Dynamic similarity in erosional processes

USGS Publications Warehouse

Scheidegger, A.E.

1963-01-01

A study is made of the dynamic similarity conditions obtaining in a variety of erosional processes. The pertinent equations for each type of process are written in dimensionless form; the similarity conditions can then easily be deduced. The processes treated are: raindrop action, slope evolution and river erosion. ?? 1963 Istituto Geofisico Italiano.

New similarity of triangular fuzzy number and its application.

PubMed

Zhang, Xixiang; Ma, Weimin; Chen, Liping

2014-01-01

The similarity of triangular fuzzy numbers is an important metric for application of it. There exist several approaches to measure similarity of triangular fuzzy numbers. However, some of them are opt to be large. To make the similarity well distributed, a new method SIAM (Shape's Indifferent Area and Midpoint) to measure triangular fuzzy number is put forward, which takes the shape's indifferent area and midpoint of two triangular fuzzy numbers into consideration. Comparison with other similarity measurements shows the effectiveness of the proposed method. Then, it is applied to collaborative filtering recommendation to measure users' similarity. A collaborative filtering case is used to illustrate users' similarity based on cloud model and triangular fuzzy number; the result indicates that users' similarity based on triangular fuzzy number can obtain better discrimination. Finally, a simulated collaborative filtering recommendation system is developed which uses cloud model and triangular fuzzy number to express users' comprehensive evaluation on items, and result shows that the accuracy of collaborative filtering recommendation based on triangular fuzzy number is higher.

Fewer doses of HPV vaccine result in immune response similar to three-dose regimen

Cancer.gov

NCI scientists report that two doses of a human papillomavirus (HPV) vaccine, trademarked as Cervarix, resulted in similar serum antibody levels against two of the most carcinogenic types of HPV (16 and 18), compared to a standard three dose regimen.

International normalized ratio (INR) testing in Europe: between-laboratory comparability of test results obtained by Quick and Owren reagents.

PubMed

Meijer, Piet; Kynde, Karin; van den Besselaar, Antonius M H P; Van Blerk, Marjan; Woods, Timothy A L

2018-04-12

This study was designed to obtain an overview of the analytical quality of the prothrombin time, reported as international normalized ratio (INR) and to assess the variation of INR results between European laboratories, the difference between Quick-type and Owren-type methods and the effect of using local INR calibration or not. In addition, we assessed the variation in INR results obtained for a single donation in comparison with a pool of several plasmas. A set of four different lyophilized plasma samples were distributed via national EQA organizations to participating laboratories for INR measurement. Between-laboratory variation was lower in the Owren group than in the Quick group (on average: 6.7% vs. 8.1%, respectively). Differences in the mean INR value between the Owren and Quick group were relatively small (<0.20 INR). Between-laboratory variation was lower after local INR calibration (CV: 6.7% vs. 8.6%). For laboratories performing local calibration, the between-laboratory variation was quite similar for the Owren and Quick group (on average: 6.5% and 6.7%, respectively). Clinically significant differences in INR results (difference in INR>0.5) were observed between different reagents. No systematic significant differences in the between-laboratory variation for a single-plasma sample and a pooled plasma sample were observed. The comparability for laboratories using local calibration of their thromboplastin reagent is better than for laboratories not performing local calibration. Implementing local calibration is strongly recommended for the measurement of INR.

Paternity tests in Mexico: Results obtained in 3005 cases.

PubMed

García-Aceves, M E; Romero Rentería, O; Díaz-Navarro, X X; Rangel-Villalobos, H

2018-04-01

National and international reports regarding the paternity testing activity scarcely include information from Mexico and other Latin American countries. Therefore, we report different results from the analysis of 3005 paternity cases analyzed during a period of five years in a Mexican paternity testing laboratory. Motherless tests were the most frequent (77.27%), followed by trio cases (20.70%); the remaining 2.04% included different cases of kinship reconstruction. The paternity exclusion rate was 29.58%, higher but into the range reported by the American Association of Blood Banks (average 24.12%). We detected 65 mutations, most of them involving one-step (93.8% and the remaining were two-step mutations (6.2%) thus, we were able to estimate the paternal mutation rate for 17 different STR loci: 0.0018 (95% CI 0.0005-0.0047). Five triallelic patterns and 12 suspected null alleles were detected during this period; however, re-amplification of these samples with a different Human Identification (HID) kit confirmed the homozygous genotypes, which suggests that most of these exclusions actually are one-step mutations. HID kits with ≥20 STRs detected more exclusions, diminishing the rate of inconclusive results with isolated exclusions (<3 loci), and leading to higher paternity indexes (PI). However, the Powerplex 21 kit (20 STRs) and Powerplex Fusion kit (22 STRs) offered similar PI (p = 0.379) and average number of exclusions (PE) (p = 0.339) when a daughter was involved in motherless tests. In brief, besides to report forensic parameters from paternity tests in Mexico, results describe improvements to solve motherless paternity tests using HID kits with ≥20 STRs instead of one including 15 STRs. Copyright © 2018 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

Obtaining patient test results from clinical laboratories: a survey of state law for pharmacists.

PubMed

Witry, Matthew J; Doucette, William R

2009-01-01

To identify states with laws that restrict to whom clinical laboratories may release copies of laboratory test results and to describe how these laws may affect pharmacists' ability to obtain patient laboratory test results. Researchers examined state statutes and administrative codes for all 50 states and the District of Columbia at the University of Iowa Law Library between June and July 2007. Researchers also consulted with lawyers, state Clinical Laboratory Improvement Amendments officers, and law librarians. Laws relating to the study objective were analyzed. 34 jurisdictions do not restrict the release of laboratory test results, while 17 states have laws that restrict to whom clinical laboratories can send copies of test results. In these states, pharmacists will have to use alternative sources, such as physician offices, to obtain test results. Pharmacists must consider state law before requesting copies of laboratory test results from clinical laboratories. This may be an issue that state pharmacy associations can address to increase pharmacist access to important patient information.

Ultra-accurate collaborative information filtering via directed user similarity

NASA Astrophysics Data System (ADS)

Guo, Q.; Song, W.-J.; Liu, J.-G.

2014-07-01

A key challenge of the collaborative filtering (CF) information filtering is how to obtain the reliable and accurate results with the help of peers' recommendation. Since the similarities from small-degree users to large-degree users would be larger than the ones in opposite direction, the large-degree users' selections are recommended extensively by the traditional second-order CF algorithms. By considering the users' similarity direction and the second-order correlations to depress the influence of mainstream preferences, we present the directed second-order CF (HDCF) algorithm specifically to address the challenge of accuracy and diversity of the CF algorithm. The numerical results for two benchmark data sets, MovieLens and Netflix, show that the accuracy of the new algorithm outperforms the state-of-the-art CF algorithms. Comparing with the CF algorithm based on random walks proposed by Liu et al. (Int. J. Mod. Phys. C, 20 (2009) 285) the average ranking score could reach 0.0767 and 0.0402, which is enhanced by 27.3% and 19.1% for MovieLens and Netflix, respectively. In addition, the diversity, precision and recall are also enhanced greatly. Without relying on any context-specific information, tuning the similarity direction of CF algorithms could obtain accurate and diverse recommendations. This work suggests that the user similarity direction is an important factor to improve the personalized recommendation performance.

Learning context-sensitive shape similarity by graph transduction.

PubMed

Bai, Xiang; Yang, Xingwei; Latecki, Longin Jan; Liu, Wenyu; Tu, Zhuowen

2010-05-01

Shape similarity and shape retrieval are very important topics in computer vision. The recent progress in this domain has been mostly driven by designing smart shape descriptors for providing better similarity measure between pairs of shapes. In this paper, we provide a new perspective to this problem by considering the existing shapes as a group, and study their similarity measures to the query shape in a graph structure. Our method is general and can be built on top of any existing shape similarity measure. For a given similarity measure, a new similarity is learned through graph transduction. The new similarity is learned iteratively so that the neighbors of a given shape influence its final similarity to the query. The basic idea here is related to PageRank ranking, which forms a foundation of Google Web search. The presented experimental results demonstrate that the proposed approach yields significant improvements over the state-of-art shape matching algorithms. We obtained a retrieval rate of 91.61 percent on the MPEG-7 data set, which is the highest ever reported in the literature. Moreover, the learned similarity by the proposed method also achieves promising improvements on both shape classification and shape clustering.

Dreaming and waking: similarities and differences revisited.

PubMed

Kahan, Tracey L; LaBerge, Stephen P

2011-09-01

Dreaming is often characterized as lacking high-order cognitive (HOC) skills. In two studies, we test the alternative hypothesis that the dreaming mind is highly similar to the waking mind. Multiple experience samples were obtained from late-night REM sleep and waking, following a systematic protocol described in Kahan (2001). Results indicated that reported dreaming and waking experiences are surprisingly similar in their cognitive and sensory qualities. Concurrently, ratings of dreaming and waking experiences were markedly different on questions of general reality orientation and logical organization (e.g., the bizarreness or typicality of the events, actions, and locations). Consistent with other recent studies (e.g., Bulkeley & Kahan, 2008; Kozmová & Wolman, 2006), experiences sampled from dreaming and waking were more similar with respect to their process features than with respect to their structural features. Copyright © 2010 Elsevier Inc. All rights reserved.

Improved collaborative filtering recommendation algorithm of similarity measure

NASA Astrophysics Data System (ADS)

Zhang, Baofu; Yuan, Baoping

2017-05-01

The Collaborative filtering recommendation algorithm is one of the most widely used recommendation algorithm in personalized recommender systems. The key is to find the nearest neighbor set of the active user by using similarity measure. However, the methods of traditional similarity measure mainly focus on the similarity of user common rating items, but ignore the relationship between the user common rating items and all items the user rates. And because rating matrix is very sparse, traditional collaborative filtering recommendation algorithm is not high efficiency. In order to obtain better accuracy, based on the consideration of common preference between users, the difference of rating scale and score of common items, this paper presents an improved similarity measure method, and based on this method, a collaborative filtering recommendation algorithm based on similarity improvement is proposed. Experimental results show that the algorithm can effectively improve the quality of recommendation, thus alleviate the impact of data sparseness.

Convection of viscous fluids: Energetics, self-similarity, experiments, geophysical applications and analogies

NASA Technical Reports Server (NTRS)

Golitsyn, G. S.

1977-01-01

The main results were the formulas for the mean convection velocities, of a viscous fluid and for the mean temperature difference in the bulk of the convecting fluid. These were obtained: by scaling analysis of the Boussinesq equations, by analysis of the energetics of the process, and by using similarity and dimensional arguments. The last approach defines the criteria of similarity and allows the proposition of some self-similarity hypotheses. By several simple new ways, an expression for the efficiency coefficient gamma of the thermal convection was also obtained. An analogy is pointed out between non-turbulent convection of a viscous fluid and the structure of turbulence for scales less than Kolmogorov's internal viscous microscale of turbulence.

Quantitative assessment of the impact of biomedical image acquisition on the results obtained from image analysis and processing.

PubMed

Koprowski, Robert

2014-07-04

Dedicated, automatic algorithms for image analysis and processing are becoming more and more common in medical diagnosis. When creating dedicated algorithms, many factors must be taken into consideration. They are associated with selecting the appropriate algorithm parameters and taking into account the impact of data acquisition on the results obtained. An important feature of algorithms is the possibility of their use in other medical units by other operators. This problem, namely operator's (acquisition) impact on the results obtained from image analysis and processing, has been shown on a few examples. The analysed images were obtained from a variety of medical devices such as thermal imaging, tomography devices and those working in visible light. The objects of imaging were cellular elements, the anterior segment and fundus of the eye, postural defects and others. In total, almost 200'000 images coming from 8 different medical units were analysed. All image analysis algorithms were implemented in C and Matlab. For various algorithms and methods of medical imaging, the impact of image acquisition on the results obtained is different. There are different levels of algorithm sensitivity to changes in the parameters, for example: (1) for microscope settings and the brightness assessment of cellular elements there is a difference of 8%; (2) for the thyroid ultrasound images there is a difference in marking the thyroid lobe area which results in a brightness assessment difference of 2%. The method of image acquisition in image analysis and processing also affects: (3) the accuracy of determining the temperature in the characteristic areas on the patient's back for the thermal method - error of 31%; (4) the accuracy of finding characteristic points in photogrammetric images when evaluating postural defects - error of 11%; (5) the accuracy of performing ablative and non-ablative treatments in cosmetology - error of 18% for the nose, 10% for the cheeks, and 7% for the

Improved personalized recommendation based on a similarity network

NASA Astrophysics Data System (ADS)

Wang, Ximeng; Liu, Yun; Xiong, Fei

2016-08-01

A recommender system helps individual users find the preferred items rapidly and has attracted extensive attention in recent years. Many successful recommendation algorithms are designed on bipartite networks, such as network-based inference or heat conduction. However, most of these algorithms define the resource-allocation methods for an average allocation. That is not reasonable because average allocation cannot indicate the user choice preference and the influence between users which leads to a series of non-personalized recommendation results. We propose a personalized recommendation approach that combines the similarity function and bipartite network to generate a similarity network that improves the resource-allocation process. Our model introduces user influence into the recommender system and states that the user influence can make the resource-allocation process more reasonable. We use four different metrics to evaluate our algorithms for three benchmark data sets. Experimental results show that the improved recommendation on a similarity network can obtain better accuracy and diversity than some competing approaches.

Analysis of multiplex gene expression maps obtained by voxelation.

PubMed

An, Li; Xie, Hongbo; Chin, Mark H; Obradovic, Zoran; Smith, Desmond J; Megalooikonomou, Vasileios

2009-04-29

Gene expression signatures in the mammalian brain hold the key to understanding neural development and neurological disease. Researchers have previously used voxelation in combination with microarrays for acquisition of genome-wide atlases of expression patterns in the mouse brain. On the other hand, some work has been performed on studying gene functions, without taking into account the location information of a gene's expression in a mouse brain. In this paper, we present an approach for identifying the relation between gene expression maps obtained by voxelation and gene functions. To analyze the dataset, we chose typical genes as queries and aimed at discovering similar gene groups. Gene similarity was determined by using the wavelet features extracted from the left and right hemispheres averaged gene expression maps, and by the Euclidean distance between each pair of feature vectors. We also performed a multiple clustering approach on the gene expression maps, combined with hierarchical clustering. Among each group of similar genes and clusters, the gene function similarity was measured by calculating the average gene function distances in the gene ontology structure. By applying our methodology to find similar genes to certain target genes we were able to improve our understanding of gene expression patterns and gene functions. By applying the clustering analysis method, we obtained significant clusters, which have both very similar gene expression maps and very similar gene functions respectively to their corresponding gene ontologies. The cellular component ontology resulted in prominent clusters expressed in cortex and corpus callosum. The molecular function ontology gave prominent clusters in cortex, corpus callosum and hypothalamus. The biological process ontology resulted in clusters in cortex, hypothalamus and choroid plexus. Clusters from all three ontologies combined were most prominently expressed in cortex and corpus callosum. The experimental

Similarly shaped letters evoke similar colors in grapheme-color synesthesia.

PubMed

Brang, David; Rouw, Romke; Ramachandran, V S; Coulson, Seana

2011-04-01

Grapheme-color synesthesia is a neurological condition in which viewing numbers or letters (graphemes) results in the concurrent sensation of color. While the anatomical substrates underlying this experience are well understood, little research to date has investigated factors influencing the particular colors associated with particular graphemes or how synesthesia occurs developmentally. A recent suggestion of such an interaction has been proposed in the cascaded cross-tuning (CCT) model of synesthesia, which posits that in synesthetes connections between grapheme regions and color area V4 participate in a competitive activation process, with synesthetic colors arising during the component-stage of grapheme processing. This model more directly suggests that graphemes sharing similar component features (lines, curves, etc.) should accordingly activate more similar synesthetic colors. To test this proposal, we created and regressed synesthetic color-similarity matrices for each of 52 synesthetes against a letter-confusability matrix, an unbiased measure of visual similarity among graphemes. Results of synesthetes' grapheme-color correspondences indeed revealed that more similarly shaped graphemes corresponded with more similar synesthetic colors, with stronger effects observed in individuals with more intense synesthetic experiences (projector synesthetes). These results support the CCT model of synesthesia, implicate early perceptual mechanisms as driving factors in the elicitation of synesthetic hues, and further highlight the relationship between conceptual and perceptual factors in this phenomenon. Copyright © 2011 Elsevier Ltd. All rights reserved.

Musical structure analysis using similarity matrix and dynamic programming

NASA Astrophysics Data System (ADS)

Shiu, Yu; Jeong, Hong; Kuo, C.-C. Jay

2005-10-01

Automatic music segmentation and structure analysis from audio waveforms based on a three-level hierarchy is examined in this research, where the three-level hierarchy includes notes, measures and parts. The pitch class profile (PCP) feature is first extracted at the note level. Then, a similarity matrix is constructed at the measure level, where a dynamic time warping (DTW) technique is used to enhance the similarity computation by taking the temporal distortion of similar audio segments into account. By processing the similarity matrix, we can obtain a coarse-grain music segmentation result. Finally, dynamic programming is applied to the coarse-grain segments so that a song can be decomposed into several major parts such as intro, verse, chorus, bridge and outro. The performance of the proposed music structure analysis system is demonstrated for pop and rock music.

Orthographic similarity: the case of "reversed anagrams".

PubMed

Morris, Alison L; Still, Mary L

2012-07-01

How orthographically similar are words such as paws and swap, flow and wolf, or live and evil? According to the letter position coding schemes used in models of visual word recognition, these reversed anagrams are considered to be less similar than words that share letters in the same absolute or relative positions (such as home and hose or plan and lane). Therefore, reversed anagrams should not produce the standard orthographic similarity effects found using substitution neighbors (e.g., home, hose). Simulations using the spatial coding model (Davis, Psychological Review 117, 713-758, 2010), for example, predict an inhibitory masked-priming effect for substitution neighbor word pairs but a null effect for reversed anagrams. Nevertheless, we obtained significant inhibitory priming using both stimulus types (Experiment 1). We also demonstrated that robust repetition blindness can be obtained for reversed anagrams (Experiment 2). Reversed anagrams therefore provide a new test for models of visual word recognition and orthographic similarity.

Correlation between protein sequence similarity and x-ray diffraction quality in the protein data bank.

PubMed

Lu, Hui-Meng; Yin, Da-Chuan; Ye, Ya-Jing; Luo, Hui-Min; Geng, Li-Qiang; Li, Hai-Sheng; Guo, Wei-Hong; Shang, Peng

2009-01-01

As the most widely utilized technique to determine the 3-dimensional structure of protein molecules, X-ray crystallography can provide structure of the highest resolution among the developed techniques. The resolution obtained via X-ray crystallography is known to be influenced by many factors, such as the crystal quality, diffraction techniques, and X-ray sources, etc. In this paper, the authors found that the protein sequence could also be one of the factors. We extracted information of the resolution and the sequence of proteins from the Protein Data Bank (PDB), classified the proteins into different clusters according to the sequence similarity, and statistically analyzed the relationship between the sequence similarity and the best resolution obtained. The results showed that there was a pronounced correlation between the sequence similarity and the obtained resolution. These results indicate that protein structure itself is one variable that may affect resolution when X-ray crystallography is used.

Behavioral similarity measurement based on image processing for robots that use imitative learning

NASA Astrophysics Data System (ADS)

Sterpin B., Dante G.; Martinez S., Fernando; Jacinto G., Edwar

2017-02-01

In the field of the artificial societies, particularly those are based on memetics, imitative behavior is essential for the development of cultural evolution. Applying this concept for robotics, through imitative learning, a robot can acquire behavioral patterns from another robot. Assuming that the learning process must have an instructor and, at least, an apprentice, the fact to obtain a quantitative measurement for their behavioral similarity, would be potentially useful, especially in artificial social systems focused on cultural evolution. In this paper the motor behavior of both kinds of robots, for two simple tasks, is represented by 2D binary images, which are processed in order to measure their behavioral similarity. The results shown here were obtained comparing some similarity measurement methods for binary images.

Kernel approach to molecular similarity based on iterative graph similarity.

PubMed

Rupp, Matthias; Proschak, Ewgenij; Schneider, Gisbert

2007-01-01

Similarity measures for molecules are of basic importance in chemical, biological, and pharmaceutical applications. We introduce a molecular similarity measure defined directly on the annotated molecular graph, based on iterative graph similarity and optimal assignments. We give an iterative algorithm for the computation of the proposed molecular similarity measure, prove its convergence and the uniqueness of the solution, and provide an upper bound on the required number of iterations necessary to achieve a desired precision. Empirical evidence for the positive semidefiniteness of certain parametrizations of our function is presented. We evaluated our molecular similarity measure by using it as a kernel in support vector machine classification and regression applied to several pharmaceutical and toxicological data sets, with encouraging results.

Quantitative Comparison of Tandem Mass Spectra Obtained on Various Instruments

NASA Astrophysics Data System (ADS)

Bazsó, Fanni Laura; Ozohanics, Oliver; Schlosser, Gitta; Ludányi, Krisztina; Vékey, Károly; Drahos, László

2016-08-01

The similarity between two tandem mass spectra, which were measured on different instruments, was compared quantitatively using the similarity index (SI), defined as the dot product of the square root of peak intensities in the respective spectra. This function was found to be useful for comparing energy-dependent tandem mass spectra obtained on various instruments. Spectral comparisons show the similarity index in a 2D "heat map", indicating which collision energy combinations result in similar spectra, and how good this agreement is. The results and methodology can be used in the pharma industry to design experiments and equipment well suited for good reproducibility. We suggest that to get good long-term reproducibility, it is best to adjust the collision energy to yield a spectrum very similar to a reference spectrum. It is likely to yield better results than using the same tuning file, which, for example, does not take into account that contamination of the ion source due to extended use may influence instrument tuning. The methodology may be used to characterize energy dependence on various instrument types, to optimize instrumentation, and to study the influence or correlation between various experimental parameters.

Self-similar motion of a Nambu-Goto string

NASA Astrophysics Data System (ADS)

Igata, Takahisa; Houri, Tsuyoshi; Harada, Tomohiro

2016-09-01

We study the self-similar motion of a string in a self-similar spacetime by introducing the concept of a self-similar string, which is defined as the world sheet to which a homothetic vector field is tangent. It is shown that in Nambu-Goto theory, the equations of motion for a self-similar string reduce to those for a particle. Moreover, under certain conditions such as the hypersurface orthogonality of the homothetic vector field, the equations of motion for a self-similar string simplify to the geodesic equations on a (pseudo)Riemannian space. As a concrete example, we investigate a self-similar Nambu-Goto string in a spatially flat Friedmann-Lemaître-Robertson-Walker expanding universe with self-similarity and obtain solutions of open and closed strings, which have various nontrivial configurations depending on the rate of the cosmic expansion. For instance, we obtain a circular solution that evolves linearly in the cosmic time while keeping its configuration by the balance between the effects of the cosmic expansion and string tension. We also show the instability for linear radial perturbation of the circular solutions.

Visualizing Similarity of Appearance by Arrangement of Cards

PubMed Central

Nakatsuji, Nao; Ihara, Hisayasu; Seno, Takeharu; Ito, Hiroshi

2016-01-01

This study proposes a novel method to extract the configuration of the psychological space by directly measuring subjects' similarity rating without computational work. Although multidimensional scaling (MDS) is well-known as a conventional method for extracting the psychological space, the method requires many pairwise evaluations. The times taken for evaluations increase in proportion to the square of the number of objects in MDS. The proposed method asks subjects to arrange cards on a poster sheet according to the degree of similarity of the objects. To compare the performance of the proposed method with the conventional one, we developed similarity maps of typefaces through the proposed method and through non-metric MDS. We calculated the trace correlation coefficient among all combinations of the configuration for both methods to evaluate the degree of similarity in the obtained configurations. The threshold value of trace correlation coefficient for statistically discriminating similar configuration was decided based on random data. The ratio of the trace correlation coefficient exceeding the threshold value was 62.0% so that the configurations of the typefaces obtained by the proposed method closely resembled those obtained by non-metric MDS. The required duration for the proposed method was approximately one third of the non-metric MDS's duration. In addition, all distances between objects in all the data for both methods were calculated. The frequency for the short distance in the proposed method was lower than that of the non-metric MDS so that a relatively small difference was likely to be emphasized among objects in the configuration by the proposed method. The card arrangement method we here propose, thus serves as a easier and time-saving tool to obtain psychological structures in the fields related to similarity of appearance. PMID:27242611

Results of the 2013 UT modeling benchmark obtained with models implemented in CIVA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Toullelan, Gwénaël; Raillon, Raphaële; Chatillon, Sylvain

The 2013 Ultrasonic Testing (UT) modeling benchmark concerns direct echoes from side drilled holes (SDH), flat bottom holes (FBH) and corner echoes from backwall breaking artificial notches inspected with a matrix phased array probe. This communication presents the results obtained with the models implemented in the CIVA software: the pencilmodel is used to compute the field radiated by the probe, the Kirchhoff approximation is applied to predict the response of FBH and notches and the SOV (Separation Of Variables) model is used for the SDH responses. The comparison between simulated and experimental results are presented and discussed.

Comparison of results obtained with various sensors used to measure fluctuating quantities in jets.

NASA Technical Reports Server (NTRS)

Parthasarathy, S. P.; Massier, P. F.; Cuffel, R. F.

1973-01-01

An experimental investigation has been conducted to compare the results obtained with six different instruments that sense fluctuating quantities in free jets. These sensors are typical of those that have recently been used by various investigators who are engaged in experimental studies of jet noise. Intensity distributions and two-point correlations with space separation and time delay were obtained. The static pressure, density, and velocity fluctuations are well correlated over the entire cross section of the jet and the cross-correlations persist for several jet diameters along the flow direction. The eddies appear to be flattened in the flow direction by a ratio of 0.4.

Self-similarity of waiting times in fracture systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Niccolini, G.; Bosia, F.; Carpinteri, A.

2009-08-15

Experimental and numerical results are presented for a fracture experiment carried out on a fiber-reinforced element under flexural loading, and a statistical analysis is performed for acoustic emission waiting-time distributions. By an optimization procedure, a recently proposed scaling law describing these distributions for different event magnitude scales is confirmed by both experimental and numerical data, thus reinforcing the idea that fracture of heterogeneous materials has scaling properties similar to those found for earthquakes. Analysis of the different scaling parameters obtained for experimental and numerical data leads us to formulate the hypothesis that the type of scaling function obtained depends onmore » the level of correlation among fracture events in the system.« less

Two Measurement Methods of Leaf Dry Matter Content Produce Similar Results in a Broad Range of Species

PubMed Central

Vaieretti, María Victoria; Díaz, Sandra; Vile, Denis; Garnier, Eric

2007-01-01

Background and Aims Leaf dry matter content (LDMC) is widely used as an indicator of plant resource use in plant functional trait databases. Two main methods have been proposed to measure LDMC, which basically differ in the rehydration procedure to which leaves are subjected after harvesting. These are the ‘complete rehydration’ protocol of Garnier et al. (2001, Functional Ecology 15: 688–695) and the ‘partial rehydration’ protocol of Vendramini et al. (2002, New Phytologist 154: 147–157). Methods To test differences in LDMC due to the use of different methods, LDMC was measured on 51 native and cultivated species representing a wide range of plant families and growth forms from central-western Argentina, following the complete rehydration and partial rehydration protocols. Key Results and Conclusions The LDMC values obtained by both methods were strongly and positively correlated, clearly showing that LDMC is highly conserved between the two procedures. These trends were not altered by the exclusion of plants with non-laminar leaves. Although the complete rehydration method is the safest to measure LDMC, the partial rehydration procedure produces similar results and is faster. It therefore appears as an acceptable option for those situations in which the complete rehydration method cannot be applied. Two notes of caution are given for cases in which different datasets are compared or combined: (1) the discrepancy between the two rehydration protocols is greatest in the case of high-LDMC (succulent or tender) leaves; (2) the results suggest that, when comparing many studies across unrelated datasets, differences in the measurement protocol may be less important than differences among seasons, years and the quality of local habitats. PMID:17353207

Obtaining orthotropic elasticity tensor using entries zeroing method.

NASA Astrophysics Data System (ADS)

Gierlach, Bartosz; Danek, Tomasz

2017-04-01

A generally anisotropic elasticity tensor obtained from measurements can be represented by a tensor belonging to one of eight material symmetry classes. Knowledge of symmetry class and orientation is helpful for describing physical properties of a medium. For each non-trivial symmetry class except isotropic this problem is nonlinear. A common method of obtaining effective tensor is a choosing its non-trivial symmetry class and minimizing Frobenius norm between measured and effective tensor in the same coordinate system. Global optimization algorithm has to be used to determine the best rotation of a tensor. In this contribution, we propose a new approach to obtain optimal tensor, with the assumption that it is orthotropic (or at least has a similar shape to the orthotropic one). In orthotropic form tensor 24 out of 36 entries are zeros. The idea is to minimize the sum of squared entries which are supposed to be equal to zero through rotation calculated with optimization algorithm - in this case Particle Swarm Optimization (PSO) algorithm. Quaternions were used to parametrize rotations in 3D space to improve computational efficiency. In order to avoid a choice of local minima we apply PSO several times and only if we obtain similar results for the third time we consider it as a correct value and finish computations. To analyze obtained results Monte-Carlo method was used. After thousands of single runs of PSO optimization, we obtained values of quaternion parts and plot them. Points concentrate in several points of the graph following the regular pattern. It suggests the existence of more complex symmetry in the analyzed tensor. Then thousands of realizations of generally anisotropic tensor were generated - each tensor entry was replaced with a random value drawn from normal distribution having a mean equal to measured tensor entry and standard deviation of the measurement. Each of these tensors was subject of PSO based optimization delivering quaternion for optimal

A similarity based agglomerative clustering algorithm in networks

NASA Astrophysics Data System (ADS)

Liu, Zhiyuan; Wang, Xiujuan; Ma, Yinghong

2018-04-01

The detection of clusters is benefit for understanding the organizations and functions of networks. Clusters, or communities, are usually groups of nodes densely interconnected but sparsely linked with any other clusters. To identify communities, an efficient and effective community agglomerative algorithm based on node similarity is proposed. The proposed method initially calculates similarities between each pair of nodes, and form pre-partitions according to the principle that each node is in the same community as its most similar neighbor. After that, check each partition whether it satisfies community criterion. For the pre-partitions who do not satisfy, incorporate them with others that having the biggest attraction until there are no changes. To measure the attraction ability of a partition, we propose an attraction index that based on the linked node's importance in networks. Therefore, our proposed method can better exploit the nodes' properties and network's structure. To test the performance of our algorithm, both synthetic and empirical networks ranging in different scales are tested. Simulation results show that the proposed algorithm can obtain superior clustering results compared with six other widely used community detection algorithms.

Networks of plants: how to measure similarity in vegetable species.

PubMed

Vivaldo, Gianna; Masi, Elisa; Pandolfi, Camilla; Mancuso, Stefano; Caldarelli, Guido

2016-06-07

Despite the common misconception of nearly static organisms, plants do interact continuously with the environment and with each other. It is fair to assume that during their evolution they developed particular features to overcome similar problems and to exploit possibilities from environment. In this paper we introduce various quantitative measures based on recent advancements in complex network theory that allow to measure the effective similarities of various species. By using this approach on the similarity in fruit-typology ecological traits we obtain a clear plant classification in a way similar to traditional taxonomic classification. This result is not trivial, since a similar analysis done on the basis of diaspore morphological properties do not provide any clear parameter to classify plants species. Complex network theory can then be used in order to determine which feature amongst many can be used to distinguish scope and possibly evolution of plants. Future uses of this approach range from functional classification to quantitative determination of plant communities in nature.

Using Riemannian geometry to obtain new results on Dikin and Karmarkar methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oliveira, P.; Joao, X.; Piaui, T.

1994-12-31

We are motivated by a 1990 Karmarkar paper on Riemannian geometry and Interior Point Methods. In this talk we show 3 results. (1) Karmarkar direction can be derived from the Dikin one. This is obtained by constructing a certain Z(x) representation of the null space of the unitary simplex (e, x) = 1; then the projective direction is the image under Z(x) of the affine-scaling one, when it is restricted to that simplex. (2) Second order information on Dikin and Karmarkar methods. We establish computable Hessians for each of the metrics corresponding to both directions, thus permitting the generation ofmore » {open_quotes}second order{close_quotes} methods. (3) Dikin and Karmarkar geodesic descent methods. For those directions, we make computable the theoretical Luenberger geodesic descent method, since we are able to explicit very accurate expressions of the corresponding geodesics. Convergence results are given.« less

Clustering by reordering of similarity and Laplacian matrices: Application to galaxy clusters

NASA Astrophysics Data System (ADS)

Mahmoud, E.; Shoukry, A.; Takey, A.

2018-04-01

Similarity metrics, kernels and similarity-based algorithms have gained much attention due to their increasing applications in information retrieval, data mining, pattern recognition and machine learning. Similarity Graphs are often adopted as the underlying representation of similarity matrices and are at the origin of known clustering algorithms such as spectral clustering. Similarity matrices offer the advantage of working in object-object (two-dimensional) space where visualization of clusters similarities is available instead of object-features (multi-dimensional) space. In this paper, sparse ɛ-similarity graphs are constructed and decomposed into strong components using appropriate methods such as Dulmage-Mendelsohn permutation (DMperm) and/or Reverse Cuthill-McKee (RCM) algorithms. The obtained strong components correspond to groups (clusters) in the input (feature) space. Parameter ɛi is estimated locally, at each data point i from a corresponding narrow range of the number of nearest neighbors. Although more advanced clustering techniques are available, our method has the advantages of simplicity, better complexity and direct visualization of the clusters similarities in a two-dimensional space. Also, no prior information about the number of clusters is needed. We conducted our experiments on two and three dimensional, low and high-sized synthetic datasets as well as on an astronomical real-dataset. The results are verified graphically and analyzed using gap statistics over a range of neighbors to verify the robustness of the algorithm and the stability of the results. Combining the proposed algorithm with gap statistics provides a promising tool for solving clustering problems. An astronomical application is conducted for confirming the existence of 45 galaxy clusters around the X-ray positions of galaxy clusters in the redshift range [0.1..0.8]. We re-estimate the photometric redshifts of the identified galaxy clusters and obtain acceptable values

Protein-protein interaction network-based detection of functionally similar proteins within species.

PubMed

Song, Baoxing; Wang, Fen; Guo, Yang; Sang, Qing; Liu, Min; Li, Dengyun; Fang, Wei; Zhang, Deli

2012-07-01

Although functionally similar proteins across species have been widely studied, functionally similar proteins within species showing low sequence similarity have not been examined in detail. Identification of these proteins is of significant importance for understanding biological functions, evolution of protein families, progression of co-evolution, and convergent evolution and others which cannot be obtained by detection of functionally similar proteins across species. Here, we explored a method of detecting functionally similar proteins within species based on graph theory. After denoting protein-protein interaction networks using graphs, we split the graphs into subgraphs using the 1-hop method. Proteins with functional similarities in a species were detected using a method of modified shortest path to compare these subgraphs and to find the eligible optimal results. Using seven protein-protein interaction networks and this method, some functionally similar proteins with low sequence similarity that cannot detected by sequence alignment were identified. By analyzing the results, we found that, sometimes, it is difficult to separate homologous from convergent evolution. Evaluation of the performance of our method by gene ontology term overlap showed that the precision of our method was excellent. Copyright © 2012 Wiley Periodicals, Inc.

Near-Infrared Scintillation of Liquid Argon: Recent Results Obtained with the NIR Facility at Fermilab

DOE Office of Scientific and Technical Information (OSTI.GOV)

Escobar, C. O.; Rubinov, P.; Tilly, E.

After a short review of previous attempts to observe and measure the near-infrared scintillation in liquid argon, we present new results obtained with NIR, a dedicated cryostat at the Fermilab Proton Assembly Building (PAB). The new results give confidence that the near-infrared light can be used as the much needed light signal in large liquid argon time projection chambers.11 pages,

Comparing Cognitive Interviewing and Online Probing: Do They Find Similar Results?

ERIC Educational Resources Information Center

Meitinger, Katharina; Behr, Dorothée

2016-01-01

This study compares the application of probing techniques in cognitive interviewing (CI) and online probing (OP). Even though the probing is similar, the methods differ regarding typical mode setting, sample size, level of interactivity, and goals. We analyzed probing answers to the International Social Survey Programme item battery on specific…

Asymptotic structure and similarity solutions for three-dimensional turbulent boundary layers

NASA Technical Reports Server (NTRS)

Degani, A. T.; Walker, J. D. A.

1989-01-01

The asymptotic structure of the three-dimensional turbulent boundary layer is investigated in the limit of large Reynolds numbers. A self-consistent, but relatively complex, two-layer structure exists and the simplest situation, corresponding to a plane of symmetry, is considered in this paper as a first step. The adjustment of the streamwise velocity to relative rest, through an outer defect layer and then an inner wall layer, is similar to that in two-dimensional flow. The adjustment of the cross-streamwise velocity is more complicated and it is shown that two terms in the expansion are required to obtain useful results, and in particular to obtain the velocity skew angle at the wall near the symmetry plane. The conditions under which self-similarity is achieved near a plane of symmetry are investigated. A set of ordinary differential equations is developed which describe the streamwise and cross-streamwise velocities near a plane of symmetry in a self-similar flow through two orders of magnitude. Calculated numerical solutions of these equations yield trends which are consistent with experimental observations.

Towards Personalized Medicine: Leveraging Patient Similarity and Drug Similarity Analytics

PubMed Central

Zhang, Ping; Wang, Fei; Hu, Jianying; Sorrentino, Robert

2014-01-01

The rapid adoption of electronic health records (EHR) provides a comprehensive source for exploratory and predictive analytic to support clinical decision-making. In this paper, we investigate how to utilize EHR to tailor treatments to individual patients based on their likelihood to respond to a therapy. We construct a heterogeneous graph which includes two domains (patients and drugs) and encodes three relationships (patient similarity, drug similarity, and patient-drug prior associations). We describe a novel approach for performing a label propagation procedure to spread the label information representing the effectiveness of different drugs for different patients over this heterogeneous graph. The proposed method has been applied on a real-world EHR dataset to help identify personalized treatments for hypercholesterolemia. The experimental results demonstrate the effectiveness of the approach and suggest that the combination of appropriate patient similarity and drug similarity analytics could lead to actionable insights for personalized medicine. Particularly, by leveraging drug similarity in combination with patient similarity, our method could perform well even on new or rarely used drugs for which there are few records of known past performance. PMID:25717413

Results of Investigative Tests of Gas Turbine Engine Compressor Blades Obtained by Electrochemical Machining

NASA Astrophysics Data System (ADS)

Kozhina, T. D.; Kurochkin, A. V.

2016-04-01

The paper highlights results of the investigative tests of GTE compressor Ti-alloy blades obtained by the method of electrochemical machining with oscillating tool-electrodes, carried out in order to define the optimal parameters of the ECM process providing attainment of specified blade quality parameters given in the design documentation, while providing maximal performance. The new technological methods suggested based on the results of the tests; in particular application of vibrating tool-electrodes and employment of locating elements made of high-strength materials, significantly extend the capabilities of this method.

Legionella in water samples: how can you interpret the results obtained by quantitative PCR?

PubMed

Ditommaso, Savina; Ricciardi, Elisa; Giacomuzzi, Monica; Arauco Rivera, Susan R; Zotti, Carla M

2015-02-01

Evaluation of the potential risk associated with Legionella has traditionally been determined from culture-based methods. Quantitative polymerase chain reaction (qPCR) is an alternative tool that offers rapid, sensitive and specific detection of Legionella in environmental water samples. In this study we compare the results obtained by conventional qPCR (iQ-Check™ Quanti Legionella spp.; Bio-Rad) and by culture method on artificial samples prepared in Page's saline by addiction of Legionella pneumophila serogroup 1 (ATCC 33152) and we analyse the selective quantification of viable Legionella cells by the qPCR-PMA method. The amount of Legionella DNA (GU) determined by qPCR was 28-fold higher than the load detected by culture (CFU). Applying the qPCR combined with PMA treatment we obtained a reduction of 98.5% of the qPCR signal from dead cells. We observed a dissimilarity in the ability of PMA to suppress the PCR signal in samples with different amounts of bacteria: the effective elimination of detection signals by PMA depended on the concentration of GU and increasing amounts of cells resulted in higher values of reduction. Using the results from this study we created an algorithm to facilitate the interpretation of viable cell level estimation with qPCR-PMA. Copyright © 2014 Elsevier Ltd. All rights reserved.

Fibonacci chain polynomials: Identities from self-similarity

NASA Technical Reports Server (NTRS)

Lang, Wolfdieter

1995-01-01

Fibonacci chains are special diatomic, harmonic chains with uniform nearest neighbor interaction and two kinds of atoms (mass-ratio r) arranged according to the self-similar binary Fibonacci sequence ABAABABA..., which is obtained by repeated substitution of A yields AB and B yields A. The implications of the self-similarity of this sequence for the associated orthogonal polynomial systems which govern these Fibonacci chains with fixed mass-ratio r are studied.

A new definition and properties of the similarity value between two protein structures.

PubMed

Saberi Fathi, S M

2016-10-01

Knowledge regarding the 3D structure of a protein provides useful information about the protein's functional properties. Particularly, structural similarity between proteins can be used as a good predictor of functional similarity. One method that uses the 3D geometrical structure of proteins in order to compare them is the similarity value (SV). In this paper, we introduce a new definition of the SV measure for comparing two proteins. To this end, we consider the mass of the protein's atoms and concentrate on the number of protein's atoms to be compared. This defines a new measure, called the weighted similarity value (WSV), adding physical properties to geometrical properties. We also show that our results are in good agreement with the results obtained by TM-SCORE and DALILITE. WSV can be of use in protein classification and in drug discovery.

An assessment of consistence of exhaust gas emission test results obtained under controlled NEDC conditions

NASA Astrophysics Data System (ADS)

Balawender, K.; Jaworski, A.; Kuszewski, H.; Lejda, K.; Ustrzycki, A.

2016-09-01

Measurements concerning emissions of pollutants contained in automobile combustion engine exhaust gases is of primary importance in view of their harmful impact on the natural environment. This paper presents results of tests aimed at determining exhaust gas pollutant emissions from a passenger car engine obtained under repeatable conditions on a chassis dynamometer. The test set-up was installed in a controlled climate chamber allowing to maintain the temperature conditions within the range from -20°C to +30°C. The analysis covered emissions of such components as CO, CO2, NOx, CH4, THC, and NMHC. The purpose of the study was to assess repeatability of results obtained in a number of tests performed as per NEDC test plan. The study is an introductory stage of a wider research project concerning the effect of climate conditions and fuel type on emission of pollutants contained in exhaust gases generated by automotive vehicles.

Advanced Models and Algorithms for Self-Similar IP Network Traffic Simulation and Performance Analysis

NASA Astrophysics Data System (ADS)

Radev, Dimitar; Lokshina, Izabella

2010-11-01

The paper examines self-similar (or fractal) properties of real communication network traffic data over a wide range of time scales. These self-similar properties are very different from the properties of traditional models based on Poisson and Markov-modulated Poisson processes. Advanced fractal models of sequentional generators and fixed-length sequence generators, and efficient algorithms that are used to simulate self-similar behavior of IP network traffic data are developed and applied. Numerical examples are provided; and simulation results are obtained and analyzed.

Case study, comparison of trial burn results from similar sulfuric acid regeneration plants

DOE Office of Scientific and Technical Information (OSTI.GOV)

Milaszewski, M.; Johns, T.; Dickerson, W.F.

The primary business of Rhodia Eco Services (Rhodia) is the regeneration of sulfuric acid. Sulfuric acid regeneration requires thermal decomposition of acid to sulfur dioxide, and remaking the acid through chemical reaction. The sulfuric acid regeneration furnace is the ideal place to process pumpable wastes for energy recovery and for thermal destruction. Rhodia is regulated by the Boiler and Industrial Furnace (BIF) regulations (40 CFR 266, Subpart H). The Hammond, Indiana plant is an interim status BIF facility and the Houston, Texas facility is renewing its RCRA incineration permit as a BIF facility. Both plants have conducted BIF Trial Burnsmore » with very similar results. The performance levels demonstrated were at levels better than RCRA/BIF standards for destruction and removal efficiency, metal, HCl/Cl, particulate, dioxin/furan, and organic emissions.« less

Self-similar gravity wave spectra resulting from the modulation of bound waves

NASA Astrophysics Data System (ADS)

Michel, Guillaume; Semin, Benoît; Cazaubiel, Annette; Haudin, Florence; Humbert, Thomas; Lepot, Simon; Bonnefoy, Félicien; Berhanu, Michaël; Falcon, Éric

2018-05-01

We experimentally study the properties of nonlinear surface gravity waves in a large-scale basin. We consider two different configurations: a one-dimensional (1D) monochromatic wave forcing, and a two-dimensional (2D) forcing with bichromatic waves satisfying resonant-wave interaction conditions. For the 1D forcing, we find a discrete wave-energy spectrum dominated at high frequencies by bound waves whose amplitudes decrease as a power law of the frequency. Bound waves (e.g., to the carrier) are harmonics superimposed on the carrier wave propagating with the same phase velocity as the one of the carrier. When a narrow frequency random modulation is applied to this carrier, the high-frequency part of the wave-energy spectrum becomes continuous with the same frequency-power law. Similar results are found for the 2D forcing when a random modulation is also applied to both carrier waves. Our results thus show that all these nonlinear gravity wave spectra are dominated at high frequencies by the presence of bound waves, even in the configuration where resonant interactions occur. Moreover, in all these configurations, the power-law exponent of the spectrum is found to depend on the forcing amplitude with the same trend as the one found in previous gravity wave turbulence experiments. Such a set of bound waves may thus explain this dependence that was previously poorly understood.

Glucose Meters: A Review of Technical Challenges to Obtaining Accurate Results

PubMed Central

Tonyushkina, Ksenia; Nichols, James H.

2009-01-01

, anemia, hypotension, and other disease states. This article reviews the challenges involved in obtaining accurate glucose meter results. PMID:20144348

Node similarity within subgraphs of protein interaction networks

NASA Astrophysics Data System (ADS)

Penner, Orion; Sood, Vishal; Musso, Gabriel; Baskerville, Kim; Grassberger, Peter; Paczuski, Maya

2008-06-01

We propose a biologically motivated quantity, twinness, to evaluate local similarity between nodes in a network. The twinness of a pair of nodes is the number of connected, labeled subgraphs of size n in which the two nodes possess identical neighbours. The graph animal algorithm is used to estimate twinness for each pair of nodes (for subgraph sizes n=4 to n=12) in four different protein interaction networks (PINs). These include an Escherichia coli PIN and three Saccharomyces cerevisiae PINs - each obtained using state-of-the-art high-throughput methods. In almost all cases, the average twinness of node pairs is vastly higher than that expected from a null model obtained by switching links. For all n, we observe a difference in the ratio of type A twins (which are unlinked pairs) to type B twins (which are linked pairs) distinguishing the prokaryote E. coli from the eukaryote S. cerevisiae. Interaction similarity is expected due to gene duplication, and whole genome duplication paralogues in S. cerevisiae have been reported to co-cluster into the same complexes. Indeed, we find that these paralogous proteins are over-represented as twins compared to pairs chosen at random. These results indicate that twinness can detect ancestral relationships from currently available PIN data.

Investigating Correlation between Protein Sequence Similarity and Semantic Similarity Using Gene Ontology Annotations.

PubMed

Ikram, Najmul; Qadir, Muhammad Abdul; Afzal, Muhammad Tanvir

2018-01-01

Sequence similarity is a commonly used measure to compare proteins. With the increasing use of ontologies, semantic (function) similarity is getting importance. The correlation between these measures has been applied in the evaluation of new semantic similarity methods, and in protein function prediction. In this research, we investigate the relationship between the two similarity methods. The results suggest absence of a strong correlation between sequence and semantic similarities. There is a large number of proteins with low sequence similarity and high semantic similarity. We observe that Pearson's correlation coefficient is not sufficient to explain the nature of this relationship. Interestingly, the term semantic similarity values above 0 and below 1 do not seem to play a role in improving the correlation. That is, the correlation coefficient depends only on the number of common GO terms in proteins under comparison, and the semantic similarity measurement method does not influence it. Semantic similarity and sequence similarity have a distinct behavior. These findings are of significant effect for future works on protein comparison, and will help understand the semantic similarity between proteins in a better way.

Functional grouping of similar genes using eigenanalysis on minimum spanning tree based neighborhood graph.

PubMed

Jothi, R; Mohanty, Sraban Kumar; Ojha, Aparajita

2016-04-01

Gene expression data clustering is an important biological process in DNA microarray analysis. Although there have been many clustering algorithms for gene expression analysis, finding a suitable and effective clustering algorithm is always a challenging problem due to the heterogeneous nature of gene profiles. Minimum Spanning Tree (MST) based clustering algorithms have been successfully employed to detect clusters of varying shapes and sizes. This paper proposes a novel clustering algorithm using Eigenanalysis on Minimum Spanning Tree based neighborhood graph (E-MST). As MST of a set of points reflects the similarity of the points with their neighborhood, the proposed algorithm employs a similarity graph obtained from k(') rounds of MST (k(')-MST neighborhood graph). By studying the spectral properties of the similarity matrix obtained from k(')-MST graph, the proposed algorithm achieves improved clustering results. We demonstrate the efficacy of the proposed algorithm on 12 gene expression datasets. Experimental results show that the proposed algorithm performs better than the standard clustering algorithms. Copyright © 2016 Elsevier Ltd. All rights reserved.

Influence of heterogeneity on second-kind self-similar solutions for viscous gravity currents

DOE PAGES

Zheng, Zhong; Christov, Ivan  C.; Stone, Howard  A.

2014-05-01

We report experimental, theoretical and numerical results on the effects of horizontal heterogeneities on the propagation of viscous gravity currents. We use two geometries to highlight these effects: (a) a horizontal channel (or crack) whose gap thickness varies as a power-law function of the streamwise coordinate; (b) a heterogeneous porous medium whose permeability and porosity have power-law variations. We demonstrate that two types of self-similar behaviours emerge as a result of horizontal heterogeneity: (a) a first-kind self-similar solution is found using dimensional analysis (scaling) for viscous gravity currents that propagate away from the origin (a point of zero permeability); (b)more » a second-kind self-similar solution is found using a phase-plane analysis for viscous gravity currents that propagate toward the origin. These theoretical predictions, obtained using the ideas of self-similar intermediate asymptotics, are compared with experimental results and numerical solutions of the governing partial differential equation developed under the lubrication approximation. All three results are found to be in good agreement.« less

Higher similarity in beta topography between tasks than subjects.

PubMed

Basile, Luis F H; Sato, João R; Pasquini, Henrique A; Velasques, Bruna; Ribeiro, Pedro; Anghinah, Renato

2018-05-01

We have recently provided evidence for highly idiosyncratic topographic distributions of beta oscillations (as well as slow potentials) across individuals. More recently, by emphasizing the analysis of similarity instead of differences across tasks, we concluded that differences between an attention task and quiet resting may be negligible or at least unsystematic across subjects. Due to the possibility that individual differences could be due to noise in a wide sense or some inherent instability of beta activity, we designed a replication study to explicitly test whether pairs of individuals matched for head size and shape would still present less similar beta topography than each individual between sessions or tasks. We used independent component analysis (ICA) for an exhaustive decomposition of beta activity in a visual attention task and in quiet resting, recorded by 256-channel EEG in 20 subjects, on two separate days. We evaluated whether each ICA component obtained in one task and in one given individual could be explained by a linear regression model based on the topographic patterns of the complementary task (correlation between one component with a linear combination of components from complementary conditions), of the same task in a second session and of a matched individual. Results again showed a high topographic similarity between conditions, as previously seen between reasoning and simple visual attention beta correlates. From an overall number of 16 components representing brain activity obtained for the tasks (out of 60 originally computed where the remaining were considered noise), over 92% could satisfactorily be explained by the complementary task. Although the similarity between sessions was significantly smaller than between tasks on each day, the similarity between sessions was statistically higher than that between subjects in a highly significant way. We discuss the possible biases of group spatial averaging and the emphasis on differences

Salient value similarity, social trust, and attitudes toward wildland fire management strategies

Treesearch

Jerry J. Vaske; James D. Absher; Alan D. Bright

2007-01-01

Using the salient value similarity (SVS) model, we predicted that social trust mediated the relationship between SVS and attitudes toward prescribed burns and mechanical thinning. Data were obtained from a mail survey (n = 532) of Colorado residents living in the wildland-urban interface. Results indicated that respondents shared the same values as U...

Self-similarity in incompressible Navier-Stokes equations.

PubMed

Ercan, Ali; Kavvas, M Levent

2015-12-01

The self-similarity conditions of the 3-dimensional (3D) incompressible Navier-Stokes equations are obtained by utilizing one-parameter Lie group of point scaling transformations. It is found that the scaling exponents of length dimensions in i = 1, 2, 3 coordinates in 3-dimensions are not arbitrary but equal for the self-similarity of 3D incompressible Navier-Stokes equations. It is also shown that the self-similarity in this particular flow process can be achieved in different time and space scales when the viscosity of the fluid is also scaled in addition to other flow variables. In other words, the self-similarity of Navier-Stokes equations is achievable under different fluid environments in the same or different gravity conditions. Self-similarity criteria due to initial and boundary conditions are also presented. Utilizing the proposed self-similarity conditions of the 3D hydrodynamic flow process, the value of a flow variable at a specified time and space can be scaled to a corresponding value in a self-similar domain at the corresponding time and space.

Airglow during ionospheric modifications by the sura facility radiation. experimental results obtained in 2010

NASA Astrophysics Data System (ADS)

Grach, S. M.; Klimenko, V. V.; Shindin, A. V.; Nasyrov, I. A.; Sergeev, E. N.; A. Yashnov, V.; A. Pogorelko, N.

2012-06-01

We present the results of studying the structure and dynamics of the HF-heated volume above the Sura facility obtained in 2010 by measurements of ionospheric airglow in the red (λ = 630 nm) and green (λ = 557.7 nm) lines of atomic oxygen. Vertical sounding of the ionosphere (followed by modeling of the pump-wave propagation) and measurements of stimulated electromagnetic emission were used for additional diagnostics of ionospheric parameters and the processes occurring in the heated volume.

Wordform Similarity Increases With Semantic Similarity: An Analysis of 100 Languages.

PubMed

Dautriche, Isabelle; Mahowald, Kyle; Gibson, Edward; Piantadosi, Steven T

2017-11-01

Although the mapping between form and meaning is often regarded as arbitrary, there are in fact well-known constraints on words which are the result of functional pressures associated with language use and its acquisition. In particular, languages have been shown to encode meaning distinctions in their sound properties, which may be important for language learning. Here, we investigate the relationship between semantic distance and phonological distance in the large-scale structure of the lexicon. We show evidence in 100 languages from a diverse array of language families that more semantically similar word pairs are also more phonologically similar. This suggests that there is an important statistical trend for lexicons to have semantically similar words be phonologically similar as well, possibly for functional reasons associated with language learning. Copyright © 2016 Cognitive Science Society, Inc.

Marital assortment for genetic similarity.

PubMed

Eckman, Ronael E; Williams, Robert; Nagoshi, Craig

2002-10-01

The present study involved analyses of a Caucasian American sample (n=949) and a Japanese American sample (n=400) for factors supporting Genetic Similarity Theory (GST). The analyses found no evidence for the presence of genetic similarity between spouses in either sample for the blood group analyses of nine loci. All results indicated random mating for blood group genes. The results did not provide consistent substantial support to show that spousal similarity is correlated with the degree of genetic component of a trait for a set of seventeen individual differences variables, with only the Caucasian sample yielding significant correlations for this analysis. A third analysis examining the correlation between presence of spousal genetic similarity and spousal similarity on observable traits was not performed because spousal genetic similarity was not observed in either sample. The overall implication of the study is that GST is not supported as an explanation for spousal similarity in humans.

Concurrence of rule- and similarity-based mechanisms in artificial grammar learning.

PubMed

Opitz, Bertram; Hofmann, Juliane

2015-03-01

A current theoretical debate regards whether rule-based or similarity-based learning prevails during artificial grammar learning (AGL). Although the majority of findings are consistent with a similarity-based account of AGL it has been argued that these results were obtained only after limited exposure to study exemplars, and performance on subsequent grammaticality judgment tests has often been barely above chance level. In three experiments the conditions were investigated under which rule- and similarity-based learning could be applied. Participants were exposed to exemplars of an artificial grammar under different (implicit and explicit) learning instructions. The analysis of receiver operating characteristics (ROC) during a final grammaticality judgment test revealed that explicit but not implicit learning led to rule knowledge. It also demonstrated that this knowledge base is built up gradually while similarity knowledge governed the initial state of learning. Together these results indicate that rule- and similarity-based mechanisms concur during AGL. Moreover, it could be speculated that two different rule processes might operate in parallel; bottom-up learning via gradual rule extraction and top-down learning via rule testing. Crucially, the latter is facilitated by performance feedback that encourages explicit hypothesis testing. Copyright © 2015 Elsevier Inc. All rights reserved.

Similarity estimation for reference image retrieval in mammograms using convolutional neural network

NASA Astrophysics Data System (ADS)

Muramatsu, Chisako; Higuchi, Shunichi; Morita, Takako; Oiwa, Mikinao; Fujita, Hiroshi

2018-02-01

Periodic breast cancer screening with mammography is considered effective in decreasing breast cancer mortality. For screening programs to be successful, an intelligent image analytic system may support radiologists' efficient image interpretation. In our previous studies, we have investigated image retrieval schemes for diagnostic references of breast lesions on mammograms and ultrasound images. Using a machine learning method, reliable similarity measures that agree with radiologists' similarity were determined and relevant images could be retrieved. However, our previous method includes a feature extraction step, in which hand crafted features were determined based on manual outlines of the masses. Obtaining the manual outlines of masses is not practical in clinical practice and such data would be operator-dependent. In this study, we investigated a similarity estimation scheme using a convolutional neural network (CNN) to skip such procedure and to determine data-driven similarity scores. By using CNN as feature extractor, in which extracted features were employed in determination of similarity measures with a conventional 3-layered neural network, the determined similarity measures were correlated well with the subjective ratings and the precision of retrieving diagnostically relevant images was comparable with that of the conventional method using handcrafted features. By using CNN for determination of similarity measure directly, the result was also comparable. By optimizing the network parameters, results may be further improved. The proposed method has a potential usefulness in determination of similarity measure without precise lesion outlines for retrieval of similar mass images on mammograms.

Comparison of visual field test results obtained through Humphrey matrix frequency doubling technology perimetry versus standard automated perimetry in healthy children.

