Objective To construct an executable model of a hypoxia response network (HRN) and to analyze the dynamic evolution mechanism of an HRN including randomness as well as concurrency based on computer simulation. Methods Specific evolution rules and Gillespie algorithm were adoped to study the dynamic evolution of the structural model based on the construction of a structural model of an HRN using stochastic Petri net ( SPN ) .Results Dynamic evolution laws of an HRN were obtained and the simulation results were consistent with laboratory results in response to descript switch-like behavior of an HRN .Conclusion A visualization model of the HRN can be achieved using SPN method.Simulation results achieved by executing the model based on stochastic simulation using specific kinetic parameters can serve as a nice complement to traditional laboratory results , which can help shed light on the structure and function characteristics of an HRN.

Objective To observe the sleeping time and analyze its impact on the psychological state and quality of life of patients with type 2 diabetes .Methods Convenience sampling was used to recruit 365 patients with type 2 diabetes in Jiangsu Province Hospital on Integration of Chinese and Western Medicine Affiliated to Nanjing University of Chinese Medicine between April 2014 and April 2015 .All the patients were divided into two groups according to the six-hour cut-off point of sleeping time .They were investigated by means of World Health Organization Quality of Life-BREF ( WHOQOL-BREF), Diabetes Distress Scale ( DDS) and General Self-Efficacy Scale ( GSES).Data were analyzed by t-test, chi-square test, Mann-Whitney U test and multivariate regression analysis .Results The average sleeping time was 7.03 h, and the sleeping time of 109 patients was less than 6 h.Patients with less sleeping time had lower quality of life and self-efficacy scores as well as higher diabetes distress scores than those with sleeping time more than 6 h.The differences were statistically significant (P<0.05).Regression analysis showed that sleeping time was the factor of quality of life (β=0.117, P=0.047), self-efficacy (β=0.136, P=0.024) and diabetes distress(β=-0.118, P=0.046).Conclusion Sleeping time affects the psychological state and quality of life of patients with type 2 diabetes.The medical should pay more attention to the quality of sleep of such patients .

Objective To evaluate the clinical efficiency of posterior unilateral open-door laminoplasty and leverage titanium plate internal fixation in the treatment of cervical spondylotic myelopathy ( CSM ) with multi-segmental spinal stenosis.Methods Between Mar 2011 and May 2015, 25 patients with multi-segmental CSM with multi-segmental spinal stenosis were treated by posterior unilateral open-door laminoplasty and leverage fixation .There were 16 males and 9 females, whose mean age was 60.6 ±9.9 years during the surgery.The change of clinical symptoms and signs was recorded during follow-up,and they all received X-ray and MRI.In all the patients, the preoperative and postoperative neurological function, the cervical curvature,cervical vertebra tube volume and axial symptoms were measured , recorded and analyzed. There was statistically significant difference (P<0.05) in the mean Japanese Orthopaedic Association (JOA) score, and Visual Analogue Scale ( VAS) .Results All the 25 patients were followed up for more than 6 months ( 6-24 months ) .No symptoms of C5 nerve root were found in our series .According to the JOA score and VSA score ,the neurological functions of each patient were significantly improved .The preoperative JOA score was 10.16 ±1.35 and the improvement rate 61.24%. There was statistically significant difference between the preoperative VSA score and the postoperative one (6.68 ±1.12 vs 2.32 ±0.84) ( P<0.05).The preoperative and postoperative meansurement of the spinal vertebrai canal diameter was (9.22 ±2.01) and (15.64 ±2.08) mm, respectively,so there was statistically significant difference (P <0.05), indicating that the cavical spinal canal was increased after operation .Conclusion Leverage titanium plate internal fixation can effectively help maintain the expanded vertebral canal after unilateral open -door laminoplasty ,reduce the incidence of postoperative axial symptoms , and maintain the cervical physical curvature .

