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Solvent accessibility in native and isolated domain environments: general features and implications to interface predictability

Raih MF, Ahmad S, Zheng R, Mohamed R

Biophys Chem, 2005 Apr 1;114(1):63-9.
PMID: 15792862

A non-redundant database of 4536 structural domains, comprising more than 790,000 residues, has been used for the calculation of their solvent accessibility in the native protein environment and then in the isolated domain environment. Nearly 140,000 (18%) residues showed a change in accessible surface area in the above two conditions. General features of this change under these two circumstances have been pointed out. Propensities of these interfacing amino acid residues have been calculated and their variation for different secondary structure types has been analyzed. Actual amount of surface area lost by different secondary structures is higher in the case of helix and strands compared to coil and other conformations. Overall change in surface area in hydrophobic and uncharged residues is higher than that in charged residues. An attempt has been made to know the predictability of interface residues from sequence environments. This analysis and prediction results have significant implications towards determining interacting residues in proteins and for the prediction of protein-protein, protein-ligand, protein-DNA and similar interactions.
Fulltext Do cryptic species exist in Hoplobatrachus rugulosus? An examination using four nuclear genes, the cyt b gene and the complete MT genome

Yu D, Zhang J, Li P, Zheng R, Shao C

PLoS One, 2015;10(4):e0124825.
PMID: 25875761 DOI: 10.1371/journal.pone.0124825

he Chinese tiger frog Hoplobatrachus rugulosus is widely distributed in southern China, Malaysia, Myanmar, Thailand, and Vietnam. It is listed in Appendix II of CITES as the only Class II nationally-protected frog in China. The bred tiger frog known as the Thailand tiger frog, is also identified as H. rugulosus. Our analysis of the Cyt b gene showed high genetic divergence (13.8%) between wild and bred samples of tiger frog. Unexpected genetic divergence of the complete mt genome (14.0%) was also observed between wild and bred samples of tiger frog. Yet, the nuclear genes (NCX1, Rag1, Rhod, Tyr) showed little divergence between them. Despite this and their very similar morphology, the features of the mitochondrial genome including genetic divergence of other genes, different three-dimensional structures of ND5 proteins, and gene rearrangements indicate that H. rugulosus may be a cryptic species complex. Using Bayesian inference, maximum likelihood, and maximum parsimony analyses, Hoplobatrachus was resolved as a sister clade to Euphlyctis, and H. rugulosus (BT) as a sister clade to H. rugulosus (WT). We suggest that we should prevent Thailand tiger frogs (bred type) from escaping into wild environments lest they produce hybrids with Chinese tiger frogs (wild type).
Fulltext An improved arithmetic optimization algorithm with forced switching mechanism for global optimization problems

Zheng R, Jia H, Abualigah L, Liu Q, Wang S

Math Biosci Eng, 2022 01;19(1):473-512.
PMID: 34903000 DOI: 10.3934/mbe.2022023

Arithmetic optimization algorithm (AOA) is a newly proposed meta-heuristic method which is inspired by the arithmetic operators in mathematics. However, the AOA has the weaknesses of insufficient exploration capability and is likely to fall into local optima. To improve the searching quality of original AOA, this paper presents an improved AOA (IAOA) integrated with proposed forced switching mechanism (FSM). The enhanced algorithm uses the random math optimizer probability (RMOP) to increase the population diversity for better global search. And then the forced switching mechanism is introduced into the AOA to help the search agents jump out of the local optima. When the search agents cannot find better positions within a certain number of iterations, the proposed FSM will make them conduct the exploratory behavior. Thus the cases of being trapped into local optima can be avoided effectively. The proposed IAOA is extensively tested by twenty-three classical benchmark functions and ten CEC2020 test functions and compared with the AOA and other well-known optimization algorithms. The experimental results show that the proposed algorithm is superior to other comparative algorithms on most of the test functions. Furthermore, the test results of two training problems of multi-layer perceptron (MLP) and three classical engineering design problems also indicate that the proposed IAOA is highly effective when dealing with real-world problems.
Fulltext A Hybrid SSA and SMA with Mutation Opposition-Based Learning for Constrained Engineering Problems

Wang S, Liu Q, Liu Y, Jia H, Abualigah L, Zheng R, et al.