PubMed

Kocabeyoglu, Sibel; Uzun, Salih; Mocan, Mehmet Cem; Bozkurt, Banu; Irkec, Murat; Orhan, Mehmet

2013-10-01

The aim of this study was to compare the visual field test results in healthy children obtained via the Humphrey matrix 24-2 threshold program and standard automated perimetry (SAP) using the Swedish interactive threshold algorithm (SITA)-Standard 24-2 test. This prospective study included 55 healthy children without ocular or systemic disorders who underwent both SAP and frequency doubling technology (FDT) perimetry visual field testing. Visual field test reliability indices, test duration, global indices (mean deviation [MD], and pattern standard deviation [PSD]) were compared between the 2 tests using the Wilcoxon signed-rank test and paired t-test. The performance of the Humphrey field analyzer (HFA) 24-2 SITA-standard and frequency-doubling technology Matrix 24-2 tests between genders were compared with Mann-Whitney U-test. Fifty-five healthy children with a mean age of 12.2 ± 1.9 years (range from 8 years to 16 years) were included in this prospective study. The test durations of SAP and FDT were similar (5.2 ± 0.5 and 5.1 ± 0.2 min, respectively, P = 0.651). MD and the PSD values obtained via FDT Matrix were significantly higher than those obtained via SAP (P < 0.001), and fixation losses and false negative errors were significantly less with SAP (P < 0.05). A weak positive correlation between the two tests in terms of MD (r = 0.352, P = 0.008) and PSD (r = 0.329, P = 0.014) was observed. Children were able to complete both the visual test algorithms successfully within 6 min. However, SAP testing appears to be associated with less depression of the visual field indices of healthy children. FDT Matrix and SAP should not be used interchangeably in the follow-up of children.

An iterative transformation procedure for numerical solution of flutter and similar characteristics-value problems

NASA Technical Reports Server (NTRS)

Gossard, Myron L

1952-01-01

An iterative transformation procedure suggested by H. Wielandt for numerical solution of flutter and similar characteristic-value problems is presented. Application of this procedure to ordinary natural-vibration problems and to flutter problems is shown by numerical examples. Comparisons of computed results with experimental values and with results obtained by other methods of analysis are made.

Biosimilar Insulins: How Similar is Similar?

PubMed Central

Heinemann, Lutz; Hompesch, Marcus

2011-01-01

Biosimilar insulins (BIs) are viewed as commercially attractive products by a number of companies. In order to obtain approval in the European Union or the United States, where there is not a single BI currently on the market, a manufacturer needs to demonstrate that a given BI has a safety and efficacy profile that is similar to that of the “original” insulin formulation that is already on the market. As trivial as this may appear at first glance, it is not trivial at all for a good number of reasons that will be discussed in this commentary. As with protein manufacturing, modifications in the structure of the insulin molecule can take place (which can have serious consequences for the biological effects induced), so a rigid and careful assessment is absolutely necessary. The example of Marvel's failed application with the European Medicines Agency provides insights into the regulatory and clinical challenges surrounding the matter of BI. Although a challenging BI approval process might be regarded as a hurdle to keep companies out of certain markets, it is fair to say that the potential safety and efficacy issues surrounding BI are substantial and relevant and do warrant a careful and evidence-driven approval process. PMID:21722590

Biosimilar insulins: how similar is similar?

PubMed

Heinemann, Lutz; Hompesch, Marcus

2011-05-01

Biosimilar insulins (BIs) are viewed as commercially attractive products by a number of companies. In order to obtain approval in the European Union or the United States, where there is not a single BI currently on the market, a manufacturer needs to demonstrate that a given BI has a safety and efficacy profile that is similar to that of the "original" insulin formulation that is already on the market. As trivial as this may appear at first glance, it is not trivial at all for a good number of reasons that will be discussed in this commentary. As with protein manufacturing, modifications in the structure of the insulin molecule can take place (which can have serious consequences for the biological effects induced), so a rigid and careful assessment is absolutely necessary. The example of Marvel's failed application with the European Medicines Agency provides insights into the regulatory and clinical challenges surrounding the matter of BI. Although a challenging BI approval process might be regarded as a hurdle to keep companies out of certain markets, it is fair to say that the potential safety and efficacy issues surrounding BI are substantial and relevant and do warrant a careful and evidence-driven approval process. © 2011 Diabetes Technology Society.

Tensor-product kernel-based representation encoding joint MRI view similarity.

PubMed

Alvarez-Meza, A; Cardenas-Pena, D; Castro-Ospina, A E; Alvarez, M; Castellanos-Dominguez, G

2014-01-01

To support 3D magnetic resonance image (MRI) analysis, a marginal image similarity (MIS) matrix holding MR inter-slice relationship along every axis view (Axial, Coronal, and Sagittal) can be estimated. However, mutual inference from MIS view information poses a difficult task since relationships between axes are nonlinear. To overcome this issue, we introduce a Tensor-Product Kernel-based Representation (TKR) that allows encoding brain structure patterns due to patient differences, gathering all MIS matrices into a single joint image similarity framework. The TKR training strategy is carried out into a low dimensional projected space to get less influence of voxel-derived noise. Obtained results for classifying the considered patient categories (gender and age) on real MRI database shows that the proposed TKR training approach outperforms the conventional voxel-wise sum of squared differences. The proposed approach may be useful to support MRI clustering and similarity inference tasks, which are required on template-based image segmentation and atlas construction.

A similarity measure method combining location feature for mammogram retrieval.

PubMed

Wang, Zhiqiong; Xin, Junchang; Huang, Yukun; Li, Chen; Xu, Ling; Li, Yang; Zhang, Hao; Gu, Huizi; Qian, Wei

2018-05-28

Breast cancer, the most common malignancy among women, has a high mortality rate in clinical practice. Early detection, diagnosis and treatment can reduce the mortalities of breast cancer greatly. The method of mammogram retrieval can help doctors to find the early breast lesions effectively and determine a reasonable feature set for image similarity measure. This will improve the accuracy effectively for mammogram retrieval. This paper proposes a similarity measure method combining location feature for mammogram retrieval. Firstly, the images are pre-processed, the regions of interest are detected and the lesions are segmented in order to get the center point and radius of the lesions. Then, the method, namely Coherent Point Drift, is used for image registration with the pre-defined standard image. The center point and radius of the lesions after registration are obtained and the standard location feature of the image is constructed. This standard location feature can help figure out the location similarity between the image pair from the query image to each dataset image in the database. Next, the content feature of the image is extracted, including the Histogram of Oriented Gradients, the Edge Direction Histogram, the Local Binary Pattern and the Gray Level Histogram, and the image pair content similarity can be calculated using the Earth Mover's Distance. Finally, the location similarity and content similarity are fused to form the image fusion similarity, and the specified number of the most similar images can be returned according to it. In the experiment, 440 mammograms, which are from Chinese women in Northeast China, are used as the database. When fusing 40% lesion location feature similarity and 60% content feature similarity, the results have obvious advantages. At this time, precision is 0.83, recall is 0.76, comprehensive indicator is 0.79, satisfaction is 96.0%, mean is 4.2 and variance is 17.7. The results show that the precision and recall of this

Assessing semantic similarity of texts - Methods and algorithms

NASA Astrophysics Data System (ADS)

Rozeva, Anna; Zerkova, Silvia

2017-12-01

Assessing the semantic similarity of texts is an important part of different text-related applications like educational systems, information retrieval, text summarization, etc. This task is performed by sophisticated analysis, which implements text-mining techniques. Text mining involves several pre-processing steps, which provide for obtaining structured representative model of the documents in a corpus by means of extracting and selecting the features, characterizing their content. Generally the model is vector-based and enables further analysis with knowledge discovery approaches. Algorithms and measures are used for assessing texts at syntactical and semantic level. An important text-mining method and similarity measure is latent semantic analysis (LSA). It provides for reducing the dimensionality of the document vector space and better capturing the text semantics. The mathematical background of LSA for deriving the meaning of the words in a given text by exploring their co-occurrence is examined. The algorithm for obtaining the vector representation of words and their corresponding latent concepts in a reduced multidimensional space as well as similarity calculation are presented.

Nuclear markers reveal that inter-lake cichlids' similar morphologies do not reflect similar genealogy.

PubMed

Kassam, Daud; Seki, Shingo; Horic, Michio; Yamaoka, Kosaku

2006-08-01

The apparent inter-lake morphological similarity among East African Great Lakes' cichlid species/genera has left evolutionary biologists asking whether such similarity is due to sharing of common ancestor or mere convergent evolution. In order to answer such question, we first used Geometric Morphometrics, GM, to quantify morphological similarity and then subsequently used Amplified Fragment Length Polymorphism, AFLP, to determine if similar morphologies imply shared ancestry or convergent evolution. GM revealed that not all presumed morphological similar pairs were indeed similar, and the dendrogram generated from AFLP data indicated distinct clusters corresponding to each lake and not inter-lake morphological similar pairs. Such results imply that the morphological similarity is due to convergent evolution and not shared ancestry. The congruency of GM and AFLP generated dendrograms imply that GM is capable of picking up phylogenetic signal, and thus GM can be potential tool in phylogenetic systematics.

The Gender Similarities Hypothesis

ERIC Educational Resources Information Center

Hyde, Janet Shibley

2005-01-01

The differences model, which argues that males and females are vastly different psychologically, dominates the popular media. Here, the author advances a very different view, the gender similarities hypothesis, which holds that males and females are similar on most, but not all, psychological variables. Results from a review of 46 meta-analyses…

Estimating the similarity of alternative Affymetrix probe sets using transcriptional networks

PubMed Central

2013-01-01

Background The usefulness of the data from Affymetrix microarray analysis depends largely on the reliability of the files describing the correspondence between probe sets, genes and transcripts. Particularly, when a gene is targeted by several probe sets, these files should give information about the similarity of each alternative probe set pair. Transcriptional networks integrate the multiple correlations that exist between all probe sets and supply much more information than a simple correlation coefficient calculated for two series of signals. In this study, we used the PSAWN (Probe Set Assignment With Networks) programme we developed to investigate whether similarity of alternative probe sets resulted in some specific properties. Findings PSAWNpy delivered a full textual description of each probe set and information on the number and properties of secondary targets. PSAWNml calculated the similarity of each alternative probe set pair and allowed finding relationships between similarity and localisation of probes in common transcripts or exons. Similar alternative probe sets had very low negative correlation, high positive correlation and similar neighbourhood overlap. Using these properties, we devised a test that allowed grouping similar probe sets in a given network. By considering several networks, additional information concerning the similarity reproducibility was obtained, which allowed defining the actual similarity of alternative probe set pairs. In particular, we calculated the common localisation of probes in exons and in known transcripts and we showed that similarity was correctly correlated with them. The information collected on all pairs of alternative probe sets in the most popular 3’ IVT Affymetrix chips is available in tabular form at http://bns.crbm.cnrs.fr/download.html. Conclusions These processed data can be used to obtain a finer interpretation when comparing microarray data between biological conditions. They are particularly well

Similarity solutions of reaction–diffusion equation with space- and time-dependent diffusion and reaction terms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ho, C.-L.; Lee, C.-C., E-mail: chieh.no27@gmail.com

2016-01-15

We consider solvability of the generalized reaction–diffusion equation with both space- and time-dependent diffusion and reaction terms by means of the similarity method. By introducing the similarity variable, the reaction–diffusion equation is reduced to an ordinary differential equation. Matching the resulting ordinary differential equation with known exactly solvable equations, one can obtain corresponding exactly solvable reaction–diffusion systems. Several representative examples of exactly solvable reaction–diffusion equations are presented.

Fault Detection of Aircraft System with Random Forest Algorithm and Similarity Measure

PubMed Central

Park, Wookje; Jung, Sikhang

2014-01-01

Research on fault detection algorithm was developed with the similarity measure and random forest algorithm. The organized algorithm was applied to unmanned aircraft vehicle (UAV) that was readied by us. Similarity measure was designed by the help of distance information, and its usefulness was also verified by proof. Fault decision was carried out by calculation of weighted similarity measure. Twelve available coefficients among healthy and faulty status data group were used to determine the decision. Similarity measure weighting was done and obtained through random forest algorithm (RFA); RF provides data priority. In order to get a fast response of decision, a limited number of coefficients was also considered. Relation of detection rate and amount of feature data were analyzed and illustrated. By repeated trial of similarity calculation, useful data amount was obtained. PMID:25057508

Scaling Relations and Self-Similarity of 3-Dimensional Reynolds-Averaged Navier-Stokes Equations.

PubMed

Ercan, Ali; Kavvas, M Levent

2017-07-25

Scaling conditions to achieve self-similar solutions of 3-Dimensional (3D) Reynolds-Averaged Navier-Stokes Equations, as an initial and boundary value problem, are obtained by utilizing Lie Group of Point Scaling Transformations. By means of an open-source Navier-Stokes solver and the derived self-similarity conditions, we demonstrated self-similarity within the time variation of flow dynamics for a rigid-lid cavity problem under both up-scaled and down-scaled domains. The strength of the proposed approach lies in its ability to consider the underlying flow dynamics through not only from the governing equations under consideration but also from the initial and boundary conditions, hence allowing to obtain perfect self-similarity in different time and space scales. The proposed methodology can be a valuable tool in obtaining self-similar flow dynamics under preferred level of detail, which can be represented by initial and boundary value problems under specific assumptions.

Web Image Search Re-ranking with Click-based Similarity and Typicality.

PubMed

Yang, Xiaopeng; Mei, Tao; Zhang, Yong Dong; Liu, Jie; Satoh, Shin'ichi

2016-07-20

In image search re-ranking, besides the well known semantic gap, intent gap, which is the gap between the representation of users' query/demand and the real intent of the users, is becoming a major problem restricting the development of image retrieval. To reduce human effects, in this paper, we use image click-through data, which can be viewed as the "implicit feedback" from users, to help overcome the intention gap, and further improve the image search performance. Generally, the hypothesis visually similar images should be close in a ranking list and the strategy images with higher relevance should be ranked higher than others are widely accepted. To obtain satisfying search results, thus, image similarity and the level of relevance typicality are determinate factors correspondingly. However, when measuring image similarity and typicality, conventional re-ranking approaches only consider visual information and initial ranks of images, while overlooking the influence of click-through data. This paper presents a novel re-ranking approach, named spectral clustering re-ranking with click-based similarity and typicality (SCCST). First, to learn an appropriate similarity measurement, we propose click-based multi-feature similarity learning algorithm (CMSL), which conducts metric learning based on clickbased triplets selection, and integrates multiple features into a unified similarity space via multiple kernel learning. Then based on the learnt click-based image similarity measure, we conduct spectral clustering to group visually and semantically similar images into same clusters, and get the final re-rank list by calculating click-based clusters typicality and withinclusters click-based image typicality in descending order. Our experiments conducted on two real-world query-image datasets with diverse representative queries show that our proposed reranking approach can significantly improve initial search results, and outperform several existing re-ranking approaches.

A transversal approach to predict gene product networks from ontology-based similarity

PubMed Central

Chabalier, Julie; Mosser, Jean; Burgun, Anita

2007-01-01

Background Interpretation of transcriptomic data is usually made through a "standard" approach which consists in clustering the genes according to their expression patterns and exploiting Gene Ontology (GO) annotations within each expression cluster. This approach makes it difficult to underline functional relationships between gene products that belong to different expression clusters. To address this issue, we propose a transversal analysis that aims to predict functional networks based on a combination of GO processes and data expression. Results The transversal approach presented in this paper consists in computing the semantic similarity between gene products in a Vector Space Model. Through a weighting scheme over the annotations, we take into account the representativity of the terms that annotate a gene product. Comparing annotation vectors results in a matrix of gene product similarities. Combined with expression data, the matrix is displayed as a set of functional gene networks. The transversal approach was applied to 186 genes related to the enterocyte differentiation stages. This approach resulted in 18 functional networks proved to be biologically relevant. These results were compared with those obtained through a standard approach and with an approach based on information content similarity. Conclusion Complementary to the standard approach, the transversal approach offers new insight into the cellular mechanisms and reveals new research hypotheses by combining gene product networks based on semantic similarity, and data expression. PMID:17605807

Optimization of the parameters for obtaining zirconia-alumina coatings, made by flame spraying from results of numerical simulation

NASA Astrophysics Data System (ADS)

Ferrer, M.; Vargas, F.; Peña, G.

2017-12-01

The K-Sommerfeld values (K) and the melting percentage (% F) obtained by numerical simulation using the Jets et Poudres software were used to find the projection parameters of zirconia-alumina coatings by thermal spraying flame, in order to obtain coatings with good morphological and structural properties to be used as thermal insulation. The experimental results show the relationship between the Sommerfeld parameter and the porosity of the zirconia-alumina coatings. It is found that the lowest porosity is obtained when the K-Sommerfeld value is close to 45 with an oxidant flame, on the contrary, when superoxidant flames are used K values are close 52, which improve wear resistance.

Salient object detection: manifold-based similarity adaptation approach

NASA Astrophysics Data System (ADS)

Zhou, Jingbo; Ren, Yongfeng; Yan, Yunyang; Gao, Shangbing

2014-11-01

A saliency detection algorithm based on manifold-based similarity adaptation is proposed. The proposed algorithm is divided into three steps. First, we segment an input image into superpixels, which are represented as the nodes in a graph. Second, a new similarity measurement is used in the proposed algorithm. The weight matrix of the graph, which indicates the similarities between the nodes, uses a similarity-based method. It also captures the manifold structure of the image patches, in which the graph edges are determined in a data adaptive manner in terms of both similarity and manifold structure. Then, we use local reconstruction method as a diffusion method to obtain the saliency maps. The objective function in the proposed method is based on local reconstruction, with which estimated weights capture the manifold structure. Experiments on four bench-mark databases demonstrate the accuracy and robustness of the proposed method.

Obtaining the Electron Angular Momentum Coupling Spectroscopic Terms, jj

ERIC Educational Resources Information Center

Orofino, Hugo; Faria, Roberto B.

2010-01-01

A systematic procedure is developed to obtain the electron angular momentum coupling (jj) spectroscopic terms, which is based on building microstates in which each individual electron is placed in a different m[subscript j] "orbital". This approach is similar to that used to obtain the spectroscopic terms under the Russell-Saunders (LS) coupling…

A few ways of calculating the similarity parameter kappa* for real gases. [increase Reynolds number in cryogenic wind tunnels

NASA Technical Reports Server (NTRS)

Lorenz-Meyer, W.

1977-01-01

In connection with the question on the applicability of test results obtained from cryogenic wind tunnels to the large-scale model the similarity parameter is referred to. A simple method is given for calculating the similarity parameter. From the numerical values obtained it can be deduced that nitrogen behaves practically like an ideal gas when it is close to the saturation point and in a pressure range up to 4 bar. The influence of this parameter on the pressure distribution of a supercritical profile confirms this finding.

The gender similarities hypothesis.

PubMed

Hyde, Janet Shibley

2005-09-01

The differences model, which argues that males and females are vastly different psychologically, dominates the popular media. Here, the author advances a very different view, the gender similarities hypothesis, which holds that males and females are similar on most, but not all, psychological variables. Results from a review of 46 meta-analyses support the gender similarities hypothesis. Gender differences can vary substantially in magnitude at different ages and depend on the context in which measurement occurs. Overinflated claims of gender differences carry substantial costs in areas such as the workplace and relationships. Copyright (c) 2005 APA, all rights reserved.

New high-definition thickness data obtained at tropical glaciers: preliminary results from Antisana volcano (Ecuador) using GPR prospection

NASA Astrophysics Data System (ADS)

Zapata, Camilo; Andrade, Daniel; Córdova, Jorge; Maisincho, Luis; Carvajal, Juan; Calispa, Marlon; Villacís, Marcos

2014-05-01

The study of tropical glaciers has been a significant contribution to the understanding of glacier dynamics and climate change. Much of the data and results have been obtained by analyzing plan-view images obtained by air- and space-borne sensors, as well as depth data obtained by diverse methodologies at selected points on the glacier surface. However, the measurement of glacier thicknesses has remained an elusive task in tropical glaciers, often located in rough terrains where the application of geophysical surveys (i.e. seismic surveys) requires logistics sometimes hardly justified by the amount of obtained data. In the case of Ecuador, however, where most glaciers have developed on active volcanoes and represent sources/reservoirs of fresh water, the precise knowledge of such information is fundamental for scientific research but also in order to better assess key aspects for the society. The relatively recent but fast development of the GPR technology has helped to obtain new highdefinition thickness data at Antisana volcano that will be used to: 1) better understand the dynamics and fate of tropical glaciers; 2) better estimate the amount of fresh water stored in the glaciers; 3) better assess the hazards associated with the sudden widespread melting of glaciers during volcanic eruptions. The measurements have been obtained at glaciers 12 and 15 of Antisana volcano, with the help of a commercial GPR equipped with a 25 MHz antenna. A total of 30 transects have been obtained, covering a distance of more than 3 km, from the glacier ablation zone, located at ~ 4600 masl, up to the level of 5200 masl. The preliminary results show a positive correlation between altitude and glacier thickness, with maximum and minimum calculated values reaching up to 80 m, and down to 15 m, respectively. The experience gained at Antisana volcano will be used to prepare a more widespread GPR survey in the glaciers of Cotopaxi volcano, whose implications in terms of volcanic hazards

Method for obtaining oxygen from lunar or similar soil

NASA Technical Reports Server (NTRS)

Downs, W. R. (Inventor)

1973-01-01

Recovery of oxygen from soil containing metal oxides such as alumina, silica, calcia, magnesia, and ilmenite wherein the material containing the oxides is placed in a vessel and reacted with fluorine to provide oxygen and metal fluorides. The oxygen produced from the reaction is recovered and stored, after further purifying processes, and the metal fluorides are further reacted with potassium vapor to provide potassium fluoride and free metals. The potassium fluoride is than subjected to electrolysis whereby the potassium and fluorine are separated and are recycled for further use in the system. Valuable free metals are recovered for other uses.

What difference reveals about similarity.

PubMed

Sagi, Eyal; Gentner, Dedre; Lovett, Andrew

2012-08-01

Detecting that two images are different is faster for highly dissimilar images than for highly similar images. Paradoxically, we showed that the reverse occurs when people are asked to describe how two images differ--that is, to state a difference between two images. Following structure-mapping theory, we propose that this disassociation arises from the multistage nature of the comparison process. Detecting that two images are different can be done in the initial (local-matching) stage, but only for pairs with low overlap; thus, "different" responses are faster for low-similarity than for high-similarity pairs. In contrast, identifying a specific difference generally requires a full structural alignment of the two images, and this alignment process is faster for high-similarity pairs. We described four experiments that demonstrate this dissociation and show that the results can be simulated using the Structure-Mapping Engine. These results pose a significant challenge for nonstructural accounts of similarity comparison and suggest that structural alignment processes play a significant role in visual comparison. Copyright © 2012 Cognitive Science Society, Inc.

Operationalization of Sign Language Phonological Similarity and its Effects on Lexical Access.

PubMed

Williams, Joshua T; Stone, Adam; Newman, Sharlene D

2017-07-01

Cognitive mechanisms for sign language lexical access are fairly unknown. This study investigated whether phonological similarity facilitates lexical retrieval in sign languages using measures from a new lexical database for American Sign Language. Additionally, it aimed to determine which similarity metric best fits the present data in order to inform theories of how phonological similarity is constructed within the lexicon and to aid in the operationalization of phonological similarity in sign language. Sign repetition latencies and accuracy were obtained when native signers were asked to reproduce a sign displayed on a computer screen. Results indicated that, as predicted, phonological similarity facilitated repetition latencies and accuracy as long as there were no strict constraints on the type of sublexical features that overlapped. The data converged to suggest that one similarity measure, MaxD, defined as the overlap of any 4 sublexical features, likely best represents mechanisms of phonological similarity in the mental lexicon. Together, these data suggest that lexical access in sign language is facilitated by phonologically similar lexical representations in memory and the optimal operationalization is defined as liberal constraints on overlap of 4 out of 5 sublexical features-similar to the majority of extant definitions in the literature. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Coupling effect of nodes popularity and similarity on social network persistence

PubMed Central

Jin, Xiaogang; Jin, Cheng; Huang, Jiaxuan; Min, Yong

2017-01-01

Network robustness represents the ability of networks to withstand failures and perturbations. In social networks, maintenance of individual activities, also called persistence, is significant towards understanding robustness. Previous works usually consider persistence on pre-generated network structures; while in social networks, the network structure is growing with the cascading inactivity of existed individuals. Here, we address this challenge through analysis for nodes under a coevolution model, which characterizes individual activity changes under three network growth modes: following the descending order of nodes’ popularity, similarity or uniform random. We show that when nodes possess high spontaneous activities, a popularity-first growth mode obtains highly persistent networks; otherwise, with low spontaneous activities, a similarity-first mode does better. Moreover, a compound growth mode, with the consecutive joining of similar nodes in a short period and mixing a few high popularity nodes, obtains the highest persistence. Therefore, nodes similarity is essential for persistent social networks, while properly coupling popularity with similarity further optimizes the persistence. This demonstrates the evolution of nodes activity not only depends on network topology, but also their connective typology. PMID:28220840

Coupling effect of nodes popularity and similarity on social network persistence

NASA Astrophysics Data System (ADS)

Jin, Xiaogang; Jin, Cheng; Huang, Jiaxuan; Min, Yong

2017-02-01

Network robustness represents the ability of networks to withstand failures and perturbations. In social networks, maintenance of individual activities, also called persistence, is significant towards understanding robustness. Previous works usually consider persistence on pre-generated network structures; while in social networks, the network structure is growing with the cascading inactivity of existed individuals. Here, we address this challenge through analysis for nodes under a coevolution model, which characterizes individual activity changes under three network growth modes: following the descending order of nodes’ popularity, similarity or uniform random. We show that when nodes possess high spontaneous activities, a popularity-first growth mode obtains highly persistent networks; otherwise, with low spontaneous activities, a similarity-first mode does better. Moreover, a compound growth mode, with the consecutive joining of similar nodes in a short period and mixing a few high popularity nodes, obtains the highest persistence. Therefore, nodes similarity is essential for persistent social networks, while properly coupling popularity with similarity further optimizes the persistence. This demonstrates the evolution of nodes activity not only depends on network topology, but also their connective typology.

Coupling effect of nodes popularity and similarity on social network persistence.

PubMed

Jin, Xiaogang; Jin, Cheng; Huang, Jiaxuan; Min, Yong

2017-02-21

Network robustness represents the ability of networks to withstand failures and perturbations. In social networks, maintenance of individual activities, also called persistence, is significant towards understanding robustness. Previous works usually consider persistence on pre-generated network structures; while in social networks, the network structure is growing with the cascading inactivity of existed individuals. Here, we address this challenge through analysis for nodes under a coevolution model, which characterizes individual activity changes under three network growth modes: following the descending order of nodes' popularity, similarity or uniform random. We show that when nodes possess high spontaneous activities, a popularity-first growth mode obtains highly persistent networks; otherwise, with low spontaneous activities, a similarity-first mode does better. Moreover, a compound growth mode, with the consecutive joining of similar nodes in a short period and mixing a few high popularity nodes, obtains the highest persistence. Therefore, nodes similarity is essential for persistent social networks, while properly coupling popularity with similarity further optimizes the persistence. This demonstrates the evolution of nodes activity not only depends on network topology, but also their connective typology.

Geodetic results from ISAGEX data. [for obtaining center of mass coordinates for geodetic camera sites

NASA Technical Reports Server (NTRS)

Marsh, J. G.; Douglas, B. C.; Walls, D. M.

1974-01-01

Laser and camera data taken during the International Satellite Geodesy Experiment (ISAGEX) were used in dynamical solutions to obtain center-of-mass coordinates for the Astro-Soviet camera sites at Helwan, Egypt, and Oulan Bator, Mongolia, as well as the East European camera sites at Potsdam, German Democratic Republic, and Ondrejov, Czechoslovakia. The results are accurate to about 20m in each coordinate. The orbit of PEOLE (i=15) was also determined from ISAGEX data. Mean Kepler elements suitable for geodynamic investigations are presented.

Relevance similarity: an alternative means to monitor information retrieval systems

PubMed Central

Dong, Peng; Loh, Marie; Mondry, Adrian

2005-01-01

Background Relevance assessment is a major problem in the evaluation of information retrieval systems. The work presented here introduces a new parameter, "Relevance Similarity", for the measurement of the variation of relevance assessment. In a situation where individual assessment can be compared with a gold standard, this parameter is used to study the effect of such variation on the performance of a medical information retrieval system. In such a setting, Relevance Similarity is the ratio of assessors who rank a given document same as the gold standard over the total number of assessors in the group. Methods The study was carried out on a collection of Critically Appraised Topics (CATs). Twelve volunteers were divided into two groups of people according to their domain knowledge. They assessed the relevance of retrieved topics obtained by querying a meta-search engine with ten keywords related to medical science. Their assessments were compared to the gold standard assessment, and Relevance Similarities were calculated as the ratio of positive concordance with the gold standard for each topic. Results The similarity comparison among groups showed that a higher degree of agreements exists among evaluators with more subject knowledge. The performance of the retrieval system was not significantly different as a result of the variations in relevance assessment in this particular query set. Conclusion In assessment situations where evaluators can be compared to a gold standard, Relevance Similarity provides an alternative evaluation technique to the commonly used kappa scores, which may give paradoxically low scores in highly biased situations such as document repositories containing large quantities of relevant data. PMID:16029513

Low-Energy Nuclear Reactions Resulting as Picometer Interactions with Similarity to K-Shell Electron Capture

NASA Astrophysics Data System (ADS)

Hora, H.; Miley, G. H.; Li, X. Z.; Kelly, J. C.; Osman, F.

2006-02-01

Since the appeal by Brian Josephson at the meeting of the Nobel Laureates July 2004, it seems to be indicated to summarize the following serious, reproducible and confirmed observations on reactions of protons or deuterons incorporated in host metals such as palladium. Some reflections to Rutherford's discovery of nuclear physics, the Cockroft-Oliphant discovery of anomalous low-energy fusion reactions and the chemist Hahn's discovery of fission had to be included. Using gaseous atmosphere or discharges between palladium targets, rather significant results were seen e.g. from the "life after death" heat production of such high values per host atom that only nuclear reactions can be involved. This supports the earlier evaluation of neutron generation in fully reversible experiments with gas discharges hinting that a reasonable screening effect - preferably in the swimming electron layer - may lead to reactions at nuclear distances d of picometers with reaction probability times U of about megaseconds similar to the K-shell capture radioactivity. Further electrolytic experiments led to low-energy nuclear reactions (LENR) where the involvement of pollution could be excluded from the appearance of very seldom rare earth elements. A basically new theory for DD cross-sections is used to confirm the picometer-megasecond reactions of cold fusion. Other theoretical aspects are given from measured heavy element distributions similar to the standard abundance distribution, SAD, in the Universe with consequences on endothermic heavy nuclei generation, magic numbers and to quark-gluon plasmas.

An approach to large scale identification of non-obvious structural similarities between proteins

PubMed Central

Cherkasov, Artem; Jones, Steven JM

2004-01-01

Background A new sequence independent bioinformatics approach allowing genome-wide search for proteins with similar three dimensional structures has been developed. By utilizing the numerical output of the sequence threading it establishes putative non-obvious structural similarities between proteins. When applied to the testing set of proteins with known three dimensional structures the developed approach was able to recognize structurally similar proteins with high accuracy. Results The method has been developed to identify pathogenic proteins with low sequence identity and high structural similarity to host analogues. Such protein structure relationships would be hypothesized to arise through convergent evolution or through ancient horizontal gene transfer events, now undetectable using current sequence alignment techniques. The pathogen proteins, which could mimic or interfere with host activities, would represent candidate virulence factors. The developed approach utilizes the numerical outputs from the sequence-structure threading. It identifies the potential structural similarity between a pair of proteins by correlating the threading scores of the corresponding two primary sequences against the library of the standard folds. This approach allowed up to 64% sensitivity and 99.9% specificity in distinguishing protein pairs with high structural similarity. Conclusion Preliminary results obtained by comparison of the genomes of Homo sapiens and several strains of Chlamydia trachomatis have demonstrated the potential usefulness of the method in the identification of bacterial proteins with known or potential roles in virulence. PMID:15147578

Semantic Similarity in Biomedical Ontologies

PubMed Central

Pesquita, Catia; Faria, Daniel; Falcão, André O.; Lord, Phillip; Couto, Francisco M.

2009-01-01

In recent years, ontologies have become a mainstream topic in biomedical research. When biological entities are described using a common schema, such as an ontology, they can be compared by means of their annotations. This type of comparison is called semantic similarity, since it assesses the degree of relatedness between two entities by the similarity in meaning of their annotations. The application of semantic similarity to biomedical ontologies is recent; nevertheless, several studies have been published in the last few years describing and evaluating diverse approaches. Semantic similarity has become a valuable tool for validating the results drawn from biomedical studies such as gene clustering, gene expression data analysis, prediction and validation of molecular interactions, and disease gene prioritization. We review semantic similarity measures applied to biomedical ontologies and propose their classification according to the strategies they employ: node-based versus edge-based and pairwise versus groupwise. We also present comparative assessment studies and discuss the implications of their results. We survey the existing implementations of semantic similarity measures, and we describe examples of applications to biomedical research. This will clarify how biomedical researchers can benefit from semantic similarity measures and help them choose the approach most suitable for their studies. Biomedical ontologies are evolving toward increased coverage, formality, and integration, and their use for annotation is increasingly becoming a focus of both effort by biomedical experts and application of automated annotation procedures to create corpora of higher quality and completeness than are currently available. Given that semantic similarity measures are directly dependent on these evolutions, we can expect to see them gaining more relevance and even becoming as essential as sequence similarity is today in biomedical research. PMID:19649320

Investigation of Rossby-number similarity in the neutral boundary layer using large-eddy simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ohmstede, W.D.; Cederwall, R.T.; Meyers, R.E.

One special case of particular interest, especially to theoreticians, is the steady-state, horizontally homogeneous, autobarotropic (PLB), hereafter referred to as the neutral boundary layer (NBL). The NBL is in fact a 'rare' atmospheric phenomenon, generally associated with high-wind situations. Nevertheless, there is a disproportionate interest in this problem because Rossby-number similarity theory provides a sound approach for addressing this issue. Rossby-number similarity theory has rather wide acceptance, but because of the rarity of the 'true' NBL state, there remains an inadequate experimental database for quantifying constants associated with the Rossby-number similarity concept. Although it remains a controversial issue, it hasmore » been proposed that large-eddy simulation (LES) is an alternative to physical experimentation for obtaining basic atmospherc 'data'. The objective of the study reported here is to investigate Rossby-number similarity in the NBL using LES. Previous studies have not addressed Rossby-number similarity explicitly, although they made use of it in the interpretation of their results. The intent is to calculate several sets of NBL solutions that are ambiguous relative to the their respective Rossby numbers and compare the results for similarity, or the lack of it. 14 refs., 1 fig.« less

Main results and experience obtained on Mir space station and experiment program for Russian segment of ISS.

PubMed

Utkin, V F; Lukjashchenko, V I; Borisov, V V; Suvorov, V V; Tsymbalyuk, M M

2003-07-01

This article presents main scientific and practical results obtained in course of scientific and applied research and experiments on Mir space station. Based on Mir experience, processes of research program formation for the Russian Segment of the ISS are briefly described. The major trends of activities planned in the frames of these programs as well as preliminary results of increment research programs implementation in the ISS' first missions are also presented. c2003 Elsevier Science Ltd. All rights reserved.

Detecting similarities among distant homologous proteins by comparison of domain flexibilities.

PubMed

Pandini, Alessandro; Mauri, Giancarlo; Bordogna, Annalisa; Bonati, Laura

2007-06-01

Aim of this work is to assess the informativeness of protein dynamics in the detection of similarities among distant homologous proteins. To this end, an approach to perform large-scale comparisons of protein domain flexibilities is proposed. CONCOORD is confirmed as a reliable method for fast conformational sampling. The root mean square fluctuation of alpha carbon positions in the essential dynamics subspace is employed as a measure of local flexibility and a synthetic index of similarity is presented. The dynamics of a large collection of protein domains from ASTRAL/SCOP40 is analyzed and the possibility to identify relationships, at both the family and the superfamily levels, on the basis of the dynamical features is discussed. The obtained picture is in agreement with the SCOP classification, and furthermore suggests the presence of a distinguishable familiar trend in the flexibility profiles. The results support the complementarity of the dynamical and the structural information, suggesting that information from dynamics analysis can arise from functional similarities, often partially hidden by a static comparison. On the basis of this first test, flexibility annotation can be expected to help in automatically detecting functional similarities otherwise unrecoverable.

25 CFR 162.539 - Must I obtain a WEEL before obtaining a WSR lease?

Code of Federal Regulations, 2014 CFR

2014-04-01

... AND PERMITS Wind and Solar Resource Leases Wsr Leases § 162.539 Must I obtain a WEEL before obtaining... direct result of energy resource information gathered from a WEEL activity, obtaining a WEEL is not a...

25 CFR 162.539 - Must I obtain a WEEL before obtaining a WSR lease?

Code of Federal Regulations, 2013 CFR

2013-04-01

... AND PERMITS Wind and Solar Resource Leases Wsr Leases § 162.539 Must I obtain a WEEL before obtaining... direct result of energy resource information gathered from a WEEL activity, obtaining a WEEL is not a...

Creating Birds of Similar Feathers: Leveraging Similarity to Improve Teacher-Student Relationships and Academic Achievement

ERIC Educational Resources Information Center

Gehlbach, Hunter; Brinkworth, Maureen E.; King, Aaron M.; Hsu, Laura M.; McIntyre, Joseph; Rogers, Todd

2016-01-01

When people perceive themselves as similar to others, greater liking and closer relationships typically result. In the first randomized field experiment that leverages actual similarities to improve real-world relationships, we examined the affiliations between 315 9th grade students and their 25 teachers. Students in the treatment condition…

Generalized entropies and the similarity of texts

NASA Astrophysics Data System (ADS)

Altmann, Eduardo G.; Dias, Laércio; Gerlach, Martin

2017-01-01

We show how generalized Gibbs-Shannon entropies can provide new insights on the statistical properties of texts. The universal distribution of word frequencies (Zipf’s law) implies that the generalized entropies, computed at the word level, are dominated by words in a specific range of frequencies. Here we show that this is the case not only for the generalized entropies but also for the generalized (Jensen-Shannon) divergences, used to compute the similarity between different texts. This finding allows us to identify the contribution of specific words (and word frequencies) for the different generalized entropies and also to estimate the size of the databases needed to obtain a reliable estimation of the divergences. We test our results in large databases of books (from the google n-gram database) and scientific papers (indexed by Web of Science).

Self-similar transmission patterns induced by magnetic field effects in graphene

NASA Astrophysics Data System (ADS)

Rodríguez-González, R.; Rodríguez-Vargas, I.; Díaz-Guerrero, D. S.; Gaggero-Sager, L. M.

2018-07-01

In this work we study the propagation of Dirac electrons through Cantor-like structures in graphene. In concrete, we are considering structures with magnetic and electrostatic barriers arrange in Cantor-like fashion. The Dirac-like equation and the transfer matrix approach have been used to obtain the transmission properties. We found self-similar patterns in the transmission probability or transmittance once the magnetic field is incorporated. Moreover, these patterns can be connected with other ones at different scales through well-defined scaling rules. In particular, we have found two scaling rules that become a useful tool to describe the self-similarity of our system. The first expression is related to the generation and the second one to the length of the Cantor-like structure. As far as we know it is the first time that a special self-similar structure in conjunction with magnetic field effects give rise to self-similar transmission patterns. It is also important to remark that according to our knowledge it is fundamental to break some symmetry of graphene in order to obtain self-similar transmission properties. In fact, in our case the time-reversal symmetry is broken by the magnetic field effects.

[Rapid analysis of metronidazole tablets by optic-fiber sensing technologies and the similarity of ultraviolet spectra].

PubMed

Jin, Lu; Li, Li; Li, Xin-xia; Yang, Ting; Kong, Bin; Xu, Ping-ping

2011-02-01

The paper is to report the development of an optic-fiber sensing technology method to analyze metronidazole tablets rapidly. In this fiber-optic sensing system, the light from source delivering to probe can be dipped into simple-handling sample solution, absorbed by the solution and reflected to the fiber-optic and detected in the detection system at last. Then the drug content can be shown in the screen from the ultraviolet absorption spectra and the consistency between that obtained by this method and that in China Pharmacopoeia can be compared. With regard to data processing, a new method is explored to identify the authenticity of drugs using the similarity between the sample map and the standard pattern by full ultraviolet spectrum. The results indicate that ultraviolet spectra of tablets can be obtained from this technology and the determination results showed no significant difference as compared with the method in China Pharmacopoeia (P > 0.05), and the similarity can be a parameter to identify the authenticity of drugs.

Finding an appropriate equation to measure similarity between binary vectors: case studies on Indonesian and Japanese herbal medicines.

PubMed

Wijaya, Sony Hartono; Afendi, Farit Mochamad; Batubara, Irmanida; Darusman, Latifah K; Altaf-Ul-Amin, Md; Kanaya, Shigehiko

2016-12-07

The binary similarity and dissimilarity measures have critical roles in the processing of data consisting of binary vectors in various fields including bioinformatics and chemometrics. These metrics express the similarity and dissimilarity values between two binary vectors in terms of the positive matches, absence mismatches or negative matches. To our knowledge, there is no published work presenting a systematic way of finding an appropriate equation to measure binary similarity that performs well for certain data type or application. A proper method to select a suitable binary similarity or dissimilarity measure is needed to obtain better classification results. In this study, we proposed a novel approach to select binary similarity and dissimilarity measures. We collected 79 binary similarity and dissimilarity equations by extensive literature search and implemented those equations as an R package called bmeasures. We applied these metrics to quantify the similarity and dissimilarity between herbal medicine formulas belonging to the Indonesian Jamu and Japanese Kampo separately. We assessed the capability of binary equations to classify herbal medicine pairs into match and mismatch efficacies based on their similarity or dissimilarity coefficients using the Receiver Operating Characteristic (ROC) curve analysis. According to the area under the ROC curve results, we found Indonesian Jamu and Japanese Kampo datasets obtained different ranking of binary similarity and dissimilarity measures. Out of all the equations, the Forbes-2 similarity and the Variant of Correlation similarity measures are recommended for studying the relationship between Jamu formulas and Kampo formulas, respectively. The selection of binary similarity and dissimilarity measures for multivariate analysis is data dependent. The proposed method can be used to find the most suitable binary similarity and dissimilarity equation wisely for a particular data. Our finding suggests that all four

Parameter Set Cloning Based on Catchment Similarity for Large-scale Hydrologic Modeling

NASA Astrophysics Data System (ADS)

Liu, Z.; Kaheil, Y.; McCollum, J.

2016-12-01

Parameter calibration is a crucial step to ensure the accuracy of hydrological models. However, streamflow gauges are not available everywhere for calibrating a large-scale hydrologic model globally. Thus, assigning parameters appropriately for regions where the calibration cannot be performed directly has been a challenge for large-scale hydrologic modeling. Here we propose a method to estimate the model parameters in ungauged regions based on the values obtained through calibration in areas where gauge observations are available. This parameter set cloning is performed according to a catchment similarity index, a weighted sum index based on four catchment characteristic attributes. These attributes are IPCC Climate Zone, Soil Texture, Land Cover, and Topographic Index. The catchments with calibrated parameter values are donors, while the uncalibrated catchments are candidates. Catchment characteristic analyses are first conducted for both donors and candidates. For each attribute, we compute a characteristic distance between donors and candidates. Next, for each candidate, weights are assigned to the four attributes such that higher weights are given to properties that are more directly linked to the hydrologic dominant processes. This will ensure that the parameter set cloning emphasizes the dominant hydrologic process in the region where the candidate is located. The catchment similarity index for each donor - candidate couple is then created as the sum of the weighted distance of the four properties. Finally, parameters are assigned to each candidate from the donor that is "most similar" (i.e. with the shortest weighted distance sum). For validation, we applied the proposed method to catchments where gauge observations are available, and compared simulated streamflows using the parameters cloned by other catchments to the results obtained by calibrating the hydrologic model directly using gauge data. The comparison shows good agreement between the two models

Vertical-axis wind turbine experiments at full dynamic similarity

NASA Astrophysics Data System (ADS)

Duvvuri, Subrahmanyam; Miller, Mark; Brownstein, Ian; Dabiri, John; Hultmark, Marcus

2017-11-01

This study presents results from pressurized (upto 200 atm) wind tunnel tests of a self-spinning 5-blade model Vertical-Axis Wind Turbine (VAWT). The model is geometrically similar (scale ratio 1:22) to a commercially available VAWT, which has a rotor diameter of 2.17 meters and blade span of 3.66 meters, and is used at the Stanford university field lab. The use of pressurized air as working fluid allows for the unique ability to obtain full dynamic similarity with field conditions in terms of matched Reynolds numbers (Re), tip-speed ratios (λ), and Mach number (M). Tests were performed across a wide range of Re and λ, with the highest Re exceeding the maximum operational field Reynolds number (Remax) by a factor of 3. With an extended range of accessible Re conditions, the peak turbine power efficiency was seen to occur roughly at Re = 2 Remax and λ = 1 . Beyond Re > 2 Remax the turbine performance is invariant in Re for all λ. A clear demonstration of Reynolds number invariance for an actual full-scale wind turbine lends novelty to this study, and overall the results show the viability of the present experimental technique in testing turbines at field conditions.

Similarity Measures for Protein Ensembles

PubMed Central

Lindorff-Larsen, Kresten; Ferkinghoff-Borg, Jesper

2009-01-01

Analyses of similarities and changes in protein conformation can provide important information regarding protein function and evolution. Many scores, including the commonly used root mean square deviation, have therefore been developed to quantify the similarities of different protein conformations. However, instead of examining individual conformations it is in many cases more relevant to analyse ensembles of conformations that have been obtained either through experiments or from methods such as molecular dynamics simulations. We here present three approaches that can be used to compare conformational ensembles in the same way as the root mean square deviation is used to compare individual pairs of structures. The methods are based on the estimation of the probability distributions underlying the ensembles and subsequent comparison of these distributions. We first validate the methods using a synthetic example from molecular dynamics simulations. We then apply the algorithms to revisit the problem of ensemble averaging during structure determination of proteins, and find that an ensemble refinement method is able to recover the correct distribution of conformations better than standard single-molecule refinement. PMID:19145244

Comparison of orbital volume obtained by tomography and rapid prototyping.

PubMed

Roça, Guilherme Berto; Foggiatto, José Aguiomar; Ono, Maria Cecilia Closs; Ono, Sergio Eiji; da Silva Freitas, Renato

2013-11-01

This study aims to compare orbital volume obtained by helical tomography and rapid prototyping. The study sample was composed of 6 helical tomography scans. Eleven healthy orbits were identified to have their volumes measured. The volumetric analysis with the helical tomography utilized the same protocol developed by the Plastic Surgery Unit of the Federal University of Paraná. From the CT images, 11 prototypes were created, and their respective volumes were analyzed in 2 ways: using software by SolidWorks and by direct analysis, when the prototype was filled with saline solution. For statistical analysis, the results of the volumes of the 11 orbits were considered independent. The average orbital volume measurements obtained by the method of Ono et al was 20.51 cm, the average obtained by the SolidWorks program was 20.64 cm, and the average measured using the prototype method was 21.81 cm. The 3 methods demonstrated a strong correlation between the measurements. The right and left orbits of each patient had similar volumes. The tomographic method for the analysis of orbital volume using the Ono protocol yielded consistent values, and by combining this method with rapid prototyping, both reliability validations of results were enhanced.

Automatic search for maximum similarity between molecular electrostatic potential distributions

NASA Astrophysics Data System (ADS)

Manaut, Francesc; Sanz, Ferran; José, Jaume; Milesi, Massimo

1991-08-01

A new computer program has been developed to automatically obtain the relative position of two molecules in which the similarity between molecular electrostatic-potential distributions is greatest. These distributions are considered in a volume around the molecules, and the similarity is measured by the Spearman rank coefficient. The program has been tested using several pairs of molecules: water vs. water; phenylethylamine and phenylpropylamine vs. benzylamine; and methotrexate vs. dihydrofolic acid.

Effect of windowing on lithosphere elastic thickness estimates obtained via the coherence method: Results from northern South America

NASA Astrophysics Data System (ADS)

Ojeda, GermáN. Y.; Whitman, Dean

2002-11-01

The effective elastic thickness (Te) of the lithosphere is a parameter that describes the flexural strength of a plate. A method routinely used to quantify this parameter is to calculate the coherence between the two-dimensional gravity and topography spectra. Prior to spectra calculation, data grids must be "windowed" in order to avoid edge effects. We investigated the sensitivity of Te estimates obtained via the coherence method to mirroring, Hanning and multitaper windowing techniques on synthetic data as well as on data from northern South America. These analyses suggest that the choice of windowing technique plays an important role in Te estimates and may result in discrepancies of several kilometers depending on the selected windowing method. Te results from mirrored grids tend to be greater than those from Hanning smoothed or multitapered grids. Results obtained from mirrored grids are likely to be over-estimates. This effect may be due to artificial long wavelengths introduced into the data at the time of mirroring. Coherence estimates obtained from three subareas in northern South America indicate that the average effective elastic thickness is in the range of 29-30 km, according to Hanning and multitaper windowed data. Lateral variations across the study area could not be unequivocally determined from this study. We suggest that the resolution of the coherence method does not permit evaluation of small (i.e., ˜5 km), local Te variations. However, the efficiency and robustness of the coherence method in rendering continent-scale estimates of elastic thickness has been confirmed.

Compassion, pride, and social intuitions of self-other similarity.

PubMed

Oveis, Christopher; Horberg, E J; Keltner, Dacher

2010-04-01

Compassion and pride serve contrasting social functions: Compassion motivates care-taking behavior, whereas pride enables the signaling and negotiation of rank within social hierarchies. Across 3 studies, compassion was associated with increased perceived self-other similarity, particularly to weak or vulnerable others. In contrast, pride was associated with an enhanced sense of similarity to strong others, and a decreased sense of similarity to weak others. These findings were obtained using trait measures (Study 1) and experimental inductions (Studies 2 and 3) of compassion and pride, examining the sense of similarity to strong or weak groups (Studies 1 and 2) and unfamiliar individuals (Study 3). The influences of compassion and pride on perceived self-other similarity could not be accounted for by positive mood, nor was this effect constrained by the ingroup status of the target group or individual. Discussion focuses on the contributions these findings make to an understanding of compassion and pride.

Self-similarity criteria in anisotropic flows with viscosity stratification

NASA Astrophysics Data System (ADS)

Danaila, L.; Voivenel, L.; Varea, E.

2017-02-01

Variable-viscosity flows exhibit a faster trend towards a fully developed turbulent state since fluctuations are produced at a larger amount. A legitimate expectation is that self-similarity to be tenable earlier than in classical, single-viscosity flows. The question which begs to be answered is: which are the self-similarity criteria for variable-viscosity, density-matched, flows? The similarity assumption, i.e., all scales evolve in a similar fashion in space/time, is applied to the transport equation for one- and two-point statistics of anisotropic, variable-viscosity flows. It is shown that the similarity assumption is valid for regions of the flow where viscosity (mean values and the fluctuations root-mean-square) is uniform. In regions where viscosity gradients are important, such as the sheared region and jet boundaries, similarity is not tenable. Our claims are applicable to any decaying flow, isotropic or anisotropic. Support is provided by experimental data obtained in the near field region of a jet issuing into a more viscous environment. The viscosity ratio is 3.5.

An Update on Phased Array Results Obtained on the GE Counter-Rotating Open Rotor Model

NASA Technical Reports Server (NTRS)

Podboy, Gary; Horvath, Csaba; Envia, Edmane

2013-01-01

Beamform maps have been generated from 1) simulated data generated by the LINPROP code and 2) actual experimental phased array data obtained on the GE Counter-rotating open rotor model. The beamform maps show that many of the tones in the experimental data come from their corresponding Mach radius. If the phased array points to the Mach radius associated with a tone then it is likely that the tone is a result of the loading and thickness noise on the blades. In this case, the phased array correctly points to where the noise is coming from and indicates the axial location of the loudest source in the image but not necessarily the correct vertical location. If the phased array does not point to the Mach radius associated with a tone then some mechanism other than loading and thickness noise may control the amplitude of the tone. In this case, the phased array may or may not point to the actual source. If the source is not rotating it is likely that the phased array points to the source. If the source is rotating it is likely that the phased array indicates the axial location of the loudest source but not necessarily the correct vertical location. These results indicate that you have to be careful in how you interpret phased array data obtained on an open rotor since they may show the tones coming from a location other than the source location. With a subsonic tip speed open rotor the tones can come form locations outboard of the blade tips. This has implications regarding noise shielding.

Self-similar conductance patterns in graphene Cantor-like structures.

PubMed

García-Cervantes, H; Gaggero-Sager, L M; Díaz-Guerrero, D S; Sotolongo-Costa, O; Rodríguez-Vargas, I

2017-04-04

Graphene has proven to be an ideal system for exotic transport phenomena. In this work, we report another exotic characteristic of the electron transport in graphene. Namely, we show that the linear-regime conductance can present self-similar patterns with well-defined scaling rules, once the graphene sheet is subjected to Cantor-like nanostructuring. As far as we know the mentioned system is one of the few in which a self-similar structure produces self-similar patterns on a physical property. These patterns are analysed quantitatively, by obtaining the scaling rules that underlie them. It is worth noting that the transport properties are an average of the dispersion channels, which makes the existence of scale factors quite surprising. In addition, that self-similarity be manifested in the conductance opens an excellent opportunity to test this fundamental property experimentally.

Structural similarity based kriging for quantitative structure activity and property relationship modeling.

PubMed

Teixeira, Ana L; Falcao, Andre O

2014-07-28

Structurally similar molecules tend to have similar properties, i.e. closer molecules in the molecular space are more likely to yield similar property values while distant molecules are more likely to yield different values. Based on this principle, we propose the use of a new method that takes into account the high dimensionality of the molecular space, predicting chemical, physical, or biological properties based on the most similar compounds with measured properties. This methodology uses ordinary kriging coupled with three different molecular similarity approaches (based on molecular descriptors, fingerprints, and atom matching) which creates an interpolation map over the molecular space that is capable of predicting properties/activities for diverse chemical data sets. The proposed method was tested in two data sets of diverse chemical compounds collected from the literature and preprocessed. One of the data sets contained dihydrofolate reductase inhibition activity data, and the second molecules for which aqueous solubility was known. The overall predictive results using kriging for both data sets comply with the results obtained in the literature using typical QSPR/QSAR approaches. However, the procedure did not involve any type of descriptor selection or even minimal information about each problem, suggesting that this approach is directly applicable to a large spectrum of problems in QSAR/QSPR. Furthermore, the predictive results improve significantly with the similarity threshold between the training and testing compounds, allowing the definition of a confidence threshold of similarity and error estimation for each case inferred. The use of kriging for interpolation over the molecular metric space is independent of the training data set size, and no reparametrizations are necessary when more compounds are added or removed from the set, and increasing the size of the database will consequentially improve the quality of the estimations. Finally it is shown

Development of similarity theory for control systems

NASA Astrophysics Data System (ADS)

Myshlyaev, L. P.; Evtushenko, V. F.; Ivushkin, K. A.; Makarov, G. V.

2018-05-01

The area of effective application of the traditional similarity theory and the need necessity of its development for systems are discussed. The main statements underlying the similarity theory of control systems are given. The conditions for the similarity of control systems and the need for similarity control control are formulated. Methods and algorithms for estimating and similarity control of control systems and the results of research of control systems based on their similarity are presented. The similarity control of systems includes the current evaluation of the degree of similarity of control systems and the development of actions controlling similarity, and the corresponding targeted change in the state of any element of control systems.

A lognormal distribution of the lengths of terminal twigs on self-similar branches of elm trees.

PubMed

Koyama, Kohei; Yamamoto, Ken; Ushio, Masayuki

2017-01-11

Lognormal distributions and self-similarity are characteristics associated with a wide range of biological systems. The sequential breakage model has established a link between lognormal distributions and self-similarity and has been used to explain species abundance distributions. To date, however, there has been no similar evidence in studies of multicellular organismal forms. We tested the hypotheses that the distribution of the lengths of terminal stems of Japanese elm trees (Ulmus davidiana), the end products of a self-similar branching process, approaches a lognormal distribution. We measured the length of the stem segments of three elm branches and obtained the following results: (i) each occurrence of branching caused variations or errors in the lengths of the child stems relative to their parent stems; (ii) the branches showed statistical self-similarity; the observed error distributions were similar at all scales within each branch and (iii) the multiplicative effect of these errors generated variations of the lengths of terminal twigs that were well approximated by a lognormal distribution, although some statistically significant deviations from strict lognormality were observed for one branch. Our results provide the first empirical evidence that statistical self-similarity of an organismal form generates a lognormal distribution of organ sizes. © 2017 The Author(s).

SSL: Signal Similarity-Based Localization for Ocean Sensor Networks.

PubMed

Chen, Pengpeng; Ma, Honglu; Gao, Shouwan; Huang, Yan

2015-11-24

Nowadays, wireless sensor networks are often deployed on the sea surface for ocean scientific monitoring. One of the important challenges is to localize the nodes' positions. Existing localization schemes can be roughly divided into two types: range-based and range-free. The range-based localization approaches heavily depend on extra hardware capabilities, while range-free ones often suffer from poor accuracy and low scalability, far from the practical ocean monitoring applications. In response to the above limitations, this paper proposes a novel signal similarity-based localization (SSL) technology, which localizes the nodes' positions by fully utilizing the similarity of received signal strength and the open-air characteristics of the sea surface. In the localization process, we first estimate the relative distance between neighboring nodes through comparing the similarity of received signal strength and then calculate the relative distance for non-neighboring nodes with the shortest path algorithm. After that, the nodes' relative relation map of the whole network can be obtained. Given at least three anchors, the physical locations of nodes can be finally determined based on the multi-dimensional scaling (MDS) technology. The design is evaluated by two types of ocean experiments: a zonal network and a non-regular network using 28 nodes. Results show that the proposed design improves the localization accuracy compared to typical connectivity-based approaches and also confirm its effectiveness for large-scale ocean sensor networks.

Similar survival of patients with multiple versus single primary melanomas based on Utah Surveillance, Epidemiology, and End Results data (1973-2011).

