Biomedical subjects

Ying Wei

Publications and source records attributed to Ying Wei.

18 recordsLinked to original sources

PubMed2026

Antimicrobial resistance analysis of Klebsiella pneumoniae bloodstream infections based on a random forest algorithm: a longitudinal study based on data from tertiary hospitals in China from 2012 to 2023.

BACKGROUND: Bloodstream infections (BSIs) caused by Klebsiella pneumoniae pose a significant global health burden, complicated by rising antimicrobial resistance (AMR). This study aimed to characterize resistance patterns, identify predictors of carbapenem resistance, and develop a machine learning model to predict patient outcomes. METHODS: In a retrospective analysis of 109 279 K. pneumoniae BSIs from tertiary hospitals in China (2012-2023), 11 000 isolates underwent whole-genome sequencing (WGS) and antimicrobial susceptibility testing. Cox proportional hazards and logistic regression models identified predictors of 30-day mortality and carbapenem-resistant K. pneumoniae (CRKP), respectively. A random forest model predicted AMR trends and outcomes, evaluated by accuracy, precision, recall, and ROC-AUC using R Studio (R Studio, Inc., Boston, MA, USA). RESULTS: Carbapenem resistance occurred in 32.3% of isolates, with rates of 41.9% for third-generation cephalosporins and 41.2% for fluoroquinolones. Among sequenced isolates, ST11 with blaKPC was the dominant CRKP genotype (12.0%). blaKPC (OR 3.97, 95% CI 3.10-5.11) and blaNDM (OR 2.80, 95% CI 2.07-3.71) strongly predicted carbapenem resistance; ICU admission predicted 30-day mortality (HR 2.10, 95% CI 1.80-2.46, p<0.001). Mortality was higher in CRKP (40.2%) vs. susceptible cases (21.5%). The random forest model achieved 89.2% accuracy and 0.92 ROC-AUC, with drug share, age, and CRKP status as top predictors. CONCLUSIONS: CRKP, especially ST11-blaKPC, drives excess mortality. Key predictors highlight the urgency for enhanced AMR surveillance and targeted therapy.

Humans↗

PubMed2026

Molecular epidemiology and antimicrobial resistance of human Streptococcus suis isolates in Guangxi, China, 2015-2021.

BACKGROUND: Streptococcus suis (S. suis) is an important zoonotic pathogen and a common colonizer of the upper respiratory tract of pigs. Human infections have been reported in several regions of China, including Guangxi, but genomic and antimicrobial resistance data from this region remain limited. This study investigated the molecular epidemiology, antimicrobial susceptibility, and genomic characteristics of human S. suis isolates collected in Baise City, Guangxi, from 2015 to 2021. METHODS: This retrospective study included 39 non-duplicate clinical isolates confirmed as S. suis by whole-genome analysis. Antimicrobial susceptibility testing was performed using a broth microdilution-based system and interpreted according to the Clinical and Laboratory Standards Institute guidelines. Serotypes were determined by agglutination using type-specific antisera. Whole-genome sequencing was used for species confirmation, multilocus sequence typing, detection of antimicrobial resistance and virulence-associated genes, and core-protein phylogenetic analysis. RESULTS: The median patient age was 55 years, and 36/39 (92.3%) patients were male. Meningitis was documented in 34/39 (87.2%) patients, and hearing impairment occurred in 21/39 (53.8%). Pig- or pork-related exposure was recorded in 15/39 (38.5%) patients. Resistance was highest to tetracycline (38/39, 97.4%), followed by erythromycin and clindamycin (26/39, 66.7% each). Four isolates (10.3%) showed intermediate susceptibility to penicillin, but none were resistant. All isolates remained susceptible to ampicillin, ceftriaxone, levofloxacin, linezolid, vancomycin, and meropenem. Serotype 2 predominated (32/39, 82.1%), followed by serotype 14 (7/39, 17.9%), while ST1 (29/39, 74.4%) and ST7 (7/39, 17.9%) were the two major sequence types. Resistance genes were mainly associated with tetracyclines, macrolides, lincosamides, and aminoglycosides. All ST1 isolates carried mrp and lacked tet(40), while all ST7 isolates showed the reverse pattern. CONCLUSION: Serotype 2 and ST1 predominated among the human S. suis isolates collected at this center. Resistance to tetracycline, erythromycin, and clindamycin was common, while susceptibility to the β-lactams tested was largely preserved. Differences in virulence- and resistance-associated gene profiles were also observed between the major lineages, indicating distinct genetic characteristics among the locally circulating isolates.

