Reverse fingerprinting, similarity searching by group fusion and fingerprint bit importance

Summary Recent research has shown that using data fusion rules in fingerprint-based similarity searching can improve results over traditional searches. Group fusion scores, which use multiple reference compounds, have in particular been shown to be quite effective in increasing enrichment rates over single reference structure based searches. In this paper, the effectiveness of using data fusion with multiple reference compounds to increase similarity search recall rates was investigated using 44 biological targets and four different 2D fingerprinting systems, including a new 2D typed triangle fingerprinting system introduced here. Scaffold-hopping abilities using data fusion rules were investigated using eight (8) different classes of scaffolds active against cGMP phosphodiesterase isoform 5 (PDE5). An approach to using the reference group for ranking and visualizing important fingerprints bits, or reverse fingerprinting, was presented, and used to score and visualize important pharmacophore features within sample active molecules. Finally, similarity statistics within the reference groups were investigated and compared to recall rates.     

Community detection using global and local structural information

Community detection is of considerable importance for understanding both the structure and function of complex networks. In this paper, we introduced the general procedure of the community detection algorithms using global and local structural information, where the edge betweenness and the local similarity measures respectively based on local random walk dynamics and local cyclic structures were used. The algorithms were tested on artificial and real-world networks. The results clearly show that all the algorithms have excellent performance in the tests and the local similarity measure based on local random walk dynamics is superior to that based on local cyclic structures.     

Pressure recovery system for a high-power HF/DF laser: implementation practice

The matter of development of a high-performance pressure recovery system (PRS) for a high-power HF/DF laser is discussed. A sequence of design steps is proposed, which involves estimation of basic characteristics of PRS components with the help of one-dimensional integral and semi-empirical procedures; simulation, to be performed using three-dimensional non-stationary Navier — Stokes equations; experimental modelling aimed at verification of the calculation procedures and at refinement of obtained parameters; and a fullscale experiment. An ejector-type system providing for recovery of pressure from 12 Torr to atmospheric pressure in the gas-dynamic system of an HF/DF laser of several-tens-kilowatt power is developed. Matching conditions for parameters of individual PRS components as well as joint functioning of the PRS with a continuous chemical laser in an integral complex are analysed. Conditions for minimization of mass-dimensional characteristics of the laser-PRS complex necessary for the development of ground-based mobile systems are identified.     

Electrical and structural characterization of inhomogeneously doped semiconductors by infrared spectroscopy

An optical method is presented for thenon-destructive electrical and structural characterisation of multilayer structures. The presented concept yields the complex refractive index profiles within an arbitrary composed layer system by using the symmetrical transmission and the asymmetrical reflectivity caused by the optical inhomogeneity of a material. This method includes the superimposition of coherent multiple reflections within the refractive index profile as well as incoherent multiple reflections within the whole wafer. This analysis yields the spacial distribution of free carrier density profiles within the sample as well as the transitions between different crystal phases by using the least squares fit procedures. The results of the optical analysis are compared with other methods used to quantitatively determine density profiles and phase transitions such as SIMS, spreading resistance, stripping Hall and RBS.     

极小景深条件下显微镜大范围聚焦算法

自动聚焦是全自动显微成像中的一项关键技术。为了克服已有聚焦算法对聚焦起始点敏感及聚焦范围过小的问题,从分析大范围聚焦曲线形态入手,依据离焦距离、初始搜索方向和初始搜索范围等参量和曲线形态参数间的制约关系,将聚焦划分为六种类型,极值搜索中结合聚焦函数值的变化信息并通过启发式方式将未知类型转化为基本型,从而实现了大范围聚焦到小范围聚焦的转换。然后在聚焦曲线陡峭区范围内对曲线进行高斯拟合以获取最优焦平面。基于自行研发的全自动显微镜系统对提出的算法进行了验证,实验结果证明了该算法的有效性。     

车载图像跟踪系统中复杂场景下目标提取算法的研究

提出一种新的复杂场景下的目标图像提取方法。给出一种改进的Snake模型,并将其应用到初始模板的建立中;引入分形布朗随机场模型,利用小波分形维数和分形拟合误差确定可能的目标区域;定义了一种新的最小失配距离（MMD）相似性度量,并基于目标的特征区域进行快速相关匹配。该算法通过精确建立初始模板和采用由粗到精的目标搜索策略,既保证了目标提取的精度,又大大减少了计算量。     

