Candidate gene prioritization for non-communicable diseases based on functional information: Case studies

Candidate gene prioritization for complex non-communicable diseases is essential to understanding the mechanism and developing better means for diagnosing and treating these diseases. Many methods have been developed to prioritize candidate genes in protein-protein interaction (PPI) networks. Integrating functional information/similarity into disease-related PPI networks could improve the performance of prioritization. In this study, a candidate gene prioritization method was proposed for non-communicable diseases considering disease risks transferred between genes in weighted disease PPI networks with weights for nodes and edges based on functional information. Here, three types of non-communicable diseases with pathobiological similarity, Type 2 diabetes (T2D), coronary artery disease (CAD) and dilated cardiomyopathy (DCM), were used as case studies. Literature review and pathway enrichment analysis of top-ranked genes demonstrated the effectiveness of our method. Better performance was achieved after comparing our method with other existing methods. Pathobiological similarity among these three diseases was further investigated for common top-ranked genes to reveal their pathogenesis.

[Characteristic analysis of aeroallergens of allergic rhinitis patients in Wuhan]

Objective:To analyze the distribution characteristics of common aeroallergens in patients with allergic rhinitis（AR）in Wuhan. Method:Serum specific IgE（ssIgE）was detected in 1 983 patients with clinically diagnosed AR by Midiwiss Allergen Screen system. Data was analyzed statistically. Result:Among the 1 983 patients，1 507（76.0%）had at least one positive ssIgE. The most common aeroallergens were Dermatophagoides pteronyssinus（62.0%），mixed fungi（32.1%）and house dust（27.3%）.Single positive allergen（43.8%），dual positive allergen（28.1%）and triple positive allergen（15.4%）were the most common combinations. The proportion of single positive allergens in the juvenile group（1 to 17 years old）（35.2%）was lower than adult group（≥18 years old）（46.7%），while the proportion of multiple positive allergens was higher than adult group. The positive rates of mulberry and mixed grass in male group were higher than female group. The positive rates of house dust，cat fur and dog fur in the juvenile group were higher than the adult group，while the positive rate of mulberry，cockroach and mixed grass were lower than the adult group. In the elder group（60-88 years old），the positive rates of Dermatophagoides pteronyssinus and mixed fungi were higher than the other three groups. The positive rates of Dermatophagoides pteronyssinus in summer and autumn were higher than that in winter and spring. The positive rate of mixed grass in autumn was much higher and the positive rate of mixed trees and mulberry trees in spring was higher than summer and autumn. Conclusion:Dermatophagoides pteronyssinus，mixed fungi and house dust were the most common aeroallergens among patients with allergic rhinitis in Wuhan. The distribution characteristics in different genders，ages and seasons were different..

[Heterogeneity and clonal evolution in pediatric ETV6-RUNX1(+) acute lymphoblastic leukemia by quantitative multigene fluorescence in situ hybridization]

目的

研究儿童ETV6-RUNX1阳性急性淋巴细胞白血病（ALL）中肿瘤细胞的异质性及克隆演化情况，探讨克隆演化与预后的相关性。

方法

应用单细胞定量多基因荧光原位杂交（QM-FISH）技术对2006年2月至2011年6月收治的48例ETV6-RUNX1阳性ALL患儿的骨髓标本进行多个基因拷贝数变异的检测，并进行克隆演化分析。将4例复发患儿初诊与复发时的情况进行比较。

结果

在48例行QM-FISH检测的患儿中，初诊时为1个克隆的有34例（70.8%），2个克隆的有9例（18.8%），≥3个克隆的有5例（10.4%）。患儿的肿瘤细胞存在异质性，各亚克隆之间呈线性或树枝状演化。白血病细胞的亚克隆数与患者预后无相关性（5年总生存率：P=0.469；5年无病生存率：P=0.116）。复发克隆可能与初诊时克隆一致，也可能为新出现克隆。复发克隆为新出现克隆的患儿再次缓解时间短，预后更差。

结论

ETV6-RUNX1阳性ALL患儿肿瘤细胞存在异质性及克隆演化情况。QM-FISH有助于研究白血病细胞的克隆演化，复发克隆为新出现克隆的患儿可能预后更差。

Insecticidal activities and mechanism of extracts from neem leaves against Oxya chinensis

ABSTRACT In this study, neem leaves were successively extracted with petroleum ether, 95% ethanol and water and the insecticidal activities of these extracts against Oxya chinensis larvae were measured. The results showed that 95% ethanol extract gave the highest extraction yield and insecticidal activity, and it was further extracted with five different solvents. The petroleum ether extract from the 95% ethanol extract possessed the highest insecticidal activity with median lethal concentration values ranging from 14.93 to 55.66mg/mL. The gas chromatography-mass spectrometer analysis showed that the petroleum ether extract mainly composed of alkanes, olefin, esters and amide. The pathological examination revealed that the prominent lesions, including reduced regenerative cells in midgut and swelled and degenerated cylindrical cells, were observed in the 5th instar Oxya chinensis after treatment. The ultrastructural features showed that the cylindrical cells, microvilli and mitochondria were seriously damaged. These results suggested that the petroleum ether extract from neem leaves had potent insecticidal activity and could be a candidate insecticide.

