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1. Large Language Models in Biomedical and Health Informatics: A Review with Bibliometric Analysis

Author

Yu, Huizi, Fan, Lizhou, Li, Lingyao, Zhou, Jiayan, Ma, Zihui, Xian, Lu, Hua, Wenyue, He, Sijia, Jin, Mingyu, Zhang, Yongfeng, Gandhi, Ashvin, and Ma, Xin

Subjects
Computer Science - Digital Libraries, Computer Science - Artificial Intelligence, Computer Science - Computation and Language, Computer Science - Social and Information Networks
Abstract

Large Language Models (LLMs) have rapidly become important tools in Biomedical and Health Informatics (BHI), enabling new ways to analyze data, treat patients, and conduct research. This study aims to provide a comprehensive overview of LLM applications in BHI, highlighting their transformative potential and addressing the associated ethical and practical challenges. We reviewed 1,698 research articles from January 2022 to December 2023, categorizing them by research themes and diagnostic categories. Additionally, we conducted network analysis to map scholarly collaborations and research dynamics. Our findings reveal a substantial increase in the potential applications of LLMs to a variety of BHI tasks, including clinical decision support, patient interaction, and medical document analysis. Notably, LLMs are expected to be instrumental in enhancing the accuracy of diagnostic tools and patient care protocols. The network analysis highlights dense and dynamically evolving collaborations across institutions, underscoring the interdisciplinary nature of LLM research in BHI. A significant trend was the application of LLMs in managing specific disease categories such as mental health and neurological disorders, demonstrating their potential to influence personalized medicine and public health strategies. LLMs hold promising potential to further transform biomedical research and healthcare delivery. While promising, the ethical implications and challenges of model validation call for rigorous scrutiny to optimize their benefits in clinical settings. This survey serves as a resource for stakeholders in healthcare, including researchers, clinicians, and policymakers, to understand the current state and future potential of LLMs in BHI., Comment: 62 pages, 9 figures, 5 tables

Published
2024

2. An Empirical Study on Large Language Models in Accuracy and Robustness under Chinese Industrial Scenarios

Author

Li, Zongjie, Qiu, Wenying, Ma, Pingchuan, Li, Yichen, Li, You, He, Sijia, Jiang, Baozheng, Wang, Shuai, and Gu, Weixi

Subjects
Computer Science - Computation and Language, Computer Science - Artificial Intelligence
Abstract

Recent years have witnessed the rapid development of large language models (LLMs) in various domains. To better serve the large number of Chinese users, many commercial vendors in China have adopted localization strategies, training and providing local LLMs specifically customized for Chinese users. Furthermore, looking ahead, one of the key future applications of LLMs will be practical deployment in industrial production by enterprises and users in those sectors. However, the accuracy and robustness of LLMs in industrial scenarios have not been well studied. In this paper, we present a comprehensive empirical study on the accuracy and robustness of LLMs in the context of the Chinese industrial production area. We manually collected 1,200 domain-specific problems from 8 different industrial sectors to evaluate LLM accuracy. Furthermore, we designed a metamorphic testing framework containing four industrial-specific stability categories with eight abilities, totaling 13,631 questions with variants to evaluate LLM robustness. In total, we evaluated 9 different LLMs developed by Chinese vendors, as well as four different LLMs developed by global vendors. Our major findings include: (1) Current LLMs exhibit low accuracy in Chinese industrial contexts, with all LLMs scoring less than 0.6. (2) The robustness scores vary across industrial sectors, and local LLMs overall perform worse than global ones. (3) LLM robustness differs significantly across abilities. Global LLMs are more robust under logical-related variants, while advanced local LLMs perform better on problems related to understanding Chinese industrial terminology. Our study results provide valuable guidance for understanding and promoting the industrial domain capabilities of LLMs from both development and industrial enterprise perspectives. The results further motivate possible research directions and tooling support.

