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Zhou CB, Lu WW, Zhang YZ, Liu WY, Chen YB, Qian YQ, Zhu LH. [Analysis of non-bacterial respiratory pathogens in children in Ningbo City from 2019 to 2021]. Zhonghua Yu Fang Yi Xue Za Zhi 2022; 56:1751-1758. [PMID: 36536562 DOI: 10.3760/cma.j.cn112150-20220121-00080] [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: 06/17/2023]
Abstract
Objective: To investigate the distribution characteristics of respiratory non-bacterial pathogens in children in Ningbo from 2019 to 2021. Methods: A retrospective analysis was performed on 23 733 children with respiratory tract infection who visited the department of pediatrics of Ningbo Women and Children's Hospital from July 2019 to December 2021. There were 13 509 males (56.92%) and 10 224 females (43.08%), with an age range of 1 day to 18 years old. There were 981 cases in the neonatal group (younger than 1 month old), 5 880 cases in the infant group (1 month to younger than 1 year old), 6 552 cases in the toddler group (1 to younger than 3 years old), 7 638 cases in the preschool group (3 to younger than 7 years old), and 2 682 cases in the school-age group (7 to 18 years old). Thirteen respiratory pathogens were detected by multiple polymerase chain reaction (PCR) based on capillary electrophoresis, and SPSS 23.0 software was used for statistical analysis of the results, the count data were expressed as percentages, and the χ2 test was used for comparison between groups. Results: Of the 23 733 specimens, 13 330 were positive for respiratory pathogens, with a total positive rate of 56.17%. The positive rates of human rhinovirus (HRV) 24.05% (5 707/23 733), human respiratory syncytial virus (HRSV) 10.45% (2 480/2 3733) and mycoplasma pneumoniae (Mp) 7.03% (1 668/23 733) were in the first three. The positive rates of pathogens in the male and female children were 57.47% (7 763/13 509) and 54.45% (5 567/10 224), respectively, and the difference was statistically significant (χ2=21.488, P<0.001). The positive rates in the neonatal group, infant group, toddler group, preschool group, and school-age group were 31.80% (312/981), 54.71% (3 217/5 880), 63.23% (4 143/6 552), 59.83% (4 570/7 638), 40.57% (1 088/2 682), respectively, and the difference among the groups was statistically significant (χ2=681.225, P<0.001). The single infection rate was 47.43% (11 256/23 733), the mixed infection rate of two or more pathogens was 8.74% (2 074/23 733), most of which were mixed infections of two pathogens. HRV, HADV, HCOV, Ch disseminated in the whole year. HRSV, HMPV, Boca, HPIV occurred mostly in fall and winter. The positive rates of FluA, FluB, Mp were at a low level after the corona virus disease 2019 (COVID-19) epidemic (2020 and 2021). The positive rates of FluA, H1N1, H3N2, FluB, HADV, Mp in 2020 were significantly lower than in 2019 (P<0.05). The positive rates of HPIV, HRV, HCOV, Ch in 2020 were significantly higher than in 2019 (P<0.05). The positive rates of FluA, H1N1, H3N2, HPIV, HCOV, Mp, Ch in 2021 were significantly lower than in 2020 (P<0.05). The positive rates of Boca, HMPV, HRSV in 2021 were significantly higher than in 2020 (P<0.05). Conclusion: From 2019 to 2021, the main non-bacterial respiratory pathogens of children in Ningbo City were Mp and HRV, and the detection rates of respiratory pathogens varied among different ages, seasons and genders.
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Affiliation(s)
- C B Zhou
- Department of Clinical Laboratory,Ningbo Women and Children's Hospital,Ningbo 315012, China
| | - W W Lu
- Department of Clinical Laboratory,Ningbo Women and Children's Hospital,Ningbo 315012, China
| | - Y Z Zhang
- Department of Clinical Laboratory,Ningbo Women and Children's Hospital,Ningbo 315012, China
| | - W Y Liu
- Department of Clinical Laboratory,Ningbo Women and Children's Hospital,Ningbo 315012, China
| | - Y B Chen
- Department of Clinical Laboratory,Ningbo Women and Children's Hospital,Ningbo 315012, China
| | - Y Q Qian
- Ningbo Health Gene Technologies Co., Ltd., Ningbo 315040, China
| | - L H Zhu
- Department of Pediatrics,Ningbo Women and Children's Hospital,Ningbo 315012, China
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2
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Qian YQ, Feng ZH, Li XB, Hu ZC, Xuan JW, Wang XY, Xu HC, Chen JX. Downregulating PI3K/Akt/NF-κB signaling with allicin for ameliorating the progression of osteoarthritis:in vitroandvivostudies. Food Funct 2018; 9:4865-4875. [DOI: 10.1039/c8fo01095a] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A schematic illustration of the potential protective effects of allicin on osteoarthritis development.
