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Article: Human long noncoding RNA,

John, Kristen / Huntress, Ian / Smith, Ethan / Chou, Hsuan / Tollison, Tammy S / Covarrubias, Sergio / Crisci, Elisa / Carpenter, Susan / Peng, Xinxia

bioRxiv : the preprint server for biology

2024

Abstract: Long noncoding RNAs (lncRNAs) are a newer class of noncoding transcripts identified as key regulators of biological processes. Here we aimed to identify novel lncRNA targets that play critical roles in major human respiratory viral infections by ... ...

Abstract	Long noncoding RNAs (lncRNAs) are a newer class of noncoding transcripts identified as key regulators of biological processes. Here we aimed to identify novel lncRNA targets that play critical roles in major human respiratory viral infections by systematically mining large-scale transcriptomic datasets. Using bulk RNA-sequencing (RNA-seq) analysis, we identified a previously uncharacterized lncRNA, named virus inducible lncRNA modulator of interferon response (
Language	English
Publishing date	2024-03-29
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.03.25.586578
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Article ; Online: Inferring environmental transmission using phylodynamics: a case-study using simulated evolution of an enteric pathogen.

Dawson, Daniel / Rasmussen, David / Peng, Xinxia / Lanzas, Cristina

Journal of the Royal Society, Interface

2021 Volume 18, Issue 179, Page(s) 20210041

Abstract: Indirect (environmental) and direct (host-host) transmission pathways cannot easily be distinguished when they co-occur in epidemics, particularly when they occur on similar time scales. Phylodynamic reconstruction is a potential approach to this problem ...

Abstract	Indirect (environmental) and direct (host-host) transmission pathways cannot easily be distinguished when they co-occur in epidemics, particularly when they occur on similar time scales. Phylodynamic reconstruction is a potential approach to this problem that combines epidemiological information (temporal, spatial information) with pathogen whole-genome sequencing data to infer transmission trees of epidemics. However, factors such as differences in mutation and transmission rates between host and non-host environments may obscure phylogenetic inference from these methods. In this study, we used a network-based transmission model that explicitly models pathogen evolution to simulate epidemics with both direct and indirect transmission. Epidemics were simulated according to factorial combinations of direct/indirect transmission proportions, host mutation rates and conditions of environmental pathogen growth. Transmission trees were then reconstructed using the phylodynamic approach SCOTTI (structured coalescent transmission tree inference) and evaluated. We found that although insufficient diversity sets a lower bound on when accurate phylodynamic inferences can be made, transmission routes and assumed pathogen lifestyle affected pathogen population structure and subsequently influenced both reconstruction success and the likelihood of direct versus indirect pathways being reconstructed. We conclude that prior knowledge of the likely ecology and population structure of pathogens in host and non-host environments is critical to fully using phylodynamic techniques.
MeSH term(s)	Epidemics ; Phylogeny ; Probability
Language	English
Publishing date	2021-06-09
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2156283-0
ISSN	1742-5662 ; 1742-5689
ISSN (online)	1742-5662
ISSN	1742-5689
DOI	10.1098/rsif.2021.0041
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Pre-challenge gut microbial signature predicts RhCMV/SIV vaccine efficacy in rhesus macaques.

Brochu, Hayden N / Smith, Elise / Jeong, Sangmi / Carlson, Michelle / Hansen, Scott G / Tisoncik-Go, Jennifer / Law, Lynn / Picker, Louis J / Gale, Michael / Peng, Xinxia

bioRxiv : the preprint server for biology

2024

Abstract: Background: RhCMV/SIV vaccines protect ∼59% of vaccinated rhesus macaques against repeated limiting-dose intra-rectal exposure with highly pathogenic SIVmac239M, but the exact mechanism responsible for the vaccine efficacy is not known. It is becoming ... ...

