LPS-induced senescence of macrophages aggravates calcification and senescence of vascular smooth muscle cells via IFITM3.

BACKGROUND: Cellular senescence, macrophages infiltration, and vascular smooth muscle cells (VSMCs) osteogenic transdifferentiation participate in the pathophysiology of vascular calcification in chronic kidney disease (CKD). Senescent macrophages are involved in the regulation of inflammation in pathological diseases. In addition, senescent cells spread senescence to neighboring cells via Interferon-induced transmembrane protein3 (IFITM3). However, the role of senescent macrophages and IFITM3 in VSMCs calcification remains unexplored. AIMS: To explore the hypothesis that senescent macrophages contribute to the calcification and senescence of VSMCs via IFITM3. METHODS: Here, the macrophage senescence model was established using Lipopolysaccharides (LPS). The VSMCs were subjected to supernatants from macrophages (MCFS) or LPS-induced macrophages (LPS-MCFS) in the presence or absence of calcifying media (CM). Senescence-associated ß-galactosidase (SA-ß-gal), Alizarin red (AR), immunofluorescent staining, and western blot were used to identify cell senescence and calcification. RESULTS: The expression of IFITM3 was significantly increased in LPS-induced macrophages and the supernatants. The VSMCs transdifferentiated into osteogenic phenotype, expressing higher osteogenic differentiation markers (RUNX2) and lower VSMCs constructive makers (SM22α) when cultured with senescent macrophages supernatants. Also, senescence markers (p16 and p21) in VSMCs were significantly increased by senescent macrophages supernatants treated. However, IFITM3 knockdown inhibited this process. CONCLUSIONS: Our study showed that LPS-induced senescence of macrophages accelerated the calcification of VSMCs via IFITM3. These data provide a new perspective linking VC and aging, which may provide clues for diagnosing and treating accelerated vascular aging in patients with CKD.

TAD boundary and strength prediction by integrating sequence and epigenetic profile information.

Topologically associated domains (TADs) are one of the important higher order chromatin structures with various sizes in the eukaryotic genomes. TAD boundaries, as the flanking regions between adjacent domains, can restrict the interactions of regulatory elements, including enhancers and promoters, and are generally dynamic and variable in different cells. However, the influence of sequence and epigenetic profile-based features in the identification of TAD boundaries is largely unknown. In this work, we proposed a method called pTADS (prediction of TAD boundary and strength), to predict TAD boundaries and boundary strength across multiple cell lines with DNA sequence and epigenetic profile information. The performance was assessed in seven cell lines and three TAD calling methods. The results demonstrate that the TAD boundary can be well predicted by the selected shared features across multiple cell lines. Especially, the model can be transferable to predict the TAD boundary from one cell line to other cell lines. The boundary strength can be characterized by boundary score with good performance. The predicted TAD boundary and TAD boundary strength are further confirmed by three Hi-C contact matrix-based methods across multiple cell lines. The codes and datasets are available at https://github.com/chrom3DEpi/pTADS.

The role of HBV cccDNA in occult hepatitis B virus infection.

Occult hepatitis B virus (HBV) infection (OBI) refers to the presence of replication-competent HBV DNA in the liver, with or without HBV DNA in the blood, in individuals who tested negative for HBV surface antigen (HBsAg). In this peculiar phase of HBV infection, the covalently closed circular DNA (cccDNA) is in a low state of replication. Several advances have been made toward clarifying the mechanisms involved in such a suppression of viral activity, which seems to be mainly related to the host's immune control and epigenetic factors. Although the underlying mechanisms describing the genesis of OBI are not completely known, the presence of viral cccDNA, which remains in a low state of replication due to the host's strong immune suppression of HBV replication and gene expression, appears to be the causative factor. Through this review, we have provided an updated account on the role of HBV cccDNA in regulating OBI. We have comprehensively described the HBV cell cycle, cccDNA kinetics, current regulatory mechanisms, and the therapeutic methods of cccDNA in OBI-related diseases.