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Affiliation(s)
- Yu-Qin Qian
- Department of Orthopaedics
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University
- Second Medical College of Wenzhou Medical University
- First Medical College of Wenzhou Medical University
- Bone Research Institute
| | - Zhen-Hua Feng
- Department of Orthopaedics
- The Second Affiliated Hospital of Jiaxing University
- Jiaxing
- China
| | - Xiao-Bin Li
- Department of Orthopaedics
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University
- Second Medical College of Wenzhou Medical University
- First Medical College of Wenzhou Medical University
- Bone Research Institute
| | - Zhi-Chao Hu
- Department of Orthopaedics
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University
- Second Medical College of Wenzhou Medical University
- First Medical College of Wenzhou Medical University
- Bone Research Institute
| | - Jiang-Wei Xuan
- Department of Orthopaedics
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University
- Second Medical College of Wenzhou Medical University
- First Medical College of Wenzhou Medical University
- Bone Research Institute
| | - Xiang-yang Wang
- Department of Orthopaedics
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University
- Second Medical College of Wenzhou Medical University
- First Medical College of Wenzhou Medical University
- Bone Research Institute
| | - Hai-Chao Xu
- Department of Orthopaedics
- The Second Affiliated Hospital of Jiaxing University
- Jiaxing
- China
| | - Jiao-Xiang Chen
- Department of Orthopaedics
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University
- Second Medical College of Wenzhou Medical University
- First Medical College of Wenzhou Medical University
- Bone Research Institute
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Qian YQ, Johanson KO, McDevitt P. Nuclear magnetic resonance solution structure of truncated human GRObeta [5-73] and its structural comparison with CXC chemokine family members GROalpha and IL-8. J Mol Biol 1999; 294:1065-72. [PMID: 10600366 DOI: 10.1006/jmbi.1999.3333] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [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: 11/22/2022]
Abstract
The three-dimensional structure of a novel four amino acid truncated form of the CXC chemokine GRObeta [5-73] isolated from bone marrow stromal cells with potent hematopoietic and anti-infective activities has been determined by two-dimensional (1)H nuclear magnetic resonance (NMR) spectroscopy in solution. On the basis of 1878 upper distance constraints derived from nuclear Overhauser effects (NOE) and 314 dihedral angle constraints, a group of 20 conformers representing the solution structure of the human GRObeta [5-73] was computed with the program DYANA. At the concentrations used for NMR study, GRObeta [5-73] forms a dimer in solution that is architectured by a six-stranded antiparallel beta-sheet (residues 25 to 29, 39 to 44, 49 to 52) and a pair of helices (residues 58 to 68) with 2-fold symmetry, while the C terminus of the protein is disordered. The average of the pairwise root-mean-square deviations of individual NMR conformers relative to the mean coordinates for the backbone atoms N, C(alpha) and C' of residues 5 to 68 is 0.47 A. Overall, the global fold of GRObeta [5-73] is similar to that of the previously reported NMR structure of GROalpha and the NMR and X-ray structures of interleukin-8. Among these three CXC chemokines, GRObeta [5-73] is most similar in structure to GROalpha. Significant differences between GRObeta [5-73], GROalpha and interleukin-8 are in the N-terminal loop comprising residues 12 to 19. The N-terminal arm containing the conserved ELR motif and the loop of residues 30 to 38 containing the GPH motif are different among these three CXC chemokines. The structural differences in these two regions may be responsible for the specificity of the receptor binding and biological activity of different chemokines.
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Affiliation(s)
- Y Q Qian
- Department of Physical & Structural Chemistry, SmithKline Beecham Pharmaceuticals, King of Prussia, PA 19406, USA.
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Bao JX, Zhang LF, Shang HH, Yu ZB, Qian YQ. [Echocardiographic assessment of left ventricular structure and function after simulated weightlessness in rats]. Space Med Med Eng (Beijing) 1999; 12:88-91. [PMID: 12428650] [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: 02/27/2023]
Abstract
Objective. To investigate whether the changes in rat after simulated weightlessness are similar to those in astronaut after flight. Methods. The effects of 4 wk tail-suspension on left ventricular structure and function in rats were examined by echocardiography. Results. After 4 wk of simulated weightlessness, the thickness of both the anterior and posterior wall in left ventricle (LV) showed a general trend of decrease, but these changes were not statistically significant; the end-systolic and end-diastolic internal dimensions (ESD and EDD respectively) of LV decreased significantly; and the end-systolic volume, end-diastolic volume and stroke volume (ESV, EDV and SV respectively) were all reduced; so did the relevant indices of them. There were no significant differences in ejection fraction (EF) and fractional shortening (FS) between the tail-suspended and control groups. The left ventricular mass (LVM) and its index (LVMI) were decreased. The peak velocities of blood flow of aorta, pulmonary artery and mitral valve didn't show any significant change after simulated weightlessness. Conclusion. Medium-term simulated weightlessness may lead to a significant decrease in left ventricular internal dimension, ventricular volume, and mass, and a trend of decrease in mean left ventricular wall thickness. These changes in rats are similar to those observed in astronauts postflight.
