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Li C, Dong X, Yuan Q, Xu G, Di Z, Yang Y, Hou J, Zheng L, Chen W, Wu G. Identification of novel characteristic biomarkers and immune infiltration profile for the anaplastic thyroid cancer via machine learning algorithms. J Endocrinol Invest 2023:10.1007/s40618-023-02022-6. [PMID: 36725810 DOI: 10.1007/s40618-023-02022-6] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/24/2023] [Indexed: 02/03/2023]
Abstract
PURPOSE Anaplastic thyroid cancer (ATC) is a rare and lethal malignant cancer. In recent years, the application of molecular-driven targeted therapy and immunotherapy has markedly improved the prognosis of ATC. This study aimed to identify characteristic genes for ATC diagnosis and revealed the role of ATC characteristic genes in drug sensitivity and immune cell infiltration. METHODS We downloaded ATC RNA-sequencing data from the GEO database. Following the combination and normalization of the dataset, we first divided the combined datasets into the training cohort and the validation cohort. We identified differentially expressed genes (DEGs) in ATC by differential expression analysis in the training cohort. We used two machine learning algorithms, least absolute shrinkage and selection operator (LASSO) and support vector machine-recursive feature elimination (SVM-RFE) to identify ATC characteristic genes. The CIBERSORT algorithm was performed to calculate the abundance of various immune cells in ATC. Finally, we validated the expression of ATC characteristic genes by quantitative RT-PCR (RT-qPCR) in ATC cell lines and immunohistochemistry (IHC). RESULTS A total of 425 DEGs were identified in the training cohort, including 240 upregulated genes and 185 downregulated genes. Four ATC characteristic genes (ADM, PXDN, MMP1, and TFF3) were identified, and their diagnostic value was validated in the validation cohort (AUC in ROC analysis > 0.75). We established a practical gene expression-based nomogram to accurately predict the probability of ATC. We also found that ATC characteristic biomarkers are associated with the tumor immune microenvironment and drug sensitivity. CONCLUSION ADM, PXDN, MMP1, and TFF3 might serve as potential ATC diagnostic biomarkers and may be helpful for ATC molecular targeted therapy and immunotherapy.
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Affiliation(s)
- C Li
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - X Dong
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Q Yuan
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - G Xu
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Z Di
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Gastric and Colorectal Surgical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Y Yang
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - J Hou
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - L Zheng
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - W Chen
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China.
| | - G Wu
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China.
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Cao Z, Li G, Di Z, Chen C, Meng L, Wu M, Wang W, Zhuo Z, Kong X, Hong M, Huang Y. From a Metal–Organic Square to a Robust and Regenerable Supramolecular Self‐assembly for Methane Purification. Angew Chem Int Ed Engl 2022; 61:e202210012. [DOI: 10.1002/anie.202210012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Zhong‐Min Cao
- CAS Key Laboratory of Design and Assembly of Functional Nanostructures and Fujian Provincial Key Laboratory of Nanomaterials Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou Fujian, 350002 China
- Xiamen Key Laboratory of Rare Earth Photoelectric Functional Materials Xiamen Institute of Rare Earth Materials Haixi Institutes Chinese Academy of Sciences Xiamen Fujian, 361021 China
| | - Guo‐Ling Li
- CAS Key Laboratory of Design and Assembly of Functional Nanostructures and Fujian Provincial Key Laboratory of Nanomaterials Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou Fujian, 350002 China
- Xiamen Key Laboratory of Rare Earth Photoelectric Functional Materials Xiamen Institute of Rare Earth Materials Haixi Institutes Chinese Academy of Sciences Xiamen Fujian, 361021 China
| | - Zheng‐Yi Di
- State Key Laboratory of Structure Chemistry Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou Fujian, 350002 China
| | - Cheng Chen
- State Key Laboratory of Structure Chemistry Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou Fujian, 350002 China
| | - Ling‐Yi Meng
- CAS Key Laboratory of Design and Assembly of Functional Nanostructures and Fujian Provincial Key Laboratory of Nanomaterials Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou Fujian, 350002 China
- Xiamen Key Laboratory of Rare Earth Photoelectric Functional Materials Xiamen Institute of Rare Earth Materials Haixi Institutes Chinese Academy of Sciences Xiamen Fujian, 361021 China
| | - Mingyan Wu
- State Key Laboratory of Structure Chemistry Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou Fujian, 350002 China
