FishSizer: Software solution for efficiently measuring larval fish size

1. Length and depth of fish larvae are part of the fundamental measurements in many marine ecology studies involving early fish life history. Until now, obtaining these measurements has required intensive manual labor and the risk of inter‐ and intra‐observer variability.
2. We developed an open‐source software solution to semi‐automate the measurement process and thereby reduce both time consumption and technical variability. Using contrast‐based edge detection, the software segments images of a fish larva into “larva” and “background.” Length and depth are extracted from the “larva” segmentation while taking curvature of the larva into consideration. The graphical user interface optimizes workflow and ease of usage, thereby reducing time consumption for both training and analysis. The software allows for visual verification of all measurements.
3. A comparison of measurement methods on a set of larva images showed that this software reduces measurement time by 66%–78% relative to commonly used software.
4. Using this software instead of the commonly used manual approach has the potential to save researchers from many hours of monotonous work. No adjustment was necessary for 89% of the images regarding length (70% for depth). Hence, the only workload on most images was the visual inspection. As the visual inspection and manual dimension extraction works in the same way as currently used software, we expect no loss in accuracy.

     

用于寡核苷酸探针设计的ARB软件

探针设计是制备高质量基因芯片的重中之重。ARB软件是用于设计系统发育芯片(Phylo Chip)探针的主要软件,然而由于安装困难、相关中文文章较少等原因,阻碍了其在国内的广泛使用。本文详细介绍了ARB软件的安装方法、探针设计及其他功能。这将有助于用户快速使用ARB软件进行探针设计,促进系统发育芯片的发展及其在各领域的应用。     

Application of satellite data for investigation of dynamic processes in inland water bodies: Lake Shira (Khakasia, Siberia), a case study

This work describes avenues to use satellite information to analyse dynamic processes in aquatic ecosystems. Information for this analysis, was retrieved from AVHRR satellite sensor data. This information consisteds of time series of images of radiation temperature and turbidity. We expect this information will be of great value in analysing inland water bodies. Methods to process satellite information using original software and data processing techniques are proposed. For the investigation of the process and analyses of satellite information Shira Lake (Khakasia, Siberia) was used as a case study. To study the variability of the surface temperature and turbidity of the Lake in summer, the satellite and ground-truth data of the lake was applied. This study represents the first evaluation of the dynamic processes for Lake Shira based on satellite, ground-truth and modelling data. We developed algorithms and software to process satellite images to enable the reconstruction of time dependence of temperature and spectral reflectance of water bodies in the visible range, and to make computer-animated films visualising the spatial and temporal dynamics of the study parameters. The analyses of morphometric, meteorological and hydrological characteristics of Lake Shira have provided a realistic opportunity for processing the satellite information and to develop numerical models of variability of the hydrological regime of the lake. The results obtained demonstrate the feasibility of systematically retrieving the spatial information from the satellite data on the dynamics of the surface water temperature and of the suspended matter in the lake.     

A comprehensive software suite for the analysis of cDNAs

We have developed a comprehensive software suite for bioinformatics research of cDNAs; it is aimed at rapid characterization of the features of genes and the proteins they code. Methods implemented include the detection of translation initia- tion and termination signals, statistical analysis of codon usage, comparative study of amino acid composition, comparative modeling of the structures of product proteins, prediction of alternative splice forms, and metabolic pathway reconstruction. The software package is freely available under the GNU General Public License at http： / /www.g-language.org/ data/cdna/.     

High Throughput Screening of Gene Expression Signatures

This paper focuses on microarray image analysis and discusses a completely automated approach to image processing, which eliminates human intervention. A system for automated image processing is described, which is capable of processing image files in a batch-mode thus allowing high-throughput of microarray image analysis. Grid-placement and spot finding are achieved without operator's help. The software eliminates noise signals from the data analysis process and minimizes operator's involvement in the procedure.     

Stability analysis of pathogen-immune interaction dynamics

The paper considers models of dynamics of infectious disease in vivo from the standpoint of the mathematical analysis of stability. The models describe the interaction of the target cells, the pathogens, and the humoral immune response. The paper mainly focuses on the interior equilibrium, whose components are all positive. If the model ignores the absorption of the pathogens due to infection, the interior equilibrium is always asymptotically stable. On the other hand, if the model does consider it, the interior equilibrium can be unstable and a simple Hopf bifurcation can occur. A sufficient condition that the interior equilibrium is asymptotically stable is obtained. The condition explains that the interior equilibrium is asymptotically stable when experimental parameter values are used for the model. Moreover, the paper considers the models in which uninfected cells are involved in the immune response to pathogens, and are removed by the immune complexes. The effect of the involvement strongly affects the stability of the interior equilibria. The results are shown with the aid of symbolic calculation software.     

Kinetics of excitation trapping in intact Photosystem I of Chlamydomonas reinhardtii and Arabidopsis thaliana

We measured picosecond time-resolved fluorescence of intact Photosystem I complexes from Chlamydomonas reinhardtii and Arabidopsis thaliana. The antenna system of C. reinhardtii contains about 30-60 chlorophylls more than that of A. thaliana, but lacks the so-called red chlorophylls, chlorophylls that absorb at longer wavelength than the primary electron donor. In C. reinhardtii, the main lifetimes of excitation trapping are about 27 and 68 ps. The overall lifetime of C. reinhardtii is considerably shorter than in A. thaliana. We conclude that the amount and energies of the red chlorophylls have a larger effect on excitation trapping time in Photosystem I than the antenna size.     

Chromatographic resolution of glucosidic compounds, ginsenosides on polyethersulphone membrane, and its application to the quantitative immunoassay for ginseng saponins

A method has been devised for the chromatographic resolution of glucosidic compounds, ginseng saponins, on polyethersulphone (PES) membrane. The method results in good resolution and quantitative immunoassay for ginsenoside Rb1 (G-Rb1), G-Rc, and G-Rd in crude extracts of various ginsengs. The newly established method is simpler and applies for quantitative analysis. Ginsenosides developed by acetonitrile-water-acetic acid solvent system on a PES membrane were directly treated with a NaIO4 solution followed by bovine serum albumin (BSA), resulting in a ginsenoside-BSA conjugate on a PES membrane. Anti-G-Rb1 monoclonal antibody (MAb) was bound, and then a second antibody labeled with peroxidase directed against the first antibody. Finally a substrate reacted to the enzyme and gave staining. The stained membrane was scanned, and spots were analyzed quantitatively using NIH Image software. At least 62.5 ng of G-Rb1, G-Rc, and G-Rd were clearly detectable individually. Three ginsenosides can be analyzed quantitatively between 0.125 and 2.0 microg.     

智能化鼠多功能行为训练系统的研究

目的：研制一种微机控制的大鼠多功能行为训练检测系统－梯度电压自动驱动大鼠及微机适时显示,记录和分析实验结果。方法：采用仿windows界面,以TurboC2．0编制,利用TC直接对硬件端口操作,完成信号的采集,处理和对实验仪器的控制。结果：本系统实现了：①梯度电压自动驱动;②声,光,电不同条件刺激;③多路径自动设置;④所没数据建立数据库以SAS软件处理其结果。结论：本系统自动化程度高,操作简便,数据处理科学、准确,尤其是还可用于听觉、视觉等特殊鼠记忆模型的建立。