Objective To systematically review the efficacy of corticosteroid nasal spray plus antihistamine versus either therapy given alone or placebo in patients with allergic rhinitis (AR).Methods The PubMed, EMbase, Google Scholar and The Cochrane Library were electronically searched for randomized controlled trials ( RCTs ) about the efficacy of corticosteroid plus antihistamine for AR .The duration of the search was from the inception of the databases to April 2015 . After literature selection , data extraction and quality assessment conducted by two reviewers independently , meta-analysis was conducted using RevMan 5.3 software.Results Ten studies involving 6568 patients were finally included .The qualitative analysis showed that the combination therapy had greater efficacy than oral antihistamines alone or placebo on improving symptoms.The results of meta-analysis showed that pooled results of two trials failed to show significant difference in total nasal symptoms between combination therapy and intranasal corticosteroid alone [ WMD =-0.20, 95%CI (-0.38,-0.01),P=0.04].The cumulative meta-analysis of six RCTs showed that the combination therapy was superior to intranasal corticosteroid alone[WMD=-1.16, 95%CI( -1.49,-0.83), P<0.00001], intranasal antihistamine alone[WMD=-1.73, 95%CI( -2.08,-1.38),P<0.00001], and placebo [WMD =-2.81, 95%CI( -3.16,-2.47), P<0.00001].Conclusion Intranasal corticosteroid plus oral antihistamine has similar efficacy to intranasal corticosteroid alone, greater efficacy than oral antihistamines alone or placebo in reducing nasal symptoms for AR patients . Intranasal corticosteroid plus intranasal antihistamine is significantly superior to either therapy given alone or placebo .

Objective To establish a quick electrochemical biosensor for the detection of nucleic acid of Ebola virus . Methods The DNA tetrahedral nanostructure was self-assembled on gold surface by strong Au-S chemical bonds , leaving the target probe at the top .A biotinylated-ssDNA was introduced as the detection probe by specific binding of the captured target sequence , before avidin-horseradish peroxidase ( HRP) was used as a signal amplifier to transduce amperometric sig-nal through interactions with TMB substrate .Results The results indicated that the nucleotide sequence of Ebola virus could be recognized and detected by the sensor .The linear range for the detection of target DNA was from 1.0 ×10 -9 to 5.0 ×10 -6 mol/L,and the detection limit was 5.2 ×10 -10 mol/L.Conclusion The fabricated sensor is demonstrated to be sensitive and specific for the detection of Ebola virus nucleotide .

Objective To knock out the GP73 gene in H22 cells originating in mice using CRISPR/Cas9 gene editing system and construct H22 GP73 gene knockout stable strain for identification of its functions .Methods Two pairs of sgRNAs that could specifically identify the upstream and downstream of GP 73 gene first promoter were designed before a recombinant eukaryotic expressional plasmid was constructed using pX 459 .After enzyme digestion and sequencing , two pairs of recombinant plasmids were co-transfected into H22 cells before puromycin was used to screen positive cells and monoclonal cells which stably knocked out GP 73 gene were developed .The knockout effect was measured by Western blotting.Cell Titer 96? AQueous One Solution Assay was used to detect the effect on cell reproductive capacity when the GP73 was knocked out .The transferability was detected through wound healing test .Results The result of Western blotting suggested that GP73 protein was undetected in the construction of H22 GP73 knockout gene stable strain after transfection.The transfer and reproduction slowed down .Conclusion H22 GP73 gene knockout stable strain can be successfully built using CRISPR/Cas9 gene editing system ,thus facilitating studies on the function of GP 73 in hepatocarcinogenesis .

