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1. chinaXiv:202105.00003 [pdf]

SEPRES: Sepsis prediction via a clinical data integration system and real-world studies in the intensive care unit

Chen, Qiyu; Li, Ranran; Lin, Chihche; Lai, Chiming; Chen, Dechang; Qu, Hongping; Huang, Yaling; Lu, Wenlian; Tang, Yaoqing; Li, Lei
Subjects: Medicine, Pharmacy >> Clinical Medicine

Background: Sepsis is vital in critical care medicine, and early detection and intervention are key to survival. We aimed to establish an early warning system for sepsis based on a data integration system that can be implemented in the intensive care unit (ICU). Methods: We trained the LightGBM and multilayer perceptron on the open-source database Medical Information Mart for Intensive Care for sepsis prediction. An ensemble sepsis prediction model was established based on the transfer learning and ensemble learning technique on the private dataset of Ruijin Hospital. The Shapley Additive Explanations analysis was applied to present feature importance on the prediction inference. With the development of data-integrating hub to collect and transmit data from different brands of ICU medical devices, the data integration system was established to receive, integrate, standardize, and store the real-time clinical data. In this way, the sepsis prediction model developed in the ICU of the Ruijin Hospital for the real-world study of sepsis early warning on ICU management. The trial was registered with (NCT05088850). Findings: Our best early warning model achieved an area under the receiver operating characteristic curve (AUC) of 0·9833 in the task of detecting sepsis in 4-h preceding on the open-source database, while our ensemble model achieved an AUC of 0·9065?0·9436 in the retrospective research from 1?5-h preceding on the private database, and 0·8636?0·8992 in real-time real-world studies using the data integration system in the ICU of the Ruijin Hospital. In the continuous early warning process of patients admitted to the ICU, 22 patients who met the diagnostic criteria for sepsis during hospitalization were predicted as positive cases; 29 patients without sepsis were predicted as negative cases. Additionally, 17 patients were predicted as false-positive cases; in six patients with sepsis during ICU stay, the predicted probabilities at different time nodes were all less than the warning threshold 0·7 and predicted as false-negative cases. Interpretation: Machine learning models could allow accurate and real-time inference to detect sepsis onset within 5-h preceding at most with the help of the data integration system. We identified the features such as age, antibiotics, ventilation, and net balance to be important for the sepsis prediction inference. We argue that this system has promising potential to improve ICU management by helping medical practitioners identify at-sepsis-risk patients and prepare for timely diagnosis and intervention. Funding: Shanghai Municipal Science and Technology Major Project, the ZHANGJIANG LAB, and the Science and Technology Commission of Shanghai Municipality.

submitted time 2021-11-22 Hits61Downloads672 Comment 0

2. chinaXiv:202110.00002 [pdf]

Transplantation of a Beating Heart: A First in Human

Yin Shengli; Rong Jian; Chen Yinghua; Cao Lu; Liu Yunqi; Mo Shaoyan; Li Hanzhao; Jiang Nan; Xiong Mai; Shi Han; Wang Tielong; Shi Yongxu; Zhu Yanlin; Liang Mengya; Xiong Wei; Chen Yili; Xu Guixing; Chen Xiaoxiang; Chen Xiaojun; Yin Meixian
Subjects: Medicine, Pharmacy >> Clinical Medicine

Ischemia and reperfusion injury (IRI), an inevitable component in organ transplantation, contributes to inferior graft survival, compromised organ quality and limitations in organ availability. The heart is most vulnerable to IRI and tolerated ischemic times are very short. We present an entire novel heart transplant procedure during which the donor heart was continuously perfused, oxygenated at normothermia and transplanted while beating. The dynamic electrocardiogram and echocardiogram indicated an absence of ischemic injury and excellent function of the donor heart during the entire procedure. This ischemia-free beating heart transplantation (IFBHT) avoids graft IRI. The approach has thus the potential to improve transplant outcome while improving organ utilization.

