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Article ; Online: Exosomes Promote Atherosclerosis Progression by Regulating Circ_100696/miR-503-5p/PAPPA Axis-Mediated Vascular Smooth Muscle Cells Proliferation and Migration.

Liu, Jing / Zhang, Xiangyang / Yu, Zhaoxia / Zhang, Tieliang

2023 Volume 64, Issue 5, Page(s) 918–927

Abstract: Circular RNAs (circRNAs) are known to play a crucial role in the progression of atherosclerosis (AS). In this study, we aim to explore the function of oxidized low-density lipoprotein (ox-LDL)-induced macrophage-derived exosomal circ_100696 in AS.THP-1 ... ...

Abstract	Circular RNAs (circRNAs) are known to play a crucial role in the progression of atherosclerosis (AS). In this study, we aim to explore the function of oxidized low-density lipoprotein (ox-LDL)-induced macrophage-derived exosomal circ_100696 in AS.THP-1 macrophages were induced by ox-LDL to mimic AS cell model. A quantitative real-time polymerase chain reaction (qRT-PCR) assay was applied to determine the expression of circ_100696, microRNA-503-5p (miR-503-5p), and pregnancy-associated plasma protein A (PAPPA). The morphology and size distribution of exosomes were examined by transmission electron microscopy (TEM) and nanoparticle tracking analysis (NTA). Western blot assay was performed for protein levels. Cell proliferation was assessed using 5-ethynyl-2'-deoxyuridine (EdU) assay. Flow cytometry analysis was performed to analyze the cell cycle. Wound-healing assay and transwell assay were done to examine cell migration. RNA pull-down assay, dual-luciferase reporter assay, and RNA immunoprecipitation (RIP) assay were employed to analyze the relationship among circ_100696, miR-503-5p, and PAPPA.Circ_100696 level was increased in ox-LDL-induced THP-1 macrophages and ox-LDL-treated THP-1 macrophage-derived exosomes (OM-Exo). OM-Exo promoted the proliferation, cell cycle, and migration of vascular smooth muscle cells (VSMCs). Circ_100696 was upregulated in VSMCs cocultured with OM-Exo. Circ_100696 knockdown reversed the effects of OM-Exo on VSMC proliferation and migration. Circ_100696 was demonstrated to function as the sponge for miR-503-5p, and miR-503-5p directly targeted PAPPA. Circ_100696 overexpression facilitated VSMC proliferation and migration, with miR-503-5p upregulation or PAPPA silencing reversing these effects. Moreover, circ_100696 overexpression promoted PAPPA expression by targeting miR-503-5p.OM-Exo promoted VSMC growth and migration by regulating the circ_100696/miR-503-5p/PAPPA axis, thereby promoting AS progression.
MeSH term(s)	Humans ; Atherosclerosis/genetics ; Cell Proliferation/genetics ; Exosomes/genetics ; Lipoproteins, LDL ; MicroRNAs/genetics ; Muscle, Smooth, Vascular ; RNA, Circular/genetics ; THP-1 Cells
Chemical Substances	Lipoproteins, LDL ; MicroRNAs ; MIRN503 microRNA, human ; RNA, Circular
Language	English
Publishing date	2023-09-16
Publishing country	Japan
Document type	Journal Article
ZDB-ID	2187806-7
ISSN	1349-3299 ; 1349-2365
ISSN (online)	1349-3299
ISSN	1349-2365
DOI	10.1536/ihj.23-089
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Article ; Online: Intranasal Delivery of Ketamine Induces Cortical Disinhibition.

Qiao, Xin / Grieco, Steven F / Yu, Zhaoxia / Holmes, Todd C / Xu, Xiangmin

eNeuro

2024 Volume 11, Issue 1

Abstract: Our previous studies find that subcutaneously administered (s.c.) subanesthetic ketamine promotes sustained cortical disinhibition and plasticity in adult mouse binocular visual cortex (bV1). We hypothesized that intranasal delivery (i.n.) of ... ...