Published
2024

4. Research on the performance of plate and roll capacitor deionization devices based on supercapacitor carbon electrodes(基于超级电容活性炭电极的板式与卷式电容去离子装置的性能研究)

Author

翁琦辉(WENG Qihui), 陈涵(CHEN Han), 贺斯佳(HE Sijia), 张燚(ZHANG Yi), and 杨岳平(YANG Yueping)

Subjects
capacitive deionization(电容去离子), super capacitor activated carbon(超级电容活性炭), unit configuration(装置构型), Electronic computers. Computer science, QA75.5-76.95, Physics, QC1-999
Abstract

Capacitive deionization is an energy-saving and environmentally friendly brackish water desalination technology. The performance of capacitive deionization is influenced by two significant factors: electrode materials and device configurations. Three types of commercially available supercapacitor carbons AC1, AC2, and AC3 were used to characterize and optimize them for electrode production. The results demonstrate that AC2 activated carbon exhibits the highest specific surface area (1 908.4 m2·g-1) and specific capacitance (67.8 F·g-1). And AC2's internal pore resistance is also the lowest. Therefore, AC2 was chosen as the electrode material to study the operation of plate and roll devices under different experimental conditions. The optimal working voltage of the two configurations was 1.6 V, the temperature was 25 ℃, the optimal flow rate of the plate device was 60 mL·min-1, and for the roll device it was 360 mL·min-1. Under the optimal working conditions, the desalination amount per unit area and current efficiency of the roll device are 1 569.7 mg·m-2 and 46.7% respectively, much bigger than 696.5 mg·m-2 and 11.3% of the plate device. These results indicate that the roll device outperforms the plate device in terms of desalination performance and charge efficiency.(电容去离子是一种节能环保的新兴盐水淡化技术，电极材料与装置是影响电容去离子性能的两大重要因素。分别对3种市售超级电容活性炭AC1、AC2、AC3进行表征并择优开展后续实验，结果表明，AC2活性炭的比表面积与比电容最大，分别为1 908.4 m2·g-1和67.8 F·g-1，内部孔隙电阻最小。因此，以AC2为电极材料研究板式与卷式电容去离子装置在不同实验条件下的运行情况，发现2种装置的最佳工作电压均为1.6 V、温度均为25 ℃，最佳流速，板式装置为60 mL·min-1，卷式装置为360 mL·min-1。在最佳工作条件下，卷式装置的单位面积脱盐量与电荷效率分别为1 569.7 mg·m-2和46.7%，远大于板式装置的696.5 mg·m-2和11.3%，卷式装置具有更强的脱盐性能与能量利用率。)

Published
2024
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8. Supply chain innovation : an integrating framework and aerospace cases from China

Author

He, Sijia

Subjects
HD Industries. Land use. Labor
Abstract

The relationship between supply chain management and innovation has been fragmentedly explored in the literature. Relevant arguments have been generally formulated around issues of resources, coordination and learning in supply chain management. Important arguments include engaging suppliers in buyers' research and development processes, especially in the early stage of new product development, which helps to leverage suppliers' expertise but may also lead to inevitable risks. Another fragmentation is that there is no unifying framework explaining how the activities along the supply chain can systematically impact on the buyers' innovation performance. In this context, this research develops an integrating framework of supply chain innovation (SCI) to reveal how the supply chain capabilities influence a firm's innovation performance. This research adopts a multiple case study approach to collect empirical data for two main reasons. Firstly, the process of identifying the relationship between supply chain capabilities and innovation performance is a theory-building process (Eisenhardt, 1989). Therefore, case study provides description and exploration to serve the aim of theory-building. Secondly, implementing case study approach is more suitable to serve the research objective to collect qualitative data that focuses on exploring in depth rather than breadth (Denscombe, 1998 and Eisenhardt, 1989). Because case study "focuses on instances of a particular phenomenon with a view to providing an in-depth account of events, relationships, experiences or processes that are occurring in that particular instance" (Denscombe, 1998). We have conducted 37 intensive interviews and secondary data from 8 aerospace manufacturers in China. The case companies were selected via theoretical sampling method, and there are five case selection criteria: firstly, the case companies must be involved in manufacturing in the aerospace industry; secondly, the company must be engaged in at least one type of innovation performance; thirdly, the researched companies must come from either the manufacturer and supplier side of the supply chain; last but not least, the company must be at the higher tier of the complex aerospace manufacturing supply chain (at least tier 1-2). The data were analysed by following Yin's (2018) guidelines and thematic analysis methods (Braun and Clarke, 2006) to explore the relationship between supply chain capabilities and innovation performance. The main contribution of this research is that it extends the existing literatures to provide an integrating framework of SCI that incorporates discussions from different aspects of operations theories. It provides case studies from eight companies from China, including two leading enterprises in the aerospace manufacturing industry in the domestic market. The research looks from both the manufacturers' side and suppliers' side, aiming to provide a more comprehensive framework and explains how innovation performance can be enhanced through SCI.