Improving the Transduction Efficiency and Antitumor Effect of Conditionally Replicative Adenovirus by Application of 6-cyclohexyl Methyl-ß-D-maltoside.

As a tumor-targeting oncolytic adenovirus (Ad), conditionally replicating adenovirus (CRAd) can access the cell interior by binding to coxsackievirus-Ad receptors (CARs) and specifically replicate and destroy cancer cells without lethal effects on normal cells. The transduction efficiency of CRAd is highly dependent on the number of CARs on the cell membrane. However, not all tumor cells highly express CARs; therefore, improving the transduction efficiency of CRAd is beneficial for improving its antitumor effect. In this study, 6-cyclohexyl methyl-ß-D-maltoside (6-ß-D), as maltoside transfection agent, showed several advantages, including high transfection efficiency, low toxicity, and potential for intensive use and easy operation. With pretreatment of cancer cells with low concentration of 6-ß-D (≤5 µg/mL), the transduction efficiency of "model" Ad (eGFP-Ad) was improved 18-fold compared to eGFP-Ad alone. 6-ß-D improved the antitumor effect of CRAd while being safe for normal cells, in which treatment with 6-ß-D helped the lethal effects of CRAd at a multiplicity-of-infection ratio of 10 (MOI 10) achieve the oncolytic outcomes of MOI 50. This means that if CRAd is combined with 6-ß-D, the amount of CRAd used in clinical practice could be greatly reduced without diminishing its curative effect or exposing patients to the potential side effects of high-titer CRAd. Finally, the underlying mechanism of antitumor effect of CRAd + 6-ß-D was primarily investigated, and we found that 6-ß-D increased the virus's replication in cancer cells at the early stage of infection and activated the apoptosis signaling pathway at the late stage of the cell cycle. This research will provide an effective technical reference for further improving Ad-mediated cancer gene therapy in clinical practice.

Exploiting the Fracture in Metal-Organic Frameworks: A General Strategy for Bifunctional Atom-Precise Nanocluster/ZIF-8(300 °C) Composites.

Atom-precise nanoclusters-metal-organic framework (APNC/MOF) composites, as bifunctional material with well-defined structures, have attracted considerable attention in recent years. Despite the progress made to date, there is an urgent need to develop a generic and scalable approach for all APNCs. Herein, the authors present the Exploiting Fracture Strategy (EFS) and successfully construct a super-stable bifunctional APNC/ZIF-8(300 °C) composite overcoming the limitations of previous strategies in selecting APNCs. The EFS utilizes the fracture of ZnN in ZIF-8 after annealing at 300 °C. This method is suitable for all kinds of S/P protected APNCs with different sizes, including uncharged clusters Au1 Ag39 , Ag40 , negatively charged Au12 Ag32 , positively charged Ag46 Au24 , Au4 Cu4 and P-ligand-protected Pd3 Cl. Importantly, the generated APNC/MOF show significantly improved performances, for example, the activities of Au12 Ag32 /ZIF-8(300°C), Au4 Cu4 /ZIF-8(300°C), and Au1 Ag39 /ZIF-8(300°C) in the corresponding reactions are higher than those of Au12 Ag32 , Au4 Cu4 , and Au1 Ag39 , respectively. In particular, Au12 Ag32 /ZIF-8(300 °C) shows higher activity than Au12 Ag32 @ZIF-8. Therefore, this work offers guidance for the design of bifunctional APNC/MOF composites with excellent optimization of properties and opens up new horizons for future related nanomaterial studies and nanocatalyst designs.

Rapid, Label-Free Prediction of Antibiotic Resistance in Salmonella typhimurium by Surface-Enhanced Raman Spectroscopy.

