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Cai Z, Wang T. SARS-CoV-2 Omicron infection in a cohort of hospitalized kidney transplant recipients: Risk factors of severity. Clin Nephrol 2024; 101:238-249. [PMID: 38497686 DOI: 10.5414/cn111303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2024] [Indexed: 03/19/2024] Open
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron is a major coronavirus variant, which was prevalent in China at the end of 2022 and caused widespread infection. As an immunosuppressed group, renal transplant recipients with SARS-CoV-2 infection are prone to developing serious pneumonia or an adverse outcome event if the infection is not treated in time. Here, we analyze the possible risk factors of infection severity. MATERIALS AND METHODS 92 cases of moderate and severe SARS-CoV-2 infection after renal transplantation were collected. Statistical methods, including Fisher's tests, F test, Spearman relative values, and multi-parameter logistic regression models, were used to analyze the risk factors for severe SARS-CoV-2 infection in renal transplant recipients. RESULTS 44 cases complicated with hypertension were observed in the study cohort, among whom 30 were severe (OR: 4.63, p < 0.001). Out of 51 male patients infected with Omicron, 30 male patients presented with severe SARS-CoV-2 (OR: 2.45, p = 0.039). In renal transplant patients, hypertension comorbidity was closely correlated with clinical presentation (R = 0.369, p < 0.001). Blood routine test, chemistries, and additional indices showed increased neutrophils and C-reactive protein in patients with severe disease compared with the moderate group according to one-way analysis of variance (p = 0.004), while CD3 (p = 0.02) and CD4 (p = 0.04) showed lower expressional levels. We also observed meaningful correlations between neutrophil levels and hypertension comorbidity (R = 0.222, p = 0.034) and between interleukin-6 (IL-6) levels and diabetes comorbidity (R = 0.315, p = 0.011), with IL-6 considered a key factor in the context of coronavirus disease. CONCLUSION Renal transplant recipients were generally susceptible to infection with the Omicron variant, with a more pronounced incidence of severe illness observed in the group with hypertension comorbidity.
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Cai Z, Peng H, Sun S, He J, Luo F, Huang Y. DeepKa Web Server: High-Throughput Protein p Ka Prediction. J Chem Inf Model 2024; 64:2933-2940. [PMID: 38530291 DOI: 10.1021/acs.jcim.3c02013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
DeepKa is a deep-learning-based protein pKa predictor proposed in our previous work. In this study, a web server was developed that enables online protein pKa prediction driven by DeepKa. The web server provides a user-friendly interface where a single step of entering a valid PDB code or uploading a PDB format file is required to submit a job. Two case studies have been attached in order to explain how pKa's calculated by the web server could be utilized by users. Finally, combining the web server with post processing as described in case studies, this work suggests a quick workflow of investigating the relationship between protein structure and function that are pH dependent. The web server of DeepKa is freely available at http://www.computbiophys.com/DeepKa/main.
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Affiliation(s)
- Zhitao Cai
- College of Computer Engineering, Jimei University, Xiamen 361021, China
| | - Hao Peng
- National Pilot School of Software, Yunnan University, Kunming 650504, China
| | - Shuo Sun
- College of Computer Engineering, Jimei University, Xiamen 361021, China
| | - Jiahao He
- College of Computer Engineering, Jimei University, Xiamen 361021, China
| | - Fangfang Luo
- College of Computer Engineering, Jimei University, Xiamen 361021, China
| | - Yandong Huang
- College of Computer Engineering, Jimei University, Xiamen 361021, China
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Li S, Wang Z, Li Z, Xie S, Shan X, Cai Z. Intraosseous schwannoma of the mandible: new case series, literature update, and proposal of a classification. Int J Oral Maxillofac Surg 2024; 53:205-211. [PMID: 37716827 DOI: 10.1016/j.ijom.2023.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 08/15/2023] [Accepted: 08/29/2023] [Indexed: 09/18/2023]
Abstract
Intraosseous schwannoma of the mandible is rare, with diagnostic and therapeutic challenges. The aims of this study were to report new cases of intraosseous schwannoma of the mandible and to propose a clinical classification, providing suggestions for treatment methods. The cases of 13 patients treated at the authors' hospital and 86 cases reported previously in the literature were reviewed. The most common clinical feature was facial swelling (60/93). The rate of cortical thinning or expansion was 44.8% (43/96); widening of the inferior alveolar nerve canal on radiographs was observed in 15 patients.
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Affiliation(s)
- S Li
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Haidian District, Beijing, PR China
| | - Z Wang
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Haidian District, Beijing, PR China
| | - Z Li
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Haidian District, Beijing, PR China
| | - S Xie
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Haidian District, Beijing, PR China
| | - X Shan
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Haidian District, Beijing, PR China
| | - Z Cai
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Haidian District, Beijing, PR China.
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Yuan XL, Wu YB, Song XL, Chen Y, Lu Y, Lai XY, Shi JM, Liu LZ, Zhao YM, Yu J, Yang LX, Lan JP, Cai Z, Huang H, Luo Y. [Efficacy and prognostic factors of allogeneic hematopoietic stem cell transplantation in the treatment of secondary acute myeloid leukemia]. Zhonghua Xue Ye Xue Za Zhi 2024; 45:41-47. [PMID: 38527837 DOI: 10.3760/cma.j.cn121090-20230929-00151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Objective: To evaluate the efficacy and prognostic factors of allogeneic hematopoietic stem cell transplantation (allo-HSCT) in patients with secondary acute myeloid leukemia (sAML) . Methods: In this multicenter, retrospective clinical study, adult patients aged ≥18 years who underwent allo-HSCT for sAML at four centers of the Zhejiang Hematopoietic Stem Cell Transplantation Collaborative Group from January 2014 to November 2022 were included, and the efficacy and prognostic factors of allo-HSCT were analyzed. Results: A total of 95 patients were enrolled; 66 (69.5%) had myelodysplastic syndrome-acute myeloid leukemia (MDS-AML) , 4 (4.2%) had MDS/MPN-AML, and 25 (26.3%) had therapy-related AML (tAML) . The 3-year CIR, LFS, and overall survival (OS) rates were 18.6% (95% CI 10.2%-27.0%) , 70.6% (95% CI 60.8%-80.4%) , and 73.3% (95% CI 63.9%-82.7%) , respectively. The 3-year CIRs of the M-AML group (including MDS-AML and MDS/MPN-AML) and the tAML group were 20.0% and 16.4%, respectively (P=0.430) . The 3-year LFSs were 68.3% and 75.4%, respectively (P=0.176) . The 3-year OS rates were 69.7% and 75.4%, respectively (P=0.233) . The 3-year CIRs of the groups with and without TP53 mutations were 60.0% and 13.7%, respectively (P=0.003) ; the 3-year LFSs were 20.0% and 76.5%, respectively (P=0.002) ; and the 3-year OS rates were 40.0% and 77.6%, respectively (P=0.002) . According to European LeukmiaNet 2022 (ELN2022) risk stratification, the 3-year CIRs of patients in the low-, intermediate-, and high-risk groups were 8.3%, 17.8%, and 22.6%, respectively (P=0.639) . The three-year LFSs were 91.7%, 69.5%, and 65.6%, respectively (P=0.268) . The 3-year OS rates were 91.7%, 71.4%, and 70.1%, respectively (P=0.314) . Multivariate analysis revealed that advanced disease at allo-HSCT and TP53 mutations were independent risk factors for CIR, LFS, and OS. Conclusion: There was no significant difference in the prognosis of patients who underwent allo-HSCT among the MDS-AML, MDS/MPN-AML, and tAML groups. Advanced disease at transplantation and TP53 mutations were poor prognostic factors. ELN2022 risk stratification had limited value for predicting the prognosis of patients with sAML following allo-HSCT.
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Affiliation(s)
- X L Yuan
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine; Liangzhu Laboratory; Institute of Hematology, Zhejiang University; Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310003, China
| | - Y B Wu
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine; Liangzhu Laboratory; Institute of Hematology, Zhejiang University; Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310003, China
| | - X L Song
- Zhejiang Provincial People's Hospital, Hangzhou 310014, China
| | - Y Chen
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325035, China
| | - Y Lu
- People's Hospital Affiliated to Ningbo University, Ningbo 315000, China
| | - X Y Lai
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine; Liangzhu Laboratory; Institute of Hematology, Zhejiang University; Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310003, China
| | - J M Shi
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine; Liangzhu Laboratory; Institute of Hematology, Zhejiang University; Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310003, China
| | - L Z Liu
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine; Liangzhu Laboratory; Institute of Hematology, Zhejiang University; Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310003, China
| | - Y M Zhao
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine; Liangzhu Laboratory; Institute of Hematology, Zhejiang University; Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310003, China
| | - J Yu
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine; Liangzhu Laboratory; Institute of Hematology, Zhejiang University; Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310003, China
| | - L X Yang
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine; Liangzhu Laboratory; Institute of Hematology, Zhejiang University; Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310003, China
| | - J P Lan
- Zhejiang Provincial People's Hospital, Hangzhou 310014, China
| | - Z Cai
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine; Liangzhu Laboratory; Institute of Hematology, Zhejiang University; Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310003, China
| | - H Huang
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine; Liangzhu Laboratory; Institute of Hematology, Zhejiang University; Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310003, China
| | - Y Luo
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine; Liangzhu Laboratory; Institute of Hematology, Zhejiang University; Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou 310003, China
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Luo Y, Wu X, Cai Z, Liu F, Li L, Tu Y. The Effect of Splenic Irradiation on Mean Fluorescence Intensity Values of HLA Antibody in Presensitized Patients Waiting for Kidney Transplantation. Transplant Proc 2023; 55:2362-2371. [PMID: 37891022 DOI: 10.1016/j.transproceed.2023.09.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 08/21/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023]
Abstract
To explore the desensitization treatment of patients waiting for kidney transplantation, this article comparative analysis of the effect of splenic irradiation on mean fluorescence intensity (MFI) values of HLA antibodies of 4 presensitized patients. After splenic irradiation, the mean MFI values of HLA-I antibody in 4 patients all decreased (P ≤ .001, P ≤ .001, P ≤ .001, P ≤ .001), and 3 patients had a decrease in intensity level (P ≤ .001, P = .001, P ≤ .001); as for HLA-II antibody, the mean MFI values in 3 patients also decreased (P ≤ .001, P = .025, P = .016), 1 patient had a decrease in intensity level (P ≤ .001) and the other 2 cases had no significant changes (P = 1.000, P = .564). On the other hand, splenic irradiation reduces MFI values in different levels of HLA antibody. So, splenic irradiation can reduce the MFI values of HLA antibodies.
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Affiliation(s)
- Yu Luo
- Department of Urology, Wuhan Sixth Hospital Affiliated Hospital of Jianghan University, Wuhan, China; Department of Nephropathy & Dialysis & Kidney Transplantation, Renmin Hospital of Wuhan University, Wuhan, China.
| | - Xiongfei Wu
- Department of Nephropathy & Dialysis & Kidney Transplantation, Renmin Hospital of Wuhan University, Wuhan, China.
| | - Zhitao Cai
- Department of Nephropathy & Dialysis & Kidney Transplantation, Renmin Hospital of Wuhan University, Wuhan, China
| | - Feng Liu
- Department of Urology, Wuhan Sixth Hospital Affiliated Hospital of Jianghan University, Wuhan, China; Department of Nephropathy & Dialysis & Kidney Transplantation, Renmin Hospital of Wuhan University, Wuhan, China
| | - Lian Li
- Department of Nephropathy & Dialysis & Kidney Transplantation, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yafang Tu
- Department of Nephropathy & Dialysis & Kidney Transplantation, Renmin Hospital of Wuhan University, Wuhan, China
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Luo Y, Cai Z, Wu X, Liu F, Li L. Transcription Factor ATF3 Mediating SOCS3 Expression Aggravates Renal Ischemia-Reperfusion Injury by Activating Mitophagy. Nephron Clin Pract 2023; 148:230-244. [PMID: 37956656 DOI: 10.1159/000531912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 06/09/2023] [Indexed: 11/15/2023] Open
Abstract
INTRODUCTION Suppressor of cytokine signaling 3 (SOCS3) is highly expressed in mice with renal ischemia/reperfusion (RI/R) injury and has the potential to regulate mitophagy. On this basis, this study further investigates the possible mechanism via which SOCS3 affects RI/R by regulating mitophagy. METHOD After establishing a RI/R injury mouse model and a hypoxia/reoxygenation (H/R) cell model, the effects of silenced SOCS3 on injury and mitophagy in the above models were analyzed by ELISA, quantitative real-time polymerase chain reaction, Western blot, pathological sections, CCK-8 assay, flow cytometry, and JC-1 assay. Mechanistic studies were carried out with the help of database analysis and binding validation experiments (chromatin immunoprecipitation, dual-luciferase reporter assay, and co-immunoprecipitation). After the binding target was identified, the regulatory relationship between the target gene and SOCS3 was verified by rescue experiments. RESULT The large increase in blood urea nitrogen (BUN) and creatinine (Cr) levels verified the success of the RI/R model. SOCS3 expression was up-regulated in RI/R mice. Silenced SOCS3 alleviated kidney damage and mitochondrial abnormalities in RI/R mice and inhibited mitophagy at the molecular level. Likewise, silenced SOCS3 alleviated H/R-induced cell damage and mitophagy. Finally, activating transcription factor 3 (ATF3) was determined to bind to the promoter of SOCS3, which interacted with insulin-like growth factor 1 receptor (IGF1R). Rescue experiments confirmed the effect of ATF3 on SOCS3 expression and the underlying regulatory mechanism. CONCLUSION ATF3 mediates SOCS3 expression to promote the activation of mitophagy, thereby aggravating renal ischemia-reperfusion injury.
