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  1. Article ; Online: Ultrafast one‐pass FASTQ data preprocessing, quality control, and deduplication using fastp

    Shifu Chen

    iMeta, Vol 2, Iss 2, Pp n/a-n/a (2023)

    2023  

    Abstract: Abstract A large amount of sequencing data is generated and processed every day with the continuous evolution of sequencing technology and the expansion of sequencing applications. One consequence of such sequencing data explosion is the increasing cost ... ...

    Abstract Abstract A large amount of sequencing data is generated and processed every day with the continuous evolution of sequencing technology and the expansion of sequencing applications. One consequence of such sequencing data explosion is the increasing cost and complexity of data processing. The preprocessing of FASTQ data, which means removing adapter contamination, filtering low‐quality reads, and correcting wrongly represented bases, is an indispensable but resource intensive part of sequencing data analysis. Therefore, although a lot of software applications have been developed to solve this problem, bioinformatics scientists and engineers are still pursuing faster, simpler, and more energy‐efficient software. Several years ago, the author developed fastp, which is an ultrafast all‐in‐one FASTQ data preprocessor with many modern features. This software has been approved by many bioinformatics users and has been continuously maintained and updated. Since the first publication on fastp, it has been greatly improved, making it even faster and more powerful. For instance, the duplication evaluation module has been improved, and a new deduplication module has been added. This study aimed to introduce the new features of fastp and demonstrate how it was designed and implemented.
    Keywords adapter ; duplication ; FASTQ ; filtering ; preprocessing ; quality control ; Computer applications to medicine. Medical informatics ; R858-859.7
    Language English
    Publishing date 2023-05-01T00:00:00Z
    Publisher Wiley
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Superhydrophilic Dendritic FeP/Cu

    Li, Fang / Cao, Jing / Yu, Huiqin / Lin, Haili / Chen, Shifu

    Inorganic chemistry

    2024  Volume 63, Issue 9, Page(s) 4204–4213

    Abstract: The electrocatalytic overall urea splitting can achieve the dual goals of urea treatment and hydrogen energy acquisition. Herein, we exploited the principle of precipitation dissolution equilibrium to obtain bimetallic phosphide FeP/ ... ...

    Abstract The electrocatalytic overall urea splitting can achieve the dual goals of urea treatment and hydrogen energy acquisition. Herein, we exploited the principle of precipitation dissolution equilibrium to obtain bimetallic phosphide FeP/Cu
    Language English
    Publishing date 2024-02-22
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1484438-2
    ISSN 1520-510X ; 0020-1669
    ISSN (online) 1520-510X
    ISSN 0020-1669
    DOI 10.1021/acs.inorgchem.3c04285
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  3. Article: Corrigendum: Exploring the bi-directional relationship and shared genes between depression and stroke via NHANES and bioinformatic analysis.

    Yang, Zhanghuan / He, Maokun / Zhang, Qian / Li, Shifu / Chen, Hua / Liao, Di

    Frontiers in genetics

    2024  Volume 15, Page(s) 1405696

    Abstract: This corrects the article DOI: 10.3389/fgene.2023.1004457.]. ...

    Abstract [This corrects the article DOI: 10.3389/fgene.2023.1004457.].
    Language English
    Publishing date 2024-04-10
    Publishing country Switzerland
    Document type Published Erratum
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2024.1405696
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  4. Article ; Online: Design of p-n heterojunction between CoWO

    Li, Li / Kuang, Kaixuan / Zheng, Xiuzhen / Wang, Jiahui / Ren, Wei / Ge, Jingbiao / Zhang, Sujuan / Chen, Shifu

    Journal of colloid and interface science

    2024  Volume 663, Page(s) 981–991

    Abstract: To enhance the efficiency of photocatalytic ... ...

    Abstract To enhance the efficiency of photocatalytic H
    Language English
    Publishing date 2024-03-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 241597-5
    ISSN 1095-7103 ; 0021-9797
    ISSN (online) 1095-7103
    ISSN 0021-9797
    DOI 10.1016/j.jcis.2024.02.218
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  5. Article: Exploring the bi-directional relationship and shared genes between depression and stroke

    Yang, Zhanghuan / He, Maokun / Zhang, Qian / Li, Shifu / Chen, Hua / Liao, Di

    Frontiers in genetics

    2023  Volume 14, Page(s) 1004457

    Abstract: Background: ...