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Affiliation(s)
- J X Bao
- Department of Aerospace Physiology, The Fourth Military Medical University, Xi'an, China
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5
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Abstract
The J-domain is a highly conserved domain found in all members of the DnaJ family of molecular chaperones. The three-dimensional structure of a recombinant, uniformly 15N-labeled 77-residue polypeptide containing the complete J-domain from human Hsp40 (HDJ-1) has been determined by nuclear magnetic resonance (NMR) spectroscopy in solution. On the basis of 876 upper distance constraints derived from nuclear Overhauser effects (NOE) and 173 dihedral angle constraints, a group of 20 conformers representing the solution structure of the HDJ-1 J-domain was computed with the program DIANA and energy-minimized with the program OPAL. The average of the pairwise root-mean-square deviations of the individual NMR conformers relative to the mean coordinates for the backbone atoms N, C2 and C' of residues 4 to 54 and 4 to to 66 is 0.88 and 0.99 A respectively. The molecular architecture includes four helices composed of residues 5 to 9, 15 to 28, 40 to 54 and 60 to 66. A turn composed of residues 10 to 14 links helices I and II, and a loop composed of residues 29 to 39 containing a highly conserved tripeptide HPD (residues 31 to 33) connects the antiparallel helices II and III. The tertiary fold formed by helix I-turn-helix II-loop-helix III forms a closed structural core; the less defined helix IV stands away from the core of the domain. The side-chains of the tripeptide HPD extend out from the core of the structure in the opposite direction from helix IV. The structure supports the hypothesis that the highly conserved tripeptide could play a key role in the interaction of Hsp40 with the molecular chaperone, Hsp70.
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Affiliation(s)
- Y Q Qian
- Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, NY 10021, USA
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Affiliation(s)
- W J Gehring
- Biozentrum der Universität Basel, Switzerland
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Qian YQ, Furukubo-Tokunaga K, Resendez-Perez D, Müller M, Gehring WJ, Wüthrich K. Nuclear magnetic resonance solution structure of the fushi tarazu homeodomain from Drosophila and comparison with the Antennapedia homeodomain. J Mol Biol 1994; 238:333-45. [PMID: 7909851 DOI: 10.1006/jmbi.1994.1296] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.8] [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: 01/27/2023]
Abstract
The three-dimensional structure of a recombinant 70-residue polypeptide containing the complete fushi tarazu (ftz) homeodomain from Drosophila melanogaster has been determined by nuclear magnetic resonance (NMR) spectroscopy in solution. On the basis of 915 upper distance constraints derived from nuclear Overhauser effects and 178 dihedral angle constraints, a group of 20 conformers representing the solution structure of the ftz homeodomain was computed with the program DIANA and energy-minimized with the program OPAL. The average of the pairwise root-mean-square deviations of the individual NMR conformers relative to the mean coordinates is 0.50 A for the backbone atoms N, C alpha and C' of residues 8 to 53. The molecular architecture includes three helices comprising the residues 10 to 21, 28 to 38, and 42 to 52, a loop of residues 22 to 27 between the helices I and II, and a turn of residues 39 to 41 linking the helices II and III. Comparisons with the structure of the mutant Antennapedia homeodomain with Cys39 replaced by Ser, Antp (C39S), shows that the two proteins contain the same molecular fold for residues 8 to 53, whereas the more flexible fourth helix comprising residues 53 to 59 in the Antp (C39S) homeodomain has no counterpart in the ftz homeodomain. Considering that important intermolecular interactions in the DNA complexes with the Antp, engrailed and Mat alpha 2 homeodomains involve the fourth helix, it was rather unexpected that the stability of the complex of ftz with the BS2 operator site was found to be comparable to or even somewhat higher than that of the Antp complex with BS2. Another difference is that the Antp homeodomain is more stable with respect to thermal denaturation, with denaturation temperatures at pH 4.8 of 27 degrees C and 48 degrees C, respectively, for ftz and Antp.
