The purpose of this study was to evaluate the application value of targeted next-generation sequencing(tNGS)for rapid detection of Mycobacterium tuberculosis.From September 2021 to October 2024,1 178 clinical samples from hospitalized pa-tients at the Non-tuberculous Mycobacteria Disease Diagnosis and Treatment Center of Guangzhou Chest Hospital were collected,in-cluding 272 sputum samples,871 broncho alveolar lavage fluid(BALF)samples,and 35 other samples.These samples were analyzed with tNGS and the liquid culture+DNA microarray chip method(referred to as the"culture identification method"),and the detection results between methods were compared.The numbers of Mycobacterium tuberculosis complex(MTBC)samples identified with tNGS and the culture identification method were 172 and 127,respectively,and the numbers of non-tuberculous mycobacteria(NTM)samples detected were 517 and 474,respectively.The detection rate of Mycobacterium was 56.88%with tNGS and was significantly lower(49.49%)with the culture identification method(χ2=13.27,P<0.05).For NTM identification,when sputum was used,the detection rate of tNGS was higher than that of the culture identification method(χ2=24.14,P<0.05).However,when BALF was used,no significant difference in detection rates was observed between tNGS and the culture identification method(χ2=3.97,P=0.06).When different sample types from the same patient were analyzed with tNGS for NTM,BALF was found to be a better choice than sputum(χ2=4.05,P<0.05).However,with the culture identification method,we observed no significant difference between sample types(χ2=2.72,P=0.10).Furthermore,both the MTBC and NTM sequences detected with tNGS were significantly higher in the culture-positive group than the culture-negative group.With increasing sequence numbers,the proportion of cases in the culture-positive group progressively rose,whereas an inverse trend was observed in the culture-negative group.With clinical diagno-sis as the reference standard,the sensitivity,specificity,and Kappa value of tNGS and the culture identification method in identifying mycobacterial diseases were 85.41%,91.32%,0.74 and 74.73%,93.15%,0.63,respectively.Compared with the culture identifica-tion method,tNGS for rapid detection of Mycobacterium exhibited excellent sensitivity,specificity and consistency,and its timeliness should help clinicians make precise individualized treatment plans earlier.

The purpose of this study was to evaluate the application value of targeted next-generation sequencing(tNGS)for rapid detection of Mycobacterium tuberculosis.From September 2021 to October 2024,1 178 clinical samples from hospitalized pa-tients at the Non-tuberculous Mycobacteria Disease Diagnosis and Treatment Center of Guangzhou Chest Hospital were collected,in-cluding 272 sputum samples,871 broncho alveolar lavage fluid(BALF)samples,and 35 other samples.These samples were analyzed with tNGS and the liquid culture+DNA microarray chip method(referred to as the"culture identification method"),and the detection results between methods were compared.The numbers of Mycobacterium tuberculosis complex(MTBC)samples identified with tNGS and the culture identification method were 172 and 127,respectively,and the numbers of non-tuberculous mycobacteria(NTM)samples detected were 517 and 474,respectively.The detection rate of Mycobacterium was 56.88%with tNGS and was significantly lower(49.49%)with the culture identification method(χ2=13.27,P<0.05).For NTM identification,when sputum was used,the detection rate of tNGS was higher than that of the culture identification method(χ2=24.14,P<0.05).However,when BALF was used,no significant difference in detection rates was observed between tNGS and the culture identification method(χ2=3.97,P=0.06).When different sample types from the same patient were analyzed with tNGS for NTM,BALF was found to be a better choice than sputum(χ2=4.05,P<0.05).However,with the culture identification method,we observed no significant difference between sample types(χ2=2.72,P=0.10).Furthermore,both the MTBC and NTM sequences detected with tNGS were significantly higher in the culture-positive group than the culture-negative group.With increasing sequence numbers,the proportion of cases in the culture-positive group progressively rose,whereas an inverse trend was observed in the culture-negative group.With clinical diagno-sis as the reference standard,the sensitivity,specificity,and Kappa value of tNGS and the culture identification method in identifying mycobacterial diseases were 85.41%,91.32%,0.74 and 74.73%,93.15%,0.63,respectively.Compared with the culture identifica-tion method,tNGS for rapid detection of Mycobacterium exhibited excellent sensitivity,specificity and consistency,and its timeliness should help clinicians make precise individualized treatment plans earlier.

