Clustering algorithm based on DINNSM and its application in gene expression data analysis.

BACKGROUND: Selecting an appropriate similarity measurement method is crucial for obtaining biologically meaningful clustering modules. Commonly used measurement methods are insufficient in capturing the complexity of biological systems and fail to accurately represent their intricate interactions. OBJECTIVE: This study aimed to obtain biologically meaningful gene modules by using the clustering algorithm based on a similarity measurement method. METHODS: A new algorithm called the Dual-Index Nearest Neighbor Similarity Measure (DINNSM) was proposed. This algorithm calculated the similarity matrix between genes using Pearson's or Spearman's correlation. It was then used to construct a nearest-neighbor table based on the similarity matrix. The final similarity matrix was reconstructed using the positions of shared genes in the nearest neighbor table and the number of shared genes. RESULTS: Experiments were conducted on five different gene expression datasets and compared with five widely used similarity measurement techniques for gene expression data. The findings demonstrate that when utilizing DINNSM as the similarity measure, the clustering results performed better than using alternative measurement techniques. CONCLUSIONS: DINNSM provided more accurate insights into the intricate biological connections among genes, facilitating the identification of more accurate and biological gene co-expression modules.

Study on film forming characteristic of ε-polylysine grafted chitosan through TEMPO oxidation system and its preservation effects for pork fillet.

The present study synthesized a new type of ε-polylysine (PL) modified chitosan film (TO-CH-PL) through TEMPO (2,2,6,6-Tetramethylpiperidine) oxidation system. Firstly, the physicochemical properties of the TO-CH-PL were characterized using Fourier transform infrared spectroscopy, scanning electron microscopy, and energy dispersive spectrometer analysis. Results proved that PL was successfully grafted onto chitosan molecules. Based on the water vapor, oxygen permeability, and mechanical analysis, the TO-CH-PL film demonstrated higher physical properties than chitosan and PE films. Secondly, the TO-CH-PL film's preservation effect on pork fillets was evaluated. Due to the significant retardation of growth of the aerobic plate count (APC), total volatile basic nitrogen (TVBN), and thiobarbituric acid reactive substances (TBARS), as well as the changes of pH and color in packaged pork, TO-CH-PL film exhibited better preservation effects for the pork samples. According to the criteria of TVBN values (<15 mg/100 g), compared with CH and PE films, TO-CH-PL film can prolong the shelf life of pork for 2 to 3 days. Therefore, PL-modified chitosan films could be introduced as an alternative method to maintain the quality indices and extend the shelf life of pork during refrigerated storage.

Effects of conjugates of ε-polylysine-dextran created through Maillard reaction on quality and storage stability of the chicken gel.

The present study mainly focused on the effects of the conjugates of PL-dextran produced through the Maillard reaction on the quality and storage stability of chicken gel for 5 days at 4 ℃. According to the results of the texture profile, water retention capacity (WRC), low-field nuclear magnetic resonance (LF NMR), aerobic plate count (APC), and total volatile basic nitrogen (TVBN), ε-polylysine (PL) could improve chicken gel storage stability while decreasing the quality of protein gels (p < 0.05). Additionally, adding dextran with high or low molecular weight could significantly increase the quality of gel during storage (p < 0.05), whereas decreased storage stability could be obtained (p < 0.05). In general, conjugates formed by PL and dextran with high molecular weight were beneficial for quality maintenance. In comparison, the polymers produced from the low molecular weight of dextran could modify the storage stability of gels. Adding conjugates of dextran and PL benefited the structure formation of protein gel, while PL would retain part of antibacterial activity when crosslinked with dextran. Therefore, it could be concluded that the quality improvement effect of PL-dextran addition on gel quality was greater than its antibacterial effect, which would impact the formulation design of novel emulsion-type meat products.

The clinical prediction factors for non-culprit lesion progression in patients with acute ST elevation myocardial infarction after primary percutaneous coronary intervention.

BACKGROUND: To investigate the relationship between the clinical features and progression of non-culprit lesions in patients with ST-elevation myocardial infarction (STEMI) after primary percutaneous coronary intervention (PPCI). METHODS: A total of 480 patients (57.1 ± 9.2 y) with STEMI who underwent PPCI between January 2016 and December 2017 in Beijing Anzhen Hospital were enrolled in this study. All patients underwent PPCI as a treatment for culprit lesions. Clinical and angiographic follow-up were performed for 12 months. All patients were divided into a non-culprit lesions (NCL) progression group (205 cases) and a control group (275 cases) based on angiographic follow-up outcomes at 12 months. The clinical and angiographic features were analyzed. RESULTS: Body mass index (BMI), serum creatinine (Scr), fasting blood glucose (FBG), glycated serum albumin, glycated hemoglobin and homocysteine levels in the NCL progression group were significantly higher than those in the control group (P < 0.05). A logistic regression analysis showed that FBG (odds ratio 1.274, 95% confidence interval 1.077-1.505, P = 0.005) and Scr (odds ratio 1.020, 95% confidence interval 1.002-1.038, P = 0.027) were independent predictors of NCL progression. A partial correlation analysis showed that FBG was positively correlated with NCL progression (r = 0.231, P = 0.001). A receiver operating characteristic curve showed that the boundary point of FBG to predict NCL progression was 5.715 mmol/L, and the sensitivity was 74.4% and the specificity was 46.4%. CONCLUSION: FBG is a valuable predictor for NCL progression in patients with STEMI after PPCI.

