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Article: A Mixed Effect Similarity Matrix Regression Model (SMRmix) for Integrating Multiple Microbiome Datasets at Community Level and its Application in HIV.

He, Mengyu / Zhao, Ni

bioRxiv : the preprint server for biology

2024

Abstract: Recent studies have highlighted the importance of human microbiota in our health and diseases. However, in many areas of research, individual microbiome studies often offer inconsistent results due to the limited sample sizes and the heterogeneity in ... ...

Abstract	Recent studies have highlighted the importance of human microbiota in our health and diseases. However, in many areas of research, individual microbiome studies often offer inconsistent results due to the limited sample sizes and the heterogeneity in study populations and experimental procedures. Integrative analysis of multiple microbiome datasets is necessary. However, statistical methods that incorporate multiple microbiome datasets and account for the study heterogeneity are not available in the literature. In this paper, we develop a mixed effect similarity matrix regression (SMRmix) approach for identifying community level microbiome shifts between outcomes. SMRmix has a close connection with the microbiome kernel association test, one of the most popular approaches for such a task but is only applicable when we have a single study. Via extensive simulations, we show that SMRmix has well-controlled type I error and higher power than some potential competitors. We also applied SMRmix to data from the HIV-reanalysis consortium, a collective effort that obtained all publicly available data on gut microbiome and HIV at December 2017, and obtained consistent associations of gut microbiome with HIV infection, and with MSM status (i.e. men who have sex with men).
Language	English
Publishing date	2024-03-13
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.03.10.584315
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Article: MIDASim: a fast and simple simulator for realistic microbiome data.

He, Mengyu / Zhao, Ni / Satten, Glen A

bioRxiv : the preprint server for biology

2024

Abstract: Background: Advances in sequencing technology has led to the discovery of associations between the human microbiota and many diseases, conditions, and traits. With the increasing availability of microbiome data, many statistical methods have been ... ...

Abstract	Background: Advances in sequencing technology has led to the discovery of associations between the human microbiota and many diseases, conditions, and traits. With the increasing availability of microbiome data, many statistical methods have been developed for studying these associations. The growing number of newly developed methods highlights the need for simple, rapid, and reliable methods to simulate realistic microbiome data, which is essential for validating and evaluating the performance of these methods. However, generating realistic microbiome data is challenging due to the complex nature of microbiome data, which feature correlation between taxa, sparsity, overdispersion, and compositionality. Current methods for simulating microbiome data are deficient in their ability to capture these important features of microbiome data, or can require exorbitant computational time. Methods: We develop MIDASim ( MI crobiome DA ta Sim ulator), a fast and simple approach for simulating realistic microbiome data that reproduces the distributional and correlation structure of a template microbiome dataset. MIDASim is a two-step approach. The first step generates correlated binary indicators that represent the presence-absence status of all taxa, and the second step generates relative abundances and counts for the taxa that are considered to be present in step 1, utilizing a Gaussian copula to account for the taxon-taxon correlations. In the second step, MIDASim can operate in both a nonparametric and parametric mode. In the nonparametric mode, the Gaussian copula uses the empirical distribution of relative abundances for the marginal distributions. In the parametric mode, an inverse generalized gamma distribution is used in place of the empirical distribution. Results: We demonstrate improved performance of MIDASim relative to other existing methods using gut and vaginal data. MIDASim showed superior performance by PER-MANOVA and in terms of alpha diversity and beta dispersion in either parametric or nonparametric mode. We also show how MIDASim in parametric mode can be used to assess the performance of methods for finding differentially abundant taxa in a compositional model. Conclusions: MIDASim is easy to implement, flexible and suitable for most microbiome data simulation situations. MIDASim has three major advantages. First, MIDASim performs better in reproducing the distributional features of real data compared to other methods at both presence-absence level and relative-abundance level. MIDASim-simulated data are more similar to the template data than competing methods, as quantified using a variety of measures. Second, MIDASim makes few distributional assumptions for the relative abundances, and thus can easily accommodate complex distributional features in real data. Third, MIDASim is computationally efficient and can be used to simulate large microbiome datasets.
Language	English
Publishing date	2024-03-27
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.03.23.533996
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Article ; Online: Health-related quality of life and associated factors among people living with HIV/AIDS in Sichuan, China

Hua Zhong / Fuling Wei / Yuqing Song / Hong Chen / Zhao Ni

Frontiers in Public Health, Vol

A cross-sectional study

2023 Volume 11

Abstract: PurposeThis study aimed to explore health-related quality of life (HRQoL) and its associated factors among people living with HIV/AIDS (PLWH) in Sichuan, China.MethodsA total of 401 PLWH were recruited from the city of Panzhihua between August 2018 and ... ...

