Direct Quantification of Damaged Nucleotides in Oligonucleotides Using an Aerolysin Single Molecule Interface

DNA lesions such as metholcytosine(mC), 8-OXO-guanine (OG), inosine (I), etc. could cause genetic diseases. Identification of the varieties of lesion bases are usually beyond the capability of conventional DNA sequencing which is mainly designed to discriminate four bases only. Therefore, lesion detection remains a challenge due to massive varieties and less distinguishable readouts for structural variations at the molecular level. Moreover, standard amplification and labeling hardly work in DNA lesion detection. Herein, we designed a single molecule interface from the mutant aerolysin (K238Q), whose sensing region shows high compatibility to capture and then directly convert a minor lesion into distinguishable electrochemical readouts. Compared with previous single molecule sensing interfaces, the temporal resolution of the K238Q aerolysin nanopore is enhanced by two orders, which has the best sensing performance in all reported aerolysin nanopores. In this work, the novel K238Q could discriminate directly at least three types of lesions (mC, OG, I) without labeling and quantify modification sites under the mixed heterocomposition conditions of the oligonucleotide. Such a nanopore electrochemistry approach could be further applied to diagnose genetic diseases at high sensitivity.

Meta-analysis: Supplementary artificial light and goose reproduction

Photoperiod affects poultry reproduction, and in birds, photoperiod regulation is a complex physiological process. In modern poultry production, lighting management has become an important and effective management approach for increasing egg production. Geese are domesticated fowl and in many goose production enterprises animals are allowed to roam in outside pens during the day and are housed indoors at night, so the animals can be exposed to artificial lighting during the night periods. Supplementary artificial lighting resulted in improved reproduction in some studies, but reports have been inconsistent. To evaluate the results from previous studies of supplementary lighting on goose egg production, a meta-analysis was conducted to determine optimal supplementary artificial lighting regimens for geese egg production. Results indicated supplementary artificial light increases mean egg production, the length of the period of egg production before there is cessation of egg production capacity, and fertility. In summary, there were evaluations of data from five studies focused on White Roman geese in the meta-analysis conducted in the present study, however, examination of more breeds is necessary to make more definitive assessments of the findings from this meta-analysis.

[Matrix metalloproteinase-3 in patients with systemic lupus erythematosus and its significance in differentiating disease activity from pulmonary infections]

The purpose of this study is to investigate the matrix metalloproteinase-3 (MMP-3) levels in patients with systemic lupus erythematosus (SLE) and its significance in identifying disease activity and pulmonary infections. A total of 122 SLE patients were enrolled, including 21 with pulmonary infections, 16 with arthritis, 26 with nephritis, 10 with vasculitis, and 23 healthy controls. Serum MMP-3, C-reactive protein (CRP), serum amyloid A (SAA), and haptoglobin (HPT) levels were measured in all subjects. The results showed that the levels of MMP-3 in SLE combined with pulmonary infections [(230.10±44.92) μg/L], arthritis [(140.20±20.76) μg/L], nephritis [(155.40±23.36) μg/L] were higher than those in SLE only [(91.74±10.47) μg/L]. The levels of MMP-3 [(210.30±45.71) μg/L], CRP [(12.11±5.21) mg/L], HPT [(1.57±0.23) g/L] in active SLE combined with pulmonary infections were higher than those inactive SLE without pulmonary infections including MMP-3 [(124.00±15.22) μg/L], CRP [(7.76±2.96) mg/L], HPT [(0.89±0.09) g/L]. The levels of CRP [(10.03±2.70) mg/L], SAA [(89.22±36.77) mg/L] in active SLE with pulmonary infections and CRP[(7.76±2.96) mg/L], SAA [(60.22±19.7) mg/L] in active SLE without pulmonary infections were higher than CRP [(1.90±0.39) mg/L], SAA [(17.60±3.89) mg/L] in stable SLE with pulmonary infections. It suggests that the levels of CRP and SAA are elevated in active SLE with pulmonary infections. Serum MMP-3 in combination with CRP may assist in differentiating from SLE pulmonary infections.

