CI, 32.6 %-43.5 %) in 2010 and 39.0 % (95 % CI, 33.4 %-44.7 %) in 2017 (P for trend = 0.84), and remained unchanged in 2022 (39.1 %). For muscle-strength training, the prevalence was 17.5 % (95 % CI, 13.3 %-21.7 %) in 2010 and 18.8 % (95 % CI, 14.8 %-22.8 %) in 2017 (P for trend = 0.82). The prevalence for both activities combined was 12.4 % (95 % CI, 8.7 %-16.2 %) in 2010 and 16.6 % (95 % CI, 12.8 %-20.5 %) in 2017 (P for trend = 0.26). The prevalence of aerobic physical activity varied by educational attainment, body mass index, comorbid conditions, alcohol-drinking status, and epilepsy status. CONCLUSION: This study suggests that the adherence rate to meeting physical activity guidelines among US adults with epilepsy was at a low level and had not improved over time. This finding highlights the need for additional nationwide efforts to promote physical activity in the US population with epilepsy.

8.
J Autoimmun ; 146: 103231, 2024 Jun.
Article En | MEDLINE | ID: mdl-38692170

OBJECTIVE: To investigate the association between autoimmune diseases (AIDs) and bladder cancer (BC) at the genetic level using Mendelian randomization (MR). METHODS: Single nucleotide polymorphisms (SNPs) associated with the seven AIDs were extracted from the IEU GWAS database, and the SNPs were quality-controlled using strict screening criteria. The association between AIDs and BC risk was assessed by inverse-variance weighted (IVW), MR-Egger regression and Weighted median method. The heterogeneity of SNPs was evaluated by Cochran Q test. MR-Egger intercept test and MR-PRESSO global test were used to test the horizontal pleiotropy of SNPs. Both sides with potential causal associations were validated using the validation set. RESULTS: Our result showed that genetically predicted RA was significantly associated with an increased risk of BC (IVW OR = 1.214, 95 % CI = 1.062-1.388, P = 0.005). MS nominally increased the risk of BC (IVW OR = 1.095, 95 % CI = 1.005-1.193, P = 0.037), consistent with the results of the MR analysis of the BC validation cohort. However SLE, T1D, UC, CD, and MG were not causally associated with BC risk (P > 0.05). The sensitivity analyses showed that there was no heterogeneity or horizontal pleiotropy in our findings. CONCLUSION: This study provides evidence of a causal relationship between AIDs and BC risk at the genetic level, confirming a causal relationship between RA and MS in increasing the risk of BC.


Autoimmune Diseases , Genetic Predisposition to Disease , Genome-Wide Association Study , Mendelian Randomization Analysis , Polymorphism, Single Nucleotide , Urinary Bladder Neoplasms , Humans , Urinary Bladder Neoplasms/genetics , Urinary Bladder Neoplasms/epidemiology , Autoimmune Diseases/genetics , Autoimmune Diseases/epidemiology , Risk Factors
9.
Front Biosci (Landmark Ed) ; 29(5): 200, 2024 May 22.
Article En | MEDLINE | ID: mdl-38812311

AIMS: Changes in myocardial mitochondrial morphology and function in premature ventricular contractions (PVCs)-induced cardiomyopathy (PVCCM) remain poorly studied. Here, we investigated the effects of PVCs with different coupling intervals (CIs) on myocardial mitochondrial remodelling in a canine model of PVCCM. METHODS AND RESULTS: Twenty-one beagles underwent pacemaker implantation and were randomised into the sham (n = 7), short-coupled PVCs (SCP, n = 7), and long-coupled PVCs (LCP, n = 7) groups. Right ventricular (RV) apical bigeminy was produced for 12-week to induce PVCCM in the SCP (CI, 250 ms) and LCP (CI, 350 ms) groups. Echocardiography was performed at baseline and biweekly thereafter to evaluate cardiac function. Masson's trichrome staining measured ventricular interstitial fibrosis. The ultrastructural morphology of the myocardial mitochondria was analysed using transmission electron microscopy. Mitochondrial Ca2+ concentration, reactive oxygen species (ROS) levels, adenosine triphosphate (ATP) content, membrane potential, and electron transport chain (ETC) complex activity were measured to assess myocardial mitochondrial function. Twelve-week-PVCs led to left ventricular (LV) enlargement with systolic dysfunction, disrupted mitochondrial morphology, increased mitochondrial Ca2+ concentration and ROS levels, decreased mitochondrial ATP content and membrane potential, and impaired ETC complex activity in both the SCP and LCP groups (all p < 0.01 vs the sham group). Ventricular fibrosis was observed only in canines with LCP. Worse cardiac function and more pronounced abnormalities in mitochondrial morphology and function were observed in the LCP group than to the SCP group (all p < 0.05). CONCLUSION: We demonstrated myocardial mitochondrial abnormalities in dogs with PVCCM, characterised by abnormal mitochondrial morphology, mitochondrial Ca2+ overload, oxidative stress, and impaired mitochondrial energy metabolism. Compared to SCP, long-term LCP exposure resulted in more severe mitochondrial remodelling and cardiac dysfunction in dogs.