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Affiliation(s)
- Yu Luo
- Department of Urology, Wuhan Sixth Hospital Affiliated Hospital of Jianghan University, Wuhan, China
- Department of Nephropathy and Dialysis and Kidney Transplantation, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zhitao Cai
- Department of Nephropathy and Dialysis and Kidney Transplantation, Renmin Hospital of Wuhan University, Wuhan, China
| | - Xiongfei Wu
- Department of Nephropathy and Dialysis and Kidney Transplantation, Renmin Hospital of Wuhan University, Wuhan, China
| | - Feng Liu
- Department of Urology, Wuhan Sixth Hospital Affiliated Hospital of Jianghan University, Wuhan, China
- Department of Nephropathy and Dialysis and Kidney Transplantation, Renmin Hospital of Wuhan University, Wuhan, China
| | - Lian Li
- Department of Nephropathy and Dialysis and Kidney Transplantation, Renmin Hospital of Wuhan University, Wuhan, China
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Sahana G, Cai Z, Sanchez MP, Bouwman AC, Boichard D. Invited review: Good practices in genome-wide association studies to identify candidate sequence variants in dairy cattle. J Dairy Sci 2023:S0022-0302(23)00357-0. [PMID: 37349208 DOI: 10.3168/jds.2022-22694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 02/01/2023] [Indexed: 06/24/2023]
Abstract
Genotype data from dairy cattle selection programs have greatly facilitated GWAS to identify variants related to economic traits. Results can enhance the accuracy of genomic prediction, analyze more complex models that go beyond additive effects, elucidate the genetic architecture of a trait, and finally, decipher the underlying biology of traits. The entire process, comprising data generation, quality control, statistical analyses, interpretation of association results, and linking results to biology should be designed and executed to minimize the generation of false-positive and false-negative associations and misleading links to biological processes. This review aims to provide general guidelines for data analysis that address data quality control, association tests, adjustment for population stratification, and significance evaluation to improve the reliability of conclusions. We also provide guidance on post-GWAS strategy and the interpretation of results. These guidelines are tailored to dairy cattle, which are characterized by long-range linkage disequilibrium, large half-sib families, and routinely collected phenotypes, requiring different approaches than those applied in human GWAS. We discuss common limitations and challenges that have been overlooked in the analysis and interpretation of GWAS to identify candidate sequence variants in dairy cattle.
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Affiliation(s)
- G Sahana
- Aarhus University, Center for Quantitative Genetic and Genomics, 8830 Tjele, Denmark.
| | - Z Cai
- Aarhus University, Center for Quantitative Genetic and Genomics, 8830 Tjele, Denmark
| | - M P Sanchez
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France
| | - A C Bouwman
- Wageningen University & Research, Animal Breeding and Genomics, 6700 AH Wageningen, the Netherlands
| | - D Boichard
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France
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Cai Z, Liu T, Lin Q, He J, Lei X, Luo F, Huang Y. Basis for Accurate Protein p Ka Prediction with Machine Learning. J Chem Inf Model 2023; 63:2936-2947. [PMID: 37146199 DOI: 10.1021/acs.jcim.3c00254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
pH regulates protein structures and the associated functions in many biological processes via protonation and deprotonation of ionizable side chains where the titration equilibria are determined by pKa's. To accelerate pH-dependent molecular mechanism research in the life sciences or industrial protein and drug designs, fast and accurate pKa prediction is crucial. Here we present a theoretical pKa data set PHMD549, which was successfully applied to four distinct machine learning methods, including DeepKa, which was proposed in our previous work. To reach a valid comparison, EXP67S was selected as the test set. Encouragingly, DeepKa was improved significantly and outperforms other state-of-the-art methods, except for the constant-pH molecular dynamics, which was utilized to create PHMD549. More importantly, DeepKa reproduced experimental pKa orders of acidic dyads in five enzyme catalytic sites. Apart from structural proteins, DeepKa was found applicable to intrinsically disordered peptides. Further, in combination with solvent exposures, it is revealed that DeepKa offers the most accurate prediction under the challenging circumstance that hydrogen bonding or salt bridge interaction is partly compensated by desolvation for a buried side chain. Finally, our benchmark data qualify PHMD549 and EXP67S as the basis for future developments of protein pKa prediction tools driven by artificial intelligence. In addition, DeepKa built on PHMD549 has been proven an efficient protein pKa predictor and thus can be applied immediately to, for example, pKa database construction, protein design, drug discovery, and so on.
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Affiliation(s)
- Zhitao Cai
- College of Computer Engineering, Jimei University, Xiamen 361021, China
| | - Tengzi Liu
- College of Computer Engineering, Jimei University, Xiamen 361021, China
| | - Qiaoling Lin
- College of Computer Engineering, Jimei University, Xiamen 361021, China
| | - Jiahao He
- College of Computer Engineering, Jimei University, Xiamen 361021, China
| | - Xiaowei Lei
- College of Computer Engineering, Jimei University, Xiamen 361021, China
| | - Fangfang Luo
- College of Computer Engineering, Jimei University, Xiamen 361021, China
| | - Yandong Huang
- College of Computer Engineering, Jimei University, Xiamen 361021, China
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Zhang Z, Zhao J, Man H, Qi L, Yin H, Lv Z, Jiang Y, Dong J, Zeng M, Cai Z, Luo Z, He K, Liu H. Updating emission inventories for vehicular organic gases: Indications from cold-start and temperature effects on advanced technology cars. Sci Total Environ 2023; 882:163544. [PMID: 37076011 DOI: 10.1016/j.scitotenv.2023.163544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 05/03/2023]
Abstract
How would the organic gas emission inventories of future urban vehicles change with new features of advanced technology cars? Here, volatile organic compounds (VOCs) and intermediate volatile organic compounds (IVOCs) from a fleet of Chinese light-duty gasoline vehicles (LDGVs) were characterized by chassis dynamometer experiments to grasp the key factors affecting future inventory accuracy. Subsequently, the VOC and IVOC emissions of LDGVs in Beijing, China, from 2020 to 2035, were calculated and the spatial-temporal variations were recognized under a scenario of fleet renewal. With the tightening of emission standards (ESs), cold start contributed a larger fraction of the total unified cycle VOC emissions due to the imbalanced emission reductions between operating conditions. It took 757.47 ± 337.75 km of hot running to equal one cold-start VOC emission for the latest certified vehicles. Therefore, the future tailpipe VOC emissions would be highly dependent on discrete cold start events rather than traffic flows. By contrast, the equivalent distance was shorter and more stable for IVOCs, with an average of 8.69 ± 4.59 km across the ESs, suggesting insufficient controls. Furthermore, there were log-linear relationships between temperatures and cold-start emissions, and the gasoline direct-injection vehicles performed better adaptability under low temperatures. In the updated emission inventories, the VOC emissions were more effectively reduced than the IVOC emissions. The start emissions of VOCs were estimated to be increasingly dominant, especially in wintertime. By winter 2035, the contribution of VOC start emissions could reach 98.98 % in Beijing, while the fraction of IVOC start emissions would decrease to 59.23 %. Spatially allocation showed that the high emission regions of tailpipe organic gases from LDGVs have transferred from road networks to regions of intense human activities. Our results provide new insights into tailpipe organic gas emissions of gasoline vehicles, and can support future emission inventories and refined assessment of air quality and human health risk.
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Affiliation(s)
- Zhining Zhang
- State Key Joint Laboratory of ESPC, State Environmental Protection Key Laboratory of Sources and Control of Air Pollution Complex, School of Environment, Tsinghua University, Beijing 100084, China
| | - Junchao Zhao
- State Key Joint Laboratory of ESPC, State Environmental Protection Key Laboratory of Sources and Control of Air Pollution Complex, School of Environment, Tsinghua University, Beijing 100084, China
| | - Hanyang Man
- College of Environment and Resource Sciences, Fujian Key Laboratory of Pollution Control & Resource Reuse, Fuzhou 350007, China
| | - Lijuan Qi
- State Key Laboratory of Plateau Ecology and Agriculture, College of Eco-environmental Engineering, Qinghai University, Xining 810016, China
| | - Hang Yin
- State Environmental Protection Key Laboratory of Vehicle Emission Control and Simulation, Vehicle Emission Control Center, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Zhaofeng Lv
- State Key Joint Laboratory of ESPC, State Environmental Protection Key Laboratory of Sources and Control of Air Pollution Complex, School of Environment, Tsinghua University, Beijing 100084, China
| | - Yuheng Jiang
- State Key Joint Laboratory of ESPC, State Environmental Protection Key Laboratory of Sources and Control of Air Pollution Complex, School of Environment, Tsinghua University, Beijing 100084, China
| | - Junjie Dong
- State Key Joint Laboratory of ESPC, State Environmental Protection Key Laboratory of Sources and Control of Air Pollution Complex, School of Environment, Tsinghua University, Beijing 100084, China
| | - Meng Zeng
- State Key Joint Laboratory of ESPC, State Environmental Protection Key Laboratory of Sources and Control of Air Pollution Complex, School of Environment, Tsinghua University, Beijing 100084, China
| | - Zhitao Cai
- State Key Joint Laboratory of ESPC, State Environmental Protection Key Laboratory of Sources and Control of Air Pollution Complex, School of Environment, Tsinghua University, Beijing 100084, China
| | - Zhenyu Luo
- State Key Joint Laboratory of ESPC, State Environmental Protection Key Laboratory of Sources and Control of Air Pollution Complex, School of Environment, Tsinghua University, Beijing 100084, China
| | - Kebin He
- State Key Joint Laboratory of ESPC, State Environmental Protection Key Laboratory of Sources and Control of Air Pollution Complex, School of Environment, Tsinghua University, Beijing 100084, China
| | - Huan Liu
- State Key Joint Laboratory of ESPC, State Environmental Protection Key Laboratory of Sources and Control of Air Pollution Complex, School of Environment, Tsinghua University, Beijing 100084, China.
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Xiong YF, Cai Z, Li SC, Song YJ, Hu XM, Zheng L. [Bioinformatics analysis in metagenomic next-generation sequencing of pathogenic microorganisms: current status and challenges]. Zhonghua Yi Xue Za Zhi 2023; 103:1098-1102. [PMID: 37055228 DOI: 10.3760/cma.j.cn112137-20221208-02598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
The clinical application of metagenomic next-generation sequencing (mNGS) in the diagnosis of unknown pathogenic infections and critical infections has become increasingly valuable. Due to the huge volume of mNGS data and the complexity of clinical diagnosis and treatment, mNGS has difficulties in data analysis and interpretation in practical application. Therefore, in the process of clinical practice, it is crucial to grasp the key points of bioinformatics analysis and establish a standardized bioinformatics analysis process, which is an important step in the transformation of mNGS from laboratory to clinic. At present, bioinformatics analysis of mNGS has made great progress, but with the high requirements of clinical standardization of bioinformatics analysis and the development of computer technology, bioinformatics analysis of mNGS is also facing new challenges. This article mainly elaborates on quality control, and identification and visualization of pathogenic bacteria.
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Affiliation(s)
- Y F Xiong
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Z Cai
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - S C Li
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Y J Song
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - X M Hu
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - L Zheng
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
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Huang JC, Yu ZZ, Zou F, Li M, Cai Z, Liu GL, Li GY. [Progress in the clinical research of malignant melanoma in nasal cavity and paranasal sinuses]. Zhonghua Er Bi Yan Hou Tou Jing Wai Ke Za Zhi 2023; 58:297-302. [PMID: 36878516 DOI: 10.3760/cma.j.cn115330-20220608-00337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Affiliation(s)
- J C Huang
- Postgraduate Training Base of Shiyan Taihe Hospital of Hubei Medical College, Shiyan 442000, China
| | - Z Z Yu
- Department of Otorhinolaryngology Head and Neck Surgery, Shiyan Taihe Hospital (Affiliated Hospital of Hubei Medical College), Shiyan 442000, China
| | - F Zou
- Department of Otorhinolaryngology Head and Neck Surgery, Shiyan Taihe Hospital (Affiliated Hospital of Hubei Medical College), Shiyan 442000, China
| | - M Li
- Department of Otorhinolaryngology Head and Neck Surgery, Shiyan Taihe Hospital (Affiliated Hospital of Hubei Medical College), Shiyan 442000, China
| | - Z Cai
- Department of Otorhinolaryngology Head and Neck Surgery, Shiyan Taihe Hospital (Affiliated Hospital of Hubei Medical College), Shiyan 442000, China
| | - G L Liu
- Department of Otorhinolaryngology Head and Neck Surgery, Shiyan Taihe Hospital (Affiliated Hospital of Hubei Medical College), Shiyan 442000, China
| | - G Y Li
- Department of Otorhinolaryngology Head and Neck Surgery, Shiyan Taihe Hospital (Affiliated Hospital of Hubei Medical College), Shiyan 442000, China
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Zhang Z, Man H, Zhao J, Jiang Y, Zeng M, Cai Z, Huang C, Huang W, Zhao H, Jing S, Shi X, He K, Liu H. Primary organic gas emissions in vehicle cold start events: Rates, compositions and temperature effects. J Hazard Mater 2022; 435:128979. [PMID: 35472544 DOI: 10.1016/j.jhazmat.2022.128979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 03/31/2022] [Accepted: 04/18/2022] [Indexed: 06/14/2023]
Abstract
Identification of air toxics emitted from light-duty gasoline vehicles (LDGVs) is expected to better protect human health. Here, the volatile organic compound (VOC) and intermediate VOC (IVOC) emissions in the high-emitted start stages were measured on a chassis dynamometer under normal and extreme temperatures for China 6 LDGVs. Low temperature enhanced the emission rates (ERs) of both VOCs and IVOCs. The VOC ERs were averaged 5.19 ± 2.74 times higher when the temperature dropped from 23 °C to 0 °C, and IVOCs were less sensitive to temperature change with an enlargement of 2.27 ± 0.19 times. Aromatics (46.75 ± 2.83%) and alkanes (18.46 ± 1.21%) dominated the cold start VOC emissions under normal temperature, which was quite different from hot running emission profiles. From the perspective of emission inventories, changes in the speciated composition of VOCs and IVOCs were less important than that in the actual magnitude of ERs under cold conditions. However, changes in the ERs and emission profiles were equally important at high temperatures. Furthermore, high time-resolved measurements revealed that low temperature enhanced both the emission peak and peak duration of fuel components and incomplete combustion products during cold start, while high temperature only increased the peak concentration of fuel components.