[Association of glycosylated hemoglobin level at admission with outcomes of intracerebral hemorrhage patients]

Objective: To explore the association of the glycosylated hemoglobin (HbA1c) level at admission with 90 days functional outcome in patients with spontaneous intracerebral hemorrhage (ICH). Methods: Patients admitted to the Department of Neurology, Tongji Hospital from January to December 2017 were prospectively and continuously enrolled in this study. Clinical data were collected at admission and functional outcomes 90 days after ICH were assessed by using the modified RANKIN scale. Univariate and multivariate conditional logistic regression models were constructed. Patients were divided into four groups according to the quartile of HbA1c values. The median value of HbA1c in each group was taken as the substitute value and P for trend was calculated. The logistic regression model was fitted by restricted cubic splines to investigate the association between HbA1c level and outcome of ICH. Results: A total of 345 patients with ICH were enrolled, including 214 with favorable outcomes and 131 with poor outcomes (99 severe disability cases and 32 deaths). The risk of poor 90 days outcomes was significantly associated with HbA1c level at admission indicated by multivariate logistic regression analysis, and the P for trend test was <0.001 (middle-level group vs. low-level group: OR=2.33, 95%CI: 1.07-5.07; high-level group vs. low-level group: OR=2.52, 95%CI: 1.12-5.64; extremely high-level group vs. low-level group: OR=6.80, 95%CI: 3.01-15.34). Results from the restricted cubic spline showed that there was a linear correlation between HbA1c level at admission and poor 90 days outcomes of ICH (χ(2)=14.81, P<0.001; non- linear test: P=0.118). Compared with patients with HbA1c level of 6.5%, the risk of poor outcomes in patients with HbA1c level of <6.5% decreased linearly with the decrease in HbA1c level at admission, and the risk in patients with HbA1c level >6.5% was higher but not significantly. Conclusion: There was correlation between high HbA1c level at admission and 90 days poor outcome of ICH. High HbA1c level is an independent prediction indicator for ICH.

[The effect and mechanism of transient receptor potential M(2) in antigen-induced arthritis mice]

The purpose of this study was to explore the role and mechanism of transient receptor potential M(2) (TRPM(2)) in antigen-induced arthritis (AIA) mice. Twelve C57BL/6 mice and 12 TRPM(2) knockout mice were divided into 4 groups, includingwild type control group, wild type AIA group, TRPM(2) knockout control group and TRPM(2) knockout AIA group, with 6 mice in each group. Methylated bovine serum albumin (mBSA) was used to establish AIA mouse model. The degree of joint swelling and inflammatory cell infiltration were recorded, as well as synovial hyperplasia of the knee joints. Real-time quantitative polymerase chain reaction (PCR) was used to detect the expression of interleukin (IL)-6, IL-8, chemokine ligand 6 (CXCL-6) and tumor necrosis factor alpha (TNFα) mRNA in synovial cells of knee joints. The results showed that compared with the wild-type AIA group, the TRPM(2) knockout AIA group had more significant synovial proliferation and inflammatory cell infiltration in the synovial tissue.The neutrophil and macrophage counts rather than monocytes in the knee joints of TRPM(2) knockout AIA group were higher than those in wild-type AIA mice. The expression of IL-6, IL-8 and CXCL-6 mRNA were significantly increased in the knock out mice. In summary, TRPM(2) may inhibit inflammatory cytokines such as IL-6 and IL-8 in knee joints of AIA mice by reducing the infiltration of neutrophils and macrophages, the refore alleviates the manifestations of knee arthritis.

Influenza a virus and Streptococcus pneumonia coinfection potentially promotes bacterial colonization and enhances B lymphocyte depression and reduction

Influenza has frequently been epidemic in recent years. However, the mechanisms of severe pneumonia with postinfluenza Streptococcus pneumoniae (SP) secondary infection have not been fully understood. In this study, we explored the mechanisms of pneumonia in postinfluenza A virus (IAV) infection via a mouse model. Mice were intranasally inoculated with SP three days after IAV inoculation. We then collected samples at three time points to dynamically observe the pathological progression. In IAV infection alone, lymphocyte infiltration and widened alveolar intervals were observed. In the blood, levels of the CD19+, CD19+CD21+ and CD19+CD79β+B lymphocyte subpopulations were reduced, and IFN-γ and IL-10 were elevated. Slight atrophy was seen in the spleen, which was due to splenic B lymphocyteinitiated apoptosis through the mitochondrial pathway. When SP infection occurred after IAV infection, the pulmonary inflammation was significantly aggravated; a fair number of lymphocytes and neutrophils infiltrated simultaneously with exfoliated bronchial epithelial cells, vascular endothelial cells, widened alveolar septum and hemorrhaging. Increasing edema fluid and bacteria accumulated in the alveolar cavity. Decreased CD19+, CD19+CD21+ and CD19+CD79β+B lymphocyte subpopulations and increased interferon gamma (IFN-γ) or interleukin 10 (IL-10) were more prominent compared to those with viral infection alone. Spleen atrophy resulting from coinfection was more obvious because of massive splenic B lymphocyte apoptosis through the mitochondrial pathway compared to viral infection alone. This study shows that although inflammation caused by SP infection alone was temporary, preceding IAV infection provided favorable conditions for SP colonization and multiplication by destroying lung structure and suppressing humoral immunity. Synergistic IAV-SP coinfection is likely to facilitate more SP colonization and promote B lymphocyte-suppression and reduction. Eventually, the pneumonia worsened.

