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1.
J Chromatogr A ; 1727: 464996, 2024 May 18.
Artigo em Inglês | MEDLINE | ID: mdl-38763087

RESUMO

Supermacroporous composite cryogels with enhanced adjustable functionality have received extensive interest in bioseparation, tissue engineering, and drug delivery. However, the variations in their components significantly impactfinal properties. This study presents a two-step hybrid machine learning approach for predicting the properties of innovative poly(2-hydroxyethyl methacrylate)-poly(vinyl alcohol) composite cryogels embedded with bacterial cellulose (pHEMA-PVA-BC) based on their compositions. By considering the ratios of HEMA (1.0-22.0 wt%), PVA (0.2-4.0 wt%), poly(ethylene glycol) diacrylate (1.0-4.5 wt%), BC (0.1-1.5 wt%), and water (68.0-96.0 wt%) as investigational variables, overlay sampling uniform design (OSUD) was employed to construct a high-quality dataset for model development. The random forest (RF) model was used to classify the preparation conditions. Then four models of artificial neural network, RF, gradient boosted regression trees (GBRT), and XGBoost were developed to predict the basic properties of the composite cryogels. The results showed that the RF model achieved an accurate three-class classification of preparation conditions. Among the four models, the GBRT model exhibited the best predictive performance of the basic properties, with the mean absolute percentage error of 16.04 %, 0.85 %, and 2.44 % for permeability, effective porosity, and height of theoretical plate (1.0 cm/min), respectively. Characterization results of the representative pHEMA-PVA-BC composite cryogel showed an effective porosity of 81.01 %, a permeability of 1.20 × 10-12 m2, and a range of height of theoretical plate between 0.40-0.49 cm at flow velocities of 0.5-3.0 cm/min. These indicate that the pHEMA-PVA-BC cryogel was an excellent material with supermacropores, low flow resistance and high mass transfer efficiency. Furthermore, the model output demonstrates that the alteration of the proportions of PVA (0.2-3.5 wt%) and BC (0.1-1.5 wt%) components in composite cryogels resulted in significant changes in the material basic properties. This work represents an attempt to efficiently design and prepare target composite cryogels using machine learning and providing valuable insights for the efficient development of polymers.

2.
NPJ Precis Oncol ; 8(1): 109, 2024 May 20.
Artigo em Inglês | MEDLINE | ID: mdl-38769374

RESUMO

Pancreatic ductal adenocarcinoma (PDAC) is a highly malignant neoplasm characterized by a poor prognosis and limited therapeutic strategy. The PDAC tumor microenvironment presents a complex heterogeneity, where neutrophils emerge as the predominant constituents of the innate immune cell population. Leveraging the power of single-cell RNA-seq, spatial RNA-seq, and multi-omics approaches, we included both published datasets and our in-house patient cohorts, elucidating the inherent heterogeneity in the formation of neutrophil extracellular traps (NETs) and revealed the correlation between NETs and immune suppression. Meanwhile, we constructed a multi-omics prognostic model that suggested the patients exhibiting downregulated expression of NETs may have an unfavorable outcome. We also confirmed TLR2 as a potent prognosis factor and patients with low TLR2 expression had more effective T cells and an overall survival extension for 6 months. Targeting TLR2 might be a promising strategy to reverse immunosuppression and control tumor progression for an improved prognosis.

3.
Free Radic Biol Med ; 221: 136-154, 2024 May 18.
Artigo em Inglês | MEDLINE | ID: mdl-38763208

RESUMO

Ferroptosis, a novel form of iron-dependent non-apoptotic cell death, plays an active role in the pathogenesis of diverse diseases, including cancer. However, the mechanism through which ferroptosis is regulated in pancreatic ductal adenocarcinoma (PDAC) remains unclear. Here, our study, via combining bioinformatic analysis with experimental validation, showed that ferroptosis is inhibited in PDAC. Genome-wide sequencing further revealed that the ferroptosis activator imidazole ketone erastin (IKE) induced upregulation of the E3 ubiquitin ligase RBCK1 in PDAC cells at the transcriptional or translational level. RBCK1 depletion or knockdown rendered PDAC cells more vulnerable to IKE-induced ferroptotic death in vitro. In a mouse xenograft model, genetic depletion of RBCK1 increased the killing effects of ferroptosis inducer on PDAC cells. Mechanistically, RBCK1 interacts with and polyubiquitylates mitofusin 2 (MFN2), a key regulator of mitochondrial dynamics, to facilitate its proteasomal degradation under ferroptotic stress, leading to decreased mitochondrial reactive oxygen species (ROS) production and lipid peroxidation. These findings not only provide new insights into the defense mechanisms of PDAC cells against ferroptotic death but also indicate that targeting the RBCK1-MFN2 axis may be a promising option for treating patients with PDAC.

