The Born in Guangzhou Cohort Study enables generational genetic discoveries.

Genomic research that targets large-scale, prospective birth cohorts constitutes an essential strategy for understanding the influence of genetics and environment on human health1. Nonetheless, such studies remain scarce, particularly in Asia. Here we present the phase I genome study of the Born in Guangzhou Cohort Study2 (BIGCS), which encompasses the sequencing and analysis of 4,053 Chinese individuals, primarily composed of trios or mother-infant duos residing in South China. Our analysis reveals novel genetic variants, a high-quality reference panel, and fine-scale local genetic structure within BIGCS. Notably, we identify previously unreported East Asian-specific genetic associations with maternal total bile acid, gestational weight gain and infant cord blood traits. Additionally, we observe prevalent age-specific genetic effects on lipid levels in mothers and infants. In an exploratory intergenerational Mendelian randomization analysis, we estimate the maternal putatively causal and fetal genetic effects of seven adult phenotypes on seven fetal growth-related measurements. These findings illuminate the genetic links between maternal and early-life traits in an East Asian population and lay the groundwork for future research into the intricate interplay of genetics, intrauterine exposures and early-life experiences in shaping long-term health.

Genome-wide characterization of LEA gene family reveals a positive role of BnaA.LEA6.a in freezing tolerance in rapeseed (Brassica napus L.).

BACKGROUND: Freezing stress is one of the major abiotic stresses that causes extensive damage to plants. LEA (Late embryogenesis abundant) proteins play a crucial role in plant growth, development, and abiotic stress. However, there is limited research on the function of LEA genes in low-temperature stress in Brassica napus (rapeseed). RESULTS: Total 306 potential LEA genes were identified in B. rapa (79), B. oleracea (79) and B. napus (148) and divided into eight subgroups. LEA genes of the same subgroup had similar gene structures and predicted subcellular locations. Cis-regulatory elements analysis showed that the promoters of BnaLEA genes rich in cis-regulatory elements related to various abiotic stresses. Additionally, RNA-seq and real-time PCR results indicated that the majority of BnaLEA family members were highly expressed in senescent tissues of rapeseed, especially during late stages of seed maturation, and most BnaLEA genes can be induced by salt and osmotic stress. Interestingly, the BnaA.LEA6.a and BnaC.LEA6.a genes were highly expressed across different vegetative and reproductive organs during different development stages, and showed strong responses to salt, osmotic, and cold stress, particularly freezing stress. Further analysis showed that overexpression of BnaA.LEA6.a increased the freezing tolerance in rapeseed, as evidenced by lower relative electrical leakage and higher survival rates compared to the wild-type (WT) under freezing treatment. CONCLUSION: This study is of great significance for understanding the functions of BnaLEA genes in freezing tolerance in rapeseed and offers an ideal candidate gene (BnaA.LEA6.a) for molecular breeding of freezing-tolerant rapeseed cultivars.

Mapping the risk factors, pathogens, and antibiotic of pharyngocutaneous fistula in patients after neck open surgery.

PURPOSE: Current literature lacks consensus on risk factors for pharyngocutaneous fistula (PCF), and empirical antibiotic guidelines for PCF are limited. The aim of this study was to reduce the incidence of PCF and improve antibiotic treatment efficacy for patients with PCF after open neck surgery by analyzing their clinical characteristics, pathogenic bacteria, and antibiotic susceptibility. METHODS: This study was a 13-year single-center retrospective cohort study, including 699 patients who underwent open neck surgery for laryngeal and hypopharyngeal cancer. Univariate and multivariate logistic regression analyses were conducted to identify the risk factors associated with the occurrence of PCF after surgery. The microbial species causing PCF were analyzed, and the antibiotic sensitivity of the top three pathogens was assessed. Venn diagrams were used to illustrate the antibiotics that exhibited 100% sensitivity against all three identified pathogens. RESULTS: The incidence of PCF after open neck surgery was 8%. Logistic univariate and multivariate analyses revealed that flap reconstruction (OR = 3.62, 95% CI [2.02-6.52]), history of preoperative radiotherapy (OR = 2.01, 95% CI [1.31-2.73]), significant postoperative bleeding (OR = 1.79, 95% CI [1.11-2.69]), and history of diabetes (OR = 1.34, 95% CI [1.29-2.46]) were significantly associated with PCF occurrence. Among the 38 cases of PCF patients, the top three identified pathogens were Pseudomonas aeruginosa, Escherichia coli, and Enterobacter cloacae. The antibiotics cefepime, meropenem, ticarcillin/clavulanic acid, and cefoperazone/sulbactam showed 100% sensitivity against these top three pathogens. CONCLUSION: Special attention should be given to patients undergoing open neck surgery, especially those with intraoperative flap reconstruction, a history of preoperative radiotherapy, postoperative bleeding, or diabetes. Strengthening monitoring and care is crucial in preventing the occurrence of PCF. According to antibiotic usage guidelines and considering the distribution of pathogens in PCF patients, empirical antibiotic treatment with cefoperazone/sulbactam or ticarcillin/clavulanic acid is recommended prior to obtaining susceptibility test results.