Revealing the transient conformations of a single flavin adenine dinucleotide using an aerolysin nanopore

Flavin adenine dinucleotide (FAD) as a cofactor is involved in numerous important metabolic pathways where the biological function is intrinsically related to its transient conformations. The confined space of enzymes requires FAD set in its specific intermediate conformation. However, conventional methods only detect stable conformations of FAD molecules, while transient intermediates are hidden in ensemble measurements. There still exists a challenge to uncover the transient conformation of each FAD molecule, which hinders the understanding of the structure-activity relationship of the FAD mechanism. Here, we employ the electrochemically confined space of an aerolysin nanopore to directly characterize a series of transient conformations of every individual FAD. Based on distinguishable current blockages, the "stack", "open", and four quasi-stacked FADs are clearly determined in solution, which is further confirmed by temperature-dependent experiments and mutant aerolysin assay. Combined with molecular dynamics simulations, we achieved a direct correlation between the residual current ratio (I/I ₀) and FAD backbone angle. These results would facilitate further understanding of the structure-activity relationship in the flavoprotein.

[Clinical analysis of five cases of autism spectrum disorder complicated with epilepsy with chromosome copy number variation]

Objective: To explore the clinical features and genetic causes of autism spectrum disorder (ASD) patients with epilepsy. Methods: The clinical data of five patients with ASD and epilepsy admitted to Xuanwu Hospital between September 2017 and September 2018 were collected, including medical history, intelligence level, developmental level, physical examination, neuroimaging and electroencephalogram. High-throughput whole-genome sequencing was applied to five patients and their parents. Results: Of five patients, four were male and one was female. All five patients had mild mental retardation, and one patient had significant growth retardation and craniofacial deformity. The average epilepsy onset age was 6.3 years old (7 months to 16 years). The main epileptic type was tonic-clonic seizure with abnormal EEG results. All patients have a favorable response to anti-epileptic drugs. Whole-exome sequencing (WES) revealed copy number variation in all 5 patients. Among them, 3 cases were reported to be pathogenic, and 2 cases were not reported (chromosome 16p13.3 duplication and chromosome 21q22.3 deletion). Conclusions: The results of current study support that autism spectrum disorders with seizures is often associated with copy number variations, such as Williams-Beuren region duplication syndrome, chromosome 15q11.2 duplication syndrome and chromosome 15q11.2 deletion syndrome. We reported two novel copy number variations (chromosome 16p13.3 duplication and chromosome 21q22.3 deletion) in two autism spectrum disorder patients with epileptic seizures.

[Comparison study on the differential expression of miRNAs in rat pulmonary fibrosis induced by nanosized SiO(2) and microsized SiO(2)]