4.
Cancer Res ; 2024 May 22.
Artigo em Inglês | MEDLINE | ID: mdl-38775804

RESUMO

Pancreatic ductal adenocarcinoma (PDAC) is one of the leading causes of cancer-related death worldwide, primarily due to its rapid progression. The current treatment options for PDAC are limited, and a better understanding of the underlying mechanisms responsible for PDAC progression is required to identify improved therapeutic strategies. Here, we identified FBXO32 as an oncogenic driver in PDAC. FBXO32 was aberrantly upregulated in PDAC, and high FBXO32 expression was significantly associated with an unfavorable prognosis in PDAC patients. FRG1 deficiency promoted FBXO32 upregulation in PDAC. FBXO32 promoted cell migration and invasion in vitro and tumor growth and metastasis in vivo. Mechanistically, FBXO32 directly interacted with eEF1A1 and promoted its polyubiquitination at the K273 site, leading to enhanced activity of eEF1A1 and increased protein synthesis in PDAC cells. Moreover, FBXO32-catalyzed eEF1A1 ubiquitination boosted the translation of ITGB5 mRNA and activated FAK signaling, thereby facilitating focal adhesion assembly and driving PDAC progression. Importantly, interfering with the FBXO32-eEF1A1 axis or pharmaceutical inhibition of FAK by defactinib, an FDA-approved FAK inhibitor, substantially inhibited PDAC growth and metastasis driven by aberrantly activated FBXO32-eEF1A1 signaling. Overall, this study uncovers a mechanism by which PDAC cells rely on FBXO32-mediated eEF1A1 activation to drive progression and metastasis. FBXO32 may serve as a promising biomarker for selecting eligible PDAC patients for treatment with defactinib.

5.
Phytomedicine ; 129: 155646, 2024 Apr 27.
Artigo em Inglês | MEDLINE | ID: mdl-38733903

RESUMO

BACKGROUND: Astragalus membranaceus (AM) shows potential therapeutic benefits for managing diabetic kidney disease (DKD), a leading cause of kidney failure with no cure. However, its comprehensive effects on renal outcomes and plausible mechanisms remain unclear. PURPOSE: This systematic review and meta-analysis aimed to synthesize the effects and mechanisms of AM on renal outcomes in DKD animal models. METHODS: Seven electronic databases were searched for animal studies until September 2023. Risk of bias was assessed based on SYRCLE's Risk of Bias tool. Standardized mean difference (SMD) or mean difference (MD) were estimated for the effects of AM on serum creatinine (SCr), blood urea nitrogen (BUN), albuminuria, histological changes, oxidative stress, inflammation, fibrosis and glucolipids. Effects were pooled using random-effects models. Heterogeneity was presented as I2. Subgroup analysis investigated treatment- and animal-related factors for renal outcomes. Publication bias was assessed using funnel plots and Egger's test. Sensitivity analysis was performed to assess the results' robustness. RevMan 5.3 and Stata MP 15 software were used for statistical analysis. RESULTS: Forty studies involving 1543 animals were identified for analysis. AM treatment significantly decreased SCr (MD = -19.12 µmol/l, 95 % CI: -25.02 to -13.23), BUN (MD = -6.72 mmol/l, 95 % CI: -9.32 to -4.12), urinary albumin excretion rate (SMD = -2.74, 95 % CI: -3.57, -1.90), histological changes (SMD = -2.25, 95 % CI: -3.19 to -1.32). AM treatment significantly improved anti-oxidative stress expression (SMD = 1.69, 95 % CI: 0.97 to 2.41), and decreased inflammation biomarkers (SMD = -3.58, 95 % CI: -5.21 to -1.95). AM treatment also decreased fibrosis markers (i.e. TGF-ß1, CTGF, collagen IV, Wnt4 and ß-catenin) and increased anti-fibrosis marker BMP-7. Blood glucose, lipids and kidney size were also improved compared with the DM control group. CONCLUSION: AM could improve renal outcomes and alleviate injury through multiple signaling pathways. This indicates AM may be an option to consider for the development of future DKD therapeutics.