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Affiliation(s)
- Y Q Qian
- Institut für Molekularbiologie und Biophysik, ETH-Hönggerberg, Zürich, Switzerland
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Qian YQ, Resendez-Perez D, Gehring WJ, Wüthrich K. The des(1-6)antennapedia homeodomain: comparison of the NMR solution structure and the DNA-binding affinity with the intact Antennapedia homeodomain. Proc Natl Acad Sci U S A 1994; 91:4091-5. [PMID: 7909611 PMCID: PMC43729 DOI: 10.1073/pnas.91.9.4091] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [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: 01/27/2023] Open
Abstract
The nuclear magnetic resonance (NMR) solution structure of an N-terminally truncated mutant Antennapedia homeodomain, des(1-6)Antp(C39S), has been determined from 935 nuclear Overhauser effect upper distance constraints and 148 dihedral angle constraints by using the programs DIANA and OPAL. Twenty conformers representing the solution structure of des(1-6)Antp(C39S) have an average root-mean-square distance relative to the mean coordinates of 0.56 A for the backbone atoms of residues 8-59. Comparison with the intact Antp(C39S) homeodomain shows that the two proteins have identical molecular architectures. The removal of the N-terminal residues 1-6, which are flexibly disordered in the intact homeodomain, causes only strictly localized structure variations and does not noticeably affect the adjoining helix I from residues 10-21. The DNA-binding constant of des(1-6)Antp(C39S) is approximately 10-fold reduced relative to the intact Antp(C39S) homeodomain, which can now be attributed to the absence of the previously reported contacts of the N-terminal polypeptide segment of the intact Antp(C39S) homeodomain with the minor groove of the DNA duplex.
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Affiliation(s)
- Y Q Qian
- Institut für Molekularbiologie und Biophysik, Eidgenössiche Technische Hochschule-Hönggerberg, Zürich, Switzerland
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9
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Billeter M, Qian YQ, Otting G, Müller M, Gehring W, Wüthrich K. Determination of the nuclear magnetic resonance solution structure of an Antennapedia homeodomain-DNA complex. J Mol Biol 1993; 234:1084-93. [PMID: 7903398 DOI: 10.1006/jmbi.1993.1661] [Citation(s) in RCA: 221] [Impact Index Per Article: 7.1] [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: 01/27/2023]
Abstract
The nuclear magnetic resonance (NMR) solution structure of a complex formed by the mutant Antennapedia homeodomain with Cys39 replaced by Ser, Antp(C39S), and a 14 base-pair DNA duplex containing the BS2 operator sequence was determined using uniform 13C and 15N-labeling of the protein. Two-dimensional nuclear Overhauser enhancement spectroscopy ([1H,1H]NOESY) with 15N(omega 2)-half-filter and 13C(omega 1, omega 2)-double-half-filter, and three-dimensional heteronuclear-correlated [1H,1H]NOESY yielded a total of 855 intramolecular NOE upper distance constraints in the homeodomain, 151 upper distance constraints within the DNA duplex, and 39 intermolecular protein-DNA upper distance constraints. These data were used as the input for the structure calculation with simulated annealing followed by molecular dynamics in a water bath and energy refinement. A group of 16 conformers was thus generated which represent the solution structure of the Antp(C39S) homeodomain-DNA complex. The new structure determination confirms the salient features reported previously from a preliminary investigation of the same complex, in particular the location of the recognition helix in the major groove with the turn of the helix-turn-helix motif outside the contact area with the DNA, and the N-terminal arm of the homeodomain contacting the minor groove of the DNA. In addition, distinct amino acid side-chain-DNA contacts could be identified, and evidence was found that the invariant residue Asn51 (and possibly also Gln50) is in a slow dynamic equilibrium between two or several different DNA contact sites. The molecular dynamics calculations in a water bath yielded structures with hydration water molecules in the protein-DNA interface, which coincides with direct NMR observations of hydration waters. In the Appendix the experimental data obtained with the Antp(C39S) homeodomain-DNA complex and the techniques used for the structure calculation are evaluated using a simulated input data set derived from the X-ray crystal structure of a DNA complex with a homologous homeodomain. This study indicates that a nearly complete set of NOE upper distance constraints for the Antp(C39S) homeodomain and the protein-DNA interface was presently obtained. It further shows that the structure calculation used here yields a precise reproduction of the crystal structure from the simulated input data, and also results in hydration of the protein-DNA interface in the recalculated complex.