    Abstract Background:
    Language English
    Publishing date 2023-03-31
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2023.1004457
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  6. Article ; Online: Oxygen vacancies synergistic cobalt phosphide electron bridge modulated bismuth oxychloride/carbon nitride Z-scheme junction for efficient carbon dioxide reduction coupled with tetracycline oxidation.

    Sun, Haoyu / Jia, Xuemei / Cao, Jing / Chen, Shifu / Chen, Yong / Lin, Haili

    Journal of colloid and interface science

    2024  Volume 661, Page(s) 150–163

    Abstract: Although great progress has been made with respect to electron bridges, the electron mobility of the state-of-the-art electron bridges is far from satisfactory because of weak electrical conductivity. To overcome the above issue, cobalt phosphide (CoP), ... ...

    Abstract Although great progress has been made with respect to electron bridges, the electron mobility of the state-of-the-art electron bridges is far from satisfactory because of weak electrical conductivity. To overcome the above issue, cobalt phosphide (CoP), as a model electron bridge, was modified by superficial oxygen vacancies (OVs) and embedded into a defective bismuth oxychloride/carbon nitride (BiO
    Language English
    Publishing date 2024-01-26
    Publishing country United States
    Document type Journal Article
    ZDB-ID 241597-5
    ISSN 1095-7103 ; 0021-9797
    ISSN (online) 1095-7103
    ISSN 0021-9797
    DOI 10.1016/j.jcis.2024.01.149
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    In stock of ZB MED Bonn / Germany

    Z 71/707: Show issues

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  7. Article ; Online: Proximal Clipping and Distal High-Flow Bypass in the Treatment of Giant/Complex Intracranial Aneurysm: An Opportunity or a Risk from a Fluid-Structural Interaction Analysis.

    Li, Shifu / Huang, Zheng / Chen, Hua / Chen, Fenghua

    Cardiovascular engineering and technology

    2023  

    Abstract: Objectives: Conventional clipping and endovascular treatment are difficult to apply for some giant intracranial aneurysms (GIAs), and sometimes extracranial-to-intracranial (EC-IC) bypass becomes the optional choice. However, not all GIA patients can ... ...

    Abstract Objectives: Conventional clipping and endovascular treatment are difficult to apply for some giant intracranial aneurysms (GIAs), and sometimes extracranial-to-intracranial (EC-IC) bypass becomes the optional choice. However, not all GIA patients can benefit from it. This study aims to recognize the underlying problems.
    Methods: We included eligible patients in our care. Then, we researched from three levels: a retrospective review of clinical data, fluid-structural analysis from two representative patient-specific models, and fluid-structural interaction analysis for idealized models to investigate the hemodynamic and biomechanical mechanisms.
    Results: In this article, we report nine patients with GIA who underwent EC-IC surgery. Of them, three experienced dangerous postoperative hemorrhage, and one patient died. Among these three patients, two lacked the A1 segment of the anterior cerebral artery (ACA). The numerical simulation showed that after surgery, for the patient with an unruptured aneurysm and existence of ACA, the wall deformation, wall stress, pressure, and area of the oscillatory shear index (OSI) > 0.2 were decreased by 43%, 39%, 33%, and 13%, while the patient without A1 segment having postoperative hemorrhage showed 36%, 45%, 13%, and 55% increased, respectively. Thus, we postulated a dangerous "stump phenomenon" in such conditions and further demonstrated it from idealized models with different sizes of ACA. Finally, we found a larger anastomosis angle and smaller diameter of the graft can alleviate this effect.
    Conclusions: Neurosurgeon should cautiously evaluate the opportunity and risk for such patients who have aplasia of the A1 segment of ACA when making clinical decisions.
    Language English
    Publishing date 2023-12-13
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2543111-0
    ISSN 1869-4098 ; 1869-408X
    ISSN (online) 1869-4098
    ISSN 1869-408X
    DOI 10.1007/s13239-023-00704-z
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  8. Article ; Online: Validation study on a non-linear dynamical model of the projectile.