Published
2020

16. Large Language Models in Biomedical and Health Informatics: A Bibliometric Review

Author

Yu, Huizi, Fan, Lizhou, Li, Lingyao, Zhou, Jiayan, Ma, Zihui, Xian, Lu, Hua, Wenyue, He, Sijia, Jin, Mingyu, Zhang, Yongfeng, Gandhi, Ashvin, Ma, Xin, Yu, Huizi, Fan, Lizhou, Li, Lingyao, Zhou, Jiayan, Ma, Zihui, Xian, Lu, Hua, Wenyue, He, Sijia, Jin, Mingyu, Zhang, Yongfeng, Gandhi, Ashvin, and Ma, Xin

Abstract

Large Language Models (LLMs) have rapidly become important tools in Biomedical and Health Informatics (BHI), enabling new ways to analyze data, treat patients, and conduct research. This bibliometric review aims to provide a panoramic view of how LLMs have been used in BHI by examining research articles and collaboration networks from 2022 to 2023. It further explores how LLMs can improve Natural Language Processing (NLP) applications in various BHI areas like medical diagnosis, patient engagement, electronic health record management, and personalized medicine. To do this, our bibliometric review identifies key trends, maps out research networks, and highlights major developments in this fast-moving field. Lastly, it discusses the ethical concerns and practical challenges of using LLMs in BHI, such as data privacy and reliable medical recommendations. Looking ahead, we consider how LLMs could further transform biomedical research as well as healthcare delivery and patient outcomes. This bibliometric review serves as a resource for stakeholders in healthcare, including researchers, clinicians, and policymakers, to understand the current state and future potential of LLMs in BHI., Comment: 51 pages, 7 figures, 4 tables

Published
2024

19. An ACE2 decamer viral trap as a durable intervention solution for current and future SARS-CoV

Author

Guo, Hailong, primary, Cho, Bomsoo, additional, Hinton, Paul R., additional, He, Sijia, additional, Yu, Yongjun, additional, Ramesh, Ashwin Kumar, additional, Sivaccumar, Jwala Priyadarsini, additional, Ku, Zhiqiang, additional, Campo, Kristen, additional, Holland, Sarah, additional, Sachdeva, Sameer, additional, Mensch, Christopher, additional, Dawod, Mohamed, additional, Whitaker, Annalis, additional, Eisenhauer, Philip, additional, Falcone, Allison, additional, Honce, Rebekah, additional, Botten, Jason W., additional, Carroll, Stephen F., additional, Keyt, Bruce A., additional, Womack, Andrew W., additional, Strohl, William R., additional, Xu, Kai, additional, Zhang, Ningyan, additional, An, Zhiqiang, additional, Ha, Sha, additional, Shiver, John W., additional, and Fu, Tong-Ming, additional

Published
2023
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20. Leptin Reduction as a Required Component for Weight Loss

Author

Zhao, Shangang, primary, Li, Na, additional, Xiong, Wei, additional, Li, Guannan, additional, He, Sijia, additional, Zhang, Zhuzhen, additional, Zhu, Qingzhang, additional, Jiang, Nisi, additional, Ikejiofor, Christian, additional, Zhu, Yi, additional, Wang, May-Yun, additional, Han, Xianlin, additional, Zhang, Ningyang, additional, Herrera-Solis, Carolina, additional, Kusminski, Christine, additional, An, Zhiqiang, additional, Elmquist, Joel K., additional, and Scherer, Philipp E., additional

