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  1. Article ; Online: Development of CRISPR/Cas Delivery Systems for In Vivo Precision Genome Editing.

    Chen, Yuxuan / Ping, Yuan

    Accounts of chemical research

    2023  Volume 56, Issue 16, Page(s) 2185–2196

    Abstract: ConspectusClustered, regularly interspaced, short palindromic repeat (CRISPR)/associated protein 9 (CRISPR/Cas9) is emerging as a powerful genome-editing tool, enabling precise and targeted modifications of virtually any genomic sequence in living cells. ...

    Abstract ConspectusClustered, regularly interspaced, short palindromic repeat (CRISPR)/associated protein 9 (CRISPR/Cas9) is emerging as a powerful genome-editing tool, enabling precise and targeted modifications of virtually any genomic sequence in living cells. These technologies have potential therapeutic applications for cancers, metabolic diseases, and genetic disorders. However, several major challenges hinder the full realization of their potential. Specifically, CRISPR-Cas9 gene editors, whether delivered as plasmid DNA, mRNA/sgRNA, or ribonucleoprotein (RNP), exhibit poor membrane permeability, restricting their access to the intracellular genome, where the editing occurs. Additionally, these editors lack tissue or organ specificity, raising concerns about off-target editing at the tissue level that causes unwanted genotoxicity. Though a range of delivery carriers has been developed to deliver Cas9 editors, their effectiveness is often limited by a number of barriers at both the extracellular and intracellular levels. Moreover, the prolonged activity of Cas9 increases the risk of off-target editing at the genomic level. Therefore, it is crucial to develop efficient delivery vectors, along with molecular switches to safely regulate Cas9 activity.In this Account, we summarize our recent achievements in developing different types of materials that can efficiently deliver the plasmid DNA encoding Cas9 protein and single-guide RNA (sgRNA), or Cas9 RNP into cells to highlight the design considerations of carriers for safe and efficient delivery in vitro and in vivo. After elucidating the chemical and physical factors that are responsible for encapsulating and delivering these biomacromolecules, we further elucidate how we design the biodegradable polymeric carriers using dynamic disulfide chemistry, emphasize their safe and efficient delivery features for genome-editing biomacromolecules, and also introduce the integration of the intracellular delivery of genome-editing biomacromolecules with microneedle-based transdermal delivery to promote therapeutic genome editing for inflammatory skin disorders. Finally, we review how we exploit optical, chemical, and genetic switches to control the Cas9 activity in conjunction with targeted delivery to address the spatiotemporal specificity of gene editing in vivo and demonstrate their precision therapy against cancer and colitis treatment as proof-of-concept examples. In the final part, we will summarize the progress we have made and propose the future directions that may impact the field based on our own research outcomes.
    Language English
    Publishing date 2023-08-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1483291-4
    ISSN 1520-4898 ; 0001-4842
    ISSN (online) 1520-4898
    ISSN 0001-4842
    DOI 10.1021/acs.accounts.3c00279
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: scMLC: an accurate and robust multiplex community detection method for single-cell multi-omics data.

    Chen, Yuxuan / Zheng, Ruiqing / Liu, Jin / Li, Min

    Briefings in bioinformatics

    2024  Volume 25, Issue 2

    Abstract: Clustering cells based on single-cell multi-modal sequencing technologies provides an unprecedented opportunity to create high-resolution cell atlas, reveal cellular critical states and study health and diseases. However, effectively integrating ... ...