| | - Wei Wang
- CAS Key Laboratory of Design and Assembly of Functional Nanostructures and Fujian Provincial Key Laboratory of Nanomaterials Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou Fujian, 350002 China
- Xiamen Key Laboratory of Rare Earth Photoelectric Functional Materials Xiamen Institute of Rare Earth Materials Haixi Institutes Chinese Academy of Sciences Xiamen Fujian, 361021 China
| | - Zhu Zhuo
- CAS Key Laboratory of Design and Assembly of Functional Nanostructures and Fujian Provincial Key Laboratory of Nanomaterials Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou Fujian, 350002 China
- Xiamen Key Laboratory of Rare Earth Photoelectric Functional Materials Xiamen Institute of Rare Earth Materials Haixi Institutes Chinese Academy of Sciences Xiamen Fujian, 361021 China
| | - Xiang‐Jian Kong
- State Key Laboratory of Physical Chemistry of Solid Surfaces Xiamen University Xiamen Fujian, 361005 China
| | - Maochun Hong
- State Key Laboratory of Structure Chemistry Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou Fujian, 350002 China
| | - You‐Gui Huang
- CAS Key Laboratory of Design and Assembly of Functional Nanostructures and Fujian Provincial Key Laboratory of Nanomaterials Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou Fujian, 350002 China
- Xiamen Key Laboratory of Rare Earth Photoelectric Functional Materials Xiamen Institute of Rare Earth Materials Haixi Institutes Chinese Academy of Sciences Xiamen Fujian, 361021 China
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Zhang P, Chen P, Jiang B, Zhang L, Li W, Di Z, Hu X, Chang H. Full scale experimental study of liquid entrainment at ADS-4 branch of CAP1400. Nuclear Engineering and Design 2019. [DOI: 10.1016/j.nucengdes.2018.11.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Yoon P, Di Z. EXPERIENCE AND PERCEPTION OF NURSES ON DEMENTIA CARE IN GERIATRIC WARDS IN A SINGAPORE HOSPITAL. Innov Aging 2017. [DOI: 10.1093/geroni/igx004.1729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- P.S. Yoon
- Geriatric Medicine, Changi General Hospital, Singapore, Singapore
| | - Z. Di
- Geriatric Medicine, Changi General Hospital, Singapore, Singapore
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Wanlong Z, Di Z, Dongmin H, Guang Y. Roles of hypothalamic neuropeptide gene expression in body mass regulation in Eothenomys miletus (Mammalia: Rodentia: Cricetidae). The European Zoological Journal 2017. [DOI: 10.1080/24750263.2017.1334840] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Z. Wanlong
- Key Laboratory of Adaptive Evolution and Ecological Conservation on Plants and Animals in Southwest Mountain Ecosystem of Yunnan Higher Education Institutes, School of Life Sciences, Yunnan Normal University, Kunming, People’s Republic of China
| | - Z. Di
- School of Life Sciences, Kunming, People’s Republic of China
| | - H. Dongmin
- Key Laboratory of Adaptive Evolution and Ecological Conservation on Plants and Animals in Southwest Mountain Ecosystem of Yunnan Higher Education Institutes, School of Life Sciences, Yunnan Normal University, Kunming, People’s Republic of China
| | - Y. Guang
- College of Life Sciences, Nanjing Normal University, Nanjing, People’s Republic of China
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Kampman N, Busch A, Bertier P, Snippe J, Hangx S, Pipich V, Di Z, Rother G, Harrington JF, Evans JP, Maskell A, Chapman HJ, Bickle MJ. Observational evidence confirms modelling of the long-term integrity of CO2-reservoir caprocks. Nat Commun 2016; 7:12268. [PMID: 27464840 PMCID: PMC4974477 DOI: 10.1038/ncomms12268] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 06/17/2016] [Indexed: 11/23/2022] Open
Abstract
Storage of anthropogenic CO2 in geological formations relies on a caprock as the primary seal preventing buoyant super-critical CO2 escaping. Although natural CO2 reservoirs demonstrate that CO2 may be stored safely for millions of years, uncertainty remains in predicting how caprocks will react with CO2-bearing brines. This uncertainty poses a significant challenge to the risk assessment of geological carbon storage. Here we describe mineral reaction fronts in a CO2 reservoir-caprock system exposed to CO2 over a timescale comparable with that needed for geological carbon storage. The propagation of the reaction front is retarded by redox-sensitive mineral dissolution reactions and carbonate precipitation, which reduces its penetration into the caprock to ∼7 cm in ∼105 years. This distance is an order-of-magnitude smaller than previous predictions. The results attest to the significance of transport-limited reactions to the long-term integrity of sealing behaviour in caprocks exposed to CO2. Anthropogenic CO2 storage, where CO2 is injected into saline geological resevoirs, relies on an impermeable caprock to seal in the CO2, but caprock reaction rates to CO2 acid brines are unclear. Here, Kampman et al. show that mineral reaction front alteration in caprocks takes place over 100,000 years.
