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Protein sequence databases generated from metagenomics and public databases produced similar soil metaproteomic results of microbial taxonomic and functional changes

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Pedosphere 2022年第4期32卷 507-520页

作者： Yi XIONG Lu zheng Xiangxiang MENG Ren Fang SHEN ping lan State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil ScienceChinese Academy of SciencesNanjing 210008China University of Chinese Academy of Sciences Beijing 100049China

Soil metaproteomics has excellent potential as a tool to elucidate the structural and functional changes in soil microbial communities in response to environmental alterations. However, soil metaproteomics is hindered by several challenges and gaps. Soil microbial communities possess extremely complex microbial composition, including many uncultured microorganisms without whole genome sequencing. Thus, how to select a suitable protein sequence database remains challenging in soil metaproteomics. In this study, the Public database and Meta-database were constructed using protein sequences from public databases and metagenomics, respectively. We comprehensively analyzed and compared the soil metaproteomic results using these two kinds of protein sequence databases for protein identification based on published soil metaproteomic raw data. The results demonstrated that many more proteins, higher sequence coverage, and even more microbial species and functional annotations could be identified using the Meta-database compared with those identified using the Public database. These findings indicated that the Meta-database was more specific as a protein sequence database. However, the follow-up in-depth metaproteomic analyses exhibited similar main results regardless of the database used. The microbial community composition at the genus level was similar between the two databases, especially the species annotations with high peptide-spectrum match and high abundance. The functional analyses in response to stress, such as the gene ontology enrichment of biological progress and molecular function and the key functional microorganisms, were also similar regardless of the database. Our analysis revealed that the Public database could also meet the demand to explore the functional responses of microbial proteins to some extent. This study provides valuable insights into the choice of protein sequence databases and their impacts on subsequent bioinformatic analysis in soil metaproteomic research and will facilitate the optimiz

关键词： bioinformatics differentially accumulated protein functional annotation functional microorganism Meta-database microbial community microbial species Public database

Invasive stratified mucin-producing carcinoma (ISMC) of the uterinecervix: An analysis of 6 cases with distinctive clinicopathologicalfeatures

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BIOCELL 2021年第5期45卷 1313-1319页

作者： TING lan SHENG QIN XIAOJIN GONG ping zheng JIAXIN YAN YANG LIU Department of Pathology Sichuan Cancer Hospital&InstituteSichuan Cancer CenterCancer Hospital affiliate to School of MedicineUESTCChengdu610000China

Invasive stratified mucin-producing carcinoma(ISMC)is a recently described histologic variant of high-risk human papillomavirus(HPV)-associated endocervical adenocarcinoma,as the putative invasive counterpart of the stratified mucin-producing intraepithelial lesion(SMILE).ISMC can display variable architectural patterns and usually coexists with other more conventional types of HPV-associated carcinomas,which makes diagnosis and differential diagnosis of ISMC is difficult for pathologists.Moreover,the prognosis of ISMC is still controversial.We analyzed 6 ISMCs with detailed pathological and clinical information.Intraepithelial lesion,including 1 high-grade squamous intraepithelial lesion and 1 SMILE,was found.Various architectures were observed(including nest,glandular,solid,trabecular,and single cell).Nuclear peripheral palisading,apoptotic bodies and mitoses,and variable cytoplasmic mucin vacuoles were seen in all of our cases.The predominance of neutrophils infiltration was seen in only 1 tumor.All the tumors infiltrated the cervical stroma in Silva pattern C manner.p63 and/or p40 was characteristically expressed in the peripheral cells in only 2 cases.High-risk HPV infection was observed in 3/3 detected cases.All the patients were alive during the follow-up time.Recognition of this infrequent tumor may help pathologists and oncologists for an accurate diagnosis and a better understanding of the clinicopathological behavior.