    Abstract Clustering cells based on single-cell multi-modal sequencing technologies provides an unprecedented opportunity to create high-resolution cell atlas, reveal cellular critical states and study health and diseases. However, effectively integrating different sequencing data for cell clustering remains a challenging task. Motivated by the successful application of Louvain in scRNA-seq data, we propose a single-cell multi-modal Louvain clustering framework, called scMLC, to tackle this problem. scMLC builds multiplex single- and cross-modal cell-to-cell networks to capture modal-specific and consistent information between modalities and then adopts a robust multiplex community detection method to obtain the reliable cell clusters. In comparison with 15 state-of-the-art clustering methods on seven real datasets simultaneously measuring gene expression and chromatin accessibility, scMLC achieves better accuracy and stability in most datasets. Synthetic results also indicate that the cell-network-based integration strategy of multi-omics data is superior to other strategies in terms of generalization. Moreover, scMLC is flexible and can be extended to single-cell sequencing data with more than two modalities.
    MeSH term(s) Multiomics ; Chromatin ; Cluster Analysis ; Algorithms ; Sequence Analysis, RNA
    Chemical Substances Chromatin
    Language English
    Publishing date 2024-03-17
    Publishing country England
    Document type Journal Article
    ZDB-ID 2068142-2
    ISSN 1477-4054 ; 1467-5463
    ISSN (online) 1477-4054
    ISSN 1467-5463
    DOI 10.1093/bib/bbae101
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Systematic Constructing FeOCl/BiVO

    Chen, Yuxuan / Li, Xiaolin / Yang, Hao / Huang, Yongchao

    Small (Weinheim an der Bergstrasse, Germany)

    2024  , Page(s) e2402406

    Abstract: Bismuth vanadate ( ... ...

    Abstract Bismuth vanadate (BiVO
    Language English
    Publishing date 2024-05-08
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2168935-0
    ISSN 1613-6829 ; 1613-6810
    ISSN (online) 1613-6829
    ISSN 1613-6810
    DOI 10.1002/smll.202402406
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Simultaneous electrocoagulation and E-peroxone coupled with ultrafiltration membrane for shale gas produced water treatment.

    Kong, Fan-Xin / Chen, Yu-Xuan / Wang, Yu-Kun / Chen, Jin-Fu

    Chemosphere

    2024  Volume 355, Page(s) 141834

    Abstract: Membrane fouling caused by the organics-coated particles was the main obstacle for the highly efficient shale gas produced water (SGPW) treatment and recycling. In this study, a novel hybrid electrocoagulation (EC) and E-peroxone process coupled with UF ( ...

    Abstract Membrane fouling caused by the organics-coated particles was the main obstacle for the highly efficient shale gas produced water (SGPW) treatment and recycling. In this study, a novel hybrid electrocoagulation (EC) and E-peroxone process coupled with UF (ECP-UF) process was proposed to examine the efficacy and elucidate the mechanism for UF fouling mitigation in assisting SGPW reuse. Compared to the TMP (transmembrane pressure) increase of -15 kPa in the EC-UF process, TMP in ECP-UF system marginally increased to -1.4 kPa for 3 filtration cycles under the current density of 15 mA/cm
    MeSH term(s) Ultrafiltration ; Natural Gas ; Hydrogen Peroxide ; Membranes, Artificial ; Water Purification/methods ; Electrocoagulation
    Chemical Substances Natural Gas ; Hydrogen Peroxide (BBX060AN9V) ; Membranes, Artificial
    Language English
    Publishing date 2024-03-31
    Publishing country England
    Document type Journal Article
    ZDB-ID 120089-6
    ISSN 1879-1298 ; 0045-6535 ; 0366-7111
    ISSN (online) 1879-1298
    ISSN 0045-6535 ; 0366-7111
    DOI 10.1016/j.chemosphere.2024.141834
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: The effect of nano-silica and silica fume on the sodium carbonate-activated slag system containing air pollution control residues.

    Ling, Xuan / Schollbach, Katrin / Chen, Yuxuan / Brouwers, H J H

    Waste management (New York, N.Y.)

    2024  Volume 176, Page(s) 52–63

    Abstract: The utilization of municipal solid waste incineration residues in alkali-activated granulated ground blast furnace slag (GGBFS) has garnered substantial interest for its potential in sustainable solid waste management and achieving a low-carbon footprint. ...