The rapid identification of bacterial antibiotic susceptibility is pivotal to the rational administration of antibacterial drugs. In this study, cefotaxime (CTX)-derived resistance in Salmonella typhimurium (abbr. CTXr-S. typhimurium) during 3 months of exposure was rapidly recorded using a portable Raman spectrometer. The molecular changes that occurred in the drug-resistant strains were sensitively monitored in whole cells by label-free surface-enhanced Raman scattering (SERS). Various degrees of resistant strains could be accurately discriminated by applying multivariate statistical analyses to bacterial SERS profiles. Minimum inhibitory concentration (MIC) values showed a positive linear correlation with the relative Raman intensities of I990/I1348, and the R2 reached 0.9962. The SERS results were consistent with the data obtained by MIC assays, mutant prevention concentration (MPC) determinations, and Kirby-Bauer antibiotic susceptibility tests (K-B tests). This preliminary proof-of-concept study indicates the high potential of the SERS method to supplement the time-consuming conventional method and help alleviate the challenges of antibiotic resistance in clinical therapy.

Rapid and label-free identification of different cancer types based on surface-enhanced Raman scattering profiles and multivariate statistical analysis.

Rapid detection and classification of cancer cells with label-free and non-destructive methods are helpful for rapid screening of cancer patients in clinical settings. Here, surface-enhanced Raman scattering (SERS) was used for rapid, unlabeled, and non-destructive detection of seven different cell types, including human cancer cells and non-tumorous cells. Au nanoparticles were used as enhanced substrates and directly added to cell surfaces. The single cellular SERS signals could be easily and stably collected in several minutes, and the cells maintained structural integrity over one hour. Different types of cells had unique Raman phenotypes. By applying multivariate statistical analysis to the Raman phenotypes, the cancer cells and non-tumorous cells were accurately identified. The high sensitivity enabled this method to discriminate subtle molecular changes in different cell types, and the accuracy reached 81.2% with principal components analysis and linear discriminant analysis. The technique provided a rapid, unlabeled, and non-destructive method for the detection and identification of various cancer types.

Insight into the Mechanism of the CuAAC Reaction by Capturing the Crucial Au4Cu4-π-Alkyne Intermediate.

The classic Fokin mechanism of the CuAAC reaction of terminal alkynes using a variety of Cu(I) catalysts is well-known to include alkyne deprotonation involving a bimetallic σ,π-alkynyl intermediate. In this study, we have designed a CNT-supported atomically precise nanocluster Au4Cu4 (noted Au4Cu4/CNT) that heterogeneously catalyzes the CuAAC reaction of terminal alkynes without alkyne deprotonation to a σ,π-alkynyl intermediate. Therefore, three nanocluster-π-alkyne intermediates [Au4Cu4(π-CH≡C-p-C6H4R)], R = H, Cl, and CH3, have been captured and characterized by MALDI-MS. This Au4Cu4/CNT system efficiently catalyzed the CuAAC reaction of terminal alkynes, and internal alkynes also undergo this reaction. DFT results further confirmed that HC≡CPh was activated by π-complexation with Au4Cu4, unlike the classic dehydrogenation mechanism involving the bimetallic σ,π-alkynyl intermediate. On the other hand, a Cu11/CNT catalyst was shown to catalyze the reaction of terminal alkynes following the classic deprotonation mechanism, and both Au11/CNT and Cu11/CNT catalysts were inactive for the AAC reaction of internal alkynes under the same conditions, which shows the specificity of Au4Cu4 involving synergy between Cu and Au in this precise nanocluster. This will offer important guidance for subsequent catalyst design.

The effects of Arabidopsis genome duplication on the chromatin organization and transcriptional regulation.

