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TransCell:In Silico Characterization of Genomic Landscape and Cellular Responses by Deep Transfer Learning

Genomics, Proteomics & Bioinformatics 2024年第2期22卷 157-170页

作者： shan-ju yeh Shreya Paithankar Ruoqiao Chen Jing Xing Mengying Sun Ke Liu Jiayu Zhou Bin Chen Department of Pediatrics and Human Development Michigan State UniversityGrand RapidsMI 49503USA Department of Pharmacology and Toxicology Michigan State UniversityGrand RapidsMI 49503USA Department of Computer Science and Engineering Michigan State UniversityEast LansingMI 48824USA

Gene expression profiling of new or modified cell lines becomes routine today;however,obtaining comprehensive molecular characterization and cellular responses for a variety of cell lines,including those derived from underrepresented groups,is not trivial when resources are *** gene expression to predict other measurements has been actively explored;however,systematic investigation of its predictive power in various measurements has not been well ***,we evaluated commonly used machine learning methods and presented TransCell,a two-step deep transfer learning framework that utilized the knowledge derived from pan-cancer tumor samples to predict molecular features and *** these models,TransCell had the best performance in predicting metabolite,gene effect score(or genetic dependency),and drug sensitivity,and had comparable performance in predicting mutation,copy number variation,and protein ***,TransCell improved the performance by over 50%in drug sensitivity prediction and achieved a correlation of 0.7 in gene effect score ***,predicted drug sensitivities revealed potential repurposing candidates for new 100 pediatric cancer cell lines,and predicted gene effect scores reflected BRAF resistance in melanoma cell ***,we investigated the predictive power of gene expression in six molecular measurement types and developed a web portal(http://***/transcell/)that enables the prediction of 352,000 genomic and cellular response features solely from gene expression profiles.

关键词： Genomics Transcriptomics Cancer dependency Drug repurposing Transfer learning

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Photocatalytic vinyl radical-mediated multicomponent 1,4-/1,8-carboimination across alkynes and olefins/(hetero)arenes

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Science China Chemistry 2024年第2期67卷 558-567页

作者： shan-shan Li Yu-Shi Jiang Xue-Ling Luo Xuming Ran Yuqiang Li Dong Wu Cheng-Xue Pan Peng-ju Xia School of Chemistry and Pharmaceutical Sciences Guangxi Normal UniversityGuilin541004China shanghai Artificial Intelligence Laboratory Shanghai200433China The Institute for Advanced Studies Wuhan UniversityWuhan430064China

We developed a highly selective and efficient multicomponent transformation by utilizing alkynes and olefins/(hetero)arenes through photoinduced energy-transfer *** reaction involves the formation of three distinct chemical bonds,namely C(sp~3)–C(sp~2),C(sp~2)–C(sp~3),and C(sp~3)–N,in a single coordinated *** strategy used a vinyl radical-mediated radical relay approach under mild conditions,exhibiting a broad substrate scope(>70 examples),excellent functional-group tolerance,and remarkable regio-and *** the utilization of a combination of experimental techniques and density functional theory(DFT),we delved deeper into the mechanistic intricacies of this distinctive *** revealed that the selective radical addition to electron-deficient alkynes,rather than olefins,was governed by the inherent reactivity of alkyl *** discovery presented a highly effective approach for the synthesis of stereodefined multisubstituted alkenes.

关键词： alkyne-olefin coupling DFT studies regio-and anti-stereoselectivity multisubstituted alkenes

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Evidence-Based Dampness-Heat ZHENG(Syndrome) in Cancer: Current Progress toward Establishing Relevant Animal Model with Pancreatic Tumor

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Chinese Journal of Integrative Medicine 2024年第1期30卷 85-95页

作者： JIAO ju-ying CHENG Chien-shan CAO Zhang-qi CHEN Lian-yu CHEN Zhen Department of Integrative Oncology Fudan University Shanghai Cancer CenterShanghai(200032)China Department of Oncology Shanghai Medical CollegeFudan UniversityShanghai(200032)China