Calcium , Cardiomyopathies , Disease Models, Animal , Mitochondria, Heart , Reactive Oxygen Species , Ventricular Premature Complexes , Animals , Dogs , Mitochondria, Heart/metabolism , Mitochondria, Heart/ultrastructure , Mitochondria, Heart/pathology , Cardiomyopathies/physiopathology , Cardiomyopathies/metabolism , Cardiomyopathies/pathology , Cardiomyopathies/etiology , Ventricular Premature Complexes/physiopathology , Ventricular Premature Complexes/metabolism , Reactive Oxygen Species/metabolism , Calcium/metabolism , Male , Adenosine Triphosphate/metabolism , Membrane Potential, Mitochondrial , Echocardiography
10.
PLoS One ; 19(5): e0303387, 2024.
Article En | MEDLINE | ID: mdl-38728351

Heavy metal pollution in farmland soil represents a considerable risk to ecosystems and human health, constituting a global concern. Focusing on a key area for the cultivation of special agricultural products in Cangxi County, we collected 228 surface soil samples. We analyzed the concentration, spatial distribution, and pollution levels of six heavy metals (Cr, Cu, Pb, Ni, Zn, and Hg) in the soil. Moreover, we investigated the sources and contribution rates of these heavy metals using Principal Component Analysis/Absolute Principal Component Scores (PCA/APCS) and Positive Matrix Factorization (PMF) models. Our findings indicate that none of the six metals exceeded the pollution thresholds for farmland soils. However, the mean concentrations of Cr and Ni surpassed the background levels of Sichuan Province. A moderate spatial correlation existed between Pb and Ni, attributable to both natural and anthropogenic factors, whereas Zn, Cu, Hg, and Cr displayed a strong spatial correlation, mainly due to natural factors. The spatial patterns of Cr, Cu, Zn, Pb, and Ni were similar, with higher concentrations in the northern and eastern regions and lower concentrations centrally. Hg's spatial distribution differed, exhibiting a broader range of lower values. The single pollution index evaluation showed that Cr and Ni were low pollution, and the other elements were no pollution. The average value of comprehensive pollution index is 0.994, and the degree of pollution is close to light pollution. Predominantly, higher pollution levels in the northern and eastern regions, lower around reservoirs. The PCA/APCS model identified two main pollution sources: agricultural traffic mixed source (65.2%) and natural parent source (17.2%). The PMF model delineated three sources: agricultural activities (32.59%), transportation (30.64%), and natural parent sources (36.77%). Comparatively, the PMF model proved more accurate and reliable, yielding findings more aligned with the study area's actual conditions.


Agriculture , Metals, Heavy , Soil Pollutants , Soil , Metals, Heavy/analysis , China , Soil Pollutants/analysis , Soil/chemistry , Environmental Monitoring/methods , Principal Component Analysis , Spatial Analysis
11.
Small ; : e2311859, 2024 Apr 21.
Article En | MEDLINE | ID: mdl-38643382

The quest for efficient hemostatic agents in emergency medicine is critical, particularly for managing massive hemorrhages in dynamic and high-pressure wound environments. Traditional self-gelling powders, while beneficial due to their ease of application and rapid action, fall short in such challenging conditions. To bridge this gap, the research introduces a novel self-gelling powder that combines ultrafast covalent gelation and robust wet adhesion, presenting a significant advancement in acute hemorrhage control. This ternary system comprises ε-polylysine (ε-PLL) and 4-arm polyethylene glycol succinyl succinate (4-arm-PEG-NHS) forming the hydrogel framework. Na2HPO4 functions as the "H+ sucker" to expedite the amidation reaction, slashing gelation time to under 10 s, crucial for immediate blood loss restriction. Moreover, PEG chains' hydrophilicity facilitates efficient absorption of interfacial blood, increasing the generated hydrogel's cross-linking density and strengthens its tissue bonding, thereby resulting in excellent mechanical and wet adhesion properties. In vitro experiments reveal the optimized formulation's exceptional tissue compliance, procoagulant activity, biocompatibility and antibacterial efficacy. In porcine models of heart injuries and arterial punctures, it outperforms commercial hemostatic agent Celox, confirming its rapid and effective hemostasis. Conclusively, this study presents a transformative approach to hemostasis, offering a reliable and potent solution for the emergency management of massive hemorrhage.