Comput Intell Neurosci, 2021;2021:6379469.
PMID: 34531910 DOI: 10.1155/2021/6379469

Based on Salp Swarm Algorithm (SSA) and Slime Mould Algorithm (SMA), a novel hybrid optimization algorithm, named Hybrid Slime Mould Salp Swarm Algorithm (HSMSSA), is proposed to solve constrained engineering problems. SSA can obtain good results in solving some optimization problems. However, it is easy to suffer from local minima and lower density of population. SMA specializes in global exploration and good robustness, but its convergence rate is too slow to find satisfactory solutions efficiently. Thus, in this paper, considering the characteristics and advantages of both the above optimization algorithms, SMA is integrated into the leader position updating equations of SSA, which can share helpful information so that the proposed algorithm can utilize these two algorithms' advantages to enhance global optimization performance. Furthermore, Levy flight is utilized to enhance the exploration ability. It is worth noting that a novel strategy called mutation opposition-based learning is proposed to enhance the performance of the hybrid optimization algorithm on premature convergence avoidance, balance between exploration and exploitation phases, and finding satisfactory global optimum. To evaluate the efficiency of the proposed algorithm, HSMSSA is applied to 23 different benchmark functions of the unimodal and multimodal types. Additionally, five classical constrained engineering problems are utilized to evaluate the proposed technique's practicable abilities. The simulation results show that the HSMSSA method is more competitive and presents more engineering effectiveness for real-world constrained problems than SMA, SSA, and other comparative algorithms. In the end, we also provide some potential areas for future studies such as feature selection and multilevel threshold image segmentation.
Production of H2-rich syngas from gasification of unsorted food waste in supercritical water

Su H, Kanchanatip E, Wang D, Zheng R, Huang Z, Chen Y, et al.

Waste Manag, 2020 Feb 01;102:520-527.
PMID: 31765972 DOI: 10.1016/j.wasman.2019.11.018

In China, waste sorting practice is not strictly followed, plastics, especially food packaging, are commonly mixed in food waste. Supercritical water gasification (SCWG) of unsorted food waste was conducted in this study, using model unsorted food waste by mixture of pure food waste and plastic. Different operating parameters including reaction temperature, residence time, and feedstock concentration were investigated. Moreover, the effect of three representative food additives namely NaCl, NaHCO3 and Na2CO3 were tested in this work. Finally, comparative analysis about SCWG of unsorted food waste, pure food waste, and plastic was studied. It was found that higher reaction temperature, longer residence time and lower feedstock concentration were advantageous for SCWG of unsorted food waste. Within the range of operating parameters in this study, when the feedstock concentration was 5 wt%, the highest H2 yield (7.69 mol/kg), H2 selectivity (82.11%), total gas yield (17.05 mol/kg), and efficiencies of SCWG (cold gas efficiency, gasification efficiency, carbon gasification efficiency, and hydrogen gasification efficiency) were obtained at 480 °C for 75 min. Also, the addition of food additives with Na+ promoted the SCWG of unsorted food waste. The Na2CO3 showed the best catalytic performance on enhancement of H2 and syngas production. This research demonstrated the positive effect of waste sorting on the SCWG of food waste, and provided novel results and information that help to overcome the problems in the process of food waste treatment and accelerate the industrial application of SCWG technology in the future.
Tai chi improves depressive symptoms among community-dwelling older persons by mediating BDNF methylation: A preliminary study

Liao S, Tan M, Li M, Ren J, Wang Y, Zheng R, et al.

Geriatr Nurs, 2022 Feb 10;44:137-142.
PMID: 35152066 DOI: 10.1016/j.gerinurse.2022.01.015

Tai Chi could alleviate depression, while the biological mechanisms underlying this effect remains unelucidated. This study recruited 18 community-dwelling older persons with a pre-post testing design, aiming to unveil the potential epigenetic effect by which Tai Chi in the alleviation of depression, using methylation of BDNF promoter as the biomarker. The methylation levels (determined by pyrosequencing using saliva samples) of the targeted BDNF sequence were positively associated with the existence and severity of depressive symptoms (measured with the 9-item Patient Health Questionnaire). Both methylation levels and depression decreased significantly after the Tai Chi intervention. Demethylation of BDNF promoter might be one of the potential mechanisms underlying the holistic depression alleviating effect of Tai Chi. BDNF methylation may potentially serve as a screening, diagnostic as well as disease activity biomarker to determine treatment effects for depression. Further adequately powered studies are needed to verify and strengthen our findings.
Quantitatively characterize the response of the hybrid grouper (Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂) under elevated temperature stress

Zheng R, Lai X, Fang C, Lin H, Huang Y, Zheng J, et al.