6.
Front Pharmacol ; 15: 1379338, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38738180

RESUMO

Background: Chinese patent medicine is commonly used in China as an important treatment mechanism to thwart the progression of chronic kidney disease (CKD) stages 3-5, among which Niaoduqing granules are a representative Chinese patent medicine; however, its long-term efficacy on CKD prognosis remains unclear. Methods: Patients were grouped according to Niaoduqing granule prescription duration (non-Niaoduqing granule (non-NDQ) group vs Niaoduqing granule (NDQ) group). Serum creatinine (SCr) variation was compared using a generalized linear mixed model (GLMM). Multivariate Cox regression models were constructed, adjusting for confounding factors, to explore the risk of composite outcomes (receiving renal replacement therapy (RRT) or having an estimated glomerular filtration rate (eGFR)<5 mL/min/1.73 m2, ≥50% decline in the eGFR from the baseline, and doubling of SCr) in individuals consuming Niaoduqing granules. Results: A total of 1,271 patients were included, with a median follow-up duration of 29.71 (12.10, 56.07) months. The mean SCr Z-scores for the non-NDQ group and NDQ group were -0.175 and 0.153, respectively, at baseline (p = 0.015). The coefficients of the NDQ group from visit 1 to visit 5 were -0.207 (95% CI: -0.346, -0.068, p = 0.004), -0.214 (95% CI: 0.389, -0.039, p = 0.017), -0.324 (95% CI: 0.538, -0.109, p = 0.003), -0.502 (95% CI: 0.761, -0.243, p = 0.000), and -0.252 (95% CI: 0.569, 0.065, p = 0.119), respectively. The survival probability was significantly higher in the NDQ group (p = 0.0039). Taking Niaoduqing granules was a significant protective factor for thwarting disease progression (model 1: HR 0.654 (95% CI 0.489-0.875, p = 0.004); model 2: HR 0.646 (95% CI 0.476, 0.877, p = 0.005); and model 3: HR 0.602 (95% CI 0.442, 0.820, p = 0.001)). Conclusion: The long-term use of Niaoduqing granules improved SCr variation and lowered the risk of CKD progression by 39.8%.

7.
Redox Rep ; 29(1): 2345455, 2024 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-38723197

RESUMO

OBJECTIVES: Cancer cells undergo metabolic reprogramming to adapt to high oxidative stress, but little is known about how metabolic remodeling enables gastric cancer cells to survive stress associated with aberrant reactive oxygen species (ROS) production. Here, we aimed to identify the key metabolic enzymes that protect gastric cancer (GC) cells from oxidative stress. METHODS: ROS level was detected by DCFH-DA probes. Multiple cell biological studies were performed to identify the underlying mechanisms. Furthermore, cell-based xenograft and patient-derived xenograft (PDX) model were performed to evaluate the role of MTHFD2 in vivo. RESULTS: We found that overexpression of MTHFD2, but not MTHFD1, is associated with reduced overall and disease-free survival in gastric cancer. In addition, MTHFD2 knockdown reduces the cellular NADPH/NADP+ ratio, colony formation and mitochondrial function, increases cellular ROS and cleaved PARP levels and induces in cell death under hypoxia, a hallmark of solid cancers and a common inducer of oxidative stress. Moreover, genetic or pharmacological inhibition of MTHFD2 reduces tumor burden in both tumor cell lines and patient-derived xenograft-based models. DISCUSSION: our study highlights the crucial role of MTHFD2 in redox regulation and tumor progression, demonstrating the therapeutic potential of targeting MTHFD2.