Boolean networks with variable number of inputs (K)

We studied a random Boolean network model with a variable number of inputs K per element. An interesting feature of this model, compared to the well-known fixed-K networks, is its higher orderliness. It seems that the distribution of connectivity alone contributes to a certain amount of order. In the present research, we tried to disentangle some of the reasons for this unexpected order. We also studied the influence of different numbers of source elements (elements with no inputs) on the network's dynamics. An analysis carried out on the networks with an average value of K=2 revealed a correlation between the number of source elements and the dynamic diversity of the network. As a diversity measure we used the number of attractors, their lengths and similarity. As a quantitative measure of the attractors' similarity, we developed two methods, one taking into account the size and the overlapping of the frozen areas, and the other in which active elements are also taken into account. As the number of source elements increases, the dynamic diversity of the networks does likewise: the number of attractors increases exponentially, while their similarity diminishes linearly. The length of attractors remains approximately the same, which indicates that the orderliness of the networks remains the same. We also determined the level of order that originates from the canalizing properties of Boolean functions and the propagation of this influence through the network. This source of order can account only for one-half of the frozen elements; the other half presumably freezes due to the complex dynamics of the network. Our work also demonstrates that different ways of assigning and redirecting connections between elements may influence the results significantly. Studying such systems can also help with modeling and understanding a complex organization and self-ordering in biological systems, especially the genetic ones.     

A comparison of psychophysical procedures for level-discrimination thresholds

Five different psychophysical procedures were used to measure level-discrimination (also called intensity discrimination) thresholds for 1-kHz tones at two levels (30 and 90 dB SPL) and two durations (10 and 500 ms). The procedures were the classic transformed up-down staircase method with a two-alternative forced-choice (2AFC) paradigm (UPD), 15- and 50-trial implementations of the method of maximum likelihood (MML) with a cued yes-no paradigm, and 18-trial implementations of ZEST using both cued yes-no and 2AFC paradigms. Results obtained from nine normal listeners show that estimates of level-discrimination thresholds for the four conditions are similar across all five procedures when different points of convergence are accounted for. The variance of threshold estimates within listener and condition was smallest for UPD, largest for the MML with 15 trials, and statistically indistinguishable among the others. The sweat factors ranged from 5.5 for MML with 50 trials to about 1.4 for UPD and ZEST. Simulations show that ideal performance of procedures may be far from real-life experience and that these deviations are likely to depend on complex interactions between listener behavior and parameter choices used for implementing the procedures. Therefore, empirical verification is important for judging the effectiveness of psychophysical procedures.     

双黄连口服液1H NMR质量稳定性分析方法研究

采用NOESYPR1D（水峰抑制）技术,测定双黄连口服液的¹H NMR谱图,用Mnova和Excel 2003软件分析处理谱图,以相似度为指标,判别分析不同厂家、不同批次的双黄连口服液中主要成分的差异. 所建立的双黄连口服液的¹H NMR质量分析方法可以有效判别不同批次双黄连口服液质量的差异. 实验方法简单、快速、稳定、重现性好,可以为中药成方制剂的质量评价提供新的思路和方法.     

可调谐地物光谱辐射源研究

介绍了一种以半导体发光二极管(LED)和溴钨灯为光源的光谱可调谐地面景物光谱辐射源,及其系统结构和控制系统设计。利用地物光谱辐射源模拟了大量不同地物光谱,在控制系统中建立了地物光谱数据库,引进了改进型遗传算法匹配出了光谱数据库中的500余种地物光谱。进而详细分析了几种典型地物的光谱匹配相似度,平均光谱匹配误差以及全波段,红,绿,蓝和近红外波段光谱匹配相似度。目标辐亮度为50W·(m2·sr)-1时,地物光谱辐射源平均光谱匹配误差在10%以内,最低可达6.0%;全波段光谱匹配相似度高于0.895,最高可达0.983;对于同一景物光谱红、绿、蓝和近红外波段(特别是绿光和近红外波段)光谱匹配相似度低于全波段,绿光和近红外波段光谱匹配相似度与红光和蓝光波段相比,最大低幅为50%。地物光谱辐射源能够用于光学遥感器的辐射定标,能有效解决光学遥感器的工作目标与定标光源光谱不匹配造成的定标误差。     

Evaluation of similarity effects in informational masking

The degree of similarity between signal and masker in informational masking paradigms has been hypothesized to contribute to informational masking. The present study attempted to quantify "similarity" using a discrimination task. Listeners discriminated various signal stimuli from a multitone complex and then detected the presence of those signals embedded in a multitone informational masker. Discriminability negatively correlated with detection threshold in an informational masking experiment, indicating that similarity between signal and the masker quality contributed to informational masking. These results suggest a method for specifying relevant signal attributes in informational masking paradigms involving similarity manipulations.     

