Proceedings of the Fourth International Conference on Biological Information and Biomedical Engineering最新文献

{"title":"An Improved MRI Reconstruction Algorithm Combining Partial Fourier and Parallel Imaging","authors":"Hongyu Guo, Mei Wang, Peng Liu, Chunsheng Li","doi":"10.1145/3403782.3403806","DOIUrl":"https://doi.org/10.1145/3403782.3403806","url":null,"abstract":"The relatively long duration of magnetic resonance imaging (MRI) limited its application in many important clinical and research scenarios, and many methods have been proposed to reduce the scan time of MRI, such as partial Fourier imaging(PF), parallel imaging and compressed sensing(CS). In order to obtain higher acceleration factors, several reconstruction methods combining half Fourier and parallel imaging have been proposed in recent years. In these methods, PF_POCSENSE is a very effective method, which apply the phase constraining to reconstruct partial Fourier and parallel sampling data. Compared with partial Fourier imaging and parallel imaging, the SNR of reconstructed image is obviously improved. However, the traditional PF_POCSENSE method converges slowly and spends longer reconstruction time, because the initial image has less information. In this paper, an iterative partial Fourier parallel imaging (PFPI) method is proposed. Firstly, the amplitude of low resolution image is used as the initial guess image. Secondly, both phase constraint and region of interest (ROI) constraint are added into the iterative process to improve image quality. Moreover, the data convex sets projection operators are optimized. More priori information is included in reconstruction process and the data projection operations also are improved, so the number of iterations is greatly reduced, and the reconstruction speed is obviously improved. The reconstruction results of phantom and in vivo data showed that the proposed algorithm can reconstruct the image with higher SNR and faster reconstruction speed than the traditional algorithm under the same acceleration factor.","PeriodicalId":260405,"journal":{"name":"Proceedings of the Fourth International Conference on Biological Information and Biomedical Engineering","volume":"90 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122537653","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A New Hierarchical Approach to Requirement Analysis Used for ICD-10 Startup Index","authors":"R. Albert, Mina Ebrahimiarjestan, Ming Yu","doi":"10.1145/3403782.3403817","DOIUrl":"https://doi.org/10.1145/3403782.3403817","url":null,"abstract":"The development of ICD 10 classification has become one of the greatest milestones that transform how Healthcare statistics are being developed and utilized. Every Healthcare entity were required to apply the ICD 10 into their reporting standards by October 1st 2015. Unfortunately, despite the major impact on the healthcare industry, most of the people are not ready yet for this technology. 70% of the healthcare entities has showed concerns about the proliferations of the tool. There is also a lack of infrastructures, financial, and operational preparation which are evident in some places. That is why, a smaller and practical model of ICD 10 are needed in order to be a buffer to make more people use this tool more efficiently and effectively. Data were gathered and observed in order to determine the directions of the development of the smaller version of ICD 10. The result of the study, will be able to help prepare the users to use the full version of ICD 10 and also to be able to implement it as a short-term solution.","PeriodicalId":260405,"journal":{"name":"Proceedings of the Fourth International Conference on Biological Information and Biomedical Engineering","volume":"25 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128809524","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of Key Genes and Signaling Pathways in Male Androgenetic Alopecia by Bioinformatics Analysis","authors":"Mengzhi Zhang, Yujia Chen, Liancheng Guan, Wen Li, Yunzhi Chen","doi":"10.1145/3403782.3403795","DOIUrl":"https://doi.org/10.1145/3403782.3403795","url":null,"abstract":"Objective: The primary aim of our research was to investigate the molecular pathogenesis and predict potential therapeutic targets of male androgenetic alopecia (MAGA) by using bioinformatics to collate and analyze gene expression profiles. Methods: The data of MAGA gene chip (GSE90594) was downloaded from GEO database, 14 pairs of normal males and MAGA scalp tissues were selected as study subjects, which were divided into alopecia group and healthy group. The online tool GEO2R was used to analyze the differentially expressed genes(DEGs) between the two groups. Gene ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, protein-protein interaction (PPI) network map construction and key node analysis