Assuntos
Metilenotetra-Hidrofolato Desidrogenase (NADP) , Oxirredução , Estresse Oxidativo , Espécies Reativas de Oxigênio , Neoplasias Gástricas , Humanos , Neoplasias Gástricas/metabolismo , Neoplasias Gástricas/patologia , Neoplasias Gástricas/genética , Metilenotetra-Hidrofolato Desidrogenase (NADP)/metabolismo , Metilenotetra-Hidrofolato Desidrogenase (NADP)/genética , Animais , Camundongos , Espécies Reativas de Oxigênio/metabolismo , Enzimas Multifuncionais/metabolismo , Enzimas Multifuncionais/genética , Linhagem Celular Tumoral , Homeostase , Aminoidrolases/metabolismo , Aminoidrolases/genética , Progressão da Doença , Ensaios Antitumorais Modelo de Xenoenxerto
8.
Drug Resist Updat ; 74: 101083, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38593500

RESUMO

AIMS: Carbapenem-resistant Klebsiella pneumonia (CRKP) is a global threat that varies by region. The global distribution, evolution, and clinical implications of the ST11 CRKP clone remain obscure. METHODS: We conducted a multicenter molecular epidemiological survey using isolates obtained from 28 provinces and municipalities across China between 2011 and 2021. We integrated sequences from public databases and performed genetic epidemiology analysis of ST11 CRKP. RESULTS: Among ST11 CRKP, KL64 serotypes exhibited considerable expansion, increasing from 1.54% to 46.08% between 2011 and 2021. Combining our data with public databases, the phylogenetic and phylogeography analyses indicated that ST11 CRKP appeared in the Americas in 1996 and spread worldwide, with key clones progressing from China's southeastern coast to the inland by 2010. Global phylogenetic analysis showed that ST11 KL64 CRKP has evolved to a virulent, resistant clade with notable regional spread. Single-nucleotide polymorphism (SNP) analysis identified BMPPS (bmr3, mltC, pyrB, ppsC, and sdaC) as a key marker for this clade. The BMPPS SNP clade is associated with high mortality and has strong anti-phagocytic and competitive traits in vitro. CONCLUSIONS: The high-risk ST11 KL64 CRKP subclone showed strong expansion potential and survival advantages, probably owing to genetic factors.


Assuntos
Antibacterianos , Infecções por Klebsiella , Klebsiella pneumoniae , Filogenia , Humanos , China/epidemiologia , Klebsiella pneumoniae/genética , Klebsiella pneumoniae/efeitos dos fármacos , Klebsiella pneumoniae/isolamento & purificação , Infecções por Klebsiella/epidemiologia , Infecções por Klebsiella/microbiologia , Infecções por Klebsiella/transmissão , Infecções por Klebsiella/tratamento farmacológico , Antibacterianos/farmacologia , Polimorfismo de Nucleotídeo Único , Enterobacteriáceas Resistentes a Carbapenêmicos/genética , Enterobacteriáceas Resistentes a Carbapenêmicos/efeitos dos fármacos , Enterobacteriáceas Resistentes a Carbapenêmicos/isolamento & purificação , Epidemiologia Molecular , Carbapenêmicos/farmacologia , Testes de Sensibilidade Microbiana , Filogeografia , Sorogrupo , Genômica/métodos
10.
Front Nutr ; 11: 1341219, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38590829

RESUMO

Introduction: Difenoconazole (DIFE) is a common pesticide used in citrus cultivation; excessive intake can cause neurological damage to the organism, and the existing colloidal gold immunochromatographic test strips cannot meet the requirements for the detection of citrus samples. Methods: Difenoconazole test strip was prepared based on the colloidal gold immunochromatographic technique (GICT), and its application in citrus samples was investigated; with colloidal gold (CG) as the probe, the optimization of GICT parameters, and the determination of reaction method, the immunochromatographic test strips for the detection of DIFE in citrus was developed, and the limit of detection (LOD), specificity, accuracy, and stability of the test strips were verified. Results: The results showed that the visual detection limit of the prepared colloidal gold immunochromatographic test strips was 0.2 mg/kg and the quantitative range was 0.06-0.6 mg/kg, and the test strips could specifically identify DIFE and have no cross-reaction with other common triazole pesticides. The detection method established in this study was verified by the GC-MS method, and the detection results achieved good consistency (R2 > 0.98). Conclusion: The test strips developed in this study have good performance and can be used for highly sensitive detection of citrus samples.

