Expanding the DNA-encoded library toolbox: identifying small molecules targeting RNA.

DNA-encoded library (DEL) technology is a powerful tool for small molecule identification in drug discovery, yet the reported DEL selection strategies were applied primarily on protein targets in either purified form or in cellular context. To expand the application of this technology, we employed DEL selection on an RNA target HIV-1 TAR (trans-acting responsive region), but found that the majority of signals were resulted from false positive DNA-RNA binding. We thus developed an optimized selection strategy utilizing RNA patches and competitive elution to minimize unwanted DNA binding, followed by k-mer analysis and motif search to differentiate false positive signal. This optimized strategy resulted in a very clean background in a DEL selection against Escherichia coli FMN Riboswitch, and the enriched compounds were determined with double digit nanomolar binding affinity, as well as similar potency in functional FMN competition assay. These results demonstrated the feasibility of small molecule identification against RNA targets using DEL selection. The developed experimental and computational strategy provided a promising opportunity for RNA ligand screening and expanded the application of DEL selection to a much wider context in drug discovery.

Integrated 16S rDNA sequencing and metabolomics to explore the intestinal changes in children and rats with dental fluorosis.

Dental fluorosis (DF) is a widely prevalent disease caused by excessive fluoride with limited awareness of its underlying pathogenesis. Here, a pilot population study was conducted to explore the pathogenesis of DF from the perspective of intestinal microbiome changes, and verified it in animal experiments combining intestinal microbiome and metabolomics. A total of 23 children were recruited in 2017 in China and divided into DF (n = 9) and control (n = 14) groups (DFG and CG, respectively). The SD rat model was established by drinking water containing sodium fluoride (NaF). Gut microbiome profiles of children and rats were analyzed by16S rDNA V3-V4 sequencing, and the intestinal metabolomics analysis of rats was performed by LC-MS methods. The 16 S rDNA sequencing revealed that the gut microbiome composition was significantly perturbed in children in DFG compared to that in CG. Acidobacteria and Thermi were specifically observed in DFG and CG, respectively. Besides, 15 fecal microbiotas were significantly altered at the genus level in DFG. Furthermore, only the expression of annotated genes for pentose and glucuronate interconversion pathway was significant lower in DFG than that in CG (P = 0.04). Notably, in NaF-treated rats, we also observed the changes of some key components of pentose and glucuronate interconversion pathway at the level of microorganisms and metabolites. Our findings suggested that the occurrence of DF is closely related to the alteration of intestinal microorganisms and metabolites annotated in the pentose and glucuronate interconversion pathway.

Extendible ghost imaging with high reconstruction quality in strong scattering medium.

Ghost imaging (GI) possesses significant application prospects in scattering imaging, which is a classic example of underdetermined conversion problem in optical field. However, even under the framework of single-pixel imaging (SPI), a challenge remains unresolved, i.e., structured patterns may be damaged by scattering media in both the emissive and receiving optical paths. In this study, an extendible ghost imaging, a numerical reproduction of the qualitative process using deep learning (DL)-based GI is presented. First, we propose and experimentally verify a brief degradation-guided reconstruction (DR) approach with a neural network to demonstrate the degradation principle of scattering, including realistic dataset simulations and a new training structure in the form of a convolutional neural network (CNN). Then, a novel photon contribution model (PCM) with redundant parameters is proposed to generate intensity sequences from the forward direction through volumetric scattering media; the redundant parameters are constructed and relate to the special output configuration in a lightweight CNN with two branches, based on a reformulated atmospheric scattering model. The proposed scheme recovers the semantics of targets and suppresses the imaging noise in the strong scattering medium, and the obtained results are very satisfactory for applications to scattering media of more practical scenarios and are available for various scattering coefficients and work distances of an imaging prototype. After using DL methods in computational imaging, we conclude that strategies embedded in optics or broader physical factors can result in solutions with better effects for unanalyzable processes.

Association between fluoride exposure and behavioural outcomes of school-age children: a pilot study in China.