PubMed

Grossman, Douglas; Farnham, James M; Hyngstrom, John; Klapperich, Marki E; Secrest, Aaron M; Empey, Sarah; Bowen, Glen M; Wada, David; Andtbacka, Robert H I; Grossmann, Kenneth; Bowles, Tawnya L; Cannon-Albright, Lisa A

2018-03-01

Survival data are mixed comparing patients with multiple primary melanomas (MPM) to those with single primary melanomas (SPM). We compared MPM versus SPM patient survival using a matching method that avoids potential biases associated with other analytic approaches. Records of 14,138 individuals obtained from the Surveillance, Epidemiology, and End Results registry of all melanomas diagnosed or treated in Utah between 1973 and 2011 were reviewed. A single matched control patient was selected randomly from the SPM cohort for each MPM patient, with the restriction that they survived at least as long as the interval between the first and second diagnoses for the matched MPM patient. Survival curves (n = 887 for both MPM and SPM groups) without covariates showed a significant survival disadvantage for MPM patients (chi-squared 39.29, P < .001). However, a multivariate Cox proportional hazards model showed no significant survival difference (hazard ratio 1.07, P = .55). Restricting the multivariate analysis to invasive melanomas also showed no significant survival difference (hazard ratio 0.99, P = .96). Breslow depth, ulceration status, and specific cause of death were not available for all patients. Patients with MPM had similar survival times as patients with SPM. Copyright © 2018 American Academy of Dermatology, Inc. Published by Elsevier Inc. All rights reserved.

Econo-ESA in semantic text similarity.

PubMed

Rahutomo, Faisal; Aritsugi, Masayoshi

2014-01-01

Explicit semantic analysis (ESA) utilizes an immense Wikipedia index matrix in its interpreter part. This part of the analysis multiplies a large matrix by a term vector to produce a high-dimensional concept vector. A similarity measurement between two texts is performed between two concept vectors with numerous dimensions. The cost is expensive in both interpretation and similarity measurement steps. This paper proposes an economic scheme of ESA, named econo-ESA. We investigate two aspects of this proposal: dimensional reduction and experiments with various data. We use eight recycling test collections in semantic text similarity. The experimental results show that both the dimensional reduction and test collection characteristics can influence the results. They also show that an appropriate concept reduction of econo-ESA can decrease the cost with minor differences in the results from the original ESA.

Comparison of Theoretical Stresses and Deflections of Multicell Wings with Experimental Results Obtained from Plastic Models

NASA Technical Reports Server (NTRS)

Zender, George W

1956-01-01

The experimental deflections and stresses of six plastic multicell-wing models of unswept, delta, and swept plan form are presented and compared with previously published theoretical results obtained by the electrical analog method. The comparisons indicate that the theory is reliable except for the evaluation of stresses in the vicinity of the leading edge of delta wings and the leading and trailing edges of swept wings. The stresses in these regions are questionable, apparently because of simplifications employed in idealizing the actual structure for theoretical purposes and because of local effects of concentrated loads.

Similarity solutions of some two-space-dimensional nonlinear wave evolution equations

NASA Technical Reports Server (NTRS)

Redekopp, L. G.

1980-01-01

Similarity reductions of the two-space-dimensional versions of the Korteweg-de Vries, modified Korteweg-de Vries, Benjamin-Davis-Ono, and nonlinear Schroedinger equations are presented, and some solutions of the reduced equations are discussed. Exact dispersive solutions of the two-dimensional Korteweg-de Vries equation are obtained, and the similarity solution of this equation is shown to be reducible to the second Painleve transcendent.

Similar call signs

DOT National Transportation Integrated Search

2010-08-18

This presentation was given at the Partnership for Safety Meeting in Washington, DC. It examines the similarities that are found when calls signs are visually similar or similar sounding. Visually similar call signs increase the chances of controller...

Eyes on crowding: crowding is preserved when responding by eye and similarly affects identity and position accuracy.

PubMed

Yildirim, Funda; Meyer, Vincent; Cornelissen, Frans W

2015-02-16

Peripheral vision guides recognition and selection of targets for eye movements. Crowding—a decline in recognition performance that occurs when a potential target is surrounded by other, similar, objects—influences peripheral object recognition. A recent model study suggests that crowding may be due to increased uncertainty about both the identity and the location of peripheral target objects, but very few studies have assessed these properties in tandem. Eye tracking can integrally provide information on both the perceived identity and the position of a target and therefore could become an important approach in crowding studies. However, recent reports suggest that around the moment of saccade preparation crowding may be significantly modified. If these effects were to generalize to regular crowding tasks, it would complicate the interpretation of results obtained with eye tracking and the comparison to results obtained using manual responses. For this reason, we first assessed whether the manner by which participants responded—manually or by eye—affected their performance. We found that neither recognition performance nor response time was affected by the response type. Hence, we conclude that crowding magnitude was preserved when observers responded by eye. In our main experiment, observers made eye movements to the location of a tilted Gabor target while we varied flanker tilt to manipulate target-flanker similarity. The results indicate that this similarly affected the accuracy of peripheral recognition and saccadic target localization. Our results inform about the importance of both location and identity uncertainty in crowding. © 2015 ARVO.

Method of synthesis of abstract images with high self-similarity

NASA Astrophysics Data System (ADS)

Matveev, Nikolay V.; Shcheglov, Sergey A.; Romanova, Galina E.; Koneva, Ð.¢atiana A.

2017-06-01

Abstract images with high self-similarity could be used for drug-free stress therapy. This based on the fact that a complex visual environment has a high affective appraisal. To create such an image we can use the setup based on the three laser sources of small power and different colors (Red, Green, Blue), the image is the pattern resulting from the reflecting and refracting by the complicated form object placed into the laser ray paths. The images were obtained experimentally which showed the good therapy effect. However, to find and to choose the object which gives needed image structure is very difficult and requires many trials. The goal of the work is to develop a method and a procedure of finding the object form which if placed into the ray paths can provide the necessary structure of the image In fact the task means obtaining the necessary irradiance distribution on the given surface. Traditionally such problems are solved using the non-imaging optics methods. In the given case this task is very complicated because of the complicated structure of the illuminance distribution and its high non-linearity. Alternative way is to use the projected image of a mask with a given structure. We consider both ways and discuss how they can help to speed up the synthesis procedure for the given abstract image of the high self-similarity for the setups of drug-free therapy.

Some Effects of Similarity Self-Disclosure

ERIC Educational Resources Information Center

Murphy, Kevin C.; Strong, Stanley R.

1972-01-01

College males were interviewed about how college had altered their friendships, values, and plans. The interviewers diclosed experiences and feelings similar to those revealed by the students. Results support Byrne's Law of Similarity in generating interpersonal attraction in the interview and suggest that the timing of self-disclosures is…

Apparent multifractality of self-similar Lévy processes

NASA Astrophysics Data System (ADS)

Zamparo, Marco

2017-07-01

Scaling properties of time series are usually studied in terms of the scaling laws of empirical moments, which are the time average estimates of moments of the dynamic variable. Nonlinearities in the scaling function of empirical moments are generally regarded as a sign of multifractality in the data. We show that, except for the Brownian motion, this method fails to disclose the correct monofractal nature of self-similar Lévy processes. We prove that for this class of processes it produces apparent multifractality characterised by a piecewise-linear scaling function with two different regimes, which match at the stability index of the considered process. This result is motivated by previous numerical evidence. It is obtained by introducing an appropriate stochastic normalisation which is able to cure empirical moments, without hiding their dependence on time, when moments they aim at estimating do not exist.

Picosecond laser welding of similar and dissimilar materials.

PubMed

Carter, Richard M; Chen, Jianyong; Shephard, Jonathan D; Thomson, Robert R; Hand, Duncan P

2014-07-01

We report picosecond laser welding of similar and dissimilar materials based on plasma formation induced by a tightly focused beam from a 1030 nm, 10 ps, 400 kHz laser system. Specifically, we demonstrate the welding of fused silica, borosilicate, and sapphire to a range of materials including borosilicate, fused silica, silicon, copper, aluminum, and stainless steel. Dissimilar material welding of glass to aluminum and stainless steel has not been previously reported. Analysis of the borosilicate-to-borosilicate weld strength compares well to those obtained using similar welding systems based on femtosecond lasers. There is, however, a strong requirement to prepare surfaces to a high (10-60 nm Ra) flatness to ensure a successful weld.

Evaluation of a statistics-based Ames mutagenicity QSAR model and interpretation of the results obtained.

PubMed

Barber, Chris; Cayley, Alex; Hanser, Thierry; Harding, Alex; Heghes, Crina; Vessey, Jonathan D; Werner, Stephane; Weiner, Sandy K; Wichard, Joerg; Giddings, Amanda; Glowienke, Susanne; Parenty, Alexis; Brigo, Alessandro; Spirkl, Hans-Peter; Amberg, Alexander; Kemper, Ray; Greene, Nigel

2016-04-01

The relative wealth of bacterial mutagenicity data available in the public literature means that in silico quantitative/qualitative structure activity relationship (QSAR) systems can readily be built for this endpoint. A good means of evaluating the performance of such systems is to use private unpublished data sets, which generally represent a more distinct chemical space than publicly available test sets and, as a result, provide a greater challenge to the model. However, raw performance metrics should not be the only factor considered when judging this type of software since expert interpretation of the results obtained may allow for further improvements in predictivity. Enough information should be provided by a QSAR to allow the user to make general, scientifically-based arguments in order to assess and overrule predictions when necessary. With all this in mind, we sought to validate the performance of the statistics-based in vitro bacterial mutagenicity prediction system Sarah Nexus (version 1.1) against private test data sets supplied by nine different pharmaceutical companies. The results of these evaluations were then analysed in order to identify findings presented by the model which would be useful for the user to take into consideration when interpreting the results and making their final decision about the mutagenic potential of a given compound. Copyright © 2015 Elsevier Inc. All rights reserved.

Counterfactual Plausibility and Comparative Similarity.

PubMed

Stanley, Matthew L; Stewart, Gregory W; Brigard, Felipe De

2017-05-01

Counterfactual thinking involves imagining hypothetical alternatives to reality. Philosopher David Lewis (1973, 1979) argued that people estimate the subjective plausibility that a counterfactual event might have occurred by comparing an imagined possible world in which the counterfactual statement is true against the current, actual world in which the counterfactual statement is false. Accordingly, counterfactuals considered to be true in possible worlds comparatively more similar to ours are judged as more plausible than counterfactuals deemed true in possible worlds comparatively less similar. Although Lewis did not originally develop his notion of comparative similarity to be investigated as a psychological construct, this study builds upon his idea to empirically investigate comparative similarity as a possible psychological strategy for evaluating the perceived plausibility of counterfactual events. More specifically, we evaluate judgments of comparative similarity between episodic memories and episodic counterfactual events as a factor influencing people's judgments of plausibility in counterfactual simulations, and we also compare it against other factors thought to influence judgments of counterfactual plausibility, such as ease of simulation and prior simulation. Our results suggest that the greater the perceived similarity between the original memory and the episodic counterfactual event, the greater the perceived plausibility that the counterfactual event might have occurred. While similarity between actual and counterfactual events, ease of imagining, and prior simulation of the counterfactual event were all significantly related to counterfactual plausibility, comparative similarity best captured the variance in ratings of counterfactual plausibility. Implications for existing theories on the determinants of counterfactual plausibility are discussed. Copyright © 2016 Cognitive Science Society, Inc.

The relative ease of obtaining a dermatologic appointment in Boston: how methods drive results.

PubMed

Weingold, David Howard; Lack, Michael Dweight; Yanowitz, Karen Leslie

2009-06-01

Recent reports have indicated long wait times for dermatologic appointments even for changing moles. Our objective was to determine the wait time for a person willing to make multiple calls and accept an appointment from any dermatologist at any satellite location for a changing mole from a dermatologist who advertised in a Boston, MA, telephone book. We telephoned each practice listed in a Boston, MA, telephone book. Patients making one call to each dermatologic practice on average obtained an appointment in 18 days. Patients calling two practices were offered an appointment on average in 7 days. Patients calling 3 practices were also offered an appointment in 1 week. We only telephoned practices listed in a Boston, MA, telephone book and we only surveyed one urban area. These results suggest that a reasonable concerned patient who was willing to make multiple calls to different providers in Boston, MA, can be seen in a timely fashion.

Proteins with similar architecture exhibit similar large-scale dynamic behavior.

PubMed Central

Keskin, O; Jernigan, R L; Bahar, I

2000-01-01

We have investigated the similarities and differences in the computed dynamic fluctuations exhibited by six members of a protein fold family with a coarse-grained Gaussian network model. Specifically, we consider the cofactor binding fragment of CysB; the lysine/arginine/ornithine-binding protein (LAO); the enzyme porphobilinogen deaminase (PBGD); the ribose-binding protein (RBP); the N-terminal lobe of ovotransferrin in apo-form (apo-OVOT); and the leucine/isoleucine/valine-binding protein (LIVBP). All have domains that resemble a Rossmann fold, but there are also some significant differences. Results indicate that similar global dynamic behavior is preserved for the members of a fold family, and that differences usually occur in regions only where specific function is localized. The present work is a computational demonstration that the scaffold of a protein fold may be utilized for diverse purposes. LAO requires a bound ligand before it conforms to the large-scale fluctuation behavior of the three other members of the family, CysB, PBGD, and RBP, all of which contain a substrate (cofactor) at the active site cleft. The dynamics of the ligand-free enzymes LIVBP and apo-OVOT, on the other hand, concur with that of unliganded LAO. The present results suggest that it is possible to construct structure alignments based on dynamic fluctuation behavior. PMID:10733987

A topic clustering approach to finding similar questions from large question and answer archives.

PubMed

Zhang, Wei-Nan; Liu, Ting; Yang, Yang; Cao, Liujuan; Zhang, Yu; Ji, Rongrong

2014-01-01

With the blooming of Web 2.0, Community Question Answering (CQA) services such as Yahoo! Answers (http://answers.yahoo.com), WikiAnswer (http://wiki.answers.com), and Baidu Zhidao (http://zhidao.baidu.com), etc., have emerged as alternatives for knowledge and information acquisition. Over time, a large number of question and answer (Q&A) pairs with high quality devoted by human intelligence have been accumulated as a comprehensive knowledge base. Unlike the search engines, which return long lists of results, searching in the CQA services can obtain the correct answers to the question queries by automatically finding similar questions that have already been answered by other users. Hence, it greatly improves the efficiency of the online information retrieval. However, given a question query, finding the similar and well-answered questions is a non-trivial task. The main challenge is the word mismatch between question query (query) and candidate question for retrieval (question). To investigate this problem, in this study, we capture the word semantic similarity between query and question by introducing the topic modeling approach. We then propose an unsupervised machine-learning approach to finding similar questions on CQA Q&A archives. The experimental results show that our proposed approach significantly outperforms the state-of-the-art methods.

Bench press and push-up at comparable levels of muscle activity results in similar strength gains.

PubMed

Calatayud, Joaquin; Borreani, Sebastien; Colado, Juan C; Martin, Fernando; Tella, Victor; Andersen, Lars L

2015-01-01

Electromyography (EMG) exercise evaluation is commonly used to measure the intensity of muscle contraction. Although researchers assume that biomechanically comparable resistance exercises with similar high EMG levels will produce similar strength gains over the long term, no studies have actually corroborated this hypothesis. This study evaluated EMG levels during 6 repetition maximum (6RM) bench press and push-up, and subsequently performed a 5-week training period where subjects were randomly divided into 3 groups (i.e., 6RM bench press group, 6RM elastic band push-up group, or control group) to evaluate muscle strength gains. Thirty university students with advanced resistance training experience participated in the 2-part study. During the training period, exercises were performed using the same loads and variables that were used during the EMG data collection. At baseline, EMG amplitude showed no significant difference between 6RM bench press and band push-up. Significant differences among the groups were found for percent change (Δ) between pretest and posttest for 6RM (p = 0.017) and for 1 repetition maximum (1RM) (p < 0.001). Six repetition maximum bench press group and 6RM elastic band push-up group improved their 1RM and 6RM (Δ ranging from 13.65 to 22.21) tests significantly with similar gains, whereas control group remains unchanged. Thus, when the EMG values are comparable and the same conditions are reproduced, the aforementioned exercises can provide similar muscle strength gains.

Saturn gravity results obtained from Pioneer 11 tracking data and earth-based Saturn satellite data

NASA Technical Reports Server (NTRS)

Null, G. W.; Lau, E. L.; Biller, E. D.; Anderson, J. D.

1981-01-01

Improved gravity coefficients for Saturn, its satellites and rings are calculated on the basis of a combination of Pioneer 11 spacecraft Doppler tracking data and earth-based determinations of Saturn natural satellite apse and node rates. Solutions are first obtained separately from the coherent Doppler tracking data obtained for the interval from August 20 to September 4, surrounding the time of closest approach, with the effects of solar plasma on radio signal propagation taken into account, and from secular rates for Mimas, Enceladus, Tethys, Dione, Rhea and Titan determined from astrometric data by Kozai (1957, 1976) and Garcia (1972). Combination of the data by the use of the Pioneer solution and corresponding unadjusted covariance matrix as a priori information for a secular rate analysis results in values for the total ring mass of essentially zero at a standard error level of 1.7 x 10 to the -6th Saturn masses, a ratio of solar mass to that of the Saturn system of 3498.09 + or - 0.22, masses of Rhea, Titan and Iapetus of 4.0 + or - 0.9, 238.8 + or - 3, and 3.4 + or - 1.3 x 10 to the -6th Saturn masses, respectively, and second and fourth zonal harmonics of 16,479 + or - 18 and -937 + or - 38, respectively. The harmonic coefficients are noted to be important as boundary conditions in the modeling of the Saturn interior.

Interdependency in Multimodel Climate Projections: Component Replication and Result Similarity

NASA Astrophysics Data System (ADS)

Boé, Julien

2018-03-01

Multimodel ensembles are the main way to deal with model uncertainties in climate projections. However, the interdependencies between models that often share entire components make it difficult to combine their results in a satisfactory way. In this study, how the replication of components (atmosphere, ocean, land, and sea ice) between climate models impacts the proximity of their results is quantified precisely, in terms of climatological means and future changes. A clear relationship exists between the number of components shared by climate models and the proximity of their results. Even the impact of a single shared component is generally visible. These conclusions are true at both the global and regional scales. Given available data, it cannot be robustly concluded that some components are more important than others. Those results provide ways to estimate model interdependencies a priori rather than a posteriori based on their results, in order to define independence weights.

BIOSSES: a semantic sentence similarity estimation system for the biomedical domain.

PubMed

Sogancioglu, Gizem; Öztürk, Hakime; Özgür, Arzucan

2017-07-15

The amount of information available in textual format is rapidly increasing in the biomedical domain. Therefore, natural language processing (NLP) applications are becoming increasingly important to facilitate the retrieval and analysis of these data. Computing the semantic similarity between sentences is an important component in many NLP tasks including text retrieval and summarization. A number of approaches have been proposed for semantic sentence similarity estimation for generic English. However, our experiments showed that such approaches do not effectively cover biomedical knowledge and produce poor results for biomedical text. We propose several approaches for sentence-level semantic similarity computation in the biomedical domain, including string similarity measures and measures based on the distributed vector representations of sentences learned in an unsupervised manner from a large biomedical corpus. In addition, ontology-based approaches are presented that utilize general and domain-specific ontologies. Finally, a supervised regression based model is developed that effectively combines the different similarity computation metrics. A benchmark data set consisting of 100 sentence pairs from the biomedical literature is manually annotated by five human experts and used for evaluating the proposed methods. The experiments showed that the supervised semantic sentence similarity computation approach obtained the best performance (0.836 correlation with gold standard human annotations) and improved over the state-of-the-art domain-independent systems up to 42.6% in terms of the Pearson correlation metric. A web-based system for biomedical semantic sentence similarity computation, the source code, and the annotated benchmark data set are available at: http://tabilab.cmpe.boun.edu.tr/BIOSSES/ . gizemsogancioglu@gmail.com or arzucan.ozgur@boun.edu.tr. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e

Measurement results obtained from air quality monitoring system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Turzanski, P.K.; Beres, R.

1995-12-31

An automatic system of air pollution monitoring operates in Cracow since 1991. The organization, assembling and start-up of the network is a result of joint efforts of the US Environmental Protection Agency and the Cracow environmental protection service. At present the automatic monitoring network is operated by the Provincial Inspection of Environmental Protection. There are in total seven stationary stations situated in Cracow to measure air pollution. These stations are supported continuously by one semi-mobile (transportable) station. It allows to modify periodically the area under investigation and therefore the 3-dimensional picture of creation and distribution of air pollutants within Cracowmore » area could be more intelligible.« less

Similarity Metrics for Closed Loop Dynamic Systems

NASA Technical Reports Server (NTRS)

Whorton, Mark S.; Yang, Lee C.; Bedrossian, Naz; Hall, Robert A.

2008-01-01

To what extent and in what ways can two closed-loop dynamic systems be said to be "similar?" This question arises in a wide range of dynamic systems modeling and control system design applications. For example, bounds on error models are fundamental to the controller optimization with modern control design methods. Metrics such as the structured singular value are direct measures of the degree to which properties such as stability or performance are maintained in the presence of specified uncertainties or variations in the plant model. Similarly, controls-related areas such as system identification, model reduction, and experimental model validation employ measures of similarity between multiple realizations of a dynamic system. Each area has its tools and approaches, with each tool more or less suited for one application or the other. Similarity in the context of closed-loop model validation via flight test is subtly different from error measures in the typical controls oriented application. Whereas similarity in a robust control context relates to plant variation and the attendant affect on stability and performance, in this context similarity metrics are sought that assess the relevance of a dynamic system test for the purpose of validating the stability and performance of a "similar" dynamic system. Similarity in the context of system identification is much more relevant than are robust control analogies in that errors between one dynamic system (the test article) and another (the nominal "design" model) are sought for the purpose of bounding the validity of a model for control design and analysis. Yet system identification typically involves open-loop plant models which are independent of the control system (with the exception of limited developments in closed-loop system identification which is nonetheless focused on obtaining open-loop plant models from closed-loop data). Moreover the objectives of system identification are not the same as a flight test and

Concentration dependence and self-similarity of photodarkening losses induced in Yb-doped fibers by comparable excitation.

PubMed

Taccheo, Stefano; Gebavi, Hrvoje; Monteville, Achille; Le Goffic, Olivier; Landais, David; Mechin, David; Tregoat, Denis; Cadier, Benoit; Robin, Thierry; Milanese, Daniel; Durrant, Tim

2011-09-26

We report on an extensive investigation of photodarkening in Yb-doped silica fibers. A set of similar fibers, covering a large Yb concentration range, was made so as to compare the photodarkening induced losses. Careful measurements were made to ensure equal and uniform inversion for all the tested fibers. The results show that, with the specific set-up, the stretching parameter obtained through fitting has a very limited variation. This gives more meaning to the fitting parameters. Results tend to indicate a square law dependence of the concentration of excited ions on the final saturated loss. We also demonstrate self-similarity of loss evolution when experimental curves are simply normalized to fitting parameters. This evidence of self-similarity also supports the possibility of introducing a preliminary figure of merit for Yb-doped fiber. This will allow the impact of photodarkening on laser/amplifier devices to be evaluated. © 2011 Optical Society of America

The self-similarly expanding Eshelby ellipsoidal inclusion: II. The Dynamic Eshelby Tensor for the expanding sphere

NASA Astrophysics Data System (ADS)

Ni, Luqun; Markenscoff, Xanthippi

2016-11-01

The field solution of a self-similarly (subsonically) expanding Eshelby ellipsoidal inclusion obtained in Part I is evaluated for the case of the expanding spherical inclusion under general uniform eigenstrain ɛij* in self-similar motion R = υt, starting from zero dimension. The particle velocity in the interior domain vanishes and the displacement gradient is constant exhibiting the Eshelby property in the self-similar dynamic case. All components of the interior and exterior Dynamic Eshelby Tensor are obtained for the sphere, with the interior ones depending on the wave speeds and the expansion speed of the inclusion, while the exterior ones depend, in addition, on the variable of self-similarity r / t and the direction of the field point. By a limiting procedure the static Eshelby tensor both interior and exterior is retrieved, thus making the static inclusion a special limit of the dynamic self-similarly expanding one. The jump of the particle velocity across the moving inclusion boundary is obtained, and it depends only on the wave and expansion speeds and the direction of the normal.

When is Chemical Similarity Significant? The Statistical Distribution of Chemical Similarity Scores and Its Extreme Values

PubMed Central

Baldi, Pierre

2010-01-01

As repositories of chemical molecules continue to expand and become more open, it becomes increasingly important to develop tools to search them efficiently and assess the statistical significance of chemical similarity scores. Here we develop a general framework for understanding, modeling, predicting, and approximating the distribution of chemical similarity scores and its extreme values in large databases. The framework can be applied to different chemical representations and similarity measures but is demonstrated here using the most common binary fingerprints with the Tanimoto similarity measure. After introducing several probabilistic models of fingerprints, including the Conditional Gaussian Uniform model, we show that the distribution of Tanimoto scores can be approximated by the distribution of the ratio of two correlated Normal random variables associated with the corresponding unions and intersections. This remains true also when the distribution of similarity scores is conditioned on the size of the query molecules in order to derive more fine-grained results and improve chemical retrieval. The corresponding extreme value distributions for the maximum scores are approximated by Weibull distributions. From these various distributions and their analytical forms, Z-scores, E-values, and p-values are derived to assess the significance of similarity scores. In addition, the framework allows one to predict also the value of standard chemical retrieval metrics, such as Sensitivity and Specificity at fixed thresholds, or ROC (Receiver Operating Characteristic) curves at multiple thresholds, and to detect outliers in the form of atypical molecules. Numerous and diverse experiments carried in part with large sets of molecules from the ChemDB show remarkable agreement between theory and empirical results. PMID:20540577

SCPRED: Accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences

PubMed Central

Kurgan, Lukasz; Cios, Krzysztof; Chen, Ke

2008-01-01

Background Protein structure prediction methods provide accurate results when a homologous protein is predicted, while poorer predictions are obtained in the absence of homologous templates. However, some protein chains that share twilight-zone pairwise identity can form similar folds and thus determining structural similarity without the sequence similarity would be desirable for the structure prediction. The folding type of a protein or its domain is defined as the structural class. Current structural class prediction methods that predict the four structural classes defined in SCOP provide up to 63% accuracy for the datasets in which sequence identity of any pair of sequences belongs to the twilight-zone. We propose SCPRED method that improves prediction accuracy for sequences that share twilight-zone pairwise similarity with sequences used for the prediction. Results SCPRED uses a support vector machine classifier that takes several custom-designed features as its input to predict the structural classes. Based on extensive design that considers over 2300 index-, composition- and physicochemical properties-based features along with features based on the predicted secondary structure and content, the classifier's input includes 8 features based on information extracted from the secondary structure predicted with PSI-PRED and one feature computed from the sequence. Tests performed with datasets of 1673 protein chains, in which any pair of sequences shares twilight-zone similarity, show that SCPRED obtains 80.3% accuracy when predicting the four SCOP-defined structural classes, which is superior when compared with over a dozen recent competing methods that are based on support vector machine, logistic regression, and ensemble of classifiers predictors. Conclusion The SCPRED can accurately find similar structures for sequences that share low identity with sequence used for the prediction. The high predictive accuracy achieved by SCPRED is attributed to the design of

Prepubertal goat oocytes from large follicles result in similar blastocyst production and embryo ploidy than those from adult goats.

PubMed

Romaguera, R; Moll, X; Morató, R; Roura, M; Palomo, M J; Catalá, M G; Jiménez-Macedo, A R; Hammami, S; Izquierdo, D; Mogas, T; Paramio, M T

2011-07-01

Developmental competence of oocytes from prepubertal females is lower than those from adult females. Oocyte development competence is positively related to follicular diameter. Most of the follicles of prepubertal goat ovaries are smaller than 3 mm. The aim of this study was to compare oocytes of two follicle sizes (< 3 mm and ≥ 3 mm) from prepubertal goats with oocytes from adult goats in relation to their in vitro production and quality of blastocysts. Oocytes from prepubertal goats were obtained from slaughterhouse ovaries and selected according to the follicle diameter whereas oocytes from adult goats were recovered in vivo by LOPU technique without prior selection of follicle size. COCs were IVM for 27 h, IVF at the conventional conditions with fresh semen and presumptive zygotes were cultured in SOF medium for 8 days. Blastocysts obtained were vitrified and after warming their blastocoele re-expansion and the ploidy by FISH technique were assessed. We found significant differences between blastocysts yield of oocytes recovered from follicles smaller than 3 mm of prepubertal goats compared to those from adult goats (5.45% vs 20. 83%, respectively) however, these differences disappear if oocytes were recovered form large follicles (18.07%). A total of 28 blastocysts were analysed and 96.43% showed mixoploidy. Age did not affect the number of embryos with abnormal ploidy or blastocyst re-expansion after warming. Furthermore, the percentage of diploid blastomeres per embryo was similar in the 3 groups studied, adult, prepubertal from follicles ≥ 3 mm and < 3 mm (68.6%, 80.8% and 73.6%, respectively). In conclusion, IVP of blastocysts coming from follicles larger than 3 mm of goats 45 days old were not different to the blastocysts produced from adult goats, both in terms of quantity and quality. Copyright © 2011 Elsevier Inc. All rights reserved.

Experimental Results Obtained with Air Liquide Cold Compression System: CERN LHC and SNS Projects

NASA Astrophysics Data System (ADS)

Delcayre, F.; Courty, J.-C.; Hamber, F.; Hilbert, B.; Monneret, E.; Toia, J.-L.

2006-04-01

Large scale collider facilities will make intensive use of superconducting magnets, operating below 2.0 K. This dictates high-capacity refrigeration systems operating below 2.0 K. These systems, making use of cryogenic centrifugal compressors in a series arrangement with room temperature screw compressors will be coupled to a refrigerator, providing a certain power at 4.5 K. A first Air Liquide Cold Compression System (CCS) unit was built and delivered to CERN in 2001. Installed at the beginning of 2002, it was commissioned and tested successfully during year 2002. A series of four sets of identical CCS were then tested in 2004. Another set of four cryogenic centrifugal compressors (CCC) has been delivered to Thomas Jefferson National Accelerator Facility (JLAB) for the Spallation Neutron Source (SNS) in 2002. These compressors were tested and commissioned from December 2004 to July 2005. The experimental results obtained with these systems will be presented and discussed: the characteristics of the CCC will be detailed. The principles of control for the CCC in series will be detailed.

Stability of similarity measurements for bipartite networks

PubMed Central

Liu, Jian-Guo; Hou, Lei; Pan, Xue; Guo, Qiang; Zhou, Tao

2016-01-01

Similarity is a fundamental measure in network analyses and machine learning algorithms, with wide applications ranging from personalized recommendation to socio-economic dynamics. We argue that an effective similarity measurement should guarantee the stability even under some information loss. With six bipartite networks, we investigate the stabilities of fifteen similarity measurements by comparing the similarity matrixes of two data samples which are randomly divided from original data sets. Results show that, the fifteen measurements can be well classified into three clusters according to their stabilities, and measurements in the same cluster have similar mathematical definitions. In addition, we develop a top-n-stability method for personalized recommendation, and find that the unstable similarities would recommend false information to users, and the performance of recommendation would be largely improved by using stable similarity measurements. This work provides a novel dimension to analyze and evaluate similarity measurements, which can further find applications in link prediction, personalized recommendation, clustering algorithms, community detection and so on. PMID:26725688

Stability of similarity measurements for bipartite networks.

PubMed

Liu, Jian-Guo; Hou, Lei; Pan, Xue; Guo, Qiang; Zhou, Tao

2016-01-04

Similarity is a fundamental measure in network analyses and machine learning algorithms, with wide applications ranging from personalized recommendation to socio-economic dynamics. We argue that an effective similarity measurement should guarantee the stability even under some information loss. With six bipartite networks, we investigate the stabilities of fifteen similarity measurements by comparing the similarity matrixes of two data samples which are randomly divided from original data sets. Results show that, the fifteen measurements can be well classified into three clusters according to their stabilities, and measurements in the same cluster have similar mathematical definitions. In addition, we develop a top-n-stability method for personalized recommendation, and find that the unstable similarities would recommend false information to users, and the performance of recommendation would be largely improved by using stable similarity measurements. This work provides a novel dimension to analyze and evaluate similarity measurements, which can further find applications in link prediction, personalized recommendation, clustering algorithms, community detection and so on.

Optimal Threshold Determination for Interpreting Semantic Similarity and Particularity: Application to the Comparison of Gene Sets and Metabolic Pathways Using GO and ChEBI

PubMed Central

Bettembourg, Charles; Diot, Christian; Dameron, Olivier

2015-01-01

Background The analysis of gene annotations referencing back to Gene Ontology plays an important role in the interpretation of high-throughput experiments results. This analysis typically involves semantic similarity and particularity measures that quantify the importance of the Gene Ontology annotations. However, there is currently no sound method supporting the interpretation of the similarity and particularity values in order to determine whether two genes are similar or whether one gene has some significant particular function. Interpretation is frequently based either on an implicit threshold, or an arbitrary one (typically 0.5). Here we investigate a method for determining thresholds supporting the interpretation of the results of a semantic comparison. Results We propose a method for determining the optimal similarity threshold by minimizing the proportions of false-positive and false-negative similarity matches. We compared the distributions of the similarity values of pairs of similar genes and pairs of non-similar genes. These comparisons were performed separately for all three branches of the Gene Ontology. In all situations, we found overlap between the similar and the non-similar distributions, indicating that some similar genes had a similarity value lower than the similarity value of some non-similar genes. We then extend this method to the semantic particularity measure and to a similarity measure applied to the ChEBI ontology. Thresholds were evaluated over the whole HomoloGene database. For each group of homologous genes, we computed all the similarity and particularity values between pairs of genes. Finally, we focused on the PPAR multigene family to show that the similarity and particularity patterns obtained with our thresholds were better at discriminating orthologs and paralogs than those obtained using default thresholds. Conclusion We developed a method for determining optimal semantic similarity and particularity thresholds. We applied

Self-Similar Compressible Free Vortices

NASA Technical Reports Server (NTRS)

vonEllenrieder, Karl

1998-01-01

Lie group methods are used to find both exact and numerical similarity solutions for compressible perturbations to all incompressible, two-dimensional, axisymmetric vortex reference flow. The reference flow vorticity satisfies an eigenvalue problem for which the solutions are a set of two-dimensional, self-similar, incompressible vortices. These solutions are augmented by deriving a conserved quantity for each eigenvalue, and identifying a Lie group which leaves the reference flow equations invariant. The partial differential equations governing the compressible perturbations to these reference flows are also invariant under the action of the same group. The similarity variables found with this group are used to determine the decay rates of the velocities and thermodynamic variables in the self-similar flows, and to reduce the governing partial differential equations to a set of ordinary differential equations. The ODE's are solved analytically and numerically for a Taylor vortex reference flow, and numerically for an Oseen vortex reference flow. The solutions are used to examine the dependencies of the temperature, density, entropy, dissipation and radial velocity on the Prandtl number. Also, experimental data on compressible free vortex flow are compared to the analytical results, the evolution of vortices from initial states which are not self-similar is discussed, and the energy transfer in a slightly-compressible vortex is considered.

Molecular similarity measures.

PubMed

Maggiora, Gerald M; Shanmugasundaram, Veerabahu

2011-01-01

Molecular similarity is a pervasive concept in chemistry. It is essential to many aspects of chemical reasoning and analysis and is perhaps the fundamental assumption underlying medicinal chemistry. Dissimilarity, the complement of similarity, also plays a major role in a growing number of applications of molecular diversity in combinatorial chemistry, high-throughput screening, and related fields. How molecular information is represented, called the representation problem, is important to the type of molecular similarity analysis (MSA) that can be carried out in any given situation. In this work, four types of mathematical structure are used to represent molecular information: sets, graphs, vectors, and functions. Molecular similarity is a pairwise relationship that induces structure into sets of molecules, giving rise to the concept of chemical space. Although all three concepts - molecular similarity, molecular representation, and chemical space - are treated in this chapter, the emphasis is on molecular similarity measures. Similarity measures, also called similarity coefficients or indices, are functions that map pairs of compatible molecular representations that are of the same mathematical form into real numbers usually, but not always, lying on the unit interval. This chapter presents a somewhat pedagogical discussion of many types of molecular similarity measures, their strengths and limitations, and their relationship to one another. An expanded account of the material on chemical spaces presented in the first edition of this book is also provided. It includes a discussion of the topography of activity landscapes and the role that activity cliffs in these landscapes play in structure-activity studies.

Prioritization of candidate disease genes by combining topological similarity and semantic similarity.

PubMed

Liu, Bin; Jin, Min; Zeng, Pan

2015-10-01

The identification of gene-phenotype relationships is very important for the treatment of human diseases. Studies have shown that genes causing the same or similar phenotypes tend to interact with each other in a protein-protein interaction (PPI) network. Thus, many identification methods based on the PPI network model have achieved good results. However, in the PPI network, some interactions between the proteins encoded by candidate gene and the proteins encoded by known disease genes are very weak. Therefore, some studies have combined the PPI network with other genomic information and reported good predictive performances. However, we believe that the results could be further improved. In this paper, we propose a new method that uses the semantic similarity between the candidate gene and known disease genes to set the initial probability vector of a random walk with a restart algorithm in a human PPI network. The effectiveness of our method was demonstrated by leave-one-out cross-validation, and the experimental results indicated that our method outperformed other methods. Additionally, our method can predict new causative genes of multifactor diseases, including Parkinson's disease, breast cancer and obesity. The top predictions were good and consistent with the findings in the literature, which further illustrates the effectiveness of our method. Copyright © 2015 Elsevier Inc. All rights reserved.

Lipid-enhancement of activated sludges obtained from conventional activated sludge and oxidation ditch processes.

PubMed

Revellame, Emmanuel D; Hernandez, Rafael; French, W Todd; Holmes, William E; Forks, Allison; Callahan, Robert

2013-11-01

Lipid-enhancement of activated sludges was conducted to increase the amount of saponifiable lipids in the sludges. The sludges were obtained from a conventional activated sludge (CAS) and an oxidation ditch process (ODP). Results showed 59-222% and 150-250% increase in saponifiable lipid content of the sludges from CAS and ODP, respectively. The fatty acid methyl ester (FAMEs) obtained from triacylglycerides was 57-67% (of total FAMEs) for enhanced CAS and 55-73% for enhanced ODP, a very significant improvement from 6% to 10% (CAS) and 4% to 8% (ODP). Regardless of the source, the enhancement resulted in sludges with similar fatty acid profile indicating homogenization of the lipids in the sludges. This study provides a potential strategy to utilize existing wastewater treatment facilities as source of significant amount of lipids for biofuel applications. Published by Elsevier Ltd.

Self-similarity of a Rayleigh–Taylor mixing layer at low Atwood number with a multimode initial perturbation

DOE PAGES

Morgan, B. E.; Olson, B. J.; White, J. E.; ...

2017-06-29

High-fidelity large eddy simulation (LES) of a low-Atwood number (A = 0.05) Rayleigh-Taylor mixing layer is performed using the tenth-order compact difference code Miranda. An initial multimode perturbation spectrum is specified in Fourier space as a function of mesh resolution such that a database of results is obtained in which each successive level of increased grid resolution corresponds approximately to one additional doubling of the mixing layer width, or generation. The database is then analyzed to determine approximate requirements for self-similarity, and a new metric is proposed to quantify how far a given simulation is from the limit of self-similarity.more » It is determined that mixing layer growth reaches a high degree of self-similarity after approximately 4.5 generations. Statistical convergence errors and boundary effects at late time, however, make it impossible to draw similar conclusions regarding the self-similar growth of more sensitive turbulence parameters. Finally, self-similar turbulence profiles from the LES database are compared with one-dimensional simulations using the k-L-a and BHR-2 Reynolds-averaged Navier-Stokes (RANS) models. The k-L-a model, which is calibrated to reproduce a quadratic turbulence kinetic energy profile for a self-similar mixing layer, is found to be in better agreement with the LES than BHR-2 results.« less

Self-similar pyramidal structures and signal reconstruction

NASA Astrophysics Data System (ADS)

Benedetto, John J.; Leon, Manuel; Saliani, Sandra

1998-03-01

Pyramidal structures are defined which are locally a combination of low and highpass filtering. The structures are analogous to but different from wavelet packet structures. In particular, new frequency decompositions are obtained; and these decompositions can be parameterized to establish a correspondence with a large class of Cantor sets. Further correspondences are then established to relate such frequency decompositions with more general self- similarities. The role of the filters in defining these pyramidal structures gives rise to signal reconstruction algorithms, and these, in turn, are used in the analysis of speech data.

A path-based measurement for human miRNA functional similarities using miRNA-disease associations

NASA Astrophysics Data System (ADS)

Ding, Pingjian; Luo, Jiawei; Xiao, Qiu; Chen, Xiangtao

2016-09-01

Compared with the sequence and expression similarity, miRNA functional similarity is so important for biology researches and many applications such as miRNA clustering, miRNA function prediction, miRNA synergism identification and disease miRNA prioritization. However, the existing methods always utilized the predicted miRNA target which has high false positive and false negative to calculate the miRNA functional similarity. Meanwhile, it is difficult to achieve high reliability of miRNA functional similarity with miRNA-disease associations. Therefore, it is increasingly needed to improve the measurement of miRNA functional similarity. In this study, we develop a novel path-based calculation method of miRNA functional similarity based on miRNA-disease associations, called MFSP. Compared with other methods, our method obtains higher average functional similarity of intra-family and intra-cluster selected groups. Meanwhile, the lower average functional similarity of inter-family and inter-cluster miRNA pair is obtained. In addition, the smaller p-value is achieved, while applying Wilcoxon rank-sum test and Kruskal-Wallis test to different miRNA groups. The relationship between miRNA functional similarity and other information sources is exhibited. Furthermore, the constructed miRNA functional network based on MFSP is a scale-free and small-world network. Moreover, the higher AUC for miRNA-disease prediction indicates the ability of MFSP uncovering miRNA functional similarity.

Incident CTS in a large pooled cohort study: associations obtained by a Job Exposure Matrix versus associations obtained from observed exposures.

PubMed

Dale, Ann Marie; Ekenga, Christine C; Buckner-Petty, Skye; Merlino, Linda; Thiese, Matthew S; Bao, Stephen; Meyers, Alysha Rose; Harris-Adamson, Carisa; Kapellusch, Jay; Eisen, Ellen A; Gerr, Fred; Hegmann, Kurt T; Silverstein, Barbara; Garg, Arun; Rempel, David; Zeringue, Angelique; Evanoff, Bradley A

2018-03-29

There is growing use of a job exposure matrix (JEM) to provide exposure estimates in studies of work-related musculoskeletal disorders; few studies have examined the validity of such estimates, nor did compare associations obtained with a JEM with those obtained using other exposures. This study estimated upper extremity exposures using a JEM derived from a publicly available data set (Occupational Network, O*NET), and compared exposure-disease associations for incident carpal tunnel syndrome (CTS) with those obtained using observed physical exposure measures in a large prospective study. 2393 workers from several industries were followed for up to 2.8 years (5.5 person-years). Standard Occupational Classification (SOC) codes were assigned to the job at enrolment. SOC codes linked to physical exposures for forceful hand exertion and repetitive activities were extracted from O*NET. We used multivariable Cox proportional hazards regression models to describe exposure-disease associations for incident CTS for individually observed physical exposures and JEM exposures from O*NET. Both exposure methods found associations between incident CTS and exposures of force and repetition, with evidence of dose-response. Observed associations were similar across the two methods, with somewhat wider CIs for HRs calculated using the JEM method. Exposures estimated using a JEM provided similar exposure-disease associations for CTS when compared with associations obtained using the 'gold standard' method of individual observation. While JEMs have a number of limitations, in some studies they can provide useful exposure estimates in the absence of individual-level observed exposures. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Regulatory challenges and approaches to characterize nanomedicines and their follow-on similars.

PubMed

Mühlebach, Stefan; Borchard, Gerrit; Yildiz, Selcan

2015-03-01

Nanomedicines are highly complex products and are the result of difficult to control manufacturing processes. Nonbiological complex drugs and their biological counterparts can comprise nanoparticles and therefore show nanomedicine characteristics. They consist of not fully known nonhomomolecular structures, and can therefore not be characterized by physicochemical means only. Also, intended copies of nanomedicines (follow-on similars) may have clinically meaningful differences, creating the regulatory challenge of how to grant a high degree of assurance for patients' benefit and safety. As an example, the current regulatory approach for marketing authorization of intended copies of nonbiological complex drugs appears inappropriate; also, a valid strategy incorporating the complexity of such systems is undefined. To demonstrate sufficient similarity and comparability, a stepwise quality, nonclinical and clinical approach is necessary to obtain market authorization for follow-on products as therapeutic alternatives, substitution and/or interchangeable products. To fill the regulatory gap, harmonized and science-based standards are needed.

Aircraft and ground vehicle friction measurements obtained under winter runway conditions

NASA Technical Reports Server (NTRS)

Yager, Thomas J.

1989-01-01

Tests with specially instrumented NASA B-737 and B-727 aircraft together with several different ground friction measuring devices have been conducted for a variety of runway surface types and wetness conditions. This effort is part of the Joint FAA/NASA Aircraft/Ground Vehicle Runway Friction Program aimed at obtaining a better understanding of aircraft ground handling performance under adverse weather conditions, and defining relationships between aircraft and ground vehicle tire friction measurements. Aircraft braking performance on dry, wet, snow-, and ice-covered runway conditions is discussed together with ground vehicle friction data obtained under similar runway conditions. For the wet, compacted snow- and ice-covered runway conditions, the relationship between ground vehicles and aircraft friction data is identified. The influence of major test parameters on friction measurements such as speed, test tire characteristics, and surface contaminant-type are discussed. The test results indicate that use of properly maintained and calibrated ground vehicles for monitoring runway friction conditions should be encouraged particularly under adverse weather conditions.

Engaging narratives evoke similar neural activity and lead to similar time perception.

PubMed

Cohen, Samantha S; Henin, Simon; Parra, Lucas C

2017-07-04

It is said that we lose track of time - that "time flies" - when we are engrossed in a story. How does engagement with the story cause this distorted perception of time, and what are its neural correlates? People commit both time and attentional resources to an engaging stimulus. For narrative videos, attentional engagement can be represented as the level of similarity between the electroencephalographic responses of different viewers. Here we show that this measure of neural engagement predicted the duration of time that viewers were willing to commit to narrative videos. Contrary to popular wisdom, engagement did not distort the average perception of time duration. Rather, more similar brain responses resulted in a more uniform perception of time across viewers. These findings suggest that by capturing the attention of an audience, narrative videos bring both neural processing and the subjective perception of time into synchrony.

Learning deep similarity in fundus photography

NASA Astrophysics Data System (ADS)

Chudzik, Piotr; Al-Diri, Bashir; Caliva, Francesco; Ometto, Giovanni; Hunter, Andrew

2017-02-01

Similarity learning is one of the most fundamental tasks in image analysis. The ability to extract similar images in the medical domain as part of content-based image retrieval (CBIR) systems has been researched for many years. The vast majority of methods used in CBIR systems are based on hand-crafted feature descriptors. The approximation of a similarity mapping for medical images is difficult due to the big variety of pixel-level structures of interest. In fundus photography (FP) analysis, a subtle difference in e.g. lesions and vessels shape and size can result in a different diagnosis. In this work, we demonstrated how to learn a similarity function for image patches derived directly from FP image data without the need of manually designed feature descriptors. We used a convolutional neural network (CNN) with a novel architecture adapted for similarity learning to accomplish this task. Furthermore, we explored and studied multiple CNN architectures. We show that our method can approximate the similarity between FP patches more efficiently and accurately than the state-of- the-art feature descriptors, including SIFT and SURF using a publicly available dataset. Finally, we observe that our approach, which is purely data-driven, learns that features such as vessels calibre and orientation are important discriminative factors, which resembles the way how humans reason about similarity. To the best of authors knowledge, this is the first attempt to approximate a visual similarity mapping in FP.

Evidence that pairing with genetically similar mates is maladaptive in a monogamous bird

USGS Publications Warehouse

Mulard, Hervé; Danchin, E.; Talbot, S.L.; Ramey, A.M.; Hatch, Shyla A.; White, J.F.; Helfenstein, F.; Wagner, R.H.

2009-01-01

Background. Evidence of multiple genetic criteria of mate choice is accumulating in numerous taxa. In many species, females have been shown to pair with genetically dissimilar mates or with extra-pair partners that are more genetically compatible than their social mates, thereby increasing their offsprings' heterozygosity which often correlates with offspring fitness. While most studies have focused on genetically promiscuous species, few studies have addressed genetically monogamous species, in which mate choice tends to be mutual. Results. Here, we used microsatellite markers to assess individual global heterozygosity and genetic similarity of pairs in a socially and genetically monogamous seabird, the black-legged kittiwake Rissa tridactyla. We found that pairs were more genetically dissimilar than expected by chance. We also identified fitness costs of breeding with genetically similar partners: (i) genetic similarity of pairs was negatively correlated with the number of chicks hatched, and (ii) offspring heterozygosity was positively correlated with growth rate and survival. Conclusion. These findings provide evidence that breeders in a genetically monogamous species may avoid the fitness costs of reproducing with a genetically similar mate. In such species that lack the opportunity to obtain extra-pair fertilizations, mate choice may therefore be under high selective pressure. ?? 2009 Mulard et al; licensee BioMed Central Ltd.

Feasibility and accuracy of molecular testing in specimens obtained with small biopsy forceps: comparison with the results of surgical specimens.

PubMed

Oki, Masahide; Yatabe, Yasushi; Saka, Hideo; Kitagawa, Chiyoe; Kogure, Yoshihito; Ichihara, Shu; Moritani, Suzuko

2015-01-01

During bronchoscopy, small biopsy forceps are increasingly used for the diagnosis of peripheral pulmonary lesions. However, it is unclear whether the formalin-fixed paraffin-embedded specimens sampled with the small biopsy forceps are suitable for the determination of genotypes which become indispensable for the management decision regarding patients with non-small cell lung cancer. The aim of this study was to evaluate the feasibility and accuracy of molecular testing in the specimens obtained with 1.5-mm small biopsy forceps. We examined specimens in 91 patients, who were enrolled in our previous 3 studies on the usefulness of thin bronchoscopes and given a diagnosis of non-small cell lung cancer by bronchoscopy with the 1.5-mm biopsy forceps, and then underwent surgical resection. An experienced pathologist examined paraffin-embedded specimens obtained by bronchoscopic biopsy or surgical resection in a blind fashion on epidermal growth factor receptor (EGFR) mutations, anaplastic lymphoma kinase (ALK) rearrangements and KRAS mutations. Twenty-five (27%), 2 (2%) and 5 (5%) patients had an EGFR mutation, ALK rearrangement and KRAS mutation, respectively, based on the results in surgical specimens. EGFR, ALK and KRAS testing with bronchoscopic specimens was feasible in 82 (90%), 86 (95%) and 83 (91%) patients, respectively. If molecular testing was feasible, the accuracy of EGFR, ALK and KRAS testing with bronchoscopic specimens for the results with surgical specimens was 98, 100 and 98%, respectively. The results of molecular testing in the formalin-fixed paraffin-embedded specimens obtained with the small forceps, in which the genotype could be evaluated, correlated well with those in surgically resected specimens.

Similarity considerations and conservation laws for magneto-static atmospheres

NASA Technical Reports Server (NTRS)

Webb, G. M.

1986-01-01

The equations of magnetohydrostatic equilibria for a plasma in a gravitational field are investigated analytically. For equilibria with one ignorable spatial coordinate, the equations reduce to a single nonlinear elliptic equation for the magnetic potential. Similarity solutions of the elliptic equation are obtained for the case of an isothermal atmosphere in a uniform gravitational field. The solutions are obtained from a consideration of the invariance group of the elliptic equation. The importance of symmetries of the elliptic equation also appears in the determination of conservation laws. It turns out that the elliptic equation can be written as a variational principle, and the symmetries of the variational functional lead (via Noether's theorem) to conservation laws for the equation. As an example of the application of the similarity solutions, a model magnetostatic atmosphere is constructed in which the current density J is proportional to the cube of the magnetic potential, and falls off exponentially with distance vertical to the base, with an 'e-folding' distance equal to the gravitational scale height. The solutions show the interplay between the gravitational force, the J x B force (B, magnetic field induction) and the gas pressure gradient.

Noncontiguous atom matching structural similarity function.

PubMed

Teixeira, Ana L; Falcao, Andre O

2013-10-28

Measuring similarity between molecules is a fundamental problem in cheminformatics. Given that similar molecules tend to have similar physical, chemical, and biological properties, the notion of molecular similarity plays an important role in the exploration of molecular data sets, query-retrieval in molecular databases, and in structure-property/activity modeling. Various methods to define structural similarity between molecules are available in the literature, but so far none has been used with consistent and reliable results for all situations. We propose a new similarity method based on atom alignment for the analysis of structural similarity between molecules. This method is based on the comparison of the bonding profiles of atoms on comparable molecules, including features that are seldom found in other structural or graph matching approaches like chirality or double bond stereoisomerism. The similarity measure is then defined on the annotated molecular graph, based on an iterative directed graph similarity procedure and optimal atom alignment between atoms using a pairwise matching algorithm. With the proposed approach the similarities detected are more intuitively understood because similar atoms in the molecules are explicitly shown. This noncontiguous atom matching structural similarity method (NAMS) was tested and compared with one of the most widely used similarity methods (fingerprint-based similarity) using three difficult data sets with different characteristics. Despite having a higher computational cost, the method performed well being able to distinguish either different or very similar hydrocarbons that were indistinguishable using a fingerprint-based approach. NAMS also verified the similarity principle using a data set of structurally similar steroids with differences in the binding affinity to the corticosteroid binding globulin receptor by showing that pairs of steroids with a high degree of similarity (>80%) tend to have smaller differences

SoRS: Social recommendation using global rating reputation and local rating similarity

NASA Astrophysics Data System (ADS)

Qian, Fulan; Zhao, Shu; Tang, Jie; Zhang, Yanping

2016-11-01

Recommendation is an important and also challenging problem in online social networks. It needs to consider not only users' personalized interests, but also social relations between users. Indeed, in practice, users are often inclined to accept recommendations from friends or opinion leaders (users with high reputations). In this paper, we present a novel recommendation framework, social recommendation using global rating reputation and local rating similarity, which combine user reputation and social similarity based on ratings. User reputation can be obtained by iteratively calculating the correlation of historical ratings of user and intrinsic qualities of items. We view the user reputation as the user's global influence and the similarity based on rating of social relation as the user's local influence, introduce it in the basic social recommender model. Thus users with high reputation have a strong influence on the others, and on the other hand, the effect of a user with low reputation has been weakened. The recommendation accuracy of proposed framework can be improved by effectively removing nature noise because of less rigorous user ratings and strengthening the effect of user influence with high reputation. We also improve the similarity based on ratings by avoiding the high similarity with the less common ratings between friends. We evaluate our approach on three datasets including Movielens, Epinions and Douban. Empirical results demonstrate that proposed framework achieves significant improvements on recommendation accuracy. User reputation and local similarity which are both based on ratings have a lot of helpful in improvement of prediction accuracy. The reputation also can help to improve the recommendation precision with the small training sets.

Tableau Calculus for the Logic of Comparative Similarity over Arbitrary Distance Spaces

NASA Astrophysics Data System (ADS)

Alenda, Régis; Olivetti, Nicola

The logic CSL (first introduced by Sheremet, Tishkovsky, Wolter and Zakharyaschev in 2005) allows one to reason about distance comparison and similarity comparison within a modal language. The logic can express assertions of the kind "A is closer/more similar to B than to C" and has a natural application to spatial reasoning, as well as to reasoning about concept similarity in ontologies. The semantics of CSL is defined in terms of models based on different classes of distance spaces and it generalizes the logic S4 u of topological spaces. In this paper we consider CSL defined over arbitrary distance spaces. The logic comprises a binary modality to represent comparative similarity and a unary modality to express the existence of the minimum of a set of distances. We first show that the semantics of CSL can be equivalently defined in terms of preferential models. As a consequence we obtain the finite model property of the logic with respect to its preferential semantic, a property that does not hold with respect to the original distance-space semantics. Next we present an analytic tableau calculus based on its preferential semantics. The calculus provides a decision procedure for the logic, its termination is obtained by imposing suitable blocking restrictions.

First results obtained within the European 'LAMA' programme (Large Active Mirrors in Aluminium)

NASA Astrophysics Data System (ADS)

Rozelot, J.-P.

1993-11-01

To investigate the feasibility of large size aluminum mirrors, studies have been undertaken in cooperation with European Southern Observatory (ESO), in the framework of a European program. The first phase, which is just now ended, addressed the following items: (1) tests to select the best aluminum alloy, (2) aluminum welding, homogeneity and stability, (3) aluminum high-precision machining, (4) nickel coating, (5) polishing of the nickel layer, (6) active optics. Furthermore, tests have been conducted to demonstrate that the quality of the mirrors is not altered at various temperatures and after a large number of aluminizing and cleaning cycles (corresponding to about 50 years' life). The mirror shape (whose specifications are fully compliant with those of the Very Large Telescope (VLT), as the program is conducted in cooperation with ESO) was computed under several causes of deformations: evidencing gravity as the predominant effect, and very low distortions as the high thermal conductivity limits the thermal transverse gradient to 0.025 C. Results show that it is quite possible to obtain high optical quality mirrors, mainly due to recent progress both in metallurgical processes (high precision machining -7 microns rms-) and active optics, that permit to correct residual aberrations of the surface. Such an alternative to classical glass mirrors will presently stand as a safe, economical solution that saves manufacturing time, for monolithic or segmented mirrors for innovative telescopes (e.g., lunar interferometric network).

Microstructure and mechanical behavior of porous Ti-6Al-4V parts obtained by selective laser melting.

PubMed

Sallica-Leva, E; Jardini, A L; Fogagnolo, J B

2013-10-01

Rapid prototyping allows titanium porous parts with mechanical properties close to that of bone tissue to be obtained. In this article, porous parts of the Ti-6Al-4V alloy with three levels of porosity were obtained by selective laser melting with two different energy inputs. Thermal treatments were performed to determine the influence of the microstructure on the mechanical properties. The porous parts were characterized by both optical and scanning electron microscopy. The effective modulus, yield and ultimate compressive strength were determined by compressive tests. The martensitic α' microstructure was observed in all of the as-processed parts. The struts resulting from the processing conditions investigated were thinner than those defined by CAD models, and consequently, larger pores and a higher experimental porosity were achieved. The use of the high-energy input parameters produced parts with higher oxygen and nitrogen content, their struts that were even thinner and contained a homogeneous porosity distribution. Greater mechanical properties for a given relative density were obtained using the high-energy input parameters. The as-quenched martensitic parts showed yield and ultimate compressive strengths similar to the as-processed parts, and these were greater than those observed for the fully annealed samples that had the lamellar microstructure of the equilibrium α+β phases. The effective modulus was not significantly influenced by the thermal treatments. A comparison between these results and those of porous parts with similar geometry obtained by selective electron beam melting shows that the use of a laser allows parts with higher mechanical properties for a given relative density to be obtained. Copyright © 2013 Elsevier Ltd. All rights reserved.