Physical and compositional analysis of differently cultured 3D human skin equivalents by confocal Raman spectroscopy

Three-dimensional skin equivalents are increasingly gaining acceptance as non-animal based experimental models of human skin. They are particularly suited to studying differences in physical and compositional properties of normal and diseased skin and their impact on the skin's barrier function. Typically, a culture protocol yielding a model of normal skin is modified to create a model simulating a pathology. Skin layer thicknesses and lipid/protein contents are compared using methods that are invasive, precluding further experiments on the same replicates, and which may be prone to artefacts. We show here that confocal Raman spectroscopy (CRS) is a valuable method for non-invasive discrimination of skin equivalents grown under different culture conditions. Using 3D full-thickness skin equivalents developed in-house, we measure significant differences in stratum corneum and viable epidermis apparent thicknesses resulting from a 7-day difference in the cultures' air-lift phase and from supplementation of the culture medium with interleukin 4. Furthermore, stratum corneum thicknesses obtained by CRS are up to 2.6-fold higher than values measured from histological photomicrographs. Regarding composition, CRS reveals the differential effects of the culture protocol modifications on ceramide, cholesterol and protein composition as a function of depth in the stratum corneum.

Random D1–A1–D1–A2 terpolymers based on diketopyrrolopyrrole and benzothiadiazolequinoxaline (BTQx) derivatives for high-performance polymer solar cells

The overall power conversion efficiency of the polymer solar cell based on P13 (DPP/BTQx ratio is 1/1) showed the highest value of 9.20% with a V_oc of 0.86 V, J_sc of 15.74 mA cm⁻², and FF of 0.68.

[Airway inflammation in sleep disordered breathing children: preliminary results]

Objective:To assess the clinical significance of nasal nitric oxide(NNO) levels in children with sleep disordered breathing(SDB).Method:Thirty children with SDB and twenty healthy children were enrolled. The NNO levels were measured non-invasively using a NIOX MINO system. SPSS statistics 20.0 software was used to analyze the data. Result:Compared to healthy children,NNO level was significant higher in children with SDB(Z=-2.215,P<0.05) .Correlation analysis showed that SDB children's NNO level was directly correlated with AHI(r=0.429,P<0.05),and it was inversely correlated with nadir SaO2(r=-0.482,P<0.01).But NNO level was not significantly correlated with other polysomnographic parameters. Conclusion:Our data suggested that NNO levels might be useful for evaluating the disease severity in SDB children.

Logistic-function-based nonlinear companding transform for asymmetrical hybrid optical orthogonal frequency division multiplexing visible light communications systems

In this paper, a logistic-function-based nonlinear companding transform (LNCT) is proposed to reduce the peak-to-average power ratio of asymmetrical hybrid optical orthogonal frequency division multiplexing (AHO-OFDM) signals in visible light communications (VLC). First, the positive and negative amplitudes of the bipolar AHO-OFDM signal are divided into two groups as the positive and nonnegative groups. Then, a peak detection is employed frame-by-frame to locate the group where the maximum peak occurs. Finally, the piecewise companding transform consisting of the nonlinear logistic function and a linear function is performed on the amplitude groups with and without the maximum peak, respectively. The simulation results show that the proposed LNCT scheme outperforms the classical linear nonsymmetrical transform method in terms of the complementary cumulative distribution function with a competing bit error rate performance, thus demonstrating its application potential in AHO-OFDM-based VLC systems.

