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Single-cell omics: experimental workflow, data analyses and applications

Science China Life sciences 2025年第1期68卷 5-102页

作者： Fengying Sun Haoyan Li Dongqing Sun Shaliu Fu Lei Gu Xin Shao Qinqin Wang Xin Dong Bin Duan Feiyang Xing Jun Wu Minmin Xiao Fangqing Zhao Jing-Dong J.Han Qi Liu Xiaohui Fan Chen Li Chenfei Wang Tieliu Shi Department of Clinical Laboratory the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City) Pharmaceutical Informatics Institute College of Pharmaceutical SciencesZhejiang University Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University) Ministry of EducationOrthopaedic DepartmentTongji HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Frontier Science Center for Stem Cells School of Life Sciences and TechnologyTongji University Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine Shanghai East HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Research Institute of Intelligent Computing Zhejiang Lab Shanghai Research Institute for Intelligent Autonomous Systems Center for Single-cell Omics School of Public HealthShanghai Jiao Tong University School of Medicine National Key Laboratory of Chinese Medicine Modernization Innovation Center of Yangtze River DeltaZhejiang University Center for Bioinformatics and Computational Biology Shanghai Key Laboratory of Regulatory Biologythe Institute of Biomedical Sciences and School of Life SciencesEast China Normal University Beijing Institutes of Life Science Chinese Academy of Sciences Peking-Tsinghua Center for Life sciences Academy for Advanced Interdisciplinary StudiesCenter for Quantitative Biology (CQB)Peking University Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases Women's HospitalZhejiang University School of Medicine Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE School of StatisticsEast China Normal University

Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular features. Our exploration of how the genomes orchestrate the formation and maintenance of each cell, and control the cellular phenotypes of various organismsis, is both captivating and intricate. Since the inception of the first single-cell RNA technology, technologies related to single-cell sequencing have experienced rapid advancements in recent years. These technologies have expanded horizontally to include single-cell genome, epigenome,proteome, and metabolome, while vertically, they have progressed to integrate multiple omics data and incorporate additional information such as spatial sc RNA-seq and CRISPR screening. Single-cell omics represent a groundbreaking advancement in the biomedical field,offering profound insights into the understanding of complex diseases, including cancers. Here, we comprehensively summarize recent advances in single-cell omics technologies, with a specific focus on the methodology section. This overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.

关键词： single-cell sequencing genome epigenome proteomics metabolomics multimodal spatial transcriptomics CRISPR screening

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Exposure to air pollutants in Vietnam:Assessing potential risk for tourists

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Journal of Environmental sciences 2018年第11期30卷 147-154页

作者： Pallavi Pant Whitney Huynh Richard E.Peltier Department of Environmental health sciences School of Public Health and Health SciencesUniversity of Massachusetts

Tourism can form an important component of a nation＇s GDP, and Vietnam is among the most visited countries in Southeast Asia. Most studies on personal exposure focus on the general population, or occupational cohorts with exposure to specific pollutants. However, short-term exposure to air pollutants while visiting regions with high levels of air pollution can lead to acute health effects. A personal exposure study was conducted across three cities in Vietnam to estimate exposure to particulate matter （PM2.5） and black carbon for tourists. Measurements were conducted during the wet season in 2014 in Ho Chi Minh City, Da Lat and Nha Trang using portable instrumentation. Average 24-hr PM2.5 and BC exposures were estimated as 18.9 ± 9.24 and 3.41 ± 1.33 μg/m3 and among the three cities, Ho Chi Minh was found to have the highest PM2.5 concentrations. Environmental tobacco smoke, commuting and street food stands were found to contribute to highest levels of exposure to PM2.s and BC across all cities.