DHAV 3CD targets IRF7 and RIG-I proteins to block the type I interferon upstream signaling pathway.

Duck hepatitis A virus type 1 (DHAV-1) is an acute, highly lethal infectious agent that infects ducklings and causes up to 95% mortality in ducklings up to 1 week of age, posing a significant economic threat to the duck farming industry. Previous studies have found that the proteolytic enzyme 3 C encoded by DHAV-1 can inhibit the IRF7 protein from blocking the upstream signaling pathway of the type I interferon to promote viral replication. However, there are still few studies on the mechanism of DHAV-1 in immune evasion. Here, we demonstrate that the DHAV-1 3CD protein can interact with IRF7 protein and reduce IRF7 protein expression without directly affecting IRF7 protein nuclear translocation. Further studies showed that the 3CD protein could reduce the expression of RIG-I protein without affecting its transcription level. Furthermore, we found that the 3CD protein interacted with the N-terminal structural domain of RIG-I protein, interfered with the interaction between RIG-I and MAVS, and degraded RIG-I protein through the proteasomal degradation pathway, thereby inhibiting its mediated antiviral innate immunity to promote DHAV-1 replication. These data suggest a novel immune evasion mechanism of DHAV-1 mediated by the 3CD protein, and the results of this experiment are expected to improve the understanding of the biological functions of the viral precursor protein and provide scientific data to elucidate the mechanism of DHAV-1 infection and pathogenesis.

Incremental predictive value of platelet parameters for preeclampsia: results from a large prospective cohort study.

BACKGROUND: Platelet parameters during pregnancy were associated with the risk of preeclampsia (PE), but the predictive value of these parameters for PE remained unclear. Our aim was to clarify the individual and incremental predictive value of platelet parameters, including platelet count (PC), mean platelet volume (MPV), plateletcrit (PCT), and platelet distribution width (PDW) for PE. METHODS: This study was based on the Born in Guangzhou Cohort Study in China. Data on platelet parameters were extracted from medical records of routine prenatal examinations. Receiver operating characteristic (ROC) curve was performed to analyze the predictive ability of platelet parameters for PE. Maternal characteristic factors proposed by NICE and ACOG were used to develop the base model. Detection rate (DR), integrated discrimination improvement (IDI) and continuous net reclassification improvement (NRI) were calculated compared with the base model to assess the incremental predictive value of platelet parameters. RESULTS: A total of 30,401 pregnancies were included in this study, of which 376 (1.24%) were diagnosed with PE. Higher levels of PC and PCT were observed at 12-19 gestational weeks in women who developed PE later. However, no platelet parameters before 20 weeks of gestation reliably distinguished between PE complicated pregnancy and non-PE complicated pregnancy, with all values of the areas under the ROC curves (AUC) below 0.70. The addition of platelet parameters at 16-19 gestational weeks to the base model increased the DR for preterm PE from 22.9 to 31.4% at a fixed false positive rate of 5%, improved the AUC from 0.775 to 0.849 (p = 0.015), and yielded a NRI of 0.793 (p < 0.001), and an IDI of 0.0069 (p = 0.035). Less but significant improvement in prediction performance was also observed for term PE and total PE when all the four platelet parameters were added to the base model. CONCLUSIONS: Although no single platelet parameter at the early stage of pregnancy identified PE with high accuracy, the addition of platelet parameters to known independent risk factors could improve the prediction of PE.

