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  1. Article ; Online: Interval estimate of causal effect in summary data based Mendelian randomization in the presence of winner's curse.

    Wang, Kai

    Genetic epidemiology

    2024  Volume 48, Issue 2, Page(s) 74–84

    Abstract: This research focuses on the interval estimation of the causal effect of an exposure on an outcome using the summary data-based Mendelian randomization (SMR) method while accounting for the winner's curse caused by the selection of single nucleotide ... ...

    Abstract This research focuses on the interval estimation of the causal effect of an exposure on an outcome using the summary data-based Mendelian randomization (SMR) method while accounting for the winner's curse caused by the selection of single nucleotide polymorphism instruments. This issue is understudied and is important as the point estimate is biased. Since Fieller's theorem and its variations are not suitable for constructing a confidence interval, we use the box method. This box method is known to be conservative and thus provides a lower bound on the coverage level. To assess the performance of the box method, we use simulation studies and compare it with the support interval we proposed earlier and the Wald interval derived from the SMR method. All three methods are applied to a study of causal genes for Alzheimer's disease. Overall, the box method presents an alternative for constructing interval estimates for a causal effect while addressing the winner's curse issue.
    MeSH term(s) Humans ; Mendelian Randomization Analysis ; Models, Genetic ; Computer Simulation ; Polymorphism, Single Nucleotide ; Genome-Wide Association Study
    Language English
    Publishing date 2024-01-28
    Publishing country United States
    Document type Journal Article
    ZDB-ID 605785-8
    ISSN 1098-2272 ; 0741-0395
    ISSN (online) 1098-2272
    ISSN 0741-0395
    DOI 10.1002/gepi.22545
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Support Interval for Two-Sample Summary Data-Based Mendelian Randomization.

    Wang, Kai

    Genes

    2023  Volume 14, Issue 1

    Abstract: The summary-data-based Mendelian randomization (SMR) method is gaining popularity in estimating the causal effect of an exposure on an outcome. In practice, the instrument SNP is often selected from the genome-wide association study (GWAS) on the ... ...

    Abstract The summary-data-based Mendelian randomization (SMR) method is gaining popularity in estimating the causal effect of an exposure on an outcome. In practice, the instrument SNP is often selected from the genome-wide association study (GWAS) on the exposure but no correction is made for such selection in downstream analysis, leading to a biased estimate of the effect size and invalid inference. We address this issue by using the likelihood derived from the sampling distribution of the estimated SNP effects in the exposure GWAS and the outcome GWAS. This likelihood takes into account how the instrument SNPs are selected. Since the effective sample size is 1, the asymptotic theory does not apply. We use a support for a profile likelihood as an interval estimate of the causal effect. Simulation studies indicate that this support has robust coverage while the confidence interval implied by the SMR method has lower-than-nominal coverage. Furthermore, the variance of the two-stage least squares estimate of the causal effect is shown to be the same as the variance used for SMR for one-sample data when there is no selection.
    MeSH term(s) Genome-Wide Association Study ; Mendelian Randomization Analysis/methods ; Causality ; Computer Simulation ; Sample Size
    Language English
    Publishing date 2023-01-13
    Publishing country Switzerland
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2527218-4
    ISSN 2073-4425 ; 2073-4425
    ISSN (online) 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes14010211
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Cr

    Wang, Kai

    Journal of computational chemistry

    2023  Volume 44, Issue 19, Page(s) 1667–1672

    Abstract: In this work, we investigated the structural evolution, electronic and magnetic properties of ... ...

    Abstract In this work, we investigated the structural evolution, electronic and magnetic properties of Cr
    MeSH term(s) Algorithms ; Cluster Analysis ; Electronics ; Isomerism
    Language English
    Publishing date 2023-04-21
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1479181-X
    ISSN 1096-987X ; 0192-8651
    ISSN (online) 1096-987X
    ISSN 0192-8651
    DOI 10.1002/jcc.27117
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  4. Article ; Online: GPDOCK: highly accurate docking strategy for metalloproteins based on geometric probability.

    Wang, Kai

    Briefings in bioinformatics

    2023  Volume 24, Issue 1

    Abstract: Accurately predicting the interaction modes for metalloproteins remains extremely challenging in structure-based drug design and mechanism analysis of enzymatic catalysis due to the complexity of metal coordination in metalloproteins. Here, we report a ... ...