    Liang, Jun / Fan, Xuanhua / Wang, Yuancen / Xiao, Shifu / Chen, Hongyong

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 13470

    Abstract: Based on the theoretical approach of multi-body interaction dynamics, a theoretical model is constructed to simulate the nonlinear response amplification of the projectile structure. The accuracy and universality of the theoretical model were verified by ...

    Abstract Based on the theoretical approach of multi-body interaction dynamics, a theoretical model is constructed to simulate the nonlinear response amplification of the projectile structure. The accuracy and universality of the theoretical model were verified by comparing the response data calculated by the theoretical model with the experimental data. The results show that the theoretical model can predict the acceleration and strain response of the projectile structure more accurately, providing a non-linear dynamic analysis method for the projectile structure from the perspective of structural dynamics.
    Language English
    Publishing date 2023-08-18
    Publishing country England
    Document type Journal Article
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-023-40619-2
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  9. Article ; Online: Integrative analysis of multi-omics data to identify three immune-related genes in the formation and progression of intracranial aneurysms.

    Li, Shifu / Zhang, Qian / Huang, Zheng / Chen, Fenghua

    Inflammation research : official journal of the European Histamine Research Society ... [et al.

    2023  Volume 72, Issue 5, Page(s) 1001–1019

    Abstract: Objective and design: The prevalence of intracranial aneurysms (IAs) has increased globally. We performed bioinformatics analysis to identify key biomarkers associated with IA formation.: Methods and results: We conducted a comprehensive analysis ... ...

    Abstract Objective and design: The prevalence of intracranial aneurysms (IAs) has increased globally. We performed bioinformatics analysis to identify key biomarkers associated with IA formation.
    Methods and results: We conducted a comprehensive analysis combined with multi-omics data and methods to identify immune-related genes (IRGs) and immunocytes involved in IAs. Functional enrichment analyses showed enhanced immune responses and suppressed organizations of extracellular matrix (ECM) during aneurysm progression. xCell analyses showed that the abundance of B cells, macrophages, mast cells, and monocytes significantly increased from levels in control to unruptured aneurysms and to ruptured aneurysms. Of 21 IRGs identified by overlapping, a three-gene (CXCR4, S100B, and OSM) model was constructed through LASSO logistic regression. The diagnostic ability of the three biomarkers in discriminating aneurysms from the control samples demonstrated a favorable diagnostic value. Among the three genes, OSM and CXCR4 were up-regulated and hypomethylated in IAs, while S100B was down-regulated and hypermethylated. The expression of the three IRGs was further validated by qRT-PCR and immunohistochemistry and mouse IA model using scRNA-seq analysis.
    Conclusion: The present study demonstrated heightened immune response and suppressed ECM organization in aneurysm formation and rupture. The three-gene immune-related signature (CCR4, S100B, and OSM) model may facilitate IA diagnosis and prevention.
    MeSH term(s) Animals ; Mice ; Intracranial Aneurysm/genetics ; Intracranial Aneurysm/diagnosis ; Intracranial Aneurysm/epidemiology ; Multiomics ; Biomarkers ; Aneurysm, Ruptured/diagnosis ; Aneurysm, Ruptured/epidemiology ; Aneurysm, Ruptured/genetics
    Chemical Substances Biomarkers
    Language English
    Publishing date 2023-04-04
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 1221794-3
    ISSN 1420-908X ; 1023-3830
    ISSN (online) 1420-908X
    ISSN 1023-3830
    DOI 10.1007/s00011-023-01725-z
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 675: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  10. Article ; Online: Decorating Zn

    Yang, Yang / Ren, Wei / Zheng, Xiuzhen / Meng, Sugang / Cai, Chun / Fu, Xianliang / Chen, Shifu

    ACS applied materials & interfaces

    2022  

    Abstract: Photocatalytic ... ...

    Abstract Photocatalytic H
    Language English
    Publishing date 2022-12-01
    Publishing country United States
    Document type Journal Article
    ISSN 1944-8252
    ISSN (online) 1944-8252
    DOI 10.1021/acsami.2c13859
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