12.
Sci Rep ; 14(1): 9525, 2024 Apr 25.
Article En | MEDLINE | ID: mdl-38664530

The goal of blind image super-resolution (BISR) is to recover the corresponding high-resolution image from a given low-resolution image with unknown degradation. Prior related research has primarily focused effectively on utilizing the kernel as prior knowledge to recover the high-frequency components of image. However, they overlooked the function of structural prior information within the same image, which resulted in unsatisfactory recovery performance for textures with strong self-similarity. To address this issue, we propose a two stage blind super-resolution network that is based on kernel estimation strategy and is capable of integrating structural texture as prior knowledge. In the first stage, we utilize a dynamic kernel estimator to achieve degradation presentation embedding. Then, we propose a triple path attention groups consists of triple path attention blocks and a global feature fusion block to extract structural prior information to assist the recovery of details within images. The quantitative and qualitative results on standard benchmarks with various degradation settings, including Gaussian8 and DIV2KRK, validate that our proposed method outperforms the state-of-the-art methods in terms of fidelity and recovery of clear details. The relevant code is made available on this link as open source.

13.
J Gen Intern Med ; 39(8): 1452-1473, 2024 Jun.
Article En | MEDLINE | ID: mdl-38592606

BACKGROUND: The effect of clinical interventions may vary by patients' frailty status. Understanding treatment effect heterogeneity by frailty could lead to frailty-guided treatment strategies and reduce overtreatment and undertreatment. This systematic review aimed to examine the effect modification by frailty in randomized controlled trials (RCTs) that evaluate pharmacological, non-pharmacological, and multicomponent interventions. METHODS: We searched PubMed, Web of Science, EMBASE, and ClinicalTrial.gov, from their inception to 8 December 2023. Two reviewers independently extracted trial data and examined the study quality with senior authors. RESULTS: Sixty-one RCTs that evaluated the interaction between frailty and treatment effects in older adults were included. Frailty was evaluated using different tools such as the deficit accumulation frailty index, frailty phenotype, and other methods. The effect of several pharmacological interventions (e.g., edoxaban, sacubitril/valsartan, prasugrel, and chemotherapy) varied according to the degree of frailty, whereas other treatments (e.g., antihypertensives, vaccinations, osteoporosis medications, and androgen medications) demonstrated consistent benefits across different frailty levels. Some non-pharmacological interventions had greater benefits in patients with higher (e.g., chair yoga, functional walking, physical rehabilitation, and higher dose exercise program) or lower (e.g., intensive lifestyle intervention, psychosocial intervention) levels of frailty, while others (e.g., resistance-type exercise training, moderate-intensive physical activity, walking and nutrition or walking) produced similar intervention effects. Specific combined interventions (e.g., hospital-based disease management programs) demonstrated inconsistent effects across different frailty levels. DISCUSSION: The efficacy of clinical interventions often varied by frailty levels, suggesting that frailty is an important factor to consider in recommending clinical interventions in older adults. REGISTRATION: PROSPERO registration number CRD42021283051.


Frailty , Randomized Controlled Trials as Topic , Humans , Randomized Controlled Trials as Topic/methods , Frailty/therapy , Aged , Frail Elderly
14.
Food Chem X ; 22: 101361, 2024 Jun 30.
Article En | MEDLINE | ID: mdl-38633738

The changes in the qualities and sweet-substance levels of Junzao jujube during variable-temperature drying (VTD) were investigated. The results showed that VTD retains the original color of jujube, reduces its hardness and chewiness, and decreases its wrinkling while shortening the drying time by 13.2% compared with that of constant temperature drying (CTD). "Electronic-tongue" taste analysis showed that the sweetness of VTD jujube is significantly higher than that for CTD. This is shown to be related to the contents of sucrose, fructose, and glucose, as well as the activities of invertase and sucrose synthase enzymes. In addition, the content trends for sweet amino acids are correlated with the temperature gradient used in VTD. Thus, the present study elucidates the factors governing the transformation of sugar substances in jujube during VTD, as well as providing a practical reference for the application of VTD in the jujube industry.