Autopolyploidy is widespread in higher plants and important for agricultural yield and quality. However, the effects of genome duplication on the chromatin organization and transcriptional regulation are largely unknown in plants. Using High-throughput Chromosome Conformation Capture (Hi-C), we showed that autotetraploid Arabidopsis presented more inter-chromosomal interactions and fewer short-range chromatin interactions compared with its diploid progenitor. In addition, genome duplication contributed to the switching of some loose and compact structure domains with altered H3K4me3 and H3K27me3 histone modification status. 539 genes were identified with altered transcriptions and chromatin interactions in autotetraploid Arabidopsis. Especially, we found that genome duplication changed chromatin looping and H3K27me3 histone modification in Flowering Locus C. We propose that genome doubling modulates the transcription genome-wide by changed chromatin interactions and at the specific locus by altered chromatin loops and histone modifications.

sRNAPrimerDB: comprehensive primer design and search web service for small non-coding RNAs.

MOTIVATION: Small non-coding RNAs (ncRNAs), especially microRNAs (miRNAs) and piwi-interacting RNAs (piRNAs), play key roles in many biological processes. However, only a few tools can be used to develop the optimal primer or probe design for the expression profile of small ncRNAs. Here, we developed sRNAPrimerDB, the first automated primer designing and query web service for small ncRNAs. RESULTS: The primer online designing module of sRNAPrimerDB is composed of primer design algorithms and quality evaluation of the polymerase chain reaction (PCR) primer. Five types of primers, namely, generic or specific reverse transcription primers, specific PCR primers pairs, TaqMan probe, double-hairpin probe and hybridization probe for different small ncRNA detection methods, can be designed and searched using this service. The quality of PCR primers is further evaluated using melting temperature, primer dimer, hairpin structure and specificity. Moreover, the sequence and size of each amplicon are also provided for the subsequent experiment verification. At present, 531 306 and 2 941 669 primer pairs exist across 223 species for miRNAs and piRNAs, respectively, according to sRNAPrimerDB. Several primers designed by sRNAPrimerDB are further successfully validated by subsequent experiments. AVAILABILITY AND IMPLEMENTATION: sRNAPrimerDB is a valuable platform that can be used to detect small ncRNAs. This module can be publicly accessible at http://www.srnaprimerdb.com or http://123.57.239.141. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Hierarchical cooperation of transcription factors from integration analysis of DNA sequences, ChIP-Seq and ChIA-PET data.

BACKGROUND: Chromosomal architecture, which is constituted by chromatin loops, plays an important role in cellular functions. Gene expression and cell identity can be regulated by the chromatin loop, which is formed by proximal or distal enhancers and promoters in linear DNA (1D). Enhancers and promoters are fundamental non-coding elements enriched with transcription factors (TFs) to form chromatin loops. However, the specific cooperation of TFs involved in forming chromatin loops is not fully understood. RESULTS: Here, we proposed a method for investigating the cooperation of TFs in four cell lines by the integrative analysis of DNA sequences, ChIP-Seq and ChIA-PET data. Results demonstrate that the interaction of enhancers and promoters is a hierarchical and dynamic complex process with cooperative interactions of different TFs synergistically regulating gene expression and chromatin structure. The TF cooperation involved in maintaining and regulating the chromatin loop of cells can be regulated by epigenetic factors, such as other TFs and DNA methylation. CONCLUSIONS: Such cooperation among TFs provides the potential features that can affect chromatin's 3D architecture in cells. The regulation of chromatin 3D organization and gene expression is a complex process associated with the hierarchical and dynamic prosperities of TFs.

Label-Free Exosomal Detection and Classification in Rapid Discriminating Different Cancer Types Based on Specific Raman Phenotypes and Multivariate Statistical Analysis.

Exosomes contain different functional bimolecular characteristics related to physiological or pathological processes and are now recognized as new biomarkers in different human cancers. Rapid detection and classification of cancer-related exosomes might be helpful in the rapid screening of patients that may have cancer. Here, we report a surface enhanced Raman scattering technology for rapid and label-free exosomal detection (Exo-SERS) to aid in the discrimination of different cancer cells based on specific Raman phenotypes and multivariate statistical analysis. The results demonstrated that exosomes derived from both tumor cells and normal cells exhibit special, unique Raman phenotypes. Using the Exo-SERS method, the cancer cells were accurately discriminated from normal cells, and subtle molecular changes between the different cell types could be detected with high sensitive. This research provides a rapid, label-free and non-destructive manner for detecting and discriminating between cancer types.