Published
2023
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25. LRG1 is an adipokine that mediates obesity-induced hepatosteatosis and insulin resistance

Author

He, Sijia, Ryu, Jiyoon, Liu, Juanhong, Luo, Hairong, Lv, Ying, Langlais, Paul R., Wen, Jie, Dong, Feng, Sun, Zhe, Xia, Wenjuan, Lynch, Jane L., Duggirala, Ravindranath, Nicholson, Bruce J., Zang, Mengwei, Shi, Yuguang, Zhang, Fang, Liu, Feng, Bai, Juli, and Dong, Lily Q.

Subjects
Glycoproteins -- Health aspects, Obesity -- Genetic aspects -- Complications and side effects -- Care and treatment, Insulin resistance -- Genetic aspects -- Development and progression -- Care and treatment, Health care industry
Abstract

Dysregulation in adipokine biosynthesis and function contributes to obesity- induced metabolic diseases. However, the identities and functions of many of the obesity-induced secretory molecules remain unknown. Here, we report the identification of leucine-rich alpha-2-glycoprotein 1 (LRG1) as an obesity- associated adipokine that exacerbates high fat diet-induced hepatosteatosis and insulin resistance. Serum levels of LRG1 were markedly elevated in obese humans and mice compared with their respective controls. LRG1 deficiency in mice greatly alleviated diet-induced hepatosteatosis, obesity, and insulin resistance. Mechanistically, LRG1 bound with high selectivity to the liver and promoted hepatosteatosis by increasing de novo lipogenesis and suppressing fatty acid p-oxidation. LRG1 also inhibited hepatic insulin signaling by downregulating insulin receptor substrates 1 and 2. Our study identified LRG1 as a key molecule that mediates the crosstalk between adipocytes and hepatocytes in diet-induced hepatosteatosis and insulin resistance. Suppressing LRG1 expression and function may be a promising strategy for the treatment of obesity-related metabolic diseases., Introduction Adipose tissue dysfunction plays a critical role in the development of insulin resistance (IR), a major risk factor for type 2 diabetes, fatty liver diseases, and cardiovascular complication (1, [...]

Published
2021
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32. Cancer Cells Enter an Adaptive Persistence to Survive Radiotherapy and Repopulate Tumor

Author

Zhao, Yucui, primary, Lu, Tingting, additional, Song, Yanwei, additional, Wen, Yanqin, additional, Deng, Zheng, additional, Fan, Jiahui, additional, Zhao, Minghui, additional, Zhao, Ruyi, additional, Luo, Yuntao, additional, xie, Jianzhu, additional, Hu, Binjie, additional, Sun, Haoran, additional, Wang, Yiwei, additional, He, Sijia, additional, Gong, Yanping, additional, Cheng, Jin, additional, Liu, Xinjian, additional, Yu, Liang, additional, Li, Jikun, additional, Li, Chuanyuan, additional, Shi, Yongyong, additional, and Huang, Qian, additional

Published
2023
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42. Paramārtha’s Ultimate Truth and the Development of Chinese Buddhism’s Ultimate Truth

Author

He, Sijia Wang and Huanhuan

Subjects
Jiejie Jing解節經, Paramārtha, ultimate truth, three truths
Abstract

This paper discusses the development of ideas of the ultimate in the thought of Chinese Buddhism in the Northern and Southern Dynasties. The concept of ultimate truth is, along with that of conventional truth, a core concept in Mahāyāna Buddhism. During the Sui Dynasty, Chinese Buddhism developed the unique perspective of the Three Truths, the foundation for which was formed during the Southern and Northern Dynasties. This begins with Jie jie Jing 解節經 (in full, Foshuo Jiejie Jing 佛說解節經) by Paramārtha (499–569), which is a partial translation of Saṃdhinirmocanasūtra and presents the theory of ultimate truth (paramārtha) to Chinese Buddhists. Through a comparison of Jiejie Jing with other Chinese and Tibetan translations of Saṃdhinirmocana-sūtra, we establish Paramārtha’s thoughts on the ultimate. The relationship between Paramārtha’s thought on the ultimate and the development of the Three Truths is evaluated in a comparison of Paramārtha’s thoughts on ultimate truth with the thinking of nearly contemporary Chinese monks.