Objective This study aims to analyze the proteomic characteristics of peripheral blood in patients with lung cancer coexistent with pulmonary tuberculosis(LC-PTB),identify the differential proteins compared with lung cancer(LC)patients,and conduct functional analysis on these proteins.Methods The study included 8 LC-PTB patients and 10 LC patients.The LC patients were newly diagnosed and confirmed by pathology and did not receive any anti-tumor treatment before,while the PTB patients were Mycobacterium tuberculosis positive at the time of sampling.Liquid chromatography-tandem mass spectrometry(LC-MS/MS)was applied to perform proteomic mass spectrometry to assess the differential proteins,and then functional analysis was conducted via bioinformatics.Results A total of 5,185 proteins were detected between two groups.Through differential expression screening,190 proteins(58 upregulated and 132 downregulated)were identified to be differentially expressed.Subcellular localization analysis revealed that the differential proteins were mainly concentrated in the cytoplasm,nucleus,and extracellular matrix.KEGG pathway and GO analysis showed the roles of differential proteins in biological processes including immune response,metabolism,and secretion regulation.Protein interaction network analysis highlighted the importance of SORT1,SAR1B,RPS6KB1,VWF,SHC1,SRPRB,CTSD,TARDBP,RPLP0,PSMA2,RPS6,XPO1,PRKACB,and HLA-DRB1 in LC-PTB.Additionally,the expression changes in proteins like ADA2,MAP3K1,and GLS2 might be closely associated with the development of LC-PTB.Conclusions The proteomic profile comprehensively described the proteomic characteristics of LC-PTB and identified numerous differentially expressed proteins,which could provide further clues for research on biological mechanism of LC-PTB.

Objective To investigating the microbial communities and physicochemical properties of soil and distribution of Oncomelania hupensis snails in marshlands along the Yangtze River basin at different types of land use, and to examine the effects of soil microorganisms and physicochemical properties on snail distribution, so as to provide insights into snail control and schistosomiasis prevention in marshland along the Yangtze River basin. Methods Marshlands with four types of land use were selected along the Yangtze River basin on April 2021, including poplar forest-crops integrated planting, reed areas, agricultural cultivation lands and ditches. The distribution of snails and physicochemical properties of soil were investigated in marshlands with different types of land use, and the V3 to V4 regions of the bacterial 16S ribosomal RNA (16S rRNA) gene, fungal internal transcribed spacer-1 (ITS1) gene and algal ribulose-bisphosphate carboxylase (rbcL) gene in soils were subjected to high-throughput sequencing. The occurrence of frames with living snails and density of living snails were compared in marshland with different types of land use. The associations of soil microorganisms and physicochemical properties with the density of living snails were examined using Pearson correlation analysis, and the contributions of soil microorganisms and physicochemical properties to the density of living snails were evaluated using variance partitioning analysis. Results In marshlands with four types of land use, the greatest occurrence of frames with living snails [(4.94 ± 2.14)%] and density of living snails [(0.070 ± 0.026) snails/0.1 m²] were seen in ditches, and the lowest were found in [(1.23 ± 1.23)%] agricultural cultivation lands [(0.016 ± 0.019) snails/0.1 m²]. A total of 2 phyla, 5 classes, 8 orders, 9 families and 11 genera of algae were detected in soils at four types of land use, with Chlorophyta as the dominant phylum and Pseudoneochloris as the dominant genus. A total of 44 phyla, 134 classes, 281 orders, 338 families and 516 genera of bacteria were detected in soils at four types of land use, with Proteobacteria and Acidobacteriota as the dominant phyla and uncultured Acidobacterium, MND1, Mitrospira, Haliangium and Sphingomonas as dominant genera. A total of 11 phyla, 41 classes, 108 orders, 223 families and 408 genera of fungi were detected in soils at four types of land use, with phyla Ascomycota, Basidiomycota and Mortierellomycota presenting high relative abundances and genera Cladorrhinum, Mortierella and Humicola presenting high relative abundances. Pearson correlation analysis revealed that the density of living snails correlated negatively with the relative abundance of Proteobacteria (r = −0.965, P < 0.05) and soil electronic conductivity (r = −0.962, P < 0.05) and positively with soil moisture (r = 0.951, P < 0.05). Variance partitioning analysis demonstrated that the physicochemical properties and microorganisms of soil contributed 69% and 10% to the density of living snails, respectively. Conclusion The diversity of microbial communities varies in soils at different types of land use in marshland along the Yangtze River basin, and the physicochemical properties and microorganisms of soils may affect the distribution of O. hupensis snails.

