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Machine-Learning-Assisted Design of Deep Eutectic Solvents Based on Uncovered Hydrogen Bond Patterns

Engineering 2024年第8期39卷 74-83页

作者： Usman L.Abbas Yuxuan Zhang Joseph Tapia Selim Md Jin Chen Jian Shi Qing Shao department of Chemical and Materials Engineering University of KentuckyLexingtonKY 40506USA department of Biosystems and Agricultural Engineering University of KentuckyLexingtonKY 40506USA Institute for biomedical informatics Department of Computer ScienceUniversity of KentuckyLexingtonKY 40506USA

Non-ionic deep eutectic solvents(DESs)are non-ionic designer solvents with various applications in catalysis,extraction,carbon capture,and ***,discovering new DES candidates is challenging due to a lack of efficient tools that accurately predict DES *** search for DES relies heavily on intuition or trial-and-error processes,leading to low success rates or missed *** that hydrogen bonds(HBs)play a central role in DES formation,we aim to identify HB features that distinguish DES from non-DES systems and use them to develop machine learning(ML)models to discover new DES *** first analyze the HB properties of 38 known DES and 111 known non-DES systems using their molecular dynamics(MD)simulation *** analysis reveals that DES systems have two unique features compared to non-DES systems:The DESs have①more imbalance between the numbers of the two intra-component HBs and②more and stronger inter-component *** on these results,we develop 30 ML models using ten algorithms and three types of HB-based *** model performance is first benchmarked using the average and minimal receiver operating characteristic(ROC)-area under the curve(AUC)*** also analyze the importance of individual features in the models,and the results are consistent with the simulation-based statistical ***,we validate the models using the experimental data of 34 *** extra trees forest model outperforms the other models in the validation,with an ROC-AUC of *** work illustrates the importance of HBs in DES formation and shows the potential of ML in discovering new DESs.

关键词： Machine learning Deep eutectic solvents Molecular dynamics simulations Hydrogen bond Molecular design

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An artificial intelligence diabetes management architecture based on 5G

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Digital Communications and Networks 2024年第1期10卷 75-82页

作者： Ruochen Huang Wei Feng Shan Lu Tao shan Changwei Zhang Yun Liu department of Geriatrics The First Affiliated Hospital of Nanjing Medical UniversityNanjing210096China department of Information The First Afliated Hospital of Nanjing Medical UniversityNanjing210096China department of Medical informatics School of Biomedical Engineering and InformaticsNanjing Medical UniversityNanjing211166China department of Outpatient The First Affiliated Hospital of Nanjing Medical UniversityNanjing210096China Jiangsu Key Laboratory of Wireless Communications Nanjing University of Posts and TelecommunicationsNanjing210003China

Along with the development of 5G network and Internet of Things technologies,there has been an explosion in personalized healthcare *** the 5G and Artificial Intelligence(Al)is introduced into diabetes management architecture,it can increase the efficiency of existing systems and complications of diabetes can be handled more effectively by taking advantage of *** this article,we propose a 5G-based Artificial Intelligence Diabetes Management architecture(AIDM),which can help physicians and patients to manage both acute complications and chronic *** AIDM contains five layers:the sensing layer,the transmission layer,the storage layer,the computing layer,and the application *** build a test bed for the transmission and application ***,we apply a delay-aware RA optimization based on a double-queue model to improve access efficiency in smart hospital wards in the transmission *** application layer,we build a prediction model using a deep forest *** on real-world data show that our AIDM can enhance the efficiency of diabetes management and improve the screening rate of diabetes as well.