Abstract	PurposeThis study aimed to explore health-related quality of life (HRQoL) and its associated factors among people living with HIV/AIDS (PLWH) in Sichuan, China.MethodsA total of 401 PLWH were recruited from the city of Panzhihua between August 2018 and January 2019. Demographic characteristics and disease-related data were collected by self-administered questionnaires and medical system records. Health-related quality of life (HRQoL) was measured by the medical outcome study HIV health survey (MOS-HIV), which measured ten subdimensions and two summarized dimensions, the physical health summary score (PHS) and the mental health summary score (MHS). Logistic regression models were used to explore the variables independently associated with quality of life.ResultsThe PHS and MHS measured by MOS-HIV were 53.66 ± 6.80 and 51.31 ± 7.66, respectively. Younger age, higher educational level, no methadone use, higher CD4 lymphocyte counts, less symptom counts and heathy BMI significantly were associated with higher HRQOL in the univariate χ2-test analysis. Education level was found to have a significant influence on patients' quality of life, both in physical health (P = 0.022) and mental health (P = 0.002) dimensions. Younger age (P = 0.032), higher CD4 lymphocyte counts (P = 0.007), less symptom counts (P < 0.001) and health BMI level (P < 0.001) were positively related to the PHS of quality of life in the multivariable logistic regression model.ConclusionThe HRQoL of PLWH in Sinchuan Province was relatively low. Age, educational level, methadone use, CD4 lymphocyte counts, symptom counts and BMI were positively related to quality of life. This study indicates that health caregivers should pay more attention to comorbidity issues and mental health in PLWH, especially for those with lower education levels, unhealthy body mass index, more symptomatic presentation and older age.
Keywords	HIV ; health-related quality of life ; China ; influencing factors ; cross-sectional study ; Public aspects of medicine ; RA1-1270
Subject code	360
Language	English
Publishing date	2023-03-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Study on the antidepressive effects and mechanism of raw and fried Ziziphi Spinosae Semen via metabolomics and gut microbiota analysis.

Du, Chenhui / Han, Rui / Wu, Jiang / Zhao, Ni / Pei, Xiangping / Qin, Xuemei / Yan, Yan

Biomedical chromatography : BMC

2024 , Page(s) e5873

Abstract: Ziziphi Spinosae Semen (ZSS) and fried ZSS (FZSS) have been used for treating insomnia and depression in China. However, the potential influence of chemical variations on their efficacy remains unclear. This study demonstrated that compared with ZSS, ... ...

Abstract	Ziziphi Spinosae Semen (ZSS) and fried ZSS (FZSS) have been used for treating insomnia and depression in China. However, the potential influence of chemical variations on their efficacy remains unclear. This study demonstrated that compared with ZSS, FZSS exhibited an increase in the content of seven compounds, while the fatty oil content decreased. Both ZSS and FZSS exhibited antidepressive effects in a chronic unpredictable mild stress rat model, indicating a synergistic regulation of deficiencies in 5-hydroxytryptamine in the brain and the hyperactivation of severe peripheral inflammation. ZSS demonstrated a superior modulatory effect compared with FZSS, as indicated by integrated pharmacodynamic index, metabolic profile, and relative distance value. The potential mechanism underlying their antidepressive effects involved the modulation of gut microbiota structure to alleviate excessive inflammatory responses and imbalanced tryptophan metabolism. Correlation analysis indicated that the higher fatty oil contents should be comprehensively considered as the main reason for ZSS's superior antidepressive effects, achieved through the regulation of pyroglutamic acid levels.
Language	English
Publishing date	2024-04-08
Publishing country	England
Document type	Journal Article
ZDB-ID	632848-9
ISSN	1099-0801 ; 0269-3879
ISSN (online)	1099-0801
ISSN	0269-3879
DOI	10.1002/bmc.5873
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Article ; Online: The Gut-Brain-Sleep Connection in Older Adults: What Do We Learn From the Microbiome?