Objective: To explore the correlation between expression level of miRNAs and pulmonary fibrosis on the basis of comparison the differential expression of miRNAs in rat pulmonary fibrosis induced by nano SiO(2) and micron SiO(2). Methods: Thirty-six healthy male SD rats weighting 180-220 g were randomly divided into 3 groups. They were instilled intratracheally with 1 ml suspension of saline, 25 mg/ml nanosized SiO(2) and microsized SiO(2) particles and sacrificed at 60 d and 90 d postexposure from each group with six rats. The change of pathological morphology and ultrastructure of lung were observed by optical and transmission electron microscopy. The differentially expressed microRNAs in lung tissue of the rats after instilled intrachcally nanosized SiO(2) and microsized SiO(2) particles at 60 d and 90 d were determined by Illumina HiSeq 2 000 sequencing technique. Target prediction for miRNAs was conducted by databases of Target-scan. Function-significant enrichment analysis and signal pathway analysis for predicted target genes were respectively conducted by the GO and the KEGG, then target genes related to pulmonary fibrosis were screened out. Results: Light microscope examination showed that wide bronchi, vessels, interlobular septa and slight fibrous connective tissue proliferation at 60 d and 90 d postexposure in 25 mg/ml nanosized SiO(2) group. A few fused nodules at 30 d postexposure, a lot of fused nodules at 60 d postexposure, fibrous cell nodules and compensatory emphysema around alveolar at 90 d postexposure in 25 mg/mL microsized SiO(2) group were observed. Electron microscopy demonstrated swelling and vacuolar degeneration of osmiophilic lamellar bodies in type Ⅱ alveolar epithelial cells, collagen fiber and elastic fiber hyperplasia in pulmonary interstitial at 60 d, 90 d postexposure in 25 mg/ml nanosized SiO(2) group. Increased and vacuoloid changed osmiophilic lamellar bodies in type Ⅱ alveolar epithelial cells, collagen fiber and elastic fiber hyperplasia in the interstitial at 60 d, 90 d postexposure in 25 mg/ml microsized SiO(2) group were observed. Comparing to saline control group, the number of miRNA up-regulated expression was 50, 70, and down-regulated expression was 22 and 24 at 60 d, 90 d postexposure in 25 mg/ml nanosized SiO(2) group respectively. There were 91,70 miRNAs up-regulated expression and 34,78 miRNAs down-regulated expression at 60 d, 90 d postexposure in 25 mg/ml microscale SiO(2) group. The common miRNA of differential up-regulated expression are miRNA-18a and miRNA-702-3p, down-regulated expression are miRNA-541, miRNA-127 and miRNA-379 both in nanosized SiO(2) and microscale SiO(2) group. The target genes related to pulmonary fibrosis were CTGF, IGF, BMP7, FGF7, TGF-β RIII, IGF1R and TGF-β1 respectively. Their biologic functions are to regulate signal pathway of TGF-β, MAPK and Wnt, and activation of fibroblast. Conclusion: These findings suggested that same dose of nanosized SiO(2) particles could cause mainly characterized by pulmonary interstitial fibrosis differing from silicotic nodule caused by microsized SiO(2). miRNA-18a, miRNA-702-3p, miRNA-541, miRNA-127 and miRNA-379 may play a role in the process of pulmonary fibrosis in nanosized SiO(2) and microscale SiO(2) by regulating its target genes.

HIV-1 persistence in the central nervous system: viral and host determinants during antiretroviral therapy

Despite remarkable therapeutic advances in the past two decades, the elimination of human immunodeficiency virus type 1 (HIV-1) from latent reservoirs constitutes a major barrier to eradication and preventing neurological disease associated with HIV/AIDS. Invasion of the central nervous system (CNS) by HIV-1 occurs early in infection, leading to viral infection and productive persistence in brain macrophage-like cells (BMCs) including resident microglia and infiltrating macrophages. HIV-1 persistence in the brain and chronic neuroinflammation occur despite effective treatment with antiretroviral therapy (ART). This review examines the evidence from clinical studies, in vivo and in vitro models for HIV-1 CNS persistence, as well as therapeutic considerations in targeting latent CNS reservoirs.

Single Molecule Study of Hydrogen Bond Interactions Between Single Oligonucleotide and Aerolysin Sensing Interface

The aerolysin nanopore displays a charming sensing capability for single oligonucleotide discrimination. When reading from the electrochemical signal, stronger interaction between the aerolysin nanopore and oligonucleotide represent prolonged duration time, thereby amplifying the hidden but intrinsic signal thus improving the sensitivity. In order to further understand and optimize the performance of the aerolysin nanopore, we focus on the investigation of the hydrogen bond interaction between nanopore, and analytes. Taking advantage of site-direct mutagenesis, single residue is replaced. According to whole protein sequence screening, the region near K238 is one of the key sensing regions. Such a positively charged amino acid is then mutagenized into cysteine and tyrosine denoted as K238C, and K238Y. As (dA)₄ traverses the pores, K238C dramatically produces a six times longer duration time than the WT aerolysin nanopore at the voltage of +120 mV. However, K238Y shortens the dwell time which suggests the acceleration of the translocation causing poor sensitivity. Referring to our previous findings in K238G, and K238F, our results suggest that the hydrogen bond does not dominate the dynamic translocation process, but enhances the interaction between pores and analytes confined in such nanopore space. These insights give detailed information for the rational design of the sensing mechanism of the aerolysin nanopore, thereby providing further understanding for the weak interactions between biomolecules and the confined space for nanopore sensing.