关键词： Diabetes 5G Artificial intelligence Deep forest Smart hospital ward

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Reconstructing cell lineage trees with genomic barcoding:approaches and applications

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Journal of genetics and Genomics 2024年第1期51卷 35-47页

作者： Zizhang Li Wenjing Yang Peng Wu Yuyan Shan Xiaoyu Zhang Feng Chen Junnan Yang Jian-Rong Yang Advanced Medical Technology Center The First Affiliated HospitalZhongshan School of MedicineSun Yat-sen UniversityGuangzhouGuangdong 510080China department of genetics and biomedical informatics Zhongshan School of MedicineSun Yat-sen UniversityGuangzhouGuangdong 510080China Key Laboratory of Tropical Disease Control Ministry of EducationSun Yat-sen UniversityGuangzhouGuangdong 510080China

In multicellular organisms,developmental history of cell divisions and functional annotation of terminal cells can be organized into a cell lineage tree(CLT).The reconstruction of the CLT has long been a major goal in developmental biology and other related *** technological advancements,especially those in editable genomic barcodes and single-cell high-throughput sequencing,have sparked a new wave of experimental methods for reconstructing *** we review the existing experimental approaches to the reconstruction of CLT,which are broadly categorized as either image-based or DNA barcode-based *** addition,we present a summary of the related literature based on the biological insight pro-vided by the obtained ***,we discuss the challenges that will arise as more and better CLT data become available in the near *** barcoding-based CLT reconstructions and analyses,due to their wide applicability and high scalability,offer the potential for novel biological discoveries,especially those related to general and systemic properties of the developmental process.

关键词： Cell lineage tree Developmental regulation Biotechnology Computational biology

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Isolation and culture of human primary osteoblasts:Comparing the effects of differences in method details on osteoblast characteristics

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Genes & Diseases 2024年第2期11卷 546-549页

作者： Fei Chen Yan Zhang Pai Peng Xiao-Ting Huang Zi-Han Qiu Bao-Cheng Liu Tie-Lin Yang Bo Yang Yan Guo Key Laboratory of biomedical Information Engineering of Ministry of Education Biomedical Informatics & Genomics CenterSchool of Life Science and TechnologyXi'an Jiaotong UniversityXi'anShaanxi 710049China department of Orthopaedics Shannxi Provincial People's Hospital (The Third Affiliated Hospital of Xi'an Jiaotong University)Xi'anShaanxi 710068China

Osteoblasts are essential in the maintenance of human bone homeostasis.1 The abnormal formation and impaired differentiation ability of osteoblasts are pivotal factors leading to bone-related diseases,suggesting that an indepth study of osteoblasts can provide novel treatment strategies for these diseases.2 Human primary osteoblasts are precious experimental models in bone-related research.3 However,the isolation and culture of human primary osteoblasts still have some difficulties and ***,we refined a method to isolate and culture human primary osteoblasts by taking cancellous bone through a bone tissue sampler and pre-digesting it with pancreatin,which makes the process easier,cheaper,and more ***,we compared the effects of the subtle changes in isolation and culture methods on the phenotype of human primary osteoblasts and examined the differences in morphology,proliferation,and differentiation between micro-explants cultured osteoblasts(MECOBs)and explants cultured osteoblasts(EC-OBs).

关键词： impaired culture details

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Ferroptosis mediators vary in metabolic syndrome,type-2 diabetes,and hypercholesterolemia:A meta-analysis report

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Genes & Diseases 2024年第3期11卷 109-112页

作者： Indra Kundu Ashlesha Pande Tannishtha Das Susan Idicula-Thomas biomedical informatics Centre Indian Council of Medical Research-National Institute for Research in Reproductive and Child HealthMumbaiMaharashtra 400012India department of Biotechnology St.Xavier's CollegeKolkataWest Bengal 700016India

Metabolic syndrome(MetS)is a complex disorder characterized by the coexistence of phenotypes such as obesity,hypertension,hyperglycemia,high triglyceride level,and low level of high-density lipoprotein *** majorly dri... 详细信息

关键词： obesity cholesterol diabetes

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Exploring unconventional attributes of red blood cells and their potential applications in biomedicine

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Protein & Cell 2024年第5期15卷 315-330页

作者： Alkmini T.Anastasiadi Vasiliki-Zoi Arvaniti Krystalyn E.Hudson Anastasios G.Kriebardis Constantinos Stathopoulos Angelo D’Alessandro Steven L.Spitalnik Vassilis L.Tzounakas department of Biochemistry School of MedicineUniversity of Patras26504 PatrasGreece department of Pathology and Cell Biology Columbia University Irving Medical CenterNew York CityNY 10032USA Laboratory of Reliability and Quality Control in Laboratory Hematology(HemQcR) Department of Biomedical SciencesSchool of Health&Caring SciencesUniversity of West Attica(UniWA)12243 EgaleoGreece department of Biochemistry and Molecular genetics University of Colorado Anschutz Medical Campus13001 AuroraCOUSA Present address:Institute for Fundamental biomedical Research(IFBR) Biomedical Sciences Research Center“Alexander Fleming”Vari11527 AthensGreece

