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Ye G, He S, Pan R, Zhu L, Zhou D, Lu R. Research on DCE-MRI Images Based on Deep Transfer Learning in Breast Cancer Adjuvant Curative Effect Prediction. JOURNAL OF HEALTHCARE ENGINEERING 2022; 2022:4477099. [PMID: 35251566 PMCID: PMC8890845 DOI: 10.1155/2022/4477099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/21/2022] [Accepted: 01/27/2022] [Indexed: 11/17/2022]
Abstract
Breast cancer is a serious threat to women's physical and mental health. In recent years, its incidence has been on the rise and it has become the top female malignant tumor in China. At present, adjuvant chemotherapy for breast cancer has become the standard mode of breast cancer treatment, but the response results usually need to be completed after the implementation of adjuvant chemotherapy, and the optimization of the treatment plan and the implementation of breast-conserving therapy need to be based on accurate estimation of the pathological response. Therefore, to predict the efficacy of adjuvant chemotherapy for breast cancer patients is to find a predictive method that is conducive to individualized choice of chemotherapy regimens. This article introduces the research of DCE-MRI images based on deep transfer learning in breast cancer adjuvant curative effect prediction. Deep transfer learning algorithms are used to process images, and then, the features of breast cancer after adjuvant chemotherapy are collected through image feature collection. Predictions are made, and the research results show that the accuracy of the prediction reaches 70%.
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Affiliation(s)
- Guolin Ye
- Department of Breast Surgery, The First People's Hospital of Foshan, Foshan 528000, China
| | - Suqun He
- Department of Breast Surgery, The First People's Hospital of Foshan, Foshan 528000, China
| | - Ruilin Pan
- Department of Breast Surgery, The First People's Hospital of Foshan, Foshan 528000, China
| | - Lewei Zhu
- Department of Breast Surgery, The First People's Hospital of Foshan, Foshan 528000, China
| | - Dan Zhou
- Department of Breast Surgery, The First People's Hospital of Foshan, Foshan 528000, China
| | - RuiLiang Lu
- MRI Room, The First People's Hospital of Foshan, Foshan 528000, China
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Toquenaga Y, Gagné T. The Evidential Statistics of Genetic Assembly: Bootstrapping a Reference Sequence. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.614374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The reference sequences play an essential role in genome assembly, like type specimens in taxonomy. Those references are also samples obtained at some time and location with a specific method. How can we evaluate or discriminate uncertainties of the reference itself and assembly methods? Here we bootstrapped 50 random read data sets from a small circular genome of a Escherichia coli bacteriophage, phiX174, and tried to reconstruct the reference with 14 free assembly programs. Nine out of 14 assembly programs were capable of circular genome reconstruction. Unicycler correctly reconstructed the reference for 44 out of 50 data sets, but each reconstructed contig of the failed six data sets had minor defects. The other assembly software could reconstruct the reference with minor defects. The defect regions differed among the assembly programs, and the defect locations were far from randomly distributed in the reference genome. All contigs of Trinity included one, but Minia had two perfect copies other than an imperfect reference copy. The centroid of contigs for assembly programs except Unicycler differed from the reference with 75bases at most. Nonmetric multidimensional scaling (NMDS) plots of the centroids indicated that even the reference sequence was located slightly off from the estimated location of the true reference. We propose that the combination of bootstrapping a reference, making consensus contigs as centroids in an edit distance, and NMDS plotting will provide an evidential statistic way of genetic assembly for non-fragmented base sequences.
