1.LitCovid-AGAC: cellular and molecular level annotation data set based on COVID-19
Sizhuo OUYANG ; Yuxing WANG ; Kaiyin ZHOU ; Jingbo XIA
Genomics & Informatics 2021;19(3):e23-
Currently, coronavirus disease 2019 (COVID-19) literature has been increasing dramatically, and the increased text amount make it possible to perform large scale text mining and knowledge discovery. Therefore, curation of these texts becomes a crucial issue for Bio-medical Natural Language Processing (BioNLP) community, so as to retrieve the important information about the mechanism of COVID-19. PubAnnotation is an aligned annotation system which provides an efficient platform for biological curators to upload their annotations or merge other external annotations. Inspired by the integration among multiple useful COVID-19 annotations, we merged three annotations resources to LitCovid data set, and constructed a cross-annotated corpus, LitCovid-AGAC. This corpus consists of 12 labels including Mutation, Species, Gene, Disease from PubTator, GO, CHEBI from OGER, Var, MPA, CPA, NegReg, PosReg, Reg from AGAC, upon 50,018 COVID-19 abstracts in LitCovid. Contain sufficient abundant information being possible to unveil the hidden knowledge in the pathological mechanism of COVID-19.
2.Analysis of regional homogeneity and functional connectivity among the depression and bipolar disorder with mixed features patients
Yue LIU ; Rui LIU ; Lin GUAN ; Xinyi LIU ; Jingjing ZHOU ; Kaiyin HUANG ; Shunli LU ; Aihong YU
Chinese Journal of Radiology 2023;57(7):741-747
Objective:To investigate the regional homogeneity (ReHo) among the major depressive disorder patients without mixed features (MDD noMF), major depressive disorder with mixed features (MMF), bipolar disorder with mixed features (BMF) and bipolar disorder patients without mixed features (BD noMF) patients, and to explore the brain activity and functional connectivity patterns of the MMF and BMF patients. Methods:This was a cross-sectional study. The MDD noMF patients (MDD noMF group), MMF patients (MMF group), BMF patients (BMF group), BD noMF patients (BD noMF group), and age-and gender-matched healthy controls (HC group) were recruited from Beijing Anding Hospital, Capital Medical University between April, 2021 and June, 2022. All the participants underwent resting-state functional MRI scanning. The ReHo values was computed with the DPABI software based on the MATLAB. Firstly, the difference in ReHo among the patients with MDD noMF, MMF, BMF, BD noMF and HC group were estimated by the analysis of covariance and the post-hoc method (LSD or Games-Howell). And then, the brain regions with significant different ReHo values were selected as the seeds to calculate the functional connectivity with the whole brain. Results:A total of 29 cases in the MDD noMF group, 24 cases in the MMF group, 26 cases in the BMF group, 29 cases in the BD noMF group, and 42 in the HC group were included. The differences in ReHo values in the left fusiform and the left precuneus of the 5 groups were statistically significant ( P<0.05). Among of them, the ReHo values of the left fusiform were lower in the MMF, BMF and BD noMF groups compared with the HC group ( P<0.05), while the ReHo values of the left precuneus in MDD noMF, MMF, BMF and BD noMF groups were higher than that in the HC group ( P<0.05). The ReHo value of the left fusiform was lower in the MMF group compared with the MDD noMF group ( P=0.001); the ReHo value of the left fusiform was lower in the BMF group compared with the MDD noMF and BD noMF groups ( P<0.05). The functional connectivity between the left fusiform and vermis, left insula, right putamen, and left medial superior frontal gyrus, and functional connectivity between the left precuneus and right superior frontal gyrus (dorsolateral) showed significant difference among the MDD noMF, MMF, BMF, BD noMF and HC groups ( P<0.05). Compared with HC group, MDD noMF, MMF, BD noMF groups showed higher functional connectivity between the left fusiform and the vermis, and MDD noMF, MMF, BMF, BD noMF group showed higher functional connectivityy between the the left fusiform and the left insula, left medial superior frontal gyrus and right putamen ( P<0.05). Compared with the MDD noMF group, the MMF, BMF and BD noMF groups showed higher functional connectivity between the left fusiform and the left insula ( P<0.05). Compared with the MDD noMF group, the BMF and BD noMF groups had higher functional connectivity between the left fusiform and the left medial superior frontal gyrus ( P<0.05). The BMF group showed higher functional connectivity of the left fusiform with the right putamen than the MDD noMF and BD noMF groups. Additonally, the BMF and BD noMF groups showed higher functional connectivity between the left precuneus and the right superior frontal gyrus (dorsolateral) than HC, MDD noMF and MMF groups ( P<0.05). Conclusions:MMF and BMF patients have local abnormalities of functional activity synchronization in the left fusiform and precuneus and abnormal functional connectivity patterns with multiple brain regions. MMF and BMF patients have specific neuroimaging features compared to MDD noMF or BD noMF patients and also share similar neuroimaging pathogenesis.