11.
iScience ; 27(4): 109406, 2024 Apr 19.
Artigo em Inglês | MEDLINE | ID: mdl-38510132

RESUMO

Nuclear factor kappa B (NF-κB) plays a pivotal role in the development of pancreatic cancer, and its phosphorylation has previously been linked to the regulation of NUAK2. However, the regulatory connection between NF-κB and NUAK2, as well as NUAK2's role in pancreatic cancer, remains unclear. In this study, we observed that inhibiting NUAK2 impeded the proliferation, migration, and invasion of pancreatic cancer cells while triggering apoptosis. NUAK2 overexpression partially resisted apoptosis and reversed the inhibitory effects of the NF-κB inhibitor. NF-κB transcriptionally regulated NUAK2 transcription by binding to the promoter region of NUAK2. Mechanistically, NUAK2 knockdown remarkably reduced the expression levels of p-SMAD2/3 and SMAD2/3, resulting in decreased nuclear translocation of SMAD4. In SMAD4-negative cells, NUAK2 knockdown impacted FAK signaling by downregulating SMAD2/3. Moreover, NUAK2 knockdown heightened the sensitivity of pancreatic cancer cells to gemcitabine, suggesting that NUAK2 inhibitors could be a promising strategy for pancreatic cancer treatment.

12.
Front Endocrinol (Lausanne) ; 15: 1334609, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38390199

RESUMO

Background: Diabetic kidney disease (DKD) has become the leading cause of kidney failure, causing a significant socioeconomic burden worldwide. The usual care for DKD fails to achieve satisfactory effects in delaying the persistent loss of renal function. A Chinese herbal medicine, Tangshen Qushi Formula (TQF), showed preliminary clinical benefits with a sound safety profile for people with stage 2-4 DKD. We present the protocol of an ongoing clinical trial investigating the feasibility, efficacy, and safety of TQF compared to placebo in delaying the progressive decline of renal function for people with stage 2-4 DKD. Methods: A mixed methods research design will be used in this study. A randomized, double-blind, placebo-controlled pilot trial will evaluate the feasibility, efficacy, and safety of TQF compared to placebo on kidney function for people with stage 2-4 DKD. An embedded semi-structured interview will explore the acceptability of TQF granules and trial procedures from the participant's perspective. Sixty eligible participants with stage 2-4 DKD will be randomly allocated to the treatment group (TQF plus usual care) or the control group (TQF placebo plus usual care) at a 1:1 ratio for 48-week treatment and 12-week follow-up. Participants will be assessed every 12 weeks. The feasibility will be assessed as the primary outcome. The changes in the estimated glomerular filtration rate, urinary protein/albumin, renal function, glycemic and lipid markers, renal composite endpoint events, and dampness syndrome of Chinese medicine will be assessed as the efficacy outcomes. Safety outcomes such as liver function, serum potassium, and adverse events will also be evaluated. The data and safety monitoring board will be responsible for the participants' benefits, the data's credibility, and the results' validity. The intent-to-treat and per-protocol analysis will be performed as the primary statistical strategy. Discussion: Conducting a rigorously designed pilot trial will be a significant step toward establishing the feasibility and acceptability of TQF and trial design. The study will also provide critical information for future full-scale trial design to further generate new evidence supporting clinical practice for people with stage 2-4 DKD. Trial registration number: https://www.chictr.org.cn/, identifier ChiCTR2200062786.


Assuntos
Diabetes Mellitus , Nefropatias Diabéticas , Medicamentos de Ervas Chinesas , Humanos , Nefropatias Diabéticas/tratamento farmacológico , Medicamentos de Ervas Chinesas/uso terapêutico , Projetos Piloto , Resultado do Tratamento , Rim , Ensaios Clínicos Controlados Aleatórios como Assunto
13.
Nat Commun ; 15(1): 67, 2024 01 02.
Artigo em Inglês | MEDLINE | ID: mdl-38167298

RESUMO

The acquisition of exogenous mobile genetic material imposes an adaptive burden on bacteria, whereas the adaptational evolution of virulence plasmids upon entry into carbapenem-resistant Klebsiella pneumoniae (CRKP) and its impact remains unclear. To better understand the virulence in CRKP, we characterize virulence plasmids utilizing a large genomic data containing 1219 K. pneumoniae from our long-term surveillance and publicly accessible databases. Phylogenetic evaluation unveils associations between distinct virulence plasmids and serotypes. The sub-lineage ST11-KL64 CRKP acquires a pK2044-like virulence plasmid from ST23-KL1 hypervirulent K. pneumoniae, with a 2698 bp region deletion in all ST11-KL64. The deletion is observed to regulate methionine metabolism, enhance antioxidant capacity, and further improve survival of hypervirulent CRKP in macrophages. The pK2044-like virulence plasmid discards certain sequences to enhance survival of ST11-KL64, thereby conferring an evolutionary advantage. This work contributes to multifaceted understanding of virulence and provides insight into potential causes behind low fitness costs observed in bacteria.