Obtaining coincident image observations for Mission to Planet Earth science data return

NASA Technical Reports Server (NTRS)

Newman, Lauri Kraft; Folta, David C.; Farrell, James P.

1994-01-01

One objective of the Mission to Planet Earth (MTPE) program involves comparing data from various instruments on multiple spacecraft to obtain a total picture of the Earth's systems. To correlate image data from instruments on different spacecraft, these spacecraft must be able to image the same location on the Earth at approximately the same time. Depending on the orbits of the spacecraft involved, complicated operational details must be considered to obtain such observations. If the spacecraft are in similar orbits, close formation flying or synchronization techniques may be used to assure coincident observations. If the orbits are dissimilar, the launch time of the second satellite may need to be restricted in order to align its orbit with that of the first satellite launched. This paper examines strategies for obtaining coincident observations for spacecraft in both similar and dissimilar orbits. Although these calculations may be performed easily for coplanar spacecraft, the non-coplanar case involves additional considerations which are incorporated into the algorithms presented herein.

A hierarchical knowledge-based approach for retrieving similar medical images described with semantic annotations

PubMed Central

Kurtz, Camille; Beaulieu, Christopher F.; Napel, Sandy; Rubin, Daniel L.

2014-01-01

Computer-assisted image retrieval applications could assist radiologist interpretations by identifying similar images in large archives as a means to providing decision support. However, the semantic gap between low-level image features and their high level semantics may impair the system performances. Indeed, it can be challenging to comprehensively characterize the images using low-level imaging features to fully capture the visual appearance of diseases on images, and recently the use of semantic terms has been advocated to provide semantic descriptions of the visual contents of images. However, most of the existing image retrieval strategies do not consider the intrinsic properties of these terms during the comparison of the images beyond treating them as simple binary (presence/absence) features. We propose a new framework that includes semantic features in images and that enables retrieval of similar images in large databases based on their semantic relations. It is based on two main steps: (1) annotation of the images with semantic terms extracted from an ontology, and (2) evaluation of the similarity of image pairs by computing the similarity between the terms using the Hierarchical Semantic-Based Distance (HSBD) coupled to an ontological measure. The combination of these two steps provides a means of capturing the semantic correlations among the terms used to characterize the images that can be considered as a potential solution to deal with the semantic gap problem. We validate this approach in the context of the retrieval and the classification of 2D regions of interest (ROIs) extracted from computed tomographic (CT) images of the liver. Under this framework, retrieval accuracy of more than 0.96 was obtained on a 30-images dataset using the Normalized Discounted Cumulative Gain (NDCG) index that is a standard technique used to measure the effectiveness of information retrieval algorithms when a separate reference standard is available. Classification

Phonological similarity and orthographic similarity affect probed serial recall of Chinese characters.

PubMed

Lin, Yi-Chen; Chen, Hsiang-Yu; Lai, Yvonne C; Wu, Denise H

2015-04-01

The previous literature on working memory (WM) has indicated that verbal materials are dominantly retained in phonological representations, whereas other linguistic information (e.g., orthography, semantics) only contributes to verbal WM minimally, if not negligibly. Although accumulating evidence has suggested that multiple linguistic components jointly support verbal WM, the visual/orthographic contribution has rarely been addressed in alphabetic languages, possibly due to the difficulty of dissociating the effects of word forms from the effects of their pronunciations in relatively shallow orthography. In the present study, we examined whether the orthographic representations of Chinese characters support the retention of verbal materials in this language of deep orthography. In Experiments 1a and 2, we independently manipulated the phonological and orthographic similarity of horizontal and vertical characters, respectively, and found that participants' accuracy of probed serial recall was reduced by both similar pronunciations and shared phonetic radicals in the to-be-remembered stimuli. Moreover, Experiment 1b showed that only the effect of phonological, but not that of orthographic, similarity was affected by concurrent articulatory suppression. Taken together, the present results indicate the indispensable contribution of orthographic representations to verbal WM of Chinese characters, and suggest that the linguistic characteristics of a specific language not only determine long-term linguistic-processing mechanisms, but also delineate the organization of verbal WM for that language.

A general framework for regularized, similarity-based image restoration.

PubMed

Kheradmand, Amin; Milanfar, Peyman

2014-12-01

Any image can be represented as a function defined on a weighted graph, in which the underlying structure of the image is encoded in kernel similarity and associated Laplacian matrices. In this paper, we develop an iterative graph-based framework for image restoration based on a new definition of the normalized graph Laplacian. We propose a cost function, which consists of a new data fidelity term and regularization term derived from the specific definition of the normalized graph Laplacian. The normalizing coefficients used in the definition of the Laplacian and associated regularization term are obtained using fast symmetry preserving matrix balancing. This results in some desired spectral properties for the normalized Laplacian such as being symmetric, positive semidefinite, and returning zero vector when applied to a constant image. Our algorithm comprises of outer and inner iterations, where in each outer iteration, the similarity weights are recomputed using the previous estimate and the updated objective function is minimized using inner conjugate gradient iterations. This procedure improves the performance of the algorithm for image deblurring, where we do not have access to a good initial estimate of the underlying image. In addition, the specific form of the cost function allows us to render the spectral analysis for the solutions of the corresponding linear equations. In addition, the proposed approach is general in the sense that we have shown its effectiveness for different restoration problems, including deblurring, denoising, and sharpening. Experimental results verify the effectiveness of the proposed algorithm on both synthetic and real examples.

Mining Diagnostic Assessment Data for Concept Similarity

ERIC Educational Resources Information Center

Madhyastha, Tara; Hunt, Earl

2009-01-01

This paper introduces a method for mining multiple-choice assessment data for similarity of the concepts represented by the multiple choice responses. The resulting similarity matrix can be used to visualize the distance between concepts in a lower-dimensional space. This gives an instructor a visualization of the relative difficulty of concepts…

Quality of courses evaluated by 'predictions' rather than opinions: Fewer respondents needed for similar results.

PubMed

Cohen-Schotanus, Janke; Schönrock-Adema, Johanna; Schmidt, Henk G

2010-01-01

A well-known problem with student surveys is a too low response rate. Experiences with predicting electoral outcomes, which required much smaller sample sizes, inspired us to adopt a similar approach to course evaluation. We expected that having respondents estimate the average opinions of their peers required fewer respondents for comparable outcomes than giving own opinions. Two course evaluation studies were performed among successive first-year medical students (N = 380 and 450, respectively). Study 1: Half the cohort gave opinions on nine questions, while the other half predicted the average outcomes. A prize was offered for the three best predictions (motivational remedy). Study 2: Half the cohort gave opinions, a quarter made predictions without a prize and a quarter made predictions with previous year's results as prior knowledge (cognitive remedy). The numbers of respondents required for stable outcomes were determined following an iterative process. Differences between numbers of respondents required and between average scores were analysed with ANOVA. In both studies, the prediction conditions required significantly fewer respondents (p < 0.001) for comparable outcomes. The informed prediction condition required the fewest respondents (N < 20). Problems with response rates can be reduced by asking respondents to predict evaluation outcomes rather than giving opinions.

Similar herpes zoster incidence across Europe: results from a systematic literature review

PubMed Central

2013-01-01

Background Herpes zoster (HZ) is caused by reactivation of the varicella-zoster virus (VZV) and mainly affects individuals aged ≥50 years. The forthcoming European launch of a vaccine against HZ (Zostavax®) prompts the need for a better understanding of the epidemiology of HZ in Europe. Therefore the aim of this systematic review was to summarize the available data on HZ incidence in Europe and to describe age-specific incidence. Methods The Medline database of the National Library of Medicine was used to conduct a comprehensive literature search of population-based studies of HZ incidence published between 1960 and 2010 carried out in the 27 member countries of the European Union, Iceland, Norway and Switzerland. The identified articles were reviewed and scored according to a reading grid including various quality criteria, and HZ incidence data were extracted and presented by country. Results The search identified 21 studies, and revealed a similar annual HZ incidence throughout Europe, varying by country from 2.0 to 4.6/1 000 person-years with no clearly observed geographic trend. Despite the fact that age groups differed from one study to another, age-specific HZ incidence rates seemed to hold steady during the review period, at around 1/1 000 children <10 years, around 2/1 000 adults aged <40 years, and around 1–4/1 000 adults aged 40–50 years. They then increased rapidly after age 50 years to around 7–8/1 000, up to 10/1 000 after 80 years of age. Our review confirms that in Europe HZ incidence increases with age, and quite drastically after 50 years of age. In all of the 21 studies included in the present review, incidence rates were higher among women than men, and this difference increased with age. This review also highlights the need to identify standardized surveillance methods to improve the comparability of data within European Union Member States and to monitor the impact of VZV immunization on the epidemiology of HZ. Conclusions

Similarity of High-Resolution Tandem Mass Spectrometry Spectra of Structurally Related Micropollutants and Transformation Products

NASA Astrophysics Data System (ADS)

Schollée, Jennifer E.; Schymanski, Emma L.; Stravs, Michael A.; Gulde, Rebekka; Thomaidis, Nikolaos S.; Hollender, Juliane

2017-12-01

High-resolution tandem mass spectrometry (HRMS2) with electrospray ionization is frequently applied to study polar organic molecules such as micropollutants. Fragmentation provides structural information to confirm structures of known compounds or propose structures of unknown compounds. Similarity of HRMS2 spectra between structurally related compounds has been suggested to facilitate identification of unknown compounds. To test this hypothesis, the similarity of reference standard HRMS2 spectra was calculated for 243 pairs of micropollutants and their structurally related transformation products (TPs); for comparison, spectral similarity was also calculated for 219 pairs of unrelated compounds. Spectra were measured on Orbitrap and QTOF mass spectrometers and similarity was calculated with the dot product. The influence of different factors on spectral similarity [e.g., normalized collision energy (NCE), merging fragments from all NCEs, and shifting fragments by the mass difference of the pair] was considered. Spectral similarity increased at higher NCEs and highest similarity scores for related pairs were obtained with merged spectra including measured fragments and shifted fragments. Removal of the monoisotopic peak was critical to reduce false positives. Using a spectral similarity score threshold of 0.52, 40% of related pairs and 0% of unrelated pairs were above this value. Structural similarity was estimated with the Tanimoto coefficient and pairs with higher structural similarity generally had higher spectral similarity. Pairs where one or both compounds contained heteroatoms such as sulfur often resulted in dissimilar spectra. This work demonstrates that HRMS2 spectral similarity may indicate structural similarity and that spectral similarity can be used in the future to screen complex samples for related compounds such as micropollutants and TPs, assisting in the prioritization of non-target compounds. [Figure not available: see fulltext.

Boron neutron capture therapy (BNCT) for newly-diagnosed glioblastoma: comparison of clinical results obtained with BNCT and conventional treatment.

PubMed

Kageji, Teruyoshi; Nagahiro, Shinji; Mizobuchi, Yoshifumi; Matsuzaki, Kazuhito; Nakagawa, Yoshinobu; Kumada, Hiroaki

2014-01-01

The purpose of this study was to evaluate the clinical outcome of boron neutron capture therapy (BNCT) and conventional treatment in patients with newly diagnosed glioblastoma. Since 1998 we treated 23 newly-diagosed GBM patients with BNCT without any additional chemotherapy. Their median survival time was 19.5 months; the 2-, 3-, and 5-year survival rates were 31.8%, 22.7%, and 9.1%, respectively. The clinical results of BNCT in patients with GBM are similar to those of recent conventional treatments based on radiotherapy with concomitant and adjuvant temozolomide.

Unsupervised Classification of PolSAR Data Using a Scattering Similarity Measure Derived From a Geodesic Distance

NASA Astrophysics Data System (ADS)

Ratha, Debanshu; Bhattacharya, Avik; Frery, Alejandro C.

2018-01-01

In this letter, we propose a novel technique for obtaining scattering components from Polarimetric Synthetic Aperture Radar (PolSAR) data using the geodesic distance on the unit sphere. This geodesic distance is obtained between an elementary target and the observed Kennaugh matrix, and it is further utilized to compute a similarity measure between scattering mechanisms. The normalized similarity measure for each elementary target is then modulated with the total scattering power (Span). This measure is used to categorize pixels into three categories i.e. odd-bounce, double-bounce and volume, depending on which of the above scattering mechanisms dominate. Then the maximum likelihood classifier of [J.-S. Lee, M. R. Grunes, E. Pottier, and L. Ferro-Famil, Unsupervised terrain classification preserving polarimetric scattering characteristics, IEEE Trans. Geos. Rem. Sens., vol. 42, no. 4, pp. 722731, April 2004.] based on the complex Wishart distribution is iteratively used for each category. Dominant scattering mechanisms are thus preserved in this classification scheme. We show results for L-band AIRSAR and ALOS-2 datasets acquired over San Francisco and Mumbai, respectively. The scattering mechanisms are better preserved using the proposed methodology than the unsupervised classification results using the Freeman-Durden scattering powers on an orientation angle (OA) corrected PolSAR image. Furthermore, (1) the scattering similarity is a completely non-negative quantity unlike the negative powers that might occur in double- bounce and odd-bounce scattering component under Freeman Durden decomposition (FDD), and (2) the methodology can be extended to more canonical targets as well as for bistatic scattering.

Standardization of a fluconazole bioassay and correlation of results with those obtained by high-pressure liquid chromatography.

PubMed Central

Rex, J H; Hanson, L H; Amantea, M A; Stevens, D A; Bennett, J E

1991-01-01

An improved bioassay for fluconazole was developed. This assay is sensitive in the clinically relevant range (2 to 40 micrograms/ml) and analyzes plasma, serum, and cerebrospinal fluid specimens; bioassay results correlate with results obtained by high-pressure liquid chromatography (HPLC). Bioassay and HPLC analyses of spiked plasma, serum, and cerebrospinal fluid samples (run as unknowns) gave good agreement with expected values. Analysis of specimens from patients gave equivalent results by both HPLC and bioassay. HPLC had a lower within-run coefficient of variation (less than 2.5% for HPLC versus less than 11% for bioassay) and a lower between-run coefficient of variation (less than 5% versus less than 12% for bioassay) and was more sensitive (lower limit of detection, 0.1 micrograms/ml [versus 2 micrograms/ml for bioassay]). The bioassay is, however, sufficiently accurate and sensitive for clinical specimens, and its relative simplicity, low sample volume requirement, and low equipment cost should make it the technique of choice for analysis of routine clinical specimens. PMID:1854166

Chest Press Exercises With Different Stability Requirements Result in Similar Muscle Damage Recovery in Resistance-Trained Men.

PubMed

Ferreira, Diogo V; Ferreira-Júnior, João B; Soares, Saulo R S; Cadore, Eduardo L; Izquierdo, Mikel; Brown, Lee E; Bottaro, Martim

2017-01-01

Ferreira, DV, Ferreira-Júnior, JB, Soares, SRS, Cadore, EL, Izquierdo, M, Brown, LE, and Bottaro, M. Chest press exercises with different stability requirements result in similar muscle damage recovery in resistance trained men. J Strength Cond Res 31(1): 71-79, 2017-This study investigated the time course of 96 hours of muscle recovery after 3 different chest press exercises with different stability requirements in resistance-trained men. Twenty-seven men (23.5 ± 3.8 years) were randomly assigned to one of the 3 groups: (a) Smith machine bench press; (b) barbell bench press; or (c) dumbbell bench press. Participants performed 8 sets of 10 repetition maximum with 2 minutes rest between sets. Muscle thickness, peak torque (PT), and soreness were measured pre, post, 24, 48, 72, and 96 hours after exercise. There were no differences in the time course of PT or muscle thickness values of the pectoralis major (p = 0.98 and p = 0.91, respectively) or elbow extensors (p = 0.07 and p = 0.86, respectively) between groups. Muscle soreness of the pectoralis major was also not different between groups (p > 0.05). However, the Smith machine and barbell groups recovered from triceps brachii muscle soreness by 72 hours after exercise (p > 0.05), whereas the dumbbell group did not present any triceps brachii muscle soreness after exercise (p > 0.05). In conclusion, resistance-trained men experience similar muscle damage recovery after Smith machine, barbell, and dumbbell chest press exercise. However, muscle soreness of the elbow extensors takes a longer time to recover after using a barbell chest press exercise.

[Similarity system theory to evaluate similarity of chromatographic fingerprints of traditional Chinese medicine].

PubMed

Liu, Yongsuo; Meng, Qinghua; Jiang, Shumin; Hu, Yuzhu

2005-03-01

The similarity evaluation of the fingerprints is one of the most important problems in the quality control of the traditional Chinese medicine (TCM). Similarity measures used to evaluate the similarity of the common peaks in the chromatogram of TCM have been discussed. Comparative studies were carried out among correlation coefficient, cosine of the angle and an improved extent similarity method using simulated data and experimental data. Correlation coefficient and cosine of the angle are not sensitive to the differences of the data set. They are still not sensitive to the differences of the data even after normalization. According to the similarity system theory, an improved extent similarity method was proposed. The improved extent similarity is more sensitive to the differences of the data sets than correlation coefficient and cosine of the angle. And the character of the data sets needs not to be changed compared with log-transformation. The improved extent similarity can be used to evaluate the similarity of the chromatographic fingerprints of TCM.

Similarity-Dissimilarity Competition in Disjunctive Classification Tasks

PubMed Central

Mathy, Fabien; Haladjian, Harry H.; Laurent, Eric; Goldstone, Robert L.

2013-01-01

Typical disjunctive artificial classification tasks require participants to sort stimuli according to rules such as “x likes cars only when black and coupe OR white and SUV.” For categories like this, increasing the salience of the diagnostic dimensions has two simultaneous effects: increasing the distance between members of the same category and increasing the distance between members of opposite categories. Potentially, these two effects respectively hinder and facilitate classification learning, leading to competing predictions for learning. Increasing saliency may lead to members of the same category to be considered less similar, while the members of separate categories might be considered more dissimilar. This implies a similarity-dissimilarity competition between two basic classification processes. When focusing on sub-category similarity, one would expect more difficult classification when members of the same category become less similar (disregarding the increase of between-category dissimilarity); however, the between-category dissimilarity increase predicts a less difficult classification. Our categorization study suggests that participants rely more on using dissimilarities between opposite categories than finding similarities between sub-categories. We connect our results to rule- and exemplar-based classification models. The pattern of influences of within- and between-category similarities are challenging for simple single-process categorization systems based on rules or exemplars. Instead, our results suggest that either these processes should be integrated in a hybrid model, or that category learning operates by forming clusters within each category. PMID:23403979

#nowplaying Madonna: a large-scale evaluation on estimating similarities between music artists and between movies from microblogs.

PubMed

Schedl, Markus

2012-01-01

Different term weighting techniques such as [Formula: see text] or BM25 have been used intensely for manifold text-based information retrieval tasks. Their use for modeling term profiles for named entities and subsequent calculation of similarities between these named entities have been studied to a much smaller extent. The recent trend of microblogging made available massive amounts of information about almost every topic around the world. Therefore, microblogs represent a valuable source for text-based named entity modeling. In this paper, we present a systematic and comprehensive evaluation of different term weighting measures , normalization techniques , query schemes , index term sets , and similarity functions for the task of inferring similarities between named entities, based on data extracted from microblog posts . We analyze several thousand combinations of choices for the above mentioned dimensions, which influence the similarity calculation process, and we investigate in which way they impact the quality of the similarity estimates. Evaluation is performed using three real-world data sets: two collections of microblogs related to music artists and one related to movies. For the music collections, we present results of genre classification experiments using as benchmark genre information from allmusic.com. For the movie collection, we present results of multi-class classification experiments using as benchmark categories from IMDb. We show that microblogs can indeed be exploited to model named entity similarity with remarkable accuracy, provided the correct settings for the analyzed aspects are used. We further compare the results to those obtained when using Web pages as data source.

Rice- or pork-based diets with similar calorie and content result in different rat gut microbiota.

PubMed

Qi, Xiaozhe; Xu, Wentao; Guo, Mingzhang; Chen, Siyuan; Liu, Yifei; He, Xiaoyun; Huang, Kunlun

2017-11-01

Rice is the most important food crop, and pork is the most widely eaten meat in the world. In this study, we compared the gut microbiota of the rats fed with rice or pork mixed diets, which have similar caloric contents. The physiological indices (body weights, hematology, serum chemistry, organ weights and histopathology) of two groups were all within the normal range. Two diets did not induce difference in the diversity of gut bacteria. However, Firmicutes were significantly higher in rice diet group, while Bacteroidetes were enriched in pork diet group. Butyrate and the bacteria enzymes β-glucuronidase, β-glucosidase and nitroreductase in the feces were all drastically higher in pork diet group. This study indicates that different diets with similar calorie and nutritional composition could change the community structure but not the diversity of rat fecal microbiota.

Surface similarity-based molecular query-retrieval

PubMed Central

Singh, Rahul

2007-01-01

Background Discerning the similarity between molecules is a challenging problem in drug discovery as well as in molecular biology. The importance of this problem is due to the fact that the biochemical characteristics of a molecule are closely related to its structure. Therefore molecular similarity is a key notion in investigations targeting exploration of molecular structural space, query-retrieval in molecular databases, and structure-activity modelling. Determining molecular similarity is related to the choice of molecular representation. Currently, representations with high descriptive power and physical relevance like 3D surface-based descriptors are available. Information from such representations is both surface-based and volumetric. However, most techniques for determining molecular similarity tend to focus on idealized 2D graph-based descriptors due to the complexity that accompanies reasoning with more elaborate representations. Results This paper addresses the problem of determining similarity when molecules are described using complex surface-based representations. It proposes an intrinsic, spherical representation that systematically maps points on a molecular surface to points on a standard coordinate system (a sphere). Molecular surface properties such as shape, field strengths, and effects due to field super-positioningcan then be captured as distributions on the surface of the sphere. Surface-based molecular similarity is subsequently determined by computing the similarity of the surface-property distributions using a novel formulation of histogram-intersection. The similarity formulation is not only sensitive to the 3D distribution of the surface properties, but is also highly efficient to compute. Conclusion The proposed method obviates the computationally expensive step of molecular pose-optimisation, can incorporate conformational variations, and facilitates highly efficient determination of similarity by directly comparing molecular surfaces

Understanding similarity of groundwater systems with empirical copulas

NASA Astrophysics Data System (ADS)

Haaf, Ezra; Kumar, Rohini; Samaniego, Luis; Barthel, Roland

2016-04-01

Within the classification framework for groundwater systems that aims for identifying similarity of hydrogeological systems and transferring information from a well-observed to an ungauged system (Haaf and Barthel, 2015; Haaf and Barthel, 2016), we propose a copula-based method for describing groundwater-systems similarity. Copulas are an emerging method in hydrological sciences that make it possible to model the dependence structure of two groundwater level time series, independently of the effects of their marginal distributions. This study is based on Samaniego et al. (2010), which described an approach calculating dissimilarity measures from bivariate empirical copula densities of streamflow time series. Subsequently, streamflow is predicted in ungauged basins by transferring properties from similar catchments. The proposed approach is innovative because copula-based similarity has not yet been applied to groundwater systems. Here we estimate the pairwise dependence structure of 600 wells in Southern Germany using 10 years of weekly groundwater level observations. Based on these empirical copulas, dissimilarity measures are estimated, such as the copula's lower- and upper corner cumulated probability, copula-based Spearman's rank correlation - as proposed by Samaniego et al. (2010). For the characterization of groundwater systems, copula-based metrics are compared with dissimilarities obtained from precipitation signals corresponding to the presumed area of influence of each groundwater well. This promising approach provides a new tool for advancing similarity-based classification of groundwater system dynamics. Haaf, E., Barthel, R., 2015. Methods for assessing hydrogeological similarity and for classification of groundwater systems on the regional scale, EGU General Assembly 2015, Vienna, Austria. Haaf, E., Barthel, R., 2016. An approach for classification of hydrogeological systems at the regional scale based on groundwater hydrographs EGU General Assembly

Self-similarity in nature

NASA Astrophysics Data System (ADS)

Timashev, S. F.

2000-02-01

A general phenomenological approach to the analysis of experimental temporal, spatial and energetic series for extracting truly physical non-model parameters ("passport data") is presented, which may be used to characterize and distinguish the evolution as well as the spatial and energetic structure of any open nonlinear dissipative system. This methodology is based on a postulate concerning the crucial information contained in the sequences of non-regularities of the measured dynamic variable (temporal, spatial, energetic). In accordance with this approach, multi-parametric formulas for dynamic variable power spectra as well as for structural functions of different orders are identical for every spatial-temporal-energetic level of the system under consideration. In effect, this entails the introduction of a new kind of self-similarity in Nature. An algorithm has been developed for obtaining as many "passport data" as are necessary for the characterization of a dynamic system. Applications of this approach in the analysis of various experimental series (temporal, spatial, energetic) demonstrate its potential for defining adequate phenomenological parameters of different dynamic processes and structures.

A novel approach to molecular similarity

NASA Astrophysics Data System (ADS)

Cooper, David L.; Allan, Neil L.

1989-09-01

We review briefly the general problem of assessing the similarity between one molecule and another. We propose a novel approach to the quantitative estimation of the similarity of two electron distributions. The procedure is based on momentum space concepts, and avoids many of the difficulties associated with the usual position space definitions. Results are presented for the model systems CH3CH2CH3, CH3OCH3, CH3SCH3, H2O and H2S.

Self-similar space-time evolution of an initial density discontinuity

NASA Astrophysics Data System (ADS)

Rekaa, V. L.; Pécseli, H. L.; Trulsen, J. K.

2013-07-01

The space-time evolution of an initial step-like plasma density variation is studied. We give particular attention to formulate the problem in a way that opens for the possibility of realizing the conditions experimentally. After a short transient time interval of the order of the electron plasma period, the solution is self-similar as illustrated by a video where the space-time evolution is reduced to be a function of the ratio x/t. Solutions of this form are usually found for problems without characteristic length and time scales, in our case the quasi-neutral limit. By introducing ion collisions with neutrals into the numerical analysis, we introduce a length scale, the collisional mean free path. We study the breakdown of the self-similarity of the solution as the mean free path is made shorter than the system length. Analytical results are presented for charge exchange collisions, demonstrating a short time collisionless evolution with an ensuing long time diffusive relaxation of the initial perturbation. For large times, we find a diffusion equation as the limiting analytical form for a charge-exchange collisional plasma, with a diffusion coefficient defined as the square of the ion sound speed divided by the (constant) ion collision frequency. The ion-neutral collision frequency acts as a parameter that allows a collisionless result to be obtained in one limit, while the solution of a diffusion equation is recovered in the opposite limit of large collision frequencies.

Benefits from living together? Clades whose species use similar habitats may persist as a result of eco-evolutionary feedbacks.

PubMed

Prinzing, Andreas; Ozinga, Wim A; Brändle, Martin; Courty, Pierre-Emmanuel; Hennion, Françoise; Labandeira, Conrad; Parisod, Christian; Pihain, Mickael; Bartish, Igor V

2017-01-01

Contents 66 I. 67 II. 68 III. 69 IV. 70 V. 73 VI. 75 VII. 77 78 References 78 SUMMARY: Recent decades have seen declines of entire plant clades while other clades persist despite changing environments. We suggest that one reason why some clades persist is that species within these clades use similar habitats, because such similarity may increase the degree of co-occurrence of species within clades. Traditionally, co-occurrence among clade members has been suggested to be disadvantageous because of increased competition and enemy pressure. Here, we hypothesize that increased co-occurrence among clade members promotes mutualist exchange, niche expansion or hybridization, thereby helping species avoid population decline from environmental change. We review the literature and analyse published data for hundreds of plant clades (genera) within a well-studied region and find major differences in the degree to which species within clades occupy similar habitats. We tentatively show that, in clades for which species occupy similar habitats, species tend to exhibit increased co-occurrence, mutualism, niche expansion, and hybridization - and rarely decline. Consistently, throughout the geological past, clades whose species occupied similar habitats often persisted through long time-spans. Overall, for many plant species, the occupation of similar habitats among fellow clade members apparently reduced their vulnerability to environmental change. Future research should identify when and how this previously unrecognized eco-evolutionary feedback operates. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

The effects of intermittency on statistical characteristics of turbulence and scale similarity of breakdown coefficients

NASA Astrophysics Data System (ADS)

Novikov, E. A.

1990-05-01

The influence of intermittency on turbulent diffusion is expressed in terms of the statistics of the dissipation field. The high-order moments of relative diffusion are obtained by using the concept of scale similarity of the breakdown coefficients (bdc). The method of bdc is useful for obtaining new models and general results, which then can be expressed in terms of multifractals. In particular, the concavity and other properties of spectral codimension are proved. Special attention is paid to the logarithmically periodic modulations. The parametrization of small-scale intermittent turbulence, which can be used for large-eddy simulation, is presented. The effect of molecular viscosity is taken into account in the spirit of the renorm group, but without spectral series, ɛ expansion, and fictitious random forces.

Investigation on the effect of nonlinear processes on similarity law in high-pressure argon discharges

NASA Astrophysics Data System (ADS)

Fu, Yangyang; Parsey, Guy M.; Verboncoeur, John P.; Christlieb, Andrew J.

2017-11-01

In this paper, the effect of nonlinear processes (such as three-body collisions and stepwise ionizations) on the similarity law in high-pressure argon discharges has been studied by the use of the Kinetic Global Model framework. In the discharge model, the ground state argon atoms (Ar), electrons (e), atom ions (Ar+), molecular ions (Ar2+), and fourteen argon excited levels Ar*(4s and 4p) are considered. The steady-state electron and ion densities are obtained with nonlinear processes included and excluded in the designed models, respectively. It is found that in similar gas gaps, keeping the product of gas pressure and linear dimension unchanged, with the nonlinear processes included, the normalized density relations deviate from the similarity relations gradually as the scale-up factor decreases. Without the nonlinear processes, the parameter relations are in good agreement with the similarity law predictions. Furthermore, the pressure and the dimension effects are also investigated separately with and without the nonlinear processes. It is shown that the gas pressure effect on the results is less obvious than the dimension effect. Without the nonlinear processes, the pressure and the dimension effects could be estimated from one to the other based on the similarity relations.

An Exploration of Kernel Equating Using SAT® Data: Equating to a Similar Population and to a Distant Population. Research Report. ETS RR-07-17

ERIC Educational Resources Information Center

Liu, Jinghua; Low, Albert C.

2007-01-01

This study applied kernel equating (KE) in two scenarios: equating to a very similar population and equating to a very different population, referred to as a distant population, using SAT® data. The KE results were compared to the results obtained from analogous classical equating methods in both scenarios. The results indicate that KE results are…

The baryonic self similarity of dark matter

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alard, C., E-mail: alard@iap.fr

2014-06-20

The cosmological simulations indicates that dark matter halos have specific self-similar properties. However, the halo similarity is affected by the baryonic feedback. By using momentum-driven winds as a model to represent the baryon feedback, an equilibrium condition is derived which directly implies the emergence of a new type of similarity. The new self-similar solution has constant acceleration at a reference radius for both dark matter and baryons. This model receives strong support from the observations of galaxies. The new self-similar properties imply that the total acceleration at larger distances is scale-free, the transition between the dark matter and baryons dominatedmore » regime occurs at a constant acceleration, and the maximum amplitude of the velocity curve at larger distances is proportional to M {sup 1/4}. These results demonstrate that this self-similar model is consistent with the basics of modified Newtonian dynamics (MOND) phenomenology. In agreement with the observations, the coincidence between the self-similar model and MOND breaks at the scale of clusters of galaxies. Some numerical experiments show that the behavior of the density near the origin is closely approximated by a Einasto profile.« less

Context-dependent similarity effects in letter recognition.

PubMed

Kinoshita, Sachiko; Robidoux, Serje; Guilbert, Daniel; Norris, Dennis

2015-10-01

In visual word recognition tasks, digit primes that are visually similar to letter string targets (e.g., 4/A, 8/B) are known to facilitate letter identification relative to visually dissimilar digits (e.g., 6/A, 7/B); in contrast, with letter primes, visual similarity effects have been elusive. In the present study we show that the visual similarity effect with letter primes can be made to come and go, depending on whether it is necessary to discriminate between visually similar letters. The results support a Bayesian view which regards letter recognition not as a passive activation process driven by the fixed stimulus properties, but as a dynamic evidence accumulation process for a decision that is guided by the task context.

Oligosaccharide composition is similar in drusen and dense deposits in membranoproliferative glomerulonephritis type II.

PubMed

D'souza, Yvonne B; Jones, Carolyn J P; Short, Colin D; Roberts, Ian S D; Bonshek, Richard E

2009-04-01

Drusen are a feature of age-related macular degeneration (AMD). Lesions similar in appearance to drusen are also found in the fundi of patients with membranoproliferative glomerulonephritis type II (dense deposit disease, DDD). The lamina densa of the glomerular basement membrane, in DDD, is transformed into an electron-dense structure by deposition of microscopically homogeneous material. Our study sought to compare the saccharide composition of drusen and dense deposits in the formalin-fixed, paraffin-embedded tissue from the eye and kidney. Six eye specimens were obtained from patients diagnosed with AMD but another eye was obtained from a patient with partial lipodystrophy, who died after renal failure presumably because of DDD. The kidney specimens were from three biopsy-proven cases of DDD. Glycosylation patterns were measured by the binding of 19 biotinylated lectins before and after neuraminidase pre-treatment. High mannose, bi/tri-antennary non-bisected and bisected complex N-glycan, N-acetyl glucosamine, galactose, and sialic acid residues were found in both drusen and dense deposits. Treatment with neuraminidase exposed subterminal galactose in both sites and sparse N-acetyl galactosamine residues in drusen alone. Our study found similar pathologic oligosaccharide structures in the eye and kidney, suggesting that drusen may be a common end result of retinal and glomerular disease.

FunSimMat: a comprehensive functional similarity database

PubMed Central

Schlicker, Andreas; Albrecht, Mario

2008-01-01

Functional similarity based on Gene Ontology (GO) annotation is used in diverse applications like gene clustering, gene expression data analysis, protein interaction prediction and evaluation. However, there exists no comprehensive resource of functional similarity values although such a database would facilitate the use of functional similarity measures in different applications. Here, we describe FunSimMat (Functional Similarity Matrix, http://funsimmat.bioinf.mpi-inf.mpg.de/), a large new database that provides several different semantic similarity measures for GO terms. It offers various precomputed functional similarity values for proteins contained in UniProtKB and for protein families in Pfam and SMART. The web interface allows users to efficiently perform both semantic similarity searches with GO terms and functional similarity searches with proteins or protein families. All results can be downloaded in tab-delimited files for use with other tools. An additional XML–RPC interface gives automatic online access to FunSimMat for programs and remote services. PMID:17932054

TumorMap: Exploring the Molecular Similarities of Cancer Samples in an Interactive Portal

PubMed Central

Newton, Yulia; Novak, Adam M.; Swatloski, Teresa; McColl, Duncan C.; Chopra, Sahil; Graim, Kiley; Weinstein, Alana S.; Baertsch, Robert; Salama, Sofie R.; Ellrott, Kyle; Chopra, Manu; Goldstein, Theodore C.; Haussler, David; Morozova, Olena; Stuart, Joshua M.

2017-01-01

Vast amounts of molecular data are being collected on tumor samples, which provide unique opportunities for discovering trends within and between cancer subtypes. Such cross-cancer analyses require computational methods that enable intuitive and interactive browsing of thousands of samples based on their molecular similarity. We created a portal called TumorMap to assist in exploration and statistical interrogation of high-dimensional complex “omics” data in an interactive and easily interpretable way. In the TumorMap, samples are arranged on a hexagonal grid based on their similarity to one another in the original genomic space and are rendered with Google’s Map technology. While the important feature of this public portal is the ability for the users to build maps from their own data, we pre-built genomic maps from several previously published projects. We demonstrate the utility of this portal by presenting results obtained from The Cancer Genome Atlas project data. PMID:29092953

A blended design in acute care training: similar learning results, less training costs compared with a traditional format.

PubMed

Dankbaar, Mary E W; Storm, Diana J; Teeuwen, Irene C; Schuit, Stephanie C E

2014-09-01

Introduction There is a demand for more attractive and efficient training programmes in postgraduate health care training. This retrospective study aims to show the effectiveness of a blended versus traditional face-to-face training design. For nurses in postgraduate Acute and Intensive Care training, the effectiveness of a blended course design was compared with a traditional design. Methods In a first pilot study 57 students took a traditional course (2-h lecture and 2-h workshop) and 46 students took a blended course (2-h lecture and 2-h online self-study material). Test results were compared for both groups. After positive results in the pilot study, the design was replicated for the complete programme in Acute and Intensive Care. Now 16 students followed the traditional programme (11 days face-to-face education) and 31 students did the blended programme (7 days face-to-face and 40 h online self-study). An evaluation was done after the pilot and course costs were calculated. Results Results show that the traditional and blended groups were similar regarding the main characteristics and did not differ in learning results for both the pilot and the complete programme. Student evaluations of both designs were positive; however, the blended group were more confident that they had achieved the learning objectives. Training costs were reduced substantially. Conclusion The blended training design offers an effective and attractive training solution, leading to a significant reduction in costs.

Semantic similarity between ontologies at different scales

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Qingpeng; Haglin, David J.

In the past decade, existing and new knowledge and datasets has been encoded in different ontologies for semantic web and biomedical research. The size of ontologies is often very large in terms of number of concepts and relationships, which makes the analysis of ontologies and the represented knowledge graph computational and time consuming. As the ontologies of various semantic web and biomedical applications usually show explicit hierarchical structures, it is interesting to explore the trade-offs between ontological scales and preservation/precision of results when we analyze ontologies. This paper presents the first effort of examining the capability of this idea viamore » studying the relationship between scaling biomedical ontologies at different levels and the semantic similarity values. We evaluate the semantic similarity between three Gene Ontology slims (Plant, Yeast, and Candida, among which the latter two belong to the same kingdom—Fungi) using four popular measures commonly applied to biomedical ontologies (Resnik, Lin, Jiang-Conrath, and SimRel). The results of this study demonstrate that with proper selection of scaling levels and similarity measures, we can significantly reduce the size of ontologies without losing substantial detail. In particular, the performance of Jiang-Conrath and Lin are more reliable and stable than that of the other two in this experiment, as proven by (a) consistently showing that Yeast and Candida are more similar (as compared to Plant) at different scales, and (b) small deviations of the similarity values after excluding a majority of nodes from several lower scales. This study provides a deeper understanding of the application of semantic similarity to biomedical ontologies, and shed light on how to choose appropriate semantic similarity measures for biomedical engineering.« less

A quantum molecular similarity analysis of changes in molecular electron density caused by basis set flotation and electric field application

NASA Astrophysics Data System (ADS)

Simon, Sílvia; Duran, Miquel

1997-08-01

Quantum molecular similarity (QMS) techniques are used to assess the response of the electron density of various small molecules to application of a static, uniform electric field. Likewise, QMS is used to analyze the changes in electron density generated by the process of floating a basis set. The results obtained show an interrelation between the floating process, the optimum geometry, and the presence of an external field. Cases involving the Le Chatelier principle are discussed, and an insight on the changes of bond critical point properties, self-similarity values and density differences is performed.

Conventional physical therapy and physical therapy based on reflex stimulation showed similar results in children with myelomeningocele.

PubMed

Aizawa, Carolina Y P; Morales, Mariana P; Lundberg, Carolina; Moura, Maria Clara D Soares de; Pinto, Fernando C G; Voos, Mariana C; Hasue, Renata H

2017-03-01

We aimed to investigate whether infants with myelomeningocele would improve their motor ability and functional independence after ten sessions of physical therapy and compare the outcomes of conventional physical therapy (CPT) to a physical therapy program based on reflex stimulation (RPT). Twelve children were allocated to CPT (n = 6, age 18.3 months) or RPT (n = 6, age 18.2 months). The RPT involved proprioceptive neuromuscular facilitation. Children were assessed with the Gross Motor Function Measure and the Pediatric Evaluation of Disability Inventory before and after treatment. Mann-Whitney tests compared the improvement on the two scales of CPT versus RPT and the Wilcoxon test compared CPT to RPT (before vs. after treatment). Possible correlations between the two scales were tested with Spearman correlation coefficients. Both groups showed improvement on self-care and mobility domains of both scales. There were no differences between the groups, before, or after intervention. The CPT and RPT showed similar results after ten weeks of treatment.

Similarity Based Semantic Web Service Match

NASA Astrophysics Data System (ADS)

Peng, Hui; Niu, Wenjia; Huang, Ronghuai

Semantic web service discovery aims at returning the most matching advertised services to the service requester by comparing the semantic of the request service with an advertised service. The semantic of a web service are described in terms of inputs, outputs, preconditions and results in Ontology Web Language for Service (OWL-S) which formalized by W3C. In this paper we proposed an algorithm to calculate the semantic similarity of two services by weighted averaging their inputs and outputs similarities. Case study and applications show the effectiveness of our algorithm in service match.

The LANDSAT system operated in Brazil by CNPq/INPE - results obtained in the area of mapping and future perspectives

NASA Technical Reports Server (NTRS)

Dejesusparada, N. (Principal Investigator); Barbosa, M. N.

1981-01-01

The LANDSAT system, operated in the country by CNPg/INPE since 1973, systematically acquires, produces, and distributes both multispectral and panchromatic images obtained through remote sensing satellites to thousands of researchers and technicians involved in the natural resources survey. To cooperate in the solution of national problems, CNPq/INPE is developing efforts in the area of manipulation of those images with the objective of making them useful as planimetric bases for the simple revision of already published maps or for its utilization as basic material in regions not yet reliability mapped. The results obtained from performed tests are presented and the existing limitations are discussed. The new system purchased to handle data from the next series of LANDSAT as well as from MAPSAT and SPOT which will be in operation within the 80's decade, and are designed not only for natural resources survey but also for the solution of cartographic problems.

Direct simulation of a self-similar plane wake

NASA Technical Reports Server (NTRS)

Moser, Robert D.; Rogers, Michael M.

1994-01-01

Direct simulations of two time-developing turbulent wakes have been performed. Initial conditions for the simulations were obtained from two realizations of a direct simulation of a turbulent boundary layer at momentum thickness Reynolds number 670. In addition, extra two dimensional disturbances were added in one of the cases to mimic two dimensional forcing. The unforced wake is allowed to evolve long enough to attain self similarity. The mass-flux Reynolds number (equivalent to the momentum thickness Reynolds number in spatially developing wakes) is 2000, which is high enough for a short k(exp -5/3) range to be evident in the streamwise one dimensional velocity spectrum. Several turbulence statistics have been computed by averaging in space and over the self-similar period in time. The growth rate in the unforced flow is low compared to experiments, but when this growth-rate difference is accounted for, the statistics of the unforced case are in reasonable agreement with experiments. However, the forced case is significantly different. The growth rate, turbulence Reynolds number, and turbulence intensities are as much as ten times larger in the forced case. In addition, the forced flow exhibits large-scale structures similar to those observed in transitional wakes, while the unforced flow does not.

Robust hashing with local models for approximate similarity search.

PubMed

Song, Jingkuan; Yang, Yi; Li, Xuelong; Huang, Zi; Yang, Yang

2014-07-01

Similarity search plays an important role in many applications involving high-dimensional data. Due to the known dimensionality curse, the performance of most existing indexing structures degrades quickly as the feature dimensionality increases. Hashing methods, such as locality sensitive hashing (LSH) and its variants, have been widely used to achieve fast approximate similarity search by trading search quality for efficiency. However, most existing hashing methods make use of randomized algorithms to generate hash codes without considering the specific structural information in the data. In this paper, we propose a novel hashing method, namely, robust hashing with local models (RHLM), which learns a set of robust hash functions to map the high-dimensional data points into binary hash codes by effectively utilizing local structural information. In RHLM, for each individual data point in the training dataset, a local hashing model is learned and used to predict the hash codes of its neighboring data points. The local models from all the data points are globally aligned so that an optimal hash code can be assigned to each data point. After obtaining the hash codes of all the training data points, we design a robust method by employing l2,1 -norm minimization on the loss function to learn effective hash functions, which are then used to map each database point into its hash code. Given a query data point, the search process first maps it into the query hash code by the hash functions and then explores the buckets, which have similar hash codes to the query hash code. Extensive experimental results conducted on real-life datasets show that the proposed RHLM outperforms the state-of-the-art methods in terms of search quality and efficiency.

New Similarity Reductions and Compacton Solutions for Boussinesq-Like Equations with Fully Nonlinear Dispersion

NASA Astrophysics Data System (ADS)

Yan, Zhen-Ya

2001-10-01

In this paper, similarity reductions of Boussinesq-like equations with nonlinear dispersion (simply called B(m,n) equations) utt=(u^n)xx+(u^m)xxxx, which is a generalized model of Boussinesq equation utt=(u^2)xx+uxxxx and modified Bousinesq equation utt=(u^3)xx+uxxxx, are considered by using the direct reduction method. As a result, several new types of similarity reductions are found. Based on the reduction equations and some simple transformations, we obtain the solitary wave solutions and compacton solutions (which are solitary waves with the property that after colliding with other compacton solutions, they re-emerge with the same coherent shape) of B(1,n) equations and B(m,m) equations, respectively. The project supported by National Key Basic Research Development Project Program of China under Grant No. G1998030600 and Doctoral Foundation of China under Grant No. 98014119

Race, Gender and Reciprocity Effects on Friendship Similarity during Early Adolescence.

ERIC Educational Resources Information Center

Clark, M. L.; Ayers, Marla

One hundred and thirty-six 7th and 8th graders were studied in order to investigate the effects of race, gender, and reciprocity on friendship similarity and proximity in early adolescence. Six measures were administered to participants to obtain data on their friendship choices, friendship proximity, degree of friendship satisfaction and…

Determining similarity in histological images using graph-theoretic description and matching methods for content-based image retrieval in medical diagnostics

PubMed Central

2012-01-01

Background Computer-based analysis of digitalized histological images has been gaining increasing attention, due to their extensive use in research and routine practice. The article aims to contribute towards the description and retrieval of histological images by employing a structural method using graphs. Due to their expressive ability, graphs are considered as a powerful and versatile representation formalism and have obtained a growing consideration especially by the image processing and computer vision community. Methods The article describes a novel method for determining similarity between histological images through graph-theoretic description and matching, for the purpose of content-based retrieval. A higher order (region-based) graph-based representation of breast biopsy images has been attained and a tree-search based inexact graph matching technique has been employed that facilitates the automatic retrieval of images structurally similar to a given image from large databases. Results The results obtained and evaluation performed demonstrate the effectiveness and superiority of graph-based image retrieval over a common histogram-based technique. The employed graph matching complexity has been reduced compared to the state-of-the-art optimal inexact matching methods by applying a pre-requisite criterion for matching of nodes and a sophisticated design of the estimation function, especially the prognosis function. Conclusion The proposed method is suitable for the retrieval of similar histological images, as suggested by the experimental and evaluation results obtained in the study. It is intended for the use in Content Based Image Retrieval (CBIR)-requiring applications in the areas of medical diagnostics and research, and can also be generalized for retrieval of different types of complex images. Virtual Slides The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1224798882787923. PMID:23035717

Natural texture retrieval based on perceptual similarity measurement

NASA Astrophysics Data System (ADS)

Gao, Ying; Dong, Junyu; Lou, Jianwen; Qi, Lin; Liu, Jun

2018-04-01

A typical texture retrieval system performs feature comparison and might not be able to make human-like judgments of image similarity. Meanwhile, it is commonly known that perceptual texture similarity is difficult to be described by traditional image features. In this paper, we propose a new texture retrieval scheme based on texture perceptual similarity. The key of the proposed scheme is that prediction of perceptual similarity is performed by learning a non-linear mapping from image features space to perceptual texture space by using Random Forest. We test the method on natural texture dataset and apply it on a new wallpapers dataset. Experimental results demonstrate that the proposed texture retrieval scheme with perceptual similarity improves the retrieval performance over traditional image features.

A novel method to remove GPR background noise based on the similarity of non-neighboring regions

NASA Astrophysics Data System (ADS)

Montiel-Zafra, V.; Canadas-Quesada, F. J.; Vera-Candeas, P.; Ruiz-Reyes, N.; Rey, J.; Martinez, J.

2017-09-01

Ground penetrating radar (GPR) is a non-destructive technique that has been widely used in many areas of research, such as landmine detection or subsurface anomalies, where it is required to locate targets embedded within a background medium. One of the major challenges in the research of GPR data remains the improvement of the image quality of stone materials by means of detection of true anisotropies since most of the errors are caused by an incorrect interpretation by the users. However, it is complicated due to the interference of the horizontal background noise, e.g., the air-ground interface, that reduces the high-resolution quality of radargrams. Thus, weak or deep anisotropies are often masked by this type of noise. In order to remove the background noise obtained by GPR, this work proposes a novel background removal method assuming that the horizontal noise shows repetitive two-dimensional regions along the movement of the GPR antenna. Specifically, the proposed method, based on the non-local similarity of regions over the distance, computes similarities between different regions of the same depth in order to identify most repetitive regions using a criterion to avoid closer regions. Evaluations are performed using a set of synthetic and real GPR data. Experimental results show that the proposed method obtains promising results compared to the classic background removal techniques and the most recently published background removal methods.

The method of similar operators in the study of the spectra of the adjacency matrices of graphs

NASA Astrophysics Data System (ADS)

Kozlukov, Serge

2018-03-01

The method of similar operators [1, 2, 3] is used to investigate spectral properties of a certain class of matrices in the context of graphs [4, 5]. Specifically, we consider the adjacency matrix of an “almost-complete graph”. Then we generalize the result to allow the matrices obtained as combinations of the Kronecker products [6, 7] and the small-norm perturbations. We derive the estimates of the spectra and the eigenvectors of such matrices.

SCPRED: accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences.

PubMed

Kurgan, Lukasz; Cios, Krzysztof; Chen, Ke

2008-05-01

Protein structure prediction methods provide accurate results when a homologous protein is predicted, while poorer predictions are obtained in the absence of homologous templates. However, some protein chains that share twilight-zone pairwise identity can form similar folds and thus determining structural similarity without the sequence similarity would be desirable for the structure prediction. The folding type of a protein or its domain is defined as the structural class. Current structural class prediction methods that predict the four structural classes defined in SCOP provide up to 63% accuracy for the datasets in which sequence identity of any pair of sequences belongs to the twilight-zone. We propose SCPRED method that improves prediction accuracy for sequences that share twilight-zone pairwise similarity with sequences used for the prediction. SCPRED uses a support vector machine classifier that takes several custom-designed features as its input to predict the structural classes. Based on extensive design that considers over 2300 index-, composition- and physicochemical properties-based features along with features based on the predicted secondary structure and content, the classifier's input includes 8 features based on information extracted from the secondary structure predicted with PSI-PRED and one feature computed from the sequence. Tests performed with datasets of 1673 protein chains, in which any pair of sequences shares twilight-zone similarity, show that SCPRED obtains 80.3% accuracy when predicting the four SCOP-defined structural classes, which is superior when compared with over a dozen recent competing methods that are based on support vector machine, logistic regression, and ensemble of classifiers predictors. The SCPRED can accurately find similar structures for sequences that share low identity with sequence used for the prediction. The high predictive accuracy achieved by SCPRED is attributed to the design of the features, which are

Comparison of polygraph data obtained from individuals involved in mock crimes and actual criminal investigations.

PubMed

Pollina, Dean A; Dollins, Andrew B; Senter, Stuart M; Krapohl, Donald J; Ryan, Andrew H

2004-12-01

In a preliminary attempt to determine the generalizability of data from laboratory mock-crime studies, the authors examined the similarities and differences among the cardiovascular, electrodermal, and respiration responses of deceptive and nondeceptive individuals elicited to crime-relevant and crime-irrelevant questions. Participants in the laboratory group were randomly assigned to nondeceptive (n = 28) or deceptive (n = 27) treatment groups, and a mock-crime scenario was used. The field participants were confirmed nondeceptive (n = 28) or deceptive (n = 39) criminal suspects who underwent polygraph examinations between 1993 and 1997. The results indicated that there were salient differences between field and similarly obtained laboratory polygraph response measures. However, accuracy of laboratory participants' classifications using logistic regression analysis was not significantly different from field participants' classification accuracy. 2004 APA, all rights reserved

Phoneme Similarity and Confusability

ERIC Educational Resources Information Center

Bailey, T.M.; Hahn, U.

2005-01-01

Similarity between component speech sounds influences language processing in numerous ways. Explanation and detailed prediction of linguistic performance consequently requires an understanding of these basic similarities. The research reported in this paper contrasts two broad classes of approach to the issue of phoneme similarity-theoretically…

Limiting similarity of competitive species and demographic stochasticity

NASA Astrophysics Data System (ADS)

Zheng, Xiu-Deng; Deng, Ling-Ling; Qiang, Wei-Ya; Cressman, Ross; Tao, Yi

2017-04-01

The limiting similarity of competitive species and its relationship with the competitive exclusion principle is still one of the most important concepts in ecology. In the 1970s, May [R. M. May, Stability and Complexity in Model Ecosystems (Princeton University, Princeton, NJ, 1973)] developed a concise theoretical framework to investigate the limiting similarity of competitive species. His theoretical results show that no limiting similarity threshold of competitive species can be identified in the deterministic model system whereby species more similar than this threshold never coexist. Theoretically, for competitive species coexisting in an unvarying environment, deterministic interspecific interactions and demographic stochasticity can be considered two sides of a coin. To investigate how the "tension" between these two forces affects the coexistence of competing species, a simple two-species competitive system based only on May's model system is transformed into an equivalent replicator equation. The effect of demographic stochasticity on the system stability is measured by the expected drift of the Lyapunov function. Our main results show that the limiting similarity of competitive species should not be considered to be an absolute measure. Specifically, very similar competitive species should be able to coexist in an environment with a high productivity level but big differences between competitive species should be necessary in an ecosystem with a low productivity level.

Molecular diversity of Clostridium botulinum and phenotypically similar strains.

PubMed

Grenda, T; Kukier, E; Sieradzki, Z; Goldsztejn, M; Kwiatek, K

2016-12-01

This study was undertaken to examine phenotypic and genetic features of strains preliminary classified as Clostridium botulinum species. The phenotypic characteristics were assessed with different culture media and biochemical tests. The genetic characterization included detection of botulinum toxin genes by PCR and macrorestriction analysis with SmaI, XhoI and SacII by PFGE (Pulsed-field Gel Electrophoresis). Despite similar biochemical properties of all analysed strains, only 47% of them contained genes determining toxicity specific to C. botulinum species. The most valuable differentiation of C. botulinum and C. botulinum-like strains was obtained after SmaI digestion. The highest affinity was observed among C. botulinum type B profiles which was even up to 100%. It was found 100% of affinity between C. botulinum and C. botulinum-like strains, however, the similarity among C. botulinum and C. botulinum-like was generally lower than 80%.

Contrasting Ecosystem-Effects of Morphologically Similar Copepods

PubMed Central

Matthews, Blake; Hausch, Stephen; Winter, Christian; Suttle, Curtis A.; Shurin, Jonathan B.

2011-01-01

Organisms alter the biotic and abiotic conditions of ecosystems. They can modulate the availability of resources to other species (ecosystem engineering) and shape selection pressures on other organisms (niche construction). Very little is known about how the engineering effects of organisms vary among and within species, and, as a result, the ecosystem consequences of species diversification and phenotypic evolution are poorly understood. Here, using a common gardening experiment, we test whether morphologically similar species and populations of Diaptomidae copepods (Leptodiaptomus ashlandi, Hesperodiaptomus franciscanus, Skistodiaptomus oregonensis) have similar or different effects on the structure and function of freshwater ecosystems. We found that copepod species had contrasting effects on algal biomass, ammonium concentrations, and sedimentation rates, and that copepod populations had contrasting effects on prokaryote abundance, sedimentation rates, and gross primary productivity. The average size of ecosystem-effect contrasts between species was similar to those between populations, and was comparable to those between fish species and populations measured in previous common gardening experiments. Our results suggest that subtle morphological variation among and within species can cause multifarious and divergent ecosystem-effects. We conclude that using morphological trait variation to assess the functional similarity of organisms may underestimate the importance of species and population diversity for ecosystem functioning. PMID:22140432

Self-similar transmission properties of aperiodic Cantor potentials in gapped graphene

NASA Astrophysics Data System (ADS)

Rodríguez-González, Rogelio; Rodríguez-Vargas, Isaac; Díaz-Guerrero, Dan Sidney; Gaggero-Sager, Luis Manuel

2016-01-01

We investigate the transmission properties of quasiperiodic or aperiodic structures based on graphene arranged according to the Cantor sequence. In particular, we have found self-similar behaviour in the transmission spectra, and most importantly, we have calculated the scalability of the spectra. To do this, we implement and propose scaling rules for each one of the fundamental parameters: generation number, height of the barriers and length of the system. With this in mind we have been able to reproduce the reference transmission spectrum, applying the appropriate scaling rule, by means of the scaled transmission spectrum. These scaling rules are valid for both normal and oblique incidence, and as far as we can see the basic ingredients to obtain self-similar characteristics are: relativistic Dirac electrons, a self-similar structure and the non-conservation of the pseudo-spin.

Flame speed and self-similar propagation of expanding turbulent premixed flames.

PubMed

Chaudhuri, Swetaprovo; Wu, Fujia; Zhu, Delin; Law, Chung K

2012-01-27

In this Letter we present turbulent flame speeds and their scaling from experimental measurements on constant-pressure, unity Lewis number expanding turbulent flames, propagating in nearly homogeneous isotropic turbulence in a dual-chamber, fan-stirred vessel. It is found that the normalized turbulent flame speed as a function of the average radius scales as a turbulent Reynolds number to the one-half power, where the average radius is the length scale and the thermal diffusivity is the transport property, thus showing self-similar propagation. Utilizing this dependence it is found that the turbulent flame speeds from the present expanding flames and those from the Bunsen geometry in the literature can be unified by a turbulent Reynolds number based on flame length scales using recent theoretical results obtained by spectral closure of the transformed G equation.

Flame Speed and Self-Similar Propagation of Expanding Turbulent Premixed Flames

NASA Astrophysics Data System (ADS)

Chaudhuri, Swetaprovo; Wu, Fujia; Zhu, Delin; Law, Chung K.