Statistical comparison of reverberation times measured by the integrated impulse response and interrupted noise methods, computationally simulated with ODEON software, and calculated by Sabine, Eyring and Arau-Puchades’ formulas

This paper evaluates several procedures to determine the reverberation time, RT, in a classroom. These procedures are: (1) measurement by the integrated impulse response method, (2) measurement by the interrupted noise method, (3) computer simulation using ODEON Version 9.0 software, and (4) calculations using the Sabine, Eyring, and Arau-Puchades formulas. The resulting data are analyzed statistically to verify their similarity. No statistical difference was found between the values obtained by the two measuring methods. The computer simulation produced accurate data. The best formula for calculating RT in the classroom in question is Eyring’s formula.     

Raman spectral detection and assessment of thin organic layers on metal substrates: systematic approach from substrate preparation to map evaluation

Raman spectral mapping of thin organic layers on metal substrates is an important analytical tool to characterize these systems. Surface‐enhanced Raman scattering (SERS) spectroscopy is a suitable technique for analysis of such layers. Development of new SERS‐active surfaces with repeatable properties and without disturbing adsorbed species is one of the important steps for reliable assessment of the thin organic layers designed. This paper presents new SERS‐active substrates suitable for both macro (millimeter scale) and microscopic (micrometer scale) spectral mapping, which allow easy regeneration for repetitive experiments. Both gold and silver SERS‐active surfaces prepared by electrochemical deposition were tested. Complete map data evaluation utilities were newly designed and applied, using both ordinarily used and newly modified mathematical algorithms and chemometric procedures. Evaluation of data starts with finite impulse response (FIR) filtration algorithms to eliminate spectral interferences in individual spectra. Principal component analysis was used for transformation of multidimensional data to understandable dimensions. Various mathematical/statistical techniques were then used for data visualization as spectral maps and for similarity testing. Copyright © 2008 John Wiley & Sons, Ltd.     

Application of hyperspectral imaging for characterization of intramuscular fat distribution in beef

In this study, a hyperspectral imaging system in the spectral region of 400–1000 nm was used for visualization and determination of intramuscular fat concentration in beef samples. Hyperspectral images were acquired for beef samples, and spectral information was then extracted from each single sample from the fat and non-fat regions. The intramuscular fat content was chemically extracted and quantified for the same samples. Chemometrics including analysis of variance (ANOVA) and spectral similarity measures involving spectral angle measure (SAM), and Euclidian distance measure (EDM) were then used to analyze the data. An ANOVA analysis indicates that the two selected spectral variables (e.g., 650.4–736.4 nm) are effective to generate ratio image for visualization of the intramuscular fat distribution in beef. The spectral similarity analysis methods, which is based on the quantifying the spectral similarities by using predetermined endmember spectrum vector, provided comparable results for characterization and detection of intramuscular fat in beef. In term of overall classification accuracy, spectral similarity measure methods outperformed the ratio image of selected bands based on the result of ANOVA analysis. The results demonstrate that proposed technique has a potential for fast and nondestructive determination of intramuscular fat in beef.     

ANNOYANCE AND SPECTRAL CONTRAST ARE CUES FOR SIMILARITY AND PREFERENCE OF SOUNDS

Previous research has suggested that perceived similarity is based on primarily cognitive processes, whereas preferences are based to a larger extent on affective processes. This was put to an empirical test utilizing 15 complex sounds as stimuli and 25 subjects for the assessments. Various versions of multidimensional scaling were used as a method of comparison. The results show that data analyses must take into account individual differences in similarity and non-preference. Contrary to the hypothesis expressed, both similarity and non-preference were found to be based mainly on affective responses because a major proportion of the explained variance originated from the perceived annoyance of sound. This was not true for perceived loudness or for the acoustic variables of Zwicker's loudness and Aures' sharpness. Spectral contrast calculated as the number of maxima in the normalized Zwicker's specific loudness spectra was found to be the best acoustic candidate for explaining at the individual level what properties of sound cause them to be perceived as similar or non-preferred.     