Assuntos
Antioxidantes , Enterobacteriáceas Resistentes a Carbapenêmicos , Klebsiella pneumoniae/genética , Filogenia , Aclimatação , Enterobacteriáceas Resistentes a Carbapenêmicos/genética , Carbapenêmicos/farmacologia , Antibacterianos/farmacologia
14.
Syst Rev ; 13(1): 23, 2024 01 12.
Artigo em Inglês | MEDLINE | ID: mdl-38217017

RESUMO

BACKGROUND: Diabetic kidney disease (DKD) is a common and severe complication of diabetes that can lead to end-stage renal disease with no cure. The first-line drugs recommended by clinical guidelines fail to achieve satisfactory effects for people with DKD. A Chinese herbal medicine Tangshen Qushi Formula (TQF) shows preliminary efficacy and safety in preserving renal function for people with DKD, but the effects on comprehensive renal outcomes remain unclear. We will conduct a systematic review and meta-analysis to evaluate the effects of TQF herbs and their compounds identified from ultra-high performance liquid chromatography-MS/MS in diabetic animal models with renal outcomes. METHODS: This protocol complies with the guideline Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols. We will include studies investigating the effects of TQF herbs and compounds on diabetic rats or mice with renal outcomes. Six electronic databases will be searched from their inception to February 2023. Quality assessment will be conducted using SYRCLE's risk of bias tool. Standardized or weighted mean differences will be estimated for renal outcomes (creatinine, urea, proteinuria, histological changes, oxidative stress, inflammation, and kidney fibrosis). Data will be pooled using random-effects models. Heterogeneity across studies will be expressed as I2. Sensitivity analyses will explore treatment effects in adjusted models and within subgroups. Funnel plots and Egger's test will be used to explore publication bias. DISCUSSION: The results of this review will provide valuable insights into the potential effects of TQF in managing DKD. The limitation is that the included studies will be animal studies from specific databases, and the interpretation of the findings must be cautious. SYSTEMATIC REVIEW REGISTRATION: PROSPERO CRD42023432895. Registered on 19 July 2023 ( https://www.crd.york.ac.uk/PROSPERO/#recordDetails ).


Assuntos
Diabetes Mellitus Experimental , Nefropatias Diabéticas , Plantas Medicinais , Animais , Humanos , Camundongos , Ratos , Diabetes Mellitus Experimental/complicações , Diabetes Mellitus Experimental/tratamento farmacológico , Nefropatias Diabéticas/tratamento farmacológico , Nefropatias Diabéticas/prevenção & controle , Rim , Metanálise como Assunto , Revisões Sistemáticas como Assunto/métodos , Espectrometria de Massas em Tandem
15.
Biomark Res ; 12(1): 11, 2024 Jan 25.
Artigo em Inglês | MEDLINE | ID: mdl-38273337

RESUMO

Neoplastic cells need to adapt their gene expression pattern to survive in an ever-changing or unfavorable tumor microenvironment. Protein synthesis (or mRNA translation), an essential part of gene expression, is dysregulated in cancer. The emergence of distinct translatomic technologies has revolutionized oncological studies to elucidate translational regulatory mechanisms. Ribosome profiling can provide adequate information on diverse aspects of translation by aiding in quantitatively analyzing the intensity of translating ribosome-protected fragments. Here, we review the primary currently used translatomics techniques and highlight their advantages and disadvantages as tools for translatomics studies. Subsequently, we clarified the areas in which ribosome profiling could be applied to better understand translational control. Finally, we summarized the latest advances in cancer studies using ribosome profiling to highlight the extensive application of this powerful and promising translatomic tool.