2012-01-01

In this Letter we present turbulent flame speeds and their scaling from experimental measurements on constant-pressure, unity Lewis number expanding turbulent flames, propagating in nearly homogeneous isotropic turbulence in a dual-chamber, fan-stirred vessel. It is found that the normalized turbulent flame speed as a function of the average radius scales as a turbulent Reynolds number to the one-half power, where the average radius is the length scale and the thermal diffusivity is the transport property, thus showing self-similar propagation. Utilizing this dependence it is found that the turbulent flame speeds from the present expanding flames and those from the Bunsen geometry in the literature can be unified by a turbulent Reynolds number based on flame length scales using recent theoretical results obtained by spectral closure of the transformed G equation.

Holos: A collaborative environment for similarity-based holistic approaches.

PubMed

Lê, Tâm Minh; Brard, Margot; Lê, Sébastien

2017-10-01

Through this article, we aim to introduce Holos-a new collaborative environment that allows researchers to carry out experiments based on similarity assessments between stimuli, such as in projective-mapping and sorting tasks. An important feature of Holos is its capacity to assess real-time individual processes during the task. Within the Holos environment, researchers can design experiments on its platform, which can handle four kinds of stimuli: concepts, images, sounds, and videos. In addition, researchers can share their study resources within the scientific community, including stimuli, experimental protocols, and/or the data collected. With a dedicated Android application combined with a tactile human-machine interface, subjects can perform experiments using a tablet to obtain similarity measures between stimuli. On the tablet, the stimuli are displayed as icons that can be dragged with one finger to position them, depending on the ways they are perceived. By recording the x,y coordinates of the stimuli while subjects move the icons, the obtained data can reveal the cognitive processes of the subjects during the experiment. Such data, named digit-tracking data, can be analyzed with the SensoMineR package. In this article, we describe how researchers can design an experiment, how subjects can perform the experiment, and how digit-tracking data can be statistically analyzed within the Holos environment. At the end of the article, a short exemplary experiment is presented.

Predicting the performance of fingerprint similarity searching.

PubMed

Vogt, Martin; Bajorath, Jürgen

2011-01-01

Fingerprints are bit string representations of molecular structure that typically encode structural fragments, topological features, or pharmacophore patterns. Various fingerprint designs are utilized in virtual screening and their search performance essentially depends on three parameters: the nature of the fingerprint, the active compounds serving as reference molecules, and the composition of the screening database. It is of considerable interest and practical relevance to predict the performance of fingerprint similarity searching. A quantitative assessment of the potential that a fingerprint search might successfully retrieve active compounds, if available in the screening database, would substantially help to select the type of fingerprint most suitable for a given search problem. The method presented herein utilizes concepts from information theory to relate the fingerprint feature distributions of reference compounds to screening libraries. If these feature distributions do not sufficiently differ, active database compounds that are similar to reference molecules cannot be retrieved because they disappear in the "background." By quantifying the difference in feature distribution using the Kullback-Leibler divergence and relating the divergence to compound recovery rates obtained for different benchmark classes, fingerprint search performance can be quantitatively predicted.

Similarity and Congruence.

ERIC Educational Resources Information Center

Herman, Daniel L.

This instructional unit is an introduction to the common properties of similarity and congruence. Manipulation of objects leads to a recognition of these properties. The ASA, SAS, and SSS theorems are not mentioned. Limited use is made in the application of the properties of size and shape preserved by similarity or congruence. A teacher's guide…

A similarity based approach to identify homogeneous regions for seasonal forecasting

NASA Astrophysics Data System (ADS)

Schick, Simon; Rössler, Ole; Weingartner, Rolf

2015-04-01

Seasonal runoff forecasting using statistical models is challenged by a large number of candidate predictors and a general weak predictor-predictand relationship. As the area of the target basin increases, often also the available data sets do, thus reinforcing the predictor selection challenge. We propose an approach which follows the idea of 'divide and conquer' as developed in computational sciences and machine learning: First, the macroscale target basin is partitioned into homogeneous regions using all its gauged mesoscale subbasins. Second, one representative subbasin per homogeneous region is identified, for which models are fitted and applied. Third, the resulting forecasts are combined at the scale of the macroscale target basin. This approach requires a suitable method to identify homogeneous regions and representative subbasins. We suggest a way based on hydrological similarity, as catchment similarity estimated with respect to physiographic-climatic descriptors does not necessarily imply similar runoff response. Each descriptor is derived from daily runoff series and aimed to reflect a specific catchment characteristic: autocorrelation coefficient, parameters of fitted Gamma distribution and low/high flow indices (based on daily runoff values) fluctuation of the standard deviation within the yearly cycle (based on weekly runoff values) dominant harmonics obtained from the discrete Fourier transform (based on monthly runoff values) long term trend (based on yearly runoff values) Where necessary, the runoff series first need to be standardized, aggregated, detrended or deseasonalized. As a preliminary study we present the results of a cluster analysis for the Swiss Rhine River as macroscale target basin, which leads to about 40 mesoscale subbasins with runoff series for the period 1991-2010. Problems we have to address include the choice of a clustering algorithm, the identification of an appropriate number of regions and the selection of representative

Similarity, not complexity, determines visual working memory performance.

PubMed

Jackson, Margaret C; Linden, David E J; Roberts, Mark V; Kriegeskorte, Nikolaus; Haenschel, Corinna

2015-11-01

A number of studies have shown that visual working memory (WM) is poorer for complex versus simple items, traditionally accounted for by higher information load placing greater demands on encoding and storage capacity limits. Other research suggests that it may not be complexity that determines WM performance per se, but rather increased perceptual similarity between complex items as a result of a large amount of overlapping information. Increased similarity is thought to lead to greater comparison errors between items encoded into WM and the test item(s) presented at retrieval. However, previous studies have used different object categories to manipulate complexity and similarity, raising questions as to whether these effects are simply due to cross-category differences. For the first time, here the relationship between complexity and similarity in WM using the same stimulus category (abstract polygons) are investigated. The authors used a delayed discrimination task to measure WM for 1-4 complex versus simple simultaneously presented items and manipulated the similarity between the single test item at retrieval and the sample items at encoding. WM was poorer for complex than simple items only when the test item was similar to 1 of the encoding items, and not when it was dissimilar or identical. The results provide clear support for reinterpretation of the complexity effect in WM as a similarity effect and highlight the importance of the retrieval stage in governing WM performance. The authors discuss how these findings can be reconciled with current models of WM capacity limits. (c) 2015 APA, all rights reserved).

Some Remarks on Similarity and Soliton Solutions of Nonlinear Klein-Gordon Equation

NASA Astrophysics Data System (ADS)

Tajiri, Masayoshi

1984-11-01

The three-dimensional nonlinear Klein-Gordon [, Higgs field and Yang-Milles] (3D-KG [, H and YM]) equation is first reduced to the 2D nonlinear Schrödinger (2D-NLS) and 2D-KG [, H and YM] equations, and secondly to the 1D-NLS and 1D-KG [, H and YM] equations by similarity transformations. It is shown that similar type soliton solutions of the 3D-KG, H and YM equations, which have singularity on a plane in (x, y, z, t) space, are obtained by substituting the soliton solutions of the 1D-NLS or 1D-KG (or H) equation into the similarity transformations. The soliton solutions of the YM equation are also investigated.

Similarity indices of meteo-climatic gauging stations: definition and comparison.

PubMed

Barca, Emanuele; Bruno, Delia Evelina; Passarella, Giuseppe

2016-07-01

Space-time dependencies among monitoring network stations have been investigated to detect and quantify similarity relationships among gauging stations. In this work, besides the well-known rank correlation index, two new similarity indices have been defined and applied to compute the similarity matrix related to the Apulian meteo-climatic monitoring network. The similarity matrices can be applied to address reliably the issue of missing data in space-time series. In order to establish the effectiveness of the similarity indices, a simulation test was then designed and performed with the aim of estimating missing monthly rainfall rates in a suitably selected gauging station. The results of the simulation allowed us to evaluate the effectiveness of the proposed similarity indices. Finally, the multiple imputation by chained equations method was used as a benchmark to have an absolute yardstick for comparing the outcomes of the test. In conclusion, the new proposed multiplicative similarity index resulted at least as reliable as the selected benchmark.

Sub-Network Kernels for Measuring Similarity of Brain Connectivity Networks in Disease Diagnosis.

PubMed

Jie, Biao; Liu, Mingxia; Zhang, Daoqiang; Shen, Dinggang

2018-05-01

As a simple representation of interactions among distributed brain regions, brain networks have been widely applied to automated diagnosis of brain diseases, such as Alzheimer's disease (AD) and its early stage, i.e., mild cognitive impairment (MCI). In brain network analysis, a challenging task is how to measure the similarity between a pair of networks. Although many graph kernels (i.e., kernels defined on graphs) have been proposed for measuring the topological similarity of a pair of brain networks, most of them are defined using general graphs, thus ignoring the uniqueness of each node in brain networks. That is, each node in a brain network denotes a particular brain region, which is a specific characteristics of brain networks. Accordingly, in this paper, we construct a novel sub-network kernel for measuring the similarity between a pair of brain networks and then apply it to brain disease classification. Different from current graph kernels, our proposed sub-network kernel not only takes into account the inherent characteristic of brain networks, but also captures multi-level (from local to global) topological properties of nodes in brain networks, which are essential for defining the similarity measure of brain networks. To validate the efficacy of our method, we perform extensive experiments on subjects with baseline functional magnetic resonance imaging data obtained from the Alzheimer's disease neuroimaging initiative database. Experimental results demonstrate that the proposed method outperforms several state-of-the-art graph-based methods in MCI classification.

A Weighted Multipath Measurement Based on Gene Ontology for Estimating Gene Products Similarity

PubMed Central

Liu, Lizhen; Dai, Xuemin; Song, Wei; Lu, Jingli

2014-01-01

Abstract Many different methods have been proposed for calculating the semantic similarity of term pairs based on gene ontology (GO). Most existing methods are based on information content (IC), and the methods based on IC are used more commonly than those based on the structure of GO. However, most IC-based methods not only fail to handle identical annotations but also show a strong bias toward well-annotated proteins. We propose a new method called weighted multipath measurement (WMM) for estimating the semantic similarity of gene products based on the structure of the GO. We not only considered the contribution of every path between two GO terms but also took the depth of the lowest common ancestors into account. We assigned different weights for different kinds of edges in GO graph. The similarity values calculated by WMM can be reused because they are only relative to the characteristics of GO terms. Experimental results showed that the similarity values obtained by WMM have a higher accuracy. We compared the performance of WMM with that of other methods using GO data and gene annotation datasets for yeast and humans downloaded from the GO database. We found that WMM is more suited for prediction of gene function than most existing IC-based methods and that it can distinguish proteins with identical annotations (two proteins are annotated with the same terms) from each other. PMID:25229994

Similarity principles for the biology of pelagic animals

PubMed Central

Barenblatt, G. I.; Monin, A. S.

1983-01-01

A similarity principle is formulated according to which the statistical pattern of the pelagic population is identical in all scales sufficiently large in comparison with the molecular one. From this principle, a power law is obtained analytically for the pelagic animal biomass distribution over the animal sizes. A hypothesis is presented according to which, under fixed external conditions, the oxygen exchange intensity of an animal is governed only by its mass and density and by the specific absorbing capacity of the animal's respiratory organ. From this hypothesis a power law is obtained by the method of dimensional analysis for the exchange intensity mass dependence. The known empirical values of the exponent of this power law are interpreted as an indication that the oxygen-absorbing organs of the animals can be represented as so-called fractal surfaces. In conclusion the biological principle of the decrease in specific exchange intensity with increase in animal mass is discussed. PMID:16593327

Semantic similarity measures in the biomedical domain by leveraging a web search engine.

PubMed

Hsieh, Sheau-Ling; Chang, Wen-Yung; Chen, Chi-Huang; Weng, Yung-Ching

2013-07-01

Various researches in web related semantic similarity measures have been deployed. However, measuring semantic similarity between two terms remains a challenging task. The traditional ontology-based methodologies have a limitation that both concepts must be resided in the same ontology tree(s). Unfortunately, in practice, the assumption is not always applicable. On the other hand, if the corpus is sufficiently adequate, the corpus-based methodologies can overcome the limitation. Now, the web is a continuous and enormous growth corpus. Therefore, a method of estimating semantic similarity is proposed via exploiting the page counts of two biomedical concepts returned by Google AJAX web search engine. The features are extracted as the co-occurrence patterns of two given terms P and Q, by querying P, Q, as well as P AND Q, and the web search hit counts of the defined lexico-syntactic patterns. These similarity scores of different patterns are evaluated, by adapting support vector machines for classification, to leverage the robustness of semantic similarity measures. Experimental results validating against two datasets: dataset 1 provided by A. Hliaoutakis; dataset 2 provided by T. Pedersen, are presented and discussed. In dataset 1, the proposed approach achieves the best correlation coefficient (0.802) under SNOMED-CT. In dataset 2, the proposed method obtains the best correlation coefficient (SNOMED-CT: 0.705; MeSH: 0.723) with physician scores comparing with measures of other methods. However, the correlation coefficients (SNOMED-CT: 0.496; MeSH: 0.539) with coder scores received opposite outcomes. In conclusion, the semantic similarity findings of the proposed method are close to those of physicians' ratings. Furthermore, the study provides a cornerstone investigation for extracting fully relevant information from digitizing, free-text medical records in the National Taiwan University Hospital database.

Representational Similarity of Body Parts in Human Occipitotemporal Cortex.

PubMed

Bracci, Stefania; Caramazza, Alfonso; Peelen, Marius V

2015-09-23

Regions in human lateral and ventral occipitotemporal cortices (OTC) respond selectively to pictures of the human body and its parts. What are the organizational principles underlying body part responses in these regions? Here we used representational similarity analysis (RSA) of fMRI data to test multiple possible organizational principles: shape similarity, physical proximity, cortical homunculus proximity, and semantic similarity. Participants viewed pictures of whole persons, chairs, and eight body parts (hands, arms, legs, feet, chests, waists, upper faces, and lower faces). The similarity of multivoxel activity patterns for all body part pairs was established in whole person-selective OTC regions. The resulting neural similarity matrices were then compared with similarity matrices capturing the hypothesized organizational principles. Results showed that the semantic similarity model best captured the neural similarity of body parts in lateral and ventral OTC, which followed an organization in three clusters: (1) body parts used as action effectors (hands, feet, arms, and legs), (2) noneffector body parts (chests and waists), and (3) face parts (upper and lower faces). Whole-brain RSA revealed, in addition to OTC, regions in parietal and frontal cortex in which neural similarity was related to semantic similarity. In contrast, neural similarity in occipital cortex was best predicted by shape similarity models. We suggest that the semantic organization of body parts in high-level visual cortex relates to the different functions associated with the three body part clusters, reflecting the unique processing and connectivity demands associated with the different types of information (e.g., action, social) different body parts (e.g., limbs, faces) convey. Significance statement: While the organization of body part representations in motor and somatosensory cortices has been well characterized, the principles underlying body part representations in visual cortex

Reliability and Accuracy of Static Parameters Obtained From Ink and Pressure Platform Footprints.

PubMed

Zuil-Escobar, Juan Carlos; Martínez-Cepa, Carmen Belén; Martín-Urrialde, Jose Antonio; Gómez-Conesa, Antonia

2016-09-01

The purpose of this study was to evaluate the accuracy and the intrarater reliability of arch angle (AA), Staheli Index (SI), and Chippaux-Smirak Index (CSI) obtained from ink and pressure platform footprints. We obtained AA, SI, and CSI measurements from ink pedigraph footprints and pressure platform footprints in 40 healthy participants (aged 25.65 ± 5.187 years). Intrarater reliability was calculated for all parameters obtained using the 2 methods. Standard error of measurement and minimal detectable change were also calculated. A repeated-measure analysis of variance was used to identify differences between ink and pressure platform footprints. Intraclass correlation coefficient and Bland and Altman plots were used to assess similar parameters obtained using different methods. Intrarater reliability was >0.9 for all parameters and was slightly higher for the ink footprints. No statistical difference was reported in repeated-measure analysis of variance for any of the parameters. Intraclass correlation coefficient values from AA, SI, and CSI that were obtained using ink footprints and pressure platform footprints were excellent, ranging from 0.797 to 0.829. However, pressure platform overestimated AA and underestimated SI and CSI. Our study revealed that AA, SI, and CSI were similar regardless of whether the ink or pressure platform method was used. In addition, the parameters indicated high intrarater reliability and were reproducible. Copyright © 2016. Published by Elsevier Inc.

Scale-Similar Models for Large-Eddy Simulations

NASA Technical Reports Server (NTRS)

Sarghini, F.

1999-01-01

Scale-similar models employ multiple filtering operations to identify the smallest resolved scales, which have been shown to be the most active in the interaction with the unresolved subgrid scales. They do not assume that the principal axes of the strain-rate tensor are aligned with those of the subgrid-scale stress (SGS) tensor, and allow the explicit calculation of the SGS energy. They can provide backscatter in a numerically stable and physically realistic manner, and predict SGS stresses in regions that are well correlated with the locations where large Reynolds stress occurs. In this paper, eddy viscosity and mixed models, which include an eddy-viscosity part as well as a scale-similar contribution, are applied to the simulation of two flows, a high Reynolds number plane channel flow, and a three-dimensional, nonequilibrium flow. The results show that simulations without models or with the Smagorinsky model are unable to predict nonequilibrium effects. Dynamic models provide an improvement of the results: the adjustment of the coefficient results in more accurate prediction of the perturbation from equilibrium. The Lagrangian-ensemble approach [Meneveau et al., J. Fluid Mech. 319, 353 (1996)] is found to be very beneficial. Models that included a scale-similar term and a dissipative one, as well as the Lagrangian ensemble averaging, gave results in the best agreement with the direct simulation and experimental data.

Studies on microstructure, mechanical and pitting corrosion behaviour of similar and dissimilar stainless steel gas tungsten arc welds

NASA Astrophysics Data System (ADS)

Mohammed, Raffi; Dilkush; Srinivasa Rao, K.; Madhusudhan Reddy, G.

2018-03-01

In the present study, an attempt has been made to weld dissimilar alloys of 5mm thick plates i.e., austenitic stainless steel (316L) and duplex stainless steel (2205) and compared with that of similar welds. Welds are made with conventional gas tungsten arc welding (GTAW) process with two different filler wires namely i.e., 309L and 2209. Welds were characterized using optical microscopy to observe the microstructural changes and correlate with mechanical properties using hardness, tensile and impact testing. Potentio-dynamic polarization studies were carried out to observe the pitting corrosion behaviour in different regions of the welds. Results of the present study established that change in filler wire composition resulted in microstructural variation in all the welds with different morphology of ferrite and austenite. Welds made with 2209 filler showed plate like widmanstatten austenite (WA) nucleated at grain boundaries. Compared to similar stainless steel welds inferior mechanical properties was observed in dissimilar stainless steel welds. Pitting corrosion resistance is observed to be low for dissimilar stainless steel welds when compared to similar stainless steel welds. Overall study showed that similar duplex stainless steel welds having favorable microstructure and resulted in better mechanical properties and corrosion resistance. Relatively dissimilar stainless steel welds made with 309L filler obtained optimum combination of mechanical properties and pitting corrosion resistance when compared to 2209 filler and is recommended for industrial practice.

Application of discrete Fourier inter-coefficient difference for assessing genetic sequence similarity.

PubMed

King, Brian R; Aburdene, Maurice; Thompson, Alex; Warres, Zach

2014-01-01

Digital signal processing (DSP) techniques for biological sequence analysis continue to grow in popularity due to the inherent digital nature of these sequences. DSP methods have demonstrated early success for detection of coding regions in a gene. Recently, these methods are being used to establish DNA gene similarity. We present the inter-coefficient difference (ICD) transformation, a novel extension of the discrete Fourier transformation, which can be applied to any DNA sequence. The ICD method is a mathematical, alignment-free DNA comparison method that generates a genetic signature for any DNA sequence that is used to generate relative measures of similarity among DNA sequences. We demonstrate our method on a set of insulin genes obtained from an evolutionarily wide range of species, and on a set of avian influenza viral sequences, which represents a set of highly similar sequences. We compare phylogenetic trees generated using our technique against trees generated using traditional alignment techniques for similarity and demonstrate that the ICD method produces a highly accurate tree without requiring an alignment prior to establishing sequence similarity.

Student and Professor Similarity: Exploring the Effects of Gender and Relative Age

ERIC Educational Resources Information Center

Gehrt, Kenneth; Louie, Therese A.; Osland, Asbjorn

2015-01-01

The authors examined student responses to faculty traits. Earlier findings revealing a preference for male instructors were obtained before female faculty and students were prevalent on college campuses and may have reflected a male demographic similarity effect. It was hypothesized that students would more favorably evaluate faculty who were…

Similarity analysis between quantum images

NASA Astrophysics Data System (ADS)

Zhou, Ri-Gui; Liu, XingAo; Zhu, Changming; Wei, Lai; Zhang, Xiafen; Ian, Hou

2018-06-01

Similarity analyses between quantum images are so essential in quantum image processing that it provides fundamental research for the other fields, such as quantum image matching, quantum pattern recognition. In this paper, a quantum scheme based on a novel quantum image representation and quantum amplitude amplification algorithm is proposed. At the end of the paper, three examples and simulation experiments show that the measurement result must be 0 when two images are same, and the measurement result has high probability of being 1 when two images are different.

Explosion Source Similarity Analysis via SVD

NASA Astrophysics Data System (ADS)

Yedlin, Matthew; Ben Horin, Yochai; Margrave, Gary

2016-04-01

An important seismological ingredient for establishing a regional seismic nuclear discriminant is the similarity analysis of a sequence of explosion sources. To investigate source similarity, we are fortunate to have access to a sequence of 1805 three-component recordings of quarry blasts, shot from March 2002 to January 2015. The centroid of these blasts has an estimated location 36.3E and 29.9N. All blasts were detonated by JPMC (Jordan Phosphate Mines Co.) All data were recorded at the Israeli NDC, HFRI, located at 30.03N and 35.03E. Data were first winnowed based on the distribution of maximum amplitudes in the neighborhood of the P-wave arrival. The winnowed data were then detrended using the algorithm of Cleveland et al (1990). The detrended data were bandpass filtered between .1 to 12 Hz using an eighth order Butterworth filter. Finally, data were sorted based on maximum trace amplitude. Two similarity analysis approaches were used. First, for each component, the entire suite of traces was decomposed into its eigenvector representation, by employing singular-valued decomposition (SVD). The data were then reconstructed using 10 percent of the singular values, with the resulting enhancement of the S-wave and surface wave arrivals. The results of this first method are then compared to the second analysis method based on the eigenface decomposition analysis of Turk and Pentland (1991). While both methods yield similar results in enhancement of data arrivals and reduction of data redundancy, more analysis is required to calibrate the recorded data to charge size, a quantity that was not available for the current study. References Cleveland, R. B., Cleveland, W. S., McRae, J. E., and Terpenning, I., Stl: A seasonal-trend decomposition procedure based on loess, Journal of Official Statistics, 6, No. 1, 3-73, 1990. Turk, M. and Pentland, A., Eigenfaces for recognition. Journal of cognitive neuroscience, 3(1), 71-86, 1991.

Quality assessment of protein model-structures based on structural and functional similarities

PubMed Central

2012-01-01

Background Experimental determination of protein 3D structures is expensive, time consuming and sometimes impossible. A gap between number of protein structures deposited in the World Wide Protein Data Bank and the number of sequenced proteins constantly broadens. Computational modeling is deemed to be one of the ways to deal with the problem. Although protein 3D structure prediction is a difficult task, many tools are available. These tools can model it from a sequence or partial structural information, e.g. contact maps. Consequently, biologists have the ability to generate automatically a putative 3D structure model of any protein. However, the main issue becomes evaluation of the model quality, which is one of the most important challenges of structural biology. Results GOBA - Gene Ontology-Based Assessment is a novel Protein Model Quality Assessment Program. It estimates the compatibility between a model-structure and its expected function. GOBA is based on the assumption that a high quality model is expected to be structurally similar to proteins functionally similar to the prediction target. Whereas DALI is used to measure structure similarity, protein functional similarity is quantified using standardized and hierarchical description of proteins provided by Gene Ontology combined with Wang's algorithm for calculating semantic similarity. Two approaches are proposed to express the quality of protein model-structures. One is a single model quality assessment method, the other is its modification, which provides a relative measure of model quality. Exhaustive evaluation is performed on data sets of model-structures submitted to the CASP8 and CASP9 contests. Conclusions The validation shows that the method is able to discriminate between good and bad model-structures. The best of tested GOBA scores achieved 0.74 and 0.8 as a mean Pearson correlation to the observed quality of models in our CASP8 and CASP9-based validation sets. GOBA also obtained the best

A literature-driven method to calculate similarities among diseases.

PubMed

Kim, Hyunjin; Yoon, Youngmi; Ahn, Jaegyoon; Park, Sanghyun

2015-11-01

"Our lives are connected by a thousand invisible threads and along these sympathetic fibers, our actions run as causes and return to us as results". It is Herman Melville's famous quote describing connections among human lives. To paraphrase the Melville's quote, diseases are connected by many functional threads and along these sympathetic fibers, diseases run as causes and return as results. The Melville's quote explains the reason for researching disease-disease similarity and disease network. Measuring similarities between diseases and constructing disease network can play an important role in disease function research and in disease treatment. To estimate disease-disease similarities, we proposed a novel literature-based method. The proposed method extracted disease-gene relations and disease-drug relations from literature and used the frequencies of occurrence of the relations as features to calculate similarities among diseases. We also constructed disease network with top-ranking disease pairs from our method. The proposed method discovered a larger number of answer disease pairs than other comparable methods and showed the lowest p-value. We presume that our method showed good results because of using literature data, using all possible gene symbols and drug names for features of a disease, and determining feature values of diseases with the frequencies of co-occurrence of two entities. The disease-disease similarities from the proposed method can be used in computational biology researches which use similarities among diseases. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

SGFSC: speeding the gene functional similarity calculation based on hash tables.

PubMed

Tian, Zhen; Wang, Chunyu; Guo, Maozu; Liu, Xiaoyan; Teng, Zhixia

2016-11-04

In recent years, many measures of gene functional similarity have been proposed and widely used in all kinds of essential research. These methods are mainly divided into two categories: pairwise approaches and group-wise approaches. However, a common problem with these methods is their time consumption, especially when measuring the gene functional similarities of a large number of gene pairs. The problem of computational efficiency for pairwise approaches is even more prominent because they are dependent on the combination of semantic similarity. Therefore, the efficient measurement of gene functional similarity remains a challenging problem. To speed current gene functional similarity calculation methods, a novel two-step computing strategy is proposed: (1) establish a hash table for each method to store essential information obtained from the Gene Ontology (GO) graph and (2) measure gene functional similarity based on the corresponding hash table. There is no need to traverse the GO graph repeatedly for each method with the help of the hash table. The analysis of time complexity shows that the computational efficiency of these methods is significantly improved. We also implement a novel Speeding Gene Functional Similarity Calculation tool, namely SGFSC, which is bundled with seven typical measures using our proposed strategy. Further experiments show the great advantage of SGFSC in measuring gene functional similarity on the whole genomic scale. The proposed strategy is successful in speeding current gene functional similarity calculation methods. SGFSC is an efficient tool that is freely available at http://nclab.hit.edu.cn/SGFSC . The source code of SGFSC can be downloaded from http://pan.baidu.com/s/1dFFmvpZ .

Suspect filler similarity in eyewitness lineups: a literature review and a novel methodology.

PubMed

Fitzgerald, Ryan J; Oriet, Chris; Price, Heather L

2015-02-01

Eyewitness lineups typically contain a suspect (guilty or innocent) and fillers (known innocents). The degree to which fillers should resemble the suspect is a complex issue that has yet to be resolved. Previously, researchers have voiced concern that eyewitnesses would be unable to identify their target from a lineup containing highly similar fillers; however, our literature review suggests highly similar fillers have only rarely been shown to have this effect. To further examine the effect of highly similar fillers on lineup responses, we used morphing software to create fillers of moderately high and very high similarity to the suspect. When the culprit was in the lineup, a higher correct identification rate was observed in moderately high similarity lineups than in very high similarity lineups. When the culprit was absent, similarity did not yield a significant effect on innocent suspect misidentification rates. However, the correct rejection rate in the moderately high similarity lineup was 20% higher than in the very high similarity lineup. When choosing rates were controlled by calculating identification probabilities for only those who made a selection from the lineup, culprit identification rates as well as innocent suspect misidentification rates were significantly higher in the moderately high similarity lineup than in the very high similarity lineup. Thus, very high similarity fillers yielded costs and benefits. Although our research suggests that selecting the most similar fillers available may adversely affect correct identification rates, we recommend additional research using fillers obtained from police databases to corroborate our findings.

TumorMap: Exploring the Molecular Similarities of Cancer Samples in an Interactive Portal.

PubMed

Newton, Yulia; Novak, Adam M; Swatloski, Teresa; McColl, Duncan C; Chopra, Sahil; Graim, Kiley; Weinstein, Alana S; Baertsch, Robert; Salama, Sofie R; Ellrott, Kyle; Chopra, Manu; Goldstein, Theodore C; Haussler, David; Morozova, Olena; Stuart, Joshua M

2017-11-01

Vast amounts of molecular data are being collected on tumor samples, which provide unique opportunities for discovering trends within and between cancer subtypes. Such cross-cancer analyses require computational methods that enable intuitive and interactive browsing of thousands of samples based on their molecular similarity. We created a portal called TumorMap to assist in exploration and statistical interrogation of high-dimensional complex "omics" data in an interactive and easily interpretable way. In the TumorMap, samples are arranged on a hexagonal grid based on their similarity to one another in the original genomic space and are rendered with Google's Map technology. While the important feature of this public portal is the ability for the users to build maps from their own data, we pre-built genomic maps from several previously published projects. We demonstrate the utility of this portal by presenting results obtained from The Cancer Genome Atlas project data. Cancer Res; 77(21); e111-4. ©2017 AACR . ©2017 American Association for Cancer Research.

Alphabetic letter identification: Effects of perceivability, similarity, and bias☆

PubMed Central

Mueller, Shane T.; Weidemann, Christoph T.

2012-01-01

The legibility of the letters in the Latin alphabet has been measured numerous times since the beginning of experimental psychology. To identify the theoretical mechanisms attributed to letter identification, we report a comprehensive review of literature, spanning more than a century. This review revealed that identification accuracy has frequently been attributed to a subset of three common sources: perceivability, bias, and similarity. However, simultaneous estimates of these values have rarely (if ever) been performed. We present the results of two new experiments which allow for the simultaneous estimation of these factors, and examine how the shape of a visual mask impacts each of them, as inferred through a new statistical model. Results showed that the shape and identity of the mask impacted the inferred perceivability, bias, and similarity space of a letter set, but that there were aspects of similarity that were robust to the choice of mask. The results illustrate how the psychological concepts of perceivability, bias, and similarity can be estimated simultaneously, and how each make powerful contributions to visual letter identification. PMID:22036587

Consumption of Milk Protein or Whey Protein Results in a Similar Increase in Muscle Protein Synthesis in Middle Aged Men

PubMed Central

Mitchell, Cameron J.; McGregor, Robin A.; D’Souza, Randall F.; Thorstensen, Eric B.; Markworth, James F.; Fanning, Aaron C.; Poppitt, Sally D.; Cameron-Smith, David

2015-01-01

The differential ability of various milk protein fractions to stimulate muscle protein synthesis (MPS) has been previously described, with whey protein generally considered to be superior to other fractions. However, the relative ability of a whole milk protein to stimulate MPS has not been compared to whey. Sixteen healthy middle-aged males ingested either 20 g of milk protein (n = 8) or whey protein (n = 8) while undergoing a primed constant infusion of ring 13C6 phenylalanine. Muscle biopsies were obtained 120 min prior to consumption of the protein and 90 and 210 min afterwards. Resting myofibrillar fractional synthetic rates (FSR) were 0.019% ± 0.009% and 0.021% ± 0.018% h−1 in the milk and whey groups respectively. For the first 90 min after protein ingestion the FSR increased (p < 0.001) to 0.057% ± 0.018% and 0.052% ± 0.024% h−1 in the milk and whey groups respectively with no difference between groups (p = 0.810). FSR returned to baseline in both groups between 90 and 210 min after protein ingestion. Despite evidence of increased rate of digestion and leucine availability following the ingestion of whey protein, there was similar activation of MPS in middle-aged men with either 20 g of milk protein or whey protein. PMID:26506377

Personality similarity in negotiations: Testing the dyadic effects of similarity in interpersonal traits and the use of emotional displays on negotiation outcomes.

PubMed

Wilson, Kelly Schwind; DeRue, D Scott; Matta, Fadel K; Howe, Michael; Conlon, Donald E

2016-10-01

We build on the small but growing literature documenting personality influences on negotiation by examining how the joint disposition of both negotiators with respect to the interpersonal traits of agreeableness and extraversion influences important negotiation processes and outcomes. Building on similarity-attraction theory, we articulate and demonstrate how being similarly high or similarly low on agreeableness and extraversion leads dyad members to express more positive emotional displays during negotiation. Moreover, because of increased positive emotional displays, we show that dyads with such compositions also tend to reach agreements faster, perceive less relationship conflict, and have more positive impressions of their negotiation partner. Interestingly, these results hold regardless of whether negotiating dyads are similar in normatively positive (i.e., similarly agreeable and similarly extraverted) or normatively negative (i.e., similarly disagreeable and similarly introverted) ways. Overall, these findings demonstrate the importance of considering the dyad's personality configuration when attempting to understand the affective experience as well as the downstream outcomes of a negotiation. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Pressure probe and isopiestic psychrometer measure similar turgor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nonami, H.; Boyer, J.S.; Steudle, E.

1987-03-01

Turgor measured with a miniature pressure probe was compared to that measured with an isopiestic thermocouple psychrometer in mature regions of soybean (Glycine max (L.) Merr.) stems. The probe measured turgor directly in cells of intact stems whereas the psychrometer measured the water potential and osmotic potential of excised stem segments and turgor was calculated by difference. When care was taken to prevent dehydration when working with the pressure probe, and diffusive resistance and dilution errors with the psychrometer, both methods gave similar values of turgor whether the plants were dehydrating or rehydrating. This finding, together with the previously demonstratedmore » similarity in turgor measured with the isopiestic psychrometer and a pressure chamber, indicates that the pressure probe provides accurate measurements of turgor despite the need to penetrate the cell. On the other hand, it suggest that as long as precautions are taken to obtain accurate values for the water potential and osmotic potential, turgor can be determined by isopiestic psychrometry in tissues not accessible to the pressure probe for physical reasons.« less

Pressure probe and isopiestic psychrometer measure similar turgor.

PubMed

Nonami, H; Boyer, J S; Steudle, E

1987-03-01

Turgor measured with a miniature pressure probe was compared to that measured with an isopiestic thermocouple psychrometer in mature regions of soybean (Glycine max [L.] Merr.) stems. The probe measured turgor directly in cells of intact stems whereas the psychrometer measured the water potential and osmotic potential of excised stem segments and turgor was calculated by difference. When care was taken to prevent dehydration when working with the pressure probe, and diffusive resistance and dilution errors with the psychrometer, both methods gave similar values of turgor whether the plants were dehydrating or rehydrating. This finding, together with the previously demonstrated similarity in turgor measured with the isopiestic psychrometer and a pressure chamber, indicates that the pressure probe provides accurate measurements of turgor despite the need to penetrate the cell. On the other hand, it suggests that as long as precautions are taken to obtain accurate values for the water potential and osmotic potential, turgor can be determined by isopiestic psychrometry in tissues not accessible to the pressure probe for physical reasons.

simDEF: definition-based semantic similarity measure of gene ontology terms for functional similarity analysis of genes.

PubMed

Pesaranghader, Ahmad; Matwin, Stan; Sokolova, Marina; Beiko, Robert G

2016-05-01

Measures of protein functional similarity are essential tools for function prediction, evaluation of protein-protein interactions (PPIs) and other applications. Several existing methods perform comparisons between proteins based on the semantic similarity of their GO terms; however, these measures are highly sensitive to modifications in the topological structure of GO, tend to be focused on specific analytical tasks and concentrate on the GO terms themselves rather than considering their textual definitions. We introduce simDEF, an efficient method for measuring semantic similarity of GO terms using their GO definitions, which is based on the Gloss Vector measure commonly used in natural language processing. The simDEF approach builds optimized definition vectors for all relevant GO terms, and expresses the similarity of a pair of proteins as the cosine of the angle between their definition vectors. Relative to existing similarity measures, when validated on a yeast reference database, simDEF improves correlation with sequence homology by up to 50%, shows a correlation improvement >4% with gene expression in the biological process hierarchy of GO and increases PPI predictability by > 2.5% in F1 score for molecular function hierarchy. Datasets, results and source code are available at http://kiwi.cs.dal.ca/Software/simDEF CONTACT: ahmad.pgh@dal.ca or beiko@cs.dal.ca Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Estimating mutual information using B-spline functions – an improved similarity measure for analysing gene expression data

PubMed Central

Daub, Carsten O; Steuer, Ralf; Selbig, Joachim; Kloska, Sebastian

2004-01-01

Background The information theoretic concept of mutual information provides a general framework to evaluate dependencies between variables. In the context of the clustering of genes with similar patterns of expression it has been suggested as a general quantity of similarity to extend commonly used linear measures. Since mutual information is defined in terms of discrete variables, its application to continuous data requires the use of binning procedures, which can lead to significant numerical errors for datasets of small or moderate size. Results In this work, we propose a method for the numerical estimation of mutual information from continuous data. We investigate the characteristic properties arising from the application of our algorithm and show that our approach outperforms commonly used algorithms: The significance, as a measure of the power of distinction from random correlation, is significantly increased. This concept is subsequently illustrated on two large-scale gene expression datasets and the results are compared to those obtained using other similarity measures. A C++ source code of our algorithm is available for non-commercial use from kloska@scienion.de upon request. Conclusion The utilisation of mutual information as similarity measure enables the detection of non-linear correlations in gene expression datasets. Frequently applied linear correlation measures, which are often used on an ad-hoc basis without further justification, are thereby extended. PMID:15339346

Distributed Efficient Similarity Search Mechanism in Wireless Sensor Networks

PubMed Central

Ahmed, Khandakar; Gregory, Mark A.

2015-01-01

The Wireless Sensor Network similarity search problem has received considerable research attention due to sensor hardware imprecision and environmental parameter variations. Most of the state-of-the-art distributed data centric storage (DCS) schemes lack optimization for similarity queries of events. In this paper, a DCS scheme with metric based similarity searching (DCSMSS) is proposed. DCSMSS takes motivation from vector distance index, called iDistance, in order to transform the issue of similarity searching into the problem of an interval search in one dimension. In addition, a sector based distance routing algorithm is used to efficiently route messages. Extensive simulation results reveal that DCSMSS is highly efficient and significantly outperforms previous approaches in processing similarity search queries. PMID:25751081

Self-similar cosmological solutions with dark energy. I. Formulation and asymptotic analysis

NASA Astrophysics Data System (ADS)

Harada, Tomohiro; Maeda, Hideki; Carr, B. J.

2008-01-01

Based on the asymptotic analysis of ordinary differential equations, we classify all spherically symmetric self-similar solutions to the Einstein equations which are asymptotically Friedmann at large distances and contain a perfect fluid with equation of state p=(γ-1)μ with 0<γ<2/3. This corresponds to a “dark energy” fluid and the Friedmann solution is accelerated in this case due to antigravity. This extends the previous analysis of spherically symmetric self-similar solutions for fluids with positive pressure (γ>1). However, in the latter case there is an additional parameter associated with the weak discontinuity at the sonic point and the solutions are only asymptotically “quasi-Friedmann,” in the sense that they exhibit an angle deficit at large distances. In the 0<γ<2/3 case, there is no sonic point and there exists a one-parameter family of solutions which are genuinely asymptotically Friedmann at large distances. We find eight classes of asymptotic behavior: Friedmann or quasi-Friedmann or quasistatic or constant-velocity at large distances, quasi-Friedmann or positive-mass singular or negative-mass singular at small distances, and quasi-Kantowski-Sachs at intermediate distances. The self-similar asymptotically quasistatic and quasi-Kantowski-Sachs solutions are analytically extendible and of great cosmological interest. We also investigate their conformal diagrams. The results of the present analysis are utilized in an accompanying paper to obtain and physically interpret numerical solutions.

Self-similar cosmological solutions with dark energy. I. Formulation and asymptotic analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harada, Tomohiro; Maeda, Hideki; Centro de Estudios Cientificos

2008-01-15

Based on the asymptotic analysis of ordinary differential equations, we classify all spherically symmetric self-similar solutions to the Einstein equations which are asymptotically Friedmann at large distances and contain a perfect fluid with equation of state p=({gamma}-1){mu} with 0<{gamma}<2/3. This corresponds to a 'dark energy' fluid and the Friedmann solution is accelerated in this case due to antigravity. This extends the previous analysis of spherically symmetric self-similar solutions for fluids with positive pressure ({gamma}>1). However, in the latter case there is an additional parameter associated with the weak discontinuity at the sonic point and the solutions are only asymptotically 'quasi-Friedmann',more » in the sense that they exhibit an angle deficit at large distances. In the 0<{gamma}<2/3 case, there is no sonic point and there exists a one-parameter family of solutions which are genuinely asymptotically Friedmann at large distances. We find eight classes of asymptotic behavior: Friedmann or quasi-Friedmann or quasistatic or constant-velocity at large distances, quasi-Friedmann or positive-mass singular or negative-mass singular at small distances, and quasi-Kantowski-Sachs at intermediate distances. The self-similar asymptotically quasistatic and quasi-Kantowski-Sachs solutions are analytically extendible and of great cosmological interest. We also investigate their conformal diagrams. The results of the present analysis are utilized in an accompanying paper to obtain and physically interpret numerical solutions.« less

Bovine lactoferrin binds oleic acid to form an anti-tumor complex similar to HAMLET.

PubMed

Fang, Bing; Zhang, Ming; Tian, Mai; Jiang, Lu; Guo, Hui Yuan; Ren, Fa Zheng

2014-04-04

α-Lactalbumin (α-LA) can bind oleic acid (OA) to form HAMLET-like complexes, which exhibited highly selective anti-tumor activity in vitro and in vivo. Considering the structural similarity to α-LA, we conjectured that lactoferrin (LF) could also bind OA to obtain a complex with anti-tumor activity. In this study, LF-OA was prepared and its activity and structural changes were compared with α-LA-OA. The anti-tumor activity was evaluated by methylene blue assay, while the apoptosis mechanism was analyzed using flow cytometry and Western blot. Structural changes of LF-OA were measured by fluorescence spectroscopy and circular dichroism. The interactions of OA with LF and α-LA were evaluated by isothermal titration calorimetry (ITC). LF-OA was obtained by heat-treatment at pH8.0 with LD50 of 4.88, 4.95 and 4.62μM for HepG2, HT29, and MCF-7 cells, respectively, all of which were 10 times higher than those of α-LA-OA. Similar to HAMLET, LF-OA induced apoptosis in tumor cells through both death receptor- and mitochondrial-mediated pathways. Exposure of tryptophan residues and the hydrophobic regions as well as the loss of tertiary structure were observed in LF-OA. Besides these similarities, LF showed different secondary structure changes when compared with α-LA, with a decrease of α-helix and β-turn and an increase of β-sheet and random coil. ITC results showed that there was a higher binding number of OA to LF than to α-LA, while both of the proteins interacted with OA through van der Waals forces and hydrogen bonds. This study provides a theoretical basis for further exploration of protein-OA complexes. Copyright © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

An Experimental Study on the Iso-Content-Based Angle Similarity Measure.

ERIC Educational Resources Information Center

Zhang, Jin; Rasmussen, Edie M.

2002-01-01

Retrieval performance of the iso-content-based angle similarity measure within the angle, distance, conjunction, disjunction, and ellipse retrieval models is compared with retrieval performance of the distance similarity measure and the angle similarity measure. Results show the iso-content-based angle similarity measure achieves satisfactory…

Earthquake Fingerprints: Representing Earthquake Waveforms for Similarity-Based Detection

NASA Astrophysics Data System (ADS)

Bergen, K.; Beroza, G. C.

2016-12-01

New earthquake detection methods, such as Fingerprint and Similarity Thresholding (FAST), use fast approximate similarity search to identify similar waveforms in long-duration data without templates (Yoon et al. 2015). These methods have two key components: fingerprint extraction and an efficient search algorithm. Fingerprint extraction converts waveforms into fingerprints, compact signatures that represent short-duration waveforms for identification and search. Earthquakes are detected using an efficient indexing and search scheme, such as locality-sensitive hashing, that identifies similar waveforms in a fingerprint database. The quality of the search results, and thus the earthquake detection results, is strongly dependent on the fingerprinting scheme. Fingerprint extraction should map similar earthquake waveforms to similar waveform fingerprints to ensure a high detection rate, even under additive noise and small distortions. Additionally, fingerprints corresponding to noise intervals should have mutually dissimilar fingerprints to minimize false detections. In this work, we compare the performance of multiple fingerprint extraction approaches for the earthquake waveform similarity search problem. We apply existing audio fingerprinting (used in content-based audio identification systems) and time series indexing techniques and present modified versions that are specifically adapted for seismic data. We also explore data-driven fingerprinting approaches that can take advantage of labeled or unlabeled waveform data. For each fingerprinting approach we measure its ability to identify similar waveforms in a low signal-to-noise setting, and quantify the trade-off between true and false detection rates in the presence of persistent noise sources. We compare the performance using known event waveforms from eight independent stations in the Northern California Seismic Network.

Weighted augmented Jacobian matrix with a variable coefficient method for kinematics mapping of space teleoperation based on human-robot motion similarity

NASA Astrophysics Data System (ADS)

Shi, Zhong; Huang, Xuexiang; Hu, Tianjian; Tan, Qian; Hou, Yuzhuo

2016-10-01

Space teleoperation is an important space technology, and human-robot motion similarity can improve the flexibility and intuition of space teleoperation. This paper aims to obtain an appropriate kinematics mapping method of coupled Cartesian-joint space for space teleoperation. First, the coupled Cartesian-joint similarity principles concerning kinematics differences are defined. Then, a novel weighted augmented Jacobian matrix with a variable coefficient (WAJM-VC) method for kinematics mapping is proposed. The Jacobian matrix is augmented to achieve a global similarity of human-robot motion. A clamping weighted least norm scheme is introduced to achieve local optimizations, and the operating ratio coefficient is variable to pursue similarity in the elbow joint. Similarity in Cartesian space and the property of joint constraint satisfaction is analysed to determine the damping factor and clamping velocity. Finally, a teleoperation system based on human motion capture is established, and the experimental results indicate that the proposed WAJM-VC method can improve the flexibility and intuition of space teleoperation to complete complex space tasks.

Statistical self-similarity of hotspot seamount volumes modeled as self-similar criticality

USGS Publications Warehouse

Tebbens, S.F.; Burroughs, S.M.; Barton, C.C.; Naar, D.F.

2001-01-01

The processes responsible for hotspot seamount formation are complex, yet the cumulative frequency-volume distribution of hotspot seamounts in the Easter Island/Salas y Gomez Chain (ESC) is found to be well-described by an upper-truncated power law. We develop a model for hotspot seamount formation where uniform energy input produces events initiated on a self-similar distribution of critical cells. We call this model Self-Similar Criticality (SSC). By allowing the spatial distribution of magma migration to be self-similar, the SSC model recreates the observed ESC seamount volume distribution. The SSC model may have broad applicability to other natural systems.

Gender similarities and differences.

PubMed

Hyde, Janet Shibley

2014-01-01

Whether men and women are fundamentally different or similar has been debated for more than a century. This review summarizes major theories designed to explain gender differences: evolutionary theories, cognitive social learning theory, sociocultural theory, and expectancy-value theory. The gender similarities hypothesis raises the possibility of theorizing gender similarities. Statistical methods for the analysis of gender differences and similarities are reviewed, including effect sizes, meta-analysis, taxometric analysis, and equivalence testing. Then, relying mainly on evidence from meta-analyses, gender differences are reviewed in cognitive performance (e.g., math performance), personality and social behaviors (e.g., temperament, emotions, aggression, and leadership), and psychological well-being. The evidence on gender differences in variance is summarized. The final sections explore applications of intersectionality and directions for future research.

Determining similarity in histological images using graph-theoretic description and matching methods for content-based image retrieval in medical diagnostics.

PubMed

Sharma, Harshita; Alekseychuk, Alexander; Leskovsky, Peter; Hellwich, Olaf; Anand, R S; Zerbe, Norman; Hufnagl, Peter

2012-10-04

Computer-based analysis of digitalized histological images has been gaining increasing attention, due to their extensive use in research and routine practice. The article aims to contribute towards the description and retrieval of histological images by employing a structural method using graphs. Due to their expressive ability, graphs are considered as a powerful and versatile representation formalism and have obtained a growing consideration especially by the image processing and computer vision community. The article describes a novel method for determining similarity between histological images through graph-theoretic description and matching, for the purpose of content-based retrieval. A higher order (region-based) graph-based representation of breast biopsy images has been attained and a tree-search based inexact graph matching technique has been employed that facilitates the automatic retrieval of images structurally similar to a given image from large databases. The results obtained and evaluation performed demonstrate the effectiveness and superiority of graph-based image retrieval over a common histogram-based technique. The employed graph matching complexity has been reduced compared to the state-of-the-art optimal inexact matching methods by applying a pre-requisite criterion for matching of nodes and a sophisticated design of the estimation function, especially the prognosis function. The proposed method is suitable for the retrieval of similar histological images, as suggested by the experimental and evaluation results obtained in the study. It is intended for the use in Content Based Image Retrieval (CBIR)-requiring applications in the areas of medical diagnostics and research, and can also be generalized for retrieval of different types of complex images. The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1224798882787923.

Protein structural similarity search by Ramachandran codes

PubMed Central

Lo, Wei-Cheng; Huang, Po-Jung; Chang, Chih-Hung; Lyu, Ping-Chiang

2007-01-01

Background Protein structural data has increased exponentially, such that fast and accurate tools are necessary to access structure similarity search. To improve the search speed, several methods have been designed to reduce three-dimensional protein structures to one-dimensional text strings that are then analyzed by traditional sequence alignment methods; however, the accuracy is usually sacrificed and the speed is still unable to match sequence similarity search tools. Here, we aimed to improve the linear encoding methodology and develop efficient search tools that can rapidly retrieve structural homologs from large protein databases. Results We propose a new linear encoding method, SARST (Structural similarity search Aided by Ramachandran Sequential Transformation). SARST transforms protein structures into text strings through a Ramachandran map organized by nearest-neighbor clustering and uses a regenerative approach to produce substitution matrices. Then, classical sequence similarity search methods can be applied to the structural similarity search. Its accuracy is similar to Combinatorial Extension (CE) and works over 243,000 times faster, searching 34,000 proteins in 0.34 sec with a 3.2-GHz CPU. SARST provides statistically meaningful expectation values to assess the retrieved information. It has been implemented into a web service and a stand-alone Java program that is able to run on many different platforms. Conclusion As a database search method, SARST can rapidly distinguish high from low similarities and efficiently retrieve homologous structures. It demonstrates that the easily accessible linear encoding methodology has the potential to serve as a foundation for efficient protein structural similarity search tools. These search tools are supposed applicable to automated and high-throughput functional annotations or predictions for the ever increasing number of published protein structures in this post-genomic era. PMID:17716377

Link-Based Similarity Measures Using Reachability Vectors

PubMed Central

Yoon, Seok-Ho; Kim, Ji-Soo; Ryu, Minsoo; Choi, Ho-Jin

2014-01-01

We present a novel approach for computing link-based similarities among objects accurately by utilizing the link information pertaining to the objects involved. We discuss the problems with previous link-based similarity measures and propose a novel approach for computing link based similarities that does not suffer from these problems. In the proposed approach each target object is represented by a vector. Each element of the vector corresponds to all the objects in the given data, and the value of each element denotes the weight for the corresponding object. As for this weight value, we propose to utilize the probability of reaching from the target object to the specific object, computed using the “Random Walk with Restart” strategy. Then, we define the similarity between two objects as the cosine similarity of the two vectors. In this paper, we provide examples to show that our approach does not suffer from the aforementioned problems. We also evaluate the performance of the proposed methods in comparison with existing link-based measures, qualitatively and quantitatively, with respect to two kinds of data sets, scientific papers and Web documents. Our experimental results indicate that the proposed methods significantly outperform the existing measures. PMID:24701188

Similarity of Turbulent Energy Scale Budget Equation of a Round Turbulent Jet

NASA Astrophysics Data System (ADS)

Sadeghi, Hamed; Lavoie, Philippe; Pollard, Andrew

2014-11-01

A novel extension to the similarity-based form of the transport equation for the second-order velocity structure function of <(δq) 2 > along the jet centreline (see Danaila et al., 2004) has been obtained. This new self-similar equation has the desirable benefit of requiring less extensive measurements to calculate the inhomogeneous (decay and production) terms of the transport equation. According to this equation, the normalized third-order structure function can be uniquely determined when the normalized second-order structure function, the power-law exponent of and the decay rate constants of and are available. In addition, on the basis of the current similarity analysis, the similarity assumptions in combination with power-law decay of mean velocity (U ~(x -x0) - 1) are strong enough to imply power-law decay of fluctuations ( ~(x -x0) m). The similarity solutions are then tested against new experimental data, which were taken along the centreline of a round jet at ReD = 50 , 000 . For the present set of initial conditions, exhibits a power-law behaviour with m = - 1 . 83 . This work was supported by grants from NSERC (Canada).

Probability of coincidental similarity among the orbits of small bodies - I. Pairing

NASA Astrophysics Data System (ADS)

Jopek, Tadeusz Jan; Bronikowska, Małgorzata

2017-09-01

Probability of coincidental clustering among orbits of comets, asteroids and meteoroids depends on many factors like: the size of the orbital sample searched for clusters or the size of the identified group, it is different for groups of 2,3,4,… members. Probability of coincidental clustering is assessed by the numerical simulation, therefore, it depends also on the method used for the synthetic orbits generation. We have tested the impact of some of these factors. For a given size of the orbital sample we have assessed probability of random pairing among several orbital populations of different sizes. We have found how these probabilities vary with the size of the orbital samples. Finally, keeping fixed size of the orbital sample we have shown that the probability of random pairing can be significantly different for the orbital samples obtained by different observation techniques. Also for the user convenience we have obtained several formulae which, for given size of the orbital sample can be used to calculate the similarity threshold corresponding to the small value of the probability of coincidental similarity among two orbits.

Using SQL Databases for Sequence Similarity Searching and Analysis.

PubMed

Pearson, William R; Mackey, Aaron J

2017-09-13

Relational databases can integrate diverse types of information and manage large sets of similarity search results, greatly simplifying genome-scale analyses. By focusing on taxonomic subsets of sequences, relational databases can reduce the size and redundancy of sequence libraries and improve the statistical significance of homologs. In addition, by loading similarity search results into a relational database, it becomes possible to explore and summarize the relationships between all of the proteins in an organism and those in other biological kingdoms. This unit describes how to use relational databases to improve the efficiency of sequence similarity searching and demonstrates various large-scale genomic analyses of homology-related data. It also describes the installation and use of a simple protein sequence database, seqdb_demo, which is used as a basis for the other protocols. The unit also introduces search_demo, a database that stores sequence similarity search results. The search_demo database is then used to explore the evolutionary relationships between E. coli proteins and proteins in other organisms in a large-scale comparative genomic analysis. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

Generalized self-similar unsteady gas flows behind the strong shock wave front

NASA Astrophysics Data System (ADS)

Bogatko, V. I.; Potekhina, E. A.

2018-05-01

Two-dimensional (plane and axially symmetric) nonstationary gas flows behind the front of a strong shock wave are considered. All the gas parameters are functions of the ratio of Cartesian coordinates to some degree of time tn, where n is a self-similarity index. The problem is solved in Lagrangian variables. It is shown that the resulting system of partial differential equations is suitable for constructing an iterative process. ¢he "thin shock layer" method is used to construct an approximate analytical solution of the problem. The limit solution of the problem is constructed. A formula for determining the path traversed by a gas particle in the shock layer along the front of a shock wave is obtained. A system of equations for determining the first approximation corrections is constructed.

Three-Dimensional Evaluation of Similarity of Right and Left Knee Joints

PubMed Central

Jang, Ki-Mo; Park, Jong-Hoon; Chang, Minho; Kim, Youngjun; Lee, Deukhee; Park, Sehyung; Wang, Joon Ho

2017-01-01

Purpose The purpose of this study was to evaluate the anatomical similarity of three-dimensional (3D) morphometric parameters between right and left knees. Materials and Methods Ten fresh-frozen paired cadaveric knees were tested. Following dissection, footprint areas of the anterior cruciate ligament (ACL) and posterior cruciate ligament (PCL) were measured. Surface scanning was performed using a 3D scanner. Scanned data were reproduced and morphometric parameters were measured on specialized software. After making mirror models, we compared footprint center positions of the ACL and PCL of both sides and calculated the average deviation of 3D alignment between the right- and left-side models. Results No significant side-to-side differences were found in any morphometric parameters. Bony shapes displayed a side-to-side difference of <1 mm. Distal femoral and proximal tibial volumes did not present side-to-side differences, either; the average 3D deviations of alignment between the right and left sides were 0.8±0.4/1.1±0.6 mm (distal femur/proximal tibia). Center-to-center distances between the right and left ACL footprints were 2.6/2.7 mm (femur/tibia) for the anteromedial bundle and 2.4/2.8 mm for the posterolateral bundle. They were 1.9/1.5 mm for the anterolateral bundle and 2.2/1.8 mm for the posteromedial bundle of the PCL. Conclusions There was a remarkable 3D morphometric similarity between right and left knees. Our results might support the concept of obtaining morphologic reference data from the uninvolved contralateral knee. PMID:29046046

Saccharomyces cerevisiae × Saccharomyces uvarum hybrids generated under different conditions share similar winemaking features.