Abstract	Background: RhCMV/SIV vaccines protect ∼59% of vaccinated rhesus macaques against repeated limiting-dose intra-rectal exposure with highly pathogenic SIVmac239M, but the exact mechanism responsible for the vaccine efficacy is not known. It is becoming evident that complex interactions exist between gut microbiota and the host immune system. Here we aimed to investigate if the rhesus gut microbiome impacts RhCMV/SIV vaccine-induced protection. Methods: Three groups of 15 rhesus macaques naturally pre-exposed to RhCMV were vaccinated with RhCMV/SIV vaccines. Rectal swabs were collected longitudinally both before SIV challenge (after vaccination) and post challenge and were profiled using 16S rRNA based microbiome analysis. Results: We identified ∼2,400 16S rRNA amplicon sequence variants (ASVs), representing potential bacterial species/strains. Global gut microbial profiles were strongly associated with each of the three vaccination groups, and all animals tended to maintain consistent profiles throughout the pre-challenge phase. Despite vaccination group differences, using newly developed compositional data analysis techniques we identified a common gut microbial signature predictive of vaccine protection outcome across the three vaccination groups. Part of this microbial signature persisted even after SIV challenge. We also observed a strong correlation between this microbial signature and an early signature derived from whole blood transcriptomes in the same animals. Conclusions: Our findings indicate that changes in gut microbiomes are associated with RhCMV/SIV vaccine-induced protection and early host response to vaccination in rhesus macaques.
Language	English
Publishing date	2024-02-28
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.02.27.582186
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Article ; Online: Orbital- and millennial-scale Asian winter monsoon variability across the Pliocene-Pleistocene glacial intensification.

Ao, Hong / Liebrand, Diederik / Dekkers, Mark J / Roberts, Andrew P / Jonell, Tara N / Jin, Zhangdong / Song, Yougui / Liu, Qingsong / Sun, Qiang / Li, Xinxia / Huang, Chunju / Qiang, Xiaoke / Zhang, Peng

Nature communications

2024 Volume 15, Issue 1, Page(s) 3364

Abstract: Intensification of northern hemisphere glaciation (iNHG), ~2.7 million years ago (Ma), led to establishment of the Pleistocene to present-day bipolar icehouse state. Here we document evolution of orbital- and millennial-scale Asian winter monsoon (AWM) ... ...

Abstract	Intensification of northern hemisphere glaciation (iNHG), ~2.7 million years ago (Ma), led to establishment of the Pleistocene to present-day bipolar icehouse state. Here we document evolution of orbital- and millennial-scale Asian winter monsoon (AWM) variability across the iNHG using a palaeomagnetically dated centennial-resolution grain size record between 3.6 and 1.9 Ma from a previously undescribed loess-palaeosol/red clay section on the central Chinese Loess Plateau. We find that the late Pliocene-early Pleistocene AWM was characterized by combined 41-kyr and ~100-kyr cycles, in response to ice volume and atmospheric CO
Language	English
Publishing date	2024-04-19
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-47274-9
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Article ; Online: Corrigendum to "A novel immune checkpoint siglec-15 antibody inhibits LUAD by modulating mφ polarization in TME" [Pharmacol. Res. 181 (2022) 106269].

Xiao, Xuejun / Peng, Yan / Wang, Zheyue / Zhang, Louqian / Yang, Tingting / Sun, Yangyang / Chen, Yufeng / Zhang, Wenqing / Chang, Xinxia / Huang, Wen / Tian, Shuning / Feng, Zhenqing / Xinhua, Nabi / Tang, Qi / Mao, Yuan

Pharmacological research

2022 Volume 182, Page(s) 106327

Language	English
Publishing date	2022-06-27
Publishing country	Netherlands
Document type	Published Erratum
ZDB-ID	1003347-6
ISSN	1096-1186 ; 0031-6989 ; 1043-6618
ISSN (online)	1096-1186
ISSN	0031-6989 ; 1043-6618
DOI	10.1016/j.phrs.2022.106327
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Article ; Online: A review for modified Li composite anode

Yang Xinxia / Peng Yi / Hou Jia / Liu Yifan / Jian Xian

Nanotechnology Reviews, Vol 9, Iss 1, Pp 1610-

Principle, preparation and challenge

2020 Volume 1624

Abstract: As the most common energy storage technology on the market, lithium-ion batteries are widely used in various industries and have a profound impact on our daily lives, with the characteristics of high voltage, high capacity, good safety performance, and ... ...