The Diagnostic Value of Procalcitonin Versus Other Biomarkers in Prediction of Bloodstream Infection.

BACKGROUND: We compared the diagnostic utility of procalcitonin (PCT), C-reactive protein (CRP), and hematological markers, including white blood cell count (WBC), neutrophils (NEU), percentage of neutrophils (NEU%), lymphocytes (LYM), neutrophil-lymphocyte count ratio (NLCR), and platelet count (PLT) for predicting bloodstream infection (BSI), which was confirmed by blood culture (BC). METHODS: A retrospective analysis was conducted for 1807 inpatients. The level of PCT, CRP, blood cells, and blood culture results were compared between the positive blood culture group and negative blood culture group; each indicator was analyzed in the performance of bacterial BSI diagnosis by drawing ROC curves. RESULTS: Blood cultures were positive in 230 patients; hence, the prevalence of bacteremia was 12.7%. There were significant differences in the median value for each marker between positive group BCs and negative group BCs (p < 0.05). The areas under the receiver operating characteristic curves (ROC-AUCs) of PCT, CRP, WBC, NEU, NUE%, LYM, NLCR, and PLT for discriminating positive BCs from negative BCs were 0.811, 0.654, 0.612, 0.634, 0.684, 0.595, 0.682, and 0.633 respectively. PCT concentrations of gram-negative (14.94 ng/mL, IQR 2.93  48.76) were significantly higher than gram-positive (4.74 ng/mL, IQR 1.22  17.5) and fungal (1.47 ng/mL, IQR 0.66  35.34). CONCLUSIONS: PCT proved to be the most reliable predictor of BSI, second were NEU% and NLCR. A higher PCT level was found in patients with a gram-negative BSI compared to gram-positive BSI and fungal BSI.

Overexpression of MexAB-OprM efflux pump in carbapenem-resistant Pseudomonas aeruginosa.

Efflux pump systems are one of the most important mechanisms conferring multidrug resistance in Pseudomonas aeruginosa. MexAB-OprM efflux pump is one of the largest multi-drug resistant efflux pumps with high-level expression, which is controlled by regulatory genes mexR, nalC, and nalD. This study investigated the role of efflux pump MexAB-OprM in 75 strains of carbapenem-resistant P. aeruginosa and evaluated the influence of point mutation of the regulatory genes. The minimum inhibitory concentrations of imipenem and meropenem, with or without MC207110, an efflux pump inhibitor, were determined by agar dilution method to select the positive strains for an overexpressed active efflux pump. Carba NP test and EDTA-disk synergy test were used for the detection of carbapenemase and metallo-ß-lactamases, respectively. The gene mexA, responsible for the fusion protein structure, and the reference gene rpoD of the MexAB-OprM pump were amplified by real-time PCR. The quantity of relative mRNA expression was determined simultaneously. By PCR method, the efflux regulatory genes mexR, nalC, and nalD and outer membrane protein OprD2 were amplified for the strains showing overexpression of MexAB-OprM and subsequently analyzed by BLAST. Among the 75 P. aeruginosa strains, the prevalence of efflux pump-positive phenotype was 17.3 % (13/75). Carba NP test and EDTA-disk synergy test were all negative in the 13 strains. PCR assay results showed that ten strains overexpressed the MexAB-OprM efflux pump and were all positive for the regulatory genes mexR, nalC, and nalD. Sequence analysis indicated that of the ten isolates, nine had a mutation (Gly â†’ Glu) at 71st amino acid position in NalC, and eight also had a mutation (Ser â†’ Arg) at 209th position in NalC. Only one strain had a mutation (Thr â†’ Ile) at the 158th amino acid position in NalD, whereas eight isolates had mutations in MexR. In conclusion, overexpression of efflux pump MexAB-OprM plays an important role in carbapenem-resistant P. aeruginosa. The mutations of regulatory genes may be a main factor contributing to overexpression of MexAB-OprM.