Abstract	Our previous studies find that subcutaneously administered (s.c.) subanesthetic ketamine promotes sustained cortical disinhibition and plasticity in adult mouse binocular visual cortex (bV1). We hypothesized that intranasal delivery (i.n.) of subanesthetic ketamine may have similar actions. To test this, we delivered ketamine (10 mg/kg, i.n.) to adult mice and then recorded excitatory pyramidal neurons or PV+ interneurons in L2/3 of bV1 slices. In pyramidal neurons the baseline IPSC amplitudes from mice treated with ketamine are significantly weaker than those in control mice. Acute bath application of neuregulin-1 (NRG1) to cortical slices increases these IPSC amplitudes in mice treated with ketamine but not in controls. In PV+ interneurons, the baseline EPSC amplitudes from mice treated with ketamine are significantly weaker than those in control mice. Acute bath application of NRG1 to cortical slices increases these EPSC amplitudes in mice treated with ketamine but not in controls. We also found that mice treated with ketamine exhibit increased pCREB staining in L2/3 of bV1. Together, our results show that a single intranasal delivery of ketamine reduces PV+ interneuron excitation and reduces pyramidal neuron inhibition and that these effects are acutely reversed by NRG1. These results are significant as they show that intranasal delivery of ketamine induces cortical disinhibition, which has implications for the treatment of psychiatric, neurologic, and ophthalmic disorders.
MeSH term(s)	Mice ; Animals ; Ketamine/pharmacology ; Pyramidal Cells/physiology ; Interneurons ; Neuronal Plasticity/physiology ; Parvalbumins/pharmacology
Chemical Substances	Esketamine (50LFG02TXD) ; Ketamine (690G0D6V8H) ; Parvalbumins
Language	English
Publishing date	2024-01-17
Publishing country	United States
Document type	Journal Article
ZDB-ID	2800598-3
ISSN	2373-2822 ; 2373-2822
ISSN (online)	2373-2822
ISSN	2373-2822
DOI	10.1523/ENEURO.0107-23.2023
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Article: Ultrasonographic Features and Pregnancy Outcomes of Complications in Monochorionic Twin Pregnancy During Various Pregnancy Periods.

Ding, Yunfei / Li, Jian / Liu, Wei / Anniwaer, Ankaerjiang / Li, Bo / Chen, Yutang / Yu, Zhaoxia

Alternative therapies in health and medicine

2024

Abstract: Objective: It was to explore the ultrasonic characteristics of complications of twin pregnancies with monochorionic diamniotic (MCDA) during various pregnancy periods and the differences in pregnancy outcomes.: Methods: One hundred pregnant women ... ...

Abstract	Objective: It was to explore the ultrasonic characteristics of complications of twin pregnancies with monochorionic diamniotic (MCDA) during various pregnancy periods and the differences in pregnancy outcomes. Methods: One hundred pregnant women with MCDA were included in the study. They were rolled into a complication group (44 cases) and a non-complication group (56 cases) according to whether they had complications. The pulsatility index (PI), resistance index (RI), and systolic/diastolic (S/D) values of ultrasound in pregnant women and the final neonatal situation at each time period were compared and analyzed. Results: In pregnant women with twin-twin transfusion syndrome (TTTS), there was no significant difference in RI and S/D values between the larger and smaller twin during pregnancy (P > .05). Compared to the group without complications, the incidence of neonatal death was significantly increased in the complication group, and the newborn's weight, length, head circumference, and Apgar score were significantly lower (P < .05). In pregnant women with selective intrauterine growth restriction (sIUGR), the RI and PI values of the larger twin were significantly higher than those of the smaller twin during pregnancy, and S/D values were significantly lower (P < .05). The newborns in the group without complications had significantly higher body weight, length, and head circumference (P < .05). In pregnant women with gestational diabetes mellitus (GDM), there was no significant difference in RI and S/D values between the larger and smaller twin during pregnancy (P > .05), and there were no significant differences in other indicators compared to the group without complications. In pregnant women with premature rupture of membrane (PROM), there was no significant difference in RI and S/D values between the larger and smaller twin during pregnancy (P > .05), but the newborns in the group without complications had significantly higher weight, length, Apgar score, and lower incidence of neonatal death (P < .05). In pregnant women with preeclampsia (PE), there was no significant difference in RI and S/D values between the larger and smaller twin during pregnancy (P > .05), and there were no significant differences in other indicators compared to the group without complications (P > .05). Conclusion: Pregnant women with sIUGR had significantly higher RI and PI values in the larger twin and significantly lower S/D values compared to the smaller twin during pregnancy, while no significant differences were observed for other complications. The combination of TTTS and PROM decreased the birth weight, body length, head circumference, and Apgar score of twins and increased the mortality rate.
Language	English
Publishing date	2024-03-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	1225073-9
ISSN	1078-6791
ISSN	1078-6791
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Zs.A 4504: Show issues