关键词： Invasive stratified mucin-producing carcinoma ISMC Stratified mucin-producing intraepithelial lesion SMILE Cervical carcinoma Human papillomavirus

Evaluation of internal and shell stiffness in the differential diagnosis of breast non-mass lesions by shear wave elastography

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World Journal of Clinical Cases 2020年第12期8卷 2510-2519页

作者： ping Xu Mei Wu Min Yang Juan Xiao zheng-Min Ruan lan-Ying Wu Department of Ultrasound Beijing Shijitan Hospital Affiliated to Capital Medical UniversityBeijing 100038China Department of Ultrasound The Second Hospital of Shandong UniversityJinan 250033Shandong ProvinceChina Evidence-based Medicine Center The Second Hospital of Shandong UniversityJinan 250033Shandong ProvinceChina

BACKGROUND The diagnostic specificity of conventional ultrasound for breast non-mass lesions(NMLs)is low at approximately 21%-43%.Shear wave elastography(SWE)can distinguish benign from malignant lesions by evaluating the internal and peripheral stiffness.SWE has good reproducibility and high diagnostic efficacy.However,there are very few independent studies on the diagnostic value of SWE in breast NMLs.AIM To determine the value of SWE in the differential diagnosis of breast NMLs.METHODS This study enrolled a total of 118 patients with breast NMLs who underwent SWE examinations in the Beijing Shijitan Hospital Affiliated to Capital Medical University and The Second Hospital of Shandong University from January 2019 to January 2020.The internal elastic parameters of the lesions were recorded,including maximum(Emax),mean(Emean)and minimum elastic values and the standard deviation.The following peripheral parameters were noted:Presence of a“stiff rim”sign;Emax,and Emean elasticity values within 1 mm,1.5 mm,2 mm,2.5 mm and 3 mm from the edge of NMLs.The receiver operating characteristic curve of each parameter was drawn,and the areas under the curve were calculated.RESULTS Emax,Emean and elastic values,and the standard deviation of the internal elastic values in malignant NMLs were significantly higher than those in benign NMLs(P<0.05).The percentage with the“stiff rim”sign in malignant NMLs was significantly higher than that in the benign group(P<0.05),and Emax and Emean at the shell of 1 mm,1.5 mm,2 mm,2.5 mm and 3 mm in the malignant group were all higher than those in the benign group(P<0.05).Of the surrounding elasticity values,Emax of the shell at 2.5 mm in malignant NMLs had maximum areas under the curve of 0.900,and the corresponding sensitivity and specificity were 94.57%and 85.86%,respectively.CONCLUSION The“stiff rim”sign and multiple quantitative elastic values within and around the lesion had good diagnostic performance in the differential diagnosis of breast NMLs.Emax in peripheral tissue had better dia

关键词： Breast tumor Shear wave elastography Non-mass lesions Stiff rim sign Ultrasound Diagnosis

Ruthenium deposited on MCM-41 as efficient catalyst for hydrolytic dehydrogenation of ammonia borane and methylamine borane

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Chinese Chemical Letters 2015年第11期26卷 1345-1350页

作者： lan Wen Zhong zheng Wei Luo ping Cai Gong-Zhen Cheng College of Chemistry and Molecular Sciences Wuhan University Suzhou Institute of Wuhan University

Ultrafine Ru nanoparticles are successfully deposited on MCM-41 by using a simple liquid impregnation- reduction method, and further investigated for catalytic hydrolysis of ammonia borane and methylamine borane. Among all the catalysts tested, 1.12wt% Ru/MCM-41 exhibits the highest catalytic activity, with turnover frequency value of 288 min^-1

关键词： MCM-41Ru nanoparticlesHydrogen storageAmmonia boraneMethyiamine

Computerized tomography-guided therapeutic percutaneous puncture catheter drainage-combined with somatostatin for severe acute pancreatitis: An analysis of efficacy and safety

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World Journal of Gastrointestinal Surgery 2024年第1期16卷 59-66页

作者： Xue-lan zheng Wan-Ling Li Yan-ping Lin Ting-Long Huang Department of Critical Care Medicine The Second Affiliated Hospital of Fujian Medical UniversityQuanzhou 362000Fujian ProvinceChina CT Room The Second Affiliated Hospital of Fujian Medical UniversityQuanzhou 362000Fujian ProvinceChina