15.
Cancer Cell Int ; 24(1): 143, 2024 Apr 22.
Article En | MEDLINE | ID: mdl-38649887

The relationship between the immune cell and tumor occurrence and progression remains unclear. Profiling alterations in the tumor immune microenvironment (TIME) at high resolution is crucial to identify factors influencing cancer progression and enhance the effectiveness of immunotherapy. However, traditional sequencing methods, including bulk RNA sequencing, exhibit varying degrees of masking the cellular heterogeneity and immunophenotypic changes observed in early and late-stage tumors. Single-cell RNA sequencing (scRNA-seq) has provided significant and precise TIME landscapes. Consequently, this review has highlighted TIME cellular and molecular changes in tumorigenesis and progression elucidated through recent scRNA-seq studies. Specifically, we have summarized the cellular heterogeneity of TIME at different stages, including early, late, and metastatic stages. Moreover, we have outlined the related variations that may promote tumor occurrence and metastasis in the single-cell era. The widespread applications of scRNA-seq in TIME will comprehensively redefine the understanding of tumor biology and furnish more effective immunotherapy strategies.

16.
Methods ; 225: 44-51, 2024 May.
Article En | MEDLINE | ID: mdl-38518843

The process of virtual screening relies heavily on the databases, but it is disadvantageous to conduct virtual screening based on commercial databases with patent-protected compounds, high compound toxicity and side effects. Therefore, this paper utilizes generative recurrent neural networks (RNN) containing long short-term memory (LSTM) cells to learn the properties of drug compounds in the DrugBank, aiming to obtain a new and virtual screening compounds database with drug-like properties. Ultimately, a compounds database consisting of 26,316 compounds is obtained by this method. To evaluate the potential of this compounds database, a series of tests are performed, including chemical space, ADME properties, compound fragmentation, and synthesizability analysis. As a result, it is proved that the database is equipped with good drug-like properties and a relatively new backbone, its potential in virtual screening is further tested. Finally, a series of seedling compounds with completely new backbones are obtained through docking and binding free energy calculations.


Deep Learning , Molecular Docking Simulation , Molecular Docking Simulation/methods , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/pharmacology , Drug Evaluation, Preclinical/methods , Humans , Databases, Pharmaceutical , Neural Networks, Computer , Databases, Chemical
17.
Phys Rev E ; 109(2-1): 024119, 2024 Feb.
Article En | MEDLINE | ID: mdl-38491572

Complex molecular details of transcriptional regulation can be coarse-grained by assuming that reaction waiting times for promoter-state transitions, the mRNA synthesis, and the mRNA degradation follow general distributions. However, how such a generalized two-state model is analytically solved is a long-standing issue. Here we first present analytical formulas of burst-size distributions for this model. Then, we derive an iterative equation for the mRNA moment-generating function, by which mRNA raw and binomial moments of any order can be conveniently calculated. The analytical results obtained in the special cases of phase-type waiting-time distributions not only provide insights into the mechanisms of complex transcriptional regulations but also bring conveniences for experimental data-based statistical inferences.


Models, Genetic , Waiting Lists , Stochastic Processes , Transcription, Genetic , RNA, Messenger/genetics , RNA, Messenger/metabolism
18.
Integr Cancer Ther ; 23: 15347354241235590, 2024.
Article En | MEDLINE | ID: mdl-38439687

BACKGROUND: The surgical intervention serves as the paramount and prevalent remedy for individuals afflicted with colorectal malignancies, with the significance of perioperative stewardship and convalescence being indisputable. Prehabilitation coupled with preoperative lifestyle modulation has demonstrated efficacy in patients subjected to certain classifications of abdominal procedures. However, the evidence pertaining to its impact on those battling colorectal cancer remains equivocal. METHODS: A meta-analysis, grounded in pairwise contrast, of randomized controlled trials (RCTs) was orchestrated, coupled with a systematic review, to probe the efficacy of preoperative lifestyle modulation and prehabilitation on patients' postoperative functionality and recuperation. An exhaustive exploration of 8 electronic databases and trial registries was undertaken to encompass all pertinent RCTs disseminated in English or Chinese from January 2012 through December 2022. Employing a random-effects model, we evaluated parameters such as the 6-minute walk test (6 MWT), complications, quality of life (QoL), aggregate and postoperative duration of hospitalization (tLHS and postLHS), and healthcare expenditure (HExp) for postoperative patients. RESULTS: A total of 28 RCTs were incorporated into the systematic review and meta-analysis. Relative to conventional preoperative care, rehabilitation or preoperative lifestyle management was found to enhance postoperative 6MWT (SMD 1.30, 95% CI 0.30 to 2.29) and diminish the complication rate (OR 0.53, 95% CI 0.40 to 0.69). Nonetheless, no significant discrepancies were observed in QoL (SMD 1.81, 95% CI -0.26 to 3.87), tLHS (SMD -0.26, 95% CI -0.68 to 0.15), and postLHS (SMD -1.46, 95% CI -3.12 to 0.20) between the groups. HExp could not be evaluated due to a lack of sufficient data for synthesis. Most pooled outcomes exhibited significant heterogeneity, urging a cautious interpretation. Subgroup analysis revealed that nutritional interventions could mitigate the incidence of complications, and preoperative exercise could improve tLHS and postLHS. A combined approach of physical, nutritional, and psychological intervention or prehabilitation proved superior to any single intervention in enhancing postoperative capabilities. CONCLUSION: This meta-analysis delineated the efficacy of preoperative interventions on postoperative capabilities in patients with colorectal cancer, thereby offering evidence for clinical practice. It was concluded that preoperative interventions are unequivocally beneficial for postoperative functional recovery and the reduction of complication rates in patients with colorectal cancer. Nonetheless, the acquisition of more high-level evidence is still necessitated to further ascertain the effectiveness of this strategy for other patient groups and to establish its best practices. The heterogeneity in the pooled outcomes underlines the need for future studies to be more uniform in their design and reporting, which would facilitate more robust and reliable meta-analyses.