关键词： Vietnam PM2.5 BC Exposure ETS Commute

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A Novel Self-Supervised Learning Network for Binocular Disparity Estimation

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Computer Modeling in Engineering & sciences 2025年第1期142卷 209-229页

作者： Jiawei Tian Yu Zhou Xiaobing Chen Salman A.AlQahtani Hongrong Chen Bo Yang Siyu Lu Wenfeng Zheng Department of Computer Science and Engineering Major in Bio Artificial IntelligenceHanyang UniversityAnsan-si15577Republic of Korea school of Electrical and Computer Engineering Louisiana State UniversityBaton RougeLA 70803USA Department of Computer Engineering College of Computer and Information SciencesKing Saud UniversityRiyadh11574Saudi Arabia school of Automation University of Electronic Science and Technology of ChinaChengdu610054China

Two-dimensional endoscopic images are susceptible to interferences such as specular reflections and monotonous texture illumination,hindering accurate three-dimensional lesion reconstruction by surgical *** study proposes a novel end-to-end disparity estimation model to address these *** approach combines a Pseudo-Siamese neural network architecture with pyramid dilated convolutions,integrating multi-scale image information to enhance robustness against lighting *** study introduces a Pseudo-Siamese structure-based disparity regression model that simplifies left-right image comparison,improving accuracy and *** model was evaluated using a dataset of stereo endoscopic videos captured by the Da Vinci surgical robot,comprising simulated silicone heart sequences and real heart video *** results demonstrate significant improvement in the network’s resistance to lighting interference without substantially increasing ***,the model exhibited faster convergence during training,contributing to overall performance *** study advances endoscopic image processing accuracy and has potential implications for surgical robot applications in complex environments.

关键词： Parallax estimation parallax regression model self-supervised learning Pseudo-Siamese neural network pyramid dilated convolution binocular disparity estimation

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Visualizing traumatic brain injury:ocular clues for diagnosis and assessment

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Neural Regeneration Research 2025年第5期20卷 1399-1400页

作者： Morteza Abyadeh Vivek Gupta Yuyi You Joao A.Paulo Mehdi Mirzaei ProGene Technologies Pty Ltd SydneyNSWAustralia Department of Clinical Medicine Faculty of MedicineHealth and Human SciencesMacquarie Medical SchoolMacquarie UniversityMacquarie ParkNorth RydeSydneyNSWAustralia Department of Cell Biology Harvard Medical SchoolBostonMAUSA

Traumatic brain injury (TBI) is defined as damage to the brain resulting from an external sudden physical force or shock to the *** is considered a silent public health epidemic causing significant death and disability *** were 64,000 TBI related deaths reported in the USA in 2020,with about US$76 billion in direct and indirect medical costs annually.

关键词： diagnosis ocular injury

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In vitro evaluation of inorganic and methyl mercury mediated cytotoxic effect on neural cells derived from different animal species

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Journal of Environmental sciences 2016年第3期28卷 138-145页

作者： Jing Tong Youwei Wang Yuanan Lu Institute of TCM & Natural Products School of Pharmaceutical SciencesWuhan University Department of public health sciences University of Hawaii at Manoa Global health Center School of Public HealthWuhan University

To extend the current understanding of the mercury-mediated cytotoxic effect,five neural cell lines established from different animal species were comparatively analyzed using three different endpoint bioassays：thiazolyl blue tetrazolium bromide,3-（4,5-dimethylthiazol-2-yl）-2,5-diphenyl tetrazolium bromide assay（MTT）,neutral red uptake assay（NRU）,and Coomassie blue assay（CB）.Following a 24-hr exposure to selected concentrations of mercury chloride（HgCl_2） and methylmercury（Ⅱ） chloride（MeHgCl）,the cytotoxic effect on test cells was characterized by comparing their 50%inhibition concentration（IC_（50）） *** results indicated that both these forms of mercury were toxic to all the neural cells,but at very different *** IC_（50）values of MeHgCl among these cell lines ranged from 1.15±0.22 to 10.31 ± 0.70 μmol/L while the IC_（50） values for HgCl_2 were much higher,ranging from 6.44 ± 0.36 to 160.97±19.63 μmol/L,indicating the more toxic nature of *** IC_（50） ratio between HgCl_2and MeHgCl ranged from 1.75 to 96.0,which confirms that organic mercury is much more toxic to these neural cells than inorganic *** these cell lines,HGST-BR and TriG44 derived from marine sea turtles showed a significantly high tolerance to HgCl_2 as compared to the three mammalian neural *** these neural cells,SK-N-SH represented the most sensitive cells to both chemical forms of mercury.