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Affiliation(s)
- M Billeter
- Institut für Molekularbiologie und Biophysik Eidgenössische Technische Hochschule-Hönggerberg, Zürich, Switzerland
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Qian YQ, Otting G, Billeter M, Müller M, Gehring W, Wüthrich K. Nuclear magnetic resonance spectroscopy of a DNA complex with the uniformly 13C-labeled Antennapedia homeodomain and structure determination of the DNA-bound homeodomain. J Mol Biol 1993; 234:1070-83. [PMID: 7903397 DOI: 10.1006/jmbi.1993.1660] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.0] [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: 01/27/2023]
Abstract
A 1:1 complex formed by the mutant Antennapedia(C39S) homeodomain and a 14 base-pair DNA duplex (molecular weight approximately 18,000) was prepared in which the protein was uniformly 13C-labeled. Using two-dimensional nuclear Overhauser enhancement (NOE) spectroscopy with 13C(omega 1, omega 2)-double-half-filter and three-dimensional 13C-correlated NOE spectroscopy, nearly complete sequence-specific resonance assignments were obtained for both the protein and the DNA in the complex. On this basis conformational constraints needed for a three-dimensional structure determination were collected. Using 855 intramolecular distance constraints as input, the structure of the DNA-bound Antp(C39S) homeodomain was calculated with the program DIANA, followed by restrained energy minimization with the program OPAL. A group of 20 conformers characterizes a well-defined structure for residues 8 to 56, with an average of 0.5 A of the pairwise root-mean-square deviations calculated for the backbone atoms of the individual conformers relative to the mean coordinates. The quality of the resulting structure is comparable to the one for the free protein, and the global fold of the free Antp(C39S) homeodomain was found to be conserved in the DNA complex. The structure of the DNA-bound protein was the starting point for the subsequent structure determination of the complete Antp(C39S) homeodomain-DNA complex in solution.
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Affiliation(s)
- Y Q Qian
- Institut für Molekularbiologie und Biophysik Eidgenössische Technische Hochschule-Hönggerberg, Zürich, Switzerland
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Wang TB, Niizeki M, Harada T, Ishikawa R, Qian YQ, Saito K. Establishment of somatic hybrid cell lines between Zea mays L. (maize) and Triticum sect, trititrigia MacKey (trititrigia). Theor Appl Genet 1993; 86:371-376. [PMID: 24193485 DOI: 10.1007/bf00222104] [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: 06/24/1992] [Accepted: 10/20/1992] [Indexed: 06/02/2023]
Abstract
Somatic hybrid cell lines were constructed by the fusion of protoplasts isolated from cell suspensions of Zea mays L. (maize, 2n = 20) and Triticum sect, trititrigia MacKey (trititrigia, 2n = 35), a perennial hybrid of T. durum Desf. and Elytrigia intermedium (Host) Nevski. Iodoacetamide-inactivated protoplasts of maize were fused with trititrigia protoplasts, which were sensitive to the PEG/DMSO fusion treatment at high pH and high calcium. Based on physiological complementation, approximately 0.002% of the total protoplasts cultured following fusion treatment developed into cell colonies, and 79 lines of them, almost a half, were singled out and subcultured. Among the subcultured lines three were, in comparison with the parents, identified as somatic hybrids by their coupled XbaI restriction patterns of total DNAs probed with the ribosomal DNA of rice. Southern analysis of the digested total DNAs with a mitochondrial gene, atpA., from pea, or a chloroplast gene, trnK, from rice, revealed that all the hybrids carried only the organellar DNAs of trititrigia, which excluded the possibilities of a chimeric callus or any DNA contamination. Cytogenetically, one hybrid was mixoploid with a 2n of 46-67 in which chromosomal endoreduplication, characterized by the appearance of diplochromosomes, was occasionally observed. Its hybridity was reconfirmed by the fact that it bore the satellite chromosomes of both maize and trititrigia, which were distinguishable from each other by size. In contrast, the other two hybrids were aneuploids. The potential of gene transfer between Zea and Triticum species was thus conclusively established.
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Affiliation(s)
- T B Wang
- Plant Breeding Laboratory, Faculty of Agriculture, Hirosaki University, Hirosaki, 036, Aomori-Ken, Japan
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12
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Qian YQ, Otting G, Furukubo-Tokunaga K, Affolter M, Gehring WJ, Wüthrich K. NMR structure determination reveals that the homeodomain is connected through a flexible linker to the main body in the Drosophila Antennapedia protein. Proc Natl Acad Sci U S A 1992; 89:10738-42. [PMID: 1359544 PMCID: PMC50417 DOI: 10.1073/pnas.89.22.10738] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.3] [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: 11/18/2022] Open
Abstract
The secondary structure of an N-terminally elongated Antennapedia (Antp) homeodomain (HD) polypeptide containing residues -14 to 67, where residues 1-60 constitute the HD, has been determined by NMR in solution. This polypeptide contains the conserved motif -Tyr-Pro-Trp-Met- (YPWM) at positions -9 to -6. Despite the hydrophobic nature of this tetrapeptide motif, the N-terminal arm consisting of residues -14 to 6 is flexibly disordered, and the well-defined part of the HD structure with residues 7-59 is indistinguishable from that of the shorter Antp HD polypeptide (where positions 0, 1, and 67 are methionine, arginine, and glycine, respectively). In vitro biochemical studies showed that the stability and specificity of the DNA binding previously observed for the shorter Antp HD polypeptide is preserved in the elongated polypeptide. These results strongly support the view that the HD is connected through a flexible linker to the main body in the Antp protein and that the minor groove contacts by the N-terminal arm (residues 1-6) in the Antp HD-DNA complex are an intrinsic feature of the DNA-binding interactions of the intact Antp protein.