submitted time 2021-10-02 Hits3005Downloads269 Comment 0

3. chinaXiv:202108.00058 [pdf]

Metagenomic evidence for the coexistence of SARS and H1N1 in patients from 2007-2012 flu seasons

Qi Liu; Zhenglin Du; Sihui Zhu; Wenming Zhao; Hua Chen; Yongbiao Xue
Subjects: Biology >> Microbiology

By re-analzying public metagenomic data from 101 patients infected with influenza A virus during the 2007-2012 H1N1 flu seasons in France, we identified 22 samples with SARS-CoV sequences. In 3 of them, the SARS genome sequences could be fully assembled out of each. These sequences are highly similar (99.99% and 99.7%) to the artificially constructed recombinant 5 SARS-CoV (SARSr-CoV) strains generated by the J. Craig Venter Institute in USA. Moreover, samples from different flu seasons have different SARS-CoV strains, and the divergence between these strains cannot be explained by natural evolution. Our study also shows that retrospective studies using public metagenomic data from past major epidemic outbreaks serves as a genomic strategy for the research of origins or spread of infectious diseases.

submitted time 2021-08-11 Hits8800Downloads979 Comment 0

4. chinaXiv:202107.00039 [pdf]

Tracing the origin of SARS-CoV-2: lessons learned from the past

Qihui Wang; Hua Chen; Yi Shi; Alice C. Hughes; William J. Liu; Jingkun Jiang; George F. Gao; Yongbiao Xue; Yigang Tong
Subjects: Biology >> Virology

新冠病毒的起源仍不清楚。了解新冠病毒如何、何时以及在何处从其天然宿主传播给人类对于预防未来由冠状病毒引发的疫情至关重要。 从与病原体无休止的战斗中吸取教训,结合目前已知的关于新冠病毒起源和中间宿主的研究数据,我们提出全球多个地点都有可能是新冠病毒的起源地。

submitted time 2021-07-28 Hits9535Downloads1297 Comment 0

5. chinaXiv:202107.00013 [pdf]

On the origin of SARS-CoV-2–The blind watchmaker argument

Chung-I Wu; Haijun Wen; Jian Lu; Xiao-dong Su; Alice C. Hughes; Weiwei Zhai; Chen Chen; Hua Chen; Mingkun Li; Shuhui Song; Zhaohui Qian; Qihui Wang; Bingjie Chen; Zixiao Guo; Yongsen Ruan; Xuemei Lu; Fuwen Wei; Li Jin; Le Kang; Yongbiao Xue
Subjects: Biology >> Virology

In the comparison with SARS-CoV of 2003, SARS-CoV-2 is extremely well adapted to the human populations and its adaptive shift from the animal host to humans must have been even more extensive. By the blind watchmaker argument, such an adaptive shift can only happen prior to the onset of the current pandemic and with the aid of step-by-step selection. In this view, SARS-CoV-2 could not have possibly evolved in an animal market in a big city and even less likely in a laboratory. Discussions of the origin of SARS-CoV-2 need to factor in the long process of adaptive shift and some models have indeed advanced in that direction.

submitted time 2021-07-17 Hits8537Downloads818 Comment 0

6. chinaXiv:202107.00008 [pdf]