    Abstract The utilization of municipal solid waste incineration residues in alkali-activated granulated ground blast furnace slag (GGBFS) has garnered substantial interest for its potential in sustainable solid waste management and achieving a low-carbon footprint. However, incorporating these residues often leads to the deterioration of mechanical properties. This study revealed the role of silica fume (SF) and nano-silica (NS) derived from olivine within a sodium carbonate-activated GGBFS system incorporating air pollution control (APC) residues. The dosage of silica additives and APC residues ranges from 0 - 6 wt% and 0-15 wt%, respectively. The mechanical properties, reaction kinetics, phase composition, microstructure and carbonation resistance of the blended binder were investigated. Results indicated that SF slightly improved the early compressive strength with the formation of C-(A)-S-H gel (Ca/Si = 1.47, Al/Si = 0.23), hemicarboaluminate and hydrotalcite; reactive NS retarded the activation of GGBFS and inhibited the formation of hemicarboaluminate and hydrotalcite, while promoting the formation of C-A-S-H gel (Ca/Si = 1.01, Al/Si = 0.23), resulting in an impressive 80.3 % enhancement in compressive strength. Notably, NS-modified samples exhibited decreased carbonation resistance due to increased porosity and C-(A)-S-H gels that are vulnerable to carbonation. Conversely, 2 % SF addition decreased the diffusion rate of CO
    MeSH term(s) Silicon Dioxide ; Aluminum Hydroxide ; Air Pollution ; Carbonates ; Magnesium Hydroxide
    Chemical Substances hydrotalcite (17432CG1KU) ; sodium carbonate (45P3261C7T) ; Silicon Dioxide (7631-86-9) ; Aluminum Hydroxide (5QB0T2IUN0) ; Carbonates ; Magnesium Hydroxide (NBZ3QY004S)
    Language English
    Publishing date 2024-01-22
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2001471-5
    ISSN 1879-2456 ; 0956-053X
    ISSN (online) 1879-2456
    ISSN 0956-053X
    DOI 10.1016/j.wasman.2024.01.028
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Association between ondansetron use and mortality of patients on mechanical ventilation in the intensive care unit: a retrospective cohort study.

    Tao, Lili / Chen, Yuxuan / Chang, Ping / An, Shengli

    Annals of translational medicine

    2023  Volume 11, Issue 2, Page(s) 43

    Abstract: Background: Basic studies show that selective 5-hydroxytryptamine type 3 (5-HT: Methods: The Medical Information Mart for Intensive Care-IV (MIMIC-IV) database was reviewed to identify patients on mechanical ventilation (aged >16 years) in the ICU, ... ...

    Abstract Background: Basic studies show that selective 5-hydroxytryptamine type 3 (5-HT
    Methods: The Medical Information Mart for Intensive Care-IV (MIMIC-IV) database was reviewed to identify patients on mechanical ventilation (aged >16 years) in the ICU, which was divided into two groups according to whether ondansetron is used. Demographic characteristics, medical history data, clinical parameters, diagnosis and treatment measures were included as covariates. Ondansetron use was defined as any kind of ondansetron administration regardless of the dose before the induction of mechanical ventilation. The primary outcome was in-hospital death. Hazard ratios (HRs) with 95% confidence intervals (CIs) were calculated by multivariable Cox regression. Propensity score matching (PSM) and inverse probability of treatment weighting (IPTW) were performed to further adjust for confounding factors. Kaplan-Meier (KM) curves with log-rank test were also performed.
    Results: A total of 18,566 patients on mechanical ventilation were included (5,735 with ondansetron use). The overall in-hospital mortality rate of patients on mechanical ventilation was 18.9% (3,512/18,566). Approximately 13.0% (746/5,735) and 21.6% (2,766/12,831) in-hospital mortality rates occurred in the ondansetron and non-ondansetron use groups, respectively. Multivariable regression indicated that ondansetron usage was associated with a 33% and 32% lower risk of in-hospital and 60-day death (HR =0.77, 95% CI: 0.70-0.85, P<0.001; HR =0.68, 95% CI: 0.62-0.75, P<0.001) in the whole sample. Multivariable regression post-PSM indicated that ondansetron usage was associated with a 38% and 31% lower risk of in-hospital and 60-day death (HR =0.62, 95% CI: 0.56-0.68, P<0.001; HR =0.69, 95% CI: 0.62-0.77, P<0.001). Log-rank test for the KM curve of ondansetron and 60-day death was statistically significant (P<0.001). The duration of ventilator use pre- and post-PSM was statistically different (P<0.001 and P=0.007) in the two groups.
    Conclusions: Ondansetron usage was significantly associated with a lower mortality risk of ventilated patients in the ICU. The 5-HT3 receptor antagonist use is may be new potential adjunctive therapeutic strategy for patients on mechanical ventilation in the ICU.
    Language English
    Publishing date 2023-01-12
    Publishing country China
    Document type Journal Article
    ZDB-ID 2893931-1
    ISSN 2305-5847 ; 2305-5839
    ISSN (online) 2305-5847
    ISSN 2305-5839
    DOI 10.21037/atm-22-6256
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: A framework for sample size calculations in longitudinal surveys to measure net and gross changes.