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Affiliation(s)
- Zhining Zhang
- State Key Joint Laboratory of ESPC, State Environmental Protection Key Laboratory of Sources and Control of Air Pollution Complex, School of Environment, Tsinghua University, Beijing 100084, China
| | - Hanyang Man
- Key Laboratory of Pollution Control and Resource Recycling of Fujian Province, College of Environmental Science and Engineering, Fujian Normal University, Fuzhou 350007, China
| | - Junchao Zhao
- State Key Joint Laboratory of ESPC, State Environmental Protection Key Laboratory of Sources and Control of Air Pollution Complex, School of Environment, Tsinghua University, Beijing 100084, China
| | - Yuheng Jiang
- State Key Joint Laboratory of ESPC, State Environmental Protection Key Laboratory of Sources and Control of Air Pollution Complex, School of Environment, Tsinghua University, Beijing 100084, China
| | - Meng Zeng
- State Key Joint Laboratory of ESPC, State Environmental Protection Key Laboratory of Sources and Control of Air Pollution Complex, School of Environment, Tsinghua University, Beijing 100084, China
| | - Zhitao Cai
- State Key Joint Laboratory of ESPC, State Environmental Protection Key Laboratory of Sources and Control of Air Pollution Complex, School of Environment, Tsinghua University, Beijing 100084, China
| | - Cheng Huang
- State Environmental Protection Key Laboratory of Formation and Prevention of Urban Air Pollution Complex, Shanghai Academy of Environmental Sciences, Shanghai 200233, China
| | - Wendong Huang
- Shanghai Motor Vehicle Inspection Certification & Tech Innovation Center Co., Ltd, Shanghai 201805, China
| | - Haiguang Zhao
- State Environmental Protection Key Laboratory of Vehicle Emission Control and Simulation, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Shengao Jing
- State Environmental Protection Key Laboratory of Formation and Prevention of Urban Air Pollution Complex, Shanghai Academy of Environmental Sciences, Shanghai 200233, China
| | - Xu Shi
- Shanghai Motor Vehicle Inspection Certification & Tech Innovation Center Co., Ltd, Shanghai 201805, China
| | - Kebin He
- State Key Joint Laboratory of ESPC, State Environmental Protection Key Laboratory of Sources and Control of Air Pollution Complex, School of Environment, Tsinghua University, Beijing 100084, China
| | - Huan Liu
- State Key Joint Laboratory of ESPC, State Environmental Protection Key Laboratory of Sources and Control of Air Pollution Complex, School of Environment, Tsinghua University, Beijing 100084, China.
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van Egmond S, Cai Z, Nava V, Rapaport B, Ko J, Chiou A, Sarin K, Tang J, Bousheri S, Zhang L, Linos E. 349 Development of a digital tool for home-based monitoring of skin disease for older adults. J Invest Dermatol 2022. [PMCID: PMC9296962 DOI: 10.1016/j.jid.2022.05.358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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van Egmond S, de Vere Hunt I, Cai Z, Rizk N, Wakkee M, Chren M, Goldfarb N, Simard J, Linos E. 374 529 dermatologists’ perspectives on active surveillance for low-risk basal cell carcinoma. J Invest Dermatol 2022. [DOI: 10.1016/j.jid.2022.05.383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Wang Z, Zhao Z, Xia Y, Cai Z, Wang C, Shen Y, Liu R, Qin H, Jia J, Yuan G. Potential biomarkers in the fibrosis progression of nonalcoholic steatohepatitis (NASH). J Endocrinol Invest 2022; 45:1379-1392. [PMID: 35226336 DOI: 10.1007/s40618-022-01773-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/17/2022] [Indexed: 12/13/2022]
Abstract
PURPOSE Fibrosis is the only histological feature reflecting the severity and prognosis of nonalcoholic steatohepatitis (NASH). We aim to explore novel genes associated with fibrosis progression in NASH. METHODS Two human RNA-seq datasets were downloaded from the public database. Weighted gene co-expression network analysis (WGCNA) was used to identify their co-expressed modules and further bioinformatics analysis was performed to identify hub genes within the modules. Finally, based on two single-cell RNA-seq datasets from mice and one microarray dataset from human, we further observed the expression of hub genes in different cell clusters and liver tissues. RESULTS 7 hub genes (SPP1, PROM1, SOX9, EPCAM, THY1, CD34 and MCAM) associated with fibrosis progression were identified. Single-cell RNA-seq analysis revealed that those hub genes were expressed by different cell clusters such as cholangiocytes, natural killer (NK) cells, and hepatic stellate cells (HSCs). We also found that SPP1 and CD34 serve as markers of different HSCs clusters, which are associated with inflammatory response and fibrogenesis, respectively. Further study suggested that SPP1, SOX9, MCAM and THY1 might be related to NASH-associated hepatocellular carcinoma (HCC). Receiver operating characteristic (ROC) analysis showed that the high expression of these genes could well predict the occurrence of HCC. At the same time, there were significant differences in metabolism-related pathway changes between different HCC subtypes, and SOX9 may be involved in these changes. CONCLUSIONS The present study identified novel genes associated with NASH fibrosis and explored their effects on fibrosis from a single-cell perspective that might provide new ideas for the early diagnosis, monitoring, evaluation, and prediction of fibrosis progression in NASH.
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Affiliation(s)
- Z Wang
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, Jiangsu, China
| | - Z Zhao
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, Jiangsu, China
| | - Y Xia
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, Jiangsu, China
| | - Z Cai
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, Jiangsu, China
| | - C Wang
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, Jiangsu, China
| | - Y Shen
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, Jiangsu, China
| | - R Liu
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, Jiangsu, China
| | - H Qin
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, Jiangsu, China
| | - J Jia
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, Jiangsu, China.
| | - G Yuan
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, Jiangsu, China.
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Cai Z, Mu M, Zhang B. P-223 An eleven-lncRNA signature predicts overall survival in patients with gastric cancer. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.04.313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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Mu M, Cai Z, Shen C, Wang J, Zhao Z, Zhang B. P-220 The efficacy of preoperative imatinib in locally advanced gastrointestinal stromal tumors: A single-center retrospective analysis. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.04.310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Cai Z, Zhao Z, Mu M, Shen C, Zhang B. P-215 Liver transplantation for hilar cholangiocarcinoma: A systematic review and meta-analysis. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.04.305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Cai Z, Chen WM. [Interpretation of treatment of relapsed/refractory multiple myeloma patients in the guidelines for the diagnosis and management of multiple myeloma in China(2022 revision)]. Zhonghua Nei Ke Za Zhi 2022; 61:469-473. [PMID: 35488595 DOI: 10.3760/cma.j.cn112138-20220414-00278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Z Cai
- Department of Bone Marrow Transplantation,the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - W M Chen
- Department of Hematology,Beijing Chao-yang Hospital,Capital Medical University, Beijing 100020, China
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Cai Z, Huang Y, Tang JH, Zhang R, Chen JK, Wang J, Ma YY. [Heparin-binding hemagglutinin as a composition antigen of tuberculosis vaccine exerts protective immune effects by inducing IL-17]. Zhonghua Yu Fang Yi Xue Za Zhi 2022; 56:370-376. [PMID: 35381662 DOI: 10.3760/cma.j.cn112150-20211206-01122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
To explore the protective immune effect induced by mucosal delivery heparin-binding hemagglutinin (HBHA)-a candidate vaccine antigen of Mycobacterium tuberculosis. Female C57BL/6 mice were between 6 and 8 weeks of age before experimental use. Thirty mice received different immunization strategies and were randomly divided into the control group, the early secreting antigen target-6 (ESAT-6) intranasal immunization group, the HBHA intranasal immunization group, the BCG priming PBS control group, or BCG priming HBHA boost group, 6 mice in each group. In order to analyzed the immune effect, the concentrations of plasma Interleukin-17A (IL-17A) and other cytokines were measured by ELISA. Quantitative real-time PCR analyses were performed to detect the relative quantity (RQ) mRNA of IL-17A in the lung. The lung tissue sections were stained to detect the formation of the tertiary lymphoid structures. The chemokines contributed to formation of the tertiary lymphoid structures were also measured. Flow cytometry was used to detect the frequency of Th1 and Th17 cells in the system. Sixty mice in the BCG priming PBS control group and the BCG priming HBHA boost group were sacrificed at different time points after infection to count the lung bacterial burden. The concentrations of plasma IL-17A and relative quantity of lung IL-17A mRNA were highest in the BCG priming HBHA boost group [(14.76±4.73) pg/mL,RQ (12.27±6.71)], which was significantly higher than the control group [(5.57±2.95) pg/mL,RQ (1.30±0.97)] (t=4.213, P<0.001; t=5.984, P<0.001), and also significantly higher than the BCG priming PBS control group [(6.81±2.18) pg/mL,RQ (1.44±1.16)] (t=3.646 P=0.001; t=6.185 P<0.001). Compared with the BCG priming PBS control group (0.38±0.38)% the frequency of spleen Th17 cells were also significantly increased (t=-0.280, P=0.048) in the BCG-primary HBHA boost group (1.02±0.34)%. In addition, HBHA boosting could promote better formation of the tertiary lymphoid structures in the lung, and decrease the bacterial load on the early stage after BCG challenge. Collectively, mucosal delivery of HBHA can effectively enhance the protective effect after BCG vaccination, and it is a potential candidate vaccine component.
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Affiliation(s)
- Z Cai
- Department of Clinical Laboratory, Air Force Medical Center, Beijing 100142, China
| | - Y Huang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - J H Tang
- Department of Clinical Laboratory, Air Force Medical Center, Beijing 100142, China
| | - R Zhang
- Department of Clinical Laboratory, the First Affiliated Hospital, Air Force Medical University, Xi'an 710032, China
| | - J K Chen
- Department of Clinical Laboratory, the First Affiliated Hospital, Air Force Medical University, Xi'an 710032, China
| | - J Wang
- Department of Clinical Laboratory, the First Affiliated Hospital, Air Force Medical University, Xi'an 710032, China
| | - Y Y Ma
- Department of Clinical Laboratory, Air Force Medical Center, Beijing 100142, China
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Cai Z, Luo F, Wang Y, Li E, Huang Y. Protein p K a Prediction with Machine Learning. ACS Omega 2021; 6:34823-34831. [PMID: 34963965 PMCID: PMC8697405 DOI: 10.1021/acsomega.1c05440] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/24/2021] [Indexed: 05/23/2023]
Abstract
Protein pK a prediction is essential for the investigation of the pH-associated relationship between protein structure and function. In this work, we introduce a deep learning-based protein pK a predictor DeepKa, which is trained and validated with the pK a values derived from continuous constant-pH molecular dynamics (CpHMD) simulations of 279 soluble proteins. Here, the CpHMD implemented in the Amber molecular dynamics package has been employed (Huang Y.J. Chem. Inf. Model.2018, 58, 1372-1383). Notably, to avoid discontinuities at the boundary, grid charges are proposed to represent protein electrostatics. We show that the prediction accuracy by DeepKa is close to that by CpHMD benchmarking simulations, validating DeepKa as an efficient protein pK a predictor. In addition, the training and validation sets created in this study can be applied to the development of machine learning-based protein pK a predictors in the future. Finally, the grid charge representation is general and applicable to other topics, such as the protein-ligand binding affinity prediction.
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Cai Z, Ding M, Chen R, Zhu J, Li L, Wu X. Primary hyperoxaluria diagnosed after kidney transplantation: a case report and literature review. BMC Nephrol 2021; 22:393. [PMID: 34837989 PMCID: PMC8626922 DOI: 10.1186/s12882-021-02546-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 09/29/2021] [Indexed: 12/02/2022] Open
Abstract
Background Primary hyperoxaluria (PH) is a rare inherited autosomal recessive disease caused by disturbed glyoxylate metabolism. The disease is characterized by calcium oxalate crystal deposition in various organs, especially in the kidney. Due to the lack of current understanding of PH, nearly all patients are only initially diagnosed with PH when recurrent lithiasis and progressive end-stage renal disease occur. Many cases are not diagnosed in patients until renal allograft insufficiency occurs after renal transplantation. This case report and literature review aim to emphasize the need for careful pre-transplant PH screening of patients with bilateral nephrocalcinosis or nephrolithiasis. Case presentation Renal allograft insufficiency was diagnosed as PH after kidney transplantation. Here, we detail the complete clinical course, including computed tomography images of the original kidney and renal graft, histopathological images of a biopsy of the transplanted kidney, the results of laboratory and molecular genetic tests, and the treatment. In addition, we reviewed the literature from 2000 to 2021 and analyzed 19 reported cases of PH diagnosed after kidney transplantation, and provide a summary of the characteristics, complications, treatment, and prognosis of these cases. Conclusions By reviewing and analyzing these cases, we concluded that patients with a history of nephrocalcinosis or nephrolithiasis in both kidneys need preoperative screening for PH and appropriate treatment before kidney transplantation. Delayed graft function caused by PH is easily misdiagnosed as acute rejection, and needle biopsy should be performed at an early stage. Supplementary Information The online version contains supplementary material available at 10.1186/s12882-021-02546-0.
