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  1. Article ; Online: Enhanced architecture and implementation of spectrum shaping codes.

    Wang, Bingrui / Xie, Zhaopeng / Zhang, Xingang

    PeerJ. Computer science

    2024  Volume 10, Page(s) e1883

    Abstract: Spectral shaping codes are modulation codes widely used in communication and data storage systems. This research enhances the algorithms employed in constructing spectral shaping codes for hardware implementation. We present a parallel scrambling ... ...

    Abstract Spectral shaping codes are modulation codes widely used in communication and data storage systems. This research enhances the algorithms employed in constructing spectral shaping codes for hardware implementation. We present a parallel scrambling calculation with a time complexity of
    Language English
    Publishing date 2024-02-21
    Publishing country United States
    Document type Journal Article
    ISSN 2376-5992
    ISSN (online) 2376-5992
    DOI 10.7717/peerj-cs.1883
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  2. Article ; Online: Development of Son of Sevenless Homologue 1 (SOS1) Modulators To Treat Cancers by Regulating RAS Signaling.

    Luo, Guangmei / Wang, Bingrui / Hou, Qiangqiang / Wu, Xiaoxing

    Journal of medicinal chemistry

    2023  Volume 66, Issue 7, Page(s) 4324–4341

    Abstract: Son of sevenless homologue 1 (SOS1) protein is universally expressed in cells and plays an important role in the RAS signaling pathway. Specifically, this protein interacts with RAS in response to upstream stimuli to promote guanine nucleotide exchange ... ...

    Abstract Son of sevenless homologue 1 (SOS1) protein is universally expressed in cells and plays an important role in the RAS signaling pathway. Specifically, this protein interacts with RAS in response to upstream stimuli to promote guanine nucleotide exchange in RAS and activates the downstream signaling pathways. Thus, targeting SOS1 is a new approach for treating RAS-driven cancers. In this Perspective, we briefly summarize the structural and functional aspects of SOS1 and focus on recent advances in the discovery of activators, inhibitors, and PROTACs that target SOS1. This review aims to provide a timely and updated overview on the strategies for targeting SOS1 in cancer therapy.
    MeSH term(s) Humans ; Nuclear Family ; SOS1 Protein/metabolism ; Signal Transduction ; Neoplasms/drug therapy
    Chemical Substances SOS1 Protein
    Language English
    Publishing date 2023-03-28
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 218133-2
    ISSN 1520-4804 ; 0022-2623
    ISSN (online) 1520-4804
    ISSN 0022-2623
    DOI 10.1021/acs.jmedchem.2c01729
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    Zs.B 151: Show issues Location:
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  3. Article ; Online: PTransIPs: Identification of Phosphorylation Sites Enhanced by Protein PLM Embeddings.

    Xu, Ziyang / Zhong, Haitian / He, Bingrui / Wang, Xueying / Lu, Tianchi

    IEEE journal of biomedical and health informatics

    2024  Volume PP

    Abstract: Phosphorylation is pivotal in numerous fundamental cellular processes and plays a significant role in the onset and progression of various diseases. The accurate identification of these phosphorylation sites is crucial for unraveling the molecular ... ...

    Abstract Phosphorylation is pivotal in numerous fundamental cellular processes and plays a significant role in the onset and progression of various diseases. The accurate identification of these phosphorylation sites is crucial for unraveling the molecular mechanisms within cells and during viral infections, potentially leading to the discovery of novel therapeutic targets. In this study, we develop PTransIPs, a new deep learning framework for the identification of phosphorylation sites. Independent testing results demonstrate that PTransIPs outperforms existing state-of-the-art (SOTA) methods, achieving AUCs of 0.9232 and 0.9660 for the identification of phosphorylated S/T and Y sites, respectively. PTransIPs contributes from three aspects. 1) PTransIPs is the first to apply protein pre-trained language model (PLM) embeddings to this task. It utilizes ProtTrans and EMBER2 to extract sequence and structure embeddings, respectively, as additional inputs into the model, effectively addressing issues of dataset size and overfitting, thus enhancing model performance; 2) PTransIPs is based on Transformer architecture, optimized through the integration of convolutional neural networks and TIM loss function, providing practical insights for model design and training; 3) The encoding of amino acids in PTransIPs enables it to serve as a universal framework for other peptide bioactivity tasks, with its excellent performance shown in extended experiments of this paper. Our code, data and models are publicly available at https://github.com/StatXzy7/PTransIPs.
    Language English
    Publishing date 2024-03-14
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2695320-1
    ISSN 2168-2208 ; 2168-2194
    ISSN (online) 2168-2208
    ISSN 2168-2194
    DOI 10.1109/JBHI.2024.3377362
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  4. Article ; Online: Climate extremes drive the phenology of a dominant species in meadow steppe under gradual warming.