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Article ; Online: Circ_0026218 ameliorates oxidized low-density lipoprotein-induced vascular endothelial cell dysfunction by regulating miR-188-3p/TLR4/NF-κB pathway.

Liu, Jing / Zhang, Xiangyang / Yu, Zhaoxia / Zhang, Tieliang

Cardiovascular drugs and therapy

2022 Volume 38, Issue 2, Page(s) 263–277

Abstract: Background: Circular RNAs (circRNAs) have shown important regulatory roles in cardiovascular diseases, including atherosclerosis (AS). However, the role and mechanism of circ_0026218 in AS remain unclear.: Methods: The cell model of AS in vitro was ... ...

Abstract	Background: Circular RNAs (circRNAs) have shown important regulatory roles in cardiovascular diseases, including atherosclerosis (AS). However, the role and mechanism of circ_0026218 in AS remain unclear. Methods: The cell model of AS in vitro was established by stimulating human umbilical vein endothelial cells (HUVECs) with oxidized low-density lipoprotein (ox-LDL). In addition, circ_0026218, microRNA-188-3p (miR-188-3p), and toll-like receptor 4 (TLR4) expression was determined via real-time quantitative polymerase chain reaction (RT-qPCR) in serum samples from AS patients and healthy volunteers. Cell proliferation was assessed using Cell Counting Kit-8 (CCK-8) assay and 5-ethynyl-2'-deoxyuridine (EdU) assay. Cell apoptosis was measured using flow cytometry. The inflammatory response was assessed using enzyme-linked immunosorbent assay (ELISA). Oxidative stress level was assessed using corresponding kits. Nitric oxide (NO) level was examined using NO detection assay. The interaction between miR-188-3p and circ_0026218 or TLR4 was determined via dual-luciferase reporter, RNA immunoprecipitation (RIP), and RNA pull-down assays. Exosomes were observed using transmission electron microscopy (TEM). The size distribution of exosomes was analyzed using nanoparticle tracking analysis (NTA). Results: Ox-LDL treatment caused HUVEC dysfunction by inhibiting cell proliferation and promoting apoptosis, inflammation, and oxidative stress. Circ_0026218 was upregulated in AS serum samples and ox-LDL-treated HUVECs. Knockdown of circ_0026218 attenuated ox-LDL-induced dysfunction in HUVECs. MiR-188-3p acted as a target of circ_0026218, and miR-188-3p downregulation reversed the suppression role of circ_0026218 knockdown on ox-LDL-induced HUVEC disorder. TLR4 was a target of miR-188-3p, and miR-188-3p overexpression alleviated ox-LDL-induced dysfunction in HUVECs by targeting TLR4. Circ_0026218 could deregulate the TLR4/NF-κB pathway by sponging the miR-188-3p. Importantly, circ_0026218 was overexpressed in exosomes from ox-LDL-treated HUVECs and could be delivered via exosomes. Conclusion: Circ_0026218 knockdown attenuated ox-LDL-induced dysfunction in HUVECs via regulating miR-188-3p/TLR4/NF-κB pathway.
MeSH term(s)	Humans ; NF-kappa B ; Toll-Like Receptor 4/genetics ; Lipoproteins, LDL/toxicity ; Human Umbilical Vein Endothelial Cells ; Apoptosis ; Atherosclerosis/genetics ; Atherosclerosis/prevention & control ; Cell Proliferation ; MicroRNAs/genetics
Chemical Substances	NF-kappa B ; Toll-Like Receptor 4 ; oxidized low density lipoprotein ; Lipoproteins, LDL ; MicroRNAs ; TLR4 protein, human ; MIRN188 microRNA, human
Language	English
Publishing date	2022-12-31
Publishing country	United States
Document type	Journal Article
ZDB-ID	639068-7
ISSN	1573-7241 ; 0920-3206
ISSN (online)	1573-7241
ISSN	0920-3206
DOI	10.1007/s10557-022-07416-x
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Zs.B 3057: Show issues

