Molecular Dynamics Simulation of Macromolecules Using Graphics Processing Unit

Molecular dynamics (MD) simulation is a powerful computational tool to study the behavior of macromolecular systems. But many simulations of this field are limited in spatial or temporal scale by the available computational resource. In recent years, graphics processing unit (GPU) provides unprecedented computational power for scientific applications. Many MD algorithms suit with the multithread nature of GPU. In this paper, MD algorithms for macromolecular systems that run entirely on GPU are presented. Compared to the MD simulation with free software GROMACS on a single CPU core, our codes achieve about 10 times speed-up on a single GPU. For validation, we have performed MD simulations of polymer crystallization on GPU, and the results observed perfectly agree with computations on CPU. Therefore, our single GPU codes have already provided an inexpensive alternative for macromolecular simulations on traditional CPU clusters and they can also be used as a basis to develop parallel GPU programs to further speedup the computations.Comment: 21 pages, 16 figure

Morinda Officinalis

Varicoceles (VCs) are the predominant cause of male infertility and are a risk factor for chronic venous disease. Morinda officinalis (M. officinalis) is a traditional Chinese medicine used to tonify the kidney and strengthen yang. In this study, we evaluated the effects of water-soluble polysaccharides extracted from M. officinalis (MOPs) on gonadotropin-release hormone (GnRH) secretion in a classic experimental left VC (ELV) rat model. Intragastric administration of MOPs at a dose ranging from 50 mg kg−1 to 100 mg kg−1 facilitated improvements in sperm parameters and seminiferous epithelial structures, modulated serum hormone profiles, and stimulated GnRH synthesis and release in the hypothalamus. MOPs also promoted spinogenesis and functional spine maturation in the arcuate nuclei (Arc), wherein they acted mainly on Kiss1 and GnRH neurons. Moreover, MOP-mediated Kisspeptin-GPR54 pathway upregulation and MAPK phosphorylation activation may have been responsible for increases in GnRH synthesis and release. Collectively, the findings of this study indicate that MOPs were effective in stimulating GnRH secretion, possibly by upregulating the Kiss1/GPR54 pathway and enhancing synaptic plasticity, and that MOPs can serve as a therapy for early VCs

Proteomic Analysis of the Hepatopancreas of Chinese Mitten Crabs (Eriocheir sinensis) Fed With a Linoleic Acid or α-Linolenic Acid Diet

As representatives of n-6 and n-3 fatty acids, many studies have analyzed the use of soybean oil and linseed oil rich in linoleic acid (18:2n-6, LA) and α-linolenic acid (18:3n-3, LNA) as better substitutes for fish oil. In aquatic animals, different dietary ratios of LA and LNA could have significant effects on growth, lipid metabolism, immune response, and reproduction. To assess the nutritive value of these two fatty acids in Chinese mitten crab (Eriocheir sinensis), we performed transcriptome analysis and label-free quantification proteomic analysis of the hepatopancreas from mitten crabs fed with LA or LNA diet. Parallel reaction monitoring was used to confirm the reliability of the proteomic analysis. A total of 186 proteins were differentially expressed with fold change ≥1.5 or ≤0.666. Among the 186 proteins, 116 were upregulated and 70 were downregulated in the LA than LNA. Most of these proteins participate in cellular process and metabolism process and have molecular functions such as binding and catalytic activity; the cellular component of these proteins are cell, cell part, membrane, and membrane part. A total of 18 proteins were identified to be related to lipid, carbohydrate, and protein metabolism, and they mainly participate in digestive enzyme activities, fatty acid transport, and glycolysis. Our results provide new insights for further investigation into the replacement of fish oil from mitten crabs with vegetable oils and enable us to better understand the different roles and nutrition value of LA and LNA in mitten crabs

Cell Signaling of Caenorhabditis elegans in Response to Enterotoxigenic Escherichia coli Infection and Lactobacillus zeae Protection