[Prognostic significance of combined TERT and IDH gene mutation analysis in diffusely infiltrating gliomas]

Objective: To investigate the status and prognostic significance of TERT and IDH1/2 genes mutations in diffusely infiltrating gliomas. Methods: Hot spot mutations of TERT and IDH1/2 genes were detected by DNA sequencing in 236 cases of gliomas at West China Hospital from 2012 to 2016, including pilocytic astrocytoma (WHO grade Ⅰ, 16 cases), diffuse astrocytoma and oligodendroglioma (WHO grade Ⅱ, 89 cases), anaplastic astrocytoma and oligodendroglioma (WHO grade Ⅲ, 72 cases) and glioblastoma (WHO grade Ⅳ, 59 cases). The prognostic significance of TERT and IDH1/2 hot spot mutations was evaluated. Results: No IDH or TERT mutations were detected in pilocytic gliomas. TERT promoter mutation frequency was higher in patients aged ≥40 years(60.8%, 93/153) than in patients aged <40 years (32.8%, 22/67; P<0.01). TERT promoter mutation rate was also significantly higher in oligodendroglioma (87.5% , 56/64) than that in astrocytoma(37.8%, 59/156; P<0.01). Young age (<40 years), oligodendroglioma and IDH1 mutation were favorable prognostic factors for diffusely infiltrating astrocytic and oligodendroglial tumors. TERT mutation alone was not of prognostic significance. Diffusely infiltrating astrocytic and oligodendroglial tumors were divided into four molecular subtypes according to TERT and IDH1 mutation status: IDH(+ )/TERT(+ ), IDH(+ )/TERT(-), IDH(-)/TERT(-) and IDH(-)/TERT(+ ). There was significant prognostic difference among the 4 subtypes. Conclusions: Combined IDH and TERT gene mutation analysis may be useful for prognostic subgrouping. Notably, IDH1 wild-type cases can be further subdivided into TERT(+ ) or (-) subgroups with significant prognostic difference.

VEGFR1 Signaling Regulates IL-4-Mediated Arginase 1 Expression in Macrophages

BACKGROUND

Macrophages undergo polarization or activation in response to environmental stimuli, an essential process for proper immune response. Meanwhile, excessive activation of macrophages causes autoimmune diseases. It is therefore crucial to prevent over-activation of macrophage in order to maintain the proper immune response. Arginase 1 (Arg-1) plays a critical role in coordinating the immune response by regulating availability of arginine.

OBJECTIVE

To understand the mechanism of Arg-1 regulation.

METHODS

Real-time PCR and Western Blot analysis were utilized to examine the Arg-1 levels expressed from the VEGFR1-deleted and VEGFR1-TK-deficient bone marrowderived macrophages (BMDMs).

RESULTS

The VEGFR1-mediated signaling suppressed IL-4-induced Arg-1 expression. Deletion of VEGFR1 resulted in elevated Arg-1 expression and the tyrosine kinase domain of VEGFR1 was required for the suppression. Each of three ligands of VEGFR1, VEGF-A, VEGF-B and PIGF, mediated the inhibition to the similar degree.

CONCLUSION

Our findings identified a novel function of the VEGFR1 signaling in avoiding over-expression of Arginase 1 potentially to maintain the proper innate immune response.

Determination of the maximum tolerated dose of intranasal sufentanil and midazolam in Chinese: a pilot study

BACKGROUND

The purpose of this study was to determine the maximum tolerated dose (MTD, the dose of causing 10% respiratory depression) of intranasal sufentanil (SUF) and midazolam (MID) for sedation during gastroscopy by continual reassessment method (CRM).

METHODS

Patients (18-65 years old) scheduled for gastroscopy were recruited in this study. Subjects received intranasal SUF and MID for sedation. The dose of MID (5 mg) was fixed, while the dose of SUF was increased progressively (six incremental doses ranging from 0-0.60 μg/kg, n = 3 for each dose). The first cohort received a conservative, predetermined dose of 5 mg MID and 0 μg/kg SUF, subsequent cohorts received doses of SUF that were determined by the responses of all previous patients using Bayesian-based software. The dose allocated to the next cohort is the one with an updated posterior response probability closest to 10%.

RESULTS

Thirty Chinese patients scheduled for gastroscopy were included. Probability of respiratory depression at each dose was as follows: 5 mg MID + 0 μg/kg SUF, 0.4%; 5 mg MID + 0.1 μg/kg SUF, 0.8%; 5 mg MID + 0.2 μg/kg SUF, 1.8%; 5 mg MID + 0.3 μg/kg SUF, 3.7%; 5 mg MID + 0.4 μg/kg SUF, 9.9%; 5 mg MID + 0.5 μg/kg SUF, 17.8%; 5 mg MID + 0.6 μg/kg SUF, 36.0%.

CONCLUSION

The MTD of intranasal MID and SUF for sedation during gastroscopy causing 10% respiratory depression is 5 mg MID + 0.4 μg/kg SUF, based on CRM.