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Affiliation(s)
- Zhitao Cai
- Center of Nephrology, Dialysis and Transplantation, Renmin Hospital of Wuhan University, No.238 Jiefang Road, Wuchang District, Wuhan, 430060, Hubei, China
| | - Mao Ding
- Center of Nephrology, Dialysis and Transplantation, Renmin Hospital of Wuhan University, No.238 Jiefang Road, Wuchang District, Wuhan, 430060, Hubei, China
| | - Rengui Chen
- Center of Nephrology, Dialysis and Transplantation, Renmin Hospital of Wuhan University, No.238 Jiefang Road, Wuchang District, Wuhan, 430060, Hubei, China
| | - Jiefu Zhu
- Center of Nephrology, Dialysis and Transplantation, Renmin Hospital of Wuhan University, No.238 Jiefang Road, Wuchang District, Wuhan, 430060, Hubei, China
| | - Lian Li
- Center of Nephrology, Dialysis and Transplantation, Renmin Hospital of Wuhan University, No.238 Jiefang Road, Wuchang District, Wuhan, 430060, Hubei, China
| | - Xiongfei Wu
- Center of Nephrology, Dialysis and Transplantation, Renmin Hospital of Wuhan University, No.238 Jiefang Road, Wuchang District, Wuhan, 430060, Hubei, China.
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Zhang Y, Betran AP, Li X, Liu D, Yuan N, Shang L, Lin W, Tu S, Wang L, Wu X, Zhu T, Zhang Y, Lu Z, Zheng L, Gu C, Fang J, Liu Z, Ma L, Cai Z, Yang X, Li H, Zhang H, Zhao X, Yan L, Wang L, Sun X, Luo Q, Liu L, Zhu J, Qin W, Yao Q, Dong S, Yang Y, Cui Z, He Y, Feng X, He L, Zhang H, Zhang L, Wang X, Souza JP, Qi H, Duan T, Zhang J. What is an appropriate caesarean delivery rate for China: a multicentre survey. BJOG 2021; 129:138-147. [PMID: 34559941 PMCID: PMC9297886 DOI: 10.1111/1471-0528.16951] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2021] [Indexed: 11/30/2022]
Abstract
Objective To assess the current status of caesarean delivery (CD) in China, propose reference CD rates for China overall, and by regions, investigate the main indications for CDs and identify possible areas for safe reduction. Design A multicentre cross‐sectional study. Setting A total of 94 hospitals across 23 provinces in China. Population A total of 73 977 randomly selected deliveries. Methods We used a modified Robson classification to characterise CDs in subgroups and by regions, and the World Health Organization (WHO) C‐Model to calculate reference CD rates. Main outcome measures CD rates in China. Results In 2015–2016, the overall CD rate in China was 38.9% (95% CI 38.6–39.3%). Considering the obstetric characteristics of the population, the multivariable model‐based reference CD rate was estimated at 28.5% (95% CI 28.3–28.8%). Accordingly, an absolute reduction of 10.4% (or 26.7% relative reduction) may be considered. The CD rate varied substantially by region. Previous CD was the most common indication in all regions, accounting for 38.2% of all CDs, followed by maternal request (9.8%), labour dystocia (8.3%), fetal distress (7.7%) and malpresentation (7.6%). Overall, 12.7% of women had prelabour CDs, contributing to 32.8% of the total CDs. Conclusions Nearly 39% of births were delivered by caesarean in China but a reduction of this rate by a quarter may be considered attainable. Repeat CD contributed more than one‐third of the total CDs. Given the large variation in maternal characteristics, region‐specific or even hospital‐specific reference CD rates are needed for precision management of CD. Tweetable abstract The caesarean rate in 2015–2016 in China was 38.9%, whereas the reference rate was 28.5%. The caesarean rate in 2015–2016 in China was 38.9%, whereas the reference rate was 28.5%. Linked article This article is commented on by M Varner, p. 148 in this issue. To view this mini commentary visit https://doi.org/10.1111/1471-0528.16953.
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Affiliation(s)
- Y Zhang
- Ministry of Education - Shanghai Key Laboratory of Children's Environmental Health, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - A P Betran
- UNDP/UNFPA/UNICEF/WHO/World Bank Special Programme of Research, Development and Research Training in Human Reproduction, Department of Reproductive Health and Research, World Health Organization (WHO), Geneva, Switzerland
| | - X Li
- Obstetrics and Gynaecology Hospital of Fudan University, Shanghai, China
| | - D Liu
- Dongguan City Maternal and Child Health Hospital, Southern Medical University, Guangdong, China
| | - N Yuan
- Department of Obstetrics and Gynaecology, The Second Hospital Affiliated to Shaanxi University of Chinese Medicine, Shaanxi, China
| | - L Shang
- Department of Obstetrics, The Maternal and Child Health Hospital of Xinxiang, Henan, China
| | - W Lin
- Department of Obstetrics, The Maternal and Child Health Hospital of Dalian, Liaoning, China
| | - S Tu
- Department of Obstetrics and Gynaecology, Southwest Medical University, Sichuan, China
| | - L Wang
- Department of Obstetrics and Gynaecology, The First Hospital Affiliated to Kunming Medical University, Yunnan, China
| | - X Wu
- Department of Obstetrics, Jiangsu Women and Child Health Hospital, Jiangsu, China
| | - T Zhu
- The First People's Hospital of Zhaotong, Kunming Medical University, Yunnan, China
| | - Y Zhang
- Department of Obstetrics, The Maternal and Child Health Hospital of Qujing, Yunnan, China
| | - Z Lu
- Suining Central Hospital, Chongqing Medical University, Sichuan, China
| | - L Zheng
- Taizhou Hospital of Zhejiang Province, Zhejiang, China
| | - C Gu
- Yangzhou Maternal and Child Care Service Centre, Jiangsu, China
| | - J Fang
- Qingdao Chengyang People's Hospital, Shandong First Medical University, Shandong, China
| | - Z Liu
- Department of Obstetrics, The Maternal and Child Health Hospital of Baoji, Shaanxi, China
| | - L Ma
- Yanshi City People's Hospital, Henan, China
| | - Z Cai
- Department of Obstetrics and Gynaecology, Aviation Hospital of Beijing, China Medical University, Beijing, China
| | - X Yang
- Department of Obstetrics, The Maternal and Child Health Hospital of Luohu District, Shenzhen, China
| | - H Li
- Yanan University Affiliated Hospital, Shaanxi, China
| | - H Zhang
- Haikou Hospital of the Maternal and Child Health, Hainan, China
| | - X Zhao
- The First People's Hospital of Taizhou, Wenzhou Medical University, Zhejiang, China
| | - L Yan
- The Second Affiliated Hospital of Hebei North University, Hebei, China
| | - L Wang
- Department of Obstetrics and Gynaecology, The 174th Hospital of the Chinese People's Liberation Army, Xiamen University, Fujian, China
| | - X Sun
- Puyang Maternal and Child Care Centres, Henan, China
| | - Q Luo
- Luzhou People's Hospital, Sichuan, China
| | - L Liu
- Affiliated Hospital of Jiangsu University, Jiangsu, China
| | - J Zhu
- The Second People's Hospital of Tongxiang, Zhejiang, China
| | - W Qin
- Department of Obstetrics and Gynaecology, Aviation Hospital of Beijing, China Medical University, Beijing, China
| | - Q Yao
- The Central Hospital of Shaoyang, University of South China, Hunan, China
| | - S Dong
- Affiliated Hospital of Zunyi Medical University, Guizhou, China
| | - Y Yang
- The First Affiliated Hospital of Anhui Medical University, Anhui, China
| | - Z Cui
- Department of Obstetrics, The Maternal and Child Health Hospital of Cangzhou, Hebei, China
| | - Y He
- The Second People's Hospital of Qingyuan City, Guangdong, China
| | - X Feng
- Department of Obstetrics and Gynaecology, Fujian Medical University Union Hospital, Fujian Medical University, Fujian, China
| | - L He
- The People's Hospital of Pengzhou, Sichuan, China
| | - H Zhang
- Department of Obstetrics, Eastern District of the Fourth Hospital of Hebei Medical University, Hebei, China
| | - L Zhang
- Ministry of Education - Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - X Wang
- Department of Obstetrics and Gynaecology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - J P Souza
- Department of Social Medicine, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, São Paulo, Brazil
| | - H Qi
- Department of Obstetrics and Gynaecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - T Duan
- Department of Obstetrics, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - J Zhang
- Ministry of Education - Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Zhang W, Han F, Wu X, Wang Z, Wang Y, Guo X, Chen S, Qiu T, Li H, Tu Y, Zhong Z, He J, Liu B, Zhang H, Cai Z, Zhang L, Lu X, Zhu L, Chen D, Zhou J, Sun Q, Chen Z. COVID-19 in the immunocompromised population: data from renal allograft recipients throughout full cycle of the outbreak in Hubei province, China. Chin Med J (Engl) 2021; 135:228-230. [PMID: 34762388 PMCID: PMC8769129 DOI: 10.1097/cm9.0000000000001538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Indexed: 01/08/2023] Open
Affiliation(s)
- Weijie Zhang
- Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
- Key Laboratory of Organ Transplantation, Ministry of Education, National Health Commission, Chinese Academy of Medical Sciences, Wuhan, Hubei 430030, China
| | - Fei Han
- Organ Transplantation Research Institute of Sun Yat-sen University, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510000, China
| | - Xiongfei Wu
- Center of Nephrology and Dialysis, Transplantation, Renmin Hospital of Wuhan University, Wuhan, Hubei 430030, China
| | - Zhendi Wang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Yanfeng Wang
- Zhongnan Hospital of Wuhan University, Institute of Hepatobiliary Diseases of Wuhan University, Transplant Center of Wuhan University, Wuhan, Hubei 430030, China
| | - Xiaojun Guo
- Dongfeng Hospital, Hubei University of Medicine, Shiyan, Hubei 442008, China
| | - Song Chen
- Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
- Key Laboratory of Organ Transplantation, Ministry of Education, National Health Commission, Chinese Academy of Medical Sciences, Wuhan, Hubei 430030, China
| | - Tao Qiu
- Department of Transplantation, Renmin Hospital, Wuhan University, Wuhan, Hubei 430030, China
| | - Heng Li
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Yafang Tu
- Center of Nephrology and Dialysis, Transplantation, Renmin Hospital of Wuhan University, Wuhan, Hubei 430030, China
| | - Zibiao Zhong
- Zhongnan Hospital of Wuhan University, Institute of Hepatobiliary Diseases of Wuhan University, Transplant Center of Wuhan University, Wuhan, Hubei 430030, China
| | - Jiannan He
- Organ Transplantation Research Institute of Sun Yat-sen University, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510000, China
| | - Bin Liu
- Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
- Key Laboratory of Organ Transplantation, Ministry of Education, National Health Commission, Chinese Academy of Medical Sciences, Wuhan, Hubei 430030, China
| | - Hui Zhang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Zhitao Cai
- Center of Nephrology and Dialysis, Transplantation, Renmin Hospital of Wuhan University, Wuhan, Hubei 430030, China
| | - Long Zhang
- Department of Transplantation, Renmin Hospital, Wuhan University, Wuhan, Hubei 430030, China
| | - Xia Lu
- Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
- Key Laboratory of Organ Transplantation, Ministry of Education, National Health Commission, Chinese Academy of Medical Sciences, Wuhan, Hubei 430030, China
| | - Lan Zhu
- Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
- Key Laboratory of Organ Transplantation, Ministry of Education, National Health Commission, Chinese Academy of Medical Sciences, Wuhan, Hubei 430030, China
| | - Dong Chen
- Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
- Key Laboratory of Organ Transplantation, Ministry of Education, National Health Commission, Chinese Academy of Medical Sciences, Wuhan, Hubei 430030, China
| | - Jiangqiao Zhou
- Department of Transplantation, Renmin Hospital, Wuhan University, Wuhan, Hubei 430030, China
| | - Qiquan Sun
- Organ Transplantation Research Institute of Sun Yat-sen University, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510000, China
| | - Zhishui Chen
- Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
- Key Laboratory of Organ Transplantation, Ministry of Education, National Health Commission, Chinese Academy of Medical Sciences, Wuhan, Hubei 430030, China
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James R, Admire B, Sisserson T, Cai Z, Dumas M, Inge L, Baumann J, Towne P, Dalvi D, ElGabry E. 1125P Analytical assessment of a diagnostic immunohistochemical assay for the detection of folate receptor-ɑ in epithelial ovarian cancers. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.08.767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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26
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Cai Z, Wang W, Pan BH, Xie C, Yang P, Wang XW, Ouyang Y, Liu GQ, Wu KM, Le TM, Huang JH. [Choices of emergency treatment and surgical method for ruptured abdominal aortic aneurysms]. Zhonghua Yi Xue Za Zhi 2021; 101:2288-2292. [PMID: 34333943 DOI: 10.3760/cma.j.cn112137-20201216-03368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To investigate the emergency management process of ruptured abdominal aortic aneurysm (RAAA), and analyze the perioperative mortality factors of different surgical methods. Methods: The emergency data and hospitalization data of 91 patients with ruptured abdominal aortic aneurysm in Xiangya Hospital of Central South University from June 2010 to June 2019 were retrospectively analyzed.Twelve of the patients died preoperatively due to excessive blood loss, and the remaining 79 patients were hospitalized for open surgery (OSR) or endovascular repair (EVAR).The differences in age, time to hospital arrival, emergency preparation time, first creatinine value, emergency infusion volume, preoperative drop in blood pressure, preoperative use of vasoactive drugs and iliac artery involvement were compared between preoperative death group (n=12) and preoperative survival group (n=79), OSR group (n=50) and EVAR group (n=29), postoperative death group (n=23) and postoperative survival group (n=56). Results: Seventy-nine patients received open surgery or endovascular repair, and 23 died after operation. Age, time to hospital arrival, first creatinine value and emergency infusion volume were (77±11) years, (18±5)h, (469±150) μmol/L, (4 140±1 743) ml in the preoperative death group and (70±10) years, (12±8) h, (228±174) μmol/L, (1 358±1 211) ml in the preoperative survival group, respectively, and the differences were statistically significant (all P<0.05). There were no significant differences in preoperative data, intraoperative treatment and postoperative perioperative mortality between the open surgery group and the endovascular repair group (all P>0.05). The intraoperative blood loss, operation time and aortic occlusion rate in the endovascular repair group were 100 (50, 175) ml, (3.2±0.9) h, 13.8%, respectively, which were better than that in the open surgery group 1700 (600, 3425) ml, (5.2±1.1) h, 100%. The differences were statistically significant (all P<0.05). Age, emergency preparation time, first creatinine value, emergency infusion volume, blood pressure decline rate and vasoactive drug utilization rate in the death group were (77±8) years, (4.1±1.7) h, (456±172) μmol/L, (2 024±1 687) ml, 100%, 100%, respectively, and (68±10) years, (2.7±2.2) h, (135±26) μmol/L, (1 085±825) ml, 21.4%, 12.5% in the survival group, respectively. The differences were statistically significant (all P<0.05). Conclusions: Age, emergency preparation time, first creatinine value, emergency infusion volume, decreased blood pressure and use of vasoactive drugs are all associated with perioperative death in patients with ruptured abdominal aortic aneurysm. EVAR surgery is a better choice if conditions exist.