    Hongchao, Ji / Guang, Yang / Xiaomin, Lv / Bingrui, Jia / Zhenzhu, Xu / Yuhui, Wang

    The Science of the total environment

    2023  Volume 869, Page(s) 161687

    Abstract: Plant phenology in terrestrial ecosystems, especially in the Northern Hemisphere, is expected to change owing to the projected increasing frequency and intensity of climate extremes in the context of global warming. Although such changes under mean ... ...

    Abstract Plant phenology in terrestrial ecosystems, especially in the Northern Hemisphere, is expected to change owing to the projected increasing frequency and intensity of climate extremes in the context of global warming. Although such changes under mean climate change have been extensively reported in the literature, little is known about the impacts of climate extremes. In this study, climatic changes and their effects on plant phenology were characterized using long-term climatic and phenological data from the start and end of the growing season (SOS and EOS, respectively) from 2005 to 2020 for Stipa baicalensis, a dominant species in a temperate meadow steppe. The results showed that the temperature, including the mean and minimum temperatures, and extreme warm indices significantly increased; however, annual precipitation, and the frequency of extreme cold and precipitation events decreased. The SOS of S. baicalensis was initially earlier and later, whereas the EOS trended to be delayed. However, the growing season (LOS) was slightly prolonged. Compared with the indices under mean temperature, the pre-season (before SOS or EOS) minimum temperature dominantly affected SOS and EOS, whereas the mean and extreme precipitation slightly affected them. Furthermore, the findings showed that plant phenology responded to extreme temperatures quicker and stronger than mean temperatures. This study provides insight into how key extreme climatic factors could affect plant phenophases and improve and refine the phenological model. This could also be useful in enhancing grassland ecosystem management and sustainable development.
    MeSH term(s) Ecosystem ; Grassland ; Climate Change ; Global Warming ; Hot Temperature ; Temperature ; Plants ; Seasons
    Language English
    Publishing date 2023-01-19
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 121506-1
    ISSN 1879-1026 ; 0048-9697
    ISSN (online) 1879-1026
    ISSN 0048-9697
    DOI 10.1016/j.scitotenv.2023.161687
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  5. Article ; Online: Rockburst hazard assessment and prevention and control strategies in the Ruihai gold mine

    Pengxiang Li / Zongwen Wang / Bingrui Chen / Jianping Peng / Bochao Zhang / Jinshuai Zhao / Houlin Xie

    Frontiers in Earth Science, Vol

    2024  Volume 11

    Abstract: Ruihai gold mine is a super large underwater gold mine with an initial mining depth of more than 1,400 m. Deep mining may face rockburst disaster. In order to scientifically control the potential rockburst risk, ensure the safety of underground personnel ...

    Abstract Ruihai gold mine is a super large underwater gold mine with an initial mining depth of more than 1,400 m. Deep mining may face rockburst disaster. In order to scientifically control the potential rockburst risk, ensure the safety of underground personnel and equipment, and realize the safe and efficient mining of the mine, it is necessary to evaluate the rockburst risk of the mine and formulate appropriate rockburst risk warning and mitigation strategies. XRD mineral composition analysis and conventional rock mechanical tests were carried out on the parent rock granite samples. The results show that there are differences in the lithologic composition and rock mechanics parameters of the three colors of granite, which are preliminarily determined as three kinds of granite; The rockburst tendency of three kinds of granites is evaluated by using three classical rockburst criteria, and the discrimination results of the three rockburst criteria are not completely consistent or even contradictory. The application limitations rockburst risk assessment based on index criteria are discussed and analyzed in detail. It is proposed to apply microseismic monitoring technology to warn and manage the rockburst risk of Ruihai gold mine in development and mining stages, and put forward microseismic monitoring layout schemes and targeted rockburst prevention and control measures in different stages. The research results can provide reference for similar projects.
    Keywords deep buried mine ; rockburst criterion ; microseismic monitoring ; warning and mitigation rockburst ; rockburst risk ; Science ; Q
    Language English
    Publishing date 2024-01-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
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  6. Article ; Online: A Red-Emission Fluorescent Probe for Intracellular Biothiols and Hydrogen Sulfide Imaging in Living Cells.

    Wang, Yuanfan / Zhang, Shengxiang / Liu, Tianle / Chen, Junning / Yuan, Bingrui / Lu, Cuntao / Bo, Xiumei / Xu, Zhou

    Molecules (Basel, Switzerland)

    2024  Volume 29, Issue 7

    Abstract: This research centers on the development and synthesis of a longwave fluorescence probe, labeled ... ...