Learning Shapelets for Improving Single-Molecule Nanopore Sensing

The nanopore technique employs a nanoscale cavity to electrochemically confine individual molecules, achieving ultrasensitive single-molecule analysis based on evaluating the amplitude and duration of the ionic current. However, each nanopore sensing interface has its own intrinsic sensing ability, which does not always efficiently generate distinctive blockade currents for multiple analytes. Therefore, analytes that differ at only a single site often exhibit similar blockade currents or durations in nanopore experiments, which often produces serious overlap in the resulting statistical graphs. To improve the sensing ability of nanopores, herein we propose a novel shapelet-based machine learning approach to discriminate mixed analytes that exhibit nearly identical blockade current amplitudes and durations. DNA oligomers with a single-nucleotide difference, 5'-AAAA-3' and 5'-GAAA-3', are employed as model analytes that are difficult to identify in aerolysin nanopores at 100 mV. First, a set of the most informative and discriminative segments are learned from the time-series data set of blockade current signals using the learning time-series shapelets (LTS) algorithm. Then, the shapelet-transformed representation of the signals is obtained by calculating the minimum distance between the shapelets and the original signals. A simple logistic classifier is used to identify the two types of DNA oligomers in accordance with the corresponding shapelet-transformed representation. Finally, an evaluation is performed on the validation data set to show that our approach can achieve a high F₁ score of 0.933. In comparison with the conventional statistical methods for the analysis of duration and residual current, the shapelet-transformed representation provides clearly discriminated distributions for multiple analytes. Taking advantage of the robust LTS algorithm, one could anticipate the real-time analysis of nanopore events for the direct identification and quantification of multiple biomolecules in a complex real sample (e.g., serum) without labels and time-consuming mutagenesis.

Evaluation and comparison of the diagnostic performance of routine blood tests in predicting liver fibrosis in chronic hepatitis B infection

Background & aims: Biopsy is the gold standard for staging liver fibrosis, but it may be accompanied by complications. As an alternative, non-invasive markers such as transient elastography (for liver fibrosis) and certain combinations of routine blood markers (liver function tests, full blood count) have been developed although their clinical significance remains controversial. Here, we compare the diagnostic values of non-invasive markers for liver fibrosis in patients with chronic hepatitis B infection. Methods: Transient elastography and routine laboratory tests were performed in 196 patients. Diagnostic performances were compared and were assessed based on the area under the curve (AUC) of a receiver operating characteristic (ROC) analysis. Results: Elevated GGT to platelet ratio (GPR), the fibrosis index FIB-4 [based on age, AST, platelets and ALT], platelet to lymphocyte ratio (PLR) and total bilirubin were independent predictors of liver stiffness defined by transient elastography (all P < 0.001). The AUCs of GPR in predicting both advanced fibrosis and cirrhosis were significantly larger than that of FIB-4 (P = 0.037 and P = 0.008, respectively) and AST-to-platelet ratio index (APRI) (P = 0.008 and P = 0.005). FIB-4, APRI and red cell volume distribution width-to-platelet ratio (RPR) had similar diagnostic values in discriminating different levels of liver fibrosis. Conclusions: GPR showed the best diagnostic value and RPR and PLR are easily available and inexpensive markers in evaluating fibrosis and cirrhosis. The diagnostic values of these laboratory markers are useful in diagnosing advanced fibrosis or cirrhosis, and in confirming the different levels of liver fibrosis.

Ligustilide, a major bioactive component of Angelica sinensis, promotes bone formation via the GPR30/EGFR pathway

Angelica sinensis (Oliv.) Diels is a widely-used traditional Chinese herbal medicine in treating osteoporosis. Ligustilide (LIG) is the main component of A. sinensis and is considered to be the most effective biologically active ingredient in this plant. LIG has been found to have multiple pharmacological activities, such as anti-atherosclerosis, neuroprotection, anticancer, anti-inflammatory and analgesic. However, little is known regarding its anti-osteoporotic effects. The aims of this study were to investigate any protective effect of LIG on bone formation. The results showed that LIG significantly ameliorated inhibition of bone formation in zebrafish caused by prednisolone. LIG promoted osteoblast differentiation, including that of the pre-osteoblastic cell line MC3T3-E1 and bone marrow mesenchymal stem cells. LIG greatly improved the viability of MC3T3-E1 cells exposed to H₂O₂, attenuated H₂O₂-induced apoptosis and increased the expression of Bcl-2. Furthermore, LIG treatment lead to marked activation of phosphorylated EGFR and ERK1/2. These effects could be obviously inhibited by blocking GPR30 signaling with the specific inhibitor G15. Collectively, the results reveal that GPR30 is a positive switch for LIG to increase bone formation via regulation of EGFR, and these results provide evidence for the potential of LIG to treat osteoporosis.