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Affiliation(s)
- Y Q Qian
- Institut für Molekularbiologie und Biophysik, Eidgenössiche Technische Hochschule-Hönggerberg, Zürich, Switzerland
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Billeter M, Neri D, Otting G, Qian YQ, Wüthrich K. Precise vicinal coupling constants 3JHN alpha in proteins from nonlinear fits of J-modulated [15N,1H]-COSY experiments. J Biomol NMR 1992; 2:257-274. [PMID: 1392569 DOI: 10.1007/bf01875320] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Improved experimental schemes for the recently introduced J-modulated [15N,1H]-correlation experiment for measurements of the homonuclear amide proton-C alpha proton vicinal coupling constants, 3JHN alpha, in uniformly 15N-labeled proteins are described, and a nonlinear fit procedure is presented for quantitative evaluation of 3JHN alpha. The method was first tested with the N-terminal DNA-binding domain of the 434 repressor (M = 7.3 kDa), where at 13 degrees C precise values of 3JHN alpha in the range 2.0-9.5 Hz were obtained for all residues with resolved 15N-1H cross peaks. It was then applied to the Antennapedia homeodomain complexed to a synthetic 14-base pair DNA fragment (molecular weight of the complex approximately 18 kDa). The 3JHN alpha values measured were found to be in excellent agreement with those predicted from the secondary structure of this protein in the complex.
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Affiliation(s)
- M Billeter
- Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule-Hönggerberg, Zürich, Switzerland
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Affolter M, Percival-Smith A, Müller M, Billeter M, Qian YQ, Otting G, Wüthrich K, Gehring WJ. Similarities between the homeodomain and the Hin recombinase DNA-binding domain. Cell 1991; 64:879-80. [PMID: 2001587 DOI: 10.1016/0092-8674(91)90311-l] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Güntert P, Qian YQ, Otting G, Müller M, Gehring W, Wüthrich K. Structure determination of the Antp (C39----S) homeodomain from nuclear magnetic resonance data in solution using a novel strategy for the structure calculation with the programs DIANA, CALIBA, HABAS and GLOMSA. J Mol Biol 1991; 217:531-40. [PMID: 1671604 DOI: 10.1016/0022-2836(91)90755-u] [Citation(s) in RCA: 104] [Impact Index Per Article: 3.2] [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: 12/28/2022]
Abstract
The structure of a mutant Antennapedia homeodomain, Antp(C39----S), from Drosophila melanogaster was determined using a set of new programs introduced in the accompanying paper. An input dataset of 957 distance constraints and 171 dihedral angle constraints was collected using two-dimensional n.m.r. experiments with the 15N-labeled protein. The resulting high quality structure for Antp(C39----S), with an average root-mean-square deviation of 0.53 A between the backbone atoms of residues 7 to 59 in 20 energy-refined distance geometry structures and the mean structure, is nearly identical to the previously reported structure of the wild-type Antp homeodomain. The only significant difference is in the connection between helices III and IV, which was found to be less kinked than was indicated by the structure determination for Antp. The main emphasis of the presentation in this paper is on a detailed account of the practical use of a novel strategy for the computation of nuclear magnetic resonance structures of proteins with the combined use of the programs DIANA, CALIBA, HABAS and GLOMSA.
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Affiliation(s)
- P Güntert
- Institut für Molekularbiologie und Biophysik Eidgenösische Technische Hochschule-Hönggerberg, Zürich, Switzerland
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Gehring WJ, Müller M, Affolter M, Percival-Smith A, Billeter M, Qian YQ, Otting G, Wüthrich K. The structure of the homeodomain and its functional implications. Trends Genet 1990; 6:323-9. [PMID: 1980756 DOI: 10.1016/0168-9525(90)90253-3] [Citation(s) in RCA: 148] [Impact Index Per Article: 4.4] [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: 12/29/2022]
Abstract
The three-dimensional structure of the homeodomain, as determined by nuclear magnetic resonance spectroscopy, reveals the presence of a helix-turn-helix motif, similar to the one found in prokaryotic gene regulatory proteins. Isolated homeodomains bind with high affinity to specific DNA sequences. Thus, the structure-function relationship is highly conserved in evolution.