Cancer is one of the deadliest diseases affecting the health of human beings. With limited therapeutic options available, complementary and alternative medicine has been widely adopted in cancer management and is increasingly becoming accepted by both patients and healthcare workers alike. Chinese medicine characterized by its unique diagnostic and treatment system is the most widely applied complementary and alternative medicine. It emphasizes symptoms and ZHENG(syndrome)-based treatment combined with contemporary disease diagnosis and further stratifies patients into individualized medicine subgroups. As a representative cancer with the highest degree of malignancy, pancreatic cancer is traditionally classified into the "amassment and accumulation". Emerging perspectives define the core pathogenesis of pancreatic cancer as "dampness-heat" and the respective treatment "clearing heat and resolving dampness" has been demonstrated to prolong survival in pancreatic cancer patients, as has been observed in many other cancers. This clinical advantage encourages an exploration of the essence of dampness-heat ZHENG(DHZ) in cancer and investigation into underlying mechanisms of action of herbal formulations against dampness-heat. However, at present, there is a lack of understanding of the molecular characteristics of DHZ in cancer and no standardized and widely accepted animal model to study this core syndrome in vivo. The shortage of animal models limits the ability to uncover the antitumor mechanisms of herbal medicines and to assess the safety profile of the natural products derived from them. This review summarizes the current research on DHZ in cancer in terms of the clinical aspects, molecular landscape, and animal models. This study aims to provide comprehensive insight that can be used for the establishment of a future standardized ZHENG-based cancer animal model.

关键词： cancer Chinese medicine syndrome ZHENG dampness-heat syndrome animal model pancreatic tumor evaluation methods

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End-to-End Paired Ambisonic-Binaural Audio Rendering

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IEEE/CAA Journal of Automatica Sinica 2024年第2期11卷 502-513页

作者： Yin Zhu Qiuqiang Kong junjie Shi Shilei Liu Xuzhou Ye ju-Chiang Wang Hongming shan junping Zhang shanghai Key Laboratory of Intelligent Information Processing School of Computer ScienceFudan UniversityShanghai 200433China Beijing ByteDance Technology Co.Ltd. Shanghai 201102China. Chinese University of Hong Kong Hong KongChina IEEE Institute of Science and Technology for Brain-Inspired Intelligence and MOE Frontiers Center for Brain Science Fudan UniversityShanghai 200433 shanghai Center for Brain Science and Brain-Inspired Technology Shanghai 200031China

Binaural rendering is of great interest to virtual reality and immersive media. Although humans can naturally use their two ears to perceive the spatial information contained in sounds, it is a challenging task for machines to achieve binaural rendering since the description of a sound field often requires multiple channels and even the metadata of the sound sources. In addition, the perceived sound varies from person to person even in the same sound field. Previous methods generally rely on individual-dependent head-related transferred function(HRTF)datasets and optimization algorithms that act on HRTFs. In practical applications, there are two major drawbacks to existing methods. The first is a high personalization cost, as traditional methods achieve personalized needs by measuring HRTFs. The second is insufficient accuracy because the optimization goal of traditional methods is to retain another part of information that is more important in perception at the cost of discarding a part of the information. Therefore, it is desirable to develop novel techniques to achieve personalization and accuracy at a low cost. To this end, we focus on the binaural rendering of ambisonic and propose 1) channel-shared encoder and channel-compared attention integrated into neural networks and 2) a loss function quantifying interaural level differences to deal with spatial information. To verify the proposed method, we collect and release the first paired ambisonic-binaural dataset and introduce three metrics to evaluate the content information and spatial information accuracy of the end-to-end methods. Extensive experimental results on the collected dataset demonstrate the superior performance of the proposed method and the shortcomings of previous methods.