PubMed

Origone, Andrea Cecilia; Rodríguez, María Eugenia; Oteiza, Juan Martín; Querol, Amparo; Lopes, Christian Ariel

2018-01-01

Interspecific hybrids among species in the Saccharomyces genus are frequently detected in anthropic habitats and can also be obtained easily in the laboratory. This occurs because the most important genetic barriers among Saccharomyces species are post-zygotic. Depending on several factors, including the involved strains, the hybridization mechanism and stabilization conditions, hybrids that bear differential genomic constitutions, and hence phenotypic variability, can be obtained. In the present study, Saccharomyces cerevisiae × Saccharomyces uvarum hybrids were constructed using genetically and physiologically different S. uvarum parents at distinct temperatures (13 and 20°C). The effect of those variables on the main oenological features of the wines obtained with these hybrids was evaluated. Hybrids were successfully obtained in all cases. However, genetic stabilization based on successive fermentations in white wine at 13°C was significantly longer than that at 20°C. Our results demonstrated that, irrespective of the S. uvarum parent and temperature used for hybrid generation and stabilization, similar physicochemical and aromatic features were found in wines. The hybrids generated herein were characterized by low ethanol production, high glycerol synthesis and the capacity to grow at low temperature and to produce malic acid with particular aroma profiles. These features make these hybrids useful for the new winemaking industry within the climate change era frame. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Characterization of Linum usitatissimum L. oil obtained from different extraction technique and in vitro antioxidant potential of supercritical fluid extract

PubMed Central

Chauhan, Rishika; Chester, Karishma; Khan, Yasmeen; Tamboli, Ennus Tajuddin; Ahmad, Sayeed

2015-01-01

Aim: Present investigation was aimed to characterize the fixed oil of Linum usitatissimum L. using five different extraction methods: Supercritical fluid extraction (SFE), ultrasound-assistance, soxhlet extraction, solvent extraction, and three phase partitioning method. Materials and Methods: The SFE conditions (temperature, pressure, and volume of CO2) were optimized prior for better yield. The extracted oils were analyzed and compared for their physiochemical parameters, high performance thin layer chromatography (HPTLC), gas chromatography-mass spectrometry (GC-MS), and Fourier-transformed infrared spectroscopy (FT-IR) fingerprinting. Antioxidant activity was also determined using 1,1-diphenyl-2-picrylhydrazyl and superoxide scavenging method. Result: The main fatty acids were α-linolenic acid, linoleic acid, palmitic acid, and stearic acid as obtained by GC-MS. HPTLC analysis revealed the presence of similar major components in chromatograms. Similarly, the pattern of peaks, as obtained in FT-IR and GC-MS spectra of same oils by different extraction methods, were superimposable. Conclusion: Analysis reported that the fixed oil of L. usitatissimum L. is a good source of n-3 fatty acid with the significant antioxidant activity of oil obtained from SFE extraction method. PMID:26681884

A diagnostic technique used to obtain cross range radiation centers from antenna patterns

NASA Technical Reports Server (NTRS)

Lee, T. H.; Burnside, W. D.

1988-01-01

A diagnostic technique to obtain cross range radiation centers based on antenna radiation patterns is presented. This method is similar to the synthetic aperture processing of scattered fields in the radar application. Coherent processing of the radiated fields is used to determine the various radiation centers associated with the far-zone pattern of an antenna for a given radiation direction. This technique can be used to identify an unexpected radiation center that creates an undesired effect in a pattern; on the other hand, it can improve a numerical simulation of the pattern by identifying other significant mechanisms. Cross range results for two 8' reflector antennas are presented to illustrate as well as validate that technique.

Salient value similarity, social trust and attitudes toward wildland fire management strategies

Treesearch

J.J. Vaske; J.D. Absher; A.D. Bright

2007-01-01

We predicted that social trust in the USDA Forest Service would mediate the relationship between shared value similarity (SVS) and attitudes toward prescribed burning and mechanical thinning. Data were obtained from a mail survey (n = 532) of rural Colorado residents living in the wildland urban interface (WUI). A structural equation analysis was used to assess the...

Reversing the similarity effect: The effect of presentation format.

PubMed

Cataldo, Andrea M; Cohen, Andrew L

2018-06-01

A context effect is a change in preference that occurs when alternatives are added to a choice set. Models of preferential choice that account for context effects largely assume a within-dimension comparison process. It has been shown, however, that the format in which a choice set is presented can influence comparison strategies. That is, a by-alternative or by-dimension grouping of the dimension values encourage within-alternative or within-dimension comparisons, respectively. For example, one classic context effect, the compromise effect, is strengthened by a by-dimension presentation format. Extrapolation from this result suggests that a second context effect, the similarity effect, will actually reverse when stimuli are presented in a by-dimension format. In the current study, we presented participants with a series of apartment choice sets designed to elicit the similarity effect, with either a by-alternative or by-dimension presentation format. Participants in the by-alternative condition demonstrated a standard similarity effect; however, participants in the by-dimension condition demonstrated a strong reverse similarity effect. The present data can be accounted for by Multialternative Decision Field Theory (MDFT) and the Multiattribute Linear Ballistic Accumulator (MLBA), but not Elimination by Aspects (EBA). Indeed, when some weak assumptions of within-dimension processes are met, MDFT and the MLBA predict the reverse similarity effect. These modeling results suggest that the similarity effect is governed by either forgetting and inhibition (MDFT), or attention to positive or negative differences (MLBA). These results demonstrate that flexibility in the comparison process needs to be incorporated into theories of preferential choice. Copyright © 2018 Elsevier B.V. All rights reserved.

Visual similarity in short-term recall for where and when.

PubMed

Jalbert, Annie; Saint-Aubin, Jean; Tremblay, Sébastien

2008-03-01

Two experiments examined the effects of visual similarity on short-term recall for where and when in the visual spatial domain. A series of squares of similar or dissimilar colours were serially presented at various locations on the screen. At recall, all coloured squares were simultaneously presented in a random order at the bottom of the screen, and the locations used for presentation were indicated by white squares. Participants were asked to place the colours at their appropriate location in their presentation order. Performance for location (where) and order (when) was assessed separately. Results revealed that similarity severely hinders both memory for what was where and memory for what was when, under quiet and articulatory suppression conditions. These results provide further evidence that similarity has a major impact on processing relational information in memory.

Processes of Similarity Judgment

ERIC Educational Resources Information Center

Larkey, Levi B.; Markman, Arthur B.

2005-01-01

Similarity underlies fundamental cognitive capabilities such as memory, categorization, decision making, problem solving, and reasoning. Although recent approaches to similarity appreciate the structure of mental representations, they differ in the processes posited to operate over these representations. We present an experiment that…

Accurate segmenting of cervical tumors in PET imaging based on similarity between adjacent slices.

PubMed

Chen, Liyuan; Shen, Chenyang; Zhou, Zhiguo; Maquilan, Genevieve; Thomas, Kimberly; Folkert, Michael R; Albuquerque, Kevin; Wang, Jing

2018-06-01

Because in PET imaging cervical tumors are close to the bladder with high capacity for the secreted 18 FDG tracer, conventional intensity-based segmentation methods often misclassify the bladder as a tumor. Based on the observation that tumor position and area do not change dramatically from slice to slice, we propose a two-stage scheme that facilitates segmentation. In the first stage, we used a graph-cut based algorithm to obtain initial contouring of the tumor based on local similarity information between voxels; this was achieved through manual contouring of the cervical tumor on one slice. In the second stage, initial tumor contours were fine-tuned to more accurate segmentation by incorporating similarity information on tumor shape and position among adjacent slices, according to an intensity-spatial-distance map. Experimental results illustrate that the proposed two-stage algorithm provides a more effective approach to segmenting cervical tumors in 3D 18 FDG PET images than the benchmarks used for comparison. Copyright © 2018 Elsevier Ltd. All rights reserved.

Common neighbour structure and similarity intensity in complex networks

NASA Astrophysics Data System (ADS)

Hou, Lei; Liu, Kecheng

2017-10-01

Complex systems as networks always exhibit strong regularities, implying underlying mechanisms governing their evolution. In addition to the degree preference, the similarity has been argued to be another driver for networks. Assuming a network is randomly organised without similarity preference, the present paper studies the expected number of common neighbours between vertices. A symmetrical similarity index is accordingly developed by removing such expected number from the observed common neighbours. The developed index can not only describe the similarities between vertices, but also the dissimilarities. We further apply the proposed index to measure of the influence of similarity on the wring patterns of networks. Fifteen empirical networks as well as artificial networks are examined in terms of similarity intensity and degree heterogeneity. Results on real networks indicate that, social networks are strongly governed by the similarity as well as the degree preference, while the biological networks and infrastructure networks show no apparent similarity governance. Particularly, classical network models, such as the Barabási-Albert model, the Erdös-Rényi model and the Ring Lattice, cannot well describe the social networks in terms of the degree heterogeneity and similarity intensity. The findings may shed some light on the modelling and link prediction of different classes of networks.

Genetic similarity analysis within Pyropia yezoensis blades developed from both conchospores and blade archeospores using AFLP(1).

PubMed

He, Linwen; Zhu, Jianyi; Lu, Qinqin; Niu, Jianfeng; Zhang, Baoyu; Lin, Apeng; Wang, Guangce

2013-06-01

Pyropia yezoensis (Ueda) M. S. Hwang et H. G. Choi (previously called Porphyra yezoensis) is an economically important alga. The blades generated from conchospores are genetic chimeras, which are not suitable for genetic similarity analysis. In this study, two types of blades from a single filament of P. yezoensis sporophyte filament were obtained. One type, ConB, consisted of 40 blades that had germinated from conchospores. The other type, ArcB, consisted of 88 blades that had germinated from archeospores released from ConB. Both of them were analyzed by amplified fragment length polymorphism. The low genetic similarity levels for both conchospore-germinated and archeospore-germinated blades demonstrated that the conchcelis we used was cross-fertilized. Furthermore, a higher polymorphic loci ratio (98.6%) was detected in ArcB than in ConB (80.7%), and the average genetic similarity of ArcB (average 0.61) was lower than that of ConB (average 0.71). These differences indicated that genetic analysis using ArcB gives more accurate results. © 2013 Phycological Society of America.

Differences and similarities in cross-cultural perceptions of boundaries: a comparison of results from two studies.

PubMed

Miller, Patrice Marie; Bener, Abdulbari; Ghuloum, Suhaila; Commons, Michael Lamport; Burgut, F Tuna

2012-01-01

There has been substantial literature on boundary excursions in clinician-patient relationships; however, very little empirical research exists. Even less information exists on how perceptions of this issue might differ across cultures. Prior to this study, empirical data on various kinds of boundary excursions were collected in different cultural contexts. First, clinicians from the U.S. and Brazil were asked to rate 173 boundary excursions for both their perceived harmfulness and their professional unacceptability (Miller et al., 2006). In a second study, colleagues from Qatar administered a slightly modified version to mental health care professional staff of a hospital in Doha, Qatar (Ghuloum et al., 2011). In this paper, the results of these two separate studies are compared. The results showed some similarities and some differences in perceptions of the boundary behaviors. For example, both sets of cultures seem to agree that certain behaviors are seriously harmful and/or professionally unacceptable. These behaviors include some frankly sexual behavior, such as having sexual intercourse with a patient, as well as behavior related to doing business with the patient, and some disclosing behavior. There are also significant cultural differences in perceptions of how harmful some of the behaviors are. Qatari practitioners seemed to rate certain behaviors that within therapy mix disclosing or personal behavior with therapy as more harmful, but behaviors that involved interacting with patients outside of therapy as less serious. A factor analysis suggested that participants in U.S./Brazil saw a much larger number of behaviors as making up a set of Core Boundary Violations, whereas Qatari respondents separated sexual behaviors from others. Finally, a Rasch analysis showed that both cultures perceived a continuum of boundary behaviors, from those that are least harmful or unprofessional to those that are highly harmful or unprofessional. One interpretation is that

Polynomial Conjoint Analysis of Similarities: A Model for Constructing Polynomial Conjoint Measurement Algorithms.

ERIC Educational Resources Information Center

Young, Forrest W.

A model permitting construction of algorithms for the polynomial conjoint analysis of similarities is presented. This model, which is based on concepts used in nonmetric scaling, permits one to obtain the best approximate solution. The concepts used to construct nonmetric scaling algorithms are reviewed. Finally, examples of algorithmic models for…

Breast mass detection in tomosynthesis projection images using information-theoretic similarity measures

NASA Astrophysics Data System (ADS)

Singh, Swatee; Tourassi, Georgia D.; Lo, Joseph Y.

2007-03-01

The purpose of this project is to study Computer Aided Detection (CADe) of breast masses for digital tomosynthesis. It is believed that tomosynthesis will show improvement over conventional mammography in detection and characterization of breast masses by removing overlapping dense fibroglandular tissue. This study used the 60 human subject cases collected as part of on-going clinical trials at Duke University. Raw projections images were used to identify suspicious regions in the algorithm's high-sensitivity, low-specificity stage using a Difference of Gaussian (DoG) filter. The filtered images were thresholded to yield initial CADe hits that were then shifted and added to yield a 3D distribution of suspicious regions. These were further summed in the depth direction to yield a flattened probability map of suspicious hits for ease of scoring. To reduce false positives, we developed an algorithm based on information theory where similarity metrics were calculated using knowledge databases consisting of tomosynthesis regions of interest (ROIs) obtained from projection images. We evaluated 5 similarity metrics to test the false positive reduction performance of our algorithm, specifically joint entropy, mutual information, Jensen difference divergence, symmetric Kullback-Liebler divergence, and conditional entropy. The best performance was achieved using the joint entropy similarity metric, resulting in ROC A z of 0.87 +/- 0.01. As a whole, the CADe system can detect breast masses in this data set with 79% sensitivity and 6.8 false positives per scan. In comparison, the original radiologists performed with only 65% sensitivity when using mammography alone, and 91% sensitivity when using tomosynthesis alone.

Path similarity skeleton graph matching.

PubMed

Bai, Xiang; Latecki, Longin Jan

2008-07-01

This paper presents a novel framework to for shape recognition based on object silhouettes. The main idea is to match skeleton graphs by comparing the shortest paths between skeleton endpoints. In contrast to typical tree or graph matching methods, we completely ignore the topological graph structure. Our approach is motivated by the fact that visually similar skeleton graphs may have completely different topological structures. The proposed comparison of shortest paths between endpoints of skeleton graphs yields correct matching results in such cases. The skeletons are pruned by contour partitioning with Discrete Curve Evolution, which implies that the endpoints of skeleton branches correspond to visual parts of the objects. The experimental results demonstrate that our method is able to produce correct results in the presence of articulations, stretching, and occlusion.

The similia principle: results obtained in a cellular model system.

PubMed

Wiegant, Fred; Van Wijk, Roeland

2010-01-01

This paper describes the results of a research program focused on the beneficial effect of low dose stress conditions that were applied according to the similia principle to cells previously disturbed by more severe stress conditions. In first instance, we discuss criteria for research on the similia principle at the cellular level. Then, the homologous ('isopathic') approach is reviewed, in which the initial (high dose) stress used to disturb cellular physiology and the subsequent (low dose) stress are identical. Beneficial effects of low dose stress are described in terms of increased cellular survival capacity and at the molecular level as an increase in the synthesis of heat shock proteins (hsps). Both phenomena reflect a stimulation of the endogenous cellular self-recovery capacity. Low dose stress conditions applied in a homologous approach stimulate the synthesis of hsps and enhance survival in comparison with stressed cells that were incubated in the absence of low dose stress conditions. Thirdly, the specificity of the low dose stress condition is described where the initial (high dose) stress is different in nature from the subsequently applied (low dose) stress; the heterologous or 'heteropathic' approach. The results support the similia principle at the cellular level and add to understanding of how low dose stress conditions influence the regulatory processes underlying self-recovery. In addition, the phenomenon of 'symptom aggravation' which is also observed at the cellular level, is discussed in the context of self-recovery. Finally, the difference in efficiency between the homologous and the heterologous approach is discussed; a perspective is indicated for further research; and the relationship between studies on the similia principle and the recently introduced concept of 'postconditioning hormesis' is emphasized. Copyright 2009 The Faculty of Homeopathy. Published by Elsevier Ltd. All rights reserved.

Average is Boring: How Similarity Kills a Meme's Success

NASA Astrophysics Data System (ADS)

Coscia, Michele

2014-09-01

Every day we are exposed to different ideas, or memes, competing with each other for our attention. Previous research explained popularity and persistence heterogeneity of memes by assuming them in competition for limited attention resources, distributed in a heterogeneous social network. Little has been said about what characteristics make a specific meme more likely to be successful. We propose a similarity-based explanation: memes with higher similarity to other memes have a significant disadvantage in their potential popularity. We employ a meme similarity measure based on semantic text analysis and computer vision to prove that a meme is more likely to be successful and to thrive if its characteristics make it unique. Our results show that indeed successful memes are located in the periphery of the meme similarity space and that our similarity measure is a promising predictor of a meme success.

Average is boring: how similarity kills a meme's success.

PubMed

Coscia, Michele

2014-09-26

Every day we are exposed to different ideas, or memes, competing with each other for our attention. Previous research explained popularity and persistence heterogeneity of memes by assuming them in competition for limited attention resources, distributed in a heterogeneous social network. Little has been said about what characteristics make a specific meme more likely to be successful. We propose a similarity-based explanation: memes with higher similarity to other memes have a significant disadvantage in their potential popularity. We employ a meme similarity measure based on semantic text analysis and computer vision to prove that a meme is more likely to be successful and to thrive if its characteristics make it unique. Our results show that indeed successful memes are located in the periphery of the meme similarity space and that our similarity measure is a promising predictor of a meme success.

Classification of wheat: Badhwar profile similarity technique

NASA Technical Reports Server (NTRS)

Austin, W. W.

1980-01-01

The Badwar profile similarity classification technique used successfully for classification of corn was applied to spring wheat classifications. The software programs and the procedures used to generate full-scene classifications are presented, and numerical results of the acreage estimations are given.

High Contrast Imaging in the Visible: First Experimental Results at the Large Binocular Telescope

NASA Astrophysics Data System (ADS)

Pedichini, F.; Stangalini, M.; Ambrosino, F.; Puglisi, A.; Pinna, E.; Bailey, V.; Carbonaro, L.; Centrone, M.; Christou, J.; Esposito, S.; Farinato, J.; Fiore, F.; Giallongo, E.; Hill, J. M.; Hinz, P. M.; Sabatini, L.

2017-08-01

In 2014 February, the System for High contrast And coronography from R to K at VISual bands (SHARK-VIS) Forerunner, a high contrast experimental imager operating at visible wavelengths, was installed at the Large Binocular Telescope (LBT). Here we report on the first results obtained by recent on-sky tests. These results show the extremely good performance of the LBT Extreme Adaptive Optics (ExAO) system at visible wavelengths, both in terms of spatial resolution and contrast achieved. Similarly to what was done by Amara & Quanz (2012), we used the SHARK-VIS Forerunner data to quantitatively assess the contrast enhancement. This is done by injecting several different synthetic faint objects in the acquired data and applying the angular differential imaging (ADI) technique. A contrast of the order of 5 × 10-5 is obtained at 630 nm for angular separations from the star larger than 100 mas. These results are discussed in light of the future development of SHARK-VIS and compared to those obtained by other high contrast imagers operating at similar wavelengths.

Transformation and Alignment in Similarity

ERIC Educational Resources Information Center

Hodgetts, Carl J.; Hahn, Ulrike; Chater, Nick

2009-01-01

This paper contrasts two structural accounts of psychological similarity: structural alignment (SA) and Representational Distortion (RD). SA proposes that similarity is determined by how readily the structures of two objects can be brought into alignment; RD measures similarity by the complexity of the transformation that "distorts" one…

Results from CrIS-ATMS Obtained Using the AIRS Science Team Retrieval Methodology

NASA Technical Reports Server (NTRS)

Susskind, Joel; Kouvaris, Louis C.; Iredell, Lena

2013-01-01

AIRS was launched on EOS Aqua in May 2002, together with AMSU-A and HSB (which subsequently failed early in the mission), to form a next generation polar orbiting infrared and microwave atmospheric sounding system. AIRS/AMSU had two primary objectives. The first objective was to provide real-time data products available for use by the operational Numerical Weather Prediction Centers in a data assimilation mode to improve the skill of their subsequent forecasts. The second objective was to provide accurate unbiased sounding products with good spatial coverage that are used to generate stable multi-year climate data sets to study the earth's interannual variability, climate processes, and possibly long-term trends. AIRS/AMSU data for all time periods are now being processed using the state of the art AIRS Science Team Version-6 retrieval methodology. The Suomi-NPP mission was launched in October 2011 as part of a sequence of Low Earth Orbiting satellite missions under the "Joint Polar Satellite System" (JPSS). NPP carries CrIS and ATMS, which are advanced infra-red and microwave atmospheric sounders that were designed as follow-ons to the AIRS and AMSU instruments. The main objective of this work is to assess whether CrIS/ATMS will be an adequate replacement for AIRS/AMSU from the perspective of the generation of accurate and consistent long term climate data records, or if improved instruments should be developed for future flight. It is critical for CrIS/ATMS to be processed using an algorithm similar to, or at least comparable to, AIRS Version-6 before such an assessment can be made. We have been conducting research to optimize products derived from CrIS/ATMS observations using a scientific approach analogous to the AIRS Version-6 retrieval algorithm. Our latest research uses Version-5.70 of the CrIS/ATMS retrieval algorithm, which is otherwise analogous to AIRS Version-6, but does not yet contain the benefit of use of a Neural-Net first guess start-up system

Sample selection in foreign similarity regions for multicrop experiments

NASA Technical Reports Server (NTRS)

Malin, J. T. (Principal Investigator)

1981-01-01

The selection of sample segments in the U.S. foreign similarity regions for development of proportion estimation procedures and error modeling for Argentina, Australia, Brazil, and USSR in AgRISTARS is described. Each sample was chosen to be similar in crop mix to the corresponding indicator region sample. Data sets, methods of selection, and resulting samples are discussed.

Scientific results obtained by the Busot observatory

NASA Astrophysics Data System (ADS)

García-Lozano, R.; Rodes, J. J.; Torrejón, J. M.; Bernabéu, G.; Berná, J. Á.

2016-12-01

We present the discovery of three new W UMa systems by our group as a part of a photometric follow-up of variable stars carried out with the Busot observatory 36 cm robotic telescope in collaboration with the X-ray astronomy group at University of Alicante (Alicante, Spain). Specifically we show the high limiting magnitude to detect moving objects (V˜ 21 mag), and the high stability and accuracy attained in photometry which allow us to measure very shallow planet transits.

PHOG analysis of self-similarity in aesthetic images

NASA Astrophysics Data System (ADS)

Amirshahi, Seyed Ali; Koch, Michael; Denzler, Joachim; Redies, Christoph

2012-03-01

In recent years, there have been efforts in defining the statistical properties of aesthetic photographs and artworks using computer vision techniques. However, it is still an open question how to distinguish aesthetic from non-aesthetic images with a high recognition rate. This is possibly because aesthetic perception is influenced also by a large number of cultural variables. Nevertheless, the search for statistical properties of aesthetic images has not been futile. For example, we have shown that the radially averaged power spectrum of monochrome artworks of Western and Eastern provenance falls off according to a power law with increasing spatial frequency (1/f2 characteristics). This finding implies that this particular subset of artworks possesses a Fourier power spectrum that is self-similar across different scales of spatial resolution. Other types of aesthetic images, such as cartoons, comics and mangas also display this type of self-similarity, as do photographs of complex natural scenes. Since the human visual system is adapted to encode images of natural scenes in a particular efficient way, we have argued that artists imitate these statistics in their artworks. In support of this notion, we presented results that artists portrait human faces with the self-similar Fourier statistics of complex natural scenes although real-world photographs of faces are not self-similar. In view of these previous findings, we investigated other statistical measures of self-similarity to characterize aesthetic and non-aesthetic images. In the present work, we propose a novel measure of self-similarity that is based on the Pyramid Histogram of Oriented Gradients (PHOG). For every image, we first calculate PHOG up to pyramid level 3. The similarity between the histograms of each section at a particular level is then calculated to the parent section at the previous level (or to the histogram at the ground level). The proposed approach is tested on datasets of aesthetic and

The Effects of Similarity on High-Level Visual Working Memory Processing.

PubMed

Yang, Li; Mo, Lei

2017-01-01

Similarity has been observed to have opposite effects on visual working memory (VWM) for complex images. How can these discrepant results be reconciled? To answer this question, we used a change-detection paradigm to test visual working memory performance for multiple real-world objects. We found that working memory for moderate similarity items was worse than that for either high or low similarity items. This pattern was unaffected by manipulations of stimulus type (faces vs. scenes), encoding duration (limited vs. self-paced), and presentation format (simultaneous vs. sequential). We also found that the similarity effects differed in strength in different categories (scenes vs. faces). These results suggest that complex real-world objects are represented using a centre-surround inhibition organization . These results support the category-specific cortical resource theory and further suggest that centre-surround inhibition organization may differ by category.

Pollinators show flower colour preferences but flowers with similar colours do not attract similar pollinators

PubMed Central

Reverté, Sara; Retana, Javier; Gómez, José M.; Bosch, Jordi

2016-01-01

Background and aims Colour is one of the main floral traits used by pollinators to locate flowers. Although pollinators show innate colour preferences, the view that the colour of a flower may be considered an important predictor of its main pollinators is highly controversial because flower choice is highly context-dependent, and initial innate preferences may be overridden by subsequent associative learning. Our objective is to establish whether there is a relationship between flower colour and pollinator composition in natural communities. Methods We measured the flower reflectance spectrum and pollinator composition in four plant communities (85 plant species represented by 109 populations, and 32 305 plant–pollinator interactions in total). Pollinators were divided into six taxonomic groups: bees, ants, wasps, coleopterans, dipterans and lepidopterans. Key Results We found consistent associations between pollinator groups and certain colours. These associations matched innate preferences experimentally established for several pollinators and predictions of the pollination syndrome theory. However, flowers with similar colours did not attract similar pollinator assemblages. Conclusions The explanation for this paradoxical result is that most flower species are pollination generalists. We conclude that although pollinator colour preferences seem to condition plant–pollinator interactions, the selective force behind these preferences has not been strong enough to mediate the appearance and maintenance of tight colour-based plant–pollinator associations. PMID:27325897

IsoCleft Finder – a web-based tool for the detection and analysis of protein binding-site geometric and chemical similarities

PubMed Central

Najmanovich, Rafael

2013-01-01

IsoCleft Finder is a web-based tool for the detection of local geometric and chemical similarities between potential small-molecule binding cavities and a non-redundant dataset of ligand-bound known small-molecule binding-sites. The non-redundant dataset developed as part of this study is composed of 7339 entries representing unique Pfam/PDB-ligand (hetero group code) combinations with known levels of cognate ligand similarity. The query cavity can be uploaded by the user or detected automatically by the system using existing PDB entries as well as user-provided structures in PDB format. In all cases, the user can refine the definition of the cavity interactively via a browser-based Jmol 3D molecular visualization interface. Furthermore, users can restrict the search to a subset of the dataset using a cognate-similarity threshold. Local structural similarities are detected using the IsoCleft software and ranked according to two criteria (number of atoms in common and Tanimoto score of local structural similarity) and the associated Z-score and p-value measures of statistical significance. The results, including predicted ligands, target proteins, similarity scores, number of atoms in common, etc., are shown in a powerful interactive graphical interface. This interface permits the visualization of target ligands superimposed on the query cavity and additionally provides a table of pairwise ligand topological similarities. Similarities between top scoring ligands serve as an additional tool to judge the quality of the results obtained. We present several examples where IsoCleft Finder provides useful functional information. IsoCleft Finder results are complementary to existing approaches for the prediction of protein function from structure, rational drug design and x-ray crystallography. IsoCleft Finder can be found at: http://bcb.med.usherbrooke.ca/isocleftfinder. PMID:24555058

Pressure Probe and Isopiestic Psychrometer Measure Similar Turgor 1

PubMed Central

Nonami, Hiroshi; Boyer, John S.; Steudle, Ernst

1987-01-01

Turgor measured with a miniature pressure probe was compared to that measured with an isopiestic thermocouple psychrometer in mature regions of soybean (Glycine max [L.] Merr.) stems. The probe measured turgor directly in cells of intact stems whereas the psychrometer measured the water potential and osmotic potential of excised stem segments and turgor was calculated by difference. When care was taken to prevent dehydration when working with the pressure probe, and diffusive resistance and dilution errors with the psychrometer, both methods gave similar values of turgor whether the plants were dehydrating or rehydrating. This finding, together with the previously demonstrated similarity in turgor measured with the isopiestic psychrometer and a pressure chamber, indicates that the pressure probe provides accurate measurements of turgor despite the need to penetrate the cell. On the other hand, it suggests that as long as precautions are taken to obtain accurate values for the water potential and osmotic potential, turgor can be determined by isopiestic psychrometry in tissues not accessible to the pressure probe for physical reasons. PMID:16665293

Inferring gene ontologies from pairwise similarity data

PubMed Central

Kramer, Michael; Dutkowski, Janusz; Yu, Michael; Bafna, Vineet; Ideker, Trey

2014-01-01

Motivation: While the manually curated Gene Ontology (GO) is widely used, inferring a GO directly from -omics data is a compelling new problem. Recognizing that ontologies are a directed acyclic graph (DAG) of terms and hierarchical relations, algorithms are needed that: analyze a full matrix of gene–gene pairwise similarities from -omics data;infer true hierarchical structure in these data rather than enforcing hierarchy as a computational artifact; andrespect biological pleiotropy, by which a term in the hierarchy can relate to multiple higher level terms. Methods addressing these requirements are just beginning to emerge—none has been evaluated for GO inference. Methods: We consider two algorithms [Clique Extracted Ontology (CliXO), LocalFitness] that uniquely satisfy these requirements, compared with methods including standard clustering. CliXO is a new approach that finds maximal cliques in a network induced by progressive thresholding of a similarity matrix. We evaluate each method’s ability to reconstruct the GO biological process ontology from a similarity matrix based on (a) semantic similarities for GO itself or (b) three -omics datasets for yeast. Results: For task (a) using semantic similarity, CliXO accurately reconstructs GO (>99% precision, recall) and outperforms other approaches (<20% precision, <20% recall). For task (b) using -omics data, CliXO outperforms other methods using two -omics datasets and achieves ∼30% precision and recall using YeastNet v3, similar to an earlier approach (Network Extracted Ontology) and better than LocalFitness or standard clustering (20–25% precision, recall). Conclusion: This study provides algorithmic foundation for building gene ontologies by capturing hierarchical and pleiotropic structure embedded in biomolecular data. Contact: tideker@ucsd.edu PMID:24932003

FISim: A new similarity measure between transcription factor binding sites based on the fuzzy integral

PubMed Central

Garcia, Fernando; Lopez, Francisco J; Cano, Carlos; Blanco, Armando

2009-01-01

Background Regulatory motifs describe sets of related transcription factor binding sites (TFBSs) and can be represented as position frequency matrices (PFMs). De novo identification of TFBSs is a crucial problem in computational biology which includes the issue of comparing putative motifs with one another and with motifs that are already known. The relative importance of each nucleotide within a given position in the PFMs should be considered in order to compute PFM similarities. Furthermore, biological data are inherently noisy and imprecise. Fuzzy set theory is particularly suitable for modeling imprecise data, whereas fuzzy integrals are highly appropriate for representing the interaction among different information sources. Results We propose FISim, a new similarity measure between PFMs, based on the fuzzy integral of the distance of the nucleotides with respect to the information content of the positions. Unlike existing methods, FISim is designed to consider the higher contribution of better conserved positions to the binding affinity. FISim provides excellent results when dealing with sets of randomly generated motifs, and outperforms the remaining methods when handling real datasets of related motifs. Furthermore, we propose a new cluster methodology based on kernel theory together with FISim to obtain groups of related motifs potentially bound by the same TFs, providing more robust results than existing approaches. Conclusion FISim corrects a design flaw of the most popular methods, whose measures favour similarity of low information content positions. We use our measure to successfully identify motifs that describe binding sites for the same TF and to solve real-life problems. In this study the reliability of fuzzy technology for motif comparison tasks is proven. PMID:19615102

Measurement of steroids in rats after exposure to an endocrine disruptor: mass spectrometry and radioimmunoassay demonstrate similar results.

PubMed

Riffle, Brandy W; Henderson, W Matthew; Laws, Susan C

2013-01-01

Commercially available radioimmunoassays (RIAs) are frequently used to evaluate the effects of endocrine disrupting chemicals (EDCs) on steroidogenesis in rats. Currently there are limited data comparing steroid concentrations in rats as measured by RIAs to those obtained using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). This study evaluates the concordance of serum and urine steroid concentrations as quantified by select RIA kits and LC-MS/MS following exposure to an EDC, atrazine (ATR). Adult male rats were orally dosed with ATR (200 mg/kg/day) or methylcellulose (1%, vehicle control) for 5 days. Serum was collected and separated into aliquots for analysis. Serum was assayed by RIA for androstenedione (ANDRO), corticosterone (CORT), estradiol (E2), estrone (E1), progesterone (P4), and testosterone (T). Serum was extracted prior to LC-MS/MS analysis with positive electrospray ionization in multiple-reaction monitoring mode for ANDRO, CORT, P4, and T. E1 and E2 concentrations were quantified similarly by LC-MS/MS, following derivatization with dansyl chloride. To compare CORT values from urine, pregnant adult rats were orally dosed with either ATR (100 mg/kg/day) or methylcellulose for 5 days (i.e., gestational days 14-18). Urine samples were collected daily and assayed for CORT by RIA and LC-MS/MS as described above. Data analyses demonstrated significant agreement between the two detection methods as assessed by Pearson product-moment correlation coefficient, Bland-Altman analysis, and the interclass correlation coefficient. No statistically significant differences were observed between RIA and LC-MS/MS means for any of the steroids assayed. These findings indicate a significant correlation between the measurement of steroids within rat serum and urine using RIA kits and LC-MS/MS. Differences in the absolute measurements existed, but these were not statistically significant. These findings indicate that steroids may be reliably

Identification and classification of similar looking food grains

NASA Astrophysics Data System (ADS)

Anami, B. S.; Biradar, Sunanda D.; Savakar, D. G.; Kulkarni, P. V.

2013-01-01

This paper describes the comparative study of Artificial Neural Network (ANN) and Support Vector Machine (SVM) classifiers by taking a case study of identification and classification of four pairs of similar looking food grains namely, Finger Millet, Mustard, Soyabean, Pigeon Pea, Aniseed, Cumin-seeds, Split Greengram and Split Blackgram. Algorithms are developed to acquire and process color images of these grains samples. The developed algorithms are used to extract 18 colors-Hue Saturation Value (HSV), and 42 wavelet based texture features. Back Propagation Neural Network (BPNN)-based classifier is designed using three feature sets namely color - HSV, wavelet-texture and their combined model. SVM model for color- HSV model is designed for the same set of samples. The classification accuracies ranging from 93% to 96% for color-HSV, ranging from 78% to 94% for wavelet texture model and from 92% to 97% for combined model are obtained for ANN based models. The classification accuracy ranging from 80% to 90% is obtained for color-HSV based SVM model. Training time required for the SVM based model is substantially lesser than ANN for the same set of images.

Material Total Mass Loss in Vacuum Obtained From Various Outgassing Systems

NASA Technical Reports Server (NTRS)

Scialdone, John; Isaac, Peggy; Clatterbuck, Carroll; Hunkeler, Ronald

2000-01-01

Several instruments including the Cahn Microbalance, the Knudsen Cell, the micro-CVCM, and the vacuum Thermogravimetric Analyzer (TGA) were used in the testing of a graphite/epoxy (GR/EP) composite that is proposed for use as a rigidizing element of an inflatable deployment system. This GR/EP will be cured in situ. The purpose of this testing is to estimate the gaseous production resulting from the curing of the GR/EP composite, to predict the resulting pressure, and to calculate the required venting. Every test was conducted under vacuum at 125 degrees C for 24 hours. Upon comparison of the results, the ASTM E-595 was noted to have given readings that were consistently lower than those obtained using the other instruments, which otherwise provided similar results. The GR/EP was tested using several different geometric arrangements. This paper describes the analysis evaluating the molecular and continuum flow of the outgassing products issuing from the exit port of the ASTM E-595 system. The effective flow conductance provided by the physical dimensions of the vent passage of the ASTM E-595 system and that of the material sample among other factors were investigated to explain the reduced amount of outgassing released during the 24-hour test period.

Investigating Pharmacological Similarity by Charting Chemical Space.

PubMed

Buonfiglio, Rosa; Engkvist, Ola; Várkonyi, Péter; Henz, Astrid; Vikeved, Elisabet; Backlund, Anders; Kogej, Thierry

2015-11-23

In this study, biologically relevant areas of the chemical space were analyzed using ChemGPS-NP. This application enables comparing groups of ligands within a multidimensional space based on principle components derived from physicochemical descriptors. Also, 3D visualization of the ChemGPS-NP global map can be used to conveniently evaluate bioactive compound similarity and visually distinguish between different types or groups of compounds. To further establish ChemGPS-NP as a method to accurately represent the chemical space, a comparison with structure-based fingerprint has been performed. Interesting complementarities between the two descriptions of molecules were observed. It has been shown that the accuracy of describing molecules with physicochemical descriptors like in ChemGPS-NP is similar to the accuracy of structural fingerprints in retrieving bioactive molecules. Lastly, pharmacological similarity of structurally diverse compounds has been investigated in ChemGPS-NP space. These results further strengthen the case of using ChemGPS-NP as a tool to explore and visualize chemical space.

Average is Boring: How Similarity Kills a Meme's Success

PubMed Central

Coscia, Michele

2014-01-01

Every day we are exposed to different ideas, or memes, competing with each other for our attention. Previous research explained popularity and persistence heterogeneity of memes by assuming them in competition for limited attention resources, distributed in a heterogeneous social network. Little has been said about what characteristics make a specific meme more likely to be successful. We propose a similarity-based explanation: memes with higher similarity to other memes have a significant disadvantage in their potential popularity. We employ a meme similarity measure based on semantic text analysis and computer vision to prove that a meme is more likely to be successful and to thrive if its characteristics make it unique. Our results show that indeed successful memes are located in the periphery of the meme similarity space and that our similarity measure is a promising predictor of a meme success. PMID:25257730

EEG Sleep Stages Classification Based on Time Domain Features and Structural Graph Similarity.

PubMed

Diykh, Mohammed; Li, Yan; Wen, Peng

2016-11-01

The electroencephalogram (EEG) signals are commonly used in diagnosing and treating sleep disorders. Many existing methods for sleep stages classification mainly depend on the analysis of EEG signals in time or frequency domain to obtain a high classification accuracy. In this paper, the statistical features in time domain, the structural graph similarity and the K-means (SGSKM) are combined to identify six sleep stages using single channel EEG signals. Firstly, each EEG segment is partitioned into sub-segments. The size of a sub-segment is determined empirically. Secondly, statistical features are extracted, sorted into different sets of features and forwarded to the SGSKM to classify EEG sleep stages. We have also investigated the relationships between sleep stages and the time domain features of the EEG data used in this paper. The experimental results show that the proposed method yields better classification results than other four existing methods and the support vector machine (SVM) classifier. A 95.93% average classification accuracy is achieved by using the proposed method.

Similarity constraints in testing of cooled engine parts

NASA Technical Reports Server (NTRS)

Colladay, R. S.; Stepka, F. S.

1974-01-01

A study is made of the effect of testing cooled parts of current and advanced gas turbine engines at the reduced temperature and pressure conditions which maintain similarity with the engine environment. Some of the problems facing the experimentalist in evaluating heat transfer and aerodynamic performance when hardware is tested at conditions other than the actual engine environment are considered. Low temperature and pressure test environments can simulate the performance of actual size prototype engine hardware within the tolerance of experimental accuracy if appropriate similarity conditions are satisfied. Failure to adhere to these similarity constraints because of test facility limitations or other reasons, can result in a number of serious errors in projecting the performance of test hardware to engine conditions.

Interfacial and Mechanical Behavior of AA5456 Filling Friction-Stir-Welded Lap Joints Using Similar and Dissimilar Pins

NASA Astrophysics Data System (ADS)

Behmand, Saleh Alaei; Mirsalehi, Seyyed Ehsan; Omidvar, Hamid; Safarkhanian, Mohammad Ali

2016-10-01

In this article, filling friction stir welding (FFSW) of the remaining exit holes of AA5456 alloy friction-stir-welded lap joints was studied. For this purpose, the influences of different rotating speeds, holding times, and pin materials, AA5456 and AA2024, on the metallurgical structure and joint strength were investigated. The observations showed that defect-free lap joints are successfully obtainable by this method using similar and dissimilar consumable pins. The results indicated that the higher rotating speed and holding time adversely affect the weld performance. The best result was achieved for 30 seconds holding time, 500 rpm rotating speed, and AA2024 consumable pin. In this condition, a lap shear strength of 10 pct higher than that of the nonfilled joint, equivalent to about 94 pct of the original defect-free FSW joint, was obtained, whereas the GTAW filled joint showed only approximately 87 pct of the continuous FSW joint strength.

Toward a Social Psychology of Diagnosis: Similarity, Attraction, and Clinical Evaluation.

ERIC Educational Resources Information Center

Mazer, Donald B.

1979-01-01

Clinicians and undergraduates evaluated a client similar or dissimilar to themselves in political radicalism. Results document the presence of diagnostic bias, but only among student subjects is bias a function of similarity. For clinicians, the more radical client is seen as less disturbed. Similarity-attraction relationships were absent in both…

Similarity increases altruistic punishment in humans

PubMed Central

Mussweiler, Thomas; Ockenfels, Axel

2013-01-01

Humans are attracted to similar others. As a consequence, social networks are homogeneous in sociodemographic, intrapersonal, and other characteristics—a principle called homophily. Despite abundant evidence showing the importance of interpersonal similarity and homophily for human relationships, their behavioral correlates and cognitive foundations are poorly understood. Here, we show that perceived similarity substantially increases altruistic punishment, a key mechanism underlying human cooperation. We induced (dis)similarity perception by manipulating basic cognitive mechanisms in an economic cooperation game that included a punishment phase. We found that similarity-focused participants were more willing to punish others’ uncooperative behavior. This influence of similarity is not explained by group identity, which has the opposite effect on altruistic punishment. Our findings demonstrate that pure similarity promotes reciprocity in ways known to encourage cooperation. At the same time, the increased willingness to punish norm violations among similarity-focused participants provides a rationale for why similar people are more likely to build stable social relationships. Finally, our findings show that altruistic punishment is differentially involved in encouraging cooperation under pure similarity vs. in-group conditions. PMID:24218611

Challenges in Obtaining Estimates of the Risk of Tuberculosis Infection During Overseas Deployment.

PubMed

Mancuso, James D; Geurts, Mia

2015-12-01

Estimates of the risk of tuberculosis (TB) infection resulting from overseas deployment among U.S. military service members have varied widely, and have been plagued by methodological problems. The purpose of this study was to estimate the incidence of TB infection in the U.S. military resulting from deployment. Three populations were examined: 1) a unit of 2,228 soldiers redeploying from Iraq in 2008, 2) a cohort of 1,978 soldiers followed up over 5 years after basic training at Fort Jackson in 2009, and 3) 6,062 participants in the 2011-2012 National Health and Nutrition Examination Survey (NHANES). The risk of TB infection in the deployed population was low-0.6% (95% confidence interval [CI]: 0.1-2.3%)-and was similar to the non-deployed population. The prevalence of latent TB infection (LTBI) in the U.S. population was not significantly different among deployed and non-deployed veterans and those with no military service. The limitations of these retrospective studies highlight the challenge in obtaining valid estimates of risk using retrospective data and the need for a more definitive study. Similar to civilian long-term travelers, risks for TB infection during deployment are focal in nature, and testing should be targeted to only those at increased risk. © The American Society of Tropical Medicine and Hygiene.

A graph-based semantic similarity measure for the gene ontology.

PubMed

Alvarez, Marco A; Yan, Changhui

2011-12-01

Existing methods for calculating semantic similarities between pairs of Gene Ontology (GO) terms and gene products often rely on external databases like Gene Ontology Annotation (GOA) that annotate gene products using the GO terms. This dependency leads to some limitations in real applications. Here, we present a semantic similarity algorithm (SSA), that relies exclusively on the GO. When calculating the semantic similarity between a pair of input GO terms, SSA takes into account the shortest path between them, the depth of their nearest common ancestor, and a novel similarity score calculated between the definitions of the involved GO terms. In our work, we use SSA to calculate semantic similarities between pairs of proteins by combining pairwise semantic similarities between the GO terms that annotate the involved proteins. The reliability of SSA was evaluated by comparing the resulting semantic similarities between proteins with the functional similarities between proteins derived from expert annotations or sequence similarity. Comparisons with existing state-of-the-art methods showed that SSA is highly competitive with the other methods. SSA provides a reliable measure for semantics similarity independent of external databases of functional-annotation observations.

Wavelet energy-guided level set-based active contour: a segmentation method to segment highly similar regions.

PubMed

Achuthan, Anusha; Rajeswari, Mandava; Ramachandram, Dhanesh; Aziz, Mohd Ezane; Shuaib, Ibrahim Lutfi

2010-07-01

This paper introduces an approach to perform segmentation of regions in computed tomography (CT) images that exhibit intra-region intensity variations and at the same time have similar intensity distributions with surrounding/adjacent regions. In this work, we adapt a feature computed from wavelet transform called wavelet energy to represent the region information. The wavelet energy is embedded into a level set model to formulate the segmentation model called wavelet energy-guided level set-based active contour (WELSAC). The WELSAC model is evaluated using several synthetic and CT images focusing on tumour cases, which contain regions demonstrating the characteristics of intra-region intensity variations and having high similarity in intensity distributions with the adjacent regions. The obtained results show that the proposed WELSAC model is able to segment regions of interest in close correspondence with the manual delineation provided by the medical experts and to provide a solution for tumour detection. Copyright 2010 Elsevier Ltd. All rights reserved.

A similarity-based data warehousing environment for medical images.

PubMed

Teixeira, Jefferson William; Annibal, Luana Peixoto; Felipe, Joaquim Cezar; Ciferri, Ricardo Rodrigues; Ciferri, Cristina Dutra de Aguiar

2015-11-01

A core issue of the decision-making process in the medical field is to support the execution of analytical (OLAP) similarity queries over images in data warehousing environments. In this paper, we focus on this issue. We propose imageDWE, a non-conventional data warehousing environment that enables the storage of intrinsic features taken from medical images in a data warehouse and supports OLAP similarity queries over them. To comply with this goal, we introduce the concept of perceptual layer, which is an abstraction used to represent an image dataset according to a given feature descriptor in order to enable similarity search. Based on this concept, we propose the imageDW, an extended data warehouse with dimension tables specifically designed to support one or more perceptual layers. We also detail how to build an imageDW and how to load image data into it. Furthermore, we show how to process OLAP similarity queries composed of a conventional predicate and a similarity search predicate that encompasses the specification of one or more perceptual layers. Moreover, we introduce an index technique to improve the OLAP query processing over images. We carried out performance tests over a data warehouse environment that consolidated medical images from exams of several modalities. The results demonstrated the feasibility and efficiency of our proposed imageDWE to manage images and to process OLAP similarity queries. The results also demonstrated that the use of the proposed index technique guaranteed a great improvement in query processing. Copyright © 2015 Elsevier Ltd. All rights reserved.

Walkable Worlds give a Rich Self-Similar Structure to the Real Line

NASA Astrophysics Data System (ADS)

Rosinger, Elemér E.

2010-05-01

It is a rather universal tacit and unquestioned belief—and even more so among physicists—that there is one and only one real line, namely, given by the coodinatisation of Descartes through the usual field R of real numbers. Such a dramatically limiting and thus harmful belief comes, unknown to equally many, from the similarly tacit acceptance of the ancient Archimedean Axiom in Euclid's Geometry. The consequence of that belief is a similar belief in the uniqueness of the coordinatization of the plane by the usual field C of complex numbers, and therefore, of the various spaces, manifolds, etc., be they finite or infinite dimensional, constructed upon the real or complex numbers, including the Hilbert spaces used in Quantum Mechanics. A near total lack of awareness follows therefore about the rich self-similar structure of other possible coordinatisations of the real line, possibilities given by various linearly ordered scalar fields obtained through the ultrapower construction. Such fields contain as a rather small subset the usual field R of real numbers. The concept of walkable world, which has highly intuitive and pragmatic algebraic and geometric meaning, illustrates the mentioned rich self-similar structure.

Similar or Different?: The Importance of Similarities and Differences for Support between Siblings

ERIC Educational Resources Information Center

Voorpostel, Marieke; van der Lippe, Tanja; Dykstra, Pearl A.; Flap, Henk

2007-01-01

Using a large-scale Dutch national sample (N = 7,126), the authors examine the importance of similarities and differences in the sibling dyad for the provision of support. Similarities are assumed to enhance attraction and empathy; differences are assumed to be related to different possibilities for exchange. For helping with housework, helping…

Finding Protein and Nucleotide Similarities with FASTA

PubMed Central

Pearson, William R.

2016-01-01

The FASTA programs provide a comprehensive set of rapid similarity searching tools ( fasta36, fastx36, tfastx36, fasty36, tfasty36), similar to those provided by the BLAST package, as well as programs for slower, optimal, local and global similarity searches ( ssearch36, ggsearch36) and for searching with short peptides and oligonucleotides ( fasts36, fastm36). The FASTA programs use an empirical strategy for estimating statistical significance that accommodates a range of similarity scoring matrices and gap penalties, improving alignment boundary accuracy and search sensitivity (Unit 3.5). The FASTA programs can produce “BLAST-like” alignment and tabular output, for ease of integration into existing analysis pipelines, and can search small, representative databases, and then report results for a larger set of sequences, using links from the smaller dataset. The FASTA programs work with a wide variety of database formats, including mySQL and postgreSQL databases (Unit 9.4). The programs also provide a strategy for integrating domain and active site annotations into alignments and highlighting the mutational state of functionally critical residues. These protocols describe how to use the FASTA programs to characterize protein and DNA sequences, using protein:protein, protein:DNA, and DNA:DNA comparisons. PMID:27010337

Finding Protein and Nucleotide Similarities with FASTA.

PubMed

Pearson, William R

2016-03-24

The FASTA programs provide a comprehensive set of rapid similarity searching tools (fasta36, fastx36, tfastx36, fasty36, tfasty36), similar to those provided by the BLAST package, as well as programs for slower, optimal, local, and global similarity searches (ssearch36, ggsearch36), and for searching with short peptides and oligonucleotides (fasts36, fastm36). The FASTA programs use an empirical strategy for estimating statistical significance that accommodates a range of similarity scoring matrices and gap penalties, improving alignment boundary accuracy and search sensitivity. The FASTA programs can produce "BLAST-like" alignment and tabular output, for ease of integration into existing analysis pipelines, and can search small, representative databases, and then report results for a larger set of sequences, using links from the smaller dataset. The FASTA programs work with a wide variety of database formats, including mySQL and postgreSQL databases. The programs also provide a strategy for integrating domain and active site annotations into alignments and highlighting the mutational state of functionally critical residues. These protocols describe how to use the FASTA programs to characterize protein and DNA sequences, using protein:protein, protein:DNA, and DNA:DNA comparisons. Copyright © 2016 John Wiley & Sons, Inc.

Parallel Immunizations of Rabbits Using the Same Antigen Yield Antibodies with Similar, but Not Identical, Epitopes

PubMed Central

Hjelm, Barbara; Forsström, Björn; Löfblom, John; Rockberg, Johan; Uhlén, Mathias

2012-01-01

A problem for the generation of polyclonal antibodies is the potential difficulties for obtaining a renewable resource due to batch-to-batch variations when the same antigen is immunized into several separate animals. Here, we have investigated this issue by determining the epitopes of antibodies generated from parallel immunizations of rabbits with recombinant antigens corresponding to ten human protein targets. The epitopes were mapped by both a suspension bead array approach using overlapping synthetic 15-mer peptides and a bacterial display approach using expression of random fragments of the antigen on the surface of bacteria. Both methods determined antibody binding with the aid of fluorescent-based analysis. In addition, one polyclonal antibody was fractionated by peptide-specific affinity capture for in-depth comparison of epitopes. The results show that the same antigen immunized in several rabbits yields polyclonal antibodies with similar epitopes, but with larger differences in the relative amounts of antibodies to the different epitopes. In some cases, unique epitopes were observed for one of the immunizations. The results suggest that polyclonal antibodies generated by repeated immunizations do not display an identical epitope pattern, although many of the epitopes are similar. PMID:23284606

The impact of bereaved parents' perceived grief similarity on relationship satisfaction.

PubMed

Buyukcan-Tetik, Asuman; Finkenauer, Catrin; Schut, Henk; Stroebe, Margaret; Stroebe, Wolfgang

2017-06-01

The present research focused on bereaved parents' perceived grief similarity, and aimed to investigate the concurrent and longitudinal effects of the perceptions that the partner has less, equal, or more grief intensity than oneself on relationship satisfaction. Participants of our longitudinal study were 229 heterosexual bereaved Dutch couples who completed questionnaires 6, 13, and 20 months after the loss of their child. Average age of participants was 40.7 (SD = 9.5). Across 3 study waves, participants' perceived grief similarity and relationship satisfaction were assessed. To control for their effects, own grief level, child's gender, expectedness of loss, parent's age, parent's gender, and time were also included in the analyses. Consistent with the hypotheses, cross-sectional results revealed that bereaved parents who perceived dissimilar levels of grief (less or more grief) had lower relationship satisfaction than bereaved parents who perceived similar levels of grief. This effect remained significant controlling for the effects of possible confounding variables and actual similarity in grief between partners. We also found that perceived grief similarity at the first study wave was related to the highest level of relationship satisfaction at the second study wave. Moreover, results showed that perceived grief similarity was associated with a higher level in partner's relationship satisfaction. Results are discussed considering the comparison and similarity in grief across bereaved partners after child loss. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Self-Similarity of Plasmon Edge Modes on Koch Fractal Antennas.

PubMed

Bellido, Edson P; Bernasconi, Gabriel D; Rossouw, David; Butet, Jérémy; Martin, Olivier J F; Botton, Gianluigi A

2017-11-28

We investigate the plasmonic behavior of Koch snowflake fractal geometries and their possible application as broadband optical antennas. Lithographically defined planar silver Koch fractal antennas were fabricated and characterized with high spatial and spectral resolution using electron energy loss spectroscopy. The experimental data are supported by numerical calculations carried out with a surface integral equation method. Multiple surface plasmon edge modes supported by the fractal structures have been imaged and analyzed. Furthermore, by isolating and reproducing self-similar features in long silver strip antennas, the edge modes present in the Koch snowflake fractals are identified. We demonstrate that the fractal response can be obtained by the sum of basic self-similar segments called characteristic edge units. Interestingly, the plasmon edge modes follow a fractal-scaling rule that depends on these self-similar segments formed in the structure after a fractal iteration. As the size of a fractal structure is reduced, coupling of the modes in the characteristic edge units becomes relevant, and the symmetry of the fractal affects the formation of hybrid modes. This analysis can be utilized not only to understand the edge modes in other planar structures but also in the design and fabrication of fractal structures for nanophotonic applications.

Semantic similarity measure in biomedical domain leverage web search engine.

PubMed

Chen, Chi-Huang; Hsieh, Sheau-Ling; Weng, Yung-Ching; Chang, Wen-Yung; Lai, Feipei

2010-01-01

Semantic similarity measure plays an essential role in Information Retrieval and Natural Language Processing. In this paper we propose a page-count-based semantic similarity measure and apply it in biomedical domains. Previous researches in semantic web related applications have deployed various semantic similarity measures. Despite the usefulness of the measurements in those applications, measuring semantic similarity between two terms remains a challenge task. The proposed method exploits page counts returned by the Web Search Engine. We define various similarity scores for two given terms P and Q, using the page counts for querying P, Q and P AND Q. Moreover, we propose a novel approach to compute semantic similarity using lexico-syntactic patterns with page counts. These different similarity scores are integrated adapting support vector machines, to leverage the robustness of semantic similarity measures. Experimental results on two datasets achieve correlation coefficients of 0.798 on the dataset provided by A. Hliaoutakis, 0.705 on the dataset provide by T. Pedersen with physician scores and 0.496 on the dataset provided by T. Pedersen et al. with expert scores.

Similar herpes zoster incidence across Europe: results from a systematic literature review.

PubMed

Pinchinat, Sybil; Cebrián-Cuenca, Ana M; Bricout, Hélène; Johnson, Robert W

2013-04-10

Herpes zoster (HZ) is caused by reactivation of the varicella-zoster virus (VZV) and mainly affects individuals aged ≥50 years. The forthcoming European launch of a vaccine against HZ (Zostavax®) prompts the need for a better understanding of the epidemiology of HZ in Europe. Therefore the aim of this systematic review was to summarize the available data on HZ incidence in Europe and to describe age-specific incidence. The Medline database of the National Library of Medicine was used to conduct a comprehensive literature search of population-based studies of HZ incidence published between 1960 and 2010 carried out in the 27 member countries of the European Union, Iceland, Norway and Switzerland. The identified articles were reviewed and scored according to a reading grid including various quality criteria, and HZ incidence data were extracted and presented by country. The search identified 21 studies, and revealed a similar annual HZ incidence throughout Europe, varying by country from 2.0 to 4.6/1 000 person-years with no clearly observed geographic trend. Despite the fact that age groups differed from one study to another, age-specific HZ incidence rates seemed to hold steady during the review period, at around 1/1 000 children <10 years, around 2/1 000 adults aged <40 years, and around 1-4/1 000 adults aged 40-50 years. They then increased rapidly after age 50 years to around 7-8/1 000, up to 10/1 000 after 80 years of age. Our review confirms that in Europe HZ incidence increases with age, and quite drastically after 50 years of age. In all of the 21 studies included in the present review, incidence rates were higher among women than men, and this difference increased with age. This review also highlights the need to identify standardized surveillance methods to improve the comparability of data within European Union Member States and to monitor the impact of VZV immunization on the epidemiology of HZ. Available data in Europe have shortcomings which

False memory for orthographically versus semantically similar words in adolescents with dyslexia: a fuzzy-trace theory perspective.

PubMed

Obidziński, Michał; Nieznański, Marek

2017-10-01

The presented research was conducted in order to investigate the connections between developmental dyslexia and the functioning of verbatim and gist memory traces-assumed in the fuzzy-trace theory. The participants were 71 high school students (33 with dyslexia and 38 without learning difficulties). The modified procedure and multinomial model of Stahl and Klauer (simplified conjoint recognition model) was used to collect and analyze data. Results showed statistically significant differences in four of the model parameters: (a) the probability of verbatim trace recollection upon presentation of orthographically similar stimulus was higher in the control than dyslexia group, (b) the probability of verbatim trace recollection upon presentation of semantically similar stimulus was higher in the control than dyslexia group, (c) the probability of gist trace retrieval upon presentation of semantically similar stimulus was higher in the dyslexia than control group, and (d) the probability of gist trace retrieval upon target stimulus presentation (in the semantic condition) was higher in the control than dyslexia group. The obtained results suggest differences of memory functioning in terms of verbatim and gist trace retrieval between people with and without dyslexia on specific, elementary cognitive processes postulated by the fuzzy-trace theory. These can indicate new approaches in the education of persons with developmental dyslexia, focused on specific impairments and the strengths of their memory functioning.

Influence of increment thickness on the similarity of composite shade: a pilot study.