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Otting G, Qian YQ, Billeter M, Müller M, Affolter M, Gehring WJ, Wüthrich K. Protein--DNA contacts in the structure of a homeodomain--DNA complex determined by nuclear magnetic resonance spectroscopy in solution. EMBO J 1990. [PMID: 1976507 PMCID: PMC552035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The 1:1 complex of the mutant Antp(C39----S) homeodomain with a 14 bp DNA fragment corresponding to the BS2 binding site was studied by nuclear magnetic resonance (NMR) spectroscopy in aqueous solution. The complex has a molecular weight of 17,800 and its lifetime is long compared with the NMR chemical shift time scale. Investigations of the three-dimensional structure were based on the use of the fully 15N-labelled protein, two-dimensional homonuclear proton NOESY with 15N(omega 2) half-filter, and heteronuclear three-dimensional NMR experiments. Based on nearly complete sequence-specific resonance assignments, both the protein and the DNA were found to have similar conformations in the free form and in the complex. A sufficient number of intermolecular 1H-1H Overhauser effects (NOE) could be identified to enable a unique docking of the protein on the DNA, which was achieved with the use of an ellipsoid algorithm. In the complex there are intermolecular NOEs between the elongated second helix in the helix-turn-helix motif of the homeodomain and the major groove of the DNA. Additional NOE contacts with the DNA involve the polypeptide loop immediately preceding the helix-turn-helix segment, and Arg5. This latter contact is of special interest, both because Arg5 reaches into the minor groove and because in the free Antp(C39----S) homeodomain no defined spatial structure could be found for the apparently flexible N-terminal segment comprising residues 0-6.
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Qian YQ, Billeter M, Otting G, Müller M, Gehring WJ, Wüthrich K. The structure of the Antennapedia homeodomain determined by NMR spectroscopy in solution: comparison with prokaryotic repressors. Cell 1989; 59:573-80. [PMID: 2572329 DOI: 10.1016/0092-8674(89)90040-8] [Citation(s) in RCA: 369] [Impact Index Per Article: 10.5] [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: 01/01/2023]
Abstract
The structure of the Antennapedia homeodomain from Drosophila melanogaster was determined by nuclear magnetic resonance spectroscopy in solution. It includes three well-defined helices (residues 10-21, 28-38, and 42-52) and a more flexible fourth helix (residues 53-59). Residues 30-50 form a helix-turn-helix motif virtually identical to those observed in various prokaryotic repressors. Further comparisons of the homeodomain with prokaryotic repressors showed that there are also significant differences in the molecular architectures. Overall, these studies support the view that the third helix of the homeodomain may function as the DNA recognition site. The elongation of the third helix by the fourth helix is a structured element that so far appears to be unique to the Antennapedia homeodomain.
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Affiliation(s)
- Y Q Qian
- Institut für Molekularbiologie und Biophysik Eidgenössische Technische Hochschule-Hönggerberg, Zürich, Switzerland
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Luo CH, Chen J, Yang XJ, Li YQ, Xu B, Zheng DY, Qian YQ. [Influence of zinc deprivation on thymus, spleen development and adenosine deaminase activity in young rats]. Hua Xi Yi Ke Da Xue Xue Bao 1989; 20:199-202. [PMID: 2591934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
This study on the thymus and spleen development and ADA activity was done in young rats with zinc deprivation and supplementation. The serum zinc level, body weight, absolute and relative weight, and ADA activity of the thymus and spleen were compared between the experimental rats and the control group. Above indications were all decreased; especially both the thymus weight and the thymus ADA activity were markedly decreased in the zinc deficient group. The averages of thymic absolute weight, relative weight and ADA activity were dropped by 61.32%, 54.54% and 47.59%, respectively. After zinc supplementation for one month, all the body weight, weight of the thymus and spleen, and ADA activity of the spleen were recovered to the control group's level, while ADA activity of the thymus was 33.03% higher than that of the control group. Our data suggested that zinc was not only an important trace element in maintaining the growth of the body, the development of the thymus and spleen, but it may be an important agent to activate the ADA or to prompt synthesis of ADA.
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Haruyama H, Qian YQ, Wüthrich K. Static and transient hydrogen-bonding interactions in recombinant desulfatohirudin studied by 1H nuclear magnetic resonance measurements of amide proton exchange rates and pH-dependent chemical shifts. Biochemistry 1989; 28:4312-7. [PMID: 2548573 DOI: 10.1021/bi00436a028] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [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: 01/01/2023]
Abstract
With proton nuclear magnetic resonance spectroscopy at 22 degrees C and pD 4.5, individual exchange rates in the range from 2 X 10(-5) to 1 X 10(-1) min-1 were observed for 23 amide protons in recombinant desulfatohirudin. The remaining 38 backbone amide protons exchange more rapidly than 1 X 10(-1) min-1. All 23 slowly exchanging protons are located in the polypeptide segment from residue 4 to residue 42, which forms a well-defined globular domain. Three different breathing modes of this molecular region are manifested in the exchange data, which appear to be correlated with the location of the three disulfide bonds. Chemical shift changes larger than 0.15 ppm between pH 2.5 and pH 5.0 arising from through-space interactions with carboxyl groups were observed for seven backbone amide protons. Two of these shifts can be explained by hydrogen bonds in the core of the protein, Gly 25 NH-Glu 43 O epsilon and Ser 32 NH-Asp 33 O delta, and two others by intraresidual NH-O epsilon interactions in Glu 61 and Glu 62. The remaining three pH shifts for Glu 35, Cys 39, and Ile 59 imply the existence of transient interactions between the molecular core and the flexible C-terminal segment 49-65, which have so far not been characterized by nuclear Overhauser effects or other conformational constraints.