    Elkasabi, Mahmoud / Suzer-Gurtekin, Z Tuba / Chen, Yuxuan

    PloS one

    2023  Volume 18, Issue 9, Page(s) e0291449

    Abstract: In longitudinal surveys, repeated measurements are collected from the same sample units over time to measure gross change (i.e., change at the level of individual sample members). Longitudinal samples are sometimes supplemented by fresh sample to measure ...

    Abstract In longitudinal surveys, repeated measurements are collected from the same sample units over time to measure gross change (i.e., change at the level of individual sample members). Longitudinal samples are sometimes supplemented by fresh sample to measure net change (i.e., change at the aggregate level). That is, in each measurement wave, while one part of the sample is newly recruited (fresh), another part overlaps with previously interviewed sample (repeated interviews). Many aspects of survey design of longitudinal surveys have been studied extensively, such as definition of target population, sample design, survey weighting, intervals between interviews, nonresponse, and panel attrition. Although the impact of the overlap between samples on the statistical power has been studied, sample size determination lacks a formulation that takes account of these factors in longitudinal surveys that aim to measure net and gross changes simultaneously. In this study, we propose a framework for sample size calculation to measure net and gross changes in estimated means or proportions concurrently in longitudinal surveys. We present a framework to compute panel and fresh sample sizes for varying levels of net and gross change. Finally, we illustrate the framework using nchange, an R package we developed to execute the algorithm of the proposed framework. The framework and the R package will support researchers to determine sample sizes targeting specific power of analysis with respect to measuring net and gross changes in rotating- or split-panel surveys.
    MeSH term(s) Humans ; Sample Size ; Algorithms ; Dietary Supplements ; Research Personnel ; Longitudinal Studies
    Language English
    Publishing date 2023-09-21
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0291449
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  8. Article ; Online: Pyroptosis-related lncRNA prognostic signatures for cutaneous melanoma and tumor microenvironment status.

    Deng, Huiling / Chen, Yuxuan / An, Ran / Wang, Jiecong

    Epigenomics

    2023  Volume 15, Issue 12, Page(s) 657–675

    Abstract: Aims: ...

    Abstract Aims:
    MeSH term(s) Humans ; Melanoma/genetics ; Skin Neoplasms/genetics ; RNA, Long Noncoding/genetics ; Prognosis ; Pyroptosis/genetics ; Tumor Microenvironment/genetics ; Melanoma, Cutaneous Malignant
    Chemical Substances RNA, Long Noncoding
    Language English
    Publishing date 2023-08-14
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2537199-X
    ISSN 1750-192X ; 1750-1911
    ISSN (online) 1750-192X
    ISSN 1750-1911
    DOI 10.2217/epi-2023-0139
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Do the New Rural Pension Scheme promote the health status of chronic patients in old age? -Evidence from CHARLS 2018 in China.

    Liang, Qihong / Chen, Yuxuan / Zhang, Zheng / An, Shengli

    BMC public health

    2023  Volume 23, Issue 1, Page(s) 2506

    Abstract: Background: Many researchers have examined the impact of social insurance on health in elderly. However, in most cases, they have only demonstrated correlational results and have not been able to determine causal effects, possibly because confounding ... ...