16.
Antimicrob Agents Chemother ; 68(3): e0117523, 2024 Mar 06.
Artigo em Inglês | MEDLINE | ID: mdl-38259089

RESUMO

Staphylococcus aureus sequence type (ST) 5 has spread worldwide; however, phylogeographic studies on the evolution of global phylogenetic and Asian clades of ST5 are lacking. This study included 368 ST5 genome sequences, including 111 newly generated sequences. Primary phylogenetic analysis suggested that there are five clades, and geographical clustering of ST5 methicillin-resistant S. aureus (MRSA) was linked to the acquisition of S. aureus pathogenicity islands (SaPIs; enterotoxin gene island) and integration of the prophage φSa3. The most recent common ancestor of global S. aureus ST5 dates back to the mid-1940s, coinciding with the clinical introduction of penicillin. Bayesian phylogeographic inference allowed to ancestrally trace the Asian ST5 MRSA clade to Japan, which may have spread to major cities in China and Korea in the 1990s. Based on a pan-genome-wide association study, the emergence of Asian ST5 clades was attributed to the gain of prophages, SaPIs, and plasmids, as well as the coevolution of resistance genes. Clade IV displayed greater genomic diversity than the Asian MRSA clades. Collectively, our study provides in-depth insights into the global evolution of S. aureus ST5 mainly in China and the United States and reveals that different S. aureus ST5 clades have arisen independently in different parts of the world, with limited geographic dispersal across continents.


Assuntos
Staphylococcus aureus Resistente à Meticilina , Infecções Estafilocócicas , Humanos , Staphylococcus aureus/genética , Staphylococcus aureus Resistente à Meticilina/genética , Filogenia , Estudo de Associação Genômica Ampla , Teorema de Bayes , Genótipo , Infecções Estafilocócicas/tratamento farmacológico , Infecções Estafilocócicas/epidemiologia , Variação Genética/genética
17.
Comput Biol Chem ; 108: 108000, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-38070456

RESUMO

Non-coding RNA (ncRNA) plays an important role in many fundamental biological processes, and it may be closely associated with many complex human diseases. NcRNAs exert their functions by interacting with proteins. Therefore, identifying novel ncRNA-protein interactions (NPIs) is important for understanding the mechanism of ncRNAs role. The computational approach has the advantage of low cost and high efficiency. Machine learning and deep learning have achieved great success by making full use of sequence information and structure information. Graph neural network (GNN) is a deep learning algorithm for complex network link prediction, which can extract and discover features in graph topology data. In this study, we propose a new computational model called GATLGEMF. We used a line graph transformation strategy to obtain the most valuable feature information and input this feature information into the attention network to predict NPIs. The results on four benchmark datasets show that our method achieves superior performance. We further compare GATLGEMF with the state-of-the-art existing methods to evaluate the model performance. GATLGEMF shows the best performance with the area under curve (AUC) of 92.41% and 98.93% on RPI2241 and NPInter v2.0 datasets, respectively. In addition, a case study shows that GATLGEMF has the ability to predict new interactions based on known interactions. The source code is available at https://github.com/JianjunTan-Beijing/GATLGEMF.


Assuntos
Algoritmos , Núcleo Celular , Humanos , Aprendizado de Máquina , Redes Neurais de Computação , RNA não Traduzido
18.
Diabetes Obes Metab ; 26(2): 602-610, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-37936340

RESUMO

AIM: To assess temporal trends of chronic kidney disease (CKD) attributable to type 2 diabetes (T2D) globally and in five sociodemographic index (SDI) regions. MATERIALS AND METHODS: We extracted the population data and CKD burden attributable to T2D from the Global Burden of Disease Study 2019. We evaluated the trends of disability-adjusted life years (DALYs), mortality, prevalence and incidence through age-period-cohort modelling, and calculated net drifts (overall annual percentage changes), local drifts (annual percentage changes in each age group), longitudinal age curves (fitted longitudinal age-specific rates), period relative risks (RRs) and cohort RRs. RESULTS: From 1990 to 2019, the global burden of CKD attributable to T2D showed increasing trends in general. The burden of CKD attributable to T2D was highest in the middle SDI region and lowest in the low SDI region. Age effects increased with age, and peaked at the ages of 75-79 and 80-84 years for incidence and prevalence, respectively. Period RRs in the burden of CKD attributable to T2D increased, with the high SDI being the most remarkable in DALYs and mortality, and the middle SDI being the most notable in incidence. Cohort RRs showed unfavourable trends in incidence and prevalence among recent cohorts. CONCLUSIONS: After a lengthy period of multi-initiative diabetes management, the high-middle SDI region exhibited improvement. However, unresolved issues and improvement gaps were still remarkable. Future efforts to reduce the burden of CKD attributable to T2D in the population should prioritize addressing the unfavourable patterns identified.