Published
2021
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44. IP-10 Promotes Latent HIV Infection in Resting Memory CD4+ T Cells via LIMK-Cofilin Pathway

Author

Wang, Zhuo, primary, Yin, Xiaowan, additional, Ma, Meichen, additional, Ge, Hongchi, additional, Lang, Bin, additional, Sun, Hong, additional, He, Sijia, additional, Fu, Yajing, additional, Sun, Yu, additional, Yu, Xiaowen, additional, Zhang, Zining, additional, Cui, Hualu, additional, Han, Xiaoxu, additional, Xu, Junjie, additional, Ding, Haibo, additional, Chu, Zhenxing, additional, Shang, Hong, additional, Wu, Yuntao, additional, and Jiang, Yongjun, additional

Published
2021
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45. Targeted delivery of lopinavir to HIV reservoirs in the mesenteric lymphatic system by lipophilic ester prodrug approach

Author

Qin, Chaolong, Chu, Yenju, Feng, Wanshan, Fromont, Christophe, He, Sijia, Ali, Joseph, Lee, Jong Bong, Zgair, Atheer, Berton, Mattia, Bettonte, Sara, Liu, Ruiling, Yang, Lei, Monmaturapoj, Teerapong, Alonso, Allen, Vetrugno, Daria, Ee, Shi Ying, Sheriston, Charles, Wu, Yuntao, Stocks, Michael J., Fischer, Peter M., and Gershkovich, Pavel

Abstract

© 2020 Elsevier B.V. The combined antiretroviral therapy (cART) can efficiently suppress HIV replication, but the cessation of cART usually results in viral rebound, mostly due to the presence of viral reservoirs. The mesenteric lymphatic system, including mesenteric lymph nodes (MLNs), is an important viral reservoir into which antiretroviral drugs poorly penetrate. In this work, we proposed a novel lipophilic ester prodrug approach, combined with oral lipid-based formulation, to efficiently deliver lopinavir (LPV) to the mesenteric lymph and MLNs. A series of prodrugs was designed using an in-silico model for prediction of affinity to chylomicrons (CMs), and then synthesized. The potential for mesenteric lymphatic targeting and bioconversion to LPV in physiologically relevant media was assessed in vitro and ex vivo. Subsequently, LPV and selected prodrug candidates were evaluated for their in vivo pharmacokinetics and biodistribution in rats. Oral co-administration of lipids alone could not facilitate the delivery of unmodified LPV to the mesenteric lymphatic system and resulted in undetectable levels of LPV in these tissues. However, a combination of the lipophilic prodrug approach with lipid-based formulation resulted in efficient targeting of LPV to HIV reservoirs in mesenteric lymph and MLNs. The maximum levels of LPV in mesenteric lymph were 1.6- and 16.9-fold higher than protein binding-adjusted IC90 (PA-IC90) of LPV for HIV-1 (140 ng/mL) following oral administration of simple alkyl ester prodrug and activated ester prodrug, respectively. Moreover, the concentrations of LPV in MLNs were 1.1- and 7.2-fold higher than PA-IC90 following administration of simple alkyl ester prodrug and activated ester prodrug, respectively. Furthermore, the bioavailability of LPV was also substantially increased following oral administration of activated ester prodrug compared to unmodified LPV. This approach, especially if can be translated to other antiretroviral drugs, has potential for reducing the size of HIV reservoirs within the mesenteric lymphatic system.

Published
2021

47. Additional file 1 of Adult-onset CNS myelin sulfatide deficiency is sufficient to cause Alzheimer’s disease-like neuroinflammation and cognitive impairment

Author

Qiu, Shulan, Palavicini, Juan Pablo, Wang, Jianing, Gonzalez, Nancy S., He, Sijia, Dustin, Elizabeth, Zou, Cheng, Ding, Lin, Bhattacharjee, Anindita, Van Skike, Candice E., Galvan, Veronica, Dupree, Jeffrey L., and Han, Xianlin

Abstract

Additional file 1: Supplementary figures and figure legends.