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Article ; Online: Handsome or Rugged? : A Speed-Dating Study of Ovulatory Shifts in Women's Preferences for Masculinity in Men.

Wu, Karen / Chen, Chuansheng / Yu, Zhaoxia

Human nature (Hawthorne, N.Y.)

2022

Abstract: We tested the good genes ovulatory shift hypothesis through speed-dating, an ecologically valid paradigm with real life consequences. Fifteen speed-dating sessions of 262 single Asian Americans were held. We analyzed 850 speed-dates involving 132 men and ...

Abstract	We tested the good genes ovulatory shift hypothesis through speed-dating, an ecologically valid paradigm with real life consequences. Fifteen speed-dating sessions of 262 single Asian Americans were held. We analyzed 850 speed-dates involving 132 men and 100 normally ovulating women, finding ovulatory shifts in the desirability of men with more masculine facial measurements (smaller eye-mouth-eye angle, larger lower face to full face height ratio, and smaller facial width to lower face height ratio) in the predicted direction. However, there was no support for ovulatory shifts in preferences for men's self-reported height. In addition, the expected shifts were not found for women's second date offers to men. Therefore, with natural stimuli and in a competitive dating scenario, we partially replicated previously documented ovulatory shifts in women's preferences for men.
Language	English
Publishing date	2022-12-10
Publishing country	United States
Document type	Journal Article
ZDB-ID	1020326-6
ISSN	1936-4776 ; 1045-6767
ISSN (online)	1936-4776
ISSN	1045-6767
DOI	10.1007/s12110-022-09434-y
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Article ; Online: Bayesian nonparametric analysis for the detection of spikes in noisy calcium imaging data

D'Angelo, Laura / Canale, Antonio / Yu, Zhaoxia / Guindani, Michele

Biometrics. 2023 June, v. 79, no. 2 p.1370-1382

2023

Abstract: Recent advancements in miniaturized fluorescence microscopy have made it possible to investigate neuronal responses to external stimuli in awake behaving animals through the analysis of intracellular calcium signals. An ongoing challenge is deconvolving ... ...

Abstract	Recent advancements in miniaturized fluorescence microscopy have made it possible to investigate neuronal responses to external stimuli in awake behaving animals through the analysis of intracellular calcium signals. An ongoing challenge is deconvolving the temporal signals to extract the spike trains from the noisy calcium signals' time series. In this article, we propose a nested Bayesian finite mixture specification that allows the estimation of spiking activity and, simultaneously, reconstructing the distributions of the calcium transient spikes' amplitudes under different experimental conditions. The proposed model leverages two nested layers of random discrete mixture priors to borrow information between experiments and discover similarities in the distributional patterns of neuronal responses to different stimuli. Furthermore, the spikes' intensity values are also clustered within and between experimental conditions to determine the existence of common (recurring) response amplitudes. Simulation studies and the analysis of a dataset from the Allen Brain Observatory show the effectiveness of the method in clustering and detecting neuronal activities.
Keywords	Bayesian theory ; brain ; calcium ; data collection ; fluorescence microscopy ; neurons ; time series analysis
Language	English
Dates of publication	2023-06
Size	p. 1370-1382.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	213543-7
ISSN	0099-4987 ; 0006-341X
ISSN	0099-4987 ; 0006-341X
DOI	10.1111/biom.13626
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Bayesian nonparametric analysis for the detection of spikes in noisy calcium imaging data.