Ginsenoside Rg3 improves microcystin-induced cardiotoxicity through the miR-128-3p/MDM4 axis.

Microcystin (MC) is the byproduct of cyanobacteria metabolism that is associated with oxidative stress and heart damage. This study aimed to investigate the effect of ginsenoside Rg3 on MC-induced cardiotoxicity. A mouse model of myocardial infarction was constructed by oral MC administration. H9C2 cells were used for in vitro analysis. Cellular oxidative stress, apoptosis, and the relationship between miR-128-3p and double minute 4 protein (MDM4) were analyzed. MiR-128-3p expression was upregulated in vitro and in vivo after MC treatment, which was downregulated after Rg3 treatment. Left ventricular ejection fraction (LVEF) and left ventricular systolic pressure (LVSP) were increased and left ventricular end-diastolic pressure (LVEDP) was decreased after Rg3 treatment. Moreover, Rg3 alleviated MC-induced pathological changes and apoptosis in myocardial tissues. Meanwhile, Rg3 treatment decreased the lactate dehydrogenase (LDH) and malondialdehyde (MDA) levels and inhabited cell apoptosis and oxidative stress in MC-treated myocardial cells. MiR-128-3p overexpression attenuated the protective effect of Rg3 on MC-induced cardiotoxicity. MiR-128-3p negatively regulated MDM4 expression. This study revealed that Rg3 alleviated MC-induced cardiotoxicity through the miR-128-3p/MDM4 axis, which emphasized the potential of Rg3 as a therapeutic agent for MC-induced cardiotoxicity, and miR-128-3p as a target for the Rg3 therapy.

Platelet parameters and risk of hypertension disorders of pregnancy: a propensity score adjusted analysis.

While the role of platelets in cardiovascular diseases among the general population has been widely reported, evidence is inconsistent regarding the association between platelet indices with hypertension in pregnant women. In this study, we explored the associations between platelet parameters before 20 gestational weeks, an understudied period, with hypertensive disorders of pregnancy (HDP), including preeclampsia/eclampsia (PEEC) and gestational hypertension (GH). Based on the Born in Guangzhou Cohort Study, 12053 singleton pregnant women with platelet parameters, including platelet count (PC), mean platelet volume (MPV), plateletcrit (PCT), and platelet distribution width (PDW) measured at 14-19 gestational weeks were included. Conventional multivariable adjustment and propensity score analysis were used to control for confounders. The restricted cubic spline showed that the risk of PEEC increased linearly for PC, and non-linearly for PCT. For GH, the risk increased linearly for PC, MPV, and PCT, and non-linearly for PDW. When these indices were categorized into quintiles, women with higher PC and PCT were associated with increased risk of both PEEC and GH. Women with MPV exceeding the second quintile (≥ 8.8 fL) had a greater risk for GH, but not for PEEC. When HDP was classified into two groups (early- vs late-onset) based on the occurrence time, significant associations persisted for early-onset PEEC, early-onset GH, and late-onset GH. In conclusion, increased PC and PCT before 20 weeks of gestation were both associated with higher risk of PEEC and GH, while elevated MPV was only linked to GH.

Concentration profiles of per- and polyfluoroalkyl substances in major sources to the environment.

A review of published literature was conducted to present the concentrations and composition profiles of per- and polyfluoroalkyl substances (PFAS) from significant sources to the environment. The major sources of PFAS to the environment are categorized under direct and indirect sources. The characteristic compounds and concentrations are summarized as found from direct sources such as manufacturing facilities, aqueous film-forming foam (AFFF) applications, metal coating operations, and textile and paper coating operations; and from indirect sources such as landfills and wastewater treatment plants (WWTPs). The major findings are: 1) among the aqueous matrices for which data were reviewed, groundwater impacted by AFFF contamination showed the highest median concentrations for both perfluorooctanoic acid (PFOA) and perfluorooctane sulfonic acid (PFOS), while the second-highest median concentrations were associated with landfill leachates for PFOA and metal-plating sources for PFOS; 2) many of the unknown polyfluorinated precursors present in AFFF-impacted sites could potentially convert to persistent PFAS by abiotic or biotic transformation, and therefore could act as the long-term source of contamination to the environment; 3) part per billion (ppb) concentrations of PFAS were detected in water bodies surrounding fluorochemical manufacturing plants; 4) in consumer products such as textile, paper, and personal care products, PFOA concentrations were an order of magnitude higher compared to other PFAS; 5) biotransformation products such as fluorotelomer carboxylic acids (FTCAs) and perfluoroalkyl acids (PFAAs) are detected in landfill leachates and WWTP effluents; and 6) many studies have shown increased PFAA concentrations in WWTP effluents compared to influents. This work provides a comprehensive review of the literature on the PFAS concentration and composition trends of select non-polymeric PFAS in different sources.