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Affiliation(s)
- Z Cai
- Department of Vascular Surgery, Xiangya Hospital, Central South University, Changsha 413000, China
| | - W Wang
- Department of Vascular Surgery, Xiangya Hospital, Central South University, Changsha 413000, China
| | - B H Pan
- Department of Vascular Surgery, Xiangya Hospital, Central South University, Changsha 413000, China
| | - C Xie
- Department of Vascular Surgery, Xiangya Hospital, Central South University, Changsha 413000, China
| | - P Yang
- Department of Vascular Surgery, Xiangya Hospital, Central South University, Changsha 413000, China
| | - X W Wang
- Department of Vascular Surgery, Xiangya Hospital, Central South University, Changsha 413000, China
| | - Y Ouyang
- Department of Vascular Surgery, Xiangya Hospital, Central South University, Changsha 413000, China
| | - G Q Liu
- Department of Vascular Surgery, Xiangya Hospital, Central South University, Changsha 413000, China
| | - K M Wu
- Department of Vascular Surgery, Xiangya Hospital, Central South University, Changsha 413000, China
| | - T M Le
- Department of Vascular Surgery, Xiangya Hospital, Central South University, Changsha 413000, China
| | - J H Huang
- Department of Vascular Surgery, Xiangya Hospital, Central South University, Changsha 413000, China
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Mu M, Cai Z, Shen C, Wang J, Zhang B. P-93 The characteristics and prognosis of extragastrointestinal stromal tumors: A single center retrospective analysis of 31 patients. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.05.148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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28
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Cai Z, Liu C, Shen C, Jiang Z, Mu M, Zhang B. P-227 Comparative safety and tolerability of approved PARP inhibitors in cancer: A systematic review and network meta-analysis. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.05.281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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29
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Vicente-Serrano SM, Peña-Angulo D, Murphy C, López-Moreno JI, Tomas-Burguera M, Domínguez-Castro F, Tian F, Eklundh L, Cai Z, Alvarez-Farizo B, Noguera I, Camarero JJ, Sánchez-Salguero R, Gazol A, Grainger S, Conradt T, Boincean B, El Kenawy A. The complex multi-sectoral impacts of drought: Evidence from a mountainous basin in the Central Spanish Pyrenees. Sci Total Environ 2021; 769:144702. [PMID: 33736257 DOI: 10.1016/j.scitotenv.2020.144702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/18/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
We analyzed the impacts of drought severity on a variety of sectors in a topographically complex basin (the upper Aragón basin 2181 km2) in the Central Spanish Pyrenees. Using diverse data sources including meteorological and hydrological observations, remote sensing and tree rings, we analyze the possible hydrological implications of drought occurrence and severity on water availability in various sectors, including downstream impacts on irrigation water supply for crop production. Results suggest varying responses in forest activity, secondary growth, plant phenology, and crop yield to drought impacts. Specifically, meteorological droughts have distinct impacts downstream, mainly due to water partitioning between streamflow and irrigation channels that transport water to crop producing areas. This implies that drought severity can extend beyond the physical boundaries of the basin, with impacts on crop productivity. This complex response to drought impacts makes it difficult to develop objective basin-scale operational definitions for monitoring drought severity. Moreover, given the high spatial variability in responses to drought across sectors, it is difficult to establish reliable drought thresholds from indices that are relevant across all socio-economic sectors. The anthropogenic impacts (e.g. water regulation projects, ecosystem services, land cover and land use changes) pose further challenges to assessing the response of different systems to drought severity. This study stresses the need to consider the seasonality of drought impacts and appropriate drought time scales to adequately assess and understand their complexity.
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Affiliation(s)
- S M Vicente-Serrano
- Instituto Pirenaico de Ecología, Consejo Superior de Investigaciones Científicas (IPE-CSIC), Zaragoza, Spain.
| | - D Peña-Angulo
- Instituto Pirenaico de Ecología, Consejo Superior de Investigaciones Científicas (IPE-CSIC), Zaragoza, Spain
| | - C Murphy
- Irish Climate Analysis and Research UnitS (ICARUS), Department of Geography, Maynooth University, Maynooth, Ireland
| | - J I López-Moreno
- Instituto Pirenaico de Ecología, Consejo Superior de Investigaciones Científicas (IPE-CSIC), Zaragoza, Spain
| | - M Tomas-Burguera
- Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas (EEAD-CSIC), Zaragoza, Spain
| | - F Domínguez-Castro
- Aragonese Agency for Research and Development Researcher (ARAID), Spain; Department of Geography, University of Zaragoza, Zaragoza, Spain
| | - F Tian
- Department of Geography, Lund University, Lund, Sweden
| | - L Eklundh
- Department of Geography, Lund University, Lund, Sweden
| | - Z Cai
- Department of Geography, Lund University, Lund, Sweden
| | - B Alvarez-Farizo
- Instituto Pirenaico de Ecología, Consejo Superior de Investigaciones Científicas (IPE-CSIC), Zaragoza, Spain
| | - I Noguera
- Instituto Pirenaico de Ecología, Consejo Superior de Investigaciones Científicas (IPE-CSIC), Zaragoza, Spain
| | - J J Camarero
- Instituto Pirenaico de Ecología, Consejo Superior de Investigaciones Científicas (IPE-CSIC), Zaragoza, Spain
| | - R Sánchez-Salguero
- Departamento Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - A Gazol
- Instituto Pirenaico de Ecología, Consejo Superior de Investigaciones Científicas (IPE-CSIC), Zaragoza, Spain
| | - S Grainger
- Irish Climate Analysis and Research UnitS (ICARUS), Department of Geography, Maynooth University, Maynooth, Ireland
| | - T Conradt
- Potsdam Institute for Climate Impact Research, Potsdam, Germany
| | - B Boincean
- Selectia Research Institute Of Field Crops, Balti, Republic of Moldova
| | - A El Kenawy
- Department of Geography, Mansoura University, Mansoura, Egypt; Department of Geography, Sultan Qaboos University, Al Khoud, Muscat, Oman
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Lun MH, Jin XY, Wang MY, Cai Z, Du W, Huang ZQ. Ulinastatin improves myocardial ischemia-reperfusion injury in rats through endoplasmic reticulum stress-induced apoptosis pathway. Eur Rev Med Pharmacol Sci 2021; 24:5742-5749. [PMID: 32495910 DOI: 10.26355/eurrev_202005_21366] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
OBJECTIVE To investigate the protective role of ulinastatin (UTI) on myocardial ischemia-reperfusion (I/R) injury in rats via endoplasmic reticulum stress (ERS)-induced apoptosis pathway. MATERIALS AND METHODS A total of 60 rats were randomly divided into normal group (n=20), myocardial I/R model group (model group, n=20), and myocardial I/R model+UTI treatment group (treatment group, n=20). The myocardial function indicators [creatinine (Scr) and creatine kinase (CK)] were detected. Enzyme-linked immunosorbent assay (ELISA) was performed to measure serum levels of tumor necrosis factor-alpha (TNF-α), interleukin-6 (IL-6), and matrix metalloproteinase-9 (MMP-9). Meanwhile, the contents of reactive oxygen species (ROS), superoxide dismutase (SOD), and malondialdehyde (MDA) in rat left ventricular tissues were determined by ELISA as well. The cardiac function indexes were determined via magnetic resonance imaging (MRI) and echocardiography (ECG). Terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate-biotin nick end labeling (TUNEL) staining assay was carried out to detect the apoptosis of myocardial tissues. Additionally, the expression levels of endoplasmic reticulum stress and apoptosis genes were measured through quantitative Reverse Transcription-Polymerase Chain Reaction (qRT-PCR) assay and Western blotting analysis, respectively. RESULTS Serum levels of alanine aminotransferase (ALT), CK, and Scr in model group were significantly higher than those in normal group (p<0.05). Besides, rats in model group had significantly lowered SOD, ejection fraction (EF, %), and fractional shortening (FS, %) than those in normal group (p<0.05). In addition, remarkably increased contents of TNF-α, IL-6, MMP-9, MDA, and ROS, as well as higher left ventricular end-diastolic diameter (LVEDd) and left ventricular end-systolic diameter (LVESd) were observed in model group in comparison with normal group (p<0.05). TUNEL staining results revealed that there were more apoptotic cells in model group than that in the other two groups (p<0.05). Expression levels of cysteine aspartic acid-specific protease 12 (Caspase-12) and glucose-regulated protein 78 (GRP78) were evidently higher in model group than those in normal group (p<0.05), while the expression level of B-cell lymphoma 2 (Bcl-2) was clearly lower in model group than that in normal group (p<0.05). UTI treatment partially reversed the above expression changes (p<0.05). CONCLUSIONS UTI has a protective effect against myocardial I/R injury in rats by repressing the occurrence of ERS-induced apoptosis.
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Affiliation(s)
- M-H Lun
- Department of Anesthesiology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, China.
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Ke J, Liu F, Tu Y, Cai Z, Luo Y, Wu X. PARP1-RNA interaction analysis: PARP1 regulates the expression of extracellular matrix-related genes in HK-2 renal proximal tubular epithelial cells. FEBS Lett 2021; 595:1375-1387. [PMID: 33641169 DOI: 10.1002/1873-3468.14065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/17/2021] [Accepted: 02/21/2021] [Indexed: 12/11/2022]
Abstract
Recent studies suggest that Poly(ADP-ribose) polymerase 1 (PARP1) acts as an RNA-binding protein in a majority of renal diseases with tubular cell injury. However, detailed knowledge of RNA targets and the RNA-binding regions for PARP1 is unknown. Herein, mapping of iRIP-seq reads in HK-2 renal tubular epithelial cells showed a biased distribution at coding sequence (CDS) and intron regions that is specific to these cells. A total of 1708 differentially expressed genes were identified after PARP1 knockdown using RNA-seq. Furthermore, transcriptome analysis also showed that selective variable splicing was globally regulated by PARP1 in HK-2 cells. By comparison of PARP1 RNA-seq and iRIP-seq data, we found 68 overlapping genes that are enriched in 'extracellular matrix' pathway. Follow-up identification of their interactions may contribute vital insights into the regulatory role of PARP1 as an RNA-binding protein in HK-2 cells.
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Affiliation(s)
- Jing Ke
- Department of Nephrology, Renmin Hospital of Wuhan University, China
| | - Feng Liu
- Department of Nephrology, Renmin Hospital of Wuhan University, China
| | - Yafang Tu
- Department of Nephrology, Renmin Hospital of Wuhan University, China
| | - Zhitao Cai
- Department of Nephrology, Renmin Hospital of Wuhan University, China
| | - Yu Luo
- Department of Nephrology, Renmin Hospital of Wuhan University, China
| | - Xiongfei Wu
- Department of Nephrology, Renmin Hospital of Wuhan University, China
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Wang J, Wu X, Tu Y, Dang J, Cai Z, Liao W, Quan W, Wei Y. An integrated analysis of lncRNA and mRNA expression profiles in the kidneys of mice with lupus nephritis. PeerJ 2021; 9:e10668. [PMID: 33628632 PMCID: PMC7894116 DOI: 10.7717/peerj.10668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 12/08/2020] [Indexed: 12/13/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are persistently expressed and have been described as potential biomarkers and therapeutic targets in various diseases. However, there is limited information regarding lncRNA expression in the tissue of kidney exhibiting lupus nephritis (LN)a serious complication of systemic lupus erythematosus (SLE). In this study, RNA sequencing (RNA-seq) was performed to characterize the lncRNA and mRNA expression in kidney tissues from LN (MRL/lpr) and control mice. We identified 12,979 novel lncRNAs in mouse. The expression profiles of both mRNAs and lncRNAs were differed significantly between LN and control mice. In particular, there were more upregulated lncRNAs and mRNAs than downregulated ones in the kidney tissues of LN mice. However, GO analysis showed that more downregulated genes were enriched in immune and inflammatory response-associated pathways. KEGG analysis showed that both downregulated and upregulated genes were enriched in a number of pathways, including the SLE pathway, and approximately half of these SLE-associated genes encoded inflammatory factors. Moreover, we observed that 2,181 DElncRNAs may have targeted and regulated the expression of 778 mRNAs in LN kidney tissues. The results of this study showed that 11 DElncRNAs targeted and were co-expressed with six immune and SLE-associated genes. qPCR analysis confirmed that lncRNA Gm20513 positively regulated the expression of the SLE-associated gene H2-Aa. In conclusion, the results of our study demonstrates that lncRNAs influence the progression of LN and provide some cues for further study of lncRNAs in LN. These results regarding the lncRNA-mRNAregulatory network may have important value in LN diagnosis and therapy.