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Zhao Z, Zhu K, Tang D, Wang Y, Wang Y, Zhang G, Geng Y, Yu H. Comparative Analysis of Mitochondrial Genome Features among Four Clonostachys Species and Insight into Their Systematic Positions in the Order Hypocreales. Int J Mol Sci 2021; 22:ijms22115530. [PMID: 34073831 PMCID: PMC8197242 DOI: 10.3390/ijms22115530] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/10/2021] [Accepted: 05/17/2021] [Indexed: 12/31/2022] Open
Abstract
The mycoparasite fungi of Clonostachys have contributed to the biological control of plant fungal disease and nematodes. The Clonostachys fungi strains were isolated from Ophiocordyceps highlandensis, Ophiocordycepsnigrolla and soil, which identified as Clonostachyscompactiuscula, Clonostachysrogersoniana, Clonostachyssolani and Clonostachys sp. To explore the evolutionary relationship between the mentioned species, the mitochondrial genomes of four Clonostachys species were sequenced and assembled. The four mitogenomes consisted of complete circular DNA molecules, with the total sizes ranging from 27,410 bp to 42,075 bp. The GC contents, GC skews and AT skews of the mitogenomes varied considerably. Mitogenomic synteny analysis indicated that these mitogenomes underwent gene rearrangements. Among the 15 protein-coding genes within the mitogenomes, the nad4L gene exhibited the least genetic distance, demonstrating a high degree of conservation. The selection pressure analysis of these 15 PCGs were all below 1, indicating that PCGs were subject to purifying selection. Based on protein-coding gene calculation of the significantly supported topologies, the four Clonostachys species were divided into a group in the phylogenetic tree. The results supplemented the database of mitogenomes in Hypocreales order, which might be a useful research tool to conduct a phylogenetic analysis of Clonostachys. Additionally, the suitable molecular marker was significant to study phylogenetic relationships in the Bionectriaceae family.
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Affiliation(s)
- Zhiyuan Zhao
- College of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, China;
- The International Joint Research Center for Sustainable Utilization of Cordyceps Bioresources in China and Southeast Asia, Yunnan University, Kunming 650091, China; (K.Z.); (D.T.); (Y.W.); (Y.W.); (G.Z.)
| | - Kongfu Zhu
- The International Joint Research Center for Sustainable Utilization of Cordyceps Bioresources in China and Southeast Asia, Yunnan University, Kunming 650091, China; (K.Z.); (D.T.); (Y.W.); (Y.W.); (G.Z.)
| | - Dexiang Tang
- The International Joint Research Center for Sustainable Utilization of Cordyceps Bioresources in China and Southeast Asia, Yunnan University, Kunming 650091, China; (K.Z.); (D.T.); (Y.W.); (Y.W.); (G.Z.)
| | - Yuanbing Wang
- The International Joint Research Center for Sustainable Utilization of Cordyceps Bioresources in China and Southeast Asia, Yunnan University, Kunming 650091, China; (K.Z.); (D.T.); (Y.W.); (Y.W.); (G.Z.)
| | - Yao Wang
- The International Joint Research Center for Sustainable Utilization of Cordyceps Bioresources in China and Southeast Asia, Yunnan University, Kunming 650091, China; (K.Z.); (D.T.); (Y.W.); (Y.W.); (G.Z.)
| | - Guodong Zhang
- The International Joint Research Center for Sustainable Utilization of Cordyceps Bioresources in China and Southeast Asia, Yunnan University, Kunming 650091, China; (K.Z.); (D.T.); (Y.W.); (Y.W.); (G.Z.)
| | - Yupeng Geng
- College of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, China;
- Correspondence: (Y.G.); (H.Y.)
| | - Hong Yu
- College of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, China;
- The International Joint Research Center for Sustainable Utilization of Cordyceps Bioresources in China and Southeast Asia, Yunnan University, Kunming 650091, China; (K.Z.); (D.T.); (Y.W.); (Y.W.); (G.Z.)
- Correspondence: (Y.G.); (H.Y.)
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Wu M, Qian X, Qin M, Tu T, Zhang R. Characterization of the complete mitochondrial genome of Caryopemon giganteus Pic (Coleoptera: Chrysomelidae: Bruchinae). Mitochondrial DNA B Resour 2020; 5:929-931. [PMID: 33366814 PMCID: PMC7748735 DOI: 10.1080/23802359.2020.1719927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
We sequenced, assembled, and annotated the complete mitochondrial genome of the seed beetle Caryopemon giganteus, which represents the first report in the tribe Caryopemini from the subfamily Bruchinae of Chrysomelidae. The circular mitochondrial genome of the species contains 15,727 bases, 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and a non-coding region. The GC content of the genome is 25.3%, which is higher than any other reported mitochondrial genomes within Bruchinae. The 16S ribosomal RNA gene and the 12S ribosomal RNA gene are 1284 and 835 bp in length, respectively. 12 PCGs started with the typical ATN codon, except for ND1 initiated with TTG. Five PCGs have the typical stop codon of TAA or TGA, while the remainder PCGs are terminated with incomplete stop codons (TA or T). The phylogenetic analysis based on a combination of 13 genes of the mitochondrial genomes of six species of Bruchinae and 23 species from other 10 subfamilies of Chrysomelidae recovered a generally well resolved and strongly supported tree topology, which shows that C. giganteus has the basalmost position in Bruchinae.