D'Angelo, Laura / Canale, Antonio / Yu, Zhaoxia / Guindani, Michele

Biometrics

2022 Volume 79, Issue 2, Page(s) 1370–1382

Abstract	Recent advancements in miniaturized fluorescence microscopy have made it possible to investigate neuronal responses to external stimuli in awake behaving animals through the analysis of intracellular calcium signals. An ongoing challenge is deconvolving the temporal signals to extract the spike trains from the noisy calcium signals' time series. In this article, we propose a nested Bayesian finite mixture specification that allows the estimation of spiking activity and, simultaneously, reconstructing the distributions of the calcium transient spikes' amplitudes under different experimental conditions. The proposed model leverages two nested layers of random discrete mixture priors to borrow information between experiments and discover similarities in the distributional patterns of neuronal responses to different stimuli. Furthermore, the spikes' intensity values are also clustered within and between experimental conditions to determine the existence of common (recurring) response amplitudes. Simulation studies and the analysis of a dataset from the Allen Brain Observatory show the effectiveness of the method in clustering and detecting neuronal activities.
MeSH term(s)	Animals ; Bayes Theorem ; Calcium ; Computer Simulation ; Brain ; Cluster Analysis
Chemical Substances	Calcium (SY7Q814VUP)
Language	English
Publishing date	2022-03-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	213543-7
ISSN	1541-0420 ; 0099-4987 ; 0006-341X
ISSN (online)	1541-0420
ISSN	0099-4987 ; 0006-341X
DOI	10.1111/biom.13626
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Zs.B 72: Show issues

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Article ; Online: PTX3 Protects Intestinal Mucosal Barrier Damage in Sepsis Through Toll-Like Receptor Signaling Pathway.

Li, Jian / Li, Yan / Chai, Ruifeng / Yu, Xiangyou / Yu, Zhaoxia

Inflammation

2022 Volume 45, Issue 6, Page(s) 2339–2351

Abstract: This study aims to confirm the protective effect of Pentraxin 3 (PTX3) on intestinal mucosal barrier damage in sepsis in animal and cell models and explore its mechanism. Analysis of the GSE147775 gene set revealed that the level of PTX3 was upregulated ... ...

