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Zhuang M, Chen Z, Yang Y, Kettunen L, Wang H. Annotation-efficient training of medical image segmentation network based on scribble guidance in difficult areas. Int J Comput Assist Radiol Surg 2024; 19:87-96. [PMID: 37233894 DOI: 10.1007/s11548-023-02931-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 04/19/2023] [Indexed: 05/27/2023]
Abstract
PURPOSE The training of deep medical image segmentation networks usually requires a large amount of human-annotated data. To alleviate the burden of human labor, many semi- or non-supervised methods have been developed. However, due to the complexity of clinical scenario, insufficient training labels still causes inaccurate segmentation in some difficult local areas such as heterogeneous tumors and fuzzy boundaries. METHODS We propose an annotation-efficient training approach, which only requires scribble guidance in the difficult areas. A segmentation network is initially trained with a small amount of fully annotated data and then used to produce pseudo labels for more training data. Human supervisors draw scribbles in the areas of incorrect pseudo labels (i.e., difficult areas), and the scribbles are converted into pseudo label maps using a probability-modulated geodesic transform. To reduce the influence of the potential errors in the pseudo labels, a confidence map of the pseudo labels is generated by jointly considering the pixel-to-scribble geodesic distance and the network output probability. The pseudo labels and confidence maps are iteratively optimized with the update of the network, and the network training is promoted by the pseudo labels and the confidence maps in turn. RESULTS Cross-validation based on two data sets (brain tumor MRI and liver tumor CT) showed that our method significantly reduces the annotation time while maintains the segmentation accuracy of difficult areas (e.g., tumors). Using 90 scribble-annotated training images (annotated time: ~ 9 h), our method achieved the same performance as using 45 fully annotated images (annotation time: > 100 h) but required much shorter annotation time. CONCLUSION Compared to the conventional full annotation approaches, the proposed method significantly saves the annotation efforts by focusing the human supervisions on the most difficult regions. It provides an annotation-efficient way for training medical image segmentation networks in complex clinical scenario.
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Affiliation(s)
- Mingrui Zhuang
- School of Biomedical Engineering, Faculty of Medicine, Dalian University of Technology, Dalian, 116024, China
| | - Zhonghua Chen
- School of Biomedical Engineering, Faculty of Medicine, Dalian University of Technology, Dalian, 116024, China
- Faculty of Information Technology, University of Jyväskylä, 40100, Jyvaskyla, Finland
| | - Yuxin Yang
- School of Biomedical Engineering, Faculty of Medicine, Dalian University of Technology, Dalian, 116024, China
| | - Lauri Kettunen
- Faculty of Information Technology, University of Jyväskylä, 40100, Jyvaskyla, Finland
| | - Hongkai Wang
- School of Biomedical Engineering, Faculty of Medicine, Dalian University of Technology, Dalian, 116024, China.
- Liaoning Key Laboratory of Integrated Circuit and Biomedical Electronic System, Dalian, China.
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Zhao T, Wang C, Zhang S, Chen L, Han B, Liu H, Xie M, Cai X, Zhang S, Zhou Y, Li G, Liu B, Du J, Zeng J, Liu Y, Lu Q, Cui F. What Causes the Discrepancy in SARS-CoV-2 Vaccine Between Parental Hesitancy for Themselves and for Their Children During Lockdown Period? J Epidemiol Glob Health 2023; 13:422-434. [PMID: 37378822 PMCID: PMC10468446 DOI: 10.1007/s44197-023-00122-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Parents are usually the decision-makers for vaccinations of children. Therefore, it is important to understand parental beliefs and attitudes toward severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine for themselves and their children when it was approved for children age 3-17. METHOD A cross-sectional survey based on an anonymous online questionnaire for parents was conducted in seven provinces of China, and demographic information, vaccination history, parental decision motives, and health belief model toward themselves and their children were collected, respectively. RESULTS The overall parental hesitancy rate toward themselves was 20.30%, and that toward their children was 7.80%. More parental concerns on disease severity (odd ratio [OR] = 1.11, 95% confidence interval [CI]: 1.01-1.61) and susceptibility (OR = 1.29, 95% CI: 1.01-1.63) of children could be the causes of discrepancy in hesitancy for themselves and for their children. Parents who hesitated to vaccinate themselves might also be hesitated to vaccinate their children (β = 0.077, P < 0.001). CONCLUSION Threat perception may lead to inconsistencies in parental vaccination decisions toward themselves and toward their children. Correcting misinformation and strengthening education about COVID-19 are of great significance in addressing vaccine hesitancy among parents and children.