Down-regulation of JARID1B expression inhibits cell proliferation, induces apoptosis and blocks cell cycle in human acute lymphoblastic leukemia cells

OBJECTIVE

Acute lymphocytic leukemia (ALL) is a multi-factorial blood disease with unknown pathogenesis. Histone H3K4 methylation was significantly reduced in ALL patients, whereas jumonji AT-rich interactive domain 1B (JARID1B) was the specific demethylase of H3K4me. This study explores the expression level of JARID1B in ALL patients and down-regulated JARID1B expression in ALL cells to explore the function of JARID1B in ALL.

PATIENTS AND METHODS

JARID1B mRNA expression level in ALL patients was detected by Real-time PCR. The peripheral blood mononuclear cells from healthy volunteers were selected as control. JARID1B shRNA was transfected with MOLT-4 cells and BALL-1 cells. JARID1B protein expression and H3K4me2 and H3K4me3 levels were detected by Western blot assay. Cell proliferation was assessed by 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2-H-tetrazolium bromide (MTT) assay. Cell apoptosis and cell cycle were determined by flow cytometry. Bcl-2, Bax, Procaspase 3, and cyclin P21 expressions were evaluated by Western blot assay.

RESULTS

JARID1B mRNA expression in primary bone marrow cells from ALL patients was significantly higher than that of healthy volunteers (p<0.05). The levels of histone H3K4me3 and H3K4me2 were up-regulated after JARID1B shRNA transfection. JARID1B shRNA significantly inhibited the proliferation of MOLT-4 and BALL-1 cells, induced apoptosis, and blocked cell cycle in G0/G1 phase compared with the control group (p<0.05).

CONCLUSIONS

JARID1B is highly expressed in ALL. Down-regulating its expression inhibited leukemia cell proliferation, promoted apoptosis, and blocked cell cycle in G0/G1 phase through histone H3K4 methylation. JARID1B is an oncogene in ALL.

Correction: Physical and compositional analysis of differently cultured 3D human skin equivalents by confocal Raman spectroscopy

Correction for 'Physical and compositional analysis of differently cultured 3D human skin equivalents by confocal Raman spectroscopy' by Y. Dancik, et al., Analyst, 2018, DOI: .

A high precision flat crystal spectrometer compatible for ultra-high vacuum light source

We report on a flat crystal spectrometer (FCS) featuring a differently pumped rotary feedthrough and double detectors connected to a crystal chamber by extendable bellows built at the Shanghai EBIT Laboratory. It was designed to overcome defects such as oil contamination, little distance from the detector to the crystal and others of an early FCS equipped at the same laboratory, but still keeps a large detectable angle range of detectors and brings new features and functions such as the Bond method measurement and double-crystal measurement which are based on the two-detector and large bellow design. This new FCS could cover an energy range of measurable photons from 570 eV to 10 keV and reach a vacuum better than 6 × 10^-10 Torr and thus is compatible for coupling directly to ultra-high vacuum light sources. Off-line tests of the FCS were undertaken where Kα x-rays from solid titanium were measured and analyzed. Measurements of transitions in He-like argon ions were performed when the spectrometer was directly connected to Shanghai EBIT, and the width of the x-ray source was monitored simultaneously using an x-ray slit imaging system. An observed spectral line broadening was 0.869 eV corresponding to a resolving power of 3600, including Doppler broadening of the x-ray source. Taking account of the measured source width, we made simulations using the SHADOW 3 code and got a nominal resolving power of 6500 for the spectrometer. This high nominal resolving power is due to a longer distance from the crystal to the detector, comparing with that in the early FCS.

The association between MICA/MICB polymorphism and respiratory syncytial virus infection in children

MICA/MICB gene polymorphisms are related to several cancers and infectious diseases, but there are no reports on the association between MICA/MICB gene polymorphisms and respiratory syncytial virus (RSV) infection. To clarify the association between MICA/MICB gene polymorphisms and infection of RSV in children, we collected fresh blood samples from paediatric patients with and without pneumonia after RSV infection. The MICA/MICB alleles were characterized by PCR sequence-specific primers (PCR-SSP) and PCR sequence-based genotyping (PCR-SBT), and then, the frequency of the MICA/MICB alleles and haplotypes was calculated. The results showed that the frequencies of MICA*002:01 and MICA-A9 in RSV-infected patients were significantly lower than in controls (9% vs. 20%, pc = 0.04). The allele frequency of MICA*002:01 in pneumonia patients (8%) and nonpneumonia patients (9%) was significantly lower than in controls (20%, pc = 0.02). MICA*002:01-MICB*008(Δrel = 0.616), MICA*009-MICB*016 (Δrel = 0.506), and MICA*045-MICB*014 (Δrel = 0.700) showed linkage disequilibrium in patients infected with RSV. The haplotype frequency of MICA*002:01-MICB*005:02 in RSV-infected patients was significantly lower than in controls (10% vs. 16%, pc = 0.033). In conclusion, allele MICA*002:01/A9 and haplotype MICA*002:01-MICB*005:02 were negatively associated with RSV respiratory tract infections.