Abstract	As the most common energy storage technology on the market, lithium-ion batteries are widely used in various industries and have a profound impact on our daily lives, with the characteristics of high voltage, high capacity, good safety performance, and long cycle life. Lithium metal was first used in the anode of lithium-ion batteries. However, the inherent growth of lithium dendrites and the instability of the SEI film limit the practical application of lithium metal materials. Despite this, lithium metal is still an ideal anode material to meet the growing demands for electronic equipment and electric vehicles due to its extremely high theoretical specific capacity, low density, and the lowest negative electrochemical potential. With the urgent need to develop new energy storage technologies, the research on lithium metal anodes has once again received extensive attention. In this review, the research progress in the modification of composite lithium metal electrode materials is summarized, including lithium/alloy composite electrode, lithium/carbon-based materials composite electrode and artificial SEI film. The possible directions for future development of lithium metal electrode are also prospected.
Keywords	lithium-ion battery ; lithium metal anode ; modification ; Technology ; T ; Chemical technology ; TP1-1185 ; Physical and theoretical chemistry ; QD450-801
Subject code	540
Language	English
Publishing date	2020-12-01T00:00:00Z
Publisher	De Gruyter
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Concurrent Asian monsoon strengthening and early modern human dispersal to East Asia during the last interglacial.

Proceedings of the National Academy of Sciences of the United States of America

2024 Volume 121, Issue 3, Page(s) e2308994121

Abstract: The relationship between ... ...

Abstract	The relationship between initial
MeSH term(s)	Humans ; Africa ; Asia ; Asia, Eastern ; Asian People ; Human Migration ; Weather
Language	English
Publishing date	2024-01-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2308994121
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Zs.A 1148: Show issues

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Article ; Online: Phylogeny-guided microbiome OTU-specific association test (POST)

Caizhi Huang / Benjamin J. Callahan / Michael C. Wu / Shannon T. Holloway / Hayden Brochu / Wenbin Lu / Xinxia Peng / Jung-Ying Tzeng

Microbiome, Vol 10, Iss 1, Pp 1-

2022 Volume 15

Abstract: Abstract Background The relationship between host conditions and microbiome profiles, typically characterized by operational taxonomic units (OTUs), contains important information about the microbial role in human health. Traditional association testing ... ...

Abstract	Abstract Background The relationship between host conditions and microbiome profiles, typically characterized by operational taxonomic units (OTUs), contains important information about the microbial role in human health. Traditional association testing frameworks are challenged by the high dimensionality and sparsity of typical microbiome profiles. Phylogenetic information is often incorporated to address these challenges with the assumption that evolutionarily similar taxa tend to behave similarly. However, this assumption may not always be valid due to the complex effects of microbes, and phylogenetic information should be incorporated in a data-supervised fashion. Results In this work, we propose a local collapsing test called phylogeny-guided microbiome OTU-specific association test (POST). In POST, whether or not to borrow information and how much information to borrow from the neighboring OTUs in the phylogenetic tree are supervised by phylogenetic distance and the outcome-OTU association. POST is constructed under the kernel machine framework to accommodate complex OTU effects and extends kernel machine microbiome tests from community level to OTU level. Using simulation studies, we show that when the phylogenetic tree is informative, POST has better performance than existing OTU-level association tests. When the phylogenetic tree is not informative, POST achieves similar performance as existing methods. Finally, in real data applications on bacterial vaginosis and on preterm birth, we find that POST can identify similar or more outcome-associated OTUs that are of biological relevance compared to existing methods. Conclusions Using POST, we show that adaptively leveraging the phylogenetic information can enhance the selection performance of associated microbiome features by improving the overall true-positive and false-positive detection. We developed a user friendly R package POSTm which is freely available on CRAN ( https://CRAN.R-project.org/package=POSTm ). Video Abstract.
Keywords	Association test ; Phylogenetic tree ; Kernel machine regression ; Microbial ecology ; QR100-130
Language	English
Publishing date	2022-06-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Engineering c-Met-CAR NK-92 cells as a promising therapeutic candidate for lung adenocarcinoma.

Peng, Yan / Zhang, Wenqing / Chen, Yufeng / Zhang, Louqian / Shen, Hongyu / Wang, Zheyue / Tian, Shuning / Yang, Xiaohui / Cui, Daixun / He, Yiting / Chang, Xinxia / Feng, Zhenqing / Tang, Qi / Mao, Yuan

Pharmacological research

2023 Volume 188, Page(s) 106656

Abstract: Mesenchymal-epithelial transition factor (C-Met) has been acknowledged as a significant therapeutic target for treating lung adenocarcinoma (LUAD). However, the potential application of chimeric antigen receptors (CAR)-modified natural killer (NK) cells ... ...