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Affiliation(s)
- Mingsong Wu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xin Qian
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Ming Qin
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Tieyao Tu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Runzhi Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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Liu P, Liao C, Xu J, Staines CL, Dai X. The Cassidinae beetles of Longnan County (Jiangxi, China): overview and community composition. Biodivers Data J 2019; 7:e39053. [PMID: 31666798 PMCID: PMC6814652 DOI: 10.3897/bdj.7.e39053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 10/16/2019] [Indexed: 11/27/2022] Open
Abstract
There are few reports on the community composition and diversity pattern of the Cassidinae species of China. Compared to the neighbouring provinces of Guangdong, Fujian and Zhejiang, the Cassidinae richness in Jiangxi Province is under-reported. Longnan City, a biodiversity hotspot in Jiangxi Province, was chosen to obtain the first overview of the Cassidinae beetles. The sample coverage curves for the three sample sites reached an asymptote which indicated sampling was sufficient for data analysis. A total of eight tribes, 16 genera, 59 species and 1590 individuals of Cassidinae beetles were collected. Most belonged to the tribe Hispini (1121 individuals; 70.5%), followed by the tribe Cassidini (161 individuals; 10.13%) and the tribe Oncocephalini (159 individuals; 10.0%). The remainder (149 individuals) belonged to five tribes (Gonophorini, Basiprionotini, Callispini, Notosacanthini and Aspidimorphini). The tribes Notosacanthini, Aspidimorphini and Oncocephalini were newly recorded for Jiangxi Province. There were 14 families, 27 genera and 39 species of host plants of Cassidinae beetles in Longnan County. Cassidinae larvae mainly feed on the plant families Poaceae, Rosaceae, Lamiaceae and Rubiaceae. Most host-plant associations are new reords for the beetle species. This research, together with our planned future work in China, may help to explain the geographical distribution, diversity patterns and host plant associations of these beetles.
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Affiliation(s)
- Peng Liu
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou, ChinaLeafminer Group, School of Life Sciences, Gannan Normal UniversityGanzhouChina
| | - Chengqing Liao
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou, ChinaLeafminer Group, School of Life Sciences, Gannan Normal UniversityGanzhouChina
| | - Jiasheng Xu
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou, ChinaLeafminer Group, School of Life Sciences, Gannan Normal UniversityGanzhouChina
| | - Charles L. Staines
- Smithsonian Environmental Research Center, Edgewater, United States of AmericaSmithsonian Environmental Research CenterEdgewaterUnited States of America
| | - Xiaohua Dai
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou, ChinaLeafminer Group, School of Life Sciences, Gannan Normal UniversityGanzhouChina
- National Navel-Orange Engineering Research Center, Ganzhou, ChinaNational Navel-Orange Engineering Research CenterGanzhouChina
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Li Q, Xiang D, Wan Y, Wu Q, Wu X, Ma C, Song Y, Zhao G, Huang W. The complete mitochondrial genomes of five important medicinal Ganoderma species: Features, evolution, and phylogeny. Int J Biol Macromol 2019; 139:397-408. [DOI: 10.1016/j.ijbiomac.2019.08.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/10/2019] [Accepted: 08/01/2019] [Indexed: 12/31/2022]
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Li Q, Liao M, Yang M, Xiong C, Jin X, Chen Z, Huang W. Characterization of the mitochondrial genomes of three species in the ectomycorrhizal genus Cantharellus and phylogeny of Agaricomycetes. Int J Biol Macromol 2018; 118:756-769. [DOI: 10.1016/j.ijbiomac.2018.06.129] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/23/2018] [Accepted: 06/26/2018] [Indexed: 12/15/2022]
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Li Q, Yang M, Chen C, Xiong C, Jin X, Pu Z, Huang W. Characterization and phylogenetic analysis of the complete mitochondrial genome of the medicinal fungus Laetiporus sulphureus. Sci Rep 2018; 8:9104. [PMID: 29904057 PMCID: PMC6002367 DOI: 10.1038/s41598-018-27489-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 05/24/2018] [Indexed: 12/22/2022] Open
Abstract
The medicinal fungus Laetiporus sulphureus is widely distributed worldwide. To screen for molecular markers potentially useful for phylogenetic analyses of this species and related species, the mitochondrial genome of L. sulphureus was sequenced and assembled. The complete circular mitochondrial genome was 101,111 bp long, and contained 38 protein-coding genes (PCGs), 2 rRNA genes, and 25 tRNA genes. Our BLAST search aligned about 6.1 kb between the mitochondrial and nuclear genomes of L. sulphureus, indicative of possible gene transfer events. Both the GC and AT skews in the L. sulphureus mitogenome were negative, in contrast to the other seven Polyporales species tested. Of the 15 PCGs conserved across the seven species of Polyporales, the lengths of 11 were unique in the L. sulphureus mitogenome. The Ka/Ks of these 15 PCGs were all less than 1, indicating that PCGs were subject to purifying selection. Our phylogenetic analysis showed that three single genes (cox1, cob, and rnl) were potentially useful as molecular markers. This study is the first publication of a mitochondrial genome in the family Laetiporaceae, and will facilitate the study of population genetics and evolution in L. sulphureus and other species in this family.