Preventive Effect of Moderate Altitude on Non-Culprit Lesion Progression in Patients with Acute Myocardial Infarction.

Wang, Jian, Cheng-Ying Yan, Wu Wang, and Tian-Zhen Wang. Preventive effect of moderate altitude on non-culprit lesion (NCL) progression in patients with acute myocardial infarction. High Alt Med Biol. 23:345-351, 2022. Background: Ischemic postconditioning may prevent NCL progression in patients with acute myocardial infarction. Moderate altitude (1,500-2,500 m) resembles ischemic postconditioning; however, the preventive effect of moderate altitude on NCL progression is unknown. Methods: We investigated the preventive effect of moderate altitude on NCL progression in patients with ST-segment elevation myocardial infarction (STEMI) after primary percutaneous coronary intervention (PPCI). This study was an observational study. Two-hundred patients with STEMI living in Beijing, which is an average of 43.5 m above sea level (a low-altitude region), who underwent PPCI were enrolled (the control group). A further 200 patients with STEMI living in Xining, which is an average of 2,261 m above sea level (moderate-altitude region), who underwent PPCI were enrolled (the moderate-altitude group). NCL progression and related clinical factors were compared between the two groups. Results: The rate of NCL progression 12 months after PPCI in the moderate-altitude group was significantly lower compared with the control group (p < 0.01). There were 158 patients without NCL progression (group A) and 42 patients with NCL progression (group B) in the control group and 186 patients without NCL progression (group C) and 14 patients with NCL progression (group D) in the moderate-altitude group. Serum adrenaline and noradrenaline concentrations in group B were significantly higher compared with group A (p < 0.001), and serum adrenaline and noradrenaline concentrations in group D were significantly higher compared with group C (p < 0.001). Serum adrenaline, noradrenaline, and C-reactive protein concentrations in patients without NCL progression (n = 344) were significantly lower compared with patients with NCL progression (n = 56) (p < 0.01). Conclusions: Moderate altitude may prevent NCL progression. Moderate altitude may be useful for clinical rehabilitation in patients with STEMI after PPCI.

A functional analysis of the effects of the molecular weight of dextran on ε-polylysine-dextran conjugate created through the maillard reaction.

The present study mainly examines the effects of molecular weight of dextran on the reaction rate and functional characteristics between ε-polylysine (PL) and dextran. The reaction kinetics, grafting degree and gel permeation chromatography are employed to evaluate the reaction rate and extent of these lard reaction. We find low activation energy (Ea) values that indicate that dextran with high molecular weight (HMD) exhibits a higher reaction rate with PL than that that of dextran with middle molecular weight (MMD) and low molecular weight (LMD). As for the functional characteristics of the formed conjugate, the conjugate of PL-HMD possesses a higher emulsifying activity, and PL-LMD exhibits higher antimicrobial activity than other molecular weight of dextran. We observe that long heating time at high temperatures can induce the partial degradation of the formed conjugates, which is reflected in the decreasing of the emulsifying and antimicrobial activity of PL-dextran conjugates.

Ischemic postconditioning protects nonculprit coronary arteries against ischemia-reperfusion injury via downregulating miR-92a, miR-328 and miR-494.

BACKGROUND: Nonculprit lesions are closely related to the prognosis of patients with ST-segment elevation myocardial infarction (STEMI). Our previous research found that ischemic postconditioning (IP) could inhibit the progression of nonculprit lesions. However, the mechanism by which IP regulates the occurrence and development of nonculprit lesions remains unclear. METHODS: Firstly, a rabbit ischemia-reperfusion (IR) model was constructed. Next, the morphological characteristics of the coronary arterial tissues and myocardial tissues of the rabbits were observed using hematoxylin-eosin (H&E) staining. Then, western blot was performed to detect the expressions of AT1, Cx43, ß-tubulin, Bax, Bcl-2 and cleaved caspase 3. Finally, to further confirm the effect of IP on nonculprit coronary arterial tissues, an in vitro model of oxygen and glucose deprivation/reperfusion (OGD/R) was established. RESULTS: IR notably induced the cells apoptosis in nonculprit coronary arterial tissues and in myocardial tissues, while IR-induced cell apoptosis was significantly inhibited by IP. In addition, IP protected nonculprit coronary arterial tissues against IR via downregulating miR-92a, miR-328 and miR-494 and mRNA AT1, Cx43 and ß-tubulin. Consistently, OGD/R-induced injury of Human umbilical vein endothelial cells (HUVECs) was reversed by IP. CONCLUSIONS: In this study, IP could protect nonculprit coronary arteries against IR injury via downregulating miR-92a, miR-328 and miR-494. Our findings may provide new directions for the treatment of nonculprit lesions.