Enterotoxigenic Escherichia coli (ETEC) infection causes the death of Caenorhabditis elegans, which can be prevented by certain Lactobacillus isolates. The host response of C. elegans to ETEC infection and its regulation by the isolates are, however, largely unclear. This study has revealed that, in agreement with the results of life-span assays, the expression of the genes encoding p38 mitogen-activated protein kinase (MAPK) pathway (nsy-1, sek-1, and pmk-1), insulin/insulin-like growth factor (DAF/IGF) pathway (daf-16), or antimicrobial peptides (lys-7, spp-1, and abf-3) and other defensing molecules (abf-2, clec-85) was upregulated significantly when the wild-type nematode (N2) was subjected to ETEC infection. This upregulation was further enhanced by the pretreatment with Lactobacillus zeae LB1, but not with L. casei CL11. Mutants defective in the cell signaling of C. elegans were either more susceptible (defective in NSY-1, SEK-1, PMK-1, or DAF16) or more resistant (defective in AGE-1, DBL-1, SKN-1, or SOD-3) to ETEC infection compared with the wild-type. Mutants defective in antimicrobial peptides (LYS-7, SPP1, or ABF-3) were also more susceptible. In addition, mutants that are defective in NSY-1, SEK-1, PMK-1, DAF16, ABF-3, LYS-7, or SPP1 showed no response to the protection from L. zeae LB1. The expression of the genes encoding antimicrobial peptides (lys-7, spp-1, and abf-3) and other defensing molecules (abf-2, clec-60, and clec-85) were almost all upregulated in AGE-1- or DBL-1-defective mutant compared with the wild-type, which was further enhanced by the pretreatment of L. zeae LB1. The expression of these genes was, however, mostly downregulated in NSY-1- or DAF-16-defective mutant. These results suggest that L. zeae LB1 regulates C. elegans signaling through the p38 MAPK and DAF/IGF pathways to control the production of antimicrobial peptides and defensing molecules to combat ETEC infection

mHealth Series: Text messaging data collection of infant and young child feeding practice in rural China – a feasibility study

Face–to–face interviews by trained field workers are commonly used in household surveys. However, this data collection method is labor–intensive, time–consuming, expensive, prone to interviewer and recall bias and not easily scalable to increase sample representativeness. The study explored the feasibility of using text messaging to collect information on infant and young child feeding practice in rural China

Probiotics are beneficial for liver cirrhosis: a systematic review and meta-analysis of randomized control trials

IntroductionGut dysbiosis may play a pivotal role in the pathogenesis of cirrhosis and the severity of complications. Numerous studies have investigated the probiotics as treatments for cirrhosis. However, there is still a lack of definitive evidence confirming the beneficial effects of probiotics on cirrhosis.MethodsDatabases including PubMed, Embase, Web of Science, and the Cochrane Library were systematically searched for randomized controlled trials that compared the effects of probiotic intervention and control treatments, including placebo, no treatment, and active control, on cirrhosis, published from inception to February 2024. Outcomes included hepatic encephalopathy (HE) reversal, safety and tolerability of probiotics, liver function, quality of life, and other cirrhotic-related outcomes. A meta-analysis was conducted to synthesize evidence.ResultsThirty studies were included. The quantitative synthesis results showed that compared with the control group, probiotics significantly reverse minimal hepatic encephalopathy (MHE) (risk ratio [RR] 1.54, 95% confidence interval [CI] 1.03 to 2.32) and improve HE (RR 1.94, 95% CI 1.24 to 3.06). Additionally, probiotics demonstrated higher safety and tolerability by causing a lower incidence of serious adverse events (RR 0.71, 95% CI 0.58 to 0.87). Probiotics could potentially improve liver function by reducing the Model for End-Stage Liver Disease (MELD) scores (standardized mean difference [SMD] -0.57, 95% CI -0.85 to −0.30), and displayed favorable changes in quality of life (SMD 0.51, 95% CI 0.27 to 0.75) and gut flora (SMD 1.67, 95% CI 1.28 to 2.06).ConclusionThis systematic review and meta-analysis offers compelling evidence that probiotics are beneficial for cirrhosis by demonstrating reversal of HE, potential for liver function improvements, enhancements in quality of life, and regulation of gut dysbiosis. Furthermore, the apparent safety profile suggests that probiotics are a promising intervention for treating cirrhosis.Clinical trial registration numberCRD42023478380