BACKGROUND Severe acute pancreatitis(SAP),a condition with rapid onset,critical condition and unsatisfactory prognosis,poses a certain threat to human health,warranting optimization of relevant treatment plans to improve treatment efficacy.AIM To evaluate the efficacy and safety of computerized tomography-guided the-rapeutic percutaneous puncture catheter drainage(CT-TPPCD)combined with somatostatin(SS)in the treatment of SAP.METHODS Forty-two SAP patients admitted to The Second Affiliated Hospital of Fujian Medical University from June 2020 to June 2023 were selected.On the basis of routine treatment,20 patients received SS therapy(control group)and 22 patients were given CT-TPPCD plus SS intervention(research group).The efficacy,safety(pancreatic fistula,intra-abdominal hemorrhage,sepsis,and organ dysfunction syndrome),abdominal bloating and pain relief time,bowel recovery time,hospital stay,inflammatory indicators(C-reactive protein,interleukin-6,and pro-calcitonin),and Acute Physiology and Chronic Health Evaluation(APACHE)II score of both groups were evaluated for comparison.RESULTS Compared with the control group,the research group had a markedly higher total effective rate,faster abdominal bloating and pain relief and bowel recovery,INTRODUCTION Pancreatitis,an inflammatory disease occurring in the pancreatic tissue,is classified as either acute or chronic and is associated with high morbidity and mortality,imposing a socioeconomic burden[1,2].The pathogenesis of this disease involves early protease activation,activation of nuclear factor kappa-B-related inflammatory reactions,and infiltration of immune cells[3].Severe acute pancreatitis(SAP)is a serious condition involving systemic injury and subsequent possible organ failure,accounting for 20%of all acute pancreatitis cases[4].SAP is also characterized by rapid onset,critical illness and unsatisfactory prognosis and is correlated with serious adverse events such as systemic inflammatory response syn-drome and acute lung injury,threatening the health of pa

关键词： Computerized tomography guidance Therapeutic percutaneous puncture catheter drainage Somatostatin Severe acute pancreatitis Efficacy and safety

Role of in vitamin D in irritable bowel syndrome

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World Journal of Clinical Cases 2023年第12期11卷 2677-2683页

作者： Xiao-lan Yu Qi-Qi Wu Lian-ping He Yong-Feng zheng School of Medicine Taizhou UniversityJiaojiang 318000Zhejiang ProvinceChina Department of Anesthesiology Affiliated People’s Hospital of Jiangsu UniversityZhenjiang 212002Jiangsu ProvinceChina

Irritable bowel syndrome(IBS)is a common chronic functional gastrointestinal disorder affecting 10%-22%of adults.Its development is closely related to the gut microbiota,and the inflammatory and immune responses triggered by the gut microbiota can lead to IBS.Vitamin D(VD)effectively treats IBS with fewer side effects by improving gut microbiota,immune regulation,and anti-inflammatory effects.In the future,it is necessary to carry out epidemiological studies on the relationship between VD and IBS,clinical studies on the efficacy of supplementing VD to improve IBS,and animal studies on the mechanism of VD improving IBS.Therefore,this paper discussed the relationship between VD and IBS.

关键词： Irritable bowel syndrome Vitamin D Gut microbiota Immune response Mental status

Donor-specific antibodies,glomerulitis,and human leukocyte antigen B eplet mismatch are risk factors for peritubular capillary C4d deposition in renal allografts

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Chinese Medical Journal 2021年第23期134卷 2874-2881页

作者： Jin zheng Hui Guo Hui-Lin Gong ping lan Chen-Guang Ding Yang Li Xiao-Ming Ding Wu-Jun Xue Department of Kidney Transplantation The First Affiliated Hospital of Xi’an Jiaotong UniversityXi’anShaanxi 710061China Institute of Organ Transplantation Tongji Hospital affiliated to Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei 430030China Department of Pathology The First Affiliated Hospital of Xi’an Jiaotong UniversityXi’anShaanxi 710061China Department of Nephrology The First Affiliated Hospital of Xi’an Jiaotong UniversityXi’anShaanxi 710061China.