关键词： In vitro cytotoxicity Neural cell lines HgCl_2 MeHgCl

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Magnetic resonance imaging evaluation and nuclear receptor binding SET domain protein 1 mutation in the Sotos syndrome with attention-deficit/hyperactivity disorder

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World Journal of Clinical Cases 2025年第2期13卷 5-9页

作者： Wei Zhu Shanghai XiRong information Science and Technology Co. LtdNational Science and Technology ParkSchool of Life Sciences and TechnologyTongji UniversityShanghai 200092China

Sotos syndrome is characterized by overgrowth features and is caused by alterations in the nuclear receptor binding SET domain protein 1 ***/hyperactivity disorder(ADHD)is considered a neurodevelopment and psychiatric disorder in *** characteristics and clinical presentation could play an important role in the diagnosis of Sotos syndrome and *** resonance imaging(MRI)has been used to assess medical images in Sotos syndrome and *** images process is considered to display in MRI while wavelet fusion has been used to integrate distinct images for achieving more complete information in single image in this *** the future,genetic mechanisms and artificial intelligence related to medical images could be used in the clinical diagnosis of Sotos syndrome and ADHD.

关键词： Sotos syndrome Attention-deficit/hyperactivity disorder Genetic mutation Magnetic resonance imaging Wavelet fusion

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Prevalence and Early Signs of Autism Spectrum Disorder(ASD) among 18-36 Month Old Children in Tianjin of China

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Biomedical and Environmental sciences 2014年第6期27卷 453-461页

作者： HUANG Jun Ping CUI Shan Shan HAN Yu IRVA Hertz-Picciotto QI Li Hong ZHANG Xin school of public health Tianjin Medical University Department of public health sciences University of California Davis

Objective The aim of this study is to estimate the prevalence of autism spectrum disorder （ASD） among 18-36 month old children in the Tianjin Municipality of China, and to identify early signs of autistic children and the predictability of each individual symptom. Methods A total of 8 000 children were screened to do a questionnaire based on CHAT modified to include more early signs of autism at the age of 28-36 months. Then the at-risk children were reexamined 1.5 years later and ASD children were identified based on DSM-IV. Early signs of autism were analyzed retrospectively by using discriminant function analysis performed among ASD children, children not followed up and children followed up but failing to meet ASD criteria. Results Three hundred and sixty seven children were screened as being at-risk to ASD, and 22 of them were identified as having ASD in the subsequent diagnosis. The prevalence of ASD was 27.5 per 10 000 in Tianjin of China with a male to female ratio of 4：1. Items addressing social interactions and communications had higher predictability than other items to distinguish autistic children from non-autistic ones. Pretend play, functional play, showing and reading parents＇ facial expressions distinguished autistic children from those not followed up, nevertheless those followed up but failing to meet ASD criteria were not included.Conclusion The prevalence of ASD found in our study was lower than that reported in some studies by western researchers. Autism has its specific symptoms, such as deficits in social awareness, social relatedness, and social referencing.

关键词： Autism spectrum disorder Prevalence Early signs Discriminant function analysis

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Polychlorinated biphenyls and omega-3 fatty acid exposure from fish consumption,and thyroid cancer among New York anglers

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Journal of Environmental sciences 2016年第3期28卷 270-277页

作者： Alyson Haslam Sara Wagner Robb Matthew R.Bonner William Lindblad Joey Allegra Ye Shen John E.Vena Department of Epidemiology and Biostatistics College of Public HealthUniversity of Georgia Department of Epidemiology and Environmental health School of Public Health and Health ProfessionsUniversity of Buffalo Department of public health sciences School of MedicineMedical University of South Carolina

