基于De Bruijn图的De Novo序列组装软件性能分析

随着新一代测序技术的发展,一些新的全基因组组装算法应运而生,特别是针对第三代高通量测序仪产生的海量短序列的组装软件被不断开发出来,这些组装软件渐渐走向市场。但是,由于这些组装软件的适用性和其性能的差别,选择一款性能优良的组装工具或者开发并行高吞吐的组装工具成为了当前面临的一大难题。本文选取基于 De Bruijn 图算法开发的 4 款 De Novo 组装的软件（Velvet、SOAPdenovo、IDBA、ABySS）对 4 种物种的基因组的模拟数据进行测试,并从软件的算法、组装性能和组装质量 3 个方面分析这 4 个软件的性能,同时根据其算法特点推断影响这些软件性能的关键因素,并给出软件的使用建议以及开发并行序列组装工具来组装超大规模的基因数据应该注意的问题。     

Caustic imaging of gallium droplets using mirror electron microscopy

We discuss a new interpretation of mirror electron microscopy (MEM) images, whereby electric field distortions caused by surface topography and/or potential variations are sufficiently large to create caustics in the image contrast. Using a ray-based trajectory method, we consider how a family of rays overlaps to create caustics in the vicinity of the imaging plane of the magnetic objective lens. Such image caustics contain useful information on the surface topography and/or potential, and can be directly related to surface features. Specifically we show how a through-focus series of MEM images can be used to extract the contact angle of a Ga droplet on a GaAs (001) surface.     

Ricci flow-based spherical parameterization and surface registration

This paper presents an improved Euclidean Ricci flow method for spherical parameterization. We subsequently invent a scale space processing built upon Ricci energy to extract robust surface features for accurate surface registration. Since our method is based on the proposed Euclidean Ricci flow, it inherits the properties of Ricci flow such as conformality, robustness and intrinsicalness, facilitating efficient and effective surface mapping. Compared with other surface registration methods using curvature or sulci pattern, our method demonstrates a significant improvement for surface registration. In addition, Ricci energy can capture local differences for surface analysis as shown in the experiments and applications.     

Analysis of distribution time of multiple files in a P2P network

Peer-to-Peer (P2P) file sharing attracts much attention due to its scalability and robustness. One important metric in measuring the performance of a P2P file sharing system is the amount of time required for all peers to get the files. We refer this time as the file distribution time. Researchers have proposed protocols to minimize the file distribution time under different situation. However, most works are based on the single-file scenario. On the other hand, there are studies showing that in a file sharing application, users may download multiple files at the same time. In this paper, we analyze the minimum time needed to distribute multiple files. We develop an explicit expression for the minimum amount of time needed to distribute multiple files in a heterogeneous P2P fluid model. Unlike the single-file scenario, we demonstrate that the theoretical lower bound in multi-file is not always achievable. With a comprehensive consideration of all the configurations, we elaborate how to partition the bandwidth capacities of both seeds and leechers for a particular file such that the finish time is optimal.     

The fate of 14C-radiolabelled diclofenac and 4'-hydroxydiclofenac in membrane bioreactor treatment of wastewater

This study aimed at enhancing knowledge on the fate of diclofenac (DF), together with its main human metabolite 4'-hydroxydiclofenac (4'OHDF), during wastewater treatment by using a laboratory-scale membrane bioreactor (MBR). The reactor was fed continuously with non-radiolabelled diclofenac for a one month period prior to a single pulse of a 14C-radiolabelled solution of DF and 4'OHDF. The solution spike contained approximately 25% 4'OHDF and 65% DF, which corresponds to the ratio observed in municipal sewage, as well as traces of two other metabolites. The radioactivity was monitored for a total of twelve days in the various output streams. The calculation of the complete mass balance in the system demonstrated that the major part of the radioactivity left the reactor with the permeate (88.7%), while 2.1% was recovered in the excess sludge. Negligible amounts were recovered in the off-gas traps and on the membranes. Chromatographic analyses of effluent samples, by means of HPLC-MS coupled in parallel to a radiodetector, displayed a different pattern than the one of the spiked solution. It showed the occurrence of three additional metabolites.     

Treatment of linear alkylbenzene sulfonate (LAS) wastewater by internal electrolysis--biological contact oxidation process

Surfactant wastewater is usually difficult to treat due to its toxicity and poor biodegradability. A separate physico-chemical or biochemical treatment method achieves a satisfactory effect with difficulty. In this study, treatment of the wastewater collected from a daily chemical plant by the combination processes of Fe/C internal electrolysis and biological contact oxidation was investigated. For the internal electrolysis process, the optimal conditions were: pH = 4-5, Fe/C = (10-15):1, air-water ratio = (10-20):1 and hydraulic retention time (HRT)= 2 h. For the biological contact oxidation process, the optimal conditions were: HRT = 12 h, DO = 4.0-5.0 mg/L. Treated by the above combined processes, the effluent could meet the I-grade criteria specified in Integrated Wastewater Discharge Standard of China (GB 8978-1996). The results provide valuable information for full-scale linear alkylbenzene sulfonate wastewater treatment.     

Seasonal factors influencing the failure of buried water reticulation pipes

While the use of environmental factors in the analysis and prediction of failures of buried reticulation pipes in cold environments has been the focus of extensive work, the same cannot be said for failures occurring on pipes in other (non-freezing) environments. A novel analysis of pipe failures in such an environment is the subject of this paper. An exploratory statistical analysis was undertaken, identifying a peak in failure rates during mid to late summer. This peak was found to correspond to a peak in the rate of circumferential failures, whilst the rate of longitudinal failures remained constant. Investigation into the effect of climate on failure rates revealed that the peak in failure rates occurs due to differential soil movement as the result of shrinkage in expansive soils.     

Spectrophotometric characterization of human impacted surface waters in the Moselle watershed

In order to characterize the pollution discharged into the Moselle River and some of its tributaries, spectroscopic techniques, namely UV-vis spectroscopy and synchronous fluorescence spectroscopy, have been combined. UV-visible spectra were analysed using the maximum of the second derivative at 225 nm (related to nitrates), the SUVA254 and E2/E3 indices (related to the nature of organic matter). Synchronous fluorescence spectra (delta lambda = 50 nm) presented different shapes depending upon the type of pollution. The pollution results from anthropogenic activities: untreated domestic sewage due to misconnections in a periurban river, effluent from urban WWTPS, agricultural runoff (nitrates) in several streams, discharge from a paper mill (humic-like substances due to wood processing) and from steel mills (PAHs).     

三峡库区水资源保护规划的编制思路

三峡水库是国家重要的战略淡水资源库,也是重要的生态环境敏感区。保护好库区水资源, 对于保障库区居民用水安全,促进库区生态环境保护与区域经济社会和谐发展具有十分重要的意义。通过分析三峡工程进入试运行期后,库区水资源保护面临的主要问题,论述了开展三峡库区水资源保护规划的重要性和必要性,并探讨了编制三峡库区水资源保护规划的指导思想、原则及主要工作思路,可为编制三峡库区水资源保护规划提供参考。