Objective To separate human γ-tubulin ring complexes (γTuRC) .Methods Cell lysates prepared from 293FT cells were separated using gel filtration chromatography .Then, the eluate fractions containing γTuRC or γ-tubulin small complexes (γTuSC ) were determined by immunoblotting .Results As the constitutive components of γTuRC,γ-tubulin,γ-tubulin complex protein 2 (GCP2), GCP3 and GCP4 were eluted and enriched in the fourth fraction .The molecular mass of eluates in the fourth fraction was about 2000 ×10 3 .Following γTuRC, the constitutive components ofγTuSC including γ-tubulin, GCP2 and GCP3 were eluted and enriched in the fourteenth fraction .The molecular mass of eluates in the fourteenth fraction was about 310 ×10 3 .Unassembled free components were washed out in the eighteenth and subsequent fractions .γTuRC could be detected in the corresponding fractions by negative-PAGE separation .ConclusionγTuRC and γTuSC were successfully separated from the unassembled free components in the fourth ( 4#) and fourteenth (14#) eluted fraction, respectively.The eluates containing ofγTuRC orγTuSC can be used for microtubule assembly research.

Objective To explore the role of the transcriptional factor activator protein (AP)-1 in mediating vascular endothelial growth factor ( VEGF) expression in human bronchial epithelial cells exposed to PM 2.5.Methods Beas-2B cells was treated with PM2.5.Luciferase assay was used to detect the activation status of AP-1 and transcription of VEGF in the Beas-2B cells.The induced activation of c-Jun, ATF2 and VEGF expression was tested by Western blotting assay.Results PM2.5 induced transactivation of the transcriptional factor AP-1, accompanied by phosphorylation of the AP-1 components, c-Jun and ATF2 in Beas-2B cells.Moreover, when AP-1 activation was inhibited by knocking down c-Jun or ATF2 expressions, induction of VEGF expression was partially attenuated in Beas-2B cells.Conclusion AP-1 is a critical transcriptional factor in mediating PM2.5-induced VEGF expression and inflammatory responses in human bronchial epithelial cells.

Objective To investigate the effect of DNA-dependent protein kinase catalytic subunit (DNA-PKcs) on autophagy induction by ionizing radiation ( IR ) .Methods The cell model of knocking-down DNA-PKcs expression was constructed by transfecting HeLa cells with a pSicoR-based lentivirus vector expressing DNA-PKcs specific shRNA .Cellular growth activity and radiosensitivity were detected by cell countingkit ( CCK)-8 assay.The expression of autophagy related proteins was detected by Western blotting hybridization .Autophagy was also detected by monitoring the autophagic marker green fluorescere protein ( GFP )-light chain 3 ( LC3 ) puncta per cell under an immunofluorescent microscope .Results A cellular model of knocking-down DNA-PKcs expression was successfully generated by transfecting the specific shRNA against DNA-PKcs.Depression of DNA-PKcs significantly decreased the growth activity of HeLa cells and increased the cellular sensitivity to ionizing radiation .Both the expression changes of P 62 and LC3 proteins and immunofluorescent GFP-LC3 puncta observation indicated that knocking-down DNA-PKcs prompted the induction of autophagy by ionizing radiation . Moreover, inactivation of DNA-PKcs led to a decreased phosphorylation of mammalian target of sirolimus ( Rapamycin, RAPA) ( mTOR) at S2481 site.Conclusion Depression of DNA-PKcs expression prompts the induction of autophagy by IR and cellular radiosensitivity .mTOR signaling may be involved in the regulation of autophagy processing by DNA-PKcs.

With the rapid development of biotechnology such as NGS and proteomics , bioinformatics has seen an explo-sion in diversity and complexity in terms of data , tools and demands .The traditional computing environment , including ded-icated workstations and virtual machines , are no longer suitable under such circumstances .As a rising container technolo-gy, Docker, which is characterized by light weight , openness and security ,has provided an innovative solution to analysis and processing of biological big data and attracted increasing attention from bioinformatics developers and users .Consider-ing the demands and features of development , deployment and application of bioinformatics tools in the age of big data , this paper analyzes the advantages of Docker in this field , introduces some actual cases and discusses current deficiencies and future improvement .