[Quantification of optical coherence tomographic angiography images in type 2 diabetic patients]

Objective: To quantify optical coherence tomographic angiography (OCTA) images and to explore potential clinical values of each parameter in diabetic patients. Methods: A case-control and cross-sectional study of diabetic (129 eyes) and healthy (32 eyes) subjects was conducted. 3-mm OCTA scan, fundus photography and best corrected visual acuity measurement were performed. Image-pro plus was used to calculate microvascular and foveal avascular indices in nonsegmented and segmented OCTA images. Intraclass correlation coefficient and relative standard deviation were used to examine the reliability, reproducibility and accuracy. Correlation of each parameter was calculated, and so was the area under the receiver operating characteristic curve. Results: Vessel density (VD) of diabetic patients measured in the nonsegmented retinal layer (RL) and superficial retinal layer (SRL) was 49.146%±6.097%, 44.038%±5.641%, respectively, significantly lower than healthy subjects 52.212%±6.250%, 46.698%±5.417% (t=2.534, 2.405; P=0.012, 0.017), and vessel length (VL) was (19.905±2.285)mm, (17.596±2.149)mm, (14.479±2.091)mm in the three layers, which was significantly shorter than that in the healthy control group (21.037±2.185)mm, (18.739±1.994)mm, (15.343±2.266)mm (t=2.529, 2.731, 2.059; P=0.012, 0.007, 0.041). Compared with non-diabetes, foveal avascular zone (FAZ) in diabetes was (0.441±0.167)mm(2), larger compared to health eyes 0.352±0.109mm(2) (t=-2.831, P=0.005). FAZ demonstrated a negative correlation with VD and VL in RL or SRL(r=-0.227, -0.338; P<0.05) (r=-0.241, -0.332; P<0.05), while best corrected visual acuity showed a negative correlation with VL in each layer (r=-0.225, -0.201, -0.250; P=0.01, 0.022, 0.004), and VD in DRL (r=-0.197, P=0.026). All parameters showed high reproducibility between graders(intraclass correlation coefficient>0.965), while relative standard deviation was greater than 3.049%. AR had the highest area under the receiver operating characteristic curve (0.737), compared with AI (0.724). Conclusions: Our study demonstrates good reliability, reproducibility and accuracy of quantification of OCTA images and reveals changes of VD, VL and FAZ in diabetes, which may occur earlier than vision impairment. AR and AL may have great values in prompting early diabetic retinopathy in diabetic patients. (Chin J Ophthalmol, 2019, 55:273-279).

[Comparison of two serological methods in screening gastric cancer and its precancerous condition]

Objective: To compare the diagnostic value of the old "ABC" method [serum pepsinogen(PG) combined with Helicobacter pylori (Hp) IgG antibody] and the new "ABC" method [serum pepsinogen plus gastrin-17(G-17)] in screening gastric cancer and its precancerous condition. Methods: Serum PG, G-17 and Hp-IgG were quantified by enzyme-linked immunosorbent assay (ELISA) in 278 subjects. Subjects were grouped according to the criteria of two methods. The gastroscopy and pathological biopsy were gold standard. Results: The positive rate of old "ABC" method was 74.46% (207/278), which was 54.68% of new "ABC" method (151/278). For the diagnosis of gastric cancer, the sensitivity and specificity of the old "ABC" method were 90.74% and 29.46% respectively, with diagnostic coincidence rate 41.37%. The sensitivity and specificity of the new "ABC" method were 92.59% and 54.46% respectively, with diagnostic coincidence rate 61.87%. As to the diagnosis of pre-cancerous state, the sensitivity and specificity of the old "ABC" method were 75.81% and 36.00%, with diagnostic coincidence rate 58.03%. The sensitivity and specificity of the new "ABC" method were 62.10% and 75.00%, with diagnostic coincidence rate 67.86%. Conclusions: Compared with the old "ABC" method, the new "ABC" method has higher sensitivity, specificity and diagnostic coincidence rate for the diagnosis of gastric cancer, yet higher specificity and lower sensitivity for the diagnosis of precancerous conditions.

A lithium-ion-active aerolysin nanopore for effectively trapping long single-stranded DNA

Wild-type aerolysin (AeL) nanopores allow direct single nucleotide discrimination of very short oligonucleotides (≤10 nt) without labelling, which shows great potential for DNA sensing. To achieve real applications, one major obstacle of AeL is its poor capture ability of long single-stranded DNA (ssDNA, >10 nt). Here, we have proposed a novel and robust strategy for the electrostatic focusing of long ssDNA into a lithium-chloride (LiCl)-active AeL. By using this method, for the first time we have demonstrated AeL detection of ssDNA longer than 100 nt. Due to screening more negative charges, LiCl improves AeL capture ability of long ssDNA (i.e. 60 nt) by 2.63- to 10.23-fold compared to KCl. Further calculations and molecular dynamics simulations revealed that strong binding between Li+ and the negatively charged residue neutralized the AeL, leading to a reduction in the energy barrier for ssDNA capture. These findings facilitate the future high-throughput applications of AeL in genetic and epigenetic diagnostics.