NURBS: a database of experimental and predicted nuclear receptor binding sites of mouse.

SUMMARY: Nuclear receptors (NRs) are a class of transcription factors playing important roles in various biological processes. An NR often impacts numerous genes and different NRs share overlapped target networks. To fulfil the need for a database incorporating binding sites of different NRs at various conditions for easy comparison and visualization to improve our understanding of NR binding mechanisms, we have developed NURBS, a database for experimental and predicted nuclear receptor binding sites of mouse (NURBS). NURBS currently contains binding sites across the whole-mouse genome of 8 NRs identified in 40 chromatin immunoprecipitation with massively parallel DNA sequencing experiments. All datasets are processed using a widely used procedure and same statistical criteria to ensure the binding sites derived from different datasets are comparable. NURBS also provides predicted binding sites using NR-HMM, a Hidden Markov Model (HMM) model. AVAILABILITY: The GBrowse-based user interface of NURBS is freely accessible at http://shark.abl.ku.edu/nurbs/. NR-HMM and all results can be downloaded for free at the website. CONTACT: jwfang@ku.edu

[Expression of CC-chemokine ligand 18 (CCL18) in the serum and pleural effusion of non-small-cell lung cancer patients and its regulatory effect on the differentiation of monocyte-derived dendritic cells].

OBJECTIVE: To compare the CC-chemokine ligand 18 (CCL18) expression in the serum and malignant pleural effusion (MPE) of NSCLC patients and explore its regulatory effect on differentiation of monocyte-derived dendritic cells (Mo-DC). METHODS: CCL18 levels in the serum and MPE from 62 NSCLC patients were quantitated by immunoassay. CCL18 in sera from 26 healthy individuals, 28 exudative pleural effusions from inflammatory pulmonary diseases and 17 transudative pleural effusions from non-inflammatory diseases were used as control. Mo-DC was generated by culturing NSCLC-derived monocytes with GM-CSF and IL-4 in the presence or absence of CCL18. The mean fluorescent intensity (MFI) of CD14, CD80, CD83, CD86 and HLA-DR were analyzed by flow cytometry (FCM). Mo-DC was then co-cultured with purified T cells and the percence of CD25(+)FoxP3(+) cells was assayed by FCM. RESULTS: CCL18 levels in the sera of NSCLC patients and healthy individuals were (132.70 ± 15.52) ng/ml and (18.44 ± 0.99) ng/ml, respectively (P < 0.001). The levels of CCL18 in MPE, exudative PE and transudative PE were (155.6 ± 13.58) ng/ml, (190.4 ± 22.33) ng/ml and (20.89 ± 3.03) ng/ml, respectively. CCL18 in the MPE was significantly higher than that in transudates (P < 0.001), however, no significant difference was observed between CCL18 expression in exudative PE and MPE (P = 0.172). Of note, a moderate positive correlation (r = 0.421, P < 0.01) was observed between CCL18 levels in the paired MPE and serum of NSCLC. In the healthy control group, Mo-DC cultured in the presence of CCL18 showed 31.4 ± 15.8 (MFI) of CD14 expression, which was significantly higher than that in Mo-DC cultured in the absence of CCL18 (18.5 ± 8.9, P < 0.05). In contrast, the expressions of MFI of CD80, CD83, CD86 and HLA-DR were significantly decreased upon CCL18 induction (P < 0.05). In the NSCLC group, GM-CSF+IL-4+CCL18 induced a MFI of 45.2 ± 13.8 of CD14 expression in Mo-DC, which was also significantly higher than that of GM-CSF+ IL-4 induction (22.6 ± 10.5, P < 0.01). Similarly, the expressions of MFI of CD80, CD83, CD86 and HLA-DR were significantly decreased in the presence of CCL18 (P < 0.05). Furthermore, the MFI of CD14, CD83, CD86 and HLA-DR had significant differences between GM-CSF/IL-4/CCL18-induced Mo-DC derived from NSCLC patients and healthy control (P < 0.05). Finally, CD4(+) T cells co-cultured with NSCLC-derived, GM-CSF/IL-4/CCL18-treated Mo-DC had significantly higher percent of CD25(+)FoxP3(+) cells compared with that of CD4(+) T cells stimulated with Mo-DC induced by GM-CSF/IL-4(P < 0.01). CONCLUSIONS: CCL18 is present at a high level in MPE and serum of NSCLC patients complicated with pleural effusion and a moderate positive correlation exists between CCL18 levels in the two fluids. CCL18 inhibits maturation of Mo-DC, which consequently stimulates T cells to differentiate into CD25(+)FoxP3(+) regulatory T cells.