庞峻峰; 高洁; 张立勇; Nahid F. Mivechi ; 柯蓝
Subjects: Medicine, Pharmacy >> Pharmacology

肿瘤血管生成是癌症的一个特征。一些抗血管生成的抗癌药物已被证明临床有疗效。我们之前的研究显示,在包括口腔癌在内的人类实体瘤中,GT198 蛋白(基因符号PSMC3IP,又称为Hop2)是一个诱导血管生成的癌蛋白。本研究结果表明,十几种临床抗癌化疗药物,和几种临床成功的抗癌草药,都能直接抑制GT198蛋白靶点。GT198是一个能与DNA结合的DNA修复蛋白。利用体外DNA结合法检测GT198活性,我们测试了129个美国NCI收集的临床抗癌化疗药物。发现体外直接抑制GT198的化药包括但不限于米托蒽醌、多柔比星(阿霉素)、紫杉醇、依托泊苷、放线菌素D和伊马替尼(格列卫)。紫杉醇和依托泊苷具有较高的结合亲和力,而多柔比星由于竞争性抑制GT198,具有较高的结合效力。由于GT198与DNA拓扑异构酶有蛋白序列同源性,而DNA拓扑异构酶是过去认为的药物靶点,因此,GT198蛋白很可能是个以前未被认知的药物新靶点。为了寻求更高效的GT198抑制剂,我们进一步测试了几种抗癌草药的提取物。发现具有高亲和力和高效力的阳性抑制草药都是临床上已经有成功历史的抗癌草药,包括牙买加的多香果(Allspice)、中国的皂角刺(Gleditsia sinensis L.),和厄瓜多尔的BIRM。我们使用有机化学方法对多香果进行了部分纯化,证明用GT198为靶标,以体外DNA结合法追踪测活,可以高效快速纯化天然产物。综上表明,此项研究揭示了GT198是多种抗癌化药的新靶点。这项研究还提供了一个鉴定化合物与纯化天然产物的优异药物靶标。特别关键的是,这项研究为快速分离高效低毒的抗癌中草药提供了绝佳机会。

submitted time 2021-07-12 Hits8540Downloads504 Comment 0

7. chinaXiv:202106.00110 [pdf]


赵晨阳; 魏利龙; 魏静; 高友鹤
Subjects: Biology >> Biochemistry


submitted time 2021-06-25 Hits7867Downloads622 Comment 0

8. chinaXiv:202105.00077 [pdf]


祝锐; 刘玉红; 王体春; 陈龙聪; 谢正祥
Subjects: Computer Science >> Computer Application Technology
Subjects: Engineering and technical science >> Optical Engineering


submitted time 2021-05-24 Hits6625Downloads691 Comment 0

9. chinaXiv:202105.00003 [pdf]

Sepsis prediction via the clinical data integration system in the ICU

Chen, Qiyu; Li, Ranran; Lin, Zhizhe; Lai, Zhiming; Xue, Peijiao; Jiang, Jingfeng; Lu, Wenlian; Li, Lei; Tang, Yaoqing
Subjects: Medicine, Pharmacy >> Clinical Medicine

Sepsis is an essential issue in critical care medicine, and early detection and intervention are key for survival. We established the sepsis early warning system based on a data integration platform that can be implemented in ICU. The sepsis early warning module can detect the onset of sepsis 5 hours proceeding, and the data integration platform integrates, standardizes, and stores information from different medical devices, making the inference of the early warning module possible. Our best early warning model got an AUC of 0.9833 in the task of detect sepsis in 4 hours proceeding on the open-source database. Our data integration platform has already been operational in a hospital for months.

submitted time 2021-05-07 Hits14231Downloads675 Comment 0

10. chinaXiv:202104.00020 [pdf]

Bacterial and viral therapies of cancer background, mechanism and perspective

Qinglin Dong, Xiangying Xing
Subjects: Medicine, Pharmacy >> Preclinical Medicine

Bacterial and viral therapies of cancer are highly promising, yet their mechanisms are incompletely understood, hindering their improvement and application. In this paper, We (1) review briefly the genesis and progress of bacterial and viral therapies of cancer, (2) compare and evaluate the proposed mechanisms of bacterial and viral therapies of cancer and present the unifying mechanism that bacteria/viruses stimulate cancer cells to produce antibacterial/antiviral proteins, which also serve as the responsive cancer antigens triggering host anticancer immune response, and (3) provide a perspective on the exploitation of non-human and non-animal bacteria and viruses, particularly protist-infecting bacteria and viruses and bacterial virus (bacteriophage/phage), for cancer treatment and prevention.

submitted time 2021-04-29 Hits11360Downloads790 Comment 0

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