PubMed

Roselino, Lourenco de Moraes Rego; Garcia, Lucas da Fonseca Roberti; Sousa, Ana Beatriz Silva; Pires-de-Souza, Fernanda de Carvalho Panzeri

2012-01-01

The aim of this study was to evaluate the similarity in shade between increments of different composite thicknesses. Fifty test specimens 12 mm in diameter were fabricated and separated into five groups (n = 10) according to sample thickness: 0.5 mm, 1.0 mm, 1.5 mm, 2.0 mm, and 2.5 mm. Specimens were polished with water abrasive papers and silicone points. Next, based on the CIE L*a*b* system, test specimens were submitted to color readouts, and the values obtained for the coordinates L*, a*, and b* for each thickness were compared using one-way ANOVA and a Tukey test (P < 0.05). The results demonstrated that there was a reduction in coordinate L* as the test specimen thickness increased, with statistically significant differences (P < 0.05), except for 2.0 mm and 2.5 mm thicknesses (P > 0.05). Samples 1.5 mm thick presented less variation of a*, while a greater variation occurred for samples 2.5 mm thick, with a significant difference in comparison with the other thicknesses (P < 0.05), except for 2.0 mm (P > 0.05). Samples 0.5 mm thick presented a greater variation of b*, while the lowest variation in this coordinate occurred for samples 2.5 mm thick, which was significantly different from the other samples (P < 0.05). It was concluded that different composite thicknesses do not present similarity of color and have an influence on the final result of esthetic restorations.

Virtual reality balance training for elderly: Similar skiing games elicit different challenges in balance training.

PubMed

de Vries, Aijse W; Faber, Gert; Jonkers, Ilse; Van Dieen, Jaap H; Verschueren, Sabine M P

2018-01-01

Virtual Reality (VR) balance training may have advantages over regular exercise training in older adults. However, results so far are conflicting potentially due to the lack of challenge imposed by the movements in those games. Therefore, the aim of this study was to assess to which extent two similar skiing games challenge balance, as reflected in center of mass (COM) movements relative to their Functional Limits of Stability (FLOS). Thirty young and elderly participants performed two skiing games, one on the Wii Balance board (Wiiski), which uses a force plate, and one with the Kinect sensor (Kinski), which performs motion tracking. During gameplay, kinematics were captured using seven opto-electronical cameras. FLOS were obtained for eight directions. The influence of games and trials on COM displacement in each of the eight directions, and maximal COM speed, were tested with Generalized Estimated Equations. In all directions with anterior and medio-lateral, but not with a posterior component, subjects showed significantly larger maximal %FLOS displacements during the Kinski game than during the Wiiski game. Furthermore, maximal COM displacement, and COM speed in Kinski remained similar or increased over trials, whereas for Wiiski it decreased. Our results show the importance of assessing the movement challenge in games used for balance training. Similar games impose different challenges, with the control sensors and their gain settings playing an important role. Furthermore, adaptations led to a decrease in challenge in Wiiski, which might limit the effectiveness of the game as a balance-training tool. Copyright © 2017 Elsevier B.V. All rights reserved.

Similarity of Cortical Activity Patterns Predicts generalization Behavior

PubMed Central

Engineer, Crystal T.; Perez, Claudia A.; Carraway, Ryan S.; Chang, Kevin Q.; Roland, Jarod L.; Sloan, Andrew M.; Kilgard, Michael P.

2013-01-01

Humans and animals readily generalize previously learned knowledge to new situations. Determining similarity is critical for assigning category membership to a novel stimulus. We tested the hypothesis that category membership is initially encoded by the similarity of the activity pattern evoked by a novel stimulus to the patterns from known categories. We provide behavioral and neurophysiological evidence that activity patterns in primary auditory cortex contain sufficient information to explain behavioral categorization of novel speech sounds by rats. Our results suggest that category membership might be encoded by the similarity of the activity pattern evoked by a novel speech sound to the patterns evoked by known sounds. Categorization based on featureless pattern matching may represent a general neural mechanism for ensuring accurate generalization across sensory and cognitive systems. PMID:24147140

Does the COPD assessment test (CAT(TM)) questionnaire produce similar results when self- or interviewer administered?

PubMed

Agusti, A; Soler-Cataluña, J J; Molina, J; Morejon, E; Garcia-Losa, M; Roset, M; Badia, X

2015-10-01

The COPD assessment test (CAT) is a questionnaire that assesses the impact of chronic obstructive pulmonary disease (COPD) on health status, but some patients have difficulties filling it up by themselves. We examined whether the mode of administration of the Spanish version of CAT (self vs. interviewer) influences its scores and/or psychometric properties. Observational, prospective study in 49 Spanish centers that includes clinically stable COPD patients (n = 153) and patients hospitalized because of an exacerbation (ECOPD; n = 224). The CAT was self-administered (CAT-SA) or administered by an interviewer (CAT-IA) based on the investigator judgment of the patient's capacity. To assess convergent validity, the Saint George's Respiratory Disease Questionnaire (SGRQ) and the London Chest Activity of Daily Living (LCADL) instrument were also administered. Psychometric properties were compared across modes of administration. A total of 118 patients (31 %) completed the CAT-SA and 259 (69 %) CAT-IA. Multiple regression analysis showed that mode of administration did not affect CAT scores. The CAT showed excellent psychometric properties in both modes of administration. Internal consistency coefficients (Cronbach's alpha) were high (0.86 for CAT-SA and 0.85 for CAT-IA) as was test-retest reliability (intraclass correlation coefficients of 0.83 for CAT-SA and CAT-IA). Correlations with SGRQ and LCADL were moderate to strong both in CAT-SA and CAT-IA, indicating good convergent validity. Similar results were observed when testing longitudinal validity. The mode of administration does not influence CAT scores or its psychometric properties. Hence, both modes of administration can be used in clinical practice depending on the physician judgment of patient's capacity.

Fuzzy measures on the Gene Ontology for gene product similarity.

PubMed

Popescu, Mihail; Keller, James M; Mitchell, Joyce A

2006-01-01

One of the most important objects in bioinformatics is a gene product (protein or RNA). For many gene products, functional information is summarized in a set of Gene Ontology (GO) annotations. For these genes, it is reasonable to include similarity measures based on the terms found in the GO or other taxonomy. In this paper, we introduce several novel measures for computing the similarity of two gene products annotated with GO terms. The fuzzy measure similarity (FMS) has the advantage that it takes into consideration the context of both complete sets of annotation terms when computing the similarity between two gene products. When the two gene products are not annotated by common taxonomy terms, we propose a method that avoids a zero similarity result. To account for the variations in the annotation reliability, we propose a similarity measure based on the Choquet integral. These similarity measures provide extra tools for the biologist in search of functional information for gene products. The initial testing on a group of 194 sequences representing three proteins families shows a higher correlation of the FMS and Choquet similarities to the BLAST sequence similarities than the traditional similarity measures such as pairwise average or pairwise maximum.

Lemurs and macaques show similar numerical sensitivity.

PubMed

Jones, Sarah M; Pearson, John; DeWind, Nicholas K; Paulsen, David; Tenekedjieva, Ana-Maria; Brannon, Elizabeth M

2014-05-01

We investigated the precision of the approximate number system (ANS) in three lemur species (Lemur catta, Eulemur mongoz, and Eulemur macaco flavifrons), one Old World monkey species (Macaca mulatta) and humans (Homo sapiens). In Experiment 1, four individuals of each nonhuman primate species were trained to select the numerically larger of two visual arrays on a touchscreen. We estimated numerical acuity by modeling Weber fractions (w) and found quantitatively equivalent performance among all four nonhuman primate species. In Experiment 2, we tested adult humans in a similar procedure, and they outperformed the four nonhuman species but showed qualitatively similar performance. These results indicate that the ANS is conserved over the primate order.

Scalable gastroscopic video summarization via similar-inhibition dictionary selection.

PubMed

Wang, Shuai; Cong, Yang; Cao, Jun; Yang, Yunsheng; Tang, Yandong; Zhao, Huaici; Yu, Haibin

2016-01-01

This paper aims at developing an automated gastroscopic video summarization algorithm to assist clinicians to more effectively go through the abnormal contents of the video. To select the most representative frames from the original video sequence, we formulate the problem of gastroscopic video summarization as a dictionary selection issue. Different from the traditional dictionary selection methods, which take into account only the number and reconstruction ability of selected key frames, our model introduces the similar-inhibition constraint to reinforce the diversity of selected key frames. We calculate the attention cost by merging both gaze and content change into a prior cue to help select the frames with more high-level semantic information. Moreover, we adopt an image quality evaluation process to eliminate the interference of the poor quality images and a segmentation process to reduce the computational complexity. For experiments, we build a new gastroscopic video dataset captured from 30 volunteers with more than 400k images and compare our method with the state-of-the-arts using the content consistency, index consistency and content-index consistency with the ground truth. Compared with all competitors, our method obtains the best results in 23 of 30 videos evaluated based on content consistency, 24 of 30 videos evaluated based on index consistency and all videos evaluated based on content-index consistency. For gastroscopic video summarization, we propose an automated annotation method via similar-inhibition dictionary selection. Our model can achieve better performance compared with other state-of-the-art models and supplies more suitable key frames for diagnosis. The developed algorithm can be automatically adapted to various real applications, such as the training of young clinicians, computer-aided diagnosis or medical report generation. Copyright © 2015 Elsevier B.V. All rights reserved.

Preliminary Results from Duplex Procedure for Obtain of Fe Based Materials for Automotive Applications

NASA Astrophysics Data System (ADS)

Crăciun, R. C.; Stanciu, S.; Geantă, V.; Voiculescu, I.; Manole, V.; Gârneţ, I. A.; Alexandru, A.; Cimpoesu, N.; Săndulache, F.

2017-06-01

Abstract Iron based materials still represent a high percentage from metallic materials used in industry, in general, and in automotive industry, in particular. In this case we used a duplex process in order to obtain the FeMnSiAl experimental alloy for a more efficient use of various units. In the first stage iron, manganese, silicon and aluminum were melted and mixed together using arc melting technology and for the second stage the alloy was re-melt for homogeneity in an induction furnace. Chemical composition, after each melting step, was analyzed using EDS Bruker detector for various areas and microstructural characterization using SEM, VegaTescan LMH II with SE detector, equipment. This alloy is proposed as a metallic approach of mechanical dumpers used in automotive industry for low and medium impact contacts.

Self-similar expansion of adiabatic electronegative dusty plasma

NASA Astrophysics Data System (ADS)

Shahmansouri, M.; Bemooni, A.; Mamun, A. A.

2017-12-01

The self-similar expansion of an adiabatic electronegative dusty plasma (consisting of inertialess adiabatic electrons, inertialess adiabatic ions and inertial adiabatic negatively charged dust fluids) is theoretically investigated by employing the self-similar approach. It is found that the effects of the plasma adiabaticity (represented by the adiabatic index ) and dusty plasma parameters (determined by dust temperature and initial dust population) significantly modify the nature of the plasma expansion. The implications of our results are expected to play an important role in understanding the physics of the expansion of space and laboratory electronegative dusty plasmas.

Effect of between-category similarity on basic-level superiority in pigeons

PubMed Central

Lazareva, Olga F.; Soto, Fabián A.; Wasserman, Edward A.

2010-01-01

Children categorize stimuli at the basic level faster than at the superordinate level. We hypothesized that between-category similarity may affect this basic-level superiority effect. Dissimilar categories may be easy to distinguish at the basic level but be difficult to group at the superordinate level, whereas similar categories may be easy to group at the superordinate level but be difficult to distinguish at the basic level. Consequently, similar basic-level categories may produce a superordinate-before-basic learning trend, whereas dissimilar basic-level categories may result in a basic-before-superordinate learning trend. We tested this hypothesis in pigeons by constructing superordinate-level categories out of basic-level categories with known similarity. In Experiment 1, we experimentally evaluated the between-category similarity of four basic-level photographic categories using multiple fixed interval-extinction training (Astley & Wasserman, 1992). We used the resultant similarity matrices in Experiment 2 to construct two superordinate-level categories from basic-level categories with high between-category similarity (cars and persons; chairs and flowers). We then trained pigeons to concurrently classify those photographs into either the proper basic-level category or the proper superordinate-level category. Under these conditions, the pigeons learned the superordinate-level discrimination faster than the basic-level discrimination, confirming our hypothesis that basic-level superiority is affected by between-category similarity. PMID:20600696

A Model of Generating Visual Place Cells Based on Environment Perception and Similar Measure.

PubMed

Zhou, Yang; Wu, Dewei

2016-01-01

It is an important content to generate visual place cells (VPCs) in the field of bioinspired navigation. By analyzing the firing characteristic of biological place cells and the existing methods for generating VPCs, a model of generating visual place cells based on environment perception and similar measure is abstracted in this paper. VPCs' generation process is divided into three phases, including environment perception, similar measure, and recruiting of a new place cell. According to this process, a specific method for generating VPCs is presented. External reference landmarks are obtained based on local invariant characteristics of image and a similar measure function is designed based on Euclidean distance and Gaussian function. Simulation validates the proposed method is available. The firing characteristic of the generated VPCs is similar to that of biological place cells, and VPCs' firing fields can be adjusted flexibly by changing the adjustment factor of firing field (AFFF) and firing rate's threshold (FRT).

A Model of Generating Visual Place Cells Based on Environment Perception and Similar Measure

PubMed Central

2016-01-01

It is an important content to generate visual place cells (VPCs) in the field of bioinspired navigation. By analyzing the firing characteristic of biological place cells and the existing methods for generating VPCs, a model of generating visual place cells based on environment perception and similar measure is abstracted in this paper. VPCs' generation process is divided into three phases, including environment perception, similar measure, and recruiting of a new place cell. According to this process, a specific method for generating VPCs is presented. External reference landmarks are obtained based on local invariant characteristics of image and a similar measure function is designed based on Euclidean distance and Gaussian function. Simulation validates the proposed method is available. The firing characteristic of the generated VPCs is similar to that of biological place cells, and VPCs' firing fields can be adjusted flexibly by changing the adjustment factor of firing field (AFFF) and firing rate's threshold (FRT). PMID:27597859

Quality assessment of protein model-structures based on structural and functional similarities.

PubMed

Konopka, Bogumil M; Nebel, Jean-Christophe; Kotulska, Malgorzata

2012-09-21

Experimental determination of protein 3D structures is expensive, time consuming and sometimes impossible. A gap between number of protein structures deposited in the World Wide Protein Data Bank and the number of sequenced proteins constantly broadens. Computational modeling is deemed to be one of the ways to deal with the problem. Although protein 3D structure prediction is a difficult task, many tools are available. These tools can model it from a sequence or partial structural information, e.g. contact maps. Consequently, biologists have the ability to generate automatically a putative 3D structure model of any protein. However, the main issue becomes evaluation of the model quality, which is one of the most important challenges of structural biology. GOBA--Gene Ontology-Based Assessment is a novel Protein Model Quality Assessment Program. It estimates the compatibility between a model-structure and its expected function. GOBA is based on the assumption that a high quality model is expected to be structurally similar to proteins functionally similar to the prediction target. Whereas DALI is used to measure structure similarity, protein functional similarity is quantified using standardized and hierarchical description of proteins provided by Gene Ontology combined with Wang's algorithm for calculating semantic similarity. Two approaches are proposed to express the quality of protein model-structures. One is a single model quality assessment method, the other is its modification, which provides a relative measure of model quality. Exhaustive evaluation is performed on data sets of model-structures submitted to the CASP8 and CASP9 contests. The validation shows that the method is able to discriminate between good and bad model-structures. The best of tested GOBA scores achieved 0.74 and 0.8 as a mean Pearson correlation to the observed quality of models in our CASP8 and CASP9-based validation sets. GOBA also obtained the best result for two targets of CASP8, and

Representation of Semantic Similarity in the Left Intraparietal Sulcus: Functional Magnetic Resonance Imaging Evidence

PubMed Central

Neyens, Veerle; Bruffaerts, Rose; Liuzzi, Antonietta G.; Kalfas, Ioannis; Peeters, Ronald; Keuleers, Emmanuel; Vogels, Rufin; De Deyne, Simon; Storms, Gert; Dupont, Patrick; Vandenberghe, Rik

2017-01-01

According to a recent study, semantic similarity between concrete entities correlates with the similarity of activity patterns in left middle IPS during category naming. We examined the replicability of this effect under passive viewing conditions, the potential role of visuoperceptual similarity, where the effect is situated compared to regions that have been previously implicated in visuospatial attention, and how it compares to effects of object identity and location. Forty-six subjects participated. Subjects passively viewed pictures from two categories, musical instruments and vehicles. Semantic similarity between entities was estimated based on a concept-feature matrix obtained in more than 1,000 subjects. Visuoperceptual similarity was modeled based on the HMAX model, the AlexNet deep convolutional learning model, and thirdly, based on subjective visuoperceptual similarity ratings. Among the IPS regions examined, only left middle IPS showed a semantic similarity effect. The effect was significant in hIP1, hIP2, and hIP3. Visuoperceptual similarity did not correlate with similarity of activity patterns in left middle IPS. The semantic similarity effect in left middle IPS was significantly stronger than in the right middle IPS and also stronger than in the left or right posterior IPS. The semantic similarity effect was similar to that seen in the angular gyrus. Object identity effects were much more widespread across nearly all parietal areas examined. Location effects were relatively specific for posterior IPS and area 7 bilaterally. To conclude, the current findings replicate the semantic similarity effect in left middle IPS under passive viewing conditions, and demonstrate its anatomical specificity within a cytoarchitectonic reference frame. We propose that the semantic similarity effect in left middle IPS reflects the transient uploading of semantic representations in working memory. PMID:28824405

Defying geometric similarity: Shape centralization in male UK offshore workers.

PubMed

Stewart, Arthur D; Ledingham, Robert J; Furnace, Graham; Williams, Hector; Nevill, Alan M

2017-05-06

Applying geometric similarity predictions of body dimensions to specific occupational groups has the potential to reveal useful ergonomic and health implications. This study assessed a representative sample of the male UK offshore workforce, and examined how body dimensions from sites typifying musculoskeletal development or fat accumulation, differed from predicted values. A cross sectional sample was obtained across seven weight categories using quota sampling, to match the wider workforce. In total, 588 UK offshore workers, 84 from each of seven weight categories, were measured for stature, mass and underwent 3D body scans which yielded 22 dimensional measurements. Each measurement was modeled using a body-mass power law (adjusting for age), to derive its exponent, which was compared against that predicted from geometric similarity. Mass scaled to stature 1.73 (CI: 1.44-2.02). Arm and leg volume increased by mass 0.8 , and torso volume increased by mass 1.1 in contrast to mass 1.0 predicted by geometric similarity. Neck girth increased by mass 0.33 as expected, while torso girth and depth dimensions increased by mass 0.53-0.72 , all substantially greater than assumed by geometric similarity. After controlling for age, offshore workers experience spectacular "super-centralization" of body shape, with greatest gains in abdominal depth and girth dimensions in areas of fat accumulation, and relative dimensional loss in limbs. These findings are consistent with the antecedents of sarcopenic obesity, and should be flagged as a health concern for this workforce, and for future targeted research and lifestyle interventions. © 2016 Wiley Periodicals, Inc.

Retrieval evaluation and distance learning from perceived similarity between endomicroscopy videos.

PubMed

André, Barbara; Vercauteren, Tom; Buchner, Anna M; Wallace, Michael B; Ayache, Nicholas

2011-01-01

Evaluating content-based retrieval (CBR) is challenging because it requires an adequate ground-truth. When the available groundtruth is limited to textual metadata such as pathological classes, retrieval results can only be evaluated indirectly, for example in terms of classification performance. In this study we first present a tool to generate perceived similarity ground-truth that enables direct evaluation of endomicroscopic video retrieval. This tool uses a four-points Likert scale and collects subjective pairwise similarities perceived by multiple expert observers. We then evaluate against the generated ground-truth a previously developed dense bag-of-visual-words method for endomicroscopic video retrieval. Confirming the results of previous indirect evaluation based on classification, our direct evaluation shows that this method significantly outperforms several other state-of-the-art CBR methods. In a second step, we propose to improve the CBR method by learning an adjusted similarity metric from the perceived similarity ground-truth. By minimizing a margin-based cost function that differentiates similar and dissimilar video pairs, we learn a weight vector applied to the visual word signatures of videos. Using cross-validation, we demonstrate that the learned similarity distance is significantly better correlated with the perceived similarity than the original visual-word-based distance.

Polyphasic characterization of Gluconacetobacter diazotrophicus isolates obtained from different sugarcane varieties

PubMed Central

Guedes, Helma V.; dos Santos, Samuel T.; Perin, Liamara; Teixeira, Kátia R. dos S.; Reis, Veronica M.; Baldani, José I.

2008-01-01

A polyphasic approach was applied to characterize 35 G. diazotrophicus isolates obtained from sugarcane varieties cultivated in Brazil. The isolates were analyzed by phenotypic (use of different carbon sources) and genotypic tests (ARDRA and RISA–RFLP techniques). Variability among the isolates was observed in relation to the carbon source use preference. Glucose and sucrose were used by all isolates in contrast to myo-inositol, galactose and ribose that were not metabolized. The results of the analysis showed the presence of two groups clustered at 68% of similarity. The genetic distance was higher when RISA-RFLP analysis was used. Analysis of 16S rDNA sequences from isolates showed that all of them belonged to the G. diazotrophicus species. Neither effect of the plant part nor sugarcane variety was observed during the cluster analysis. The observed metabolic and genetic variability will be helpful during the strain selection studies for sugarcane inoculation in association with sugarcane breeding programs. PMID:24031296

Walking on a user similarity network towards personalized recommendations.

PubMed

Gan, Mingxin

2014-01-01

Personalized recommender systems have been receiving more and more attention in addressing the serious problem of information overload accompanying the rapid evolution of the world-wide-web. Although traditional collaborative filtering approaches based on similarities between users have achieved remarkable success, it has been shown that the existence of popular objects may adversely influence the correct scoring of candidate objects, which lead to unreasonable recommendation results. Meanwhile, recent advances have demonstrated that approaches based on diffusion and random walk processes exhibit superior performance over collaborative filtering methods in both the recommendation accuracy and diversity. Building on these results, we adopt three strategies (power-law adjustment, nearest neighbor, and threshold filtration) to adjust a user similarity network from user similarity scores calculated on historical data, and then propose a random walk with restart model on the constructed network to achieve personalized recommendations. We perform cross-validation experiments on two real data sets (MovieLens and Netflix) and compare the performance of our method against the existing state-of-the-art methods. Results show that our method outperforms existing methods in not only recommendation accuracy and diversity, but also retrieval performance.

Walking on a User Similarity Network towards Personalized Recommendations

PubMed Central

Gan, Mingxin

2014-01-01

Personalized recommender systems have been receiving more and more attention in addressing the serious problem of information overload accompanying the rapid evolution of the world-wide-web. Although traditional collaborative filtering approaches based on similarities between users have achieved remarkable success, it has been shown that the existence of popular objects may adversely influence the correct scoring of candidate objects, which lead to unreasonable recommendation results. Meanwhile, recent advances have demonstrated that approaches based on diffusion and random walk processes exhibit superior performance over collaborative filtering methods in both the recommendation accuracy and diversity. Building on these results, we adopt three strategies (power-law adjustment, nearest neighbor, and threshold filtration) to adjust a user similarity network from user similarity scores calculated on historical data, and then propose a random walk with restart model on the constructed network to achieve personalized recommendations. We perform cross-validation experiments on two real data sets (MovieLens and Netflix) and compare the performance of our method against the existing state-of-the-art methods. Results show that our method outperforms existing methods in not only recommendation accuracy and diversity, but also retrieval performance. PMID:25489942

Global invariants of paths and curves for the group of all linear similarities in the two-dimensional Euclidean space

NASA Astrophysics Data System (ADS)

Khadjiev, Djavvat; Ören, Idri˙s; Pekşen, Ömer

Let E2 be the 2-dimensional Euclidean space, LSim(2) be the group of all linear similarities of E2 and LSim+(2) be the group of all orientation-preserving linear similarities of E2. The present paper is devoted to solutions of problems of global G-equivalence of paths and curves in E2 for the groups G = LSim(2),LSim+(2). Complete systems of global G-invariants of a path and a curve in E2 are obtained. Existence and uniqueness theorems are given. Evident forms of a path and a curve with the given global invariants are obtained.

Concept Similarity in Publications Precedes Cross-disciplinary Collaboration

PubMed Central

Post, Andrew R.; Harrison, James H.

2008-01-01

Innovative science frequently occurs as a result of cross-disciplinary collaboration, the importance of which is reflected by recent NIH funding initiatives that promote communication and collaboration. If shared research interests between collaborators are important for the formation of collaborations, methods for identifying these shared interests across scientific domains could potentially reveal new and useful collaboration opportunities. MEDLINE represents a comprehensive database of collaborations and research interests, as reflected by article co-authors and concept content. We analyzed six years of citations using information retrieval-based methods to compute articles’ conceptual similarity, and found that articles by basic and clinical scientists who later collaborated had significantly higher average similarity than articles by similar scientists who did not collaborate. Refinement of these methods and characterization of found conceptual overlaps could allow automated discovery of collaboration opportunities that are currently missed. PMID:18999254

Concept similarity in publications precedes cross-disciplinary collaboration.

PubMed

Post, Andrew R; Harrison, James H

2008-11-06

Innovative science frequently occurs as a result of cross-disciplinary collaboration, the importance of which is reflected by recent NIH funding initiatives that promote communication and collaboration. If shared research interests between collaborators are important for the formation of collaborations,methods for identifying these shared interests across scientific domains could potentially reveal new and useful collaboration opportunities. MEDLINE represents a comprehensive database of collaborations and research interests, as reflected by article co-authors and concept content. We analyzed six years of citations using information retrieval based methods to compute articles conceptual similarity, and found that articles by basic and clinical scientists who later collaborated had significantly higher average similarity than articles by similar scientists who did not collaborate.Refinement of these methods and characterization of found conceptual overlaps could allow automated discovery of collaboration opportunities that are currently missed.

Analysis of perceived similarity between pairs of microcalcification clusters in mammograms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Juan; Jing, Hao; Wernick, Miles N.

2014-05-15

Purpose: Content-based image retrieval aims to assist radiologists by presenting example images with known pathology that are visually similar to the case being evaluated. In this work, the authors investigate several fundamental issues underlying the similarity ratings between pairs of microcalcification (MC) lesions on mammograms as judged by radiologists: the degree of variability in the similarity ratings, the impact of this variability on agreement between readers in retrieval of similar lesions, and the factors contributing to the readers’ similarity ratings. Methods: The authors conduct a reader study on a set of 1000 image pairs of MC lesions, in which amore » group of experienced breast radiologists rated the degree of similarity between each image pair. The image pairs are selected, from among possible pairings of 222 cases (110 malignant, 112 benign), based on quantitative image attributes (features) and the results of a preliminary reader study. Next, the authors apply analysis of variance (ANOVA) to quantify the level of variability in the readers’ similarity ratings, and study how the variability in individual reader ratings affects consistency between readers. The authors also measure the extent to which readers agree on images which are most similar to a given query, for which the Dice coefficient is used. To investigate how the similarity ratings potentially relate to the attributes underlying the cases, the authors study the fraction of perceptually similar images that also share the same benign or malignant pathology as the query image; moreover, the authors apply multidimensional scaling (MDS) to embed the cases according to their mutual perceptual similarity in a two-dimensional plot, which allows the authors to examine the manner in which similar lesions relate to one another in terms of benign or malignant pathology and clustered MCs. Results: The ANOVA results show that the coefficient of determination in the reader similarity ratings

Similarity to the self influences cortical recruitment during impression formation

PubMed Central

Leshikar, Eric D.; Cassidy, Brittany S.; Gutchess, Angela H.

2015-01-01

Prior work has shown that whether or not someone is similar to the self influences person memory—a type of self-reference effect for others. In this study, we were interested in understanding the neural regions supporting the generation of impressions and subsequent memory for targets who vary in similarity to the self. Participants underwent fMRI scanning while forming positive or negative impressions of face-behavior pairs. We tested participants’ memory for their generated impressions, and then back-sorted the impression trials (encoding) into different levels of self-similarity (high, medium, low) using a self-similarity post-test that came after recognition. Extending prior behavioral work, our data confirmed our hypothesis that memory would be highest for self-similar others and lowest for self-dissimilar others. Dorsal anterior cingulate cortex (dACC) activity increased with self-similarity (high > medium > low) to targets, regardless of later memory for them. An analysis of regions supporting impression memory revealed a double dissociation within medial temporal lobe regions: for similar others, amygdala recruitment supported memory, whereas for dissimilar others, hippocampal activation supported memory. These results suggest that self-similarity influences evaluation and memory for targets, but also affects the underlying neural resources engaged when thinking about others who vary in self-similarity. PMID:26558615

Similarity to the Self Affects Memory for Impressions of Others

PubMed Central

Leshikar, Eric D.; Gutchess, Angela H.

2017-01-01

The present studies investigated whether similarity to the self influenced memory for impressions of others. We predicted that similarity to the self would facilitate impression memory for others, paralleling the self-reference effect found when information is processed relative to the self. We were interested in how the initial valence of the impression, whether positive or negative, affected impression memory. Across two experiments, participants formed impressions while viewing faces paired with traits and behaviors. After recognition, participants rated the self-descriptiveness of the studied traits allowing impression memory to be sorted into high-, medium-, and low-self-similarity. For positive impressions, similar others were remembered better than dissimilar others. For negative impressions, similar others were remembered more poorly than dissimilar others. These results illustrate that similarity to the self has multifaceted effects on person memory, leading to memory enhancement in the case of people given positive impressions, but reducing memory for people associated with negative impressions. PMID:28936392

Signal-noise separation based on self-similarity testing in 1D-timeseries data

NASA Astrophysics Data System (ADS)

Bourdin, Philippe A.

2015-08-01

The continuous improvement of the resolution delivered by modern instrumentation is a cost-intensive part of any new space- or ground-based observatory. Typically, scientists later reduce the resolution of the obtained raw-data, for example in the spatial, spectral, or temporal domain, in order to suppress the effects of noise in the measurements. In practice, only simple methods are used that just smear out the noise, instead of trying to remove it, so that the noise can nomore be seen. In high-precision 1D-timeseries data, this usually results in an unwanted quality-loss and corruption of power spectra at selected frequency ranges. Novel methods exist that are based on non-local averaging, which would conserve much of the initial resolution, but these methods are so far focusing on 2D or 3D data. We present here a method specialized for 1D-timeseries, e.g. as obtained by magnetic field measurements from the recently launched MMS satellites. To identify the noise, we use a self-similarity testing and non-local averaging method in order to separate different types of noise and signals, like the instrument noise, non-correlated fluctuations in the signal from heliospheric sources, and correlated fluctuations such as harmonic waves or shock fronts. In power spectra of test data, we are able to restore significant parts of a previously know signal from a noisy measurement. This method also works for high frequencies, where the background noise may have a larger contribution to the spectral power than the signal itself. We offer an easy-to-use software tools set, which enables scientists to use this novel technique on their own noisy data. This allows to use the maximum possible capacity of the instrumental hardware and helps to enhance the quality of the obtained scientific results.

Learning semantic and visual similarity for endomicroscopy video retrieval.

PubMed

Andre, Barbara; Vercauteren, Tom; Buchner, Anna M; Wallace, Michael B; Ayache, Nicholas

2012-06-01

Content-based image retrieval (CBIR) is a valuable computer vision technique which is increasingly being applied in the medical community for diagnosis support. However, traditional CBIR systems only deliver visual outputs, i.e., images having a similar appearance to the query, which is not directly interpretable by the physicians. Our objective is to provide a system for endomicroscopy video retrieval which delivers both visual and semantic outputs that are consistent with each other. In a previous study, we developed an adapted bag-of-visual-words method for endomicroscopy retrieval, called "Dense-Sift," that computes a visual signature for each video. In this paper, we present a novel approach to complement visual similarity learning with semantic knowledge extraction, in the field of in vivo endomicroscopy. We first leverage a semantic ground truth based on eight binary concepts, in order to transform these visual signatures into semantic signatures that reflect how much the presence of each semantic concept is expressed by the visual words describing the videos. Using cross-validation, we demonstrate that, in terms of semantic detection, our intuitive Fisher-based method transforming visual-word histograms into semantic estimations outperforms support vector machine (SVM) methods with statistical significance. In a second step, we propose to improve retrieval relevance by learning an adjusted similarity distance from a perceived similarity ground truth. As a result, our distance learning method allows to statistically improve the correlation with the perceived similarity. We also demonstrate that, in terms of perceived similarity, the recall performance of the semantic signatures is close to that of visual signatures and significantly better than those of several state-of-the-art CBIR methods. The semantic signatures are thus able to communicate high-level medical knowledge while being consistent with the low-level visual signatures and much shorter than them

Tests of peak flow scaling in simulated self-similar river networks

USGS Publications Warehouse

Menabde, M.; Veitzer, S.; Gupta, V.; Sivapalan, M.

2001-01-01

The effect of linear flow routing incorporating attenuation and network topology on peak flow scaling exponent is investigated for an instantaneously applied uniform runoff on simulated deterministic and random self-similar channel networks. The flow routing is modelled by a linear mass conservation equation for a discrete set of channel links connected in parallel and series, and having the same topology as the channel network. A quasi-analytical solution for the unit hydrograph is obtained in terms of recursion relations. The analysis of this solution shows that the peak flow has an asymptotically scaling dependence on the drainage area for deterministic Mandelbrot-Vicsek (MV) and Peano networks, as well as for a subclass of random self-similar channel networks. However, the scaling exponent is shown to be different from that predicted by the scaling properties of the maxima of the width functions. ?? 2001 Elsevier Science Ltd. All rights reserved.

Learning to distinguish similar objects

NASA Astrophysics Data System (ADS)

Seibert, Michael; Waxman, Allen M.; Gove, Alan N.

1995-04-01

This paper describes how the similarities and differences among similar objects can be discovered during learning to facilitate recognition. The application domain is single views of flying model aircraft captured in silhouette by a CCD camera. The approach was motivated by human psychovisual and monkey neurophysiological data. The implementation uses neural net processing mechanisms to build a hierarchy that relates similar objects to superordinate classes, while simultaneously discovering the salient differences between objects within a class. Learning and recognition experiments both with and without the class similarity and difference learning show the effectiveness of the approach on this visual data. To test the approach, the hierarchical approach was compared to a non-hierarchical approach, and was found to improve the average percentage of correctly classified views from 77% to 84%.

Perceptions of similarity and responsibility attributions to an acquaintance sexual assault victim.

PubMed

Amacker, Amanda M; Littleton, Heather L

2013-11-01

Individuals view similar rape victims as less responsible for the rape than victims perceived as dissimilar. However, it is unclear if individuals hold victims they perceive as similar less responsible for the assault, or if individuals view themselves as more similar to victims they do not view as responsible for the assault. The current study, therefore, examined the temporal relationship between these constructs. A total of 167 college women listened to a date narrative that ended in sexual assault, consensual sex, or no sexual activity (these last two served as controls). Results supported that participants viewed themselves as less similar to the woman in the narrative when the date ended in sexual assault. Only similarity ratings made following learning that the woman was sexually assaulted predicted responsibility attributions suggesting that viewing a victim as responsible for the assault results in decreased perceptions of similarity toward her. Implications and suggestions for future research are discussed.

Color-size Relations of Disc Galaxies with Similar Stellar Masses

NASA Astrophysics Data System (ADS)

Fu, W.; Chang, R. X.; Shen, S. Y.; Zhang, B.

2011-01-01

To investigate the correlations between colors and sizes of disc galaxies with similar stellar masses, a sample of 7959 local face-on disc galaxies is collected from the main galaxy sample of the Seventh Data Release of Sloan Digital Sky Survey (SDSS DR7). Our results show that, under the condition that the stellar masses of disc galaxies are similar, the relation between u-r and size is weak, while g-r, r-i and r-z colors decrease with disk size. This means that the color-size relations of disc galaxies with similar stellar masses do exist, i.e., the more extended disc galaxies with similar stellar masses tend to have bluer colors. An artificial sample is constructed to confirm that this correlation is not driven by the color-stellar mass relations and size-stellar mass relation of disc galaxies. Our results suggest that the mass distribution of disk galaxies may have an important influence on their stellar formation history, i.e., the galaxies with more extended mass distribution evolve more slowly.

Comparison of Various Similarity Measures for Average Image Hash in Mobile Phone Application

NASA Astrophysics Data System (ADS)

Farisa Chaerul Haviana, Sam; Taufik, Muhammad

2017-04-01

One of the main issue in Content Based Image Retrieval (CIBR) is similarity measures for resulting image hashes. The main key challenge is to find the most benefits distance or similarity measures for calculating the similarity in term of speed and computing costs, specially under limited computing capabilities device like mobile phone. This study we utilize twelve most common and popular distance or similarity measures technique implemented in mobile phone application, to be compared and studied. The results show that all similarity measures implemented in this study was perform equally under mobile phone application. This gives more possibilities for method combinations to be implemented for image retrieval.

Birds of a feather sit together: physical similarity predicts seating choice.

PubMed

Mackinnon, Sean P; Jordan, Christian H; Wilson, Anne E

2011-07-01

Across four studies, people sat (or reported they would sit) closer to physically similar others. Study 1 revealed significant aggregation in seating patterns on two easily observed characteristics: glasses wearing and sex. Study 2 replicated this finding with a wider variety of physical traits: race, sex, glasses wearing, hair length, and hair color. The overall tendency for people to sit beside physically similar others remained significant when controlling for sex and race, suggesting people aggregate on physical dimensions other than broad social categories. Study 3 conceptually replicated these results in a laboratory setting. The more physically similar participants were to a confederate, the closer they sat before an anticipated interaction when controlling for sex, race, and attractiveness similarity. In Study 4, overall physical similarity and glasses wearing similarity predicted self-reported seating distance. These effects were mediated by perceived attitudinal similarity. Liking and inferred acceptance also received support as mediators for glasses wearing similarity. © 2011 by the Society for Personality and Social Psychology, Inc

The Roles of Similarity in Transfer: Determinants of Similarity-Based Reminding and Mapping

DTIC Science & Technology

1991-06-02

Psychology , Northwestern University, 2029 Sheridan Road, Evanston, IL 60208. Reproduction in whole or part is permitted for any purpose of the United...ADDRESS (City, State, and ZIPCode) 10 SOURCE OF FUNDING NUMBERS Department of Psychology PROGRAM PROJECT TASK WORK UNIT 603 E. Daniel ELEMENT NO NO NO...according to 3 whether the stimuli (in an S-R pair) or the responses are similar from training to test . Ellis (1965), while agreeing that similarity is

Techniques for obtaining subjective response to vertical vibration

NASA Technical Reports Server (NTRS)

Clarke, M. J.; Oborne, D. J.

1975-01-01

Laboratory experiments were performed to validate the techniques used for obtaining ratings in the field surveys carried out by the University College of Swansea. In addition, attempts were made to evaluate the basic form of the human response to vibration. Some of the results obtained by different methods are described.

Outgassing Total Mass Loss Obtained with Micro-CVCM and Other Vacuum Systems

NASA Technical Reports Server (NTRS)

Scialdone, John; Isaac, Peggy; Clatterbuck, Carroll; Hunkeler, Ronald; Powers, Edward I. (Technical Monitor)

2000-01-01

Several instruments including the Cahn Microbalance, the Knudsen Cell, the micro-CVCM, and the vacuum Thermogravimetric Analyzer (TGA) were used in the testing of a graphite epoxy (GR/EP) composite that is proposed for use as a rigidizing element of an inflatable deployment system. This GR/EP will be cured in situ. The purpose of this testing is to estimate the gaseous production resulting from the curing of the GR/EP composite, to predict the resulting pressure, and to calculate the required venting. Every test was conducted under vacuum at 125 C for 24 hours. Upon comparison of the results, the ASTM E-595 was noted to have given readings that were consistently lower than those obtained using the other instruments, which otherwise provided similar results. The GR/EP was tested using several different geometric arrangements. This paper describes the analysis evaluating the molecular and continuum flow of the outgassing products issuing from the exit port of the ASTM E-595 system. The effective flow conductance provided by the physical dimensions of the vent passage of the ASTM E-595 system and that of the material sample among other factors were investigated to explain the reduced amount of outgassing released during the 24-hour test period,

Outgassing Total Mass Loss Obtained with Micro-CVCM and other Vacuum Systems

NASA Technical Reports Server (NTRS)

Scialdone, John J.; Isaac, Peggy A.; Clatterbuck, Carroll H.; Hunkeler, Ronald E.; Powers, Edward I. (Technical Monitor)

2000-01-01

Several instruments including the Cahn Microbalance the Knudsen Cell, the micro-CVCM, and the vacuum Thermogravimetric Analyzer (TGA) were used in the testing of a graphite epoxy (GR/EP) composite that is proposed for use as a rigidizing element of an inflatable deployment system. This GR/EP will be cured in situ. The purpose of this testing is to estimate the gaseous production resulting from the curing of the GR/EP composite, to predict the resulting pressure, and to calculate the required venting. Every test was conducted under vacuum at 125 C for 24 hours. Upon comparison of the results, the ASTM E-595 was noted to have given readings that were consistently lower than those obtained using the other instruments, which otherwise provided similar results. The GR/EP was tested using several different geometric arrangements. This paper describes the analysis evaluating the molecular and continuum flow of the outgassing products issuing from the exit port of the ASTM E-595 system. The effective flow conductance provided by the physical dimensions of the vent passage of the ASTM E-595 system and that of the material sample among other factors were investigated to explain the reduced amount of outgassing released during the 24-hour test period

Domain similarity based orthology detection.

PubMed

Bitard-Feildel, Tristan; Kemena, Carsten; Greenwood, Jenny M; Bornberg-Bauer, Erich

2015-05-13

Orthologous protein detection software mostly uses pairwise comparisons of amino-acid sequences to assert whether two proteins are orthologous or not. Accordingly, when the number of sequences for comparison increases, the number of comparisons to compute grows in a quadratic order. A current challenge of bioinformatic research, especially when taking into account the increasing number of sequenced organisms available, is to make this ever-growing number of comparisons computationally feasible in a reasonable amount of time. We propose to speed up the detection of orthologous proteins by using strings of domains to characterize the proteins. We present two new protein similarity measures, a cosine and a maximal weight matching score based on domain content similarity, and new software, named porthoDom. The qualities of the cosine and the maximal weight matching similarity measures are compared against curated datasets. The measures show that domain content similarities are able to correctly group proteins into their families. Accordingly, the cosine similarity measure is used inside porthoDom, the wrapper developed for proteinortho. porthoDom makes use of domain content similarity measures to group proteins together before searching for orthologs. By using domains instead of amino acid sequences, the reduction of the search space decreases the computational complexity of an all-against-all sequence comparison. We demonstrate that representing and comparing proteins as strings of discrete domains, i.e. as a concatenation of their unique identifiers, allows a drastic simplification of search space. porthoDom has the advantage of speeding up orthology detection while maintaining a degree of accuracy similar to proteinortho. The implementation of porthoDom is released using python and C++ languages and is available under the GNU GPL licence 3 at http://www.bornberglab.org/pages/porthoda .

Scale effects and a method for similarity evaluation in micro electrical discharge machining

NASA Astrophysics Data System (ADS)

Liu, Qingyu; Zhang, Qinhe; Wang, Kan; Zhu, Guang; Fu, Xiuzhuo; Zhang, Jianhua

2016-08-01

Electrical discharge machining(EDM) is a promising non-traditional micro machining technology that offers a vast array of applications in the manufacturing industry. However, scale effects occur when machining at the micro-scale, which can make it difficult to predict and optimize the machining performances of micro EDM. A new concept of "scale effects" in micro EDM is proposed, the scale effects can reveal the difference in machining performances between micro EDM and conventional macro EDM. Similarity theory is presented to evaluate the scale effects in micro EDM. Single factor experiments are conducted and the experimental results are analyzed by discussing the similarity difference and similarity precision. The results show that the output results of scale effects in micro EDM do not change linearly with discharge parameters. The values of similarity precision of machining time significantly increase when scaling-down the capacitance or open-circuit voltage. It is indicated that the lower the scale of the discharge parameter, the greater the deviation of non-geometrical similarity degree over geometrical similarity degree, which means that the micro EDM system with lower discharge energy experiences more scale effects. The largest similarity difference is 5.34 while the largest similarity precision can be as high as 114.03. It is suggested that the similarity precision is more effective in reflecting the scale effects and their fluctuation than similarity difference. Consequently, similarity theory is suitable for evaluating the scale effects in micro EDM. This proposed research offers engineering values for optimizing the machining parameters and improving the machining performances of micro EDM.

Clustering and visualizing similarity networks of membrane proteins.

PubMed

Hu, Geng-Ming; Mai, Te-Lun; Chen, Chi-Ming

2015-08-01

We proposed a fast and unsupervised clustering method, minimum span clustering (MSC), for analyzing the sequence-structure-function relationship of biological networks, and demonstrated its validity in clustering the sequence/structure similarity networks (SSN) of 682 membrane protein (MP) chains. The MSC clustering of MPs based on their sequence information was found to be consistent with their tertiary structures and functions. For the largest seven clusters predicted by MSC, the consistency in chain function within the same cluster is found to be 100%. From analyzing the edge distribution of SSN for MPs, we found a characteristic threshold distance for the boundary between clusters, over which SSN of MPs could be properly clustered by an unsupervised sparsification of the network distance matrix. The clustering results of MPs from both MSC and the unsupervised sparsification methods are consistent with each other, and have high intracluster similarity and low intercluster similarity in sequence, structure, and function. Our study showed a strong sequence-structure-function relationship of MPs. We discussed evidence of convergent evolution of MPs and suggested applications in finding structural similarities and predicting biological functions of MP chains based on their sequence information. © 2015 Wiley Periodicals, Inc.

Personality Trait Similarity Between Spouses in Four Cultures

PubMed Central

Martin, Thomas A.; H⊆ebí ková, Martina; Urbánek, Tomáš; Boomsma, Dorret I.; Willemsen, Gonneke; Costa, Paul T.

2008-01-01

We examined patterns of trait similarity (assortative mating) in married couples in four cultures, using both self-reports and spouse ratings on versions of the Revised NEO Personality Inventory. There was evidence of a subtle but pervasive perceived contrast bias in the spouse rating data. However, there was strong agreement across methods of assessment and moderate agreement across cultures in the pattern of results. Most assortment effects were small, but correlations exceeding .40 were seen for a subset of traits, chiefly from the Openness and Agreeableness domains. Except in Russia, where more positive assortment was seen for younger couples, comparisons of younger and older cohorts showed little systematic difference. This suggested that mate selection, rather than convergence over time, accounted for similarity. Future research on personality similarity in dyads can utilize different designs, but should assess personality at both domain and the facet levels. PMID:18665894

Discrete Self-Similarity in Interfacial Hydrodynamics and the Formation of Iterated Structures.

PubMed

Dallaston, Michael C; Fontelos, Marco A; Tseluiko, Dmitri; Kalliadasis, Serafim

2018-01-19

The formation of iterated structures, such as satellite and subsatellite drops, filaments, and bubbles, is a common feature in interfacial hydrodynamics. Here we undertake a computational and theoretical study of their origin in the case of thin films of viscous fluids that are destabilized by long-range molecular or other forces. We demonstrate that iterated structures appear as a consequence of discrete self-similarity, where certain patterns repeat themselves, subject to rescaling, periodically in a logarithmic time scale. The result is an infinite sequence of ridges and filaments with similarity properties. The character of these discretely self-similar solutions as the result of a Hopf bifurcation from ordinarily self-similar solutions is also described.

Measuring transferring similarity via local information

NASA Astrophysics Data System (ADS)

Yin, Likang; Deng, Yong

2018-05-01

Recommender systems have developed along with the web science, and how to measure the similarity between users is crucial for processing collaborative filtering recommendation. Many efficient models have been proposed (i.g., the Pearson coefficient) to measure the direct correlation. However, the direct correlation measures are greatly affected by the sparsity of dataset. In other words, the direct correlation measures would present an inauthentic similarity if two users have a very few commonly selected objects. Transferring similarity overcomes this drawback by considering their common neighbors (i.e., the intermediates). Yet, the transferring similarity also has its drawback since it can only provide the interval of similarity. To break the limitations, we propose the Belief Transferring Similarity (BTS) model. The contributions of BTS model are: (1) BTS model addresses the issue of the sparsity of dataset by considering the high-order similarity. (2) BTS model transforms uncertain interval to a certain state based on fuzzy systems theory. (3) BTS model is able to combine the transferring similarity of different intermediates using information fusion method. Finally, we compare BTS models with nine different link prediction methods in nine different networks, and we also illustrate the convergence property and efficiency of the BTS model.

[Pain registries and similar data collections : A systematic review].

PubMed

Freytag, A; Scriba, B; Kaiser, U; Meißner, W

2016-12-01

Registries and similar data collections are a valuable addition to prospective studies as they provide data from real life treatment. In pain medicine only few such data collections exist so far. Aim of the study was to identify German-language registries or similar data collections that record patient-reported and pain-associated outcomes together with other data. A systematic search was carried out, which included the following sources: the data bases PubMed/MEDLINE and Embase, the German Registry for Clinical Trials (DRKS), ClinicalTrials.gov and registry portals known to us. Furthermore, an extended internet search was carried out via Google Scholar. References from personal scientific contacts and from operators of registries were also included. Questionnaires regarding registry items were sent to registry operators. Out of 381 search hits, 37 potentially relevant projects received a questionnaire and 35 answered. From the 35 responders 23 registries or similar data collections fulfilling inclusion criteria could be identified: 5 primarily pain-associated, 3 therapy-associated, 2 population-associated and 13 disease-associated (rheumatism/arthritis 5, joints/spine 4, hernias 1 and cancer 3). The reader obtains contact information on relevant data collections associated with pain, the contents, objectives and the pain assessment instruments applied. This review could give an important impulse for increased networking in health services research on pain. A limitation of the study was that identification of registries was made difficult due to an inconsistent definition and application of the term "registry", incomplete or insufficiently updated registry portals, missing scientific publications as well as two non-responders.

Vere-Jones' self-similar branching model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saichev, A.; Institute of Geophysics and Planetary Physics, University of California, Los Angeles, California 90095; Sornette, D.

2005-11-01

Motivated by its potential application to earthquake statistics as well as for its intrinsic interest in the theory of branching processes, we study the exactly self-similar branching process introduced recently by Vere-Jones. This model extends the ETAS class of conditional self-excited branching point-processes of triggered seismicity by removing the problematic need for a minimum (as well as maximum) earthquake size. To make the theory convergent without the need for the usual ultraviolet and infrared cutoffs, the distribution of magnitudes m{sup '} of daughters of first-generation of a mother of magnitude m has two branches m{sup '}m with exponent {beta}+d, where {beta} and d are two positive parameters. We investigate the condition and nature of the subcritical, critical, and supercritical regime in this and in an extended version interpolating smoothly between several models. We predict that the distribution of magnitudes of events triggered by a mother of magnitude m over all generations has also two branches m{sup '}m with exponent {beta}+h, with h=d{radical}(1-s), where s is the fraction of triggered events. This corresponds to a renormalization of the exponent d into h by the hierarchy of successive generations of triggered events. For a significant part of the parameter space, the distribution of magnitudes over a full catalog summed over an average steady flow of spontaneous sources (immigrants) reproduces the distribution of the spontaneous sources with a single branch and is blind to the exponents {beta},d of the distribution of triggered events. Since the distribution of earthquake magnitudes is usually obtained with catalogs including many sequences, we conclude that the two branches of the distribution of aftershocks are not directly observable and the model is compatible with real seismic catalogs. In summary, the exactly self-similar Vere-Jones model provides an

A study of concept-based similarity approaches for recommending program examples

NASA Astrophysics Data System (ADS)

Hosseini, Roya; Brusilovsky, Peter

2017-07-01

This paper investigates a range of concept-based example recommendation approaches that we developed to provide example-based problem-solving support in the domain of programming. The goal of these approaches is to offer students a set of most relevant remedial examples when they have trouble solving a code comprehension problem where students examine a program code to determine its output or the final value of a variable. In this paper, we use the ideas of semantic-level similarity-based linking developed in the area of intelligent hypertext to generate examples for the given problem. To determine the best-performing approach, we explored two groups of similarity approaches for selecting examples: non-structural approaches focusing on examples that are similar to the problem in terms of concept coverage and structural approaches focusing on examples that are similar to the problem by the structure of the content. We also explored the value of personalized example recommendation based on student's knowledge levels and learning goal of the exercise. The paper presents concept-based similarity approaches that we developed, explains the data collection studies and reports the result of comparative analysis. The results of our analysis showed better ranking performance of the personalized structural variant of cosine similarity approach.

Semantic Similarity between Web Documents Using Ontology

NASA Astrophysics Data System (ADS)

Chahal, Poonam; Singh Tomer, Manjeet; Kumar, Suresh

2018-06-01

The World Wide Web is the source of information available in the structure of interlinked web pages. However, the procedure of extracting significant information with the assistance of search engine is incredibly critical. This is for the reason that web information is written mainly by using natural language, and further available to individual human. Several efforts have been made in semantic similarity computation between documents using words, concepts and concepts relationship but still the outcome available are not as per the user requirements. This paper proposes a novel technique for computation of semantic similarity between documents that not only takes concepts available in documents but also relationships that are available between the concepts. In our approach documents are being processed by making ontology of the documents using base ontology and a dictionary containing concepts records. Each such record is made up of the probable words which represents a given concept. Finally, document ontology's are compared to find their semantic similarity by taking the relationships among concepts. Relevant concepts and relations between the concepts have been explored by capturing author and user intention. The proposed semantic analysis technique provides improved results as compared to the existing techniques.

Semantic Similarity between Web Documents Using Ontology

NASA Astrophysics Data System (ADS)

Chahal, Poonam; Singh Tomer, Manjeet; Kumar, Suresh

2018-03-01

The World Wide Web is the source of information available in the structure of interlinked web pages. However, the procedure of extracting significant information with the assistance of search engine is incredibly critical. This is for the reason that web information is written mainly by using natural language, and further available to individual human. Several efforts have been made in semantic similarity computation between documents using words, concepts and concepts relationship but still the outcome available are not as per the user requirements. This paper proposes a novel technique for computation of semantic similarity between documents that not only takes concepts available in documents but also relationships that are available between the concepts. In our approach documents are being processed by making ontology of the documents using base ontology and a dictionary containing concepts records. Each such record is made up of the probable words which represents a given concept. Finally, document ontology's are compared to find their semantic similarity by taking the relationships among concepts. Relevant concepts and relations between the concepts have been explored by capturing author and user intention. The proposed semantic analysis technique provides improved results as compared to the existing techniques.

A hybrid algorithm for selecting head-related transfer function based on similarity of anthropometric structures

NASA Astrophysics Data System (ADS)

Zeng, Xiang-Yang; Wang, Shu-Guang; Gao, Li-Ping

2010-09-01

As the basic data for virtual auditory technology, head-related transfer function (HRTF) has many applications in the areas of room acoustic modeling, spatial hearing and multimedia. How to individualize HRTF fast and effectively has become an opening problem at present. Based on the similarity and relativity of anthropometric structures, a hybrid HRTF customization algorithm, which has combined the method of principal component analysis (PCA), multiple linear regression (MLR) and database matching (DM), has been presented in this paper. The HRTFs selected by both the best match and the worst match have been applied into obtaining binaurally auralized sounds, which are then used for subjective listening experiments and the results are compared. For the area in the horizontal plane, the localization results have shown that the selection of HRTFs can enhance the localization accuracy and can also abate the problem of front-back confusion.

Research of obtaining TiO2 by sol-gel method using titanium isopropoxide TIP and tetra-n-butyl orthotitanate TNB

NASA Astrophysics Data System (ADS)

Gómez de Salazar, J. M.; Nutescu Duduman, C.; Juárez Gonzalez, M.; Palamarciuc, I.; Barrena Pérez, M. I.; Carcea, I.

2016-08-01

Titanium dioxide crystallises in three polymorphs: anatase, rutile and brookite. Rutile is most stable form of the TiO2 polymorphs. In this paper we concentrate on obtaining rutile and anatase, both used in various applications. The chosen method is sol-gel, which is a reliable method used for obtaining titanium oxides. We prepared titanium dioxide with using titanium isopropoxide (TIP) with chemical construction (C12H28O4Ti) and tetra-n-butyl orthotitanate (TNB) with chemical construction (C16H36O4Ti). The experiments were carried out in order to compare the results of the samples with similar reaction conditions, but with different precursors, thus concluding which precursor gives best results. Using different analysis techniques as X-ray Diffraction (XRD), Fourier Transform Infrared Spectroscopy (FTIR), Scanning Electron Microscopy (SEM), Transmission Electron Microscopy (TEM) and Thermogravimetric Analysis (TGA) we characterised the samples morphologically and structurally.

Similarity network fusion for aggregating data types on a genomic scale.

PubMed

Wang, Bo; Mezlini, Aziz M; Demir, Feyyaz; Fiume, Marc; Tu, Zhuowen; Brudno, Michael; Haibe-Kains, Benjamin; Goldenberg, Anna

2014-03-01

Recent technologies have made it cost-effective to collect diverse types of genome-wide data. Computational methods are needed to combine these data to create a comprehensive view of a given disease or a biological process. Similarity network fusion (SNF) solves this problem by constructing networks of samples (e.g., patients) for each available data type and then efficiently fusing these into one network that represents the full spectrum of underlying data. For example, to create a comprehensive view of a disease given a cohort of patients, SNF computes and fuses patient similarity networks obtained from each of their data types separately, taking advantage of the complementarity in the data. We used SNF to combine mRNA expression, DNA methylation and microRNA (miRNA) expression data for five cancer data sets. SNF substantially outperforms single data type analysis and established integrative approaches when identifying cancer subtypes and is effective for predicting survival.

Thematic Relations Affect Similarity via Commonalities

ERIC Educational Resources Information Center

Golonka, Sabrina; Estes, Zachary

2009-01-01

Thematic relations are an important source of perceived similarity. For instance, the "rowing" theme of boats and oars increases their perceived similarity. The mechanism of this effect, however, has not been specified previously. The authors investigated whether thematic relations affect similarity by increasing commonalities or by…

BEAUTY: an enhanced BLAST-based search tool that integrates multiple biological information resources into sequence similarity search results.