[Expressions of FOXO1/3a/4/6 in human testis and their roles in testicular aging].

OBJECTIVE: To investigate the expression rules of FOXO1a, FOXO3a, FOXO4 and FOXO6 proteins in the human testis, and explore their roles in the development and progression of testicular aging. METHODS: We collected the para-carcinoma testis tissue from 4 testis cancer patients aged 28, 31, 32 and 46 years, and the testis tissue from another 2 PCa patients aged 66 and 81 years after castration surgery from January 2018 to December 2020. We detected the expressions of FOXO1a, FOXO3a, FOXO4 and FOXO6 proteins in the testis tissue by Western blot, determined the locations of FOXO1a, FOXO3a, FOXO4 and FOXO6 in the testis cells by immunofluorescence staining, and performed semi-quantitative and statistical analyses using image J and SPSS 23.0 software, respectively. RESULTS: The expression levels of FOXO1a and FOXO3a proteins were significantly decreased in the testis tissue of the elderly patients (P < 0.01), with an age-dependent reduction in the proportion of the positive cells. No statistically significant difference was observed in the expression levels of FOXO4 and FOXO6 between different age groups. FOXO1a was mainly expressed at the base of the seminiferous tubules, FOXO3a and FOXO4 in the Leydig cells, and FOXO6 in the seminiferous tubules. In addition, FOXO4 underwent age-related nuclear translocation in the senescent Leydig cells, suggesting its involvement in the aging of Leydig cells. CONCLUSION: FOXO1a/3a/4 may be closely related to human testicular aging and corresponding pathological changes, but its underlying mechanism remains to be further explored.

Natural Ingredients from Medicine Food Homology as Chemopreventive Reagents against Type 2 Diabetes Mellitus by Modulating Gut Microbiota Homoeostasis.

Type 2 diabetes mellitus (T2DM) is a noteworthy worldwide public health problem. It represents a complex metabolic disorder, mainly characterized as hyperglycemia and lipid dysfunction. The gut microbiota dysbiosis has been proposed to play a role in the development of diabetes. Recently, there has been considerable interest in the use of medicine food homology (MFH) and functional food herbs (FF) to ameliorate diabetes and lead to a natural and healthy life. Hence, this review compiles some reports and findings to demonstrate that the practical use of the MFH/FF can modulate the homoeostasis of gut microbiota, thereby ameliorating the development of T2DM. The results provided useful data to support further investigation of the functional basis and application of MFH/FF to treat T2DM through maintaining intestinal homeostasis.

Combination of white tea and peppermint demonstrated synergistic antibacterial and anti-inflammatory activities.

BACKGROUND: White tea, considered to be the oldest form of tea, is becoming a popular beverage for its organoleptic characteristics. Peppermint tea, used as a herbal remedy for centuries, is now also very popular throughout the world as herbal tea. What interested us was that in ancient China, peppermint was used in combination with tea as a detoxification or anti-inflammatory agent. However, there are few reports on the combined use of white tea and peppermint. Therefore, this study aims to investigate the antibacterial and anti-inflammatory activities of white tea in combination with peppermint. RESULTS: A synergistic inhibitory effect against four bacterial strains, especially against Staphylococcus argenteus, was observed in the combination of white tea and peppermint in vitro. In addition, the combined formula demonstrated a stronger anti-inflammatory effect in vivo than either of the two used alone, which was associated with the decrease of the pro-inflammatory cytokines of interleukin-6 (IL-6), interleukin-1beta (IL-1ß), tumor necrosis factor-alpha (TNF-α), cyclooxygenase-2 (COX-2) and inducible nitric oxide synthase (iNOS). In a further mechanism study, it was found that white tea and peppermint inhibited the phosphorylation of p-IκB-α and mitogen-activated protein kinase (MAPK) at different degrees. While the enhanced anti-inflammatory effect of the combined formula was associated with the combination of NF-κB down-regulation and p-MAPK inhibition. CONCLUSION: In our study, it was for the first time shown that when white tea was combined with peppermint, the antibacterial and anti-inflammatory effects were enhanced. The results suggested an effective application of white tea in combination with peppermint as a potential antibacterial and anti-inflammatory functional food. © 2020 Society of Chemical Industry.