Streptococcus suis↗

PubMed2026

Pulmonary fibrosis after COVID-19 is characterized by airway abnormalities and elevated club cell secretory protein-16.

BACKGROUNDThere are no known serum biomarkers that provide mechanistic insight or prognostic enrichment for post-COVID-19 pulmonary fibrosis.METHODSWe tested associations of serum biomarkers with radiographic fibrosis-like abnormalities (reticulation, traction bronchiectasis, or honeycombing) on thoracic computed tomography (CT) scans 4 months, 15 months, and 3 years after hospitalization in an American discovery cohort of severe-to-critical COVID-19 survivors, and externally validated findings in 2 Canadian cohorts of moderate-to-critical COVID-19 survivors. In the discovery cohort, we investigated the dose-response relationship of the biomarker with CT-derived airway-to-lung ratio. We performed single-cell RNA sequencing (scRNA-seq) of transbronchial lung biopsies from COVID-19 survivors obtained 3 years after COVID-19 hospitalization and conducted immunofluorescence analysis of COVID-19 lung explants.RESULTSAmong 150 discovery cohort participants, only higher levels of circulating club cell secretory protein-16 (CC16, encoded by the SCGB1A1 gene) at hospital discharge, 4 months, 15 months, and 3 years were associated with thoracic CT fibrosis-like abnormalities in cross-sectional and longitudinal analyses. Higher CC16 levels were associated with thoracic CT fibrosis-like abnormalities in 2 validation cohorts (n = 56 and n = 37). CC16 levels were linearly associated with increased airway-to-lung ratio. scRNA-seq revealed increased proportions of epithelial cells expressing SCGB1A1 and SCGB1A1/MUC5B in COVID-19 survivors with fibrosis. Immunofluorescence analysis of COVID-19 lung explants demonstrated increased numbers of SCGB1A1-expressing epithelial cells only in small (<100 μm) airways, with 3-fold more CC16/MUC5B-coexpressing cells in respiratory bronchioles..CONCLUSION. Higher CC16 levels are associated with CT fibrosis-like abnormalities for up to 3 years following moderate-to-critical COVID-19. Increased CC16 reflects dysregulated small airway epithelial progenitor cell remodeling and increased expansion of CC16+MUC5B+ epithelial cells in respiratory bronchioles after COVID-19.TRIAL REGISTRATIONNot applicable.FUNDINGDepartment of Defense, NIH, and Japan Society for the Promotion of Science for Young Scientists.

Humans↗

PubMed2026

Identification and characterization of the HSP gene family in the Chinese giant salamander: Expression patterns under combined environmental stress.

BACKGROUND: The Chinese giant salamander (Andrias davidianus) is a critically endangered living fossil species that is highly sensitive to changes in water temperature. However, systematic studies on the heat shock protein (HSP) gene family and its response mechanisms to environmental stress in this species remain limited. This study utilized transcriptome data from captive-bred salamanders exposed to combined temperature and pathogen stress. Bioinformatics tools were employed to identify the HSP gene family of A. davidianus (AndHSP) and to analyze their evolution, structure, and function, thereby revealing their regulatory mechanisms in response to environmental stress. RESULTS: A total of 72 AndHSPs were identified and classified into five subfamilies. Phylogenetic analysis revealed that each subfamily is evolutionarily conserved and functionally related. Gene expression analysis demonstrated that pathogen infection induced the expression of AndHSPs, and elevated temperature significantly intensified this response. Nine key differentially expressed genes were identified, predominantly from the AndHSP70 subfamily, with AndHSP70-18 exhibiting rapid heat-induced expression. Tissue-specific analysis showed high expression of AndHSP60 in the spleen. A qPCR validation confirmed the reliability of the transcriptome expression results. CONCLUSIONS: This study presents the first systematic identification of the AndHSP gene family and elucidates its cooperative stress response mechanisms under combined temperature and pathogen stress. These findings provide a molecular basis for understanding the species' environmental adaptation and have important implications for its conservation and artificial breeding.