Mueller, Noel T / Liu, Tiange / Debelius, Justine / Zhao, Ni

The journals of gerontology. Series A, Biological sciences and medical sciences

2023 Volume 78, Issue 10, Page(s) 1933–1934

MeSH term(s)	Male ; Humans ; Aged ; Gastrointestinal Microbiome ; Osteoporotic Fractures ; Brain ; Sleep ; Microbiota
Language	English
Publishing date	2023-10-07
Publishing country	United States
Document type	Editorial ; Comment
ZDB-ID	1223643-3
ISSN	1758-535X ; 1079-5006
ISSN (online)	1758-535X
ISSN	1079-5006
DOI	10.1093/gerona/glad049
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Article ; Online: Editorial

Zhao Ni / Santi Martini / Erin M. Spaulding / Arief Hargono / Seth Shay Martin

Frontiers in Public Health, Vol

Future trends and directions of using mHealth strategies to prevent and treat cardiovascular diseases

2023 Volume 11

Keywords	mobile health ; mHealth ; cardiovascular diseases ; strategies ; trends ; prevention ; Public aspects of medicine ; RA1-1270
Language	English
Publishing date	2023-07-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
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Article ; Online: Ion Migration in Perovskite Light-Emitting Diodes: Mechanism, Characterizations, and Material and Device Engineering.

Li, Nan / Jia, Yongheng / Guo, Yuwei / Zhao, Ni

Advanced materials (Deerfield Beach, Fla.)

2022 Volume 34, Issue 19, Page(s) e2108102

Abstract: In recent years, perovskite light-emitting diodes (PeLEDs) have emerged as a promising new lighting technology with high external quantum efficiency, color purity, and wavelength tunability, as well as, low-temperature processability. However, the ... ...

Abstract	In recent years, perovskite light-emitting diodes (PeLEDs) have emerged as a promising new lighting technology with high external quantum efficiency, color purity, and wavelength tunability, as well as, low-temperature processability. However, the operational stability of PeLEDs is still insufficient for their commercialization. The generation and migration of ionic species in metal halide perovskites has been widely acknowledged as the primary factor causing the performance degradation of PeLEDs. Herein, this topic is systematically discussed by considering the fundamental and engineering aspects of ion-related issues in PeLEDs, including the material and processing origins of ion generation, the mechanisms driving ion migration, characterization approaches for probing ion distributions, the effects of ion migration on device performance and stability, and strategies for ion management in PeLEDs. Finally, perspectives on remaining challenges and future opportunities are highlighted.
Language	English
Publishing date	2022-03-18
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	1474949-X
ISSN	1521-4095 ; 0935-9648
ISSN (online)	1521-4095
ISSN	0935-9648
DOI	10.1002/adma.202108102
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Article: New Perspectives on the Aberrant Alveolar Repair of Idiopathic Pulmonary Fibrosis.

Wang, Zhao Ni / Tang, Xiao Xiao

Frontiers in cell and developmental biology

2020 Volume 8, Page(s) 580026

Abstract: Idiopathic pulmonary fibrosis (IPF) is a chronic lung disease of unknown etiology and high mortality. Current therapeutic strategies have limited efficacy and the prognosis remains poor. Based on the histological observations of IPF lung tissues and ... ...

Abstract	Idiopathic pulmonary fibrosis (IPF) is a chronic lung disease of unknown etiology and high mortality. Current therapeutic strategies have limited efficacy and the prognosis remains poor. Based on the histological observations of IPF lung tissues and experimental studies using lung fibrosis animal models, it is gradually accepted that impaired epithelial regeneration after lung injury is a critical mechanism underlying the pathogenesis of pulmonary fibrosis. The central role of AEC2 in this process has been well-elucidated, while the contribution of other lung progenitor/stem cells is less discussed. Recently, increasing studies have identified several non-AEC2 epithelial progenitor/stem cells with great plasticity to transform into mature AECs and reconstitute alveolar epithelium after lung injury. However, why these cells do not function as alternate stem cells to regenerate alveolar epithelium in IPF is still unknown. In this review, we discuss the contribution of lung epithelial progenitor/stem cells in the aberrant alveolar regeneration, and provide a novel perspective on the mechanism of IPF pathogenesis, in which non-AEC2 progenitors may play an essential role.
Language	English
Publishing date	2020-09-30
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2737824-X
ISSN	2296-634X
ISSN	2296-634X
DOI	10.3389/fcell.2020.580026
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Article ; Online: A powerful microbial group association test based on the higher criticism analysis for sparse microbial association signals.