一种改进的弱光谱畸变PCA融合方法

针对用PCA融合方法进行高光谱遥感影像和高分影像融合会出现一定程度的光谱失真问题,提出了一种改进的弱光谱畸变PCA融合方法。采用NCUT(normalized cut)影像分割算法,将复杂的高光谱遥感影像对象化, 增加融合样本的线性可分性, 从而削弱传统PCA融合产生的光谱畸变;运用图论和聚类理论生成表达像素间相似度的权重矩阵和若干掩膜,并用这些掩膜切割高光谱影像与高分影像,再分别融合其对应匹配的子区域对象,最后将所有子区域融合结果拼接成一幅影像。使用Hyperion高光谱数据和Rapid Eye高分影像进行实验,结果表明：该方法在保证融合结果空间分辨率提升和纹理信息不变的前提下,光谱保真能力优于传统的PCA融合方法。     

Interlaboratory beta source calibration using TL and OSL on natural quartz

Laboratories using luminescence methods for dose reconstruction have to make interlaboratory source calibrations—initially this will be a single isotope beta or gamma source using one particular reference material. The procedure requires not only the administration of exact doses to the material but also the uniform handling of the dosimetric material and standardization of the procedures. An interlaboratory calibration of an Sr-90 beta source was recently carried out by our five laboratories which are involved in a retrospective project. The reference material was quartz but there were difficulties finding sufficient suitable quartz. Five different batches were obtained from the Merck company and tested for sensitivity, linearity and stability of the 340°C peak, the 1992 batch was found to be the most appropriate. The irradiations were performed at the Secondary Standard Dosimetry Laboratory at GSF using a Co-60 source as well as the in situ measurements with an ionization chamber, calibrated to the primary standards of PTB Braunschweig. Irradiated and unirradiated quartz was distributed to the five laboratories and although different procedures were used for thermoluminescence and optically stimulated luminescence, the source calibrations for the different laboratories agreed within ±3% compared to the previous calibrations of the laboratories.     

Quantifying complex patterns of bioacoustic variation: use of a neural network to compare killer whale (Orcinus orca) dialects

A quantitative measure of acoustic similarity is crucial to any study comparing vocalizations of different species, social groups, or individuals. The goal of this study was to develop a method of extracting frequency contours from recordings of pulsed vocalizations and to test a nonlinear index of acoustic similarity based on the error of an artificial neural network at classifying them. Since the performance of neural networks depends on the amount of consistent variation in the training data, this technique can be used to assess such variation from samples of acoustic signals. The frequency contour extraction and the neural network index were tested on samples of one call type shared by nine social groups of killer whales. For comparison, call similarity was judged by three human subjects in pairwise classification tasks. The results showed a significant correlation between the neural network index and the similarity ratings by the subjects. Both measures of acoustic similarity were significantly correlated with the groups' association patterns, indicating that both methods of quantifying acoustic similarity are biologically meaningful. An index based on neural network analysis therefore represents an objective and repeatable means of measuring acoustic similarity, and allows comparison of results across studies, species and time.     

基于多尺度滤波和线检测算子的视网膜血管检测

视网膜血管分割在眼底图像分析中具有重要作用。结合多尺度Hessian矩阵滤波和线检测算子,提出了一种有效的血管检测方法。首先利用多尺度Hessian矩阵的特征值构建血管相似性函数,实现血管增强;然后采用改进的线检测算子,提取反映血管测度的特征;最后采用SVM实现血管检测。实验结果表明,该方法只需要较少的训练样本即可达到与其他方法相当的准确率,且在灵敏性上具有更好的性能。     

An Orientation‐Independent Imaging Technique for the Classification of Blood Cells

This study presents an orientation independent imaging technique for the classification and recognition of blood cells with relevant applications to related problems in cytometry and medical diagnosis. The proposed method integrates three important aspects towards its practical implementation: 1. The use of the principal component (PC) transform to reorient in an optimal fashion the image data and to make of the feature matching an orientation independent process; 2. The establishment of similarity measures to quantify the matching process of the shape of the blood cell populations with any chosen degree of certainty; and 3. The application of the recognition and classification processes once all the similarity measurements are gathered. An extension of this two‐dimensional (2‐D) method to a three‐dimensional (3‐D) base is proposed. Results of this technique using real‐world image data of blood cell populations are given. It is appropriate to note that although the images used here are real‐world samples of blood cell populations, other samples containing different biological specimens could have been used just as well.