关键词： Ambisonic attention binaural rendering neural network

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dECM restores macrophage immune homeostasis and alleviates iron overload to promote DTPI healing

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Regenerative Biomaterials 2024年第2期3卷 100-113页

作者： ju Zhang Ruijuan Si Yu Gao Hui shan Qi Su Zujian Feng Pingsheng Huang Deling Kong Weiwei Wang Tianjin Key Laboratory of Biomaterial Research Institute of Biomedical EngineeringChinese Academy of Medical Sciences and Peking Union Medical CollegeTianjin300192China School of Nursing Qingdao UniversityNingde RoadShinan DistrictQingdaoShandong266071China Cancer Hospital of Tianjin Medical University North Huanhu West RoadTianjinChina The Affliated Hospital of Qingdao University 16 Jjiangsu RoadShinan DistrictQingdaoChina 5NankaiUniver aniin300071.China

Due to its highly insidious and rapid progression,deep tissue pressure injury(DTPI)is a clinical *** previous study found that DTPI may be a skeletal muscle injury dominated by macrophage immune dysfunction due to excessive iron *** extracellular matrix(dECM)hydrogel promotes skeletal muscle injury ***,its role in po-larizing macrophages and regulating iron metabolism in DTPI remains ***,porcine dECM hydrogel was prepared,and its therapeutic function and mechanism in repairing DTPI were *** stimulus of dECM hydrogel toward RAW264.7 cells resulted in a significantly higher percentage of CD2o6+macrophages and notably decreased intracellular divalent iron *** mice DTPI model,dECM hydrogel treatment promoted M1 to M2 macrophage conversion,improved iron metabolism and reduced oxidative stress in the early stage of *** the remodeling phase,the dECM hydrogel remarkably enhanced revascularization and accelerated skeletal muscle ***,the immunomodulation of dEcM hydrogels in vivo was mainly involved in the P13k/Akt signaling pathway,as revealed by GO and KEGG pathway analysis,which may ameliorate the iron deposition and promote the healing of *** findings indicate that dECM hydrogel is promising in skeletal muscle repair,inflammation resolution and tissue injury healing by effectively restoring macrophage immune homeostasis and normalizing iron metabolism.

关键词： Deep tissue pressure injury hydrogel immunomodulation tissue repair

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Circ_0004592:An auxiliary diagnostic biomarker for gastric cancer

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World Journal of Gastrointestinal Oncology 2024年第6期16卷 2757-2768页

作者： shan Kong Yan-Hua Xu Ming Zheng Shao-Qing ju Heng-Chuan Shi Department of Laboratory Medicine Jiangsu Province Official HospitalNanjing 210000Jiangsu ProvinceChina Department of Laboratory Medicine Northern Jiangsu People’s HospitalYangzhou 225000Jiangsu ProvinceChina Department of Laboratory Medicine The Affiliated Hospital of Nantong UniversityNantong 226001Jiangsu ProvinceChina

BACKGROUND Gastric cancer(GC)has a high mortality rate,and robust diagnostic biomarkers are currently ***,the clinical relevance of circular RNAs(circRNAs)as GC biomarkers remains largely *** To evaluate the potential of novel circRNA circ_0004592 in the early screening and prognosis of *** High-throughput sequencing of circRNAs was performed to screen for potential target ***_0004592 expression was examined in GC tissues,cells,and *** samples were collected from healthy subjects’patients,as well as from patients with benign lesions,precancerous lesions,and GC,whereafter the diagnostic accuracy of circ_0004592 was *** correlation between circ_0004592 levels in plasma and clinicopathological data of patients with GC was further *** Circ_0004592 was upregulated in both the tissue and plasma of patients with ***,circ_0004592 expression was higher in patients with precancerous lesions than in healthy controls while being highest in patients with *** the same patient,the postoperative plasma level of circ_0004592 was lower than that in the preoperative ***,circ_0004592 level was significantly correlated with tumor differentiation,tumor depth,and lymph node *** area under the curve(AUC)of plasma circ_0004592 exhibited high sensitivity and specificity for differentiating patients with GC from healthy *** based on circ_0004592,carcinoembryonic antigen,and cancer antigen 199 achieved a superior AUC and was highly *** Plasma circ_0004592 may represent a potential non-invasive auxiliary diagnostic biomarker for patients with GC.