Assuntos
Diabetes Mellitus Tipo 2 , Insuficiência Renal Crônica , Humanos , Anos de Vida Ajustados por Qualidade de Vida , Diabetes Mellitus Tipo 2/complicações , Diabetes Mellitus Tipo 2/epidemiologia , Carga Global da Doença , Insuficiência Renal Crônica/epidemiologia , Insuficiência Renal Crônica/etiologia , Estudos de Coortes
19.
Front Psychol ; 14: 1146260, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-38090183

RESUMO

Background: The health of office workers has become a major concern under the pressure of increasingly fierce job competition. As countries have gradually promoted healthy buildings, there is an urgent need to create and construct healthy office environments. Although the WELL Building Standard proposed management and design strategies based on the principles of health and medicine, it does not consider group characteristics or gender differences. Purpose: This study aims to apply the theory of planned behavior to healthy building design and supplement the important role of gender and group characteristics in behavioral guidance based on architectural strategies and user behaviors to improve the relevant building evaluation system. Methods: This study adopted a questionnaire survey and structural equation model. Four WELL-certified healthy office buildings in Nanshan District, Shenzhen, were selected for the survey. Based on the theory of planned behavior, structural equation models for men and women were established, compared, and analyzed. The factors affecting the health behaviors of the two groups and the actual effectiveness of various building optimization strategies were discussed, and an optimization direction for gender differences was proposed. Results: The findings indicated differences between male and female staff in their individual characteristics and implementation of health behaviors. Management strategies, subjective design strategies in assistance and guidance, and objective design strategies in spatial planning can promote the health behaviors of the two groups. However, the design strategies of result feedback and detail optimization only appeared to have a significant positive effect on female staff, whereas the intelligent automation design strategies only had an obvious intervention effect on men's health behaviors. Significance: This study found that the theory of planned behavior in the field of social psychology could be applied to relevant research on architectural design and emphasized the influence of gender. It can not only provide the optimization direction for the evaluation standards of relevant healthy buildings but also promote the implementation of health behaviors in office groups and provide new ideas for promoting the development of healthy buildings.

20.
Ophthalmol Sci ; 3(4): 100401, 2023 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-38025160

RESUMO

Purpose: To develop and validate a deep learning model that can transform color fundus (CF) photography into corresponding venous and late-phase fundus fluorescein angiography (FFA) images. Design: Cross-sectional study. Participants: We included 51 370 CF-venous FFA pairs and 14 644 CF-late FFA pairs from 4438 patients for model development. External testing involved 50 eyes with CF-FFA pairs and 2 public datasets for diabetic retinopathy (DR) classification, with 86 952 CF from EyePACs, and 1744 CF from MESSIDOR2. Methods: We trained a deep-learning model to transform CF into corresponding venous and late-phase FFA images. The translated FFA images' quality was evaluated quantitatively on the internal test set and subjectively on 100 eyes with CF-FFA paired images (50 from external), based on the realisticity of the global image, anatomical landmarks (macula, optic disc, and vessels), and lesions. Moreover, we validated the clinical utility of the translated FFA for classifying 5-class DR and diabetic macular edema (DME) in the EyePACs and MESSIDOR2 datasets. Main Outcome Measures: Image generation was quantitatively assessed by structural similarity measures (SSIM), and subjectively by 2 clinical experts on a 5-point scale (1 refers real FFA); intragrader agreement was assessed by kappa. The DR classification accuracy was assessed by area under the receiver operating characteristic curve. Results: The SSIM of the translated FFA images were > 0.6, and the subjective quality scores ranged from 1.37 to 2.60. Both experts reported similar quality scores with substantial agreement (all kappas > 0.8). Adding the generated FFA on top of CF improved DR classification in the EyePACs and MESSIDOR2 datasets, with the area under the receiver operating characteristic curve increased from 0.912 to 0.939 on the EyePACs dataset and from 0.952 to 0.972 on the MESSIDOR2 dataset. The DME area under the receiver operating characteristic curve also increased from 0.927 to 0.974 in the MESSIDOR2 dataset. Conclusions: Our CF-to-FFA framework produced realistic FFA images. Moreover, adding the translated FFA images on top of CF improved the accuracy of DR screening. These results suggest that CF-to-FFA translation could be used as a surrogate method when FFA examination is not feasible and as a simple add-on to improve DR screening. Financial Disclosures: Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.

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