1.Combining hydrophobicity with PSSM for protein secondary structure prediction using BP neural network
Huiyun YANG ; Ouyan SHI ; Xin TIAN
International Journal of Biomedical Engineering 2008;31(5):261-264
Objective Since predicting protein secondary structure is the basis of predicting protein spacial structure, it is important to improve the prediction accuracy of secondary structure. Methods A two-stage BP neural network was constructed based on the method of combining hydrophobicity of amino acid residues with PSSM which contains evolution information. CB513 dataset was employed in our study. After excluding the protein chains containing X,B and those with sequence length shorter than 30 amino acids, 492 protein chains in the dataset were used. The results of protein secondary structure prediction of our study were compared with those from the networks using only PSSN as their inputs. Accuracy of the network was tested by 4-fold cross-validation. Results In our study, α-helix was predicted with an averaged accuracy of nearly 79%, sensitivity of 79% and specificity of 91%. Total prediction accuracy of secondary structure reached 75.96%, which was higher than that of only using PSSM as input. Conclusion The new method developed can better predict protein secondary structure, especially α-helix with a higher accuracy.
2.Study on Absorption of Troxerutin onto Infusion Systems of Polyvinyl Chloride
Zhisheng REN ; Huiyun NIU ; Yan SHI
China Pharmacy 2005;0(13):-
0.05).CONCLUSION:In the study,PVC infusion systems have no adsorption effect on troxerutin.
3.Hidden Markov model for protein structural class prediction based on MATLAB
Huiyun YANG ; Ouyan SHI ; Haixuan QIAO ; Xin TIAN
International Journal of Biomedical Engineering 2012;(6):350-352,372
Objective Predicting protein structural class is the basis for predicting protein spatial structure,so it is important to improve the prediction accuracy of protein structural class.Methods We proposed 3-state and 8-state Hidden Markov model (HMM),and applied these HMMs to the prediction of protein structural class,respectively.We evaluated their accuracy on two different datasets through the rigorous jackknife cross-validation test.Results Prediction ability of 8-state HMM and 3-state HMM to all α class were excellent,the prediction accuracy of 3-state HMM even reached above 95%.Compared with Chou data set,the prediction accuracy of Zhou data set for all β class and α/β class of was improved,while overall prediction accuracy increased by 2%.Conclusion HMM is an effective method to predict protein structural class.
4.Analysis of combined screening results for hearing and deafness in 842 newborns in Dalian
Huiyun YANG ; Shijun LI ; Jing ZHANG ; Wenxiu ZHU ; Xiaoxue LIU ; Ming SHI
Chinese Journal of Postgraduates of Medicine 2023;46(5):461-465
Objective:To analyze the results of the joint screening of newborn hearing and deafness genes in Dalian to provide a reference for the prevention and control of hereditary deafness.Methods:Eight hundred and forty-two neonates born in Dalian Women and Children′s Medical Group from January 1, 2022 to May 30, 2022 were screened retrospectively, using AABR (automatic brainstem evoked potential). And 20 mutation sites of common genetic deafness 4 genes , including GJB2, GJB3, SLC26A4 (PDS) and mitochondrial genes associated with drug-induced deafness (MT-RNRI)(12SrRNA), were detected by high-throughput sequencing.Results:Among the 842 newborns, 840 passed hearing screening (99.8%); 36 cases (4.3%) passed the hearing screening but not the hearing loss gene screening; 804 cases passed through the both screening (95.5%); 2 cases (0.24%) failed in the both screening. 38 cases of deafness gene mutations were detected, with a total carrying rate of 4.51% (38/842). Among them, the carrying rates of heterozygous mutations in GJB2, GJB3, SLC26A4 (PDS), MT-RNRI (12SrRNA) were 1.90%, 0.24%, 1.30%, and 0.95%, respectively. The carrying rates of GJB2/GJB3 composite heterozygous mutations were 0.12%.Conclusions:The combined screening of neonatal hearing and deafness genes can reduce the missed rate of hearing screening. The carrier rate of neonatal deafness gene in Dalian is 4.51%, with the highest GJB 2 carrier rate, followed by SLC26A4 (PDS) carrier rate.
5.Preparation,characterization and gastric mucosal permeability of evodiamine phospholipid complex self- microemulsifying drug delivery system
Shuoyao SONG ; Guiqian YANG ; Ling TAO ; Xiangchun SHEN ; Huan ZHANG ; Herong LI ; Shouli WANG ; Huiyun SHI ; Wen LIU
China Pharmacy 2022;33(9):1056-1062
OBJE CTIVE To prepare and characterize evodiamine phospholipid complex self-microemulsifying drug delivery system(EVO-PC-SMEDDS),and to investigate its gastric mucosal permeability. METHODS EVO-PC-SMEDDS was prepared , and particle size ,polydispersity(PDI)and Zeta potential were tested ,and microscopic observation was carried out. The stability of EVO-PC-SMEDDS in simulated gastric liquid with different pH (1.2,2.0,4.0,7.0)was investigated. The entrapment efficiency and drug-loading amount of the preparation were determined ,and the in vitro release was investigated. The gastric mucosal permeability of EVO-PC-SMEDDS was studied by combining rat gastric mucosal tissue and Ussing Chamber technology. RESULTS The particle size of EVO-PC-SMEDDS was (53.63±1.51)nm,PDI and Zeta potential were 0.217±0.017 and (-12.20±0.15)mV,entrapment efficiency was (95.25±0.97)% and drug-loading amount was (19.30±1.21)mg/g. EVO-PC- SMEDDS exhibited a uniformly dispersed round spherical shape under transmission electron microscope. Stability experiments showed that EVO-PC-SMEDDS exhibited no significant change in particle size ,PDI and Zeta potential under the simulated gastric fluid with different pH and showed excellent stability. Results of in vitro release test showed that compared with evodiamine (EVO),in vitro accumulative release of EVO-PC-SMEDDS were enhanced 6.83-fold,which was in line with the first-order kinetic release model. Results of gastric mucosal permeability showed that gastric mucosal permeation transport ,permeation rate , permeation flux and area under curve of cumulative permeability of EVO-PC-SMEDDS were higher than those of EVO , respectively. CONCLUSIONS EVO-PC-SMEDDS is prepared N successfully and shows good stability. It could significantly improve the release behavior and gastric mucosal permeability of EVO.