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Affiliation(s)
- N Kampman
- Shell Global Solutions International, Kessler Park 1, 2288 GS Rijswijk, The Netherlands.,Department of Earth Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EQ, UK
| | - A Busch
- Shell Global Solutions International, Kessler Park 1, 2288 GS Rijswijk, The Netherlands
| | - P Bertier
- Clay and Interface Mineralogy, RWTH Aachen University, Bunsenstrasse 8, 52072 Aachen, Germany
| | - J Snippe
- Shell Global Solutions International, Kessler Park 1, 2288 GS Rijswijk, The Netherlands
| | - S Hangx
- High Pressure and Temperature Laboratory, Utrecht University, PO Box 80 021, 3508 TA Utrecht, The Netherlands
| | - V Pipich
- Jülich Centre for Neutron Science (JCNS), Forschungszentrum Jülich GmbH, Outstation at Heinz Maier-Leibnitz Zentrum (MLZ),1 Lichtenbergstrasse, 85747 Garching, Germany
| | - Z Di
- Jülich Centre for Neutron Science (JCNS), Forschungszentrum Jülich GmbH, Outstation at Heinz Maier-Leibnitz Zentrum (MLZ),1 Lichtenbergstrasse, 85747 Garching, Germany
| | - G Rother
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - J F Harrington
- British Geological Survey, Environmental Science Centre, Keyworth, Nottingham NG12 5GG, UK
| | - J P Evans
- Department of Geology, Utah State University, 4505 Old Main Hill, Logan, Utah 84322-4505, USA
| | - A Maskell
- Department of Earth Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EQ, UK
| | - H J Chapman
- Department of Earth Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EQ, UK
| | - M J Bickle
- Department of Earth Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EQ, UK
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Zhao LP, Di Z, Zhang L, Wang L, Ma L, Lv Y, Hong Y, Wei H, Chen HD, Gao XH. Association of SPINK5 gene polymorphisms with atopic dermatitis in Northeast China. J Eur Acad Dermatol Venereol 2011; 26:572-7. [PMID: 21585560 DOI: 10.1111/j.1468-3083.2011.04120.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
BACKGROUND Defect in the SPINK5 gene is known to be implicated in Netherton syndrome (NS), and has been suggested to be a locus predisposing to atopy in general. Coding polymorphisms in SPINK5 exons 13, 14 and 26 have been reported to be associated with atopic dermatitis (AD), asthma and high level of IgE. OBJECTIVES To examine whether the SPINK5 gene polymorphisms are associated with AD in Northeast China, and to assess how variants influence selected phenotypic traits. METHODS A case-control study was conducted on four non-synonymous polymorphisms in the coding region of SPINK5 in AD and controls. The SPINK5 gene polymorphisms were analyzed using the PCR and RFLP methods. RESULTS For the four non-synonymous SNPs, A1103G(Asn368Ser), G1156A(Asp386Asn), G1258A(Glu420Lys), G2475T(Glu825Asp) in SPINK5, the allelic frequencies in the AD cohort were 0.55 for 1103G, 0.57 for 1156A, 0.54for 1258A, 0.62 for 2475T, consistent with those already published in the original British and Japanese cohorts. The T allele of SNP 2475G > T was found to be significantly associated with AD. There were significant differences in genotype frequencies for G1258A(Glu420Lys) and G2475T(Glu825Asp) but not for A1103G(Asn368Ser) and G1156A(Asp386Asn). Genotypes GA(420Glu/Lys), TT (2475Asp/Asp) and GT(2475Glu/Asp) were significantly more frequent in AD. However, the SPINK5 gene polymorphisms was found not to be associated with AD in regard to either serum IgE levels, concurrent allergic asthma or early onset of AD. CONCLUSIONS Our study confirms the association between SPINK5 and AD.
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Affiliation(s)
- L P Zhao
- Department of Dermatology, No.1 Hospital of China Medical University, Shenyang, China
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Papadakis CM, Darko C, Di Z, Troll K, Metwalli E, Timmann A, Reiter G, Förster S. Surface-induced breakout crystallization in cylinder-forming P(I-b-EO) diblock copolymer thin films. Eur Phys J E Soft Matter 2011; 34:7. [PMID: 21267706 DOI: 10.1140/epje/i2011-11007-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Accepted: 12/21/2010] [Indexed: 05/30/2023]
Abstract
We have found very slow crystallization in thin films of cylinder-forming poly(isoprene-b-ethyleneoxide) (P(I-b -EO)) diblock copolymers with PEO being the minority block. The film was crystallized at room temperature after melting at 62 °C. Imaging methods were combined with X-ray reflectometry and grazing-incidence small-angle X-ray scattering and diffraction. Initially, hexagonally packed, amorphous PEO cylinders lie in the film plane. After 148 days, crystallized, finger-like terraces were observed over the entire film surface. The terrace height is 20% higher than the repeat distance in the as-prepared film. Thus, at the film surface, the cylinders have been destroyed by crystalline lamellae lying in the film plane. The PEO chain stems are perpendicular to the substrate surface and are once-folded and fully interdigitated. The substrate-near layers still consist of the hexagonally packed, amorphous PEO cylinders within the PI matrix.