To assess the association between fluoride exposure and children's behavioural outcomes, we recruited 325 resident school-age children (7-13 years old) lived in Tongxu County of Henan Province in China. We measured urinary fluoride (UF) concentrations using the ion-selective electrode method. Children's behavioural outcomes were assessed by Conners' Parent Rating Scale-Revised, including conduct problems, learning problems, psychosomatic problems, impulsive-hyperactive, anxiety, and ADHD index. It turned out that each 1.0 mg/L increment in UF concentration corresponded with an elevation in the psychosomatic problem score of 4.01 (95% CI: 2.74, 5.28) and a 97% (OR = 1.97, 95% CI: 1.19, 3.27) increase in the prevalence of psychosomatic problems after adjusting for potential influencing factors. The sensitivity analysis results were consistent with those observed in our preliminary analysis. Our study suggests that fluoride exposure is positively related to the behavioural problem in school-age children, psychosomatic problem in particular.

Synthetic system design method for off-axis stabilized zoom systems with a high zoom ratio.

Stabilized zoom systems possess the advantages such as the simplified system layout, improved system stability, enhanced imaging performance, and a high zoom speed. The complex system design to achieve high performances requires calculations or investigations of the initial system for optimization and improvements, and thus, specific design techniques are pursued. In this study, we propose an automatic optical design scheme of synthetic characteristics for the off-axis stabilized zoom systems, which using focal length variable (FLV) opto-electronic elements and with a high zoom ratio. The study aims at evaluating and synthetically achieving the zooming properties and the image quality balance of entire focus imaging. The multi-element stabilized zoom systems are characterized using the Gaussian brackets expressions and their optimal solution ranges for high zoom ratios are deduced to achieve non-defocusing imaging in specific stroke ranges of FLV elements. Then considering the analytical characterization of the off-axis-induced primary aberrations at multi-conjugate positions, we use a conic surface to deduce the basic expression of the nodal aberration. Thereby the nonlinear global merit function is established with a semi-empirical mathematical model based on nodal aberration theory and nonlinear zoom equation for maintaining the stability of focal length and image plane drift. And the theory of Pareto Optimality is employed in the process of verifying the superiority of the solutions. Finally, a series of solutions for a high zoom ratio and aberration compensation are implemented and the optimal configurations with conical surfaces for an off-axis stabilized zoom system are obtained.

Description method with automatically configurable Gaussian radial basis function for complex freeform surface.

The description of deformable mirror (DM) surface, which is usually a complex freeform surface, affects the measurement speed and accuracy in a real-time interferometric measurement system with a DM as the dynamic compensator. We propose an accurate and fast description method with automatically configurable Gaussian radial basis function. The distribution and shape factors of GRBFs are related to the complexity of the surface with sufficient flexibility to improve the accuracy, and the fitting results are automatically obtained using a traversal optimization algorithm, which can improve the fitting speed by reducing the number of time-consuming calculations. The feasibility is verified by numerical and practical experiment.

Attenuation of Pb-induced Aß generation and autophagic dysfunction via activation of SIRT1: Neuroprotective properties of resveratrol.

This study examined the neuroprotective properties of resveratrol (Res) and its target sirtuin1 (SIRT1) against lead (Pb)-mediated toxicity and discovered that both resveratrol treatment and SIRT1 overexpression restored blocked autophagic flux as well as reduced ß-amyloid (Aß) contents. Four-week-old male C57BL/6 mice were employed to consumed 0.2% Pb(Ac)2 solution or deionized water for 3 months followed by 12 months of Res (50 mg/kg BW) or vehicle gavage. In in vitro study, SH-SY5Y cells were pretreated with the SIRT1 activator SRT1720 (2 µM) or the inhibitor EX527 (2 µM) for 2 h, then 25 µM of Pb(Ac)2 was added and incubated for 48 h. Western blotting, RT-qPCR, enzyme-linked immunosorbent assay (ELISA), and Lyso-Tracker Red Staining were next used to estimate the potential alterations of the autophagic pathway as well as BACE1-mediated amyloid processing in response to Pb exposure, respectively. Our data revealed that Res treatment or SIRT1 activation resisted the induction of autophagy by Pb exposure through inhibition of LC3 and Beclin-1 expression and promoted the degradation of Aß and Tau phosphorylation. Besides, the SIRT1 activator (SRT1720) downregulated the expression of BACE1, the rate-limiting enzyme for Aß production, by inhibiting the activation of nuclear factor-κB (NF-κB) in Pb-treated SH-SY5Y cells, which resulted in reduced Aß production. Collectively, we verified the role of Res-SIRT1-autophagy as well as the SIRT1-NF-κB-BACE1 pathway in Pb-induced neuronal cell injury by in vivo or in vitro models. Our findings further elucidate the important role of SIRT1 and Res in counteracting Pb neurotoxicity, which may provide new interventions and targets for the subsequent treatment of neurodegenerative diseases.