were also performed in the present study. Results: The results of GEO2R analysis showed that 214 differentially expressed genes (DEGs) were identified, including 50 up-regulated genes and 164 down-regulated genes. GO enrichment analysis showed that DEGs were mainly enriched in immune response, intermediate filaments, hair growth cycle, epidermis development and structural constituent, aging and other terms. KEGG pathway analysis results showed that DEGs was mainly enriched in cytokine-cytokine receptor interaction, cell adhesion molecules, chemokine, synthesis and degradation of ketone bodies, IL-17 signaling pathway as well as other. PPI analysis results suggested that a total of 128 genes and 1235 interactions participated in the construction of PPI network map, including eight key DEGs and two important gene clusters. Conclusion: The pathogenesis of MAGA was closely related to multiple genes and pathways in the body. Among them, KRT82, KRTAP24-1, KRT39, KRTAP3-1, KRTAP12-1, KRTAP26-1, KRTAP3-2 and KRTAP17-1 might play key roles. Further related study will be carried out for experimental and clinical verification.","PeriodicalId":260405,"journal":{"name":"Proceedings of the Fourth International Conference on Biological Information and Biomedical Engineering","volume":"7 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116787026","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Method of Non-invasive Fetal Electrocardiogram Denoising Based on Stationary Wavelet Transform and Spatially Selective Noise Filtration","authors":"Yue Zhang, Shuai Yu","doi":"10.1145/3403782.3403801","DOIUrl":"https://doi.org/10.1145/3403782.3403801","url":null,"abstract":"The non-invasive fetal electrocardiogram can provide significant clinical diagnostic information for the fetal health condition. However, since the signal is collected from the abdomen of the pregnant woman, its signal-to-noise ratio is low and it contains a lot of noise, which causes much trouble for the extraction of the fetal electrocardiogram. The non-invasive fetal electrocardiogram is non-stationary, and the noise may overlap with the useful signal in the frequency domain. To solve this challenging denoising work, we propose a method based on stationary wavelet transform and spatially selective noise filtration. The method is evaluated in the synthetic dataset and clinic dataset, and the experiment results show that this method performs better than other two methods. Moreover, the filtered signal is clearer, and the contour is smoother, which is helpful for fetal electrocardiogram morphological analysis and visualization.","PeriodicalId":260405,"journal":{"name":"Proceedings of the Fourth International Conference on Biological Information and Biomedical Engineering","volume":"7 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115138160","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chimeric Antigen Receptor T-Cell Immunotherapy for Cancer","authors":"D. Luo","doi":"10.1145/3403782.3403802","DOIUrl":"https://doi.org/10.1145/3403782.3403802","url":null,"abstract":"Cancer is a disease which causes a high death rate each year. The traditional therapies for treating cancers, for example, radiotherapy and chemotherapy, can cause the damage effect on both cancer cells and normal cells. Therefore, new immune therapies, Chimeric Antigen Receptor T-Cell (CAR-T cell) immunotherapy which can recognize the receptor on the surface of tumor cells specifically, and use the immune response to kill the cancer cells. The effects by the CAR-T cell treatment will be better than the normal therapies. However, there are several disadvantages for the CAR-T cell therapy. In this review, we will introduce the current researches about CAR-T treatment used in the solid cancers and leukemia, and propose some possible solutions and some future directions.","PeriodicalId":260405,"journal":{"name":"Proceedings of the Fourth International Conference on Biological Information and Biomedical Engineering","volume":"6 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126640325","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clone and Analysis of Atrazine Chlorohydrolase Gene of Arthrobacter sp. T3AB1 Isolated from Northeast China","authors":"Fengshan Yang, Mengyi Li, Cong Sun, Siying Li, Yukun Ma, Haiyan Fu, Chunguang Liu","doi":"10.1145/3403782.3403787","DOIUrl":"https://doi.org/10.1145/3403782.3403787","url":null,"abstract":"Atrazine is a triazine herbicide widely used throughout the world in crop fields but it can cause long residual effects such as a phytotoxic response to the subsequent crop. Therefore, it is an urgent issue to effectively control and solve the contaminant of atrazine regularly in rain, ground water and crop fields. In this study, we reported one bacterial strain of Arthrobacter sp. T3AB1. It was capable of