Knowledge, attitude, and practice towards bacterial multidrug-resistance and structural equation modeling analysis among intensive care unit nurses and physicians.

BACKGROUND: The intensive care unit (ICU) is a department with a high risk of MDR bacteria, and ICU nurses and physicians play critical roles in bacterial multidrug resistance (MDR) prevention. OBJECTIVES: To explore the knowledge, attitudes, and practice (KAP) towards bacterial MDR among ICU nurses and physicians. METHODS: A self-designed questionnaire was administered to collect data. Structural equation modeling (SEM) was applied to assess the associations among study variables. RESULTS: A total of 369 questionnaires were collected; 43 questionnaires were excluded due to self-contradictory on the trap question or the obviously repeated pattern. Finally, 326 (88.35%) valid questionnaires were included in the analysis. The knowledge, attitudes, and practice were 13.57 ± 1.69 (90.47%, possible range: 0-15), 38.75 ± 2.23 (96.88%, possible range: 8-40), and 47.40 ± 3.59 (94.80%, possible range: 10-50). The SEM showed that knowledge had a direct effect on attitude with a direct effect value of 0.61 (P < 0.001) and a direct negative effect on practice with a direct effect value of -0.30 (P = 0.009). The direct effect of attitude on practice was 0.89 (P < 0.001); the indirect effect of knowledge through attitude on practice was 0.52 (P < 0.001). Job satisfaction had a direct effect on attitude and practice, with an effect value of 0.52 (P = 0.030) and 0.75 (P = 0.040). Being a physician (OR = 0.354, 95%CI: 0.159-0.790, P = 0.011), 5-9.9 years of practice (OR = 4.534, 95%CI: 1.878-8.721, P < 0.001), and ≥ 10 years of practice (OR = 3.369, 95%CI: 1.301-8.721, P = 0.012) were independently associated with good knowledge. The attitude scores (OR = 1.499, 95%CI: 1.227-1.830, P < 0.001), male gender (OR = 0.390, 95%CI: 0.175-0.870, P = 0.022), and 5-9.9 years of experience (OR = 0.373, 95%CI: 0.177-0.787, P = 0.010) were independently associated with proactive practice. CONCLUSION: Nurses and physicians in the ICU showed good knowledge, positive attitudes, and proactive practice toward bacterial MDR. Nurses and physicians' knowledge had a direct effect on their attitude, while attitude might directly influence the practice and also play a mediating role between knowledge and practice. Job satisfaction might directly support the positive attitude and practice toward bacterial MDR.

The functional role of cellular senescence during vascular calcification in chronic kidney disease.