Revealing the distribution characteristics of antibiotic resistance genes and bacterial communities in animal-aerosol-human in a chicken farm: From One-Health perspective.

Antibiotics in breeding industry can enter the environment through multiple pathways, thus accelerating the emergence and spread of antibiotic resistance genes (ARGs), among which aerosol transmission is easily achieved and often overlooked. To elucidate the role of aerosols in this situation, the present study investigated the distribution characteristics of 107 ARG subtypes (targeting to eight different ARG types) and nine mobile genetic elements (MGEs) and bacterial community in animal (chicken cloaca), environment (aerosols) and human (nasopharynx) of a chicken farm (n = 42) in Henan Province. In total, 116 ARG subtypes and MGEs were identified in the poultry farm. The total bacterial concentration of aerosols inside the chicken house (3.117 × 104 CFU/m3) exceeded the corresponding limit. The microbial communities in the samples of cloaca swab (C) and the workers' nasopharyngeal swab (N) were closer, while the abundance distribution of ARGs/ MGEs in cloacal swab (C) and aerosol (AI) in chicken house were much similar. There were certain consistency of the microbial community structure and the distribution of ARGs among the three groups of chicken cloaca, air aerosol, and workers' nasopharynx. Our results highlighted that animal breeding does have a certain impact on the surrounding environment and human, and aerosols play an important role in this process.

Resveratrol improved hippocampal neurogenesis following lead exposure in rats through activation of SIRT1 signaling.

Lead (Pb) poses a potential environmental risk factor for cognitive dysfunction during early life and childhood. Resveratrol is considered a promising antioxidant with respect to the prevention of cognitive deficits and act as a potent SIRT1 agonist. Herein, this study aims to investigate the profile of neurogenesis markers following Pb exposure and to determine the regulatory role of resveratrol in this process. We confirmed firstly the protective effects of resveratrol against Pb-induced impairments of hippocampal neurogenesis in Male SD rats. Pb exposure early in life caused the altered expression of Ki-67, NeuN, caspase-3 and SIRT1 signaling, thereby resulting in spatial cognitive impairment of adolescent rats. As expected, resveratrol reduced cognitive damage and promoted neurogenesis in Pb-induced injury by regulation of SIRT1 pathway. Collectively, our study establishes the efficacy of resveratrol as a neuroprotective agent and provides a strong rationale for further studies on SIRT1-mediated mechanisms of neuroprotective functions.

The independent risks and specific biomarker of breast cancer-related ischemic stroke.

AIM: This retrospective study was designed to investigate the independent risks and specific biomarker for breast cancer-related ischemic stroke (BCRS). METHODS: Clinical features and laboratory findings were compared between BCRS group and breast cancer group without stroke, and further multivariate analyses were performed to predict independent risks factors for BCRS patients. A receiver operator characteristic (ROC) curve analysis was configured to estimate the diagnostic efficacy of each independent risk and the product of these risks and to obtain the optimal cut-off value of diagnosis, which was termed the BCRS Index. RESULTS: BCRS patients had elevated plasma D-dimer and CA153 levels and platelet-to-lymphocyte ratio (PLR), as well as more patients received endocrine therapy (all p ＜ 0.05). Moreover, multivariate analysis revealed that D-dimer levels (odds ratio [OR]: 1.002; 95% confidence interval [CI]: 1.001-1.003; p = 0.000), CA153 levels (OR: 1.005; 95% CI: 1.001-1.008; p = 0.007), PLR (OR: 1.010; 95% CI: 1.004-1.015; p = 0.001), and endocrine therapy (OR: 1.268; 95% CI: 1.087-1.479; p = 0.003) were identified as independent risks of BCRS. Furthermore, ROC analysis displayed that the product of risks had the best diagnostic efficacy, of which the area under the curve was 0.846 ± 0.28. The optimum cut-off point was 2.37 × 106/mL, which was termed the BCRS Index with higher diagnostic accuracy and validity. CONCLUSIONS: Endocrine therapy, as well as elevated plasma D-dimer and CA153 levels and PLR values may be independent risks for BCRS. Furthermore, BCRS Index should be served as a novel specific biomarker for BCRS, which is useful to distinguish BCRS for clinicians.