utilizing Atrazine as the sole nitrogen and carbon source isolated from the corn field in Nehe (Heilongjiang, China) where had seriously suffered the phytotoxicity of atrazine. The exoenzyme and endoenzyme extracted from T3AB1 and cell debris were all assayed for enzyme activities and the critical genes that could degrade atrazine was cloned by PCR; the specific expression of trzN gene was analyzed by Quantitative Real-time PCR (qRT-PCR). Our results indicated that the endoenzyme showed higher activities in a pH 6.0 phosphate buffer and could degrade 93.61% of atrazine. sequence analysis of the trzN, atzB and atzC genes demonstrated that these genes had very highly conserved domains. We also obtain the full length of trzN gene (1371-bp in length, accession no. GU459314). Compared to the reported hydrolases, seven mutation sites were found in this gene: 67F/F/Y→Y, 117E/Q/E→E, 197E/E/E→H, 305W/W/W→S, 299P/S/P/→P, 342A/A/A→T and 331D/D/D→E. QRT-PCR suggested that the trzN gene expression of T3AB1 strain cultured in 100 mg/L MSM+AT(Mineral salt medium including Atrazine) for 36 h was up-regulated, nearly twice as much as that in LB medium at the same time. It will be the molecular evidence and lay the foundation for the research of atrazine catabolic pathway by T3AB1 in the future.","PeriodicalId":260405,"journal":{"name":"Proceedings of the Fourth International Conference on Biological Information and Biomedical Engineering","volume":"40 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123525986","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of Key Genes and Pathways Associated with Chronic Obstructive Pulmonary Disease Based on Bioinformatics Analysis","authors":"Huaiquan Liu, Yunzhi Chen, Xing Zhu, Mengzhi Zhang, Wen Li","doi":"10.1145/3403782.3403803","DOIUrl":"https://doi.org/10.1145/3403782.3403803","url":null,"abstract":"Objective: Chronic obstructive pulmonary disease (COPD) is recognized as a common preventable respiratory disease whose character is incompletely reversible airflow limitation. However, its specific pathogenesis is still not fully understood. Here we sought to identify novel biomarkers or targets for COPD. Methods: We performed expression profiling through gene arrays contained lung tissue data of 14 COPD patients and 5 non-smokers from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) are identified by using the GEO2R tool with standard of the |log(FC)|>2 and P<0.05. Then the DAVID 6.8 databases were used to do the Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the DEGs. The String 11.0 database was applied for constructing the protein-protein interaction (PPI) network. We used Cytoscape 3.6.0 software to create a PPI interaction module. Results: A total of 133 DEGs were discovered from GEO2R, including 78 up-regulated genes and 55 down-regulated genes. GO enrichment analysis showed that up-regulated genes were involved in cell chemotaxis, cytokine activity and external stimuli response, the down-regulated genes had influenced on membrane organization and neurogenesis, and the all DEGs were mainly involved in cell chemotaxis, cytokine activity, external stimuli response and response to bacterium. KEGG pathway analysis showed that up-regulated genes were mainly involved in Toll-like receptors(TLR), phosphoinositide-3-kinase/protein kinase (PI3K-Akt), fork head box class O (FoxO) and tumor necrosis factor (TNF), and down-regulated genes mainly had influenced on estrogen and cell adhesion molecules (CAMs) signaling pathways, and all DEGs were mainly involved in interaction with cytokine and cytokine receptor, Chemokine and IL-17 signaling pathway. A total of 4 hub genes (degree≥9) were obtained from the PPI network, including interleukin6 (IL6), CC chemokine ligand 20 (CCL20), secreted phosphoprotein 1 (SPP1) and epithelial neutrophil activating peptide-78 (CXCL5). When we used the MCODE plug-in in Cytoscape 3.6.0 software, we found an important gene group. Through KEGG analysis of those gene groups, there are signaling pathways stated out, including immune response, inflammatory response, reninangiotensin system, tyrosine kinase-signal transducers and transcriptional activators (Jak-STAT), phagosome and others. Conclusion: This study indicates that IL6, CCL20, SPP1, CXCL5 and the pathways involved were crucial to the COPD pathophysiology. These key genes and pathways are valuable for further investigations. This study provides a better understanding of the gene expression profile in COPD pathophysiology.","PeriodicalId":260405,"journal":{"name":"Proceedings of the Fourth International Conference on Biological Information and Biomedical Engineering","volume":"46 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132303922","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Simple Residual Network for Lung Nodule Classification","authors":"Lei