PubMed

Worley, K C; Wiese, B A; Smith, R F

1995-09-01

BEAUTY (BLAST enhanced alignment utility) is an enhanced version of the NCBI's BLAST data base search tool that facilitates identification of the functions of matched sequences. We have created new data bases of conserved regions and functional domains for protein sequences in NCBI's Entrez data base, and BEAUTY allows this information to be incorporated directly into BLAST search results. A Conserved Regions Data Base, containing the locations of conserved regions within Entrez protein sequences, was constructed by (1) clustering the entire data base into families, (2) aligning each family using our PIMA multiple sequence alignment program, and (3) scanning the multiple alignments to locate the conserved regions within each aligned sequence. A separate Annotated Domains Data Base was constructed by extracting the locations of all annotated domains and sites from sequences represented in the Entrez, PROSITE, BLOCKS, and PRINTS data bases. BEAUTY performs a BLAST search of those Entrez sequences with conserved regions and/or annotated domains. BEAUTY then uses the information from the Conserved Regions and Annotated Domains data bases to generate, for each matched sequence, a schematic display that allows one to directly compare the relative locations of (1) the conserved regions, (2) annotated domains and sites, and (3) the locally aligned regions matched in the BLAST search. In addition, BEAUTY search results include World-Wide Web hypertext links to a number of external data bases that provide a variety of additional types of information on the function of matched sequences. This convenient integration of protein families, conserved regions, annotated domains, alignment displays, and World-Wide Web resources greatly enhances the biological informativeness of sequence similarity searches. BEAUTY searches can be performed remotely on our system using the "BCM Search Launcher" World-Wide Web pages (URL is < http:/ /gc.bcm.tmc.edu:8088/ search-launcher/launcher.html > ).

Similar Genetic Mechanisms Underlie the Parallel Evolution of Floral Phenotypes

PubMed Central

Zhang, Wenheng; Kramer, Elena M.; Davis, Charles C.

2012-01-01

The repeated origin of similar phenotypes is invaluable for studying the underlying genetics of adaptive traits; molecular evidence, however, is lacking for most examples of such similarity. The floral morphology of neotropical Malpighiaceae is distinctive and highly conserved, especially with regard to symmetry, and is thought to result from specialization on oil-bee pollinators. We recently demonstrated that CYCLOIDEA2–like genes (CYC2A and CYC2B) are associated with the development of the stereotypical floral zygomorphy that is critical to this plant–pollinator mutualism. Here, we build on this developmental framework to characterize floral symmetry in three clades of Malpighiaceae that have independently lost their oil bee association and experienced parallel shifts in their floral morphology, especially in regard to symmetry. We show that in each case these species exhibit a loss of CYC2B function, and a strikingly similar shift in the expression of CYC2A that is coincident with their shift in floral symmetry. These results indicate that similar floral phenotypes in this large angiosperm clade have evolved via parallel genetic changes from an otherwise highly conserved developmental program. PMID:22558314

Information filtering based on transferring similarity.

PubMed

Sun, Duo; Zhou, Tao; Liu, Jian-Guo; Liu, Run-Ran; Jia, Chun-Xiao; Wang, Bing-Hong

2009-07-01

In this Brief Report, we propose an index of user similarity, namely, the transferring similarity, which involves all high-order similarities between users. Accordingly, we design a modified collaborative filtering algorithm, which provides remarkably higher accurate predictions than the standard collaborative filtering. More interestingly, we find that the algorithmic performance will approach its optimal value when the parameter, contained in the definition of transferring similarity, gets close to its critical value, before which the series expansion of transferring similarity is convergent and after which it is divergent. Our study is complementary to the one reported in [E. A. Leicht, P. Holme, and M. E. J. Newman, Phys. Rev. E 73, 026120 (2006)], and is relevant to the missing link prediction problem.

A WordNet-Based Near-Synonyms and Similar-Looking Word Learning System

ERIC Educational Resources Information Center

Sun, Koun-Tem; Huang, Yueh-Min; Liu, Ming-Chi

2011-01-01

Near-Synonyms and Similar-Looking (NSSL) words can create confusion for English as Foreign Language Learners as a result of a type of lexical error that often occurs when they confuse similar-looking words that are near synonyms to have the same meaning. Particularly, this may occur if the similar-looking words have the same translated meaning.…

Semantic shape similarity-based contour tracking evaluation

NASA Astrophysics Data System (ADS)

Zhang, Xiaoqin; Luo, Wenhan; Zhao, Li; Li, Wei; Hu, Weiming

2011-10-01

One major problem of contour-based tracking is how to evaluate the accuracy of tracking results due to nonrigid and deformative properties of contours. We propose a shape context-based evaluation measure that considers the semantic shape similarity between the tracked contour and ground-truth contour. In addition, a pyramid match kernel is introduced for shape histogram matching, which can effectively deal with the contours with different scales. Experimental results demonstrate, compared to two start-of-art evaluation measures, our measure effectively captures the local shape information and thus is more consistent with human vision.

Perceiving similarity and comprehending metaphor.

PubMed

Marks, L E; Hammeal, R J; Bornstein, M H

1987-01-01

We conducted a series of 3 experiments to assess the comprehension of 4 types of cross-modal (synesthetic) similarities in nearly 500 3.5-13.5-year-old children and more than 100 adults. We tested both perceptual and verbal (metaphoric) modes. Children of all ages and adults matched pitch to brightness and loudness to brightness, thereby showing that even very young children recognize perceptual similarities between hearing and vision. Children did not consistently recognize similarity between pitch and size until about age 11. This difference in developmental timetables is compatible with the view that pitch-brightness and loudness-brightness similarities are intrinsic characteristics of perception (characteristics based, perhaps, on common sensory codes), whereas pitch-size similarity may be learned (perhaps through association of size with resonance properties). In a parallel verbal task, even 4-year-old children showed at least some capacity to translate meanings metaphorically from one modality to another (e.g., rating "low pitched" as dim and "high pitched" as bright). But not all literal meanings produced metaphoric equivalents in the youngest children (e.g., rating "sunlight" brighter but not louder than "moonlight"). Improvements with age in making metaphoric translations of synesthetic expressions paralleled increasing differentiation of meanings along literal dimensions and increasing capacity to integrate meanings of components in compound expressions. We postulate that perceptual knowledge about objects and events is represented in terms of locations in a multidimensional space; cross-modal similarities imply that the space is also multimodal. Verbal processes later gain access to this graded perceptual knowledge, thus permitting the interpretation of synesthetic metaphors according to the rules of cross-modal perception.

Similarity between the superconductivity in the graphene with the spin transport in the two-dimensional antiferromagnet in the honeycomb lattice

NASA Astrophysics Data System (ADS)

Lima, L. S.

2017-02-01

We have used the Dirac's massless quasi-particles together with the Kubo's formula to study the spin transport by electrons in the graphene monolayer. We have calculated the electric conductivity and verified the behavior of the AC and DC currents of this system, that is a relativistic electron plasma. Our results show that the AC conductivity tends to infinity in the limit ω → 0 , similar to the behavior obtained for the spin transport in the two-dimensional frustrated antiferromagnet in the honeycomb lattice. We have made a diagrammatic expansion for the Green's function and we have not gotten significative change in the results.

Cosmogenic radionuclides on LDEF: An unexpected Be-10 result

NASA Technical Reports Server (NTRS)

Gregory, J. C.; Albrecht, A.; Herzog, G.; Klein, J.; Middleton, R.; Dezfouly-Arjomandy, B.; Harmon, B. A.

1993-01-01

Following the discovery of the atmospheric derived cosmogenic radionuclide Be-7 on the Long Duration Exposure Facility (LDEF), a search began for other known nuclides produced by similar mechanisms. None of the others have the narrow gamma-ray line emission of Be-7 decay which enabled its rapid detection and quantification. A search for Be-10 atoms on LDEF clamp plates using accelerator mass spectrometry is described. An unexpected result was obtained.

Determining the semantic similarities among Gene Ontology terms.

PubMed

Taha, Kamal

2013-05-01

We present in this paper novel techniques that determine the semantic relationships among GeneOntology (GO) terms. We implemented these techniques in a prototype system called GoSE, which resides between user application and GO database. Given a set S of GO terms, GoSE would return another set S' of GO terms, where each term in S' is semantically related to each term in S. Most current research is focused on determining the semantic similarities among GO ontology terms based solely on their IDs and proximity to one another in the GO graph structure, while overlooking the contexts of the terms, which may lead to erroneous results. The context of a GO term T is the set of other terms, whose existence in the GO graph structure is dependent on T. We propose novel techniques that determine the contexts of terms based on the concept of existence dependency. We present a stack-based sort-merge algorithm employing these techniques for determining the semantic similarities among GO terms.We evaluated GoSE experimentally and compared it with three existing methods. The results of measuring the semantic similarities among genes in KEGG and Pfam pathways retrieved from the DBGET and Sanger Pfam databases, respectively, have shown that our method outperforms the other three methods in recall and precision.

Discuss Similarity Using Visual Intuition

ERIC Educational Resources Information Center

Cox, Dana C.; Lo, Jane-Jane

2012-01-01

The change in size from a smaller shape to a larger similar shape (or vice versa) is created through continuous proportional stretching or shrinking in every direction. Students cannot solve similarity tasks simply by iterating or partitioning a composed unit, strategies typically used on numerical proportional tasks. The transition to thinking…

Structural covariance of brain region volumes is associated with both structural connectivity and transcriptomic similarity.

PubMed

Yee, Yohan; Fernandes, Darren J; French, Leon; Ellegood, Jacob; Cahill, Lindsay S; Vousden, Dulcie A; Spencer Noakes, Leigh; Scholz, Jan; van Eede, Matthijs C; Nieman, Brian J; Sled, John G; Lerch, Jason P

2018-05-18

An organizational pattern seen in the brain, termed structural covariance, is the statistical association of pairs of brain regions in their anatomical properties. These associations, measured across a population as covariances or correlations usually in cortical thickness or volume, are thought to reflect genetic and environmental underpinnings. Here, we examine the biological basis of structural volume covariance in the mouse brain. We first examined large scale associations between brain region volumes using an atlas-based approach that parcellated the entire mouse brain into 318 regions over which correlations in volume were assessed, for volumes obtained from 153 mouse brain images via high-resolution MRI. We then used a seed-based approach and determined, for 108 different seed regions across the brain and using mouse gene expression and connectivity data from the Allen Institute for Brain Science, the variation in structural covariance data that could be explained by distance to seed, transcriptomic similarity to seed, and connectivity to seed. We found that overall, correlations in structure volumes hierarchically clustered into distinct anatomical systems, similar to findings from other studies and similar to other types of networks in the brain, including structural connectivity and transcriptomic similarity networks. Across seeds, this structural covariance was significantly explained by distance (17% of the variation, up to a maximum of 49% for structural covariance to the visceral area of the cortex), transcriptomic similarity (13% of the variation, up to maximum of 28% for structural covariance to the primary visual area) and connectivity (15% of the variation, up to a maximum of 36% for structural covariance to the intermediate reticular nucleus in the medulla) of covarying structures. Together, distance, connectivity, and transcriptomic similarity explained 37% of structural covariance, up to a maximum of 63% for structural covariance to the

Limiting similarity and Darwin's naturalization hypothesis: understanding the drivers of biotic resistance against invasive plant species.

PubMed

Yannelli, F A; Koch, C; Jeschke, J M; Kollmann, J

2017-03-01

Several hypotheses have been proposed to explain biotic resistance of a recipient plant community based on reduced niche opportunities for invasive alien plant species. The limiting similarity hypothesis predicts that invasive species are less likely to establish in communities of species holding similar functional traits. Likewise, Darwin's naturalization hypothesis states that invasive species closely related to the native community would be less successful. We tested both using the invasive alien Ambrosia artemisiifolia L. and Solidago gigantea Aiton, and grassland species used for ecological restoration in central Europe. We classified all plant species into groups based on functional traits obtained from trait databases and calculated the phylogenetic distance among them. In a greenhouse experiment, we submitted the two invasive species at two propagule pressures to competition with communities of ten native species from the same functional group. In another experiment, they were submitted to pairwise competition with native species selected from each functional group. At the community level, highest suppression for both invasive species was observed at low propagule pressure and not explained by similarity in functional traits. Moreover, suppression decreased asymptotically with increasing phylogenetic distance to species of the native community. When submitted to pairwise competition, suppression for both invasive species was also better explained by phylogenetic distance. Overall, our results support Darwin's naturalization hypothesis but not the limiting similarity hypothesis based on the selected traits. Biotic resistance of native communities against invasive species at an early stage of establishment is enhanced by competitive traits and phylogenetic relatedness.

Rheumatic Heart Disease and Myxomatous Degeneration: Differences and Similarities of Valve Damage Resulting from Autoimmune Reactions and Matrix Disorganization.

PubMed

Martins, Carlo de Oliveira; Demarchi, Lea; Ferreira, Frederico Moraes; Pomerantzeff, Pablo Maria Alberto; Brandao, Carlos; Sampaio, Roney Orismar; Spina, Guilherme Sobreira; Kalil, Jorge; Cunha-Neto, Edecio; Guilherme, Luiza

2017-01-01

Autoimmune inflammatory reactions leading to rheumatic fever (RF) and rheumatic heart disease (RHD) result from untreated Streptococcus pyogenes throat infections in individuals who exhibit genetic susceptibility. Immune effector mechanisms have been described that lead to heart tissue damage culminating in mitral and aortic valve dysfunctions. In myxomatous valve degeneration (MXD), the mitral valve is also damaged due to non-inflammatory mechanisms. Both diseases are characterized by structural valve disarray and a previous proteomic analysis of them has disclosed a distinct profile of matrix/structural proteins differentially expressed. Given their relevance in organizing valve tissue, we quantitatively evaluated the expression of vimentin, collagen VI, lumican, and vitronectin as well as performed immunohistochemical analysis of their distribution in valve tissue lesions of patients in both diseases. We identified abundant expression of two isoforms of vimentin (45 kDa, 42 kDa) with reduced expression of the full-size protein (54 kDa) in RHD valves. We also found increased vitronectin expression, reduced collagen VI expression and similar lumican expression between RHD and MXD valves. Immunohistochemical analysis indicated disrupted patterns of these proteins in myxomatous degeneration valves and disorganized distribution in rheumatic heart disease valves that correlated with clinical manifestations such as valve regurgitation or stenosis. Confocal microscopy analysis revealed a diverse pattern of distribution of collagen VI and lumican into RHD and MXD valves. Altogether, these results demonstrated distinct patterns of altered valve expression and tissue distribution/organization of structural/matrix proteins that play important pathophysiological roles in both valve diseases.

Document similarity measures and document browsing

NASA Astrophysics Data System (ADS)

Ahmadullin, Ildus; Fan, Jian; Damera-Venkata, Niranjan; Lim, Suk Hwan; Lin, Qian; Liu, Jerry; Liu, Sam; O'Brien-Strain, Eamonn; Allebach, Jan

2011-03-01

Managing large document databases is an important task today. Being able to automatically com- pare document layouts and classify and search documents with respect to their visual appearance proves to be desirable in many applications. We measure single page documents' similarity with respect to distance functions between three document components: background, text, and saliency. Each document component is represented as a Gaussian mixture distribution; and distances between dierent documents' components are calculated as probabilistic similarities between corresponding distributions. The similarity measure between documents is represented as a weighted sum of the components' distances. Using this document similarity measure, we propose a browsing mechanism operating on a document dataset. For these purposes, we use a hierarchical browsing environment which we call the document similarity pyramid. It allows the user to browse a large document dataset and to search for documents in the dataset that are similar to the query. The user can browse the dataset on dierent levels of the pyramid, and zoom into the documents that are of interest.

Weighted similarity-based clustering of chemical structures and bioactivity data in early drug discovery.

PubMed

Perualila-Tan, Nolen Joy; Shkedy, Ziv; Talloen, Willem; Göhlmann, Hinrich W H; Moerbeke, Marijke Van; Kasim, Adetayo

2016-08-01

The modern process of discovering candidate molecules in early drug discovery phase includes a wide range of approaches to extract vital information from the intersection of biology and chemistry. A typical strategy in compound selection involves compound clustering based on chemical similarity to obtain representative chemically diverse compounds (not incorporating potency information). In this paper, we propose an integrative clustering approach that makes use of both biological (compound efficacy) and chemical (structural features) data sources for the purpose of discovering a subset of compounds with aligned structural and biological properties. The datasets are integrated at the similarity level by assigning complementary weights to produce a weighted similarity matrix, serving as a generic input in any clustering algorithm. This new analysis work flow is semi-supervised method since, after the determination of clusters, a secondary analysis is performed wherein it finds differentially expressed genes associated to the derived integrated cluster(s) to further explain the compound-induced biological effects inside the cell. In this paper, datasets from two drug development oncology projects are used to illustrate the usefulness of the weighted similarity-based clustering approach to integrate multi-source high-dimensional information to aid drug discovery. Compounds that are structurally and biologically similar to the reference compounds are discovered using this proposed integrative approach.

SDL: Saliency-Based Dictionary Learning Framework for Image Similarity.

PubMed

Sarkar, Rituparna; Acton, Scott T

2018-02-01

In image classification, obtaining adequate data to learn a robust classifier has often proven to be difficult in several scenarios. Classification of histological tissue images for health care analysis is a notable application in this context due to the necessity of surgery, biopsy or autopsy. To adequately exploit limited training data in classification, we propose a saliency guided dictionary learning method and subsequently an image similarity technique for histo-pathological image classification. Salient object detection from images aids in the identification of discriminative image features. We leverage the saliency values for the local image regions to learn a dictionary and respective sparse codes for an image, such that the more salient features are reconstructed with smaller error. The dictionary learned from an image gives a compact representation of the image itself and is capable of representing images with similar content, with comparable sparse codes. We employ this idea to design a similarity measure between a pair of images, where local image features of one image, are encoded with the dictionary learned from the other and vice versa. To effectively utilize the learned dictionary, we take into account the contribution of each dictionary atom in the sparse codes to generate a global image representation for image comparison. The efficacy of the proposed method was evaluated using three tissue data sets that consist of mammalian kidney, lung and spleen tissue, breast cancer, and colon cancer tissue images. From the experiments, we observe that our methods outperform the state of the art with an increase of 14.2% in the average classification accuracy over all data sets.

Narcissists of a Feather Flock Together: Narcissism and the Similarity of Friends.

PubMed

Maaß, Ulrike; Lämmle, Lena; Bensch, Doreen; Ziegler, Matthias

2016-03-01

Who is willing to expose himself or herself to narcissists on a long-term basis? Studies that address the interactions of narcissists focus mainly on their interactions with strangers. Hence, the aim of the present study was to investigate the extent to which two best friends' similarity in narcissism would influence their similarities in other personality profiles. A total of 290 best friends' dyads filled out measurements of the whole Dark Triad as well as the Big Five. For each personality domain, profile similarity and its dependence on the similarity in the Dark Triad were determined. Results showed that the friends' similarity in narcissism significantly predicted similarity in all Big Five domains. For the general Big Five similarity as well as extraversion, the effect of narcissism similarity was stronger for male than female or mixed friends. Similarity in psychopathy and Machiavellianism significantly predicted all domains except for openness and extraversion, respectively. © 2016 by the Society for Personality and Social Psychology, Inc.

Evaluation of two transport aircraft and several ground test vehicle friction measurements obtained for various runway surface types and conditions. A summary of test results from joint FAA/NASA Runway Friction Program

NASA Technical Reports Server (NTRS)

Yager, Thomas J.; Vogler, William A.; Baldasare, Paul

1990-01-01

Tests with specially instrumented NASA Boeing 737 and 727 aircraft together with several different ground friction measuring devices were conducted for a variety of runway surface types and conditions. These tests are part of joint FAA/NASA Aircraft/Ground Vehicle Runway Friction Program aimed at obtaining a better understanding of aircraft ground handling performance under adverse weather conditions and defining relationships between aircraft and ground vehicle tire friction measurements. Aircraft braking performance on dry, wet, snow and ice-covered runway conditions is discussed as well as ground vehicle friction data obtained under similar runway conditions. For a given contaminated runway surface condition, the correlation between ground vehicles and aircraft friction data is identified. The influence of major test parameters on friction measurements such as speed, test tire characteristics, type and amount of surface contaminant, and ambient temperature are discussed. The effect of surface type on wet friction levels is also evaluated from comparative data collected on grooved and ungrooved concrete and asphalt surfaces.

Similar or Different? The Role of the Ventrolateral Prefrontal Cortex in Similarity Detection

PubMed Central

Garcin, Béatrice; Volle, Emmanuelle; Dubois, Bruno; Levy, Richard

2012-01-01

Patients with frontal lobe syndrome can exhibit two types of abnormal behaviour when asked to place a banana and an orange in a single category: some patients categorize them at a concrete level (e.g., “both have peel”), while others continue to look for differences between these objects (e.g., “one is yellow, the other is orange”). These observations raise the question of whether abstraction and similarity detection are distinct processes involved in abstract categorization, and that depend on separate areas of the prefrontal cortex (PFC). We designed an original experimental paradigm for a functional magnetic resonance imaging (fMRI) study involving healthy subjects, confirming the existence of two distinct processes relying on different prefrontal areas, and thus explaining the behavioural dissociation in frontal lesion patients. We showed that: 1) Similarity detection involves the anterior ventrolateral PFC bilaterally with a right-left asymmetry: the right anterior ventrolateral PFC is only engaged in detecting physical similarities; 2) Abstraction per se activates the left dorsolateral PFC. PMID:22479551

Chirped self-similar optical pulses in tapered centrosymmetric nonlinear waveguides doped with resonant impurities

NASA Astrophysics Data System (ADS)

He, J. R.; Xu, S. L.; Xue, L.

2017-11-01

Exact chirped self-similar optical pulses propagating in tapered centrosymmetric nonlinear waveguides doped with resonant impurities are reported. The propagation behaviors of the pulses are studied by tailoring of the tapering function. Numerical simulations and stability analysis reveal that the tapering can be used to postpone the wave dispersion and the addition of a small cubic self-focusing term to the governing equation could stabilize the chirped bright pulses. An example of possible experimental protocol that may generate the pulses in realistic waveguides is given. The obtained chirped self-similar optical pulses are particularly useful in the design of amplifying or attenuating pulse compressors for chirped solitary waves in tapered centrosymmetric nonlinear waveguides doped with resonant impurities.

Biorthogonal projected energies of a Gutzwiller similarity transformed Hamiltonian.

PubMed

Wahlen-Strothman, J M; Scuseria, G E

2016-12-07

We present a method incorporating biorthogonal orbital-optimization, symmetry projection, and double-occupancy screening with a non-unitary similarity transformation generated by the Gutzwiller factor [Formula: see text], and apply it to the Hubbard model. Energies are calculated with mean-field computational scaling with high-quality results comparable to coupled cluster singles and doubles. This builds on previous work performing similarity transformations with more general, two-body Jastrow-style correlators. The theory is tested on 2D lattices ranging from small systems into the thermodynamic limit and is compared to available reference data.

Similarity Judgments: From Classical to Complex Vector Psychological Spaces

NASA Astrophysics Data System (ADS)

Barque Duran, Albert; Pothos, Emmanuel M.; Yearsley, James M.; Hampton, James A.; Busemeyer, Jerome R.; Trueblood, Jennifer S.

This chapter reviews progress with applications of quantum theory in understanding human similarity judgments. We first motivate and subsequently describe the quantum similarity model (QSM), which was proposed by Pothos, Busemeyer and Trueblood (2013), primarily as a way to cover the empirical findings reported in Tversky (1977). We then show how the QSM encompasses Tversky's (1977) results, specifically in relation to violations of symmetry, violations of the triangle inequality and the diagnosticity effect. We next consider a list of challenges of the QSM and open issues for further research.

SU-E-T-212: Comparison of TG-43 Dosimetric Parameters of Low and High Energy Brachytherapy Sources Obtained by MCNP Code Versions of 4C, X and 5

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zehtabian, M; Zaker, N; Sina, S

2015-06-15

Purpose: Different versions of MCNP code are widely used for dosimetry purposes. The purpose of this study is to compare different versions of the MCNP codes in dosimetric evaluation of different brachytherapy sources. Methods: The TG-43 parameters such as dose rate constant, radial dose function, and anisotropy function of different brachytherapy sources, i.e. Pd-103, I-125, Ir-192, and Cs-137 were calculated in water phantom. The results obtained by three versions of Monte Carlo codes (MCNP4C, MCNPX, MCNP5) were compared for low and high energy brachytherapy sources. Then the cross section library of MCNP4C code was changed to ENDF/B-VI release 8 whichmore » is used in MCNP5 and MCNPX codes. Finally, the TG-43 parameters obtained using the MCNP4C-revised code, were compared with other codes. Results: The results of these investigations indicate that for high energy sources, the differences in TG-43 parameters between the codes are less than 1% for Ir-192 and less than 0.5% for Cs-137. However for low energy sources like I-125 and Pd-103, large discrepancies are observed in the g(r) values obtained by MCNP4C and the two other codes. The differences between g(r) values calculated using MCNP4C and MCNP5 at the distance of 6cm were found to be about 17% and 28% for I-125 and Pd-103 respectively. The results obtained with MCNP4C-revised and MCNPX were similar. However, the maximum difference between the results obtained with the MCNP5 and MCNP4C-revised codes was 2% at 6cm. Conclusion: The results indicate that using MCNP4C code for dosimetry of low energy brachytherapy sources can cause large errors in the results. Therefore it is recommended not to use this code for low energy sources, unless its cross section library is changed. Since the results obtained with MCNP4C-revised and MCNPX were similar, it is concluded that the difference between MCNP4C and MCNPX is their cross section libraries.« less

Natural cellulose fibers from switchgrass with tensile properties similar to cotton and linen.

PubMed

Reddy, Narendra; Yang, Yiqi

2007-08-01

We report the production and characteristics of natural cellulose fibers obtained from the leaves and stems of switchgrass. In this paper, the composition, structure and properties of fibers obtained from the leaves and stem of switchgrass have been studied in comparison to the common natural cellulose fibers, such as cotton, linen and kenaf. The leaves and stems of switchgrass have tensile properties intriguingly similar to that of linen and cotton, respectively. Fibers were obtained from the leaves and stems of switchgrass using a simple alkaline extraction and the structure and properties of the fibers were studied. Fibers obtained from switchgrass leaves have crystallinity of 51%, breaking tenacity of 5.5 g per denier (715 MPa) and breaking elongation of 2.2% whereas the corresponding values for fibers obtained from switchgrass stems are 46%, 2.7 g per denier and 6.8%, respectively. Switchgrass is a relatively easy to grow and high yield biomass crop that can be source to partially substitute the natural and synthetic fibers currently in use. We hope that this research will stimulate interests in using switchgrass as a novel fiber crop in addition to being promoted as a potential source for biofuels. (c) 2007 Wiley Periodicals, Inc.

Low serum vitamin K in PXE results in defective carboxylation of mineralization inhibitors similar to the GGCX mutations in the PXE-like syndrome.

PubMed

Vanakker, Olivier M; Martin, Ludovic; Schurgers, Leon J; Quaglino, Daniela; Costrop, Laura; Vermeer, Cees; Pasquali-Ronchetti, Ivonne; Coucke, Paul J; De Paepe, Anne

2010-06-01

Soft-tissue mineralization is a tightly regulated process relying on the activity of systemic and tissue-specific inhibitors and promoters of calcium precipitation. Many of these, such as matrix gla protein (MGP) and osteocalcin (OC), need to undergo carboxylation to become active. This post-translational modification is catalyzed by the gammaglutamyl carboxylase GGCX and requires vitamin K (VK) as an essential co-factor. Recently, we described a novel phenotype characterized by aberrant mineralization of the elastic fibers resulting from mutations in GGCX. Because of the resemblance with pseudoxanthoma elasticum (PXE), a prototype disorder of elastic fiber mineralization, it was coined the PXE-like syndrome. As mutations in GGCX negatively affect protein carboxylation, it is likely that inactive inhibitors of calcification contribute to ectopic mineralization in PXE-like syndrome. Because of the remarkable similarities with PXE, we performed a comparative study of various forms of VK-dependent proteins in serum, plasma (using ELISA), and dermal tissues (using immunohistochemistry) of PXE-like and PXE patients using innovative, conformation-specific antibodies. Furthermore, we measured VK serum concentrations (using HPLC) in PXE-like and PXE samples to evaluate the VK status. In PXE-like patients, we noted an accumulation of uncarboxylated Gla proteins, MGP, and OC in plasma, serum, and in the dermis. Serum levels of VK were normal in these patients. In PXE patients, we found similar, although not identical results for the Gla proteins in the circulation and dermal tissue. However, the VK serum concentration in PXE patients was significantly decreased compared with controls. Our findings allow us to conclude that ectopic mineralization in the PXE-like syndrome and in PXE results from a deficient protein carboxylation of VK-dependent inhibitors of calcification. Although in PXE-like patients this is due to mutations in the GGCX gene, a deficiency of the

A community detection algorithm based on structural similarity

NASA Astrophysics Data System (ADS)

Guo, Xuchao; Hao, Xia; Liu, Yaqiong; Zhang, Li; Wang, Lu

2017-09-01

In order to further improve the efficiency and accuracy of community detection algorithm, a new algorithm named SSTCA (the community detection algorithm based on structural similarity with threshold) is proposed. In this algorithm, the structural similarities are taken as the weights of edges, and the threshold k is considered to remove multiple edges whose weights are less than the threshold, and improve the computational efficiency. Tests were done on the Zachary’s network, Dolphins’ social network and Football dataset by the proposed algorithm, and compared with GN and SSNCA algorithm. The results show that the new algorithm is superior to other algorithms in accuracy for the dense networks and the operating efficiency is improved obviously.

Deep Convolutional Neural Networks Outperform Feature-Based But Not Categorical Models in Explaining Object Similarity Judgments

PubMed Central

Jozwik, Kamila M.; Kriegeskorte, Nikolaus; Storrs, Katherine R.; Mur, Marieke

2017-01-01

Recent advances in Deep convolutional Neural Networks (DNNs) have enabled unprecedentedly accurate computational models of brain representations, and present an exciting opportunity to model diverse cognitive functions. State-of-the-art DNNs achieve human-level performance on object categorisation, but it is unclear how well they capture human behavior on complex cognitive tasks. Recent reports suggest that DNNs can explain significant variance in one such task, judging object similarity. Here, we extend these findings by replicating them for a rich set of object images, comparing performance across layers within two DNNs of different depths, and examining how the DNNs’ performance compares to that of non-computational “conceptual” models. Human observers performed similarity judgments for a set of 92 images of real-world objects. Representations of the same images were obtained in each of the layers of two DNNs of different depths (8-layer AlexNet and 16-layer VGG-16). To create conceptual models, other human observers generated visual-feature labels (e.g., “eye”) and category labels (e.g., “animal”) for the same image set. Feature labels were divided into parts, colors, textures and contours, while category labels were divided into subordinate, basic, and superordinate categories. We fitted models derived from the features, categories, and from each layer of each DNN to the similarity judgments, using representational similarity analysis to evaluate model performance. In both DNNs, similarity within the last layer explains most of the explainable variance in human similarity judgments. The last layer outperforms almost all feature-based models. Late and mid-level layers outperform some but not all feature-based models. Importantly, categorical models predict similarity judgments significantly better than any DNN layer. Our results provide further evidence for commonalities between DNNs and brain representations. Models derived from visual features

Sexual Preference Similarity, Attitude Similarity, and Perceived Counselor Credibility and Attractiveness.

ERIC Educational Resources Information Center

Atkinson, Donald R.; And Others

1981-01-01

Examined the effect of membership group and attitudinal similarity on perceived counselor credibility and attractiveness. Homosexual men (N=84) rated the counselor's credibility and attractiveness after listening to a recorded counseling interview. The counselor was rated more expert, trustworthy, and attractive when he stated a sexual preference…

Sequence-similar, structure-dissimilar protein pairs in the PDB.

PubMed

Kosloff, Mickey; Kolodny, Rachel

2008-05-01

It is often assumed that in the Protein Data Bank (PDB), two proteins with similar sequences will also have similar structures. Accordingly, it has proved useful to develop subsets of the PDB from which "redundant" structures have been removed, based on a sequence-based criterion for similarity. Similarly, when predicting protein structure using homology modeling, if a template structure for modeling a target sequence is selected by sequence alone, this implicitly assumes that all sequence-similar templates are equivalent. Here, we show that this assumption is often not correct and that standard approaches to create subsets of the PDB can lead to the loss of structurally and functionally important information. We have carried out sequence-based structural superpositions and geometry-based structural alignments of a large number of protein pairs to determine the extent to which sequence similarity ensures structural similarity. We find many examples where two proteins that are similar in sequence have structures that differ significantly from one another. The source of the structural differences usually has a functional basis. The number of such proteins pairs that are identified and the magnitude of the dissimilarity depend on the approach that is used to calculate the differences; in particular sequence-based structure superpositioning will identify a larger number of structurally dissimilar pairs than geometry-based structural alignments. When two sequences can be aligned in a statistically meaningful way, sequence-based structural superpositioning provides a meaningful measure of structural differences. This approach and geometry-based structure alignments reveal somewhat different information and one or the other might be preferable in a given application. Our results suggest that in some cases, notably homology modeling, the common use of nonredundant datasets, culled from the PDB based on sequence, may mask important structural and functional information. We

Management Careers in Professional Sport and College/University Athletics: Results of a Survey Evaluation.

ERIC Educational Resources Information Center

Beitel, Patricia A.; And Others

This study assessed the needs of management positions and obtained evaluations of sport management programs by management personnel from different sport program perspectives, i.e., professional sport and college/university athletics. Results of survey identified: (1) specific similarities and differences in the criteria for both hiring sport…

Meta-Storms: efficient search for similar microbial communities based on a novel indexing scheme and similarity score for metagenomic data.

PubMed

Su, Xiaoquan; Xu, Jian; Ning, Kang

2012-10-01

It has long been intriguing scientists to effectively compare different microbial communities (also referred as 'metagenomic samples' here) in a large scale: given a set of unknown samples, find similar metagenomic samples from a large repository and examine how similar these samples are. With the current metagenomic samples accumulated, it is possible to build a database of metagenomic samples of interests. Any metagenomic samples could then be searched against this database to find the most similar metagenomic sample(s). However, on one hand, current databases with a large number of metagenomic samples mostly serve as data repositories that offer few functionalities for analysis; and on the other hand, methods to measure the similarity of metagenomic data work well only for small set of samples by pairwise comparison. It is not yet clear, how to efficiently search for metagenomic samples against a large metagenomic database. In this study, we have proposed a novel method, Meta-Storms, that could systematically and efficiently organize and search metagenomic data. It includes the following components: (i) creating a database of metagenomic samples based on their taxonomical annotations, (ii) efficient indexing of samples in the database based on a hierarchical taxonomy indexing strategy, (iii) searching for a metagenomic sample against the database by a fast scoring function based on quantitative phylogeny and (iv) managing database by index export, index import, data insertion, data deletion and database merging. We have collected more than 1300 metagenomic data from the public domain and in-house facilities, and tested the Meta-Storms method on these datasets. Our experimental results show that Meta-Storms is capable of database creation and effective searching for a large number of metagenomic samples, and it could achieve similar accuracies compared with the current popular significance testing-based methods. Meta-Storms method would serve as a suitable

Privacy-preserving matching of similar patients.

PubMed

Vatsalan, Dinusha; Christen, Peter

2016-02-01

The identification of similar entities represented by records in different databases has drawn considerable attention in many application areas, including in the health domain. One important type of entity matching application that is vital for quality healthcare analytics is the identification of similar patients, known as similar patient matching. A key component of identifying similar records is the calculation of similarity of the values in attributes (fields) between these records. Due to increasing privacy and confidentiality concerns, using the actual attribute values of patient records to identify similar records across different organizations is becoming non-trivial because the attributes in such records often contain highly sensitive information such as personal and medical details of patients. Therefore, the matching needs to be based on masked (encoded) values while being effective and efficient to allow matching of large databases. Bloom filter encoding has widely been used as an efficient masking technique for privacy-preserving matching of string and categorical values. However, no work on Bloom filter-based masking of numerical data, such as integer (e.g. age), floating point (e.g. body mass index), and modulus (numbers wrap around upon reaching a certain value, e.g. date and time), which are commonly required in the health domain, has been presented in the literature. We propose a framework with novel methods for masking numerical data using Bloom filters, thereby facilitating the calculation of similarities between records. We conduct an empirical study on publicly available real-world datasets which shows that our framework provides efficient masking and achieves similar matching accuracy compared to the matching of actual unencoded patient records. Copyright © 2015 Elsevier Inc. All rights reserved.

Quantifying similarity in reliability surfaces using the probability of agreement

DOE PAGES

Stevens, Nathaniel T.; Anderson-Cook, Christine Michaela

2017-03-30

When separate populations exhibit similar reliability as a function of multiple explanatory variables, combining them into a single population is tempting. This can simplify future predictions and reduce uncertainty associated with estimation. However, combining these populations may introduce bias if the underlying relationships are in fact different. The probability of agreement formally and intuitively quantifies the similarity of estimated reliability surfaces across a two-factor input space. An example from the reliability literature demonstrates the utility of the approach when deciding whether to combine two populations or to keep them as distinct. As a result, new graphical summaries provide strategies formore » visualizing the results.« less

Quantifying similarity in reliability surfaces using the probability of agreement

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stevens, Nathaniel T.; Anderson-Cook, Christine Michaela

When separate populations exhibit similar reliability as a function of multiple explanatory variables, combining them into a single population is tempting. This can simplify future predictions and reduce uncertainty associated with estimation. However, combining these populations may introduce bias if the underlying relationships are in fact different. The probability of agreement formally and intuitively quantifies the similarity of estimated reliability surfaces across a two-factor input space. An example from the reliability literature demonstrates the utility of the approach when deciding whether to combine two populations or to keep them as distinct. As a result, new graphical summaries provide strategies formore » visualizing the results.« less

Comparison of sigma(o) obtained from the conventional definition with sigma(o) appearing in the radar equation for randomly rough surfaces

NASA Technical Reports Server (NTRS)

Levine, D. M.

1981-01-01

A comparison is made of the radar cross section of rough surface calculated in one case from the conventional definition and obtained in the second case directly from the radar equation. The validity of the conventional definition representing the cross section appearing in the radar equation is determined. The analysis is executed in the special case of perfectly conducting, randomly corrugated surfaces in the physical optics limit. The radar equation is obtained by solving for the radiation scattered from an arbitrary source back to a colocated antenna. The signal out of the receiving antenna is computed from this solution and the result put into a form recognizeable as the radar equation. The conventional definition is obtained by solving a similar problem but for backscatter from an incident planewave. It is shown that these tow forms for sigma are the same if the observer is far enough from the surface.

Driven similarity renormalization group: Third-order multireference perturbation theory.

PubMed

Li, Chenyang; Evangelista, Francesco A

2017-03-28

A third-order multireference perturbation theory based on the driven similarity renormalization group (DSRG-MRPT3) approach is presented. The DSRG-MRPT3 method has several appealing features: (a) it is intruder free, (b) it is size consistent, (c) it leads to a non-iterative algorithm with O(N 6 ) scaling, and (d) it includes reference relaxation effects. The DSRG-MRPT3 scheme is benchmarked on the potential energy curves of F 2 , H 2 O 2 , C 2 H 6 , and N 2 along the F-F, O-O, C-C, and N-N bond dissociation coordinates, respectively. The nonparallelism errors of DSRG-MRPT3 are consistent with those of complete active space third-order perturbation theory and multireference configuration interaction with singles and doubles and show significant improvements over those obtained from DSRG second-order multireference perturbation theory. Our efficient implementation of the DSRG-MRPT3 based on factorized electron repulsion integrals enables studies of medium-sized open-shell organic compounds. This point is demonstrated with computations of the singlet-triplet splitting (Δ ST =E T -E S ) of 9,10-anthracyne. At the DSRG-MRPT3 level of theory, our best estimate of the adiabatic Δ ST is 3.9 kcal mol -1 , a value that is within 0.1 kcal mol -1 from multireference coupled cluster results.

Driven similarity renormalization group: Third-order multireference perturbation theory

DOE PAGES

Li, Chenyang; Evangelista, Francesco A.

2017-03-28

Here, a third-order multireference perturbation theory based on the driven similarity renormalization group (DSRG-MRPT3) approach is presented. The DSRG-MRPT3 method has several appealing features: (a) it is intruder free, (b) it is size consistent, (c) it leads to a non-iterative algorithm with O(N 6) scaling, and (d) it includes reference relaxation effects. The DSRG-MRPT3 scheme is benchmarked on the potential energy curves of F 2, H 2O 2, C 2H 6, and N 2 along the F–F, O–O, C–C, and N–N bond dissociation coordinates, respectively. The nonparallelism errors of DSRG-MRPT3 are consistent with those of complete active space third-order perturbationmore » theory and multireference configuration interaction with singles and doubles and show significant improvements over those obtained from DSRG second-order multireference perturbation theory. Our efficient implementation of the DSRG-MRPT3 based on factorized electron repulsion integrals enables studies of medium-sized open-shell organic compounds. This point is demonstrated with computations of the singlet-triplet splitting (Δ ST = E T–E S) of 9,10-anthracyne. At the DSRG-MRPT3 level of theory, our best estimate of the adiabatic Δ ST is 3.9 kcal mol –1, a value that is within 0.1 kcal mol –1 from multireference coupled cluster results.« less

Driven similarity renormalization group: Third-order multireference perturbation theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Chenyang; Evangelista, Francesco A.

Here, a third-order multireference perturbation theory based on the driven similarity renormalization group (DSRG-MRPT3) approach is presented. The DSRG-MRPT3 method has several appealing features: (a) it is intruder free, (b) it is size consistent, (c) it leads to a non-iterative algorithm with O(N 6) scaling, and (d) it includes reference relaxation effects. The DSRG-MRPT3 scheme is benchmarked on the potential energy curves of F 2, H 2O 2, C 2H 6, and N 2 along the F–F, O–O, C–C, and N–N bond dissociation coordinates, respectively. The nonparallelism errors of DSRG-MRPT3 are consistent with those of complete active space third-order perturbationmore » theory and multireference configuration interaction with singles and doubles and show significant improvements over those obtained from DSRG second-order multireference perturbation theory. Our efficient implementation of the DSRG-MRPT3 based on factorized electron repulsion integrals enables studies of medium-sized open-shell organic compounds. This point is demonstrated with computations of the singlet-triplet splitting (Δ ST = E T–E S) of 9,10-anthracyne. At the DSRG-MRPT3 level of theory, our best estimate of the adiabatic Δ ST is 3.9 kcal mol –1, a value that is within 0.1 kcal mol –1 from multireference coupled cluster results.« less

[Bad results obtained from the current public health policies and recommendations of hydration].

PubMed

San Mauro Martín, Ismael; Romo Orozco, Denisse Aracely; Mendive Dubourdieu, Paula; Garicano Vilar, Elena; Valente, Ana; Betancor, Fabiana; Morales Hurtado, Alexis Daniel; Garagarza, Cristina

2016-07-19

Achieving an adequate intake of water is crucial within a balanced diet. For that purpose, dietary guidelines for healthy eating and drinking are an important consideration and need to be updated and disseminated to the population. We aimed to evaluate the liquid intake habits of a Mediterranean and Latin American population (Spain-Portugal and Mexico-Uruguay) and if they support the current recommendations of hydration by the EFSA. A record of fluid intake was obtained from 1168 participants from 4 countries above; and then compared with current consensus about hydration 1600 mL/day (female) and 2000 mL/day (male). The average fluid intake slightly surpassed the recommended: mean of 2049 mL/day (2,223 mL in males, 1,938 mL in females). Portugal stood out due to its lower intake (mean of 1,365 mL/day). Water contributed the largest part to total fluid intake (37%) in all countries (mean of 1365 mL/day). Hot beverages (18%) and milk and derivates (17%) follow water in highest consumption. The 20% of males and only 0.3% of females knew recommendations of hydration, while 63.3% of males and 62% of females followed them. Only 8.4% of people who follow the recommendations know them. The people studied surpassed the recommendation, although majority they didn´t know it. Future research should examine actual beverage consumption patterns and evaluate if the current consensuses are correctly adapted to the population needs. Hydration's policies should be transmitted to the population for their knowledge and adequate compliance.

Comparison of Dissolution Similarity Assessment Methods for Products with Large Variations: f2 Statistics and Model-Independent Multivariate Confidence Region Procedure for Dissolution Profiles of Multiple Oral Products.

PubMed

Yoshida, Hiroyuki; Shibata, Hiroko; Izutsu, Ken-Ichi; Goda, Yukihiro

2017-01-01

The current Japanese Ministry of Health Labour and Welfare (MHLW)'s Guideline for Bioequivalence Studies of Generic Products uses averaged dissolution rates for the assessment of dissolution similarity between test and reference formulations. This study clarifies how the application of model-independent multivariate confidence region procedure (Method B), described in the European Medical Agency and U.S. Food and Drug Administration guidelines, affects similarity outcomes obtained empirically from dissolution profiles with large variations in individual dissolution rates. Sixty-one datasets of dissolution profiles for immediate release, oral generic, and corresponding innovator products that showed large variation in individual dissolution rates in generic products were assessed on their similarity by using the f 2 statistics defined in the MHLW guidelines (MHLW f 2 method) and two different Method B procedures, including a bootstrap method applied with f 2 statistics (BS method) and a multivariate analysis method using the Mahalanobis distance (MV method). The MHLW f 2 and BS methods provided similar dissolution similarities between reference and generic products. Although a small difference in the similarity assessment may be due to the decrease in the lower confidence interval for expected f 2 values derived from the large variation in individual dissolution rates, the MV method provided results different from those obtained through MHLW f 2 and BS methods. Analysis of actual dissolution data for products with large individual variations would provide valuable information towards an enhanced understanding of these methods and their possible incorporation in the MHLW guidelines.

Similarity solutions for unsteady flow behind an exponential shock in a self-gravitating non-ideal gas with azimuthal magnetic field

NASA Astrophysics Data System (ADS)

Nath, G.; Pathak, R. P.; Dutta, Mrityunjoy

2018-01-01

Similarity solutions for the flow of a non-ideal gas behind a strong exponential shock driven out by a piston (cylindrical or spherical) moving with time according to an exponential law is obtained. Solutions are obtained, in both the cases, when the flow between the shock and the piston is isothermal or adiabatic. The shock wave is driven by a piston moving with time according to an exponential law. Similarity solutions exist only when the surrounding medium is of constant density. The effects of variation of ambient magnetic field, non-idealness of the gas, adiabatic exponent and gravitational parameter are worked out in detail. It is shown that the increase in the non-idealness of the gas or the adiabatic exponent of the gas or presence of magnetic field have decaying effect on the shock wave. Consideration of the isothermal flow and the self-gravitational field increase the shock strength. Also, the consideration of isothermal flow or the presence of magnetic field removes the singularity in the density distribution, which arises in the case of adiabatic flow. The result of our study may be used to interpret measurements carried out by space craft in the solar wind and in neighborhood of the Earth's magnetosphere.

Linked Forests: Semantic similarity of geographical concepts "forest"

NASA Astrophysics Data System (ADS)

Čerba, Otakar; Jedlička, Karel

2016-01-01

Linked Data represents the new trend in geoinformatics and geomatics. It produces a structure of objects (in a form of concepts or terms) interconnected by object relations expressing a type of semantic relationships of various concepts. The research published in this article studies, if objects connected by above mentioned relations are more similar than objects representing the same phenomenon, but standing alone. The phenomenon "forest" and relevant geographical concepts were chosen as the domain of the research. The concepts similarity (Tanimoto coefficient as a specification of Tversky index) was computed on the basis of explicit information provided by thesauri containing particular concepts. Overall in the seven thesauri (AGROVOC, EuroVoc, GEMET, LusTRE/EARTh, NAL, OECD and STW) there was tested if the "forest" concept interconnected by the relation skos:exactMatch are more similar than other, not interlinked concepts. The results of the research are important for the sharing and combining of geographical data, information and knowledge. The proposed methodology can be reused to a comparison of other geographical concepts.

Brand name confusion: Subjective and objective measures of orthographic similarity.

PubMed

Burt, Jennifer S; McFarlane, Kimberley A; Kelly, Sarah J; Humphreys, Michael S; Weatherall, Kimberlee; Burrell, Robert G

2017-09-01

Determining brand name similarity is vital in areas of trademark registration and brand confusion. Students rated the orthographic (spelling) similarity of word pairs (Experiments 1, 2, and 4) and brand name pairs (Experiment 5). Similarity ratings were consistently higher when words shared beginnings rather than endings, whereas shared pronunciation of the stressed vowel had small and less consistent effects on ratings. In Experiment 3 a behavioral task confirmed the similarity of shared beginnings in lexical processing. Specifically, in a task requiring participants to decide whether 2 words presented in the clear (a probe and a later target) were the same or different, a masked prime word preceding the target shortened response latencies if it shared its initial 3 letters with the target. The ratings of students for word and brand name pairs were strongly predicted by metrics of orthographic similarity from the visual word identification literature based on the number of shared letters and their relative positions. The results indicate a potential use for orthographic metrics in brand name registration and trademark law. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Relations between premise similarity and inductive strength.

PubMed

Heit, Evan; Feeney, Aidan

2005-04-01

According to the diversity principle, diverse evidence is strong evidence. There has been considerable evidence that people respect this principle in inductive reasoning. However, exceptions may be particularly informative. Medin, Coley, Storms, and Hayes (2003) introduced a relevance theory of inductive reasoning and used this theory to predict exceptions, including the nondiversity-by-property-reinforcement effect. A new experiment in which this phenomenon was investigated is reported here. Subjects made inductive strength judgments and similarity judgments for stimuli from Medin et al. (2003). The inductive strength judgments showed the same pattern as that in Medin et al. (2003); however, the similarity judgments suggested that the pattern should be interpreted as a diversity effect, rather than as a nondiversity effect. It is concluded that the evidence regarding the predicted nondiversity-by-property-reinforcement effect does not give distinctive support for relevance theory, although this theory does address other results.

Similarity of WISC-R and WAIS-R Scores at Age 16.

ERIC Educational Resources Information Center

Sandoval, Jonathan; And Others

1988-01-01

Examined similarity of scores of 30 learning disabled students (aged 16 and 17) on the Wechsler Intelligence Scale for Children-Revised (WISC-R) and the Wechsler Adult Intelligence Scale-Revised (WAIS-R). Results documented similarity between WISC-R and WAIS-R for 16 year-olds who were learning disabled and had average intellectual ability.…

Self-Similar Subsets of Symmetric Cantor Sets

NASA Astrophysics Data System (ADS)

Zeng, Ying

This paper concerns the affine embeddings of general symmetric Cantor sets. Under certain condition, we show that if a self-similar set F can be affinely embedded into a symmetric Cantor set E, then their contractions are rationally commensurable. Our result supports Conjecture 1.2 in [D. J. Feng, W. Huang and H. Rao, Affine embeddings and intersections of Cantor sets, J. Math. Pures Appl. 102 (2014) 1062-1079].

Thai Language Sentence Similarity Computation Based on Syntactic Structure and Semantic Vector

NASA Astrophysics Data System (ADS)

Wang, Hongbin; Feng, Yinhan; Cheng, Liang

2018-03-01

Sentence similarity computation plays an increasingly important role in text mining, Web page retrieval, machine translation, speech recognition and question answering systems. Thai language as a kind of resources scarce language, it is not like Chinese language with HowNet and CiLin resources. So the Thai sentence similarity research faces some challenges. In order to solve this problem of the Thai language sentence similarity computation. This paper proposes a novel method to compute the similarity of Thai language sentence based on syntactic structure and semantic vector. This method firstly uses the Part-of-Speech (POS) dependency to calculate two sentences syntactic structure similarity, and then through the word vector to calculate two sentences semantic similarity. Finally, we combine the two methods to calculate two Thai language sentences similarity. The proposed method not only considers semantic, but also considers the sentence syntactic structure. The experiment result shows that this method in Thai language sentence similarity computation is feasible.

Results of the new processing of images obtained from the surface of Venus in a TV experiment onboard the VENERA-9 lander (1975)

NASA Astrophysics Data System (ADS)

Ksanfomality, L. V.

2012-09-01

Data on the results of the analysis of the content of re-processed panorama of the VENERA-9 lander are presented. The panorama was transmitted historically for the first time from the surface of Venus in 1975. The low noise of the VENERA-9 data allowed allocating a large object of an unusual regular structure. Earlier, its fuzzy image was repeatedly cited in the literature being interpreted as a "strange stone". The complex shape and its other features suggest that the object may be a real habitant of the planet. It is not excluded that another similar object observed was damaged during the VENERA-9 landing. From the evidence of its movement and position of some other similar objects it is concluded that because of the limited energy capacity, the physical action of the Venusian fauna may be much slower than that of the Earth fauna. Another question considered is what sources of energy could be used by life in the conditions of the high temperature oxygenless atmosphere of the planet. It is natural to assume that, like on Earth, the Venusian fauna is heterotrophic and should be based on hypothetical flora, using photosynthesis (based on an unknown high temperature biophysical mechanism).

Drug Promiscuity in PDB: Protein Binding Site Similarity Is Key.

PubMed

Haupt, V Joachim; Daminelli, Simone; Schroeder, Michael

2013-01-01

Drug repositioning applies established drugs to new disease indications with increasing success. A pre-requisite for drug repurposing is drug promiscuity (polypharmacology) - a drug's ability to bind to several targets. There is a long standing debate on the reasons for drug promiscuity. Based on large compound screens, hydrophobicity and molecular weight have been suggested as key reasons. However, the results are sometimes contradictory and leave space for further analysis. Protein structures offer a structural dimension to explain promiscuity: Can a drug bind multiple targets because the drug is flexible or because the targets are structurally similar or even share similar binding sites? We present a systematic study of drug promiscuity based on structural data of PDB target proteins with a set of 164 promiscuous drugs. We show that there is no correlation between the degree of promiscuity and ligand properties such as hydrophobicity or molecular weight but a weak correlation to conformational flexibility. However, we do find a correlation between promiscuity and structural similarity as well as binding site similarity of protein targets. In particular, 71% of the drugs have at least two targets with similar binding sites. In order to overcome issues in detection of remotely similar binding sites, we employed a score for binding site similarity: LigandRMSD measures the similarity of the aligned ligands and uncovers remote local similarities in proteins. It can be applied to arbitrary structural binding site alignments. Three representative examples, namely the anti-cancer drug methotrexate, the natural product quercetin and the anti-diabetic drug acarbose are discussed in detail. Our findings suggest that global structural and binding site similarity play a more important role to explain the observed drug promiscuity in the PDB than physicochemical drug properties like hydrophobicity or molecular weight. Additionally, we find ligand flexibility to have a minor

Similarity of Symbol Frequency Distributions with Heavy Tails

NASA Astrophysics Data System (ADS)

Gerlach, Martin; Font-Clos, Francesc; Altmann, Eduardo G.

2016-04-01

Quantifying the similarity between symbolic sequences is a traditional problem in information theory which requires comparing the frequencies of symbols in different sequences. In numerous modern applications, ranging from DNA over music to texts, the distribution of symbol frequencies is characterized by heavy-tailed distributions (e.g., Zipf's law). The large number of low-frequency symbols in these distributions poses major difficulties to the estimation of the similarity between sequences; e.g., they hinder an accurate finite-size estimation of entropies. Here, we show analytically how the systematic (bias) and statistical (fluctuations) errors in these estimations depend on the sample size N and on the exponent γ of the heavy-tailed distribution. Our results are valid for the Shannon entropy (α =1 ), its corresponding similarity measures (e.g., the Jensen-Shanon divergence), and also for measures based on the generalized entropy of order α . For small α 's, including α =1 , the errors decay slower than the 1 /N decay observed in short-tailed distributions. For α larger than a critical value α*=1 +1 /γ ≤2 , the 1 /N decay is recovered. We show the practical significance of our results by quantifying the evolution of the English language over the last two centuries using a complete α spectrum of measures. We find that frequent words change more slowly than less frequent words and that α =2 provides the most robust measure to quantify language change.

Similarity-transformed dyson mapping and SDG-interacting boson hamiltonian

NASA Astrophysics Data System (ADS)

Navrátil, P.; Dobeš, J.

1991-10-01

The sdg-interacting boson hamiltonian is constructed from the fermion shell-model input. The seniority boson mapping as given by the similarity-transformed Dyson boson mapping is used. The s, d, and g collective boson amplitudes are determined consistently from the mapped hamiltonian. Influence of the starting shell-model parameters is discussed. Calculations for the Sm isotopic chain and for the 148Sm, 150Nd, and 196Pt nuclei are presented. Calculated energy levels as well as E2 and E4 properties agree rather well with experimental ones. To obtain such agreement, the input shell-model parameters cannot be fixed at a constant set for several nuclei but have to be somewhat varied, especially in the deformed region. Possible reasons for this variation are discussed. Effects of the explicit g-boson consideration are shown.

A tale of two pectins: Diverse fine structures can result from identical processive PME treatments on similar high DM subtrates

USDA-ARS?s Scientific Manuscript database

The effects of a processive pectin-methylesterase treatment on two different pectins, both possessing a high degree of methylesterification, were investigated. While the starting samples were purportedly very similar in fine structure, and even though the sample-averaged degree of methylesterificati...

An integrative approach for measuring semantic similarities using gene ontology.

PubMed

Peng, Jiajie; Li, Hongxiang; Jiang, Qinghua; Wang, Yadong; Chen, Jin

2014-01-01

Gene Ontology (GO) provides rich information and a convenient way to study gene functional similarity, which has been successfully used in various applications. However, the existing GO based similarity measurements have limited functions for only a subset of GO information is considered in each measure. An appropriate integration of the existing measures to take into account more information in GO is demanding. We propose a novel integrative measure called InteGO2 to automatically select appropriate seed measures and then to integrate them using a metaheuristic search method. The experiment results show that InteGO2 significantly improves the performance of gene similarity in human, Arabidopsis and yeast on both molecular function and biological process GO categories. InteGO2 computes gene-to-gene similarities more accurately than tested existing measures and has high robustness. The supplementary document and software are available at http://mlg.hit.edu.cn:8082/.

Query Auto-Completion Based on Word2vec Semantic Similarity

NASA Astrophysics Data System (ADS)

Shao, Taihua; Chen, Honghui; Chen, Wanyu

2018-04-01

Query auto-completion (QAC) is the first step of information retrieval, which helps users formulate the entire query after inputting only a few prefixes. Regarding the models of QAC, the traditional method ignores the contribution from the semantic relevance between queries. However, similar queries always express extremely similar search intention. In this paper, we propose a hybrid model FS-QAC based on query semantic similarity as well as the query frequency. We choose word2vec method to measure the semantic similarity between intended queries and pre-submitted queries. By combining both features, our experiments show that FS-QAC model improves the performance when predicting the user’s query intention and helping formulate the right query. Our experimental results show that the optimal hybrid model contributes to a 7.54% improvement in terms of MRR against a state-of-the-art baseline using the public AOL query logs.

Balancing the popularity bias of object similarities for personalised recommendation

NASA Astrophysics Data System (ADS)

Hou, Lei; Pan, Xue; Liu, Kecheng