Colorectal Neoplasms , Preoperative Exercise , Humans , Life Style , Quality of Life , Asian People , Colorectal Neoplasms/surgery
19.
Nutr Metab Cardiovasc Dis ; 34(4): 1008-1013, 2024 Apr.
Article En | MEDLINE | ID: mdl-38413359

BACKGROUND AND AIMS: Uric acid, the end-product of purine metabolism within the human body, has been the subject of studies exploring its potential association with cardiovascular and cerebrovascular diseases. However, the precise relationship between uric acid levels and heart failure remains elusive. METHODS AND RESULTS: In this particular study, aggregated data from genome-wide association studies on uric acid and heart failure were utilized to perform a two-sample Mendelian randomization (MR) analysis utilizing R software. The aim was to uncover any causal link between these variables. The primary outcome was assessed using inverse variance weighted (IVW) methodology, while sensitivity analyses employed MR-Egger, weighted median (WME), and MR Pleiotropy RESidual Sum and Outlier (MR-PRESSO) techniques. IVW results revealed a possible causal relationship between elevated uric acid levels and an increased risk of heart failure (OR: 1.09, 95 % CI: 1.01-1.17, P < 0.05). Encouragingly, the directions provided by MR-Egger and WME aligned with IVW findings, and no anomalies were detected in the remaining sensitivity analyses. CONCLUSION: These outcomes indicate the stability of the results of the study, thereby suggesting that heightened uric acid levels may contribute to an augmented risk of heart failure.


Heart Failure , Uric Acid , Humans , Genome-Wide Association Study , Mendelian Randomization Analysis , Heart Failure/diagnosis , Heart Failure/epidemiology , Heart Failure/genetics , Software
20.
BMC Cardiovasc Disord ; 24(1): 128, 2024 Feb 28.
Article En | MEDLINE | ID: mdl-38418967

OBJECTIVE: Calcific aortic valve disease (CAVD) is the leading cause of angina, heart failure, and death from aortic stenosis. However, the molecular mechanisms of its progression, especially the complex disease-related transcriptional regulatory mechanisms, remain to be further elucidated. METHODS: This study used porcine valvular interstitial cells (PVIC) as a model. We used osteogenic induced medium (OIM) to induce calcium deposition in PVICs to calcify them, followed by basic fibroblast growth factor (bFGF) treatment to inhibit calcium deposition. Transcriptome sequencing was used to study the mRNA expression profile of PVICs and its related transcriptional regulation. We used DaPars to further examine alternative polyadenylation (APA) between different treatment groups. RESULTS: We successfully induced calcium deposition of PVICs through OIM. Subsequently, mRNA-seq was used to identify differentially expressed mRNAs for three different treatments: control, OIM-induced and OIM-induced bFGF treatment. Global APA events were identified in the OIM and bFGF treatment groups by bioinformatics analysis. Finally, it was discovered and proven that catalase (CAT) is one of the potential targets of bFGF-induced APA regulation. CONCLUSION: We described a global APA change in a calcium deposition model related to CAVD. We revealed that transcriptional regulation of the CAT gene may contribute to bFGF-induced calcium deposition inhibition.


Aortic Valve Stenosis , Aortic Valve/pathology , Calcinosis , Swine , Animals , Aortic Valve Stenosis/metabolism , Aortic Valve/metabolism , Calcium/metabolism , Fibroblast Growth Factor 2/genetics , Fibroblast Growth Factor 2/pharmacology , Polyadenylation , Cells, Cultured , Calcinosis/metabolism , RNA, Messenger/genetics , RNA, Messenger/metabolism
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