    Abstract Accurately predicting the interaction modes for metalloproteins remains extremely challenging in structure-based drug design and mechanism analysis of enzymatic catalysis due to the complexity of metal coordination in metalloproteins. Here, we report a docking method for metalloproteins based on geometric probability (GPDOCK) with unprecedented accuracy. The docking tests of 10 common metal ions with 9360 metalloprotein-ligand complexes demonstrate that GPDOCK has an accuracy of 94.3% in predicting binding pose. What is more, it can accurately realize the docking of metalloproteins with ligand when one or two water molecules are engaged in the metal ion coordination. Since GPDOCK only depends on the three-dimensional structure of metalloprotein and ligand, structure-based machine learning model is employed for the scoring of binding poses, which significantly improves computational efficiency. The proposed docking strategy can be an effective and efficient tool for drug design and further study of binding mechanism of metalloproteins. The manual of GPDOCK and the code for the logistical regression model used to re-rank the docking results are available at https://github.com/wangkai-zhku/GPDOCK.git.
    MeSH term(s) Metalloproteins/chemistry ; Metalloproteins/metabolism ; Protein Binding ; Ligands ; Machine Learning ; Catalysis ; Molecular Docking Simulation ; Binding Sites
    Chemical Substances Metalloproteins ; Ligands
    Language English
    Publishing date 2023-01-15
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2068142-2
    ISSN 1477-4054 ; 1467-5463
    ISSN (online) 1477-4054
    ISSN 1467-5463
    DOI 10.1093/bib/bbac620
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: The Yin-Yang Definition Model of Mental Health: The Mental Health Definition in Chinese Culture.

    Wang, Kai

    Frontiers in psychology

    2022  Volume 13, Page(s) 832076

    Abstract: It is a common aim of psychologists to construct a definition model with universal cultural applicability for mental health. These models can be divided into two types in terms of definition: One is the negative mental health definition model based on ... ...

    Abstract It is a common aim of psychologists to construct a definition model with universal cultural applicability for mental health. These models can be divided into two types in terms of definition: One is the negative mental health definition model based on the absence of mental illness symptoms; the other is the definition model of positive mental health based on subjective feelings, such as happiness and social identity. However, neither of these definitions can properly explain Chinese people's understanding of mental health or how mental health is dealt with in Chinese culture. This paper proposes a Yin-Yang definition model of mental health based on the theory of personality of Confucianism and Taoism. This model not only properly describes the understanding of mental health in traditional Chinese culture, but also explains East Asian psychotherapy and mental health practices in the context of Chinese culture.
    Language English
    Publishing date 2022-03-24
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2563826-9
    ISSN 1664-1078
    ISSN 1664-1078
    DOI 10.3389/fpsyg.2022.832076
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Support Interval for Two-Sample Summary Data-Based Mendelian Randomization

    Wang, Kai

    Genes (Basel). 2023 Jan. 13, v. 14, no. 1

    2023  

    Abstract: The summary-data-based Mendelian randomization (SMR) method is gaining popularity in estimating the causal effect of an exposure on an outcome. In practice, the instrument SNP is often selected from the genome-wide association study (GWAS) on the ... ...

    Abstract The summary-data-based Mendelian randomization (SMR) method is gaining popularity in estimating the causal effect of an exposure on an outcome. In practice, the instrument SNP is often selected from the genome-wide association study (GWAS) on the exposure but no correction is made for such selection in downstream analysis, leading to a biased estimate of the effect size and invalid inference. We address this issue by using the likelihood derived from the sampling distribution of the estimated SNP effects in the exposure GWAS and the outcome GWAS. This likelihood takes into account how the instrument SNPs are selected. Since the effective sample size is 1, the asymptotic theory does not apply. We use a support for a profile likelihood as an interval estimate of the causal effect. Simulation studies indicate that this support has robust coverage while the confidence interval implied by the SMR method has lower-than-nominal coverage. Furthermore, the variance of the two-stage least squares estimate of the causal effect is shown to be the same as the variance used for SMR for one-sample data when there is no selection.
    Keywords confidence interval ; genome-wide association study ; mathematical theory ; sample size ; variance
    Language English
    Dates of publication 2023-0113
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article ; Online
    ZDB-ID 2527218-4
    ISSN 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes14010211
    Database NAL-Catalogue (AGRICOLA)

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  7. Article: The "One Mind, Two Aspects" Model of the Self: The Self Model and Self-Cultivation Theory of Chinese Buddhism.