Published
2021
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48. Targeted delivery of lopinavir to HIV reservoirs in the mesenteric lymphatic system by lipophilic ester prodrug approach

Author

Universidad de Sevilla. Departamento de Nutrición y Bromatología, Toxicología y Medicina Legal, Qin, Chaolong, Chu, Yen Ju, Feng, Wanshan, Fromont, Christophe, He, Sijia, Ali, Joseph, Lee, Jong Bong, Zgair, Atheer, Medrano Padial, Concepción, Fischer, Peter M., Gershkovich, Pavel, Universidad de Sevilla. Departamento de Nutrición y Bromatología, Toxicología y Medicina Legal, Qin, Chaolong, Chu, Yen Ju, Feng, Wanshan, Fromont, Christophe, He, Sijia, Ali, Joseph, Lee, Jong Bong, Zgair, Atheer, Medrano Padial, Concepción, Fischer, Peter M., and Gershkovich, Pavel

Abstract

The combined antiretroviral therapy (cART) can efficiently suppress HIV replication, but the cessation of cART usually results in viral rebound, mostly due to the presence of viral reservoirs. The mesenteric lymphatic system, including mesenteric lymph nodes (MLNs), is an important viral reservoir into which antiretroviral drugs poorly penetrate. In this work, we proposed a novel lipophilic ester prodrug approach, combined with oral lipid-based formulation, to efficiently deliver lopinavir (LPV) to the mesenteric lymph and MLNs. A series of prodrugs was designed using an in-silico model for prediction of affinity to chylomicrons (CMs), and then synthesized. The potential for mesenteric lymphatic targeting and bioconversion to LPV in physiologically relevant media was assessed in vitro and ex vivo. Subsequently, LPV and selected prodrug candidates were evaluated for their in vivo pharmacokinetics and biodistribution in rats. Oral co-administration of lipids alone could not facilitate the delivery of unmodified LPV to the mesenteric lymphatic system and resulted in undetectable levels of LPV in these tissues. However, a combination of the lipophilic prodrug approach with lipid-based formulation resulted in efficient targeting of LPV to HIV reservoirs in mesenteric lymph and MLNs. The maximum levels of LPV in mesenteric lymph were 1.6- and 16.9-fold higher than protein binding-adjusted IC90 (PA-IC90) of LPV for HIV-1 (140 ng/mL) following oral administration of simple alkyl ester prodrug and activated ester prodrug, respectively. Moreover, the concentrations of LPV in MLNs were 1.1- and 7.2-fold higher than PA-IC90 following administration of simple alkyl ester prodrug and activated ester prodrug, respectively. Furthermore, the bioavailability of LPV was also substantially increased following oral administration of activated ester prodrug compared to unmodified LPV. This approach, especially if can be translated to other antiretroviral drugs, has potential for reducing

Published
2021

50. Viruses

Author

He, Sijia, Waheed, Abdul A., Hetrick, Brian, Dabbagh, Deemah, Akhrymuk, Ivan V., Kehn-Hall, Kylene, Freed, Eric O., Wu, Yuntao, and Biomedical Sciences and Pathobiology

Subjects
integumentary system, coronavirus, pseudovirion, cellular antiviral factor
Abstract

P-selectin glycoprotein ligand-1 (PSGL-1) is a cell surface glycoprotein that binds to P-, E-, and L-selectins to mediate the tethering and rolling of immune cells on the surface of the endothelium for cell migration into inflamed tissues. PSGL-1 has been identified as an interferon-γ (INF-γ)-regulated factor that restricts HIV-1 infectivity, and has recently been found to possess broad-spectrum antiviral activities. Here we report that the expression of PSGL-1 in virus-producing cells impairs the incorporation of SARS-CoV and SARS-CoV-2 spike (S) glycoproteins into pseudovirions and blocks pseudovirus attachment and infection of target cells. These findings suggest that PSGL-1 may potentially inhibit coronavirus replication in PSGL-1+ cells Published version

Published
2020

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