We need to talk about red blood *** cells are defined as cells containing distinct nuclei and other membranous ***,red blood cells(RBCs)lack a nucleus and organelles—perhaps to limit the generation of reactive oxygen species(Zhang et al.,2011)—and are filled with hemoglobin(Hb).This oxygen carrier is limited to the cytosol by the cell membrane and cytoskeleton,which maintain cellular integrity and deformability as RBCs pass through narrow capillaries(Gratzer,1994)to perform their primary function of gas exchange.

关键词： membranous maintain

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Validity of fatty liver prediction scores for diagnosis of fatty liver by Fibroscan

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Hepatobiliary & Pancreatic Diseases International 2024年第4期23卷 353-360页

作者： Seogsong Jeong Sun Jae Park Seong Kyun Na Sang Min Park Byung-Cheol Song Yun Hwan Oh department of biomedical Sciences Seoul National University Graduate SchoolSeoul 03080Korea department of biomedical informatics CHA University School of MedicineCHA UniversitySeongnam 13488Korea department of Internal Medicine Inje University College of MedicineSeoul 50834Korea department of Family Medicine Seoul National University HospitalSeoul National University College of MedicineSeoul 03080Korea department of Internal Medicine Jeju National University HospitalJeju National University College of MedicineJeju 63241Korea department of Family Medicine Jeju National University HospitalJeju National University College of MedicineJeju 63241Korea department of Family Medicine Chung-Ang University Gwangmyeong HospitalChung-Ang University College of MedicineGwangmyeong 14353Korea

Background:The Korea National Health and Nutrition Examination Survey nonalcoholic fatty liver disease(K-NAFLD)score was recently developed with the intent to operationally define nonalcoholic fatty liver disease(NAFLD).However,there remained an external validation that confirmed its diagnostic performance,especially in patients with alcohol consumption or hepatitis virus ***:Diagnostic accuracy of the K-NAFLD score was evaluated in a hospital-based cohort consisting of 1388 participants who received Fibroscan®.Multivariate-adjusted logistic regression models and the contrast estimation of receiver operating characteristic curves were used for validation of the K-NAFLD score,fatty liver index(FLI),and hepatic steatosis index(HSI).Results:K-NAFLD-moderate[adjusted odds ratio(aOR)=2.53,95%confidence interval(CI):1.13-5.65]and K-NAFLD-high(aOR=4.14,95%CI:1.69-10.13)groups showed higher risks of fatty liver compared to the K-NAFLD-low group after adjustments for demographic and clinical characteristics,and FLI-moderate and FLI-high groups revealed aORs of 2.05(95%CI:1.22-3.43)and 1.51(95%CI:0.78-2.90),*** addition,the HSI was less predictive for Fibroscan®-defined fatty *** K-NAFLD and FLI also demonstrated high accuracy in the prediction of fatty liver in patients with alcohol consumption and chronic hepatitis virus infection,and the adjusted area under curve values were comparable between K-NAFLD and ***:Externally validation of the K-NAFLD and FLI showed that these scores may be a useful,noninvasive,and non-imaging modality for the identification of fatty *** addition,these scores also predicted fatty liver in patients with alcohol consumption and chronic hepatitis virus infection.