Background:The complement system plays an important role in the immune response to transplantation,and the diagnostic significance of peritubular capillary(PTC)C4d deposition(C4d+)in grafts is controversial.The study aimed to fully investigate the risk factors for PTC C4d+and analyze its significance in biopsy pathology of kidney transplantation.Methods:This retrospective study included 124 cases of kidney transplant with graft biopsy and donor-specific antibody(DSA)testing from January 2017 to December 2019 in a single center.The effects of recipient pathological indicators,eplet mismatch(MM),and DSAs on PTC C4d+were examined using univariate and multivariate logistic regression analyses.Results:In total,35/124(28%)were PTC C4d+,including 21 with antibody-mediated rejection(AMR),eight with renal tubular injury,three with T cell-mediated rejection,one with glomerular disease,and two others.Univariate analysis revealed that DSAs(P<0.001),glomerulitis(P<0.001),peritubular capillaritis(P<0.001),and human leukocyte antigen(HLA)B eplet MM(P=0.010)were the influencing factors of PTC C4d+.According to multivariate analysis,DSAs(odds ratio[OR]:9.608,95%confidence interval[CI]:2.742–33.668,P<0.001),glomerulitis(OR:3.581,95%CI:1.246–10.289,P=0.018),and HLA B eplet MM(OR:1.166,95%CI:1.005–1.353,P=0.042)were the independent risk factors for PTC C4d+.In receiver operating characteristic curve analysis,the area under the curve was increased to 0.831 for predicting PTC C4d+when considering glomerulitis,DSAs,and HLA B eplet MM.The proportions of HLA I DSAs and PTC C4d+in active antibody-mediated rejection were 12/17 and 15/17,respectively;the proportions of HLA class II DSAs and PTC C4d+in chronic AMR were 8/12 and 7/12,respectively.Furthermore,the higher the PTC C4d+score was,the more serious the urinary occult blood and proteinuria of recipients at the time of biopsy.Conclusions:PTC C4d+was mainly observed in AMR cases.DSAs,glomerulitis,and HLA B eplet MM are the independent risk factors for PTC C4d+.

关键词： Kidney transplantation C4d deposition donor-specific antibody Glomerulitis human leukocyte antigen eplet

Anoxic biodegradation of dimethyl phthalate (DMP) by activated sludge cultures under nitrate-reducing conditions

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Journal of Environmental Sciences 2007年第10期19卷 1252-1256页

作者： WU Dong-lei HU Bao-lan zheng ping Qaisar Mahmood Department of Environmental Engineering Zhejiang University Hangzhou 310029 China

Worldwide extensive use of plasticized plastics has resulted in phthalates pollution in different environment. Nitrates from industry and agriculture are also widely disseminated in the soils, natural waters and wastewaters. Dimethyl phthalate （DMP） biodegradation by activated sludge cultures under nitrate-reducing conditions was investigated. Under one optimized condition, DMP was biodegraded from 102.20 mg/L to undetectable level in 56 h under anoxic conditions and its reaction fitted well with the first-order kinetics. Using the high-performance liquid chromatography （HPLC） and liquid chromatography mass spectrometry （LC-MS） analysis, mono-methyl phthalate （MMP） and phthalic acid （PA） were detected as the major intermediates of DMP biodegradation. When combined with the determination of chemical oxygen demand （CODer） removal capacity and pH, DMP was found to be mineralized completely under anoxic conditions. The biodegradation pathway was proposed as DMP → MMP→ PA→…→ CO2 ＋ H2O. The molar ratio of DMP to nitrate consumed was found to be 9.0：1, which agrees well with the theoretical stoichiometric values of DMP biodegradation by nitrate-reducing bacteria. The results of the non-linear simulation showed that the optimum pH and temperature for the degradation were 7.56 and 31.4℃, respectively.

关键词： biodegradation dimethyl phthalate phthalic acid nitrate reduction mineralization

Massive Preparation of Coumarone-indene Resin-based Hyper-crosslinked Polymers for Gas Adsorption

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Chinese Journal of Polymer Science 2018年第10期36卷 1168-1174页

作者： Ke Tian Ting-Ting Zhu ping lan zheng-Chen Wu Wei Hu Fei-Fei Xie Lei Li College of Materials and Fujian Provincial Key Laboratory of Materials Genome Xiamen University Material and Textile College Jiaxing University

Hyper-crosslinked polymers （HCPs） are promising materials for gas capture and storage because of their low cost and easy preparation. In this work, we report the massive preparation of coumarone-indene resin-based hyper-crosslinked polymers via one-step Friedel-Crafts alkylation. Low-cost coumarone-indene resin serves as the new building block and chloroform is employed as both solvent and external crosslinker. A maximum surface area of 966 m2·g-1 is achieved, which is comparable with that of previously-reported coal tar-based porous organic polymers. Most importantly, a large number of heteroatoms including inherent oxygen atoms and introduced chlorine atoms in obtianed HCPs further enhance the interaction between specific sorbate molecule and adsorbent. Therefore, optimal structural and chemical property endow the new coumarone-indene resin-based HCPs with decent gas storage capacity （14.60 wt% at 273 K and 0.1 MPa for CO2; 1.18 wt% at 77.3 K and 0.1 MPa for H2）. These results demonstrate that new HCPs are potential candidates for applications in CO2 and H2 capture.

关键词： Coumarone-indene resin Friedel-Crafts alkylation Gas adsorption Microporous organic polymers