Text Messaging Data Collection for Monitoring an Infant Feeding Intervention Program in Rural China: Feasibility Study

BACKGROUND: An effective data collection method is crucial for high quality monitoring of health interventions. The traditional face-to-face data collection method is labor intensive, expensive, and time consuming. With the rapid increase of mobile phone subscribers, text messaging has the potential to be used for evaluation of population health interventions in rural China. OBJECTIVE: The objective of this study was to explore the feasibility of using text messaging as a data collection tool to monitor an infant feeding intervention program. METHODS: Participants were caregivers of children aged 0 to 23 months in rural China who participated in an infant feeding health education program. We used the test-retest method. First, we collected data with a text messaging survey and then with a face-to-face survey for 2 periods of 3 days. We compared the response rate, data agreement, costs, and participants’ acceptability of the two methods. Also, we interviewed participants to explore their reasons for not responding to the text messages and the reasons for disagreement in the two methods. In addition, we evaluated the most appropriate time during the day for sending text messages. RESULTS: We included 258 participants; 99 (38.4%) participated in the text messaging survey and 177 (68.6%) in the face-to-face survey. Compared with the face-to-face survey, the text messaging survey had much lower response rates to at least one question (38.4% vs 68.6%) and to all 7 questions (27.9% vs 67.4%) with moderate data agreement (most kappa values between .5 and .75, the intraclass correlation coefficients between .53 to .72). Participants who took part in both surveys gave the same acceptability rating for both methods (median 4.0 for both on a 5-point scale, 1=disliked very much and 5=liked very much). The costs per questionnaire for the text messaging method were much lower than the costs for the face-to-face method: ¥19.7 (US $3.13) versus ¥33.9 (US$5.39) for all questionnaires, and ¥27.1 (US $4.31) versus ¥34.4 (US$5.47) for completed questionnaires. The main reasons for not replying were that participants did not receive text messages, they were too busy to reply, or they did not see text messages in time. The main reasons for disagreement in responses were that participants forgot their answers in the text messaging survey and that they changed their minds. We found that participants were more likely to reply to text messages immediately during 2 time periods: 8 AM to 3 PM and 8 PM to 9 PM. CONCLUSIONS: The text messaging method had reasonable data agreement and low cost, but a low response rate. Further research is needed to evaluate effectiveness of measures that can increase the response rate, especially in collecting longitudinal data by text messaging

Polysaccharide Extracted from Laminaria japonica

This study aimed to determine the effect of topically applied Laminaria polysaccharide (LP) on skin aging. We applied ointment containing LP (10, 25, and 50 μg/g) or vitamin E (10 μg/g) to the dorsal skin of aging mice for 12 months and young control mice for 4 weeks. Electron microscopy analysis of skin samples revealed that LP increased dermal thickness and skin collagen content. Tissue inhibitor of metalloprotease- (TIMP-) 1 expression was upregulated while that of matrix metalloproteinase- (MMP-) 1 was downregulated in skin tissue of LP-treated as compared to untreated aging mice. Additionally, phosphorylation of c-Jun N-terminal kinase (JNK) and p38 was higher in aging skin than in young skin, while LP treatment suppressed phospho-JNK expression. LP application also enhanced the expression of antioxidative enzymes in skin tissue, causing a decrease in malondialdehyde levels and increases in superoxide dismutase, catalase, and glutathione peroxidase levels relative to those in untreated aging mice. These results indicate that LP inhibits MMP-1 expression by preventing oxidative stress and JNK phosphorylation, thereby delaying skin collagen breakdown during aging