关键词： Biomarker Circular RNA Diagnosis Gastric cancer Plasma

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CircZFR promotes colorectal cancer progression via stabilizing BCLAF1 and regulating the miR-3127-5p/RTKN2 axis

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Science China(Life Sciences) 2024年第9期67卷 1881-1898页

作者： Jiaxin Chen Huijuan Wang Jianbin Xu Engeng Chen Qing Meng Jiawei Wang Haoyi Xiang Wei Zhou Ge shan Zhenyu ju Zhangfa Song Department of Colorectal Surgery Sir Run Run Shaw HospitalZhejiang University School of MedicineHangzhou 310016China Key Laboratory of Biological Treatment of Zhejiang Province Hangzhou 310016China Department of Pulmonary and Critical Care Medicine Regional medical center for National Institute of Respiratory DiseaseSir Run Run Shaw HospitalZhejiang University School of MedicineHangzhou 310016China Key Laboratory of Regenerative Medicine of Ministry of Education Institute of Aging and Regenerative MedicineJinan UniversityGuangzhou 510632China Department of Breast Surgery the Second Affiliated HospitalZhejiang University School of MedicineHangzhou 310009China Department of Orthopedic Surgery the Second Affiliated HospitalZhejiang University School of MedicineHangzhou 310009China

Aberrant expression of circular RNAs(circ RNAs)is frequently linked to colorectal cancer(CRC).Here,we identified circ ZFR as a promising biomarker for CRC diagnosis and *** ZFR was upregulated in CRC tissues and serum exosomes and its level was linked to cancer incidence,advanced-stages,and *** both in vitro and in vivo settings,circ ZFR promoted the growth and spread while suppressing apoptosis of *** with circ ZFR overexpression promoted the proliferation and migration of cocultured CRC ***,epithelial splicing regulatory protein 1(ESRP1)in CRC cells may enhance the production of circ ***2-associated transcription factor 1(BCLAF1)bound to circ ZFR,which prevented its ubiquitinated ***,circ ZFR sponged mi R-3127-5p to boost rhotekin 2(RTKN2)*** TCP1-CD-QDs nanocarrier was able to carry and deliver circ ZFR si RNA(si-circ ZFR)to the vasculature of CRC tissues and cells,which inhibited the growth of tumors in patient-derived xenograft(PDX)*** together,our results show that circ ZFR is an oncogenic circ RNA,which promotes the development and spread of CRC in a BCLAF1 and mi R-3127-5p-dependent *** ZFR is a possible serum biopsy marker for the diagnosis and a desirable target for further treatment of CRC.

关键词： circZFR exosome ESRP1 BCLAF1 miR-3127-5p nanoparticle(NP)

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Outcomes of combined mitochondria and mesenchymal stem cellsderived exosome therapy in rat acute respiratory distress syndrome and sepsis

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World Journal of Stem Cells 2024年第6期16卷 690-707页

作者： Kun-Chen Lin Wen-Feng Fang jui-Ning yeh John Y Chiang Hsin-ju Chiang Pei-Lin Shao Pei-Hsun Sung Hon-Kan Yip Department of Anesthesiology Kaohsiung Chang Gung Memorial HospitalKaohsiung 83301TaiwanChina Division of Pulmonary and Critical Care Medicine Department of Internal MedicineKaohsiung Chang Gung Memorial HospitalChang Gung University College of MedicineKaohsiung 83301TaiwanChina Department of Cardiology The First Affiliated Hospital of Jinan UniversityGuangzhou 510630Guangdong ProvinceChina Department of Computer Science and Engineering National Sun Yat-sen UniversityKaohsiung 804201TaiwanChina Department of Healthcare Administration and Medical Informatics Kaohsiung Medical UniversityKaohsiung 80708TaiwanChina School of Medicine Chung Shan Medical UniversityTaichung 40201TaiwanChina Department of Nursing Asia UniversityTaichung 41354TaiwanChina Division of Cardiology Department of Internal MedicineKaohsiung Chang Gung Memorial Hospital and Chang Gung University College of MedicineKaohsiung 83301TaiwanChina Institute for Translational Research in Biomedicine Kaohsiung Chang Gung Memorial HospitalKaohsiung 83301TaiwanChina Center for Shockwave Medicine and Tissue Engineering Kaohsiung Chang Gung Memorial HospitalKaohsiung 83301TaiwanChina Department of Medical Research China Medical University HospitalChina Medical UniversityTaichung 40402TaiwanChina School of Medicine College of MedicineChang Gung UniversityTaoyuan 33302TaiwanChina