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Affiliation(s)
- C M Papadakis
- Technische Universität München, Physikdepartment, Fachgebiet Physik weicher Materie/Lehrstuhl für funktionelle Materialien, James-Franck-Str. 1, 85747 Garching, Germany.
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Pei W, Huai-Zhang S, Shan-Cai X, Cheng G, Di Z. Isolated hypoglossal nerve palsy due to endovascular treatment of a dural arteriovenous fistula with Onyx-18. Interv Neuroradiol 2010; 16:286-9. [PMID: 20977862 DOI: 10.1177/159101991001600310] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2010] [Accepted: 05/02/2010] [Indexed: 10/20/2022] Open
Abstract
We describe a patient with dural arteriovenous fistula (DAVF) treated with Onyx-18 who developed isolated hypoglossal nerve palsy. This is the first case of isolated hypoglossal nerve palsy caused by Onyx-18 embolization. This complication suggests that over embolization with Onyx-18 in the treatment of hypoglossal canal DAVFs should be avoided, and transvenous embolization may be safer. Furthermore, prednisolone therapy should be carried out in the prophase of nerve palsy.
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Affiliation(s)
- W Pei
- Department of Neurosurgery, The first Affiliated Hospital Harbin Medical University, Harbin Heilongjiang, China
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Rauth C, Ackermann D, Blaum K, Block M, Chaudhuri A, Di Z, Eliseev S, Ferrer R, Habs D, Herfurth F, Hessberger FP, Hofmann S, Kluge HJ, Maero G, Martín A, Marx G, Mukherjee M, Neumayr JB, Plass WR, Rahaman S, Rodríguez D, Scheidenberger C, Schweikhard L, Thirolf PG, Vorobjev G, Weber C. First Penning trap mass measurements beyond the proton drip line. Phys Rev Lett 2008; 100:012501. [PMID: 18232754 DOI: 10.1103/physrevlett.100.012501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2006] [Revised: 07/19/2007] [Indexed: 05/25/2023]
Abstract
The masses of six neutron-deficient rare holmium and thulium isotopes close to the proton drip line were determined with the SHIPTRAP Penning trap mass spectrometer. For the first time the masses of the proton-unbound isotopes 144,145Ho and 147,148Tm were directly measured. The proton separation energies were derived from the measured mass values and compared to predictions from mass formulas. The new values of the proton separation energies are used to determine the location of the proton drip line for holmium and thulium more accurately.
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Affiliation(s)
- C Rauth
- Gesellschaft für Schwerionenforschung (GSI), Planckstrasse 1, 64291 Darmstadt, Germany
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Abstract
AIM To investigate the effects of somatostatin analogs (SSa) on apoptosis of pancreatic acinar cells and apoptosis-regulated gene bax, and p53 in treating acute pancreatitis in mice. METHODS In cerulein-induced pancreatitis, with or without treatment of somatostatin, analogs (Octreotide) in CD-1 (BALB/c x DBetaAlpha/1) mice, apoptosis of pancreatic acinar cells was detected by using the TdT-mediated dUTP nick-end labeling (TUNEL) method, and the expression of apoptosis-regulated gene bax and p53 was determined by using the streptavidin-peroxidase immunohistochemical technique and the RT-PCR method, respectively. RESULTS On HE staining, acinar cells in the pancreas showed pyknotic nuclei and the formation of apoptotic bodies, which are the typical morphological features of apoptosis. Regarding TUNEL use, the apoptotic index of pancreatic acinar cells in the non-treated group at 5 and 14 h after induction of acute pancreatitis was significantly lower than those of the SSa-treated group, respectively (P < 0.01). On immunohistochemistry and RT-PCR, there was an expression of neither bax nor p53 in normal pancreatic tissues. The expression of bax in the SSa-treated group at 5 and 14 h after treatment of SSa was markedly higher than those of the non-treated group, respectively (P < 0.01), but there was no significant difference in the expression of p53 between the SSa-treated group and the non-treated group. CONCLUSIONS The induction of apoptosis in pancreatic acinar cells injury to reduce inflammatory reaction might be one of the mechanisms of SSa in treating acute pancreatitis in mice, and the mechanisms of apoptosis probably correlated with the expression of apoptosis-regulated gene bax, but have no relationship with the expression of p53.
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Affiliation(s)
- Y Yuan
- Department of Gastroenterology, Ruijin Hospital, Shanghai Second Medical University, Shanghai, China.
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