Fluoride exposure and intelligence in school-age children: evidence from different windows of exposure susceptibility.

BACKGROUND: The intellectual loss induced by fluoride exposure has been extensively studied, but the association between fluoride exposure in different susceptibility windows and children's intelligence is rarely reported. Hence, we conducted a cross-sectional study to explore the association between fluoride exposure in prenatal and childhood periods and intelligence quotient (IQ). METHODS: We recruited 633 local children aged 7-13 years old randomly from four primary schools in Kaifeng, China in 2017. The children were divided into four groups, of which included: control group (CG, n = 228), only prenatal excessive fluoride exposure group (PFG, n = 107), only childhood excessive fluoride exposure group (CFG, n = 157), both prenatal and childhood excessive fluoride exposure group (BFG, n = 141). The concentrations of urinary fluoride (UF) and urinary creatinine (UCr) were determined by fluoride ion-selective electrode assay and a creatinine assay kit (picric acid method), respectively. The concentration of UCr-adjusted urinary fluoride (CUF) was calculated. IQ score was assessed using the second revision of the Combined Raven's Test-The Rural in China (CRT-RC2). Threshold and saturation effects analysis, multiple linear regression analysis and logistic regression analysis were conducted to analyze the association between fluoride exposure and IQ. RESULTS: The mean IQ score in PFG was respectively lower than those in CG, CFG and BFG (P < 0.05). The odds of developing excellent intelligence among children in PFG decreased by 51.1% compared with children in CG (OR = 0.489, 95% CI: 0.279, 0.858). For all the children, CUF concentration of ≥1.7 mg/L was negatively associated with IQ scores (ß = - 4.965, 95% CI: - 9.198, - 0.732, P = 0.022). In children without prenatal fluoride exposure, every 1.0 mg/L increment in the CUF concentration of ≥2.1 mg/L was related to a reduction of 11.4 points in children's IQ scores (95% CI: - 19.2, - 3.5, P = 0.005). CONCLUSIONS: Prenatal and childhood excessive fluoride exposures may impair the intelligence development of school children. Furthermore, children with prenatal fluoride exposure had lower IQ scores than children who were not prenatally exposed; therefore the reduction of IQ scores at higher levels of fluoride exposure in childhood does not become that evident.

Epigenetic modification of H3K4 and oxidative stress are involved in MC-LR-induced apoptosis in testicular cells of SD rats.

Microcystin-leucine arginine (MC-LR) is a cyclic heptapeptide, produced by aquatic cyanobacteria such as microcystis, with strong reproductive toxicity which poses greater threat to the reproductive abilities of humans and animals. By exploring the role of trimethylation of histone H3 at lysine 4 (H3K4me3) and the role of oxidative stress in MC-LR-induced apoptosis in testicular Sertoli cells in Sprague-Dawley (SD) rats, this study indicated that MC-LR increased the expression levels of apoptosis-related genes by raising the levels of H3K4me3. 5'-Deoxy-5'-methylthioadenosine (MTA), the inhibitor of H3K4me3, reduced apoptosis, indicating for the first time that epigenetic modification is closely related to the testicular reproductive toxicity induced by MC-LR. MC-LR also induced oxidative stress by stimulating the generation of reactive oxygen species (ROS), and subsequently triggering mitochondria-mediated apoptotic pathway by decreasing mitochondrial membrane potential and increasing the levels of Bax, Bcl-2, Caspase-3, and so on. MC-LR-induced apoptosis of testicular cells could be decreased after pretreatment with oxidative stress inhibitor N-acetyl-cysteine (NAC). Furthermore, the pathological damage to mitochondria and testes were observed in SD rats. These results show that MC-LR can induce apoptosis by raising the levels of H3K4me3, and pretreatment with MTA can ameliorate the MC-LR-induced apoptosis of cocultured cells by lowering the levels of H3K4me3. Furthermore, NAC has a protective effect on MC-LR-induced apoptosis of testicular cells in SD rats by inhibiting the oxidative stress.