Direct Sensing of Single Native RNA with a Single-Biomolecule Interface of Aerolysin Nanopore

RNA sensing is of vital significance to advance our comprehension of gene expression and to further benefit medical diagnostics. Taking advantage of the excellent sensing capability of the aerolysin nanopore as a single-biomolecule interface, we for the first time achieved the direct characterization of single native RNA of Poly(A)₄ and Poly(U)₄. Poly(A)₄ induces ∼10% larger blockade current amplitude than Poly(U)₄. The statistical duration of Poly(A)₄ is 18.83 ± 1.08 ms, which is 100 times longer than that of Poly(U)₄. Our results demonstrated that the capture of RNA homopolymers is restricted by the biased diffusion. The translocation of RNA needs to overcome a lower free-energy barrier than that of DNA. Moreover, the strong RNA-aerolysin interaction is attributed to the hydroxyl in pentose, which prolongs the translocation time. This study opens an avenue for aerolysin nanopores to directly achieve RNA sensing, including discrimination of RNA epigenetic modification and selective detection of miRNA.

Identification of Essential Sensitive Regions of the Aerolysin Nanopore for Single Oligonucleotide Analysis

The aerolysin nanopore channel is one of the confined spaces for single molecule analysis which displays high spatial and temporal resolution for the discrimination of single nucleotides, identification of DNA base modification, and analyzing the structural transition of DNAs. However, to overcome the challenge of achieving the ultimate goal of the widespread real analytical application, it is urgent to probe the sensing regions of the aerolysin to further improve the sensitivity. In this paper, we explore the sensing regions of the aerolysin nanopore by a series of well-designed mutant nanopore experiments combined with molecular dynamics simulations-based electrostatic analysis. The positively charged lumen-exposed Lys-238, identified as one of the key sensing sites due to the presence of a deep valley in the electrostatic potentials, was replaced by different charged and sized amino acids. The results show that the translocation time of oligonucleotides through the nanopore can be readily modulated by the choice of the target amino acid at the 238 site. In particular, a 7-fold slower translocation at a voltage bias of +120 mV is observed with respect to the wild-type aerolysin, which provides a high resolution for methylated cytosine discrimination. We further determine that both the electrostatic properties and geometrical structure of the aerolysin nanopore are crucial to its sensing ability. These insights open ways for rationally designing the sensing mechanism of the aerolysin nanopore, thus providing a novel paradigm for nanopore sensing.

[The significance of clinical indicators of different Gram-stained bacteria resulted in secondary intracranial infection after craniocerebral operation]

Objective: To compare and analyze the clinical characteristics and laboratory parameters of central nervous system (CNS) infection caused by different Gram-stained bacteria after craniocerebral surgery, and to provide a preliminary basis for early anti-infection treatment to reduce the use of extended-spectrum antibiotics and the generation of resistant strains. Methods: A single center retrospective study was conducted to investigate the clinical data of patients with intracranial infection after craniocerebral surgery from January 2012 to December 2016 in PLA general hospital. The general conditions, clinical features, laboratory parameters, antibiotic treatments and prognosis were analyzed. Results: A toal of 813 cases of CNS infection after craniocerebral surgery were found during the 5-year period, with an incidence rate of 5.43% (813/14 986). The positive rate of cerebrospinal fluid (CSF)culture was 9.72% (79/813). According to the criteria, 71 cases were included in the study. Among all the cases, 64.8% (46/71) of which were Gram-positive bacteria (G(+) ) and 35.2% (25/71) were identified as Gram-negative bacteria (G(-)). The duration between surgery and meningitis events, as well as the period of antibiotic treatment for G(+) bacteria group were 5.0 (4.0, 6.0) days and (18.3±6.8) days, which were shorter than those of the G(-) bacteria group 9.0(7.0, 11.0) days and (29.2±9.9) days (Z=-6.184, t=-5.245, both P<0.01) , and the differences were statistically significant. The serum procalcitonin concentration in the G(+) group was lower than that in G(-) group [1.02(0.83, 1.27)μg/L vs 2.68(1.97, 5.07)μg/L, Z=-5.719, P<0.01]. The cerebrospinal fluid glucose content was higher than that of G(-) bacteria group[(2.13±1.30) mmol/L vs (1.09±0.95) mmol/L, t=3.512, P<0.01]. The protein level was lower than that of G(-) bacteria group [(1 615.93±848.83) mg/L vs (2 480.60±1 105.28) mg/L, t=-3.679, P<0.01]. Serum C-reactive protein concentrations in the two groups did not show any statistical significance [(96.2±46.1) mg/L vs (117.8±46.3) mg/L, t=-1.884, P>0.05]. In addition, the mortality rate of the G(-) bacteria group was 16.0% (4/25), and 0 in G(+) bacteria group. Conclusion: The time of onset of intracranial infection, serum PCT concentration, and cerebrospinal fluid glucose and protein content caused by Gram-positive bacteria and Gram-negative bacteria are found to be significantly different, and these findings could serve as a preliminary guide for the selection of antibiotics in early experiential anti-infective treatments without the etiology report.