Mar Environ Res, 2024 Nov;202:106758.
PMID: 39305860 DOI: 10.1016/j.marenvres.2024.106758

Global warming may affect the health of marine species. However, the collected information on quantitative assessment of response in fish under elevated temperature is poorly defined. The present study aimed to quantitatively evaluate the effects of the hybrid grouper (Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂) under elevated temperature (33 °C and 36 °C, ET1 and ET2) stress for 14 days. As endpoints, we examined changes in body growth, hemato-immunological parameters, liver oxidative stress markers, as well as changes of the stomach digestive enzymes. Compared to the control, the body weight was significantly decreased in ET2 group for 14 d exposure, and a remarkable change of differential leukocyte counts of the ﬁsh was observed in ET1 group at 3 d and in ET2 group at 14 d. The respiratory burst activity of the hybrid grouper leukocytes markedly decreased in the treatment groups after 14-d exposure. Overall, the antioxidant enzyme activities and transcriptional levels of superoxide dismutase (SOD), catalase (CAT), glutathione reductase (GR), and glutathione peroxidase (GSH-PX) were markedly inhibited in the liver for 3-d and 14-d exposure. The expression levels of nf-κb mRNA were significantly inhibited while the expression levels of atp2b1 mRNA were significantly induced after 14-d exposure. The activities of pepsin and lipase in the stomach were significantly reduced. In addition, an innovative hazard classification system (ET-HCS) was developed to quantitatively characterize the stress response of the fish following elevated temperature treatments. The stress level of ET2 group for 14-d exposure was ranked as level IV (high stress), and the other treatments were ranked as level II (low stress). Taken together, the findings of this study further extend our understanding of quantitative assessment of response in fish under high-temperature stress, which provides valuable information for improving countermeasures of mariculture industry.
Features of BSCL2 related congenital generalized lipodystrophy in China: long-term follow-up of three patients and literature review

Su X, Lin Y, Liu L, Mei H, Xu A, Zeng C, et al.

J Pediatr Endocrinol Metab, 2023 Jan 27;36(1):74-80.
PMID: 36433712 DOI: 10.1515/jpem-2022-0372

OBJECTIVES: Congenital generalized lipodystrophy (CGL) is a group of rare autosomal inherited diseases characterized by a widespread loss of adipose tissue. The main purpose of this study was to evaluate the features of Chinese patients with CGL2.
METHODS: Three patients diagnosed with CGL2 from our center were reviewed. Data on clinical features, results of laboratory analyses, and previous treatments were retrospectively collected. This study also reviewed studies that reported patients diagnosed with CGL2 in the last 30 years.
RESULTS: All patients presented a lack of subcutaneous fat, hypertriglyceridemia, reversed triangular faces, acanthosis nigricans, and hepatomegaly within the first six months of life. All three patients developed splenomegaly, and mental retardation in later life. Dietary control dramatically lowered triglyceride levels in all patients. One patient presented with diabetes mellitus at 1 year-old. Although combined therapy with low fat diet and metformin maintained normal levels of blood lipid and glucose, this patient developed hypertrophic cardiomyopathy at the age of three. By a literature review on all Chinese cases with CGL2, it is known that classic manifestations such as hypertriglyceridemia, hepatomegaly and diabetes mellitus can occur shortly after birth, and early diagnosis and treatment can improve quality of life. In this cohort, the most frequent variations are c.782dupG and c.974dup in the BSCL2 gene. However, the same genotype may have different clinical phenotypes in patients with CGL2.
CONCLUSIONS: This study not only described the clinical and genetic features of three patients with CGL2 in China, but also reviewed literature about CGL2 around the world.