    Abstract This research centers on the development and synthesis of a longwave fluorescence probe, labeled as
    MeSH term(s) Hydrogen Sulfide ; Fluorescent Dyes ; Diagnostic Imaging ; Cysteine ; Glutathione ; Homocysteine ; Sulfhydryl Compounds
    Chemical Substances Hydrogen Sulfide (YY9FVM7NSN) ; Fluorescent Dyes ; Cysteine (K848JZ4886) ; Glutathione (GAN16C9B8O) ; Homocysteine (0LVT1QZ0BA) ; Sulfhydryl Compounds
    Language English
    Publishing date 2024-03-31
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 1413402-0
    ISSN 1420-3049 ; 1431-5165 ; 1420-3049
    ISSN (online) 1420-3049
    ISSN 1431-5165 ; 1420-3049
    DOI 10.3390/molecules29071572
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  7. Article ; Online: Lamina Cribrosa Insertions Into the Sclera Are Sparser, Narrower, and More Slanted in the Anterior Lamina.

    Ji, Fengting / Islam, Mohammad R / Wang, Bingrui / Hua, Yi / Sigal, Ian A

    Investigative ophthalmology & visual science

    2024  Volume 65, Issue 4, Page(s) 35

    Abstract: Purpose: The lamina cribrosa (LC) depends on the sclera for support. The support must be provided through the LC insertions. Although a continuous insertion over the whole LC periphery is often assumed, LC insertions are actually discrete locations ... ...

    Abstract Purpose: The lamina cribrosa (LC) depends on the sclera for support. The support must be provided through the LC insertions. Although a continuous insertion over the whole LC periphery is often assumed, LC insertions are actually discrete locations where LC collagenous beams meet the sclera. We hypothesized that LC insertions vary in number, size, and shape by quadrant and depth.
    Methods: Coronal cryosections through the full LCs from six healthy monkey eyes were imaged using instant polarized light microscopy. The images were registered into a stack, on which we manually marked LC insertion outlines, nothing their position in-depth and quadrant (inferior, superior, nasal, or temporal). From the marks, we determined the insertion number, width, angle to the canal wall (90 degrees = perpendicular), and insertion ratio (fraction of LC periphery represented by insertions). Using linear mixed effect models, we determined if the insertion characteristics were associated with depth or quadrant.
    Results: Insertions in the anterior LC were sparser, narrower, and more slanted than those in deeper LC (P values < 0.001). There were more insertions spanning a larger ratio of the canal wall in the middle LC than in the anterior and posterior (P values < 0.001). In the nasal quadrant, the insertion angles were significantly smaller (P < 0.001).
    Conclusions: LC insertions vary substantially and significantly over the canal. The sparser, narrower, and more slanted insertions of the anterior-most LC may not provide the robust support afforded by insertions of the middle and posterior LC. These variations may contribute to the progressive deepening of the LC and regional susceptibility to glaucoma.
    MeSH term(s) Sclera/anatomy & histology ; Animals ; Optic Disk/anatomy & histology ; Optic Disk/diagnostic imaging ; Microscopy, Polarization ; Macaca mulatta ; Male
    Language English
    Publishing date 2024-04-22
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 391794-0
    ISSN 1552-5783 ; 0146-0404
    ISSN (online) 1552-5783
    ISSN 0146-0404
    DOI 10.1167/iovs.65.4.35
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  8. Article: Conservation planning for the endemic and endangered medicinal plants under the climate change and human disturbance: a case study of

    Zou, Hui / Chen, Bingrui / Zhang, Boyan / Zhou, Xinyu / Zhang, Xiyuan / Zhang, Xinxin / Wang, Jianwei

    Frontiers in plant science

    2023  Volume 14, Page(s) 1184556

    Abstract: Human activities and climate change have significantly impacted the quantity and sustainable utilization of medicinal plants. ...

    Abstract Human activities and climate change have significantly impacted the quantity and sustainable utilization of medicinal plants.
    Language English
    Publishing date 2023-07-26
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2613694-6
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2023.1184556
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  9. Article ; Online: Systematic elucidation of the mechanism of Jingyin granule in the treatment of Novel Coronavirus (COVID-19) Pneumonia via Network Pharmacology.

    Wang, Bingrui / Sun, Xuehua / Kong, Xiaoni / Gao, Yueqiu

    International journal of medical sciences

    2021  Volume 18, Issue 7, Page(s) 1648–1656

    Abstract: Background: ...

    Abstract Background:
    MeSH term(s) Humans ; Molecular Targeted Therapy ; Phytotherapy ; COVID-19 Drug Treatment
    Language English
    Publishing date 2021-02-05
    Publishing country Australia
    Document type Journal Article
    ZDB-ID 2151424-0
    ISSN 1449-1907 ; 1449-1907
    ISSN (online) 1449-1907
    ISSN 1449-1907
    DOI 10.7150/ijms.53575
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  10. Article: Targeted sequencing and clinical strategies in children with autism spectrum disorder: A cohort study.

    Hu, Chunchun / Wang, Yi / Li, Chunyang / Mei, Lianni / Zhou, Bingrui / Li, Dongyun / Li, Huiping / Xu, Qiong / Xu, Xiu

    Frontiers in genetics

    2023  Volume 14, Page(s) 1083779

    Abstract: Objectives: ...

    Abstract Objectives:
    Language English
    Publishing date 2023-02-28
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2023.1083779
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