Bao, Tao Bao, Yunfei Zheng, Jianjun Xia","doi":"10.1145/3403782.3403808","DOIUrl":"https://doi.org/10.1145/3403782.3403808","url":null,"abstract":"Purpose: Lung nodules have very diverse shapes, sizes, densities and textures, which makes predicting the malignancy of lung nodules a very challenging problem. In this paper, we propose a simple global-local residual network to classify pulmonary nodules as benign or malignant. Methods: Different from previous models, we suppose that global features effect lung nodule classification tasks before local features logically. Thus, we propose to use Self-Attention mechanism to detect global features firstly. After that, inceptionlike module is introduced to extract multi-scale local features. The detected local features would be treated as complementary part of global features with residual connection. Results: We trained and validated the proposed network on the public and comprehensive LIDC-IDRI dataset. The comparison with five state-of-the-art models and five self-designed methods shows that, the proposed GLR network achieved state-of-the-art results with an AUC of 96.07%. Conclusions: On the basis of the present results, the GLR network works well on predicting the malignancy of lung nodules.","PeriodicalId":260405,"journal":{"name":"Proceedings of the Fourth International Conference on Biological Information and Biomedical Engineering","volume":"108 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128498901","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Study of sEMG-based Detection Methods of Wrist Muscle Lesions","authors":"Zhuangzhi Li, Hanwu He, Yu-Wei Wei, Junhua Wang","doi":"10.1145/3403782.3403816","DOIUrl":"https://doi.org/10.1145/3403782.3403816","url":null,"abstract":"This paper aims to explore the effectiveness of surface electromyography (sEMG) features obtained by wavelet packet analyse for the detection of lesion degree in wrist muscle, so as to provide an auxiliary reference in clinical diagnosis for rehabilitation physicians. From October 2018 to April 2019, 35 1patients with wrist muscle lesion were recruited and their sEMG signals of flexor carpi radialis, flexor carpi ulnaris, extensor carpi radialis longus and extensor carpi radialis brevis during dorsal extension, palmar flexion, Radial flexion and ulnar flexion were recorded. Wavelet packet analyse was conducted on these signals to obtain the eigenvalue coefficients of decomposed wavelet packets, which were used to analyze the position of muscle lesions, and meanwhile, the reliability of these eigenvalue coefficients was verified by dEMG. Relatively large difference was demonstrated in the muscle feature parameters of patients with wrist muscle lesion after sEMG feature extraction, and the eigenvalue of sEMG signals obtained by wavelet packet analyse can reach a good effectiveness in the detection of lesion degree in wrist muscle.","PeriodicalId":260405,"journal":{"name":"Proceedings of the Fourth International Conference on Biological Information and Biomedical Engineering","volume":"117 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121962141","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptome Analysis for the Effect of Tartary Buckwheat Polysaccharides on the Type 2 Diabetes Model Mice","authors":"Q. Ren, Litao Zhang, Bo Gao","doi":"10.1145/3403782.3403813","DOIUrl":"https://doi.org/10.1145/3403782.3403813","url":null,"abstract":"Diabetes mellitus is the most common metabolic disease in the world. The clinical symptoms represent hyperglycemia and low insulin secretion. Type 2 diabetes mellitus (T2DM) accounts for the majority of all diabetic patients (approximately 90%). Our previous study found that tartary buckwheat polysaccharides (TBP) had a good hypoglycemic effect on the T2DM model mice induced by streptozotocin (STZ). However, the underlying mechanism of TBP on hypoglycemic effect is still unclear. In the present study, RNA sequencing (RNA-seq) was applied to study the changes of transcriptome in the liver of mice in the T2DM model group. Compared with model group, 1191 DEGs (differently expressed genes) were screened in the TBP treatment group, in which 313 genes were up-regulated and 878 down-regulated. The KEGG, GO, and KOG analysis of DEGs indicated that many DEGs were associated with glycometabolism. In the T2DM pathway, there are only 5 DEGs including GLUT4, HK3, SOCS3, PYK, and GCK. qRT-PCR further confirm their expressions. All the results indicated that GLUT4, HK3, SOCS3, PYK, and GCK might play important roles in the hypoglycemic mechanism of TBP.","PeriodicalId":260405,"journal":{"name":"Proceedings of the Fourth International Conference on Biological Information and Biomedical Engineering","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125847031","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}