Increasing trends in incidence of preterm birth among 2.5 million newborns in Guangzhou, China, 2001 to 2016: an age-period-cohort analysis.

BACKGROUND: The incidence of preterm birth (PTB, < 37 weeks of gestation) has been increasing in China and many other countries in recent years. However, the causes of the increase were not well understood. The current study aims to examine the contribution of maternal age, period of delivery, and maternal birth cohorts to long-term trends in preterm birth in Guangzhou, China. METHODS: In a retrospective population-based study, data were obtained from 2,535,000 singleton live births with 20-43 gestational weeks from 2001 to 2016 and recorded in the Guangzhou Perinatal Health Care and Delivery Surveillance System, in China. The age-period-cohort models were applied to investigate the temporal changes in incidences of PTB, stratified by parity. RESULTS: The incidence of preterm birth steadily increased from 5.1% in 2001 to 5.9% in 2016, with larger rise in primiparous mothers (from 5.0 to 5.9%) compared to multiparous mothers (from 5.6 to 5.9%). A J-shaped and a V-shaped relationship were found between maternal age and PTB among primiparous and multiparous mothers, respectively. A linear cohort effect was found among primiparous mothers with the lowest risk of PTB [risk ratio (RR) = 0.81, 95% confidence interval (CI): 0.74 to 0.89] in 1961 and the highest risk (RR = 1.06, 95% CI: 1.00 to 1.13) in 1997 compared to the mothers born in 1981. An inverse U-shaped association between maternal birth cohort and PTB was found in multiparous mothers. There were weak decreasing period effects on the trend of overall PTB among multiparous mothers and on the trend of extremely (< 27 weeks) or very (28-31 weeks) PTB among both parity groups during the period of 2001-2012. CONCLUSIONS: Our findings showed the PTB incidences had been increasing in the past 16 years in Guangzhou, China and both maternal age and cohort effects contributed to these trends. Further studies are recommended on the impact of altered maternal age and parity on premature births and corresponding public education and public health policies.

Effect of a two-stage intervention package on the cesarean section rate in Guangzhou, China: A before-and-after study.

BACKGROUND: The cesarean section (CS) rate has risen globally during the last two decades. Effective and feasible strategies are needed to reduce it. The aim of this study was to assess the CS rate change after a two-stage intervention package that was designed to reduce the overall CS rate in Guangzhou, China. METHODS AND FINDINGS: This intervention package was implemented by the Health Commission of Guangzhou Municipality in 2 stages (October 2010-September 2014 and October 2014-December 2016) and included programs for population health education, skills training for healthcare professionals, equipment and technical support for local healthcare facilities, and capacity building for the maternal near-miss care system. A retrospective repeated cross-sectional study was conducted to evaluate influences of the intervention on CS rates. A pre-intervention period from January 2008 to September 2010 served as the baseline. The primary outcome was the CS rate, and the secondary outcomes included maternal mortality ratio (MMR) and perinatal mortality rate (PMR), all obtained from the Guangzhou Perinatal Health Care and Delivery Surveillance System (GPHCDSS). The Cochran-Armitage test was used to examine the trends of the overall CS rate, MMR, and PMR across different stages. Segmented linear regression analysis was used to assess the change of the CS rate over the intervention period. A total of 1,921,932 records of births and 108 monthly CS rates from 2008 to 2016 were analyzed. The monthly CS rate declined across the intervention stages (Z = 75.067, p < 0.001), with an average rate of 42.4% at baseline, 39.8% at Stage 1, and 35.0% at Stage 2. The CS rate declined substantially among nulliparous women who delivered term singletons, with an accelerating decreasing trend observed across Stage 1 and Stage 2 (the difference in slopes: -0.09 [95% CI -0.16 to -0.02] between Stage 1 and baseline, p = 0.014; -0.11 [95% CI -0.20 to -0.02] between Stage 1 and Stage 2, p = 0.017). The CS rate in the remaining population increased during baseline and Stage 1 and subsequently decreased during Stage 2. The sensitivity analysis suggested no immediate impact of the universal two-child policy on the trend of the CS rate. The MMR (Z = -4.368, p < 0.001) and PMR (Z = -13.142, p < 0.001) declined by stage over the intervention period. One of the main limitations of the study is the lack of a parallel control group. Moreover, the influence of temporal changes in the study population on the CS rate was unknown. Given the observational nature of the present study, causality cannot be confirmed. CONCLUSIONS: Apparent decline in the overall CS rate was observed in Guangzhou, China, after the implementation of a two-stage intervention package. The decline was most evident among nulliparous women who delivered term singletons. Despite some limitations for causal inference, Guangzhou's experience in controlling the CS rate by implementing composite interventions with public health education and perinatal healthcare service improvement could have implications for other similar areas with high rates of CS.