Animals↗

PubMed2006

Urokinase receptors are required for alpha 5 beta 1 integrin-mediated signaling in tumor cells.

Up-regulation of urokinase receptors is common during tumor progression and thought to promote invasion and metastasis. Urokinase receptors bind urokinase and a set of beta1 integrins, but it remains unclear to what degree urokinase receptor/integrin binding is important to beta1 integrin signaling. Using site-directed mutagenesis, single amino acid mutants of the urokinase receptor were identified that fail to associate with either alpha3beta1 (D262A) or alpha5beta1 (H249A) but associate normally with urokinase. To study the effects of these mutations on beta1 integrin function, endogenous urokinase receptors were first stably silenced in tumor cell lines HT1080 and H1299, and then wild type or mutant receptors were expressed. Knockdown of urokinase receptors resulted in markedly reduced fibronectin and alpha5beta1-dependent ERK activation and metalloproteinase MMP-9 expression. Re-expression of wild type or D262A mutant receptors but not the alpha5beta1 binding-deficient H249A mutant reconstituted fibronectin responses. Because urokinase receptor.alpha5beta1 complexes bind in the fibronectin heparin-binding domain (Type III 12-14) whereas alpha5beta1 primarily binds in the RGD-containing domain (Type III 7-10), signaling pathways leading to ERK and MMP-9 responses were dissected. Binding to III 7-10 led to Src/focal adhesion kinase activation, whereas binding to III 7-14 caused Rac 1 activation. Tumor cells engaging fibronectin required both Type III 7-10- and 12-14-initiated signals to activate ERK and up-regulate MMP-9. Thus urokinase receptor binding to alpha5beta1 is required for maximal responses to fibronectin and tumor cell invasion, and this operates through an enhanced Src/Rac/ERK signaling pathway.

Cell Line, Tumor↗

PubMed2006

Structure-directing role of amines in the ionothermal synthesis.

The structure-directing effect of amine has been observed in the ionothermal synthesis of aluminophosphate molecular sieves in 1-butyl-3-methylimidazolium bromide ionic liquid. The seven different amines we tested have an influence on the crystallization dynamics and the final product, leading to the formation of pure AFI and ATV structures.

Journal Article↗

PubMed2006

Quantile regression methods for reference growth charts.

Estimation of reference growth curves for children's height and weight has traditionally relied on normal theory to construct families of quantile curves based on samples from the reference population. Age-specific parametric transformation has been used to significantly broaden the applicability of these normal theory methods. Non-parametric quantile regression methods offer a complementary strategy for estimating conditional quantile functions. We compare estimated reference curves for height using the penalized likelihood approach of Cole and Green with quantile regression curves based on data used for modern Finnish reference charts. An advantage of the quantile regression approach is that it is relatively easy to incorporate prior growth and other covariates into the analysis of longitudinal growth data. Quantile specific autoregressive models for unequally spaced measurements are introduced and their application to diagnostic screening is illustrated.

Adolescent↗

PubMed2006

Functional relevance of urinary-type plasminogen activator receptor-alpha3beta1 integrin association in proteinase regulatory pathways.