Silk fibroin (SF) as a natural biopolymer has become a popular material for biomedical applications due to its minimal immunogenicity, tunable biodegradability, and high biocompatibility. Nowadays, various techniques have been developed for the applications of SF in bioengineering. Most of the literature reviews focus on the SF-based biomaterials and their different forms of applications such as films, hydrogels, and scaffolds. SF is also valuable as a coating on other substrate materials for biomedicine; however, there are few reviews related to SF-coated biomaterials. Thus, in this review, we focused on the surface modification of biomaterials using SF coatings, demonstrated their various preparation methods on substrate materials, and introduced the latest procedures. The diverse applications of SF coatings for biomedicine are discussed, including bone, ligament, skin, mucosa, and nerve regeneration, and dental implant surface modification. SF coating is conducive to inducing cell adhesion and migration, promoting hydroxyapatite (HA) deposition and matrix mineralization, and inhibiting the Notch signaling pathway, making it a promising strategy for bone regeneration. In addition, SF-coated composite scaffolds can be considered prospective candidates for ligament regeneration after injury. SF coating has been proven to enhance the mechanical properties of the substrate material, and render integral stability to the dressing material during the regeneration of skin and mucosa. Moreover, SF coating is a potential strategy to accelerate nerve regeneration due to its dielectric properties, mechanical flexibility, and angiogenesis promotion effect. In addition, SF coating is an effective and popular means for dental implant surface modification to promote osteogenesis around implants made of different materials. Thus, this review can be of great benefit for further improvements in SF-coated biomaterials, and will undoubtedly contribute to clinical transformation in the future.
Biocompatible Materials/chemistry* ; Silk/chemistry* ; Fibroins/pharmacology* ; Dental Implants ; Osteogenesis ; Tissue Scaffolds/chemistry* ; Tissue Engineering/methods*

Objective: To establish a standard operation procedure (SOP) for ribosome genotyping (ribotyping) on Clostridioides (C.) difficile, supplement and verify ribotyping typing library, so as to improve the comparability of data between different laboratories and to develop surveillance network of C. difficil in China. Methods: Molecular typing of 54 reference strains from the United States and Europe of C. difficile were performed by using the SOP referencing correspondence from abroad and from our laboratory with a BioNumerics 7.6 software to estimate the reference library of types of C. difficile. Identification of 374 clinical and animal isolates of C. difficile from 13 cities in China between 2010 and 2018, to supplement the library information. Kappa test was used to evaluate the consistency. Results: Results of capillary electrophoresis of reference strains appeared clear and stable, which guaranteed the clustering results being fast and accurate. Results from the supplementary typing showed that there were 84 types of isolates, of which 25 RT types were consistent with reference strains from abroad, while 58 RT types were different from referenced types. In the 40 referenced types, 15 RT types were not found in this study. In the consistency evaluation, the Kappa value was 0.891 and (P<0.01), showing the two Molecular typing as consistent and with close resemblance. Conclusions The result of capillary electrophoresis by applying SOP for ribotyping on C. difficile base on QIAxcel capillary electrophoresis system, appeared clear and stable. The standardized library seemed more easily used for comparability and data sharing between the laboratories.

Objective: To study the pathological features, immunophenotypes, differential diagnoses and prognostic parameters of collecting duct carcinoma of the kidney (CDC). Methods: Clinical imaging, histopathology, immunohistochemistry, and survival data of 10 patients at First Affiliated Hospital of Nanjing Medical University from January 2009 to August 2017 were retrospectively analyzed along with a review of literatures. Results: The clinical symptoms of CDC were not specific, and image examinations showed space-occupying mass lesions. Tumors were mainly located in renal medulla with grey and firm cut face and the presence of focal hemorrhage and necrosis. Microscopically, there were predominant tubular or tubular-papillary structures with associated focal sarcomatoid areas, desmoplastic stromal reaction and lymphoplasmacytic cells infiltration. Tumor cells had marked cytological atypia with high grade nuclei, conspicuous nucleolus and numerous mitoses. Immunohistochemically, tumor cells were strongly positive for CK19, E-cadherin, vimentin, HCK, CK7 and PAX8. The main treatment was radical nephrectomy in the patients. Seven cases died of CDC with median survival of 10 months. Conclusions CDC is a rare, highly aggressive malignancy of kidney with poor prognosis. Definitive diagnosis should be made by histology and immunohistochemistry. Differential diagnoses include papillary renal cell carcinoma(type Ⅱ), renal medullary carcinoma, infiltrating high grade urothelial carcinoma, renal pelvis adenocarcinoma and metastatic adenocarcinomas.