Knockdown of SIRT1 inhibits proliferation and promotes apoptosis of paclitaxel-resistant human cervical cancer cells.

Cervical cancer (CC), a common gynecological cancer, is a primary cause of cancer-related death in women, worldwide. This study investigates the role of Sirtuin 1 (SIRT1) in paclitaxel (PTX)-resistant CC lines. We used qPCR and Western blots to measure SIRT1 mRNA and protein expressions in 10 matched clinical cancer tissues. We compared the expression levels of SIRT1 between sensitive CC cell lines and PTX-resistant cell lines. Subsequently, we used SIRT1 siRNA to knockdown the expression of SIRT1, and then measured cell proliferation, cell apoptosis rate, cell cycle distribution, and expression levels of Bcl-2 and Bax in PTX-sensitive Hela cell line, PTX-resistant Hela and Sila-resistant cell lines. Finally, we detected the location and expression of MRP (multidrug resistance-associated proteins) using immunofluorescence. We found that SIRT1 expression was higher in PTX-sensitive CC tissues than in normal tissues, and significantly higher in PTX-resistant CC tissues than in PTX-sensitive CC tissues. We further demonstrated that knockdown of SIRT1 in PTX-resistant CC cell lines and PTX-sensitive CC cell line inhibited cell proliferation and promoted cell apoptosis. In addition, we observed that blocking SIRT1 expression in PTX-resistant CC cell lines significantly decreased MRP expression. SIRT1 exhibited high expression levels in both PTX-resistant cell lines and patients. Our results suggest that SIRT1 serves as a potential therapeutic target in PTX-resistant CC.

Maternal IGF1 and IGF1R polymorphisms and the risk of spontaneous preterm birth.

BACKGROUND: The insulin-like growth factor (IGF) pathway was involved in the occurrence of spontaneous preterm birth (SPTB), but little is known regarding the relationship between genetic variations in IGF pathway and the risk of SPTB. We aimed to investigate the associations of IGF1 rs972936 and IGF1 receptor (IGF1R) rs2229765 polymorphisms with SPTB risk in a Chinese population. METHOD: A total of 114 cases of SPTB and 250 controls of term delivery were included from Guangzhou Women and Children's Medical Center, China. The odds ratios (ORs) and the corresponding 95% confidence intervals (CIs) were calculated using multivariate logistic regression. RESULTS: We found that the GA and GA/AA genotypes of IGF1 rs972936 were associated with an increased risk of SPTB, and the adjusted ORs (95% CI) were 1.74 (1.01-3.02) and 1.75 (1.04-2.93) respectively. Women carrying GA and GA/AA genotypes of IGF1R rs2229765 had a reduced risk compared to those with the GG genotype (0.60 [0.37-0.98] and 0.64 [0.40-1.00] respectively). There were significant interactions between IGF1 rs972936 and GDM status (P for interaction=.02), as well as between IGF1R rs2229765 and pre-pregnancy BMI (P for interaction <.001) on the risk of SPTB. CONCLUSION: Our findings suggest that polymorphisms of IGF1 rs972936 and IGF1R rs2229765 were associated with the risk of SPTB in Chinese pregnant women and these effects depend on the maternal metabolic status.