Squamous cell carcinoma of the oral cavity is characterized by persistent, disorganized expression of integrin alpha3beta1 and enhanced production of urinary-type plasminogen activator (uPA) and its receptor (uPAR) relative to normal oral mucosa. Because multivalent aggregation of alpha3beta1 integrin up-regulates uPA and induces a dramatic co-clustering of uPAR, we explored the hypothesis that lateral ligation of alpha3beta1 integrin by uPAR contributes to uPA regulation in oral mucosal cells. To investigate mechanisms by which uPAR/alpha3beta1 binding enhances uPA expression, integrin-dependent signal activation was assessed. Both Src and ERK1/2 were phosphorylated in response to integrin aggregation, and blocking Src kinase activity completely abrogated ERK1/2 activation and uPA induction, whereas inhibition of epidermal growth factor receptor tyrosine kinase activity did not alter uPA expression. Proteinase up-regulation occurred at the transcriptional level and mutation of the AP1 (-1967) site in the uPA promoter blocked the uPAR/integrin-mediated transcriptional activation. Because uPAR is redistributed to clustered alpha3beta1 integrins, the requirement for uPAR/alpha3beta1 interaction in uPA regulation was assessed. Clustering of alpha3beta1 in the presence of a peptide (alpha325) that disrupts uPAR/alpha3beta1 integrin binding prevented uPA induction. Depletion of cell surface uPAR using small interfering RNA also blocked uPA induction following integrin alpha3beta1 clustering. These results were confirmed using a genetic strategy in which alpha3 null epithelial cells reconstituted with wild type alpha3 integrin, but not a mutant alpha3 unable to bind uPAR, induced uPA expression upon integrin clustering, confirming the critical role of uPAR in integrin-regulated proteinase expression. Disruption of uPAR/alpha3beta1 binding using peptide alpha325 or small interfering RNA blocked filopodia formation and matrix invasion, indicating that this interaction stimulates invasive behavior. Together these data support a model wherein matrix-induced clustering ofalpha3beta1 integrin promotes uPAR/alpha3beta1 interaction, thereby potentiating cellular signal transduction pathways culminating in activation of uPA expression and enhanced uPA-dependent invasive behavior.

Animals↗

PubMed2005

Regulation of alpha5beta1 integrin conformation and function by urokinase receptor binding.

Urokinase-type plasminogen activator receptors (uPARs), up-regulated during tumor progression, associate with beta1 integrins, localizing urokinase to sites of cell attachment. Binding of uPAR to the beta-propeller of alpha3beta1 empowers vitronectin adhesion by this integrin. How uPAR modifies other beta1 integrins remains unknown. Using recombinant proteins, we found uPAR directly binds alpha5beta1 and rather than blocking, renders fibronectin (Fn) binding by alpha5beta1 Arg-Gly-Asp (RGD) resistant. This resulted from RGD-independent binding of alpha5beta1-uPAR to Fn type III repeats 12-15 in addition to type III repeats 9-11 bound by alpha5beta1. Suppression of endogenous uPAR by small interfering RNA in tumor cells promoted weaker, RGD-sensitive Fn adhesion and altered overall alpha5beta1 conformation. A beta1 peptide (res 224NLDSPEGGF232) that models near the known alpha-chain uPAR-binding region, or a beta1-chain Ser227Ala point mutation, abrogated effects of uPAR on alpha5beta1. Direct binding and regulation of alpha5beta1 by uPAR implies a modified "bent" integrin conformation can function in an alternative activation state with this and possibly other cis-acting membrane ligands.

Amino Acid Sequence↗

PubMed2005

A nationwide survey of physician office visits found that inappropriate antibiotic prescriptions were issued for bacterial respiratory tract infections in ambulatory patients.

OBJECTIVE: Correlations between probabilities of resistance and the frequencies with which antibiotics were prescribed for treating bacterial respiratory infections were examined in a nationwide ambulatory population. STUDY DESIGN AND SETTING: The data of a nationwide probability sample survey of visits to physician offices in the United States in 1999 were used to conduct this study of drug use. A clinical pharmacologist identified antibiotics prescribed during those visits using a large online database. The participating physicians diagnosed the bacterial respiratory infections. An infectious disease expert determined the probabilities of bacterial resistance from a nationwide antibiotic surveillance database. RESULTS: Various bacterial respiratory infections were diagnosed during 6.5% of physician office visits in 1999. One or more antibiotics were prescribed during 51.0% of those visits. The probabilities of resistance to the most frequently prescribed antibiotics varied from 20% to 40% and showed a weak positive correlation with the frequencies of antibiotic prescriptions. CONCLUSION: A significant number of inappropriate antibiotic prescriptions were issued for infections with a high probability of bacterial resistance to the prescribed antibiotics.