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Affiliation(s)
- H Haruyama
- Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule--Hönggerberg, Zürich, Switzerland
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Otting G, Qian YQ, Müller M, Affolter M, Gehring W, Wüthrich K. Secondary structure determination for the Antennapedia homeodomain by nuclear magnetic resonance and evidence for a helix-turn-helix motif. EMBO J 1988; 7:4305-9. [PMID: 2907480 PMCID: PMC455146 DOI: 10.1002/j.1460-2075.1988.tb03329.x] [Citation(s) in RCA: 103] [Impact Index Per Article: 2.9] [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: 11/08/2022] Open
Abstract
The homeodomain encoded by the Antennapedia (Antp) gene of Drosophila was studied in aqueous solution by nuclear magnetic resonance (NMR). Sequence-specific resonance assignments have been obtained for the complete polypeptide chain of 68 amino acid residues. The secondary structure determined from nuclear Overhauser effects (NOE) and information about slowly exchanging amide protons includes three helical segments consisting of the residues 10-21, 28-38 and 42-52, respectively. Combination of the presently available NMR data with computer modeling provided preliminary evidence for the presence of a helix-turn-helix motif in the homeodomain. Near the turn, this supersecondary structure appears to be very similar to the DNA binding site in the 434 and P22 c2 repressors, but both helices in the homeodomain include 2-3 additional residues when compared with these prokaryotic DNA-binding proteins.
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Affiliation(s)
- G Otting
- Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule-Hönggerberg, Zürich, Switzerland
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Qian YQ. [Advances and current status of vascular grafts]. Zhonghua Wai Ke Za Zhi 1988; 26:633-5. [PMID: 3072166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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23
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Wang MR, Tang ST, Qian YQ, Kang Y. [Investigation on sexual development of children between 7 and 15 years in rural areas of Deyang County, Sichuan Province]. Hua Xi Yi Ke Da Xue Xue Bao 1988; 19:293-6. [PMID: 3253176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Huang G, Zheng DY, Qian YQ. [Serum prolactin level of lactating mothers and its relation to milk volume]. Hua Xi Yi Ke Da Xue Xue Bao 1987; 18:265-8. [PMID: 3679179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Abstract
Reoxidation of the reduced insulin A and B chains in 8 M urea leads to a recovery of native insulin of 2-7% whereas in 6 M guanidine or 0.5 mM dodecylsulfate very little, if any, resynthesis of insulin could be detected. Considering all the possibilities of different oligomeric forms containing one or both of the chains, the yield in 8 M urea is well over the yield as calculated from random joining of the chains and the yield in guanidine or dodecylsulfate is to be expected. It is concluded that some interaction and pairing of the chains occur even in the presence of 8 M urea.
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Qian YQ, Feng CN, Lin QT. [Surgical treatment of thoracoabdominal aortic aneurysms]. Zhonghua Wai Ke Za Zhi 1987; 25:283-6, 316. [PMID: 3677934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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27
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Wu DL, Qian YQ, Xu HM. [Massive hemorrhage of the lower gastrointestinal tract]. Zhonghua Wai Ke Za Zhi 1987; 25:136-8, 188. [PMID: 3497785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Chai ZK, Qian YQ. [Early diagnosis and reoperation for local recurrence after radical operation for rectal cancer]. Zhonghua Wai Ke Za Zhi 1986; 24:395-7, 445. [PMID: 3028730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Qian YQ, Li QT, Feng CN. [Evaluation of terminal esophago-proximal gastrectomy in the treatment of massive upper gastrointestinal hemorrhage due to portal hypertension]. Zhonghua Wai Ke Za Zhi 1984; 22:732-4, 781-2. [PMID: 6336169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Lin CH, Wang RS, Ma XZ, Qian YQ, Chen QS, Zhang YT. Gastric carcinoma. Study of lymphatic metastasis. Chin Med J (Engl) 1984; 97:741-6. [PMID: 6443262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
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Qian YQ. [Vascular malformations of the duodenum, small intestine and colon]. Zhonghua Wai Ke Za Zhi 1983; 21:679-81. [PMID: 6676015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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32
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Qian YQ. [Diarrhea and massive melena due to periarteritis nodosa of colon (author's transl)]. Zhonghua Wai Ke Za Zhi 1982; 20:78-9. [PMID: 6124372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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