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Affiliation(s)
- Tianshuo Zhao
- Department of Laboratorial Science and Technology, School of Public Health, Peking University, Beijing, 100191, People's Republic of China
- Vaccine Research Center, School of Public Health, Peking University, Beijing, 100191, People's Republic of China
| | - Chao Wang
- Department of Laboratorial Science and Technology, School of Public Health, Peking University, Beijing, 100191, People's Republic of China
- Vaccine Research Center, School of Public Health, Peking University, Beijing, 100191, People's Republic of China
| | - Sihui Zhang
- Department of Laboratorial Science and Technology, School of Public Health, Peking University, Beijing, 100191, People's Republic of China
- Vaccine Research Center, School of Public Health, Peking University, Beijing, 100191, People's Republic of China
| | - Linyi Chen
- Department of Laboratorial Science and Technology, School of Public Health, Peking University, Beijing, 100191, People's Republic of China
- Vaccine Research Center, School of Public Health, Peking University, Beijing, 100191, People's Republic of China
| | - Bingfeng Han
- Department of Laboratorial Science and Technology, School of Public Health, Peking University, Beijing, 100191, People's Republic of China
- Vaccine Research Center, School of Public Health, Peking University, Beijing, 100191, People's Republic of China
| | - Hanyu Liu
- Department of Laboratorial Science and Technology, School of Public Health, Peking University, Beijing, 100191, People's Republic of China
- Vaccine Research Center, School of Public Health, Peking University, Beijing, 100191, People's Republic of China
| | - Mingzhu Xie
- Department of Laboratorial Science and Technology, School of Public Health, Peking University, Beijing, 100191, People's Republic of China
- Vaccine Research Center, School of Public Health, Peking University, Beijing, 100191, People's Republic of China
| | - Xianming Cai
- Department of Laboratorial Science and Technology, School of Public Health, Peking University, Beijing, 100191, People's Republic of China
- Vaccine Research Center, School of Public Health, Peking University, Beijing, 100191, People's Republic of China
| | - Shanshan Zhang
- Department of Laboratorial Science and Technology, School of Public Health, Peking University, Beijing, 100191, People's Republic of China
- Vaccine Research Center, School of Public Health, Peking University, Beijing, 100191, People's Republic of China
| | - Yiguo Zhou
- Department of Laboratorial Science and Technology, School of Public Health, Peking University, Beijing, 100191, People's Republic of China
- Vaccine Research Center, School of Public Health, Peking University, Beijing, 100191, People's Republic of China
| | - Guoxing Li
- Department of Laboratorial Science and Technology, School of Public Health, Peking University, Beijing, 100191, People's Republic of China
- Vaccine Research Center, School of Public Health, Peking University, Beijing, 100191, People's Republic of China
- Puyang Center for Disease Control and Prevention, Henan, 457005, People's Republic of China
| | - Bei Liu
- Department of Laboratorial Science and Technology, School of Public Health, Peking University, Beijing, 100191, People's Republic of China
- Vaccine Research Center, School of Public Health, Peking University, Beijing, 100191, People's Republic of China
| | - Juan Du
- Department of Laboratorial Science and Technology, School of Public Health, Peking University, Beijing, 100191, People's Republic of China
- Vaccine Research Center, School of Public Health, Peking University, Beijing, 100191, People's Republic of China
| | - Jing Zeng
- Department of Laboratorial Science and Technology, School of Public Health, Peking University, Beijing, 100191, People's Republic of China
- Vaccine Research Center, School of Public Health, Peking University, Beijing, 100191, People's Republic of China
| | - Yaqiong Liu
- Department of Laboratorial Science and Technology, School of Public Health, Peking University, Beijing, 100191, People's Republic of China
- Vaccine Research Center, School of Public Health, Peking University, Beijing, 100191, People's Republic of China
| | - Qingbin Lu
- Department of Laboratorial Science and Technology, School of Public Health, Peking University, Beijing, 100191, People's Republic of China
- Vaccine Research Center, School of Public Health, Peking University, Beijing, 100191, People's Republic of China
| | - Fuqiang Cui
- Department of Laboratorial Science and Technology, School of Public Health, Peking University, Beijing, 100191, People's Republic of China.
- Vaccine Research Center, School of Public Health, Peking University, Beijing, 100191, People's Republic of China.