Koh, Hyunwook / Zhao, Ni

Microbiome

2020 Volume 8, Issue 1, Page(s) 63

Abstract: Background: In human microbiome studies, it is crucial to evaluate the association between microbial group (e.g., community or clade) composition and a host phenotype of interest. In response, a number of microbial group association tests have been ... ...

Abstract	Background: In human microbiome studies, it is crucial to evaluate the association between microbial group (e.g., community or clade) composition and a host phenotype of interest. In response, a number of microbial group association tests have been proposed, which account for the unique features of the microbiome data (e.g., high-dimensionality, compositionality, phylogenetic relationship). These tests generally fall in the class of aggregation tests which amplify the overall group association by combining all the underlying microbial association signals, and, therefore, they are powerful when many microbial species are associated with a given host phenotype (i.e., low sparsity). However, in practice, the microbial association signals can be highly sparse, and this is especially the situation where we have a difficulty to discover the microbial group association. Methods: Here, we introduce a powerful microbial group association test for sparse microbial association signals, namely, microbiome higher criticism analysis (MiHC). MiHC is a data-driven omnibus test taken in a search space spanned by tailoring the higher criticism test to incorporate phylogenetic information and/or modulate sparsity levels and including the Simes test for excessively high sparsity levels. Therefore, MiHC robustly adapts to diverse phylogenetic relevance and sparsity levels. Results: Our simulations show that MiHC maintains a high power at different phylogenetic relevance and sparsity levels with correct type I error controls. We also apply MiHC to four real microbiome datasets to test the association between respiratory tract microbiome and smoking status, the association between the infant's gut microbiome and delivery mode, the association between the gut microbiome and type 1 diabetes status, and the association between the gut microbiome and human immunodeficiency virus status. Conclusions: In practice, the true underlying association pattern on the extent of phylogenetic relevance and sparsity is usually unknown. Therefore, MiHC can be a useful analytic tool because of its high adaptivity to diverse phylogenetic relevance and sparsity levels. MiHC can be implemented in the R computing environment using our software package freely available at https://github.com/hk1785/MiHC.
MeSH term(s)	Computational Biology ; Humans ; Microbiota ; Software
Language	English
Publishing date	2020-05-11
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2697425-3
ISSN	2049-2618 ; 2049-2618
ISSN (online)	2049-2618
ISSN	2049-2618
DOI	10.1186/s40168-020-00834-9
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Book ; Online: Early ChatGPT User Portrait through the Lens of Data

Deng, Yuyang / Zhao, Ni / Huang, Xin

2023

Abstract: Since its launch, ChatGPT has achieved remarkable success as a versatile conversational AI platform, drawing millions of users worldwide and garnering widespread recognition across academic, industrial, and general communities. This paper aims to point a ...

Abstract	Since its launch, ChatGPT has achieved remarkable success as a versatile conversational AI platform, drawing millions of users worldwide and garnering widespread recognition across academic, industrial, and general communities. This paper aims to point a portrait of early GPT users and understand how they evolved. Specific questions include their topics of interest and their potential careers; and how this changes over time. We conduct a detailed analysis of real-world ChatGPT datasets with multi-turn conversations between users and ChatGPT. Through a multi-pronged approach, we quantify conversation dynamics by examining the number of turns, then gauge sentiment to understand user sentiment variations, and finally employ Latent Dirichlet Allocation (LDA) to discern overarching topics within the conversation. By understanding shifts in user demographics and interests, we aim to shed light on the changing nature of human-AI interaction and anticipate future trends in user engagement with language models. Comment: 6 pages, 5 figures, 2023 IEEE International Conference on Big Data (BigData), to be published
Keywords	Computer Science - Human-Computer Interaction ; Computer Science - Artificial Intelligence ; Computer Science - Computation and Language ; Computer Science - Machine Learning
Subject code	004
Publishing date	2023-12-10
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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