BACKGROUND The treatment of acute respiratory distress syndrome(ARDS)complicated by sepsis syndrome(SS)remains *** To investigate whether combined adipose-derived mesenchymal-stem-cells(ADMSCs)-derived exosome(EXAD)and exogenous mitochondria(mitoEx)protect the lung from ARDS complicated by *** In vitro study,including L2 cells treated with lipopolysaccharide(LPS)and in vivo study including male-adult-SD rats categorized into groups 1(sham-operated-control),2(ARDS-SS),3(ARDS-SS+EXAD),4(ARDS-SS+mitoEx),and 5(ARDS-SS+EXAD+mitoEx),were included in the present *** In vitro study showed an abundance of mitoEx found in recipient-L2 cells,resulting in significantly higher mitochondrial-cytochrome-C,adenosine triphosphate and relative mitochondrial DNA levels(Pjunctions[occluding/β-catenin/zonula occludens(ZO)-1/E-cadherin]exhibited an opposite pattern of inflam-mation(all Pjury/fibrosis area and inflammatory/DNA-damaged markers(CD68+/γ-H2AX)displayed an identical pattern of SaO2%among the groups(all P<0.0001).The pro

关键词： Acute respiratory distress syndrome Sepsis syndrome Exosomes Mitochondria Adipose tissue-derived mesenchymal stem cells Inflammation

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当代中国特色身体批评范式的形态、进路与价值

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中南民族大学学报（人文社会科学版） 2024年第2期44卷 161-171,188页

作者：龚举善李慧中南民族大学文学与新闻传播学院湖北武汉430074

当代中国特色社会历史批评视域中的身体批评,依托新中国社会主义革命、建设、改革三大社会情境,凝聚为政治身体批评、经济身体批评、审美身体批评等三种主流范式。当代中国特色身体批评范式的历史转换,总体上凸显出既合规律又合目的的... 详细信息

当代中国特色社会历史批评视域中的身体批评,依托新中国社会主义革命、建设、改革三大社会情境,凝聚为政治身体批评、经济身体批评、审美身体批评等三种主流范式。当代中国特色身体批评范式的历史转换,总体上凸显出既合规律又合目的的三大文化进路:一是从政治主位到生命主体,二是从一元规定到多维诉求,三是从平面表述到立体呈现。当代中国特色身体批评三大主流范式及其现代转进,有助于女性文学写作的叙事规范,有益于审美现代性的当代实现,有利于社会历史批评的品质优化。

关键词：当代中国特色身体批评范式形态进路价值

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《大浴女》器物叙事的范型、机制与功效

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北方民族大学学报（哲学社会科学版） 2024年第3期 150-160页

作者：刘仁丽龚举善中南民族大学文学与新闻传播学院湖北武汉430074

置身于“物转向”的当代语境之下,具有诗性气质的器物书写在文学叙事中绽放着独特的艺术光彩。作为当代文学器物叙事的典范之作,铁凝的《大浴女》通过生活型器物、身份型器物和仪式型器物的分型连类书写,显示了相应社会阶层在特定历史... 详细信息

置身于“物转向”的当代语境之下,具有诗性气质的器物书写在文学叙事中绽放着独特的艺术光彩。作为当代文学器物叙事的典范之作,铁凝的《大浴女》通过生活型器物、身份型器物和仪式型器物的分型连类书写,显示了相应社会阶层在特定历史时期个体性、亲历性的创伤记忆与情感体验。细究该作器物叙事的系统生成,外因性社会情境、内因性主体选择以及活态性文本呈现堪称三大发动机制。器物的本原性和生成性特征,使之享有调控叙事节奏、隐喻作品意旨、增显“家国同构”的艺术功效。经由器物叙事话语分析以抵达生命美学的诗意追求,对中国当代小说器物叙事的“宽窄逻辑”建构不乏启示意义。

关键词：《大浴女》器物叙事范型机制功效

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