Abstract	This study aims to confirm the protective effect of Pentraxin 3 (PTX3) on intestinal mucosal barrier damage in sepsis in animal and cell models and explore its mechanism. Analysis of the GSE147775 gene set revealed that the level of PTX3 was upregulated in the lipopolysaccharide (LPS)-induced rat sepsis model. The mice sepsis model was established by cecal ligation perforation (CLP), and the cell inflammation model was induced by LPS. Cell apoptosis and the expression of apoptosis-related protein were detected by flow cytometry and Western blotting. The PTX3 level was significantly upregulated in the mice sepsis model. Intestinal mucosal barrier damage was aggravated and inflammatory factor expression was upregulated after PTX3 downregulation in sepsis mice. After upregulation of PTX3, intestinal mucosal barrier damage was alleviated and inflammatory factor expression was decreased in sepsis mice. Further data mining suggested that the anti-inflammatory effect of PTX3 might be realized through inhibition of the toll-like receptor (TLR) signaling pathway. Moreover, compared with the LPS group, downregulation of PTX3 increased cell apoptosis and the levels of BCL2-associated X (Bax), myeloperoxidase (MPO), tumor necrosis factor-alfa (TNF-α), interleukin 1 beta (IL-1β), and interferon-gamma (IFN-γ), and decreased the levels of B-cell lymphoma-2 (Bcl-2), zona occludens (ZO)-1, and occludin. On the contrary, overexpression of PTX3 reduced cell apoptosis and the levels of Bax, MPO, TNF-α, IL-1β, and IFN-γ. Moreover, downregulation of PTX3 reversed the inhibitive effects on cell apoptosis and inflammation and promotive effects on the levels of Zo-1 and occludin induced by CLI-095 (a TLR signaling pathway inhibitor). In the CLP-induced mice sepsis model and LPS-induced cell inflammation model, PTX3 inhibits inflammatory response and reduces intestinal mucosal barrier damage through the TLR signaling pathway.
MeSH term(s)	Animals ; Mice ; bcl-2-Associated X Protein/metabolism ; Disease Models, Animal ; Inflammation/metabolism ; Interferon-gamma/metabolism ; Intestinal Mucosa/metabolism ; Lipopolysaccharides ; Occludin ; Sepsis/metabolism ; Signal Transduction ; Toll-Like Receptors/metabolism ; Tumor Necrosis Factor-alpha/metabolism ; Acute-Phase Proteins/metabolism
Chemical Substances	bcl-2-Associated X Protein ; Interferon-gamma (82115-62-6) ; Lipopolysaccharides ; Occludin ; PTX3 protein (148591-49-5) ; Toll-Like Receptors ; Tumor Necrosis Factor-alpha ; Acute-Phase Proteins
Language	English
Publishing date	2022-06-10
Publishing country	United States
Document type	Journal Article
ZDB-ID	434408-x
ISSN	1573-2576 ; 0360-3997
ISSN (online)	1573-2576
ISSN	0360-3997
DOI	10.1007/s10753-022-01696-z
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Article ; Online: The Role of MicroRNAs in Predicting the Neurological Outcome of Patients with Subarachnoid Hemorrhage: A Meta-analysis.

Li, Jian / Liu, Wei / Anniwaer, Ankaerjiang / Li, Bo / Chen, Yutang / Yu, Zhaoxia / Yu, Xiangyou

Cellular and molecular neurobiology

2023 Volume 43, Issue 6, Page(s) 2883–2893

Abstract: Subarachnoid hemorrhage (SAH) is a hemorrhagic cerebrovascular disease with an extremely poor prognosis. The molecular mechanism and biomarkers involved in neurological outcome after SAH still need to be explored. This study assessed the microRNA ... ...