Method for Training Convolutional Neural Networks for In Situ Plankton Image Recognition and Classification Based on the Mechanisms of the Human Eye.

In this study, we propose a method for training convolutional neural networks to make them identify and classify images with higher classification accuracy. By combining the Cartesian and polar coordinate systems when describing the images, the method of recognition and classification for plankton images is discussed. The optimized classification and recognition networks are constructed. They are available for in situ plankton images, exploiting the advantages of both coordinate systems in the network training process. Fusing the two types of vectors and using them as the input for conventional machine learning models for classification, support vector machines (SVMs) are selected as the classifiers to combine these two features of vectors, coming from different image coordinate descriptions. The accuracy of the proposed model was markedly higher than those of the initial classical convolutional neural networks when using the in situ plankton image data, with the increases in classification accuracy and recall rate being 5.3% and 5.1% respectively. In addition, the proposed training method can improve the classification performance considerably when used on the public CIFAR-10 dataset.

Dynamic Deformation Measurement of Specular Surface with Deflectometry and Speckle Digital Image Correlation.

The deformation measurement of a specular surface is of great importance during the quality inspection and installation of optical elements or wafers, especially those with large apertures. We propose a deflectometry method with speckle digital image correlation (DeSDIC) to realize the dynamic and high-accuracy measurement of the deformation on specular surfaces, with a simple system structure and robustness to noises and environmental vibrations. Random speckle pattern displayed on liquid crystal display is reflected by the original surface under test (SUT), and the distorted pattern is recorded by a camera. This originally distorted pattern is taken as the reference image, and the patterns captured afterwards are digitally correlated with the reference image to calculate the gradient change and deformation of the SUT. The theoretical relationships and an experimental one-step calibration scheme are proposed. Both static and dynamic deformations of a deformable mirror were experimentally measured to demonstrate the feasibility and accuracy of DeSDIC, which is comparable to phase-measuring deflectometry and interferometry.

Trends of SHBG and ABP levels in male farmers: Influences of environmental fluoride exposure and ESR alpha gene polymorphisms.

A number of epidemiological studies have reported that chronic exposure to high concentrations of fluoride not only causes dental and skeletal fluorosis but additionally affects serum levels of reproductive hormones. However, possible interaction between fluoride exposure and estrogen receptor alpha (ESRα) gene polymorphisms on sex hormone-binding globulin (SHBG) and androgen binding protein (ABP) of male farmers has not been detailed. Here, we conducted a cross-sectional study including 348 male farmers with different fluoride exposure levels from drinking water in Henan province of China to explore effects of fluoride exposure and ESRα genetic variation on serum SHBG and ABP levels. We found serum SHBG levels in male farmers from the high exposure group to be lower than those of the low exposure group. We also found that concentrations of SHBG affected ABP levels. Furthermore, fluoride exposure and single nucleotide polymorphisms at the XbaI and rs3798577 loci of the ESRα gene affected serum ABP levels. Our findings suggest that chronic fluoride exposure from drinking water is associated with alterations of serum SHBG and ABP concentrations in local male farmers and that the effect of fluoride exposure on ABP levels vary depending on ESRα gene polymorphisms.

p53-Dependent pathway and the opening of mPTP mediate the apoptosis of co-cultured Sertoli-germ cells induced by microcystin-LR.