Objective To investigate the dynamic changes of regulatory T cells (Treg ) and the surface expression of programmed death (PD)‐1 and the level of transforming growth factor (TGF )‐βduring antiviral treatment in patients with chronic hepatitis C (CHC) .Methods Eighty‐six CHC patients referred to the First Affiliated Hospital of Zhengzhou University from October 2012 to October 2013 were included ,and all of them were administered with pegylated interferon α‐2a and ribavirin .Thirty healthy controls were enrolled .The percentage of Treg cells ,PD‐1 expression and TGF‐β level were analyzed by flow cytometry at baseline and at time of achieving rapid virological response (RVR ) , early viral virological (EVR ) , end‐of‐treatment virological response (ETVR ) and sustained virological response (SVR) ,or not achieving SVR .Comparison between two groups was analyzed by t test .Results Among 86 CHC patients ,the proportions of RVR ,EVR ,ETVR ,and SVR at week 24 of follow‐up were 29 cases ,67 cases ,79 cases and 67 cases ,respectively .Percentage of Treg cells in CHC patients was much higher than that in healthy controls (10 .31 ± 5 .61 vs 2 .18 ± 0 .65 ,t = 2 .28 , P< 0 .05) .During antiviral therapy ,percentages of Treg cells declined ,not only in CHC patients with HCV genotype 1b (at baseline , RVR ,EVR ,and ETVR :14 .44 ± 3 .78 ,11 .01 ± 1 .79 ,8 .24 ± 2 .98 ,and 5 .36 ± 1 .47 ,respectively ) ,but also in those infected with HCV genotype 2a (at baseline ,RVR ,EVR ,and ETVR :12 .34 ± 2 .82 ,8 .99 ± 1 .68 ,7 .53 ± 2 .96 ,and 4 .79 ± 1 .23 ,respectively ) .Expressions of PD‐1 and TGF‐β also decreased .At baseline ,the expressions of PD‐1 in patients with SVR and without SVR were 29 .11 ± 14 .65 and 37 .73 ± 11 .65 ,respectively (t = 2 .15 , P = 0 .04) ,and the levels of TGF‐β were 41 .20 ± 18 .96 and 56 .75 ± 14 .42 ,respectively (t= 2 .66 ,P< 0 .01) .At week 24 ,the expressions of PD‐1 in patients with SVR and without SVR were 10 .36 ± 4 .81 and 36 .46 ± 10 .52 ,respectively (t= 13 .95 ,P< 0 .01) ,and the levels of TGF‐β were 10 .06 ± 4 .64 and 45 .23 ± 17 .85 , respectively ( t = 11 .85 , P < 0 .01 ) . Conclusions Percentages of Treg cells and expressions of PD‐1 and TGF‐β decrease during antiviral treatment in CHC patients .Thus ,it could be of assist to predict the treatment response by monitoring these parameters .

Objective To study the effect of SKF96365 and NiCl2 on cyclopiazonic acid (CPA) induced intracellular calcium cation concentration ([Ca2+ ]i ) change in rat distal pulmonary arterial smooth muscle cells (PASMC) .Methods The rat distal PASMC were isolated and cultured .The effects of CPA ,SKF96365 and NiCl2 on [Ca2+ ]i in PASMC were tested by fluorescence microscope and InCyte [Ca2+ ]i measurement system .Results PASMC were incubated with Ca2+‐free Krebs solution containing 5μmol/L nifedipine ,10 μmol/L CPA caused a small transient increase in [Ca2+ ]i ;after restoration of extracellular Ca2+ to 2 .5 mmol/L ,10 μmol/L CPA caused marked increases in [Ca2+ ]i in PASMC incubated with Krebs solution containing 5 μmol/L nife‐dipine .Both 50 μmol/L SKF96365 and 500 μmol/L NiCl2 distinctly attenuated the increases in [Ca2+ ]i caused by 10 μmol/L CPA in PASMC .However ,neither 50 μmol/L SKF96365 nor 500 μmol/L NiCl2 affected the increases in [Ca2+ ]i caused by 60 mmol/L KCl in PASMC .Conclusion CPA induced increases in [Ca2+ ]i may related to Ca2+ release from sarcoplasmic reticulum and the in‐flux of Ca2+ through store‐operated Ca2+ channels (SOCC) in rat distal PASMC .Both SKF96365 and NiCl2 could selectively block SOCC and attenuated the influx of Ca2+ through SOCC in PASMC .