Fish from the Great Lakes contain polychlorinated biphenyls（PCBs）which have been shown to disrupt endocrine function and mimic thyroid hormones,but they also contain beneficial omega-3 fatty acids that may offer protection against endocrine *** purpose of this study was to examine the effects of Lake Ontario fish consumption and the estimated consumption of PCBs and omega-3 fatty acids on the risk of thyroid cancer in a group of sport *** from the New York State Angler Cohort Study were followed for cancer incidence from 1991–***-seven cases of incident thyroid cancer and 108 controls were included in the *** estimated fish consumption,estimated omega-3 fatty acid consumption,and estimated PCB consumption from Lake Ontario fish were examined for an association with the incidence of thyroid cancer,while matching on sex,and controlling for age and smoking *** from logistic regression indicate no significant associations between fish consumption,short-term estimated omega-3 fatty acids,or estimated PCB consumption from Great Lakes fish and the development of thyroid cancer,but it was suggested that long-term omega-3 fatty acid from Great Lakes fish may be protective of the development of thyroid *** conclusion,fish consumption,with the possible concomitant PCBs,from the Great Lakes does not appear to increase the risk of thyroid cancer in New York *** research is needed in order to separate the individual health effects of PCBs from omega-3 fatty acids contained within the fish.

关键词： Polychlorinated biphenyls Omega-3 fatty acids Thyroid cancer Lake Ontario Fish consumption

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Anti-nitric oxide production, anti-proliferation and antioxidant effects of the aqueous extract from Tithonia diversifolia

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Asian Pacific Journal of Tropical Biomedicine 2016年第11期6卷 950-956页

作者： Poonsit Hiransai Jitbanjong Tangpong Chuthamat Kumbuar Namon Hoonheang Onrunee Rodpech Padchara Sangsuk Urairat Kajklangdon Waraphorn Inkaow Molecular Medicine and Cancer Biology Research Unit School of Allied Health Sciences and Public Health Walailak University Department of Medical Technology School of Allied Health Sciences and Public Health Walailak University Biomedical sciences Research Unit School of Allied Health Sciences and Public Health Walailak University

Objective: To determine the cytotoxicity, reduction in nitric oxide production and antioxidative activity of the aqueous leaf extract from Tithonia diversifolia(T. diversifolia) in an in vitro ***: Leaves of T. diversifolia were collected from natural habitats and extracted with distilled water using the decoction method. The cytotoxic effect of the extract in terms of cell viability was determined using RAW264.7 cells and human peripheral blood mononuclear cells(PBMCs) via the mitochondrial respiration method using the MTT reagent. The effect of the extract on lipopolysaccharide(LPS)-induced nitric oxide production in RAW264.7 cells was measured using the Griess reagent. The chemical antioxidant was evaluated by ABTS- and DPPH-radical scavenging ***: The half-maximal cytotoxic concentration values were 145.87 mg/m L and73.67 mg/m L for human PBMCs and RAW264.7 cells, respectively. In the presence of phytohemagglutinin-M, the IC_(50) on PBMCs proliferation was 4.42 mg/m L. The noncytotoxic range of the extracts inhibited LPS-induced nitrite production in RAW264.7 cells with an IC_(50) value of 11.63 mg/m L. To determine the anti-oxidative properties, the N-acetyl cysteine equivalent antioxidant capacity of the extract was(32.62 ± 1.87) and(20.99 ± 2.79)mg N-acetyl cysteine/g extract, respectively determined by the ABTS-radical and DPPHradical assay. However, the extract did not confer death protection in a hydrogen peroxideinduced RAW264.7 co-culturing ***: Our study demonstrated the immunomodulation caused by the aqueous leaf extract of T. diversifolia, resulting from the inhibition of phytohemagglutinin-Minduced PBMCs proliferation and LPS-induced nitric oxide production in RAW264.7macrophages. Although the anti-oxidative activity was presented in the chemical-based anti-oxidant assay, the extract cannot protect cell death from stress conditions.

关键词： Tithonia diversifolia Anti-nitric oxide production Anti-proliferation Antioxidant

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Effects of Omethoate on Liver Insulin Signaling in Mice

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Biomedical and Environmental sciences 2018年第8期31卷 627-631页

作者： WANG Yuan LI Yu Ling MENG Fan Zhu HOU Bao Lian ZHUANG Chuan Ning XIONG Shu Han REN Shu Ping Department of Occupational and Environmental health School of Public Health Jilin University Department of information Retrieval School of Public Health Jilin University

According to the report of the International Diabetes Federation, there were 382 million people affected with diabetes in 2013 and it is expected that this number will increase to 592 million by the year 2035;. Diabet... 详细信息

关键词： Akt PI Effects of Omethoate on Liver Insulin Signaling in Mice PGC IRS

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