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Affiliation(s)
- Juan Wang
- Nephrology Department, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Xiongfei Wu
- Nephrology Department, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Yafang Tu
- Nephrology Department, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Jianzhong Dang
- Nephrology Department, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Zhitao Cai
- Nephrology Department, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Wenjing Liao
- Nephrology Department, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Weili Quan
- ABLife BioBigData Institute, Wuhan, Hubei, China
| | - Yaxun Wei
- Center for Genome Analysis, ABLife Inc., Wuhan, Hubei, China
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Cai Z, Zhang J, He Y, Xia L, Dong X, Chen G, Zhou Y, Hu X, Zhong S, Wang Y, Chen H, Xie D, Liu X, Liu J. Liquid biopsy by combining 5-hydroxymethylcytosine signatures of plasma cell-free DNA and protein biomarkers for diagnosis and prognosis of hepatocellular carcinoma. ESMO Open 2021; 6:100021. [PMID: 33508734 PMCID: PMC7841321 DOI: 10.1016/j.esmoop.2020.100021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/29/2020] [Accepted: 11/14/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Liquid biopsy based on 5-hydroxymethylcytosine (5hmC) signatures of plasma cell-free DNA (cfDNA) originating from tumor cells provides a novel approach for early diagnosis in hepatocellular carcinoma (HCC). Here, we sought to develop a reliable model using cfDNA 5hmC signatures and protein biomarkers for diagnosis and prognosis of HCC. PATIENTS AND METHODS We carried out genome-wide 5hmC sequencing of cfDNA samples collected from 165 healthy volunteers, 62 liver cirrhosis (LC) patients and 135 HCC patients. A sensitive 5hmC diagnostic model was developed based on 5hmC signatures selected by sparse Partial Least Squares Discriminant Analysis and cross-validation to define the weighted diagnostic score (wd-score). Then, we combined protein biomarkers with the wd-score to build a more robust score (HCC score) by logistic regression. RESULTS The distribution pattern of differential 5hmC regions could clearly distinguish HCC patients, LC patients and healthy volunteers. The wd-score based on 64 5hmC signatures in cfDNA achieves 93.24% of area under the curve (AUC) to distinguish HCC patients from non-HCC patients, and the HCC score by combing protein biomarkers achieves 92.75% of AUC to distinguish HCC patients from LC patients. Meanwhile, the HCC score showed high capacity for screening high recurrence risk patients after receiving surgical resection, and appeared to be an independent indicator for both relapse-free survival (P = 0.00865) and overall survival (P = 0.000739). Furthermore, the values of the HCC score in patients' longitudinal plasma samples were positively associated with tumor burden dynamics during follow-up. CONCLUSION We have developed and validated a novel non-invasive liquid biopsy strategy for HCC diagnosis, prognosis and surveillance during HCC progression.
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Affiliation(s)
- Z Cai
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, P. R. China; Mengchao Med-X Center, Fuzhou University, Fuzhou, P. R. China
| | - J Zhang
- Frontier Science Center for Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, P. R. China
| | - Y He
- Frontier Science Center for Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, P. R. China; Laboratory of Nervous System Disease and Brain Functions, Clinical Research Institute, The Affiliated Hospital of Southwest Medical University, Luzhou, P. R. China
| | - L Xia
- Frontier Science Center for Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, P. R. China
| | - X Dong
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, P. R. China; Mengchao Med-X Center, Fuzhou University, Fuzhou, P. R. China
| | - G Chen
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, P. R. China; Mengchao Med-X Center, Fuzhou University, Fuzhou, P. R. China
| | - Y Zhou
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, P. R. China; Mengchao Med-X Center, Fuzhou University, Fuzhou, P. R. China
| | - X Hu
- Frontier Science Center for Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, P. R. China
| | - S Zhong
- Tailai Inc., Shanghai, P. R. China
| | - Y Wang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, P. R. China; Mengchao Med-X Center, Fuzhou University, Fuzhou, P. R. China
| | - H Chen
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, P. R. China
| | - D Xie
- Frontier Science Center for Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, P. R. China.
| | - X Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, P. R. China; Mengchao Med-X Center, Fuzhou University, Fuzhou, P. R. China.
| | - J Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, P. R. China; Mengchao Med-X Center, Fuzhou University, Fuzhou, P. R. China.
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Qiu L, Han XY, He DH, Zhu F, Zhao Y, Zhu WW, Zheng GF, Yang Y, Wu WW, Cai Z, Yang XC, He JS. [The effect of peripheral blood cell score on the prognosis of multiple myeloma patients treated with bortezomib]. Zhonghua Xue Ye Xue Za Zhi 2021; 41:756-761. [PMID: 33113608 PMCID: PMC7595856 DOI: 10.3760/cma.j.issn.0253-2727.2020.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
目的 评估外周血细胞检测结果在以硼替佐米为一线治疗的多发性骨髓瘤(MM)患者中的预后作用。 方法 回顾性分析2014年1月至2016年12月浙江大学医学院附属第一医院和浙江省舟山医院收治的155例初诊MM患者的临床数据,患者均一线接受以硼替佐米为基础方案的治疗。分析外周血细胞检测结果,包括ANC、单核细胞计数(AMC)、HGB、红细胞平均体积(MCV)、PLT以及其他临床特征对MM患者的预后评估作用。 结果 AMC(>0.6×109/L)、MCV(>99.1fl)以及PLT(<150×109/L)明显影响MM患者无进展生存(PFS)和总生存(OS),以上3个因子分别赋值1分,形成血细胞积分。结果显示,64例(41.3%)积分0,57例(36.8%)积分1,32例(20.6%)积分2,2例(1.3%)积分3,4组患者中位PFS时间分别为42.8、26.5、15.8、6.4个月(P<0.001),中位OS时间分别为未达到和48.2、31.1、31.4个月(P=0.001)。多因素分析提示,血细胞积分(2~3对0~1)和骨髓浆细胞比例(>30%对≤30%)为PFS的独立预后因素(HR分别为1.95和1.76),而患者年龄(>65岁对≤65岁)、R-ISS分期(Ⅲ期对Ⅰ~Ⅱ期)和血细胞积分(2~3对0~1)是OS的独立预后因素(HR分别为2.08、2.13和2.12)。 结论 血细胞积分简单易得,可用于新药时代初治MM患者的预后评估,但仍需扩大病例并进行前瞻性研究进一步明确。
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Affiliation(s)
- L Qiu
- Department of Hematological Oncology and Chemotherapy, Zhoushan Hospital, Zhoushan 316004, China
| | - X Y Han
- Hematology and Bone Marrow Transplantation, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - D H He
- Hematology and Bone Marrow Transplantation, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - F Zhu
- Department of Hematological Oncology and Chemotherapy, Zhoushan Hospital, Zhoushan 316004, China
| | - Y Zhao
- Hematology and Bone Marrow Transplantation, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - W W Zhu
- Department of Hematological Oncology and Chemotherapy, Zhoushan Hospital, Zhoushan 316004, China
| | - G F Zheng
- Hematology and Bone Marrow Transplantation, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Y Yang
- Hematology and Bone Marrow Transplantation, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - W W Wu
- Hematology and Bone Marrow Transplantation, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Z Cai
- Hematology and Bone Marrow Transplantation, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - X C Yang
- Department of Hematological Oncology and Chemotherapy, Zhoushan Hospital, Zhoushan 316004, China
| | - J S He
- Hematology and Bone Marrow Transplantation, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
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Yang D, Boesch H, Liu Y, Somkuti P, Cai Z, Chen X, Di Noia A, Lin C, Lu N, Lyu D, Parker RJ, Tian L, Wang M, Webb A, Yao L, Yin Z, Zheng Y, Deutscher NM, Griffith DWT, Hase F, Kivi R, Morino I, Notholt J, Ohyama H, Pollard DF, Shiomi K, Sussmann R, Té Y, Velazco VA, Warneke T, Wunch D. Toward High Precision XCO 2 Retrievals From TanSat Observations: Retrieval Improvement and Validation Against TCCON Measurements. J Geophys Res Atmos 2020; 125:e2020JD032794. [PMID: 33777605 PMCID: PMC7983077 DOI: 10.1029/2020jd032794] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 07/22/2020] [Accepted: 07/24/2020] [Indexed: 06/12/2023]
Abstract
TanSat is the 1st Chinese carbon dioxide (CO2) measurement satellite, launched in 2016. In this study, the University of Leicester Full Physics (UoL-FP) algorithm is implemented for TanSat nadir mode XCO2 retrievals. We develop a spectrum correction method to reduce the retrieval errors by the online fitting of an 8th order Fourier series. The spectrum-correction model and its a priori parameters are developed by analyzing the solar calibration measurement. This correction provides a significant improvement to the O2 A band retrieval. Accordingly, we extend the previous TanSat single CO2 weak band retrieval to a combined O2 A and CO2 weak band retrieval. A Genetic Algorithm (GA) has been applied to determine the threshold values of post-screening filters. In total, 18.3% of the retrieved data is identified as high quality compared to the original measurements. The same quality control parameters have been used in a footprint independent multiple linear regression bias correction due to the strong correlation with the XCO2 retrieval error. Twenty sites of the Total Column Carbon Observing Network (TCCON) have been selected to validate our new approach for the TanSat XCO2 retrieval. We show that our new approach produces a significant improvement on the XCO2 retrieval accuracy and precision when compared to TCCON with an average bias and RMSE of -0.08 ppm and 1.47 ppm, respectively. The methods used in this study can help to improve the XCO2 retrieval from TanSat and subsequently the Level-2 data production, and hence will be applied in the TanSat operational XCO2 processing.
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Affiliation(s)
- D. Yang
- Earth Observation Science, School of Physics and AstronomyUniversity of LeicesterUK
- Institute of Atmospheric PhysicsChinese Academy of SciencesChina
- Shanghai Advanced Research InstituteChinese Academy of SciencesShanghaiChina
| | - H. Boesch
- Earth Observation Science, School of Physics and AstronomyUniversity of LeicesterUK
- National Centre for Earth ObservationUniversity of LeicesterUK
| | - Y. Liu
- Institute of Atmospheric PhysicsChinese Academy of SciencesChina
- Shanghai Advanced Research InstituteChinese Academy of SciencesShanghaiChina
| | - P. Somkuti
- Earth Observation Science, School of Physics and AstronomyUniversity of LeicesterUK
- National Centre for Earth ObservationUniversity of LeicesterUK
- Colorado State UniversityFort CollinsCOUSA
| | - Z. Cai
- Institute of Atmospheric PhysicsChinese Academy of SciencesChina
| | - X. Chen
- Institute of Atmospheric PhysicsChinese Academy of SciencesChina
| | - A. Di Noia
- Earth Observation Science, School of Physics and AstronomyUniversity of LeicesterUK
- National Centre for Earth ObservationUniversity of LeicesterUK
| | - C. Lin
- Changchun Institute of Optics, Fine Mechanics and PhysicsChina
| | - N. Lu
- National Satellite Meteorological Center, China Meteorological AdministrationChina
| | - D. Lyu
- Institute of Atmospheric PhysicsChinese Academy of SciencesChina
| | - R. J. Parker
- Earth Observation Science, School of Physics and AstronomyUniversity of LeicesterUK
- National Centre for Earth ObservationUniversity of LeicesterUK
| | - L. Tian
- Shanghai Engineering Center for MicrosatellitesChina
| | - M. Wang
- Shanghai Advanced Research InstituteChinese Academy of SciencesShanghaiChina
| | - A. Webb
- Earth Observation Science, School of Physics and AstronomyUniversity of LeicesterUK
- National Centre for Earth ObservationUniversity of LeicesterUK
| | - L. Yao
- Institute of Atmospheric PhysicsChinese Academy of SciencesChina
| | - Z. Yin
- Shanghai Engineering Center for MicrosatellitesChina
| | - Y. Zheng
- Changchun Institute of Optics, Fine Mechanics and PhysicsChina
| | - N. M. Deutscher
- Centre for Atmospheric Chemistry, School of Earth, Atmospheric and Life SciencesUniversity of WollongongNSWAustralia
| | - D. W. T. Griffith
- Centre for Atmospheric Chemistry, School of Earth, Atmospheric and Life SciencesUniversity of WollongongNSWAustralia
| | - F. Hase
- Karlsruhe Institute of Technology, IMK‐IFUGarmisch‐PartenkirchenGermany
| | - R. Kivi
- Space and Earth Observation CentreFinnish Meteorological InstituteFinland
| | - I. Morino
- National Institute for Environmental Studies (NIES)TsukubaIbarakiJapan
| | - J. Notholt
- Institute of Environmental Physics (IUP)University of BremenBremenGermany
| | - H. Ohyama
- National Institute for Environmental Studies (NIES)TsukubaIbarakiJapan
| | - D. F. Pollard
- National Institute of Water and Atmospheric Research Ltd (NIWA)LauderNew Zealand
| | - K. Shiomi
- Japan Aerospace Exploration AgencyJapan
| | - R. Sussmann
- Karlsruhe Institute of Technology, IMK‐IFUGarmisch‐PartenkirchenGermany
| | - Y. Té
- Laboratoire d'Etudes du Rayonnement et de la Matière en Astrophysique et Atmosphères (LERMA‐IPSL)Sorbonne Université, CNRS, Observatoire de Paris, PSL UniversitéParisFrance
| | - V. A. Velazco
- Centre for Atmospheric Chemistry, School of Earth, Atmospheric and Life SciencesUniversity of WollongongNSWAustralia
| | - T. Warneke
- Institute of Environmental Physics (IUP)University of BremenBremenGermany
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Cai Z, Klein T, Geenen L, Tu L, Tian S, Van Den Bosch A, De Rijke Y, Reiss I, Boersma E, Duncker D, Boomars K, Guignabert C, Merkus D. Lower plasma melatonin levels predict worse long-term survival in pulmonary arterial hypertension. Eur Heart J 2020. [DOI: 10.1093/ehjci/ehaa946.3815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Exogenous melatonin has been reported to be beneficial in the treatment of pulmonary hypertension (PH) in animal models. Multiple mechanisms may be involved, with melatonin exerting anti-oxidant and anti-inflammatory effects, as well as inducing vasodilation and cardio-protection. However, endogenous levels of melatonin in treatment-naïve pulmonary arterial hypertension (PAH) patients and their clinical significance are still unknown.