关键词： Nonalcoholic fatty liver disease Fatty liver index Hepatic steatosis index

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Bioinformatic approaches of liquid–liquid phase separation in human disease

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中华医学杂志(英文版) 2024年第16期137卷 1912-1925页

作者： Sun Jun Chen Yilong Bi Ruiye Yuan Yong Yu Haopeng department of Thoracic Surgery and West China biomedical Big Data Center West China Hospital Sichuan University Chengdu Sichuan China Med-X Center for informatics Sichuan University Chengdu Sichuan China department of Orthognathic and TMJ Surgery State Key Laboratory of Oral Diseases National Clinical Research Center for Oral Diseases West China Hospital of Stomatology Sichuan University Chengdu Sichuan China

Biomolecular aggregation within cellular environments via liquid–liquid phase separation (LLPS) spontaneously forms droplet-like structures, which play pivotal roles in diverse biological processes. These structures are closely associated with a range of diseases, including neurodegenerative disorders, cancer and infectious diseases, highlighting the significance of understanding LLPS mechanisms for elucidating disease pathogenesis, and exploring potential therapeutic interventions. In this review, we delineate recent advancements in LLPS research, emphasizing its pathological relevance, therapeutic considerations, and the pivotal role of bioinformatic tools and databases in facilitating LLPS investigations. Additionally, we undertook a comprehensive analysis of bioinformatic resources dedicated to LLPS research in order to elucidate their functionality and applicability. By providing comprehensive insights into current LLPS-related bioinformatics resources, this review highlights its implications for human health and disease.

关键词： Phase separation Liquid–liquid phase separation Disease Phase separation databases Bioinformatic tools

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SCFD1 in amyotrophic lateral sclerosis: reconciling a genetic association with in vivo functional analysis

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Neural Regeneration Research 2024年第6期19卷 1201-1202页

作者： Ruben J.Cauchi Centre for Molecular Medicine and Biobanking Biomedical Sciences BuildingDepartment of Physiology and Biochemistry Faculty of Medicine and Surgery University of Malta

Amyotrophic lateral sclerosis(ALS) is a neurodegenerative disease characterized by progressive loss of upper and lower motor neurons,resulting in muscle weakness and spasticity,eventually leading to death due to respiratory *** by our group of a casecontrol cohort from an isolated island population have found that genetics plays a significant role in disease etiology(Farrugia Wismayer et al.,2023).

关键词： PROTEIN SLY1

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High-yield and rapid isolation of extracellular vesicles by flocculation via orbital acoustic trapping:FLOAT

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Microsystems & Nanoengineering 2024年第1期10卷 313-323页

作者： Joseph Rufo Peiran Zhang Zeyu Wang Yuyang Gu Kaichun Yang Joseph Rich Chuyi Chen Ruoyu Zhong Ke Jin Ye He Jianping Xia Ke Li Jiarong Wu Yingshi Ouyang Yoel Sadovsky Luke P.Lee Tony Jun Huang department of Mechanical Engineering and Materials Science Duke UniversityDurhamNCUSA department of biomedical Engineering Duke UniversityDurhamNCUSA department of Obstetrics Gynecologyand Reproductive SciencesMagee-Womens Research InstituteUniversity of PittsburghPittsburghPAUSA department of Microbiology and Molecular genetics School of MedicineUniversity of PittsburghPittsburghPAUSA Renal Division and Division of Engineering in Medicine Department of MedicineBrigham and Women’s HospitalHarvard Medical SchoolBostonMAUSA department of Bioengineering Department of Electrical Engineering and Computer ScienceUniversity of CaliforniaBerkeleyBerkeleyCAUSA department of Biophysics Institute of Quantum BiophysicsSungkyunkwan UniversitySuwonKorea

Extracellular vesicles(EVs)have been identified as promising biomarkers for the noninvasive diagnosis of various ***,challenges in separating EVs from soluble proteins have resulted in variable EV recovery rates and low ***,we report a high-yield(>90%)and rapid(<10 min)EV isolation method called FLocculation via Orbital Acoustic Trapping(FLOAT).The FLOAT approach utilizes an acoustofluidic droplet centrifuge to rotate and controllably heat liquid *** adding a thermoresponsive polymer flocculant,nanoparticles as small as 20 nm can be rapidly and selectively concentrated at the center of the *** demonstrate the ability of FLOAT to separate urinary EVs from the highly abundant Tamm-Horsfall protein,addressing a significant obstacle in the development of EV-based liquid *** to its high-yield nature,FLOAT reduces biofluid starting volume requirements by a factor of 100(from 20 mL to 200µL),demonstrating its promising potential in point-of-care diagnostics.

关键词： trapping utilize separating

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