6.Chronic hypoperfusion due to intracranial large artery stenosis is not associated with cerebral β-amyloid deposition and brain atrophy.
Dongyu FAN ; Huiyun LI ; Dongwan CHEN ; Yang CHEN ; Xu YI ; Heng YANG ; Qianqian SHI ; Fangyang JIAO ; Yi TANG ; Qiming LI ; Fangyang WANG ; Shunan WANG ; Rongbing JIN ; Fan ZENG ; Yanjiang WANG
Chinese Medical Journal 2022;135(5):591-597
BACKGROUND:
Insufficient cerebral perfusion is suggested to play a role in the development of Alzheimer disease (AD). However, there is a lack of direct evidence indicating whether hypoperfusion causes or aggravates AD pathology. We investigated the effect of chronic cerebral hypoperfusion on AD-related pathology in humans.
METHODS:
We enrolled a group of cognitively normal patients (median age: 64 years) with unilateral chronic cerebral hypoperfusion. Regions of interest with the most pronounced hypoperfusion changes were chosen in the hypoperfused region and were then mirrored in the contralateral hemisphere to create a control region with normal perfusion. 11C-Pittsburgh compound-positron emission tomography standard uptake ratios and brain atrophy indices were calculated from the computed tomography images of each patient.
RESULTS:
The median age of the 10 participants, consisting of 4 males and 6 females, was 64 years (47-76 years). We found that there were no differences in standard uptake ratios of the cortex (volume of interest [VOI]: P = 0.721, region of interest [ROI]: P = 0.241) and grey/white ratio (VOI: P = 0.333, ROI: P = 0.445) and brain atrophy indices (Bicaudate, Bifrontal, Evans, Cella, Cella media, and Ventricular index, P > 0.05) between the hypoperfused regions and contralateral normally perfused regions in patients with unilateral chronic cerebral hypoperfusion.
CONCLUSION
Our findings suggest that chronic hypoperfusion due to large vessel stenosis may not directly induce cerebral β-amyloid deposition and neurodegeneration in humans.
Aged
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Alzheimer Disease/pathology*
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Amyloid beta-Peptides/metabolism*
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Arteries
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Atrophy
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Brain/metabolism*
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Cerebral Cortex/metabolism*
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Cerebrovascular Circulation
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Constriction, Pathologic/pathology*
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Female
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Humans
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Magnetic Resonance Imaging/methods*
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Male
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Middle Aged
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Positron-Emission Tomography/methods*
7.Formulation Optimization of Zuojin Pectin Capsule and Its Protective Effect on Gastric Ulcer Model Rats
Guiqian YANG ; Wen LIU ; Ling TAO ; Xiangchun SHEN ; Shuoyao SONG ; Huan ZHANG ; Herong LI ; Shouli WANG ; Huiyun SHI
China Pharmacy 2021;32(19):2327-2335
OBJECTIVE:To optimize the form ulation of Zuojin pectin c apsules,and to prepare modern Zuojin pectin capsules with protective effects against gastric ulcers. METHODS :The formulation of Zuojin pectin capsules was optimized with orthogonal test with the contents of pectin ,soluble starch and dextrin as factors ,using formability ,moisture absorption and flow ability as indicators. Zuojin pectin capsule was prepared by wet granulation filling method with Zuojin extract powder as raw material. The contents of palmatine hydrochloride ,berberine hydrochloride ,evodiamine and rutaecarpin were evaluated by HPLC. Basket method was used to investigate the release behavior of the capsule in 0.1 mol/L HCl solution. The gastric ulcer model of rats was established by intragastric administration of 75% ethanol. Gastric ulcer index ,the inhibition rate of gastric ulcer and the pathological sections were used as indexes to investigate the protective effect of Zuojin pectin capsules (the doses were 54,108, 216 mg/kg)on gastric ulcer. RESULTS :The optimal formulation of Zuojin pectin capsules included 45% pectin,12% soluble starch,27% dextrin and 1% xylitol. Results of in vitro drug , release showed that palmatine hydrochloride and berberine, hydrochloride in Zuojin pectin capsules released 53.76% and No.54.82% respectively within 1 h,completely released at about 8 h, and conformed to the zero-order release behavior. 2492109374@qq.com Different doses of Zuojin pectin capsule could improve the ulcer injury of gastric tissue in gastric ulcer model rats to different extent ,and significantly reduced the gastric ulcer index(P<0.01),significantly increased the inhibition rate of gastric ulcer and the percentage of positive expression area of Schiff ’s iodate staining (P<0.01). CONCLUSIONS :Zuojin pectin capsule with protective effect on gastric ulcer and certain sustained- release effect is successfully prepared.