Microcystin-LR (MC-LR), a potent endotoxin, can induce reproductive toxicity. In order to investigate the role and mechanisms of apoptosis (p53-dependent and mitochondrial pathways) of germ cells induced by MC-LR, the co-cultured primary Sertoli-germ cells from Sprague-Dawley rats were used for the experiments. Expression levels of proteins, genes, and mitochondrial membrane potential (MMP) were obtained after exposing co-cultured Sertoli-germ cells to MC-LR with or without the addition of the p53 inhibitor, pifithrin-α (PFT-α), and MMP inhibitor, cyclosporin A (CsA). Results indicated that MC-LR could activate p53-dependent pathway-associated proteins in Sertoli-germ cells, leading to a decrease in MMP (indicating the opening of mitochondrial permeability transition pore [mPTP] and the release of Cytochrome-c [Cyt-c]) from the mitochondria into the cytoplasm and eventually the induction of apoptosis. PFT-α inhibited the expression ofp53, ameliorated the MMP of the co-cultured Sertoli-germ cells, and prevented the release of Cyt-c from the mitochondria into the cytoplasm, which reduces the occurrence of apoptosis. Similarly, the decreased release of Cyt-c from the mitochondria into the cytoplasm and the declined level of apoptosis in Sertoli-germ cells induced by MC-LR were observed after the addition of CsA. These results indicated that the apoptosis of the co-cultured Sertoli-germ cells induced by MC-LR was mediated by the p53-dependent pathway, with the involvement of the opening of mPTP.

Do Environmental Fluoride Exposure and ESRα Genetic Variation Modulate Methylation Modification on Bone Changes in Chinese Farmers?

Although increasing evidence suggests that estrogen receptor α (ESRα) genetic variation could modify bone damage caused by environmental fluoride exposure, little is known about epigenetic mechanisms in relation to bone changes. A case-control study was conducted among farmers aged 18-55 years in Henan Province, China. X-ray was used to detect bone changes. Methylation status was determined by methylation-specific PCR. Genotypes were identified by Taqman probe and real-time PCR. In this study, we found that methylation status in the promoter region of the ESRα gene was lower in bone change cases than that in controls, which was only observed in male farmers after stratification by gender. Furthermore, methylation level was negatively associated with the urinary fluoride concentration in male farmers. No significant association was found between the distribution of ESRα rs2941740 genotypes and the risk of bone changes. Multivariate logistic regression analysis showed that after adjusting for age and gender, increased serum calcium and methylation status were protective factors for bone changes. No interaction effect was observed between fluoride exposure and ESRα rs2941740 polymorphism on bone changes. In conclusion, the current work suggests that bone changes are associated with methylation status, which might be modulated by fluoride exposure in male farmers. Methylation status and bone changes were not modified by ESRα gene rs2941740 polymorphism in the promoter region.

Error analysis of the calibration of a dual-rotating-retarder Mueller matrix polarimeter.

We previously developed a Mueller matrix microscope by combining a dual-rotating-retarder device with a commercial microscope, which holds promise for pathologic diagnosis applications. In practical applications, the signals to be measured are sensitive to systematic errors, and the measurement accuracy and the instrument calibration affect the capacity to characterize the data. In conventional calibration, the initial positions of the rotating devices are constrained, causing calibration instability. To improve the calibration, we examine the mathematical model of the calibration process using previous studies, and derive a calibration algorithm with reduced error magnification. Our experimental results show the proposed algorithm improves calibration accuracy, and provides more robust results.

Optical stabilization system based on deformable mirrors for retina-like sensors.

This paper presents an optical stabilization system based on deformable mirrors (DMs) for retina-like sensors. This system achieves image stabilization by changing the reflective plate of the DM's compensating tilt angle. The mathematical model is constructed with relative parameters, and the simulation experiments and parameter analysis are discussed to verify the system's reliability. The experimental results show that this system achieved optical image stabilization. The maximum relative error of the compensation angle is 8.78%. The system is close to the diffraction limit, and the distortion is less than 0.33%. This study presents an image stabilization system and offers possible improvement in the aberrations in the system, which will provide great support to retina-like sensors.