An information-flow-based model with dissipation, saturation and direction for active pathway inference

<p>Abstract</p> <p>Background</p> <p>Biological systems process the genetic information and environmental signals through pathways. How to map the pathways systematically and efficiently from high-throughput genomic and proteomic data is a challenging open problem. Previous methods design different heuristics but do not describe explicitly the behaviours of the information flow.</p> <p>Results</p> <p>In this study, we propose new concepts of dissipation, saturation and direction to decipher the information flow behaviours in the pathways and thereby infer the biological pathways from a given source to its target. This model takes into account explicitly the common features of the information transmission and provides a general framework to model the biological pathways. It can incorporate different types of bio-molecular interactions to infer the signal transduction pathways and interpret the expression quantitative trait loci (eQTL) associations. The model is formulated as a linear programming problem and thus is solved efficiently. Experiments on the real data of yeast indicate that the reproduced pathways are highly consistent with the current knowledge.</p> <p>Conclusions</p> <p>Our model explicitly treats the biological pathways as information flows with dissipation, saturation and direction. The effective applications suggest that the three new concepts may be valid to describe the organization rules of biological pathways. The deduced linear programming should be a promising tool to infer the various biological pathways from the high-throughput data.</p

Movable Fiber-Integrated Hybrid Plasmonic Waveguide on Metal Film

A waveguide structure consisting of a tapered nanofiber on a metal film is proposed and analyzed to support highly localized hybrid plasmonic modes. The hybrid plasmonic mode can be efficiently excited through the in-line tapered fiber based on adiabatic conversion and collected by the same fiber, which is very convenient in the experiment. Due to the ultrasmall mode area of plasmonic mode, the local electromagnetic field is greatly enhanced in this movable waveguide, which is potential for enhanced coherence light emitter interactions, such as waveguide quantum electrodynamics, single emitter spectrum and nonlinear optics

Proposal for a near-field optomechanical system with enhanced linear and quadratic coupling

We propose a realistic system with separated optical and mechanical degrees of freedom, in which a high-mechanical-quality silicon nitride membrane is placed upon a high-optical-quality whispering gallery microcavity. The strongly enhanced linear optomechanical coupling, together with simultaneously low optical and mechanical losses in the present system, results in a remarkable single-photon cooperativity exceeding 300. This unprecedented cooperativity in the optomechanical system enables optical nonlinearity at low light intensities and holds great potential in generating, storing, and implementing quantum states. Moreover, the device gives rise to significantly stronger quadratic optomechanical coupling than achieved to date, which is desirable for measuring phonon shot noise with a high signal-to-noise ratio.Comment: 14 pages, 5 figure

The investigation of status of human parasites in children from Yushu

目的  调查青海省玉树县震后转移安置学生的肠道寄生虫感染情况。方法  粪便直接涂片法检查虫卵。结果  512份粪便样品中，寄生虫阳性粪便31份，感染率为6.05%。其中，结肠内阿米巴20例，感染率为3.91%；蓝氏贾第鞭毛虫8例，感染率为1.56%；蛔虫3例，感染率0.59%。结论  玉树的学生肠道寄生虫的感染率均不高于全国平均水平。Objective: To investigate the status of human parasites in children who have been evacuated here from Yushu after earthquake. Methods: Detect the eggs from smear feces samples. Results: 512 stool samples were collected and examined by microscope. The total infection rate was 6.05%, where the infection rate for entamoeba coli Grassi was 3.91%, Giardia lamblia stile was 1.56%, Ascaris Lumbricoides was 0.59%. Conclusion: Our results suggest that the infection rate of human parasites is not higher than normal rate in China

Discovering cooperative biomarkers for heterogeneous complex disease diagnoses

Biomarkers with high reproducibility and accurate prediction performance can contribute to comprehending the underlying pathogenesis of related complex diseases and further facilitate disease diagnosis and therapy. Techniques integrating gene expression profiles and biological networks for the identification of network-based disease biomarkers are receiving increasing interest. The biomarkers for heterogeneous diseases often exhibit strong cooperative effects, which implies that a set of genes may achieve more accurate outcome prediction than any single gene. In this study, we evaluated various biomarker identification methods that consider gene cooperative effects implicitly or explicitly, and proposed the gene cooperation network to explicitly model the cooperative effects of gene combinations. The gene cooperation network- enhanced method, named as MarkRank, achieves superior performance compared with traditional biomarker identification methods in both simulation studies and real data sets. The biomarkers identified by MarkRank not only have a better prediction accuracy but also have stronger topological relationships in the biological network and exhibit high specificity associated with the related diseases. Furthermore, the top genes identified by MarkRank involve crucial biological processes of related diseases and give a good prioritization for known disease genes. In conclusion, MarkRank suggests that explicit modeling of gene cooperative effects can greatly improve biomarker identification for complex diseases, especially for diseases with high heterogeneity

Research on the Determination of Cadmium in Grain by Rapid Digestion-Standard Addition

Rapid digestion-standard addition based on graphite furnace atomic absorption spectrometry(GFAAS) for determining cadmium in grain of four kinds of matrix (brown rice, corn, wheat and rice) is established, by studying on digestion conditions, optimizing the proportion of sample and nitric acid, and using digested sample to prepare standard solution. The results show that the correlation coefficients are 0.995 to 0.999. The detection limit of method is 0.003 mg/kg. The relative error between the test result and the standard value is –3.8% to –1.1%. The standard recoveries of cadmium in low, medium and high gradient are 99.1% to 103.4%, and the RSD values of the standard substances and real samples are 1.2% to 2.7%.Compared with the results of microwave digestion method, the detection values of cadmium have no significant difference (P>0.05). The method have shown advantages in terms of accuracy and precision, and it is a rapid and accurate method to calculate cadmium in large quantities of grain samples

N′-(2-Hydr­oxy-5-chloro­benzyl­idene)-4-nitro­benzohydrazide methanol solvate

The title compound, C14H10ClN3O4·CH4O, was synthesized from the reaction of 5-chloro­salicylaldehyde with 4-nitro­benzohydrazide in methanol. The Schiff base mol­ecule is nearly planar, with a dihedral angle of 9.1 (3)° between the two benzene rings. The methanol solvent mol­ecules are linked to the Schiff base mol­ecules by N—H⋯O, O—H⋯N and O—H⋯O hydrogen bonds, forming chains running parallel to the a axis