Methods and results
Plasma levels of endogenous melatonin were measured by liquid chromatography-tandem mass spectrometry in treatment-naïve PAH patients (n=43) and healthy controls (n=111). Melatonin levels were higher in PAH patients when compared with controls (Median 118.9 [IQR 109.3–147.7] versus 108.0 [102.3–115.2] pM, P<0.001) (Figure 1A). The overall mortality was 26% (11/43) during a median long-term follow-up of 42 [IQR: 32–58] months. When PAH patients were stratified into 4 groups according to the quartiles of melatonin levels, the mortality from below 1st quartile to above 4th quartile was 55% (6/11), 10% (1/10), 0% (0/12), and 40% (4/10), respectively (Figure 1B). Kaplan-Meier analysis further showed that patients with melatonin levels below the 1st quartile (<109.3 pM) had a worse long-term survival than patients with melatonin levels above the 1st quartile (Mean survival times were 46 [95% CI: 30–65] versus 68 [58–77] months, Log-rank, p=0.026) (Figure 1C).
Conclusion
Endogenous melatonin levels were increased in treatment-naïve PAH patients, and lower levels of melatonin were associated with worse long-term survival in patient with PAH, however, whether exogenous melatonin supplements may be effective as a therapeutic strategy in human PAH remains to be established.
Figure 1
Funding Acknowledgement
Type of funding source: Foundation. Main funding source(s): This work was supported by the China Scholarship Council (201606230252) as well as the Netherlands CardioVascular Research Initiative: an initiative with support of the Dutch Heart Foundation (CVON2014-11, RECONNECT), and German Center for Cardiovascular Research (DZHK81Z0600207). Instrumentation support was received from AB Sciex, ltd. for LC-MS/MS analyses performed in this study.
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Affiliation(s)
- Z Cai
- Erasmus Medical Center, Cardiology, Rotterdam, Netherlands (The)
| | - T Klein
- Erasmus Medical Center, Clinical Chemistry, Rotterdam, Netherlands (The)
| | - L.W Geenen
- Erasmus Medical Center, Cardiology, Rotterdam, Netherlands (The)
| | - L Tu
- INSERM UMR_S 999 Hôpital Marie Lannelongue and Université Paris-Saclay School of Medicine, Paris, France
| | - S Tian
- Erasmus Medical Center, Cardiology, Rotterdam, Netherlands (The)
| | | | - Y.B De Rijke
- Erasmus Medical Center, Clinical Chemistry, Rotterdam, Netherlands (The)
| | - I.K.M Reiss
- Erasmus Medical Center, Pediatrics/Neonatology, Rotterdam, Netherlands (The)
| | - E Boersma
- Erasmus University Medical Centre, Clinical Epidemiology, Rotterdam, Netherlands (The)
| | - D.J Duncker
- Erasmus Medical Center, Cardiology, Rotterdam, Netherlands (The)
| | - K.A Boomars
- Erasmus Medical Center, Pulmonary Medicine, Rotterdam, Netherlands (The)
| | - C Guignabert
- INSERM UMR_S 999 Hôpital Marie Lannelongue and Université Paris-Saclay School of Medicine, Paris, France
| | - D Merkus
- Erasmus Medical Center, Cardiology, Rotterdam, Netherlands (The)
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Cai Z, Klein T, Tu L, Geenen L, Tian S, Van Der Ley C, Van Faassen M, Kema I, Van Den Bosch A, De Rijke J, Reiss I, Duncker D, Boomars K, Guignabert C, Merkus D. Different tryptophan-kynurenine metabolism profiles in human pulmonary arterial hypertension and animal models of pulmonary hypertension. Eur Heart J 2020. [DOI: 10.1093/ehjci/ehaa946.3814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Background
De novo NAD+ synthesis through the tryptophan-kynurenine (TK) metabolism was recognized as an important pathway in improving mitochondrial function and survival of injury or apoptotic cells, which are key processes involved in the pathogenesis of pulmonary arterial hypertension (PAH). Although abnormal TK metabolism has been reported in human PAH, the difference between human and animal models of pulmonary hypertension (PH) are currently unknown.
Objective
Determine and compare TK metabolism profiles in plasma from human PAH and 3 animal models of PH.
Methods
Human plasma was collected from treatment naïve patients with PAH (n=43) and healthy controls (n=111). Animal plasma was collected from 3 animal models of PH and corresponding controls, including monocrotaline (MCT) induced PH in rat (n=7, control n=6), Sugen + hypoxia (SuHx) induced PH in rat (n=5, control n=6), and pulmonary vein banding (PVB) induced PH in swine (n=7, control n=6). TK metabolites were determined using liquid chromatography-tandem mass spectrometry (LC-MS/MS).
Results
TK metabolism was altered in the plasma from of PAH compared to healthy controls (Figure 1A). Lower tryptophan (0.8 fold vs Control, p<0.0001), maintained 3-hydroxyanthranilic acid, and higher kynurenine, 3-hydroxykynurenine, anthranilic acid, and quinolinic acid (1.5, 2.6, 2.0, 2.6 fold vs Control, respectively, p all<0.0001) were seen in the plasma from human PAH. In the rat SuHx-PH model, kynurenine (0.7 fold, p<0.01) and quinolinic acid (0.5 fold, p<0.001) were lower, while 3-hydroxyanthranilic acid (4.3 fold, p<0.001) was higher in PH compared to control (Figure 1B). However, the TK metabolism was unaltered in MCT-PH model in rat (Figure 1C), and PVB-PH model in swine (Figure 1D).
Conclusions
TK metabolism was altered in the plasma from human PAH. The TK metabolism profiles were different among 3 animal models of PH, but did not mimic the profile in human PAH. Further research is required to determine the mechanism(s) behind the abnormal TK metabolism in human PAH as well as whether these mechanisms relate to disease onset or progression.
Figure 1
Funding Acknowledgement
Type of funding source: Foundation. Main funding source(s): This work was supported by the China Scholarship Council (201606230252) as well as the Netherlands CardioVascular Research Initiative: an initiative with support of the Dutch Heart Foundation (CVON2014-11, RECONNECT), and German Center for Cardiovascular Research (DZHK81Z0600207). Instrumentation support was received from AB Sciex, ltd. for LC-MS/MS analyses performed in this study.
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Affiliation(s)
- Z Cai
- Erasmus Medical Center, Cardiology, Rotterdam, Netherlands (The)
| | - T Klein
- Erasmus Medical Center, Clinical Chemistry, Rotterdam, Netherlands (The)
| | - L Tu
- INSERM UMR_S 999 Hôpital Marie Lannelongue and Université Paris-Saclay School of Medicine, Paris, France
| | - L.W Geenen
- Erasmus Medical Center, Cardiology, Rotterdam, Netherlands (The)
| | - S Tian
- Erasmus Medical Center, Cardiology, Rotterdam, Netherlands (The)
| | - C Van Der Ley
- University Medical Center Groningen, Laboratory Medicine, Groningen, Netherlands (The)
| | - M Van Faassen
- University Medical Center Groningen, Laboratory Medicine, Groningen, Netherlands (The)
| | - I Kema
- University Medical Center Groningen, Laboratory Medicine, Groningen, Netherlands (The)
| | | | - J.B De Rijke
- Erasmus Medical Center, Clinical Chemistry, Rotterdam, Netherlands (The)
| | - I.K.M Reiss
- Erasmus Medical Center, Pediatrics/Neonatology, Rotterdam, Netherlands (The)
| | - D.J Duncker
- Erasmus Medical Center, Cardiology, Rotterdam, Netherlands (The)
| | - K.A Boomars
- Erasmus Medical Center, Pulmonary Medicine, Rotterdam, Netherlands (The)
| | - C Guignabert
- INSERM UMR_S 999 Hôpital Marie Lannelongue and Université Paris-Saclay School of Medicine, Paris, France
| | - D Merkus
- Erasmus Medical Center, Cardiology, Rotterdam, Netherlands (The)
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Ueda K, Jung S, Chen Y, Cai Z, Nakamura T. PND16 Quantifying the Burden of Migraine in JAPAN: A Propensity-Score Matched Analysis of a Population-Based Survey. Value Health Reg Issues 2020. [DOI: 10.1016/j.vhri.2020.07.404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Cai Z, Wu Y, Zhang F, Wu H. A three-gene signature and clinical outcome in pediatric acute myeloid leukemia. Clin Transl Oncol 2020; 23:866-873. [PMID: 32862280 DOI: 10.1007/s12094-020-02480-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 08/12/2020] [Indexed: 11/29/2022]
Abstract
BACKGROUND Although the 5-year survival rates in pediatric acute myeloid leukemia (AML) have improved over the last decades, there is a high relapse rate for Pediatric AML patients. METHODS In the present study, we mainly combine PCA with the LASSO technique to identify prognostic markers for Pediatric AML patients coming from the NCI TARGET database. RESULTS Three key genes (EEF1A1, RPLP2, RPL19) associated with poor prognosis of pediatric AML has been screened by both PCA and LASSO Cox regression analysis. Simultaneously, we developed a risk score model to predict the prognosis of pediatric AML, according to risk scores, the patients were divided into high- and low-risk groups based on the median risk score. Kaplan-Meier survival analysis indicated that Pediatric AML patients with the high-risk group have a poorer survival rate than those with a low-risk group (p < 0.000). The receiver operating characteristic (ROC) analysis showed that the risk model has a good performance (AUC:0.669). Moreover, the clinicopathologic correlation showed that the expression levels of three genes were related to the central nervous system (CNS) disease and chloroma. GSEA identified that those pathways including oxidative phosphorylation, apoptosis and TGFB signaling pathway were differentially enriched. CONCLUSION Taken together, those studies suggested that a gene panel that consists of three genes (EEF1A1, RPLP2, RPL19) may act as a potential prognostic marker.
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Affiliation(s)
- Z Cai
- Department of Pediatrics, The First Affiliated Hospital of University of South China, Hengyang, 421001, Hunan, China
| | - Y Wu
- Department of Pathology, The First People's Hospital of Xiangtan City, No.100 Shuyuan Road, Yuetang District, Xiangtan, 421001, Hunan, China
| | - F Zhang
- Department of Pathology, The Rushan People's Hospital of Weihai City, Shandong, 264500, China
| | - H Wu
- Department of Pathology, The First People's Hospital of Xiangtan City, No.100 Shuyuan Road, Yuetang District, Xiangtan, 421001, Hunan, China.