Improved packing of protein side chains with parallel ant colonies.

INTRODUCTION: The accurate packing of protein side chains is important for many computational biology problems, such as ab initio protein structure prediction, homology modelling, and protein design and ligand docking applications. Many of existing solutions are modelled as a computational optimisation problem. As well as the design of search algorithms, most solutions suffer from an inaccurate energy function for judging whether a prediction is good or bad. Even if the search has found the lowest energy, there is no certainty of obtaining the protein structures with correct side chains. METHODS: We present a side-chain modelling method, pacoPacker, which uses a parallel ant colony optimisation strategy based on sharing a single pheromone matrix. This parallel approach combines different sources of energy functions and generates protein side-chain conformations with the lowest energies jointly determined by the various energy functions. We further optimised the selected rotamers to construct subrotamer by rotamer minimisation, which reasonably improved the discreteness of the rotamer library. RESULTS: We focused on improving the accuracy of side-chain conformation prediction. For a testing set of 442 proteins, 87.19% of X1 and 77.11% of X12 angles were predicted correctly within 40° of the X-ray positions. We compared the accuracy of pacoPacker with state-of-the-art methods, such as CIS-RR and SCWRL4. We analysed the results from different perspectives, in terms of protein chain and individual residues. In this comprehensive benchmark testing, 51.5% of proteins within a length of 400 amino acids predicted by pacoPacker were superior to the results of CIS-RR and SCWRL4 simultaneously. Finally, we also showed the advantage of using the subrotamers strategy. All results confirmed that our parallel approach is competitive to state-of-the-art solutions for packing side chains. CONCLUSIONS: This parallel approach combines various sources of searching intelligence and energy functions to pack protein side chains. It provides a frame-work for combining different inaccuracy/usefulness objective functions by designing parallel heuristic search algorithms.

A targeted/non-targeted screening method for perfluoroalkyl carboxylic acids and sulfonates in whole fish using quadrupole time-of-flight mass spectrometry and MS(e).

A new method for measuring perfluoroalkyl contaminants (PFCs) in biological matrices has been developed. An ultra-high pressure liquid chromatograph equipped with a quadrupole time-of-flight mass spectrometer (UPLC-QToF) was optimized using a continuous precursor/product ion monitoring mode. Unlike traditional targeted studies that isolate precursor/product ion pairs, the current method alternates between two ionization energy channels to continuously capture standard electrospray ionization (low energy) and collision induced dissociation (high energy) spectra. The result is the indiscriminant acquisition of paired low and high energy spectra for all constituents eluting from the chromatographic system. This technique was evaluated for the routine analysis of perfluoroalkyl species. Using this technique, linear perfluoroalkyl carboxylic acids (C4 to C14) and perfluoroalkyl sulfonates (C4, C6, C8 and C10) exhibited a linear range spanning over three orders of magnitude and were detectable at levels less than 1 pg on column with a root mean squared signal to noise ratio of 5 to 20. Lake trout (Salvelinus namaycush) and National Institutes of Standards and Technology Standard Reference Material 1946 were used to evaluate matrix effects and the accuracy of this method when applied to a whole fish extract. The current method was also evaluated as a diagnostic tool to identify unknown PFCs using experimental fragmentation patterns, mass defect filtering and Kendrick plots.

Correlation of deregulated like-acetylglucosaminyl transferase and aberrant α-dystroglycan expression with human tongue cancer metastasis.