Adolescent↗

PubMed2005

Prediction of active sites for protein structures from computed chemical properties.

MOTIVATION: Identification of functional information for a protein from its three-dimensional (3D) structure is a major challenge in genomics. The power of theoretical microscopic titration curves (THEMATICS), when coupled with a statistical analysis, provides a method for high-throughput screening for identification of catalytic sites and binding sites with high accuracy and precision. The method requires only the 3D structure of the query protein as input, but it performs as well as other methods that depend on sequence alignments and structural similarities.

Bacterial Proteins↗

PubMed2005

Active site prediction for comparative model structures with thematics.

THEMATICS (Theoretical Microscopic Titration Curves) is a simple, reliable computational predictor of the active sites of enzymes from structure. Our method, based on well-established Finite Difference Poisson-Boltzmann techniques, identifies the ionisable residues with anomalous predicted titration behavior. A cluster of two or more such perturbed residues is a very reliable predictor of the active site. The protein does not have to bear any resemblance in sequence or structure to any previously characterized protein, but the method does require the three-dimensional structure. We now present evidence that THEMATICS can also locate the active site in structures built by comparative modeling from similar structures. Results are given for a total of 21 sets of proteins, including 21 templates and 83 comparative model structures. Detailed results are presented for three sets of orthologous proteins (Triosephosphate isomerase, 6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase, and Aspartate aminotransferase) and for one set of human homologues of Aldose reductase with different functions. THEMATICS correctly locates the active site in the model structures. This suggests that the method can be applicable to a much larger set of proteins for which an experimentally determined structure is unavailable. With a few exceptions, the predicted active sites in the comparative model structures are similar to that of the corresponding template structure.

Algorithms↗

PubMed2004

[The spectroscopic behaviour and extraction separation of Cu(II), La(III), U(VI) and Ce(IV) in two-phase aqueous systems].

In polyethylene glycol 2000 (PEG)-(NH4)2 SO4-extractant (sodium diethyldithiocarbamate, DDC) two-phase aqueous systems, spectroscopic behaviour of complexes of Cu(II), La(III), U(VI) and Ce(IV) with DDC as the extractant in PEG phase and general water phase was investigated. Comparing to DDC spectrophotometry, the new method has the advantage that the maximum wavelength of complex of Cu(II) shifts to red wavelength. Extraction mechanism and existing form of complexes of metal ions in PEG phase were studied. Effects of different acidity, quantities of DDC and salt, different surfactant on the extraction efficiency of copper(II), lanthanum(III), uranium(VI) and cerium(IV) were discussed. Experimental results show that Cu(II) was almost completely extracted in PEG phase at pH 5-8, U(VI) was partly extracted at pH 1-11, while La(III) and Ce(IV) were not extracted at pH 3-6 buffer solution. So, extraction separation of Cu(II)-La(III) and Cu(II)-Ce(IV) was carried out by controlling the solution acidity.

English Abstract↗

PubMed2003

Distinct ligand binding sites in integrin alpha3beta1 regulate matrix adhesion and cell-cell contact.

The integrin alpha3beta1 mediates cellular adhesion to the matrix ligand laminin-5. A second integrin ligand, the urokinase receptor (uPAR), associates with alpha3beta1 via a surface loop within the alpha3 beta-propeller (residues 242-246) but outside the laminin binding region, suggesting that uPAR-integrin interactions could signal differently from matrix engagement. To explore this, alpha3-/- epithelial cells were reconstituted with wild-type (wt) alpha3 or alpha3 with Ala mutations within the uPAR-interacting loop (H245A or R244A). Wt or mutant-bearing cells showed comparable expression and adhesion to laminin-5. Cells expressing wt alpha3 and uPAR dissociated in culture, with increased Src activity, up-regulation of SLUG, and down-regulation of E-cadherin and gamma-catenin. Src kinase inhibition or expression of Src 1-251 restored the epithelial phenotype. The H245A and R244A mutants were unaffected by coexpression of uPAR. We conclude that alpha3beta1 regulates both cell-cell contact and matrix adhesion, but through distinct protein interaction sites within its beta-propeller. These studies reveal an integrin- and Src-dependent pathway for SLUG expression and mesenchymal transition.