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Wang Z, Zhong C, Li D, Yan C, Yao X, Li Z. Cytotype distribution and chloroplast phylogeography of the Actinidia chinensis complex. BMC Plant Biol 2021; 21:325. [PMID: 34229602 PMCID: PMC8259359 DOI: 10.1186/s12870-021-03099-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 06/11/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Plant phylogeographic studies of species in subtropical China have mainly focused on rare and endangered species, whereas few studies have been conducted on taxa with relatively wide distribution, especially polyploid species. We investigated the cytotype and haplotype distribution pattern of the Actinidia chinensis complex, a widespread geographically woody liana with variable ploidy in subtropical China comprising two varieties, with three chloroplast fragments DNA (ndhF-rpl132, rps16-trnQ and trnE-trnT). Macroevolutionary, microevolutionary and niche modeling tools were also combined to disentangle the origin and the demographic history of the species or cytotypes. RESULTS The ploidy levels of 3338 individuals from 128 populations sampled throughout the species distribution range were estimated with flow cytometry. The widespread cytotypes were diploids followed by tetraploids and hexaploids, whereas triploids and octoploids occurred in a few populations. Thirty-one chloroplast haplotypes were detected. The genetic diversity and genetic structure were found to be high between varieties (or ploidy races) chinensis and deliciosa. Our results revealed that these two varieties inhabit significantly different climatic niche spaces. Ecological niche models (ENMs) indicate that all varieties' ranges contracted during the Last Inter Glacial (LIG), and expanded eastward or northward during the Last Glacial Maximum (LGM). CONCLUSIONS Pliocene and Plio-Pleistocene climatic fluctuations and vicariance appear to have played key roles in shaping current population structure and historical demography in the A. chinensis complex. The polyploidization process also appears to have played an important role in the historical demography of the complex through improving their adaptability to environmental changes.
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Affiliation(s)
- Zhi Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Caihong Zhong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Dawei Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Chunlin Yan
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Xiaohong Yao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.
| | - Zuozhou Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.
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Yuan Y, Xing H, Zeng W, Xu J, Mao L, Wang L, Feng W, Tao J, Wang H, Zhang H, Wang Q, Zhang G, Song X, Sun XZ. Genome-wide association and differential expression analysis of salt tolerance in Gossypium hirsutum L at the germination stage. BMC Plant Biol 2019; 19:394. [PMID: 31510912 PMCID: PMC6737726 DOI: 10.1186/s12870-019-1989-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 08/26/2019] [Indexed: 05/18/2023]
Abstract
BACKGROUND Salinity is a major abiotic stress seriously hindering crop yield. Development and utilization of tolerant varieties is the most economical way to address soil salinity. Upland cotton is a major fiber crop and pioneer plant on saline soil and thus its genetic architecture underlying salt tolerance should be extensively explored. RESULTS In this study, genome-wide association analysis and RNA sequencing were employed to detect salt-tolerant qualitative-trait loci (QTLs) and candidate genes in 196 upland cotton genotypes at the germination stage. Using comprehensive evaluation values of salt tolerance in four environments, we identified 33 significant single-nucleotide polymorphisms (SNPs), including 17 and 7 SNPs under at least two and four environments, respectively. The 17 stable SNPs were located within or near 98 candidate genes in 13 QTLs, including 35 genes that were functionally annotated to be involved in salt stress responses. RNA-seq analysis indicated that among the 98 candidate genes, 13 were stably differentially expressed. Furthermore, 12 of the 13 candidate genes were verified by qRT-PCR. RNA-seq analysis detected 6640, 3878, and 6462 differentially expressed genes at three sampling time points, of which 869 were shared. CONCLUSIONS These results, including the elite cotton accessions with accurate salt tolerance evaluation, the significant SNP markers, the candidate genes, and the salt-tolerant pathways, could improve our understanding of the molecular regulatory mechanisms under salt stress tolerance and genetic manipulation for cotton improvement.
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Affiliation(s)
- Yanchao Yuan
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, Shandong, China
- College of Life Sciences, Qingdao Agricultural University, Key Lab of Plant Biotechnology in Universities of Shandong Province, Changcheng Road 700, Qingdao, China
| | - Huixian Xing
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, Shandong, China
| | - Wenguan Zeng
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, Shandong, China
| | - Jialing Xu
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, Shandong, China
| | - Lili Mao
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, Shandong, China
| | - Liyuan Wang
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, Shandong, China
| | - Wei Feng
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, Shandong, China
| | - Jincai Tao
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, Shandong, China
| | - Haoran Wang
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, Shandong, China
| | - Haijun Zhang
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, Shandong, China
| | - Qingkang Wang
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, Shandong, China
| | - Guihua Zhang
- Heze Academy of Agricultural Sciences, Heze, China
| | - Xianliang Song
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, Shandong, China.
| | - Xue-Zhen Sun
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, Shandong, China.
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