[Comparison of efficacy between sorafenib and sunitinib as first-line therapy for metastatic renal cell carcinoma and analyze prognostic factors for survival]

Objective: To investigate the efficacy and drug related adverse reactions of sorafenib and sunitinib as first-line tyrosine-kinase inhibitors (TKIs) for patients with metastatic renal cell carcinoma (mRCC) and analyze the clinical prognostic factor for survival. Methods: The data of 271 patients with metastatic renal cell carcinoma who had complete clinicopathological data were retrospectively analyzed, including 174 cases in sorafenib group and 97 cases in sunitinib group, to access patients' overall survival (OS) and progression-free survival (PFS). Prognostic values of all characteristics were determined by using univariate and multivariate Cox regression models. Results: The objective response rates (ORR) of the sorafenib and sunitinib groups were 14.9% and 19.6%, respectively, and the disease control rates (DCR) were 85.1% and 88.6%, respectively. No significant difference was found between the sorafenib and sunitinib group in ORR (P=0.325) or DCR (P=0.408). The most common grade 3 to 4 adverse events in the sorafenib group were hand-foot syndrome (6.7%), diarrhea (2.3%), and rash (2.3%). The most common grade 3 to 4 adverse events in the sunitinib group were neutropenia (6.2%), hand-foot syndrome (6.2%), and thrombocytopenia (4.6%). During the follow-up, 97 cases death occurred and 81 cases disease progression occurred in sorafenib group. The median PFS was 12 months (95% CI: 9-15 months), and the median OS was 25 months (95% CI: 21-29 months) in sorafenib group. While 74 cases death occurred and 40 cases disease progression occurred in sunitinib group, the median PFS was 12 months (95% CI: 10-12 months) and the median OS was 23 months (95% CI: 20-32 months) in sunitinib group. No significant difference was found between the sorafenib and the sunitinib group in PFS (P=0.771) or OS (P=0.548). Multivariate analysis showed Fuhrman grades (HR=1.358, 95%CI: 1.004-1.835), number of metastatic sites (HR=1.550, 95%CI: 1.143-2.101) and MSKCC risk grade (Intermediate risk group: HR=1.621, 95%CI: 1.117-2.232; Poor risk group: HR=2.890, 95%CI: 1.942-4.298) were independent prognostic factors for PFS. Fuhrman grades (HR=2.135, 95%CI: 1.533-2.974), number of metastatic sites (HR=1.774, 95%CI: 1.279-2.461) and MSKCC risk grade (Intermediate risk group: HR=1.415, 95%CI: 1.002-1.998; Poor risk group: HR=3.161, 95%CI: 2.065-4.838) were independent prognostic factors for OS. Conclusions: The results of this study indicate that sorafenib and sunitinib are both effective as the first-line TKIs for mRCC patients and sorafenib has comparable efficacy to sunitinib. But they have differences in the incidence of adverse effects. Fuhrman grades, number of metastatic sites and MSKCC risk grade are independent prognostic factors for mRCC patients.

Study on physiological and psychological comprehensive nursing of elderly tumor patients after surgery

The aim of this study is to formulate nursing schemes for elderly tumor patients after surgery according to their clinical characteristics, and give effective guidance for alleviating the patients’ psychological anxiety. One hundred elderly tumor patients admitted to the oncology department of the Affiliated Cancer Hospital of Harbin Medical University were included and divided into an intervention group (50) and a control group (50). Nursing intervention was performed on the intervention group, and routine nursing was performed in the control group. One day before surgery, all the patients were asked to fill in a self-rating anxiety scale (SAS) and a self-rating depression scale (SDS), and their blood pressure and heart rate data were measured. After surgery, the patients were asked to fill in a form which investigated their pain degree, recovery situation and satisfaction degree. The heart rate and blood pressure of the patients in the intervention group recovered faster than those of the control group, with lower SAS and SDS scores and shorter recovery time. In conclusion, effective nursing intervention played a crucial role in the postoperative recovery of elderly tumor patients by reducing pain and anxiety degrees, which improved the patients’ satisfaction with the nursing.