Amino Acid Substitution↗

PubMed2003

Urokinase receptor and integrin interactions.

Urokinase receptors (uPAR) were initially thought to function simply as a mechanism to concentrate the urokinase/plasmin system toward the cell surface. However, extensive evidence has accumulated that this glycolipid-anchored receptor also functions in both the adhesive and signaling pathways of many migratory cells. Mechanisms by which uPAR exercises these functions involve complexing with other membrane proteins for signal transduction. One set of functional partners for uPAR on the cell surface are integrins. Recent studies point to important structural features of uPAR:integrin interactions, indicating uPAR to be a cis-acting integrin ligand. In vivo data reveal altered integrin function and cell migration when uPAR:integrin interactions are impaired. Together these observations support the idea that uPAR:integrin interactions may be a focal point of intervention in pathobiology where integrin function is crucial, such as tumor metastasis.

Amino Acid Sequence↗

PubMed2003

[Studies on chemical constituents from the root of Mirablis jalapa].

OBJECTIVE: To investigate the chemical constituents from the root of Mirabilis jalapa. METHOD: Compounds were isolated from 75% ethanolic extract of the titled herb by silica gel column chromatography, and their structures were elucidated by physical and chemical evidences and spectroscopic analysis. RESULT: Four compounds were obtained and identified as (2, 5-dioxoimidazolidin-4-yl)-urea (1), glycerin monoeicosate (2), boeravinone (3) and beta-sitosterol (4). CONCLUSION: Compound (2) is a new compound, and compound (1) was obtained from this plant for the first time.

Allantoin↗

PubMed2002

Human Na(+)/H(+) exchanger isoform 6 is found in recycling endosomes of cells, not in mitochondria.

Since the discovery of the first intracellular Na(+)/H(+) exchanger in yeast, Nhx1, multiple homologs have been cloned and characterized in plants. Together, studies in these organisms demonstrate that Nhx1 is located in the prevacuolar/vacuolar compartment of cells where it sequesters Na(+) into the vacuole, regulates intravesicular pH, and contributes to vacuolar biogenesis. In contrast, the human homolog of Nhx1, Na(+)/H(+) exchanger isoform 6 (NHE6), has been reported to localize to mitochondria when transiently expressed as a fusion with green fluorescent protein. This result warrants reevaluation because it conflicts with predictions from phylogenetic analyses. Here we demonstrate that when epitope-tagged NHE6 is transiently expressed in cultured mammalian cells, it does not colocalize with mitochondrial markers. It also does not colocalize with markers of the lysosome, late endosome, trans-Golgi network, or Golgi cisternae. Rather, NHE6 is distributed in recycling compartments and transiently appears on the plasma membrane. These results suggest that, like its homologs in yeast and plants, NHE6 is an endosomal Na(+)/H(+) exchanger that may regulate intravesicular pH and volume and contribute to lysosomal biogenesis.

Animals↗

PubMed2002

[Effect of Panax notoginseng saponins on human kidney fibroblast].

OBJECTIVE: To study the effect of Panax notoginseng saponins (PNS) on cell proliferation, type I collagen secretion and integrin beta 1 expression in human kidney fibroblast (KFB). METHODS: KFB were cultured and stimulated by PNS in vitro. The cell proliferation, type I collagen secretion and integrin beta 1 expression in KFB were measured by methyl thiazolyl tetrazolium (MTT), enzyme-linked immunoabsorbent assay (ELISA) and flowcytometry respectively. RESULTS: Within its optimal concentration range and effective time range, PNS could obviously inhibit the proliferation, type I collagen secretion and integrin beta 1 expression (all P < 0.05) in human KFB. CONCLUSION: PNS would possibly be an effective drug for renal interstitial fibrosis prevention and treatment.

Cells, Cultured↗