Abstract	Subarachnoid hemorrhage (SAH) is a hemorrhagic cerebrovascular disease with an extremely poor prognosis. The molecular mechanism and biomarkers involved in neurological outcome after SAH still need to be explored. This study assessed the microRNA expression characteristics of SAH patients with different neurological outcomes by meta-analysis. Public databases were searched from database inception until December 2022. The study reported that microRNA expression data in SAH patients with different neurological outcomes were included in the analysis. The differential expression of miRNAs was evaluated by meta-analysis. Overrepresentation analysis was performed for the targeted genes of significant miRNAs. The XGBoost algorithm was used to assess the predictive ability for neurological outcomes with clinical characteristics and significantly expressed miRNAs. Seven studies were finally included in the meta-analysis. The results showed that the levels of miR-152-3p (SMD: - 0.230; 95% CI - 0.389, - 0.070; padj = 0.041), miR-221-3p (SMD: - 0.286; 95% CI - 0.446, - 0.127; padj = 0.007), and miR-34a-5p (SMD: - 0.227; 95% CI - 0.386, - 0.067; padj = 0.041) were significantly lower in SAH patients with good neurological outcomes than in those with poor neurological outcomes. The PI3K-AKT signaling pathway may have an important role in neurological recovery after SAH. Based on the XGBoost algorithm, the neurological outcome could be accurately predicted with clinical characteristics plus the three miRNAs. The expression levels of miR-152-3p, miR-221-3p, and miR-34a-5p were significantly lower in patients with good neurological outcomes than in those with poor outcomes. These miRNAs can serve as potential predictive biomarkers for neurological outcomes. The molecular mechanism and biomarkers involved in neurological outcome after SAH still need to be explored. Our study analyzed microRNA expression characteristics of SAH patients with different neurological outcomes by meta-analysis. After analyze studies reporting the microRNA expression data in SAH patients with different neurological outcomes, results show that the levels of miR-152-3p, miR-221-3p, and miR-34a-5p were significantly lower in SAH patients with good neurological outcomes than in those with poor neurological outcomes. The PI3K-AKT signaling pathway may have an important role in neurological recovery after SAH. Based on the XGBoost algorithm, the neurological outcome could be accurately predicted with clinical characteristics plus the three miRNAs.
MeSH term(s)	Humans ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Subarachnoid Hemorrhage/genetics ; Subarachnoid Hemorrhage/metabolism ; Phosphatidylinositol 3-Kinases ; Proto-Oncogene Proteins c-akt ; Biomarkers
Chemical Substances	MicroRNAs ; Phosphatidylinositol 3-Kinases (EC 2.7.1.-) ; Proto-Oncogene Proteins c-akt (EC 2.7.11.1) ; Biomarkers ; MIRN152 microRNA, human
Language	English
Publishing date	2023-03-21
Publishing country	United States
Document type	Meta-Analysis ; Journal Article
ZDB-ID	283404-2
ISSN	1573-6830 ; 0272-4340
ISSN (online)	1573-6830
ISSN	0272-4340
DOI	10.1007/s10571-023-01327-7
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Article ; Online: To deconvolve, or not to deconvolve: Inferences of neuronal activities using calcium imaging data.

Shen, Tong / Lur, Gyorgy / Xu, Xiangmin / Yu, Zhaoxia

Journal of neuroscience methods

2021 Volume 366, Page(s) 109431

Abstract: Background: With the increasing popularity of calcium imaging in neuroscience research, choosing the right methods to analyze calcium imaging data is critical to address various scientific questions. Unlike spike trains measured using electrodes, ... ...

Abstract	Background: With the increasing popularity of calcium imaging in neuroscience research, choosing the right methods to analyze calcium imaging data is critical to address various scientific questions. Unlike spike trains measured using electrodes, fluorescence intensity traces provide an indirect and noisy measurement of the underlying neuronal activities. The observed calcium traces are either analyzed directly or deconvolved to spike trains to infer neuronal activities. When both approaches are applicable, it is unclear whether deconvolving calcium traces is a necessary step. Methods: In this article, we compare the performance of using calcium traces or their deconvolved spike trains for three common analyses: clustering, principal component analysis (PCA), and population decoding. Results: We found that (1) the two approaches lead to diverging results; (2) estimated spike trains, when smoothed or binned appropriately, usually lead to satisfactory performances, such as more accurate estimation of cluster membership; (3) although estimate spike train produce results more similar to true spike data than trace data, we found that the PCA results from trace data might better reflect the underlying neuronal ensembles (clusters); and (4) for both approaches, decobability can be improved by using denoising or smoothing methods. Comparison with existing methods: Our simulations and applications to real data suggest that estimated spike data outperform trace data in cluster analysis and give comparable results for population decoding. In addition, the decobability of estimated spike data can be slightly better than that of calcium trace data with appropriate filtering / smoothing methods. Conclusion: We conclude that spike detection might be a useful pre-processing step for certain problems such as clustering; however, the continuous nature of calcium imaging data provides a natural smoothness that might be helpful for problems such as dimensional reduction.
MeSH term(s)	Action Potentials/physiology ; Algorithms ; Calcium/metabolism ; Calcium Signaling/physiology ; Models, Neurological ; Neurons/physiology
Chemical Substances	Calcium (SY7Q814VUP)
Language	English
Publishing date	2021-11-29
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	282721-9
ISSN	1872-678X ; 0165-0270
ISSN (online)	1872-678X
ISSN	0165-0270
DOI	10.1016/j.jneumeth.2021.109431
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