    Wang, Kai

    Frontiers in psychology

    2021  Volume 12, Page(s) 652465

    Abstract: Constructing a self model with universal cultural adaptability is a common concern of cultural psychologists. These models can be divided into two types: one is the self model based on Western culture, represented by the self theory of Marsh, Cooley, ... ...

    Abstract Constructing a self model with universal cultural adaptability is a common concern of cultural psychologists. These models can be divided into two types: one is the self model based on Western culture, represented by the self theory of Marsh, Cooley, Fitts, etc.; the other is the non-self model based on Eastern culture, represented by the Mandela model of Hwang Kwang Kuo and the Taiji model of Zhen Dong Wang. However, these models do not fully explain the self structure and development of Chinese people in the context of Chinese Buddhist culture. Based on the self theory of Chinese Buddhism and inspired by the famous Buddhist work
    Language English
    Publishing date 2021-04-28
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2563826-9
    ISSN 1664-1078
    ISSN 1664-1078
    DOI 10.3389/fpsyg.2021.652465
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Contribution of cerebrospinal fluid antibody titers and sex to acute cerebral blood flow in patients with anti-NMDAR autoimmune encephalitis.

    Miao, Ailiang / Wang, Kai

    Frontiers in immunology

    2024  Volume 15, Page(s) 1299898

    Abstract: Objective: The objective of this study was to elucidate the contribution of cerebrospinal fluid (CSF) antibody titers (AT) and sex to acute cerebral blood flow (CBF) in patients diagnosed with anti-: Methods: Forty-five patients diagnosed with NMDAR ... ...

    Abstract Objective: The objective of this study was to elucidate the contribution of cerebrospinal fluid (CSF) antibody titers (AT) and sex to acute cerebral blood flow (CBF) in patients diagnosed with anti-
    Methods: Forty-five patients diagnosed with NMDAR AE were recruited from December 2016 to January 2023. The acute CBF in patients with NMDAR AE at the early stage of the disease was analyzed using arterial spin labeling. The groups were compared based on CSF AT and sex. The connectivity of the CBF in the region of interest was also compared between groups.
    Results: The patients with different CSF AT exhibited varied brain regions with CBF abnormalities compared to the healthy subjects (
    Conclusion: CSF AT and sex contributed to CBF abnormalities in the patients diagnosed with NMDAR AE. Altered CBF might potentially serve as the diagnostic marker for NMDAR AE.
    MeSH term(s) Humans ; Male ; Female ; Anti-N-Methyl-D-Aspartate Receptor Encephalitis/diagnosis ; Brain/diagnostic imaging ; Receptors, N-Methyl-D-Aspartate ; Cerebrovascular Circulation ; Encephalitis ; Hashimoto Disease
    Chemical Substances Receptors, N-Methyl-D-Aspartate
    Language English
    Publishing date 2024-03-01
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2606827-8
    ISSN 1664-3224 ; 1664-3224
    ISSN (online) 1664-3224
    ISSN 1664-3224
    DOI 10.3389/fimmu.2024.1299898
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Deep-learning-enhanced light-field microscopy.

    Wang, Kai

    Nature methods

    2021  Volume 18, Issue 5, Page(s) 459–460

    MeSH term(s) Deep Learning ; Image Processing, Computer-Assisted ; Microscopy ; Neural Networks, Computer
    Language English
    Publishing date 2021-05-04
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 2169522-2
    ISSN 1548-7105 ; 1548-7091
    ISSN (online) 1548-7105
    ISSN 1548-7091
    DOI 10.1038/s41592-021-01151-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Stability Analysis and Design of

    Wang, Kai / Xu, Wei

    Sensors (Basel, Switzerland)

    2024  Volume 24, Issue 5

    Abstract: This paper is concerned with the stability analysis and design of ... ...

    Abstract This paper is concerned with the stability analysis and design of the
    Language English
    Publishing date 2024-02-29
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2052857-7
    ISSN 1424-8220 ; 1424-8220
    ISSN (online) 1424-8220
    ISSN 1424-8220
    DOI 10.3390/s24051600
    Database MEDical Literature Analysis and Retrieval System OnLINE

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