    Abstract Background: Many researchers have examined the impact of social insurance on health in elderly. However, in most cases, they have only demonstrated correlational results and have not been able to determine causal effects, possibly because confounding biases have not been fully addressed. In this study, we investigated the health effects of the New Rural Pension Scheme (NRPS) on the elderly (age≥60 years old) with chronic diseases in rural areas, and to explore the causal relationship and effects of NRPS and health status.
    Methods: This paper used data from the 2018 China Health and Retirement Longitudinal Study (CHARLS) and applied Bayesian networks and fuzzy regression discontinuity design to conduct causal analysis. Bayesian networks were used to explore the causal directed acyclic graphs of factors related to NRPS and health status. Based on the results of Bayesian network, a fuzzy regression discontinuity design was employed to estimate the causal effect of NRPS on health status.
    Results: Among rural elderly with chronic diseases, Bayesian network mapping of causal relationships among NRPS, health status and covariates showed that age was a common cause of NRPS receipt and satisfaction with health. The results of the fuzzy regression discontinuity analysis showed that the effect of receiving NRPS on the health status was positive, but there was no statistically significant difference concerning the interval estimates. The results of the subgroup analysis with chronic obstructive pulmonary disease (COPD) and asthma indicated that the effect of NRPS receipt on the health status of elderly people with COPD was positive. There was a statistically significant effect of receiving NRPS on self-rated health description ([Formula: see text]) and health satisfaction ([Formula: see text]) in COPD population and a statistically significant effect of receiving NRPS on health satisfaction in asthma population ([Formula: see text]).
    Conclusion: This paper has confirmed the contribution and positive causal effect of NRPS on health status in a subgroup of older adults with COPD and asthma, using the CHARLS database as evidence. Thus, Chinese government should increase the take-up rate of the NRPS to enhance their positive impact on health status of elderly people with chronic diseases in rural areas.
    MeSH term(s) Humans ; Aged ; Middle Aged ; Retirement ; Longitudinal Studies ; Bayes Theorem ; Pensions ; Health Status ; Rural Population ; Chronic Disease ; Pulmonary Disease, Chronic Obstructive ; China/epidemiology ; Asthma/epidemiology
    Language English
    Publishing date 2023-12-14
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2041338-5
    ISSN 1471-2458 ; 1471-2458
    ISSN (online) 1471-2458
    ISSN 1471-2458
    DOI 10.1186/s12889-023-17430-9
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  10. Article ; Online: DeepQs: Local quality assessment of cryo-EM density map by deep learning map-model fit score.

    Feng, Ming-Feng / Chen, Yu-Xuan / Shen, Hong-Bin

    Journal of structural biology

    2023  Volume 216, Issue 1, Page(s) 108059

    Abstract: Cryogenic electron microscopy maps are valuable for determining macromolecule structures. A proper quality assessment method is essential for cryo-EM map selection or revision. This article presents DeepQs, a novel approach to estimate local quality for ... ...

    Abstract Cryogenic electron microscopy maps are valuable for determining macromolecule structures. A proper quality assessment method is essential for cryo-EM map selection or revision. This article presents DeepQs, a novel approach to estimate local quality for 3D cryo-EM density maps, using a deep-learning algorithm based on map-model fit score. DeepQs is a parameter-free method for users and incorporates structural information between map and its related atomic model into well-trained models by deep learning. More specifically, the DeepQs approach leverages the interplay between map and atomic model through predefined map-model fit score, Q-score. DeepQs can get close results to the ground truth map-model fit scores with only cryo-EM map as input. In experiments, DeepQs demonstrates the lowest root mean square error with standard method Fourier shell correlation metric and high correlation with map-model fit score, Q-score, when compared with other local quality estimation methods in high-resolution dataset (<=5 Å). DeepQs can also be applied to evaluate the quality of the post-processed maps. In both cases, DeepQs runs faster by using GPU acceleration. Our program is available at http://www.csbio.sjtu.edu.cn/bioinf/DeepQs for academic use.
    MeSH term(s) Cryoelectron Microscopy/methods ; Deep Learning ; Models, Molecular ; Microscopy, Electron ; Algorithms ; Protein Conformation
    Language English
    Publishing date 2023-12-30
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1032718-6
    ISSN 1095-8657 ; 1047-8477
    ISSN (online) 1095-8657
    ISSN 1047-8477
    DOI 10.1016/j.jsb.2023.108059
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