PURPOSE: The present study examined the correlation of α-dystroglycan (α-DG) expression and like-acetylglucosaminyl transferase (LARGE) with metastasis of human tongue cancer. MATERIALS AND METHODS: Fifty human tongue cancer tissues and 2 tongue squamous cell carcinoma cell lines (CAL27 and SCC4) were involved. Immunohistochemistry was used to detect the expression of α-DG and LARGE. Methylation-specific polymerase chain reaction was performed to assess the methylation status of the LARGE gene promoter. CAL27 and SCC4 cells were transfected with exogenous LARGE and treated with 5-aza-2'-deoxycytidine (Aza-dC), respectively. Glycol sites of α-DG were detected by western blotting. In addition, the laminin overlay assay, cell adhesion assay, and invasion assay were performed. RESULTS: Immunohistochemical results showed that decreased expression of VIA4-1 and IIH6 (antibodies that recognize the glycol sites of α-DG) were correlated with the lymph node metastasis of tongue cancer (n = 50; P = .016 and .025, respectively). Decreased LARGE expression and hypermethylation of the LARGE gene promoter were correlated with lymph node metastasis and α-DG glycosylation in human tongue cancer (n = 50; P = .043 and .015 respectively). In addition, LARGE overexpression and Aza-dC treatment actively led to restoration of functional α-DG expression, elevation of laminin binding, and decrease of migratory ability in cancer cells. CONCLUSION: The results suggested that absent α-DG expression and LARGE deregulation were closely associated with nodal metastasis of tongue cancer. Aberrant α-DG expression and glycosylation were attributed at least in part to the abnormal epigenetic modification of LARGE, especially the hypermethylation of its promoter.

Comparison of PoraPak Rxn RP and XAD-2 adsorbents for monitoring dissolved hydrophobic organic contaminants.

Accurate determination of the levels of dissolved hydrophobic organic contaminants (HOCs) is an important step in estimating the dynamics of their inputs and losses in aqueous systems. This study explores an alternative method for efficiently sampling dissolved HOCs while mitigating a number of sampling artifacts associated with traditional methods. The adsorption characteristics of a new polymeric resin, PoraPak Rxn RP (PPR), were assessed using sorption isotherm experiments and fixed bed adsorption studies. The adsorption capacities and breakthrough times for four model contaminants (phenol, p-nitrophenol, naphthalene, and 2,4,6-tribromophenol) were proportional to the contaminant's hydrophobicity. The ability of PPR to isolate dissolved polychlorinated biphenyls (PCBs) in real samples was compared with that of XAD-2, a well-known macroporous polymer that suffers from high background contamination. The results indicated that the PPR resin can be effectively used for monitoring HOCs, with low ∑PCB levels in blanks, decreasing solvent use, and reducing extraction times.

Positive relief of stroke patients with dysphagia under cluster nursing strategy.

For exploring the positive relief effect and application value of cluster nursing strategies on stroke patients with dysphagia in rehabilitation medicine. A retrospective analysis was conducted on 70 patients with stroke dysphagia admitted to the Rehabilitation Medicine Department of our hospital from June 2021 to November 2022; by comparison, patients were separated into intervention group (IG) and control group (CG) according to different degrees of swallowing difficulty, and nutritional nursing interventions were conducted on the selected research subjects. It was given routine care in the CG and a cluster nursing strategy in the IG, with a total intervention time of 5 months. Before intervention, general information of all patients was compared. Before and after intervention, the incidence of aspiration, nutritional biochemical indicators (hemoglobin, total serum protein, albumin, prealbumin, total cholesterol), grip strength, Swallowing Quality of Life score, etc were collected from the 2 groups of patients. Finally, the specific benefits were analyzed through statistical results to evaluate the intervention effect. After intervention, the explicit aspiration rate of the participants in this experiment significantly decreased, and the difference among the participants in this experiment was statistically significant (P < .05); the implicit aspiration rate was not statistically significant (P > .05). In the comparison of nursing expenses, the CG spent 5403.57 ± 815.51 yuan, while the IG spent 5237.10 ± 758.35 yuan. There was a statistically marked disparity among the participants in this experiment (t = 52.41, P < .001). In the comparison of hospitalization expenses, the cost of the CG was 9236.05 ± 3236.08 yuan; The cost of the IG was 9538.59 ± 4985.21 yuan, and there was a marked disparity among the participants in this experiment (P < .001). The significant statistical significance exists (P < .05) in the 5 indicators of hemoglobin, total protein, prealbumin, albumin, and total cholesterol, quality of life scores, and patient physical efficacy in both groups. The intervention study of cluster nursing strategy for stroke patients with dysphagia in rehabilitation medicine can effectively reduce the incidence of overt aspiration and ultimately improve their quality of life. It has high clinical application value.