Vascular calcification (VC) has emerged as a key predictor of cardiovascular events in patients with chronic kidney disease (CKD). In recent years, an expanding body of research has put forth the concept of accelerated vascular aging among CKD patients, highlighting the significance of vascular cells senescence in the process of VC. Within the milieu of uremia, senescent vascular endothelial cells (VECs) release extracellular microvesicles (MV) that promote vascular smooth muscle cells (VSMCs) senescence, thereby triggering the subsequent osteogenic phenotypic switch and ultimately contributing to the VC process. In addition, senescent vascular progenitor or stem cells with diminished ability to differentiate into VECs and VSMCS, compromise the repair of vascular integrity, on the other hand, release a cascade of molecules associated with senescence, collectively known as the senescence-associated secretory phenotype (SASP), perpetuating the senescence phenomenon. Furthermore, SASP triggers the recruitment of monocytes and macrophages, as well as adjacent VECs and VSMCs into a pro-adhesive and pro-inflammatory senescent state. This pro-inflammatory microenvironment niche not only impacts the functionality of immune cells but also influences the differentiation of myeloid immune cells, thereby amplifying the reduced ability to effectively clear senescent cells of senescent macrophages, promoted calcification of VSMCs. The objective of this paper is to provide a comprehensive review of the contribution of vascular cell senescence to the emergence and advancement of VC. Gaining a comprehensive understanding of the involvement of cellular senescence within the vessel wall is pivotal, especially when it comes to its intersection with VC. This knowledge is essential for advancing groundbreaking anti-aging therapies, aiming to effectively mitigate cardiovascular diseases.

Diagnostic prediction of complex diseases using phase-only correlation based on virtual sample template.

MOTIVATION: Complex diseases induce perturbations to interaction and regulation networks in living systems, resulting in dynamic equilibrium states that differ for different diseases and also normal states. Thus identifying gene expression patterns corresponding to different equilibrium states is of great benefit to the diagnosis and treatment of complex diseases. However, it remains a major challenge to deal with the high dimensionality and small size of available complex disease gene expression datasets currently used for discovering gene expression patterns. RESULTS: Here we present a phase-only correlation (POC) based classification method for recognizing the type of complex diseases. First, a virtual sample template is constructed for each subclass by averaging all samples of each subclass in a training dataset. Then the label of a test sample is determined by measuring the similarity between the test sample and each template. This novel method can detect the similarity of overall patterns emerged from the differentially expressed genes or proteins while ignoring small mismatches. CONCLUSIONS: The experimental results obtained on seven publicly available complex disease datasets including microarray and protein array data demonstrate that the proposed POC-based disease classification method is effective and robust for diagnosing complex diseases with regard to the number of initially selected features, and its recognition accuracy is better than or comparable to other state-of-the-art machine learning methods. In addition, the proposed method does not require parameter tuning and data scaling, which can effectively reduce the occurrence of over-fitting and bias.

Identification of properties important to protein aggregation using feature selection.

BACKGROUND: Protein aggregation is a significant problem in the biopharmaceutical industry (protein drug stability) and is associated medically with over 40 human diseases. Although a number of computational models have been developed for predicting aggregation propensity and identifying aggregation-prone regions in proteins, little systematic research has been done to determine physicochemical properties relevant to aggregation and their relative importance to this important process. Such studies may result in not only accurately predicting peptide aggregation propensities and identifying aggregation prone regions in proteins, but also aid in discovering additional underlying mechanisms governing this process. RESULTS: We use two feature selection algorithms to identify 16 features, out of a total of 560 physicochemical properties, presumably important to protein aggregation. Two predictors (ProA-SVM and ProA-RF) using selected features are built for predicting peptide aggregation propensity and identifying aggregation prone regions in proteins. Both methods are compared favourably to other state-of-the-art algorithms in cross validation. The identified important properties are fairly consistent with previous studies and bring some new insights into protein and peptide aggregation. One interesting new finding is that aggregation prone peptide sequences have similar properties to signal peptide and signal anchor sequences. CONCLUSIONS: Both predictors are implemented in a freely available web application (http://www.abl.ku.edu/ProA/). We suggest that the quaternary structure of protein aggregates, especially soluble oligomers, may allow the formation of new molecular recognition signals that guide aggregate targeting to specific cellular sites.