[Epidemiological characteristics of HBeAg reversion in chronic hepatitis B patients with HBeAg seroconversion in Jiangsu province, 2012-2014]

Objective: To understand characteristics and influencing factors of reversion of HBeAg in chronic hepatitis B patients with HBeAg sero-conversion, and provide epidemiological evidence for the regular management of chronic hepatitis B patients. Methods: From 2012 to 2014, a cohort study was conducted among the chronic hepatitis B patients with sero-conversion of HBeAg in Jiangsu province. Association between participants' demographics, ALT, HBV DNA and incidence of HBeAg reversion was analyzed by Cox regression model. HBV DNA changing trend between patients with HBeAg reversion and patients with persistent HBeAg sero-conversion was compared by repeated measure data variance analysis. Results: In 2012, there were 5 068 HBeAg seroconverted chronic hepatitis B patients aged (51.9 ± 12.8) years enrolled. By 2014, HBeAg had reversed in 121 cases with the rate of 1.3/100 person-years. The probability of HBeAg reversion decreased with the age of the patients. By Cox regression analysis, HBV DNA level was an important influencing factor for the progress of HBeAg reversion. The patients with HBV DNA≥200 000 IU/ml had a higher HBeAg reversion rate DNA (3.8/100 person-years) than those with HBV DNA <2 000 IU/ml (1.1 person-years) (HR=3.44, 95% CI: 1.91-6.20, P=0.000). Compared with the persistent HBeAg sero-conversion group, HBV DNA and ALT showed a more dramatic increase in the HBeAg reversion group (P=0.000). Conclusions: There was a certain HBeAg reversion rate in chronic hepatitis B patients with HBeAg sero-conversion. Younger chronic CHB patients with HBeAg sero-conversion and those with higher HBV DNA lever had higher HBeAg reversion rate. Following up and management of chronic CHB patients with HBeAg sero-conversion is important and helpful for the control of hepatitis B.

[A cohort study on the epidemiological characteristics of HBeAg sero-clearance in HBeAg positive chronic hepatitis B patients in Jiangsu province from 2012 to 2014]

Objective: To understand the epidemiological characteristics and influencing factors related to HBeAg sero-clearance in chronic hepatitis B patients so as to provide evidence for regular management on chronic HBV patients. Methods: From 2012 to 2014, a cohort study was conducted among HBeAg positive chronic HBV patients in Jiangsu province. Association between the characteristics and incidence of HBeAg sero-clearance was analyzed by Cox regression method. The changing trend on HBV DNA between patients with HBeAg sero-clearance and those with persistent HBeAg positive status was compared by repeated measure data variance analysis method. Results: In 2012, there were 721 HBeAg positive hepatitis B patients aged (45.2 ± 14.2) years enrolled in this study. By 2014, the follow-up observation period was 1 058 person-years, and 393 cases had lost their HBeAg status, with the rate as 37.2/100 person-years. The HBeAg sero-clearance rate was 32.4/100 person-years in hepatitis B patients who received antiviral treatment. The probability of HBeAg clearance in HBeAg positive hepatitis B patients aged ≥60 year (62.0/100 person-years) was higher than those of aged <20 year (7.0/100 person-years). The rate of HBeAg sero-clearance in HBeAg positive patients with HBV DNA <20 000 IU/ml (75.8/100 person-years) was higher than those whose HBV DNA were ≥200 000 IU/ml (16.1/100 person-years). By Cox regression analysis, the HBV DNA level was an important influencing factor on the progress of HBeAg sero-clearance. Patients with HBV DNA levle as ≥200 000 IU/ml, had a lower HBeAg clearance rate (HR=0.18, 95%CI: 0.13-0.23, P<0.001). Compared to the persistent HBeAg positive group, HBV DNA showed a more dramatic fall in the HBeAg-lost group (P<0.001). Conclusion: The rate of HBeAg sero-clearance among HBeAg positive hepatitis B patients was correlated with age and HBV DNA status of the patients that called for comprehensive management and intervention programs to develop for the HBeAg positive hepatitis B patients with different characteristics.