Abstract	Mesenchymal-epithelial transition factor (C-Met) has been acknowledged as a significant therapeutic target for treating lung adenocarcinoma (LUAD). However, the potential application of chimeric antigen receptors (CAR)-modified natural killer (NK) cells targeting c-Met in LUAD is rarely explored. In this study, bioinformatic databases were searched and a tissue microarray (TMA) was enrolled to investigate expression status and prognostic role of c-Met in LUAD. Then, four types of c-Met-CAR structures were designed and prepared. The engineering CAR-NK cells containing c-Met-CARs were transfected, verified and characterized. The tumor-inhibitory role of c-Met-CAR-NK cells was finally evaluated in vitro and in vivo. The results demonstrated that c-Met expression elevated and confirmed that high c-Met expression was significantly associated with unfavorable prognosis in LUAD. Then, C-Met-CAR-NK cells were successfully constructed and DAP10 designed in CAR structure was a favorable stimulator for NK cell activation. CCN4 containing DAP10 co-stimulator exhibited the strongest cytotoxicity compared with other CAR-NK cells. Furthermore, CCN4 cells also exerted the prominent tumor-inhibitory effect on xenograft tumor growth. Collectively, this study suggests that DAP10 is a potent stimulator in CAR structure for NK cell activation, and CCN4-based immunotherapy may represent a promising strategy for the treatment of c-Met-positive LUAD.
MeSH term(s)	Humans ; Receptors, Chimeric Antigen ; Cell Line, Tumor ; Killer Cells, Natural ; Adenocarcinoma of Lung/genetics ; Adenocarcinoma of Lung/therapy ; Adenocarcinoma of Lung/metabolism ; Lung Neoplasms/genetics ; Lung Neoplasms/therapy ; Lung Neoplasms/metabolism
Chemical Substances	Receptors, Chimeric Antigen
Language	English
Publishing date	2023-01-11
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1003347-6
ISSN	1096-1186 ; 0031-6989 ; 1043-6618
ISSN (online)	1096-1186
ISSN	0031-6989 ; 1043-6618
DOI	10.1016/j.phrs.2023.106656
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Article ; Online: Phylogeny-guided microbiome OTU-specific association test (POST).

Huang, Caizhi / Callahan, Benjamin J / Wu, Michael C / Holloway, Shannon T / Brochu, Hayden / Lu, Wenbin / Peng, Xinxia / Tzeng, Jung-Ying

Microbiome

2022 Volume 10, Issue 1, Page(s) 86

Abstract: Background: The relationship between host conditions and microbiome profiles, typically characterized by operational taxonomic units (OTUs), contains important information about the microbial role in human health. Traditional association testing ... ...

Abstract	Background: The relationship between host conditions and microbiome profiles, typically characterized by operational taxonomic units (OTUs), contains important information about the microbial role in human health. Traditional association testing frameworks are challenged by the high dimensionality and sparsity of typical microbiome profiles. Phylogenetic information is often incorporated to address these challenges with the assumption that evolutionarily similar taxa tend to behave similarly. However, this assumption may not always be valid due to the complex effects of microbes, and phylogenetic information should be incorporated in a data-supervised fashion. Results: In this work, we propose a local collapsing test called phylogeny-guided microbiome OTU-specific association test (POST). In POST, whether or not to borrow information and how much information to borrow from the neighboring OTUs in the phylogenetic tree are supervised by phylogenetic distance and the outcome-OTU association. POST is constructed under the kernel machine framework to accommodate complex OTU effects and extends kernel machine microbiome tests from community level to OTU level. Using simulation studies, we show that when the phylogenetic tree is informative, POST has better performance than existing OTU-level association tests. When the phylogenetic tree is not informative, POST achieves similar performance as existing methods. Finally, in real data applications on bacterial vaginosis and on preterm birth, we find that POST can identify similar or more outcome-associated OTUs that are of biological relevance compared to existing methods. Conclusions: Using POST, we show that adaptively leveraging the phylogenetic information can enhance the selection performance of associated microbiome features by improving the overall true-positive and false-positive detection. We developed a user friendly R package POSTm which is freely available on CRAN ( https://CRAN.R-project.org/package=POSTm ). Video Abstract.
MeSH term(s)	Computational Biology/methods ; Computer Simulation ; Female ; Humans ; Infant, Newborn ; Microbiota/genetics ; Phylogeny ; Premature Birth
Language	English
Publishing date	2022-06-07
Publishing country	England
Document type	Journal Article ; Video-Audio Media ; 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/s40168-022-01266-3
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