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Zhang EF, Yang L, Cai Z. [Prognosis of multiple myeloma: current situation, challenges and contemplation]. Zhonghua Nei Ke Za Zhi 2020; 59:493-495. [PMID: 32594681 DOI: 10.3760/cma.j.cn112138-20200318-00256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Affiliation(s)
- E F Zhang
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - L Yang
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Z Cai
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
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Deng S, Li D, Liu X, Cai Z, Wei W, Chen J, Zhang L. Serum metabolomic investigations of mulberry leaf powder supplementation in Chinese Erhualian pigs. J Anim Feed Sci 2020. [DOI: 10.22358/jafs/124043/2020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Nowell WB, Kannowski CL, Gavigan K, Cai Z, Cardoso A, Hunter T, Venkatachalam S, Birt J, Workman J, Curtis J. PARE0026 WHICH PATIENT-REPORTED OUTCOMES DO RHEUMATOLOGY PATIENTS FIND IMPORTANT TO TRACK DIGITALLY? A REAL-WORLD LONGITUDINAL STUDY IN ARTHRITISPOWER. Ann Rheum Dis 2020. [DOI: 10.1136/annrheumdis-2020-eular.1016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Background:Development of a standardized approach to assess key elements of disease activity in rheumatology clinical trials has been the goal of Outcome Measures in Rheumatology Clinical Trials (OMERACT), American College of Rheumatology (ACR), and European League Against Rheumatism (EULAR).1,2,3The core sets of measures developed include assessments and composite indices incorporating use of patient-reported outcomes (PROs) and clinical measures and clinicians’ assessments to quantify disease activity over time.2PROs are important indicators of disease activity and variability, and they are increasingly used to evaluate treatment effectiveness. Little is known about PROs that patients with rheumatic conditions find most important to convey their experience with their condition and its treatment.Objectives:To examine PROs selected by patients with rheumatic conditions in the ArthritisPower registry to identify symptoms they found most important to track digitally.Methods:Adult US patients within the ArthritisPower registry with rheumatoid arthritis (RA), psoriatic arthritis (PsA), ankylosing spondylitis (AS), systemic lupus erythematosus (SLE), osteoporosis (OP), osteoarthritis (OA), and fibromyalgia syndrome (FMS) were invited via email to participate in this study. Enrolled participants (pts) were prompted to select ≤10 PRO symptom measures they felt were important to track for their condition at baseline via the ArthritisPower app. At 3 subsequent time points (Month [m] 1, m2, m3), pts were given the option to continue tracking their previously selected PRO measures or to add, remove and/or select different measures. At m3, pts completed an exit survey to prioritize ≤5 measures from all measures selected during study participation and to specify other symptoms not available that they would have wanted to track. Measures were rank-ordered based on number of pts rating the item as their 1st, 2nd, 3rd, 4th or 5th choice and weighted by multiplying the rank number by its inverse for a single, weighted summary score for each measure. Values were summed across all pts to produce a summary score for each measure.Results:Among pts who completed initial selection of PRO assessments at baseline (N=253), 184 pts confirmed or changed PRO selections across m1-3. Mean (SD) age of pts was 55.7 (9.2) yrs, 89.3% female, 91.3% White, mean disease duration of 11.6 (10.6) yrs. The majority (64.8%) self-reported OA, followed by RA (48.6%), FMS (40.3%), PsA (26.1%), OP (21.0%), AS (15.8%) and SLE (5.9%), not mutually exclusive, and were similar to the overall ArthritisPower population. The average number of instruments (SD) selected for baseline completion was 7.0 (2.5), 7.1 (2.4) at m1, 7.2 (2.4) at m2, and 7.0 (2.5) at m3. The top 5 PROs ranked by pts overall as most important (weighted summary score) for tracking were Fatigue (71), Physical Function (58), Pain Intensity (50), Pain Interference (49), Duration of Morning Joint Stiffness (41) (Figure 1). Fatigue, Physical Function, and Pain were consistently in the top 5 across diseases while Depression was more frequent among pts with OA, AS and FMS. Pts’ PRO selections showed stability over time except for the RA Flare measure which decreased from 70.5% of RA pts at baseline to 13.6% at m3.Conclusion:The symptoms prioritized by pts included fatigue, physical function, pain, and joint stiffness. Pts‘ choices were consistent over time. These findings provide insights into symptoms rheumatology patients find most important and will be useful to inform design of future patient-centric clinical trials and real-world evidence generation.References:[1]Boers M, et al. J Rheumatol Suppl. 1994;41:86–89.[2]Felson DT, et al. Arthritis Rheum. 1993;36:729–740.[3]Tugwell P, et al. J Rheumatol. 1993;20:555–556.Disclosure of Interests:W. Benjamin Nowell: None declared, Carol L. Kannowski Shareholder of: Eli Lilly and Company, Employee of: Eli Lilly and Company, Kelly Gavigan: None declared, Zhihong Cai Shareholder of: Eli Lilly and Company, Employee of: Eli Lilly and Company, Anabela Cardoso Shareholder of: Eli Lilly and Company, Employee of: Eli Lilly and Company, Theresa Hunter Shareholder of: Eli Lilly and Company, Employee of: Eli Lilly and Company, Shilpa Venkatachalam: None declared, Julie Birt Shareholder of: Eli Lilly and Company, Employee of: Eli Lilly and Company, Jennifer Workman Shareholder of: Eli Lilly and Company, Employee of: Eli Lilly and Company, Jeffrey Curtis Grant/research support from: AbbVie, Amgen, Bristol-Myers Squibb, Corrona, Janssen, Lilly, Myriad, Pfizer, Regeneron, Roche, UCB, Consultant of: AbbVie, Amgen, Bristol-Myers Squibb, Corrona, Janssen, Lilly, Myriad, Pfizer, Regeneron, Roche, UCB
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Dong S, Nie H, Li D, Cai Z, Sun X, Huo Z, Yan X. Molecular cloning and characterization of Y-box gene (Rpybx) from Manila clam and its expression analysis in different strains under low-temperature stress. Anim Genet 2020; 51:430-438. [PMID: 32091145 DOI: 10.1111/age.12919] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/26/2020] [Indexed: 12/28/2022]
Abstract
Manila clam, Ruditapes philippinarum, is an economically important marine bivalve species. Y-box proteins are members of the cold shock proteins family and highly conserved from bacteria to humans. In this study, a novel Y-box gene (Rpybx) was cloned from the Manila clam and gene expression profiling was performed on three shell color strains (white, zebra and white zebra) and two wild populations (Southern and Northern) of R. philippinarum. The complete ORF length of Rpybx is 1367 bp, encoding 253 amino acids residues. Based on the amino acid sequence analysis and phylogenetic analysis, the Rpybx gene was identified as a member of the invertebrate Y-box proteins family. Rpybx has a similar tertiary structure to human Y-box protein YB-1. The Rpybx mRNA levels were analyzed by qPCR under acute and gradually varied cold stress. Under acute low-temperature stress, the expression of Rpybx mRNA in gills and hepatopancreas was significantly increased in all selected strains and populations (P < 0.05). The Northern population showed the lowest relative expression level of Rpybx. The expressions of Rpybx were greatly upregulated in gills and hepatopancreas of different stains and populations at 5 or -2°C under gradually varied temperature stress (P < 0.05). The results shed light on the biological function of the Rpybx gene in defending against low-temperature challenge and further exploring the molecular mechanism of cold tolerance and resistance in R. philippinarum.
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Affiliation(s)
- S Dong
- College of Fisheries and Life Science, Engineering and Technology Research Center of Shellfish Breeding of Liaoning Province, Dalian Ocean University, Dalian, 116023, China
| | - H Nie
- College of Fisheries and Life Science, Engineering and Technology Research Center of Shellfish Breeding of Liaoning Province, Dalian Ocean University, Dalian, 116023, China
| | - D Li
- College of Fisheries and Life Science, Engineering and Technology Research Center of Shellfish Breeding of Liaoning Province, Dalian Ocean University, Dalian, 116023, China
| | - Z Cai
- College of Fisheries and Life Science, Engineering and Technology Research Center of Shellfish Breeding of Liaoning Province, Dalian Ocean University, Dalian, 116023, China
| | - X Sun
- College of Fisheries and Life Science, Engineering and Technology Research Center of Shellfish Breeding of Liaoning Province, Dalian Ocean University, Dalian, 116023, China
| | - Z Huo
- College of Fisheries and Life Science, Engineering and Technology Research Center of Shellfish Breeding of Liaoning Province, Dalian Ocean University, Dalian, 116023, China
| | - X Yan
- College of Fisheries and Life Science, Engineering and Technology Research Center of Shellfish Breeding of Liaoning Province, Dalian Ocean University, Dalian, 116023, China
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Liu X, Li Z, Cai Z, Chen G, Liu J. Neoantigen profile of hepatocellular carcinoma reveals its correlation with tumour progression and clonal evolution. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz438.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Chi Y, Yao Y, Fang Z, Wang S, Huang G, Cai Q, Shang G, Wang G, Qu G, Wu Q, Jiang Y, Song J, Chen J, Zhu X, Cai Z, Bai C, Lu Y, Yu Z, Shen J, Cai J. Efficacy and safety of anlotinib in advanced leiomyosarcoma: Subgroup analysis of a phase IIB trial (ALTER0203). Ann Oncol 2019. [DOI: 10.1093/annonc/mdz283.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Fang Z, Yao Y, Cai J, Chi Y, Wang S, Huang G, Cai Q, Shang G, Wang G, Qu G, Wu Q, Jiang Y, Song J, Chen J, Cai Z, Zhu X, Bai C, Lu Y, Yu Z, Shen J. The effect of treatment line on the efficacy of anlotinib hydrochloride in advanced alveolar soft part sarcoma patients. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz283.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Huang J, Ma C, Yin J, Bai Y, Zhang G, Wang J, Yu J, Cai Z. Anatomy research of the bifrontal decompressive craniectomy with coronal incision. J Neurol Sci 2019. [DOI: 10.1016/j.jns.2019.10.423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Cai Z, Zhang B, Yin Y, Cao D. Efficacy and safety of apatinib for advanced gastrointestinal stromal tumours after failure of imatinib and sunitinib: An open-label, multicenter, single-arm, phase II trial. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz283.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Cai Z, Wang C, Chen Y, He W. An Antioxidant Role by Minocycline Via Enhancing the Activation of LKB1/AMPK Signaling in the Process of Cerebral Ischemia Injury. Curr Mol Med 2019; 18:142-151. [PMID: 30198433 DOI: 10.2174/1566524018666180907161504] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 07/22/2018] [Accepted: 09/04/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND LKB1/AMPK signaling pathway, as a metabolic checkpoint, is involved in the pathogenesis of cerebral ischemia injury. Minocycline, a tetracycline derivative, protects against cerebral ischemia via reducing inflammation, oxidative stress, and apoptosis. The aim of the study was to evaluate the influence of minocycline on oxidative biomarkers and LKB1/AMPK signaling pathway in Wistar rats with focal cerebral ischemia injury and to clarify the neuroprotective mechanism of minocycline against focal cerebral ischemia injury. METHODS The focal cerebral ischemia injury of Wistar rats was established by inserting a thread into the left middle cerebral artery. 2,3,5-Triphenyltetrazolium chloride (TTC) staining was used to label infarct volume. The levels of MDA and LPO were measured with a biochemical assay. All other items were determined by Western blotting. RESULTS Minocycline decreased cerebral infarct volume, but had no effects on neurological scores. Minocycline improved the biological activity of GPx-1/2, GSS and GR, while limited the GGT1 activity in the hippocampus of cerebral ischemia-reperfusion rats. Minocycline also elevated the biological activity of SOD and counteracted lipid peroxidation. Minocycline enhanced the activity of both LKB1 and the levels of the three AMPK subunits in the hippocampus of cerebral ischemia-reperfusion rats. CONCLUSION Minocycline effectively inhibits oxidative stress via modulating antioxidative enzymes and activating the LKB1/AMPK signaling pathway in the process of acute cerebral infarct.
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Affiliation(s)
- Z Cai
- Department of Neurology, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing 400013, Chongqing, China
| | - C Wang
- Department of Neurology, Renmin Hospital, Hubei University of Medicine, Shiyan 442000, Hubei Province, China
| | - Y Chen
- Department of Neurology, Renmin Hospital, Hubei University of Medicine, Shiyan 442000, Hubei Province, China
| | - W He
- Department of Neurology, Renmin Hospital, Hubei University of Medicine, Shiyan 442000, Hubei Province, China
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Tu Y, Wu X, Yu F, Dang J, Wang J, Wei Y, Cai Z, Zhou Z, Liao W, Li L, Zhang Y. Tristetraprolin specifically regulates the expression and alternative splicing of immune response genes in HeLa cells. BMC Immunol 2019; 20:13. [PMID: 31046669 PMCID: PMC6498542 DOI: 10.1186/s12865-019-0292-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 04/08/2019] [Indexed: 01/03/2023] Open
Abstract
Background Tristetraprolin (TTP) is an RNA binding protein that plays a critical role in regulating proinflammatory immune responses by destabilizing target mRNAs via binding to their AU-rich elements (AREs) in the 3′-UTRs of mRNAs. A recent CLIP-seq study revealed that TTP-binding sites are enriched in the intronic regions of RNA. TTP is also a nuclear protein that exhibits putative DNA-binding activity. These features suggested that TTP might regulate gene transcription and/or alternative splicing of pre-mRNAs in the absence of stimulation. Results To elucidate the regulatory pattern of TTP, we cloned and overexpressed the human TTP-encoding gene, ZFP36, in HeLa cells in the absence of inflammatory stimuli. The transcriptomes of the control and ZFP36-overexpressing cells were sequenced and subjected to analysis and validation. Upon ZFP36 overexpression, the expression of genes associated with innate immunity, including those in the type I interferon signaling pathway and viral response, were specifically upregulated, implying a transcriptional regulatory mechanism associated with the predicted DNA binding activity of TTP. TTP preferentially regulated the alternative splicing of genes involved in the positive regulation of the I-κB/NF-κB cascade and the TRIF-dependent toll-like receptor, MAPK, TNF, and T cell receptor signaling pathways. Conclusions Our findings indicated that TTP may regulate the immune response via the regulation of alternative splicing and potentially transcription, which greatly expands the current understanding of the mechanisms of TTP-mediated gene regulation. Electronic supplementary material The online version of this article (10.1186/s12865-019-0292-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yafang Tu
- Nephrology Department, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuchang District, Wuhan, 430060, Hubei, China.
| | - Xiongfei Wu
- Nephrology Department, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuchang District, Wuhan, 430060, Hubei, China
| | - Fengyun Yu
- Laboratory for Genome Regulation and Human Health, ABLife Inc., Optics Valley International Biomedical Park, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, 430075, Hubei, China.,Center for Genome Analysis, ABLife Inc., Optics Valley International Biomedical Park, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, 430075, Hubei, China
| | - Jianzhong Dang
- Department of Geriatrics, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuchang District, Wuhan, 430060, Hubei, China
| | - Juan Wang
- Nephrology Department, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuchang District, Wuhan, 430060, Hubei, China
| | - Yaxun Wei
- Center for Genome Analysis, ABLife Inc., Optics Valley International Biomedical Park, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, 430075, Hubei, China
| | - Zhitao Cai
- Nephrology Department, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuchang District, Wuhan, 430060, Hubei, China
| | - Zhipeng Zhou
- Laboratory for Genome Regulation and Human Health, ABLife Inc., Optics Valley International Biomedical Park, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, 430075, Hubei, China.,Center for Genome Analysis, ABLife Inc., Optics Valley International Biomedical Park, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, 430075, Hubei, China
| | - Wenliang Liao
- Nephrology Department, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuchang District, Wuhan, 430060, Hubei, China
| | - Lian Li
- Nephrology Department, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuchang District, Wuhan, 430060, Hubei, China
| | - Yi Zhang
- Laboratory for Genome Regulation and Human Health, ABLife Inc., Optics Valley International Biomedical Park, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, 430075, Hubei, China.,Center for Genome Analysis, ABLife Inc., Optics Valley International Biomedical Park, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, 430075, Hubei, China
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