The alleles of AGT and HIF1A gene affect the risk of hypertension in plateau residents.

Plateau essential hypertension is a common chronic harmful disease of permanent residents in plateau areas. Studies have shown some single nucleotide polymorphisms (SNPs) associations with hypertension, but few have been verified in plateau area-lived people. In this paper, we examined some hypertension-related gene loci to analyze the relationship between risk SNPs and plateau essential hypertension in residents in Qinghai-Tibet plateau area. We screened hypertension-related SNPs from the literature, Clinvar database, GHR database, GTR database, and GWAS database, and then selected 101 susceptible SNPs for detection. Illumina MiSeq NGS platform was used to perform DNA sequencing on the blood samples from 185 Tibetan dwellings of Qinghai, and bioinformatic tools were used to make genotyping. Genetic models adjusted by gender and age were used to calculate the risk effects of genotypes. Four known SNPs as well as a new locus were found associated with PHE, which were rs2493134 (AGT), rs9349379 (PHACTR1), rs1371182 (CYP2C56P-PRPS1P1), rs567481079 (CYP2C56P-PRPS1P1), and chr14:61734822 (HIF1A). Among them, genotypes of rs2493134, rs9349379, and rs567481079 were risk factors, genotypes of rs1371182 and chr14:61734822 were protective factors. The rs2493134 in AGT was found associated with an increased risk of the plateau essential hypertension by 3.24-, 3.24-, and 2.06-fold in co-dominant, dominant, and Log-additive models, respectively. The rs9349379 in PHACTR1 is associated with a 2.61-fold increased risk of plateau essential hypertension according to the dominant model. This study reveals that the alleles of AGT, HIF1A, and PHACTR1 are closely related to plateau essential hypertension risk in the plateau Tibetan population.

Systematic Review and Meta-Analysis of Comparing Phacoemulsification Combined with goniosynechialysis to other mainstream procedures in treating patients with angle-closure glaucoma.

BACKGROUND: The aim of this meta-analysis is to compare the efficacy and safety of combined phacoemulsification (Phaco) with goniosynechialysis (GSL) to either Phaco or to Phaco combined with trabeculectomy or trabeculectomy alone in patients with angle closure glaucoma (ACG). METHODS: Five main electronic databases were searched for the eligible studies. Intraocular pressure (IOP) decrease was set as the primary outcome, while anti-glaucomatous medication decrease, changes of anterior chamber depth (ACD), range of peripheral anterior synechia (PAS), and complication occurrence were the secondary outcomes. Standard mean difference (SMD) and relative risk (RR) were the size effects for continuous and binomial data, respectively. Either fixed-effects model or random-effects model was chosen to pool the data based on the heterogeneities. RESULTS: A total of 7 eligible studies were included. The combined data showed the IOP decreased more significantly after Phaco-GSL than that after Phaco alone (SMD = -0.42,95%CI: -0.70 - 0.14, I = 17.6%, Z = 2.90, P = .004). However, there were no distinct differences regarding medication decrease (SMD =  -0.25,95%CI: -0.70 - 0.21, I = 0%, Z = 1.06, P = 0.29), ACD, the range of PAS and complication occurrence rate when compared Phaco-GSL to Phaco. Moreover, Phaco-GSL was comparable to Phaco-trabeculectomy/trabeculectomy in decreasing IOP (SMD =  -0.08, 95%CI = -0.32 - 0.15, I = 0%, Z = 0.70, P = .49). CONCLUSIONS: Phaco-GSL might be an optimal procedure to treat ACG with concomitant cataract due to its bleb-less nature, and its capacity for lowering IOP seems superior to Phaco alone and comparable to Phaco-trabeculectomy/trabeculectomy.

PRODH gene is associated with executive function in schizophrenic families.

The aim of this study was to investigate the relationship between polymorphisms in the PRODH and COMT genes and selected neurocognitive functions. Six SNPs in PRODH and two SNPs in COMT were genotyped in 167 first-episode schizophrenic families who had been assessed by a set of 14 neuropsychological tests. Neuropsychological measures were selected as quantitative traits for association analysis. The haplotype of SNPs PRODH 1945T/C and PRODH 1852G/A was associated with impaired performance on the Tower of Hanoi, a problem-solving task mainly reflecting planning capacity. There was no significant evidence for association with any other neuropsychological traits for other SNPs or haplotypes of paired SNPs in the two genes. This study takes previous findings of association between PRODH and schizophrenia further by associating variation within the gene with performance on a neurocognitive trait characteristic of the illness. It fails to confirm previous reports of an association between COMT and cognitive function.