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Affiliation(s)
- Qiang Li
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, P.R. China.,Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, P.R. China
| | - Mei Yang
- Panzhihua City Academy of Agricultural and Forest Sciences, Panzhihua, 617061, Sichuan, P.R. China
| | - Cheng Chen
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, P.R. China
| | - Chuan Xiong
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, P.R. China
| | - Xin Jin
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, P.R. China
| | - Zhigang Pu
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, P.R. China. .,Sichuan Academy of Agricultural Sciences, 106 # Shizishan Rd, Chengdu, 610061, Sichuan, China.
| | - Wenli Huang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, P.R. China. .,Sichuan Academy of Agricultural Sciences, 106 # Shizishan Rd, Chengdu, 610061, Sichuan, China.
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Comparative mitogenomics reveals large-scale gene rearrangements in the mitochondrial genome of two Pleurotus species. Appl Microbiol Biotechnol 2018; 102:6143-6153. [DOI: 10.1007/s00253-018-9082-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 05/02/2018] [Accepted: 05/04/2018] [Indexed: 12/18/2022]
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Sayadi A, Immonen E, Tellgren-Roth C, Arnqvist G. The Evolution of Dark Matter in the Mitogenome of Seed Beetles. Genome Biol Evol 2017; 9:2697-2706. [PMID: 29048527 PMCID: PMC5737749 DOI: 10.1093/gbe/evx205] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2017] [Indexed: 12/14/2022] Open
Abstract
Animal mitogenomes are generally thought of as being economic and optimized for rapid replication and transcription. We use long-read sequencing technology to assemble the remarkable mitogenomes of four species of seed beetles. These are the largest circular mitogenomes ever assembled in insects, ranging from 24,496 to 26,613 bp in total length, and are exceptional in that some 40% consists of non-coding DNA. The size expansion is due to two very long intergenic spacers (LIGSs), rich in tandem repeats. The two LIGSs are present in all species but vary greatly in length (114-10,408 bp), show very low sequence similarity, divergent tandem repeat motifs, a very high AT content and concerted length evolution. The LIGSs have been retained for at least some 45 my but must have undergone repeated reductions and expansions, despite strong purifying selection on protein coding mtDNA genes. The LIGSs are located in two intergenic sites where a few recent studies of insects have also reported shorter LIGSs (>200 bp). These sites may represent spaces that tolerate neutral repeat array expansions or, alternatively, the LIGSs may function to allow a more economic translational machinery. Mitochondrial respiration in adult seed beetles is based almost exclusively on fatty acids, which reduces the need for building complex I of the oxidative phosphorylation pathway (NADH dehydrogenase). One possibility is thus that the LIGSs may allow depressed transcription of NAD genes. RNA sequencing showed that LIGSs are partly transcribed and transcriptional profiling suggested that all seven mtDNA NAD genes indeed show low levels of transcription and co-regulation of transcription across sexes and tissues.
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Affiliation(s)
- Ahmed Sayadi
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Sweden
| | - Elina Immonen
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Sweden
| | - Christian Tellgren-Roth
- National Genomics Infrastructure, Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Göran Arnqvist
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Sweden
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